Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021227.1 Corchorus olitorius cultivar O-4 contig21260, 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: 90364
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:567 original size:21 final size:21
Alignment explanation
Indices: 541--583 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
531 AATTTACGTG
*
541 TTCTTACACGATTGGAATGAC
1 TTCTTACACGATTGAAATGAC
*
562 TTCTTACACGGTTGAAATGAC
1 TTCTTACACGATTGAAATGAC
583 T
1 T
584 AGCAATGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (21 bp):
TTCTTACACGATTGAAATGAC
Found at i:780 original size:39 final size:39
Alignment explanation
Indices: 726--805 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
716 TACACAACCA
* * *
726 AAAAAATTGACTAGAATTTTGTCCCATATGACCAAATTG
1 AAAAAATCGACTAGAATTTTATCCCACATGACCAAATTG
765 AAAAAATCGACTAGAATTTTATCCCACATGACCAAATTG
1 AAAAAATCGACTAGAATTTTATCCCACATGACCAAATTG
804 AA
1 AA
806 TTGTTAGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (39 bp):
AAAAAATCGACTAGAATTTTATCCCACATGACCAAATTG
Found at i:6442 original size:14 final size:15
Alignment explanation
Indices: 6423--6451 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6413 ATGATGATGC
6423 CTTTTT-CTTTTTTT
1 CTTTTTCCTTTTTTT
6437 CTTTTTCCTTTTTTT
1 CTTTTTCCTTTTTTT
6452 AAGATACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTCCTTTTTTT
Found at i:10149 original size:20 final size:20
Alignment explanation
Indices: 10124--10163 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
10114 TTATTTTTTA
**
10124 AAAATAAATTTCAATAAAAT
1 AAAATAAATTAAAATAAAAT
*
10144 AAAATATATTAAAATAAAAT
1 AAAATAAATTAAAATAAAAT
10164 TATTTAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAATTAAAATAAAAT
Found at i:10156 original size:15 final size:14
Alignment explanation
Indices: 10124--10167 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
10114 TTATTTTTTA
* *
10124 AAAATAAATTTCAAT
1 AAAATAAAATT-ATT
10139 AAAATAAAATATATT
1 AAAATAAAAT-TATT
10154 AAAATAAAATTATT
1 AAAATAAAATTATT
10168 TAATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 21 0.81
16 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAAAATTATT
Found at i:10170 original size:15 final size:15
Alignment explanation
Indices: 10138--10167 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10128 TAAATTTCAA
10138 TAAAATAAAATATAT
1 TAAAATAAAATATAT
10153 TAAAATAAAAT-TAT
1 TAAAATAAAATATAT
10167 T
1 T
10168 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:14503 original size:31 final size:31
Alignment explanation
Indices: 14468--14633 Score: 197
Period size: 31 Copynumber: 5.4 Consensus size: 31
14458 TTTGTGCACT
**
14468 TGGCATGCCACATGTCACTTTTTGAAACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* **
14499 TGGCATGTCACATGTCACTTTTTGAAACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
**
14530 TGGCATGCCATGTGTCACTTTTTGGTACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* * ** *
14561 TGACGTGATACGTGTCACTTTTTGGTACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
** *
14592 TGGTGTGCCACATGTCACTTTTTGGTACACG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
