Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014999.1 Corchorus capsularis cultivar CVL-1 contig15020, 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: 23045
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--49 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 ATGATG
7 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
49 T
1 T
50 TTGTACATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1951 original size:115 final size:114
Alignment explanation
Indices: 1742--1966 Score: 342
Period size: 115 Copynumber: 2.0 Consensus size: 114
1732 AAATAACTTG
* *
1742 AAAAGAAAAAACTAAGAAAAAGTTAATGCGATTTGTAACTAGTAATGTAAGACACTCAAGTTTGA
1 AAAAGAAAAAACTAAGAAAAAGCTAATGCGATTTGTAACTAGTAATGAAAGACACTCAAGTTTGA
* * *
1807 TTCTTTATAGTTTTTCATTAGCAAAGAGTTAACAGCTTATCTTAATCTA
66 TTCCTTAAAGTTTTTCATTAGCAAAGAGTTAACAGCTTACCTTAATCTA
* * *
1856 AAAAGAAAAAAACTAAGAAAAAGCTAATGCGATTTGTAATTAGTAATGAAAGGCACTCGAGTTTG
1 AAAAG-AAAAAACTAAGAAAAAGCTAATGCGATTTGTAACTAGTAATGAAAGACACTCAAGTTTG
* * *
1921 ATTCCTTAAAGTTTTTCATTAGTAAGGAGTTAACGGCTTACCTTAA
65 ATTCCTTAAAGTTTTTCATTAGCAAAGAGTTAACAGCTTACCTTAA
1967 CCTTGAAGAT
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
114 5 0.05
115 94 0.95
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (114 bp):
AAAAGAAAAAACTAAGAAAAAGCTAATGCGATTTGTAACTAGTAATGAAAGACACTCAAGTTTGA
TTCCTTAAAGTTTTTCATTAGCAAAGAGTTAACAGCTTACCTTAATCTA
Found at i:16230 original size:2 final size:2
Alignment explanation
Indices: 16223--16251 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16213 ATGTTCCTAT
16223 TA 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 TA T
16252 GACTAATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19055 original size:59 final size:59
Alignment explanation
Indices: 18983--19104 Score: 235
Period size: 59 Copynumber: 2.1 Consensus size: 59
18973 ACTTGAAAGT
18983 TTCAATTTTGTAATTGTTTTACTAGATTCTATCACCTGATTATTATGTTACTAGATTCG
1 TTCAATTTTGTAATTGTTTTACTAGATTCTATCACCTGATTATTATGTTACTAGATTCG
*
19042 TTCAATTTTGTAATTGTTTTACTAGATTCTTTCACCTGATTATTATGTTACTAGATTCG
1 TTCAATTTTGTAATTGTTTTACTAGATTCTATCACCTGATTATTATGTTACTAGATTCG
19101 TTCA
1 TTCA
19105 CCTGATTCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (59 bp):
TTCAATTTTGTAATTGTTTTACTAGATTCTATCACCTGATTATTATGTTACTAGATTCG
Found at i:19066 original size:30 final size:29
Alignment explanation
Indices: 18983--19072 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
18973 ACTTGAAAGT
18983 TTCAATTTTGTAATTGTTTTACTAGATTC
1 TTCAATTTTGTAATTGTTTTACTAGATTC
** * * *
19012 TATC-A-CCTGATTATTATGTTACTAGATTC
1 T-TCAATTTTG-TAATTGTTTTACTAGATTC
19041 GTTCAATTTTGTAATTGTTTTACTAGATTC
1 -TTCAATTTTGTAATTGTTTTACTAGATTC
19071 TT
1 TT
19073 TCACCTGATT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
28 2 0.04
29 22 0.48
30 20 0.43
31 2 0.04
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.52
Consensus pattern (29 bp):
TTCAATTTTGTAATTGTTTTACTAGATTC
Found at i:19099 original size:29 final size:29
Alignment explanation
Indices: 19001--19111 Score: 127
Period size: 29 Copynumber: 3.8 Consensus size: 29
18991 TGTAATTGTT
19001 TTACTAGATTC-TATCACCTGATTATTATG
1 TTACTAGATTCGT-TCACCTGATTATTATG
** * * *
19030 TTACTAGATTCGTTCAATTTTG-TAATTGTT
1 TTACTAGATTCGTTC-A-CCTGATTATTATG
*
19060 TTACTAGATTCTTTCACCTGATTATTATG
1 TTACTAGATTCGTTCACCTGATTATTATG
19089 TTACTAGATTCGTTCACCTGATT
1 TTACTAGATTCGTTCACCTGATT
19112 CTAAGGTTCT
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.03
29 41 0.62
30 21 0.32
31 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (29 bp):
TTACTAGATTCGTTCACCTGATTATTATG
Found at i:20538 original size:71 final size:71
Alignment explanation
Indices: 20422--20564 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
20412 TCCCCTTACA
20422 ATGTACAGTGGATGAGAGCTGTTGCTGTGAGTTACATGAAGTTTTCTCCTAATTATTTATAGTGG
1 ATGTACAGTGGATGAGAGCTGTTGCTGTGAGTTACATGAAGTTTTCTCCTAATTATTTATAGTGG
20487 GGGACG
66 GGGACG
20493 ATGTACAGTGGATGAGAGCTGTTGCTGTGAGTTACATGAAGTTTTCTCCTAATTATTTATAGTGG
1 ATGTACAGTGGATGAGAGCTGTTGCTGTGAGTTACATGAAGTTTTCTCCTAATTATTTATAGTGG
20558 GGGACG
66 GGGACG
20564 A
1 A
20565 GAGACTTGTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.35
Consensus pattern (71 bp):
ATGTACAGTGGATGAGAGCTGTTGCTGTGAGTTACATGAAGTTTTCTCCTAATTATTTATAGTGG
GGGACG
Found at i:22512 original size:19 final size:20
Alignment explanation
Indices: 22485--22530 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
22475 GTTAACCATT
22485 GTTTAGTTAATTAACAGATA
1 GTTTAGTTAATTAACAGATA
*
22505 GTTT-GTTAATTAACAGTTA
1 GTTTAGTTAATTAACAGATA
22524 G-TTAGTT
1 GTTTAGTT
22531 TGTTAGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 2 0.08
19 18 0.75
20 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
GTTTAGTTAATTAACAGATA
Done.