Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 138 of 171
Found at i:42622035 original size:10 final size:9
Alignment explanation
Indices: 42621974--42622037 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
42621964 CACTTAAGCA
42621974 ATTAATAAAT
1 ATTAA-AAAT
*
42621984 TTTAAAAAT
1 ATTAAAAAT
*
42621993 TTTAAAAAT
1 ATTAAAAAT
42622002 -TTCAAAAAT
1 ATT-AAAAAT
42622011 GA-TAAAAAT
1 -ATTAAAAAT
*
42622020 ATTAAAATT
1 ATTAAAAAT
42622029 ATCTAAAAA
1 AT-TAAAAA
42622038 AGATAAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
8 3 0.07
9 33 0.72
10 10 0.22
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:42622046 original size:27 final size:27
Alignment explanation
Indices: 42621986--42622045 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
42621976 TAATAAATTT
* *
42621986 TAAAAATTTTAAAAATTTCAAAAATGA
1 TAAAAATATTAAAAATTTCAAAAAAGA
42622013 TAAAAATATT-AAAATTATCTAAAAAAGA
1 TAAAAATATTAAAAATT-TC-AAAAAAGA
42622041 TAAAA
1 TAAAA
42622046 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 11 0.38
28 12 0.41
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (27 bp):
TAAAAATATTAAAAATTTCAAAAAAGA
Found at i:42629554 original size:3 final size:3
Alignment explanation
Indices: 42629541--42629580 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
42629531 ATATTTTTGT
42629541 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
42629581 TTTTTTTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:42639632 original size:51 final size:49
Alignment explanation
Indices: 42639576--42639865 Score: 269
Period size: 51 Copynumber: 5.7 Consensus size: 49
42639566 CTCATTTCAT
*
42639576 TTCATACTCACGATAACA-TATAGTCATCGGACCTCTTATTCCAT-ATAGGAA
1 TTCATACTCACGATAACACT-TAGTCATCGGACCT-TTAATCCATCAT-GG-A
* *
42639627 TTCATATGCTCATGATAACACTGAGTCATCGGACCTTTAATCCATCATGGA
1 TTCATA--CTCACGATAACACTTAGTCATCGGACCTTTAATCCATCATGGA
* ** * *
42639678 TTCATTTACTCACGATGACACTTAGTCATCACACCTTTAATACATCCTGGA
1 TTCA--TACTCACGATAACACTTAGTCATCGGACCTTTAATCCATCATGGA
* * * *
42639729 TTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATACATCCTGGA
1 TTCA--TACTCACGATAACACTTAGTCATCGGACCTTTAATCCATCATGGA
* * * *
42639780 TTCATTTACTCATGATGACACTTAGTCATCGAACCTTTAATCCATCCTGGA
1 TTCA--TACTCACGATAACACTTAGTCATCGGACCTTTAATCCATCATGGA
* **
42639831 TTCATTTACTCACAATGGCACTTAGTCATCGGACC
1 TTCA--TACTCACGATAACACTTAGTCATCGGACC
42639866 CTTTCGTTTA
Statistics
Matches: 214, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
51 175 0.82
52 10 0.05
53 28 0.13
54 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (49 bp):
TTCATACTCACGATAACACTTAGTCATCGGACCTTTAATCCATCATGGA
Found at i:42639756 original size:102 final size:102
Alignment explanation
Indices: 42639626--42639865 Score: 365
Period size: 102 Copynumber: 2.4 Consensus size: 102
42639616 CCATATAGGA
* * * * *
42639626 ATTCATATGCTCATGATAACACTGAGTCATCGGACCTTTAATCCATCATGGATTCATTTACTCAC
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATACATCATGGATTCATTTACTCAC
42639691 GATGACACTTAGTCATC-ACACCTTTAATACATCCTGG
66 GATGACACTTAGTCATCGA-ACCTTTAATACATCCTGG
* *
42639728 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATACATCCTGGATTCATTTACTCAT
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATACATCATGGATTCATTTACTCAC
*
42639793 GATGACACTTAGTCATCGAACCTTTAATCCATCCTGG
66 GATGACACTTAGTCATCGAACCTTTAATACATCCTGG
** *
42639830 ATTCATTTACTCACAATGGCACTTAGTCATCGGACC
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACC
42639866 CTTTCGTTTA
Statistics
Matches: 126, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
102 125 0.99
103 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (102 bp):
ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATACATCATGGATTCATTTACTCAC
GATGACACTTAGTCATCGAACCTTTAATACATCCTGG
Found at i:42645028 original size:16 final size:16
Alignment explanation
Indices: 42645004--42645045 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
42644994 GTCATACTTG
*
42645004 CTCAGCTGTACAAACT
1 CTCATCTGTACAAACT
42645020 CTCATCTGTACAAACT
1 CTCATCTGTACAAACT
42645036 CTCATCTGTA
1 CTCATCTGTA
42645046 ATCTGCCACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (16 bp):
CTCATCTGTACAAACT
Found at i:42646755 original size:51 final size:49
Alignment explanation
Indices: 42646699--42646933 Score: 206
Period size: 51 Copynumber: 4.6 Consensus size: 49
42646689 CTCATTTCAT
*
42646699 TTCATACTCACGATAACTTA-T-AGTCATCGGACCTCTTATTCCAT-ATAGGAA
1 TTCATACTCACGATAAC--ACTGAGTCATCGGACCT-TTAATCCATCAT-GG-A
42646750 TTCATATGCTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGGA
1 TTCATA--CTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGGA
* * * * *
42646801 TTCATTTACTCACGATTACACTTAGTCATCAGACCTTTAATACATCCTGGA
1 TTCA--TACTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGGA
* * * * *
42646852 TTCATTTACTCACGATGACACTTAGTCATCGAACCTTTAATCCATCCTAGA
1 TTCA--TACTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGGA
* * *
42646903 TTCATTTACCCACGATGACACTTAGTCATCG
1 TTCA--TACTCACGATAACACTGAGTCATCG
42646934 AACCCTTTCG
Statistics
Matches: 165, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
51 126 0.76
52 11 0.07
53 28 0.17
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (49 bp):
TTCATACTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGGA
Found at i:42646934 original size:51 final size:51
Alignment explanation
Indices: 42646749--42646937 Score: 272
Period size: 51 Copynumber: 3.7 Consensus size: 51
42646739 CCATATAGGA
* * * * * *
42646749 ATTCATATGCTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGAACCTTTAATCCATCCTGG
* *
42646800 ATTCATTTACTCACGATTACACTTAGTCATC-AGACCTTTAATACATCCTGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGA-ACCTTTAATCCATCCTGG
*
42646851 ATTCATTTACTCACGATGACACTTAGTCATCGAACCTTTAATCCATCCTAG
1 ATTCATTTACTCACGATGACACTTAGTCATCGAACCTTTAATCCATCCTGG
*
42646902 ATTCATTTACCCACGATGACACTTAGTCATCGAACC
1 ATTCATTTACTCACGATGACACTTAGTCATCGAACC
42646938 CTTTCGTTTA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
51 124 0.99
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGAACCTTTAATCCATCCTGG
Found at i:42656721 original size:14 final size:14
Alignment explanation
Indices: 42656684--42656730 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
42656674 CGTGTAGTCT
*
42656684 TATAATATT-ATAA
1 TATAATATTAAAAA
42656697 TATAATATTAAAAA
1 TATAATATTAAAAA
42656711 TA-AATATTTAAAAAA
1 TATAATA-TT-AAAAA
42656726 TATAA
1 TATAA
42656731 GATGAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 13 0.45
14 7 0.24
15 7 0.24
16 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATAATATTAAAAA
Found at i:42657957 original size:14 final size:14
Alignment explanation
Indices: 42657920--42657966 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
42657910 AGGAGTGTTT
*
42657920 TATAATATT-ATAA
1 TATAATATTAAAAA
42657933 TATAATATTAAAAA
1 TATAATATTAAAAA
42657947 TA-AATATTTAAAAAA
1 TATAATA-TT-AAAAA
42657962 TATAA
1 TATAA
42657967 GATGAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 13 0.45
14 7 0.24
15 7 0.24
16 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATAATATTAAAAA
Found at i:42660812 original size:162 final size:162
Alignment explanation
Indices: 42660391--42660875 Score: 611
Period size: 163 Copynumber: 3.0 Consensus size: 162
42660381 TTATATGTCG
* * *
42660391 TGAGTGTTGTATAAATGCTTATTTTGCTTTGGTTATTGGAATCATAAACCTTTCACTATACTTAA
1 TGAGTGTTATATAAATG-TTATTTTGCTTTTGTTATTGGAATAATAAACCTTTCACTATACTTAA
*
42660456 ATCTTTATTTTC-TCATAGATATTTATTTTGTTTTTGTTTTAATACCTAAATTAGCTTTCAAAT-
65 ATCTTTATTTTCTTC-TAGATACTTATTTTGTTTTTGTTTTAATACCTAAATTAGCTTTCAAATA
* *
42660519 TATATCTTTTAACGATGCTTAAGGTTTATATTTTA
129 TACATCTTTTAATGATGCTTAA-GTTTATATTTTA
* * * * * *
42660554 TGAGTGTTATATAAATGGTTATTTTGCTCTTGTTATTAGAATTATACACCTTTTAGTATACTTAA
1 TGAGTGTTATATAAAT-GTTATTTTGCTTTTGTTATTGGAATAATAAACCTTTCACTATACTTAA
* ** * * * * *
42660619 TTCTGCATTTTATTGTAGATGCTTA-TTTGTTTTTGTTTTAATACCTAAA-TGGATTTTCAAACT
65 ATCTTTATTTTCTTCTAGATACTTATTTTGTTTTTGTTTTAATACCTAAATTAG-CTTTCAAA-T
42660682 ATACATCTTTTAATGATGCTTAAGTTTATATTTTA
128 ATACATCTTTTAATGATGCTTAAGTTTATATTTTA
** * * *
42660717 TGAGTGTTATATAAATGTT-TTTTTTTTTTGTTATCGGAATAATAAATCTTTCACTATACCTAAA
1 TGAGTGTTATATAAATGTTATTTTGCTTTTGTTATTGGAATAATAAACCTTTCACTATACTTAAA
*
42660781 TCTTTATTTTCTTCTAGATACTTATTTTGTTTTTGTTTTAATACCTAGATTAGCTTTCAAATTAT
66 TCTTTATTTTCTTCTAGATACTTATTTTGTTTTTGTTTTAATACCTAAATTAGCTTTCAAA-TAT
* *
42660846 ACATCTTTTAATGATACTCAAAGTTTATAT
130 ACATCTTTTAATGATGCT-TAAGTTTATAT
42660876 GTTGGACTTA
Statistics
Matches: 272, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
161 54 0.20
162 84 0.31
163 112 0.41
164 22 0.08
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (162 bp):
TGAGTGTTATATAAATGTTATTTTGCTTTTGTTATTGGAATAATAAACCTTTCACTATACTTAAA
TCTTTATTTTCTTCTAGATACTTATTTTGTTTTTGTTTTAATACCTAAATTAGCTTTCAAATATA
CATCTTTTAATGATGCTTAAGTTTATATTTTA
Found at i:42661158 original size:287 final size:288
Alignment explanation
Indices: 42660595--42661162 Score: 727
Period size: 288 Copynumber: 2.0 Consensus size: 288
42660585 GTTATTAGAA
* * * *
42660595 TTATACACCTTTTAGTATACTTAATTCTGCATTTTATTGTAGATGCTTATTTGTTTTTGTTTTAA
1 TTATACACCTTTCACTATACTTAATTCTGCATTTTATTATAGATGCTTATTTGTTTATGTTTTAA
*
42660660 TACCTAAATGGATTTTCAAACTATACATCTTTTAATGATGCTTAAGTTTATATTTTATGAGTGTT
66 TACCTAAATGGATTTTCAAACTATACATCTTTTAACGATGCTTAAGTTTATATTTTATGAGTGTT
* * * * *
42660725 ATATAAATGTTTTTTTTTTTTGTTATCGGAATAATAAATCTTTCACTATACCTAAATCTTTATTT
131 ATATAAATGTTTTTTGTTTTGGTTATCGAAATAATAAATCTTTCACTATACCTAAACCTATATTT
* * * * ** *
42660790 TCTTCTAGATACTTATTTTGTTTTTGTTTTAATACCTAGATTAGCTTTCAAATTATACATCTTTT
196 TCTTCTAAATACTTATATTGATTTTGTGTTAATAAATAGAATAGCTTTCAAATTATACATCTTTT
42660855 AATGATACTCAAAGTTTATATGTTGGAC
261 AATGATACTCAAAGTTTATATGTTGGAC
*
42660883 TTATACACCTTTCACTATACTTAA-TGTGCATTTTATTATAGATGCTTATTTTGTTTATGTTTTA
1 TTATACACCTTTCACTATACTTAATTCTGCATTTTATTATAGATGCTTA-TTTGTTTATGTTTTA
* * *
42660947 CTACTTAAATTGG-TTTT-TAACTATACATCTTTTAACGATGCTTAAGGTTTATATTTTATGAGT
65 ATACCTAAA-TGGATTTTCAAACTATACATCTTTTAACGATGCTTAA-GTTTATATTTTATGAGT
* * * * *
42661010 TTTATATAATTGCTTATTTTGTTTTGGTTATTGAAATCATACA-CATTTCACTATACCTAAACCT
128 GTTATATAAATG-TT-TTTTGTTTTGGTTATCGAAATAATAAATC-TTTCACTATACCTAAACCT
* * * * * * *
42661074 ATATTTT-TTTTAAATGCTTATATTGATTTTGTGTTACTAAATA-AATGGTTTTCGAATTATATA
190 ATATTTTCTTCTAAATACTTATATTGATTTTGTGTTAATAAATAGAATAGCTTTCAAATTATACA
*
42661137 TC-TTTAATGATACTTAAAGTTTATAT
255 TCTTTTAATGATACTCAAAGTTTATAT
42661163 TTCATGGGTG
Statistics
Matches: 240, Mismatches: 34, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
287 71 0.30
288 91 0.38
289 33 0.14
290 45 0.19
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (288 bp):
TTATACACCTTTCACTATACTTAATTCTGCATTTTATTATAGATGCTTATTTGTTTATGTTTTAA
TACCTAAATGGATTTTCAAACTATACATCTTTTAACGATGCTTAAGTTTATATTTTATGAGTGTT
ATATAAATGTTTTTTGTTTTGGTTATCGAAATAATAAATCTTTCACTATACCTAAACCTATATTT
TCTTCTAAATACTTATATTGATTTTGTGTTAATAAATAGAATAGCTTTCAAATTATACATCTTTT
AATGATACTCAAAGTTTATATGTTGGAC
Found at i:42661367 original size:165 final size:164
Alignment explanation
Indices: 42660885--42661655 Score: 707
Period size: 165 Copynumber: 4.7 Consensus size: 164
42660875 TGTTGGACTT
* * * * *
42660885 ATACACCTTTCACTATACTTAATGTGC-ATTTTATTATAGATGCTTATTTTGTTTATGTTTTACT
1 ATACACCTTTCACTATACTAAATCT-CTATTTTATTATAGATACTTATTTTGTTTTTGTTTTAAT
* ** * * * * * *
42660949 A-CTTAAATTG-GTTTTTAACTATACATCTTTTAACGATGCTTAAGGTTTATATTTTATGAGTTT
65 ATC-TAAATTGACTTTCAAATTATACATATTTTAACGATGCTTAAAGTTTATATTTCATGGGTGT
* * * * * *
42661012 TATATAATTGCTTATTTTGTTTTGGTTATTGAAATC
129 TATATAAATACTTATATTGCTTTGGTTATCGGAATC
* * * * * * * * * *
42661048 ATACACATTTCACTATACCTAAACCTATATTTT-TTTTAAATGCTTATATTGATTTTGTGTTACT
1 ATACACCTTTCACTATA-CTAAATCTCTATTTTATTATAGATACTTATTTTGTTTTTGTTTTAAT
** ** * * *
42661112 AAATAAA-TGGTTTTCGAATTAT--ATATCTTTAATGATACTTAAAGTTTATATTTCATGGGTGT
65 ATCTAAATTGACTTTCAAATTATACATAT-TTTAACGATGCTTAAAGTTTATATTTCATGGGTGT
* *
42661174 TATATAAATTCTTATTTTGCTTTGGTTATCGGAATC
129 TATATAAATACTTATATTGCTTTGGTTATCGGAATC
* * * * * *
42661210 ATAAACCTTTCACTATATCTAAGTCTTTATTTTCTTCTAGATACTTATTTTGTTTTCGTTTTAAT
1 ATACACCTTTCACTATA-CTAAATCTCTATTTTATTATAGATACTTATTTTGTTTTTGTTTTAAT
* * ** *
42661275 ATCTAAATTGACTTTCAAATTATACATATTTTAATGATGCTTAAAGCTTATATGCCATGGGTGTG
65 ATCTAAATTGACTTTCAAATTATACATATTTTAACGATGCTTAAAGTTTATATTTCATGGGTGTT
* * *
42661340 ATATAAATACTTATATTGCTCTGGTTATCAGAATT
130 ATATAAATACTTATATTGCTTTGGTTATCGGAATC
* * *
42661375 ATACACCTTTCACTATACTTAAATCTGCT-TTTTATTATAGATGCTTATTTTGTTTTTATTTTTA
1 ATACACCTTTCACTATAC-TAAATCT-CTATTTTATTATAGATACTTATTTTGTTTTTGTTTTAA
* ** * * * **
42661439 TATCTAAATAGGTTTTCAAATTATACATCTTTTAACGATGCTTAAGGTTTATATTTTATAAGTGT
64 TATCTAAATTGACTTTCAAATTATACATATTTTAACGATGCTTAAAGTTTATATTTCATGGGTGT
* * *
42661504 TATATAAATGCTTA-ACTTGCTTTGATTATCGAAATC
129 TATATAAATACTTATA-TTGCTTTGGTTATCGGAATC
* * * *
42661540 ATACACCATTCACTATACCTAAACCTCTATGTTATTATAAATACTTATTTTGTTTTTGTTTTAAT
1 ATACACCTTTCACTATA-CTAAATCTCTATTTTATTATAGATACTTATTTTGTTTTTGTTTTAAT
* * * * *
42661605 ACCTACATTAACTTTCAAATTATACAT-CTTTAACCATGCTTAAAGTTTATA
65 ATCTAAATTGACTTTCAAATTATACATATTTTAACGATGCTTAAAGTTTATA
42661656 AGTCGTGGGT
Statistics
Matches: 493, Mismatches: 101, Indels: 27
0.79 0.16 0.04
Matches are distributed among these distances:
161 3 0.01
162 89 0.18
163 82 0.17
164 47 0.10
165 266 0.54
166 6 0.01
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (164 bp):
ATACACCTTTCACTATACTAAATCTCTATTTTATTATAGATACTTATTTTGTTTTTGTTTTAATA
TCTAAATTGACTTTCAAATTATACATATTTTAACGATGCTTAAAGTTTATATTTCATGGGTGTTA
TATAAATACTTATATTGCTTTGGTTATCGGAATC
Found at i:42662155 original size:164 final size:164
Alignment explanation
Indices: 42661877--42662830 Score: 651
Period size: 164 Copynumber: 5.7 Consensus size: 164
42661867 TTTCATGGGT
* * * * *
42661877 TTTTGCTTTGGTTATCGAAATCATACACCCTTCACTATACCTAAACCTCTACCTTTTGTTGTAAA
1 TTTTGCTTTGGTTATAGGAATCATACACCCTTCACTATACCTAAA--TCTACATTTTATTATAAA
* * * ** * *
42661942 CGCTTATTTTATTTTTGTTTTAATATGTAAAACGGTTTTCCAATTATATATCTTTTAACGTTACT
64 TGCTTATTTTGTTTTTATTTTAATACATAAAACGATTTTCGAATTATATATCTTTTAACG-TACT
* * *
42662007 TAAAGTTTATATTTCATGGGTATTATATAAGTGTTTA
128 TAAAGTTTATATTTCATGTGTATTATATAAATGCTTA
* * * * * * *
42662044 TTTTGCTTTAGTTATAGGAATCGTACACCTTTCACTACACTTAAATCTACATTTTATTTTATATG
1 TTTTGCTTTGGTTATAGGAATCATACACCCTTCACTATACCTAAATCTACATTTTATTATAAATG
* * *
42662109 CTT-TTTTTTTTTTACTTTAATACATAAAACGATTTTCGATTTATATA-CTTTTTAACAGTACTT
66 CTTATTTTGTTTTTATTTTAATACATAAAACGATTTTCGAATTATATATC-TTTTAAC-GTACTT
* * *
42662172 AAATTTTATATTTCAT-TGTGTTGTATAAATGCTTA
129 AAAGTTTATATTTCATGTGTATTATATAAATGCTTA
* * * * *
42662207 TTTTACTTTGGTTATTGGAATCATACACCTTTCACTATACTTAAATCTGCATTTTATTATAGAA-
1 TTTTGCTTTGGTTATAGGAATCATACACCCTTCACTATACCTAAATCTACATTTTATTATA-AAT
* ** * * * * *
42662271 GCTTATTTTGTTTTTGTTTTAATACATAAATTGGA-TTTCAAATTATACATCTTTGAGCGATCCT
65 GCTTATTTTGTTTTTATTTTAATACATAAA-ACGATTTTCGAATTATATATCTTTTAACG-TACT
*
42662335 TAATGTTTATATTT-ATGTGTATTATATAAATGCTTA
128 TAAAGTTTATATTTCATGTGTATTATATAAATGCTTA
* *
42662371 TTTTGCTTTGGCTATCA-GAATCATACACCCTTCACTATACCTAAACCT-CTATTTTATTATAAA
1 TTTTGCTTTGGTTAT-AGGAATCATACACCCTTCACTATACCTAAATCTAC-ATTTTATTATAAA
* *
42662434 TGCTTATTTTGTTTTTATTTTAATA-AGTAAAACGGTTTTCGATTTATATAATATATATATATAT
64 TGCTTATTTTGTTTTTATTTTAATACA-TAAAACGATTTTCG---------A-AT-TATATATCT
* * **
42662498 ATACATTAACGATACTTAAAGTCTATATTTCATGGGTGA-TATATAAAAACTTA
117 -T---TTAACG-TACTTAAAGTTTATATTTCATGTGT-ATTATATAAATGCTTA
* * * * ** * * *
42662551 TTTTACTTTTGTTATCGGAAACATACACTTTTTATTATACCTAAACCT-CTATTTTA-T-T--AT
1 TTTTGCTTTGGTTATAGGAATCATACACCCTTCACTATACCTAAATCTAC-ATTTTATTATAAAT
* * * * * *
42662611 GCTTATTTTACTTTTT-GTTTAATA-AGTAAATA-GGTTTTCAAATTATATATTTTTTAACTATA
65 GCTTATTTT-GTTTTTATTTTAATACA-TAAA-ACGATTTTCGAATTATATATCTTTTAAC-GTA
* * *
42662673 TTTAAAGTTTATATTTTA-GTGTACTT-TGTAAATG-TCTA
