Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011242.1 Kokia drynarioides strain JFW-HI SEQ_126220, whole genome shotgun sequence
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: 117065
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--56 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
* *
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49 AAT AAT AA
1 AAT AAT AA
57 ACGGTGGTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:436 original size:78 final size:77
Alignment explanation
Indices: 299--455 Score: 251
Period size: 78 Copynumber: 2.0 Consensus size: 77
289 TTTTGAACTT
* *
299 ACCGGTGACCGGAGATGGGGGCGCGTGGACAATCGAACGGTGCTATGGCGAAGATGCGCAACGGC
1 ACCGGTGACCGGAGATGGGGGCGCGTGGACAATCGAACGGTGCCATGGCGAAGACGCGCAACGGC
364 GCGTGGCTACGG
66 GCGTGGCTACGG
* * * *
376 ACCGGTGACCGGAGATGTGGGGCGCGTGGACGATCGGACGGTGCCATGGTGGAGACGCGCAACGG
1 ACCGGTGACCGGAGATG-GGGGCGCGTGGACAATCGAACGGTGCCATGGCGAAGACGCGCAACGG
441 CGCGTGGCTACGG
65 CGCGTGGCTACGG
454 AC
1 AC
456 TCGTAGCGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 17 0.23
78 56 0.77
ACGTcount: A:0.19, C:0.24, G:0.44, T:0.13
Consensus pattern (77 bp):
ACCGGTGACCGGAGATGGGGGCGCGTGGACAATCGAACGGTGCCATGGCGAAGACGCGCAACGGC
GCGTGGCTACGG
Found at i:1213 original size:30 final size:29
Alignment explanation
Indices: 1117--1563 Score: 313
Period size: 30 Copynumber: 15.1 Consensus size: 29
1107 TACTCCCGAG
*
1117 CTTCCAAAAATTCCATTTTTTGACCTC-AAA
1 CTTCCAAAAATTCCA--TTTTGACCCCGAAA
*
1147 GCTTCCAAAAATTCCATTTTTACCCTCG-AA
1 -CTTCCAAAAATTCCATTTTGACCC-CGAAA
*
1177 CTTCCAAAAATTCCATGTTTGACCCCGAAG
1 CTTCCAAAAATTCCAT-TTTGACCCCGAAA
* *
1207 CTTCCAAAAATTCTATTTTTACCCTC-AAA
1 CTTCCAAAAATTCCATTTTGACCC-CGAAA
* * *
1236 CTTCCAAAAATTTCATTTTTAACCCCAAAA
1 CTTCCAAAAATTCCA-TTTTGACCCCGAAA
* *
1266 CTTCAAAAAATCCCATATTT-ACCCCCG-AA
1 CTTCCAAAAATTCCAT-TTTGA-CCCCGAAA
* * * * *
1295 CATCCAAAAGTTCCATTTTTAACCTCAAAA
1 CTTCCAAAAATTCCA-TTTTGACCCCGAAA
* *
1325 CTTCCAAAAATTCTATTTTTGACCTCGAAA
1 CTTCCAAAAATTCCA-TTTTGACCCCGAAA
* * *
1355 CTTCCAAAAATTCTATTTTTGACCTCAAAA
1 CTTCCAAAAATTCCA-TTTTGACCCCGAAA
* * *
1385 CTTCCAAAAA-ACTATTTTTACCCCCG-AA
1 CTTCCAAAAATTCCATTTTGA-CCCCGAAA
*
1413 CTTCCAAAAATTCCATTTTAAACCCCGAAA
1 CTTCCAAAAATTCCATTTT-GACCCCGAAA
* *
1443 ATTCCAAAAATTCCATTTTTACCCCTG-AA
1 CTTCCAAAAATTCCATTTTGACCCC-GAAA
* * * * *
1472 CCTCTAAAATTTTCATTTTTGACCCCAAAA
1 CTTCCAAAAATTCCA-TTTTGACCCCGAAA
* *
1502 TTTTCAAAAATTACCATTTTG-CCCTCG-AA
1 CTTCCAAAAATT-CCATTTTGACCC-CGAAA
* *
1531 -TGTCCAAAAACTCCATTTTTCGACCTCGAAA
1 CT-TCCAAAAATTCCA-TTTT-GACCCCGAAA
1562 CT
1 CT
1564 CTTGAAATTA
Statistics
Matches: 337, Mismatches: 52, Indels: 53
0.76 0.12 0.12
Matches are distributed among these distances:
28 21 0.06
29 120 0.36
30 174 0.52
31 21 0.06
32 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATTCCATTTTGACCCCGAAA
Found at i:1219 original size:59 final size:59
Alignment explanation
Indices: 1094--1555 Score: 470
Period size: 59 Copynumber: 7.8 Consensus size: 59
1084 CAACTGTTTG
* * * * *
1094 AAAATTACATTTATACTCC-CGAGCTTCCAAAAATTCCATTTTTTGACCTCAAAGCTTCCA
1 AAAATTCCATTTTTAC-CCTCGAACTTCCAAAAATTCCA-TTTTTGACCCCAAAACTTCCA
* * *
1154 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATGTTTGACCCCGAAGCTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCA
* * * * *
1213 AAAATTCTATTTTTACCCTCAAACTTCCAAAAATTTCATTTTTAACCCCAAAACTTCAA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCA
* * * * * * *
1272 AAAATCCCATATTTACCCCCGAACATCCAAAAGTTCCATTTTTAACCTCAAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCA
* * *
1331 AAAATTCTATTTTTGA-CCTCGAAACTTCCAAAAATTCTATTTTTGACCTCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCA
* * * **
1391 AAAA-ACTATTTTTACCCCCGAACTTCCAAAAATTCCATTTTAAACCCCGAAAA-TTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCC-AAAACTTCCA
* * * * * *
1449 AAAATTCCATTTTTACCC-CTGAACCTCTAAAATTTTCATTTTTGACCCCAAAATTTTCA
1 AAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCA
* *
1508 AAAATTACCA-TTTTGCCCTCGAA-TGTCCAAAAACTCCATTTTTCGACC
1 AAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT-GACC
1556 TCGAAACTCT
Statistics
Matches: 337, Mismatches: 53, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
58 39 0.12
59 219 0.65
60 79 0.23
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCA
Found at i:10068 original size:26 final size:25
Alignment explanation
Indices: 10035--10089 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
10025 ATTAGTCACA
* *
10035 AAAGCTCTTTAGCAGAATCAACCAT
1 AAAGCTCTTTAACAGAATCAACCAC
10060 AAAGACTCTTTAACAGAATCAACCAC
1 AAAG-CTCTTTAACAGAATCAACCAC
10086 AAAG
1 AAAG
10090 GCTCACGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (25 bp):
AAAGCTCTTTAACAGAATCAACCAC
Found at i:10110 original size:25 final size:25
Alignment explanation
Indices: 10076--10151 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
10066 TCTTTAACAG
10076 AATCAACCACAAAGGCTCACGTATA
1 AATCAACCACAAAGGCTCACGTATA
10101 AATCAACCACAAAGGCTCACGTATA
1 AATCAACCACAAAGGCTCACGTATA
10126 AATCAACCACAAAGGCTCACGTATA
1 AATCAACCACAAAGGCTCACGTATA
10151 A
1 A
10152 CATAATTATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.45, C:0.28, G:0.12, T:0.16
Consensus pattern (25 bp):
AATCAACCACAAAGGCTCACGTATA
Found at i:17837 original size:13 final size:12
Alignment explanation
Indices: 17798--17876 Score: 50
Period size: 14 Copynumber: 5.9 Consensus size: 12
17788 TAAGCAACCA
*
17798 TTTTTTTCTTCT
1 TTTTTTTCTTTT
* *
17810 TTTTCTCCGTTTT
1 TTTTTTTC-TTTT
17823 TTCTTTTTCTTTTT
1 TT-TTTTTC-TTTT
17837 TTTTTTGTCGTTCTT
1 TTTTTT-TC-TT-TT
17852 TTTTTTTCATTATT
1 TTTTTTTC-TT-TT
*
17866 TTTTCTTCTTT
1 TTTTTTTCTTT
17877 ATTTGAACTC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
12 7 0.13
13 11 0.21
14 27 0.51
15 8 0.15
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:17839 original size:17 final size:17
Alignment explanation
