Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019697.1 Corchorus olitorius cultivar O-4 contig19730, 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: 46673
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1146 original size:31 final size:31
Alignment explanation
Indices: 1086--1146 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
1076 TTTGTTAATT
* *
1086 AAAAAACACATATAGTGTTTTCAACAAAAAA
1 AAAAAACACATATAGTGTGTTCAAAAAAAAA
1117 AAAAAACACATATA-TAGTAGTT-AAAAAAAA
1 AAAAAACACATATAGT-GT-GTTCAAAAAAAA
1147 CACAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 23 0.88
32 2 0.08
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (31 bp):
AAAAAACACATATAGTGTGTTCAAAAAAAAA
Found at i:6633 original size:23 final size:22
Alignment explanation
Indices: 6582--6633 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
6572 CGTGTAGATG
*
6582 GAGTT-AAATTCGTTATTTTGA
1 GAGTTAAAATTCATTATTTTGA
*
6603 -AGCATAAAATTCATTAATTTTGA
1 GAG-TTAAAATTCATT-ATTTTGA
6626 GAGTTAAA
1 GAGTTAAA
6634 CATTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 2 0.08
21 1 0.04
22 8 0.33
23 11 0.46
24 2 0.08
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
GAGTTAAAATTCATTATTTTGA
Found at i:15751 original size:56 final size:54
Alignment explanation
Indices: 15659--15764 Score: 194
Period size: 56 Copynumber: 1.9 Consensus size: 54
15649 GGTCCACATT
15659 AATTAATAATTAGTAATATATAATAATATAATCACATGTTTTTCATTTTTAATC
1 AATTAATAATTAGTAATATATAATAATATAATCACATGTTTTTCATTTTTAATC
15713 AATTAATAATTAGTAATATATATAATAATATAATCACATGTTTTTCATTTTT
1 AATTAATAATTAGT-A-ATATATAATAATATAATCACATGTTTTTCATTTTT
15765 TATTATCTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 14 0.28
55 1 0.02
56 35 0.70
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (54 bp):
AATTAATAATTAGTAATATATAATAATATAATCACATGTTTTTCATTTTTAATC
Found at i:22170 original size:60 final size:60
Alignment explanation
Indices: 22084--22216 Score: 239
Period size: 60 Copynumber: 2.2 Consensus size: 60
22074 GTTAATTGTT
* *
22084 CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGAC
*
22144 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGAC
22204 CAAATAAGGGCCT
1 CAAATAAGGGCCT
22217 GATCTTTTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGAC
Found at i:22216 original size:29 final size:29
Alignment explanation
Indices: 22115--22245 Score: 167
Period size: 29 Copynumber: 4.4 Consensus size: 29
22105 TCAAAATGCT
*
22115 CAAATAAGGGCATGATCTTTTAATTTGAC
1 CAAATAAGGGCCTGATCTTTTAATTTGAC
* * **
22144 CAAATAAGGGCCT-AACGTTTGCCAAAATG-C
1 CAAATAAGGGCCTGATC-TTT--TAATTTGAC
22174 TCAAATAAGGGCCTGATCTTTTAATTTGAC
1 -CAAATAAGGGCCTGATCTTTTAATTTGAC
22204 CAAATAAGGGCCTGATCTTTTAATTTGAC
1 CAAATAAGGGCCTGATCTTTTAATTTGAC
22233 CAAATAAGGGCCT
1 CAAATAAGGGCCT
22246 AACGTTATCC
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.02
29 61 0.70
30 2 0.02
31 20 0.23
32 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGCCTGATCTTTTAATTTGAC
Found at i:22236 original size:89 final size:89
Alignment explanation
Indices: 22115--22278 Score: 303
Period size: 89 Copynumber: 1.8 Consensus size: 89
22105 TCAAAATGCT
22115 CAAATAAGGGCATGATCTTTTAATTTGACCAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAA
1 CAAATAAGGGCATGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTAT-CCAAAATGCTCAAA
22179 TAAGGGCCTGATCTTTTAATTTGAC
65 TAAGGGCCTGATCTTTTAATTTGAC
*
22204 CAAATAAGGGCCTGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCCAAAATGCTCAAAT
1 CAAATAAGGGCATGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCCAAAATGCTCAAAT
22269 AAGGGCCTGA
66 AAGGGCCTGA
22279 CGTCGAAAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
89 72 0.99
90 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (89 bp):
CAAATAAGGGCATGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCCAAAATGCTCAAAT
AAGGGCCTGATCTTTTAATTTGAC
