Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 15 of 311
Found at i:4088467 original size:33 final size:33
Alignment explanation
Indices: 4088430--4088495 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4088420 CAGACCACAT
4088430 CAGTATTGGCTACTAACTTGAATTCAGTTTGGG
1 CAGTATTGGCTACTAACTTGAATTCAGTTTGGG
4088463 CAGTATTGGCTACTAACTTGAATTCAGTTTGGG
1 CAGTATTGGCTACTAACTTGAATTCAGTTTGGG
4088496 TATGATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (33 bp):
CAGTATTGGCTACTAACTTGAATTCAGTTTGGG
Found at i:4088859 original size:21 final size:21
Alignment explanation
Indices: 4088833--4088883 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
4088823 AGCGGTGGCG
*
4088833 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
4088854 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
4088875 GTGAGATTA
1 GTGAGATTA
4088884 AAAACAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.33, T:0.31
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:4094436 original size:29 final size:30
Alignment explanation
Indices: 4094404--4094469 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
4094394 ATGAATAGAT
* *
4094404 TTTTTTATTATTTTATGAGAG-TTAATTGA
1 TTTTTAATTATTTTAGGAGAGTTTAATTGA
4094433 TTTTTAATTATTTTAGGAGAGTTTAATTGA
1 TTTTTAATTATTTTAGGAGAGTTTAATTGA
4094463 TTTTTAA
1 TTTTTAA
4094470 GGATTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.58
Consensus pattern (30 bp):
TTTTTAATTATTTTAGGAGAGTTTAATTGA
Found at i:4094962 original size:27 final size:27
Alignment explanation
Indices: 4094932--4094985 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4094922 CATTGAATTA
4094932 AAGTTTATGTATAAATTTGATATCTAT
1 AAGTTTATGTATAAATTTGATATCTAT
4094959 AAGTTTATGTATAAATTTGATATCTAT
1 AAGTTTATGTATAAATTTGATATCTAT
4094986 TCCTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (27 bp):
AAGTTTATGTATAAATTTGATATCTAT
Found at i:4095196 original size:31 final size:31
Alignment explanation
Indices: 4095129--4095189 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
4095119 ATATGTTATG
* *
4095129 AAATAATGAAAATGCTAAATAAATATTATAA
1 AAATAATGAAAATGATAAATAAATATTAAAA
*
4095160 AAATAATTAAAATGATAAA-AAATA-TAAAA
1 AAATAATGAAAATGATAAATAAATATTAAAA
4095189 A
1 A
4095190 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 5 0.19
31 17 0.63
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (31 bp):
AAATAATGAAAATGATAAATAAATATTAAAA
Found at i:4095544 original size:17 final size:18
Alignment explanation
Indices: 4095509--4095544 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4095499 TATAAGTTGT
*
4095509 TAAAAAATTTTAATGTTA
1 TAAAAAATTTAAATGTTA
4095527 TAAAAAATTTAAAT-TTA
1 TAAAAAATTTAAATGTTA
4095544 T
1 T
4095545 TGTCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAAAAATTTAAATGTTA
Found at i:4097464 original size:28 final size:27
Alignment explanation
Indices: 4097415--4097470 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
4097405 TTCGTATAAC
* *
4097415 TAAATTTTGTATATTTATATGTATGAAT
1 TAAATATTGTATATTGATATGT-TGAAT
4097443 TAAATATTGTATATGTGA-ATGTTGAAT
1 TAAATATTGTATAT-TGATATGTTGAAT
4097470 T
1 T
4097471 GTGTAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 17 0.68
29 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (27 bp):
TAAATATTGTATATTGATATGTTGAAT
Found at i:4098923 original size:10 final size:10
Alignment explanation
Indices: 4098901--4098960 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
4098891 TGATGTTAAA
4098901 ATTTATTAT-T
1 ATTT-TTATAT
4098911 ATTTTTATAT
1 ATTTTTATAT
* *
4098921 ATTTGTATTT
1 ATTTTTATAT
4098931 ATTATTTAT-T
1 ATT-TTTATAT
4098941 A-TTTTATA-
1 ATTTTTATAT
4098949 ATTTTTATAT
1 ATTTTTATAT
4098959 AT
1 AT
4098961 AGTATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
8 6 0.14
9 12 0.29
10 20 0.48
11 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:4100735 original size:29 final size:29
Alignment explanation
Indices: 4100701--4100777 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
4100691 TTTGCCTTAG
4100701 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTATGTTTGAAAT
4100730 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTATGTTTGAAAT
4100759 GTTACATTTTAGTCACTTA
1 GTTACATTTTAGTCACTTA
4100778 CGTTATTGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTATGTTTGAAAT
Found at i:4113550 original size:28 final size:28
Alignment explanation
Indices: 4113510--4113564 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
4113500 GTTTATGATA
4113510 AAATAGCATGAAATTGAAGCTTCAATTG
1 AAATAGCATGAAATTGAAGCTTCAATTG
*
4113538 AAATATCATGAAATTGAAGCTTCAATT
1 AAATAGCATGAAATTGAAGCTTCAATT
4113565 TGTTTATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (28 bp):
AAATAGCATGAAATTGAAGCTTCAATTG
Found at i:4127597 original size:20 final size:19
Alignment explanation
Indices: 4127523--4127598 Score: 77
Period size: 18 Copynumber: 4.1 Consensus size: 19
4127513 ATACTCACTC
*
4127523 TCTTTTTCAATTTTC-TTT
1 TCTTTTTCAATTCTCTTTT
**
4127541 TCTTAATCAATT-TCTTTT
1 TCTTTTTCAATTCTCTTTT
4127559 TCTTTTTCAATTC-CGTTTT
1 TCTTTTTCAATTCTC-TTTT
*
4127578 TCTTTTTCTCATTCTCTTTT
1 TCTTTTTC-AATTCTCTTTT
4127598 T
1 T
4127599 GCTCTATTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 2 0.04
18 24 0.50
19 12 0.25
20 9 0.19
21 1 0.02
ACGTcount: A:0.12, C:0.20, G:0.01, T:0.67
Consensus pattern (19 bp):
TCTTTTTCAATTCTCTTTT
Found at i:4127649 original size:19 final size:18
Alignment explanation
Indices: 4127615--4127651 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4127605 TTTCGCACTC
*
4127615 TTTTTCTTTCATTTCTTT
1 TTTTTCTTTCAATTCTTT
4127633 TTTTTCTTTCAAATTCTTT
1 TTTTTCTTTC-AATTCTTT
4127652 CTTACATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTCTTTCAATTCTTT
Found at i:4146327 original size:5 final size:5
Alignment explanation
Indices: 4146317--4146348 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4146307 TTGTGTGTTC
4146317 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4146349 TCACAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4146331 original size:9 final size:9
Alignment explanation
Indices: 4146317--4146347 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4146307 TTGTGTGTTC
4146317 TTTATTTTA
1 TTTATTTTA
4146326 TTTATTTTA
1 TTTATTTTA
4146335 TTTTATTTTA
1 -TTTATTTTA
4146345 TTT
1 TTT
4146348 TTCACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4147592 original size:24 final size:24
Alignment explanation
Indices: 4147563--4147609 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4147553 TATATATACC
4147563 AATTCAATCA-ATA-TAAATTCAATA
1 AATTC-ATCACATACTAAA-TCAATA
4147587 AATTCATCACATACTAAATCAAT
1 AATTCATCACATACTAAATCAAT
4147610 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCATCACATACTAAATCAATA
Found at i:4148354 original size:36 final size:36
Alignment explanation
Indices: 4148277--4148354 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
4148267 CTTTCCCCCC
* *
4148277 TTTTTTATATTATAATATATATACTTAAACATTAAG
1 TTTTTTATATTATAATATATATACATAAACATTAAA
*
4148313 GTTTTTATATTATAATATATATA-ATAAAC-TTACACA
1 TTTTTTATATTATAATATATATACATAAACATTA-A-A
4148349 TTTTTT
1 TTTTTT
4148355 TAATCTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 3 0.08
35 6 0.17
36 27 0.75
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTTTTATATTATAATATATATACATAAACATTAAA
Found at i:4157930 original size:21 final size:21
Alignment explanation
Indices: 4157907--4157948 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4157897 TATTTTTATT
*
4157907 AAATTAATTTATATAATAAATA
1 AAATAAATTT-TATAATAAATA
*
4157929 AAATAAATTTTATATTAAAT
1 AAATAAATTTTATAATAAAT
4157949 TACTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATAAATTTTATAATAAATA
Found at i:4161844 original size:2 final size:2
Alignment explanation
Indices: 4161837--4161896 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
4161827 AGTTAATAAC
4161837 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4161879 CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA
4161897 TATATATATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4166776 original size:15 final size:15
Alignment explanation
Indices: 4166756--4166786 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4166746 GAGAACCATG
4166756 CCAAGTGAAGTTTAT
1 CCAAGTGAAGTTTAT
4166771 CCAAGTGAAGTTTAT
1 CCAAGTGAAGTTTAT
4166786 C
1 C
4166787 TCGCCAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (15 bp):
CCAAGTGAAGTTTAT
Found at i:4175774 original size:17 final size:17
Alignment explanation
Indices: 4175732--4175775 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
4175722 AAAATTATTT
* *
4175732 AATTGATAAATTAATTC
1 AATTGATTAATTAATTA
* *
4175749 AGTTAATTAATTAATTA
1 AATTGATTAATTAATTA
4175766 AATTGATTAA
1 AATTGATTAA
4175776 ATAAACAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (17 bp):
AATTGATTAATTAATTA
Found at i:4179234 original size:16 final size:15
Alignment explanation
Indices: 4179213--4179252 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
4179203 TACTGCCAAT
4179213 TGCTACATTGAATTAC
1 TGCTACATTG-ATTAC
*
4179229 TGCTACATTGATTGC
1 TGCTACATTGATTAC
*
4179244 TACTACATT
1 TGCTACATT
4179253 TGTTGGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (15 bp):
TGCTACATTGATTAC
Found at i:4181055 original size:41 final size:41
Alignment explanation
Indices: 4180998--4181081 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
4180988 TTGTTAAAAG
4180998 GTAAAAAAATCGACATTCTTTATATTTTGAAAGCTTCTACA