Indices: 17798--17841 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
17788 TAAGCAACCA
*
17798 TTTTTTTCTTCTTTTTC
1 TTTTTTTTTTCTTTTTC
***
17815 TCCGTTTTTTCTTTTTC
1 TTTTTTTTTTCTTTTTC
17832 TTTTTTTTTT
1 TTTTTTTTTT
17842 TGTCGTTCTT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTCTTTTTC
Found at i:17840 original size:18 final size:18
Alignment explanation
Indices: 17819--17858 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17809 TTTTTCTCCG
**
17819 TTTTTTCTTTTTCTTTTT
1 TTTTTTCTCGTTCTTTTT
*
17837 TTTTTTGTCGTTCTTTTT
1 TTTTTTCTCGTTCTTTTT
17855 TTTT
1 TTTT
17859 CATTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (18 bp):
TTTTTTCTCGTTCTTTTT
Found at i:17840 original size:28 final size:29
Alignment explanation
Indices: 17809--17871 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
17799 TTTTTTCTTC
*
17809 TTTTTCT-CCGTT-TTTTCTTTTTC-TTTT
1 TTTTTCTGCCGTTCTTTT-TTTTTCATTAT
* *
17836 TTTTTTTGTCGTTCTTTTTTTTTCATTAT
1 TTTTTCTGCCGTTCTTTTTTTTTCATTAT
17865 TTTTTCT
1 TTTTTCT
17872 TCTTTATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.21
28 10 0.34
29 13 0.45
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (29 bp):
TTTTTCTGCCGTTCTTTTTTTTTCATTAT
Found at i:18770 original size:20 final size:19
Alignment explanation
Indices: 18737--18806 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 19
18727 CCAAAAATAA
18737 AAAAATAAATAGAAATAAAAT
1 AAAAAT-AA-AGAAATAAAAT
18758 AAAAATAACAGAAATAATGAAGT
1 AAAAATAA-AGAAATAA--AA-T
*
18781 ATAAAATTAAATAAATAAAAT
1 A-AAAA-TAAAGAAATAAAAT
18802 AAAAA
1 AAAAA
18807 ACAATGGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 14 0.33
21 8 0.19
22 4 0.10
23 2 0.05
24 11 0.26
25 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (19 bp):
AAAAATAAAGAAATAAAAT
Found at i:29307 original size:17 final size:17
Alignment explanation
Indices: 29287--29373 Score: 86
Period size: 17 Copynumber: 5.0 Consensus size: 17
29277 TTTATTTTGG
*
29287 GTTTAAATTTAGTTTAA
1 GTTTAAATTTAATTTAA
**
29304 GTTTAAACTTTTCTTTTAA
1 GTTTAAA--TTTAATTTAA
*
29323 GTTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
29340 GTTTAAATTTAATTTGAA
1 GTTTAAATTTAATTT-AA
* *
29358 -TTTGAATTTAAATTAA
1 GTTTAAATTTAATTTAA
29374 TTAAAAAGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
16 2 0.03
17 40 0.68
18 2 0.03
19 15 0.25
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:29351 original size:12 final size:11
Alignment explanation
Indices: 29318--29375 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
29308 AAACTTTTCT
*
29318 TTTAAGTTTAAA
1 TTTAAATTT-AA
29330 TTTAAA-TTAA
1 TTTAAATTTAA
29340 GTTTAAATTTAA
1 -TTTAAATTTAA
*
29352 TTTGAATTTGAA
1 TTTAAATTT-AA
29364 TTTAAA-TTAA
1 TTTAAATTTAA
29374 TT
1 TT
29376 AAAAAGTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 6 0.15
11 18 0.45
12 16 0.40
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:30094 original size:3 final size:3
Alignment explanation
Indices: 30088--30214 Score: 166
Period size: 3 Copynumber: 42.0 Consensus size: 3
30078 ATATATATTA
30088 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
30136 AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT AAT AA- ATAT CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * *
30181 AAT AAT GAT AAT ATT AATT AAT ATT AAT ATT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
30215 TTTAAATAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.01
3 103 0.96
4 3 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:30537 original size:3 final size:3
Alignment explanation
Indices: 30529--30559 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30519 ATACTTTTAA
30529 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
30560 GAAAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31295 original size:29 final size:30
Alignment explanation
Indices: 31239--31353 Score: 123
Period size: 29 Copynumber: 3.9 Consensus size: 30
31229 CCCTAAAGGT
* *
31239 CCCTAAACTATCCAAAAATTACATTTTTAC
1 CCCTAAACTTTCCAAAAATTCCATTTTTAC
31269 CCCTAAACTTTCC-AAAATTCCATTTTTTA-
1 CCCTAAACTTTCCAAAAATTCCA-TTTTTAC
* * *
31298 CCCT-AATTTTTCAAAAATTACCA-ATTTAC
1 CCCTAAACTTTCCAAAAATT-CCATTTTTAC
*
31327 CCCTAAAC-TTCCAAAAATTCTATTTTT
1 CCCTAAACTTTCCAAAAATTCCATTTTT
31354 TATCCAAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
28 12 0.17
29 35 0.50
30 23 0.33
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATTCCATTTTTAC
Found at i:31330 original size:58 final size:58
Alignment explanation
Indices: 31251--31493 Score: 176
Period size: 58 Copynumber: 4.3 Consensus size: 58
31241 CTAAACTATC
31251 CAAAAATTA-CATTTTTACCCCTAAACTTTCC-AAAATTCCATTTTTTA-CCCTAATTTTT
1 CAAAAATTACCA-TTTTACCCCTAAAC-TTCCAAAAATTCCATTTTTTACCCCT-ATTTTT
* *
31309 CAAAAATTACCAATTTACCCCTAAACTTCCAAAAATTCTA-TTTTT-----TA----T
1 CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTTACCCCTATTTTT
* * * *
31357 CCAAAATTCCCATTTTA-CCCTCAAACTTTCC-AAAATTTCATTTTTAACCCCTATTTTT
1 CAAAAATTACCATTTTACCCCT-AAAC-TTCCAAAAATTCCATTTTTTACCCCTATTTTT
* * * * * * * * *
31415 CCAAAATTACCAATTTACAACC-GAACTTCCAAAAATTTCATTTTTGATCCCGATTCTTC
1 CAAAAATTACCATTTTAC-CCCTAAACTTCCAAAAATTCCATTTTTTACCCCTATT-TTT
31474 CAAAAATTACCATTTTACCC
1 CAAAAATTACCATTTTACCC
31494 TCGAATGTTT
Statistics
Matches: 148, Mismatches: 19, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
47 4 0.03
48 26 0.18
49 8 0.05
52 1 0.01
53 1 0.01
54 2 0.01
57 13 0.09
58 71 0.48
59 20 0.14
60 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.01, T:0.38
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTTACCCCTATTTTT
Found at i:31442 original size:106 final size:106
Alignment explanation
Indices: 31263--31464 Score: 286
Period size: 106 Copynumber: 1.9 Consensus size: 106
31253 AAAATTACAT
* *
31263 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTTACCCTAATTTTTCAAAAATTACCAATTTACC
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTTCAAAAATTACCAATTTACA
