Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006084.1 Corchorus capsularis cultivar CVL-1 contig06102, 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: 34311
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:1346 original size:133 final size:131
Alignment explanation
Indices: 1031--1430 Score: 531
Period size: 132 Copynumber: 3.0 Consensus size: 131
1021 ACATTGTTTA
*
1031 AATTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAAC
1 AATTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAAC
* ** * * *
1096 AATTTCATTTTTACCATTTTACTATTTTAATTAAAAAACATTTTTAGATATACTTTTATATGTTT
66 TATTTC-TTTTTACCATTTTACTATTTTAATTAAAAAA-A-ACTTAGATATA--TTAAAATTTTT
1161 -AA-AT
126 AAATAT
* *
1165 --TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTAAATTAAATCTAACATCCTTATAAC
1 AATTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAAC
* *
1228 TATTTCTTTTTCACCATTTTACTAGTTTAATTAAAAAAAACTTAGATACATTAGAAATTTTTAAA
66 TATTTCTTTTT-ACCATTTTACTATTTTAATTAAAAAAAACTTAGATATATTA-AAATTTTTAAA
1293 TAT
129 TAT
* *
1296 AATTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
1 AATTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAAC
* * * *
1361 TATTTTATTTTTATCATTTTACTATTTTAATT-GAAAAAACTTAGATATATTATAATTTTTAAAA
66 TA-TTTCTTTTTACCATTTTACTATTTTAATTAAAAAAAACTTAGATATATTAAAATTTTT-AAA
1425 TAT
129 TAT
1428 AAT
1 AAT
1431 CTTTTACAAT
Statistics
Matches: 238, Mismatches: 20, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
128 2 0.01
129 6 0.03
130 10 0.04
131 15 0.06
132 117 0.49
133 80 0.34
134 8 0.03
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (131 bp):
AATTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAAC
TATTTCTTTTTACCATTTTACTATTTTAATTAAAAAAAACTTAGATATATTAAAATTTTTAAATA
T
Found at i:1444 original size:25 final size:24
Alignment explanation
Indices: 1416--1462 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
1406 TATATTATAA
1416 TTTTTA-AAATATAATCTTTTACAAT
1 TTTTTAGAAATA-AA-CTTTTACAAT
1441 TTTTTAGAAATAAACTTTTACA
1 TTTTTAGAAATAAACTTTTACA
1463 GTTATTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTTTAGAAATAAACTTTTACAAT
Found at i:2468 original size:3 final size:3
Alignment explanation
Indices: 2460--2499 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2450 AGGTAAAATT
2460 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2500 CAACATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3069 original size:15 final size:14
Alignment explanation
Indices: 3046--3079 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3036 TCAACTTATG
*
3046 TATAATATCTATATC
1 TATACTATCTATA-C
3061 TATACTATCTATAC
1 TATACTATCTATAC
3075 TATAC
1 TATAC
3080 ATTAATGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (14 bp):
TATACTATCTATAC
Found at i:3995 original size:412 final size:415
Alignment explanation
Indices: 3225--4052 Score: 1455
Period size: 412 Copynumber: 2.0 Consensus size: 415
3215 TTTGGGAACT
*
3225 TTGATTAAAAGTTACTATTTATGGGTCCCACTTTCAATAAACTAATTTTTTTCTGGAATATTTAG
1 TTGATTAAAAATTACTATTTATGGGTCCCACTTTCAATAAACTAATTTTTTTCTGGAATATTTAG
* *
3290 CAAATGATCCTTATACTTTTACGTTTTATGCTATTTAATCCCTCACAAATTCTGGGTTGGACGAT
66 CAAATGATCCTTATACTTTTACGCTTTATGCTATTTAATCCCTCACAAATTATGGGTTGGACGAT
*
3355 TTAACGTTTCAACTTTAATTCTTTTGTTTTTTTTGTTCTATTTATCCGATCAAGGTGATTCAAAT
131 TTAACGTTTCAACTTTAATTCTTTTGTATTTTTTGTTCTATTTATCCGATCAAGGTGATTCAAAT
** *
3420 ATCTATTTAAAGGTAATTTAATGATCTACAACTTCCATGAAGTACTCAAAAGGCAATTTGATTGT
196 ATCTATTTAAAGGTAATTTAATGATCTACAACTTCCATGAAGTACTCAAAACCCAATTTGAATGT
3485 TTTGATTCTAAAAAATGCTTCTGAAATTCTGTGGTCTCGATTGCCGGTCTATCTAATATTGTATA
261 TTTGATTCTAAAAAATGCTTCTGAAATTCTGTGGTCTCGATTGCCGGTCTATCTAATATTGTATA
*
3550 ATTTTAAGTCCACTTGTCCGATTGAGCTTGTTCAAGTGTTGGTTAAAAGGTTATTGTGTGATCTA
326 ATTTTAAGTCCACTTATCCGATTGAGCTTGTTCAAGTGTTGGTTAAAAGGTTATTGTGTGATCTA
3615 CAACTTTCGTCAAGGGCCCAAAACC
391 CAACTTTCGTCAAGGGCCCAAAACC
*
3640 TTGATTAAAAATTACTGTTTATGGGTCCCACTTTCAATAAACTAATTTTTTTCTGGAATATTTAG
1 TTGATTAAAAATTACTATTTATGGGTCCCACTTTCAATAAACTAATTTTTTTCTGGAATATTTAG
*