1 GTAAAAAAATCGACATTCTTTATATTTTGAAAGCTTCTACA
4181039 GTAAAAAAATCGACATTCTTTATATTTTGAAAGCTTCTACA
1 GTAAAAAAATCGACATTCTTTATATTTTGAAAGCTTCTACA
4181080 GT
1 GT
4181082 GATCGGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (41 bp):
GTAAAAAAATCGACATTCTTTATATTTTGAAAGCTTCTACA
Found at i:4182583 original size:28 final size:28
Alignment explanation
Indices: 4182543--4182599 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
4182533 CATCCAATCA
**
4182543 TTATTTTTATATTGCTTTTGAAATGTTT
1 TTATTTTTATATTGCTAGTGAAATGTTT
*
4182571 TTATTTTTATATTGGTAGTGAAATGTTT
1 TTATTTTTATATTGCTAGTGAAATGTTT
4182599 T
1 T
4182600 AAGGATTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.61
Consensus pattern (28 bp):
TTATTTTTATATTGCTAGTGAAATGTTT
Found at i:4193204 original size:207 final size:207
Alignment explanation
Indices: 4192849--4193270 Score: 501
Period size: 207 Copynumber: 2.0 Consensus size: 207
4192839 AAATTATCGT
* * * * * *
4192849 CTGTAAAATTAAGGTTCACAATCGAAGGGCTGCGACCTCTACCACAGTTAGCAAGAGCAATGTTT
1 CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCTACCACAGTTAGCAAGAGCAAAGTCT
** ** * *
4192914 CCAGCTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCAGCACAGTTAGCGAGAGCAAT
66 CCAGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCAAA
* * * * * * *
4192979 GGTCTCAGCTGTAAAATTAAGGTTCGCAGGCAAAGAG-CTGTGACCTCCATCATAGTTAGTGAGA
131 GCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTC-GCGACCTCCAACATAGTTAGCGAGA
*
4193043 GCAATA-CTCCTAA
195 GCAA-AGCTCCCAA
* * *
4193056 CTGTAAAATTAAGGTTCATAGGCGAAGAGCCGCAACCT-TCACCACAGTTAGCGAGAGCAAAG-C
1 CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCT-ACCACAGTTAGCAAGAGCAAAGTC
* * * *
4193119 TCCTAGCTAAAAAATTAAGGTTTGCAGGCTAAGAGCCACGACCTCTAGCACAATTAGCGAGAGCA
65 TCC-AGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCA
* *
4193184 AAGCTCTCAACTATAAAATTAAGGTTCGTAGACGAAGAGTCGCGACCTCCAACATAGTTAGCGAG
129 AAGCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTCGCGACCTCCAACATAGTTAGCGAG
* *
4193249 GGTAAAGCTCCCAA
194 AGCAAAGCTCCCAA
4193263 CTGTAAAA
1 CTGTAAAA
4193271 CCAAGGTTTG
Statistics
Matches: 180, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
206 5 0.03
207 174 0.97
208 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (207 bp):
CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCTACCACAGTTAGCAAGAGCAAAGTCT
CCAGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCAAA
GCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTCGCGACCTCCAACATAGTTAGCGAGAG
CAAAGCTCCCAA
Found at i:4193278 original size:69 final size:68
Alignment explanation
Indices: 4192849--4193270 Score: 378
Period size: 69 Copynumber: 6.1 Consensus size: 68
4192839 AAATTATCGT
* ** * * * * * * *
4192849 CTGTAAAATTAAGGTTCACAATCGAAGGGCTGCGACCTCTACCACAGTTAGCAAGAGCAATGTTT
1 CTGTAAAATTAAGGTTCGCAGGCGAAGAGC-GCGACCTCCAGCACAGTTAGCGAGAGCAAAGCTC
*
4192914 CCAG
65 CCAA
* * *
4192918 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCAGCACAGTTAGCGAGAGCAATGGTC
1 CTGTAAAATTAAGGTTCGCAGGCGAAGAGC-GCGACCTCCAGCACAGTTAGCGAGAGCAAAGCTC
* *
4192983 TCAG
65 CCAA
* * * * *
4192987 CTGTAAAATTAAGGTTCGCAGGCAAAGAGCTGTGACCTCCATCATAGTTAGTGAGAGCAATA-CT
1 CTGTAAAATTAAGGTTCGCAGGCGAAGAGC-GCGACCTCCAGCACAGTTAGCGAGAGCAA-AGCT
*
4193051 CCTAA
64 CCCAA
** * * *
4193056 CTGTAAAATTAAGGTTCATAGGCGAAGAGCCGCAACCTTCACCACAGTTAGCGAGAGCAAAGCTC
1 CTGTAAAATTAAGGTTCGCAGGCGAAGAG-CGCGACCTCCAGCACAGTTAGCGAGAGCAAAGCTC
* *
4193121 CTAG
65 CCAA
** * * * * *
4193125 CTAAAAAATTAAGGTTTGCAGGCTAAGAGCCACGACCTCTAGCACAATTAGCGAGAGCAAAGCTC
1 CTGTAAAATTAAGGTTCGCAGGCGAAGAG-CGCGACCTCCAGCACAGTTAGCGAGAGCAAAGCTC
*
4193190 TCAA
65 CCAA
* * * * * * *
4193194 CTATAAAATTAAGGTTCGTAGACGAAGAGTCGCGACCTCCAACATAGTTAGCGAGGGTAAAGCTC
1 CTGTAAAATTAAGGTTCGCAGGCGAAGAG-CGCGACCTCCAGCACAGTTAGCGAGAGCAAAGCTC
4193259 CCAA
65 CCAA
4193263 CTGTAAAA
1 CTGTAAAA
4193271 CCAAGGTTTG
Statistics
Matches: 290, Mismatches: 60, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
68 1 0.00
69 288 0.99
70 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (68 bp):
CTGTAAAATTAAGGTTCGCAGGCGAAGAGCGCGACCTCCAGCACAGTTAGCGAGAGCAAAGCTCC
CAA
Found at i:4199279 original size:13 final size:14
Alignment explanation
Indices: 4199244--4199282 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
4199234 GAAGATATTT
4199244 ATATATTATATATAA
1 ATATATTAT-TATAA
*
4199259 ATAAATTATTAT-A
1 ATATATTATTATAA
4199272 ATATATTATTA
1 ATATATTATTA
4199283 GTAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTATTATAA
Found at i:4206650 original size:18 final size:18
Alignment explanation
Indices: 4206627--4206661 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4206617 GAGTTAAACG
*
4206627 AATCGAGTTGTTCGAGTT
1 AATCGAGTTATTCGAGTT
4206645 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
4206662 CAACGCGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:4206725 original size:9 final size:9
Alignment explanation
Indices: 4206711--4206738 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4206701 TGAGTTTTCG
4206711 AATTCGAAT
1 AATTCGAAT
4206720 AATTCGAAT
1 AATTCGAAT
4206729 AATTCGAAT
1 AATTCGAAT
4206738 A
1 A
4206739 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:4209391 original size:12 final size:12
Alignment explanation
Indices: 4209374--4209427 Score: 60
Period size: 11 Copynumber: 4.6 Consensus size: 12
4209364 CTTCAAAAAT
4209374 AAATAAAAGATA
1 AAATAAAAGATA
4209386 AAATAAAAG-TA
1 AAATAAAAGATA
4209397 AAATTAAAAAGA-A
1 AAA-T-AAAAGATA
*
4209410 AAATAATA-ATA
1 AAATAAAAGATA
4209421 AAATAAA
1 AAATAAA
4209428 TGGACTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 1 0.03
11 15 0.42
12 11 0.31
13 9 0.25
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.19
Consensus pattern (12 bp):
AAATAAAAGATA
Found at i:4209412 original size:24 final size:25
Alignment explanation
Indices: 4209378--4209424 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
4209368 AAAAATAAAT
4209378 AAAAGATAAAATAA-AAGTAAAATTA
1 AAAAGATAAAATAATAA-TAAAATTA
4209403 AAAAGA-AAAATAATAATAAAAT
1 AAAAGATAAAATAATAATAAAAT
4209425 AAATGGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (25 bp):
AAAAGATAAAATAATAATAAAATTA
Found at i:4210354 original size:24 final size:24
Alignment explanation
Indices: 4210327--4210390 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
4210317 TTGAAAGGGA
4210327 AAAAGAAAGGGAAGGGAAA-ATAAG
1 AAAAGAAAGGGAAGGGAAAGA-AAG
**
4210351 AAAAGATGGGGAA--GAAAGAAAG
1 AAAAGAAAGGGAAGGGAAAGAAAG
4210373 AGAAAGGAAAGGGAAGGG
1 A-AAA-GAAAGGGAAGGG
4210391 GGAAGTGGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
22 8 0.26
23 4 0.13
24 18 0.58
26 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (24 bp):
AAAAGAAAGGGAAGGGAAAGAAAG
Found at i:4217050 original size:24 final size:23
Alignment explanation
Indices: 4217015--4217063 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
4217005 ACAAGGTCTT
*
4217015 ATTTTCTTGCTT-GAGTTCTAGAA
1 ATTTTCTTGCTTCGAG-TCTAAAA
*
4217038 ATTTTTTTCGCTTCGAGTCTAAAA
1 ATTTTCTT-GCTTCGAGTCTAAAA
4217062 AT
1 AT
4217064 CTTTGACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 12 0.55
25 3 0.14
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (23 bp):
ATTTTCTTGCTTCGAGTCTAAAA
Found at i:4228375 original size:13 final size:14
Alignment explanation
Indices: 4228352--4228381 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4228342 GACTTGTTCG
4228352 TATTAATTTTTTTA
1 TATTAATTTTTTTA
4228366 TATT-ATTTTTTTA
1 TATTAATTTTTTTA
4228379 TAT
1 TAT
4228382 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTAATTTTTTTA
Found at i:4229061 original size:12 final size:12
Alignment explanation
Indices: 4229046--4229084 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
4229036 TTAGAATGTT
4229046 AATTTATATTAA
1 AATTTATATTAA
*
4229058 AATTT-GATT-A
1 AATTTATATTAA
4229068 AATTTATATTAA
1 AATTTATATTAA
4229080 AATTT
1 AATTT
4229085 GATTAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
AATTTATATTAA
Found at i:4229069 original size:11 final size:11
Alignment explanation
Indices: 4229053--4229090 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4229043 GTTAATTTAT
4229053 ATTAAAATTTG
1 ATTAAAATTTG
*
4229064 ATT-AAATTTAT
1 ATTAAAATTT-G
4229075 ATTAAAATTTG
1 ATTAAAATTTG
4229086 ATTAA
1 ATTAA
4229091 CTTTATCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.26
11 11 0.48
12 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (11 bp):
ATTAAAATTTG
Found at i:4229073 original size:22 final size:22
Alignment explanation
Indices: 4229046--4229096 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4229036 TTAGAATGTT
4229046 AATTTATATTAAAATTTGATTA
1 AATTTATATTAAAATTTGATTA
4229068 AATTTATATTAAAATTTGATTA
1 AATTTATATTAAAATTTGATTA
*
4229090 ACTTTAT
1 AATTTAT
4229097 CCAGGGGCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (22 bp):
AATTTATATTAAAATTTGATTA
Found at i:4234143 original size:12 final size:12
Alignment explanation
Indices: 4234126--4234150 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4234116 TTACAGCTAG
4234126 TCTAGGAGTATT
1 TCTAGGAGTATT
4234138 TCTAGGAGTATT
1 TCTAGGAGTATT
4234150 T
1 T
4234151 TGGTGATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TCTAGGAGTATT
Found at i:4237758 original size:126 final size:126
Alignment explanation
Indices: 4237492--4237927 Score: 596
Period size: 125 Copynumber: 3.5 Consensus size: 126
4237482 AATTGTTCAT
* *
4237492 TGCATCCTGCTTGAAGCATTTTTAACACTATTTGTTCAGAAATATCTTCTCAAAATTATTTTTTC
