Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013690.1 Corchorus capsularis cultivar CVL-1 contig13711, 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: 156465
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:15228 original size:25 final size:25
Alignment explanation
Indices: 15194--15258 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
15184 TGAACTATAC
15194 ATTAGTAATTAGGAAGGACATATGA
1 ATTAGTAATTAGGAAGGACATATGA
15219 ATTAGTAATTAGGAAGGACATATGA
1 ATTAGTAATTAGGAAGGACATATGA
15244 ATTAGTAATTAGGAA
1 ATTAGTAATTAGGAA
15259 TCAATTTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (25 bp):
ATTAGTAATTAGGAAGGACATATGA
Found at i:19278 original size:26 final size:24
Alignment explanation
Indices: 19249--19301 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
19239 GTGGATTGTA
*
19249 AAATAAAATTGAATAATAAATATATT
1 AAATAAAATT-AAGAATAAA-ATATT
*
19275 AAATAAAATTAAGAATTAAATATT
1 AAATAAAATTAAGAATAAAATATT
19299 AAA
1 AAA
19302 AAATTATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.32
25 7 0.28
26 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAAAATTAAGAATAAAATATT
Found at i:22121 original size:2 final size:2
Alignment explanation
Indices: 22114--22157 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
22104 CAAAACTAAC
*
22114 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22156 AT
1 AT
22158 TAGCTACCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32007 original size:2 final size:2
Alignment explanation
Indices: 32000--32032 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31990 TTGAATCAAC
32000 TA TA TA TA 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 TA TA TA TA T
32033 TTGTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41883 original size:3 final size:3
Alignment explanation
Indices: 41875--41902 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41865 AATTCTCATC
41875 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41903 GAATAGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42598 original size:42 final size:42
Alignment explanation
Indices: 42551--42670 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
42541 TAAATTGGGG
*
42551 AACCAATGTATTAGCACATTCTCTAGATAAAATTGATAGGGA
1 AACCAATGTATTAGCACATTCTCTAGCTAAAATTGATAGGGA
42593 AACCAATGTATTAGCACATTCTCTAGCTAAAATTGATAGGGA
1 AACCAATGTATTAGCACATTCTCTAGCTAAAATTGATAGGGA
42635 AACCAATGTATTAGCACATTCTCTAGCTAAAATTGA
1 AACCAATGTATTAGCACATTCTCTAGCTAAAATTGA
42671 GCTGGATAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (42 bp):
AACCAATGTATTAGCACATTCTCTAGCTAAAATTGATAGGGA
Found at i:51529 original size:13 final size:13
Alignment explanation
Indices: 51497--51529 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
51487 TTTGGTAGAT
*
51497 AATCATCTTCATG
1 AATCATGTTCATG
51510 AATCATGTTCATG
1 AATCATGTTCATG
51523 AATCATG
1 AATCATG
51530 ATATATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (13 bp):
AATCATGTTCATG
Found at i:64429 original size:28 final size:29
Alignment explanation
Indices: 64369--64429 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
64359 GTAAAACGTC
* * **
64369 CCAAAATTAAAGTTCGGGAGGCAAAATGT
1 CCAAAATTAAAATTCAGGAGGCAAAACAT
64398 CCAAAATTAAAATTCAGGA-GCAAAACAT
1 CCAAAATTAAAATTCAGGAGGCAAAACAT
64426 CCAA
1 CCAA
64430 GCGCTATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (29 bp):
CCAAAATTAAAATTCAGGAGGCAAAACAT
Found at i:67513 original size:6 final size:6
Alignment explanation
Indices: 67504--67544 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
67494 ATACAGAGTC
67504 AGCCAT AGCCAT AGCCAT AGCCAT AGCCAT AGCCAT AGCCA
1 AGCCAT AGCCAT AGCCAT AGCCAT AGCCAT AGCCAT AGCCA
67545 GCCGCAACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (6 bp):
AGCCAT
Found at i:70316 original size:127 final size:128
Alignment explanation
Indices: 70085--70333 Score: 473
Period size: 127 Copynumber: 2.0 Consensus size: 128
70075 CCACTCAACA
*
70085 ATTATTGATATTTGTGGATTCTGAATGTGTTCTCCATTTGGTTAAGAGTTCTTCTTCTTATCATC
1 ATTATTGATATTTGTGGATTCTGAATGTGTTCTCCATTTGGTTAAGAGTTCTTATTCTTATCATC