14623 TGGCATGCCAC
1 TGGCATGCCAC
14634 GTCGGACATC
Statistics
Matches: 116, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 116 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (31 bp):
TGGCATGCCACATGTCACTTTTTGGTACACA
Found at i:19721 original size:20 final size:20
Alignment explanation
Indices: 19696--19737 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
19686 CTCTATTCCC
19696 AAATCCACAAACCCTAGAAA
1 AAATCCACAAACCCTAGAAA
19716 AAATCCACAAACCCTAGAAA
1 AAATCCACAAACCCTAGAAA
19736 AA
1 AA
19738 GTGAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.29, G:0.05, T:0.10
Consensus pattern (20 bp):
AAATCCACAAACCCTAGAAA
Found at i:20089 original size:14 final size:14
Alignment explanation
Indices: 20070--20103 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20060 CTCCACCTAA
* *
20070 TTTTTTGTGTATTC
1 TTTTTTGAGAATTC
20084 TTTTTTGAGAATTC
1 TTTTTTGAGAATTC
20098 TTTTTT
1 TTTTTT
20104 TTTCTTCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.71
Consensus pattern (14 bp):
TTTTTTGAGAATTC
Found at i:20994 original size:21 final size:21
Alignment explanation
Indices: 20968--21010 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
20958 TCCATCTGGC
20968 ATGTAATTTTTGCATTTGTAA
1 ATGTAATTTTTGCATTTGTAA
20989 ATGTAATTTTTGCATTTGTAA
1 ATGTAATTTTTGCATTTGTAA
21010 A
1 A
21011 ACAAACTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (21 bp):
ATGTAATTTTTGCATTTGTAA
Found at i:21181 original size:11 final size:11
Alignment explanation
Indices: 21161--21210 Score: 61
Period size: 10 Copynumber: 4.6 Consensus size: 11
21151 CAACCCAACT
21161 AGAA-AAAAAA
1 AGAAGAAAAAA
21171 AGAAG-AAAAA
1 AGAAGAAAAAA
21181 AGAA-AAGAAAA
1 AGAAGAA-AAAA
21192 AGAAAGAAAAAA
1 AG-AAGAAAAAA
21204 AGAAGAA
1 AGAAGAA
21211 GACCCAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 14 0.40
11 11 0.31
12 8 0.23
13 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAGAAAAAA
Found at i:21186 original size:15 final size:15
Alignment explanation
Indices: 21163--21207 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
21153 ACCCAACTAG
21163 AAAAA-AAAAGAAGA
1 AAAAAGAAAAGAAGA
21177 AAAAAGAAAAGAA-A
1 AAAAAGAAAAGAAGA
*
21191 AAGAAAGAAAAAAAGA
1 AA-AAAGAAAAGAAGA
21207 A
1 A
21208 GAAGACCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 8 0.30
15 17 0.63
16 2 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAGA
Found at i:21194 original size:18 final size:18
Alignment explanation
Indices: 21161--21212 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
21151 CAACCCAACT
*
21161 AGAAAAAAA-AAGAAGAA
1 AGAAAAAAAGAAAAAGAA
21178 A-AAAGAAAAGAAAAAGAA
1 AGAAA-AAAAGAAAAAGAA
*
21196 AGAAAAAAAGAAGAAGA
1 AGAAAAAAAGAAAAAGA
21213 CCCAACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.10
17 5 0.17
18 19 0.63
19 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAGAAAAAGAA
Found at i:23390 original size:42 final size:43
Alignment explanation
Indices: 23338--23431 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
23328 AGTGCATTAC
* *
23338 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
