Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018498.1 Corchorus olitorius cultivar O-4 contig18531, 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: 68279
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:4520 original size:63 final size:63
Alignment explanation
Indices: 4421--4676 Score: 283
Period size: 62 Copynumber: 4.1 Consensus size: 63
4411 TTAGGAAGAA
* *
4421 AATGTGACAAAACTGACCCTTT-ATCTGAAAGGGTATTTTGGGGAAATTGAAACTAAATGCAAG
1 AATGTGACAAAACTGACCCTTTGTTCTGAAAGGGTATTTT-GGGAAATTGAAACTATATGCAAG
* * * *
4484 AATGTGA-AAAAGCTAACCCTTTGTTC-GAAAGGGTATTTTGGGAAATGGAGACTATATGCGAG
1 AATGTGACAAAA-CTGACCCTTTGTTCTGAAAGGGTATTTTGGGAAATTGAAACTATATGCAAG
* * * *
4546 AAAGTGACAAAATTGACCCTTTG-TCTGAAAGGGTATTTTGGGAAATAGAGACTATTTATG-AGA
1 AATGTGACAAAACTGACCCTTTGTTCTGAAAGGGTATTTTGGGAAATTGAAACTA--TATGCA-A
4609 G
63 G
* * * * *
4610 AATGTGACAAAACTGACCCTTTG-TCCGAAAGGGTATTTT-GGAGATTAAAACTAGATGCTAG
1 AATGTGACAAAACTGACCCTTTGTTCTGAAAGGGTATTTTGGGAAATTGAAACTATATGCAAG
4671 AATGTG
1 AATGTG
4677 TCGAAACGTT
Statistics
Matches: 165, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
61 13 0.08
62 65 0.39
63 43 0.26
64 44 0.27
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (63 bp):
AATGTGACAAAACTGACCCTTTGTTCTGAAAGGGTATTTTGGGAAATTGAAACTATATGCAAG
Found at i:4640 original size:64 final size:62
Alignment explanation
Indices: 4421--4650 Score: 293
Period size: 62 Copynumber: 3.7 Consensus size: 62
4411 TTAGGAAGAA
* * * * *
4421 AATGTGACAAAACTGACCCTTTATCTGAAAGGGTATTTTGGGGAAATTGAAACTAAATGCA-AG
1 AATGTGACAAAACTGACCCTTTGTCCGAAAGGGTATTTT-GGGAAATAGAGACTATATG-AGAG
* * * *
4484 AATGTGA-AAAAGCTAACCCTTTGTTCGAAAGGGTATTTTGGGAAATGGAGACTATATGCGAG
1 AATGTGACAAAA-CTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAGACTATATGAGAG
* * *
4546 AAAGTGACAAAATTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATAGAGACTATTTATGAGAG
1 AATGTGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAGACTA--TATGAGAG
4610 AATGTGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTGG
1 AATGTGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTGG
4651 AGATTAAAAC
Statistics
Matches: 144, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
62 65 0.45
63 34 0.24
64 45 0.31
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (62 bp):
AATGTGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAGACTATATGAGAG
Found at i:9636 original size:150 final size:150
Alignment explanation
Indices: 9365--9661 Score: 549
Period size: 150 Copynumber: 2.0 Consensus size: 150
9355 GGGACATACT
*
9365 AAAAAAATGAACATGAAGATATCAATTGAAAACTAGACCTATTACTAAAAATGCTTAAGCTATGT
1 AAAAAAATGAACATGAAGATATCAATTGAAAACTAGACCTATTACTAAAAATGCTTAAGCTATAT
*
9430 GACTAAAGTGCAACTAAATTACTGAATGCTGCTAAGCCATGAAATATGTAAAAATGCCAACAGTT
66 GACTAAAGTGCAACTAAATTACCGAATGCTGCTAAGCCATGAAATATGTAAAAATGCCAACAGTT
9495 TTAGATGACTAAGAATGTAA
131 TTAGATGACTAAGAATGTAA
*
9515 AAAAAAATGAACATGAAGATATCAATTGAAAACTAGACCTATTACTAAAAGTGCTTAAGCTATAT
1 AAAAAAATGAACATGAAGATATCAATTGAAAACTAGACCTATTACTAAAAATGCTTAAGCTATAT
* *
9580 GACTAAAGTGCAACTAAATTACCGAATGGTGCTAAGCCATGAAGTATGTAAAAATGCCAACAGTT
66 GACTAAAGTGCAACTAAATTACCGAATGCTGCTAAGCCATGAAATATGTAAAAATGCCAACAGTT
9645 TTAGATGACTAAGAATG
131 TTAGATGACTAAGAATG
9662 AATTAGTTAG
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 142 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (150 bp):
