Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016461.1 Corchorus capsularis cultivar CVL-1 contig16482, 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: 40471
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1532 original size:21 final size:24
Alignment explanation
Indices: 1488--1567 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 24
1478 TATCTTAGAT
1488 ATAATATATATTACTAAATAAATA
1 ATAATATATATTACTAAATAAATA
*
1512 ATAA-ATATATT-TTAAAT-AAT-
1 ATAATATATATTACTAAATAAATA
*
1532 A-AATA-ATGAGTT-CAAAATAAATAA
1 ATAATATAT-A-TTACTAAATAAAT-A
1556 ATAATATATATT
1 ATAATATATATT
1568 TAATTACTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 9 0.20
22 8 0.18
23 7 0.16
24 7 0.16
25 5 0.11
26 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAATATATATTACTAAATAAATA
Found at i:2317 original size:20 final size:22
Alignment explanation
Indices: 2280--2319 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
2270 AATTTACCTT
2280 TATATATATATATAAATTTTCA
1 TATATATATATATAAATTTTCA
*
2302 TATAT-TATAT-TCAATTTT
1 TATATATATATATAAATTTT
2320 TCAACACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATATATATATAAATTTTCA
Found at i:2474 original size:26 final size:26
Alignment explanation
Indices: 2428--2492 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
2418 TACTAAAAAT
2428 AATAAATGTA-TTTTTTTTGAAAAGC
1 AATAAATGTATTTTTTTTTGAAAAGC
2453 AATAAATGTATTTTTTTTTGAAAAGC
1 AATAAATGTATTTTTTTTTGAAAAGC
2479 AATAAATGTATTTT
1 AATAAATGTATTTT
2493 ACAAACTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
25 10 0.26
26 29 0.74
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (26 bp):
AATAAATGTATTTTTTTTTGAAAAGC
Found at i:3212 original size:46 final size:46
Alignment explanation
Indices: 3159--3252 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
3149 GAGATTTCAA
* *
3159 TTGTATTTGTTGGGGAGGGGGTTGTTTGTTAGCTCATACATTAGCG
1 TTGTATTTGTTGGGGAGGGGGTTGTTTGTTAGCTAATACATTAACG
* *
3205 TTGTATTTGTTGGGGAGGGGGTTGTTTGTTGGCTAATAGATTAACG
1 TTGTATTTGTTGGGGAGGGGGTTGTTTGTTAGCTAATACATTAACG
3251 TT
1 TT
3253 TCAGTGATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.16, C:0.06, G:0.35, T:0.43
Consensus pattern (46 bp):
TTGTATTTGTTGGGGAGGGGGTTGTTTGTTAGCTAATACATTAACG
Found at i:5059 original size:19 final size:20
Alignment explanation
Indices: 5030--5068 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
5020 CGCGACCCGC
5030 TGTTCTTCTTCTTTTTTTTT
1 TGTTCTTCTTCTTTTTTTTT
5050 TGTT-TTCTTCTTTTTTTTT
1 TGTTCTTCTTCTTTTTTTTT
5069 CCTCTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (20 bp):
TGTTCTTCTTCTTTTTTTTT
Found at i:11785 original size:362 final size:354
Alignment explanation
Indices: 11109--11830 Score: 1047
Period size: 362 Copynumber: 2.0 Consensus size: 354
11099 AACATATAAC
* * * * *
11109 ATATATTAAAGTTGAAAATGGAATTACCCTTTTGTTTAGTTATAAGATGTACCATATTTCCCCAA
1 ATATATTAAAGTTGAAAATGAAATTACCCTTTTGTCTAGCTATAAGATGCACCACATTTCCCCAA
* *
11174 CAACAAATTGTCAGCGGTATTGCGGTACTTTCATGCTCGGTATTTTCATTATTATTGTTGATTTT
66 CAACAAATTGTCAGCGGTATTGCGGTACTTTCATGCACGGTATTTTCATTATTATTGTTGATTGT
* *