*
31328 CCTAAACTTCCAAAAA-TTCTATTTTTTATCCAAAATTCCCA
66 CCTAAACTTCCAAAAATTTC-ATTTTTGATCCAAAATTCCCA
* *
31369 TTTTA-CCCTCAAACTTTCCAAAATTTCATTTTTAACCCCT-ATTTTTCCAAAATTACCAATTTA
1 TTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAA-CCCTAATTTTTCAAAAATTACCAATTTA
*
31432 CAACC-GAACTTCCAAAAATTTCATTTTTGATCC
64 C-ACCTAAACTTCCAAAAATTTCATTTTTGATCC
31465 CGATTCTTCC
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
105 4 0.05
106 73 0.85
107 9 0.10
ACGTcount: A:0.33, C:0.26, G:0.01, T:0.40
Consensus pattern (106 bp):
TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTTCAAAAATTACCAATTTACA
CCTAAACTTCCAAAAATTTCATTTTTGATCCAAAATTCCCA
Found at i:31509 original size:59 final size:56
Alignment explanation
Indices: 31356--31556 Score: 174
Period size: 59 Copynumber: 3.4 Consensus size: 56
31346 CTATTTTTTA
* * * * *
31356 TCCAAAATTCCCATTTTACCCTCAAACTTTCCAAAATTTCATTTTTAACCCCTATTTT
1 TCCAAAATTACCATTTTACCCTCGAACTTTCAAAAATTTCATTTTTGA-CCC-ATTCT
* * *
31414 TCCAAAATTACCAATTTACAAC-CGAACTTCCAAAAATTTCATTTTTGATCCCGATTCT
1 TCCAAAATTACCATTTTAC-CCTCGAACTTTCAAAAATTTCATTTTTGA-CCC-ATTCT
* **
31472 TCCAAAAATTACCATTTTACCCTCGAA-TGTTTAAAAA-TTCTATTTTTGACCTCAAACTT
1 TCC-AAAATTACCATTTTACCCTCGAACT-TTCAAAAATTTC-ATTTTTGACC-CATTC-T
*
31531 TCCTAAAATTACCATTTTGCCCTCGA
1 TCC-AAAATTACCATTTTACCCTCGA
31557 GTTACCAAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
58 58 0.49
59 60 0.51
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (56 bp):
TCCAAAATTACCATTTTACCCTCGAACTTTCAAAAATTTCATTTTTGACCCATTCT
Found at i:31979 original size:97 final size:97
Alignment explanation
Indices: 31813--31995 Score: 244
Period size: 97 Copynumber: 1.9 Consensus size: 97
31803 GAAAACTTTA
* * *
31813 AAATCGAGGCAATATTATTTTATTTTGAGTTTTGAAAATTTGTGCCTTAACTTACTAAGCACGAT
1 AAATCGAGGCAATATTATTTTATTCTGAGTTTTGAAAATTTGTGCCTTAACTCACTAAGCACGAA
*
31878 TTTTCCTCAAATTGAAATAATTGAATACCCTT
66 TTTTCCTCAAATCGAAATAATTGAATACCCTT
* * **
31910 AAATCGAGGCAATGTT-TCTTTATCTCTGA-TTTTGAAAATTTGTGCCTTAACTCACTAGGTGCG
1 AAATCGAGGCAATATTAT-TTTAT-TCTGAGTTTTGAAAATTTGTGCCTTAACTCACTAAGCACG
* *
31973 AATTTTCTTCAAATCGAGATAAT
64 AATTTTCCTCAAATCGAAATAAT
31996 CAAATATCCT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
96 1 0.01
97 69 0.93
98 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (97 bp):
AAATCGAGGCAATATTATTTTATTCTGAGTTTTGAAAATTTGTGCCTTAACTCACTAAGCACGAA
TTTTCCTCAAATCGAAATAATTGAATACCCTT
Found at i:38455 original size:18 final size:18
Alignment explanation
Indices: 38428--38471 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38418 TAGATGCAAG
38428 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
* **
38446 GGAAAGGAAGTGAGAGAT
1 GGAAAAGAAGAAAGAGAT
38464 GAGAAAAG
1 G-GAAAAG
38472 CACGATTGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.07
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:42626 original size:28 final size:28
Alignment explanation
Indices: 42594--42654 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
42584 GAGCAGAAAG
42594 ATGATCCTCAGATCAGAGAAACTCATAT
1 ATGATCCTCAGATCAGAGAAACTCATAT
*
42622 ATGATCCTCAGATTAGAGAAACTCATAT
1 ATGATCCTCAGATCAGAGAAACTCATAT
*
42650 TTGAT
1 ATGAT
42655 ATTTAGGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (28 bp):
ATGATCCTCAGATCAGAGAAACTCATAT
Found at i:43354 original size:99 final size:99
Alignment explanation
Indices: 43139--43820 Score: 701
Period size: 99 Copynumber: 6.9 Consensus size: 99
43129 GTACCACGAA
* * * * *
43139 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACC-AAGAAGATA-TAGAGGGAAGG
1 ACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCA-AAGATACAAAAGGGAAGG
*
43202 GTTTAAGTCGCAATGACGAACCGT-GTACCTCAGA-
65 GTTTAAGTCGCAATGGCGAACC-TAGTACCTCAGAG
**
43236 AGCATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGATAAGG
1 A-CATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGG
* * *
43301 GTTTAAGTCGTAATGGTGAATCC-AGTACCACAGAG
65 GTTTAAGTCGCAATGGCGAA-CCTAGTACCTCAGAG
* * *
43336 ACATGAAGGGAAATATCTAAGCCGCAACT-GCGGATCCTA-TACCGCAAAGATACAAAACGGAAT
1 ACATGAAGGGAAAGATCTAAGCCGCAA-TGGCGGATCC-AGTACCGCAAAGATACAAAAGGGAAG
* * * *
43399 GGTTTAAGTTGCAAAGGCGAACCTTGCACCTCAGAG
64 GGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAG
* * * *
43435 ACATGAAGGGAAAGATCTAAGCCGCAACGGTGGATCTAGTACAGCAAAGATACAAAAGGGAAGGG
1 ACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGG
* * *
43500 TTTAAGTCGCAACGGCGAACCTTA-CACCACAGAG
66 TTTAAGTCGCAATGGCGAACC-TAGTACCTCAGAG
* * *
43534 ACATGAAGGGAAATATCTAAGCCGCAATGGCGGATCCAATACCGCGAAG--ACAAAAGGGAAAGG
1 ACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGG-AAGG
*
43597 G-TTAAGTCGCAACGGCGAACCTAGTACCTCAGAG
65 GTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAG
* * * * *
43631 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATCCAGTACCACGAAG--ACAAAAGGGAAAGG
1 ACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGG
* * *
43694 TTTAAGTCGCAATGGAGAACCATA-CACCTCAAAG
66 TTTAAGTCGCAATGGCGAACC-TAGTACCTCAGAG
* * * *** * * * * * ** *
43728 ACATAAAGGGAAATATTTAAGTTACAACGGTGAATCCAGTACCACGAAGGCAC-AAAGGGAAAGG
1 ACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGG
* *
43792 TTTAAGTCGCAATGGTGAACCTTGTACCT
66 TTTAAGTCGCAATGGCGAACCTAGTACCT
43821 TATAAACATA
Statistics
Matches: 503, Mismatches: 63, Indels: 37
0.83 0.10 0.06
Matches are distributed among these distances:
96 6 0.01
97 160 0.32
98 91 0.18
99 240 0.48
100 6 0.01
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (99 bp):
ACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGG
TTTAAGTCGCAATGGCGAACCTAGTACCTCAGAG
Found at i:43608 original size:48 final size:49
Alignment explanation
Indices: 43127--43803 Score: 289
Period size: 49 Copynumber: 13.8 Consensus size: 49
43117 CTACAGGTCT
* * * * *
43127 CAGTACCACGAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * * * * * *
43175 CAGTACCAAGAAGATATAGAGGGAAGGGTTTAAGTCGCAATGAC-GAAC