AAAAAAATGAACATGAAGATATCAATTGAAAACTAGACCTATTACTAAAAATGCTTAAGCTATAT
GACTAAAGTGCAACTAAATTACCGAATGCTGCTAAGCCATGAAATATGTAAAAATGCCAACAGTT
TTAGATGACTAAGAATGTAA
Found at i:9750 original size:27 final size:27
Alignment explanation
Indices: 9694--9771 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
9684 AGTGCACTTG
***
9694 AAATGA-TCAAAATGCCCCTGGACGTGC
1 AAATGACT-AAAATGCCCCTGGACACAC
*
9721 AAATGACTAAAATGCCCCTGGGCACAC
1 AAATGACTAAAATGCCCCTGGACACAC
* *
9748 AAATCACTAAAATGCCCTTGGACA
1 AAATGACTAAAATGCCCCTGGACA
9772 TGTCAATAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 42 0.98
28 1 0.02
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGGACACAC
Found at i:10131 original size:67 final size:67
Alignment explanation
Indices: 9982--10305 Score: 404
Period size: 67 Copynumber: 4.8 Consensus size: 67
9972 GACAAAACTA
* * ** * ** * *
9982 ACCCTTTGTCCGAAAGGGTATTTCTGGAAAATAAAA-GCTAAACTTAAACACAACAACCTGGTGA
1 ACCCTTTGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTAAATGCAA-AA--AGATGA
10046 AATTG
63 AATTG
** * *
10051 ACCCTCCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAATTTAAATGCAAAAAAATGAAAT
1 ACCCTTTGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTAAATGCAAAAAGATGAAAT
10116 TG
66 TG
* *
10118 ACCCTTTGACCGAAAGGGTATTTCTGGAAACGAAAATACTAAACTTAAATGCAAAAAGACGAAAT
1 ACCCTTTGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTAAATGCAAAAAGATGAAAT
10183 TG
66 TG
* * *
10185 ACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTTAAATGCAAAAAGGCT-AAA
1 ACCCTTTGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTAAATGCAAAAA-GATGAAA
*
10249 CTG
65 TTG
*
10252 ACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAAT--TAAACTTAAATGCAAAA
1 ACCCTTTGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTAAATGCAAAA
10306 CGACAAGACC
Statistics
Matches: 227, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
65 17 0.07
67 164 0.72
68 1 0.00
69 32 0.14
70 13 0.06
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (67 bp):
ACCCTTTGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTAAATGCAAAAAGATGAAAT
TG
Found at i:12176 original size:13 final size:13
Alignment explanation
Indices: 12142--12184 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
12132 TATCTGGCTG
12142 TTTGGTTTATTA-
1 TTTGGTTTATTAC
*
12154 TTCTGATTTATTAC
1 TT-TGGTTTATTAC
*
12168 TTTGGTTTATGAC
1 TTTGGTTTATTAC
12181 TTTG
1 TTTG
12185 ATTATGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.60
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:13219 original size:31 final size:29
Alignment explanation
Indices: 13177--13241 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 29
13167 CCTTAATACC
13177 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTAGCCCCTTAACTAT--ATTTTGGGA
* *
13208 CAAATTGGCCCCTTAACTATTTTTTGGGA
1 CAAATTAGCCCCTTAACTATATTTTGGGA
13237 CAAAT
1 CAAAT
13242 AAATCCCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 13 0.41
31 19 0.59
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (29 bp):
CAAATTAGCCCCTTAACTATATTTTGGGA
Found at i:14026 original size:31 final size:29
Alignment explanation
Indices: 13963--14027 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
13953 TATGGGATTT
*
13963 ATTTGTCCCAAAAAAAAGTTAAGGGGCCA
1 ATTTGTCCCAAAAAAAAGTTAAGGGGACA
* * *
13992 ATTTGTCCCAAAATGGATAGTTAAGGGGATA
