Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6675.1
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: 10459
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Found at i:445 original size:72 final size:72
Alignment explanation
Indices: 209--461 Score: 402
Period size: 73 Copynumber: 3.5 Consensus size: 72
199 ACATGTGAAC
* *
209 TGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 TGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCT
*
273 CAGCGTGT-T
63 CAACGTGTCT
*
282 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTC
1 -TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTC
347 AACGTGTCT
64 AACGTGTCT
356 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
*
421 TGTGTCT
66 CGTGTCT
428 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
462 TTCTTTCAAA
Statistics
Matches: 170, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
72 68 0.40
73 71 0.42
74 31 0.18
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (72 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
CGTGTCT
Found at i:544 original size:88 final size:88
Alignment explanation
Indices: 395--639 Score: 298
Period size: 88 Copynumber: 2.8 Consensus size: 88
385 GTTGAATTTT
* ** * **
395 GAAAACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 GAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
460 GA-TTCTTTCAAAAACATAATAAC
66 GATTTCTTTCAAAAACAGAA-AAC
* *
483 GAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 GAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * *
548 GATTTTTTTGAAAAACAGAAATC
66 GATTTCTTTCAAAAACAGAAAAC
**
571 -AAAAGGC-TTAATTGAAAATACCTCGGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 GAAAA--CAGAAATTGAAAATACCTC-G-GTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
634 AGTTGA
62 AGTTGA
640 AATTAAAACA
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
87 4 0.03
88 75 0.55
89 16 0.12
90 41 0.30
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (88 bp):
GAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTCTTTCAAAAACAGAAAAC
Found at i:825 original size:73 final size:73
Alignment explanation
Indices: 738--906 Score: 329
Period size: 73 Copynumber: 2.3 Consensus size: 73
728 ATTAAAAGGT
*
738 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
803 CCTGAGGC
66 CCTGAGGC
811 TCAACTCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
876 CCTGAGGC
66 CCTGAGGC
884 TCAACTCACCTCTCGCAATATGA
1 TCAACTCACCTCTCGCAATATGA
907 ATTAAAAAAA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 95 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (73 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
CCTGAGGC
Found at i:840 original size:127 final size:127
Alignment explanation
Indices: 612--845 Score: 328
Period size: 127 Copynumber: 1.8 Consensus size: 127
602 GTCCTGAGGC
*
612 TCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTACC
1 TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTACC
*
677 CCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATT-TTGAAAAAGTAGAAATTAAAAGGT
66 CCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTCTTGAAAAAGTAGAAATTAAAAGGT
** * * * * *
738 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAA-ACAGAAATTGAAATTACCTCATCGTG
1 TCAACCCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAAATTGAAAATACCTCAGCGTA
* * *
802 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTGA
64 CCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTCTTGA
846 CAAACAGAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
126 27 0.29
127 59 0.63
128 7 0.08
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (127 bp):
TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTACC
CCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTCTTGAAAAAGTAGAAATTAAAAGGT
Found at i:1046 original size:80 final size:73
Alignment explanation
Indices: 938--1233 Score: 258
Period size: 72 Copynumber: 3.8 Consensus size: 73
928 GTAATCTGAA
* *
938 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAAAAACAGAAATTGAAAATACCTC
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTT------GAAAACAGAAATTGAAAATACCTC
*
1003 AGCATGTGAACCGAG
60 AGCA-GTGATCCGAG
1018 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAATACCTC
1 GCTCAACTCACCTCTCGCAATATAAGTTGA------TTTTTGAAAACAGAAATTGAAAATACCTC
* *
1083 AAC-GTG-TCTTGAG
60 AGCAGTGATC-CGAG
** * * *
1096 GCTCAACTCATTTCTCGCAATATAAGTTAAATTTTGAAAACAGAAATTGAAATTACCTCAGC-GT
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGCAGT
1160 -ATCCTGAG
66 GATCC-GAG
** * * *
1168 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTACCTCAG
1 GCTCAACTCACCTCTCGCAATATAAGTTGA---TTTTTGAA-AACAGAAATTGAAAATACCTCAG
1233 C
62 C
1234 GTGCAATATG
Statistics
Matches: 187, Mismatches: 16, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
72 64 0.34
75 6 0.03
76 24 0.13
77 1 0.01
78 33 0.18
80 54 0.29
86 5 0.03
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (73 bp):
GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGCAGT
GATCCGAG
Found at i:1170 original size:72 final size:74
Alignment explanation
Indices: 980--1235 Score: 302
Period size: 72 Copynumber: 3.4 Consensus size: 74
970 TTTAAAAAAA
* **
980 AAAACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAACAGAAATTGAAAATACCTCAGC--GT-ATCCTGAGGCTCAACTCATTTCTCGCAATATAAG
1044 TTGATTTTTTTTTTTG
63 TTGA----TTTTTTTG
* * *
1060 AAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTT-
1 AAAACAGAAATTGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTG
**
1124 A-AATTTTG
66 ATTTTTTTG
* *
1132 AAAACAGAAATTGAAATTACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTG
*
1197 ATTTTTTTTT
66 A-TTTTTTTG
*
1207 AACAACAGAAATTGAAATTACCTCAGCGT
1 AA-AACAGAAATTGAAAATACCTCAGCGT
1236 GCAATATGAG
Statistics
Matches: 155, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
72 64 0.41
73 1 0.01
75 6 0.04
76 26 0.17
77 2 0.01
78 31 0.20
80 25 0.16
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (74 bp):
AAAACAGAAATTGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTG
ATTTTTTTG
Found at i:1490 original size:122 final size:126
Alignment explanation
Indices: 1236--1521 Score: 323
Period size: 122 Copynumber: 2.3 Consensus size: 126
1226 ACCTCAGCGT
* * *
1236 GCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGT
1 GCAATATGAGTTGATTTTGAAAAA-CAAAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGT
* * * * * * * * *
1301 TGATTCTTGACAAACAGAAATTGAAATTACCTTATCGTGTCCTGAGGCTCAACTCACATCTA
65 TCAATCTTGACAAACAGAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACATCTA
*
1363 GCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTT-AACTCACCTCTCGCAATATGAG-
1 GCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGG-TTCAACCCACCTCTCGCAATATGAGT
* * * *
1426 TCAAT-TT-A-AAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACCTCTC
65 TCAATCTTGACAAACAGAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACATCTA
**
1485 GCAATATGAGTTGAAATT-AAAACACAAAAATTGAAAA
1 GCAATATGAGTTGATTTTGAAAA-ACAAAAATT-AAAA
1522 TACCTCAGCG
Statistics
Matches: 137, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
121 4 0.03
122 65 0.47
123 5 0.04
124 2 0.01
125 3 0.02
126 33 0.24
127 25 0.18
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (126 bp):
GCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTT
CAATCTTGACAAACAGAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACATCTA
Found at i:1546 original size:72 final size:69
Alignment explanation
Indices: 1398--1566 Score: 230
Period size: 72 Copynumber: 2.4 Consensus size: 69
1388 AAAAATTAAA
* * * * * *
1398 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTAAATTAAAAACAAAAACTAAAAATACCTCAGCGTAC
1463 CCCG
66 CCCG
* *
1467 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAG-T-AAATTAAAA-ACAAAAACTAAAAATACCTCAGCG
1532 TACCCCG
63 TACCCCG
*
1539 AGGCTCAACTCACCTCTTGCAATATGAG
1 AGGCTCAACTCACCTCTCGCAATATGAG
1567 CTGATTTTGA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
69 27 0.31
70 1 0.01
71 7 0.08
72 53 0.60
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (69 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTAAATTAAAAACAAAAACTAAAAATACCTCAGCGTAC
CCCG
Found at i:1605 original size:321 final size:320
Alignment explanation
Indices: 1235--1894 Score: 1162
Period size: 321 Copynumber: 2.1 Consensus size: 320
1225 TACCTCAGCG
1235 TGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAG
1 TGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAG
1300 TTGATTCTTGACAAACAGAAATTGAAATTACCTTATCGTGTCCTGAGGCTCAACTCACATCTAGC
66 TTGATTCTTGACAAACAGAAATTGAAATTACCTTATCGTGTCCTGAGGCTCAACTCACATCTAGC
1365 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
131 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
*
1430 TTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
196 TTTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
* *
1495 TTGAAATT-AAAACACAAAAATTGAAAATACCTCAGCGTA-CCCCGAGGCTCAACTCACCTCT
261 TTGAAATTGAAAA-A-AAAAATTAAAAATACCTCAACG-AGCCCCGAGGCTCAACTCACCTCT
1556 TGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAG
1 TGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAG
1621 TTGATTCTTGACAAACAGAAATTGAAATTACCTTATCGTGTCCTGAGGCTCAACTCACATCTAGC
66 TTGATTCTTGACAAACAGAAATTGAAATTACCTTATCGTGTCCTGAGGCTCAACTCACATCTAGC
1686 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
131 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
* *
1751 TTTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGTAATATGAG
196 TTTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
** * ** *
1816 TTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGAGTCTTGAGGCTCAACTCATCTCT
261 TTGAAATTGAAAAAAAAAATTAAAAATACCTCAACGAGCCCCGAGGCTCAACTCACCTCT
* *
1876 CGCAATATGAGTTGATTTT
1 TGCAATATGAGCTGATTTT
1895 CCTTGGAAAG
Statistics
Matches: 324, Mismatches: 13, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
319 1 0.00
320 55 0.17
321 264 0.81
