Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013100.1 Corchorus olitorius cultivar O-4 contig13133, 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: 17545
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:385 original size:36 final size:36
Alignment explanation
Indices: 338--407 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
328 TTCAATAACC
* *
338 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
* *
374 TTACATTTTTTGTAATTTTGATTATTATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
408 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1200 original size:25 final size:24
Alignment explanation
Indices: 1172--1218 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
1162 ACGTTTGCAC
1172 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
1197 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
1219 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:1263 original size:39 final size:40
Alignment explanation
Indices: 1209--1289 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
1199 ATACCTAAGA
*
1209 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
1248 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
1288 AT
1 AT
1290 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:1901 original size:29 final size:30
Alignment explanation
Indices: 1835--1914 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 30
1825 GCTTAAATAC
*
1835 CAAAAAAATCCCTTAGCTTTTTCATTTGGGA
1 CAAATAAATCCCTTAGCTTTTT-ATTTGGGA
*
1866 CAAATAAATCCCTTATCTTTTT-TTTGGGA
1 CAAATAAATCCCTTAGCTTTTTATTTGGGA
*
1895 CAAATAAATCCCTTTGCTTT
1 CAAATAAATCCCTTAGCTTT
1915 CAAAAGTGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (30 bp):
CAAATAAATCCCTTAGCTTTTTATTTGGGA
Found at i:2907 original size:13 final size:13
Alignment explanation
Indices: 2889--2913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2879 ATTAATCTTA
2889 TTATCTTACTATC
1 TTATCTTACTATC
2902 TTATCTTACTAT
1 TTATCTTACTAT
2914 TATATAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATCTTACTATC
Found at i:5509 original size:2 final size:2
Alignment explanation
Indices: 5504--5531 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5494 AGTAATTTGA
5504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5532 TAGATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5943 original size:21 final size:21
Alignment explanation
Indices: 5919--5961 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5909 TTGGGAGATC
*
5919 AAAGCCCAGATT-CAATTGCAA
1 AAAGCCCA-ATTCCAAATGCAA
5940 AAAGCCCAATTCCAAATGCAA
1 AAAGCCCAATTCCAAATGCAA
5961 A
1 A
5962 GTAACCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.16
Consensus pattern (21 bp):
AAAGCCCAATTCCAAATGCAA
Found at i:5994 original size:6 final size:6
Alignment explanation
Indices: 5983--6020 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
5973 GATTTGATTT
*
5983 TTTTTA TTTTTA TTTTTA TTTTTT TTTATTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA T
6021 GGCATCCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:6004 original size:19 final size:19
Alignment explanation
Indices: 5981--6020 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5971 TTGATTTGAT
*
5981 TTTTTTTATTTTTATTTTTA
1 TTTTTTT-TTATTATTTTTA
6001 TTTTTTTTTATTATTTTTA
1 TTTTTTTTTATTATTTTTA
6020 T
1 T
6021 GGCATCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTATTATTTTTA
Found at i:9246 original size:36 final size:36
Alignment explanation
Indices: 9170--9246 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
9160 TTTAACTCTT
* * *
9170 TTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTAAAATA
*
9206 TTCAAATTGGGAAAGTTCCCA-CCAGTTTTCAAAATA
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTT-AAAATA