1 ATTTGTCCCAAAA--AAAAGTTAAGGGGACA
14023 ATTTG
1 ATTTG
14028 GGTATTAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (29 bp):
ATTTGTCCCAAAAAAAAGTTAAGGGGACA
Found at i:15610 original size:41 final size:42
Alignment explanation
Indices: 15545--15631 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 42
15535 AACTGAGTTT
* *
15545 TGATAATACGCAACAGTGGATGTCG-TTTGGAGATATGTGAG
1 TGATAATACGCAACAGTGGATGTCGTTTTGGAGATACGCGAG
* *
15586 TGATAATACGCAGCAGTAGG-TGTCGTTTTGGTGATACGCGAG
1 TGATAATACGCAACAGT-GGATGTCGTTTTGGAGATACGCGAG
15628 TGAT
1 TGAT
15632 GGATATCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 21 0.52
42 19 0.47
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.30
Consensus pattern (42 bp):
TGATAATACGCAACAGTGGATGTCGTTTTGGAGATACGCGAG
Found at i:17978 original size:20 final size:20
Alignment explanation
Indices: 17949--17989 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
17939 CCAAGTAGAA
17949 TAGCCAAAAGAAAATCAACT
1 TAGCCAAAAGAAAATCAACT
*
17969 TAGCCGAAAGAAAATCAACT
1 TAGCCAAAAGAAAATCAACT
17989 T
1 T
17990 GGACAGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (20 bp):
TAGCCAAAAGAAAATCAACT
Found at i:21910 original size:433 final size:435
Alignment explanation
Indices: 21423--22331 Score: 1171
Period size: 435 Copynumber: 2.1 Consensus size: 435
21413 GTTCTTTACA
* * * * *
21423 AATCAATTTAACGCTTTAG-TTTTTTTTT-TCCTTTTTGTCTGATTAAGGTGATTCAGGTGTC-T
1 AATCGATTTAACGCTTAAGTTTTTTTTTTGTTCTATTTGTCCGATTAAGGTGATTCAGGTGTCGT
* * ** **
21485 ATTAAAAAGTAATTTCATGATTTACAGCTTTCATGAAGGACTTAAAAGCCAATTTTTATGTTCCA
66 -TTAAAAAGTAATTTCATGATCTACAACTTTCATGAAAAACTTAAAAGCCAATTTTTACATTCCA
* * * * * *
21550 ATTC-CA-AAAAATGCTTCCGAAATTTGGTGATTTTGATTGCCGATCTATTTAATATCATATAAT
130 ATTCAAAGAAAAATGCTTCCCAAATTTAGTGATTTTGATTGCCGAGCTATTTAAAACCATATAAT
* *
21613 TTTCGATCAACATGTCCGATTAATA-TT-TCTCAAGTGTCGGTTAAAAGGTTATTGCATGATCTA
195 TTTAGATCAACATGTCCGATTAA-AGTTAT-TCAAGTGTCGGTTAAAAGGTTATTACATGATCTA
* * * * * *
21676 CGA-TTTCATGAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCATTAAGTGTTCAAAAGGAA
258 CGACTTTCATGAA--ACACAAAAGCTAAATTTGATCTACAAATTTCATGAAGGGTTCAAAAGGAA
* * *
21740 ATTTTTATGTTTCAAGATCTCCATCAACAAACATTTTTTTATTTTAATTATTTATG-AAATGACC
321 ATTTTTATGTTTCAAAATCTCCATCAACAAACATTTTCTTATTTGAATTATTTA-GCAAATGACC
*
21804 CTCATAT-T-TTTCTACTTTATACTACTT-AGTCCTTTACTAATTCTATCTT
385 CTCATATATATTTCTACTTTATACTA-TTAAGTCCTTTACAAATTCTATCTT
21853 AATCGATTTAACGCTTAAGCTTTTTTTTTTGTTCTATTTGTCCGATTAAGGTGATTCAGGTGTCG
1 AATCGATTTAACGCTTAAG-TTTTTTTTTTGTTCTATTTGTCCGATTAAGGTGATTCAGGTGTCG
* * *
21918 TTTAAAAGGTAATTTCATGATCTCCAACTTTCATGAAAAACTTAAAAGCCAATTTTTACATTTCA
65 TTTAAAAAGTAATTTCATGATCTACAACTTTCATGAAAAACTTAAAAGCCAATTTTTACATTCCA
* * *
21983 ATTCAAAGAAAAATGCTTCCCAAATTTAGTGGTTTTGATTGCCGGGCTATTTAAAACCGTATAAT
130 ATTCAAAGAAAAATGCTTCCCAAATTTAGTGATTTTGATTGCCGAGCTATTTAAAACCATATAAT
* * *
22048 TTTAGATCCACATGTCCGATTAAAGTTATTTAAGTGTCTGTTAAAAGGTTATTACATGATCTACG
195 TTTAGATCAACATGTCCGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTACATGATCTACG
* * *
22113 ACTTTCATGAAATACAAAAGCTAAATTTGATCTACAAATTTCGTGAAGGGTTCAAAAGGGAATTT
260 ACTTTCATGAAACACAAAAGCTAAATTTGATCTACAAATTTCATGAAGGGTTCAAAAGGAAATTT
* * * * *
22178 TTATGTTTGAAAATCTCTATCAATAAACATTTTCTTATTTGGATTATTTAGCAAATGGCCCTCAT
325 TTATGTTTCAAAATCTCCATCAACAAACATTTTCTTATTTGAATTATTTAGCAAATGACCCTCAT