322 4 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (320 bp):
TGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAG
TTGATTCTTGACAAACAGAAATTGAAATTACCTTATCGTGTCCTGAGGCTCAACTCACATCTAGC
AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
TTTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGAAATTGAAAAAAAAAATTAAAAATACCTCAACGAGCCCCGAGGCTCAACTCACCTCT
Found at i:1699 original size:127 final size:123
Alignment explanation
Indices: 1467--1840 Score: 450
Period size: 127 Copynumber: 3.0 Consensus size: 123
1457 GCGTGCCCCG
*
1467 AGGC-TCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGC
1 AGGCTTCAACTCACCTCTCGCAATATGAGTTG--ATTTAAA-ACAAAAATTGAAAATACCTCAGC
* * * * * *
1531 GTACCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAA
63 GTGCCCCGAGGCTCAACTCACATCTAGCAATATGAGTTGATTTTGAAAAA-CAAAAATTAAA
* * * * *
1593 AGG-TTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTTAT
1 AGGCTTCAACTCACCTCTCGCAATATGAGTTGA-T-TT-A-AAACAAAAATTGAAAATACCTCAG
* *
1657 CGTGTCCTGAGGCTCAACTCACATCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
62 CGTGCCCCGAGGCTCAACTCACATCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
** * * *
1719 AGGCTT-AACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTG
1 AGGCTTCAACTCACCTCTCGCAATATGAGTTGATTTAAAACAAAAATTGAAAATACCTCAGCGTG
* * *
1783 CCCCGAGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTGAAAAA-AAAAATTAAA
66 CCCCGAGGCTCAACTCACATCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
1840 A
1 A
1841 ATACCTCAAC
Statistics
Matches: 214, Mismatches: 28, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
121 11 0.05
122 64 0.30
123 1 0.00
124 3 0.01
125 2 0.01
126 65 0.30
127 66 0.31
128 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.26
Consensus pattern (123 bp):
AGGCTTCAACTCACCTCTCGCAATATGAGTTGATTTAAAACAAAAATTGAAAATACCTCAGCGTG
CCCCGAGGCTCAACTCACATCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:1865 original size:71 final size:70
Alignment explanation
Indices: 1719--1894 Score: 203
Period size: 71 Copynumber: 2.5 Consensus size: 70
1709 AAAAATTAAA
* * * * * * * *
1719 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCAGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGAG
1783 CCCCG
66 CCCCG
* *
1788 AGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGA
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAAAAAAAACTAAAAATACCTCAACGA
* **
1853 GTCTTG
65 GCCCCG
1859 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
1895 CCTTGGAAAG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
69 25 0.28
70 6 0.07
71 59 0.66
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGAG
CCCCG
Found at i:2806 original size:15 final size:14
Alignment explanation
Indices: 2782--2834 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
2772 TTCATCTTAA
* *
2782 TTTTTCTTTTTCTT
1 TTTTTTTTTTTGTT
2796 TTTTTGTTTTTTGTT
1 TTTTT-TTTTTTGTT
2811 TTTTATTTTTTTGTT
1 TTTT-TTTTTTTGTT
2826 GTTTTTTTT
1 -TTTTTTTT
2835 ATTTTTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 5 0.15
15 24 0.71
16 5 0.15
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTTGTT
Found at i:2812 original size:20 final size:21
Alignment explanation
Indices: 2783--2844 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
2773 TCATCTTAAT
* *
2783 TTTTCTTTTTCTTTTTTTGTTT
1 TTTT-TTTTTATTTTTTTGTTG
2805 TTTGTTTTTTATTTTTTTGTTG
1 TTT-TTTTTTATTTTTTTGTTG
2827 -TTTTTTTTATTTTTTTGT
1 TTTTTTTTTATTTTTTTGT
2845 CTACTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.43
21 2 0.05
22 18 0.49
23 1 0.03
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTATTTTTTTGTTG
Found at i:2813 original size:22 final size:21
Alignment explanation
Indices: 2788--2844 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
2778 TTAATTTTTC
* *
2788 TTTTTCTTTTTTTGTTTTTTGT
1 TTTTTATTTTTTTGTTTGTT-T
2810 TTTTTATTTTTTTG-TTGTTT
1 TTTTTATTTTTTTGTTTGTTT
2830 TTTTTATTTTTTTGT
1 TTTTTATTTTTTTGT
2845 CTACTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 15 0.47
21 4 0.12
22 13 0.41
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.86
Consensus pattern (21 bp):
TTTTTATTTTTTTGTTTGTTT
Found at i:2852 original size:21 final size:20
Alignment explanation
Indices: 2809--2855 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2799 TTGTTTTTTG
**
2809 TTTTTTATTTTTTTGTTGTT
1 TTTTTTATTTTTTTGTTACT
2829 TTTTTTATTTTTTTGTCTACT
1 TTTTTTATTTTTTTGT-TACT
2850 TTTTTT
1 TTTTTT
2856 CAGGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.06, C:0.04, G:0.06, T:0.83
Consensus pattern (20 bp):
TTTTTTATTTTTTTGTTACT
Found at i:2855 original size:1 final size:1
Alignment explanation
Indices: 2782--2842 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
2772 TTCATCTTAA
* * * * * * * *
2782 TTTTTCTTTTTCTTTTTTTGTTTTTTGTTTTTTATTTTTTTGTTGTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2843 GTCTACTTTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.87
Consensus pattern (1 bp):
T
Done.