Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2264
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: 27597
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:1013 original size:58 final size:58
Alignment explanation
Indices: 941--1293 Score: 255
Period size: 58 Copynumber: 6.1 Consensus size: 58
931 CTGAGTCTCG
* * * *
941 AGATCAAGGTAAATGATTTAAATGACAACAAAATTTACAAAATTACATCCAAGTCCCT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
* * * * ** **
999 AGTTCATGGAAAATGATTTAAATGACATCAAAA--TGCATTAATTGACATTAAAGTCATT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACA-AAATT-ACATCCAAGTCCCT
* * * *
1057 CGATCATGGAAAATGACCTAAATGGCATCAAAATTTATAAAATTACA-CACAAGTCCCT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATC-CAAGTCCCT
* * * * * *
1115 AGATCATGGTAAATGATCTAGATGACATCAAAATTCATAAAATTACATCTAAGTCCTT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
* * * * * * ** * * ** *
1173 ATATCATAGAAAATGACCTAAATAATATTAAAATGCATAAAATGACATAAAAGTCCTTT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCC-CT
* * * * * * *
1232 A-AACATGAAAAAATGACCTAAATGGCATCAAAATTCATAAAATTACATCCAAATCCCT
1 AGATCATG-GAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
1290 AGAT
1 AGAT
1294 TATTATCACA
Statistics
Matches: 230, Mismatches: 56, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
56 3 0.01
57 4 0.02
58 174 0.76
59 47 0.20
60 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (58 bp):
AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
Found at i:1079 original size:116 final size:116
Alignment explanation
Indices: 959--1280 Score: 310
Period size: 116 Copynumber: 2.8 Consensus size: 116
949 GTAAATGATT
* *
959 TAAATGACAACAAAATTTACAAAATTACATC-CAAGTCCCTAGTTCATGGAAAATGATTTAAATG
1 TAAATGACAACAAAATTTACAAAATTACA-CACAAGTCCCTAGATCATGGAAAATGATCTAAATG
* * *
1023 ACATCAAAATGCAT-TAATTGACAT-TAAAGTCATTCGATCATGGAAAATGACC
65 ACATCAAAATGCATAAAATT-ACATCT-AAGTCATTAGATCATAGAAAATGACC
* * * * *
1075 TAAATGGCATCAAAATTTATAAAATTACACACAAGTCCCTAGATCATGGTAAATGATCTAGATGA
1 TAAATGACAACAAAATTTACAAAATTACACACAAGTCCCTAGATCATGGAAAATGATCTAAATGA
* * *
1140 CATCAAAATTCATAAAATTACATCTAAGTCCTTATATCATAGAAAATGACC
66 CATCAAAATGCATAAAATTACATCTAAGTCATTAGATCATAGAAAATGACC
* * ** ** * * * * * * * *
1191 TAAATAATATTAAAATGCATAAAATGACATAAAAGTCCTTTA-AACATGAAAAAATGACCTAAAT
1 TAAATGACAACAAAATTTACAAAATTACACACAAGTCC-CTAGATCATG-GAAAATGATCTAAAT
* *
1255 GGCATCAAAATTCATAAAATTACATC
64 GACATCAAAATGCATAAAATTACATC
1281 CAAATCCCTA
Statistics
Matches: 172, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
115 1 0.01
116 128 0.74
117 43 0.25
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (116 bp):
TAAATGACAACAAAATTTACAAAATTACACACAAGTCCCTAGATCATGGAAAATGATCTAAATGA
CATCAAAATGCATAAAATTACATCTAAGTCATTAGATCATAGAAAATGACC
Found at i:1149 original size:174 final size:173
Alignment explanation
Indices: 800--1293 Score: 505
Period size: 174 Copynumber: 2.8 Consensus size: 173
790 TGACCCCATT
* ** * *
800 ATTCATAAAATTACATAAAAGTCCTTAGATCAT-GAAAAAT-AGCCTAAATGATATCAAAATGCA
1 ATTCACAAAATTACATCCAAGTCCCTATATCATAG-AAAATGA-CCTAAATGATATCAAAATGCA
* * * * ** *
863 TGAAATGAC-TTAAAAGTCCGTAGATCATAG-AAATAACCTAAATGGCATCAAAATTCACGAGAT
64 TAAAATGACATT-AAAGTCCTTAGATCATGGAAAATGACCTAAATGGCATCAAAATTCATAAAAT
** * * * *
926 TGTACCTGAGTCTCGAGATCAAGGTAAATGATTTAAATGACAACAAA
128 TACACC-AAGTCCCTAGATCAAGGTAAATGATCTAAATGACAACAAA
* * ** *
973 ATTTACAAAATTACATCCAAGTCCCTAGT-TCATGGAAAATGATTTAAATGACATCAAAATGCAT
1 ATTCACAAAATTACATCCAAGTCCCTA-TATCATAGAAAATGACCTAAATGATATCAAAATGCAT
* * * * *
1037 TAATTGACATTAAAGTCATTCGATCATGGAAAATGACCTAAATGGCATCAAAATTTATAAAATTA
65 AAAATGACATTAAAGTCCTTAGATCATGGAAAATGACCTAAATGGCATCAAAATTCATAAAATTA
* * *