126 CTTAAAGTTTATATTTCATGTGTA-TTATATAAATGCT-TA
** * * * * * *
42662711 TTTTATTTTGGTTATTGAAATCATATACCTTTCACTATAACTAAACCT-CTATTTTATTATAAAT
1 TTTTGCTTTGGTTATAGGAATCATACACCCTTCACTATACCTAAATCTAC-ATTTTATTATAAAT
* * * * * * *
42662775 ACTTAATTTATTTTTGTTTTAATA-AGTAAAA-TAGTTTTCAAATTATATATATTTTA
65 GCTTATTTTGTTTTTATTTTAATACA-TAAAACGA-TTTTCGAATTATATATCTTTTA
42662831 CTATACTCGT
Statistics
Matches: 636, Mismatches: 108, Indels: 89
0.76 0.13 0.11
Matches are distributed among these distances:
159 2 0.00
160 56 0.09
161 24 0.04
162 1 0.00
163 87 0.14
164 261 0.41
165 30 0.05
166 2 0.00
167 39 0.06
173 1 0.00
174 2 0.00
175 7 0.01
176 32 0.05
177 6 0.01
178 1 0.00
179 21 0.03
180 63 0.10
181 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (164 bp):
TTTTGCTTTGGTTATAGGAATCATACACCCTTCACTATACCTAAATCTACATTTTATTATAAATG
CTTATTTTGTTTTTATTTTAATACATAAAACGATTTTCGAATTATATATCTTTTAACGTACTTAA
AGTTTATATTTCATGTGTATTATATAAATGCTTA
Found at i:42662458 original size:328 final size:329
Alignment explanation
Indices: 42661877--42662483 Score: 785
Period size: 328 Copynumber: 1.8 Consensus size: 329
42661867 TTTCATGGGT
* * * *
42661877 TTTTGCTTTGGTTATCGAAATCATACACCCTTCACTATACCTAAACCTCTACCTTTTGTTGTAAA
1 TTTTACTTTGGTTATCGAAATCATACACCCTTCACTATACCTAAA-CTCTACATTTTATTATAAA
** * * * * *
42661942 CGCTTATTTTATTTTTGTTTTAATATGTAAAACGGTTTTCCAATTATATATCTTTTAACGTTACT
65 CGCTTATTTTATTTTTGTTTTAATACATAAAACGGATTTCAAATTATACATCTTTGAACGATACT
* * * *
42662007 TAAAGTTTATATTTCATGGGTATTATATAAGTGTTTATTTTGCTTTAGTTATAGGAATCGTACAC
130 TAAAGTTTATATTTCATGGGTATTATATAAATGCTTATTTTGCTTTAGCTATAGGAATCATACAC
* * * * * *
42662072 CTTTCACTACACTTAAATCTACATTTTATTTTATATGCTTTTTTTTTTTTACTTTAATACA-TAA
195 CCTTCACTACACCTAAACCTACATTTTATTATAAATGCTTTTTTGTTTTTACTTTAATA-AGTAA
42662136 AACGATTTTCGATTTATATACTTTTTAACAGTACTTAAATTTTATATTTCATTGTGTTGTATAAA
259 AACGATTTTCGATTTATATACTTTTTAACAGTACTTAAATTTTATATTTCATTGTGTTGTATAAA
42662201 TGCTTA
324 TGCTTA
* * * * *
42662207 TTTTACTTTGGTTATTGGAATCATACACCTTTCACTATACTTAAA-TCTGCATTTTATTATAGAA
1 TTTTACTTTGGTTATCGAAATCATACACCCTTCACTATACCTAAACTCTACATTTTATTATA-AA
* ** * *
42662271 -GCTTATTTTGTTTTTGTTTTAATACATAAATTGGATTTCAAATTATACATCTTTGAGCGATCCT
65 CGCTTATTTTATTTTTGTTTTAATACATAAAACGGATTTCAAATTATACATCTTTGAACGATACT
* * *
42662335 TAATGTTTATATTT-ATGTGTATTATATAAATGCTTATTTTGCTTTGGCTATCA-GAATCATACA
130 TAAAGTTTATATTTCATGGGTATTATATAAATGCTTATTTTGCTTTAGCTAT-AGGAATCATACA
* *
42662398 CCCTTCACTATACCTAAACCT-CTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGT
194 CCCTTCACTACACCTAAACCTAC-ATTTTATTATAAATGCTT-TTTTGTTTTTACTTTAATAAGT
*
42662462 AAAACGGTTTTCGATTTATATA
257 AAAACGATTTTCGATTTATATA
42662484 ATATATATAT
Statistics
Matches: 235, Mismatches: 37, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
326 1 0.00
327 75 0.32
328 117 0.50
329 2 0.01
330 40 0.17
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (329 bp):
TTTTACTTTGGTTATCGAAATCATACACCCTTCACTATACCTAAACTCTACATTTTATTATAAAC
GCTTATTTTATTTTTGTTTTAATACATAAAACGGATTTCAAATTATACATCTTTGAACGATACTT
AAAGTTTATATTTCATGGGTATTATATAAATGCTTATTTTGCTTTAGCTATAGGAATCATACACC
CTTCACTACACCTAAACCTACATTTTATTATAAATGCTTTTTTGTTTTTACTTTAATAAGTAAAA
CGATTTTCGATTTATATACTTTTTAACAGTACTTAAATTTTATATTTCATTGTGTTGTATAAATG
CTTA
Found at i:42662735 original size:340 final size:340
Alignment explanation
Indices: 42662167--42662823 Score: 781
Period size: 340 Copynumber: 1.9 Consensus size: 340
42662157 TTTTTAACAG
* * * * * ** * *
42662167 TACTTAAATTTTATATTTCATTGTGTTGTATAAATGCTTATTTTACTTTGGTTATTGGAATCATA
1 TACTTAAAGTCTATATTTCATGGTGATATATAAAAACTTATTTTACTTTGGTTATCGGAAACATA
* * *
42662232 CACCTTTCACTATACTTAAATCTGCATTTTATTATAGAAGCTTATTTTGTTTTTGTTTTAATACA
66 CACCTTTCACTATACCTAAACCTGCATTTTATTAT---AGCTTATTTTCTTTTTGTTTTAATACA
* * * *
42662297 TAAATTGGATTTCAAATTATACATCTTTGAGCGATCCTTAATGTTTATATTTATGTGTATTATAT
128 TAAATAGGATTTCAAATTATACATCTTTGAACGATACTTAAAGTTTATATTTATGTGTATTATAT
* *
42662362 AAATGCTTATTTTGCTTTGGCTATCAGAATCATACACCCTTCACTATACCTAAACCTCTATTTTA
193 AAATGCTTATTTTACTTTGGCTATCAGAATCATACACCCTTCACTATAACTAAACCTCTATTTTA
* * * * * *
42662427 TTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAAAACGGTTTTCGATTTATATAATATATAT
258 TTATAAATACTTAATTTATTTTTATTTTAATAAGTAAAACAGTTTTCAAATTATATAATATATAT
42662492 ATATATATACATTAACGA
323 ATATATATACATTAACGA
*
42662510 TACTTAAAGTCTATATTTCATGGGTGATATATAAAAACTTATTTTACTTTTGTTATCGGAAACAT
1 TACTTAAAGTCTATATTTCAT-GGTGATATATAAAAACTTATTTTACTTTGGTTATCGGAAACAT
* * *
42662575 ACACTTTTTATTATACCTAAACCT-CTATTTTATTAT-GCTTATTTTACTTTTTG-TTTAATA-A
65 ACACCTTTCACTATACCTAAACCTGC-ATTTTATTATAGCTTATTTT-CTTTTTGTTTTAATACA
* * * * * *
42662636 GTAAATAGGTTTTCAAATTATATATTTTTTAACTATATTTAAAGTTTATATTT-TAGTGTACTT-
128 -TAAATAGGATTTCAAATTATACATCTTTGAACGATACTTAAAGTTTATATTTAT-GTGTA-TTA
* * * * * *
42662699 TGTAAATG-TCTATTTTATTTTGGTTAT-TGAAATCATATACCTTTCACTATAACTAAACCTCTA
190 TATAAATGCT-TATTTTACTTTGGCTATCAG-AATCATACACCCTTCACTATAACTAAACCTCTA
* *
42662762 TTTTATTATAAATACTTAATTTATTTTTGTTTTAATAAGTAAAATAGTTTTCAAATTATATA
253 TTTTATTATAAATACTTAATTTATTTTTATTTTAATAAGTAAAACAGTTTTCAAATTATATA
42662824 TATTTTACTA
Statistics
Matches: 264, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
339 4 0.02
340 168 0.64
341 8 0.03
343 20 0.08
344 64 0.24
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (340 bp):
TACTTAAAGTCTATATTTCATGGTGATATATAAAAACTTATTTTACTTTGGTTATCGGAAACATA
CACCTTTCACTATACCTAAACCTGCATTTTATTATAGCTTATTTTCTTTTTGTTTTAATACATAA
ATAGGATTTCAAATTATACATCTTTGAACGATACTTAAAGTTTATATTTATGTGTATTATATAAA
TGCTTATTTTACTTTGGCTATCAGAATCATACACCCTTCACTATAACTAAACCTCTATTTTATTA
TAAATACTTAATTTATTTTTATTTTAATAAGTAAAACAGTTTTCAAATTATATAATATATATATA
TATATACATTAACGA
Found at i:42662816 original size:504 final size:491
Alignment explanation
Indices: 42661877--42662821 Score: 1058
Period size: 504 Copynumber: 1.9 Consensus size: 491
42661867 TTTCATGGGT
* * *
42661877 TTTTGCTTTGGTTATCGAAATCATACACCCTTCACTATACCTAAACCTCTACCTTTTGTTGTAAA
1 TTTTGCTTTGGCTATCGAAATCATACACCCTTCACTATACCTAAACCTCTA-CTTTTATTATAAA
* * * * *
42661942 CGCTTATTTTATTTTTGTTTTAATATGTAAAACGGTTTTCCAATTATATATCTTTTAACGTTACT
65 CGCTTATTTTATTTTTATTTTAATAAGTAAAACGGTTTTCAAATTATATATATTTTAACGATACT
* **** * * *
42662007 TAAAGTTTATATTTCATGGGTATTATATAAGTGTTTATTTTGCTTTAGTTATAGGAATCGTACAC
130 TAAAGTCTATATTTCATGGGTATTATATAAAAACTTATTTTACTTTAGTTATAGGAAACATACAC
* * *
42662072 CTTTCACTACACTTAAATCTACATTTTATTTTATATGCTTTTTTTTTTTTACTTTAATACATAAA
195 CTTTCACTACACCTAAACCTACATTTTA--TTATATGCTTTTTTCTTTTTACTTTAATACATAAA
* * * * *
42662137 ACGATTTTCGATTTATATACTTTTTAACAGTACTTAAATTTTATATTTCATTGTGTTGTATAAAT
258 ACGATTTTCAAATTATATACTTTTTAACAGTACTTAAAGTTTATATTTCAGTGTCTTGTATAAAT
* *
42662202 GCTTATTTTACTTTGGTTATTGGAATCATACACCTTTCACTATACTTAAATCTGCATTTTATTAT
323 GCTTATTTTACTTTGGTTATTGAAATCATACACCTTTCACTATACTTAAACCTGCATTTTATTAT
* * * * *
42662267 AGAAGCTTATTTTGTTTTTGTTTTAATACATAAATTGGATTTCAAATTATACATCTTTGAGCGAT
388 AGAAACTTAATTTATTTTTGTTTTAATACATAAAATAGATTTCAAATTATACATCTTTGAGCGAT
42662332 CCTTAATGTTTATATTTATGTGTATTATATAAATGCTTA
453 CCTTAATGTTTATATTTATGTGTATTATATAAATGCTTA
42662371 TTTTGCTTTGGCTATC-AGAATCATACACCCTTCACTATACCTAAACCTCTA-TTTTATTATAAA
1 TTTTGCTTTGGCTATCGA-AATCATACACCCTTCACTATACCTAAACCTCTACTTTTATTATAAA
* *
42662434 TGCTTATTTTGTTTTTATTTTAATAAGTAAAACGGTTTTCGATTTATATAATATATATATATATA
65 CGCTTATTTTATTTTTATTTTAATAAGTAAAACGGTTTTC---------AA-AT-TATATATAT-
*
42662499 TACATTAACGATACTTAAAGTCTATATTTCATGGGTGA-TATATAAAAACTTATTTTACTTTTGT
118 T---TTAACGATACTTAAAGTCTATATTTCATGGGT-ATTATATAAAAACTTATTTTACTTTAGT
* * * * *
42662563 TATCGGAAACATACACTTTTTATTATACCTAAACCT-CTATTTTA-T-TATGCTTATTTTACTTT
179 TATAGGAAACATACACCTTTCACTACACCTAAACCTAC-ATTTTATTATATGCTT-TTTT-CTTT
* * * *
42662625 TT-GTTTAATA-AGTAAATA-GGTTTTCAAATTATATATTTTTTAACTA-TATTTAAAGTTTATA
241 TTACTTTAATACA-TAAA-ACGATTTTCAAATTATATACTTTTTAAC-AGTACTTAAAGTTTATA
* * * *
42662686 TTTTAGTGTACTT-TGTAAATG-TCTATTTTATTTTGGTTATTGAAATCATATACCTTTCACTAT
303 TTTCAGTGT-CTTGTATAAATGCT-TATTTTACTTTGGTTATTGAAATCATACACCTTTCACTAT
*
42662749 AAC-TAAACCT-CTATTTTATTATA-AATACTTAATTTATTTTTGTTTTAATA-AGTAAAATAGT
366 -ACTTAAACCTGC-ATTTTATTATAGAA-ACTTAATTTATTTTTGTTTTAATACA-TAAAATAGA
42662810 TTTCAAATTATA
427 TTTCAAATTATA
42662822 TATATTTTAC
Statistics
Matches: 374, Mismatches: 48, Indels: 48
0.80 0.10 0.10
Matches are distributed among these distances:
492 46 0.12
493 1 0.00
494 48 0.13
501 1 0.00
502 2 0.01
503 21 0.06
504 159 0.43
505 11 0.03
506 1 0.00
507 83 0.22
508 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (491 bp):
TTTTGCTTTGGCTATCGAAATCATACACCCTTCACTATACCTAAACCTCTACTTTTATTATAAAC
GCTTATTTTATTTTTATTTTAATAAGTAAAACGGTTTTCAAATTATATATATTTTAACGATACTT
AAAGTCTATATTTCATGGGTATTATATAAAAACTTATTTTACTTTAGTTATAGGAAACATACACC
TTTCACTACACCTAAACCTACATTTTATTATATGCTTTTTTCTTTTTACTTTAATACATAAAACG
ATTTTCAAATTATATACTTTTTAACAGTACTTAAAGTTTATATTTCAGTGTCTTGTATAAATGCT
TATTTTACTTTGGTTATTGAAATCATACACCTTTCACTATACTTAAACCTGCATTTTATTATAGA
AACTTAATTTATTTTTGTTTTAATACATAAAATAGATTTCAAATTATACATCTTTGAGCGATCCT
TAATGTTTATATTTATGTGTATTATATAAATGCTTA
Found at i:42663933 original size:2 final size:2
Alignment explanation
Indices: 42663926--42663960 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42663916 CATACAGGTA
42663926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42663961 GATTTAGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42666129 original size:113 final size:113
Alignment explanation
Indices: 42665922--42666151 Score: 424
Period size: 113 Copynumber: 2.0 Consensus size: 113
42665912 ATCTTCTTCC
42665922 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAAC
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAAC
*
42665987 CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCATTATGTTT
66 CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCATTAAGTTT
*
42666035 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGTTTGAATCTTTAAAACCCATTAAC
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAAC
* *
42666100 CAAAAGATTCAATATCTTTTGTTCTAATATCTTCTTCCCATTAAGTTT
66 CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCATTAAGTTT
42666148 CTTT
1 CTTT
42666152 GAGTTAATGG
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.42
Consensus pattern (113 bp):
CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAAC
CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCATTAAGTTT
Found at i:42666472 original size:21 final size:21
Alignment explanation
Indices: 42666448--42666490 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
42666438 ACATAAGTGA
42666448 CTAA-AACGTAACATTTCAAAC
1 CTAAGAAC-TAACATTTCAAAC
*
42666469 CTAAGTGACTAACATTTCAAAC
1 CTAAG-AACTAACATTTCAAAC
42666491 ATGTGGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (21 bp):
CTAAGAACTAACATTTCAAAC
Found at i:42666873 original size:29 final size:30
Alignment explanation
Indices: 42666818--42666879 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
42666808 AAATTTTCAA
**
42666818 AAAAAATGATAAAAAATATTTTTAAAAAAT
1 AAAAAATGATAAAAAATATTTAGAAAAAAT
* * *
42666848 AAAAAAT-ATTAAAATTATTTAGAAAAGAT
1 AAAAAATGATAAAAAATATTTAGAAAAAAT
42666877 AAA
1 AAA
42666880 TTTATAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (30 bp):
AAAAAATGATAAAAAATATTTAGAAAAAAT
Found at i:42672332 original size:24 final size:24
Alignment explanation
Indices: 42672300--42672347 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42672290 AATTTAGTAG
42672300 ATCTTTTTACTAAGGTATTCCTAA
1 ATCTTTTTACTAAGGTATTCCTAA
42672324 ATCTTTTTACTAAGGTATTCCTAA
1 ATCTTTTTACTAAGGTATTCCTAA
42672348 CTTCAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (24 bp):
ATCTTTTTACTAAGGTATTCCTAA
Found at i:42673252 original size:26 final size:26
Alignment explanation
Indices: 42673201--42673253 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
42673191 TAAAACATTT
* *
42673201 TATATATTTATAACTAAATTAAAAAA
1 TATATATTTAAAACTAAATGAAAAAA
*
42673227 TATATATTTAAAATTAAATGAGAAAAA
1 TATATATTTAAAACTAAATGA-AAAAA
42673254 AAGTCTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (26 bp):
TATATATTTAAAACTAAATGAAAAAA
Found at i:42676384 original size:91 final size:91
Alignment explanation
Indices: 42676229--42676401 Score: 294
Period size: 91 Copynumber: 1.9 Consensus size: 91
42676219 TGTCCTTTAT
*
42676229 AAAATTGTTGCTAAGGCAATTGGCAATAGATTTTGGAAGTGGTTGGATAGATGTATTGATAAATC
1 AAAATTGTTGCTAAGGCAATTGGCAATAGATTTTGGAAGTAGTTGGATAGATGTATTGATAAATC
42676294 CCAGAGTGCTTTTGTCCTAGGGGAGA
66 CCAGAGTGCTTTTGTCCTAGGGGAGA
*
42676320 AAAATTGTTGCTAAGGC-ATTTGCTAATAGATTTTGGAAGTAGTTGGATAGATGTATTGATAAAT
1 AAAATTGTTGCTAAGGCAATTGGC-AATAGATTTTGGAAGTAGTTGGATAGATGTATTGATAAAT
* *
42676384 CCTAGAGTGTTTTTGTCC
65 CCCAGAGTGCTTTTGTCC
42676402 CAAGGAGGCT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 5 0.06
91 72 0.94
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (91 bp):
AAAATTGTTGCTAAGGCAATTGGCAATAGATTTTGGAAGTAGTTGGATAGATGTATTGATAAATC
CCAGAGTGCTTTTGTCCTAGGGGAGA
Found at i:42688757 original size:139 final size:139
Alignment explanation
Indices: 42688585--42688946 Score: 478
Period size: 138 Copynumber: 2.6 Consensus size: 139
42688575 TAAATCTTTT
* * * * * * *
42688585 TTTTCTTATAGATACTTATTTTATTTTTGTTTTAATACTTAAATTGGCTTTCAAAGTATATATCT
1 TTTTATTATAAATACTTACTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAACTATACATCT
42688650 TTTAACGATACTTAAAGTTTATAATTTGCTTTGATTATCGAAATCATACA-CTATTCACTATACC
66 TTTAACGATACTTAAAGTTTATAATTTGCTTTGATTATCGAAATCATACACCT-TTCACTATACC
42688714 TAAACCTCTA
130 TAAACCTCTA
* * * *
42688724 TTTTATTATAAATGCTTACTTTGTTTTTATTTTAATACCTAAATTGACTTTCAAATTATACATCT
1 TTTTATTATAAATACTTACTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAACTATACATCT
* ** * *
42688789 TTTAACGATAC-TGAAGGGTATAATTTGCTTTGATTATTGAAATCATGCACCTTTCACTATACCT
66 TTTAACGATACTTAAAGTTTATAATTTGCTTTGATTATCGAAATCATACACCTTTCACTATACCT
*
42688853 AAACCTTTA
131 AAACCTCTA
* *
42688862 TTTTATTATAAATACTTACTTTGTTTTTGTTTTAATACCTAATTTGG-TATTCAAACTATAGATC
1 TTTTATTATAAATACTTACTTTGTTTTTGTTTTAATACCTAAATTGGCT-TTCAAACTATACATC
* * * *
42688926 TTCTAATGATGCTTACAGTTT
65 TTTTAACGATACTTAAAGTTT
42688947 GTATTTTATG
Statistics
Matches: 191, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
137 1 0.01
138 118 0.62
139 72 0.38
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (139 bp):
TTTTATTATAAATACTTACTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAACTATACATCT
TTTAACGATACTTAAAGTTTATAATTTGCTTTGATTATCGAAATCATACACCTTTCACTATACCT
AAACCTCTA
Found at i:42689673 original size:167 final size:164
Alignment explanation
Indices: 42689292--42689846 Score: 607
Period size: 167 Copynumber: 3.3 Consensus size: 164
42689282 TCGTGGGTGT
* * * * ** * *
42689292 TGTTTTCAAACTATACATCTTCTAATGGTGCTTAAAGTTTATATTTTATGAGTGTAATATAAATG
1 TGTTTTCAAATTATACATCTTTTAATGATACTTAAAGTTTATATTTCGTGGGTGTTATATAAATG
* * * *
42689357 CTTATTTTGTTTTGGTGATCGAAATCATATACCTTTCACTATACCAAAAACTATATATTTTTTTA
66 CTTATTTTGATTTGGTTATCGAAATCATACACCTTTCACTATA-CTAAAACTATATA-TTTTTT-
*
42689422 ATAAATGCTTATATTGCTTTTGTTTTACTAAGTAAAAC
128 ATAAATGCTTATATTTCTTTTGTTTTACT-AGTAAAAC
* * *
42689460 GGTTTTCAAATTATATATCTTTCAACT-ATACTTAAAGTTTATATTTCGTGGGTGTTATATAAAT
1 TGTTTTCAAATTATACATCTTTTAA-TGATACTTAAAGTTTATATTTCGTGGGTGTTATATAAAT
* *
42689524 GCTTATTTTGCTTTGGTTATCGAAATCATACACCTTTCACTATATCTAAACCTATATAATTTTTT
65 GCTTATTTTGATTTGGTTATCGAAATCATACACCTTTCACTATA-CTAAAACTATAT-ATTTTTT
42689589 ATAAATGCTTATATTTCTTTTGTTTTACTCAGTAAAAC
128 ATAAATGCTTATATTTCTTTTGTTTTACT-AGTAAAAC
* *
42689627 TGTTTTCAAATTATATATCTTTTAATGATACTTTAAGTTTATATTTCGTGGGTGTTATATAAATG
1 TGTTTTCAAATTATACATCTTTTAATGATACTTAAAGTTTATATTTCGTGGGTGTTATATAAATG
* * * * * * ** *
42689692 TTTTTTTTTAGTTGATTATC-AGAATCATACACCTTTCACTATACTTAAATCTGCAT-TTTATTA
66 CTTATTTTGATTTGGTTATCGA-AATCATACACCTTTCACTATAC-TAAAACTATATATTTTTTA
** * * * *
42689755 TTGATGCTTAT-TTTTTTTTGTTTTAATACCT-AAAT
129 TAAATGCTTATATTTCTTTTGTTTTACTA-GTAAAAC
* * * * *
42689790 TGACTTTCAAATTATACATCTTTTAATGATGCTTATAGTTTATATGTCGTAGGTGTT