9242 TTCAA
1 TTCAA
9247 TTTAGCTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 7 0.19
36 29 0.81
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (36 bp):
TTCAAATTGGGAAAGTTCCCATCAAGTTTTAAAATA
Found at i:9305 original size:87 final size:88
Alignment explanation
Indices: 9142--9313 Score: 224
Period size: 87 Copynumber: 2.0 Consensus size: 88
9132 TTTCCTTCAA
* ** * *
9142 AGTTTTCAAAGTATTCAATTTAACTCTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAGTTT
1 AGTTTTCAAAATATTCAATTTAACTCTTTTCAAATTAAGAAAATTCCCATCAAGGTTTTAAGTTT
9207 TCAAATTGGG-AAAGTTCCCACC
66 TCAAATTGGGAAAAGTTCCCACC
* * *
9229 AGTTTTCAAAATATTCAATTTAGCTCCTTTTCAAATTAAGAAAATTCCCAT-TAGGTTTT-GGTT
1 AGTTTTCAAAATATTCAATTTAACT-CTTTTCAAATTAAGAAAATTCCCATCAAGGTTTTAAGTT
*
9292 TTCAATTTAGGGAAAAGTTCCC
65 TTCAAATT-GGGAAAAGTTCCC
9314 GTCATTTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 10 0.14
87 32 0.44
88 31 0.42
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (88 bp):
AGTTTTCAAAATATTCAATTTAACTCTTTTCAAATTAAGAAAATTCCCATCAAGGTTTTAAGTTT
TCAAATTGGGAAAAGTTCCCACC
Found at i:12558 original size:13 final size:13
Alignment explanation
Indices: 12540--12564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12530 TGAGATTGAT
12540 CAATTGCCGATCC
1 CAATTGCCGATCC
12553 CAATTGCCGATC
1 CAATTGCCGATC
12565 TCTTACCACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (13 bp):
CAATTGCCGATCC
Found at i:15674 original size:138 final size:140
Alignment explanation
Indices: 15295--15837 Score: 858
Period size: 141 Copynumber: 3.9 Consensus size: 140
15285 CGAAGACAAA
15295 ATTT-ATTTCATCAAGTTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGA
1 ATTTCATTTCATCAAGTTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGA
* *
15359 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAAAAACCTCCAGGTATTAATTCTGATAAATCC
66 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
*
15424 TCCAGGTATC
131 TCCGGGTATC
* *
15434 ATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAAATTTCAAAAACCTTGCTCAAGTTTG
1 ATTTCATTTCATCAAGTTTTTAATCAAAGCTGCGTTT-AAATTTCAAAAACCTTGCTCAAGGTTG
* * * *
15499 TGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAATCTTCGGGTATTAGTTCTGATAAATC
65 AGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATC
15564 CTCCGGGTATC
130 CTCCGGGTATC
* *
15575 ATTTCATTTCTTCAAG-TTTTAATCAAAGCTACGTTTAAATTTC-AAAACCTTGCTCAAGGTTGA
1 ATTTCATTTCATCAAGTTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGA
15638 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
66 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
15703 TCCGGGTATC
131 TCCGGGTATC
* * * ** *
15713 ATCTCATTTCATCATGTTGTTAATCAAATTTGCGTTTAAATTTCAAATAAACCTTGCTCAAGGTC
1 ATTTCATTTCATCAAGTTTTTAATCAAAGCTGCGTTTAAATTTC-AA-AAACCTTGCTCAAGGTT
* * *
15778 GAGTTTGCATTTGTGAGACCACCGGGCACAATTTCAGAAACCTCCGGGTATCAATTCTGA
64 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGA
15838 CTTGTCCTCC
Statistics
Matches: 370, Mismatches: 28, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
138 103 0.28
139 34 0.09
140 49 0.13
141 111 0.30
142 73 0.20
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (140 bp):
ATTTCATTTCATCAAGTTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGA
GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
TCCGGGTATC
Found at i:15850 original size:280 final size:280
Alignment explanation
Indices: 15295--15837 Score: 876
Period size: 279 Copynumber: 1.9 Consensus size: 280
15285 CGAAGACAAA
*
15295 ATTTATTTCATCAAGTTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAG
1 ATTTATTTCATCAAGTTTTTAATCAAAGCTACGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAG
15360 TTTGCATTTGTAAGACCTCCGGGCACAATTTCAAAAACCTCCAGGTATTAATTCTGATAAATCCT