1 TGCATCCTACTTGAAGCGTTTTTAACACTATTTGTTCAGAAATATCTTCTCAAAATTATTTTTTC
* * *
4237557 AGGAACTA-TGTAGAAAAAGAGCGTCCACGTGGGAGTTTTTTTCTGCAATTTTGTTGACAA
66 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTGTAATTTTGTTGACAG
* * * *
4237617 TGCATCTTGCTTGAAGTGTTTTTAACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
1 TGCATCCTACTTGAAGCGTTTTTAACACTATTTGTTCAGAAATATCTTCTCAAAATTATTTTTTC
* * * ** *
4237682 ATGAACTACTATAGAAAAAGAGCGTTCACGTGATAGCTTTTTTCTATAATTTTGTTGACAG
66 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTGTAATTTTGTTGACAG
* * * *
4237743 TGCATTCTACTTGAAGCGTTTTTGACACTA----TTCATAAATGTCTTCTCAAAATTATTTTTTC
1 TGCATCCTACTTGAAGCGTTTTTAACACTATTTGTTCAGAAATATCTTCTCAAAATTATTTTTTC
* * * *
4237804 AGGAACTACTGTAGAAAAAGAACATCCACGTGGGAGCTTTTTT-TGTAATTTTGCTGATAG
66 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTGTAATTTTGTTGACAG
* * *
4237864 TGCATCCTACTTGAAGCGTTTTTGATACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
1 TGCATCCTACTTGAAGCGTTTTTAACACTATTTGTTCAGAAATATCTTCTCAAAATTATTTTTT
4237928 TGGGGTAAAA
Statistics
Matches: 272, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
121 42 0.15
122 64 0.24
125 97 0.36
126 69 0.25
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (126 bp):
TGCATCCTACTTGAAGCGTTTTTAACACTATTTGTTCAGAAATATCTTCTCAAAATTATTTTTTC
AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTGTAATTTTGTTGACAG
Found at i:4238004 original size:26 final size:25
Alignment explanation
Indices: 4237953--4238005 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
4237943 CAATTTTGTT
*
4237953 AAAAAAATAAACACAATGTTATTTA
1 AAAAAAATAAACACAATGTTACTTA
*
4237978 AAAAAAACTAAACCCTAAT-TTACTTA
1 AAAAAAA-TAAACAC-AATGTTACTTA
4238004 AA
1 AA
4238006 TTTAACCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 14 0.58
27 3 0.12
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.26
Consensus pattern (25 bp):
AAAAAAATAAACACAATGTTACTTA
Found at i:4238060 original size:30 final size:28
Alignment explanation
Indices: 4238015--4238218 Score: 123
Period size: 34 Copynumber: 6.7 Consensus size: 28
4238005 ATTTAACCAT
4238015 AAACCCTAAACCCTAATTTAATTTATTTA
1 AAACCCTAAA-CCTAATTTAATTTATTTA
4238044 AAACCCTAGAATCCTAAATTACTTAATTTATTTAA
1 AAACCCTA-AA-CCT-AA-T--TTAATTTATTT-A
*
4238079 AAACCATAAACTCTAATTTAATTTATTTA
1 AAACCCTAAAC-CTAATTTAATTTATTTA
4238108 AAACCCT--A--T--TTTAATTTATTTA
1 AAACCCTAAACCTAATTTAATTTATTTA
* *
4238130 AAACCTATAAACCTTAAACCTTAATTTATTTA
1 AAACC-CTAAACC-T-AA-TTTAATTTATTTA
*
4238162 AAACCTTAAAAACCCTAATTTATTTAATTTATTTAA
1 AAACCCT--AAA-CCT-A---ATTTAATTTATTT-A
*
4238198 AAACCATAAACCCTAATTTAA
1 AAACCCTAAA-CCTAATTTAA
4238219 ATAATTTTTA
Statistics
Matches: 143, Mismatches: 8, Indels: 47
0.72 0.04 0.24
Matches are distributed among these distances:
22 18 0.13
23 1 0.01
24 1 0.01
25 1 0.01
27 1 0.01
28 1 0.01
29 15 0.10
30 22 0.15
31 3 0.02
32 19 0.13
33 10 0.07
34 24 0.17
35 19 0.13
36 8 0.06
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (28 bp):
AAACCCTAAACCTAATTTAATTTATTTA
Found at i:4238120 original size:22 final size:22
Alignment explanation
Indices: 4238086--4238134 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
4238076 TAAAAACCAT
*
4238086 AAACTCTAATTTAATTTATTTA
1 AAACCCTAATTTAATTTATTTA
*
4238108 AAACCCTATTTTAATTTATTTA
1 AAACCCTAATTTAATTTATTTA
4238130 AAACC
1 AAACC
4238135 TATAAACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (22 bp):
AAACCCTAATTTAATTTATTTA
Found at i:4238123 original size:52 final size:54
Alignment explanation
Indices: 4238066--4238166 Score: 147
Period size: 52 Copynumber: 1.9 Consensus size: 54
4238056 CCTAAATTAC
*
4238066 TTAATTTATTTAAAAACC-ATAAA-CTCT-AA-TTTAATTTATTTAAAACCCTATT
1 TTAATTTATTT-AAAACCTATAAACCT-TAAACCTTAATTTATTTAAAACCCTATT
4238118 TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACC
1 TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACC
4238167 TTAAAAACCC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
51 6 0.14
52 17 0.39
53 4 0.09
54 17 0.39
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (54 bp):
TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACCCTATT
Found at i:4238224 original size:34 final size:35
Alignment explanation
Indices: 4238151--4238233 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
4238141 CCTTAAACCT
**
4238151 TAATTTATTT-AAAACCTTAAAAACCCTAATTTATT
1 TAATTTATTTAAAAACC-TAAAAACCCTAATTTAAA
*
4238186 TAATTTATTTAAAAACC-ATAAACCCTAATTTAAA
1 TAATTTATTTAAAAACCTAAAAACCCTAATTTAAA
4238220 TAATTT-TTATAAAA
1 TAATTTATT-TAAAA
4238234 TAACACCAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.05
34 25 0.58
35 10 0.23
36 6 0.14
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (35 bp):
TAATTTATTTAAAAACCTAAAAACCCTAATTTAAA
Found at i:4241670 original size:14 final size:15
Alignment explanation
Indices: 4241651--4241685 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
4241641 TTTAATTTTC
4241651 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
*
4241665 AAAATTTTAAAAATA
1 AAAATTTCAAAAATA
4241680 AAAATT
1 AAAATT
4241686 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:4241715 original size:30 final size:31
Alignment explanation
Indices: 4241681--4241782 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 31
4241671 TTAAAAATAA
*
4241681 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
** *
4241711 AAATTTCATTTTGACCTTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
4241741 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
4241771 AAATTTCATTTT
1 AAATTTCATTTT
4241783 AATCCTAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 4 0.07
30 55 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:4242156 original size:3 final size:3
Alignment explanation
Indices: 4242150--4242190 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
4242140 GTGTAGGAGG
4242150 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
4242191 AGGAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4242326 original size:15 final size:16
Alignment explanation
Indices: 4242308--4242364 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
4242298 AAAATTAATT
4242308 AAAAAAACAACA-CAA
1 AAAAAAACAACAGCAA
4242323 AAAAAAACAAATCAGCCAA
1 AAAAAAAC-AA-CAG-CAA
4242342 AAAAAAACCAA-AGCAA
1 AAAAAAA-CAACAGCAA
4242358 AAAAAAA
1 AAAAAAA
4242365 GCAGCCCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.22
16 12 0.32
17 4 0.11
19 12 0.32
20 1 0.03
ACGTcount: A:0.77, C:0.18, G:0.04, T:0.02
Consensus pattern (16 bp):
AAAAAAACAACAGCAA
Found at i:4242344 original size:31 final size:30
Alignment explanation
Indices: 4242308--4242381 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 30
4242298 AAAATTAATT
*
4242308 AAAAAAACAACACAAA-AAAAAACAAATCAGCC
1 AAAAAAA-AAC-CAAACAAAAAA-AAAGCAGCC
4242340 AAAAAAAAACCAAAGCAAAAAAAAAGCAGCCC
1 AAAAAAAAACCAAA-CAAAAAAAAAGCAG-CC
4242372 AAAAAGAAAA
1 AAAAA-AAAA
4242382 GGCCCAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 4 0.11
31 9 0.24
32 20 0.54
33 4 0.11
ACGTcount: A:0.73, C:0.19, G:0.07, T:0.01
Consensus pattern (30 bp):
AAAAAAAAACCAAACAAAAAAAAAGCAGCC
Found at i:4242374 original size:16 final size:16
Alignment explanation
Indices: 4242324--4242395 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
4242314 ACAACACAAA
*
4242324 AAAAAACAAATCAG-CC
1 AAAAAA-AAAGCAGCCC
* ***
4242340 AAAAAAAAACCAAAGC
1 AAAAAAAAAGCAGCCC
4242356 AAAAAAAAAGCAGCCC
1 AAAAAAAAAGCAGCCC
4242372 AAAAAGAAAAG--GCCC
1 AAAAA-AAAAGCAGCCC
4242387 AAAAAAAAA
1 AAAAAAAAA
4242396 AGAAAAGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 4 0.09
15 14 0.30
16 24 0.51
17 5 0.11
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAGCAGCCC
Found at i:4242396 original size:15 final size:16
Alignment explanation
Indices: 4242356--4242398 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
4242346 AAACCAAAGC
4242356 AAAAAAAAAGCAGCCCA
1 AAAAAAAAAG-AGCCCA
*
4242373 AAAAGAAAAG-GCCCA
1 AAAAAAAAAGAGCCCA
4242388 AAAAAAAAAGA
1 AAAAAAAAAGA
4242399 AAAGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 14 0.61
17 9 0.39
ACGTcount: A:0.70, C:0.16, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAGCCCA
Found at i:4242534 original size:8 final size:8
Alignment explanation
Indices: 4242506--4242609 Score: 106
Period size: 8 Copynumber: 13.0 Consensus size: 8
4242496 AGCAGGCCAG
4242506 GAAAAAAA
1 GAAAAAAA
* *
4242514 GAGAGAAA
1 GAAAAAAA
4242522 G-AAAAAA
1 GAAAAAAA
4242529 GAAAAAAA
1 GAAAAAAA
*
4242537 G-AAAGAA
1 GAAAAAAA
4242544 GAAAAAAA
1 GAAAAAAA
*
4242552 G-AAAAGA
1 GAAAAAAA
4242559 GAAAAAAA
1 GAAAAAAA
*
4242567 GGAAAAAAG
1 -GAAAAAAA
*
4242576 GAAAAAAG
1 GAAAAAAA
4242584 GAAAAAAGAA
1 G-AAAAA-AA
4242594 GAAAAAAA
1 GAAAAAAA
4242602 GAAAAAAA
1 GAAAAAAA
4242610 AAGAGTTTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
7 17 0.21
8 44 0.55
9 17 0.21
10 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:4242551 original size:16 final size:15
Alignment explanation
Indices: 4242508--4242613 Score: 117
Period size: 15 Copynumber: 7.1 Consensus size: 15
4242498 CAGGCCAGGA
* *
4242508 AAAAAAGAGAGAAAG
1 AAAAAAGAAAAAAAG
4242523 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
4242538 AAAGAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
4242553 AAAAGAGAAAAAAAGG
1 AAAAAAGAAAAAAA-G
*
4242569 AAAAAAGGAAAAAAGG
1 AAAAAA-GAAAAAAAG
*
4242585 AAAAAAGAAGAAAA-
1 AAAAAAGAAAAAAAG
*
4242599 AAAGAA-AAAAAAAG
1 AAAAAAGAAAAAAAG
4242613 A
1 A
4242614 GTTTCAATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