*
22243 ATATAACTTTCTACTTTATACTATTAAGTCCTTTACAAATTCTATTTT
390 ATAT-A-TTTCTACTTTATACTATTAAGTCCTTTACAAATTCTATCTT
*
22291 ACTCGA-TTAACGCTTCAA-TTTTTTTACTTTGTTCTATTTGT
1 AATCGATTTAACGCTT-AAGTTTTTTT--TTTGTTCTATTTGT
22332 TGTCCAATTA
Statistics
Matches: 413, Mismatches: 48, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
430 17 0.04
432 9 0.02
433 90 0.22
434 105 0.25
435 107 0.26
436 17 0.04
437 11 0.03
438 57 0.14
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (435 bp):
AATCGATTTAACGCTTAAGTTTTTTTTTTGTTCTATTTGTCCGATTAAGGTGATTCAGGTGTCGT
TTAAAAAGTAATTTCATGATCTACAACTTTCATGAAAAACTTAAAAGCCAATTTTTACATTCCAA
TTCAAAGAAAAATGCTTCCCAAATTTAGTGATTTTGATTGCCGAGCTATTTAAAACCATATAATT
TTAGATCAACATGTCCGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTACATGATCTACGA
CTTTCATGAAACACAAAAGCTAAATTTGATCTACAAATTTCATGAAGGGTTCAAAAGGAAATTTT
TATGTTTCAAAATCTCCATCAACAAACATTTTCTTATTTGAATTATTTAGCAAATGACCCTCATA
TATATTTCTACTTTATACTATTAAGTCCTTTACAAATTCTATCTT
Found at i:23269 original size:22 final size:22
Alignment explanation
Indices: 23244--23511 Score: 114
Period size: 22 Copynumber: 12.0 Consensus size: 22
23234 ATTACACTAT
*
23244 TTTTGATGACCTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
*
23266 TTTTGATAACCTTCC-AATGAAA
1 TTTTGATAACC-TCCTTATGAAA
* * * *
23288 TTTTAATAACGATAC-TATGGAA
1 TTTTGATAAC-CTCCTTATGAAA
* * * **
23310 TTTCGAGAACATTTTTAT-AAA
1 TTTTGATAACCTCCTTATGAAA
** *
23331 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * * *
23353 TTTTGTTAATCTCCCTAAGGAA
1 TTTTGATAACCTCCTTATGAAA
23375 TTTTGA-AGACCTCAC-TATGAAA
1 TTTTGATA-ACCTC-CTTATGAAA
* *
23397 TTTTGATAACTTCCTAATGAAA
1 TTTTGATAACCTCCTTATGAAA
* *
23419 TTTTGATAACCAACACTATACTATGAGA
1 TTTTGATAACC-TC-C--T--TATGAAA
* * *
23447 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTCCTTATGAAA
* * *
23469 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
23491 ATTTAAAAACCTCCATATGAA
1 TTTTGATAACCTCCTTATGAA
23512 TTGTTAGTAA
Statistics
Matches: 181, Mismatches: 51, Indels: 28
0.70 0.20 0.11
Matches are distributed among these distances:
21 18 0.10
22 138 0.76
23 6 0.03
24 1 0.01
26 2 0.01
27 1 0.01
28 15 0.08
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTCCTTATGAAA
Found at i:26322 original size:6 final size:6
Alignment explanation
Indices: 26311--26367 Score: 71
Period size: 6 Copynumber: 9.5 Consensus size: 6
26301 TTTTATTTTA
* * *
26311 TTTTCT TTTTCT TTTTCT TTTTCCT CTTCCT TTTCCT TTTTCT TTTT-T
1 TTTTCT TTTTCT TTTTCT TTTT-CT TTTTCT TTTTCT TTTTCT TTTTCT
26359 TTTTCT TTT
1 TTTTCT TTT
26368 CCTGGCTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
5 5 0.11
6 36 0.80
7 4 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:26499 original size:6 final size:6
Alignment explanation
Indices: 26481--26524 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
26471 CAGCAGGCCC
* * * *
26481 CTTTTT CTCTTT CTTTTT CTTTTT TTTTTT CTTCTT CTTCTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CT
26525 CCTCCTCCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:28598 original size:76 final size:76
Alignment explanation
Indices: 28461--28612 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
28451 ACAAGGGCCC
* * *
28461 CGACTCCACCTGGGCGCCCACATAGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATAGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
