Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009724.1 Corchorus capsularis cultivar CVL-1 contig09745, 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: 71354
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:894 original size:19 final size:19
Alignment explanation
Indices: 854--891 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
844 AATTTATCCT
854 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
873 ATCT-TCTGTTGGATTTGA
1 ATCTATCTGTTGAATTTGA
891 A
1 A
892 ATCCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:5343 original size:18 final size:19
Alignment explanation
Indices: 5315--5350 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5305 GATTTATCCT
5315 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
5334 ATCT-TCTGTTGGATTTG
1 ATCTATCTGTTGAATTTG
5351 GAAATCCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.50
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:23478 original size:15 final size:15
Alignment explanation
Indices: 23460--23488 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23450 TAACTCTCCA
23460 TGGGAGAGTGATTCT
1 TGGGAGAGTGATTCT
23475 TGGGAGAGTGATTC
1 TGGGAGAGTGATTC
23489 CAGGGAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.41, T:0.31
Consensus pattern (15 bp):
TGGGAGAGTGATTCT
Found at i:23494 original size:15 final size:15
Alignment explanation
Indices: 23456--23494 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
23446 GGAATAACTC
23456 TCCATGGGAGAGTGAT
1 TCCA-GGGAGAGTGAT
**
23472 TCTTGGGAGAGTGAT
1 TCCAGGGAGAGTGAT
23487 TCCAGGGA
1 TCCAGGGA
23495 AAGTAACAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.23, C:0.13, G:0.38, T:0.26
Consensus pattern (15 bp):
TCCAGGGAGAGTGAT
Found at i:26005 original size:18 final size:18
Alignment explanation
Indices: 25982--26019 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
25972 ATGAGCAGCC
25982 TTTCATAATCATCCAAAT
1 TTTCATAATCATCCAAAT
26000 TTTCATAATCATCCAAAT
1 TTTCATAATCATCCAAAT
26018 TT
1 TT
26020 CCACCACACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTCATAATCATCCAAAT
Found at i:26180 original size:32 final size:32
Alignment explanation
Indices: 26144--26207 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
26134 ATCAAGTAGA
* * *
26144 TTGAGGCAAATCCTATGAGCTCCTTGATAGTC
1 TTGAGCCAAATCCTACGAGCTCCTAGATAGTC
26176 TTGAGCCAAATCCTACGAGCTCCTAGATAGTC
1 TTGAGCCAAATCCTACGAGCTCCTAGATAGTC
26208 CGTTAGGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (32 bp):
TTGAGCCAAATCCTACGAGCTCCTAGATAGTC
Found at i:26315 original size:6 final size:6
Alignment explanation
Indices: 26304--26360 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
26294 TGATATTTGA
* * *
26304 ATAATT ATAATT ATTATT TTAA-- ATAATT ATAATT AT-TTT ATAA-T
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
26348 -TAATT ATAATT AT
1 ATAATT ATAATT AT
26361 TGAGTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
4 6 0.15
5 6 0.15
6 28 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATAATT
Found at i:26322 original size:21 final size:20
Alignment explanation
Indices: 26297--26361 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 20
26287 TGATTTTTGA
26297 TATTTGAATAATTATAATTAT
1 TATTT-AATAATTATAATTAT
26318 TATTTTAAATAATTATAATTAT
1 TA-TTT-AATAATTATAATTAT
26340 T-TTATAATTAATTATAATTAT
1 TATT-TAA-TAATTATAATTAT
26361 T
1 T
26362 GAGTTTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
20 4 0.10
21 17 0.43
22 19 0.47
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTTAATAATTATAATTAT
Found at i:26603 original size:13 final size:13
Alignment explanation
Indices: 26585--26613 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
26575 TATTTATTAC
26585 TATATTTAATATT
1 TATATTTAATATT
26598 TATATTTAATATT
1 TATATTTAATATT
26611 TAT
1 TAT
26614 CATATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATTTAATATT
Found at i:27365 original size:13 final size:14
Alignment explanation
Indices: 27347--27376 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
27337 ATTCGAGAAG
27347 AAAAACGAA-AAAA
1 AAAAACGAAGAAAA
27360 AAAAACGAAGAAAA
1 AAAAACGAAGAAAA
27374 AAA
1 AAA
27377 TGGAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAACGAAGAAAA
Found at i:41653 original size:30 final size:28
Alignment explanation
Indices: 41586--41667 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 28
41576 AAATGTCAAA
*
41586 TAAGCTTATGAACTTTCAATTTTGCCAAT
1 TAAGCTTTTGAA-TTTCAATTTTGCCAAT
41615 TAAGCTTTTGAATTTCAATTTTGCCAAT
1 TAAGCTTTTGAATTTCAATTTTGCCAAT
* *
41643 TAAGAGCTTTTGAAATCCAATTTTG
1 T-A-AGCTTTTGAATTTCAATTTTG
41668 ACTAGATAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
28 17 0.35
29 12 0.25
30 19 0.40
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (28 bp):