13 6 0.08
14 6 0.08
15 45 0.58
16 13 0.17
17 7 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:4243193 original size:20 final size:22
Alignment explanation
Indices: 4243156--4243199 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
4243146 AATTTTGTGT
*
4243156 AAAAAAATCCAGTGTTTTCAAAA
1 AAAAAAATCCAGT-TTTCCAAAA
4243179 AAAAAAATCCA-TTTTCCAAAA
1 AAAAAAATCCAGTTTTCCAAAA
4243200 TTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAAAAATCCAGTTTTCCAAAA
Found at i:4243268 original size:18 final size:17
Alignment explanation
Indices: 4243195--4243357 Score: 143
Period size: 17 Copynumber: 9.4 Consensus size: 17
4243185 ATCCATTTTC
* *
4243195 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
4243213 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
4243231 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
* *
4243247 AAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
4243264 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
*
4243282 C-AAAATTTTACGTATTT
1 CAAAAATTTT-CGTGTTT
** *
4243299 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
4243317 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
4243334 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
4243352 CAAAAA
1 CAAAAA
4243358 AAAAAATCTC
Statistics
Matches: 117, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
16 14 0.12
17 52 0.44
18 39 0.33
19 12 0.10
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:4243300 original size:35 final size:34
Alignment explanation
Indices: 4243195--4243357 Score: 159
Period size: 35 Copynumber: 4.7 Consensus size: 34
4243185 ATCCATTTTC
* * * *
4243195 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
*
4243231 CAAAAATTTTC--GTTTTAAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
4243264 CAAAAATTTTCGTGTTTTCAAAATTTTACGTATTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
** *
4243299 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
4243334 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
4243358 AAAAAATCTC
Statistics
Matches: 104, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 5 0.05
35 65 0.62
36 9 0.09
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:4255416 original size:192 final size:192
Alignment explanation
Indices: 4255089--4255700 Score: 1129
Period size: 192 Copynumber: 3.2 Consensus size: 192
4255079 CTTTCCAAGG
4255089 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
4255154 TTTAAAAAATCAAC-CAATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGATGTATTTTTA
66 TTTAAAAAATCAACTC-ATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
4255218 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
4255281 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
4255346 TTTAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCATGCCGAGGTATTTTTAG
66 TTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
4255411 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
4255473 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
** * *
4255538 TAAAAAAAATTAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAG
66 TTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
*
4255603 TTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
4255665 AAAATCAACTCATATTGCGAG-AATGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
4255701 GGGCACGCCG
Statistics
Matches: 409, Mismatches: 10, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
191 15 0.04
192 393 0.96
193 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (192 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:4255687 original size:122 final size:123
Alignment explanation
Indices: 4255542--4255824 Score: 500
Period size: 120 Copynumber: 2.3 Consensus size: 123
4255532 AATTTTTAAA
*
4255542 AAAAATTAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
*
4255607 TGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
4255665 -AAAATCAACTCATATTGCGAGAA-TGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
4255727 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* *
4255785 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGG
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGG
4255825 CTCACATGCT
Statistics
Matches: 152, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
120 82 0.54
121 34 0.22
122 35 0.23
123 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (123 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:4255740 original size:120 final size:121
Alignment explanation
Indices: 4255542--4255857 Score: 490
Period size: 120 Copynumber: 2.6 Consensus size: 121
4255532 AATTTTTAAA
* *
4255542 AAAAATTAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAA-TGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTAGTTTA
*
4255607 TGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
64 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
4255665 -AAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCGGGCACGCCGAGGTATTTTTAGTTTATG
1 AAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCGGGCACGCCGAGGTATTTTTAGTTTATG
4255729 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * * * * *
4255785 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGA-ATGAGTTGAGCCTCGG-GCAC--GCCGAGGTATTTTTAGTT
4255850 TATGTTTT
62 TATGTTTT
4255858 TTTCAATCTA
Statistics
Matches: 179, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
120 82 0.46
121 34 0.19
122 37 0.21
123 3 0.02
125 23 0.13
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (121 bp):
AAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCGGGCACGCCGAGGTATTTTTAGTTTATG
TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:4255862 original size:16 final size:17
Alignment explanation
Indices: 4255841--4255874 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4255831 TGCTGAGGTA
*
4255841 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
4255857 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
4255874 T
1 T
4255875 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:4255985 original size:176 final size:186
Alignment explanation
Indices: 4255780--4256192 Score: 490
Period size: 193 Copynumber: 2.2 Consensus size: 186
4255770 TAATTTTTGT
*
4255780 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
* * *
4255844 TCAATTTATG-TTTT-TTTC-A-ATCT-A-TGC-T-TTTC-AAAAATCAACTTATATTGCGAGAG
64 TCAAATTATGTTTTTATTTCTATATCTAATTGCGTGTTTCAAAAAATCAACTCATATTGCAAGAG
*
4255900 GTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTGCTTTACTAA-TTCTAC
129 GTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTAC-AATTTCTAC
* *
4255958 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
* * * *
4256022 AAATTCTGTTTTTAATTTCTATTTTTTTTAATTTCTGTGTTTCAAAAAAAAATCAACTCATATTG
66 AAATTATGTTTTT-ATTTCTA---TATCTAATTGC-GTGTTTC---AAAAAATCAACTCATATTG
* * **
4256087 CAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGT
123 CAAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTACAATTTCTAC
*
4256151 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
4256193 TTTAATTTCT
Statistics
Matches: 197, Mismatches: 17, Indels: 25
0.82 0.07 0.10
Matches are distributed among these distances:
176 58 0.29
177 7 0.04
178 5 0.03
179 4 0.02
180 1 0.01
184 2 0.01
185 1 0.01
186 2 0.01
188 1 0.01
189 4 0.02
192 2 0.01
193 77 0.39
195 33 0.17
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (186 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AAATTATGTTTTTATTTCTATATCTAATTGCGTGTTTCAAAAAATCAACTCATATTGCAAGAGGT
GAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTACAATTTCTAC
Found at i:4256038 original size:85 final size:87
Alignment explanation
Indices: 4255780--4256047 Score: 307
Period size: 91 Copynumber: 3.0 Consensus size: 87
4255770 TAATTTTTGT
*
4255780 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
*
4255844 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA--C
* *
4255871 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTT
**
4255933 TCAATTTCTGCTTTACTAATTCTAC
64 TCAATTTCTG-TTTTTTAATTCTAC
* *
4255958 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
* *
4256022 AAATTCTG-TTTTTAATTTCTAT
66 AATTTCTGTTTTTTAA-TTCTAC
4256044 TTTT
1 TTTT
4256048 TTTAATTTCT
Statistics
Matches: 155, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 38 0.25
86 9 0.06
87 29 0.19
88 2 0.01
89 31 0.20
91 41 0.26
93 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (87 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAC
Found at i:4256293 original size:55 final size:54
Alignment explanation
Indices: 4256136--4256302 Score: 264
Period size: 54 Copynumber: 3.1 Consensus size: 54
4256126 TCAATTTCTA
4256136 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
4256191 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
4256245 CTTTTGCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
4256300 CTT
1 CTT
4256303 GGCTCACGTG
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
54 51 0.50
55 46 0.45
56 6 0.06
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:4256563 original size:14 final size:15
Alignment explanation
Indices: 4256544--4256578 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
4256534 TTTAATTTTC
4256544 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
*
4256558 AAAATTTTAAAAATA
1 AAAATTTCAAAAATA
4256573 AAAATT
1 AAAATT
4256579 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:4256608 original size:30 final size:30
Alignment explanation
