Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004847.1 Corchorus capsularis cultivar CVL-1 contig04865, 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: 27044
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:44 original size:2 final size:2
Alignment explanation
Indices: 37--63 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27 CATCAGGAAA
37 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
64 TATTTGCTTG
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3505 original size:19 final size:19
Alignment explanation
Indices: 3481--3545 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
3471 CGATACTTGG
3481 TAGATATATCAAATTTTGA
1 TAGATATATCAAATTTTGA
*
3500 TAG--ATAT---A--TTGG
1 TAGATATATCAAATTTTGA
3512 TAGATATATCAAATTTTGA
1 TAGATATATCAAATTTTGA
3531 TAGATATATCAAATT
1 TAGATATATCAAATT
3546 AAAGTGAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
12 6 0.16
14 5 0.14
17 5 0.14
19 21 0.57
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (19 bp):
TAGATATATCAAATTTTGA
Found at i:3515 original size:31 final size:31
Alignment explanation
Indices: 3477--3539 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3467 TACACGATAC
3477 TTGGTAGATATATCAAATTTTGATAGATATA
1 TTGGTAGATATATCAAATTTTGATAGATATA
3508 TTGGTAGATATATCAAATTTTGATAGATATA
1 TTGGTAGATATATCAAATTTTGATAGATATA
3539 T
1 T
3540 CAAATTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (31 bp):
TTGGTAGATATATCAAATTTTGATAGATATA
Found at i:3645 original size:31 final size:31
Alignment explanation
Indices: 3607--3695 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 31
3597 TATATCAGGT
3607 CCTTATTTGAGCATTTTCGATAAAATTAGAC
1 CCTTATTTGAGCATTTTCGATAAAATTAGAC
** *
3638 CCTTATTTG-GCTAAATT--A-AAAGATTGGAC
1 CCTTATTTGAGC-ATTTTCGATAAA-ATTAGAC
* *
3667 CTTTATTTGAGCATTTTCGATAACATTAG
1 CCTTATTTGAGCATTTTCGATAAAATTAG
3696 GTTCTTATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
28 3 0.07
29 18 0.41
30 4 0.09
31 17 0.39
32 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTCGATAAAATTAGAC
Found at i:3763 original size:60 final size:59
Alignment explanation
Indices: 3604--3766 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 59
3594 ATATATATCA
* *
3604 GGTCCTTATTTGAGCATTTTCGATAA-AATTAGACCCTTATTTGGCTAAATTAAAAGATT
1 GGTCCTTATTTGAGCATTTTCGATAACAATAAG-CCCTTATTTGGCTAAATTAAAAGATG
* * * **
3663 GGACCTTTATTTGAGCATTTTCGATAACATTAGGTTCTTATTTGG-TCAAATTAAAAGATCG
1 GGTCC-TTATTTGAGCATTTTCGATAACAATAAGCCCTTATTTGGCT-AAATTAAAAGAT-G
*
3724 GGTCCTTATTTGAGCATTTTAGCA-AACAATAAGCCCTTATTTG
1 GGTCCTTATTTGAGCATTTTCG-ATAACAATAAGCCCTTATTTG
3767 AGCAATTAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
59 5 0.06
60 73 0.85
61 8 0.09
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (59 bp):
GGTCCTTATTTGAGCATTTTCGATAACAATAAGCCCTTATTTGGCTAAATTAAAAGATG
Found at i:3851 original size:30 final size:31
Alignment explanation
Indices: 3817--3875 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
3807 AGTACTATTT
3817 AAAAAGGTTATTTAGTTGA-TGCCAAAAAAA
1 AAAAAGGTTATTTAGTTGATTGCCAAAAAAA
*
3847 AAAAAGGTTATTTAGTTTATTGCCAAAAA
1 AAAAAGGTTATTTAGTTGATTGCCAAAAA
3876 GGCATAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (31 bp):
AAAAAGGTTATTTAGTTGATTGCCAAAAAAA
Found at i:4076 original size:31 final size:31
Alignment explanation
Indices: 4032--4126 Score: 136
Period size: 31 Copynumber: 3.1 Consensus size: 31
4022 GTGTCCGACA
* *
4032 TGGCATGCTACGTGTACCAAAAAGTGACATG
1 TGGCATGCCACGTGTACCAAAAAGTGACACG
* *
4063 TGGCACGCCACGTGTACCACAAAGTGACACG
1 TGGCATGCCACGTGTACCAAAAAGTGACACG
* *
4094 TGTCATGCCACGTGTACCAAAAAGTGACGCG
1 TGGCATGCCACGTGTACCAAAAAGTGACACG
4125 TG
1 TG
4127 TCCCGCTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.19
Consensus pattern (31 bp):
TGGCATGCCACGTGTACCAAAAAGTGACACG
Found at i:4191 original size:31 final size:30
Alignment explanation
Indices: 4149--4316 Score: 139
Period size: 31 Copynumber: 5.6 Consensus size: 30
4139 TTAGGCTAAT
* *
4149 TGCTCAAATAAGGGCCTAAGGTTTGATAAAA
1 TGCTCAAATAAGGGCCTAACGTTTG-CAAAA
* * * **
4180 TGCCCAAATAAGGGCCTGATC-TTT-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCAAAA
4209 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTG-CAAAA
* * **
4240 TGCTCAAATAAGGGCCCCATC-TTTG-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCAAAA
*
4269 TGGTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTG-CAAAA
4300 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
4317 GTCTCACGCG
Statistics
Matches: 108, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
28 6 0.06
29 39 0.36
30 4 0.04
31 54 0.50
32 5 0.05
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTGCAAAA
Found at i:4248 original size:60 final size:60
Alignment explanation
Indices: 4153--4317 Score: 258
Period size: 60 Copynumber: 2.8 Consensus size: 60
4143 GCTAATTGCT
* ** * *
4153 CAAATAAGGGCCTAAGGTTTGATAAAATGCCCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
