Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold138
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: 1735418
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2489 characters in sequence are not A, C, G, or T
File 1 of 11
Found at i:1064 original size:2 final size:2
Alignment explanation
Indices: 1051--1085 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1041 GTTGACGATA
*
1051 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1086 TAAAATCACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4631 original size:2 final size:2
Alignment explanation
Indices: 4624--4667 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4614 TAACATATGT
4624 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4666 GA
1 GA
4668 CCTGTGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8393 original size:11 final size:11
Alignment explanation
Indices: 8336--8398 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
8326 ACATGAAAAT
8336 ATATAAATAATA
1 ATATAAAT-ATA
* *
8348 TTTTAAATATA
1 ATATAAATATA
8359 AT-TATAATAT-
1 ATATA-AATATA
8369 ATA-AAA-AT-
1 ATATAAATATA
8377 ATATAAATATA
1 ATATAAATATA
8388 ATATAAATATA
1 ATATAAATATA
8399 TACATTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
8 5 0.12
9 5 0.12
10 7 0.16
11 20 0.47
12 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATAAATATA
Found at i:10267 original size:1 final size:1
Alignment explanation
Indices: 10232--10256 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
10222 ATCTTAAATG
10232 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
10257 CCAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13491 original size:52 final size:52
Alignment explanation
Indices: 13429--13527 Score: 198
Period size: 52 Copynumber: 1.9 Consensus size: 52
13419 TAAATGGTAC
13429 AGATATTTTCATTATCTTCTATTATGTAGAATGATTCTGCAGCACAAGTGCT
1 AGATATTTTCATTATCTTCTATTATGTAGAATGATTCTGCAGCACAAGTGCT
13481 AGATATTTTCATTATCTTCTATTATGTAGAATGATTCTGCAGCACAA
1 AGATATTTTCATTATCTTCTATTATGTAGAATGATTCTGCAGCACAA
13528 AGTGGCTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (52 bp):
AGATATTTTCATTATCTTCTATTATGTAGAATGATTCTGCAGCACAAGTGCT
Found at i:13939 original size:15 final size:15
Alignment explanation
Indices: 13919--13948 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13909 CAAGACTTAA
*
13919 TCCCAATATATTTGG
1 TCCCAATATACTTGG
13934 TCCCAATATACTTGG
1 TCCCAATATACTTGG
13949 GGCCAACAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
TCCCAATATACTTGG
Found at i:15281 original size:123 final size:123
Alignment explanation
Indices: 15062--15307 Score: 474
Period size: 123 Copynumber: 2.0 Consensus size: 123
15052 AGGGTCCATA
15062 AACGCGTTGTTGATGGTTTGGAGGGCGATTCATCTCATGCACCTGCGGCTGTGGGAACCAAGGTT
1 AACGCGTTGTTGATGGTTTGGAGGGCGATTCATCTCATGCACCTGCGGCTGTGGGAACCAAGGTT
*
15127 TCAACAAGGCTGCTAGTCCCCGCCGCACAAGCTGGAAGTTTGATTGGAAAACAAGGAG
66 TCAACAAGGCTGCTAGTCCCCGCCACACAAGCTGGAAGTTTGATTGGAAAACAAGGAG
*
15185 AACGCGTTGTTGATGGTTTGGAGGGCGATTCATCTCATGCATCTGCGGCTGTGGGAACCAAGGTT
1 AACGCGTTGTTGATGGTTTGGAGGGCGATTCATCTCATGCACCTGCGGCTGTGGGAACCAAGGTT
15250 TCAACAAGGCTGCTAGTCCCCGCCACACAAGCTGGAAGTTTGATTGGAAAACAAGGAG
66 TCAACAAGGCTGCTAGTCCCCGCCACACAAGCTGGAAGTTTGATTGGAAAACAAGGAG
15308 CAATTGTCAA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (123 bp):
AACGCGTTGTTGATGGTTTGGAGGGCGATTCATCTCATGCACCTGCGGCTGTGGGAACCAAGGTT
TCAACAAGGCTGCTAGTCCCCGCCACACAAGCTGGAAGTTTGATTGGAAAACAAGGAG
Found at i:16093 original size:21 final size:20
Alignment explanation
Indices: 16045--16096 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
16035 TAAATCCGTC
* *
16045 TTATTTTGTTTTTAAAATTA
1 TTATTTTATTTTTAAAAATA
16065 TTATTTTATTTTTAAAAATA
1 TTATTTTATTTTTAAAAATA
*
16085 TTTTATTTATTT
1 TTAT-TTTATTT
16097 ATTTATATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTTTAAAAATA
Found at i:16133 original size:15 final size:15
Alignment explanation
Indices: 16113--16173 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 15
16103 ATTGAGCGTG
16113 ATATAAAGAAATAT-A
1 ATATAAA-AAATATAA
16128 ATATAATAAAATATAA
1 ATATAA-AAAATATAA
16144 ATAT---AAATATAA
1 ATATAAAAAATATAA
16156 ATATAATAAAAATATAA
1 ATAT-A-AAAAATATAA
16173 A
1 A
16174 AATATAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 12 0.31
15 12 0.31
16 6 0.15
17 9 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
ATATAAAAAATATAA
Found at i:16147 original size:6 final size:6
Alignment explanation
Indices: 16121--16184 Score: 73
Period size: 6 Copynumber: 11.0 Consensus size: 6
16111 TGATATAAAG
*
16121 AAATAT -AATAT -AATA- AAATAT AAATAT AAATAT AAATAT -AATAA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
16165 AAATAT AAAAATAT AAATAT
1 AAATAT --AAATAT AAATAT
16185 TTTAAAATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
5 17 0.33
6 28 0.55
8 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:16155 original size:37 final size:37
Alignment explanation
Indices: 16113--16184 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
16103 ATTGAGCGTG
*
16113 ATATAAAGA-AAT-ATAATATAATAAAATATAAATATAA
1 ATATAAAGATAATAAAAATAT-A-AAAATATAAATATAA
*
16150 ATATAAATATAATAAAAATATAAAAATATAAATAT
1 ATATAAAGATAATAAAAATATAAAAATATAAATAT
16185 TTTAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 21 0.68
38 4 0.13
39 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (37 bp):
ATATAAAGATAATAAAAATATAAAAATATAAATATAA
Found at i:16174 original size:8 final size:8
Alignment explanation
Indices: 16127--16181 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
16117 AAAGAAATAT
16127 AATATAATA
1 AATATAA-A
*
16136 AA-ATATA
1 AATATAAA
16143 AATAT--A
1 AATATAAA
16149 AATATAAA
1 AATATAAA
*
16157 TATAATAAA
1 AAT-ATAAA
16166 AATATAAA
1 AATATAAA
16174 AATATAAA
1 AATATAAA
16182 TATTTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
6 6 0.15
7 3 0.08
8 21 0.54
9 9 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AATATAAA
Found at i:16177 original size:31 final size:27
Alignment explanation
Indices: 16121--16184 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 27
16111 TGATATAAAG
16121 AAATATAATATAATAAAATATAAATAT
1 AAATATAATATAATAAAATATAAATAT
16148 AAATATAAATATAATAAAAATATAAAAATAT
1 AAATAT-AATATAAT-AAAATAT--AAATAT
16179 AAATAT
1 AAATAT
16185 TTTAAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 6 0.18
28 8 0.24
29 7 0.21
31 12 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
AAATATAATATAATAAAATATAAATAT
Found at i:16190 original size:25 final size:24
Alignment explanation
Indices: 16121--16207 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 24
16111 TGATATAAAG
16121 AAATAT-AATATAATAAAATATAAATAT
1 AAATATAAATATAATAAAAT-T--A-AT
16148 AAATATAAATATAATAAAAATATAA-
1 AAATATAAATATAAT-AAAAT-TAAT
**
16173 AAATATAAATATTTTAAAATTAAT
1 AAATATAAATATAATAAAATTAAT
16197 ATAATATAAAT
1 A-AATATAAAT
16208 TATTAATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.06
24 6 0.11
25 22 0.41
26 1 0.02
27 7 0.13
28 8 0.15
29 7 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AAATATAAATATAATAAAATTAAT
Found at i:19486 original size:16 final size:16
Alignment explanation
Indices: 19465--19497 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19455 CAATAAACAA
19465 GGAAATTGACACATTT
1 GGAAATTGACACATTT
19481 GGAAATTGACACATTT
1 GGAAATTGACACATTT
19497 G
1 G
19498 ACTCAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (16 bp):
GGAAATTGACACATTT
Found at i:20857 original size:3 final size:3
Alignment explanation
Indices: 20813--20842 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20803 GTTATTTATG
20813 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20843 AATCTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21221 original size:24 final size:20
Alignment explanation
Indices: 21180--21221 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
21170 AAATTCAAAT
21180 ATAAATTATAAAATAATAAA
1 ATAAATTATAAAATAATAAA
* *
21200 ATAAA-TATATAATAATTAA
1 ATAAATTATAAAATAATAAA
21219 ATA
1 ATA
21222 CATCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATTATAAAATAATAAA
Found at i:22977 original size:14 final size:14
Alignment explanation
Indices: 22958--22999 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
22948 TCATTAATTT
*
22958 TAAATATGATTAAA
1 TAAATATAATTAAA
22972 TAAATATAATATAAA
1 TAAATATAAT-TAAA
22987 TAAA-ATAATTAAA
1 TAAATATAATTAAA
23000 ATATGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 14 0.54
15 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
TAAATATAATTAAA
Found at i:23008 original size:19 final size:19
Alignment explanation
Indices: 22959--23012 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
22949 CATTAATTTT
*
22959 AAATATGATTAAATAAATA
1 AAATATGATAAAATAAATA
* * *
22978 TAATATAAATAAAATAATTA
1 AAATAT-GATAAAATAAATA
22998 AAATATGATAAAATA
1 AAATATGATAAAATA
