Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006774.1 Corchorus capsularis cultivar CVL-1 contig06795, 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: 134285
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:308 original size:2 final size:2
Alignment explanation
Indices: 301--326 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
291 ATTTATTTAC
301 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
327 GATTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8746 original size:12 final size:12
Alignment explanation
Indices: 8731--8755 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8721 CAATCCAAGG
8731 CCAACCCCAACA
1 CCAACCCCAACA
8743 CCAACCCCAACA
1 CCAACCCCAACA
8755 C
1 C
8756 TTAAAGCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (12 bp):
CCAACCCCAACA
Found at i:10475 original size:22 final size:23
Alignment explanation
Indices: 10447--10496 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
10437 TTTTTTGTTA
*
10447 ATTTTTTTTAA-TGTTTCACTGG
1 ATTTTTTTTAAGAGTTTCACTGG
10469 ATTTTTTTTAAGGAGTTTCACTGG
1 ATTTTTTTTAA-GAGTTTCACTGG
10493 ATTT
1 ATTT
10497 CTATATGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.44
24 14 0.56
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (23 bp):
ATTTTTTTTAAGAGTTTCACTGG
Found at i:10873 original size:28 final size:30
Alignment explanation
Indices: 10826--10888 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
10816 AAAATACCAA
10826 AAAACTTTTTTTGAGACATAT-AAAACCCT
1 AAAACTTTTTTTGAGACATATAAAAACCCT
**
10855 AAAACTTTTTTTTTG-CATATAAAAACCCT
1 AAAACTTTTTTTGAGACATATAAAAACCCT
10884 AAAAC
1 AAAAC
10889 CTAATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAACTTTTTTTGAGACATATAAAAACCCT
Found at i:12511 original size:28 final size:28
Alignment explanation
Indices: 12476--12530 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
12466 ACGTCAAATT
* *
12476 AAGAGACTAGAATAAATATTTACTCAAA
1 AAGAGACTAGAATAAATAATTAATCAAA
12504 AAGAGACTAGAATAAATAATTAATCAA
1 AAGAGACTAGAATAAATAATTAATCAA
12531 GAAAAAGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (28 bp):
AAGAGACTAGAATAAATAATTAATCAAA
Found at i:14636 original size:2 final size:2
Alignment explanation
Indices: 14624--14687 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
14614 TCTTCCCTTC
*
14624 CT CT AT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
14666 CT CT CT CT AT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
14688 ATCACCCTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29309 original size:34 final size:36
Alignment explanation
Indices: 29266--29339 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 36
29256 ACAAATGTAA
29266 TTGTTTTTATTAGTAAA-ACTTT-TTTGTAGACTCT
1 TTGTTTTTATTAGTAAACACTTTATTTGTAGACTCT
*
29300 TTGTTTTTATTAGTAAACCTCTTTAATTTGTAGACTCT
1 TTGTTTTTATTAGTAAA-CACTTT-ATTTGTAGACTCT
29338 TT
1 TT
29340 ATTTGTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 17 0.49
36 4 0.11
38 14 0.40
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (36 bp):
TTGTTTTTATTAGTAAACACTTTATTTGTAGACTCT
Found at i:29774 original size:21 final size:21