28526 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * *
28537 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATAG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCA
*
28599 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
28613 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATAGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
GGGCAGTGTCA
Found at i:28995 original size:22 final size:22
Alignment explanation
Indices: 28970--29197 Score: 109
Period size: 22 Copynumber: 10.5 Consensus size: 22
28960 ACTCGGTATA
28970 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
* *
28992 AAATCTTGATAA----C-TA-C
1 AAATTTTGATAACCTCCTTATG
29008 AAATTTTGATAACCTCCCAATATATG
1 AAATTTTGATAACCT-CC--T-TATG
** * *
29034 ATTTTTTGATAAGCTCATTATG
1 AAATTTTGATAACCTCCTTATG
** ** *
29056 AAATTTTTTTTTAATTTCCCTATG
1 AAA--TTTTGATAACCTCCTTATG
* * *
29080 AAATTTTGATCTACATAC-TATG
1 AAATTTTGAT-AACCTCCTTATG
29102 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CTTATG
* **
29124 AAATTTTGA-AAACTAAATTATG
1 AAATTTTGATAACCT-CCTTATG
* *
29146 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCTTATG
* *
29168 AAATTTTGATATCCTCC--CTG
1 AAATTTTGATAACCTCCTTATG
29188 AAATTTTGAT
1 AAATTTTGAT
29198 TACTACATAA
Statistics
Matches: 153, Mismatches: 35, Indels: 38
0.68 0.15 0.17
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
20 12 0.08
21 7 0.05
22 81 0.53
23 8 0.05
24 16 0.10
25 3 0.02
26 12 0.08
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATG
Found at i:29222 original size:64 final size:66
Alignment explanation
Indices: 29098--29225 Score: 152
Period size: 64 Copynumber: 2.0 Consensus size: 66
29088 ATCTACATAC
* * * * *
29098 TATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAATTATGAAATTTTGATAACCTTC
1 TATGAAATTTTGATAACCCTCTCATGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTC
29163 A
66 A
* * ** *
29164 TATGAAATTTTGAT-ATCCTC-CCTGAAATTTTGATTACTACATAATAAAAGTTTAATAACCTT
1 TATGAAATTTTGATAACCCTCTCATGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTT
29226 TCTAATTTGG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
64 33 0.63
65 5 0.10
66 14 0.27
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (66 bp):
TATGAAATTTTGATAACCCTCTCATGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTC
A
Found at i:29427 original size:88 final size:90
Alignment explanation
Indices: 29278--29495 Score: 275
Period size: 88 Copynumber: 2.4 Consensus size: 90
29268 AGAAATACCA
* * * **
29278 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
* *
29343 TCTACAAAATTTTGTTGA-CC-CCT
66 ACTACAAAATTTTGATGATCCACCT
* *
29366 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
*
29430 CACTACAAAATTTTGATGATCCAATCT
65 CACTACAAAATTTTGATGATCC-ACCT
*
29457 CTATGAAATTTTGATAATCAC-TCTATG-AGATTTGATAAC
1 CTATGAAATTTTGATAATCACAT-TATGAAAATTTGATAAC
29496 TTTCTATCAA
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
88 71 0.63
89 4 0.04
90 11 0.10
91 27 0.24
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (90 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTACAAAATTTTGATGATCCACCT
Found at i:29480 original size:22 final size:22
Alignment explanation
Indices: 29278--29697 Score: 212
Period size: 22 Copynumber: 18.9 Consensus size: 22
29268 AGAAATACCA
* *
29278 CTATGAAATTTTGGTAATCACAT
1 CTATGAAATTTTGATAACCAC-T