23013 TGTTTTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
AAATATGATAAAATAAATA
Found at i:24157 original size:13 final size:13
Alignment explanation
Indices: 24136--24174 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
24126 ACTTGGTAAC
24136 AAAAATAAAATTA
1 AAAAATAAAATTA
* *
24149 AAGAATAAAGATAA
1 AAAAATAAA-ATTA
24163 AAAAATAAAATT
1 AAAAATAAAATT
24175 TTTAATCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (13 bp):
AAAAATAAAATTA
Found at i:27187 original size:22 final size:22
Alignment explanation
Indices: 27159--27213 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
27149 TGGACATGTT
27159 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
27181 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
27203 AAAAATGCATG
1 AAAAATGCATG
27214 GTCAAAGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:28172 original size:20 final size:19
Alignment explanation
Indices: 28122--28199 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
28112 GGTAAAAAGA
28122 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
28141 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
*
28161 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* * *
28181 GAAAAATGTATTGATACAT
1 -CATAATGTATCGATACAT
28200 CAGGGTAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.89
21 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:28197 original size:40 final size:39
Alignment explanation
Indices: 28122--28199 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
28112 GGTAAAAAGA
* *
28122 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
28161 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
28200 CAGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:36535 original size:20 final size:20
Alignment explanation
Indices: 36510--36587 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
36500 GGTAAAAAGA
36510 CATAATGTATCGATACATTG
1 CATAATGTATCGATACATTG
*
36530 CATAATATATCGATACATT-
1 CATAATGTATCGATACATTG
*
36549 CATACATGTATCGATATATTG
1 CATA-ATGTATCGATACATTG
* *
36570 AAAAATGTATCGATACAT
1 CATAATGTATCGATACAT
36588 CAGGGTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.08
20 44 0.88
21 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
CATAATGTATCGATACATTG
Found at i:36894 original size:2 final size:2
Alignment explanation
Indices: 36887--36911 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36877 GATTAATCGT
36887 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36912 TCATATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37455 original size:105 final size:104
Alignment explanation
Indices: 37323--37726 Score: 393
Period size: 105 Copynumber: 3.8 Consensus size: 104
37313 AAATTATAAA
* * * **
37323 CATAAAGTAAGTGATCTTCAAAGAAGAAATCGATAATTGAATTTAAATAATTAAAAAAATGTAAA
1 CATAAAGTAAATGATCTTCAAGGAAGAAATCGATGATTGAATACAAATAATTAAAAAAATGTAAA
* * *
37388 ATCTAGAAAGATAACTTCTACAATCATATTTTAATTGTAG
66 ATCT-GAAACATAACTTCCACTATCATATTTTAATTGTAG
* * ** * *
37428 CATAGAGTAAATGATCTTCAAGGAAGAAATTGATGATTGAATACAAA-AACTTTTAAAAATATAG
1 CATAAAGTAAATGATCTTCAAGGAAGAAATCGATGATTGAATACAAATAA-TTAAAAAAATGTAA
* *
37492 AATCTAGAAACATAACTTCCACTATCAAATTTTTATTGTAG
65 AATCT-GAAACATAACTTCCACTATCATATTTTAATTGTAG
* * *
37533 CATAAAGTAAATAATCTTCAAGGTAA-AAATCGATGATT-AGATACAAATACTTAAAAAAAAGTA
1 CATAAAGTAAATGATCTTCAAGG-AAGAAATCGATGATTGA-ATACAAATAATTAAAAAAATGTA
* ** * *
37596 AAATCTGAAA-ATATTACTTCCACTATCGTATTTTGGTTGCAA
64 AAATCTGAAACATA--ACTTCCACTATCATATTTTAATTGTAG
* * * * ** * * *
37638 CATAGAGTAAATGATCTTCGAGGAATAAATCAATGATTGGGTATAAACACTTAAAAAAATGTAGA
1 CATAAAGTAAATGATCTTCAAGGAAGAAATCGATGATTGAATACAAATAATTAAAAAAATGTA-A
*
37703 AATCTGAAAACATAACTTTCACTA
65 AATCTG-AAACATAACTTCCACTA
37727 AATGATCTTC
Statistics
Matches: 247, Mismatches: 41, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
103 3 0.01
104 9 0.04
105 210 0.85
106 19 0.08
107 3 0.01
108 3 0.01
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (104 bp):
CATAAAGTAAATGATCTTCAAGGAAGAAATCGATGATTGAATACAAATAATTAAAAAAATGTAAA
ATCTGAAACATAACTTCCACTATCATATTTTAATTGTAG
Found at i:39184 original size:20 final size:21
Alignment explanation
Indices: 39143--39184 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
39133 AAAGTAGAGT
*
39143 ACAAAATTTAACTACCAAATTA
1 ACAAAATATAACTA-CAAATTA
39165 ACAAAATATAACTA-AAATTA
1 ACAAAATATAACTACAAATTA
39185 TATATTACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
ACAAAATATAACTACAAATTA
Found at i:39230 original size:3 final size:3
Alignment explanation
Indices: 39224--39273 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
39214 TTTCATCATT
39224 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39272 TT
1 TT
39274 GTTGTTGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39278 original size:3 final size:3
Alignment explanation
Indices: 39272--39300 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39262 ATTATTATTA
39272 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
39301 TTACAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:40641 original size:27 final size:27
Alignment explanation
Indices: 40605--40681 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
40595 AAAGCCACCA
*
40605 TTTGTGTTTGTCAACAATGGTGGTTAC
1 TTTGTGTTTGTCAAAAATGGTGGTTAC
* *
40632 TTTGTATTTGTCAAAAATGGTGGTTCC
1 TTTGTGTTTGTCAAAAATGGTGGTTAC
* *
40659 TTTTTGTTTGTCAAAAATTGTGG
1 TTTGTGTTTGTCAAAAATGGTGG
40682 CTTGTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (27 bp):
TTTGTGTTTGTCAAAAATGGTGGTTAC
Found at i:40772 original size:13 final size:13
Alignment explanation
Indices: 40754--40787 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
40744 AAGCTCTCTC
*
40754 ATCCCTTTCTTGT
1 ATCCCTCTCTTGT
40767 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
40780 ATCCCTCT
1 ATCCCTCT
40788 TCAATTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.38, G:0.06, T:0.47
Consensus pattern (13 bp):
ATCCCTCTCTTGT
Found at i:43263 original size:21 final size:22
Alignment explanation
Indices: 43234--43279 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
43224 TCTTTAGACA
** *
43234 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
43256 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
43277 AGT
1 AGT
43280 TTCAACATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:45215 original size:26 final size:26
Alignment explanation
Indices: 45158--45228 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
45148 CAAAAGCTGC
45158 CCTTTGTGTTTGTCAATAATGGTGGTT
1 CCTTTGTGTTTGTCAA-AATGGTGGTT
* *
45185 ACTTTGTATTTGTCAAAATGGTGGTT
1 CCTTTGTGTTTGTCAAAATGGTGGTT
*
45211 CCTTTTTGTTTGTCAAAA
1 CCTTTGTGTTTGTCAAAA
45229 ATTGTGGCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 25 0.64
27 14 0.36
ACGTcount: A:0.20, C:0.11, G:0.21, T:0.48
Consensus pattern (26 bp):
CCTTTGTGTTTGTCAAAATGGTGGTT
Found at i:45215 original size:53 final size:51
Alignment explanation
Indices: 45158--45259 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 51
45148 CAAAAGCTGC
*
45158 CCTTTGTGTTTGTCAATAATGGTGG-TTACTTTGTATTTGTCAAAA-TGGTGGTT
1 CCTTTGTGTTTGTCAAAAATGGTGGCTTA--TTG--TTTGTCAAAATTGGTGGTT
* *
45211 CCTTTTTGTTTGTCAAAAATTGTGGCTTATTGTTTGTCAAAATTGGTGG
1 CCTTTGTGTTTGTCAAAAATGGTGGCTTATTGTTTGTCAAAATTGGTGG
45260 GTGATTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
50 10 0.23
51 6 0.14
52 3 0.07
53 22 0.50
54 3 0.07
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.47
Consensus pattern (51 bp):
CCTTTGTGTTTGTCAAAAATGGTGGCTTATTGTTTGTCAAAATTGGTGGTT
Found at i:45259 original size:24 final size:25
Alignment explanation
Indices: 45193--45259 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
45183 TTACTTTGTA
*
45193 TTTGTCAAAA-TGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG-T-CTTATTG
45219 TTTGTCAAAAATT-GTGG-CTTATTG
1 TTTGTC-AAAATTGGTGGTCTTATTG
45243 TTTGTCAAAATTGGTGG
1 TTTGTCAAAATTGGTGG
45260 GTGATTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 6 0.16
24 16 0.43
26 6 0.16
27 8 0.22
28 1 0.03
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.46
Consensus pattern (25 bp):
TTTGTCAAAATTGGTGGTCTTATTG
Found at i:46226 original size:13 final size:13
Alignment explanation
Indices: 46208--46233 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46198 TACACCAAGT
46208 ATGTATCGATACA
1 ATGTATCGATACA
46221 ATGTATCGATACA
1 ATGTATCGATACA
46234 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:52441 original size:13 final size:13
Alignment explanation
Indices: 52423--52461 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
52413 ACATTTTTCT
52423 TTGTATCGATACA
1 TTGTATCGATACA
52436 TTGTATCGATACA
1 TTGTATCGATACA
*
52449 CTGTATCGATACA
1 TTGTATCGATACA
52462 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:52625 original size:20 final size:20
Alignment explanation