Alignment explanation
Indices: 29748--29787 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29738 ACTCTTTGTT
29748 TTTATTAGTAAACCTCTTTAA
1 TTTATTAGTAAACCTCTTTAA
*
29769 TTTATTAGTAAATCTCTTT
1 TTTATTAGTAAACCTCTTT
29788 TGCAGACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTATTAGTAAACCTCTTTAA
Found at i:29780 original size:55 final size:55
Alignment explanation
Indices: 29714--29826 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
29704 TGTAATTGTT
29714 TTTATTAGTAAATCTCTTTTGCAGACTCTTTGTTTTTATTAGTAAACCTCTTTAA
1 TTTATTAGTAAATCTCTTTTGCAGACTCTTTGTTTTTATTAGTAAACCTCTTTAA
29769 TTTATTAGTAAATCTCTTTTGCAGACTCTTTGTTTTTATTAGTAAACCTCTTTAA
1 TTTATTAGTAAATCTCTTTTGCAGACTCTTTGTTTTTATTAGTAAACCTCTTTAA
29824 TTT
1 TTT
29827 GTAGACTCTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (55 bp):
TTTATTAGTAAATCTCTTTTGCAGACTCTTTGTTTTTATTAGTAAACCTCTTTAA
Found at i:32292 original size:22 final size:19
Alignment explanation
Indices: 32263--32315 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
32253 ATTACTAAAT
*
32263 AAAT-AATAAATATATTTTA
1 AAATAAATAAATA-AGTTTA
32282 AATATTAAAT-AATAAGTTTA
1 AA-A-TAAATAAATAAGTTTA
32302 AAATAAATAAATAA
1 AAATAAATAAATAA
32316 TATATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 8 0.28
20 8 0.28
21 5 0.17
22 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAATAAATAAATAAGTTTA
Found at i:32941 original size:30 final size:31
Alignment explanation
Indices: 32905--32981 Score: 129
Period size: 30 Copynumber: 2.5 Consensus size: 31
32895 CTGTTGAGTT
*
32905 AACATAAGATTTGTATTTTCCT-AAAAATAA
1 AACATAAGATTTGTATTTTCCTAAAAAAAAA
32935 AACATAAGATTTGTATTTTCCTAAAAAAAAAA
1 AACATAAGATTTGTATTTTCCT-AAAAAAAAA
32967 AACATAAGATTTGTA
1 AACATAAGATTTGTA
32982 GTATATTAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 22 0.50
32 22 0.50
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (31 bp):
AACATAAGATTTGTATTTTCCTAAAAAAAAA
Found at i:38408 original size:29 final size:29
Alignment explanation
Indices: 38352--38409 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
38342 GACTATGAAT
** ** *
38352 TCTGCAAGATCTTTGTCCCCAAACAAAAA
1 TCTGCAAGATCTTTAACCAAAAAAAAAAA
38381 TCTGCAAGATCTTTAACCAAAAAAAAAAA
1 TCTGCAAGATCTTTAACCAAAAAAAAAAA
38410 AAATCTTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (29 bp):
TCTGCAAGATCTTTAACCAAAAAAAAAAA
Found at i:39154 original size:30 final size:30
Alignment explanation
Indices: 39116--39186 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
39106 ACGAAATTCA
* *
39116 ATTT-AGGATACACCGTTA-GCACTTGTGTT
1 ATTTCAGGATAAACCGTTACGCA-TTGTGTC
* *
39145 ATTTCAGGATAAAGCGTTATCGGATTGTGTC
1 ATTTCAGGATAAACCGTTA-CGCATTGTGTC
39176 ATTTCAGGATA
1 ATTTCAGGATA
39187 TGGACATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 12 0.34
31 17 0.49
32 2 0.06
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (30 bp):
ATTTCAGGATAAACCGTTACGCATTGTGTC
Found at i:41011 original size:18 final size:19
Alignment explanation
Indices: 40990--41034 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40980 CGGTTTTGGT
40990 TGTTGATAT-CAGTTTTGA
1 TGTTGATATGCAGTTTTGA
* *
41008 TGTTGATTTGCTGTTTTGA