1102 CACACAAGTCCCTAGATCATGGTAAATGATCTAGATGACATCAAA
130 CAC-CAAGTCCCTAGATCAAGGTAAATGATCTAAATGACAACAAA
* * * * *
1147 ATTCATAAAATTACATCTAAGTCCTTATATCATAGAAAATGACCTAAATAATATTAAAATGCATA
1 ATTCACAAAATTACATCCAAGTCCCTATATCATAGAAAATGACCTAAATGATATCAAAATGCATA
* * *
1212 AAATGACATAAAAGTCCTTTA-AACATGAAAAAATGACCTAAATGGCATCAAAATTCATAAAATT
66 AAATGACATTAAAGTCC-TTAGATCATG-GAAAATGACCTAAATGGCATCAAAATTCATAAAATT
*
1276 ACATCCAAATCCCTAGAT
129 ACA-CCAAGTCCCTAGAT
1294 TATTATCACA
Statistics
Matches: 263, Mismatches: 48, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
173 71 0.27
174 139 0.53
175 52 0.20
176 1 0.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (173 bp):
ATTCACAAAATTACATCCAAGTCCCTATATCATAGAAAATGACCTAAATGATATCAAAATGCATA
AAATGACATTAAAGTCCTTAGATCATGGAAAATGACCTAAATGGCATCAAAATTCATAAAATTAC
ACCAAGTCCCTAGATCAAGGTAAATGATCTAAATGACAACAAA
Found at i:7354 original size:20 final size:20
Alignment explanation
Indices: 7325--7362 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7315 TAGGCTCAAC
*
7325 GTATCGATACAATTTACTAT
1 GTATCAATACAATTTACTAT
7345 GTATCAATACAATTTACT
1 GTATCAATACAATTTACT
7363 TGGGTAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
GTATCAATACAATTTACTAT
Found at i:7446 original size:32 final size:33
Alignment explanation
Indices: 7405--7468 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
7395 CATTTCATGT
7405 TGTATCGATACAAAG-AACATGTACCGATACAA
1 TGTATCGATACAAAGCAACATGTACCGATACAA
* * *
7437 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACAAAGCAACATGTACCGATACA
7469 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACATGTACCGATACAA
Found at i:7480 original size:20 final size:21
Alignment explanation
Indices: 7457--7495 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
7447 CTAAGCAATA
7457 TGTATCGATACA-TCTAGGTG
1 TGTATCGATACATTCTAGGTG
7477 TGTATCGATACATTCTAGG
1 TGTATCGATACATTCTAGG
7496 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGGTG
Found at i:10202 original size:32 final size:33
Alignment explanation
Indices: 10141--10202 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
10131 GACCTAGACG
*
10141 TATCGATACATATTGCTTTGTATCAATACAATA
1 TATCGATACATATTGCTTAGTATCAATACAATA
*
10174 TATCGATACATGA-T-CTTAGTATCGATACA
1 TATCGATACAT-ATTGCTTAGTATCAATACA
10203 CAGCAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 13 0.50
33 12 0.46
34 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (33 bp):
TATCGATACATATTGCTTAGTATCAATACAATA
Found at i:10286 original size:13 final size:13
Alignment explanation
Indices: 10268--10298 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10258 CAATACATGG
10268 TACATTGTATCAA
1 TACATTGTATCAA
*
10281 TACATTGTATCGA
1 TACATTGTATCAA
10294 TACAT
1 TACAT
10299 AGTGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTGTATCAA
Found at i:12468 original size:21 final size:21
Alignment explanation
Indices: 12415--12475 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
12405 GATGTGCTTA
* **
12415 AAAAGAAAAAAAAAGAATTAG
1 AAAAGAAAATAAGTGAATTAG
12436 AAAAGAAAATAAGTGAATTAG
1 AAAAGAAAATAAGTGAATTAG
* *
12457 AAAAGAAGATAATTGAATT
1 AAAAGAAAATAAGTGAATT
12476 GCAAGATGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (21 bp):
AAAAGAAAATAAGTGAATTAG
Found at i:12516 original size:21 final size:21
Alignment explanation
Indices: 12490--12545 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
12480 GATGGTAATA
12490 AAGAATTAGCTAATGAA-AAC
1 AAGAATTAGCTAATGAAGAAC
*
12510 AATGAATTGGCTAA-GAAGAAC
1 AA-GAATTAGCTAATGAAGAAC
*
12531 AAGAACTTACCTAAT
1 AAGAA-TTAGCTAAT
12546 TCATTTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.21
Consensus pattern (21 bp):
AAGAATTAGCTAATGAAGAAC
Found at i:13643 original size:33 final size:32