Indices: 4256574--4256672 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
4256564 TTAAAAATAA
*
4256574 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCA-TTTGACCCCTAAACTTTTCTCT
* *
4256604 AAATTTCA-TTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTGACCCCTAAACTTTTCTCT
* **
4256632 AAATTTCACTTAGACCCCTAAAC-TTTCAAT
1 AAATTTCA-TTTGACCCCTAAACTTTTCTCT
4256662 AAATTTCATTT
1 AAATTTCATTT
4256673 TAATCCTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
27 4 0.07
28 21 0.36
29 2 0.03
30 31 0.53
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.41
Consensus pattern (30 bp):
AAATTTCATTTGACCCCTAAACTTTTCTCT
Found at i:4256616 original size:28 final size:28
Alignment explanation
Indices: 4256584--4256671 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 28
4256574 AAATTGCATT
*
4256584 TTGACCCCTAAACTTTTC-CTAAATTTCA
1 TTGACCCCTAAAC-TTTCAATAAATTTCA
* **
4256612 TTGACCCTTAAACTTTCTTTAAATTTCA
1 TTGACCCCTAAACTTTCAATAAATTTCA
4256640 CTTAGACCCCTAAACTTTCAATAAATTTCA
1 -TT-GACCCCTAAACTTTCAATAAATTTCA
4256670 TT
1 TT
4256672 TTAATCCTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.08
28 21 0.40
29 4 0.08
30 23 0.44
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (28 bp):
TTGACCCCTAAACTTTCAATAAATTTCA
Found at i:4257048 original size:3 final size:3
Alignment explanation
Indices: 4257042--4257076 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
4257032 GTGTAGGAGG
4257042 AGA AGA AGA AGA AGA AGA AG- AGA AGA AG- AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
4257077 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4257067 original size:8 final size:8
Alignment explanation
Indices: 4257045--4257080 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
4257035 TAGGAGGAGA
4257045 AGAAGAAG
1 AGAAGAAG
4257053 AAGAAGAAG
1 -AGAAGAAG
4257062 AGAAGAAG
1 AGAAGAAG
4257070 AGAAGAA-
1 AGAAGAAG
4257077 AGAA
1 AGAA
4257081 AAAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 4 0.15
8 15 0.56
9 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (8 bp):
AGAAGAAG
Found at i:4257218 original size:20 final size:20
Alignment explanation
Indices: 4257195--4257237 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4257185 AAAATTAATT
4257195 AAAAAAAAACAACACAAAAA
1 AAAAAAAAACAACACAAAAA
* * * *
4257215 AAAACAAATCAGCCCAAAAA
1 AAAAAAAAACAACACAAAAA
4257235 AAA
1 AAA
4257238 CCAAAGCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.77, C:0.19, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAAAAAAACAACACAAAAA
Found at i:4257290 original size:27 final size:24
Alignment explanation
Indices: 4257260--4257310 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
4257250 AAGCAGCCCA
4257260 AAAAGAAAAGGCCCAAAAAAGAAGAAG
1 AAAA-AAAA-GCCCAAAAAA-AAGAAG
* *
4257287 AAAAAACAGCCCAGAAAAAAGAAG
1 AAAAAAAAGCCCAAAAAAAAGAAG
4257311 CAGGCCACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 9 0.41
26 3 0.14
27 4 0.18
ACGTcount: A:0.67, C:0.14, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGCCCAAAAAAAAGAAG
Found at i:4257414 original size:7 final size:7
Alignment explanation
Indices: 4257390--4257485 Score: 90
Period size: 7 Copynumber: 13.3 Consensus size: 7
4257380 AGCAGGCCAG
4257390 GAAAAAA
1 GAAAAAA
*
4257397 GAGAGAAA
1 GA-AAAAA
4257405 GAAAAAA
1 GAAAAAA
4257412 G-AAAAA
1 GAAAAAA
*
4257418 GAAAGAA
1 GAAAAAA
4257425 GAAAAAA
1 GAAAAAA
*
4257432 GAAAAGA
1 GAAAAAA
4257439 GAAAAAAA
1 G-AAAAAA
4257447 GGAAAAAA
1 -GAAAAAA
4257455 GGAAAAAA
1 -GAAAAAA
4257463 GAAGAAAA
1 GAA-AAAA
4257471 -AAAGAAA
1 GAAA-AAA
4257478 -AAAAAA
1 GAAAAAA
4257484 GA
1 GA
4257486 GTTTCAATTC
Statistics
Matches: 76, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
6 10 0.13
7 36 0.47
8 29 0.38
9 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:4257417 original size:8 final size:8
Alignment explanation
Indices: 4257391--4257481 Score: 69
Period size: 9 Copynumber: 10.8 Consensus size: 8
4257381 GCAGGCCAGG
4257391 AAAAAAGA
1 AAAAAAGA
* *
4257399 GAGAAAG-
1 AAAAAAGA
4257406 AAAAAAGAA
1 AAAAAAG-A
4257415 AAAGAAAGA
1 AAA-AAAGA
4257424 AGAAAAA-A
1 A-AAAAAGA
*
4257432 GAAAAGAGA
1 -AAAAAAGA
4257441 AAAAAAGGA
1 AAAAAA-GA
*
4257450 AAAAAGGAA
1 AAAAAAG-A
4257459 AAAAGAAGA
1 AAAA-AAGA
4257468 AAAAAAGA
1 AAAAAAGA
4257476 AAAAAA
1 AAAAAA
4257482 AAGAGTTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
7 5 0.08
8 26 0.39
9 27 0.41
10 8 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:4257441 original size:27 final size:26
Alignment explanation
Indices: 4257402--4257480 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
4257392 AAAAAGAGAG
4257402 AAAGAAAAAAGAAAAAGAAAGAAGAAA
1 AAAGAAAAAAGAAAAA-AAAGAAGAAA
*
4257429 AAAGAAAAGAG-AAAAAAAG--GAAA
1 AAAGAAAAAAGAAAAAAAAGAAGAAA
*
4257452 AAAGGAAAAAAGAAGAAAAA-AAGAAA
1 AAA-GAAAAAAGAAAAAAAAGAAGAAA
4257478 AAA
1 AAA
4257481 AAAGAGTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 7 0.16
24 7 0.16
25 10 0.22
26 11 0.24
27 10 0.22
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAGAAAAAAAAGAAGAAA
Found at i:4257481 original size:27 final size:26
Alignment explanation
Indices: 4257391--4257481 Score: 98
Period size: 25 Copynumber: 3.5 Consensus size: 26
4257381 GCAGGCCAGG
* *
4257391 AAAAAAGAGAGAAAGAAAAAAGAA-A
1 AAAAAAGAAAAAAAGAAAAAAGAAGA
* *
4257416 AAGAAAGAAGAAAAA-AGAAAAG-AGA
1 AAAAAAGAA-AAAAAGAAAAAAGAAGA
*
4257441 AAAAAAGGAAAAAAGGAAAAAAGAAGA
1 AAAAAA-GAAAAAAAGAAAAAAGAAGA
4257468 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
4257482 AAGAGTTTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
24 1 0.02
25 23 0.43
26 20 0.38
27 9 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAAAGAAAAAAGAAGA
Found at i:4257884 original size:19 final size:18
Alignment explanation
Indices: 4257840--4257883 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
4257830 AAAATTTCTT
4257840 TTTCAAAATTTTTCGTGC
1 TTTCAAAATTTTTCGTGC
*
4257858 CTTCAAAATTTTCTCGTG-
1 TTTCAAAATTTT-TCGTGC
4257876 TTTCAAAA
1 TTTCAAAA
4257884 AAAATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (18 bp):
TTTCAAAATTTTTCGTGC
Found at i:4258157 original size:18 final size:18
Alignment explanation
Indices: 4258056--4258223 Score: 152
Period size: 17 Copynumber: 9.6 Consensus size: 18
4258046 AAAAAATCCA
* *
4258056 TTTTCCAAAATTTTTAGTG
1 TTTT-CAAAAATTTTCGTG
* *
4258075 TCTTCTAAAAATTTTTGTG
1 TTTTC-AAAAATTTTCGTG
4258094 -TTTCAAAAATTTTC--G
1 TTTTCAAAAATTTTCGTG
* *
4258109 TTTTAAAAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
4258127 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
* *
4258144 TTTTCAAAATTTTTCGTA
1 TTTTCAAAAATTTTCGTG
** *
4258162 TTTT-AAAAATCCTCTTG
1 TTTTCAAAAATTTTCGTG
4258179 TTTTCAAAAA-TTTCGGTG
1 TTTTCAAAAATTTTC-GTG
*
4258197 TTTT-GAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
4258214 TTTTCAAAAA
1 TTTTCAAAAA
4258224 AAAAATCTCG
Statistics
Matches: 119, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
15 1 0.01
16 12 0.10
17 49 0.41
18 43 0.36
19 14 0.12
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:4258223 original size:35 final size:34
Alignment explanation
Indices: 4258061--4258223 Score: 150
Period size: 35 Copynumber: 4.7 Consensus size: 34
4258051 ATCCATTTTC
* * * *
4258061 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
*
4258097 CAAAAATTTTC--GTTTTAAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
4258130 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
* ** *
4258165 TAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
4258200 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
4258224 AAAAATCTCG
Statistics
Matches: 104, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 8 0.08
35 59 0.57
36 12 0.12
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:4258238 original size:39 final size:38
Alignment explanation
Indices: 4258184--4258312 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 38
4258174 TCTTGTTTTC
*
4258184 AAAAATTTCGGTGTTTTGAAAATTTTCGTGTTTTCAAAAA
1 AAAAATCTC-GTGTTTT-AAAATTTTCGTGTTTTCAAAAA
*
4258224 AAAAATCTCGTGTTTCATAAATTTT-G-GTTTT-AAAAA
1 AAAAATCTCGTGTTTTA-AAATTTTCGTGTTTTCAAAAA
* * * *
4258260 AAATAT-T-ATGTCTTAAAATTCTCGTGTTTTCAAAACA
1 AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAA-A
*
4258297 AGAAATTCTCGTGTTT
1 A-AAAATCTCGTGTTT
4258313 CAATCGGATC
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
33 6 0.09
34 6 0.09
35 6 0.09
36 14 0.20
37 7 0.10
38 5 0.07
39 14 0.20
40 12 0.17
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (38 bp):
AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAAA
Found at i:4266349 original size:18 final size:20
Alignment explanation
Indices: 4266307--4266343 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4266297 ATATTTTATG
*
4266307 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
4266326 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
4266344 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:4268551 original size:46 final size:46
Alignment explanation
Indices: 4268499--4268819 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
4268489 AGTGTGCTCT
4268499 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4268545 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
4268591 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
4268637 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *** *
4268683 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
4268729 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * * * *
4268775 ATGACAAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
4268820 TCATGTCAAA
Statistics
Matches: 249, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 216 0.87
47 33 0.13
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:4273862 original size:53 final size:53
Alignment explanation
Indices: 4273734--4273903 Score: 218
Period size: 53 Copynumber: 3.2 Consensus size: 53
4273724 TGTGCGCCTT
* ** *
4273734 TATAAGACCATAGTTGGGCTATGGCATCTGTGCAATGTGAT-ACGTG-TTCCCG
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATT-CCG
* * * *
4273786 TATAAGACCATAGTTGGGCTATGGCTTCGGTATGATGTGATAATGTGATTCCA
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
* *
4273839 TATAAGACCATAGCTGGGCTATGGCGTCAGTGTGATGTGATAATGTGATTCCG
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
*
4273892 TATAAAACCATA
1 TATAAGACCATA
4273904 TATGGGATAT
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
52 36 0.35
53 65 0.63
54 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (53 bp):
TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
Found at i:4274841 original size:37 final size:37
Alignment explanation
Indices: 4274789--4274862 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
4274779 TGGCTTAGCC
*
4274789 ACATGGGCGTATGCCTAGGCCATGTGCCGCTCTGATA
1 ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
* * *
4274826 ACATGGGTGTGTGCCTAGGCCGTGTGCCCCTCTGATA
1 ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
4274863 CTTAAGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.16, C:0.27, G:0.31, T:0.26
Consensus pattern (37 bp):
ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
Found at i:4275463 original size:22 final size:22
Alignment explanation
Indices: 4275435--4275489 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
4275425 TTCTTCTTTG
4275435 TTTTCTCCTTTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
4275457 TTTTCTCCTCTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
4275479 TATT-TCCTTTT
1 TTTTCTCCTTTT
4275490 TCCTTATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTCTCCTTTTCTCCAAAATT
Found at i:4282651 original size:4 final size:4
Alignment explanation
Indices: 4282642--4282667 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4282632 AACAAAACAA
4282642 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
4282668 ACGTAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:4286092 original size:16 final size:14
Alignment explanation
Indices: 4286069--4286108 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
4286059 CGTCTTTCCC
4286069 TCTTTCTTTTCTCAT
1 TCTTTCTTTTCTC-T
4286084 TCTTTTCTTTTTCTCT
1 TC-TTTC-TTTTCTCT
4286100 TCTTTCTTT
1 TCTTTCTTT
4286109 AACCAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 6 0.26
16 7 0.30
17 7 0.30
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTCTTTTCTCT
Found at i:4287107 original size:21 final size:21
Alignment explanation
Indices: 4287078--4287120 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4287068 ATAAACAATA
*
4287078 TAATTGTTTTG-CTTTTTAACT
1 TAATGGTTTTGAC-TTTTAACT
4287099 TAATGGTTTTGACTTTTAACT
1 TAATGGTTTTGACTTTTAACT
4287120 T
1 T
4287121 TAGAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (21 bp):
TAATGGTTTTGACTTTTAACT
Found at i:4289936 original size:42 final size:42
Alignment explanation
Indices: 4289873--4289999 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
4289863 TTTCGTTTTC
** * *
4289873 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
4289916 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
4289957 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
4289998 TC
1 TC
4290000 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:4290061 original size:47 final size:46
Alignment explanation
Indices: 4289958--4290081 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 46
4289948 ATTCATATAT
* * * * *
4289958 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
4290004 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
4290051 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
4290082 GAAATCACTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:4290134 original size:31 final size:31
Alignment explanation
Indices: 4290099--4290247 Score: 228
Period size: 31 Copynumber: 4.8 Consensus size: 31
4290089 CTTGTCACTT
* *
4290099 GTAGCCGAAGCTACCACTATTCACTGATAAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
4290130 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
4290161 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
4290192 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
4290223 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
4290248 TGTCATTTGT
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 3 0.03
31 104 0.95
32 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:4290329 original size:50 final size:51
Alignment explanation
Indices: 4290223--4290351 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
4290213 CACTGATCAG
* * *
4290223 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
4290274 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
4290324 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
4290352 TGCCATGGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:4290486 original size:14 final size:15
Alignment explanation
Indices: 4290467--4290495 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4290457 TTTTATCATC
4290467 AACACAT-ATGAAAT
1 AACACATCATGAAAT
4290481 AACACATCATGAAAT
1 AACACATCATGAAAT
4290496 TCATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (15 bp):
AACACATCATGAAAT
Found at i:4293224 original size:12 final size:11
Alignment explanation
Indices: 4293203--4293243 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
4293193 CTCTTTTGAC
4293203 TTTTGGTTTTG
1 TTTTGGTTTTG
4293214 TTTTGGGTTTTG
1 TTTT-GGTTTTG
4293226 TTATTGGTTTTAG
1 TT-TTGGTTTT-G
4293239 TTTTG
1 TTTTG
4293244 ATTAAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.15
12 18 0.67
13 5 0.19
ACGTcount: A:0.05, C:0.00, G:0.27, T:0.68
Consensus pattern (11 bp):
TTTTGGTTTTG
Found at i:4300859 original size:41 final size:41
Alignment explanation
Indices: 4300735--4301040 Score: 359
Period size: 41 Copynumber: 7.5 Consensus size: 41
4300725 ATAACGGCAT
* * * * *
4300735 TTTTAGTAAGACGCCGCTAAA-AACAGAGCAATAGCGGTG-
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* * * * *
4300774 TTTTAGTAAAAAGCACCGCTAAA-AACAAAGCATTAGTGGCGC
1 TTTTGGT-AAAA-CGCCGCTAAAGACCAGAGCATTAGCGGCGC
* *
4300816 TTTTGGTAAAACGCCGCTAAAGACCAGAGTATTATCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
** * *
4300857 TTTTATTAAAACGCCGTTAAAGACCAGAGCATTAGCGACGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* *
4300898 TTTTGGTAAAACGCCGCTAAAGACCAGGGCATTAGCGACGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
4300939 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTA-CGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
** * *
4300979 TTTTATTAAAACGACGCTAAAGACCAGAACATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
*
4301020 TTTTGGTAAAACGTCGCTAAA
1 TTTTGGTAAAACGCCGCTAAA
4301041 AGTCATATAA
Statistics
Matches: 230, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
39 7 0.03
40 47 0.20
41 170 0.74
42 6 0.03
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (41 bp):
TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
Found at i:4301013 original size:122 final size:123
Alignment explanation
Indices: 4300803--4301040 Score: 397
Period size: 122 Copynumber: 1.9 Consensus size: 123
4300793 TAAAAACAAA
* * *
4300803 GCATTAGTGGCGCTTTTGGTAAAACGCCGCTAAAGACCAGAGTATTATCGGCGCTTTTATTAAAA
1 GCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTATCGGCGCTTTTATTAAAA
* * *
4300868 CGCCGTTAAAGACCAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGG
66 CGACGCTAAAGACCAGAACATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGG
4300926 GCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTA-CGGCGCTTTTATTAAAA
1 GCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTATCGGCGCTTTTATTAAAA
* *
4300990 CGACGCTAAAGACCAGAACATTAGCGGCGCTTTTGGTAAAACGTCGCTAAA
66 CGACGCTAAAGACCAGAACATTAGCGACGCTTTTGGTAAAACGCCGCTAAA
4301041 AGTCATATAA
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
122 63 0.59
123 44 0.41
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (123 bp):
GCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTATCGGCGCTTTTATTAAAA
CGACGCTAAAGACCAGAACATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGG
Found at i:4301280 original size:21 final size:21
Alignment explanation
Indices: 4301203--4301280 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
4301193 TTATCATTGT
4301203 AGTTTAAG-GTTTATGGTTTAA
1 AGTTTAAGAGTTTATGGTTT-A
*
4301224 AGTTTATGAGTTAACTATGGTTTA
1 AGTTTAAGAGTT---TATGGTTTA
* * *
4301248 AG-ATATATAGTTTAGGGTTTA
1 AGTTTA-AGAGTTTATGGTTTA
4301269 AGTTTAAGAGTT
1 AGTTTAAGAGTT
4301281 AACTAGTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 22 0.50
22 5 0.11
23 2 0.05
24 7 0.16
25 8 0.18
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (21 bp):
AGTTTAAGAGTTTATGGTTTA
Found at i:4307147 original size:9 final size:9
Alignment explanation
Indices: 4307130--4307170 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
4307120 CTTCTCTCAT
4307130 ATAACTTAC
1 ATAACTTAC
*
4307139 ATAATTTAC
1 ATAACTTAC
*
4307148 ATAACTCAC
1 ATAACTTAC
*
4307157 ATAACGTAC
1 ATAACTTAC
4307166 ATAAC
1 ATAAC