1 TGTTGATATGCAGTTTTGA
41027 TGGTTGAT
1 T-GTTGAT
41035 TTGTGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.16, C:0.04, G:0.27, T:0.53
Consensus pattern (19 bp):
TGTTGATATGCAGTTTTGA
Found at i:41023 original size:19 final size:19
Alignment explanation
Indices: 41001--41047 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
40991 GTTGATATCA
41001 GTTTTGAT-GTTGATTTGCT
1 GTTTTGATGGTTGATTTG-T
41020 GTTTTGATGGTTGATTTGT
1 GTTTTGATGGTTGATTTGT
41039 GTTATTGAT
1 GTT-TTGAT
41048 AATTCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.13, C:0.02, G:0.28, T:0.57
Consensus pattern (19 bp):
GTTTTGATGGTTGATTTGT
Found at i:45322 original size:22 final size:22
Alignment explanation
Indices: 45281--45328 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
45271 TGTTTAACAT
*
45281 GTTTTGACTATGCAACTTTAGA
1 GTTTTGACTATGCAAATTTAGA
*
45303 GTTTTGACTAT-CAAAATTTAGG
1 GTTTTGACTATGC-AAATTTAGA
45325 GTTT
1 GTTT
45329 GACCATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (22 bp):
GTTTTGACTATGCAAATTTAGA
Found at i:45384 original size:21 final size:21
Alignment explanation
Indices: 45355--45409 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
45345 TAAAATGTTT
*
45355 TTTGTGGTTTGATTATCGA-CC
1 TTTGTGGTTTGACTATC-ATCC
*
45376 TTTGGGGTTTGACTATCATCC
1 TTTGTGGTTTGACTATCATCC
45397 TTTGTGGTTTGAC
1 TTTGTGGTTTGAC
45410 CATGCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.13, C:0.15, G:0.25, T:0.47
Consensus pattern (21 bp):
TTTGTGGTTTGACTATCATCC
Found at i:45782 original size:20 final size:21
Alignment explanation
Indices: 45736--45783 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
45726 ATAACATGGT
* *
45736 TTGACTATCAAACTTTGGGGG
1 TTGACTAACAAACTTTGGGGC
45757 TTGACTAACAAACTTT-GGGC
1 TTGACTAACAAACTTTGGGGC
45777 TTGACTA
1 TTGACTA
45784 TTTGATACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
TTGACTAACAAACTTTGGGGC
Found at i:46650 original size:33 final size:32
Alignment explanation
Indices: 46578--46685 Score: 119
Period size: 33 Copynumber: 3.3 Consensus size: 32
46568 AAAGGATCAT
* * *
46578 GTGGCCAGTTGTGACCGGGCATGGCCGAGTCAT
1 GTGGCCGGTTGTGGCCGGGCATGGCC-AGTCAC
46611 GTGGCCGGTTGTGGCCGGGCATGGCCATGTCAC
1 GTGGCCGGTTGTGGCCGGGCATGGCCA-GTCAC
** *
46644 GTGGCCGG-TGATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTTG-TGGCCGGGCATGGCC-AGTCAC
46677 GTGGCCGGT
1 GTGGCCGGT
46686 GTTGCGCAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
32 3 0.05
33 61 0.94
34 1 0.02
ACGTcount: A:0.11, C:0.27, G:0.42, T:0.20
Consensus pattern (32 bp):
GTGGCCGGTTGTGGCCGGGCATGGCCAGTCAC
Found at i:48105 original size:77 final size:77
Alignment explanation
Indices: 47946--48133 Score: 238
Period size: 77 Copynumber: 2.4 Consensus size: 77
47936 AAACTTTGGA
* * * *
47946 ATTTGACCATGCATGTATAGTGAAATGTTTTTTGTGGTTTGGCTATCAAATTTTGGGATTTCCTA
1 ATTTGACCATGCATGTATAGTGAAATGTTTTTTGTGATTTGACTATCAAAATTTGGGATTTACTA
48011 TCAAAATGTAGGG
66 T-AAAATGTAGGG
48024 -TTTGACCATGCATGTATAGTGAAATGTTTTTTGTGATTTGACTATCAAAATTTGGG-TTTGACT
1 ATTTGACCATGCATGTATAGTGAAATGTTTTTTGTGATTTGACTATCAAAATTTGGGATTT-ACT
* *
48087 AT-AATTTTATGGG
65 ATAAAATGTA-GGG
