Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004882.1 Corchorus capsularis cultivar CVL-1 contig04900, 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: 7106
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Found at i:99 original size:21 final size:21
Alignment explanation
Indices: 75--136 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
65 ATTATTTGTA
75 GTTTGACCATTAAGATTTGGG
1 GTTTGACCATTAAGATTTGGG
* * * * *
96 GTTTCACAATGGATGCTTTGGG
1 GTTTGACCAT-TAAGATTTGGG
*
118 GTTTGACCATTAATATTTG
1 GTTTGACCATTAAGATTTG
137 AGCAAGTTGT
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (21 bp):
GTTTGACCATTAAGATTTGGG
Found at i:1159 original size:33 final size:33
Alignment explanation
Indices: 1117--1200 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
1107 TACACTGAGT
* *
1117 CTCCCCACTAGGACGGCTCAGCCACGGCGGAGC
1 CTCCCCACTAGGACGGCTCAACCACGCCGGAGC
1150 CTCCCCACTAGGGA-GGCTCAACCACGCCGGAGC
1 CTCCCCACTA-GGACGGCTCAACCACGCCGGAGC
* *
1183 CTCCCCACTGGGGCGGCT
1 CTCCCCACTAGGACGGCT
1201 TCGTCACGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 2 0.04
33 40 0.89
34 3 0.07
ACGTcount: A:0.17, C:0.43, G:0.30, T:0.11
Consensus pattern (33 bp):
CTCCCCACTAGGACGGCTCAACCACGCCGGAGC
Found at i:1357 original size:33 final size:32
Alignment explanation
Indices: 1315--1411 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 32
1305 CTGCCATGGC
1315 GTGGGGCGGCCTGCCCATGGTGAAGCCGCCCCA
1 GTGGGGCGGCCTG-CCATGGTGAAGCCGCCCCA
* **
1348 GTGGGGCGGCTCTGCCGTGGTTG-AGCCTTCCCA
1 GTGGGGCGGC-CTGCCATGG-TGAAGCCGCCCCA
* *
1381 ATGGGGCGGCTTGAGCCATGGT-AAGCCGCCC
1 GTGGGGCGGCCT--GCCATGGTGAAGCCGCCC
1412 TCTTGGGGCG
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
32 1 0.02
33 39 0.76
34 11 0.22
ACGTcount: A:0.11, C:0.32, G:0.39, T:0.18
Consensus pattern (32 bp):
GTGGGGCGGCCTGCCATGGTGAAGCCGCCCCA
Found at i:1914 original size:19 final size:19
Alignment explanation
Indices: 1890--1926 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1880 AGCCTCCCTC
1890 CCATTTTATTCCCTTTTAG
1 CCATTTTATTCCCTTTTAG
*
1909 CCATTTTATTCCTTTTTA
1 CCATTTTATTCCCTTTTA
1927 TCTTTTTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (19 bp):
CCATTTTATTCCCTTTTAG
Found at i:3309 original size:73 final size:70
Alignment explanation
Indices: 3232--3384 Score: 173
Period size: 73 Copynumber: 2.1 Consensus size: 70
3222 TAATATATCA
* * * *
3232 AGTTTTTTAATTAAAATAGTAAAATGGTAAAATA-TAAGTAATAAGGATATTAGATTTAATTATA
1 AGTTTTTTAAGTAAAATAGTAAAA---TAAAATAGTAACT-ATAAAGATATTAGATTTAATTAAA
3296 TAAAAATAG
62 TAAAAATAG
* * *
3305 AGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAAT
1 AG-TTTT--TTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAAT
3370 AAAAATAG
63 AAAAATAG
3378 AGTTTTT
1 AGTTTTT
3385 AGTTAAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
70 1 0.01
72 4 0.06
73 41 0.59
74 7 0.10
76 16 0.23
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.39
Consensus pattern (70 bp):
AGTTTTTTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAATAAA
AATAG
Found at i:3330 original size:68 final size:70
Alignment explanation
Indices: 3249--3410 Score: 195
Period size: 73 Copynumber: 2.3 Consensus size: 70
3239 TAATTAAAAT
* * *
3249 AGTAAAATGGTAAAATATAAG-TA-ATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
*
3312 AGTTG
66 AGTTA
* *
3317 AGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAATAAAAATAGAGTT
1 AGTAAAATAGTAAAAT-ATA-AGTTAC-ATAAAGATATTAGATTTAATTAAATAAAAATAGAGTT
3382 TTTAGTTA
63 TTTAGTTA
*
3390 AATAAAACTA-TAAAAATATAA
1 AGTAAAA-TAGT-AAAATATAA
3411 AAATAGAGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
68 15 0.19
69 2 0.03
70 2 0.03
71 2 0.03
72 1 0.01
73 50 0.63
74 7 0.09
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (70 bp):
AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTA
Found at i:3435 original size:39 final size:39
Alignment explanation
Indices: 3368--3524 Score: 126
Period size: 39 Copynumber: 4.2 Consensus size: 39
3358 ATTTAATTAA
3368 ATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAAAAAT
1 ATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGTAAAAAT
* *
3407 ATAAAAATAGAGTTTTTAGTTGAGTAAAATAGT--AAA-
1 ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAAAT
* *
3443 AT-AAAAT--AG---TTA--TAAATATATTATATTAAATTAA-
1 ATAAAAATAGAGTTTTTAGTTAAATA-A-AATAGTAAA--AAT
3477 ATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAAAAAT
1 ATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGTAAAAAT
3516 ATAAAAATA
1 ATAAAAATA
3525 TAAAAATAGA
Statistics
Matches: 94, Mismatches: 7, Indels: 34
0.70 0.05 0.25
Matches are distributed among these distances:
28 4 0.04
29 1 0.01
30 7 0.07
32 1 0.01
33 2 0.02
34 4 0.04
35 10 0.11
36 2 0.02
37 5 0.05
38 4 0.04
39 37 0.39
40 8 0.09
41 3 0.03
42 6 0.06
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.34
Consensus pattern (39 bp):
ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAAAT
Found at i:3513 original size:8 final size:8
Alignment explanation
Indices: 3500--3532 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
3490 TTTTAGTTAA
*
3500 ATAAAACT
1 ATAAAAAT
3508 ATAAAAAT
1 ATAAAAAT
3516 ATAAAAAT
1 ATAAAAAT
3524 ATAAAAAT
1 ATAAAAAT
3532 A
1 A
3533 GAGTTTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:3548 original size:117 final size:117
Alignment explanation
Indices: 3293--3631 Score: 568
Period size: 117 Copynumber: 2.9 Consensus size: 117
3283 AGATTTAATT
*
3293 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTAT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAG-T--TATAAATATATTAT
3358 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAAC--------TATAAAA
63 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAAATATAAAA
3405 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
*
3470 AAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAAATATAAAA
66 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAAATATAAAA
*
3522 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATGGTAAAATAAAATAGTTATAAATATATTATATT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
3587 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAAA
66 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAAA
3632 CTTAAACAAT
Statistics
Matches: 215, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
109 52 0.24
111 1 0.00
112 47 0.22
117 115 0.53
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (117 bp):
ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAAATATAAAA
Found at i:3800 original size:11 final size:11
Alignment explanation
Indices: 3780--3812 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3770 CCTTAGAAGC
*
3780 AAACACAAAAA
1 AAACAAAAAAA
3791 AAACAAAAAAA
1 AAACAAAAAAA
3802 AAA-AAAAAAA
1 AAACAAAAAAA
3812 A
1 A
3813 GTGACATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (11 bp):
AAACAAAAAAA
Done.