Found at i:22356 original size:31 final size:29
Alignment explanation
Indices: 22318--22482 Score: 120
Period size: 31 Copynumber: 5.5 Consensus size: 29
22308 TGACGTCAGA
22318 CCCTTATTTGAGCATTTTCGATAACATTAGG
1 CCCTTATTTGAGCATTTT-GA-AACATTAGG
** * * *
22349 CCCTTATTTG-GTCAAATTAAAAGATCAGG
1 CCCTTATTTGAG-CATTTTGAAACATTAGG
*
22378 TCCC-TATTTGAGCATTTTGGCAAACATTAGA
1 -CCCTTATTTGAGCATTTT-G-AAACATTAGG
** * * *
22409 CCCTTATTTG-GCCAAATTAAAAGATCAGG
1 CCCTTATTTGAG-CATTTTGAAACATTAGG
*
22438 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-G-AAACATTAGG
22469 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
22483 ATTAGCCAAA
Statistics
Matches: 101, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
29 38 0.38
30 11 0.11
31 52 0.51
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAACATTAGG
Found at i:22415 original size:60 final size:60
Alignment explanation
Indices: 22313--22478 Score: 255
Period size: 60 Copynumber: 2.8 Consensus size: 60
22303 CAAACTGACG
* * *
22313 TCAGACCCTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTATTTGGTCAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGGCA-AACATTAGGCCCTTATTTGGCCAAATTAAAAGA
*
22373 TCAGGTCCC-TATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGA
1 TCAGG-CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGA
*
22433 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 TCAGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
22479 AGCAATTAGC
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
59 3 0.03
60 90 0.93
61 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (60 bp):
TCAGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGA
Found at i:22443 original size:29 final size:28
Alignment explanation
Indices: 22346--22447 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
22336 CGATAACATT
22346 AGGCCCTTATTTGGTCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
** * * *
22375 AGGTCCC-TATTTGAGCATTTTGGCAAACATT
1 AGG-CCCTTATTTG-GCAAATT--AAAAGATC
*
22406 AGACCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
22435 AGGCCCTTATTTG
1 AGGCCCTTATTTG
22448 AGCATTTTGG
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
29 30 0.55
30 8 0.15
31 17 0.31
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (28 bp):
AGGCCCTTATTTGGCAAATTAAAAGATC
Found at i:28790 original size:122 final size:126
Alignment explanation
Indices: 28566--28792 Score: 354
Period size: 122 Copynumber: 1.8 Consensus size: 126
28556 CTTTAATCAA
* *
28566 ATATTTACCTTGTCTTTAAAGTTATGCAAATATTGGTCTGTGGCTCGGTACTTTTGTGTTTGTTG
1 ATATTTACCTTGTCTTTAAAGTTATGCAAATATTGGTCTGTGG--CGGTACTTGTGTGTTTGTTA
*
28631 TGTCTGTCTGCAGCTGCTACACCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATAT
64 TGTCTGACTGCAGCTGCTACACCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATAT
* *
28694 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGT-G-GGT-C-TGTGTGTTTGTTATG
1 ATATTTACCTTGTCTTTAAAGTTATGCAAATATTGGTCTGTGGCGGTACTTGTGTGTTTGTTATG
*
28755 TCTGACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTT
66 TCTGACTGCAGCTGCTACACCCTGTTCTGCTTCGTTTT
28793 TATGCTTATT
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
122 49 0.53
123 1 0.01
124 3 0.03
127 1 0.01
128 39 0.42
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (126 bp):
ATATTTACCTTGTCTTTAAAGTTATGCAAATATTGGTCTGTGGCGGTACTTGTGTGTTTGTTATG
TCTGACTGCAGCTGCTACACCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATAT
Found at i:33786 original size:25 final size:24
Alignment explanation
Indices: 33758--33808 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
33748 CTTAATACCC
* *
33758 TTTTCCCCCTTTTAACTTGTAGCG
1 TTTTTCCCCTTTGAACTTGTAGCG
*
33782 TTTTTCCCCTTTGAACTTTTAGCG
1 TTTTTCCCCTTTGAACTTGTAGCG
33806 TTT
1 TTT
33809 GAACATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.51
Consensus pattern (24 bp):
TTTTTCCCCTTTGAACTTGTAGCG
Done.