* * *
29301 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAACCACT
* *
29322 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAACCACT
** * * *
29344 CTACAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACCACT
*
29366 CTATGAAATTTTGATAATCACAT
1 CTATGAAATTTTGATAACCAC-T
* * *
29389 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACT
* * *
29410 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAACCACT
** *
29432 CTACAAAATTTTGATGATCCAATCT
1 CTATGAAATTTTGAT-AACC-A-CT
*
29457 CTATGAAATTTTGATAATCACT
1 CTATGAAATTTTGATAACCACT
* **
29479 CTATGAGA-TTTGATAA-CTTT
1 CTATGAAATTTTGATAACCACT
* * ***
29499 CTATCAAATTTTGGT-ATTGCT
1 CTATGAAATTTTGATAACCACT
* *
29520 -TATGAAATTGAGACTTTTATAACC-TT
1 CTATGAAA-T-----TTTGATAACCACT
*
29546 CATATGAAATTTTGATAACCACA
1 C-TATGAAATTTTGATAACCACT
** *
29569 CTAAAAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACT
** *
29591 CTAAAAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACT
* *
29613 CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCACT
* * *
29635 CCATGAAATATT-AGTAACCTC-
1 CTATGAAATTTTGA-TAACCACT
* *
29656 CTTATGAAATTTTGTTAACCACA
1 C-TATGAAATTTTGATAACCACT
29679 CTATGAAATTCTT-ATAACC
1 CTATGAAATT-TTGATAACC
29698 TCGTTGTGAC
Statistics
Matches: 305, Mismatches: 69, Indels: 47
0.72 0.16 0.11
Matches are distributed among these distances:
20 15 0.05
21 18 0.06
22 233 0.76
23 8 0.03
24 3 0.01
25 14 0.05
26 5 0.02
27 2 0.01
28 7 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACT
Found at i:29685 original size:44 final size:43
Alignment explanation
Indices: 29574--29719 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 43
29564 CCACACTAAA
** * *
29574 AAATTTTGATAACCACACTAAAAAATTTTGATAACCACAC-TATG
1 AAATTTTGATAACCACACTATGAAATTTAG-TAACCTC-CTTATG
* * *
29618 AAATTTTGATAACCTCCCCATGAAATATTAGTAACCTCCTTATG
1 AAATTTTGATAACCACACTATGAAAT-TTAGTAACCTCCTTATG
* * *
29662 AAATTTTGTTAACCACACTATGAAATTCTTA-TAACCTCGTTGTG
1 AAATTTTGATAACCACACTATGAAA-T-TTAGTAACCTCCTTATG
29706 ACAATTTTTGATAA
1 A-AA-TTTTGATAA
29720 TCTTTTTGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
43 1 0.01
44 64 0.78
45 9 0.11
46 8 0.10
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (43 bp):
AAATTTTGATAACCACACTATGAAATTTAGTAACCTCCTTATG
Found at i:29835 original size:22 final size:22
Alignment explanation
Indices: 29723--29886 Score: 136
Period size: 22 Copynumber: 7.4 Consensus size: 22
29713 TTGATAATCT
* *
29723 TTTTGATAACCTTTCTATAAAA
1 TTTTGATAACCTTCCTATGAAA
* *
29745 TTGTGATAACC-ACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* ** *
29767 CTTCAATAACCTTCCTAAGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
29789 TTTTAATAACCCGATCCTATGAAA
1 TTTTGATAA-CC-TTCCTATGAAA
*
29813 TTTTGATAACCTTCCCATGAAA
1 TTTTGATAACCTTCCTATGAAA
29835 TTTTGATAA-CTTCCATATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* * *
29857 TTTTGGTAACC-ACACTATGGAA
1 TTTTGATAACCTTC-CTATGAAA
29879 TTTTGATA
1 TTTTGATA
29887 TAATAACCAT
Statistics
Matches: 113, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
21 5 0.04
22 84 0.74
23 7 0.06
24 17 0.15
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:46114 original size:38 final size:38
Alignment explanation
Indices: 46018--46165 Score: 217
Period size: 38 Copynumber: 3.9 Consensus size: 38
46008 GGCTGTGCAT
*