1 TG-TTTTCAAATTATACATCTTTTAATGATACTTAAAGTTTATATTTCGTGGGTGTT
42689847 GTTTTCAAAC
Statistics
Matches: 335, Mismatches: 45, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
163 6 0.02
164 62 0.19
165 15 0.04
166 3 0.01
167 139 0.41
168 108 0.32
169 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.48
Consensus pattern (164 bp):
TGTTTTCAAATTATACATCTTTTAATGATACTTAAAGTTTATATTTCGTGGGTGTTATATAAATG
CTTATTTTGATTTGGTTATCGAAATCATACACCTTTCACTATACTAAAACTATATATTTTTTATA
AATGCTTATATTTCTTTTGTTTTACTAGTAAAAC
Found at i:42690334 original size:387 final size:386
Alignment explanation
Indices: 42689490--42690991 Score: 2186
Period size: 387 Copynumber: 3.9 Consensus size: 386
42689480 TTCAACTATA
** ** *
42689490 CTTAAAGTTTATATTTCGTGGGTGTTATATAAATGCTTATTTTGCTTTGGTTATCGAAATCATAC
1 CTTAAAGTTTATATTTTATGAATGTTATATAAATGCTTATTTTGCTTTGATTATCGAAATCATAC
* * *
42689555 ACCTTTCACTATATCTAAACCTATATAATTTTTTATAAATGCTTATATTTCTTTTGTTTTACTCA
66 ACCTTTCACTATACCTAAACCTATATAA-TTTTTATAAATGCTTATATTGCTTTTGTTTTACTAA
* * * *
42689620 GTAAAACTGTTTTCAAATTATATATCTTTTAATGATACTTTAAGTTTATATTTCGTGGGTGTTAT
130 GTAAAACGGTTTTCGAATTATATATCTTTTAATAATACTTAAAGTTTATATTTCGTGGGTGTTAT
* * * * * *
42689685 ATAAATGTTTTTTTTTAGTTGATTATCAGAATCATACACCTTTCACTATACTTAAATCTGCATTT
195 ATAAATGCTTATTTTGATTTGGTTATCAGAATCATACACCTTTCACTATACTTAAATCTACATTT
* *
42689750 TATTATTGATGCTTATTTT-TTTTTGTTTTAATACCTAAATTGACTTTCAAATTATACATCTTTT
260 TATTATAGATGCTTATTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAATTATACATCTTTT
** * * *
42689814 AATGATGCTTATAGTTTATATGTCGTAGGTGTTGTTTTCAAACTCTACATCTTCTAACGGTG
325 AACAATGCTTAAAGTTTATATGTCGTGGGTGTTGTTTTCAAACTATACATCTTCTAACGGTG
* * * * *
42689876 CTTAACGTTTATATTTTATGAATGTTATATAAATGCTTAGTTTGCTTTGGTTATTGAAATCATAA
1 CTTAAAGTTTATATTTTATGAATGTTATATAAATGCTTATTTTGCTTTGATTATCGAAATCATAC
* * * * * *
42689941 ACCTTTCGCGATACCTAAACCTATTTACACTTTTATAAATGCTTATACTGCTTTTGTTTTAGTAA
66 ACCTTTCACTATACCTAAACCTATATA-ATTTTTATAAATGCTTATATTGCTTTTGTTTTACTAA
* * *
42690006 GTAAAACGGTTTTCGAATTATATATCTTTTAACAATACTTAAAGTTTATATTCCGTGGCTGTTAT
130 GTAAAACGGTTTTCGAATTATATATCTTTTAATAATACTTAAAGTTTATATTTCGTGGGTGTTAT
*
42690071 ATTAATGCTTATTTTGATTTGGTTATCAGAATCATACACCTTTCACTATACTTAAATCTACATTT
195 ATAAATGCTTATTTTGATTTGGTTATCAGAATCATACACCTTTCACTATACTTAAATCTACATTT
** * * * * *
42690136 TATTATTTATGTTTATTTTATTTTTGTTTTAATACTTAAATTGGCTTTCAAATTATTCAACTTTT
260 TATTATAGATGCTTATTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAATTATACATCTTTT
* * *
42690201 AACGATGATTAAAGTTTATATGTCGTGGGTGTTGCTTTCAAACTATACATCTTCTAACGGTG
325 AACAATGCTTAAAGTTTATATGTCGTGGGTGTTGTTTTCAAACTATACATCTTCTAACGGTG
* * *
42690263 CTTAATGTTTATATTTTATGAATGTTATATAAATGCTTATTTTGCTTTGATTATCTAAATCATAT
1 CTTAAAGTTTATATTTTATGAATGTTATATAAATGCTTATTTTGCTTTGATTATCGAAATCATAC
* *
42690328 ACCTTTCACTATACCTAAACTTATATATATTTTTATAAATGATTATATTGCTTTTGTTTTACTAA
66 ACCTTTCACTATACCTAAACCTATATA-ATTTTTATAAATGCTTATATTGCTTTTGTTTTACTAA
* * *
42690393 GTAAAATGATTTTCGAATTATATATCTTTTAATAATACTTAAAGTTTATATTTCATGGGTGTTAT
130 GTAAAACGGTTTTCGAATTATATATCTTTTAATAATACTTAAAGTTTATATTTCGTGGGTGTTAT
* * ** * *
42690458 ATAAATACTTATTTTGATTTCGTTATTGGAATCATACACCTTTCACAATACTTAAATCTATATTT
195 ATAAATGCTTATTTTGATTTGGTTATCAGAATCATACACCTTTCACTATACTTAAATCTACATTT
* *
42690523 TATTATAGATGCTTATTTTGTTTTTG-TTTAATACCTAAATTAGCTTTCAAATTATATATCTTTT
260 TATTATAGATGCTTATTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAATTATACATCTTTT
*
42690587 AACAATGCTTAAAGTTTATATGTTGTGGGTGTTGTTTTCAAACTATACAT-TTCT-ACGGTG
325 AACAATGCTTAAAGTTTATATGTCGTGGGTGTTGTTTTCAAACTATACATCTTCTAACGGTG
*
42690647 CTTAAAGTTTATATTTTATGAGTGTTATATAAATGCTTATTTTGCTTT-AGTTATCGAAATCATA
1 CTTAAAGTTTATATTTTATGAATGTTATATAAATGCTTATTTTGCTTTGA-TTATCGAAATCATA
* **
42690711 CACCTGTCACTATACCTAAACCTATATTTTTTTTATAAATGCTTATATTGCTTTTGTTTTACTAA
65 CACCTTTCACTATACCTAAACCTATATAATTTTTATAAATGCTTATATTGCTTTTGTTTTACTAA
* *
42690776 GTAAAACGGTTTTCGAATTGTATATCTTTTAATGATACTTAAAGTTTATATTTCGTGGGTGTTAT
130 GTAAAACGGTTTTCGAATTATATATCTTTTAATAATACTTAAAGTTTATATTTCGTGGGTGTTAT
* * * * **
42690841 ATAAATTCTTATTTTGATTTGGTTATCAAAATCATACACCTTTCGCTATACTTAAATTTGTATTT
195 ATAAATGCTTATTTTGATTTGGTTATCAGAATCATACACCTTTCACTATACTTAAATCTACATTT
* * *
42690906 TATTATAGATACTTATTTTGTTTTTGTTTTAATACCTAAATTGGTTTTCAAATTATACATTTTTT
260 TATTATAGATGCTTATTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAATTATACATCTTTT
*
42690971 AACAATGCTTAAAATTTATAT
325 AACAATGCTTAAAGTTTATAT
42690992 TTTATGAGTG
Statistics
Matches: 999, Mismatches: 113, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
383 177 0.18
384 143 0.14
385 4 0.00
386 323 0.32
387 352 0.35
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (386 bp):
CTTAAAGTTTATATTTTATGAATGTTATATAAATGCTTATTTTGCTTTGATTATCGAAATCATAC
ACCTTTCACTATACCTAAACCTATATAATTTTTATAAATGCTTATATTGCTTTTGTTTTACTAAG
TAAAACGGTTTTCGAATTATATATCTTTTAATAATACTTAAAGTTTATATTTCGTGGGTGTTATA
TAAATGCTTATTTTGATTTGGTTATCAGAATCATACACCTTTCACTATACTTAAATCTACATTTT
ATTATAGATGCTTATTTTGTTTTTGTTTTAATACCTAAATTGGCTTTCAAATTATACATCTTTTA
ACAATGCTTAAAGTTTATATGTCGTGGGTGTTGTTTTCAAACTATACATCTTCTAACGGTG
Found at i:42690597 original size:773 final size:770
Alignment explanation
Indices: 42689512--42690991 Score: 2225
Period size: 773 Copynumber: 1.9 Consensus size: 770
42689502 ATTTCGTGGG
* *
42689512 TGTTATATAAATGCTTATTTTGCTTTGGTTATCGAAATCATACACCTTTCACTATATCTAAACCT
1 TGTTATATAAATGCTTATTTTGCTTTGATTATCGAAATCATACACCTTTCACTATACCTAAACCT
* * *
42689577 ATATAATTTTTTATAAATGCTTATATTTCTTTTGTTTTACTCAGTAAAACTGTTTTCAAATTATA
66 ATATAATTTTTTATAAATGATTATATTGCTTTTGTTTTACTAAGTAAAACTGTTTTCAAATTATA
* * * ** * *
42689642 TATCTTTTAATGATACTTTAAGTTTATATTTCGTGGGTGTTATATAAATGTTTTTTTTTAGTTGA
131 TATCTTTTAATAATACTTAAAGTTTATATTTCATGGGTGTTATATAAATACTTATTTTGAGTTGA
* * *
42689707 TTATCAGAATCATACACCTTTCACTATACTTAAATCTGCATTTTATTATTGATGCTTATTTTTTT
196 TTATCAGAATCATACACCTTTCACAATACTTAAATCTACATTTTATTATAGATGCTTATTTTTTT
** *
42689772 TTGTTTTAATACCTAAATTGACTTTCAAATTATACATCTTTTAATGATGCTTATAGTTTATATGT
261 TTGTTTTAATACCTAAATTGACTTTCAAATTATACATCTTTTAACAATGCTTAAAGTTTATATGT
* *
42689837 CGTAGGTGTTGTTTTCAAACTCTACATCTTCTAACGGTGCTTAACGTTTATATTTTATGAATGTT
326 CGTAGGTGTTGTTTTCAAACTATACAT-TTCT-ACGGTGCTTAAAGTTTATATTTTATGAATGTT
* * * *
42689902 ATATAAATGCTTAGTTTGCTTTGGTTATTGAAATCATAAACCTTTCGCGATACCTAAACCTAT-T
389 ATATAAATGCTTAGTTTGCTTTAGTTATCGAAATCATAAACCTGTCACGATACCTAAACCTATAT
*
42689966 TACACTTTTATAAATGCTTATACTGCTTTTGTTTTAGTAAGTAAAACGGTTTTCGAATTATATAT
454 T--ACTTTTATAAATGCTTATACTGCTTTTGTTTTACTAAGTAAAACGGTTTTCGAATTATATAT
*
42690031 CTTTTAACAATACTTAAAGTTTATATTCCGTGGCTGTTATATTAATGCTTATTTTGATTTGGTTA
517 CTTTTAACAATACTTAAAGTTTATATTCCGTGGCTGTTATATAAATGCTTATTTTGATTTGGTTA
* ** **
42690096 TCAGAATCATACACCTTTCACTATACTTAAATCTACATTTTATTATTTATGTTTATTTTATTTTT
582 TCAAAATCATACACCTTTCACTATACTTAAATCTACATTTTATTATAGATACTTATTTTATTTTT
* * * *
42690161 GTTTTAATACTTAAATTGGCTTTCAAATTATTCAACTTTTAACGATGATTAAAGTTTATATGTCG
647 GTTTTAATACCTAAATTGGCTTTCAAATTATACAACTTTTAACAATGATTAAAATTTATATGTCG
42690226 TGGGTGTTGCTTTCAAACTATACATCTTCTAACGGTGCTTAATGTTTATATTTTATGAA
712 TGGGTGTTGCTTTCAAACTATACATCTTCTAACGGTGCTTAATGTTTATATTTTATGAA
* * *
42690285 TGTTATATAAATGCTTATTTTGCTTTGATTATCTAAATCATATACCTTTCACTATACCTAAACTT
1 TGTTATATAAATGCTTATTTTGCTTTGATTATCGAAATCATACACCTTTCACTATACCTAAACCT
*
42690350 ATAT-ATATTTTTATAAATGATTATATTGCTTTTGTTTTACTAAGTAAAA-TGATTTTCGAATTA
66 ATATAAT-TTTTTATAAATGATTATATTGCTTTTGTTTTACTAAGTAAAACTG-TTTTCAAATTA
*
42690413 TATATCTTTTAATAATACTTAAAGTTTATATTTCATGGGTGTTATATAAATACTTATTTTGATTT
129 TATATCTTTTAATAATACTTAAAGTTTATATTTCATGGGTGTTATATAAATACTTATTTTGAGTT
** *
42690478 CG-TTATTGGAATCATACACCTTTCACAATACTTAAATCTATATTTTATTATAGATGCTTATTTT
194 -GATTATCAGAATCATACACCTTTCACAATACTTAAATCTACATTTTATTATAGATGCTTATTTT
*
42690542 GTTTTTG-TTTAATACCTAAATT-AGCTTTCAAATTATATATCTTTTAACAATGCTTAAAGTTTA
258 -TTTTTGTTTTAATACCTAAATTGA-CTTTCAAATTATACATCTTTTAACAATGCTTAAAGTTTA
* * *
42690605 TATGTTGTGGGTGTTGTTTTCAAACTATACATTTCTACGGTGCTTAAAGTTTATATTTTATGAGT
321 TATGTCGTAGGTGTTGTTTTCAAACTATACATTTCTACGGTGCTTAAAGTTTATATTTTATGAAT
* * *
42690670 GTTATATAAATGCTTATTTTGCTTTAGTTATCGAAATCATACACCTGTCACTATACCTAAACCTA
386 GTTATATAAATGCTTAGTTTGCTTTAGTTATCGAAATCATAAACCTGTCACGATACCTAAACCTA
** * *
42690735 TATTTTTTTTATAAATGCTTATATTGCTTTTGTTTTACTAAGTAAAACGGTTTTCGAATTGTATA
451 TATTACTTTTATAAATGCTTATACTGCTTTTGTTTTACTAAGTAAAACGGTTTTCGAATTATATA
** * * *
42690800 TCTTTTAATGATACTTAAAGTTTATATTTCGTGGGTGTTATATAAATTCTTATTTTGATTTGGTT
516 TCTTTTAACAATACTTAAAGTTTATATTCCGTGGCTGTTATATAAATGCTTATTTTGATTTGGTT
* * ** *
42690865 ATCAAAATCATACACCTTTCGCTATACTTAAATTTGTATTTTATTATAGATACTTATTTTGTTTT
581 ATCAAAATCATACACCTTTCACTATACTTAAATCTACATTTTATTATAGATACTTATTTTATTTT
* ** *
42690930 TGTTTTAATACCTAAATTGGTTTTCAAATTATACATTTTTTAACAATGCTTAAAATTTATAT
646 TGTTTTAATACCTAAATTGGCTTTCAAATTATACAACTTTTAACAATGATTAAAATTTATAT
42690992 TTTATGAGTG
Statistics
Matches: 633, Mismatches: 68, Indels: 15
0.88 0.09 0.02
Matches are distributed among these distances:
770 224 0.35
771 86 0.14
772 11 0.02
773 305 0.48
774 7 0.01
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.48
Consensus pattern (770 bp):
TGTTATATAAATGCTTATTTTGCTTTGATTATCGAAATCATACACCTTTCACTATACCTAAACCT
ATATAATTTTTTATAAATGATTATATTGCTTTTGTTTTACTAAGTAAAACTGTTTTCAAATTATA
TATCTTTTAATAATACTTAAAGTTTATATTTCATGGGTGTTATATAAATACTTATTTTGAGTTGA
TTATCAGAATCATACACCTTTCACAATACTTAAATCTACATTTTATTATAGATGCTTATTTTTTT
TTGTTTTAATACCTAAATTGACTTTCAAATTATACATCTTTTAACAATGCTTAAAGTTTATATGT
CGTAGGTGTTGTTTTCAAACTATACATTTCTACGGTGCTTAAAGTTTATATTTTATGAATGTTAT
ATAAATGCTTAGTTTGCTTTAGTTATCGAAATCATAAACCTGTCACGATACCTAAACCTATATTA
CTTTTATAAATGCTTATACTGCTTTTGTTTTACTAAGTAAAACGGTTTTCGAATTATATATCTTT
TAACAATACTTAAAGTTTATATTCCGTGGCTGTTATATAAATGCTTATTTTGATTTGGTTATCAA
AATCATACACCTTTCACTATACTTAAATCTACATTTTATTATAGATACTTATTTTATTTTTGTTT
TAATACCTAAATTGGCTTTCAAATTATACAACTTTTAACAATGATTAAAATTTATATGTCGTGGG
TGTTGCTTTCAAACTATACATCTTCTAACGGTGCTTAATGTTTATATTTTATGAA
Found at i:42690618 original size:164 final size:165
Alignment explanation
Indices: 42690233--42690619 Score: 408
Period size: 167 Copynumber: 2.3 Consensus size: 165
42690223 TCGTGGGTGT
* * * ** * ** *
42690233 TGCTTTCAAACTATACATCTTCTAACGGTGCTTAATGTTTATATTTTATGAATGTTATATAAATG
1 TGCTTTCAAATTATATATCTTTTAACAATGCTTAAAGTTTATA-TTTATGGGTGTTATATAAATA
* * * *
42690298 CTTATTTTGCTTTGATTATCTAAATCATATACCTTTCACTATACCTAAACTTATATATATTTTTA
65 CTTATTTTGATTTGATTATCTAAATCATACACCTTTCACAATACCTAAACTTATATATATTATTA
* *
42690363 TAAATGATTATATTGCTTTTGTTTTACTAAGTAAAA
130 TAAATGATTATATTGCTTTTGTTTTAATAACTAAAA
* * * *
42690399 TGATTTTCGAATTATATATCTTTTAATAATACTTAAAGTTTATATTTCATGGGTGTTATATAAAT
1 TG-CTTTCAAATTATATATCTTTTAACAATGCTTAAAGTTTATATTT-ATGGGTGTTATATAAAT
* *
42690464 ACTTATTTTGATTTCG-TTAT-TGGAATCATACACCTTTCACAATACTTAAA-TCTATAT-T-TT
64 ACTTATTTTGATTT-GATTATCT-AAATCATACACCTTTCACAATACCTAAACT-TATATATATT
* * * * * *
42690524 ATTATAGATGCTTATTTTGTTTTTG-TTTAATACCTAAAT
126 ATTATAAATGATTATATTGCTTTTGTTTTAATAACTAAAA
*
42690563 TAGCTTTCAAATTATATATCTTTTAACAATGCTTAAAGTTTATATGTTGTGGGTGTT
1 T-GCTTTCAAATTATATATCTTTTAACAATGCTTAAAGTTTATAT-TTATGGGTGTT
42690620 GTTTTCAAAC
Statistics
Matches: 182, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
164 57 0.31
165 25 0.14
166 8 0.04
167 91 0.50
168 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (165 bp):
TGCTTTCAAATTATATATCTTTTAACAATGCTTAAAGTTTATATTTATGGGTGTTATATAAATAC
TTATTTTGATTTGATTATCTAAATCATACACCTTTCACAATACCTAAACTTATATATATTATTAT
AAATGATTATATTGCTTTTGTTTTAATAACTAAAA
Found at i:42691007 original size:165 final size:166
Alignment explanation
Indices: 42690620--42691020 Score: 466
Period size: 165 Copynumber: 2.4 Consensus size: 166
42690610 TGTGGGTGTT
* * * *
42690620 GTTTTCAAACTATACA-TTTCT-ACGGTGCTTAAAGTTTATATTTTATGAGTGTTATATAAATGC
1 GTTTTCAAATTATACATTTTTTAACGATGCTTAAAGTTTATATTTTATGAGTGTTATATAAATAC
* * *
42690683 TTATTTTGCTTTAGTTATCGAAATCATACACCTGTCACTATACCTAAACCTATATTTTTTTTATA
66 TTATTTTGATTTAGTTATCAAAATCATACACCTGTCACTATACCTAAACCTATATTTTTATTATA
* * *
42690748 AATGCTTATATTGCTTTTGTTTTACTAAGTAAAACG
131 AATACTTATATTGCTTTTGTTTTAATAACTAAAACG
* * * * * * ** * *
42690784 GTTTTCGAATTGTATATCTTTTAATGATACTTAAAGTTTATATTTCGTGGGTGTTATATAAATTC
1 GTTTTCAAATTATACATTTTTTAACGATGCTTAAAGTTTATATTTTATGAGTGTTATATAAATAC
* * * * ** *
42690849 TTATTTTGATTTGGTTATCAAAATCATACACCTTTCGCTATACTTAAATTTGTA-TTTTATTATA
66 TTATTTTGATTTAGTTATCAAAATCATACACCTGTCACTATACCTAAACCTATATTTTTATTATA
* * * * **
42690913 GATACTTATTTTGTTTTTGTTTTAATACCTAAATTG
131 AATACTTATATTGCTTTTGTTTTAATAACTAAAACG
* *
42690949 GTTTTCAAATTATACATTTTTTAACAATGCTTAAAATTTATATTTTATGAGTGTTATATAAATAC
1 GTTTTCAAATTATACATTTTTTAACGATGCTTAAAGTTTATATTTTATGAGTGTTATATAAATAC
42691014 TTATTTT
66 TTATTTT
42691021 TCACTATACC
Statistics
Matches: 191, Mismatches: 44, Indels: 3
0.80 0.18 0.01
Matches are distributed among these distances:
164 12 0.06
165 99 0.52
166 80 0.42
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (166 bp):
GTTTTCAAATTATACATTTTTTAACGATGCTTAAAGTTTATATTTTATGAGTGTTATATAAATAC
TTATTTTGATTTAGTTATCAAAATCATACACCTGTCACTATACCTAAACCTATATTTTTATTATA
AATACTTATATTGCTTTTGTTTTAATAACTAAAACG
Found at i:42692170 original size:24 final size:24
Alignment explanation
Indices: 42692138--42692185 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42692128 CATACTCCAG
42692138 TTTGAAAGTTAGTTTTAATGGGAT
1 TTTGAAAGTTAGTTTTAATGGGAT
42692162 TTTGAAAGTTAGTTTTAATGGGAT
1 TTTGAAAGTTAGTTTTAATGGGAT
42692186 AATGGCGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (24 bp):
TTTGAAAGTTAGTTTTAATGGGAT
Found at i:42695883 original size:49 final size:48
Alignment explanation
Indices: 42695830--42696301 Score: 134
Period size: 49 Copynumber: 9.7 Consensus size: 48
42695820 ACTAAATTCG
*
42695830 CCGTTGCGACTGAAAATTTTCCCTTCATGTC-TCTGAGGTACAAGGTTCT
1 CCGTTGCGACT-AAAATTTTCCCTTCATGTCTTCT-AGGTACAAGGTTCA
* ** ** * * * *
42695879 CCGTTACGACTTAAACCTTTCCCTTTGTATCTTCTTGGTACTAGATTCA
1 CCGTTGCGAC-TAAAATTTTCCCTTCATGTCTTCTAGGTACAAGGTTCA
* * *
42695928 CCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTAAGGTACAAGGTTCG
1 CCGTTGCGACTAAAAT-TTTCCCTTCATGTCTTCT-AGGTACAAGGTTCA
* * * * * ** **
42695977 CCATTGCGACTTAAACTGTTCCCTCTGCATCT-TTGT-GGTA-TTGGATTTG
1 CCGTTGCGAC-TAAAATTTTCCCT-T-CATGTCTTCTAGGTACAAGG-TTCA
* *
42696026 CCGTTGCGGCTTAAATCTTTCCCTTCAT-T-TTCTGAGGTACAAGGTTCA
1 CCGTTGCGACTAAAAT-TTTCCCTTCATGTCTTCT-AGGTACAAGGTTCA
* * * ** * *
42696074 TCATTGCGGCTTAAACCTTTCCCTT--TGCATCTTCGT-GGTAC-TGGATTCG
1 CCGTTGCGAC-TAAAATTTTCCCTTCATG--TCTTC-TAGGTACAAGG-TTCA
* * * * * *
42696123 CTGTTGCTG-CTTAAATCCTTCCCTTCAT-T-TTTTGAGGTACCAGGTTCG
1 CCGTTGC-GACTAAAAT-TTTCCCTTCATGTCTTCT-AGGTACAAGGTTCA
* ** ** *
42696171 CCGTTGCGGCTTAAACCTTTCCCTTTGTATCTTCGT-GGTAC-AGGATTCA
1 CCGTTGCGAC-TAAAATTTTCCCTTCATGTCTTC-TAGGTACAAGG-TTCA
* * * *
42696220 CCGTTGTGGCTTAAATCTTTCCCTTCAT-T-TTCTGAGGTACAAGGTTCG
1 CCGTTGCGACTAAAAT-TTTCCCTTCATGTCTTCT-AGGTACAAGGTTCA
* * **
42696268 CTGTTGCGGCTTAAACCTTTCCCTTCATGTCTTC
1 CCGTTGCGAC-TAAAATTTTCCCTTCATGTCTTC
42696302 ATGGTAATGA
Statistics
Matches: 304, Mismatches: 79, Indels: 79
0.66 0.17 0.17
Matches are distributed among these distances:
46 7 0.02
47 9 0.03
48 101 0.33
49 160 0.53
50 18 0.06
51 9 0.03
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.39
Consensus pattern (48 bp):
CCGTTGCGACTAAAATTTTCCCTTCATGTCTTCTAGGTACAAGGTTCA
Found at i:42696103 original size:97 final size:96
Alignment explanation
Indices: 42695816--42696292 Score: 580
Period size: 97 Copynumber: 4.9 Consensus size: 96
42695806 CGTGTCTACA
** * * *
42695816 TGGTACTAAATTCGCCGTTGCGACTGAAAAT-TTTCCCTTCATGTCTCTGAGGTACAAGGTTCTC
1 TGGTACTGGATTCGCCGTTGCGGCT-TAAATCTTTCCCTTCAT-TTTCTGAGGTACAAGGTTC-C
* * * *
42695880 CGTTACGACTTAAACCTTTCCCTTTGTATCTTCT
63 CGTTGCGGCTTAAACCTTTCCCTTTGCATCTTCG
* * * *
42695914 TGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT-TTTCTGAGGTACAAGGTTC-CC
* * * *
42695979 ATTGCGACTTAAA-CTGTTCCCTCTGCATCTTTG
64 GTTGCGGCTTAAACCT-TTCCCTTTGCATCTTCG