* * *
48100 ATTTGACCATGCATATACAATGAAATGATTTTTT
1 ATTTGACCATGCATGTATAGTGAAATG-TTTTTT
48134 TTTTTAGTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
75 5 0.05
76 6 0.06
77 80 0.82
78 6 0.06
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.43
Consensus pattern (77 bp):
ATTTGACCATGCATGTATAGTGAAATGTTTTTTGTGATTTGACTATCAAAATTTGGGATTTACTA
TAAAATGTAGGG
Found at i:48371 original size:21 final size:21
Alignment explanation
Indices: 48345--48394 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
48335 TGTTGTTTCC
48345 GGTTTGACTATCAA-ACTTTGG
1 GGTTTGACTATCAACA-TTTGG
*
48366 GGTTTGACTATCATCATTTGG
1 GGTTTGACTATCAACATTTGG
48387 GGTTTGAC
1 GGTTTGAC
48395 CATGCATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (21 bp):
GGTTTGACTATCAACATTTGG
Found at i:48540 original size:287 final size:285
Alignment explanation
Indices: 47995--48558 Score: 751
Period size: 287 Copynumber: 2.0 Consensus size: 285
47985 TGGCTATCAA
* * * * **
47995 ATTTTGGGATTTCCTATCAAAATGTAGGGTTTGACCATGCATGTATAGTGAAATGTTTTTTGTGA
1 ATTTTGGGATTTACTATCAAAATGTAGGGTTTGACCATGCATGTATAATAAAATGTTGTTTCCGA
* *
48060 TTTGACTATCAAAATTTGGGTTTGACTATAATTTTATGGGATTTGACCATGCATATACAATGAAA
66 TTTGACTATCAAAATTTGGGTTTGACTATAATATTATGGGATTTGACCATGCATATACAATAAAA
* * *
48125 TGATTTTTTTTTTTAGTTTTTGTGAAATTTGAGCCTCAAATGCAAACACATATCCAATAACATGC
131 TGATTTTTGTTATTA-TTTTTGTGAAATTTGAGCCTCAAATGCAAACACATATCCAATAACATAC
* * * *
48190 AGATCTATACTATCAAATGAGAAATCTAATATTATGACTTGATATGAGTTCAATGGGATAATAAG
195 AGATCCATACTATCAAATGAGAAATCTAACATTATGACTTGATACGAGTCCAATGGGATAATAAG
48255 TTTATAATGAAATTAATGTTCAACAT
260 TTTATAATGAAATTAATGTTCAACAT
* * *
48281 ATTTTGGGGTTTTACTATCAAAATTTATGGTTTGACCATGCATGTATAATAAAATGTTGTTTCCG
1 ATTTT-GGGATTTACTATCAAAATGTAGGGTTTGACCATGCATGTATAATAAAATGTTGTTTCCG
* * * * *
48346 GTTTGACTATCAAACTTTGGGGTTTGACTATCATCATT-TGGGGTTTGACCATGCATATGCAATA
65 ATTTGACTATCAAAATTT-GGGTTTGACTATAAT-ATTATGGGATTTGACCATGCATATACAATA
* * * *
48410 AAATGATTTTTGTTATT-TTTTTGTGATATTTGAGTCTCAATATGTAAACACATATCTAATAACA
128 AAATGATTTTTGTTATTATTTTTGTGAAATTTGAGCCTCAA-ATGCAAACACATATCCAATAACA
* * *
48474 TAC-GAATCCATACTGTCAAAT-ACGAAATCTAACAGTT-TGGCTTGATACGAGTCCAATGGTAT
192 TACAG-ATCCATACTATCAAATGA-GAAATCTAACA-TTATGACTTGATACGAGTCCAATGGGAT
48536 AATAAGTTTATAATGAAATTAAT
254 AATAAGTTTATAATGAAATTAAT
48559 ATTTAAAATA
Statistics
Matches: 241, Mismatches: 30, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
286 28 0.12
287 157 0.65
288 54 0.22
289 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (285 bp):
ATTTTGGGATTTACTATCAAAATGTAGGGTTTGACCATGCATGTATAATAAAATGTTGTTTCCGA
TTTGACTATCAAAATTTGGGTTTGACTATAATATTATGGGATTTGACCATGCATATACAATAAAA
TGATTTTTGTTATTATTTTTGTGAAATTTGAGCCTCAAATGCAAACACATATCCAATAACATACA
GATCCATACTATCAAATGAGAAATCTAACATTATGACTTGATACGAGTCCAATGGGATAATAAGT
TTATAATGAAATTAATGTTCAACAT
Found at i:51559 original size:17 final size:17
Alignment explanation
Indices: 51528--51571 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
51518 TTACAAAATA
51528 AATTTATTT-AGTGAGT
1 AATTTATTTAAGTGAGT
51544 AATTTATTTAAGTGAGT
1 AATTTATTTAAGTGAGT
51561 AATTTATTTAA
1 AATTTATTTAA