70150 ACATGGCAATATCATTAATGATTGCAGGTCTCTAATTGGAAGCTTATCCAATATCAAAAGCTT
66 ACATGGCAATATCATTAATGATTGCAGGTCTCTAATTGGAAGCTTATCCAATATCAAAAGCTT
*
70213 ATTA-TGATATTTGTGGATTCTGAATGTGTTCTCCATTTGGTTAAGAGTTCTTATTCTTCTCATC
1 ATTATTGATATTTGTGGATTCTGAATGTGTTCTCCATTTGGTTAAGAGTTCTTATTCTTATCATC
70277 ACATGGCAATATCATTAATGATTGCAGGTCTCTAATTGGAAGCTTATCCAATATCAA
66 ACATGGCAATATCATTAATGATTGCAGGTCTCTAATTGGAAGCTTATCCAATATCAA
70334 GGTGGAGCAC
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
127 115 0.97
128 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (128 bp):
ATTATTGATATTTGTGGATTCTGAATGTGTTCTCCATTTGGTTAAGAGTTCTTATTCTTATCATC
ACATGGCAATATCATTAATGATTGCAGGTCTCTAATTGGAAGCTTATCCAATATCAAAAGCTT
Found at i:71730 original size:14 final size:15
Alignment explanation
Indices: 71711--71742 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
71701 GAATTGAAGA
71711 TAAGACTTTGG-ACT
1 TAAGACTTTGGAACT
71725 TAAGACTTTGGAACT
1 TAAGACTTTGGAACT
71740 TAA
1 TAA
71743 TATTATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (15 bp):
TAAGACTTTGGAACT
Found at i:72637 original size:31 final size:31
Alignment explanation
Indices: 72599--72733 Score: 135
Period size: 31 Copynumber: 4.4 Consensus size: 31
72589 TTTTGTGCAC
* * **
72599 GTGGCATGCCATGTGCCATTTTTTGAAACAT
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* *
72630 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* *
72661 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* ** * * *
72692 GTGGCGTGCCACATTTAACTTTTTGGTACAC
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
*
72723 GTGGCGTGCCA
1 GTGGCATGCCA
72734 CGTCGGACAC
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCATGTGTCACTTTTTGGTACAT
Found at i:72674 original size:62 final size:62
Alignment explanation
Indices: 72596--72730 Score: 180
Period size: 62 Copynumber: 2.2 Consensus size: 62
72586 TCCTTTTGTG
* * * * *
72596 CACGTGGCATGCCATGTGCCATTTTTTGAAACATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGACATGTGCCACTTTTTGAAACATGTGGCATGCCACATGTAACTTTTTGGTA
* ** * *
72658 CACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCGTGCCACATTTAACTTTTTGGTA
1 CACGTGGCGTGACATGTGCCACTTTTTGAAACATGTGGCATGCCACATGTAACTTTTTGGTA
72720 CACGTGGCGTG
1 CACGTGGCGTG
72731 CCACGTCGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (62 bp):
CACGTGGCGTGACATGTGCCACTTTTTGAAACATGTGGCATGCCACATGTAACTTTTTGGTA
Found at i:73837 original size:22 final size:20
Alignment explanation
Indices: 73812--73869 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
73802 AATCACTTCA
73812 ATCCCTCCCTCCTTCCTCCACC
1 ATCCCTCCCT-CTTCCTCC-CC
*
73834 ATCCC-CACTC-TCCTCCCC
1 ATCCCTCCCTCTTCCTCCCC
*
73852 AACCACTCCCTCTTCCTC
1 ATCC-CTCCCTCTTCCTC
73870 ACCTCTTCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
20 5 0.17
21 8 0.27
22 5 0.17
ACGTcount: A:0.12, C:0.62, G:0.00, T:0.26
Consensus pattern (20 bp):
ATCCCTCCCTCTTCCTCCCC
Found at i:83346 original size:29 final size:29
Alignment explanation
Indices: 83304--83362 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
83294 GCAGCATAGA
83304 TAAGGTAACCTCGCTCGCAAAACCTTTTT
1 TAAGGTAACCTCGCTCGCAAAACCTTTTT
83333 TAAGGTAACCTCGCTCGCAAAACCTTTTT
1 TAAGGTAACCTCGCTCGCAAAACCTTTTT
83362 T
1 T
83363 TTTAACGCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (29 bp):
TAAGGTAACCTCGCTCGCAAAACCTTTTT
Found at i:92002 original size:32 final size:32
Alignment explanation
Indices: 91965--92047 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
91955 AGGATCAAGA
*
91965 GTGAGTTTCTGGAATTTATTGAGGGTTTAAGG
1 GTGAGTTTCTGAAATTTATTGAGGGTTTAAGG
91997 GTGAGTTTCTGAAATTTATTGAGGGTTTAAGG
1 GTGAGTTTCTGAAATTTATTGAGGGTTTAAGG
*
92029 GCGAGTTTCTGAAATTTAT
1 GTGAGTTTCTGAAATTTAT
92048 ACACATAGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.41
Consensus pattern (32 bp):
GTGAGTTTCTGAAATTTATTGAGGGTTTAAGG
Found at i:100355 original size:37 final size:35
Alignment explanation
Indices: 100296--100367 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 35
100286 TCACTTTTTC