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * * * * * *
43223 CGTGTACCTCAGAAG-CATGAAGGGAAAGATCTAAGCCGCAATGGCGGATC
1 C-AGTACCAC-GAAGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * ** * * * * *
43273 CAGTACCGCAAAGATACA-AAAGATAAGGGTTTAAGTCGTAATGGTGAATC
1 CAGTACCACGAAG--ACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* ** * * *
43323 CAGTACCAC-AGAGACATGAAGGGAAATATCTAAGCCGCAACTGCGGATC
1 CAGTACCACGA-AGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * * * * * *
43372 CTA-TACCGCAAAGATACA-AAACGGAATGGTTTAAGTTGCAAAGGC-GAAC
1 C-AGTACCACGAAG--ACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * * * * * * *
43421 CTTGCACCTC-AGAGACATGAAGGGAAAGATCTAAGCCGCAACGGTGGATC
1 C-AGTACCACGA-AGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * * *
43471 TAGTA-CAGCAAAGATACA-AAAGGGAAGGGTTTAAGTCGCAACGGC-GAAC
1 CAGTACCA-CGAAG--ACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * ** * * *
43520 CTTA-CACCAC-AGAGACATGAAGGGAAATATCTAAGCCGCAATGGCGGATC
1 C--AGTACCACGA-AGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * * *
43570 CAATACCGCGAAGACA-AAAGGGAAAGGGTTAAGTCGCAACGGC-GAAC
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * * *
43617 CTAGTACCTC-AGAGACATGAAGGGAAAGATCTAAG-CTGCAACGGCGGATC
1 C-AGTACCACGA-AGACATAAAGGGAAAGGTTTAAGTC-GCAACGGCGGATC
* * *
43667 CAGTACCACGAAGACA-AAAGGGAAAGGTTTAAGTCGCAATGG-AGAAC
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* * ** ** * *
43714 CA-TACACCTCAAAGACATAAAGGGAAATATTTAAGTTACAACGGTGAATC
1 CAGT--ACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
* *
43764 CAGTACCACGAAGGCACAAAGGGAAAGGTTTAAGTCGCAA
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAA
43804 TGGTGAACCT
Statistics
Matches: 451, Mismatches: 137, Indels: 81
0.67 0.20 0.12
Matches are distributed among these distances:
46 1 0.00
47 10 0.02
48 90 0.20
49 230 0.51
50 108 0.24
51 12 0.03
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (49 bp):
CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGATC
Found at i:45245 original size:3 final size:3
Alignment explanation
Indices: 45239--45335 Score: 99
Period size: 3 Copynumber: 32.0 Consensus size: 3
45229 ATATATATTA
*
45239 AAT AAT AAT AAT AAT AACT -AC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
45284 AAT AAT AAT AA- ATAT CAT AAT AAT GAT AAT ATT AATT AAT ATT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
45330 ATT AAT
1 AAT AAT
45336 TTTAAATAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
2 1 0.01
3 72 0.94
4 4 0.05
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:46458 original size:29 final size:30
Alignment explanation
Indices: 46421--46760 Score: 171
Period size: 29 Copynumber: 11.7 Consensus size: 30
46411 ACCCATAAAC
*
46421 TTTCC-AAAATT-CTATTTTTGACCTTAAT
1 TTTCCAAAAATTACCATTTTTGACCTTAAT
* *
46449 TTTCCAAAAATTACCA-TTTT-ACCTCCAAAA
1 TTTCCAAAAATTACCATTTTTGACCT--TAAT
**
46479 TTT-CAAAAATT-CCATTTTTGACCCCAATT
1 TTTCCAAAAATTACCATTTTTGACCTTAA-T
* * * ** *
46508 TTTCTAAAAATTACTA-TTTTGCCCCAAAA
1 TTTCCAAAAATTACCATTTTTGACCTTAAT
* * *
46537 TTTCTAAAAATT-CCATTTTTTACCTTGATT
1 TTTCCAAAAATTACCATTTTTGACCTT-AAT
* *
46567 TTTCC-AAAATTACCA-TTTT-ACCCTCGAAC
1 TTTCCAAAAATTACCATTTTTGA-CCT-TAAT
*
46596 TTTCC-AAAATTA-CATTTTTTACCTTAATT
1 TTTCCAAAAATTACCATTTTTGACCTTAA-T
* *
46625 TTTCCAAAAATTACCA-TTTT-A-CTCCAAA
1 TTTCCAAAAATTACCATTTTTGACCT-TAAT
* * *
46653 CTTCCAAAAATT-CCA-TTTTGACCTCGATT
1 TTTCCAAAAATTACCATTTTTGACCT-TAAT
* *** **
46682 TTTCCAAAAATTACTATTTTACCCCCGAA-
1 TTTCCAAAAATTACCATTTTTGACCTTAAT
* *
46711 CTTCCAGAAATT-CCATTTTTGACCTTAAT
1 TTTCCAAAAATTACCATTTTTGACCTTAAT
*
46740 TCTTCCAAAAACTACCATTTT
1 T-TTCCAAAAATTACCATTTT
46761 ACCCCCAGAT
Statistics
Matches: 237, Mismatches: 48, Indels: 51
0.71 0.14 0.15
Matches are distributed among these distances:
27 7 0.03
28 45 0.19
29 109 0.46
30 60 0.25
31 16 0.07
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
TTTCCAAAAATTACCATTTTTGACCTTAAT
Found at i:46521 original size:59 final size:58
Alignment explanation
Indices: 46407--46822 Score: 419
Period size: 58 Copynumber: 7.1 Consensus size: 58
46397 AAAATTATAT
* *
46407 TTTTA-CCCATAAACTTTCCAAAATTCTATTTTTGACCTTAA-TTTTCCAAAAATTACCA
1 TTTTACCCCA-AAA-TTTCAAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
** * *
46465 TTTTACCTCCAAAATTTCAAAAATTCCATTTTTGACCCCAATTTTTCTAAAAATTACTA
1 TTTTACC-CCAAAATTTCAAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
* * *
46524 TTTTGCCCCAAAATTTCTAAAAATTCCATTTTTTACCTTGATTTTTCC-AAAATTACCA
1 TTTTACCCCAAAATTTC-AAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
* * * * *
46582 TTTTACCCTCGAACTTTCCAAAATTACATTTTTTACCTTAATTTTTCCAAAAATTACCA
1 TTTTACCC-CAAAATTTCAAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
* * * ** *
46641 TTTTACTCCAAACTTCCAAAAATTCCA-TTTTGACCTCGATTTTTCCAAAAATTACTA
1 TTTTACCCCAAAATTTCAAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
* * * * * *
46698 TTTTACCCCCGAACTTCCAGAAATTCCATTTTTGACCTTAATTCTTCCAAAAACTACCA
1 TTTTA-CCCCAAAATTTCAAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
* * * * ** ** *
46757 TTTTACCCCCAGATGTCTAAAAATTCCGTTTTTGA-CTTAAACTTTCTTAAAACTACCA
1 TTTTACCCCAAAATTTC-AAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
46815 TTTTACCC
1 TTTTACCC
46823 TCGAGTTACC
Statistics
Matches: 301, Mismatches: 48, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
57 31 0.10
58 148 0.49
59 119 0.40
60 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (58 bp):
TTTTACCCCAAAATTTCAAAAATTCCATTTTTGACCTTAATTTTTCCAAAAATTACCA
Found at i:46862 original size:28 final size:28
Alignment explanation
Indices: 46805--46864 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
46795 AAACTTTCTT
* *
46805 AAAACTACCATTTTACCCTCGAGTTACC
1 AAAACTACCATTTTACCCTCCAGGTACC
* *
46833 AAAATTACCATTTTGCCC-CCAGGTATCC
1 AAAACTACCATTTTACCCTCCAGGTA-CC
46861 AAAA
1 AAAA