23379 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
23424 CTAATATT
1 CTAATATT
23432 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:23833 original size:54 final size:54
Alignment explanation
Indices: 23770--23885 Score: 196
Period size: 54 Copynumber: 2.1 Consensus size: 54
23760 TTGTGCATTA
* * * *
23770 ATAGTTCAATTGCTTCAATTACATAACCTTTTACATGCAATTATATCTGCATCT
1 ATAGCTCAATTGCTTCAATTACAAAACCTTTTACAAGCAATTATATATGCATCT
23824 ATAGCTCAATTGCTTCAATTACAAAACCTTTTACAAGCAATTATATATGCATCT
1 ATAGCTCAATTGCTTCAATTACAAAACCTTTTACAAGCAATTATATATGCATCT
23878 ATAGCTCA
1 ATAGCTCA
23886 CATGCATACA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (54 bp):
ATAGCTCAATTGCTTCAATTACAAAACCTTTTACAAGCAATTATATATGCATCT
Found at i:27373 original size:16 final size:16
Alignment explanation
Indices: 27324--27367 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
27314 AGAAAAAAAC
27324 TTTTGGGGTTTCAATT
1 TTTTGGGGTTTCAATT
*
27340 TTTTAGGGTTTCAATT
1 TTTTGGGGTTTCAATT
27356 TTTTGGGGTTTC
1 TTTTGGGGTTTC
27368 GTTTTTCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.11, C:0.07, G:0.25, T:0.57
Consensus pattern (16 bp):
TTTTGGGGTTTCAATT
Found at i:28766 original size:77 final size:77
Alignment explanation
Indices: 28639--28793 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 77
28629 AATATATCTA
*
28639 TAACAATATATAATAAGAGAAATAAAAGTGCCAAAAAACCAGTTGAAAAACCTCACCACATTCAC
1 TAACAATATATAATAAGAGAAATAAAAGTACCAAAAAACCAGTTGAAAAACCTCACCACATTCAC
*
28704 CTAAGAACAAAT
66 CCAAGAACAAAT
* * *
28716 TAACAATATATAATAAGATAAATAAAAGTACCAAAAAACCAGTTGGAAAACCTCACCATATTCAC
1 TAACAATATATAATAAGAGAAATAAAAGTACCAAAAAACCAGTTGAAAAACCTCACCACATTCAC
28781 CCAAGAACAAAT
66 CCAAGAACAAAT
28793 T
1 T
28794 GTCAGGGGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.19
Consensus pattern (77 bp):
TAACAATATATAATAAGAGAAATAAAAGTACCAAAAAACCAGTTGAAAAACCTCACCACATTCAC
CCAAGAACAAAT
Found at i:29754 original size:438 final size:437
Alignment explanation
Indices: 28919--29765 Score: 1107
Period size: 438 Copynumber: 1.9 Consensus size: 437
28909 ACAAATCATG
* * * *
28919 TTTTTGCTGGATTATTTATCAAATGACCCCTATACTTTTATAATTTATGATATTTAGTTCCTCAC
1 TTTTTGCCGAATTATTTATAAAATGACCCCTATACTTTTATAATTTATGATATTTAGATCCTCAC
* * * *
28984 AAATTCTGGGTTGGACGATTGAACGTTTCAGCTTTAATTCTTTTATCTTTTGTTTTGTTTGTCCG
66 AAATTATGGGTTGGACGATTGAACGTTTCA-CTTTAATTCTTGTATCTTTTGTTCTATTTGTCCG
* *
29049 ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAACTTAATGATCTACAACTTTCATGAAGGATTCA
130 ATCAAGGTGATTCAAGTGTCTATTAAAAGGTAACTTAATGATCTACAACTTTCATGAAGGACTCA
** *
29114 AAAGCCAATTTTAATGTTTTGATTCAAAAAAATGCTTCTGAATTTTGTGGTCTCGATTGCCGGTC
195 AAAGCCAATTTTAATGTTTCAATTCAAAAAAATGCTTCTGAATTTCGTGGTCTCGATTGCCGGTC
* * * *
29179 TATTTAATATCATATAAATTTTGGTCCACTTGTCCAATTGAGGTTGTTCAAGTGTCGGTTAAAAG
260 TATTTAATATCATATAAATATCGGTCCACTTGTCCAATTGAAGTTATTCAAGTGTCGGTTAAAAG
* * * * * *
29244 GTTATTGTGTGATCTACGACTTTCGTCAAGGGTCTGAAAGCTGAATTTGATTAATGAGTTTCGTG
325 GTTAATGTGTGATCTACGACTTTCATCAAGGGCCTGAAAGCTGAACTTGATTAATGAGATTCATG
*
29309 GAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAACAATTTTT
390 AAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAACAATTTTT
* * * *
29357 TTTTTGCCGAATTATTTATAAAATGA-TCCTCATACTTTTATAGTTTATGCTATTTA-ATCCTTT
1 TTTTTGCCGAATTATTTATAAAATGACCCCT-ATACTTTTATAATTTATGATATTTAGATCC-TC
* * *
29420 AC-AATTATGGGTTGGACGATTTAACGCTTTGC-CTTTTACTT-TTGTATTTTTTGTTCTATTTG
64 ACAAATTATGGGTTGGACGATTGAACG-TTT-CAC-TTTAATTCTTGTATCTTTTGTTCTATTTG
*
29482 TCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAACTTCATGAT-TCACAACTTTCATGAAGG
126 TCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAACTTAATGATCT-ACAACTTTCATGAAGG
* * * * * * *
29546 ACTCTGATAG-CAATTTTATTGTTTCAATTCTAAAAAATGCTTTTGAAATTTCGTGGTTTTGATT
190 ACTC-AAAAGCCAATTTTAATGTTTCAATTCAAAAAAATGCTTCTG-AATTTCGTGGTCTCGATT
* ** * *
29610 GTCGGTCTATTTAATATTGTAT-AATAATCGGTCCACTTGTCCGATTGAAGTTATTCAAGTGTTG
253 GCCGGTCTATTTAATATCATATAAAT-ATCGGTCCACTTGTCCAATTGAAGTTATTCAAGTGTCG
* * * *
29674 GTTAAAATGTTAATGTGTGATCTACGACTTTCATCAAGGGCCTGAATGTTGAACTTGATTCATGA
317 GTTAAAAGGTTAATGTGTGATCTACGACTTTCATCAAGGGCCTGAAAGCTGAACTTGATTAATGA
*
29739 GATTCATGAAGGGTTCAAGAGGTAATT
382 GATTCATGAAGGGTTCAAGAGGGAATT
29766 ACTTTTGAAA
Statistics
Matches: 351, Mismatches: 49, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
436 1 0.00
437 142 0.40
438 207 0.59
439 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (437 bp):
TTTTTGCCGAATTATTTATAAAATGACCCCTATACTTTTATAATTTATGATATTTAGATCCTCAC
AAATTATGGGTTGGACGATTGAACGTTTCACTTTAATTCTTGTATCTTTTGTTCTATTTGTCCGA
TCAAGGTGATTCAAGTGTCTATTAAAAGGTAACTTAATGATCTACAACTTTCATGAAGGACTCAA
AAGCCAATTTTAATGTTTCAATTCAAAAAAATGCTTCTGAATTTCGTGGTCTCGATTGCCGGTCT
ATTTAATATCATATAAATATCGGTCCACTTGTCCAATTGAAGTTATTCAAGTGTCGGTTAAAAGG
TTAATGTGTGATCTACGACTTTCATCAAGGGCCTGAAAGCTGAACTTGATTAATGAGATTCATGA
AGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAACAATTTTT
Found at i:30923 original size:59 final size:56
Alignment explanation
Indices: 30802--30932 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 56
30792 CATGGCGGAT
* *
30802 CCGAAAGCTAAATTTG-GATTTTAGCTAAATTTGATCTACAATTTTAATGAAGGAC
1 CCGAAAGCTAAATTTGAGATTATAGCTAAATTTGACCTACAATTTTAATGAAGGAC
* * **
30857 CTGAAAGCTAAATTTGAG-TTATAGCTAAATTTGTTTGACCTACAATTTTCATGTTGGAC
1 CCGAAAGCTAAATTTGAGATTATAGCTAAA----TTTGACCTACAATTTTAATGAAGGAC
30916 CCGAAAGCTAAATTTGA
1 CCGAAAGCTAAATTTGA
30933 CCTGCAAATC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
55 25 0.39
56 1 0.02
59 38 0.59
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (56 bp):
CCGAAAGCTAAATTTGAGATTATAGCTAAATTTGACCTACAATTTTAATGAAGGAC
Found at i:31708 original size:53 final size:53
Alignment explanation
Indices: 31651--31762 Score: 197
Period size: 53 Copynumber: 2.1 Consensus size: 53
31641 AATAGAATTA
*
31651 TTCAATAGTTCATTACATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGG
1 TTCAATAGTTCACTACATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGG
* *
31704 TTCAATAGTTCACTGCATTTTGTATTATTTGGTATGTGTGTTTATTTAATAGG
1 TTCAATAGTTCACTACATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGG
31757 TTCAAT
1 TTCAAT
31763 TGAATAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (53 bp):
TTCAATAGTTCACTACATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGG
Found at i:32125 original size:30 final size:30
Alignment explanation
Indices: 32089--32149 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
32079 ATTTTTTTTC
* *
32089 CTTTGATTACCTTTAATTAGTTTTAATCAT
1 CTTTGATTACCTTTAATCAGTTTCAATCAT
32119 CTTTGATTACCTTTAATCAGTTTCAATCAT
1 CTTTGATTACCTTTAATCAGTTTCAATCAT
32149 C
1 C
32150 AATGGCCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (30 bp):
CTTTGATTACCTTTAATCAGTTTCAATCAT
Found at i:32127 original size:20 final size:20
Alignment explanation
Indices: 32099--32137 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
32089 CTTTGATTAC
**
32099 CTTTAATTAGTTTTAATCAT
1 CTTTAATTACCTTTAATCAT
*
32119 CTTTGATTACCTTTAATCA
1 CTTTAATTACCTTTAATCA
32138 GTTTCAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (20 bp):
CTTTAATTACCTTTAATCAT
Found at i:40767 original size:27 final size:27
Alignment explanation
Indices: 40729--40782 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
40719 GTAAGGGTCG
40729 ATCCCACAGGGAGGGAATAACTAAAAA
1 ATCCCACAGGGAGGGAATAACTAAAAA
40756 ATCCCACAGGGAGGGAATAACTAAAAA
1 ATCCCACAGGGAGGGAATAACTAAAAA
40783 TCACTTTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (27 bp):
ATCCCACAGGGAGGGAATAACTAAAAA
Found at i:42309 original size:21 final size:21
Alignment explanation
Indices: 42275--42315 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42265 CCCACATGGA
* *
42275 TTGCCTGAAGACCCATGTGGT
1 TTGCCTGAACACCCAGGTGGT
*
42296 TTGCCTGATCACCCAGGTGG
1 TTGCCTGAACACCCAGGTGG
42316 GCTGTGTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (21 bp):
TTGCCTGAACACCCAGGTGGT
Found at i:43821 original size:17 final size:17
Alignment explanation
Indices: 43801--43859 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
43791 ATTGAAATGG
43801 ATCAAGTTTTCAAAGTT
1 ATCAAGTTTTCAAAGTT
* ***
43818 ATCAAATTGGGAAAGTT
1 ATCAAGTTTTCAAAGTT
43835 CCCATCAAGTTTTCAAAGTT
1 ---ATCAAGTTTTCAAAGTT
43855 ATCAA
1 ATCAA
43860 ATTGGGAAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 18 0.58
20 13 0.42
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (17 bp):
ATCAAGTTTTCAAAGTT
Found at i:43842 original size:37 final size:37
Alignment explanation
Indices: 43801--43925 Score: 196
Period size: 37 Copynumber: 3.3 Consensus size: 37
43791 ATTGAAATGG
43801 ATCAAGTTTTCAAAGTTATCAAATTGGGAAAGTTCCC
1 ATCAAGTTTTCAAAGTTATCAAATTGGGAAAGTTCCC
43838 ATCAAGTTTTCAAAGTTATCAAATTGGGAAAGTTCCC
1 ATCAAGTTTTCAAAGTTATCAAATTGGGAAAGTTCCC
* *
43875 ATCAAGTTTTTTTCAAAAATTTTCAAATTGGGAAAGTTCCC
1 ATCAAG---TTTTC-AAAGTTATCAAATTGGGAAAGTTCCC
43916 ATCAAGTTTT
1 ATCAAGTTTT
43926 AGTTTTTAAT
Statistics
Matches: 82, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
37 43 0.52
38 4 0.05
40 5 0.06
41 30 0.37
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (37 bp):
ATCAAGTTTTCAAAGTTATCAAATTGGGAAAGTTCCC
Found at i:43852 original size:20 final size:20
Alignment explanation
Indices: 43829--43884 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 20
43819 TCAAATTGGG
43829 AAAGTTCCCATCAAGTTTTC
1 AAAGTTCCCATCAAGTTTTC
* ***