TAAGCTTTTGAATTTCAATTTTGCCAAT
Found at i:42371 original size:26 final size:26
Alignment explanation
Indices: 42338--42391 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
42328 GTTGAAATAA
*
42338 ATGCTTAATTTTTGTAAAAATTCATG
1 ATGCTTAATCTTTGTAAAAATTCATG
42364 ATGCTTAATCTTTGTAAAAATTCATG
1 ATGCTTAATCTTTGTAAAAATTCATG
42390 AT
1 AT
42392 TTAGGACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (26 bp):
ATGCTTAATCTTTGTAAAAATTCATG
Found at i:44730 original size:17 final size:17
Alignment explanation
Indices: 44708--44743 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
44698 GTGTCAATAG
44708 TTAATTTTCTAAATGTT
1 TTAATTTTCTAAATGTT
44725 TTAATTTTCTAAATGTT
1 TTAATTTTCTAAATGTT
44742 TT
1 TT
44744 GTTTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
TTAATTTTCTAAATGTT
Found at i:46855 original size:216 final size:218
Alignment explanation
Indices: 46461--46876 Score: 631
Period size: 216 Copynumber: 1.9 Consensus size: 218
46451 CTGTTGGAGG
**
46461 AAACGTGGTGGGGAGATGAACTAGAAAATGGAAGAGAAAGAATAGAGACTACAACTGTCTCTATA
1 AAACGTGGTGGCAAGATGAACTAGAAAATGGAAGAGAAAGAATAGAGACTACAACTGTCTCTATA
*
46526 CCATGTAATTTAATTCATTCATATATATCCATGAATTAGGACATGTGTAAAACATGCAAAGATTT
66 CCATGTAA-TT-ATTCATTCATATATATCCATGAACTAGGACATGTGTAAAACATGCAAAGATTT
* * **
46591 TAAACATGCAACACAACAAGTGTACAATACAATTTCCTGTGGAAGCC-TTTCAAAGGAAACATCA
129 TAAACATGCAACACAACAAGTGTACAATACAAATTCCTATCAAAGCCATTTCAAAGGAAACATCA
46655 TCACTGCATTGTTTGAACTTAACAT
194 TCACTGCATTGTTTGAACTTAACAT
* * *
46680 AAACGTGGTGGCCAAGATGAACTGGAAAATGGAAGAGAAGGAGTAGAGACTACAACTGTCTCTAT
1 AAACGTGGTGG-CAAGATGAACTAGAAAATGGAAGAGAAAGAATAGAGACTACAACTGTCTCTAT
* *
46745 GCCATGTAA-T-TTCATTCATATATATCCATGAACTGGGACATGTGTAAAACATGCAAAGATTTT
65 ACCATGTAATTATTCATTCATATATATCCATGAACTAGGACATGTGTAAAACATGCAAAGATTTT
* *
46808 AAACATGCAACTCAACAAGTGTGCAATACAAATTCCTATCAAAGCCTTAATTTCAAAGGAAACAT
130 AAACATGCAACACAACAAGTGTACAATACAAATTCCTATCAAAGCC---ATTTCAAAGGAAACAT
46873 CATC
192 CATC
46877 GTTGCATGAA
Statistics
Matches: 178, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
216 91 0.51
218 1 0.01
219 11 0.06
220 75 0.42
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (218 bp):
AAACGTGGTGGCAAGATGAACTAGAAAATGGAAGAGAAAGAATAGAGACTACAACTGTCTCTATA
CCATGTAATTATTCATTCATATATATCCATGAACTAGGACATGTGTAAAACATGCAAAGATTTTA
AACATGCAACACAACAAGTGTACAATACAAATTCCTATCAAAGCCATTTCAAAGGAAACATCATC
ACTGCATTGTTTGAACTTAACAT
Found at i:48521 original size:30 final size:29
Alignment explanation
Indices: 48425--48531 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
48415 TAATCTACCA
** * *
48425 TTTTGCCCCCTGAACTTGTAGCGTTTAGACG
1 TTTTGCCCCCTGAACTTCAATC--TTGGACG
* *
48456 TTTTGCCCCCCGAACTTCAATCTTGGACA
1 TTTTGCCCCCTGAACTTCAATCTTGGACG
*
48485 TTTTGCCCCCTGAACTTCAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAATCTT-GGACG
*
48515 TTTTGCCCCCTCAACTT
1 TTTTGCCCCCTGAACTT
48532 AACGGCTCCG
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 27 0.42
30 20 0.31
31 18 0.28
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.36
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTCAATCTTGGACG
Found at i:48728 original size:30 final size:31
Alignment explanation
Indices: 48693--48768 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
48683 CCGTTAGGTT
*
48693 GAGGGGACAAAACGTCCCAAAATTGAAGTTC
1 GAGGGGGCAAAACGTCCCAAAATTGAAGTTC
* * *
48724 -AGGGGGTAAAATGT-CCAAGATTGAAGTTC
1 GAGGGGGCAAAACGTCCCAAAATTGAAGTTC
*
48753 GGGGGGGCAAAACGTC
1 GAGGGGGCAAAACGTC
48769 TAAACTCTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.17
Consensus pattern (31 bp):
GAGGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:49006 original size:2 final size:2
Alignment explanation
Indices: 48999--49025 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48989 TTGATGCCAC
48999 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
49026 TCTTAGCCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50123 original size:29 final size:30
Alignment explanation
Indices: 50086--50148 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
50076 CCGTATTATA
* *
50086 TATAAATAATATAATTAAATAA-TTATATG
1 TATAAATAATAAAATTAAATAATTTATAAG
* *
50115 TATACATAATAAAATTGAATAATTTATAAG
1 TATAAATAATAAAATTAAATAATTTATAAG
50145 TATA
1 TATA
50149 TATATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (30 bp):
TATAAATAATAAAATTAAATAATTTATAAG
Found at i:50480 original size:21 final size:21
Alignment explanation
Indices: 50454--50495 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
50444 CTCTAAATGG
50454 GATATTCTATGTCACTTACAT
1 GATATTCTATGTCACTTACAT
*
50475 GATATTCTATGTTACTTACAT
1 GATATTCTATGTCACTTACAT
50496 CCCATCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
GATATTCTATGTCACTTACAT
Done.