Alignment explanation
Indices: 13597--13661 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
13587 CACACCCAGA
* * *
13597 TGTATCGATACATGCTGCTTTGTATTGATACAT
1 TGTATCGACACATG-TGCATTGTATCGATACAT
*
13630 TGTATCGACACATGTTCATTGTATCGATACAT
1 TGTATCGACACATGTGCATTGTATCGATACAT
13662 GGACAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGACACATGTGCATTGTATCGATACAT
Found at i:16000 original size:21 final size:21
Alignment explanation
Indices: 15976--16023 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
15966 AAGTAGATAT
*
15976 TAAAAAATTGGCTAATG-AAAA
1 TAAAAAATTAGCTAA-GAAAAA
*
15997 TAAAGAATTAGCTAAGAAAAA
1 TAAAAAATTAGCTAAGAAAAA
16018 TAAAAA
1 TAAAAA
16024 CTTGCATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.21
Consensus pattern (21 bp):
TAAAAAATTAGCTAAGAAAAA
Found at i:19946 original size:13 final size:13
Alignment explanation
Indices: 19928--19971 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
19918 ATACAACATT
19928 CATTGTATCGATA
1 CATTGTATCGATA
19941 CATTGTATCGATA
1 CATTGTATCGATA
*
19954 CAATGTATCGATA
1 CATTGTATCGATA
19967 CATTG
1 CATTG
19972 GGTACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:25075 original size:52 final size:52
Alignment explanation
Indices: 24997--25197 Score: 341
Period size: 52 Copynumber: 3.9 Consensus size: 52
24987 CGAAATATGA
*
24997 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
25049 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
25101 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
25153 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
25198 ATGTATCGAT
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
51 2 0.01
52 141 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:25204 original size:13 final size:13
Alignment explanation
Indices: 25186--25210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25176 CAAAGATCAG
25186 TGTATCGATACAA
1 TGTATCGATACAA
25199 TGTATCGATACA
1 TGTATCGATACA
25211 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:25291 original size:13 final size:13
Alignment explanation
Indices: 25273--25297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25263 CAAAAAAACA
25273 TGTATCGATACAT
1 TGTATCGATACAT
25286 TGTATCGATACA
1 TGTATCGATACA
25298 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:25396 original size:21 final size:21
Alignment explanation
Indices: 25355--25396 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25345 GTTGGGACCT
*
25355 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
25376 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
25397 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:26260 original size:171 final size:173
Alignment explanation
Indices: 26076--26458 Score: 644
Period size: 171 Copynumber: 2.2 Consensus size: 173
26066 TGAAGGTGTT
26076 AATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATG
1 AATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATG
* *
26141 CCAATATGTTGATACATGGCCCACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGCT
66 CCAATATGTTGATACACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGCT
26206 GATTCAAGGCCAGCTACATTGAACTTAAAGAT-G-AAGATGCC
131 GATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGATGCC
* * *
26247 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATG
1 AATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATG
* * * *
26312 CCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAAGGATGTCAATGTGCT
66 CCAATATGTTGATACACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGCT
*
26377 GATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCC
131 GATTCAAGGCCAGCTACATTGAACTTAAAGATGG-AAAGATGCC
*
