Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005350.1 Corchorus capsularis cultivar CVL-1 contig05368, 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: 5259
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Found at i:424 original size:31 final size:31
Alignment explanation
Indices: 389--454 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
379 AACTTTATGT
* *
389 TTTCCGATTGTACCCATATT-TTTAAAATATA
1 TTTCCAATTGTACCC-TATTCTTTAAAACATA
*
420 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTATTCTTTAAAACATA
451 TTTC
1 TTTC
455 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTATTCTTTAAAACATA
Found at i:597 original size:37 final size:36
Alignment explanation
Indices: 554--630 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 36
544 AATTTGACTT
554 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCATTTGTC
1 TTTGTTTCCAATCGTCCTATTTAATTTTG-C-TTTGTC
**
591 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTGTC
627 TTTG
1 TTTG
631 GTCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 12 0.32
38 15 0.41
ACGTcount: A:0.14, C:0.17, G:0.13, T:0.56
Consensus pattern (36 bp):
TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTGTC
Found at i:795 original size:19 final size:21
Alignment explanation
Indices: 763--805 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
753 TTCTTTACTA
763 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
784 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
803 TTA
1 TTA
806 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:999 original size:22 final size:22
Alignment explanation
Indices: 971--1132 Score: 89
Period size: 22 Copynumber: 7.3 Consensus size: 22
961 TGTCTCTATG
971 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* *
993 TGGTTATTATAATTTCA-AGAGGA
1 TGGTTATCAAAATTTCATA-A-GA
* *
1016 -GGTTATCAAAATTACAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
1037 TGGTTACCAAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* * *
1059 CGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
1081 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
1105 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
1127 TGGTTA
1 TGGTTA
1133 ATCATCACAA
Statistics
Matches: 110, Mismatches: 20, Indels: 20
0.73 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 85 0.77
23 3 0.03
24 18 0.16
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:1189 original size:22 final size:22
Alignment explanation
Indices: 1164--1206 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1154 GGTTATCAAA
1164 GAGATTATCAA-AATGTCATAGC
1 GAGATTAT-AAGAATGTCATAGC
*
1186 GAGATTATAAGAATTTCATAG
1 GAGATTATAAGAATGTCATAG
1207 TGTGGTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
GAGATTATAAGAATGTCATAGC
Found at i:1291 original size:22 final size:22
Alignment explanation
Indices: 1249--1291 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1239 GGGGAGCTTA
* *
1249 TCAAAATTTTATAGTGTGGTTG
1 TCAAAATTTCATAGTGAGGTTG
1271 TCAAAATTTCATA-TGAAGGTT
1 TCAAAATTTCATAGTG-AGGTT
1292 ATAAGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (22 bp):
TCAAAATTTCATAGTGAGGTTG
Found at i:1429 original size:22 final size:22
Alignment explanation
Indices: 1382--1549 Score: 97
Period size: 22 Copynumber: 7.7 Consensus size: 22
1372 TAGAGATCGG
**
1382 GTTATCAAAATTT-ATAGAAAT
1 GTTATCAAAATTTCATAGTGAT
* *
1403 ATTATCAAAATTTCATAGTGTT
1 GTTATCAAAATTTCATAGTGAT
* * * *
1425 GTTATCAAAGTTTCAAAGCGAG
1 GTTATCAAAATTTCATAGTGAT
* *
1447 GTTATCAAAATTACATAATG-T
1 GTTATCAAAATTTCATAGTGAT
* * **
1468 GATTATCAGAATTTCATAGAGGG
1 G-TTATCAAAATTTCATAGTGAT
* * * ** *
1491 GTCAACAAAATTTTATAAAGAG
1 GTTATCAAAATTTCATAGTGAT