46865 ATCACATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.35, C:0.30, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAACTACCATTTTACCCTCCAGGTACC
Found at i:47980 original size:12 final size:10
Alignment explanation
Indices: 47957--48013 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
47947 TATAAAAATA
47957 AAAAATTAAT
1 AAAAATTAAT
*
47967 AAAAATTATT
1 AAAAATTAAT
*
47977 ATAAATTAATT
1 AAAAATTAA-T
*
47988 AAAAA-TCAT
1 AAAAATTAAT
* *
47997 AAAATTTTAT
1 AAAAATTAAT
48007 AAAAATT
1 AAAAATT
48014 TAATTTATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 5 0.14
10 27 0.73
11 5 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAAATTAAT
Found at i:49825 original size:31 final size:32
Alignment explanation
Indices: 49765--49825 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
49755 TTATTTATTT
* *
49765 TGTTGACCTGACACTACCGCGTTAACAATCAG
1 TGTTGACCTGACACTACCGCATCAACAATCAG
* *
49797 TGTTGATCTGACAC-ACCGCATCATCAATC
1 TGTTGACCTGACACTACCGCATCAACAATC
49826 GATACTGGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (32 bp):
TGTTGACCTGACACTACCGCATCAACAATCAG
Found at i:56456 original size:16 final size:17
Alignment explanation
Indices: 56435--56472 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
56425 AGAAAATTTA
56435 ATTTTTCT-TCAAAAAT
1 ATTTTTCTATCAAAAAT
*
56451 ATTTTTTTACTCAAAAAT
1 ATTTTTCTA-TCAAAAAT
56469 ATTT
1 ATTT
56473 ATGAAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTCTATCAAAAAT
Found at i:57499 original size:58 final size:58
Alignment explanation
Indices: 57411--57579 Score: 182
Period size: 58 Copynumber: 2.9 Consensus size: 58
57401 GAAGTTTCGG
* * **
57411 GGTCAAAATCGAGATTTTTGGAAGTTTGGGGGTAAAATGGCT-ATTTT-GGAAAAATCAA
1 GGTCAAAATGGA-ATTTTTGAAAGTTTGGGGGTAAAAT-GCTAATTTTAAAAAAAATCAA
* * *
57469 GGTCGAAAATGGAATTTTTGAAAGTTTGGGGGTAAAATGTTAATTTTAAAAAAAATTAG
1 GGTC-AAAATGGAATTTTTGAAAGTTTGGGGGTAAAATGCTAATTTTAAAAAAAATCAA
* * * *
57528 GGTTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATG-TAATTTTTAAAAA
1 GGTCAAAATGGAATTTTTGAAAGTTTGGGGGT-AAAATGCTAATTTTAAAAAA
57580 TTTGAGTGTC
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.02
58 71 0.74
59 23 0.24
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (58 bp):
GGTCAAAATGGAATTTTTGAAAGTTTGGGGGTAAAATGCTAATTTTAAAAAAAATCAA
Found at i:57513 original size:29 final size:28
Alignment explanation
Indices: 57474--57615 Score: 88
Period size: 29 Copynumber: 4.9 Consensus size: 28
57464 ATCAAGGTCG
* * *
57474 AAAATGGAATTTTTGAAAGTTTGGGGGT
1 AAAATGTAATTTTTAAAAATTTGGGGGT
* * * *
57502 AAAATGTTAATTTTAAAAAAAATTAGGGTT
1 AAAATG-TAATTTT-TAAAAATTTGGGGGT
* ** * *
57532 AAAATGGAATTTTGGAAAGTTTGAGGGT
1 AAAATGTAATTTTTAAAAATTTGGGGGT
* *
57560 AAAAATGTAATTTTTAAAAATTTGAGTGT
1 -AAAATGTAATTTTTAAAAATTTGGGGGT
*
57589 CAAAATATAA-TTTTAAAGAAGTTTGGG
1 -AAAATGTAATTTTTAAA-AA-TTTGGG
57616 ATCAAAATAT
Statistics
Matches: 86, Mismatches: 23, Indels: 8
0.74 0.20 0.07
Matches are distributed among these distances:
28 21 0.24
29 45 0.52
30 20 0.23
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTAAAAATTTGGGGGT
Found at i:57601 original size:58 final size:58
Alignment explanation
Indices: 57410--57602 Score: 153
Period size: 58 Copynumber: 3.3 Consensus size: 58
57400 AGAAGTTTCG
* * * ** *
57410 GGGTCAAAATCGAGATTTTTGG-AAGTTTGGGGGTAAAATGGCT-ATTTT-GGAAAAATCA
1 GGGTCAAAAT--AGAATTTTGGAAAGTTTGAGGGTAAAAT-GTTAATTTTAAAAAAAATTA
* * * *
57468 AGGTCGAAAATGGAATTTTTGAAAGTTTGGGGGTAAAATGTTAATTTTAAAAAAAATTA
1 GGGTC-AAAATAGAATTTTGGAAAGTTTGAGGGTAAAATGTTAATTTTAAAAAAAATTA
* * * *
57527 GGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATG-TAATTTT-TAAAAATTTGA
1 GGGTCAAAATAGAATTTTGGAAAGTTTGAGGGT-AAAATGTTAATTTTAAAAAAAATT-A
* *
57585 GTGTCAAAATATAATTTT
1 GGGTCAAAATAGAATTTT
57603 AAAGAAGTTT
Statistics
Matches: 111, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
57 16 0.14
58 74 0.67
59 21 0.19
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGTCAAAATAGAATTTTGGAAAGTTTGAGGGTAAAATGTTAATTTTAAAAAAAATTA
Found at i:58833 original size:3 final size:3
Alignment explanation
Indices: 58775--58819 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
58765 AACTCATTTC
58775 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58820 ATGAATTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:64593 original size:28 final size:28
Alignment explanation
Indices: 64551--64621 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
64541 CAATCGAAGT
* *
64551 TAAAATGAGACTTTTTGGA-TACCGGGGG
1 TAAAATGGGAATTTTTGGACTA-CGGGGG
* *
64579 TAAAATGGTAA-TTTTGGACTTATGGGGG
1 TAAAATGGGAATTTTTGGAC-TACGGGGG
64607 TAAAATGGGAATTTT
1 TAAAATGGGAATTTT
64622 GAGAAAGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 7 0.20
28 23 0.66
29 5 0.14
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.34
Consensus pattern (28 bp):
TAAAATGGGAATTTTTGGACTACGGGGG
Found at i:64823 original size:27 final size:27
Alignment explanation
Indices: 64781--64881 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 27
64771 GGAAGTTTGG
64781 GGGTAAAATGGTAATTTTAAAAAATTA
1 GGGTAAAATGGTAATTTTAAAAAATTA
* ** *
64808 GGGTCAAAATGG-AATTTTGGAAAGTTTGG
1 GGGT-AAAATGGTAATTTT-AAAAAATT-A
*
64837 GGGTAGAATGGTAATTTTAAAAAATTA
1 GGGTAAAATGGTAATTTTAAAAAATTA
64864 GGGTCAAAATGG-AATTTT
1 GGGT-AAAATGGTAATTTT
64882 GGAAAGTTCG
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
27 20 0.34
28 29 0.49
29 10 0.17
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.33
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTAAAAAATTA
Found at i:64840 original size:56 final size:56
Alignment explanation
Indices: 64767--64953 Score: 252
Period size: 56 Copynumber: 3.3 Consensus size: 56
64757 AAATCAAGAT
64767 TTTTGG-AAGTTTGGGGGTAAAATGGTAATTTTAAAAAATTAGGGTCAAAATGGAA
1 TTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTAAAAAATTAGGGTCAAAATGGAA
*
64822 TTTTGGAAAGTTTGGGGGTAGAATGGTAATTTTAAAAAATTAGGGTCAAAATGGAA
