Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023900.1 Corchorus olitorius cultivar O-4 contig23933, 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: 67896
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1855 original size:41 final size:41
Alignment explanation
Indices: 1785--1864 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
1775 TTCAATTTCG
*
1785 TCCCTGATTTAAGATCTATTTCCTGATTTGATACAATTTAA
1 TCCCTGATTTAAGATCTATGTCCTGATTTGATACAATTTAA
* *
1826 TCCCTGATTTAGGATTCTA-GTCACT-ATTTGATTCAATTT
1 TCCCTGATTTAAGA-TCTATGTC-CTGATTTGATACAATTT
1865 GGTCCTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 28 0.82
42 6 0.18
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (41 bp):
TCCCTGATTTAAGATCTATGTCCTGATTTGATACAATTTAA
Found at i:4529 original size:15 final size:16
Alignment explanation
Indices: 4505--4544 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4495 AGTGGTTGAA
*
4505 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
4520 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
4536 AGAAAACAA
1 AGAAAACAA
4545 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:8786 original size:40 final size:41
Alignment explanation
Indices: 8716--8798 Score: 141
Period size: 40 Copynumber: 2.0 Consensus size: 41
8706 TTTAACAAGT
8716 TTAAATTTTCCAAAAAAAAACAAGTAAGGTTAAATTAAATG
1 TTAAATTTTCCAAAAAAAAACAAGTAAGGTTAAATTAAATG
* *
8757 TTAAATTTTCC-CAGAAAAACAAGTAAGGTTAAATTAAATG
1 TTAAATTTTCCAAAAAAAAACAAGTAAGGTTAAATTAAATG
8797 TT
1 TT
8799 TACTTGAGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 29 0.73
41 11 0.28
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.31
Consensus pattern (41 bp):
TTAAATTTTCCAAAAAAAAACAAGTAAGGTTAAATTAAATG
Found at i:15273 original size:23 final size:24
Alignment explanation
Indices: 15241--15286 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
15231 AAGACAATAG
15241 AAAAAGCTCTCACAAAGGAGTCCC
1 AAAAAGCTCTCACAAAGGAGTCCC
*
15265 AAAAA-CTCTCACAATGGAGTCC
1 AAAAAGCTCTCACAAAGGAGTCC
15287 TAACAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.15
Consensus pattern (24 bp):
AAAAAGCTCTCACAAAGGAGTCCC
Found at i:16094 original size:178 final size:178
Alignment explanation
Indices: 15831--16154 Score: 501
Period size: 178 Copynumber: 1.8 Consensus size: 178
15821 AAGGTGATTT
*
15831 AAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
1 AAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACCAAATTTA
* * * *
15896 ATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAACGGGAATATACGGTC
66 ATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGATTAACGGGAATAGACGG-C
*
15960 C-ACTTAATATTATATAACTTTTGCTTCAGTTGTCTAATTGAGATAATTC
129 CTACTTAATATTACATAACTTTTGCTTCAGTTGTCTAATTGAGATAATTC
* * * *
16009 AAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACCAAATTTA
1 AAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACCAAATTTA
*
16074 TTG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACGGGAATAGACGGCC
66 ATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACGGGAATAGACGGCC
16138 TACTTAATATTACATAA
130 TACTTAATATTACATAA
16155 TTTGCGCTTA
Statistics
Matches: 132, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
177 10 0.08
178 122 0.92
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (178 bp):
AAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACCAAATTTA
ATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACGGGAATAGACGGCCT
ACTTAATATTACATAACTTTTGCTTCAGTTGTCTAATTGAGATAATTC
Found at i:16709 original size:19 final size:19
Alignment explanation
Indices: 16685--16721 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
16675 TGTATCTGTA
16685 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
16704 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
16722 TGGGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.38, G:0.14, T:0.32
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:17274 original size:13 final size:13
Alignment explanation
Indices: 17256--17286 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17246 TCGGTTATGG
*
17256 ACCCAATATCCAT
1 ACCCAATATCCAA
17269 ACCCAATATCCAA
1 ACCCAATATCCAA
17282 ACCCA
1 ACCCA
17287 TTAAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (13 bp):
ACCCAATATCCAA
Found at i:18542 original size:18 final size:19
Alignment explanation
Indices: 18503--18542 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
18493 GTGCTCCCGT
18503 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
18524 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
18542 T
1 T
18543 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:19532 original size:36 final size:37
Alignment explanation
Indices: 19453--19545 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 37
19443 AGTCAACAGA
*
19453 CTAACTAAATTTAAGAGATTTACTAGCCACAAAATCTG
1 CTAATTAAATTTAAGAGATTTACTAGCCAC-AAATCTG
*
19491 CTAATTAAATTTAAGAGATTTATTAGCCAC-AATCTG
1 CTAATTAAATTTAAGAGATTTACTAGCCACAAATCTG
*
19527 CTAATTAAATTTAATAGAT
1 CTAATTAAATTTAAGAGAT
19546 AATAATTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
36 24 0.46
38 28 0.54
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (37 bp):
CTAATTAAATTTAAGAGATTTACTAGCCACAAATCTG
Found at i:19989 original size:15 final size:15
Alignment explanation
Indices: 19966--19998 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19956 TGGAAAAGTT
19966 GAAGAAAAAGGCTGA
1 GAAGAAAAAGGCTGA
*
19981 GAAGGAAAAGGCTGA
1 GAAGAAAAAGGCTGA
19996 GAA
1 GAA
19999 AGAGAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.36, T:0.06
Consensus pattern (15 bp):
GAAGAAAAAGGCTGA
Found at i:20006 original size:16 final size:15
Alignment explanation
Indices: 19971--20006 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
19961 AAGTTGAAGA
*
19971 AAAAGGCTGAGAAGG
1 AAAAGGCTGAGAAAG
19986 AAAAGGCTGAGAAAG
1 AAAAGGCTGAGAAAG
20001 AGAAAG
1 A-AAAG
20007 ATGGTGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.53, C:0.06, G:0.36, T:0.06
Consensus pattern (15 bp):
AAAAGGCTGAGAAAG
Found at i:21380 original size:33 final size:33
Alignment explanation
Indices: 21338--21404 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
21328 TCACCTCCCA
*
21338 ACTTCATTCACTTCCCACCAAGGAGTTTAATCT
1 ACTTCATTCACTTCCCACCAAAGAGTTTAATCT
21371 ACTTCATTCACTTCCCACCAAAGAGTTTAATCT
1 ACTTCATTCACTTCCCACCAAAGAGTTTAATCT
21404 A
1 A
21405 GATATAGACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (33 bp):
ACTTCATTCACTTCCCACCAAAGAGTTTAATCT
Found at i:21479 original size:17 final size:17
Alignment explanation
Indices: 21457--21512 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
21447 AAGTGGTAAA
21457 AAATATACTAAAATAAC
1 AAATATACTAAAATAAC