66 TTTGCATTTGTAAGACCTCCGGGCACAATTTCAAAAACCTCCAGGTATTAATTCTGATAAATCCT
* *
15425 CCAGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAAATTTCAAAAACCTTGC
131 CCAGGTATCATCTCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAAAATTTCAAAAACCTTGC
* * * * * * * *
15490 TCAAGTTTGTGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAATCTTCGGGTATTAGTTC
196 TCAAGGTCGAGTTTGCATTTGTAAGACCACCGGGCACAATTTCAGAAACCTCCGGGTATCAATTC
15555 TGATAAATCCTCCGGGTATC
261 TGATAAATCCTCCGGGTATC
*
15575 ATTTCATTTCTTCAAG-TTTTAATCAAAGCTACGTTTAAATTTC-AAAACCTTGCTCAAGGTTGA
1 ATTT-ATTTCATCAAGTTTTTAATCAAAGCTACGTTTAAATTTCAAAAACCTTGCTCAAGGTTGA
* *
15638 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
65 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAAAAACCTCCAGGTATTAATTCTGATAAATCC
* * *
15703 TCCGGGTATCATCTCATTTCATCATGTTGTTAATCAAATTTGCGTTT-AAATTTCAAATAAACCT
130 TCCAGGTATCATCTCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAAAATTTC-AA-AAACCT
*
15767 TGCTCAAGGTCGAGTTTGCATTTGTGAGACCACCGGGCACAATTTCAGAAACCTCCGGGTATCAA
193 TGCTCAAGGTCGAGTTTGCATTTGTAAGACCACCGGGCACAATTTCAGAAACCTCCGGGTATCAA
15832 TTCTGA
258 TTCTGA
15838 CTTGTCCTCC
Statistics
Matches: 242, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
278 7 0.03
279 127 0.52
280 98 0.40
281 10 0.04
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (280 bp):
ATTTATTTCATCAAGTTTTTAATCAAAGCTACGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAG
TTTGCATTTGTAAGACCTCCGGGCACAATTTCAAAAACCTCCAGGTATTAATTCTGATAAATCCT
CCAGGTATCATCTCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAAAATTTCAAAAACCTTGC
TCAAGGTCGAGTTTGCATTTGTAAGACCACCGGGCACAATTTCAGAAACCTCCGGGTATCAATTC
TGATAAATCCTCCGGGTATC
Found at i:16106 original size:40 final size:39
Alignment explanation
Indices: 15939--16583 Score: 502
Period size: 40 Copynumber: 16.6 Consensus size: 39
15929 TCGATTCCAG
* **
15939 AATCCTGCTCAGGATCA-TTCTTTACCAGTCGATTTCAA
1 AATCCTGCTCAGGATCATTTCTTTACCAATTAATTTCAA
* *
15977 AATCCTGCTCAGGATCTTTTCTTTACCAGTTAATTTCAA
1 AATCCTGCTCAGGATCATTTCTTTACCAATTAATTTCAA
16016 AATCCTGCTCAGGATCATTTCTTTACCAATTAATTTCAA
1 AATCCTGCTCAGGATCATTTCTTTACCAATTAATTTCAA
* * *
16055 AACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTTCTTTA-CCAATTAATTTCAA
* *
16095 AATCCTACTCAGG---A------T--C-ATTAATTTCAG
1 AATCCTGCTCAGGATCATTTCTTTACCAATTAATTTCAA
* *
16122 AATCTTGCTCAGGATCATTGT-TTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATT-TCTTTA-CCAATTAATTTCAA
* * *
16162 AACCCTACTCAGGATCATTGT-TTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATT-TCTTTA-CCAATTAATTTCAA
* * * * * *
16202 AACCCTGCTCAGGATCATTGCTTTGTCAAATCAATTTCAG
1 AATCCTGCTCAGGATCATTTCTTT-ACCAATTAATTTCAA
*
16242 AATCCTGCTCAGGATCATCTT-TTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TTCTTTA-CCAATTAATTTCAA
* * *
16282 AACCCTTCTCAGGATCATTGT-TTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATT-TCTTTA-CCAATTAATTTCAA
* *
16322 AACCCTGCTCAGGATCATTGT-TTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATT-TCTTTA-CCAATTAATTTCAA
* * * * * * *
16362 AACCCTACTCAGGATCATTGCTTTGTCAAATCAATTTCAG
1 AATCCTGCTCAGGATCATTTCTTT-ACCAATTAATTTCAA
*
16402 AATCCTGCTCAGGATCATCTT-TTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TTCTTTA-CCAATTAATTTCAA
* * * * *
16442 AACCCTGCTCATGATCATTAT-TTTATCTAGTTAATTTCAG
1 AATCCTGCTCAGGATCATT-TCTTTA-CCAATTAATTTCAA
* * * *
16482 AATCCTGCTCAGGACCATTGCTTTATCAAACTAATTTCAA
1 AATCCTGCTCAGGATCATTTCTTTA-CCAATTAATTTCAA
* * * * ** *
16522 AATCTTACTCAGGATCATTGCTCTATAAATTGAATTTCAG
1 AATCCTGCTCAGGATCATTTCTTTACCAATT-AATTTCAA
* *
16562 AATCCTGTTCAGGATCACTTCT
1 AATCCTGCTCAGGATCATTTCT
16584 GTATCATTCA
Statistics
Matches: 512, Mismatches: 68, Indels: 52
0.81 0.11 0.08