1 TTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTAAAAAATTAGGGTCAAAATGGAA
* * * * **
64878 TTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTAGAAAGTTCAAGGGTCAAAATATAA
1 TTTTGGAAAGTTTGGGGGT-AAAATGGTAA-TTTTAAAAAATT--AGGGTCAAAATGGAA
64937 TTTTGGAGAAGTTTGGG
1 TTTTGGA-AAGTTTGGG
64954 ATCAAAATAT
Statistics
Matches: 116, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
55 6 0.05
56 69 0.59
57 14 0.12
59 20 0.17
60 7 0.06
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (56 bp):
TTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTAAAAAATTAGGGTCAAAATGGAA
Found at i:64900 original size:28 final size:28
Alignment explanation
Indices: 64767--64949 Score: 124
Period size: 29 Copynumber: 6.4 Consensus size: 28
64757 AAATCAAGAT
*
64767 TTTTGG-AAGTTTGGGGGT-AAAATGGTAA
1 TTTTGGAAAG-TTGAGGGTCAAAATGG-AA
** *
64795 TTTTAAAAAATT-AGGGTCAAAATGGAA
1 TTTTGGAAAGTTGAGGGTCAAAATGGAA
* *
64822 TTTTGGAAAGTTTGGGGGT-AGAATGGTAA
1 TTTTGGAAAG-TTGAGGGTCAAAATGG-AA
** *
64851 TTTTAAAAAATT-AGGGTCAAAATGGAA
1 TTTTGGAAAGTTGAGGGTCAAAATGGAA
* *
64878 TTTTGGAAAGTTCGAGGGTAAAAATGTAA
1 TTTTGGAAAGTT-GAGGGTCAAAATGGAA
* * **
64907 TTTTTAGAAAGTTCAAGGGTCAAAATATAA
1 -TTTTGGAAAGTT-GAGGGTCAAAATGGAA
64937 TTTTGGAGAAGTT
1 TTTTGGA-AAGTT
64950 TGGGATCAAA
Statistics
Matches: 121, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
27 28 0.23
28 29 0.24
29 34 0.28
30 30 0.25
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (28 bp):
TTTTGGAAAGTTGAGGGTCAAAATGGAA
Found at i:64901 original size:29 final size:29
Alignment explanation
Indices: 64807--64949 Score: 130
Period size: 29 Copynumber: 4.9 Consensus size: 29
64797 TTAAAAAATT
*
64807 AGGGTCAAAATGGAATTTTGGAAAGTTTG
1 AGGGTCAAAATGGAATTTTGGAAAGTTCG
* * ** *
64836 GGGGT-AGAATGGTAATTTTAAAAAATT--
1 AGGGTCAAAATGG-AATTTTGGAAAGTTCG
64863 AGGGTCAAAATGGAATTTTGGAAAGTTCG
1 AGGGTCAAAATGGAATTTTGGAAAGTTCG
* * * *
64892 AGGGTAAAAATGTAATTTTTAGAAAGTTCA
1 AGGGTCAAAATGGAA-TTTTGGAAAGTTCG
**
64922 AGGGTCAAAATATAATTTTGGAGAAGTT
1 AGGGTCAAAATGGAATTTTGGA-AAGTT
64950 TGGGATCAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
27 15 0.16
28 12 0.13
29 34 0.37
30 30 0.33
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.31
Consensus pattern (29 bp):
AGGGTCAAAATGGAATTTTGGAAAGTTCG
Found at i:64949 original size:30 final size:30
Alignment explanation
Indices: 64863--64949 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
64853 TTAAAAAATT
* *
64863 AGGGTCAAAATGGAATTTTGGA-AAGTTCG
1 AGGGTCAAAATGTAATTTTGGAGAAGTTCA
* *
64892 AGGGTAAAAATGTAATTTT-TAGAAAGTTCA
1 AGGGTCAAAATGTAATTTTGGAG-AAGTTCA
*
64922 AGGGTCAAAATATAATTTTGGAGAAGTT
1 AGGGTCAAAATGTAATTTTGGAGAAGTT
64950 TGGGATCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.02
29 17 0.35
30 28 0.58
31 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (30 bp):
AGGGTCAAAATGTAATTTTGGAGAAGTTCA
Found at i:64959 original size:29 final size:30
Alignment explanation
Indices: 64861--64984 Score: 89
Period size: 29 Copynumber: 4.2 Consensus size: 30
64851 TTTTAAAAAA
**
64861 TTAGGG-TCAAAATGGAATTTTGG-AAAGT
1 TTAGGGATCAAAATATAATTTTGGAAAAGT
* * * *
64889 TCGAGGG-TAAAAATGTAATTTT-TAGAAAGT
1 T-TAGGGATCAAAATATAATTTTGGA-AAAGT
* *
64919 TCAAGGG-TCAAAATATAATTTTGGAGAAGT
1 T-TAGGGATCAAAATATAATTTTGGAAAAGT
* *
64949 TT-GGGATCAAAATATGATTTTTGAAAAGT
1 TTAGGGATCAAAATATAATTTTGGAAAAGT
64978 TTAGGGA
1 TTAGGGA
64985 CCTTTAAGGC
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
28 4 0.05
29 39 0.51
30 33 0.43
31 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
TTAGGGATCAAAATATAATTTTGGAAAAGT
Found at i:64971 original size:30 final size:29
Alignment explanation
Indices: 64792--64984 Score: 87
Period size: 29 Copynumber: 6.7 Consensus size: 29
64782 GGTAAAATGG
** *
64792 TAATTTT-AAAAAATTAGGG-TCAAAATG
1 TAATTTTGAAAAGTTTAGGGATCAAAATA
* * * * * *
64819 GAATTTTGGAAAGTTTGGGGGT-AGAATGG
1 TAATTTTGAAAAGTTTAGGGATCAAAAT-A
** *
64848 TAATTTT-AAAAAATTAGGG-TCAAAATG
1 TAATTTTGAAAAGTTTAGGGATCAAAATA
* * * * *
64875 GAATTTTGGAAAGTTCGAGGG-TAAAAATG
1 TAATTTTGAAAAGTT-TAGGGATCAAAATA
* *
64904 TAATTTTTAGAAAGTTCAAGGG-TCAAAATA
1 TAATTTTGA-AAAGTT-TAGGGATCAAAATA
*
64934 TAATTTTGGAGAAGTTT-GGGATCAAAATA
1 TAATTTT-GAAAAGTTTAGGGATCAAAATA
*
64963 TGATTTTTGAAAAGTTTAGGGA
1 T-AATTTTGAAAAGTTTAGGGA
64985 CCTTTAAGGC
Statistics
Matches: 126, Mismatches: 29, Indels: 19
0.72 0.17 0.11
Matches are distributed among these distances:
27 14 0.11
28 31 0.25
29 42 0.33
30 38 0.30
31 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.33
Consensus pattern (29 bp):
TAATTTTGAAAAGTTTAGGGATCAAAATA
Found at i:64978 original size:59 final size:59
Alignment explanation
Indices: 64807--64974 Score: 141
Period size: 56 Copynumber: 2.9 Consensus size: 59
64797 TTAAAAAATT
* * * * * * * *
64807 AGGGTCAAAATGGAATTTTGGAAAGTTTGGGGGT-AGAATGGTAA-TTTTAAAAAATT--
1 AGGGTCAAAATAGAATTTTGGAAAGTTCGAGGATAAAAAT-ATAATTTTTAGAAAGTTCA
* * *
64863 AGGGTCAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTAGAAAGTTCA
1 AGGGTCAAAATAGAATTTTGGAAAGTTCGAGGATAAAAATATAATTTTTAGAAAGTTCA
* * * *
64922 AGGGTCAAAATATAATTTTGGAGAAGTTTG-GGATCAAAATATGATTTTT-GAAA
1 AGGGTCAAAATAGAATTTTGGA-AAGTTCGAGGATAAAAATATAATTTTTAGAAA
64975 AGTTTAGGGA
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
56 36 0.38
57 14 0.15
58 4 0.04
59 35 0.37
60 6 0.06
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.32
Consensus pattern (59 bp):
AGGGTCAAAATAGAATTTTGGAAAGTTCGAGGATAAAAATATAATTTTTAGAAAGTTCA
Found at i:66158 original size:3 final size:3
Alignment explanation
Indices: 66100--66144 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
66090 TTAAACCCAT
66100 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
66145 ATGAATTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:66883 original size:17 final size:17
Alignment explanation
Indices: 66858--66923 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
66848 ATTAATTTTT