43849 AAAGTT---ATCAAATTGGG
1 AAAGTTCCCATCAAGTTTTC
43866 AAAGTTCCCATCAAGTTTT
1 AAAGTTCCCATCAAGTTTT
43885 TTTCAAAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 6
0.67 0.18 0.15
Matches are distributed among these distances:
17 13 0.50
20 13 0.50
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
AAAGTTCCCATCAAGTTTTC
Found at i:43869 original size:17 final size:17
Alignment explanation
Indices: 43812--43871 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
43802 TCAAGTTTTC
43812 AAAGTTATCAAATTGGG
1 AAAGTTATCAAATTGGG
* ***
43829 AAAGTTCCCATCAAGTTTTC
1 AAAGTT---ATCAAATTGGG
43849 AAAGTTATCAAATTGGG
1 AAAGTTATCAAATTGGG
43866 AAAGTT
1 AAAGTT
43872 CCCATCAAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 19 0.59
20 13 0.41
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (17 bp):
AAAGTTATCAAATTGGG
Found at i:43937 original size:41 final size:40
Alignment explanation
Indices: 43819--43925 Score: 157
Period size: 41 Copynumber: 2.7 Consensus size: 40
43809 TTCAAAGTTA
* * *
43819 TCAAATTGGGAAAGTTCCCATCAAG---TTTTCAAAGTTA
1 TCAAATTGGGAAAGTTCCCATCAAGTTTTTTTAAAAATTT
43856 TCAAATTGGGAAAGTTCCCATCAAGTTTTTTTCAAAAATTT
1 TCAAATTGGGAAAGTTCCCATCAAGTTTTTTT-AAAAATTT
43897 TCAAATTGGGAAAGTTCCCATCAAGTTTT
1 TCAAATTGGGAAAGTTCCCATCAAGTTTT
43926 AGTTTTTAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
37 25 0.40
40 4 0.06
41 34 0.54
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (40 bp):
TCAAATTGGGAAAGTTCCCATCAAGTTTTTTTAAAAATTT
Found at i:44186 original size:19 final size:19
Alignment explanation
Indices: 44162--44199 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
44152 GTTTATTTGC
*
44162 TTTCAACTCCCATCATTCA
1 TTTCAACTCCCAACATTCA
44181 TTTCAACTCCCAACATTCA
1 TTTCAACTCCCAACATTCA
44200 AAAATACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (19 bp):
TTTCAACTCCCAACATTCA
Found at i:46064 original size:30 final size:30
Alignment explanation
Indices: 46030--46123 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
46020 CTTCACTATC
*
46030 TTCTACCACCTCTTCCTCGTCCTCTCAAAT
1 TTCTACCACCTCTTCCTTGTCCTCTCAAAT
*
46060 TTCTACCACCTCTTCCTTGCCCTCTCAAAT
1 TTCTACCACCTCTTCCTTGTCCTCTCAAAT
* *
46090 TTCTACCACCTCTTCCTTGTCCTTTCAAAA
1 TTCTACCACCTCTTCCTTGTCCTCTCAAAT
46120 TTCT
1 TTCT
46124 GGACTTCCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.17, C:0.40, G:0.03, T:0.39
Consensus pattern (30 bp):
TTCTACCACCTCTTCCTTGTCCTCTCAAAT
Found at i:52777 original size:14 final size:14
Alignment explanation
Indices: 52758--52785 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52748 ATAATTTAAA
52758 ATAACTTAGAAGAT
1 ATAACTTAGAAGAT
52772 ATAACTTAGAAGAT
1 ATAACTTAGAAGAT
52786 TGTTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
ATAACTTAGAAGAT
Found at i:63978 original size:23 final size:23
Alignment explanation
Indices: 63944--63987 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
63934 GACAATTTCA
*
63944 GGAAGCAAGCCAATTTCAACAAG
1 GGAAGCAAGCCAATTCCAACAAG
*
63967 GGAAGCATGCCAATTCCAACA
1 GGAAGCAAGCCAATTCCAACA
63988 TTGGACCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (23 bp):