11239 TGAGGATATTTTGGGAATTTTAGGATAAAGTTACTATTTGGCGGATCCCACTCTCAACTCTCAAT
131 TGAGGATATTTTGGGAACTTTAGGATAAAATTACTATTTGGCGGAT--C-CTCT-AACTCTCAAT
* * *
11304 AAGCAAATCATTTTTTGTTGGATTATTTCTCAAATGATCATCATACTTTTATACTTTATGCTATT
192 AAACAAATAATTTTTTGTTGGATTATTTATCAAATGATCATCATACTTTTATACTTTATGCTATT
*
11369 TAATCCTTTACAATTATGGGTTGGACGATTGAATGTTTCGACTTTAATTTTTTTTTTTTCTATTT
257 TAATCCTTTACAATTATGGGTTCGACGATTGAATGTTTCGACTTTAA----TTTTTTTTCTATTT
11434 GTCCGATCAAGGTAATTCAGGAGTCTATTTAAAGATA
318 GTCCGATCAAGGTAATTCAGGAGTCTATTTAAAGATA
11471 ATATATTAAAGTTGAAAATGAAATTACCCTTTTGTCTAGCTATAAGATGCACCACA-TTCCACCA
1 ATATATTAAAGTTGAAAATGAAATTACCCTTTTGTCTAGCTATAAGATGCACCACATTTCC-CCA
* * **
11535 AGAACAAATTGTCAGGGGTATTTTGGTACTTTCATGCACGGTATTTTCATTATTATTGTTGATTG
65 ACAACAAATTGTCAGCGGTATTGCGGTACTTTCATGCACGGTATTTTCATTATTATTGTTGATTG
* * *
11600 TTGAGGGTATTTTGGGAACTTTAGGATAAAATTACTATTTGGTGGGT-C-CT-ACTCTCAATAAA
130 TTGAGGATATTTTGGGAACTTTAGGATAAAATTACTATTTGGCGGATCCTCTAACTCTCAATAAA
*
11662 CAAATAATTTTTTGTTGGATTATTTATCAAATGATCCTCATACTTTTATACTTTATGCTATTTAA
195 CAAATAATTTTTTGTTGGATTATTTATCAAATGATCATCATACTTTTATACTTTATGCTATTTAA
* *
11727 TCCTTTACAATTATGGGTTCGACGATTGAATGTTTTGGCTTTAATTCTTTTATTTTTTTCTATTT
260 TCCTTTACAATTATGGGTTCGACGATTGAATGTTTCGACTTTAA------T-TTTTTTTCTATTT
* *
11792 GTCCGATCAAGGTAATTCAGGTGTCTATTTAAAGGTA
318 GTCCGATCAAGGTAATTCAGGAGTCTATTTAAAGATA
11829 AT
1 AT
11831 TTCATGGTCT
Statistics
Matches: 330, Mismatches: 26, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
355 114 0.35
357 6 0.02
358 51 0.15
361 4 0.01
362 155 0.47
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (354 bp):
ATATATTAAAGTTGAAAATGAAATTACCCTTTTGTCTAGCTATAAGATGCACCACATTTCCCCAA
CAACAAATTGTCAGCGGTATTGCGGTACTTTCATGCACGGTATTTTCATTATTATTGTTGATTGT
TGAGGATATTTTGGGAACTTTAGGATAAAATTACTATTTGGCGGATCCTCTAACTCTCAATAAAC
AAATAATTTTTTGTTGGATTATTTATCAAATGATCATCATACTTTTATACTTTATGCTATTTAAT
CCTTTACAATTATGGGTTCGACGATTGAATGTTTCGACTTTAATTTTTTTTCTATTTGTCCGATC
AAGGTAATTCAGGAGTCTATTTAAAGATA
Found at i:15161 original size:26 final size:26
Alignment explanation
Indices: 15119--15168 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
15109 ATGATTTAGG
*
15119 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTCTTTTGA
* *
15145 GGTTACTAACACTCTTTTTTTTTT
1 GGTTACTAACACCCTTTTTCTTTT
15169 TTCAGAGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (26 bp):
GGTTACTAACACCCTTTTTCTTTTGA
Found at i:16054 original size:18 final size:19
Alignment explanation
Indices: 16031--16068 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16021 AGAAACATGT
*
16031 TACAAA-TACAAATTAAAG
1 TACAAACTACAAATAAAAG
16049 TACAAACTACAAATAAAAG
1 TACAAACTACAAATAAAAG
16068 T
1 T
16069 GCATGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (19 bp):
TACAAACTACAAATAAAAG
Found at i:35033 original size:11 final size:11
Alignment explanation
Indices: 35004--35033 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
34994 TTGACAGCGT
35004 AACAAAAACAA
1 AACAAAAACAA
*
35015 AACGAAAACAA
1 AACAAAAACAA
35026 AACAAAAA
1 AACAAAAA
35034 TGAAAAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Done.