*
66858 AATTGAAAATAAATTTA
1 AATTTAAAATAAATTTA
*
66875 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTTA
* * *
66892 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTTA
*
66909 AATTTAGAATAAATT
1 AATTTAAAATAAATT
66924 CAAACTTATT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:66901 original size:34 final size:34
Alignment explanation
Indices: 66863--66929 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
66853 TTTTTAATTG
66863 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
* *
66897 AAAATGAATTTAAATTTAGAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
66930 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:76667 original size:18 final size:18
Alignment explanation
Indices: 76640--76675 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
76630 ATGCTTGTAA
76640 TAATTAATTGT-AATTGT
1 TAATTAATTGTAAATTGT
76657 TAATATAATTGTAAATTGT
1 TAAT-TAATTGTAAATTGT
76676 AACTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
TAATTAATTGTAAATTGT
Found at i:89954 original size:3 final size:3
Alignment explanation
Indices: 89946--90008 Score: 83
Period size: 3 Copynumber: 21.3 Consensus size: 3
89936 AAACCTAACA
** * *
89946 AAT AAT AAT AA- AAT GTT GAT AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
89993 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
90009 GAGTGTAGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:90231 original size:15 final size:17
Alignment explanation
Indices: 90206--90239 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
90196 CATTAACTTT
90206 AAAAAGAAAGAAAA-AA
1 AAAAAGAAAGAAAAGAA
90222 AAAAAG-AAGAAAAGAA
1 AAAAAGAAAGAAAAGAA
90238 AA
1 AA
90240 GCCGATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAGAA
Found at i:90367 original size:15 final size:15
Alignment explanation
Indices: 90347--90375 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
90337 TGATTAGCGA
90347 TCGAATTTAATTCGG
1 TCGAATTTAATTCGG
90362 TCGAATTTAATTCG
1 TCGAATTTAATTCG
90376 ATTAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (15 bp):
TCGAATTTAATTCGG
Found at i:97033 original size:2 final size:2
Alignment explanation
Indices: 97026--97061 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
97016 AAGCTTCTTC
97026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97062 ACTTGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:97644 original size:34 final size:34
Alignment explanation
Indices: 97605--97730 Score: 96
Period size: 34 Copynumber: 3.7 Consensus size: 34
97595 ATTGTATATT
*
97605 TTATACATATTTTTTTATATATACGGTTTTATAC
1 TTATACATATTTTTTTATATATACGATTTTATAC
* * * *
97639 TTATACA-ATGTTATATATATATACTATTTTATAT
1 TTATACATAT-TTTTTTATATATACGATTTTATAC
* * * * **
97673 TTACATATATTGTTTTTATATATA-TATATATATTG
1 TTATACATATT-TTTTTATATATACGAT-TTTATAC
97708 TTATACA-ATTTTTTTTATATATA
1 TTATACATA-TTTTTTTATATATA
97731 AACAAAATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
33 2 0.03
34 48 0.66
35 23 0.32
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (34 bp):
TTATACATATTTTTTTATATATACGATTTTATAC
Found at i:97691 original size:21 final size:23
Alignment explanation
Indices: 97665--97709 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
97655 ATATATACTA
97665 TTTTATAT-T-TACATATATTGT
1 TTTTATATATATACATATATTGT
*
97686 TTTTATATATATATATATATTGT
1 TTTTATATATATACATATATTGT
97709 T
1 T
97710 ATACAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 1 0.05
23 12 0.57
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTATATATATACATATATTGT
Found at i:106685 original size:9 final size:9
Alignment explanation
Indices: 106671--106711 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
106661 TTATCTTTTA
106671 AAAAATTAT
1 AAAAATTAT
106680 AAAAATTCAT
1 AAAAATT-AT
106690 AAAAACTTAT
1 AAAAA-TTAT
*
106700 AAGAATTAT
1 AAAAATTAT
106709 AAA
1 AAA
106712 TAAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 13 0.46
10 13 0.46
11 2 0.07
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:106692 original size:20 final size:19
Alignment explanation
Indices: 106669--106711 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
106659 ATTTATCTTT
106669 TAAAAAATTATAAAAATTCA
1 TAAAAAATTATAAAAATT-A
* *
106689 TAAAAACTTATAAGAATTA
1 TAAAAAATTATAAAAATTA
106708 TAAA
1 TAAA
106712 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTA
Found at i:107025 original size:19 final size:19
Alignment explanation
Indices: 106976--107027 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
106966 TTCTATGAGT
* * **
106976 TTTTTATGATTTTTATATG
1 TTTTTATAAATTTTATACA
106995 TTTTTA-AGAATTTTATACA
1 TTTTTATA-AATTTTATACA
107014 TTTTTATAAATTTT
1 TTTTTATAAATTTT
107028 TAAATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (19 bp):
TTTTTATAAATTTTATACA
Found at i:107036 original size:29 final size:29
Alignment explanation
Indices: 106984--107062 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
106974 GTTTTTTATG
** *
106984 ATTTTTATATGTTTTTAAGA-ATTTTATAC
1 ATTTTTATAAATTTTTAA-ATATTTTAAAC
*
107013 ATTTTTATAAATTTTTAAATATTTTAAAT
1 ATTTTTATAAATTTTTAAATATTTTAAAC
* *
107042 ATGTTTTATTAATTTATAAAT
1 AT-TTTTATAAATTTTTAAAT
107063 TATTAGAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.02
29 25 0.60
30 16 0.38
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (29 bp):
ATTTTTATAAATTTTTAAATATTTTAAAC
Found at i:107133 original size:9 final size:9
Alignment explanation
Indices: 106956--107176 Score: 62
Period size: 9 Copynumber: 23.6 Consensus size: 9
106946 TTATGGGTTT
106956 TTTTTATAA
1 TTTTTATAA
* *
106965 TTTCTATGAGT
1 TTTTTAT-A-A
*
106976 TTTTTATGA
1 TTTTTATAA
*
106985 TTTTTATATG
1 TTTTTATA-A
106995 TTTTTA-AGA
1 TTTTTATA-A
*
107004 ATTTTATACA
1 TTTTTATA-A
107014 TTTTTATAAA
1 TTTTTAT-AA
107024 TTTTTA-AA
1 TTTTTATAA
*
107032 TATTTTAAATA
1 T-TTTTATA-A
107043 TGTTTTATTAA
1 T-TTTTA-TAA
*
107054 TTTATA-AA
1 TTTTTATAA
* *
107062 TTATTAGAA