Matches are distributed among these distances:
27 21 0.04
30 1 0.00
31 1 0.00
36 1 0.00
37 1 0.00
38 16 0.03
39 85 0.17
40 384 0.75
41 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (39 bp):
AATCCTGCTCAGGATCATTTCTTTACCAATTAATTTCAA
Found at i:16119 original size:27 final size:27
Alignment explanation
Indices: 16084--16140 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
16074 GCTTTATCAA
16084 ATTAATTTCAAAATCCTACTCAGGATC
1 ATTAATTTCAAAATCCTACTCAGGATC
* * *
16111 ATTAATTTCAGAATCTTGCTCAGGATC
1 ATTAATTTCAAAATCCTACTCAGGATC
16138 ATT
1 ATT
16141 GTTTTATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (27 bp):
ATTAATTTCAAAATCCTACTCAGGATC
Found at i:16253 original size:80 final size:80
Alignment explanation
Indices: 16111--16578 Score: 627
Period size: 80 Copynumber: 5.8 Consensus size: 80
16101 ACTCAGGATC
* * * * * * *
16111 ATTAATTTCAGAATCTTGCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGGA
1 ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGA
16176 TCATTGTTTTATCAA
66 TCATTGTTTTATCAA
* *
16191 ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTGTCAAATCAATTTCAGAATCCTGCTCAGGA
1 ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGA
16256 TCATCT-TTTTATCAA
66 TCAT-TGTTTTATCAA
* * * *
16271 ATTAATTTCAAAACCCTTCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGA
1 ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGA
16336 TCATTGTTTTATCAA
66 TCATTGTTTTATCAA
* * *
16351 ATTAATTTCAAAACCCTACTCAGGATCATTGCTTTGTCAAATCAATTTCAGAATCCTGCTCAGGA
1 ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGA
16416 TCATCT-TTTTATCAA
66 TCAT-TGTTTTATCAA
* ** * *
16431 ATTAATTTCAAAACCCTGCTCATGATCATTATTTTATCTAGTTAATTTCAGAATCCTGCTCAGGA
1 ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGA
* *
16496 CCATTGCTTTATCAA
66 TCATTGTTTTATCAA
* * * * * *
16511 ACTAATTTCAAAATCTTACTCAGGATCATTGCTCTAT-AAATTGAATTTCAGAATCCTGTTCAGG
1 ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATT-AATTTCAGAATCCTGCTCAGG
16575 ATCA
65 ATCA
16579 CTTCTGTATC
Statistics
Matches: 340, Mismatches: 43, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
79 5 0.01
80 333 0.98
81 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (80 bp):
ATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGA
TCATTGTTTTATCAA
Found at i:16327 original size:120 final size:120
Alignment explanation
Indices: 16111--16578 Score: 629
Period size: 120 Copynumber: 3.9 Consensus size: 120
16101 ACTCAGGATC
* * *
16111 ATTAATTTCAGAATCTTGCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGGA
1 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTTCTCAGGA
* *
16176 TCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTGTCAA
66 TCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGTTTTATCAA
* *
16231 ATCAATTTCAGAATCCTGCTCAGGATCATCT-TTTTATCAAATTAATTTCAAAACCCTTCTCAGG
1 ATTAATTTCAGAATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAAAACCCTTCTCAGG
16295 ATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGTTTTATCAA
65 ATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGTTTTATCAA
* * * * * * * *
16351 ATTAATTTCAAAACCCTACTCAGGATCATTGCTTTGTCAAATCAATTTCAGAATCCTGCTCAGGA
1 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTTCTCAGGA
* * *
16416 TCATCT-TTTTATCAAATTAATTTCAAAACCCTGCTCATGATCATTATTTTATCTA
66 TCAT-TGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGTTTTATCAA
* * * *
16471 GTTAATTTCAGAATCCTGCTCAGGACCATTGCTTTATCAAACTAATTTCAAAA-TCTTACTCAGG
1 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTT-CTCAGG
* * * * *
16535 ATCATTGCTCTAT-AAATTGAATTTCAGAATCCTGTTCAGGATCA
65 ATCATTGTTTTATCAAATT-AATTTCAAAACCCTGCTCAGGATCA
16579 CTTCTGTATC
Statistics
Matches: 307, Mismatches: 35, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
