Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013283.1 Corchorus capsularis cultivar CVL-1 contig13304, 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: 41027
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2198 original size:77 final size:77
Alignment explanation
Indices: 2071--2227 Score: 296
Period size: 77 Copynumber: 2.0 Consensus size: 77
2061 CGGTGAACCT
* *
2071 GGTGTGACCATCCAGGGGTGCGCAATTGTGGAGTGTTCGTAGCTTGCACCACTCCAAGGGTTAAG
1 GGTGTGACCATCCAGGGGTGCGCAATTGTGGAGTGTCCGTAACTTGCACCACTCCAAGGGTTAAG
2136 TCTTGGATGGCC
66 TCTTGGATGGCC
2148 GGTGTGACCATCCAGGGGTGCGCAATTGTGGAGTGTCCGTAACTTGCACCACTCCAAGGGTTAAG
1 GGTGTGACCATCCAGGGGTGCGCAATTGTGGAGTGTCCGTAACTTGCACCACTCCAAGGGTTAAG
2213 TCTTGGATGGCC
66 TCTTGGATGGCC
2225 GGT
1 GGT
2228 AATTGGCTTA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.18, C:0.22, G:0.34, T:0.25
Consensus pattern (77 bp):
GGTGTGACCATCCAGGGGTGCGCAATTGTGGAGTGTCCGTAACTTGCACCACTCCAAGGGTTAAG
TCTTGGATGGCC
Found at i:5320 original size:50 final size:49
Alignment explanation
Indices: 5245--5347 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 49
5235 AGAGATGAAA
*
5245 AAAAATGGAATTAAATTATTAAATTTTAAAATATATATTAAAAAATAATT
1 AAAAATGGAATGAAATTATTAAATTTTAAAATATATATTAAAAAATAA-T
5295 AAAAATGGAATGAAATTATTAAATTTTAAAATATATATTAAAAAATAAT
1 AAAAATGGAATGAAATTATTAAATTTTAAAATATATATTAAAAAATAAT
5344 AAAA
1 AAAA
5348 TAATTAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 5 0.10
50 47 0.90
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (49 bp):
AAAAATGGAATGAAATTATTAAATTTTAAAATATATATTAAAAAATAAT
Found at i:5354 original size:38 final size:37
Alignment explanation
Indices: 5282--5355 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 37
5272 AAAATATATA
* *
5282 TTAAAAAATAATTAAAAATGGAATGAAATTATTAAATT
1 TTAAAAAATAATTAAAAAT-GAATAAAATAATTAAATT
*
5320 TTAAAATATATATTAAAAAAT-AATAAAATAATTAAA
1 TTAAAAAATA-ATT-AAAAATGAATAAAATAATTAAA
5356 AAATTTACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 22 0.71
39 3 0.10
40 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (37 bp):
TTAAAAAATAATTAAAAATGAATAAAATAATTAAATT
Found at i:5408 original size:25 final size:25
Alignment explanation
Indices: 5379--5431 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
5369 TAACGGAAGA
5379 GTGGACTTAATGGGAACTCAACGGC
1 GTGGACTTAATGGGAACTCAACGGC
*
5404 GTGGACTTAATGGGAACTTAACGGC
1 GTGGACTTAATGGGAACTCAACGGC
5429 GTG
1 GTG
5432 TGTAGTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (25 bp):
GTGGACTTAATGGGAACTCAACGGC
Found at i:5533 original size:64 final size:64
Alignment explanation
Indices: 5432--5560 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
5422 TAACGGCGTG
*
5432 TGTAGTTCAAATGCGCTAGGGGACCTAAAAAATTACTATATTGAACCATTAGTAAAACTTTTGT
1 TGTAGTTCAAATGCGCTAGGGGACCTAAAAAATTACTATATTGAACCATTAGTAAAACCTTTGT
* *
5496 TGTAGTTCAAATGCGCTGGGGGATCTAAAAAATTACTATATTGAACCATTAGTAAAACCTTTGT
1 TGTAGTTCAAATGCGCTAGGGGACCTAAAAAATTACTATATTGAACCATTAGTAAAACCTTTGT
5560 T
1 T
5561 ACCAAATTGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (64 bp):
TGTAGTTCAAATGCGCTAGGGGACCTAAAAAATTACTATATTGAACCATTAGTAAAACCTTTGT
Found at i:6888 original size:37 final size:38
Alignment explanation
Indices: 6847--6922 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
6837 CCAGATGATA
* *
6847 TAGAATAATA-GAAAATAAAACCATGGTTGCTACTCCT
1 TAGAATAATAGGAAAAAAAAACCATGGTTACTACTCCT
6884 TAGAATAATAGGAAAAAAAAACCATGGTTACTACTCCT