Indices: 52582--52627 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
52572 AAATCTTTTG
52582 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
52603 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
52623 CAAAA
1 CAAAA
52628 CCAGCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:59366 original size:14 final size:14
Alignment explanation
Indices: 59336--59374 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
59326 TAAATTATTT
59336 AAATGAAAAATAACA
1 AAAT-AAAAATAACA
* *
59351 AAATACAAATACCA
1 AAATAAAAATAACA
59365 AAATAAAAAT
1 AAATAAAAAT
59375 TAGTATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (14 bp):
AAATAAAAATAACA
Found at i:59433 original size:24 final size:20
Alignment explanation
Indices: 59392--59433 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
59382 AAATTCAAAT
59392 ATAAATTATAAAATAATAAA
1 ATAAATTATAAAATAATAAA
* *
59412 ATAAA-TATATAATAATTAA
1 ATAAATTATAAAATAATAAA
59431 ATA
1 ATA
59434 CAACTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATTATAAAATAATAAA
Found at i:60278 original size:17 final size:17
Alignment explanation
Indices: 60256--60289 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
60246 CGCGAAATAG
60256 CAATCGCGATACCGTAA
1 CAATCGCGATACCGTAA
60273 CAATCGCGATACCGTAA
1 CAATCGCGATACCGTAA
60290 TGCCACTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (17 bp):
CAATCGCGATACCGTAA
Found at i:62350 original size:15 final size:15
Alignment explanation
Indices: 62330--62358 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62320 TCAAGGATAC
62330 TTTTAATTTTTTTTA
1 TTTTAATTTTTTTTA
62345 TTTTAATTTTTTTT
1 TTTTAATTTTTTTT
62359 CTTTGAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTAATTTTTTTTA
Found at i:63250 original size:19 final size:21
Alignment explanation
Indices: 63226--63265 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
63216 ACTATTTTGC
*
63226 ATATG-TACAC-TAATTAAAA
1 ATATGTTACACATAAATAAAA
63245 ATATGTTACACATAAATAAAA
1 ATATGTTACACATAAATAAAA
63266 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (21 bp):
ATATGTTACACATAAATAAAA
Found at i:64316 original size:1 final size:1
Alignment explanation
Indices: 64310--64336 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
64300 TAGCACTAAG
64310 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
64337 AACTTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:66908 original size:362 final size:362
Alignment explanation
Indices: 66243--67323 Score: 2162
Period size: 362 Copynumber: 3.0 Consensus size: 362
66233 TGTGCTCAGC
66243 TGGCCAAGAAATGAATCATATGCATTAAGCCCCCACCCATTAAGCCAGAGTCTATGCCCAAATTA
1 TGGCCAAGAAATGAATCATATGCATTAAGCCCCCACCCATTAAGCCAGAGTCTATGCCCAAATTA
66308 GCTTTTATGTTTCTCTTTTCTATCTCTTTTCTTTTTTCTGGAGAAAATGCAACAACAAATTTGGC
66 GCTTTTATGTTTCTCTTTTCTATCTCTTTTCTTTTTTCTGGAGAAAATGCAACAACAAATTTGGC
66373 TAATGCAATGATATGAATATAAAACCAACTTAAAATGCCAAACAGCACAATATTACACCTAATAA
131 TAATGCAATGATATGAATATAAAACCAACTTAAAATGCCAAACAGCACAATATTACACCTAATAA
66438 CAGTATACTCTCCAGTCATTGACTATATCCCTACAACAGCTTTTGATTTGAAAACATGGGAAAAG
196 CAGTATACTCTCCAGTCATTGACTATATCCCTACAACAGCTTTTGATTTGAAAACATGGGAAAAG
66503 GCGTAAAATCTCTTATTTATCTGATAATAACGCTAGTAACATGGGAGGTAACATTCTCTTTTTTA
261 GCGTAAAATCTCTTATTTATCTGATAATAACGCTAGTAACATGGGAGGTAACATTCTCTTTTTTA
66568 TATCAACGTAGTTGACTAGACCAAAACCTTTATATCA
326 TATCAACGTAGTTGACTAGACCAAAACCTTTATATCA
66605 TGGCCAAGAAATGAATCATATGCATTAAGCCCCCACCCATTAAGCCAGAGTCTATGCCCAAATTA
1 TGGCCAAGAAATGAATCATATGCATTAAGCCCCCACCCATTAAGCCAGAGTCTATGCCCAAATTA
66670 GCTTTTATGTTTCTCTTTTCTATCTCTTTTCTTTTTTCTGGAGAAAATGCAACAACAAATTTGGC
66 GCTTTTATGTTTCTCTTTTCTATCTCTTTTCTTTTTTCTGGAGAAAATGCAACAACAAATTTGGC
66735 TAATGCAATGATATGAATATAAAACCAACTTAAAATGCCAAACAGCACAATATTACACCTAATAA
131 TAATGCAATGATATGAATATAAAACCAACTTAAAATGCCAAACAGCACAATATTACACCTAATAA
66800 CAGTATACTCTCCAGTCATTGACTATATCCCTACAACAGCTTTTGATTTGAAAACATGGGAAAAG
196 CAGTATACTCTCCAGTCATTGACTATATCCCTACAACAGCTTTTGATTTGAAAACATGGGAAAAG
66865 GCGTAAAATCTCTTATTTATCTGATAATAACGCTAGTAACATGGGAGGTAACATTCTCTTTTTTA
261 GCGTAAAATCTCTTATTTATCTGATAATAACGCTAGTAACATGGGAGGTAACATTCTCTTTTTTA
66930 TATCAACGTAGTTGACTAGACCAAAACCTTTATATCA
326 TATCAACGTAGTTGACTAGACCAAAACCTTTATATCA
66967 TGGCCAAGAAATGAATCATATGCATTAAGCCCCCACCCATTAAGCCAGAGTCTATGCCCAAATTA
1 TGGCCAAGAAATGAATCATATGCATTAAGCCCCCACCCATTAAGCCAGAGTCTATGCCCAAATTA
67032 GCTTTTATGTTTCTCTTTTCTATCTCTTTTCTTTTTTCTGGAGAAAATGCAACAACAAATTTGGC
66 GCTTTTATGTTTCTCTTTTCTATCTCTTTTCTTTTTTCTGGAGAAAATGCAACAACAAATTTGGC
67097 TAATGCAATGATATGAATATAAAACCAACTTAAAATGCCAAACAGCACAATATTACACCTAATAA
131 TAATGCAATGATATGAATATAAAACCAACTTAAAATGCCAAACAGCACAATATTACACCTAATAA
67162 CAGTATACTCTCCAGTCATTGACTATATCCCTACAACAGCTTTTGATTTGAAAACATGGGAAAAG
196 CAGTATACTCTCCAGTCATTGACTATATCCCTACAACAGCTTTTGATTTGAAAACATGGGAAAAG
67227 GCGTAAAATCTCTTATTTATCTGATAATAACGCTAGTAACATGGGAGGTAACATTCTCTTTTTTA
261 GCGTAAAATCTCTTATTTATCTGATAATAACGCTAGTAACATGGGAGGTAACATTCTCTTTTTTA
67292 TATCAACGTAGTTGACTAGACCAAAACCTTTA
326 TATCAACGTAGTTGACTAGACCAAAACCTTTA
67324 AAAAACCGGT
Statistics
Matches: 719, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
362 719 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (362 bp):
TGGCCAAGAAATGAATCATATGCATTAAGCCCCCACCCATTAAGCCAGAGTCTATGCCCAAATTA
GCTTTTATGTTTCTCTTTTCTATCTCTTTTCTTTTTTCTGGAGAAAATGCAACAACAAATTTGGC
TAATGCAATGATATGAATATAAAACCAACTTAAAATGCCAAACAGCACAATATTACACCTAATAA
CAGTATACTCTCCAGTCATTGACTATATCCCTACAACAGCTTTTGATTTGAAAACATGGGAAAAG
GCGTAAAATCTCTTATTTATCTGATAATAACGCTAGTAACATGGGAGGTAACATTCTCTTTTTTA
TATCAACGTAGTTGACTAGACCAAAACCTTTATATCA
Found at i:68740 original size:8 final size:9
Alignment explanation
Indices: 68717--68743 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
68707 ATAAAATATA
68717 TTAAAAATT
1 TTAAAAATT
68726 TTAAAAATT
1 TTAAAAATT
68735 TTAAAAATT
1 TTAAAAATT
68744 ATTTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAAAATT
Found at i:68795 original size:24 final size:26
Alignment explanation
Indices: 68766--68814 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
68756 ATATTTATAT
*
68766 ATTTTATAATT-AAATTTA-AATAAA
1 ATTTTATAATTCAAATATATAATAAA
*
68790 ATTTTATTATTCAAATATATAATAA
1 ATTTTATAATTCAAATATATAATAA
68815 TTTGAATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTTATAATTCAAATATATAATAAA
Found at i:68965 original size:6 final size:6
Alignment explanation
Indices: 68954--68987 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
68944 AACACAAATA
* *
68954 TATATG TATATG TCTATG TAAATG TATATG TATA
1 TATATG TATATG TATATG TATATG TATATG TATA
68988 AATGAAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (6 bp):
TATATG
Found at i:69547 original size:31 final size:33
Alignment explanation
Indices: 69486--69547 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
69476 TTATTTTATT
69486 TAAAATATTTATATATTTAATATAGGTAAAAGTA
1 TAAAATATTTATATATTTAATATA-GTAAAAGTA
69520 TAAAATA-TTATAT-TTTAAATATA-TAAAA
1 TAAAATATTTATATATTT-AATATAGTAAAA
69548 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 5 0.19
32 3 0.11
33 12 0.44
34 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (33 bp):
TAAAATATTTATATATTTAATATAGTAAAAGTA
Found at i:69557 original size:33 final size:34
Alignment explanation
Indices: 69484--69557 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 34
69474 TTTTATTTTA
**
69484 TTTAAAATATTTATATATTTAATATAGGTAAAAG
1 TTTAAAATATTTATATATTTAATATAGAAAAAAG
* * *
69518 TATAAAATA-TTATAT-TTTAAATATATAAAAAAT
1 TTTAAAATATTTATATATTT-AATATAGAAAAAAG
69551 TTTAAAA
1 TTTAAAA
69558 AAATTAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 3 0.09
33 22 0.67
34 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (34 bp):
TTTAAAATATTTATATATTTAATATAGAAAAAAG
Found at i:69580 original size:15 final size:14
Alignment explanation
Indices: 69559--69595 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
69549 ATTTTAAAAA
69559 AATTAAATATAATT
1 AATTAAATATAATT
*
69573 ATATTAAATATATTT
1 A-ATTAAATATAATT
69588 AATTAAAT
1 AATTAAAT
69596 TCGAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTAAATATAATT
Found at i:73727 original size:37 final size:37
Alignment explanation
Indices: 73677--73749 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
73667 AAGCAGTAAC
*
73677 TTAATTGATTTTGAACTAAATTAATCCAAGGGTCAAT
1 TTAATTAATTTTGAACTAAATTAATCCAAGGGTCAAT
73714 TTAATTAATTTTGAACTAAATTAATCCAAGGGTCAA
1 TTAATTAATTTTGAACTAAATTAATCCAAGGGTCAA
73750 GCTATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (37 bp):
TTAATTAATTTTGAACTAAATTAATCCAAGGGTCAAT
Found at i:73876 original size:30 final size:33
Alignment explanation
Indices: 73824--73887 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 33
73814 ATTTTACTTA
*
73824 ATTTTATTCAATTTGAATTATAATT-TAAATAAT
1 ATTTTATTCAATTTGAAATATAATTATAAA-AAT
73857 ATTTT-TT-AATTT-AAATATAATTATAAAAAT
1 ATTTTATTCAATTTGAAATATAATTATAAAAAT
73887 A
1 A