3705 CAAATGATCC-TATACTTTTATGCTTTATGCTATTTAATCCCTCACAAATTATGGGTTGGACGAT
66 CAAATGATCCTTATACTTTTACGCTTTATGCTATTTAATCCCTCACAAATTATGGGTTGGACGAT
**
3769 TTAACGTTTCTTCTTTAATTC-TTT-TATTTTTTGTTCTATTTATCCGATCAAGGTGATTCAAAT
131 TTAACGTTTCAACTTTAATTCTTTTGTATTTTTTGTTCTATTTATCCGATCAAGGTGATTCAAAT
* * * *
3832 GTCTATTTAAAGTTAATTTAATGATCTACAACTTTCATGAAGTACTCAAAACCCAATTTTAATGT
196 ATCTATTTAAAGGTAATTTAATGATCTACAACTTCCATGAAGTACTCAAAACCCAATTTGAATGT
*
3897 TTTGATTCTAAAAAATGCTTCTGAAATTTTGTGGTCTCGATTGCCGGTCTATCTAATATTGTATA
261 TTTGATTCTAAAAAATGCTTCTGAAATTCTGTGGTCTCGATTGCCGGTCTATCTAATATTGTATA
* * *
3962 ATTTTAGGTCCACTTATCCGATTGAGTTTGTTCAAGTGTTGGTTAAACGGTTATTGTGTGATCTA
326 ATTTTAAGTCCACTTATCCGATTGAGCTTGTTCAAGTGTTGGTTAAAAGGTTATTGTGTGATCTA
4027 CAACTTTCGTCAAGGGCCCAAAACC
391 CAACTTTCGTCAAGGGCCCAAAACC
4052 T
1 T
4053 AAATTTGATT
Statistics
Matches: 393, Mismatches: 20, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
412 247 0.63
413 3 0.01
414 70 0.18
415 73 0.19
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (415 bp):
TTGATTAAAAATTACTATTTATGGGTCCCACTTTCAATAAACTAATTTTTTTCTGGAATATTTAG
CAAATGATCCTTATACTTTTACGCTTTATGCTATTTAATCCCTCACAAATTATGGGTTGGACGAT
TTAACGTTTCAACTTTAATTCTTTTGTATTTTTTGTTCTATTTATCCGATCAAGGTGATTCAAAT
ATCTATTTAAAGGTAATTTAATGATCTACAACTTCCATGAAGTACTCAAAACCCAATTTGAATGT
TTTGATTCTAAAAAATGCTTCTGAAATTCTGTGGTCTCGATTGCCGGTCTATCTAATATTGTATA
ATTTTAAGTCCACTTATCCGATTGAGCTTGTTCAAGTGTTGGTTAAAAGGTTATTGTGTGATCTA
CAACTTTCGTCAAGGGCCCAAAACC
Found at i:5123 original size:30 final size:30
Alignment explanation
Indices: 5087--5147 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
5077 TTCAAGGGGT
5087 AGGGAATGATGCGCCCAA-GGCTTATCATGG
1 AGGGAATGATGCG-CCAAGGGCTTATCATGG
*
5117 AGGGAATGATGCGTCAAGGGCTTATCATGG
1 AGGGAATGATGCGCCAAGGGCTTATCATGG
5147 A
1 A
5148 TTTGAAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.28, C:0.16, G:0.34, T:0.21
Consensus pattern (30 bp):
AGGGAATGATGCGCCAAGGGCTTATCATGG
Found at i:5212 original size:18 final size:19
Alignment explanation
Indices: 5189--5226 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5179 TTGCATGGGC
*
5189 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
5207 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
5226 T
1 T
5227 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:7821 original size:38 final size:38
Alignment explanation
Indices: 7728--7875 Score: 208
Period size: 38 Copynumber: 3.9 Consensus size: 38
7718 TCGAGTCTAG
* * *
7728 CCAACAG-TTAACCCCCAGAGACACGGGTCCACTTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
7765 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAA-CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
7804 CCAACAGTTTGACCCCCTGAGGTACGGGTCCACACTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* *
7842 CCATCAATTTAACCCCCTGAGGCACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
7876 ATGCACAGCC
Statistics
Matches: 98, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
37 4 0.04
38 63 0.64
39 31 0.32
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:8078 original size:15 final size:17
Alignment explanation
Indices: 8053--8087 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
8043 TGTATAAAAC
8053 AATTGATAATAC-ATAT
1 AATTGATAATACAATAT
8069 AATT-ATAATACAATAT
1 AATTGATAATACAATAT
8085 AAT
1 AAT
8088 CTTTGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTGATAATACAATAT
Found at i:10492 original size:15 final size:16
Alignment explanation
Indices: 10472--10505 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
10462 GTTTTCAAAG
10472 ATTATATGTATTAT-A
1 ATTATATGTATTATCA
10487 ATTATATGTATTATCA
1 ATTATATGTATTATCA
10503 ATT
1 ATT
10506 GTTTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTATATGTATTATCA
Found at i:11213 original size:48 final size:48
Alignment explanation
Indices: 11143--11712 Score: 804
Period size: 48 Copynumber: 11.9 Consensus size: 48
11133 AGACAAATCT
* * *
11143 AGCACCTTCCGACTGGGAAGGGCAAAACTGGAAATAGGCACTGAAAAT
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* *