1 TAGAATAATAGGAAAAAAAAACCATGGTTACTACTCCT
6922 T
1 T
6923 CAAATACAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 10 0.28
38 26 0.72
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (38 bp):
TAGAATAATAGGAAAAAAAAACCATGGTTACTACTCCT
Found at i:9124 original size:21 final size:21
Alignment explanation
Indices: 9100--9140 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9090 TACTCAACTC
9100 TCATTTCGCT-CTGTTGTTTCA
1 TCATTT-GCTACTGTTGTTTCA
*
9121 TCATTTGCTACTGTTTTTTC
1 TCATTTGCTACTGTTGTTTC
9141 TAACTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.10, C:0.22, G:0.12, T:0.56
Consensus pattern (21 bp):
TCATTTGCTACTGTTGTTTCA
Found at i:10401 original size:21 final size:21
Alignment explanation
Indices: 10372--10431 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
10362 TTAAACTAAA
10372 TAATAAATAATATATATTATT
1 TAATAAATAATATATATTATT
*
10393 TATTAAATAATATATTATTATT
1 TAATAAATAATATA-TATTATT
*
10415 TAATATAT-ATATATATT
1 TAATAAATAATATATATT
10432 TACAATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.11
21 18 0.51
22 13 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATAAATAATATATATTATT
Found at i:10412 original size:15 final size:15
Alignment explanation
Indices: 10392--10467 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 15
10382 TATATATTAT
10392 TTATTAAATAATATA
1 TTATTAAATAATATA
10407 TTATTATTTAATATATATA
1 TTATTA---AATA-ATATA
* *
10426 TATATT-TACAATATA
1 T-TATTAAATAATATA
*
10441 -TATTTAAT-ATATA
1 TTATTAAATAATATA
*
10454 TTACTAAATAATAT
1 TTATTAAATAATAT
10468 TACTAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
13 9 0.19
14 7 0.15
15 15 0.32
16 2 0.04
18 4 0.09
19 6 0.13
20 4 0.09
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTAAATAATATA
Found at i:10439 original size:13 final size:11
Alignment explanation
Indices: 10423--10493 Score: 56
Period size: 11 Copynumber: 6.2 Consensus size: 11
10413 TTTAATATAT
10423 ATATATATTTACA
1 ATATATATTT--A
10436 ATATATATTTA
1 ATATATATTTA
10447 ATATATATTACTA
1 ATATATATT--TA
10460 A-ATA-ATATTA
1 ATATATAT-TTA
* * *
10470 CTAAATATATA
1 ATATATATTTA
10481 ATATATATTTA
1 ATATATATTTA
10492 AT
1 AT
10494 TAGTAAAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
10 2 0.04
11 26 0.55
12 6 0.13
13 13 0.28
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATATTTA
Found at i:16119 original size:3 final size:3
Alignment explanation
Indices: 16111--16140 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16101 TTACGATTAT
*
16111 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16141 TATGTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:31726 original size:2 final size:2
Alignment explanation
Indices: 31719--31745 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31709 TCCAAATTTG
31719 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 T
31746 TGTACATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32457 original size:33 final size:33
Alignment explanation
Indices: 32415--32495 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
32405 AATGAACGAC
*
32415 AATCTTGGTATAATGGGATCATTCAAAAATACA
1 AATCTTGGTATAATGGGATCATTCAAAAATAAA
32448 AATCTTGGTATAATGGGATCATTCAAAAATAAA
1 AATCTTGGTATAATGGGATCATTCAAAAATAAA
32481 AATCTTGGTATAATG
1 AATCTTGGTATAATG
32496 TAGAAAACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (33 bp):
AATCTTGGTATAATGGGATCATTCAAAAATAAA