4307171 AACTTACTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.29
Consensus pattern (9 bp):
ATAACTTAC
Found at i:4312761 original size:21 final size:21
Alignment explanation
Indices: 4312735--4312782 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
4312725 TCAACTCAGA
4312735 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
4312756 GCGGAGGCAGCAGTGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
4312777 GAGGAG
1 GCGGAG
4312783 CAGAACAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.58, T:0.02
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:4313207 original size:43 final size:43
Alignment explanation
Indices: 4313160--4313257 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
4313150 GAACAAGACT
* * * * *
4313160 TTTAGCGACGTTTTTTATATAA-GCGTCGCTATAAGTCCTGGTC
1 TTTAGCGGCGTTTTTTA-AAAATGCGCCGCTATAAATCCTAGTC
4313203 TTTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAATCCTAGTC
1 TTTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAATCCTAGTC
4313246 TTTAGCGGCGTT
1 TTTAGCGGCGTT
4313258 ACATATAGCG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 3 0.06
43 46 0.94
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAATCCTAGTC
Found at i:4323566 original size:18 final size:19
Alignment explanation
Indices: 4323540--4323575 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4323530 GAAGATATTA
*
4323540 TTTTGTTTTATT-ATTTAT
1 TTTTATTTTATTAATTTAT
4323558 TTTTATTTTATTAATTTA
1 TTTTATTTTATTAATTTA
4323576 GGATTAAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTATTTTATTAATTTAT
Found at i:4328525 original size:21 final size:21
Alignment explanation
Indices: 4328500--4328568 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4328490 TATAATGATT
4328500 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
4328521 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
4328541 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
4328561 ATTATTAT
1 ATTATTAT
4328569 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:4328581 original size:15 final size:14
Alignment explanation
Indices: 4328555--4328585 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4328545 TATGGTTTTA
4328555 TATTAGATTATTAT
1 TATTAGATTATTAT
4328569 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
4328584 TA
1 TA
4328586 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:4339357 original size:4 final size:4
Alignment explanation
Indices: 4339343--4339409 Score: 54
Period size: 4 Copynumber: 17.0 Consensus size: 4
4339333 GCTTTCACAT
*
4339343 TAAA AAAA TAAA TAAA TAAA TAAA T-AA TAACAA TAAA -ATAA TAAA T--A
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-A-AA TAAA TA-AA TAAA TAAA
4339390 TAAA TATAA T-AA TAAA TAAA
1 TAAA TA-AA TAAA TAAA TAAA
4339410 ATTTAAGACG
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
2 2 0.04
3 7 0.13
4 35 0.67
5 5 0.10
6 3 0.06
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:4339378 original size:21 final size:19
Alignment explanation
Indices: 4339349--4339408 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
4339339 ACATTAAAAA
4339349 AATAAATAAATAAATAAAT
1 AATAAATAAATAAATAAAT
4339368 AATAACAATAAA-ATAATAAAT
1 AAT-A-AATAAATA-AATAAAT
4339389 -ATAAATATAAT-AATAAAT
1 AATAAATA-AATAAATAAAT
4339407 AA
1 AA
4339409 AATTTAAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
18 11 0.31
19 7 0.20
20 4 0.11
21 13 0.37
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAAATAAATAAATAAAT
Found at i:4339389 original size:18 final size:17
Alignment explanation
Indices: 4339343--4339411 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 17
4339333 GCTTTCACAT
*
4339343 TAAAAAAATAAAT-AAA
1 TAAAATAATAAATAAAA
4339359 T-AAATAA-ATAATAACAA
1 TAAAATAATA-AATAA-AA
4339376 TAAAATAATAAATATAAA
1 TAAAATAATAAATA-AAA
*
4339394 TATAATAATAAATAAAA
1 TAAAATAATAAATAAAA
4339411 T
1 T
4339412 TTAAGACGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.02
15 8 0.18
16 2 0.04
17 7 0.16
18 25 0.56
19 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAATAAATAAAA
Found at i:4340032 original size:13 final size:13
Alignment explanation
Indices: 4340016--4340060 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
4340006 TTATTATTAT
4340016 TTATTTAGTTTTA
1 TTATTTAGTTTTA
*
4340029 TTATTTATTTTTA
1 TTATTTAGTTTTA
4340042 -T-TTTA-TTTTA
1 TTATTTAGTTTTA
4340052 TTAATTTAG
1 TT-ATTTAG
4340061 GATTAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 1 0.04
13 16 0.59
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:4340041 original size:23 final size:24
Alignment explanation
Indices: 4340009--4340059 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
4339999 GAAGATATTA
4340009 TTATTATTTA-TTTAGTTTTATTAT
1 TTATTATTTATTTTA-TTTTATTAT
4340033 TTATT-TTTATTTTATTTTATTAAT
1 TTATTATTTATTTTATTTTATT-AT
4340057 TTA
1 TTA
4340060 GGATTAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTATTATTTATTTTATTTTATTAT
Found at i:4342882 original size:31 final size:31
Alignment explanation
Indices: 4342819--4342884 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4342809 ACTGGGCGTG
* * *
4342819 TGGGCCCACATGAGTAGTCCACACGGGCATA
1 TGGGCCCACACGAGTAGTCCAAACGAGCATA
* * *
4342850 TGGGCCCACACGGGTAGTCCAAACTAGTATA
1 TGGGCCCACACGAGTAGTCCAAACGAGCATA
4342881 TGGG
1 TGGG
4342885 TTGCTGGGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.18
Consensus pattern (31 bp):
TGGGCCCACACGAGTAGTCCAAACGAGCATA
Found at i:4346220 original size:16 final size:16
Alignment explanation
Indices: 4346198--4346231 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4346188 AACTAAAACT
4346198 TTAT-TTTTAATTTT-
1 TTATATTTTAATTTTA
4346212 TTATATTTTAATTTTA
1 TTATATTTTAATTTTA
4346228 TTAT
1 TTAT
4346232 GCATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 10 0.56
16 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATATTTTAATTTTA
Found at i:4350761 original size:3 final size:3
Alignment explanation
Indices: 4350748--4350789 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
4350738 ACAAACAATG
* *
4350748 ATA AAA ATA ATA ATA AAA ATA ATA ATA ATAA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA AT
4350790 GCAATGATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:4350765 original size:12 final size:12
Alignment explanation
Indices: 4350748--4350788 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
4350738 ACAAACAATG
4350748 ATAAAAATAATA
1 ATAAAAATAATA
4350760 ATAAAAATAATA
1 ATAAAAATAATA
4350772 ATAATAAATAATA
1 ATAA-AAATAATA
4350785 ATAA
1 ATAA
4350789 TGCAATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:4351326 original size:26 final size:27
Alignment explanation
Indices: 4351295--4351347 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
4351285 TGTACACAAT
*
4351295 ATATAATA-TATAAAAAATATATATAA
1 ATATAATATTATAAAAAATACATATAA
4351321 ATATAATATTTATAAAAAATACATATA
1 ATATAATA-TTATAAAAAATACATATA
4351348 TGGTATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
28 16 0.67
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATAATATTATAAAAAATACATATAA
Found at i:4351328 original size:15 final size:13
Alignment explanation
Indices: 4351300--4351347 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
4351290 ACAATATATA
4351300 ATATATAAAAAAT
1 ATATATAAAAAAT
4351313 ATATATAAATATAAT
1 ATATATAAA-A-AAT
*
4351328 ATTTATAAAAAAT
1 ATATATAAAAAAT
*
4351341 ACATATA
1 ATATATA
4351348 TGGTATAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 17 0.57
14 2 0.07
15 11 0.37
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATATAAAAAAT
Found at i:4351426 original size:3 final size:3
Alignment explanation
Indices: 4351413--4351445 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
4351403 GTATAAATGA
4351413 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
4351446 AATCGAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4352402 original size:26 final size:27
Alignment explanation
Indices: 4352366--4352427 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
4352356 CTTTCTTTTT
*
4352366 TTTTTTATTCCATTACCAACTTT-TCC
1 TTTTTTATTCCATTACCAACTTTCCCC
4352392 TTTTTTATTCCATTACCAACTTTCCCC
1 TTTTTTATTCCATTACCAACTTTCCCC
4352419 TTTTTTATT
1 TTTTTTATT
4352428 TTTTATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 23 0.68
27 11 0.32
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTTTATTCCATTACCAACTTTCCCC
Found at i:4355202 original size:22 final size:22
Alignment explanation
Indices: 4355167--4355208 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4355157 ATACTTATTT
* *
4355167 TATTTTACATTGATTAGAATTC
1 TATTTGACACTGATTAGAATTC
4355189 TATTTGACACTGATTAGAAT
1 TATTTGACACTGATTAGAAT
4355209 AAGGTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (22 bp):
TATTTGACACTGATTAGAATTC
Found at i:4363339 original size:21 final size:21
Alignment explanation
Indices: 4363313--4363363 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
4363303 CGCTATTTCT
* * *
4363313 AATCTCATCGCTATAGTATCC
1 AATCTCACCACTATAGTAACC
*
4363334 AATCTCACCACTATAGTAACT
1 AATCTCACCACTATAGTAACC
4363355 AATCTCACC
1 AATCTCACC
4363364 GCCACTACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.29
Consensus pattern (21 bp):
AATCTCACCACTATAGTAACC
Found at i:4364377 original size:63 final size:63
Alignment explanation
Indices: 4364291--4364662 Score: 372
Period size: 63 Copynumber: 5.9 Consensus size: 63
4364281 TGCCTTGCCC
* * * * *