119 9 0.03
120 296 0.96
121 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (120 bp):
ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTTCTCAGGA
TCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGTTTTATCAA
Found at i:16375 original size:160 final size:160
Alignment explanation
Indices: 16111--16578 Score: 724
Period size: 160 Copynumber: 2.9 Consensus size: 160
16101 ACTCAGGATC
* * *
16111 ATTAATTTCAGAA-TCTTGCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGG
1 ATTAATTTCAAAACCCTT-CTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGG
*
16175 ATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTGTCAAATCAATTTC
65 ATCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGGATCATTGCTTTGTCAAATCAATTTC
16240 AGAATCCTGCTCAGGATCATCTTTTTATCAA
130 AGAATCCTGCTCAGGATCATCTTTTTATCAA
16271 ATTAATTTCAAAACCCTTCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGA
1 ATTAATTTCAAAACCCTTCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGA
16336 TCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGGATCATTGCTTTGTCAAATCAATTTCA
66 TCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGGATCATTGCTTTGTCAAATCAATTTCA
16401 GAATCCTGCTCAGGATCATCTTTTTATCAA
131 GAATCCTGCTCAGGATCATCTTTTTATCAA
* * * * * * *
16431 ATTAATTTCAAAACCCTGCTCATGATCATTATTTTATCTAGTTAATTTCAGAATCCTGCTCAGGA
1 ATTAATTTCAAAACCCTTCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGA
* * * * * * * *
16496 CCATTGCTTTATCAAACTAATTTCAAAATCTTACTCAGGATCATTGCTCTAT-AAATTGAATTTC
66 TCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGGATCATTGCTTTGTCAAA-TCAATTTC
*
16560 AGAATCCTGTTCAGGATCA
130 AGAATCCTGCTCAGGATCA
16579 CTTCTGTATC
Statistics
Matches: 286, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
159 3 0.01
160 280 0.98
161 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (160 bp):
ATTAATTTCAAAACCCTTCTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTGCTCAGGA
TCATTGTTTTATCAAATTAATTTCAAAACCCTACTCAGGATCATTGCTTTGTCAAATCAATTTCA
GAATCCTGCTCAGGATCATCTTTTTATCAA
Found at i:16615 original size:27 final size:27
Alignment explanation
Indices: 16569--16627 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
16559 CAGAATCCTG
*
16569 TTCAGGATCACTTCTGTATCATTCAAT
1 TTCAGGATCACTTCTGTATCAGTCAAT
16596 TTCAGGATCATCCTT-T-TATCAGTCAAT
1 TTCAGGATCA--CTTCTGTATCAGTCAAT
16623 TTCAG
1 TTCAG
16628 AATCCTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 25 0.86
28 1 0.03
29 3 0.10
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (27 bp):
TTCAGGATCACTTCTGTATCAGTCAAT
Found at i:16639 original size:39 final size:40
Alignment explanation
Indices: 16596--16680 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 40
16586 ATCATTCAAT
*
16596 TTCAGGAT-CATCCTTTTATCAGTCAATTTC-AGAATCCTA
1 TTCAGGATCCATCC-TTTATCAGTCAATTTCAAAAATCCTA
* *
16635 TTCAGGATCCTTGCTTTATCAGTCAATTTCAAAAATCCTA
1 TTCAGGATCCATCCTTTATCAGTCAATTTCAAAAATCCTA
16675 TTCAGG
1 TTCAGG
16681 GCCAGTGGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
39 24 0.59
40 17 0.41
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (40 bp):
TTCAGGATCCATCCTTTATCAGTCAATTTCAAAAATCCTA
Found at i:16694 original size:40 final size:39
Alignment explanation
Indices: 16610--16697 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 39
16600 GGATCATCCT
* * *
16610 TTTATCAGTCAATTTCAGAATCCTATTCAGGATCCTTGC
1 TTTATCAGTCAATTTCAAAATCCTATTCAGGAGCCTGGC
16649 TTTATCAGTCAATTTCAAAAATCCTATTCAGG-GCCAGTGGC
1 TTTATCAGTCAATTTC-AAAATCCTATTCAGGAGCC--TGGC
16690 -TTATCAGT
1 TTTATCAGT
16698 TGATTTCAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 18 0.42
40 22 0.51
41 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (39 bp):
TTTATCAGTCAATTTCAAAATCCTATTCAGGAGCCTGGC
Done.