51572 AAGAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (17 bp):
AATTTATTTAAGTGAGT
Found at i:51673 original size:15 final size:15
Alignment explanation
Indices: 51653--51682 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51643 GATAGTTTAA
51653 TATTTTAAAAAAAAT
1 TATTTTAAAAAAAAT
*
51668 TATTTTAAAATAAAT
1 TATTTTAAAAAAAAT
51683 ACATATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTTTAAAAAAAAT
Found at i:70475 original size:21 final size:22
Alignment explanation
Indices: 70435--70475 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
70425 TTACTTCAAA
* *
70435 ACTTCATAACCTGCAAGACCAT
1 ACTTCATAAACTGAAAGACCAT
70457 ACTTCA-AAACTGAAAGACC
1 ACTTCATAAACTGAAAGACC
70476 TTCAGCTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (22 bp):
ACTTCATAAACTGAAAGACCAT
Found at i:78862 original size:15 final size:15
Alignment explanation
Indices: 78844--78893 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
78834 TAATTACTTT
78844 CTTTATAATCT-ATTG
1 CTTT-TAATCTGATTG
*
78859 CTTTTAATCTGTTTG
1 CTTTTAATCTGATTG
*
78874 CTTTTAATCTGTTTG
1 CTTTTAATCTGATTG
78889 CTTTT
1 CTTTT
78894 TTAGTTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
14 6 0.18
15 27 0.82
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.60
Consensus pattern (15 bp):
CTTTTAATCTGATTG
Found at i:78868 original size:14 final size:15
Alignment explanation
Indices: 78856--78893 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
78846 TTATAATCTA
78856 TTGCTTTTAATCTGT
1 TTGCTTTTAATCTGT
78871 TTGCTTTTAATCTGT
1 TTGCTTTTAATCTGT
78886 TTGCTTTT
1 TTGCTTTT
78894 TTAGTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.63
Consensus pattern (15 bp):
TTGCTTTTAATCTGT
Found at i:85916 original size:36 final size:36
Alignment explanation
Indices: 85876--85945 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
85866 TAATCGTACA
*
85876 AGTTTAAGTGACGATCAAGAAGTTCAAAAAGATCCG
1 AGTTTAAGTGACGATCAAGAAGCTCAAAAAGATCCG
* *
85912 AGTTTAAGTGATGGTCAAGAAGCTCAAAAAGATC
1 AGTTTAAGTGACGATCAAGAAGCTCAAAAAGATC
85946 GATATTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (36 bp):
AGTTTAAGTGACGATCAAGAAGCTCAAAAAGATCCG
Found at i:86094 original size:30 final size:32
Alignment explanation
Indices: 86035--86105 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
86025 ACAAAGTTTA
* * *
86035 TTTAACATGCATGATCTCTTCTTCTACCTTTC-
1 TTTATCATGCATAATCTC-TCTCCTACCTTTCT
86067 TTTATCATGCATAATCTC-CTCCTACCTTTCT
1 TTTATCATGCATAATCTCTCTCCTACCTTTCT
86098 TTTATCAT
1 TTTATCAT
86106 TAAAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 11 0.31
31 8 0.23
32 16 0.46
ACGTcount: A:0.20, C:0.28, G:0.04, T:0.48
Consensus pattern (32 bp):
TTTATCATGCATAATCTCTCTCCTACCTTTCT
Found at i:102540 original size:85 final size:85
Alignment explanation
Indices: 102392--102567 Score: 291
Period size: 85 Copynumber: 2.1 Consensus size: 85
102382 TGCTTCCACT
*
102392 TCTAC-TTTTACTTGGTATACAAACATTGGCATTAAAACACCCTTCCTTCAATGCGTCTATTATG
1 TCTACTTTTTACTTGGTATACAAACATTGGCATTAAAACACCCTTCCTTCAATGCATCTATTATG
102456 ATGCTATTAACAACATGTTC
66 ATGCTATTAACAACATGTTC
* * * *
102476 TCTACTTTTTACTTGGTTTACAAACATTGGTATTAAACCACCCTTTCTTCAATGCATCTATTATG