73888 AATAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 13 0.45
31 9 0.31
32 2 0.07
33 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (33 bp):
ATTTTATTCAATTTGAAATATAATTATAAAAAT
Found at i:78548 original size:38 final size:39
Alignment explanation
Indices: 78506--78589 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 39
78496 AAAACTTCAA
78506 AAAAAAAGT-CAAAAGCAAAAGCATAAA-AAAAACAAAAC
1 AAAAAAAGTACAAAAGCAAAAGCA-AAAGAAAAACAAAAC
* * * *
78544 -AAAAAAGTACAAAGGCAAAATCAAAAGGGAGAACAAAAC
1 AAAAAAAGTACAAAAGCAAAAGCAAAA-GAAAAACAAAAC
78583 AAAAAAA
1 AAAAAAA
78590 CAAAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
37 11 0.29
38 12 0.32
39 9 0.24
40 6 0.16
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.05
Consensus pattern (39 bp):
AAAAAAAGTACAAAAGCAAAAGCAAAAGAAAAACAAAAC
Found at i:79986 original size:27 final size:28
Alignment explanation
Indices: 79956--81037 Score: 821
Period size: 28 Copynumber: 38.9 Consensus size: 28
79946 CAGTCTTTTT
* *
79956 CTTTTAAAGTCCACAACTCCGTAGCAACTTTTT
1 CTTTTAAAGTCCACAACTCCGTGGC-AC----C
* ** *
79989 CTTTTAAAGTCCATAACTCTATGACACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
80017 CTTTTAAAGTCCACAACTCCGTAGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
80045 CTTTT-AAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
80072 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
80100 CTTTT-AAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
80127 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80155 CTTTT-AAGTCCATAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* **
80182 CTTTTAAAGTCCACAACTCGGTGGCTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80210 CTTTT-AAGTCCATAACTCGGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
** **
80237 CTTTTAAAGTCCACAACTTGGTGGCTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
80265 CTTTT-AAGTCTACAACTTCATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
80292 CTTTT-AAGTCCAAAACTTCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
80319 CTTTTAGAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
80347 CTTTT-AAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80374 CTTTTAAAGTCCATAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80402 CTTTT-AAGTCCAAAACTCCAG-GGCATC
1 CTTTTAAAGTCCACAACTCC-GTGGCACC
*
80429 CTTTT-AAGTTCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80456 CTTTTAAAGTCCACAACTCTGTGGCA-T
1 CTTTTAAAGTCCACAACTCCGTGGCACC
** **
80483 CTTTTTCAGTCCACAACTCTATGGCAGCC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CC
* * *
80512 CTTTTAAAGTTCACAACTCTGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
80540 C-TTTAAAGTCTATAGCTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80567 CTTTT-AGGTCCACAACTCCGAGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
80594 CTTTTAAAATCCATAACTCTGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80621 CTTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
80649 CTTTT-AACTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * * * *
80676 ATTTCAAAGCCCACAAGTCAGTGGTATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * * * *
80704 ATTTCAAAGCCCACAAGTCAGCGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * * *
80732 ATTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
80759 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT-AAAGTCCACAACTCCGTGGCACC
* * * * * * *
80788 ATTTCAAAGCCCATAACTCAGTGTCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
80816 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
80844 CTTTCAAA-ACCAACAAGTCAGTGGCAAC
1 CTTTTAAAGTCC-ACAACTCCGTGGCACC
* * * * *
80872 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* ** * ** *
80900 CTTTCAAAACCCACAAGTTAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * ** *
80928 CTTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
80956 CTTTCAAAGCCCATAAGTCAGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
** * * *
80984 CTTTTAAAACCCACAAATCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
81012 TTTTTAAAGCCCACAAGTCAGTGGCA
1 CTTTTAAAGTCCACAACTCCGTGGCA
81038 TCATTTCAAA
Statistics
Matches: 901, Mismatches: 129, Indels: 43
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.00
27 332 0.37
28 519 0.58
29 27 0.03
32 2 0.00
33 20 0.02
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCCGTGGCACC
Found at i:79992 original size:33 final size:34
Alignment explanation
Indices: 79918--80007 Score: 128
Period size: 33 Copynumber: 2.6 Consensus size: 34
79908 TTTAGTGGCA
* *
79918 TTTCTTTTCAAAGTCCACAACTCCATCGCAGTCTT
1 TTTCTTTT-AAAGTCCACAACTCCATAGCAGACTT
*
79953 TTTCTTTTAAAGTCCACAACTCCGTAGCA-ACTT
1 TTTCTTTTAAAGTCCACAACTCCATAGCAGACTT
*
79986 TTTCTTTTAAAGTCCATAACTC
1 TTTCTTTTAAAGTCCACAACTC
80008 TATGACACCC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 24 0.47
34 19 0.37
35 8 0.16
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.39
Consensus pattern (34 bp):
TTTCTTTTAAAGTCCACAACTCCATAGCAGACTT
Found at i:80056 original size:55 final size:55
Alignment explanation
Indices: 79956--81039 Score: 847
Period size: 55 Copynumber: 19.5 Consensus size: 55
79946 CAGTCTTTTT
* * * * *
79956 CTTTTAAAGTCCACAACTCCGTAGCAACTTTTTCTTTTAAAGTCCATAACTCTATGACACC
1 CTTTTAAAGTCCACAACTCCGTGGC-A----TCCTTTT-AAGTCCACAACTCTGTGGCACC
* *
80017 CTTTTAAAGTCCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
*
80072 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
*
80127 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCATAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
* * * *
80182 CTTTTAAAGTCCACAACTCGGTGGCTTCCTTTTAAGTCCATAACTCGGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
** * * *
80237 CTTTTAAAGTCCACAACTTGGTGGCTTCCTTTTAAGTCTACAACT-TCATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCT-GTGGCACC
* * *
80292 CTTTT-AAGTCCAAAACTTCGTGGCATCCTTTTAGAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTA-AGTCCACAACTCTGTGGCACC
* * * * *
80347 CTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCATAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCTGTGGCACC
* * *
80402 CTTTT-AAGTCCAAAACTCCAG-GGCATCCTTTTAAGTTCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCC-GTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
* * * *
80456 CTTTTAAAGTCCACAACTCTGTGGCATCTTTTTCAGTCCACAACTCTATGGCAGCC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCA-CC
* * * * * * *
80512 CTTTTAAAGTTCACAACTCTGTGGCATCCTTTAAAGTCTATAGCTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
* * * * *
80567 CTTTT-AGGTCCACAACTCCGAGGCACCCTTTTAAAATCCATAACTCTGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCTGTGGCACC
* * * * * *
80621 CTTTTTAAGTCCATAACTCCGTGGCACCCTTTTAACTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
* * * * * * * * * * * * *
80676 ATTTCAAAGCCCACAAGTCAGTGGTATCATTTCAAAGCCCACAAGTCAGCGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAACTCTGTGGCACC
* * * * * * * *
80732 ATTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTT--AAGTCCACAACTCTGTGGCACC
* * * * * * * * * * *
80788 ATTTCAAAGCCCATAACTCAGTGTCATCCTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAACTCTGTGGCACC
* * * * * * * * * *
80844 CTTTCAAA-ACCAACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCC-ACAACTCCGTGGCATCCTTT-TAAGTCCACAACTCTGTGGCACC
* ** * ** * * * *
80900 CTTTCAAAACCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGT-TAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAACTCT-GTGGCACC
* * * * * * ** * * *
80956 CTTTCAAAGCCCATAAGTCAGTGGCACCCTTTTAAAACCCACAAATCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCTGTGGCACC
* * * *
81012 TTTTTAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
81040 ATTTCAAAAC
Statistics
Matches: 888, Mismatches: 114, Indels: 47
0.85 0.11 0.04
Matches are distributed among these distances:
54 94 0.11
55 436 0.49
56 326 0.37
57 6 0.01
60 1 0.00
61 25 0.03
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
Found at i:80699 original size:28 final size:28
Alignment explanation
Indices: 80658--81082 Score: 557
Period size: 28 Copynumber: 15.2 Consensus size: 28
80648 CCTTTTAACT
* * *
80658 CCACAACTCCGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
80686 CCACAAGTCAGTGGTATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
80714 CCACAAGTCAGCGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
80742 CCACAAGTCAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
80770 CCACAAGTCAGTGGCA-CCATTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
* * *
80798 CCATAACTCAGTGTCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
80826 CCACAAGTCAGTGGCATCCTTTCAAAAC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
80854 CAACAAGTCAGTGGCAACCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
80882 CCACAAGTCAGTGGCATCCTTTCAAAAC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