11191 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTAAAAAC
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* *
11239 AGCACCTTCCGACCGGAAAGGGTAAAACTGGAAATAGACACTGAAAAC
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
*
11287 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAAAC
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* *
11335 AGCACCTTCCGACCAGGAAGGGCAAAACTGG--A-AGACATTGAAAAC
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* *
11380 AGCACCTTCCGACCGTGAAGGGCAAAATTGGAAATAGACACTGAAAAC
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* * * *
11428 AGTACCTTCCGACCGGGAAGGGCAAAACCGAAAATAGACACCGAAAAC
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* * *
11476 AGCACCTTCCGGCCGGGAAGGGCGAAACTGGAAATAAACACTGAAAAC
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* * * * *
11524 AGCACCTTCCGACCAGGAAGGGCGAAATTTGAAATAGACACTGAAAAT
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
*
11572 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAT
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* ** * *
11620 AGCACCTTCCAACCGGGAAGGGCAAAACTAAAAATAAACACTGAAAAT
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
* * * * *
11668 AGCCCCTTCCGACCGGTAAGGGCGAAACAGGAAATAAACACTGAA
1 AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAA
11713 CACCTTTTGA
Statistics
Matches: 466, Mismatches: 53, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
45 39 0.08
46 1 0.00
47 1 0.00
48 425 0.91
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12
Consensus pattern (48 bp):
AGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACACTGAAAAC
Found at i:21705 original size:39 final size:38
Alignment explanation
Indices: 21576--21729 Score: 247
Period size: 38 Copynumber: 4.1 Consensus size: 38
21566 ATTCGTATCA
* *
21576 GTAAGAGTGGACCCGTACCTCAAGGGGTTAAACTGTTG
1 GTAAGAGTGGACCCGTGCCTCAGGGGGTTAAACTGTTG
21614 GTAAGAGTGGACCCGTGCCTCAGGGGGTTAAACTGTTG
1 GTAAGAGTGGACCCGTGCCTCAGGGGGTTAAACTGTTG
*
21652 GTAAGAGTGAACCCGTGCCTCAGGGGGTTAAACTGATTG
1 GTAAGAGTGGACCCGTGCCTCAGGGGGTTAAACTG-TTG
* *
21691 GTAAGAGTGGACCCGTGTCTTAGGGGGTT-AACTGTTG
1 GTAAGAGTGGACCCGTGCCTCAGGGGGTTAAACTGTTG
21728 GT
1 GT
21730 TAGACTCGAG
Statistics
Matches: 109, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
37 5 0.05
38 75 0.69
39 29 0.27
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (38 bp):
GTAAGAGTGGACCCGTGCCTCAGGGGGTTAAACTGTTG
Found at i:21769 original size:6 final size:6
Alignment explanation
Indices: 21758--21789 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
21748 CGTTAACGGA
21758 TGATTG TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TG
21790 GTGTAGCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:22800 original size:14 final size:14
Alignment explanation
Indices: 22781--22808 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22771 TCCTCTGCTT
22781 TAACAAAAATAAAA
1 TAACAAAAATAAAA
22795 TAACAAAAATAAAA
1 TAACAAAAATAAAA
22809 AATAGTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (14 bp):
TAACAAAAATAAAA
Found at i:24873 original size:1 final size:1
Alignment explanation
Indices: 24862--24932 Score: 70
Period size: 1 Copynumber: 71.0 Consensus size: 1
24852 CTCTTAATTG
* * * * * * * *
24862 TTTTTTGTTTTTTTTTTGTTTTGTTTTGTTTTGTTTTTGTTTTTTTTTTTTTGTTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24927 TTTTTT
1 TTTTTT
24933 ATCTAGGGAG
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:24878 original size:11 final size:11
Alignment explanation
Indices: 24862--24932 Score: 92
Period size: 11 Copynumber: 6.3 Consensus size: 11
24852 CTCTTAATTG
24862 TTTTTTGTTTT
1 TTTTTTGTTTT
24873 TTTTTTGTTTT
1 TTTTTTGTTTT
24884 GTTTTGTT-TTGTT
1 -TTTT-TTGTT-TT
24897 TTTGTTT-TTTT
1 TTT-TTTGTTTT
24908 TTTTTTGTTTT
1 TTTTTTGTTTT
24919 TTTTTTGTTTT
1 TTTTTTGTTTT
24930 TTT
1 TTT
24933 ATCTAGGGAG
Statistics
Matches: 55, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.05
11 34 0.62
12 13 0.24
13 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TTTTTTGTTTT
Done.