* * *
21474 AAATAT-TTATAGTAA-
1 AAATATACTAAAATAAC
21489 ACAATATACTAAAATAAC
1 A-AATATACTAAAATAAC
21507 AAATAT
1 AAATAT
21513 TTATAGTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 1 0.03
16 11 0.37
17 17 0.57
18 1 0.03
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.29
Consensus pattern (17 bp):
AAATATACTAAAATAAC
Found at i:21507 original size:16 final size:16
Alignment explanation
Indices: 21458--21508 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
21448 AGTGGTAAAA
21458 AATATACTAAAATAAC
1 AATATACTAAAATAAC
* * *
21474 AA-ATATTTATAGTAAAC
1 AATATA-CTAAAAT-AAC
21491 AATATACTAAAATAAC
1 AATATACTAAAATAAC
21507 AA
1 AA
21509 ATATTTATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
15 3 0.12
16 11 0.42
17 9 0.35
18 3 0.12
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (16 bp):
AATATACTAAAATAAC
Found at i:21523 original size:33 final size:33
Alignment explanation
Indices: 21452--21523 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
21442 AAAATAAGTG
*
21452 GTAAAAAATATACTAAAATAACAAATATTTATA
1 GTAAACAATATACTAAAATAACAAATATTTATA
21485 GTAAACAATATACTAAAATAACAAATATTTATA
1 GTAAACAATATACTAAAATAACAAATATTTATA
21518 GTAAAC
1 GTAAAC
21524 GTTTAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.29
Consensus pattern (33 bp):
GTAAACAATATACTAAAATAACAAATATTTATA
Found at i:26565 original size:316 final size:316
Alignment explanation
Indices: 25992--26610 Score: 1055
Period size: 316 Copynumber: 2.0 Consensus size: 316
25982 TGAAACAATT
25992 TTGAAAACTACATTACATAAACTAATCGGGCGATAATCTTTAACCACAAATGGATGCTCACTCTT
1 TTGAAAACTACATTACATAAACTAATCGGGCGATAATCTTTAACCACAAATGGATGCTCACTCTT
* * *
26057 GGGAATTAAGACAACATTTGTATGATTGATGTCAGGTAAGTTCTGCCTTGAATTCAAGAAATTTA
66 GGGAATCAAGACAACATTTGTATGATTGATGTCAAGTAAGTTCTGCCCTGAATTCAAGAAATTTA
26122 AAACCATCTCACTAACCTTTTCCCCTACAATATGCCAATATCGTTGGAAAAACAAAGGAGTCATG
131 AAACCATCTCACTAACCTTTTCCCCTACAATATGCCAATATCGTTGGAAAAACAAAGGAGTCATG
*
26187 CCATCTGGGCCTGATAATTTATCAACTCCCATGTCGAAAGCTTCTAATCTAATTTCTTCACTTGT
196 CCATCTGGGCCTGATAATTTATCAACTCCCATGTCGAAAGCTGCTAATCTAATTTCTTCACTTGT
26252 AAAAATCCTATTCAACCGGGAGTTCATATCT-TTAGTCACCCTCCGGGCAACATTTG
261 AAAAATCCTATTCAACCGGGAGTTCATATCTGTT-GTCACCCTCCGGGCAACATTTG
* * * *
26308 TTGAAAACTACATTACATAAACTAATCGGGCGATAATCTTTAACCATACATGGATGCTGATTCTT
1 TTGAAAACTACATTACATAAACTAATCGGGCGATAATCTTTAACCACAAATGGATGCTCACTCTT
26373 GGGAATC-AGAACAACATTTGTATGATTGATGTCAAGTAAGTTCTGCCCTGAATTCAAGAAATTT
66 GGGAATCAAG-ACAACATTTGTATGATTGATGTCAAGTAAGTTCTGCCCTGAATTCAAGAAATTT
* * **
26437 AAAACCATCTCACTAACCTTTTCCCCTACAATATGCCAATATCGTTTGAAAAATAGTGGAGTCAT
130 AAAACCATCTCACTAACCTTTTCCCCTACAATATGCCAATATCGTTGGAAAAACAAAGGAGTCAT
* *
26502 GCCATCTGGGTCC-GGTGATTTATCAACTCCCATGTCGAAAGCTGCTAATCTAATTTCTTCACTT
195 GCCATCTGGG-CCTGATAATTTATCAACTCCCATGTCGAAAGCTGCTAATCTAATTTCTTCACTT
*
26566 GTAAAAATCCTATTCAACTGGGAGTTCATATCTGTTGTCACCCTC
259 GTAAAAATCCTATTCAACCGGGAGTTCATATCTGTTGTCACCCTC
26611 TTGTCAACTG
Statistics
Matches: 285, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
315 2 0.01
316 279 0.98
317 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (316 bp):
TTGAAAACTACATTACATAAACTAATCGGGCGATAATCTTTAACCACAAATGGATGCTCACTCTT
GGGAATCAAGACAACATTTGTATGATTGATGTCAAGTAAGTTCTGCCCTGAATTCAAGAAATTTA
AAACCATCTCACTAACCTTTTCCCCTACAATATGCCAATATCGTTGGAAAAACAAAGGAGTCATG