1 TCTACTTTTTACTTGGTATACAAACATTGGCATTAAAACACCCTTCCTTCAATGCATCTATTATG
*
102541 ATGCTATTACCAACATGTTC
66 ATGCTATTAACAACATGTTC
102561 TCTACTT
1 TCTACTT
102568 CTCTACCTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 5 0.06
85 80 0.94
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (85 bp):
TCTACTTTTTACTTGGTATACAAACATTGGCATTAAAACACCCTTCCTTCAATGCATCTATTATG
ATGCTATTAACAACATGTTC
Found at i:104614 original size:2 final size:2
Alignment explanation
Indices: 104607--104631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104597 GACATGTATG
104607 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
104632 TGAGCAAACA
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:104914 original size:2 final size:2
Alignment explanation
Indices: 104907--104954 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
104897 TGAATTATAA
104907 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
104949 GT GT GT
1 GT GT GT
104955 ATTCAATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:108461 original size:139 final size:132
Alignment explanation
Indices: 108198--108448 Score: 342
Period size: 139 Copynumber: 1.8 Consensus size: 132
108188 ATACCCTTAG
* *
108198 ATAAAGTTTAACCTCAAATTAATTAGGTTAGCCCCAATAAAAACAAAGTTTGATTTTAAGGGTAT
1 ATAAAGTTTAACCCCAAATTAATTAGGTTAGCCCCAATAAAAAAAAAGTTTGATTTTAAGGGTAT
* *
108263 ATCTTAAACTTAAAATATTTTTCCTAGGGTTTTGGGAAAAAAATGTATAAAGACAAAATTACTTT
66 AGCTTAAACTTAAAATATTTTTCCTAGGGTTTTGAGAAAAAAATGTAT-AAGACAAAATTACTTT
108328 ATA
130 ATA
* *
108331 ATAAAGTTTAGCCCCAAATTAATTAGTTTTAGCCCCACATTTAAAAAAAAAAGTTTGATTTTTAA
1 ATAAAGTTTAACCCCAAATTAATTAG-GTTAGCCCCA-A--T-AAAAAAAAAGTTTGA-TTTTAA
*
108396 GGGTATGGCTTAAACTTAAAATATTTATTCTCTAGGGTTTT-AGAAATAAAATG
60 GGGTATAGCTTAAACTTAAAATATTT-TTC-CTAGGGTTTTGAGAAA-AAAATG
108449 ACTAGTTAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
133 24 0.24
134 9 0.09
135 1 0.01
137 1 0.01
138 14 0.14
139 30 0.29
140 7 0.07
141 16 0.16
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (132 bp):
ATAAAGTTTAACCCCAAATTAATTAGGTTAGCCCCAATAAAAAAAAAGTTTGATTTTAAGGGTAT
AGCTTAAACTTAAAATATTTTTCCTAGGGTTTTGAGAAAAAAATGTATAAGACAAAATTACTTTA
TA
Found at i:109536 original size:22 final size:22
Alignment explanation
Indices: 109508--109549 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
109498 GGGCATAGTC
109508 GGGACTCCTTGTGAGAGCGTTT
1 GGGACTCCTTGTGAGAGCGTTT
*
109530 GGGACTCTTTGTGAGAGCGT
1 GGGACTCCTTGTGAGAGCGT
109550 GTGTCTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.38, T:0.31
Consensus pattern (22 bp):
GGGACTCCTTGTGAGAGCGTTT
Found at i:110486 original size:120 final size:125
Alignment explanation
Indices: 110268--110488 Score: 353
Period size: 120 Copynumber: 1.8 Consensus size: 125
110258 TTTCGTCAAT
* *
110268 AGGACCTTAATATTCATGACACACCCAGAACAAATAGACAATGATCAGAAACTACAAGAAAAAGA
1 AGGACCCTAATATTCATGACACACCCAGAACAAATAGACAATGATAAGAAACTACAAGAAAAAGA
110333 ATAATACCAAGCAACATAAGATGAATACATAAAAAATGAAAGCGTGTTTAAGCTCCATAC
66 ATAATACCAAGCAACATAAGATGAATACATAAAAAATGAAAGCGTGTTTAAGCTCCATAC
* * *
110393 AGGACCCTAATATTCATGACACACCGAG-A-AAA-A-A-TATGATAAGAAACTATAAGAAAAAGA