46018 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* * *
46057 AGTGGACCCATACCACAGGGGGTTAAACAGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
46095 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
* *
46133 AGTGGACCCGTGCCTCAGGGTGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
46166 CTAGACTCGA
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 9 0.09
38 60 0.60
39 31 0.31
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:46206 original size:6 final size:6
Alignment explanation
Indices: 46195--46232 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
46185 CATTAACGGA
*
46195 TGATTG TGATTG TGATTG TGATTG TGTTTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
46233 GTGCAGCCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.13, C:0.00, G:0.34, T:0.53
Consensus pattern (6 bp):
TGATTG
Found at i:46835 original size:6 final size:6
Alignment explanation
Indices: 46824--46855 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
46814 CAGGCTGCAC
46824 CACAAT CACAAT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CA
46856 TCCGTTAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:47010 original size:77 final size:75
Alignment explanation
Indices: 46885--47032 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 75
46875 TCGAGTCTAG
*
46885 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTAAGGCACGGG
1 CCAACAGTTAACCCCCTGAGGCACGGGTACACTCTTACCAACAGTTTAACCCCCTAAGGCACGGG
46950 TCCACTCTTA
66 TCCACTCTTA
* * * * * *
46960 CCAACAGTTTAACCCCCTGTGGTATGGGTACACTATTTACCATCAGTTTAACCCCCTGAGGCACG
1 CCAACAG-TTAACCCCCTGAGGCACGGGTACACT-CTTACCAACAGTTTAACCCCCTAAGGCACG
47025 GGTCCACT
64 GGTCCACT
47033 ATGCACAGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
75 7 0.11
76 22 0.34
77 35 0.55
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (75 bp):
CCAACAGTTAACCCCCTGAGGCACGGGTACACTCTTACCAACAGTTTAACCCCCTAAGGCACGGG
TCCACTCTTA
Found at i:47034 original size:39 final size:38
Alignment explanation
Indices: 46885--47032 Score: 217
Period size: 38 Copynumber: 3.9 Consensus size: 38
46875 TCGAGTCTAG
46885 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
46922 CCAACAGTTTAACCCCCTAAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * * * *
46960 CCAACAGTTTAACCCCCTGTGGTATGGGTACACTATTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT-CTTA
*
46999 CCATCAGTTTAACCCCCTGAGGCACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
47033 ATGCACAGCC
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 7 0.07
38 58 0.60
39 32 0.33
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:47228 original size:15 final size:16
Alignment explanation
Indices: 47199--47232 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
47189 ATAGGAAAAC
*
47199 AATTGATAATTCATAT
1 AATTGATAATACATAT
47215 AATT-ATAATACATAT
1 AATTGATAATACATAT
47230 AAT
1 AAT
47233 CTTAGAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTGATAATACATAT
Found at i:48946 original size:21 final size:21
Alignment explanation
Indices: 48921--48964 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
48911 AACTTATTTA
*
48921 AATTTTGATTTGCAAAGTTTG
1 AATTTTGATCTGCAAAGTTTG
*
48942 AATTTTGATCTGCAGAGTTTG
1 AATTTTGATCTGCAAAGTTTG
48963 AA
1 AA
48965 GGGAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (21 bp):
AATTTTGATCTGCAAAGTTTG
Found at i:57578 original size:7 final size:7