** *
1513 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCATAGTGAT
*
1535 GTTATCAAACTTTCA
1 GTTATCAAAATTTCA
1550 AAATGTGATT
Statistics
Matches: 113, Mismatches: 31, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
21 13 0.12
22 99 0.88
23 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAT
Found at i:1474 original size:44 final size:43
Alignment explanation
Indices: 1404--1564 Score: 139
Period size: 44 Copynumber: 3.7 Consensus size: 43
1394 TATAGAAATA
* *
1404 TTATCAAAATTTCATAGTGTTG-TTATCAAAGTTTCAAAGCGAGG
1 TTATCAAAATTTCATAATG-TGATTATCAAA-TTTCAAAGAGAGG
* * *
1448 TTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGTGATTATCA-AATTTCAAAGAGAGG
* * * * * *
1492 TCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATGTGATTATC-AAATTTCA-AAGAGAGG
* *
1536 TTATCAAACTTTCAAAATGTGATTA-CAAA
1 TTATCAAAATTTCATAATGTGATTATCAAA
1565 AATTTTCATA
Statistics
Matches: 91, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 81 0.89
45 4 0.04
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (43 bp):
TTATCAAAATTTCATAATGTGATTATCAAATTTCAAAGAGAGG
Found at i:1710 original size:22 final size:22
Alignment explanation
Indices: 1654--1976 Score: 185
Period size: 22 Copynumber: 15.0 Consensus size: 22
1644 AAACTTTTGT
*
1654 TATGGA-GTAATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
1675 -A-GGAGGATATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
1695 TATGAAGGTTATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
** *
1717 TAGTTTA-GTTTTCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
* *
1739 CA-AGAGGGTTATCAAAATTTCA
1 TATGGA-GGTTATCAAAATTTCA
* * *
1761 TA-GTATGTAGATCAAAATTTCA
1 TATGGAGGT-TATCAAAATTTCA
* * *
1783 TAGGGAGATTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
**
1805 TGAT-GAGGTTATCAAAAAATCA
1 T-ATGGAGGTTATCAAAATTTCA
* *
1827 TAGGGAGGTTATTAAAA--T--
1 TATGGAGGTTATCAAAATTTCA
* *
1845 T-TGTA-GTTATCAAGATTTCA
1 TATGGAGGTTATCAAAATTTCA
* * * *
1865 TAAGAAAGTTATCAAAATTTTA
1 TATGGAGGTTATCAAAATTTCA
* *
1887 TAGGGAGGTTTATCAAAATTTTA
1 TATGGAGG-TTATCAAAATTTCA
*
1910 TA-GGAAGATTTATCAAAATTTCA
1 TATGG-AG-GTTATCAAAATTTCA
*
1933 TA-GCGAGGTTATCACAATTTCA
1 TATG-GAGGTTATCAAAATTTCA
1955 TAGTGTGA--TTATCAAAATTTCA
1 TA-TG-GAGGTTATCAAAATTTCA
1977 GAGTGTGATT
Statistics
Matches: 235, Mismatches: 45, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
16 8 0.03
17 2 0.01
18 2 0.01
19 3 0.01
20 17 0.07
21 6 0.03
22 151 0.64
23 42 0.18
24 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TATGGAGGTTATCAAAATTTCA
Found at i:1998 original size:22 final size:23
Alignment explanation
Indices: 1919--1996 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 23
1909 ATAGGAAGAT
* * * *
1919 TTATCAA-AATTTCATAGCGAGG
1 TTATCAACAATTTCAGAGTGTGA
*
1941 TTATC-ACAATTTCATAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
1963 TTATCAA-AATTTCAGAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
1985 TTA-CTAACAATT
1 TTATC-AACAATT
1997 CATATCTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.04
22 41 0.85
23 5 0.10
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (23 bp):
TTATCAACAATTTCAGAGTGTGA
Found at i:2382 original size:2 final size:2
Alignment explanation
Indices: 2375--2402 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2365 TTGTACTGCT
2375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2403 ATCTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3851 original size:3 final size:3
Alignment explanation
Indices: 3843--3878 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3833 AATTTTGTAT
3843 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3879 AACTTCAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Done.