26421 AATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
26459 GTGCCAATGT
Statistics
Matches: 197, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
171 153 0.78
172 1 0.01
174 43 0.22
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (173 bp):
AATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATG
CCAATATGTTGATACACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGCT
GATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGATGCC
Found at i:26437 original size:52 final size:52
Alignment explanation
Indices: 26305--26516 Score: 208
Period size: 52 Copynumber: 4.2 Consensus size: 52
26295 GAAAAGTGAT
* * * * * * * *
26305 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
26359 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
26412 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
26455 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
26507 AAAGGTGCCA
1 AAAGGTGCCA
26517 CCGACTTGTG
Statistics
Matches: 130, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
43 38 0.29
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.32
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:26473 original size:43 final size:43
Alignment explanation
Indices: 26412--26501 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
26402 TAAAGATGGA
*
26412 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
26455 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
26498 AAAG
1 AAAG
26502 ATGGAAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:26546 original size:30 final size:29
Alignment explanation
Indices: 26505--27056 Score: 603
Period size: 30 Copynumber: 19.0 Consensus size: 29
26495 CTTAAAGATG
* *
26505 GAAAAGG-TGCCACCGACTTGTGGGCTTCG
1 GAAAAGGTTGCCACTGACTTGTGGGCTT-T
* *
26534 GAAAAGGGTGCCACTGATTTGTGGGCTTT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
26563 G--AAGGTTGCCACTGACTTGTGGGC-TT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
*
26589 GTAAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
*
26618 CGAAAA-ATATGCCACTGACTTGTGGGCTTTT
1 -GAAAAGGT-TGCCACTGACTTGTGGGC-TTT
**
26649 GAAAAAATATGCCACTGACTTGTGGGCTTT
1 GAAAAGGT-TGCCACTGACTTGTGGGCTTT
*
26679 -TAAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGTTGCCACTGACTTGTGGGC-TTT
*
26708 GAAAA-ATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGT-TGCCACTGACTTGTGGGC-TTT
* *
26738 GAAAAGGGTGCCACTAACTTGTGGGCTTT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
26767 G--AAGGTTGCCACTGACTTGTGGGC-TT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
*
26793 GTAAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
*
26822 CGAAAA-ATATGCCACTGACTTGTGGGCTTTT
1 -GAAAAGGT-TGCCACTGACTTGTGGGC-TTT
**
26853 GAAAAAATATGCCACTGACTTGTGGGCTTT
1 GAAAAGGT-TGCCACTGACTTGTGGGCTTT
*
26883 -TAAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGTTGCCACTGACTTGTGGGC-TTT
*
26912 GAAAA-ATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGT-TGCCACTGACTTGTGGGC-TTT
* *
26942 GAAAAGGGTGCCACTAACTTGTGGGCTTT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
26971 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGTTGCCACTGACTTGTGGGC-TTT
* ***
26999 AAAAAAAATGCCACTGACTTGTGGGCTTT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
*** *
27028 GAAAAAAATGCCACTGACTTGTGGACTTT
1 GAAAAGGTTGCCACTGACTTGTGGGCTTT
27057 TGAAGGGTGA
Statistics
Matches: 462, Mismatches: 35, Indels: 52
0.84 0.06 0.09
Matches are distributed among these distances:
26 6 0.01
27 63 0.14
28 85 0.18
29 68 0.15
30 192 0.42
31 48 0.10
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (29 bp):
GAAAAGGTTGCCACTGACTTGTGGGCTTT
Found at i:26696 original size:89 final size:86
Alignment explanation
Indices: 26507--27056 Score: 655