Found at i:32531 original size:31 final size:31
Alignment explanation
Indices: 32490--32556 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
32480 AAATCTTGGT
*
32490 ATAATGTAGAAAACAAGACCCCAAAAATTAA
1 ATAAAGTAGAAAACAAGACCCCAAAAATTAA
* * *
32521 ATAAAGTAGAAAATAAGACCTCAAAAGTTAA
1 ATAAAGTAGAAAACAAGACCCCAAAAATTAA
32552 ATAAA
1 ATAAA
32557 AAGCCTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.18
Consensus pattern (31 bp):
ATAAAGTAGAAAACAAGACCCCAAAAATTAA
Found at i:32801 original size:28 final size:28
Alignment explanation
Indices: 32739--32802 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
32729 TTTAGGCGGA
** *
32739 AAATCTTCCCTCTAATGTATCAGGCAGC
1 AAATCTTCCCTCTAATGTATCACACAAC
*
32767 AAATCTTCCCTCTGATGTATCACACAAC
1 AAATCTTCCCTCTAATGTATCACACAAC
*
32795 AAGTCTTC
1 AAATCTTC
32803 TGATGCTTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (28 bp):
AAATCTTCCCTCTAATGTATCACACAAC
Found at i:33278 original size:156 final size:157
Alignment explanation
Indices: 33096--33508 Score: 502
Period size: 156 Copynumber: 2.6 Consensus size: 157
33086 TGGCTGGATT
* *
33096 CGAGCCCTCCTTCA-TGGTGAACTAGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGCA
1 CGAGCTCTCCTT-AGTGGTGAACTAGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACAAGCA
* *
33160 TAAGTTTTTCAT-TCTAAGTCTGATTGAGATGAAACTTTGTCA-AAGGA-CTTAGATTATCTCCA
65 TAAGTTTTTCATCT-TAAGTCTGATTGAGATGAAACTTT-CCACAAGGAGCTTAGATCATCTCCA
* *
33222 TAAGACTATGGAAAAAATCCTAAGTAAAAC
128 TAAAACTATGAAAAAAATCCTAAGTAAAAC
* * *
33252 CGAGGTCTCCTTAGTGGTGAACTAGGTTTCACACCCCAAATTGTCCTTAAATGAAAAACAAGTAT
1 CGAGCTCTCCTTAGTGGTGAACTAGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACAAGCAT
* * * * * * *
33317 AAGTTTTTTATCTTAAGTC-CAATAAGGCTG-AA-TTTCCACCAGTATGCTTAGATCATCTCCAT
66 AAGTTTTTCATCTTAAGTCTGATTGA-GATGAAACTTTCCACAAGGA-GCTTAGATCATCTCCAT
*
33379 AAAACTATGAAAAAAATTCTAAGTAAAAC
129 AAAACTATGAAAAAAATCCTAAGTAAAAC
** *
33408 CGAGCTCTCCTT-GATGGTGAACT-GGTTTTCTTACCCGAAACTGTCCTTAAATGAAAAACAAGC
1 CGAGCTCTCCTTAG-TGGTGAACTAGG-TTTCACACCCCAAACTGTCCTTAAATGAAAAACAAGC
* *
33471 ATAAATTTTTCATCTTAAGTCTGTTTGAGATGAAACTT
64 ATAAGTTTTTCATCTTAAGTCTGATTGAGATGAAACTT
33509 AGCCAAGATG
Statistics
Matches: 216, Mismatches: 30, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
153 2 0.01
154 6 0.03
155 9 0.04
156 192 0.89
157 5 0.02
158 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (157 bp):
CGAGCTCTCCTTAGTGGTGAACTAGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACAAGCAT
AAGTTTTTCATCTTAAGTCTGATTGAGATGAAACTTTCCACAAGGAGCTTAGATCATCTCCATAA
AACTATGAAAAAAATCCTAAGTAAAAC
Found at i:35740 original size:17 final size:17
Alignment explanation
Indices: 35718--35750 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35708 TTAATTTCTG
*
35718 AAATTAAAAATTAAATT
1 AAATTAAAAAGTAAATT
35735 AAATTAAAAAGTAAAT
1 AAATTAAAAAGTAAAT
35751 AAAACCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAATTAAAAAGTAAATT
Found at i:36958 original size:24 final size:26
Alignment explanation
Indices: 36908--36958 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
36898 GAAATTGTTC
*
36908 TTGTTGATGAGATTGAAGAGGATGTTG
1 TTGTTGATGAGATT-AAGAGGAAGTTG
*
36935 TTGTTGATTAGATT-AG-GGAAGTTG
1 TTGTTGATGAGATTAAGAGGAAGTTG
36959 ATTAGAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 2 0.09
27 13 0.59
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.39
Consensus pattern (26 bp):
TTGTTGATGAGATTAAGAGGAAGTTG
Done.