* * * *
42696012 TGGTATTGGATTTGCCGTTGCGGCTTAAATCTTTCCCTTCATTTTCTGAGGTACAAGGTTCATCA
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTTTCTGAGGTACAAGGTTC-CCG
42696077 TTGCGGCTTAAACCTTTCCCTTTGCATCTTCG
65 TTGCGGCTTAAACCTTTCCCTTTGCATCTTCG
* * * * *
42696109 TGGTACTGGATTCGCTGTTGCTGCTTAAATCCTTCCCTTCATTTTTTGAGGTACCAGGTTCGCCG
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTTTCTGAGGTACAAGGTTC-CCG
*
42696174 TTGCGGCTTAAACCTTTCCCTTTGTATCTTCG
65 TTGCGGCTTAAACCTTTCCCTTTGCATCTTCG
* * * *
42696206 TGGTACAGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATTTTCTGAGGTACAAGGTTCGCTG
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTTTCTGAGGTACAAGGTTC-CCG
42696271 TTGCGGCTTAAACCTTTCCCTT
65 TTGCGGCTTAAACCTTTCCCTT
42696293 CATGTCTTCA
Statistics
Matches: 331, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
97 215 0.65
98 116 0.35
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (96 bp):
TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATTTTCTGAGGTACAAGGTTCCCGT
TGCGGCTTAAACCTTTCCCTTTGCATCTTCG
Found at i:42702234 original size:26 final size:26
Alignment explanation
Indices: 42702198--42702250 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
42702188 GGCGCGAAGA
42702198 TAATTATTACAAGGCAATCAAGCTTG
1 TAATTATTACAAGGCAATCAAGCTTG
42702224 TAATTATTACAAGGCAATCAAGCTTG
1 TAATTATTACAAGGCAATCAAGCTTG
42702250 T
1 T
42702251 TTGCCCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (26 bp):
TAATTATTACAAGGCAATCAAGCTTG
Found at i:42713211 original size:23 final size:24
Alignment explanation
Indices: 42713178--42713232 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
42713168 AACAATATCT
* * *
42713178 AAACAAAATTAAAAGTG-AAAGCA
1 AAACAACATTAAAAATGAAAAGAA
42713201 AAACAACATTAAAAATGACAAAGAA
1 AAACAACATTAAAAATGA-AAAGAA
42713226 AAACAAC
1 AAACAAC
42713233 CTGCAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 15 0.56
25 12 0.44
ACGTcount: A:0.67, C:0.13, G:0.09, T:0.11
Consensus pattern (24 bp):
AAACAACATTAAAAATGAAAAGAA
Found at i:42721418 original size:28 final size:28
Alignment explanation
Indices: 42721377--42721497 Score: 129
Period size: 28 Copynumber: 4.4 Consensus size: 28
42721367 TAAGACTGGT
* *
42721377 GAACTCACATATGGCGAACCCCGATGGC
1 GAACTCACCTATGGCGAACCCCTATGGC
* * **
42721405 AAACTCACCTATGGTGAACCATTATGGC
1 GAACTCACCTATGGCGAACCCCTATGGC
* *
42721433 GAACTCACCTATGGTGAA-CCCTATGGT
1 GAACTCACCTATGGCGAACCCCTATGGC
* * *
42721460 GAAGTCACCTATGGCGAACCCCTATTGT
1 GAACTCACCTATGGCGAACCCCTATGGC
42721488 GAACT-ACCTA
1 GAACTCACCTA
42721498 AATTCATTCT
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
27 27 0.35
28 51 0.65
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (28 bp):
GAACTCACCTATGGCGAACCCCTATGGC
Found at i:42721451 original size:15 final size:15
Alignment explanation
Indices: 42721373--42721497 Score: 90
Period size: 15 Copynumber: 9.0 Consensus size: 15
42721363 CTCCTAAGAC
*
42721373 TGGTGAACTCACATA
1 TGGTGAACTCACCTA
* *
42721388 TGGCGAAC-C-CCGA
1 TGGTGAACTCACCTA
**
42721401 TGGCAAACTCACCTA
1 TGGTGAACTCACCTA
*
42721416 TGGTGAAC-CA-TTA
1 TGGTGAACTCACCTA
*
42721429 TGGCGAACTCACCTA
1 TGGTGAACTCACCTA
42721444 TGGTGAA--C-CCTA
1 TGGTGAACTCACCTA
*
42721456 TGGTGAAGTCACCTA
1 TGGTGAACTCACCTA
*
42721471 TGGCGAAC-C-CCTA
1 TGGTGAACTCACCTA
*
42721484 TTGTGAACT-ACCTA
1 TGGTGAACTCACCTA
42721498 AATTCATTCT
Statistics
Matches: 86, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
12 11 0.13
13 29 0.34
14 12 0.14
15 34 0.40
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (15 bp):
TGGTGAACTCACCTA
Found at i:42721492 original size:55 final size:56
Alignment explanation
Indices: 42721373--42721497 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 56
42721363 CTCCTAAGAC
* * *
42721373 TGGTGAACTCACATATGGCGAACCCCGATGGCAAACTCACCTATGGTGAACCATTA
1 TGGTGAACTCACCTATGGCGAACCCCGATGGCAAACTCACCTATGGCGAACCACTA
* * * ** * *
42721429 TGGCGAACTCACCTATGGTGAA-CCCTATGGTGAAGTCACCTATGGCGAACCCCTA
1 TGGTGAACTCACCTATGGCGAACCCCGATGGCAAACTCACCTATGGCGAACCACTA
*
42721484 TTGTGAACT-ACCTA
1 TGGTGAACTCACCTA
42721498 AATTCATTCT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 5 0.09
55 33 0.58
56 19 0.33
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (56 bp):
TGGTGAACTCACCTATGGCGAACCCCGATGGCAAACTCACCTATGGCGAACCACTA
Found at i:42729955 original size:23 final size:23
Alignment explanation
Indices: 42729903--42729959 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
42729893 CCTATTTACT
42729903 TAATTTTAAACCCTTAAAACACC
1 TAATTTTAAACCCTTAAAACACC
*
42729926 TATTTTTAACACACC-TAAAACACC
1 TAATTTTAA-AC-CCTTAAAACACC
42729950 -AATTTTAAAC
1 TAATTTTAAAC
42729960 ATCTCCCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 2 0.07
23 15 0.50
24 11 0.37
25 2 0.07
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATTTTAAACCCTTAAAACACC
Found at i:42733954 original size:21 final size:21
Alignment explanation
Indices: 42733928--42733970 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42733918 ACACATTTTC
*
42733928 TTACTCATGATTCTTTTGTTT
1 TTACTCATGATTCTTTTCTTT
**
42733949 TTACTCATTTTTCTTTTCTTT
1 TTACTCATGATTCTTTTCTTT
42733970 T
1 T
42733971 GATTTTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (21 bp):
TTACTCATGATTCTTTTCTTT
Found at i:42733984 original size:26 final size:28
Alignment explanation
Indices: 42733938--42733993 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
42733928 TTACTCATGA
*
42733938 TTCTTTTGTTTTTACTCA-TT-TTTCTT
1 TTCTTTTGATTTTACTCATTTATTTCTT
*
42733964 TTCTTTTGATTTT-CTTTATTTATTTCTT
1 TTCTTTTGATTTTAC-TCATTTATTTCTT
42733992 TT
1 TT
42733994 TGGCTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 1 0.04
26 14 0.56
27 2 0.08
28 8 0.32
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (28 bp):
TTCTTTTGATTTTACTCATTTATTTCTT
Found at i:42736620 original size:16 final size:17
Alignment explanation
Indices: 42736599--42736638 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
42736589 CAATTAAAAT
*
42736599 TAATAAAATAA-ACAAG
1 TAATAAAATAATACAAA
42736615 TAATAAAATAATACAAA
1 TAATAAAATAATACAAA
42736632 TAATAAA
1 TAATAAA
42736639 GAACAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAATAAAATAATACAAA
Found at i:42740066 original size:13 final size:13
Alignment explanation
Indices: 42740050--42740074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42740040 TTGCTTTGCT
42740050 TTTTTATTTTTTG
1 TTTTTATTTTTTG
42740063 TTTTTATTTTTT
1 TTTTTATTTTTT
42740075 TTGTCGTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTG
Found at i:42755536 original size:59 final size:57
Alignment explanation
Indices: 42755437--42755717 Score: 209
Period size: 59 Copynumber: 4.8 Consensus size: 57
42755427 TTCGAGGTTT
* * *
42755437 AAAATAGAATTTTAGATA-TTC-AGGGGTGAAATGGTAATTTTGGAAAGAATCAGGGTCA
1 AAAATAGAATTTTTGAAAGTTCGA-GGGTAAAAT-GTAATTTTGGAAA-AATCAGGGTCA
* *
42755495 AAAATAGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAAT-TGAGGTC-
1 AAAATAGAATTTTTGAAAGTTCGAGGGTAAAAT-GTAA-TTTTGGAAAAATCAG-GGTCA
* *
42755553 -AAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGTAAATTTTAGAAAAATCAGGGTCA
1 AAAATAGAATTTTTGAAAGTTCGAGGGT-AAAATGT-AATTTTGGAAAAATCAGGGTCA
* * * * ** *
42755611 TAGATAGAA-ATTTGAAAAGTTTGAGGGTAAAAACATAATTTTTTGGAAAAAATCAAGGTCA
1 AAAATAGAATTTTTG-AAAGTTCGAGGGT-AAAATGTAA--TTTTGG-AAAAATCAGGGTCA
* * *
42755672 AAAAT-GAAATTTTAGCAATTTCGA-GGTACAAATGTAAATTTTGGAA
1 AAAATAG-AATTTTTGAAAGTTCGAGGGTA-AAATGT-AATTTTGGAA
42755718 GTATGGGGGT
Statistics
Matches: 180, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
57 42 0.23
58 32 0.18
59 54 0.30
60 23 0.13
61 26 0.14
62 3 0.02
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (57 bp):
AAAATAGAATTTTTGAAAGTTCGAGGGTAAAATGTAATTTTGGAAAAATCAGGGTCA
Found at i:42755578 original size:57 final size:58
Alignment explanation
Indices: 42755405--42755717 Score: 200
Period size: 59 Copynumber: 5.3 Consensus size: 58
42755395 CGCTCAAGGA
* * * * * *
42755405 TAAAATGGTAATTTT-TAGAAAGTTCGAGGTTTAAAATAGAATTTTAGATA-TTC-AGGGG
1 TAAAATGGTAATTTTGGA-AAAATTC-AGGGTCAAAATAGAATTTTTGAAAGTTCGA-GGG
* *
42755463 TGAAATGGTAATTTTGGAAAGAA-TCAGGGTCAAAAATAGAATTTTTGGAAGTTCGAGGG
1 TAAAATGGTAATTTTGGAAA-AATTCAGGGTC-AAAATAGAATTTTTGAAAGTTCGAGGG
* *
42755522 TAAAATGGTAATTTTTGGAAAAATTGA-GGTC-AAATGGAATTTTTGAAAGTTCGAGGG
1 TAAAATGGTAA-TTTTGGAAAAATTCAGGGTCAAAATAGAATTTTTGAAAGTTCGAGGG
* * * *
42755579 TAAAAAT-GTAAATTTTAGAAAAA-TCAGGGTCATAGATAGAA-ATTTGAAAAGTTTGAGGG
1 T-AAAATGGT-AATTTTGGAAAAATTCAGGGTCA-AAATAGAATTTTTG-AAAGTTCGAGGG
*** * * * * *
42755638 TAAAAACATAATTTTTTGGAAAAAATCAAGGTCAAAA-ATGAAATTTTAGCAATTTCGA-GG
1 TAAAATGGTAA--TTTTGGAAAAATTCAGGGTCAAAATA-G-AATTTTTGAAAGTTCGAGGG
42755698 TACAAAT-GTAAATTTTGGAA
1 TA-AAATGGT-AATTTTGGAA
42755718 GTATGGGGGT
Statistics
Matches: 203, Mismatches: 30, Indels: 43
0.74 0.11 0.16
Matches are distributed among these distances:
56 2 0.01
57 45 0.22
58 50 0.25
59 52 0.26
60 30 0.15
61 21 0.10
62 3 0.01
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (58 bp):
TAAAATGGTAATTTTGGAAAAATTCAGGGTCAAAATAGAATTTTTGAAAGTTCGAGGG
Found at i:42755586 original size:29 final size:29
Alignment explanation
Indices: 42755377--42755583 Score: 133
Period size: 29 Copynumber: 7.1 Consensus size: 29
42755367 ACCTAGGGGC
*** * * *
42755377 AAAATGGTAATTTTTGGTCGCTCAAGGAT
1 AAAATGGTAATTTTTGAAAGTTCGAGGGT
*
42755406 AAAATGGTAATTTTTAGAAAGTTCGAGGTTT
1 AAAATGGTAATTTTT-GAAAGTTCGAGG-GT
* * *
42755437 AAAATAG-AATTTTAGATA-TTC-AGGGGT
1 AAAATGGTAATTTTTGAAAGTTCGA-GGGT
* * *
42755464 GAAATGGTAATTTTGGAAAGAATC-AGGGT
1 AAAATGGTAATTTTTGAAAG-TTCGAGGGT
* *
42755493 CAAAAATAG-AATTTTTGGAAGTTCGAGGGT
1 --AAAATGGTAATTTTTGAAAGTTCGAGGGT
*
42755523 AAAATGGTAATTTTTGGAAAAATT-GA-GGT
1 AAAATGGTAATTTTT-G-AAAGTTCGAGGGT
*
42755552 CAAATGG-AATTTTTGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGAAAGTTCGAGGGT
42755580 AAAA
1 AAAA
42755584 ATGTAAATTT
Statistics
Matches: 138, Mismatches: 26, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
26 5 0.04
27 10 0.07
28 33 0.24
29 40 0.29
30 34 0.25
31 16 0.12
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTTGAAAGTTCGAGGGT
Found at i:42757526 original size:17 final size:17
Alignment explanation
Indices: 42757503--42757595 Score: 116
Period size: 17 Copynumber: 5.4 Consensus size: 17
42757493 ACATTTATTC
*
42757503 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
42757520 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* * *
42757538 ATTTAAACTCAAATTAA
1 ATTTAAATTTAAAATAA
42757555 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
42757572 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
42757589 ATTTAAA
1 ATTTAAA
42757596 ATGGGTTTGG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
16 3 0.05
17 46 0.72
18 15 0.23
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:42757560 original size:6 final size:6
Alignment explanation
Indices: 42757503--42757595 Score: 56
Period size: 6 Copynumber: 16.2 Consensus size: 6
42757493 ACATTTATTC
* * * *
42757503 ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTCAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* *
42757550 A-TTAA ATTTAA ATTTAA A-ATAA ATTT-A ATCTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
42757595 A
1 A
42757596 ATGGGTTTGG
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
4 1 0.02
5 20 0.30
6 38 0.58
7 7 0.11
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:42757562 original size:11 final size:12
Alignment explanation
Indices: 42757522--42757584 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 12
42757512 TATAATAATT
42757522 TTAAATTTGAAA-
1 TTAAATTT-AAAC
*
42757534 ATAAATTTAAAC
1 TTAAATTTAAAC
* *
42757546 TCAAA-TTAAAT
1 TTAAATTTAAAC
42757557 TTAAATTTAAA-
1 TTAAATTTAAAC
* *
42757568 ATAAATTTAATC
1 TTAAATTTAAAC
42757580 TTAAA
1 TTAAA
42757585 ATAAATTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 21 0.52
12 19 0.47
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (12 bp):
TTAAATTTAAAC
Found at i:42757597 original size:11 final size:11
Alignment explanation
Indices: 42757523--42757577 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
42757513 ATAATAATTT
42757523 TAAATTTGAAAA
1 TAAATTT-AAAA
*
42757535 TAAATTTAAAC
1 TAAATTTAAAA
*
42757546 TCAAA-TTAAATT
1 T-AAATTTAAA-A
42757558 TAAATTTAAAA
1 TAAATTTAAAA
42757569 TAAATTTAA
1 TAAATTTAA
42757578 TCTTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 21 0.57
12 16 0.43
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:42758056 original size:39 final size:39
Alignment explanation
Indices: 42758002--42758154 Score: 141
Period size: 39 Copynumber: 3.9 Consensus size: 39
42757992 TCTGCCTCAG
* *
42758002 GCTCGGGGTAGGAGATTGGTTGATGGTGATCTTCCCCAA
1 GCTCGGGGTAAGAGATTGGTTGATGATGATCTTCCCCAA
* ** * * **
42758041 GCTCGGGGTAAGAGATCGAATGACT-ATAATCTACCCCTG
1 GCTCGGGGTAAGAGATTGGTTGA-TGATGATCTTCCCCAA
* *
42758080 GCTCGGGGTAAGAGACTGGTTGACGATGAT-TTACCCCTAA
1 GCTCGGGGTAAGAGATTGGTTGATGATGATCTT-CCCC-AA
* *
42758120 -CTCGGGGTAAGAGGTTGGTTGATGATGATTTTCCC
1 GCTCGGGGTAAGAGATTGGTTGATGATGATCTTCCC
42758155 ATCAAATGGC
Statistics
Matches: 88, Mismatches: 21, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
38 1 0.01
39 84 0.95
40 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.27
Consensus pattern (39 bp):
GCTCGGGGTAAGAGATTGGTTGATGATGATCTTCCCCAA
Found at i:42758683 original size:48 final size:47
Alignment explanation
Indices: 42758631--42758732 Score: 114
Period size: 48 Copynumber: 2.1 Consensus size: 47
42758621 ACAAGGTTCA
*
42758631 CCGTTGCAACTTAAACCTCTCCCTTATGTCTTCGTGATACTGGATCCG
1 CCGTTGCAACTTAAACCTCTCCCTTATGTCTTCGCG-TACTGGATCCG
*** * * * * *
42758679 CCGTTGCGGTTTAGATCTTTCCCTTGTGTCTTCGCGTACTGGATCTG
1 CCGTTGCAACTTAAACCTCTCCCTTATGTCTTCGCGTACTGGATCCG
42758726 CCGTTGC
1 CCGTTGC
42758733 GGTCTTATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 17 0.38
48 28 0.62
ACGTcount: A:0.13, C:0.29, G:0.22, T:0.36
Consensus pattern (47 bp):
CCGTTGCAACTTAAACCTCTCCCTTATGTCTTCGCGTACTGGATCCG
Found at i:42758769 original size:97 final size:98
Alignment explanation
Indices: 42758668--42758898 Score: 320
Period size: 98 Copynumber: 2.4 Consensus size: 98
42758658 GTCTTCGTGA
* *
42758668 TACTGGATCCGCCGTTGCGGTTTAGATCTTTCCCTTGTGTCTTCG-CGTACTGGATCTGCCGTTG
1 TACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTCGTACTGGATCTGCCATTG
* * *
42758732 CGGTCTTATATCTTTCCCGTCATGTTTTTATGG
66 CAGTCTTAGATCTTTCCCATCATGTTTTTATGG
* *** *
42758765 TACTGGATCCGTCGTCATGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATCTGCCATTG
1 TACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTCGTACTGGATCTGCCATTG
* * *
42758830 CAGTCTTAGATCTTTCTCATCGTGTTTTTGTGG
66 CAGTCTTAGATCTTTCCCATCATGTTTTTATGG
* *
42758863 TACTGGATCTGCCGTTGCGACTTAGATCTTTCCCTT
1 TACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTT
42758899 CATGTCCTGA
Statistics
Matches: 114, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
97 40 0.35
98 74 0.65
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.41
Consensus pattern (98 bp):
TACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTCGTACTGGATCTGCCATTG
CAGTCTTAGATCTTTCCCATCATGTTTTTATGG
Found at i:42758870 original size:50 final size:49
Alignment explanation
Indices: 42758668--42758895 Score: 205
Period size: 49 Copynumber: 4.7 Consensus size: 49
42758658 GTCTTCGTGA
* * * * * * *
42758668 TACTGGATCCGCCGTTGCGGT-TTAGATCTTTCCCTTGTGTCTTCG-CG
1 TACTGGATCTGCCGTTGCAGTCTTAGATCTTTCCATCGTGTTTTTGTGG
* * * * *
42758715 TACTGGATCTGCCGTTGCGGTCTTATATCTTTCCCGTCATGTTTTTATGG
1 TACTGGATCTGCCGTTGCAGTCTTAGATCTTT-CCATCGTGTTTTTGTGG
* * * * * * *
42758765 TACTGGATCCGTCG-T-CATGGCTTAGATCTTTCCCTTGTGTCTTCGTGG
1 TACTGGATCTGCCGTTGCA-GTCTTAGATCTTTCCATCGTGTTTTTGTGG
*
42758813 TACTGGATCTGCCATTGCAGTCTTAGATCTTTCTCATCGTGTTTTTGTGG
1 TACTGGATCTGCCGTTGCAGTCTTAGATCTTTC-CATCGTGTTTTTGTGG
*
42758863 TACTGGATCTGCCGTTGC-GACTTAGATCTTTCC
1 TACTGGATCTGCCGTTGCAGTCTTAGATCTTTCC
