Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008549.1 Corchorus capsularis cultivar CVL-1 contig08570, 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: 27492
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:567 original size:7 final size:7
Alignment explanation
Indices: 555--588 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
545 GAGGAAGAGA
555 GAGAAAG
1 GAGAAAG
562 GAGAAAG
1 GAGAAAG
569 GAGAAAG
1 GAGAAAG
576 GAGAAAG
1 GAGAAAG
583 GAGAAA
1 GAGAAA
589 ATGAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
GAGAAAG
Found at i:659 original size:14 final size:13
Alignment explanation
Indices: 642--713 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 13
632 ATATTTTAGG
*
642 AATATAATTTATAT
1 AATATAATATAT-T
656 AATATAATATATT
1 AATATAATATATT
*
669 AATAATAATAATAAT
1 AAT-ATAAT-ATATT
684 AATAATAATATTATT
1 AAT-ATAATA-TATT
*
699 ATTAT-ATATAGTT
1 AATATAATATA-TT
712 AA
1 AA
714 ATAGTCGGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.04
13 10 0.20
14 19 0.39
15 18 0.37
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (13 bp):
AATATAATATATT
Found at i:676 original size:3 final size:3
Alignment explanation
Indices: 654--693 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
644 TATAATTTAT
*
654 ATA AT- ATA AT- ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
694 TTATTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:4369 original size:21 final size:21
Alignment explanation
Indices: 4343--4383 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4333 TCTTGAAGGC
4343 TTGAAGTCCATTGAAGATCAA
1 TTGAAGTCCATTGAAGATCAA
**
4364 TTGAAGTGTATTGAAGATCA
1 TTGAAGTCCATTGAAGATCA
4384 TAAGCCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (21 bp):
TTGAAGTCCATTGAAGATCAA
Found at i:10766 original size:21 final size:21
Alignment explanation
Indices: 10740--10780 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10730 TCTTGAAGGC
*
10740 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGATCAA
**
10761 TTGAAGAGTATTGAAGATCA
1 TTGAAGACCATTGAAGATCA
10781 TAAGCCAAGG
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:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAGACCATTGAAGATCAA
Found at i:16693 original size:67 final size:67
Alignment explanation
Indices: 16455--16901 Score: 471
Period size: 67 Copynumber: 6.7 Consensus size: 67
16445 GGGTAAAGTT
* * * * *
16455 GTATTTTCTCTTTCCAGAAATACCCTTTCTGTCAAAGGGTCATTTTTGTCTTTTCGCATTTAAGT
1 GTATTTT-TTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGT
16520 TTA
65 TTA
* ** *
16523 GTATTTTGTTTTTCAAAAAATACCCTTTCGGTCGAAGGGTCATTTTAATCTTTTCGCATTTAAAT
1 GTATTTT-TTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGT
16588 TTA
65 TTA
* * *
16591 GTAGTTTGTTTTTTCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCATCTTTT-GCATTTAGG
1 GTA-TTT-TTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAG
16655 TTTA
64 TTTA
* * * * *
16659 GTATTTTGTTTTTCCAAAAATACCCTTTCAGTGGAAGGATCATTTTCGTCTTTT-GCATTCAGGT
1 GTATTTT-TTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGT
16723 TTA
65 TTA
* * * *
16726 G--TTTTATTTTCCAAAAGTACCC-TTCTGGTCGAAAGGTCAGTTTT-GTCTTTTTC-CATTCAA
1 GTATTTTTTTTTCCAAAAATACCCTTTC-GGTCGAAGGGTCA-TTTTCGTC-TTTTCGCATTTAA
16786 GTTTA
63 GTTTA
** * * * * * *
16791 GTATTTTCATTTCCATAAATACCCTTTTGTTCGAAGGGTCAGTTTCGTCTTTTGGCATTTAGGTT
1 GTATTTTTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTT
16856 TA
66 TA
* * *
16858 G--TTTTATTTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTC
1 GTATTTTTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTC
16902 ATCAGGTTGT
Statistics
Matches: 325, Mismatches: 42, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
63 3 0.01
64 27 0.08
65 61 0.19
66 8 0.02
67 101 0.31
68 78 0.24
69 46 0.14
70 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (67 bp):
GTATTTTTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTT
TA
Found at i:16880 original size:132 final size:130
Alignment explanation
Indices: 16465--16900 Score: 468
Period size: 132 Copynumber: 3.3 Consensus size: 130
16455 GTATTTTCTC
* *
16465 TTTCCAGAAATACCCTTTCT-GTC-AAAGGGTCATTTTTGTCTTTTCGCATTTAAGTTTAGTATT
1 TTTCCAAAAATACCC-TTCTGGTCGAAA-GGTCAGTTTTGTCTTTTC-CATTTAAGTTTAGTATT
* * ** **