1 AGGACCCTAATATTCATGACACACCCAGAACAAATAGACAATGATAAGAAACTACAAGAAAAAGA
*
110453 ATAATACCCAGCAACATAAGATGAATACATAAAAAA
66 ATAATACCAAGCAACATAAGATGAATACATAAAAAA
110489 GAAGATTTGC
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
120 58 0.64
121 1 0.01
122 1 0.01
123 3 0.03
124 1 0.01
125 26 0.29
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.18
Consensus pattern (125 bp):
AGGACCCTAATATTCATGACACACCCAGAACAAATAGACAATGATAAGAAACTACAAGAAAAAGA
ATAATACCAAGCAACATAAGATGAATACATAAAAAATGAAAGCGTGTTTAAGCTCCATAC
Found at i:112824 original size:15 final size:15
Alignment explanation
Indices: 112806--112873 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
112796 TAAAGAGCAT
112806 AAAGGAAAAGGAAAG
1 AAAGGAAAAGGAAAG
*
112821 AAAGGAAAAGGGAAG
1 AAAGGAAAAGGAAAG
* *
112836 GAAGGAAAA--AAGAA
1 AAAGGAAAAGGAA-AG
*
112850 AAAGAAAAAGGAGAA-
1 AAAGGAAAAGGA-AAG
112865 AAAGGAAAA
1 AAAGGAAAA
112874 ATGGTAGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
13 1 0.02
14 8 0.19
15 30 0.71
16 2 0.05
17 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAGGAAAG
Found at i:115178 original size:41 final size:41
Alignment explanation
Indices: 115121--115388 Score: 245
Period size: 41 Copynumber: 6.4 Consensus size: 41
115111 CTTGTATTAC
* *
115121 ATGTGTTT-AGGGACTTTGATATAGATGCCTCTATGTTATAA
1 ATGTGTTTGA-GGACTTTGAAATAGATGCCTCTGTGTTATAA
*
115162 ATGTGTTTGAGGACTTTGAAAGAGAGGTGCCT-TGTGTTATAA
1 ATGTGTTTGAGGACTTTGAAATAGA--TGCCTCTGTGTTATAA
* * * *
115204 TTGTGCTTGGGGACTTT-AATATAGATGCCTATGTGTTATAA
1 ATGTGTTTGAGGACTTTGAA-ATAGATGCCTCTGTGTTATAA
* * * *
115245 ATGTGCTTGAGGACTTTTAAAAAGAATTGCCCCTGTGTTATAA
1 ATGTGTTTGAGGACTTTGAAATAG-A-TGCCTCTGTGTTATAA
* * * * *
115288 TTGTGTTTGGGGACTTTGAGATGGATGCCTCTGTGTTACAA
1 ATGTGTTTGAGGACTTTGAAATAGATGCCTCTGTGTTATAA
* * * * *
115329 ATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCTGTGTTATAA
1 ATGTGTTTGAGGACTTT-GAAATAGATGCCTCTGTGTTATAA
* *
115371 TTGTGTTTGGGGACTTTG
1 ATGTGTTTGAGGACTTTG
115389 GTTATTGGGT
Statistics
Matches: 186, Mismatches: 32, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
40 5 0.03
41 80 0.43
42 65 0.35
43 36 0.19
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (41 bp):
ATGTGTTTGAGGACTTTGAAATAGATGCCTCTGTGTTATAA
Found at i:115226 original size:83 final size:83
Alignment explanation
Indices: 115122--115388 Score: 383
Period size: 83 Copynumber: 3.2 Consensus size: 83
115112 TTGTATTACA
* * *
115122 TGTGTTTAGGGACTTTGATATAGATGCCTCTATGTTATAAATGTGTTTGAGGACTTTGAAAGAGA
1 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTT-AAAGAGA
* *
115187 GGTG-CCTTGTGTTATAAT
65 GTTGCCCCTGTGTTATAAT
* * * *
115205 TGTGCTTGGGGACTTTAATATAGATGCCTATGTGTTATAAATGTGCTTGAGGACTTTTAAAAAGA
1 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGAC-TTTAAAGAGA
*
115270 ATTGCCCCTGTGTTATAAT
65 GTTGCCCCTGTGTTATAAT
* * * *
115289 TGTGTTTGGGGACTTTGAGATGGATGCCTCTGTGTTACAAATGTGCTTGAGGACTTTAGAGAGAG
1 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAAAGAGAG
115354 TTGCCCCTGTGTTATAAT
66 TTGCCCCTGTGTTATAAT
115372 TGTGTTTGGGGACTTTG
1 TGTGTTTGGGGACTTTG
115389 GTTATTGGGT
Statistics