42758896 CTTCATGTCC
Statistics
Matches: 144, Mismatches: 30, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
47 20 0.14
48 33 0.23
49 47 0.33
50 44 0.31
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.41
Consensus pattern (49 bp):
TACTGGATCTGCCGTTGCAGTCTTAGATCTTTCCATCGTGTTTTTGTGG
Found at i:42758925 original size:98 final size:94
Alignment explanation
Indices: 42758668--42758966 Score: 298
Period size: 98 Copynumber: 3.1 Consensus size: 94
42758658 GTCTTCGTGA
* * *
42758668 TACTGGATCCGCCGTTGCGGTTTAGATCTTTCCCTTGTGTCTTCGCGTACTGGATCTGCCGTTGC
1 TACTGGATCCGCCGTTGC-GCTTAGATCTTTCCCTTGTGTCTTCGGGTACTGGATCTGCCATTGC
* * * *
42758733 GGTCTTATATCTTTCCCGTCATGTTTTTATGG
65 -GTCTTAAATCTTT-CCATCGTGTTTTTGTGG
*
42758765 TACTGGATCCGTCGTCATG-GCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATCTGCCATT
1 TACTGGATCCGCCGT--TGCGCTTAGATCTTTCCCTTGTGTCTTCG-GGTACTGGATCTGCCATT
*
42758829 GCAGTCTTAGATCTTTCTCATCGTGTTTTTGTGG
63 GC-GTCTTAAATCTTTC-CATCGTGTTTTTGTGG
* * * * *
42758863 TACTGGATCTGCCGTTGCGACTTAGATCTTTCCCTTCATGTCCT-GAGGTGCTAGGTTC-GCCAT
1 TACTGGATCCGCCGTTGCG-CTTAGATCTTTCCCTT-GTGTCTTCG-GGTACT-GGATCTGCCAT
* * * * *
42758926 TGCGACTTAAACCTTTCCCTTGTGTCTTTGTGG
62 TGCGTCTTAAATCTTTCCATCGTGTTTTTGTGG
42758959 TACTGGAT
1 TACTGGAT
42758967 TCACCAATGC
Statistics
Matches: 172, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
96 23 0.13
97 52 0.30
98 86 0.50
99 11 0.06
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.40
Consensus pattern (94 bp):
TACTGGATCCGCCGTTGCGCTTAGATCTTTCCCTTGTGTCTTCGGGTACTGGATCTGCCATTGCG
TCTTAAATCTTTCCATCGTGTTTTTGTGG
Found at i:42759032 original size:49 final size:48
Alignment explanation
Indices: 42758877--42759032 Score: 129
Period size: 48 Copynumber: 3.2 Consensus size: 48
42758867 GGATCTGCCG
* * * *
42758877 TTGCGACTTAGATCTTTCCCTTCATG-TCCTGAGGTGCTAGGTTCGCCA
1 TTGCGACTTAAATCTTT-CCTTTATGCTTCTGAGGTACTAGGTTCGCCA
* * * * *
42758925 TTGCGACTTAAACCTTTCCCTTGTGTCTT-TGTGGTACT-GGATTCACCA
1 TTGCGACTTAAATCTTTCCTTTATG-CTTCTGAGGTACTAGG-TTCGCCA
* * * * *
42758973 ATGCGGCTTAAATCTTTCCTTTTATGCTTCTGGGGTACTAAGTTCGCCG
1 TTGCGACTTAAATCTTTCC-TTTATGCTTCTGAGGTACTAGGTTCGCCA
42759022 TTGCGACTTAA
1 TTGCGACTTAA
42759033 TCCTTCCCCT
Statistics
Matches: 82, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
47 7 0.09
48 47 0.57
49 27 0.33
50 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (48 bp):
TTGCGACTTAAATCTTTCCTTTATGCTTCTGAGGTACTAGGTTCGCCA
Found at i:42759040 original size:96 final size:98
Alignment explanation
Indices: 42758851--42759094 Score: 280
Period size: 98 Copynumber: 2.5 Consensus size: 98
42758841 CTTTCTCATC
* * * * *
42758851 GTGTTTTTGTGGTACTGGA-TCTGCCGTTGCGACTTAGATCTTTCCCTTCATGTCCTGAGGTGCT
1 GTGTCTTTGTGGTACTGGATTC-ACCGATGCGGCTTAGATCTTTCCCTTCATGTCCTGAGGTACT
*
42758915 AGGTTCGCCATTGCGACTTAAACCTTT-CCC-TT
65 AAGTTCGCCATTGCGACTTAAACCTTTCCCCTTT
* * * * * *
42758947 GTGTCTTTGTGGTACTGGATTCACCAATGCGGCTTAAATCTTTCCTTTTATGCTTCTGGGGTACT
1 GTGTCTTTGTGGTACTGGATTCACCGATGCGGCTTAGATCTTTCCCTTCATG-TCCTGAGGTACT
* *
42759012 AAGTTCGCCGTTGCGACTTAATCC-TTCCCCTTT
65 AAGTTCGCCATTGCGACTTAAACCTTTCCCCTTT
* * * *
42759045 GTGTCTTCGTGGTACTGGATCCCCCGATGCGGCTTAGATTTTTCCCTTCA
1 GTGTCTTTGTGGTACTGGATTCACCGATGCGGCTTAGATCTTTCCCTTCA
42759095 CTTCATGTCT
Statistics
Matches: 122, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
96 43 0.35
97 35 0.29
98 44 0.36
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (98 bp):
GTGTCTTTGTGGTACTGGATTCACCGATGCGGCTTAGATCTTTCCCTTCATGTCCTGAGGTACTA
AGTTCGCCATTGCGACTTAAACCTTTCCCCTTT
Found at i:42759059 original size:49 final size:48
Alignment explanation
Indices: 42758527--42759060 Score: 202
Period size: 49 Copynumber: 11.0 Consensus size: 48
42758517 TAAGGTACCG
* * * **
42758527 GGTTTGCCATTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACT-
1 GGTTCGCCATTGCGACTT-AATCTTTCCCTTTATGTCTTCGTGGTACTA
* * * * * *
42758575 GGATTCGCCATTGCGGCTAAAATCTTTCCCTTTATGTCTTTGAGTTACAA
1 GG-TTCGCCATTGCGACT-TAATCTTTCCCTTTATGTCTTCGTGGTACTA
* * * * * *
42758625 GGTTCACCGTTGCAACTTAAACCTCTCCC-TTATGTCTTCGTGATACT-
1 GGTTCGCCATTGCGACTT-AATCTTTCCCTTTATGTCTTCGTGGTACTA
* * ** * *
42758672 GGATCCGCCGTTGCGGTTTAGATCTTTCCC-TTGTGTCTTCG-CGTACT-
1 GG-TTCGCCATTGCGACTTA-ATCTTTCCCTTTATGTCTTCGTGGTACTA
* * * * * * **
42758719 GGATCTGCCGTTGCGGTCTTATATCTTTCCCGTCATGTTTTTATGGTACT-
1 GGTTC-GCCATTGC-GACTTA-ATCTTTCCCTTTATGTCTTCGTGGTACTA
* *
42758769 GGATCCGTCGTCA-TG-G-CTTAGATCTTTCCC-TTGTGTCTTCGTGGTACT-
1 GG-T---TCGCCATTGCGACTTA-ATCTTTCCCTTTATGTCTTCGTGGTACTA
* * * * ** * *
42758817 GGATCTGCCATTGCAGTCTTAGATCTTTCTCATCGTGTTTTTGTGGTACT-
1 GGTTC-GCCATTGC-GACTTA-ATCTTTCCCTTTATGTCTTCGTGGTACTA
* * * * * *
42758867 GGATCTGCCGTTGCGACTTAGATCTTTCCCTTCATGTCCT-GAGGTGCTA
1 GGTTC-GCCATTGCGACTTA-ATCTTTCCCTTTATGTCTTCGTGGTACTA
* * *
42758916 GGTTCGCCATTGCGACTTAAACCTTTCCC-TTGTGTCTTTGTGGTACT-
1 GGTTCGCCATTGCGACTT-AATCTTTCCCTTTATGTCTTCGTGGTACTA
* * * * *
42758963 GGATTCACCAATGCGGCTTAAATCTTTCCTTTTATG-CTTCTGGGGTACTA
1 GG-TTCGCCATTGCGACTT-AATCTTTCCCTTTATGTCTTC-GTGGTACTA
* * * *
42759013 AGTTCGCCGTTGCGACTTAATCCTTCCCCTTTGTGTCTTCGTGGTACT
1 GGTTCGCCATTGCGACTTAAT-CTTTCCCTTTATGTCTTCGTGGTACT
42759061 GGATCCCCCG
Statistics
Matches: 365, Mismatches: 92, Indels: 57
0.71 0.18 0.11
Matches are distributed among these distances:
44 2 0.01
45 3 0.01
46 3 0.01
47 25 0.07
48 133 0.36
49 150 0.41
50 43 0.12
52 2 0.01
53 2 0.01
54 2 0.01
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (48 bp):
GGTTCGCCATTGCGACTTAATCTTTCCCTTTATGTCTTCGTGGTACTA
Found at i:42760350 original size:22 final size:21
Alignment explanation
Indices: 42760320--42760397 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 21
42760310 CAGCTCGACC
*
42760320 TCTCCTTTTCTTTTTCTTTATT
1 TCTCTTTTTCTTTTTCTTT-TT
* *
42760342 TCTCTTTTTTTTTTTTTTTTT
1 TCTCTTTTTCTTTTTCTTTTT
* *
42760363 TCTTTTTTTCCTTCTTCTTTTT
1 TCTCTTTTT-CTTTTTCTTTTT
42760385 TCT-TTTTTCTTTT
1 TCTCTTTTTCTTTT
42760398 ATTCATTGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 4 0.09
21 15 0.32
22 28 0.60
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (21 bp):
TCTCTTTTTCTTTTTCTTTTT
Found at i:42760387 original size:7 final size:7
Alignment explanation
Indices: 42760325--42760397 Score: 78
Period size: 7 Copynumber: 10.3 Consensus size: 7
42760315 CGACCTCTCC
42760325 TTTTC-T
1 TTTTCTT
42760331 TTTTCTT
1 TTTTCTT
42760338 TATTTCTCT
1 T-TTTCT-T
42760347 TTTT-TT
1 TTTTCTT
*
42760353 TTTTTTT
1 TTTTCTT
42760360 TTTTCTTT
1 TTTTC-TT
*
42760368 TTTTCCT
1 TTTTCTT
*
42760375 TCTTCTT
1 TTTTCTT
42760382 TTTTCTT
1 TTTTCTT
42760389 TTTTCTT
1 TTTTCTT
42760396 TT
1 TT
42760398 ATTCATTGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
6 10 0.18
7 30 0.53
8 15 0.26
9 2 0.04
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:42760397 original size:29 final size:29
Alignment explanation
Indices: 42760325--42760397 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
42760315 CGACCTCTCC
* *
42760325 TTTTC-TTTTTCTTTATTTCTCTTTTTTT
1 TTTTCTTTTTTCTTTTTTTCTCTTTTCTT
*
42760353 TTTTTTTTTTTCTTTTTTTC-CTTCTTCTT
1 TTTTCTTTTTTCTTTTTTTCTCTT-TTCTT
42760382 TTTTCTTTTTTCTTTT
1 TTTTCTTTTTTCTTTT
42760398 ATTCATTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 7 0.18
29 32 0.82
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (29 bp):
TTTTCTTTTTTCTTTTTTTCTCTTTTCTT
Found at i:42765928 original size:30 final size:29
Alignment explanation
Indices: 42765878--42766204 Score: 222
Period size: 29 Copynumber: 11.0 Consensus size: 29
42765868 TTTTGGTCGC
* *
42765878 TCGAGGGT-AAAATGGTAATTTTGAGAAAGG
1 TCGAGGTTAAAAATGG-AATTTTG-GAAAGT
* *
42765908 TCGAGGTTTAAAATGGAATTTTTAGG-CA-T
1 TCGAGGTTAAAAATGGAA-TTTT-GGAAAGT
* * * *
42765937 TCGAGGGT-AAAATAGTAATTTTGAAAAAGAA
1 TCGAGGTTAAAAAT-GGAATTTTG-GAAAG-T
* *
42765968 TC-AGGGTCAAAAATAGAATTTTTGG-AAGT
1 TCGA-GGTTAAAAATGGAA-TTTTGGAAAGT
* *
42765997 TTGAGGGT-AAAATGGTAATTTTTGGAAAAGT
1 TCGAGGTTAAAAATGG-AA-TTTTGG-AAAGT
*
42766028 T-GGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGAGGTTAAAAATGGAATTTTGGAAAGT
* * *
42766056 TCGAGGGTAAAAATGTAAATTTTAGAAAAG-
1 TCGAGGTTAAAAATG-GAATTTT-GGAAAGT
* *
42766086 TAGAGGTCAAAAATGGAATTTTGGAAAGT
1 TCGAGGTTAAAAATGGAATTTTGGAAAGT
* **
42766115 TCGAGGGTAAAAATGGAATTTTTGGAAAAA
1 TCGAGGTTAAAAATGGAA-TTTTGGAAAGT
42766145 TCGAGGTTAAAAATGGAATTTTGGAAAGT
1 TCGAGGTTAAAAATGGAATTTTGGAAAGT
* * * *
42766174 TCAAGGGTACAAATGTAAATTTTGGAAAGT
1 TCGAGGTTAAAAATG-GAATTTTGGAAAGT
42766204 T
1 T
42766205 TGGGGATCAA
Statistics
Matches: 234, Mismatches: 41, Indels: 44
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.00
28 26 0.11
29 82 0.35
30 79 0.34
31 35 0.15
32 11 0.05
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (29 bp):
TCGAGGTTAAAAATGGAATTTTGGAAAGT
Found at i:42765928 original size:59 final size:59
Alignment explanation
Indices: 42765857--42766201 Score: 320
Period size: 59 Copynumber: 5.8 Consensus size: 59
42765847 ACCCGAGGGC
** * * *
42765857 AAAATGGTAATTTTTGGTCGCTCGAGGGTAAAATGGTAATTTTGAGAAAGGTCGAGGTTT
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAAAGTCGAGGTTA
* * *
42765917 AAAATGGAATTTTTAGGCA-TTCGAGGGTAAAATAGTAATTTTGA-AAAAGAATC-AGGGTCA
1 AAAATGGAATTTTT-GGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAAAG--TCGA-GGTTA
* * * *
42765977 AAAATAGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTG-GAAAAGTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAA-TTTTGAGAAAAGTCGAGGTTA
* *
42766036 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAAT-GTAAATTTT-AGAAAAGTAGAGGTCA
1 AAAATGGAATTTTTGG-AAGTTCGAGGGT-AAAATGGT-AATTTTGAGAAAAGTCGAGGTTA
*
42766095 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAATGG-AATTTTTG-GAAAAATCGAGGTTA
1 AAAATGGAATTTTTGG-AAGTTCGAGGGT-AAAATGGTAA-TTTTGAGAAAAGTCGAGGTTA
*
42766154 AAAATGGAA-TTTTGGAAAGTTCAAGGGTACAAAT-GTAAATTTTG-GAAA
1 AAAATGGAATTTTTGG-AAGTTCGAGGGTA-AAATGGT-AATTTTGAGAAA
42766202 GTTTGGGGAT
Statistics
Matches: 244, Mismatches: 23, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
58 14 0.06
59 166 0.68
60 54 0.22
61 10 0.04
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.30
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAAAGTCGAGGTTA
Found at i:42765956 original size:29 final size:29
Alignment explanation
Indices: 42765850--42765958 Score: 96
Period size: 29 Copynumber: 3.7 Consensus size: 29
42765840 TTTGGATACC
* *
42765850 CGAGGGCAAAATGGTAATTTTT-GGTCGCT
1 CGAGGGTAAAATGGTAATTTTTAGG-CACT
* ** *
42765879 CGAGGGTAAAATGGTAATTTTGAGAAAGGT
1 CGAGGGTAAAATGGTAATTTTTAGGCA-CT
* *
42765909 CGAGGTTTAAAATGG-AATTTTTAGGCATT
1 CGAGG-GTAAAATGGTAATTTTTAGGCACT
*
42765938 CGAGGGTAAAATAGTAATTTT
1 CGAGGGTAAAATGGTAATTTT
42765959 GAAAAAGAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
28 7 0.11
29 32 0.51
30 16 0.25
31 8 0.13
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.32
Consensus pattern (29 bp):
CGAGGGTAAAATGGTAATTTTTAGGCACT
Found at i:42766016 original size:29 final size:31
Alignment explanation
Indices: 42765857--42766234 Score: 252
Period size: 30 Copynumber: 12.7 Consensus size: 31
42765847 ACCCGAGGGC
** *
42765857 AAAATGGTAATTTTTGG-TCGCTCGAGGGT-
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTA
* * *
42765886 AAAATGGTAA-TTTTGAGAAAGGTCGAGGTTT
1 AAAATGGTAATTTTTG-GAAAGTTCGAGGGTA
*
42765917 AAAATGG-AATTTTTAGG-CA-TTCGAGGGT-
1 AAAATGGTAATTTTT-GGAAAGTTCGAGGGTA
* * *
42765945 AAAATAGTAA-TTTTGAAAAAGAATC-AGGGTCA
1 AAAATGGTAATTTTTG-GAAAG-TTCGAGGGT-A
* *
42765977 AAAATAG-AATTTTTGG-AAGTTTGAGGGT-
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTA
42766005 AAAATGGTAATTTTTGGAAAAGTT-G-GGGTTA
1 AAAATGGTAATTTTTGG-AAAGTTCGAGGG-TA
42766036 AAAATGG-AA-TTTTGGAAAGTTCGAGGGTA
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTA
* * *
42766065 AAAAT-GTAAATTTTAGAAAAG-TAGA-GGTCA
1 AAAATGGT-AATTTTTGGAAAGTTCGAGGGT-A
42766095 AAAATGG-AA-TTTTGGAAAGTTCGAGGGTA
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTA
** *
42766124 AAAATGG-AATTTTTGGAAAAATCGAGGTTA
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTA
*
42766154 AAAATGG-AA-TTTTGGAAAGTTCAAGGGTA
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTA
* * * *
42766183 CAAAT-GTAAATTTTGGAAAGTTTG-GGGATC
1 AAAATGGTAATTTTTGGAAAGTTCGAGGG-TA
* *
42766213 AAAAT-ATAATTTTTGGACAGTT
1 AAAATGGTAATTTTTGGAAAGTT
42766235 TAAAGACCTC
Statistics
Matches: 281, Mismatches: 36, Indels: 63
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.00
28 37 0.13
29 91 0.32
30 102 0.36
31 37 0.13
32 13 0.05
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.31
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAAAGTTCGAGGGTA
Found at i:42766137 original size:118 final size:118
Alignment explanation
Indices: 42765878--42766234 Score: 401
Period size: 118 Copynumber: 3.0 Consensus size: 118
42765868 TTTTGGTCGC
* * *
42765878 TCGAGGGTAAAATGGTAA-TTTTGAGAAAGGTCGAGGTTTAAAATGGAATTTTTAGG-CA-TTCG
1 TCGAGGGTAAAATGGTAATTTTTG-GAAAAGTCGAGGTTAAAAATGGAA-TTTT-GGAAAGTTCG
42765940 AGGGT-AAAATAGT-AATTTTGAAAAAGAATCAGGGTCAAAAATAGAATTTTTGGAAGT
63 AGGGTAAAAAT-GTAAATTTTG-AAAAG-ATCAGGGTCAAAAATAGAATTTTTGGAAGT
* * *
42765997 TTGAGGGTAAAATGGTAATTTTTGGAAAAGTTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGG
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAGTCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGG
*
42766062 GTAAAAATGTAAATTTTAGAAAAG-T-AGAGGTCAAAAATGGAA-TTTTGGAAAGT
66 GTAAAAATGTAAATTTT-GAAAAGATCAG-GGTCAAAAATAGAATTTTTGG-AAGT
* *
42766115 TCGAGGGTAAAAATGG-AATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAG
1 TCGAGGGT-AAAATGGTAATTTTTGGAAAAGTCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAG
* * * ** *
42766179 GGTACAAATGTAAATTTTGGAAAGTTTGGGGATC-AAAATATAATTTTTGGACAGT
65 GGTAAAAATGTAAATTTTGAAAAGATCAGGG-TCAAAAATAGAATTTTTGGA-AGT
42766234 T
1 T
42766235 TAAAGACCTC
Statistics
Matches: 207, Mismatches: 17, Indels: 28
0.82 0.07 0.11
Matches are distributed among these distances:
117 15 0.07
118 102 0.49
119 68 0.33
120 21 0.10
121 1 0.00
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (118 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAAAGTCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGG
GTAAAAATGTAAATTTTGAAAAGATCAGGGTCAAAAATAGAATTTTTGGAAGT
Found at i:42768012 original size:7 final size:7
Alignment explanation
Indices: 42767997--42768035 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
42767987 TTACTTAGCC
*
42767997 TTTAATT
1 TTTAGTT
42768004 TTTAGTT
1 TTTAGTT
42768011 TTTAGTT
1 TTTAGTT
*
42768018 TATTTGTT
1 T-TTAGTT
42768026 TTTAGTT
1 TTTAGTT
42768033 TTT
1 TTT
42768036 TGAAACGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74
Consensus pattern (7 bp):
TTTAGTT
Found at i:42768028 original size:15 final size:14
Alignment explanation
Indices: 42767997--42768037 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
42767987 TTACTTAGCC
* *
42767997 TTTAATTTTTAGTT
1 TTTAGTTTTTTGTT
42768011 TTTAGTTTATTTGTT
1 TTTAGTTT-TTTGTT
42768026 TTTAGTTTTTTG
1 TTTAGTTTTTTG
42768038 AAACGAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (14 bp):
TTTAGTTTTTTGTT
Found at i:42770878 original size:68 final size:68
Alignment explanation
Indices: 42770762--42770904 Score: 236
Period size: 68 Copynumber: 2.1 Consensus size: 68
42770752 TTTCCTTTTG
* * *
42770762 TTTCTTA--AGTAAGATTCTCTTTTTCTTCTTTTTGGTGACTTTGTAATTTTGTCACTATTCACA
1 TTTCTTACTAGTAAGATTCTCTTTTTCTTCTTTTTGGCGAATTTATAATTTTGTCACTATTCACA
*
42770825 CGT
66 CAT
42770828 TTTCTTACTAGTAAGATTCTCTTTTTCTTCTTTTTGGCGAATTTATAATTTTGTCACTATTCACA
1 TTTCTTACTAGTAAGATTCTCTTTTTCTTCTTTTTGGCGAATTTATAATTTTGTCACTATTCACA
42770893 CAT
66 CAT
42770896 TTTCTTACT
1 TTTCTTACT
42770905 CATGATTCTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 7 0.10
68 64 0.90
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (68 bp):
TTTCTTACTAGTAAGATTCTCTTTTTCTTCTTTTTGGCGAATTTATAATTTTGTCACTATTCACA
CAT
Found at i:42770926 original size:21 final size:21