16528 TTGTTTTTCAAAAAATACCCTTTCGGTCGAAGGGTCATTTTAATCTTTTCGCATTTAAATTTAGT
63 TTGTTTTTCCAAAAATACCCTTT-AGTCGAAGGGTCATTTTCGTCTTTT-GCATTT-AGGTT--T
*
16593 AGTTTGTTT
123 AGTTT-TAT
* * * * *
16602 TTTCCAAAAATACCCTT-TCGGTGGAAGGGTCA-TTTTCATCTTTTGCATTTAGGTTTAGTATTT
1 TTTCCAAAAATACCCTTCT-GGTCGAAAGGTCAGTTTT-GTCTTTTCCATTTAAGTTTAGTATTT
* * *
16665 TGTTTTTCCAAAAATACCCTTTCAGTGGAAGGATCATTTTCGTCTTTTGCATTCAGGTTTAGTTT
64 TGTTTTTCCAAAAATACCCTTT-AGTCGAAGGGTCATTTTCGTCTTTTGCATTTAGGTTTAGTTT
16730 TAT
128 TAT
* *
16733 TTTCCAAAAGTACCCTTCTGGTCGAAAGGTCAGTTTTGTCTTTTTCCATTCAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTCTGGTCGAAAGGTCAGTTTTGTC-TTTTCCATTTAAGTTTAGTATTTT
** * * *
16798 -CATTTCCATAAATACCCTTTTGTTCGAAGGGTCAGTTTCGTCTTTTGGCATTTAGGTTTAGTTT
65 GTTTTTCCAAAAATACCCTTTAG-TCGAAGGGTCATTTTCGTCTTTT-GCATTTAGGTTTAGTTT
16862 TAT
128 TAT
* *
16865 TTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTT
1 TTTCCAAAAATACCCTTCTGGTCGAAAGGTCAGTTT
16901 CATCAGGTTG
Statistics
Matches: 256, Mismatches: 34, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
130 1 0.00
131 68 0.27
132 84 0.33
134 3 0.01
135 6 0.02
136 65 0.25
137 27 0.11
138 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (130 bp):
TTTCCAAAAATACCCTTCTGGTCGAAAGGTCAGTTTTGTCTTTTCCATTTAAGTTTAGTATTTTG
TTTTTCCAAAAATACCCTTTAGTCGAAGGGTCATTTTCGTCTTTTGCATTTAGGTTTAGTTTTAT
Found at i:17509 original size:12 final size:13
Alignment explanation
Indices: 17494--17538 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
17484 AATCTAAATT
17494 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
17506 TAAAGCAAATTAA
1 TAAAGCAGATTAA
17519 TAAAGCAGATTAA
1 TAAAGCAGATTAA
17532 TAAAGCA
1 TAAAGCA
17539 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:17545 original size:25 final size:25
Alignment explanation
Indices: 17494--17546 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
17484 AATCTAAATT
*
17494 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
17519 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
17544 TAA
1 TAA
17547 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:24188 original size:22 final size:22
Alignment explanation
Indices: 24176--24709 Score: 581
Period size: 22 Copynumber: 24.4 Consensus size: 22
24166 ACTTCCAAAC
*
24176 GTCTCAGGGCAGACTTTTAAGT
1 GTCTCAGGGCAGACTTTCAAGT
* * *
24198 GTCTCAAGGAAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
* *
24220 GTCTCAAGGCAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
* * * *
24242 GTCTCAAGGCAAACTTCCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
*
24264 GTCTCAGGGCATACTTTCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
* * *
24286 GCCTCAAGGTAGACTTTCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
*
24308 GTCTCAAGGCAGACTTTCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
* ** *
24330 GTCTCAAGTTAGACTTCCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
* ** *
24352 GTCTCAAGTTAGACTTCCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
*
24374 GTCTCAGGGTAGACTTTCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
* *
24396 GTCTCAAGGCAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
* * *
24418 GTCTCCGGGCAAACTTTCCAGT
1 GTCTCAGGGCAGACTTTCAAGT
*
24440 GTCTCAGGGTAGACTTTCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
* *
24462 GTCTCAAGGCAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
* *
24484 GTCTCCGGGCAAACTTTCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
*
24506 GTCTCAGGGCAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
* *
24528 GTCACAGGGCAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
* *
24550 GTCTCCGGGCAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
*
24572 GTCTCAGGGCAGACTTTCAAGC
1 GTCTCAGGGCAGACTTTCAAGT
* * *
24594 GCCTCAGGACAGAC-CTCTAAGT
1 GTCTCAGGGCAGACTTTC-AAGT
* * * * *
24616 GTCTCAAGGAAAACTTT-TAGC
1 GTCTCAGGGCAGACTTTCAAGT
24637 GTCTCAGGGCAGACTTTCAAGT
1 GTCTCAGGGCAGACTTTCAAGT
*
24659 GTCTCAGGGCAGACTATC-AGT
1 GTCTCAGGGCAGACTTTCAAGT
*
24680 GTCTCAGGGCAGACTTT-TAGT
1 GTCTCAGGGCAGACTTTCAAGT
24701 GTCTCAGGG
1 GTCTCAGGG
24710 TAGGATTTTA
Statistics
Matches: 440, Mismatches: 68, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
21 49 0.11
22 390 0.89
23 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (22 bp):
GTCTCAGGGCAGACTTTCAAGT
Done.