80910 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
80938 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
80966 CCATAAGTCAGTGGCACCCTTTTAAAAC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
80994 CCACAAATCAGTGGCATCTTTTTAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
81022 CCACAAGTCAGTGGCATCATTTCAAAAC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
81050 CCATAAGTCAGTGGCA-CATTTTGAAAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
81078 CCACA
1 CCACA
81083 CAACTCAGCA
Statistics
Matches: 352, Mismatches: 42, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
27 2 0.01
28 348 0.99
29 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:82266 original size:2 final size:2
Alignment explanation
Indices: 82259--82291 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
82249 TTACTTGTTT
82259 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
82292 TGAAAATCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:86156 original size:67 final size:68
Alignment explanation
Indices: 86080--86221 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 68
86070 TGAACTTTGA
86080 ATTTTGAAAACTTTA-TTTTAAAATTTCAAATAAAATGTTTTTATTTTTCTTCT-TATCATTAGC
1 ATTTTGAAAACTTTATTTTTAAAATTTCAAATAAAATGTTTTTATTTTTCTTCTCT-TCATTAGC
86143 TTAG
65 TTAG
* *
86147 ATTTTGAAAACTTTATTTTTAAAATTTCAAATAAAATGTTTTTATTTTTTTTCTCTTCATTAGTT
1 ATTTTGAAAACTTTATTTTTAAAATTTCAAATAAAATGTTTTTATTTTTCTTCTCTTCATTAGCT
86212 TAG
66 TAG
86215 ATTTTGA
1 ATTTTGA
86222 TTGTGAGAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
67 15 0.21
68 55 0.77
69 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (68 bp):
ATTTTGAAAACTTTATTTTTAAAATTTCAAATAAAATGTTTTTATTTTTCTTCTCTTCATTAGCT
TAG
Found at i:87266 original size:17 final size:18
Alignment explanation
Indices: 87244--87283 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
87234 AGATATTACC
*
87244 TTAATTTT-TTAAAAATT
1 TTAATTTTATTAAAAATA
87261 TTAATTTTATTAAAAATA
1 TTAATTTTATTAAAAATA
87279 TTAAT
1 TTAAT
87284 AGACTAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTTATTAAAAATA
Found at i:88618 original size:19 final size:20
Alignment explanation
Indices: 88598--88635 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
88588 TATATATGAT
88598 AAAATCAAAATCATATCATA
1 AAAATCAAAATCATATCATA
* *
88618 AAAATTAACATCATATCA
1 AAAATCAAAATCATATCA
88636 ACAAACAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATCAAAATCATATCATA
Found at i:93006 original size:13 final size:13
Alignment explanation
Indices: 92988--93012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92978 CAAAGATCAG
92988 TGTATCGATACAA
1 TGTATCGATACAA
93001 TGTATCGATACA
1 TGTATCGATACA
93013 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:93090 original size:33 final size:33
Alignment explanation
Indices: 93053--93119 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
93043 AGTAGCTTAA
93053 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
93086 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
93119 A
1 A
93120 AATCGTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:93093 original size:13 final size:13
Alignment explanation
Indices: 93075--93099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93065 CAAAAAAATA
93075 TGTATCGATACAT
1 TGTATCGATACAT
93088 TGTATCGATACA
1 TGTATCGATACA
93100 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:94937 original size:3 final size:3
Alignment explanation
Indices: 94924--94966 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
94914 ATGTTTTGAA
94924 ATT ACTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
94967 TCTTGTAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:96711 original size:218 final size:217
Alignment explanation
Indices: 96426--96825 Score: 552
Period size: 218 Copynumber: 1.8 Consensus size: 217
96416 CCTTTTGGGT
* * * * *
96426 CTTTGAATTTATTGGATCTTAAAATTATTTTTTACTTCGAATTACATATCAGATACTTATTAGGC
1 CTTTAAATTTATGGGATCTTAAAATTATTTTTGACTTCGAATTACACATCAGATACTTAGTAGGC
** * * * *
96491 TTAAAGGTTTCATATTGTTAAATAGGTTTAAATTTTTAGATTGAACCG-GCCTATATCCATATGC
66 TTAAAGGTTAAAAATTGTTAAATAAGTTTAAATTTTTAGATTAAACCGAGCC-ATATCCATATCC
* * **
96555 ATATGCAATGTTT-ATTTACTAAAAACTCATTTTTTTTATCGTTCATCTTTCAATTTTATCAAGT
130 ATATACAATGTTTAATTT-CTAAAAACTCATTTTTTTAATCAATCATCTTTCAATTTTATCAAGT
96619 CAATTTGAAGTTCATATTTCTAGC
194 CAATTTGAAGTTCATATTTCTAGC
* * ** *
96643 CTTTAAATTTATGGGATTTTAAAATTATTTTTGGGCTTCGAATTACACATTGGATCCTTAGTAGG
1 CTTTAAATTTATGGGATCTTAAAATTATTTTT-GACTTCGAATTACACATCAGATACTTAGTAGG
* * *
96708 CTTAATGGTTAAAAATTGTTAAATAAGTTTAAATTTTTAGATTAAATCGATCCATATCCATATCC
65 CTTAAAGGTTAAAAATTGTTAAATAAGTTTAAATTTTTAGATTAAACCGAGCCATATCCATATCC
96773 ATATACAATGTTTAATTTCTAAAAACTCATTTTTTTAATCAATCATCTTTCAA
130 ATATACAATGTTTAATTTCTAAAAACTCATTTTTTTAATCAATCATCTTTCAA
96826 ATAGAGAAAA
Statistics
Matches: 157, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
217 29 0.18
218 122 0.78
219 6 0.04
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (217 bp):
CTTTAAATTTATGGGATCTTAAAATTATTTTTGACTTCGAATTACACATCAGATACTTAGTAGGC
TTAAAGGTTAAAAATTGTTAAATAAGTTTAAATTTTTAGATTAAACCGAGCCATATCCATATCCA
TATACAATGTTTAATTTCTAAAAACTCATTTTTTTAATCAATCATCTTTCAATTTTATCAAGTCA
ATTTGAAGTTCATATTTCTAGC
Found at i:98200 original size:2 final size:2
Alignment explanation
Indices: 98193--98222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
98183 AAATATTTTA
98193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98223 TGCTGTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98407 original size:16 final size:16
Alignment explanation
Indices: 98388--98420 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
98378 TTTTATCACT
98388 ACATCAATTTATCTTG
1 ACATCAATTTATCTTG
*
98404 ACATTAATTTATCTTG
1 ACATCAATTTATCTTG
98420 A
1 A
98421 ATGGTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (16 bp):
ACATCAATTTATCTTG
Found at i:102703 original size:20 final size:20
Alignment explanation
Indices: 102677--102718 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
102667 ATTTTTATAA
102677 AAAATTATT--TAT-TTATT
1 AAAATTATTAATATGTTATT
102694 AAAATTATTAATATGTTATT
1 AAAATTATTAATATGTTATT
102714 AAAAT
1 AAAAT
102719 AAATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
19 3 0.14
20 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AAAATTATTAATATGTTATT
Found at i:103718 original size:13 final size:13
Alignment explanation
Indices: 103702--103727 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
103692 TTATTAATCA
103702 TTATTATTTAAAT
1 TTATTATTTAAAT
103715 TTATTATTTAAAT
1 TTATTATTTAAAT
103728 AATAAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATTTAAAT
Found at i:103749 original size:16 final size:16
Alignment explanation
Indices: 103730--103760 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
103720 ATTTAAATAA
*
103730 TAAAGTATTAAATTAT
1 TAAAATATTAAATTAT
103746 TAAAATATTAAATTA
1 TAAAATATTAAATTA
103761 AGATTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAAATATTAAATTAT
Found at i:104247 original size:22 final size:23
Alignment explanation
Indices: 104207--104256 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
104197 TTATATTTTT
* *
104207 ATAATTTTAATTAATATGATGTG
1 ATAATTTAAATTAATATGAGGTG
*
104230 ATAATTTAAATTTA-ATGAGGTG
1 ATAATTTAAATTAATATGAGGTG
104252 -TAATT
1 ATAATT
104257 GTCTATGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 7 0.29
23 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (23 bp):
ATAATTTAAATTAATATGAGGTG
Found at i:104361 original size:31 final size:30
Alignment explanation
Indices: 104302--104382 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
104292 AAGATTTGTA
* * * *
104302 TTAAATTAAATTTGATTTTATTTTTTAATGAT
1 TTAAGTTAAGTTTGA-TTTAATTTTTAAT-AG
104334 TTAAGTTAAGTTTGATTTAATTTTTAATAG
1 TTAAGTTAAGTTTGATTTAATTTTTAATAG
*
104364 TTAGAGTTAAGTTTAATTT
1 TTA-AGTTAAGTTTGATTT
104383 GATCATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.09
31 26 0.60
32 13 0.30
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (30 bp):
TTAAGTTAAGTTTGATTTAATTTTTAATAG
Found at i:104453 original size:14 final size:14
Alignment explanation
Indices: 104434--104463 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
104424 TTAATTAATT
*
104434 ATAATATATAAATA
1 ATAATATAAAAATA
104448 ATAATATAAAAATA
1 ATAATATAAAAATA
104462 AT
1 AT
104464 TTTAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATAAAAATA
Found at i:109101 original size:28 final size:28
Alignment explanation
Indices: 109067--109140 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
109057 GAAATAAAGC
*
109067 CGGGGTTGGGGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCCTCAAAAATAA
* *
109095 CGGGGTTGGAGTATCTCCTCGAAAATAA
1 CGGGGTTGGAGTATCCCCTCAAAAATAA
109123 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