GGAAGCAAGCCAATTCCAACAAG
Found at i:64347 original size:8 final size:8
Alignment explanation
Indices: 64334--64360 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
64324 GTTAAAGTAT
64334 GTTTAATG
1 GTTTAATG
64342 GTTTAATG
1 GTTTAATG
64350 GTTTAATG
1 GTTTAATG
64358 GTT
1 GTT
64361 CGAGTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (8 bp):
GTTTAATG
Found at i:68001 original size:18 final size:18
Alignment explanation
Indices: 67978--68012 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
67968 CCAAAAACAG
*
67978 AAACAGAAACTTATAAAA
1 AAACAGAAACTCATAAAA
67996 AAACAGAAACTCATAAA
1 AAACAGAAACTCATAAA
68013 CTTGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.06, T:0.14
Consensus pattern (18 bp):
AAACAGAAACTCATAAAA
Found at i:68021 original size:24 final size:24
Alignment explanation
Indices: 67994--68052 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
67984 AAACTTATAA
67994 AAAAACAGAAACTCATAAACTTGT
1 AAAAACAGAAACTCATAAACTTGT
*
68018 AAAAACAGAAACTTATAAACTTGT
1 AAAAACAGAAACTCATAAACTTGT
68042 AAAAACAGAAA
1 AAAAACAGAAA
68053 GTTTGAGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.59, C:0.14, G:0.08, T:0.19
Consensus pattern (24 bp):
AAAAACAGAAACTCATAAACTTGT
Found at i:69085 original size:15 final size:15
Alignment explanation
Indices: 69065--69155 Score: 92
Period size: 15 Copynumber: 6.1 Consensus size: 15
69055 TAGGCTGAGA
*
69065 TGCATTAGAAGGCCC
1 TGCATTAGATGGCCC
69080 TGCATTAGATGGCCC
1 TGCATTAGATGGCCC
*
69095 TGCATGAGATGGCCC
1 TGCATTAGATGGCCC
* **
69110 CGCAGCAGATGGCCC
1 TGCATTAGATGGCCC
**
69125 TGCACGAGATGGCCC
1 TGCATTAGATGGCCC
* **
69140 CGCAGCAGATGGCCC
1 TGCATTAGATGGCCC
69155 T
1 T
69156 ACCCCAACAG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 64 1.00
ACGTcount: A:0.21, C:0.32, G:0.31, T:0.16
Consensus pattern (15 bp):
TGCATTAGATGGCCC
Found at i:69109 original size:30 final size:30
Alignment explanation
Indices: 69086--69155 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
69076 GCCCTGCATT
69086 AGATGGCCCTGCATGAGATGGCCCCGCAGC
1 AGATGGCCCTGCATGAGATGGCCCCGCAGC
*
69116 AGATGGCCCTGCACGAGATGGCCCCGCAGC
1 AGATGGCCCTGCATGAGATGGCCCCGCAGC
69146 AGATGGCCCT
1 AGATGGCCCT
69156 ACCCCAACAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.20, C:0.34, G:0.33, T:0.13
Consensus pattern (30 bp):
AGATGGCCCTGCATGAGATGGCCCCGCAGC
Found at i:69375 original size:24 final size:24
Alignment explanation
Indices: 69347--69400 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
69337 CATTTGGCAA
* *
69347 ATTCTCCCCCTCTTCCAAAGGCCC
1 ATTCTCCCCATCTTCCAAAGGACC
*
69371 ATTCTCCCCATCTTCTAAAGGACC
1 ATTCTCCCCATCTTCCAAAGGACC
69395 ATTCTC
1 ATTCTC
69401 AATGAGTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.07, T:0.30
Consensus pattern (24 bp):
ATTCTCCCCATCTTCCAAAGGACC
Found at i:81180 original size:31 final size:28
Alignment explanation
Indices: 81145--81207 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 28
81135 CTTAATACCT
81145 AAATTAG-CCCTTTAACTATTCATTTTGGGAC
1 AAATTAGCCCCTTT-ACT-TT--TTTTGGGAC
*
81176 AAATTGGCCCCTTTACTTTTTTTGGGAC
1 AAATTAGCCCCTTTACTTTTTTTGGGAC