* *
100296 CTTTTTTTTTTTTTGGATAACACACTTTTTCCTCT
1 CTTTTTTTTTTTTGGGAAAACACACTTTTTCCTCT
100331 CTTTTTTTTTTTTGGGCGAAAACACACTTTTTCCTCT
1 CTTTTTTTTTTTT-GG-GAAAACACACTTTTTCCTCT
100368 TAAATTCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 13 0.39
36 1 0.03
37 19 0.58
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.56
Consensus pattern (35 bp):
CTTTTTTTTTTTTGGGAAAACACACTTTTTCCTCT
Found at i:113969 original size:34 final size:34
Alignment explanation
Indices: 113926--113991 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
113916 TGATCTCTAC
*
113926 TTCTCTTTGAGAATAGAAAGAAGGCATCCATTTA
1 TTCTCTTTGAGAAAAGAAAGAAGGCATCCATTTA
113960 TTCTCTTTGAGAAAAGAAAGAAGGCATCCATT
1 TTCTCTTTGAGAAAAGAAAGAAGGCATCCATT
113992 GCCAAGTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (34 bp):
TTCTCTTTGAGAAAAGAAAGAAGGCATCCATTTA
Found at i:118661 original size:2 final size:2
Alignment explanation
Indices: 118656--118687 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
118646 CCCCCCTCCC
118656 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
118688 ACTTCCGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:133076 original size:21 final size:21
Alignment explanation
Indices: 133050--133097 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
133040 AAACTAACAG
* *
133050 AACCCATATAAAGCGACACAA
1 AACCCATATAAAACAACACAA
133071 AACCCATATAAAACAACACAA
1 AACCCATATAAAACAACACAA
133092 AACCCA
1 AACCCA
133098 AATGCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.31, G:0.04, T:0.08
Consensus pattern (21 bp):
AACCCATATAAAACAACACAA
Found at i:133421 original size:15 final size:17
Alignment explanation
Indices: 133396--133428 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
133386 CGGAATGTGA
133396 GTTTAATTTGTA-ATTT
1 GTTTAATTTGTACATTT
133412 GTTT-ATTTGTACATTT
1 GTTTAATTTGTACATTT
133428 G
1 G
133429 ATAGGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.61
Consensus pattern (17 bp):
GTTTAATTTGTACATTT
Found at i:146966 original size:2 final size:2
Alignment explanation
Indices: 146959--146997 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
146949 ATATGGTGGG
146959 AT AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
146998 GATGGTTGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:146985 original size:19 final size:19
Alignment explanation
Indices: 146961--147000 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
146951 ATGGTGGGAT
146961 ATATATATATATATATATG
1 ATATATATATATATATATG
146980 ATATATATATATATATATG
1 ATATATATATATATATATG
146999 AT
1 AT
147001 GGTTGGATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
ATATATATATATATATATG
Found at i:153592 original size:3 final size:3
Alignment explanation
Indices: 153584--153618 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
153574 AAAAGTATAT
153584 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
153619 CATATTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:154290 original size:106 final size:105
Alignment explanation
Indices: 154073--154330 Score: 360
Period size: 106 Copynumber: 2.5 Consensus size: 105
154063 TTTCTAACCA
* **
154073 TTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATAATATATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATAATATATTTTATTTC
* * *
154136 TAAAAACCTATAGCAACATTATTAATTATGGAATTTACCC
66 TAAAAACCTACAGCAAAATTATTAATTATGAAATTTACCC
* ** *
154176 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATAATATATTTTATTTC
* *
154241 TAAAACCCTACATG-ATAAATTATTAATTTTGAAATTTACCC
66 TAAAAACCTACA-GCA-AAATTATTAATTATGAAATTTACCC
*
154282 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAATGAAATTAA
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
154331 GGCTAAACTT
Statistics
Matches: 137, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
103 23 0.17
104 15 0.11
105 29 0.21
106 70 0.51
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (105 bp):
TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATAATATATTTTATTTC
TAAAAACCTACAGCAAAATTATTAATTATGAAATTTACCC
Done.