109141 GATGAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAA
Found at i:109204 original size:104 final size:106
Alignment explanation
Indices: 108983--109213 Score: 349
Period size: 104 Copynumber: 2.2 Consensus size: 106
108973 TTTTGGAAAT
* *
108983 AATAACGGGGTTGGAGTATCTCCTTGAAAATAACGGGGTTGGAGTATCCCCAGTTGTGAAAAATC
1 AATAACGGGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCAG-TATGAAAAATC
* * *
109048 GATATTTTAGAAATAAAGCCGGGGTTGGGGTATCCCCTCAAA
65 GATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAAA
*
109090 AATAACGGGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCC-G-ATGAAAAATTG
1 AATAACGGGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCAGTATGAAAAATCG
* * **
109153 ATGTTTTAGAAATAAAACTAGGGTTGGAGTATCCCCTCGGA
66 ATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAAA
109194 AATAACGGGGTTGGAGTATC
1 AATAACGGGGTTGGAGTATC
109214 CCCGATTATG
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
104 63 0.55
106 1 0.01
107 50 0.44
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (106 bp):
AATAACGGGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCAGTATGAAAAATCG
ATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAAA
Found at i:109267 original size:79 final size:76
Alignment explanation
Indices: 109097--109267 Score: 209
Period size: 76 Copynumber: 2.2 Consensus size: 76
109087 AAAAATAACG
* * * * *
109097 GGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAG
1 GGGTTGAAATATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAAGTCATGTTTTAG
109162 AAATAAAACTA
66 AAATAAAACTA
* * * *
109173 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAGTCAGTGTTT
1 GGGTTGAAATATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGA--AAAAGTCA-TGTTT
*
109238 TAGAAATAAAA-TC
63 TAGAAATAAAACTA
109251 GGAGTTGAAATATCCCC
1 GG-GTTGAAATATCCCC
109268 GATTGCGGAG
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
76 46 0.55
78 9 0.11
79 28 0.34
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (76 bp):
GGGTTGAAATATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAAGTCATGTTTTAG
AAATAAAACTA
Found at i:109268 original size:51 final size:51
Alignment explanation
Indices: 109210--109317 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
109200 GGGGTTGGAG
* *
109210 TATCCCCGATT-ATGAAAAGTCAGTGTTTTAGAAATAAAATCGGAGTTGAAA
1 TATCCCCGATTGAGGAAAA-TCAGTGTTTTAGAAATAAAACCGGAGTTGAAA
* * ** * *
109261 TATCCCCGATTGCGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGAAG
1 TATCCCCGATTGAGGAAAATCAGTGTTTTAGAAATAAAACCGGAGTTGAAA
109312 TATCCC
1 TATCCC
109318 TTCGGAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 44 0.92
52 4 0.08
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
TATCCCCGATTGAGGAAAATCAGTGTTTTAGAAATAAAACCGGAGTTGAAA
Found at i:109399 original size:130 final size:130
Alignment explanation
Indices: 109148--109382 Score: 373
Period size: 130 Copynumber: 1.8 Consensus size: 130
109138 CCCGATGAAA
* * *
109148 AATTGATGTTTTAGAAATAAAACTAGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTAT
1 AATTGATGTTTTAGAAATAAAACCAGGGTTGAAGTATCCCCTCGGAAATAACGGGGTTGGAGCAT
109213 CCCCGATTATGAAAAGTCAGTGTTTTAGAAATAAAATCGGAGTTGAAATATCCCCGATTGCGGAG
66 CCCCGATTATGAAAAGTCAGTGTTTTAGAAATAAAATCGGAGTTGAAATATCCCCGATTGCGGAG
* * *
109278 AATTGGTGTTTTAGAAATAAAACCGGGGTTGAAGTATCCCTTCGGAAATAACGGGGTTGGAGCAT
1 AATTGATGTTTTAGAAATAAAACCAGGGTTGAAGTATCCCCTCGGAAATAACGGGGTTGGAGCAT
* * *
109343 CCCCGATTATGAAAAAT-TGATGTTTTAGAAATGAAATCGG
66 CCCCGATTATGAAAAGTCAG-TGTTTTAGAAATAAAATCGG
109383 GATTGCAGTA
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
129 1 0.01
130 94 0.99
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (130 bp):
AATTGATGTTTTAGAAATAAAACCAGGGTTGAAGTATCCCCTCGGAAATAACGGGGTTGGAGCAT
CCCCGATTATGAAAAGTCAGTGTTTTAGAAATAAAATCGGAGTTGAAATATCCCCGATTGCGGAG
Found at i:111790 original size:13 final size:13
Alignment explanation
Indices: 111772--111797 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
111762 ACAAAGATCG
111772 ATGTATCGATACA
1 ATGTATCGATACA
111785 ATGTATCGATACA
1 ATGTATCGATACA
111798 TTCTACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:111874 original size:19 final size:21
Alignment explanation
Indices: 111850--111901 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
111840 AGCGATACAC
111850 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGTA
*
111869 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTTACTGTA
111890 TGTATCGATACA
1 TGTATCGATACA
111902 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTTACTGTA
Found at i:115172 original size:21 final size:20
Alignment explanation
Indices: 115142--115180 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
115132 CACATTTTTG
115142 TCTAAATGTATCGATACATT
1 TCTAAATGTATCGATACATT
115162 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCGATACA
115181 AGGTCCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCGATACATT
Found at i:115235 original size:13 final size:13
Alignment explanation
Indices: 115217--115369 Score: 62
Period size: 13 Copynumber: 11.9 Consensus size: 13
115207 TTCAACAATT
115217 TGTATCGATACAA
1 TGTATCGATACAA
115230 TGTATCGATACATAA
1 TGTATCGATAC--AA
115245 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
115262 TGTATCGCTACGAA
1 TGTATCGATAC-AA
* * *
115276 -GCTATTGCTAAGGAAA
1 TG-TATCGAT-A--CAA
115292 TGTATCGATAC-A
1 TGTATCGATACAA
115304 T-TA-CG--A-AA
1 TGTATCGATACAA
*
115312 TGTATCGATACAT
1 TGTATCGATACAA
115325 TGTATCGATAC-A
1 TGTATCGATACAA
115337 T-TA-CG--A-AA
1 TGTATCGATACAA
*
115345 TGTATCGATACAT
1 TGTATCGATACAA
115358 TGTATCGATACA
1 TGTATCGATACA
115370 TGGATCTTTG
Statistics
Matches: 107, Mismatches: 9, Indels: 48
0.65 0.05 0.29
Matches are distributed among these distances:
8 6 0.06
9 4 0.04
10 8 0.07
11 4 0.04
12 5 0.05
13 47 0.44
14 8 0.07
15 4 0.04
16 7 0.07
17 3 0.03
19 11 0.10
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:115313 original size:20 final size:20
Alignment explanation
Indices: 115288--115358 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
115278 TATTGCTAAG
115288 GAAATGTATCGATACATTAC
1 GAAATGTATCGATACATTAC
115308 GAAATGTATCGATACA-T--
1 GAAATGTATCGATACATTAC
115325 ----TGTATCGATACATTAC
1 GAAATGTATCGATACATTAC
115341 GAAATGTATCGATACATT
1 GAAATGTATCGATACATT
115359 GTATCGATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
13 12 0.27
14 1 0.02
19 1 0.02
20 30 0.68
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (20 bp):
GAAATGTATCGATACATTAC
Found at i:115330 original size:33 final size:33
Alignment explanation
Indices: 115292--115370 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
115282 GCTAAGGAAA
115292 TGTATCGATACATTACGAAATGTATCGATACAT
1 TGTATCGATACATTACGAAATGTATCGATACAT
115325 TGTATCGATACATTACGAAATGTATCGATACAT
1 TGTATCGATACATTACGAAATGTATCGATACAT
115358 TGTATCGATACAT
1 TGTATCGATACAT
115371 GGATCTTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATTACGAAATGTATCGATACAT
Found at i:115370 original size:13 final size:13
Alignment explanation
Indices: 115312--115370 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
115302 CATTACGAAA
115312 TGTATCGATACAT
1 TGTATCGATACAT
115325 TGTATCGATACA-
1 TGTATCGATACAT
115337 T-TA-CGA-A-A-
1 TGTATCGATACAT
115345 TGTATCGATACAT
1 TGTATCGATACAT
115358 TGTATCGATACAT
1 TGTATCGATACAT
115371 GGATCTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.05
9 3 0.07
10 6 0.15
11 3 0.07
12 2 0.05
13 25 0.61
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:124387 original size:17 final size:17
Alignment explanation
Indices: 124365--124409 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
124355 TAGGTTATTG
124365 ATACTCTTAAATAATGT
1 ATACTCTTAAATAATGT
*
124382 ATACTCCTAAATAATGT
1 ATACTCTTAAATAATGT
*
124399 -TTCTCTTAAAT
1 ATACTCTTAAAT
124410 TCTTGCATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (17 bp):
ATACTCTTAAATAATGT
Found at i:127307 original size:21 final size:21
Alignment explanation
Indices: 127283--127339 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
127273 AAAAAATTTA
*
127283 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTCGTAG
*
127304 AATGTATCGATACATTCGTGG
1 AATGTATCGATACATTCGTAG
127325 AATGTATCGATACAT
1 AATGTATCGATACAT
127340 CCTACAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTCGTAG
Found at i:127419 original size:19 final size:19
Alignment explanation
Indices: 127395--127462 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
127385 AATTCAACAA
127395 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
127414 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
127429 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
127446 ATTGTTTCGATACATAA
1 TTTGTATCGATACATAA
127463 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:127434 original size:13 final size:13