Alignment explanation
Indices: 42770900--42770942 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42770890 ACACATTTTC
*
42770900 TTACTCATGATTCTTTTGTTT
1 TTACTCATGATTCTTTTCTTT
**
42770921 TTACTCATTTTTCTTTTCTTT
1 TTACTCATGATTCTTTTCTTT
42770942 T
1 T
42770943 GATTTTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (21 bp):
TTACTCATGATTCTTTTCTTT
Found at i:42770956 original size:26 final size:28
Alignment explanation
Indices: 42770910--42770965 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
42770900 TTACTCATGA
*
42770910 TTCTTTTGTTTTTACTCA-TT-TTTCTT
1 TTCTTTTGATTTTACTCATTTATTTCTT
*
42770936 TTCTTTTGATTTT-CTTTATTTATTTCTT
1 TTCTTTTGATTTTAC-TCATTTATTTCTT
42770964 TT
1 TT
42770966 TAGCTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 1 0.04
26 14 0.56
27 2 0.08
28 8 0.32
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (28 bp):
TTCTTTTGATTTTACTCATTTATTTCTT
Found at i:42773552 original size:16 final size:17
Alignment explanation
Indices: 42773531--42773572 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
42773521 CAATTAAAAT
*
42773531 TAATAAAATAA-ACAAG
1 TAATAAAATAATACAAA
42773547 TAATAAAATAATACAAA
1 TAATAAAATAATACAAA
42773564 TAATTAAAA
1 TAA-TAAAA
42773573 ACAAACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.48
17 7 0.30
18 5 0.22
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (17 bp):
TAATAAAATAATACAAA
Found at i:42775069 original size:3 final size:3
Alignment explanation
Indices: 42775061--42775092 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42775051 CTATAGCCTA
42775061 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42775093 ACAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42776854 original size:13 final size:13
Alignment explanation
Indices: 42776838--42776862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42776828 TTGCTTTGCT
42776838 TTTTTATTTTTTG
1 TTTTTATTTTTTG
42776851 TTTTTATTTTTT
1 TTTTTATTTTTT
42776863 TTGTCGTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTG
Found at i:42792327 original size:59 final size:58
Alignment explanation
Indices: 42792208--42792495 Score: 239
Period size: 58 Copynumber: 4.9 Consensus size: 58
42792198 TTCAAAAAGT
** * * * * *
42792208 TCGAGGTTTAAAATGGAATTTTAGATA-TTCAAGGGTGAAATGGT-GATTTTGGAAAGAA
1 TCGAGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAT-GTAAATTTTGGAAA-AA
* * *
42792266 TCGAGGTCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAA
1 TCGAGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAT-GTAAATTTTGGAAAAA
* * * * *
42792325 TCGGGGTC--AAATGGAATTATTGAAAGTTTGGGGGTAAAAATGTAAATTTTAGAAAAA
1 TCGAGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGT-AAAATGTAAATTTTGGAAAAA
* * * ** *
42792382 TC-AGGGTCAAAAATGGAAATTTAGAAAGTT-GGGGGTAAAAACATAATTTTTGGAAAAAA
1 TCGA-GGTCAAAAATGGAATTTTTGAAAGTTCGAGGGT-AAAATGTAAATTTTGG-AAAAA
* * *
42792441 T-AAGGTCAAAAATGGAATTTTGGAAATTTCGAGGGTACAAATGTAAATTTTGGAA
1 TCGAGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGTA-AAATGTAAATTTTGGAA
42792496 GTACAGGGAT
Statistics
Matches: 187, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
57 42 0.22
58 71 0.38
59 65 0.35
60 9 0.05
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (58 bp):
TCGAGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGTAAAATGTAAATTTTGGAAAAA
Found at i:42792331 original size:29 final size:30
Alignment explanation
Indices: 42792245--42792495 Score: 91
Period size: 29 Copynumber: 8.6 Consensus size: 30
42792235 TTCAAGGGTG
* *
42792245 AAATGGTGA-TTTTGGAAAGAATCGAGGTCAA
1 AAATGGTAATTTTTGGAAA-AATCGGGGT-AA
* **
42792276 AAATAG-AATTTTTGG-AAGTTCGAGGGT-A
1 AAATGGTAATTTTTGGAAAAATCG-GGGTAA
*
42792304 AAATGGTAATTTTTGGAAAAATCGGGGT-C
1 AAATGGTAATTTTTGGAAAAATCGGGGTAA
* ** *
42792333 AAATGG-AATTATT-GAAAGTTTGGGGGTAA
1 AAATGGTAATTTTTGGAAA-AATCGGGGTAA
* * *
42792362 AAAT-GTAAATTTTAGAAAAATCAGGGTCAA
1 AAATGGTAATTTTTGGAAAAATCGGGGT-AA
* * ** *
42792392 AAATGG-AA-ATTTAGAAAGTTGGGGGTAA
1 AAATGGTAATTTTTGGAAAAATCGGGGTAA
** **
42792420 AAA-CATAATTTTTGGAAAAAAT-AAGGTCAA
1 AAATGGTAATTTTTGG-AAAAATCGGGGT-AA
** *
42792450 AAATGG-AA-TTTTGGAAATTTCGAGGGTAC
1 AAATGGTAATTTTTGGAAAAATCG-GGGTAA
*
42792479 AAAT-GTAAATTTTGGAA
1 AAATGGTAATTTTTGGAA
42792496 GTACAGGGAT
Statistics
Matches: 161, Mismatches: 40, Indels: 39
0.67 0.17 0.16
Matches are distributed among these distances:
27 4 0.02
28 31 0.19
29 69 0.43
30 45 0.28
31 12 0.07
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.29
Consensus pattern (30 bp):
AAATGGTAATTTTTGGAAAAATCGGGGTAA
Found at i:42793533 original size:3 final size:3
Alignment explanation
Indices: 42793523--42793588 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
42793513 TTTTTTTTAA
* * * * *
42793523 TAT T-T TAT TAT TAT TAT TAT AAT TAT TAC TAC CAT TCT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42793570 TAT TAT TATT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT
42793589 AAAAACTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:42794352 original size:17 final size:18
Alignment explanation
Indices: 42794329--42794422 Score: 88
Period size: 17 Copynumber: 5.4 Consensus size: 18
42794319 ACATTTATTC
*
42794329 ATTTAAATTT-ATAATAA
1 ATTTAAATTTGAAAATAA
*
42794346 TTTTAAATTTGAAAATAA
1 ATTTAAATTTGAAAATAA
* **
42794364 ATTTAAACTT-AACTTAA
1 ATTTAAATTTGAAAATAA
* *
42794381 ATTTAAATTTTAAAACAA
1 ATTTAAATTTGAAAATAA
42794399 ATTT-AATCTT-AAAATAA
1 ATTTAAAT-TTGAAAATAA
42794416 ATTTAAA
1 ATTTAAA
42794423 ATGGGTTTGG
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
17 36 0.58
18 26 0.42
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTTAAATTTGAAAATAA
Found at i:42794368 original size:35 final size:34
Alignment explanation
Indices: 42794329--42794422 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
42794319 ACATTTATTC
* *
42794329 ATTTAAATTTATAATAATTTTAAATTTGAAAATAA
1 ATTTAAATTTA-AATAAATTTAAATTTGAAAACAA
* * *
42794364 ATTTAAACTTAACTTAAATTTAAATTTTAAAACAA
1 ATTTAAATTTAA-ATAAATTTAAATTTGAAAACAA
42794399 ATTT-AATCTTAAAATAAATTTAAA
1 ATTTAAAT-TT-AAATAAATTTAAA
42794423 ATGGGTTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
34 3 0.06
35 44 0.90
36 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (34 bp):
ATTTAAATTTAAATAAATTTAAATTTGAAAACAA
Found at i:42795064 original size:137 final size:138
Alignment explanation
Indices: 42794817--42795071 Score: 345
Period size: 137 Copynumber: 1.9 Consensus size: 138
42794807 GGATAACTAC
* ** * * *
42794817 AATCTGCCTCAGGCTCGGGGTAGGAGATTGGTTGATGGTGATCTTCCCTAAGCTCGGGGTAAGAG
1 AATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTGATAATGATCTGCCCTAAGCTAGGGGTAAAAG
* * **
42794882 ATCGAATGGCTATAATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGACGATGATTGCCCATCAA
66 ATCAAATGACTATAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACGATGATTGCCCATCAA
42794947 ATGGCTGG
131 ATGGCTGG
* * *
42794955 AATCTGGCC-CAGGCTCGGGGTAAGAGATTGGTTGATAATGATCTGCTC-GAGGTAGGGGTAAAA
1 AATCT-GCCTCAGGCTCGGGGTAAGAGATTGGTTGATAATGATCTGCCCTAAGCTAGGGGTAAAA
*
42795018 GATCAAATGACT-TCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATG
65 GATCAAATGACTAT-AATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACGATG
42795072 TAACTTCACT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
136 1 0.01
137 58 0.57
138 39 0.39
139 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (138 bp):
AATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTGATAATGATCTGCCCTAAGCTAGGGGTAAAAG
ATCAAATGACTATAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACGATGATTGCCCATCAA
ATGGCTGG
Found at i:42795468 original size:48 final size:48
Alignment explanation
Indices: 42795348--42795927 Score: 445
Period size: 48 Copynumber: 11.9 Consensus size: 48
42795338 TCCCGTCAAA
* * * * *
42795348 TCTTCGTGGTACTGAATTCGCCATTGCGGCTCAAATCTTTCCCTTTATG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCC-TTGTG
* * ** ** * *
42795397 TC-TCTGAGGTACAAGG-TTTGCCGTTGCAACTTAAACCTTTCCCTTATG
1 TCTTC-GTGGTAC-TGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTGTG
* * *
42795445 TCTTCGCGGTACTGGATCCGCCGTTACGGCTTATATCTTTCCCTTGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTGTG
* ** * *
42795493 TCTTCGTGGTACTAGATATGCCGTTACGGCTTAGATCTTTCCCTTGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTGTG
* * * *
42795541 TCTTCGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTTGTC
1 TCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAAATCTTTCCC-TTGTG
* * * ** * *
42795591 TTTTTGTGGTACTGGATCCGTCGTCACGGCTTAGATCTTTCTCTTGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTGTG
* *
42795639 TCTTCGTGGTACTGGATCCGCAGTTGCGGTCTTAGATCTTT-CCTGTCGTG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTAAATCTTTCCCT-T-GTG
* * * * * *
42795689 TTTTTGTGATACTGGATCTGCCGTTGCGGCTTAGATCTTTCCCTTCATG
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTT-GTG
* * * * * * *
42795738 TCCT-GAGGTGCTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTGTG
1 TCTTCGTGGTACT-GGATCCGCCGTTGCGGCTTAAATCTTTCCCTTGTG
* * * * *
42795785 TCTTTGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTT-CCTTTTA
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTGTG
* * * * * *
42795832 TGCTTCTGAGGTACT-AAGTTCGCCGTTGCGACTTAAACCTTCCCCTTTGTG
1 T-CTTC-GTGGTACTGGA-TCCGCCGTTGCGGCTTAAATCTTTCCC-TTGTG
* *
42795883 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATTTTTCCCTT
1 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTT
42795928 CATTTCATGT
Statistics
Matches: 425, Mismatches: 87, Indels: 39
0.77 0.16 0.07
Matches are distributed among these distances:
47 15 0.04
48 198 0.47
49 144 0.34
50 64 0.15
51 4 0.01
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (48 bp):
TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTGTG
Found at i:42795640 original size:98 final size:98
Alignment explanation
Indices: 42795433--42795927 Score: 443
Period size: 98 Copynumber: 5.1 Consensus size: 98
42795423 CAACTTAAAC
* * * *
42795433 CTTTCCCTTATGTCTTCGCGGTACTGGATCCGCCGTTACGG-CTTATATCTTTCCC-TTGTGTCT
1 CTTTCCCTTGTGTCTTCGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTTGTGTTT
* * *
42795496 TCGTGGTACTAGATATGCCGTTACGGCTTAGAT
66 TTGTGGTACTGGATCTGCCGTTACGGCTTAGAT
* *
42795529 CTTTCCCTTGTGTCTTCGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTTGTCTTT
1 CTTTCCCTTGTGTCTTCGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTTGTGTTT
* * *
42795594 TTGTGGTACTGGATCCGTCGTCACGGCTTAGAT
66 TTGTGGTACTGGATCTGCCGTTACGGCTTAGAT
* * * * *
42795627 CTTTCTCTTGTGTCTTCGTGGTACTGGATCCGCAGTTGCGGTCTTAGATCTTTCCTGTCGTGTTT
1 CTTTCCCTTGTGTCTTCGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTTGTGTTT
* *
42795692 TTGTGATACTGGATCTGCCGTTGCGGCTTAGAT
66 TTGTGGTACTGGATCTGCCGTTACGGCTTAGAT
* * * * * * * * *
42795725 CTTTCCCTTCATGTCCT-GAGGTGCTAGG-TTCGCCATTGC-GACTTAAACCTTTCCC-TTGTGT
1 CTTTCCCTT-GTGTCTTCGCGGTACT-GGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTTGTGT
* * * *
42795786 CTTTGTGGTACTGGAT-TCGCCATTGCGGCTTAAAT
64 TTTTGTGGTACTGGATCT-GCCGTTACGGCTTAGAT
* * * * * * * * * *
42795821 CTTT-CCTTTTATGCTTCTGAGGTACT-AAGTTCGCCGTTGC-GACTTAAACCTTCCCCTTTGTG
1 CTTTCCCTTGTGT-CTTC-GCGGTACTGGA-TCCGCCGTTGCGGTCTTAGATCTTTCCCGTTGTG
* * * *
42795883 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGAT
63 TTTTTGTGGTACTGGATCTGCCGTTACGGCTTAGAT
*
42795919 TTTTCCCTT
1 CTTTCCCTT
42795928 CATTTCATGT
Statistics
Matches: 333, Mismatches: 53, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
94 2 0.01
95 7 0.02
96 76 0.23
97 57 0.17
98 180 0.54
99 11 0.03
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (98 bp):
CTTTCCCTTGTGTCTTCGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTTGTGTTT
TTGTGGTACTGGATCTGCCGTTACGGCTTAGAT
Found at i:42795640 original size:146 final size:147
Alignment explanation
Indices: 42795452--42795731 Score: 404
Period size: 146 Copynumber: 1.9 Consensus size: 147
42795442 ATGTCTTCGC
* * * *
42795452 GGTACTGGATCCGCCGTTACGGCTTATATCTTTCCCTTGTGTCTTCGTGGTACTAGATATGCCGT
1 GGTACTGGATCCGCCGTCACGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTAGATACGCAGT
*
42795517 TACGG-CTTAGATCTTTCCCT-T-GTGTCTTCGCGGTACTGGATCTGCCGTTGCGGTCTTAGATC
66 TACGGTCTTAGATCTTT-CCTGTCGTGTCTTCGCGATACTGGATCTGCCGTTGCGG-CTTAGATC
42795579 TTTCCCGTTGTCTTTTTGT
129 TTTCCCGTTGTCTTTTTGT
* * * *
42795598 GGTACTGGATCCGTCGTCACGGCTTAGATCTTTCTCTTGTGTCTTCGTGGTACTGGATCCGCAGT
1 GGTACTGGATCCGCCGTCACGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTAGATACGCAGT
* * * *
42795663 TGCGGTCTTAGATCTTTCCTGTCGTGTTTTTGTGATACTGGATCTGCCGTTGCGGCTTAGATCTT
66 TACGGTCTTAGATCTTTCCTGTCGTGTCTTCGCGATACTGGATCTGCCGTTGCGGCTTAGATCTT
42795728 TCCC
131 TCCC
42795732 TTCATGTCCT
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
146 64 0.54
147 26 0.22
148 28 0.24
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (147 bp):
GGTACTGGATCCGCCGTCACGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTAGATACGCAGT
TACGGTCTTAGATCTTTCCTGTCGTGTCTTCGCGATACTGGATCTGCCGTTGCGGCTTAGATCTT
TCCCGTTGTCTTTTTGT
Found at i:42795783 original size:146 final size:144
Alignment explanation
Indices: 42795452--42795828 Score: 368
Period size: 146 Copynumber: 2.6 Consensus size: 144
42795442 ATGTCTTCGC
* * * * * * * *
42795452 GGTACTGGATCCGCCGTTACGGCTTATATCTTTCCCTTGTGTCTTCGTGGTACTAGATATGCCGT
1 GGTACTGGATCCGCCATCACGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATACGCAGT
* *
42795517 TACGGCTTAGATCTTTCCCTTGTGTCTTCGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTT
66 TGCGGCTTAGATCTTT-CCTTGTGTCTTCGCGATACTGGATCTGCCGTTGCGGTCTTAGATCTTT
** *
42795582 CCCGTTGTCTTTTTGT
130 CCCG-TGTCTTCCTGA
* * * * * * *
42795598 GGTACTGGATCCGTCGTCACGGCTTAGATCTTTCTCTTGTGTCTTCGTGGTACTGGATCCGCAGT
1 GGTACTGGATCCGCCATCACGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATACGCAGT
* * *
42795663 TGCGGTCTTAGATCTTTCCTGTCGTGTTTTTGTGATACTGGATCTGCCGTTGCGG-CTTAGATCT
66 TGCGG-CTTAGATCTTTCCT-T-GTGTCTTCGCGATACTGGATCTGCCGTTGCGGTCTTAGATCT
42795727 TTCCC-T-TCATGTCCTGA
128 TTCCCGTGTC-T-TCCTGA
* * ** * *
42795744 GGTGCTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTTGTGGTACTGGATTCGCCA
1 GGTACT-GGATCCGCCATCACGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATACG-CA
*
42795808 -TTGCGGCTTAAATCTTTCCTT
64 GTTGCGGCTTAGATCTTTCCTT
42795829 TTATGCTTCT
Statistics
Matches: 195, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
144 3 0.02
145 15 0.08
146 119 0.61
147 30 0.15
148 28 0.14
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (144 bp):
GGTACTGGATCCGCCATCACGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATACGCAGT
TGCGGCTTAGATCTTTCCTTGTGTCTTCGCGATACTGGATCTGCCGTTGCGGTCTTAGATCTTTC
CCGTGTCTTCCTGA
Found at i:42802833 original size:117 final size:117
Alignment explanation
Indices: 42802710--42803030 Score: 361
Period size: 117 Copynumber: 2.7 Consensus size: 117
42802700 TTTTTATCGC
** * * *
42802710 TCGAGGGTAAAATGGTAA-TTTTGAGAAAGGTCGAGGTTTAAAATGGAATTTTTAGGCA-TTCGG
1 TCGAGGGTAAAATGGTAATTTTTG-GAAAAATCGAGGTTAAAAATGGAATTTTT-GGAAGTTCGA
** *
42802773 GGGT-AAATGGT-AATTTT-GAAAAGAATCGGGGTCAAAAATAGAATTTTTTGAA-GT
64 GGGTAAAAT-GTAAATTTTAG-AAA-AATCGAAGTCAAAAATAGAA-TTTTGGAACGT
* * *
42802827 TCGAGGGTAAAATGGTAATTTTTGGAAAAATTGGGGTTAAAAATGGAA-GTTTGGAAGTTCGAGG
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGG
*
42802891 GTAAAAATGTAAATTTTAGAAAAATCGAAGTCAAAAATGGAATTTTGGAACGT
66 GT-AAAATGTAAATTTTAGAAAAATCGAAGTCAAAAATAGAATTTTGGAACGT
* * * *
42802944 TCGAGGGTAAAAAT-GTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTCAAG
1 TCGAGGGT-AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAG
42803008 GGTACAAATGTAAATTTTAGAAA
65 GGTA-AAATGTAAATTTTAGAAA
42803031 GTTTGGGGAT
Statistics
Matches: 175, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
115 3 0.02
116 18 0.10
117 98 0.56
118 55 0.31
119 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.30
Consensus pattern (117 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGG
GTAAAATGTAAATTTTAGAAAAATCGAAGTCAAAAATAGAATTTTGGAACGT
Found at i:42802863 original size:59 final size:56
Alignment explanation
Indices: 42802710--42803030 Score: 286
Period size: 59 Copynumber: 5.5 Consensus size: 56
42802700 TTTTTATCGC
** ** *
42802710 TCGAGGGTAAAATGGTAATTTTGAGAAAGGTCGAGGTTTAAAATGGAATTTTTAGGCA-T
1 TCGAGGGTAAAAT-GTAATTTTG-GAAAAATCGAGGTCAAAAATGGAA-TTTT-GGAAGT
* * * * *
42802769 TCGGGGGT-AAATGGTAATTTTGAAAAGAATCGGGGTCAAAAATAGAATTTTTTGAAGT
1 TCGAGGGTAAAAT-GTAATTTTGGAAA-AATCGAGGTCAAAAATGGAA-TTTTGGAAGT
* * * *
42802827 TCGAGGGTAAAATGGTAATTTTTGGAAAAATTGGGGTTAAAAATGGAAGTTTGGAAGT
1 TCGAGGGTAAAAT-GTAA-TTTTGGAAAAATCGAGGTCAAAAATGGAATTTTGGAAGT
* *
42802885 TCGAGGGTAAAAATGTAAATTTTAGAAAAATCGAAGTCAAAAATGGAATTTTGGAACGT
1 TCGAGGGT-AAAATGT-AATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTGGAA-GT
* * *
42802944 TCGAGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTAGAAAGT
1 TCGAGGGT-AAAATGTAA-TTTTGGAAAAATCGAGGTCAAAAATGGAATTTT-GGAAGT
* *
42803003 TCAAGGGTACAAATGTAAATTTTAGAAA
1 TCGAGGGTA-AAATGT-AATTTTGGAAA
42803031 GTTTGGGGAT
Statistics
Matches: 221, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
57 5 0.02
58 93 0.42
59 110 0.50
60 13 0.06
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.30
Consensus pattern (56 bp):
TCGAGGGTAAAATGTAATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTGGAAGT
Found at i:42802892 original size:29 final size:28
Alignment explanation
Indices: 42802710--42803017 Score: 139
Period size: 29 Copynumber: 10.5 Consensus size: 28
42802700 TTTTTATCGC
*
42802710 TCGAGGGT-AAAATGGTAATTTTGAGAAAGG
1 TCGAGGGTAAAAATGG-AATTTTG-G-AAGT
* * *
42802740 TCGAGGTTTAAAATGGAATTTTTAGGCA-T
1 TCGAGGGTAAAAATGGAA-TTTT-GGAAGT
* * *
42802769 TCGGGGGT--AAATGGTAATTTTGAAAAGAA
1 TCGAGGGTAAAAATGG-AATTTTG-GAAG-T
* *
42802798 TCG-GGGTCAAAAATAGAATTTTTTGAAGT
1 TCGAGGGT-AAAAATGGAA-TTTTGGAAGT
*
42802827 TCGAGGGT-AAAATGGTAATTTTTGGAAAAAT
1 TCGAGGGTAAAAATGG-AA-TTTTGG--AAGT
*
42802858 T-G-GGGTTAAAAATGGAAGTTTGGAAGT
1 TCGAGGG-TAAAAATGGAATTTTGGAAGT
* * **
42802885 TCGAGGGTAAAAATGTAAATTTTAGAAAAA
1 TCGAGGGTAAAAATG-GAATTTT-GGAAGT
*
42802915 TCGA-AGTCAAAAATGGAATTTTGGAACGT
1 TCGAGGGT-AAAAATGGAATTTTGGAA-GT
* **
42802944 TCGAGGGTAAAAATGTAATTTTTGGAAAAA
1 TCGAGGGTAAAAATGGAA-TTTTGG-AAGT
* * *
42802974 TCAAGGTTAAAAATGGAATTTTAGAAAGT
1 TCGAGGGTAAAAATGGAATTTT-GGAAGT
* *
42803003 TCAAGGGTACAAATG
1 TCGAGGGTAAAAATG
42803018 TAAATTTTAG
Statistics
Matches: 212, Mismatches: 39, Indels: 55
0.69 0.13 0.18
Matches are distributed among these distances:
26 1 0.00
27 15 0.07
28 24 0.11
29 76 0.36
30 61 0.29
31 34 0.16
32 1 0.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (28 bp):
TCGAGGGTAAAAATGGAATTTTGGAAGT
Found at i:42803031 original size:30 final size:30
Alignment explanation
Indices: 42802881--42803033 Score: 134
Period size: 30 Copynumber: 5.2 Consensus size: 30
42802871 GGAAGTTTGG
*
42802881 AAGTTCGAGGGTAAAAATGTAAATTTTAGA
1 AAGTTCAAGGGTAAAAATGTAAATTTTAGA
** * *
42802911 AAAATCGAA--GTCAAAAATG-GAATTTTGGA
1 AAGTTC-AAGGGT-AAAAATGTAAATTTTAGA
* * * *
42802940 ACGTTCGAGGGTAAAAATGTAATTTTTGGA
1 AAGTTCAAGGGTAAAAATGTAAATTTTAGA
** * *
42802970 AAAATCAAGGTTAAAAATG-GAATTTTAGA
1 AAGTTCAAGGGTAAAAATGTAAATTTTAGA
*
42802999 AAGTTCAAGGGTACAAATGTAAATTTTAGA
1 AAGTTCAAGGGTAAAAATGTAAATTTTAGA
42803029 AAGTT
1 AAGTT
42803034 TGGGGATCAA
Statistics
Matches: 93, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
28 1 0.01
29 42 0.45
30 49 0.53
31 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (30 bp):
AAGTTCAAGGGTAAAAATGTAAATTTTAGA
Found at i:42804086 original size:3 final size:3
Alignment explanation
Indices: 42804080--42804106 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42804070 TACTACTATT
42804080 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
42804107 TTATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42804111 original size:3 final size:3
Alignment explanation
Indices: 42804105--42804131 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42804095 ATAATAATAA
42804105 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
42804132 AAAAACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42804618 original size:25 final size:25
Alignment explanation
Indices: 42804590--42804650 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
42804580 GCTATGGTAG
* *
42804590 TGGTAATGGCAGA-GCAGGTTGAAGC
1 TGGTGATGGCA-ACGCAAGTTGAAGC
*
42804615 TGGTGGTGGCAACGCAAGTTGAAGC
1 TGGTGATGGCAACGCAAGTTGAAGC
42804640 TGGTGATGGCA
1 TGGTGATGGCA
42804651 CTGTTGATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.25, C:0.13, G:0.41, T:0.21
Consensus pattern (25 bp):
TGGTGATGGCAACGCAAGTTGAAGC
Found at i:42804923 original size:17 final size:17
Alignment explanation
Indices: 42804900--42805010 Score: 134
Period size: 17 Copynumber: 6.4 Consensus size: 17
42804890 ACATTTATTC
*
42804900 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
42804917 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* * *
42804935 ATTTAAACTCAAATTAA
1 ATTTAAATTTAAAATAA
42804952 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
42804969 ATTTAAATTTTAAAACAA
1 ATTTAAA-TTTAAAATAA
42804987 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
42805004 ATTTAAA
1 ATTTAAA
42805011 ATGGGTTTGG
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 50 0.63
18 28 0.35
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:42804939 original size:35 final size:33
Alignment explanation
Indices: 42804900--42805010 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 33
42804890 ACATTTATTC
*
42804900 ATTTAAATTTATAATAATTTTAAATTTGAAAATAA
1 ATTTAAATTTA-AATAAATTTAAATTT-AAAATAA
* *
42804935 ATTTAAACTCAAATTAAATTTAAATTTAAAATAA
1 ATTTAAATTTAAA-TAAATTTAAATTTAAAATAA
*
42804969 ATTTAAATTTTAAAACAAATTT-AATCTTAAAATAA
1 ATTTAAA-TTT-AAATAAATTTAAAT-TTAAAATAA
42805004 ATTTAAA
1 ATTTAAA
42805011 ATGGGTTTGG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
34 19 0.29
35 44 0.67
36 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (33 bp):
ATTTAAATTTAAATAAATTTAAATTTAAAATAA
Found at i:42804957 original size:6 final size:6
Alignment explanation
Indices: 42804900--42804978 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
42804890 ACATTTATTC
* * * *
42804900 ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTCAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
*
42804947 A-TTAA ATTTAA ATTTAA A-ATAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
42804979 TAAAACAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
4 1 0.02
5 13 0.23
6 38 0.67
7 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:42804959 original size:23 final size:23
Alignment explanation
Indices: 42804932--42804978 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
42804922 AATTTGAAAA
*
42804932 TAAATTTAAACTCAAA-TTAAATT
1 TAAATTTAAAAT-AAATTTAAATT
42804955 TAAATTTAAAATAAATTTAAATT
1 TAAATTTAAAATAAATTTAAATT
42804978 T
1 T
42804979 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAATTTAAAATAAATTTAAATT
Found at i:42804962 original size:52 final size:52
Alignment explanation
Indices: 42804900--42805010 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 52
42804890 ACATTTATTC
* * * *
42804900 ATTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTCAAATTAA
1 ATTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTCAAAATAA
* * *
42804952 ATTTAAATTTAAAATAAATTTAAATTTTAAAACAAATTTAATCTTAAAATAA
1 ATTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTCAAAATAA
42805004 ATTTAAA
1 ATTTAAA
42805011 ATGGGTTTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (52 bp):
ATTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTCAAAATAA
Found at i:42805012 original size:11 final size:11
Alignment explanation
Indices: 42804920--42804975 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
42804910 ATAATAATTT
42804920 TAAATTTGAAAA
1 TAAATTT-AAAA
*
42804932 TAAATTTAAAC
1 TAAATTTAAAA
*
42804943 TCAAA-TTAAATT
1 T-AAATTTAAA-A
42804955 TAAATTTAAAA
1 TAAATTTAAAA
42804966 TAAATTTAAA
1 TAAATTTAAA
42804976 TTTTAAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 22 0.58
12 16 0.42
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:42811435 original size:29 final size:30
Alignment explanation
Indices: 42811398--42811466 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
42811388 ACGATAATAT
*
42811398 AAGTGACTAAAACATAACAT-TTCAAACAA
1 AAGTGACTAAAACATAACATAGTCAAACAA
** *
42811427 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACATAACAT-AGTCAAACAA
42811458 AAGTGACTA
1 AAGTGACTA
42811467 TTTCGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (30 bp):
AAGTGACTAAAACATAACATAGTCAAACAA
Found at i:42814571 original size:22 final size:24
Alignment explanation
Indices: 42814531--42814581 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
42814521 ACCTATATAT
42814531 TTAAAAAAATTTAACAA-TTAA-A
1 TTAAAAAAATTTAACAATTTAATA
*
42814553 TTAAAAAAA-TTATCAAATTTAATA
1 TTAAAAAAATTTAAC-AATTTAATA
42814577 TTAAA
1 TTAAA
42814582 TATTGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 11 0.44
23 4 0.16
24 6 0.24
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAAAAAATTTAACAATTTAATA
Found at i:42815304 original size:41 final size:40
Alignment explanation
Indices: 42815259--42815349 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 40
42815249 TAAAAATTAT
* *
42815259 TTATATTAAAAAACATTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTAACATAAATATAATAAATA-TTTA
* * *
42815300 TTATACTAAAAAACACTAATATTAATATAATAAATATTTA
1 TTATATTAAAAAACACTAACATAAATATAATAAATATTTA
*
42815340 TTGTATTAAA
1 TTATATTAAA
42815350 TATAATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 12 0.28
41 31 0.72
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAAACACTAACATAAATATAATAAATATTTA
Found at i:42819531 original size:35 final size:35
Alignment explanation
Indices: 42819491--42819558 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
42819481 TAAAAATGTT
42819491 CAAAAAT-AGTAATTTCCCAAAATAAAAAGTTTTGA
1 CAAAAATGA-TAATTTCCCAAAATAAAAAGTTTTGA
* * * *
42819526 CAAAAATGATAGTTTCCTAAAATGATAAGTTTT
1 CAAAAATGATAATTTCCCAAAATAAAAAGTTTT
42819559 TGTCGAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (35 bp):
CAAAAATGATAATTTCCCAAAATAAAAAGTTTTGA
Found at i:42820193 original size:97 final size:97
Alignment explanation
Indices: 42820018--42820210 Score: 255
Period size: 97 Copynumber: 2.0 Consensus size: 97
42820008 AACCTTGGAA
*
42820018 AAGGATATTTGATTATCTCGATTTGAAGAAAAGTCACACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAAATTTTCA
* *
42820083 GAATCAGAGATAAAGAAACATTCCCTCGATTC
66 AAATCAGAAATAAAGAAACATTCCCTCGATTC
* *** *
42820115 AAGGGTATTTGATTAT-TCCGATTTGAAGAAAAATCGTGCCTAGTACGTTAAGGCACAAATTTTC
1 AAGGATATTTGATTATCT-CGATTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAAATTTTC
* * *
42820179 AAAACTC-GAAATAAAGGAATATTGCCTCGATT
65 AAAA-TCAGAAATAAAGAAACATTCCCTCGATT
42820211 TTAAAGGTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 1 0.01
97 80 0.96
98 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (97 bp):
AAGGATATTTGATTATCTCGATTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAGAAACATTCCCTCGATTC
Found at i:42820530 original size:29 final size:30
Alignment explanation
Indices: 42820498--42820944 Score: 287
Period size: 29 Copynumber: 15.2 Consensus size: 30
42820488 GTTCAAGGTC
* *
42820498 AAAAATGGAATTTTTGGACA-TTCGAGGAT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
* *
42820527 -AAAATAGTAA-TTTTGAAAAGCTT-G-GGGT
1 AAAAAT-GGAATTTTTGGAAAG-TTCGAGGGT
* * *
42820555 CAAAAATGGGATTTTTGGATA-TTCGGGGGT
1 -AAAAATGGAATTTTTGGAAAGTTCGAGGGT
* **
42820585 -AAAATGGTCATTTTTGG-AAGTTTTAGGGTT
1 AAAAATGG-AATTTTTGGAAAGTTCGAGGG-T
* * * *
42820615 AAAAATGGGATTTTTGGACACTT-GGGGGT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
**
42820644 -AAAATGGTAATTTTTGGAATTTTCGA-GGT
1 AAAAATGG-AATTTTTGGAAAGTTCGAGGGT
*
42820673 AAAAAATGGAATTTTTGGACA-TTCGAGGGT
1 -AAAAATGGAATTTTTGGAAAGTTCGAGGGT
42820703 -AAAATGGTAATTTTTGG-AAGTTTCGA-GGT
1 AAAAATGG-AATTTTTGGAAAG-TTCGAGGGT
**
42820732 CAAAAATGGAA-TTTTAAAAAGTTCG-GGAGT
1 -AAAAATGGAATTTTTGGAAAGTTCGAGG-GT
* *
42820762 AAAAATGTAATTTTT-GAAAGTTTTG-GGGT
1 AAAAATGGAATTTTTGGAAAG-TTCGAGGGT
*
42820791 CAAAAATGGAA-TTTTGGAAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAAGTTCGAGGGT
* *
42820821 AAAAATGTAATTTTTGGAAACTTCG-GGGT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
*
42820850 CAAAAATAGAA-TTTTGGAATA-TTCGAGGGT
1 -AAAAATGGAATTTTTGGAA-AGTTCGAGGGT
** * * *
42820880 AAAAATAAAATTTTTGGAAAATTTG-GGCT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT
*
42820909 CAAAAATGGAA-TTTTGGAAAGTTCAAGGGT
1 -AAAAATGGAATTTTTGGAAAGTTCGAGGGT
*
42820939 CAAAAT
1 AAAAAT
42820945 ATGATTTCTT
Statistics
Matches: 332, Mismatches: 47, Indels: 78
0.73 0.10 0.17
Matches are distributed among these distances:
28 40 0.12
29 138 0.42
30 130 0.39
31 24 0.07
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAAGTTCGAGGGT
Found at i:42820532 original size:58 final size:59
Alignment explanation
Indices: 42820449--42820923 Score: 402
Period size: 59 Copynumber: 8.1 Consensus size: 59
42820439 TAAACGGTAA
* * * * *
42820449 TTTTGAACACTTCGAGGGGTAAAATAGTAATTTTCGG-AGGTTCAAGGTCAAAAATGGAAT
1 TTTTGGACA-TTCGA-GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* * * * * *
42820509 TTTTGGACATTCGAGGATAAAATAGTAA-TTTTGAAAAGCTT-GGGGTCAAAAATGGGAT
1 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTG-GAAGTTTCGAGGTCAAAAATGGAAT
* * * * * *
42820567 TTTTGGATATTCGGGGGTAAAATGGTCATTTTTGGAAGTTT-TAGGGTTAAAAATGGGAT
1 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAAT
* * *
42820626 TTTTGGACACTT-GGGGGTAAAATGGTAATTTTTGGAATTTTCGAGGTAAAAAATGGAAT
1 TTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAAT
42820685 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA-
1 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAAT
** * * * *
42820743 TTTTAAAAAGTTCG-GGAGTAAAAAT-GTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAA-
1 TTTTGGACA-TTCGAGG-GT-AAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* * ** * *
42820802 TTTTGGAAAGTTTGAGGGTAAAAAT-GTAATTTTTGGAAACTTCGGGGTCAAAAATAGAA-
1 TTTTGGACA-TTCGAGGGT-AAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* ** *
42820861 TTTTGGAATATTCGAGGGTAAAAAT-AAAATTTTTGGAAAATTT-G-GGCTCAAAAATGGAAT
1 TTTTGG-ACATTCGAGGGT-AAAATGGTAATTTTTGG-AAGTTTCGAGG-TCAAAAATGGAAT
42820921 TTT
1 TTT
42820924 GGAAAGTTCA
Statistics
Matches: 353, Mismatches: 47, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
57 4 0.01
58 67 0.19
59 254 0.72
60 28 0.08
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.34
Consensus pattern (59 bp):
TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAAT
Found at i:42820897 original size:30 final size:31
Alignment explanation
Indices: 42820494--42820943 Score: 238
Period size: 30 Copynumber: 15.3 Consensus size: 31
42820484 GGAGGTTCAA
*
42820494 GGTCAAAAATGGAATTTTTGG-ACATTCGAG
1 GGTCAAAAATGGAATTTTTGGAATATTCGAG
* * *
42820524 GAT--AAAATAGTAA-TTTT-GAAAAGCTT-G-G
1 GGTCAAAAAT-GGAATTTTTGGAATA--TTCGAG
* *
42820552 GGTCAAAAATGGGATTTTTGG-ATATTCGGG
1 GGTCAAAAATGGAATTTTTGGAATATTCGAG
* *
42820582 GGT--AAAATGGTCATTTTTGGAAGT-TT-TAG
1 GGTCAAAAATGG-AATTTTTGGAA-TATTCGAG
* * * *
42820611 GGTTAAAAATGGGATTTTTGGACA-CTT-GGG
1 GGTCAAAAATGGAATTTTTGGA-ATATTCGAG
*
42820641 GGT--AAAATGGTAATTTTTGGAATTTTCGA-
1 GGTCAAAAATGG-AATTTTTGGAATATTCGAG
* *
42820670 GGTAAAAAATGGAATTTTTGG-ACATTCGAG
1 GGTCAAAAATGGAATTTTTGGAATATTCGAG
42820700 GGT--AAAATGGTAATTTTTGGAAGT-TTCGA-
1 GGTCAAAAATGG-AATTTTTGGAA-TATTCGAG
* *
42820729 GGTCAAAAATGGAA-TTTT-AAAAAGTTCG-G
1 GGTCAAAAATGGAATTTTTGGAATA-TTCGAG
* * *
42820758 GAGT-AAAAATGTAATTTTTGAAAGT-TTTG-G
1 G-GTCAAAAATGGAATTTTTGGAA-TATTCGAG
*
42820788 GGTCAAAAATGGAA-TTTTGGAA-AGTTTGAG
1 GGTCAAAAATGGAATTTTTGGAATA-TTCGAG
*