CCATCTGGGCCTGATAATTTATCAACTCCCATGTCGAAAGCTGCTAATCTAATTTCTTCACTTGT
AAAAATCCTATTCAACCGGGAGTTCATATCTGTTGTCACCCTCCGGGCAACATTTG
Found at i:34733 original size:29 final size:29
Alignment explanation
Indices: 34691--34785 Score: 172
Period size: 29 Copynumber: 3.3 Consensus size: 29
34681 TCATGGCTTG
*
34691 TCTTAAATCCTTCGCAATTAAAGCTCCAA
1 TCTTCAATCCTTCGCAATTAAAGCTCCAA
34720 TCTTCAATCCTTCGCAATTAAAGCTCCAA
1 TCTTCAATCCTTCGCAATTAAAGCTCCAA
*
34749 TCTTCAATCCTTCGCTATTAAAGCTCCAA
1 TCTTCAATCCTTCGCAATTAAAGCTCCAA
34778 TCTTCAAT
1 TCTTCAAT
34786 TCCCGTAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (29 bp):
TCTTCAATCCTTCGCAATTAAAGCTCCAA
Found at i:38721 original size:16 final size:16
Alignment explanation
Indices: 38700--38730 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
38690 TTTCATTGTT
38700 TTGCTTTGATTGATTA
1 TTGCTTTGATTGATTA
38716 TTGCTTTGATTGATT
1 TTGCTTTGATTGATT
38731 GCATATTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.19, T:0.58
Consensus pattern (16 bp):
TTGCTTTGATTGATTA
Found at i:38846 original size:12 final size:13
Alignment explanation
Indices: 38818--38850 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
38808 TTATGACTTA
38818 TATGATGTGATTGC
1 TATGAT-TGATTGC
38832 TATGATTGA-TGC
1 TATGATTGATTGC
38844 TATGATT
1 TATGATT
38851 TACTTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 3 0.16
14 6 0.32
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (13 bp):
TATGATTGATTGC
Found at i:39704 original size:41 final size:41
Alignment explanation
Indices: 39658--39885 Score: 273
Period size: 41 Copynumber: 5.5 Consensus size: 41
39648 CTAAAGTTGT
39658 CAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCC
1 CAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCC
* * * * *
39699 CAAACACAATTATAACACA-AGGGCAATTCTCTCTAAAAGTCCT
1 CAAACACATTTATAACACAGA-GGC-A-TCTATATCAAAGTCCC
* *
39742 CAAACACATTTATAACACAGAGGCATCCATA-CTAGAGTCCC
1 CAAACACATTTATAACACAGAGGCATCTATATC-AAAGTCCC
* * *
39783 CAAACACAATTATAACACAGGGGCACCTCTAT-TCTAAAGTCCT
1 CAAACACATTTATAACACAGAGGCA--TCTATATC-AAAGTCCC
*
39826 CAAACACATTTATAACACAGAGGCATATATATCAAAGTCCC
1 CAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCC
39867 CAAACACATTTATAACACA
1 CAAACACATTTATAACACA
39886 AGGGCGATTC
Statistics
Matches: 157, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 83 0.53
42 4 0.03
43 68 0.43
44 1 0.01
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22
Consensus pattern (41 bp):
CAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCC
Found at i:39781 original size:84 final size:83
Alignment explanation
Indices: 39606--39900 Score: 414
Period size: 84 Copynumber: 3.5 Consensus size: 83
39596 CCCAATAACT
* **
39606 AAAGTCCCCAAGA-ACAATTATAACACAGGGGCAATTCTCTTTCTAAAGTTGTCAAACACATTTA
1 AAAGTCCCCAA-ACACAATTATAACACAAGGGCAATTCTC--TCTAAAGTCCTCAAACACATTTA
39670 TAACACAGAGGCATCTATATC
63 TAACACAGAGGCATCTATATC
39691 AAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTCTAAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTCT-AAAGTCCTCAAACACATTTATA
*
39756 ACACAGAGGCATCCATA-C
65 ACACAGAGGCATCTATATC
* * ** *
39774 TAGAGTCCCCAAACACAATTATAACACAGGGGCACCTCTATTCTAAAGTCCTCAAACACATTTAT
1 -AAAGTCCCCAAACACAATTATAACACAAGGGCAATTCT-CTCTAAAGTCCTCAAACACATTTAT
*
39839 AACACAGAGGCATATATATC
64 AACACAGAGGCATCTATATC
* *