Alignment explanation
Indices: 127416--127440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127406 ACATAAGTTT
127416 TGTATCGATACAA
1 TGTATCGATACAA
127429 TGTATCGATACA
1 TGTATCGATACA
127441 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:127438 original size:32 final size:32
Alignment explanation
Indices: 127397--127459 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
127387 TTCAACAATT
*
127397 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
127429 TGTATCGATACATAAGTATTGTTTCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
127460 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:127520 original size:13 final size:13
Alignment explanation
Indices: 127502--127527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127492 CATTTTTCTG
127502 TGTATCGATACAT
1 TGTATCGATACAT
127515 TGTATCGATACAT
1 TGTATCGATACAT
127528 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:127523 original size:33 final size:33
Alignment explanation
Indices: 127482--127548 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
127472 GCCAAGGAAA
***
127482 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
127515 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
127548 T
1 T
127549 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:129957 original size:28 final size:27
Alignment explanation
Indices: 129890--129962 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
129880 CTTCACAATC
* *
129890 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
129917 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
129945 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
129963 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:130007 original size:51 final size:51
Alignment explanation
Indices: 129945--130115 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
129935 TTATTTCTGA
* * *
129945 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
129996 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
130049 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
130101 GAGGATACTCCAACC
1 GGGGATACTCCAACC
130116 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:130135 original size:28 final size:27
Alignment explanation
Indices: 130103--130179 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
130093 TCACAATCGA
130103 GGATACTCCAACCTCGTTATTTCATC-AG
1 GGATACTCCAACCTCGTTATTTC--CGAG
* *
130131 GGATACTCCAACCCCGTTACTTCCGAG
1 GGATACTCCAACCTCGTTATTTCCGAG
*
130158 GGAACACTCCAACCTCGTTATT
1 GG-ATACTCCAACCTCGTTATT
130180 ATCTCCAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 4 0.10
28 37 0.88
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (27 bp):
GGATACTCCAACCTCGTTATTTCCGAG
Found at i:136151 original size:28 final size:29
Alignment explanation
Indices: 136106--136162 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
136096 AAAGAACAGC
*
136106 GAATTAATCAAAATAATA-ATAAAATAAA
1 GAATTAATCAAAATAATAGACAAAATAAA
*
136134 GAATTAATCCAACA-AATAGACAAAATAAA
1 GAATTAAT-CAAAATAATAGACAAAATAAA
136163 AAAGACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (29 bp):
GAATTAATCAAAATAATAGACAAAATAAA
Found at i:144706 original size:20 final size:20
Alignment explanation
Indices: 144683--144732 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
144673 ATTAAAATAC
144683 ATTGATACAT-GATCAAATGT
1 ATTGATACATAGATC-AATGT
* *
144703 ATTGATATATAGGTCAATGT
1 ATTGATACATAGATCAATGT
144723 ATTGATACAT
1 ATTGATACAT
144733 TTTGGTCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (20 bp):
ATTGATACATAGATCAATGT
Found at i:144745 original size:21 final size:22
Alignment explanation
Indices: 144714--144755 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
144704 TTGATATATA
*
144714 GGTCAATGTATTGATACATTTT
1 GGTCAATGTATGGATACATTTT
144736 GGTC-ATGTATGGATACATTT
1 GGTCAATGTATGGATACATTT
144756 GATTTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (22 bp):
GGTCAATGTATGGATACATTTT
Found at i:145895 original size:12 final size:12
Alignment explanation
Indices: 145878--145908 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
145868 GGTTTATAAT
145878 ATGCTTGACAAA
1 ATGCTTGACAAA
145890 ATGCTTGACAAA
1 ATGCTTGACAAA
145902 ATGCTTG
1 ATGCTTG
145909 CTTTGATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (12 bp):
ATGCTTGACAAA
Found at i:150597 original size:20 final size:20
Alignment explanation
Indices: 150545--150585 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
150535 TAATGATAAA
*
150545 AATATAAATATTAAATGTAG
1 AATATAAATATTAAATATAG
150565 AATATAAATATTAAATATAG
1 AATATAAATATTAAATATAG
150585 A
1 A
150586 TATGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (20 bp):
AATATAAATATTAAATATAG
Found at i:150645 original size:21 final size:23
Alignment explanation
Indices: 150603--150650 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
150593 TATTACTTAC
*
150603 ATAACAATATGATAATTAAAAA-
1 ATAACAATATGATAATGAAAAAT
150625 ATAA-AATATGAT-ATGATAAAAT
1 ATAACAATATGATAATGA-AAAAT
150647 ATAA
1 ATAA
150651 TAATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 12 0.52
22 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
ATAACAATATGATAATGAAAAAT
Found at i:152534 original size:15 final size:13
Alignment explanation
Indices: 152503--152547 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 13
152493 AAGGTTCTTA
152503 TTTT-TATAT-TT
1 TTTTATATATATT
152514 TTTTATATATCATT
1 TTTTATATAT-ATT
152528 ATTTTATATATATT
1 -TTTTATATATATT
152542 TTTTAT
1 TTTTAT
152548 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.13
12 5 0.17
13 6 0.20
14 5 0.17
15 10 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATATATATT
Found at i:155114 original size:155 final size:155
Alignment explanation
Indices: 154913--155270 Score: 407
Period size: 155 Copynumber: 2.3 Consensus size: 155
154903 GTTCTAATGC
* * * *
154913 AAAATTACTAAAATACTCTAAAGTATACCTTTAACGTGAAAGTATCTCGCTAAC-C-ACAAAGGA
1 AAAATTACAAAAATACTCTAAGGTATACCTTTGACGTGAAAGTATCTCGATAACTCTA-AAA-GA
* * * * *
154976 CTTAAAAATGATCATAAACACGATGAACATATCATAAATGTATATCTTTAACATAAAAACATCCT
64 CTTAAAAATGATCATAAACACGACGAACATATCATAAATGAACACCTTCAACATAAAAACATCCT
* *
155041 AGTGACAACCTAGGACTCAGTTCTAA-
129 AGTAACAACCTAGGACTCAGTTATAAG
* *
155067 AAAATTACAAAAATACTCATAAGGTATACTTTTGACGTGAAAGTATCTTGATAACTCTAAAAGAC
1 AAAATTACAAAAATACTC-TAAGGTATACCTTTGACGTGAAAGTATCTCGATAACTCTAAAAGAC
* *** * * * *
155132 TTAAAAATGATTATAAATGGGACGAACCTATCATAAATGAACACCTTCAGCATAAGAGCATCCTA
65 TTAAAAATGATCATAAACACGACGAACATATCATAAATGAACACCTTCAACATAAAAACATCCTA
* *
155197 GTAACAACCTAGGATTTAGTTATAAG
130 GTAACAACCTAGGACTCAGTTATAAG
** * * *
155223 AAAATTATGAAAATATCTCTAGGGTATACCTTTGACATAAAAGTATCT
1 AAAATTACAAAAATA-CTCTAAGGTATACCTTTGACGTGAAAGTATCT
155271 TAATAACCTT
Statistics
Matches: 170, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
154 17 0.10
155 107 0.63
156 42 0.25
157 4 0.02
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.28
Consensus pattern (155 bp):
AAAATTACAAAAATACTCTAAGGTATACCTTTGACGTGAAAGTATCTCGATAACTCTAAAAGACT
TAAAAATGATCATAAACACGACGAACATATCATAAATGAACACCTTCAACATAAAAACATCCTAG
TAACAACCTAGGACTCAGTTATAAG
Found at i:155832 original size:157 final size:157
Alignment explanation
Indices: 155660--155988 Score: 428
Period size: 157 Copynumber: 2.1 Consensus size: 157
155650 AGTTTTATCT
* * ** *
155660 TTAGAACAAAATTTTTGAATAAACCTGC-TAAACTTTCTAATTTTGTAAATTAGTCCTTACATAA
1 TTAGAACAAAATTTTTGAATAAA-CTCCATAAACTTTCTAAATTTACAAATTAATCCTTACATAA
* * * * **
155724 TTAAAACA-TAGAATTAAATATCCAATAAATCAAAGTCAACATACAAAACACATCAAAAAGTTAC
65 TTAAAACACCA-AATTAAACATCAAAGAAATCAAAACCAACATACAAAACACATCAAAAAGTTAC
** *
155788 AAAGGAGGTTCGGCCAAGCACTTTTGGCC
129 AAAGGAGGTTCAACCAAGCACCTTTGGCC
* * *
155817 TTAGAACAAAATTTTTGAATAAACTCCATAAACTTTTTAAATTTACAAATTAATCTTTATATAAT
1 TTAGAACAAAATTTTTGAATAAACTCCATAAACTTTCTAAATTTACAAATTAATCCTTACATAAT
*
155882 TAAAACACCAAATTAAGCATCAAAGAAATCAAAACCAACATACAAAACACATCAAAAAGTTACAA
66 TAAAACACCAAATTAAACATCAAAGAAATCAAAACCAACATACAAAACACATCAAAAAGTTACAA
* * **
155947 AGGAGGTTTAACCAAGTACCTTTGGTT
131 AGGAGGTTCAACCAAGCACCTTTGGCC
155974 TTAGAACAAAATTTT
1 TTAGAACAAAATTTT
155989 CAATATTTAC
Statistics
Matches: 148, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
156 3 0.02
157 144 0.97
158 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (157 bp):
TTAGAACAAAATTTTTGAATAAACTCCATAAACTTTCTAAATTTACAAATTAATCCTTACATAAT
TAAAACACCAAATTAAACATCAAAGAAATCAAAACCAACATACAAAACACATCAAAAAGTTACAA
AGGAGGTTCAACCAAGCACCTTTGGCC
Found at i:157321 original size:115 final size:115
Alignment explanation
Indices: 157124--157355 Score: 376
Period size: 115 Copynumber: 2.0 Consensus size: 115
157114 CATAAAAATT
* * * * *
157124 AACTAGAAGGATTAAATTATAAAAATTAAAAATTATGTATTTACAATAACATTTTAAATAATCAA
1 AACTACAAGGACTAAATTACAAAAATTAAAAATTATGTACTTACAATAAAATTTTAAATAATCAA