42820818 GGT-AAAAATGTAATTTTTGGAA-ACTTCG-G
1 GGTCAAAAATGGAATTTTTGGAATA-TTCGAG
*
42820847 GGTCAAAAATAGAA-TTTTGGAATATTCGAG
1 GGTCAAAAATGGAATTTTTGGAATATTCGAG
** * *
42820877 GGT-AAAAATAAAATTTTTGGAAAATTTG-G
1 GGTCAAAAATGGAATTTTTGGAATATTCGAG
* *
42820906 GCTCAAAAATGGAA-TTTTGGAA-AGTTCAAG
1 GGTCAAAAATGGAATTTTTGGAATA-TTCGAG
42820936 GGTCAAAA
1 GGTCAAAA
42820944 TATGATTTCT
Statistics
Matches: 333, Mismatches: 40, Indels: 94
0.71 0.09 0.20
Matches are distributed among these distances:
27 1 0.00
28 41 0.12
29 129 0.39
30 135 0.41
31 27 0.08
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (31 bp):
GGTCAAAAATGGAATTTTTGGAATATTCGAG
Found at i:42822106 original size:16 final size:16
Alignment explanation
Indices: 42822080--42822117 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42822070 TTAGTATTAT
*
42822080 TATTA-TTATTATTAA
1 TATTATTTATTATAAA
*
42822095 TGTTATTTATTATAAA
1 TATTATTTATTATAAA
42822111 TATTATT
1 TATTATT
42822118 ATGCATTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTATTTATTATAAA
Found at i:42822823 original size:13 final size:14
Alignment explanation
Indices: 42822805--42822855 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
42822795 TTTGAGCGTG
42822805 TGTAA-TTGGACTT
1 TGTAATTTGGACTT
*
42822818 TGTAATTTGGACCT
1 TGTAATTTGGACTT
* *
42822832 T-TAAGTTGG-GTT
1 TGTAATTTGGACTT
42822844 TGTAATTTGGAC
1 TGTAATTTGGAC
42822856 ATTAATTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
12 2 0.07
13 19 0.66
14 8 0.28
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.45
Consensus pattern (14 bp):
TGTAATTTGGACTT
Found at i:42822933 original size:17 final size:17
Alignment explanation
Indices: 42822873--42822952 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
42822863 TAAATAAATT
*
42822873 TAAACTTAATATTTATAA
1 TAAACTTAA-ATTTAAAA
* **
42822891 TAAATTTAAATTCCAAA
1 TAAACTTAAATTTAAAA
** * *
42822908 TGGATTTAAATTTAATA
1 TAAACTTAAATTTAAAA
42822925 TAAACTTAAATTTAAAA
1 TAAACTTAAATTTAAAA
*
42822942 TAAATTTAAAT
1 TAAACTTAAAT
42822953 CTGTTGGGTC
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 40 0.83
18 8 0.17
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAACTTAAATTTAAAA
Found at i:42824939 original size:39 final size:39
Alignment explanation
Indices: 42824832--42824945 Score: 147
Period size: 39 Copynumber: 2.9 Consensus size: 39
42824822 TTATCAAATT
* * * *
42824832 ACTAAATTGGTAGTGACATTGTAAACATTACAATACAAT
1 ACTAAACTGGTAGTGACATTGTAAACACTGCAATACAAC
*
42824871 ACTGAACTGGTAGTGACATTGTAAACACTGCAATACAAC
1 ACTAAACTGGTAGTGACATTGTAAACACTGCAATACAAC
* ** *
42824910 ACTAAACTGATAGTGACACAGTAAACACTGTAATAC
1 ACTAAACTGGTAGTGACATTGTAAACACTGCAATAC
42824946 TATACTGAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (39 bp):
ACTAAACTGGTAGTGACATTGTAAACACTGCAATACAAC
Found at i:42824988 original size:39 final size:38
Alignment explanation
Indices: 42824869--42825019 Score: 104
Period size: 39 Copynumber: 3.9 Consensus size: 38
42824859 TTACAATACA
* * * * ** *
42824869 ATACTGAACTGGTAGTGACATTGTAAACACTGCAATACA
1 ATACTAAACTGGCAATGACACTGTAAACACTG-TGTACT
* ** * * *
42824908 ACACTAAACTGATAGTGACACAGTAAACACTGTAATACT
1 ATACTAAACTGGCAATGACACTGTAAACACTGT-GTACT
* **
42824947 ATACTGAGTTGGCAATGACACTGTAAACACTGTGTAGCT
1 ATACTAAACTGGCAATGACACTGTAAACACTGTGTA-CT
* * *
42824986 ATATTAAACTGGCAGTAACACTGTAAACACTGTG
1 ATACTAAACTGGCAATGACACTGTAAACACTGTG
42825020 ATGTTACTTC
Statistics
Matches: 88, Mismatches: 22, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
38 2 0.02
39 86 0.98
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (38 bp):
ATACTAAACTGGCAATGACACTGTAAACACTGTGTACT
Found at i:42827453 original size:23 final size:23
Alignment explanation
Indices: 42827381--42827550 Score: 134
Period size: 23 Copynumber: 7.3 Consensus size: 23
42827371 TATAGGAAAC
* *
42827381 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
42827403 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
42827424 AGGAAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* * *
42827450 AAACAAAGAGTACACAAAGTTCT
1 AAACAGAGAGCACACAAAGTGCT
*
42827473 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
42827496 AATCAGAGTGCACACACAA-TGCT
1 AAACAGAGAGCACACA-AAGTGCT
* *
42827519 AATAACAGAGAGCACGAGACA-TGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
42827544 AAACAGA
1 AAACAGA
42827551 AAGCGCGCTA
Statistics
Matches: 120, Mismatches: 18, Indels: 19
0.76 0.11 0.12
Matches are distributed among these distances:
21 17 0.14
23 63 0.52
24 4 0.03
25 28 0.23
26 8 0.07
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:42827503 original size:69 final size:67
Alignment explanation
Indices: 42827381--42827520 Score: 174
Period size: 69 Copynumber: 2.0 Consensus size: 67
42827371 TATAGGAAAC
* * *
42827381 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGAAACAGAGAGCACACACAG
1 AAACAAAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--GAAACAGAGAGCACACACAA
42827446 TGCT
64 TGCT
* * *
42827450 AAACAAAGAGTACACAAAGTTCTAATCAGAGAGCACACAAAGTGCT-AATCAGAGTGCACACACA
1 AAACAAAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAAACAGAGAGCACACACA
42827514 ATGCT
63 ATGCT
42827519 AA
1 AA
42827521 TAACAGAGAG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
69 34 0.55
70 10 0.16
71 11 0.18
72 7 0.11
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.14
Consensus pattern (67 bp):
AAACAAAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAAACAGAGAGCACACACAATG
CT
Found at i:42837056 original size:101 final size:99
Alignment explanation
Indices: 42836811--42837606 Score: 633
Period size: 101 Copynumber: 7.9 Consensus size: 99
42836801 TCAATCCGAT
* * * * ** * *
42836811 CCACTGCAACTTC-AGGGATATAGGATTTGATGTTGTAACTTCCTCTTGCTCCAGTGTATCTCCA
1 CCACTACAACTTCAAGGG-TATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACAACTTCA
* * * * * *
42836875 AGGAAATAATATTTTCTTCTATAGCTTCAATCTGA
65 GGGAGATAAGATTTGCTTCTGTAGCTTTAATCTGA
* ** * * *
42836910 TCCACTGCAACTTC-AGGGATATAGGATTTGATGACGTAGTTTCATCTTGCTCCACTGCATCTTC
1 -CCACTACAACTTCAAGGG-TATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACAACTTC
* * *
42836974 AGGTAGATAAGATTTGCTTGCTGCAACTTTAATCTGA
64 AGGGAGATAAGATTTGCTT-CTGTAGCTTTAATCTGA
* * *
42837011 CCTACTACAACTTCAAGGGTATAGGATTT-AGTGTTGTAGCCTCATCTTGCTCCATTGCAACTTC
1 CC-ACTACAACTTCAAGGGTATAGGATTTGA-TGTTGTAGCTTCATCTTGCTCCACTACAACTTC
* * *
42837075 AAGGAG--AAGATTTG-TTATTGTAGCTTTAATTTGA
64 AGGGAGATAAGATTTGCTT-CTGTAGCTTTAATCTGA
* * * * *
42837109 TCCATTGCAACTTC-AGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTTCACTACAGCTTC
1 -CCACTACAACTTCAAGGG-TATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACAACTTC
* * *
42837173 AAGGAGATAAAGATTTGCTTTTGTAGCTTCAATCCT-A
64 AGGGAGAT-AAGATTTGCTTCTGTAGCTTTAAT-CTGA
*** * *** * * * *
42837210 TCCACTACAACTTCAATAATATAAGATTTGATGACATAACTTCCTCTTGCTCCATTACATCTTCA
1 -CCACTACAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACAACTTCA
*
42837275 GGGAGATAAGATTTGCTTTCTGTAACTTTAATCTGA
65 GGGAGATAAGATTTGC-TTCTGTAGCTTTAATCTGA
* * * ** * * * **
42837311 CCCACTACAACTTTAGGGGTATAAGATTCAATGTTATAGCCTCATCTTACTCCACTGTAACTTCA
1 -CCACTACAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACAACTTCA
* ** * *
42837376 GGGAGATAAGATTTTCTAT-TGTAATTTTAGTCCGA
65 GGGAGATAAGATTTGCT-TCTGTAGCTTTAATCTGA
* * * *
42837411 CCAACAACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTTATCTTGCTACACTACAACTTCA
1 CC-ACTACAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACAACTTCA
* *
42837476 GGGAGATAAAGATTTGCTT-TCGTAGCTTCAATATGA
65 GGGAGAT-AAGATTTGCTTCT-GTAGCTTTAATCTGA
** * *
42837512 CCCACTGTAACTTCAAGGGTATAGGATTCGATGTTGTAGATTCAT-TATGCTCCACTACAACTTC
1 -CCACTACAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCT-TGCTCCACTACAACTTC
* * *
42837576 AGGGAGATAAATATTTACTTCTGTAGTTTTA
64 AGGGAGAT-AAGATTTGCTTCTGTAGCTTTA
42837607 CTCCATTCCA
Statistics
Matches: 563, Mismatches: 111, Indels: 43
0.79 0.15 0.06
Matches are distributed among these distances:
97 4 0.01
98 67 0.12
99 13 0.02
100 157 0.28
101 311 0.55
102 11 0.02
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (99 bp):
CCACTACAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACAACTTCAG
GGAGATAAGATTTGCTTCTGTAGCTTTAATCTGA
Found at i:42837097 original size:48 final size:50
Alignment explanation
Indices: 42836757--42837203 Score: 164
Period size: 50 Copynumber: 8.9 Consensus size: 50
42836747 AAAATTATCC
* * * * * * * *
42836757 TGCTCCATTGCATCTTCAAGGGGATAGGACTCGCTAATATAGTTTCAATC-
1 TGCTCCATTGCAACTTCAAGGAGATAGGATTTGATATTGTAGCTTC-ATCT
* * * * * * * *
42836807 CGATCCACTGCAACTTCAGGGATATAGGATTTGATGTTGTAACTTCCTCT
1 TGCTCCATTGCAACTTCAAGGAGATAGGATTTGATATTGTAGCTTCATCT
* * * * * ** ** *
42836857 TGCTCCAGTGTATCTCCAAGGAAATAATATTTTCT-TCTATAGCTTCAATC-
1 TGCTCCATTGCAACTTCAAGGAGATAGGATTTGATAT-TGTAGCTTC-ATCT
* * * * * *
42836907 TGATCCACTGCAACTTCAGGGATATAGGATTTGATGA-CGTAGTTTCATCT
1 TGCTCCATTGCAACTTCAAGGAGATAGGATTTGAT-ATTGTAGCTTCATCT
* * * * * * *
42836957 TGCTCCACTGCATCTTC-AGGTAGATAAGATTTGCT-TGCTGCAACTTTAATC-
1 TGCTCCATTGCAACTTCAAGG-AGATAGGATTTGATAT--TGTAGC-TTCATCT
* * * * *
42837008 TGAC-CTACTACAACTTCAAGG-GTATAGGATTT-AGTGTTGTAGCCTCATCT
1 TG-CTCCATTGCAACTTCAAGGAG-ATAGGATTTGA-TATTGTAGCTTCATCT
* *
42837058 TGCTCCATTGCAACTTCAAGGAGA-A-GATTTGTTATTGTAGCTTTAAT-T
1 TGCTCCATTGCAACTTCAAGGAGATAGGATTTGATATTGTAGC-TTCATCT
* * * * *
42837106 TGATCCATTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCT
1 TGCTCCATTGCAACTTCAAGGAGATAGGATTTGATATTGTAGCTTCATCT
* * * * * * *
42837156 TGCTTCACTACAGCTTCAAGGAGATAAAGATTTGCTTTTGTAGCTTCA
1 TGCTCCATTGCAACTTCAAGGAGAT-AGGATTTGATATTGTAGCTTCA
42837204 ATCCTATCCA
Statistics
Matches: 282, Mismatches: 90, Indels: 49
0.67 0.21 0.12
Matches are distributed among these distances:
48 35 0.12
49 22 0.08
50 171 0.61
51 44 0.16
52 10 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (50 bp):
TGCTCCATTGCAACTTCAAGGAGATAGGATTTGATATTGTAGCTTCATCT
Found at i:42837425 original size:201 final size:201
Alignment explanation
Indices: 42837216--42837585 Score: 465
Period size: 201 Copynumber: 1.8 Consensus size: 201
42837206 CCTATCCACT
* * * * *
42837216 ACAACTTCAATAATATAAGATTTGATGACATAACTTCCTCTTGCTCCATTACATCTTCAGGGAGA
1 ACAACTTCAAGAATATAAGATTTGATGACATAACTTCATCTTGCTACACTACAACTTCAGGGAGA
* * * *
42837281 T-AAGATTTGCTTTCTGTAACTTTAATCTGACCCACTACAACTTTAGGGGTATAAGATTCAATGT
66 TAAAGATTTGCTTTC-GTAACTTCAATATGACCCACTACAACTTCAAGGGTATAAGATTCAATGT
* **
42837345 TATAGCCTCATCT-TACTCCACTGTAACTTCAGGGAGATAAGATTTTCTATTGTAATTTTAGTCC
130 TATAGACTCAT-TATACTCCACTACAACTTCAGGGAGATAAGATTTTCTATTGTAATTTTAGTCC
42837409 GACCAACA
194 GACCAACA
** *** * *
42837417 ACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTTATCTTGCTACACTACAACTTCAGGGAGA
1 ACAACTTCAAGAATATAAGATTTGATGACATAACTTCATCTTGCTACACTACAACTTCAGGGAGA
* ** * *
42837482 TAAAGATTTGCTTTCGTAGCTTCAATATGACCCACTGTAACTTCAAGGGTATAGGATTCGATGTT
66 TAAAGATTTGCTTTCGTAACTTCAATATGACCCACTACAACTTCAAGGGTATAAGATTCAATGTT
* * *
42837547 GTAGATTCATTATGCTCCACTACAACTTCAGGGAGATAA
131 ATAGACTCATTATACTCCACTACAACTTCAGGGAGATAA
42837586 ATATTTACTT
Statistics
Matches: 140, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
200 1 0.01
201 126 0.90
202 13 0.09
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (201 bp):
ACAACTTCAAGAATATAAGATTTGATGACATAACTTCATCTTGCTACACTACAACTTCAGGGAGA
TAAAGATTTGCTTTCGTAACTTCAATATGACCCACTACAACTTCAAGGGTATAAGATTCAATGTT
ATAGACTCATTATACTCCACTACAACTTCAGGGAGATAAGATTTTCTATTGTAATTTTAGTCCGA
CCAACA
Found at i:42837471 original size:50 final size:50
Alignment explanation
Indices: 42836810--42837576 Score: 272
Period size: 50 Copynumber: 15.3 Consensus size: 50
42836800 TTCAATCCGA
* * * *
42836810 TCCACTGCAACTTC-AGGGATATAGGATTTGATGTTGTAACTTCCTCTTGC
1 TCCACTACAACTTCAAGGG-TATAAGATTTGATGTTGTAGCTTCATCTTGC
* ** * * ** * ** * *
42836860 TCCAGTGTATCTCCAAGGAAATAATATTTTCT-TCTATAGCTTCAATC-TGA
1 TCCACTACAACTTCAAGGGTATAAGATTTGATGT-TGTAGCTTC-ATCTTGC
* * ** *
42836910 TCCACTGCAACTTC-AGGGATATAGGATTTGATGACGTAGTTTCATCTTGC
1 TCCACTACAACTTCAAGGG-TATAAGATTTGATGTTGTAGCTTCATCTTGC
* * * * * * *
42836960 TCCACTGCATCTTC-A-GGTAGATAAGATTTGCTTGCTGCAACTTTAATC-TGAC
1 TCCACTACAACTTCAAGGGT--ATAAGATTTG-ATGTTGTAGC-TTCATCTTG-C
* * *
42837012 -CTACTACAACTTCAAGGGTATAGGATTT-AGTGTTGTAGCCTCATCTTGC
1 TCCACTACAACTTCAAGGGTATAAGATTTGA-TGTTGTAGCTTCATCTTGC
* * * * * * *
42837061 TCCATTGCAACTTCAA-GG-AGAAGATTTGTTATTGTAGCTTTAAT-TTGA
1 TCCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGC-TTCATCTTGC
* * * *
42837109 TCCATTGCAACTTC-AGGGATATAGGATTTGATGTCGTAGCTTCATCTTGC
1 TCCACTACAACTTCAAGGG-TATAAGATTTGATGTTGTAGCTTCATCTTGC
* * * * * *
42837159 TTCACTACAGCTTCAAGGAG-ATAAAGATTTGCTTTTGTAGCTTCAATCCT-A
1 TCCACTACAACTTCAAGG-GTAT-AAGATTTGATGTTGTAGCTTC-ATCTTGC
*** *** * *
42837210 TCCACTACAACTTCAATAATATAAGATTTGATGACATAACTTCCTCTTGC
1 TCCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGC
* * * * * * *
42837260 TCCATTACATCTTC-AGGGAGATAAGATTTGCTTTCTGTAACTTTAATC-TGAC
1 TCCACTACAACTTCAAGGG-TATAAGATTTGATGT-TGTAGC-TTCATCTTG-C
* * ** * * *
42837312 -CCACTACAACTTTAGGGGTATAAGATTCAATGTTATAGCCTCATCTTAC
1 TCCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGC
** * ** * ** * *
42837361 TCCACTGTAACTTC-AGGGAGATAAGATTTTCTATTGTAATTTTAGTC-CGAC
1 TCCACTACAACTTCAAGGG-TATAAGATTTGATGTTGTAGCTTCA-TCTTG-C
* * *
42837412 -CAACAACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTTATCTTGC
1 TCCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGC
* * * *
42837461 TACACTACAACTTC-AGGGAGATAAAGATTTGCT-TTCGTAGCTTCAAT-ATGAC
1 TCCACTACAACTTCAAGGG-TAT-AAGATTTGATGTT-GTAGCTTC-ATCTTG-C
** * * *
42837513 -CCACTGTAACTTCAAGGGTATAGGATTCGATGTTGTAGATTCAT-TATGC
1 TCCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCT-TGC
42837562 TCCACTACAACTTCA
1 TCCACTACAACTTCA
42837577 GGGAGATAAA
Statistics
Matches: 506, Mismatches: 161, Indels: 100
0.66 0.21 0.13
Matches are distributed among these distances:
47 1 0.00
48 35 0.07
49 45 0.09
50 265 0.52
51 130 0.26
52 27 0.05
53 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (50 bp):
TCCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGC
Found at i:42845622 original size:26 final size:26
Alignment explanation
Indices: 42845572--42845656 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 26
42845562 ATGATGATGG
* *
42845572 TAAAATAAAAATACAT-ACATGAATAA
1 TAAAAT-AAAATAAATAACATAAATAA
42845598 TAAAATAAAATAAATAACACT-AATAA
1 TAAAATAAAATAAATAACA-TAAATAA
* * *
42845624 -ATAATACAATTAATAACATAAATAA
1 TAAAATAAAATAAATAACATAAATAA
*
42845649 AAAAATAA
1 TAAAATAA
42845657 TAGTAATGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
24 1 0.02
25 28 0.57
26 19 0.39
27 1 0.02
ACGTcount: A:0.68, C:0.07, G:0.01, T:0.24
Consensus pattern (26 bp):
TAAAATAAAATAAATAACATAAATAA
Found at i:42845843 original size:3 final size:3
Alignment explanation
Indices: 42845830--42845864 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
42845820 ACCGAAAATA
42845830 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
42845865 ATAAATAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:42846377 original size:42 final size:42
Alignment explanation
Indices: 42846316--42846399 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
42846306 TGAATGGAGA
*
42846316 TGTAACATCCGCGTTATTGAATCGGAGTTGGAACAGTAATAG
1 TGTAACATCCGCGTGATTGAATCGGAGTTGGAACAGTAATAG
* * *
42846358 TGTAACATCTGCGTGATTGAATCGGATTTGGAACAGTGATAG
1 TGTAACATCCGCGTGATTGAATCGGAGTTGGAACAGTAATAG
42846400 AGTACAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (42 bp):
TGTAACATCCGCGTGATTGAATCGGAGTTGGAACAGTAATAG
Found at i:42848326 original size:18 final size:18
Alignment explanation
Indices: 42848303--42848339 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42848293 TTTGTGATCA
*
42848303 AAATTGAAAGTGAATGTG
1 AAATTGAAAGTGAAAGTG
*
42848321 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
42848339 A
1 A
42848340 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Done.