Alignment explanation
Indices: 57562--57612 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
57552 TAGTTATTCC
57562 AAAT-AA
1 AAATAAA
57568 AAATAAA
1 AAATAAA
57575 AAATAAAAA
1 AAAT--AAA
*
57584 TAAATAAT
1 -AAATAAA
57592 AAATAAA
1 AAATAAA
57599 AAATAAA
1 AAATAAA
57606 TAAATAA
1 -AAATAA
57613 CACTTAGTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 4 0.11
7 19 0.50
8 8 0.21
9 3 0.08
10 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAATAAA
Found at i:57580 original size:13 final size:13
Alignment explanation
Indices: 57562--57605 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
57552 TAGTTATTCC
57562 AAATAAAAATAAA
1 AAATAAAAATAAA
57575 AAATAAAAATAAA
1 AAATAAAAATAAA
*
57588 TAAT--AAATAAA
1 AAATAAAAATAAA
57599 AAATAAA
1 AAATAAA
57606 TAAATAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.37
13 17 0.63
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:57590 original size:4 final size:4
Alignment explanation
Indices: 57568--57612 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
57558 TTCCAAATAA
57568 AAAT AAA- AAAT -AA- AAAT AAAT -AAT AAAT AAA- AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
57611 AA
1 AA
57613 CACTTAGTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
3 13 0.36
4 23 0.64
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:57597 original size:11 final size:11
Alignment explanation
Indices: 57562--57612 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
57552 TAGTTATTCC
57562 AAATAAA-AAT
1 AAATAAATAAT
57572 AAA-AAATAA-
1 AAATAAATAAT
57581 AAATAAATAAT
1 AAATAAATAAT
*
57592 AAATAAAAAAT
1 AAATAAATAAT
57603 AAATAAATAA
1 AAATAAATAA
57613 CACTTAGTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 6 0.17
10 11 0.31
11 19 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:59889 original size:12 final size:12
Alignment explanation
Indices: 59872--59899 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
59862 GAGAAAGAGA
59872 GAGAAGGAGAAG
1 GAGAAGGAGAAG
59884 GAGAAGGAGAAG
1 GAGAAGGAGAAG
59896 GAGA
1 GAGA
59900 GAAAGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (12 bp):
GAGAAGGAGAAG
Found at i:59906 original size:18 final size:19
Alignment explanation
Indices: 59861--59906 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
59851 AAATGGAAAA
59861 AGAGAAAG-AGAGAGAAGG
1 AGAGAAAGAAGAGAGAAGG
*
59879 AGA-AGGAGAAG-GAGAAGG
1 AGAGA-AAGAAGAGAGAAGG
59897 AGAGAAAGAA
1 AGAGAAAGAA
59907 AGAAAAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (19 bp):
AGAGAAAGAAGAGAGAAGG
Found at i:61153 original size:16 final size:18
Alignment explanation
Indices: 61113--61155 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
61103 TAATTCATAC
*
61113 TTTAAACATCTTAATTTA
1 TTTAAATATCTTAATTTA
*
61131 CTTAAATATC-TAA-TTA
1 TTTAAATATCTTAATTTA
61147 TTTAAATAT
1 TTTAAATAT
61156 TCAACCTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAATATCTTAATTTA
Found at i:67549 original size:22 final size:22
Alignment explanation
Indices: 67505--67549 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
67495 AAATATTACC
* ***
67505 ATAATTATTTTTGCCAGTCATA
1 ATAAATATTTTTGCCAAAAATA
67527 ATAAATATTTTTGCCAAAAATA
1 ATAAATATTTTTGCCAAAAATA
67549 A
1 A
67550 AATTATGAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (22 bp):
ATAAATATTTTTGCCAAAAATA
Done.