Matches: 163, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
83 99 0.61
84 64 0.39
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (83 bp):
TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAAAGAGAG
TTGCCCCTGTGTTATAAT
Found at i:119733 original size:17 final size:17
Alignment explanation
Indices: 119713--119761 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
119703 GCTGCCACGT
*
119713 GATTCCTGTTGCAGTGC
1 GATTCCTGTTGCAGCGC
*
119730 GATTCCTGTTGCAGCGT
1 GATTCCTGTTGCAGCGC
*
119747 GATTCCTATTGCAGC
1 GATTCCTGTTGCAGC
119762 CTGACTCCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.35
Consensus pattern (17 bp):
GATTCCTGTTGCAGCGC
Found at i:119748 original size:34 final size:34
Alignment explanation
Indices: 119696--119760 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
119686 GTCCTTCCGT
*
119696 GATTCCTGCTGCCACGTGATTCCTGTTGCAGTGC
1 GATTCCTGCTGCCACGTGATTCCTATTGCAGTGC
*
119730 GATTCCTGTTG-CAGCGTGATTCCTATTGCAG
1 GATTCCTGCTGCCA-CGTGATTCCTATTGCAG
119761 CCTGACTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.14, C:0.26, G:0.26, T:0.34
Consensus pattern (34 bp):
GATTCCTGCTGCCACGTGATTCCTATTGCAGTGC
Found at i:133355 original size:35 final size:35
Alignment explanation
Indices: 133314--133556 Score: 258
Period size: 35 Copynumber: 6.7 Consensus size: 35
133304 CAGTAATAAG
* *
133314 CAACTTAATTCAGGGTAATTAAGCAAGTCGGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* *
133349 CAACTTAATTCAGGGTAATTAAGTAATTAAGCAATTAAGCAAT
1 CAACTTAATTCAGGGTAATTAAG----TAAG----TCAGTAAT
*
133392 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
133427 CAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* * * *
133462 CAACTTTAATTCAAGGTAATTAAGTGAGTTAATGAAT
1 CAAC-TTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
*
133499 -AACTTAATTCAGGGTAATTAAGT-AGTTCAATAAGT
1 CAACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-T
133534 -AACTTAATTCAGGGTAATTAAGT
1 CAACTTAATTCAGGGTAATTAAGT
133557 TTAGTAAGAA
Statistics
Matches: 182, Mismatches: 14, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.02
35 113 0.62
36 28 0.15
37 3 0.02
39 6 0.03
43 28 0.15
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (35 bp):
CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
Found at i:133503 original size:71 final size:70
Alignment explanation
Indices: 133389--133556 Score: 227
Period size: 71 Copynumber: 2.4 Consensus size: 70
133379 GCAATTAAGC
*
133389 AATCAACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAG
1 AATCAACTTAATTCAGGGTAATTAAGTAATTAAGTAATCAACTTAATTCAGGGTAATTAAGT-AG
*
133454 -TCAGT
65 TTCAAT
* *
133459 AATCAACTTTAATTCAAGGTAATTAAGTGAGTTAA-TGAAT-AACTTAATTCAGGGTAATTAAGT
1 AATCAAC-TTAATTCAGGGTAATTAAGT-AATTAAGT-AATCAACTTAATTCAGGGTAATTAAGT
133522 AGTTCAAT
63 AGTTCAAT
133530 AAGT-AACTTAATTCAGGGTAATTAAGT
1 AA-TCAACTTAATTCAGGGTAATTAAGT
133557 TTAGTAAGAA
Statistics
Matches: 88, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
70 28 0.32
71 52 0.59
72 8 0.09
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (70 bp):
AATCAACTTAATTCAGGGTAATTAAGTAATTAAGTAATCAACTTAATTCAGGGTAATTAAGTAGT
TCAAT
Done.