4364291 GTGTGTCTCAAATATAAACTCAGTGAGTCACACGGCCTAGACACACGCCCGTGTGTCTTGCCT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * * * * **
4364354 ATATGCCTCTAATAAAAACTCAGTGAGTTATACGGCTTGGACACACGCCCGTGTGTCTTGTCT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * ** * *
4364417 ATGTG-CATCTAATATGAACTCAGTGAGTGACACGGCCTGGACACACGCCTATGTGTCTCACCC
1 GTGTGAC-TCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * *
4364480 GTGTGACTCTAATATGAATTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * ** * ** *
4364543 GTATGACTCTAATATGAACTTAGTGAGTTACA-AACCTGGACATACGCTTGTGTGTCTCA-CT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * * *
4364604 CGTGTGACTCTAATATAAACTCAGTGTGTTACACGGCCTAGATACATGCCCATGTGTCT
1 -GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCT
4364663 CACCCATATG
Statistics
Matches: 256, Mismatches: 49, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
61 2 0.01
62 51 0.20
63 202 0.79
64 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (63 bp):
GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
Found at i:4364503 original size:126 final size:126
Alignment explanation
Indices: 4364301--4364673 Score: 417
Period size: 126 Copynumber: 3.0 Consensus size: 126
4364291 GTGTGTCTCA
* * * ** ** * *
4364301 AATATAAACTCAGTGAGTCACACGGCCTAGACACACGCCCGTGTGTCTTGCCTATATGCCTCTAA
1 AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
* * * *** *
4364366 TAAAAACTCAGTGAGTTATACGGCTTGGACACACGCCCGTGTGTCTTGTCTATGTG-CATCT
66 TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGAC-TCT
* *
4364427 AATATGAACTCAGTGAGTGACACGGCCTGGACACACGCCTATGTGTCTCACCCGTGTGACTCTAA
1 AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
* * *
4364492 TATGAATTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTGTATGACTCT
66 TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGACTCT
* * ** * * *
4364553 AATATGAACTTAGTGAGTTACA-AACCTGGACATACGCTTGTGTGTCTCACTCGTGTGACTCTAA
1 AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
* * * * * *
4364617 TATAAACTCAGTGTGTTACACGGCCTAGATACATGCCCATGTGTCTCACCCATATGA
66 TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGA
4364674 TTCCTGTATC
Statistics
Matches: 208, Mismatches: 38, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
125 84 0.40
126 123 0.59
127 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (126 bp):
AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGACTCT
Found at i:4367640 original size:12 final size:12
Alignment explanation
Indices: 4367623--4367653 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4367613 GTCTAAATAC
4367623 TATATATATATT
1 TATATATATATT
4367635 TATATATATATT
1 TATATATATATT
4367647 TATATAT
1 TATATAT
4367654 TATGTATACA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATATATATT
Found at i:4372487 original size:25 final size:25
Alignment explanation
Indices: 4372453--4372508 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
4372443 CCCAGATCAG
*
4372453 TTCATAGAAAGATCTAGCACAAGCT
1 TTCATGGAAAGATCTAGCACAAGCT
4372478 TTCATGGAAAGATCTAGCACAAGCT
1 TTCATGGAAAGATCTAGCACAAGCT
4372503 TTCATG
1 TTCATG
4372509 AAGCAGTACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (25 bp):
TTCATGGAAAGATCTAGCACAAGCT
Found at i:4377653 original size:804 final size:804
Alignment explanation
Indices: 4375534--4377753 Score: 4248
Period size: 801 Copynumber: 2.8 Consensus size: 804
4375524 CCCCACACGA
4375534 GGAGATGAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGA
1 GGAGATGAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGA
4375599 CCTTATTGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGC
66 CCTTATTGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGC
* *
4375664 TAAGTACTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATAGAAGCCGGTTCAGCAAAAG
131 TAAGTACTGACATTGTGGTACACAGGCTCCCCACCAAAGAAGAATGGAAGCCGGTTCAGCAAAAG
*
4375729 CTTCGAAGGATGTGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGC
196 CTTCGAAGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGC
*
4375794 TGGTTTCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAG
261 TAGTTTCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAG
4375859 GTGGAAAAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTC
326 GTGGAAAAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTC
4375924 CCGTTGCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGA
391 CCGTTGCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGA
4375989 TGGTTTCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGA
456 TGGTTTCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGA
4376054 CCATGTGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATAT
521 CCATGTGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATAT
* *
4376119 CGGAGAGCCATGGTGACCCTATTCCATGATGATATCAACGATGTGAGTGACGTTGCTACTAATTC
586 CAGAGAGCCATGGTAACCCTATTCCATGATGATATCAACGATGTGAGTGACGTTGCTACTAATTC
4376184 AGAGTCCCCTTTTGAGCGGGATATGTGTCTAGAGGGATCTCAGGACTTTGAGGATGACGGAGACT
651 AGAGTCCCCTTTTGAGCGGGATATGTGTCTAGAGGGATCTCAGGACTTTGAGGATGACGGAGACT
4376249 GTAACTCATCCCTTGATTTGTTAAGGATGGTAGAACACGAGGAGAAACAGATTCTACCCTATAAA
716 GTAACTCATCCCTTGATTTGTTAAGGATGGTAGAACACGAGGAGAAACAGATTCTACCCTATAAA
4376314 GAGACCGTAGAAGTCGTGAACTTG
781 GAGACCGTAGAAGTCGTGAACTTG
* *
4376338 GGAGATGAACTAGAAAAGAAAAAAGTAAATATC---GCTTGTATTACCACAGAGACAAAGCGGAA
1 GGAGATGAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGA
4376400 CCTTATTGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGC
66 CCTTATTGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGC
4376465 TAAGTACTGACATTGTGGTACACAGGCTCCCCACCAAAGAAGAATGGAAGCCGGTTCAGCAAAAG
131 TAAGTACTGACATTGTGGTACACAGGCTCCCCACCAAAGAAGAATGGAAGCCGGTTCAGCAAAAG
*
4376530 CTTCGAAGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAAAAGCAATTTGATGC
196 CTTCGAAGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGC
*
4376595 TAGTTTCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCCTCCCCGTCCCTAAAAAAG
261 TAGTTTCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAG
4376660 GTGGAAAAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTC
326 GTGGAAAAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTC
4376725 CCGTTGCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGA
391 CCGTTGCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGA
*
4376790 TGGTTTCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTAA
456 TGGTTTCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGA
4376855 CCATGTGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATAT
521 CCATGTGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATAT
4376920 CAGAGAGCCATGGTAACCCTATTCCATGATGATATCAACGATGTGAGTGACGTTGCTACTAATTC
586 CAGAGAGCCATGGTAACCCTATTCCATGATGATATCAACGATGTGAGTGACGTTGCTACTAATTC
*
4376985 AGAGTCCCCTTTTGAGCGGGATATGTGTTTAGAGGGATCTCAGGACTTTGAGGATGACGGAGACT
651 AGAGTCCCCTTTTGAGCGGGATATGTGTCTAGAGGGATCTCAGGACTTTGAGGATGACGGAGACT
4377050 GTAACTCATCCCTTGATTTGTTAAGGATGGTAGAACACGAGGAGAAACAGATTCTACCCTATAAA
716 GTAACTCATCCCTTGATTTGTTAAGGATGGTAGAACACGAGGAGAAACAGATTCTACCCTATAAA
4377115 GAGACCGTAGAAGTCGTGAACTTG
781 GAGACCGTAGAAGTCGTGAACTTG
*
4377139 GGAGACGAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGA
1 GGAGATGAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGA
*
4377204 CCTTATTGAGTTACTCCAAGAGTTCAAGGATGCCTTTGCATGGTCATATCAAGATATGCCTGGGC
66 CCTTATTGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGC
*
4377269 TAAGTACTGACATTGTGGTGCACAGGCTCCCCACCAAAGAAGAATGGAAGCCGGTTCAGCAAAAG
131 TAAGTACTGACATTGTGGTACACAGGCTCCCCACCAAAGAAGAATGGAAGCCGGTTCAGCAAAAG
4377334 CTTCGAAGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGC
196 CTTCGAAGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGC
4377399 TAGTTTCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAG
261 TAGTTTCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAG
* *
4377464 GTGGTAAAGTACGGATGTGTGTAGACTACATAGACTTAAACAAAGCCAGCCCGAAGGATAATTTC
326 GTGGAAAAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTC
* *
4377529 CCGTTGCCTCATATTGACACCTTAGTGGATAACACGACAGGTTACTCACTCTTTTCCTTCATGGA
391 CCGTTGCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGA
4377594 TGGTTTCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGA
456 TGGTTTCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGA
4377659 CCATGTGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATAT
521 CCATGTGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATAT
4377724 CAGAGAGCCATGGTAACCCTATTCCATGAT
586 CAGAGAGCCATGGTAACCCTATTCCATGAT
4377754 ATGATGCATA
Statistics
Matches: 1389, Mismatches: 24, Indels: 6
0.98 0.02 0.00
Matches are distributed among these distances:
801 788 0.57
804 601 0.43
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (804 bp):
GGAGATGAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGA
CCTTATTGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGC
TAAGTACTGACATTGTGGTACACAGGCTCCCCACCAAAGAAGAATGGAAGCCGGTTCAGCAAAAG
CTTCGAAGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGC
TAGTTTCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAG
GTGGAAAAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTC
CCGTTGCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGA
TGGTTTCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGA
CCATGTGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATAT
CAGAGAGCCATGGTAACCCTATTCCATGATGATATCAACGATGTGAGTGACGTTGCTACTAATTC
AGAGTCCCCTTTTGAGCGGGATATGTGTCTAGAGGGATCTCAGGACTTTGAGGATGACGGAGACT
GTAACTCATCCCTTGATTTGTTAAGGATGGTAGAACACGAGGAGAAACAGATTCTACCCTATAAA
GAGACCGTAGAAGTCGTGAACTTG
Done.