157189 TGTGATAATTTTCAATAACAAATAAATTTTAATATCCAAGAAGAAAAGAA
66 TGTGATAATTTTCAATAACAAATAAATTTTAATATCCAAGAAGAAAAGAA
* *
157239 AACTACAAGGACTAAATTACAAAAATTTAAAATTATGTACTTACAATAAAATTTTATATAATCAA
1 AACTACAAGGACTAAATTACAAAAATTAAAAATTATGTACTTACAATAAAATTTTAAATAATCAA
*
157304 TGTGTTTAA-TTTCAATAACAAATAAATTTTAATATCCAAGAAGAAAAGAA
66 TGTG-ATAATTTTCAATAACAAATAAATTTTAATATCCAAGAAGAAAAGAA
157354 AA
1 AA
157356 ATATTAAAAT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
115 105 0.97
116 3 0.03
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (115 bp):
AACTACAAGGACTAAATTACAAAAATTAAAAATTATGTACTTACAATAAAATTTTAAATAATCAA
TGTGATAATTTTCAATAACAAATAAATTTTAATATCCAAGAAGAAAAGAA
Found at i:157942 original size:150 final size:150
Alignment explanation
Indices: 157433--157980 Score: 513
Period size: 151 Copynumber: 3.6 Consensus size: 150
157423 AAAAAATGCG
* * *
157433 AAACTCATAAGATAGATTGAATTTTTACAAAATAATTCAATATGAATTTAATAAA-AATATTTGA
1 AAACTCATAA-ATAAATTGAATTTTT-CAAAA-AATTTAATATGAA-TTAAAAAATAATATTTGA
* * * * * * * * *
157497 TGAATTTTAAAAATT-TAAGCTGAGAAAAATCCTATCAAA-ACATATACGAAA-TAGAAAACTTC
62 AGAATTTTGAAGATTATAAACTTAGAAAAATCATACCAAAGAAATTTAC-AAAGTAGAAAACTTC
*
157559 GTATCTTGGT-ATAAGAAAAATTCTA
126 GTATCTCGGTAAT-AGAAAAATTCTA
* * **
157584 AAACTCATAAAATAAATAGAAATTTTTGAAACAAATTTAATATGGGTTAAAAAATAATATTTGAA
1 AAACTCAT-AAATAAATTG-AATTTTTCAAA-AAATTTAATATGAATTAAAAAATAATATTTGAA
* *** * * *
157649 GAATTTTGAAGATTATAAACTTAGAAAAATCCTACCAAAGAAATTTATGGAGAAGAAAGCTCCGT
63 GAATTTTGAAGATTATAAACTTAGAAAAATCATACCAAAGAAATTTACAAAGTAGAAAACTTCGT
* * *
157714 -TTTCGGTAGTAGGAAAATTCTA
128 ATCTCGGTAATAGAAAAATTCTA
* * * *
157736 AATCTCATAAATAAATTGAATTTTTCAAAACTAATTTAACATAAATTAAATAATAATATTTGAAG
1 AAACTCATAAATAAATTGAATTTTTCAAAA--AATTTAATATGAATTAAAAAATAATATTTGAAG
* * *
157801 TATTTTGAA-AGTTATAAACTCTA-AAAAATCATA-CAGAGGAATTTACAAAGTAGAAAACTTCG
64 AATTTTGAAGA-TTATAAACT-TAGAAAAATCATACCAAAGAAATTTACAAAGTAGAAAACTTCG
**
157863 TATCTCCATAATAGAAAAATTCTA
127 TATCTCGGTAATAGAAAAATTCTA
* * *
157887 AAACTCATAAA-AAATTGAATTTTTCAAAAAGGATTTAATATGCATTAAAAAATAATATTTAAAA
1 AAACTCATAAATAAATTGAATTTTTCAAAAA--ATTTAATATGAATTAAAAAATAATATTTGAAG
* * *
157951 AATTTTAAAAATTATAAATTTAGAAAAATC
64 AATTTTGAAGATTATAAACTTAGAAAAATC
157981 CTACTAGATA
Statistics
Matches: 322, Mismatches: 58, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
148 1 0.00
149 3 0.01
150 106 0.33
151 139 0.43
152 57 0.18
153 16 0.05
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (150 bp):
AAACTCATAAATAAATTGAATTTTTCAAAAAATTTAATATGAATTAAAAAATAATATTTGAAGAA
TTTTGAAGATTATAAACTTAGAAAAATCATACCAAAGAAATTTACAAAGTAGAAAACTTCGTATC
TCGGTAATAGAAAAATTCTA
Found at i:157977 original size:26 final size:24
Alignment explanation
Indices: 157931--157979 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
157921 TTAATATGCA
157931 TTAAAAAATAATATTTAAAAAATT
1 TTAAAAAATAATATTTAAAAAATT
157955 TTAAAAATTATAA-ATTTAGAAAAAT
1 TTAAAAA--ATAATATTTA-AAAAAT
157980 CCTACTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TTAAAAAATAATATTTAAAAAATT
Found at i:159201 original size:21 final size:21
Alignment explanation
Indices: 159177--159218 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
159167 TAGAAAGGTG
159177 TTGGCCGAGACAGAACCATAC
1 TTGGCCGAGACAGAACCATAC
*
159198 TTGGCCGAGACGGAACCATAC
1 TTGGCCGAGACAGAACCATAC
159219 AAACCAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (21 bp):
TTGGCCGAGACAGAACCATAC
Found at i:159311 original size:43 final size:43
Alignment explanation
Indices: 159198--159301 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
159188 AGAACCATAC
* * *
159198 TTGGCCGA-GACGGAACCATACAAACCAACAATTTAGAAAGGTG
1 TTGGCC-ACGACGAAACCATACGAACCAACAAGTTAGAAAGGTG
* *
159241 TTGGCCAGGACGAAACCATACGAACCAACGAGTTAGAAAGGTG
1 TTGGCCACGACGAAACCATACGAACCAACAAGTTAGAAAGGTG
*
159284 TTGGCCACGATGAAACCA
1 TTGGCCACGACGAAACCA
159302 AGCATACCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.02
43 53 0.98
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (43 bp):
TTGGCCACGACGAAACCATACGAACCAACAAGTTAGAAAGGTG
Found at i:159397 original size:41 final size:41
Alignment explanation
Indices: 159347--159431 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 41
159337 CCATACGAGT
*
159347 CAATAAAGGAAGTGTGTTGGTCGGGACGAAACCATATGAAC
1 CAATAAAGGAAGTGTGTTGGCCGGGACGAAACCATATGAAC
* * * * *
159388 CAATGAAGGAATTGTGTTGGCCGGGATGAAACTATATGTAC
1 CAATAAAGGAAGTGTGTTGGCCGGGACGAAACCATATGAAC
159429 CAA
1 CAA
159432 CGAGAGAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.22
Consensus pattern (41 bp):
CAATAAAGGAAGTGTGTTGGCCGGGACGAAACCATATGAAC
Found at i:159786 original size:79 final size:79
Alignment explanation
Indices: 159655--159870 Score: 236
Period size: 79 Copynumber: 2.7 Consensus size: 79
159645 GGTGGGGACG
* * * * * *
159655 AAACCATAC-ATGCCAATGAGGGAAGGGTATTGGCCAAGATAAAACTATATGAATCAACGAAGGA
1 AAACCATACGA-GTCAATGAAGAAAGGGTATTGGCCGAGATAAAACCATATGAATCAACGAAGAA
* *
159719 AAGTTGATCACGACC
65 AAATTGATCACGACA
* * * *
159734 AAACCATACGAGTCAATGAAGAAAGGGTGTTGGTCGAGATGAAACCATATGAACCAACGAAGAAA
1 AAACCATACGAGTCAATGAAGAAAGGGTATTGGCCGAGATAAAACCATATGAATCAACGAAGAAA
***
159799 AATTGATTGGGACA
66 AATTGATCACGACA
* ** * *
159813 AAACCTTACGAGTCAACAAAGAAAGGGTATTGGCCGAGACAAAACCATATAAATCAAC
1 AAACCATACGAGTCAATGAAGAAAGGGTATTGGCCGAGATAAAACCATATGAATCAAC
159871 AAAAGCGTTA
Statistics
Matches: 112, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
79 111 0.99
80 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (79 bp):
AAACCATACGAGTCAATGAAGAAAGGGTATTGGCCGAGATAAAACCATATGAATCAACGAAGAAA
AATTGATCACGACA
Found at i:159796 original size:41 final size:41
Alignment explanation
Indices: 159567--159798 Score: 127
Period size: 41 Copynumber: 5.7 Consensus size: 41
159557 GGCATTGGCT
* * *
159567 GAGATGAAACCATCCGAACCAACGAAGAAAGGGTGTTGGCC
1 GAGACGAAACCATACGAACCAACGAAGAAAGGGTGTTGGTC
* * * * *
159608 AAGACGAAACAATACGAACTAACAAAGGAAA-GGTGTTGGTG
1 GAGACGAAACCATACGAACCAACGAA-GAAAGGGTGTTGGTC
* * * * * * *
159649 GGGACGAAACCATAC-ATGCCAATGAGGGAAGGGTATTGGCC
1 GAGACGAAACCATACGA-ACCAACGAAGAAAGGGTGTTGGTC
* ** * * * *
159690 AAGATAAAACTATATGAATCAACGAAGGAAA----GTTGATC
1 GAGACGAAACCATACGAACCAACGAA-GAAAGGGTGTTGGTC
* ** *
159728 -ACGACCAAACCATACGAGTCAATGAAGAAAGGGTGTTGGTC
1 GA-GACGAAACCATACGAACCAACGAAGAAAGGGTGTTGGTC
* *
159769 GAGATGAAACCATATGAACCAACGAAGAAA
1 GAGACGAAACCATACGAACCAACGAAGAAA
159799 AATTGATTGG
Statistics
Matches: 133, Mismatches: 47, Indels: 22
0.66 0.23 0.11
Matches are distributed among these distances:
37 5 0.04
38 22 0.17
40 4 0.03
41 93 0.70
42 9 0.07
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (41 bp):
GAGACGAAACCATACGAACCAACGAAGAAAGGGTGTTGGTC
Found at i:163365 original size:2 final size:2
Alignment explanation
Indices: 163358--163384 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
163348 ATAAGTTGCC
163358 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 A
163385 GTTTAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:163802 original size:7 final size:7
Alignment explanation
Indices: 163792--163838 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
163782 AATAAAAAAT
*
163792 AATTATA
1 AATTTTA
163799 AATTTTA
1 AATTTTA
*
163806 AATTTCA
1 AATTTTA
*
163813 AATTTCA
1 AATTTTA
163820 AATTTTA
1 AATTTTA
163827 AATTTTA
1 AATTTTA
163834 AATTT
1 AATTT
163839 AATATCATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (7 bp):
AATTTTA
Found at i:164019 original size:11 final size:11
Alignment explanation
Indices: 164005--164049 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
163995 TTTTTTACCC
*
164005 TTTTTATTTTA
1 TTTTTATATTA
164016 TTTTTATATTA
1 TTTTTATATTA
* * *
164027 TATTCATCTTA
1 TTTTTATATTA
164038 TTTTTATATTA
1 TTTTTATATTA
164049 T
1 T
164050 AATCAACTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:175644 original size:7 final size:7
Alignment explanation
Indices: 175632--175664 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
175622 GTTTTCTTGC
175632 TGTTTAA
1 TGTTTAA
175639 TGTTTAA
1 TGTTTAA
175646 TGTTTAA
1 TGTTTAA
175653 TGTTTAA
1 TGTTTAA
175660 TGTTT
1 TGTTT
175665 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (7 bp):
TGTTTAA
Found at i:180831 original size:19 final size:19
Alignment explanation
Indices: 180804--180841 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
180794 CACTTGAAAG
180804 GTGACTTTACATTGCCTAT
1 GTGACTTTACATTGCCTAT
*
180823 GTGATTTTACATTGCCTAT
1 GTGACTTTACATTGCCTAT
180842 AAAAGGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (19 bp):
GTGACTTTACATTGCCTAT
Found at i:183194 original size:2 final size:2
Alignment explanation
Indices: 183187--183220 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
183177 TGCCTTCGAT
183187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
183221 GCCTATGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.