Period size: 89 Copynumber: 6.3 Consensus size: 86
26497 TAAAGATGGA
* * * * **
26507 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGT
1 AAAGGTTGCCACTGACTTGTGGGCTT-TGAAAA-GTTGCCACTGACTTGTGGGCTTTTGAAAAAT
*
26569 -TGCCACTGACTTGTGGGCTTGT
64 ATGCCACTGACTTGTGGGCTTTT
*
26591 AAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAAA
1 AAAGGTTGCCACTGACTTGTGGGCTTT-GAAAAGT-TGCCACTGACTTGTGGGCTTTTG-AAAAA
26656 TATGCCACTGACTTGTGGGCTTTT
63 TATGCCACTGACTTGTGGGCTTTT
* **
26680 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGC-TTTGAAAAGT-TGCCACTGACTTGTGGGCTTTTGAAAAAT
* *
26745 GTGCCACTAACTTGTGGGC-TTT
64 ATGCCACTGACTTGTGGGCTTTT
* * *
26767 GAAGGTTGCCACTGACTTGTGGGC-TTGTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG-AAAAGTTGCCACTGACTTGTGGGCTTTTGAAAAATA
26831 TGCCACTGACTTGTGGGCTTTT
65 TGCCACTGACTTGTGGGCTTTT
** * *
26853 GAAAAAATATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAA
1 --AAAGGT-TGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTTTGAAAAA
26918 TATGCCACTGACTTGTGGGCTTTT
63 TATGCCACTGACTTGTGGGCTTTT
* * * * *
26942 GAAAAGGGTGCCACTAACTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTAAAAAAA
1 --AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTTTGAAAAAT
*
27006 ATGCCACTGACTTGTGGGCTTTGA
64 ATGCCACTGACTTGTGGGCTTT-T
*** *
27030 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAGGTTGCCACTGACTTGTGGGCTTT
27057 TGAAGGGTGA
Statistics
Matches: 413, Mismatches: 38, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
84 5 0.01
85 87 0.21
86 33 0.08
87 80 0.19
88 47 0.11
89 156 0.38
90 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (86 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTTTGAAAAATAT
GCCACTGACTTGTGGGCTTTT
Found at i:26869 original size:204 final size:204
Alignment explanation
Indices: 26512--27060 Score: 974
Period size: 204 Copynumber: 2.7 Consensus size: 204
26502 ATGGAAAAGG
* ** * *
26512 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAGGTTGCCACTG
26577 ACTTGTGGGCTTGTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATATGCCACTGACTTGTG
66 ACTTGTGGGCTTGTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATATGCCACTGACTTGTG
26642 GGCTTTTGAAAAAATATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTT
131 GGCTTTTGAAAAAATATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTT
26707 TGAAAAATA
196 TGAAAAATA
26716 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAGGTTGCCACTG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAGGTTGCCACTG
26781 ACTTGTGGGCTTGTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATATGCCACTGACTTGTG
66 ACTTGTGGGCTTGTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATATGCCACTGACTTGTG
26846 GGCTTTTGAAAAAATATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTT
131 GGCTTTTGAAAAAATATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTT
26911 TGAAAAATA
196 TGAAAAATA
26920 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAGGTTGCCACTG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAGGTTGCCACTG
* *** *
26985 ACTTGTGGGCTTTTAAAAAAAATGCCACTGACTTGTGGGCTTT-GAAAAAAATGCCACTGACTTG
66 ACTTGTGGGCTTGT--AAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATATGCCACTGACTTG
*
27049 TGGACTTTTGAA
129 TGGGCTTTTGAA
27061 GGGTGATGAA
Statistics
Matches: 332, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
204 277 0.83
205 31 0.09
206 24 0.07
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (204 bp):
TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAGGTTGCCACTG
ACTTGTGGGCTTGTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAATATGCCACTGACTTGTG
GGCTTTTGAAAAAATATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTT
TGAAAAATA
Done.