39859 AAAGTCCCCAAACACATTTATAACACAAGGGCGATTCTCTCT
1 AAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTCT
39901 TTGGCAAAGG
Statistics
Matches: 187, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
83 7 0.04
84 140 0.75
85 40 0.21
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (83 bp):
AAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTCTAAAGTCCTCAAACACATTTATAA
CACAGAGGCATCTATATC
Found at i:39964 original size:2 final size:2
Alignment explanation
Indices: 39957--39981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39947 ATTCCTAACT
39957 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39982 CAAAGGCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43596 original size:26 final size:26
Alignment explanation
Indices: 43517--43596 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
43507 GATCACCTAG
* * *
43517 GGGCACTTTGGTCATTTTCAAGAATCTAG
1 GGGCATTTTGGTCATTTT-AAG-TTC-AA
*
43546 GGGCATTTTGGTCATTTGACA-TTCAA
1 GGGCATTTTGGTCATTTTA-AGTTCAA
43572 GGGCATTTTGGTCATTTTAAGTTCA
1 GGGCATTTTGGTCATTTTAAGTTCA
43597 CTTTTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 1 0.02
26 23 0.52
27 2 0.05
28 1 0.02
29 17 0.39
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.39
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTTAAGTTCAA
Found at i:45923 original size:82 final size:82
Alignment explanation
Indices: 45778--45938 Score: 268
Period size: 82 Copynumber: 2.0 Consensus size: 82
45768 TTTCCGTGTT
* *
45778 CAATTTGGCCCCTAATTTAGGATTCTATTTACTATTTGATACAATTTAGTCCCTAATTAAGGATT
1 CAATTTGGCCCCTAATTTACGATTCTACTTACTATTTGATACAATTTAGTCCCTAATTAAGGATT
*
45843 CTATTTACTATTTGATA
66 CTAATTACTATTTGATA
* *
45860 CAATTTGGCCCCTAATTTACGATTCTACTTACTATTTGATACAATTTAGTCCCTGATTTAGGATT
1 CAATTTGGCCCCTAATTTACGATTCTACTTACTATTTGATACAATTTAGTCCCTAATTAAGGATT
*
45925 CTAATTACTGTTTG
66 CTAATTACTATTTG
45939 GCTCAATTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.43
Consensus pattern (82 bp):
CAATTTGGCCCCTAATTTACGATTCTACTTACTATTTGATACAATTTAGTCCCTAATTAAGGATT
CTAATTACTATTTGATA
Found at i:45946 original size:41 final size:41
Alignment explanation
Indices: 45778--45952 Score: 235
Period size: 41 Copynumber: 4.3 Consensus size: 41
45768 TTTCCGTGTT
*
45778 CAATTTGGCCCCTAATTTAGGATTCTATTTACTATTTGATA
1 CAATTTGGTCCCTAATTTAGGATTCTATTTACTATTTGATA
* *
45819 CAATTTAGTCCCTAATTAAGGATTCTATTTACTATTTGATA
1 CAATTTGGTCCCTAATTTAGGATTCTATTTACTATTTGATA
* * *
45860 CAATTTGGCCCCTAATTTACGATTCTACTTACTATTTGATA
1 CAATTTGGTCCCTAATTTAGGATTCTATTTACTATTTGATA
* * * * *
45901 CAATTTAGTCCCTGATTTAGGATTCTAATTACTGTTTGGCT-
1 CAATTTGGTCCCTAATTTAGGATTCTATTTACTATTT-GATA
45942 CAATTTGGTCC
1 CAATTTGGTCC
45953 TTATTTTCTT
Statistics
Matches: 117, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 115 0.98
42 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (41 bp):
CAATTTGGTCCCTAATTTAGGATTCTATTTACTATTTGATA
Found at i:67253 original size:19 final size:17
Alignment explanation
Indices: 67216--67255 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
67206 CTTTAAAATT
*
67216 TGAAAAACTTTGATGGA
1 TGAAAAACTTTGATAGA
67233 TGAAAAACTTGATGATAGA
1 TGAAAAACTT--TGATAGA
67252 TGAA
1 TGAA
67256 TATAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
19 10 0.50
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28
Consensus pattern (17 bp):
TGAAAAACTTTGATAGA
Done.