1 TTTTTATAA
*
107071 TTTATA-AGA
1 TTTTTATA-A
107080 TATTTTAT-A
1 T-TTTTATAA
*
107089 TTTTTATAC
1 TTTTTATAA
* *
107098 TCTTGATAA
1 TTTTTATAA
* *
107107 GTTTGTATTACT
1 -TTTTTA-TA-A
107119 TTTTTATAA
1 TTTTTATAA
107128 TTTTTATAA
1 TTTTTATAA
* *
107137 GTCTATATCAA
1 -TTTTTAT-AA
*
107148 TTTTAAT-A
1 TTTTTATAA
107156 -TTTT-TAA
1 TTTTTATAA
*
107163 TTTTTCTAA
1 TTTTTATAA
107172 TTTTT
1 TTTTT
107177 TTATAAATTT
Statistics
Matches: 154, Mismatches: 36, Indels: 44
0.66 0.15 0.19
Matches are distributed among these distances:
6 1 0.01
7 4 0.03
8 21 0.14
9 57 0.37
10 45 0.29
11 25 0.16
12 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:109672 original size:22 final size:20
Alignment explanation
Indices: 109622--109679 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
109612 GGGCCGAAAC
109622 TTTTTTTA-TATAATTCTAT
1 TTTTTTTATTATAATTCTAT
** *
109641 TTTTAATATTAGTAAATTTTAT
1 TTTTTTTATTA-T-AATTCTAT
109663 TTTTTTTATTCATAATT
1 TTTTTTTATT-ATAATT
109680 TTTCTCGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.20
20 2 0.07
21 5 0.17
22 16 0.53
23 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTTTATTATAATTCTAT
Found at i:113209 original size:75 final size:75
Alignment explanation
Indices: 113125--113321 Score: 376
Period size: 75 Copynumber: 2.6 Consensus size: 75
113115 AAATGTGAAT
113125 ATATTCTAAGAGGATATAAATAACCCACTGAAAACAAATTTAATTTGATGATATTCTTTTTCAAT
1 ATATTCTAAGAGGATATAAATAACCCACTGAAAACAAATTTAATTTGATGATATTCTTTTTCAAT
113190 GCCACTCATC
66 GCCACTCATC
*
113200 ATATTCTAAGAGGATATAAATAACCCACCGAAAACAAATTTAATTTGATGATATTCTTTTTCAAT
1 ATATTCTAAGAGGATATAAATAACCCACTGAAAACAAATTTAATTTGATGATATTCTTTTTCAAT
*
113265 GCCTCTCATC
66 GCCACTCATC
113275 ATATTCTAAGAGGATATAAATAACCCACTGAAAACAAATTTAATTTG
1 ATATTCTAAGAGGATATAAATAACCCACTGAAAACAAATTTAATTTG
113322 TAGGTCATAG
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 119 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.34
Consensus pattern (75 bp):
ATATTCTAAGAGGATATAAATAACCCACTGAAAACAAATTTAATTTGATGATATTCTTTTTCAAT
GCCACTCATC
Found at i:114552 original size:16 final size:17
Alignment explanation
Indices: 114531--114566 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
114521 TAATAGAGTA
*
114531 AAAGTAGTTAAAAC-AT
1 AAAGTAATTAAAACAAT
114547 AAAGTAATTAAAACAAT
1 AAAGTAATTAAAACAAT
114564 AAA
1 AAA
114567 TGAATGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (17 bp):
AAAGTAATTAAAACAAT
Found at i:116121 original size:59 final size:59
Alignment explanation
Indices: 116086--116545 Score: 557
Period size: 59 Copynumber: 7.8 Consensus size: 59
116076 GATGTCCCAA
* * * * * *
116086 GGTCAAAAATGGGATTTTAGGAGGTTCGAGGGTAAAATTGTAATTTTTAAAAGGTTCGA
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAGGTTCGG
** * * *
116145 GGTCAAAAATTAGATTTTTGGAAGTCCGAGGGTAAGATGGTAATTTTAAGAAGGTTCGG
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAGGTTCGG
* * * *
116204 GGCCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGGGAAGGTTCGG
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAGGTTCGG
* * * **
116263 GGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTGGGAAAGTTTAG
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAGGTTCGG
* * * * *
116322 GGTCAAAAATGGTATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGGGAAGATTCGT
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAGGTTCGG
* * * * *
116381 AGTAAAAAATGAGATTTTTGGAAGTTCG-GGGATAAAATGGTAATTTTGGGAAGATTCGG
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAATGGTAATTTTGAGAAGGTTCGG
* * * *
116440 GGTAAAAAATGGGATTTTTGGAAGTTTG-GGAGTAAAATGGTAATTTTGGGAAGGTTTGG
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAATGGTAATTTTGAGAAGGTTCGG
*
116499 GGTCAAAAATGGGATTTTTGGAAGTTC-AGGGGTAAAATGGTACTTTT
1 GGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTT
116546 TGGATAGTTT
Statistics
Matches: 352, Mismatches: 45, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
58 3 0.01
59 346 0.98
60 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (59 bp):
GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAGAAGGTTCGG
Found at i:116141 original size:30 final size:30
Alignment explanation
Indices: 116099--116549 Score: 219
Period size: 30 Copynumber: 15.3 Consensus size: 30
116089 CAAAAATGGG
*
116099 ATTTTAGG-AGGTTCGAGGGTAAAATTGTA
1 ATTTTTGGAAGGTTCGAGGGTAAAATTGTA
** *
116128 ATTTTTAAAAGGTTCGA-GGTCAAAAAT-TA
1 ATTTTTGGAAGGTTCGAGGGT-AAAATTGTA
* * *
116157 GATTTTTGGAA-GTCCGAGGGTAAGATGGTA
1 -ATTTTTGGAAGGTTCGAGGGTAAAATTGTA
** * *
116187 ATTTTAAGAAGGTTCG-GGGCCAAAAATG-A
1 ATTTTTGGAAGGTTCGAGGG-TAAAATTGTA
* *
116216 GATTTTTGGAA-GTTCGGGGGTAAAATGGTA
1 -ATTTTTGGAAGGTTCGAGGGTAAAATTGTA
* * **
116246 ATTTTGGGAAGGTTCG-GGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGAGGGT-AAAATTGTA
* *
116276 ATTTTTGGAA-GTTTGAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGAGGGTAAAATTGTA
* * * *
116305 ATTTTGGGAAAGTT-TAGGGTCAAAAATGGT-
1 ATTTTTGGAAGGTTCGAGGGT--AAAATTGTA
* *
116335 ATTTTTGGAA-GTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGAGGGTAAAATTGTA
* * *
116364 ATTTTGGGAAGATTCGTA--GTAAAAAATG-A
1 ATTTTTGGAAGGTTCG-AGGGT-AAAATTGTA
*
116393 GATTTTTGGAA-GTTCG-GGGATAAAATGGTA
1 -ATTTTTGGAAGGTTCGAGGG-TAAAATTGTA
* * * **
116423 ATTTTGGGAAGATTCG-GGGTAAAAAATGGG
1 ATTTTTGGAAGGTTCGAGGGT-AAAATTGTA
* *
116453 ATTTTTGGAA-GTTTG-GGAGTAAAATGGTA
1 ATTTTTGGAAGGTTCGAGG-GTAAAATTGTA
* * * **
116482 ATTTTGGGAAGGTTTG-GGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGAGGGT-AAAATTGTA
*
116512 ATTTTTGGAA-GTTC-AGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGA-GGGTAAAATTGTA
*
116541 CTTTTTGGA
1 ATTTTTGGA
116550 TAGTTTAGGG
Statistics
Matches: 317, Mismatches: 72, Indels: 66
0.70 0.16 0.15
Matches are distributed among these distances:
28 8 0.03
29 148 0.47
30 153 0.48
31 8 0.03
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (30 bp):
ATTTTTGGAAGGTTCGAGGGTAAAATTGTA
Done.