** *
4213 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
4273 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTG
4318 TCTCACGCGT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
Found at i:4283 original size:29 final size:29
Alignment explanation
Indices: 4184--4284 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
4174 ATAAAATGCC
** * *
4184 CAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCCCATCTTTGAATTTGGT
* * ** *
4213 CAAATAAGGG-CCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCCCATC-TTTG--AATTTGGT
4244 CAAATAAGGGCCCCATCTTTGAATTTGGT
1 CAAATAAGGGCCCCATCTTTGAATTTGGT
4273 CAAATAAGGGCC
1 CAAATAAGGGCC
4285 TAACGTTTGC
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 3 0.05
29 30 0.55
31 18 0.33
32 4 0.07
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCCCATCTTTGAATTTGGT
Found at i:4387 original size:31 final size:31
Alignment explanation
Indices: 4345--4477 Score: 166
Period size: 31 Copynumber: 4.4 Consensus size: 31
4335 ACTGACATCG
4345 GGCCCTTATTTGAGCATTTTCGATAACGTTA
1 GGCCCTTATTTGAGCATTTTCGATAACGTTA
*
4376 GGCTCTTATTTGAGCATTTTCGATAACGTTA
1 GGCCCTTATTTGAGCATTTTCGATAACGTTA
** * **
4407 GGCCCTTATTTG-GCAAAATT--A-AAAGATCG
1 GGCCCTTATTTGAGC-ATTTTCGATAACG-TTA
4436 GGCCCTTATTTGAGCATTTTCGATAACGTTA
1 GGCCCTTATTTGAGCATTTTCGATAACGTTA
4467 GGCCCTTATTT
1 GGCCCTTATTT
4478 AGCCAAATTA
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.04
29 17 0.20
30 4 0.05
31 57 0.68
32 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (31 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTA
Found at i:4451 original size:60 final size:60
Alignment explanation
Indices: 4380--4543 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 60
4370 ACGTTAGGCT
**
4380 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGGGCC
1 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGAACC
* *
4440 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCGAACC
1 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGAACC
* * *
4500 CTTATTTGAGCATTTT-GACAAACATTAGGCTCTTATTTGAGCAA
1 CTTATTTGAGCATTTTCGA-TAACGTTAGGCCCTTATTTG-GCAA
4544 TTAGCCATTT
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
59 2 0.02
60 88 0.95
61 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (60 bp):
CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGAACC
Found at i:4987 original size:110 final size:109
Alignment explanation
Indices: 4784--4997 Score: 392
Period size: 110 Copynumber: 2.0 Consensus size: 109
4774 ATTTTGATGT
* *
4784 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTCTTGTTTGGTATGTGTGCTTATTTA
1 TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTATTTA
*
4849 ATAGGTTCAATTGAATAAACAACACAATTAATCATAATAGGTGC
66 ATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTGC
4893 TTGTATTTTTCCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTATTT
1 TTGTATTTTT-CTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTATTT
4958 AATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
65 AATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
4998 TATATATATA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
109 10 0.10
110 91 0.90
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (109 bp):
TTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTATTTA
ATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTGC
Found at i:7071 original size:38 final size:38
Alignment explanation
Indices: 7025--7101 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
7015 CATCTGTTAA
7025 TGGAATGTTAAAAAACCCTGTCCTTTATATCCTCTCTG
1 TGGAATGTTAAAAAACCCTGTCCTTTATATCCTCTCTG
* *
7063 TGGAATGTTAAAAAACTCTGTTCTTTATATCCTCTCTG
1 TGGAATGTTAAAAAACCCTGTCCTTTATATCCTCTCTG
7101 T
1 T
7102 TAATGGAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (38 bp):
TGGAATGTTAAAAAACCCTGTCCTTTATATCCTCTCTG
Found at i:7896 original size:35 final size:35
Alignment explanation
Indices: 7850--7916 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
7840 TAATATTAAA
7850 GGTATTTTAGTAATTGACTAATTAAGATTTTTATG
1 GGTATTTTAGTAATTGACTAATTAAGATTTTTATG
* *
7885 GGTATTTTAGTAATTGATTAATTCAGATTTTT
1 GGTATTTTAGTAATTGACTAATTAAGATTTTT
7917 GAGTTCGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (35 bp):
GGTATTTTAGTAATTGACTAATTAAGATTTTTATG
Found at i:7971 original size:18 final size:18
Alignment explanation
Indices: 7945--7983 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
7935 AGTAGTAATA
*
7945 ATAAGATAGTAAGATAAG
1 ATAAAATAGTAAGATAAG
7963 ATAAAATAGTAAGATAAG
1 ATAAAATAGTAAGATAAG
7981 ATA
1 ATA
7984 TATATTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (18 bp):
ATAAAATAGTAAGATAAG
Found at i:27018 original size:2 final size:2
Alignment explanation
Indices: 27011--27044 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27001 GAGCAAAAGA
27011 AT AT AT AT 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 AT AT AT AT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.