81204 AAAT
1 AAAT
81208 AAATCCCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 13 0.43
30 2 0.07
31 9 0.30
32 6 0.20
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (28 bp):
AAATTAGCCCCTTTACTTTTTTTGGGAC
Found at i:84015 original size:22 final size:22
Alignment explanation
Indices: 83986--84066 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
83976 TGAATATTTT
83986 TATAAAATTTTGATAATTACCC
1 TATAAAATTTTGATAATTACCC
* ** *
84008 TATTAAATTTTGATAACCACCA
1 TATAAAATTTTGATAATTACCC
84030 TATAAAATTTTGATAATTA-CC
1 TATAAAATTTTGATAATTACCC
*
84051 TATAAAATTGTGATAA
1 TATAAAATTTTGATAA
84067 ACTCCATATG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 16 0.32
22 34 0.68
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (22 bp):
TATAAAATTTTGATAATTACCC
Found at i:84074 original size:43 final size:44
Alignment explanation
Indices: 83986--84088 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 44
83976 TGAATATTTT
* * *
83986 TATAAAATTTTGATAATTACCCTATTAAATTTTGATAACCACCA
1 TATAAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCA
*
84030 TATAAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCCA
1 TATAAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCA
* *
84073 TATGAAACTTTGATAA
1 TATAAAATTTTGATAA
84089 CCTAACTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 34 0.64
44 19 0.36
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.38
Consensus pattern (44 bp):
TATAAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCA
Found at i:84103 original size:65 final size:64
Alignment explanation
Indices: 83986--84110 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 64
83976 TGAATATTTT
* * * * *
83986 TATAAAATTTTGATAATTACCCTATTAAATTTTGATAACCACCATATAAAATTTTGATAATTACC
1 TATAAAATTGTGATAA-TACCCTATGAAACTTTGATAACCAACATATAAAATTTTAATAATTACC
*
84051 TATAAAATTGTGATAA-ACTCCATATGAAACTTTGATAACCTAAC-TATGAAATTTTAATAA
1 TATAAAATTGTGATAATAC-CC-TATGAAACTTTGATAACC-AACATATAAAATTTTAATAA
84111 ATTTTCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
63 2 0.04
64 2 0.04
65 45 0.88
66 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (64 bp):
TATAAAATTGTGATAATACCCTATGAAACTTTGATAACCAACATATAAAATTTTAATAATTACC
Found at i:86294 original size:22 final size:21
Alignment explanation
Indices: 86269--86328 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
86259 ATTATTTTTA
86269 AATATATAAATATATACTATGT
1 AATATATAAATATATACT-TGT
*
86291 AATATATAACATATATAGTTGT
1 AATATATAA-ATATATACTTGT
*
86313 ATTATATAAATTATAT
1 AATATATAAA-TATAT
86329 TTATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 25 0.74
23 8 0.24
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (21 bp):
AATATATAAATATATACTTGT
Found at i:89325 original size:23 final size:23
Alignment explanation
Indices: 89277--89325 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
89267 TTATGAATCG
**
89277 AAAAAAATTGAGATTTGTTTCAC
1 AAAAAAATTGAGATTTGTGACAC
*
89300 AAAAAAATTTGAGATTTG-GACTC
1 AAAAAAA-TTGAGATTTGTGACAC
89323 AAA
1 AAA
89326 TCGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (23 bp):
AAAAAAATTGAGATTTGTGACAC
Done.