Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020062.1 Corchorus olitorius cultivar O-4 contig20095, 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: 10170
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:264 original size:29 final size:28
Alignment explanation
Indices: 197--301 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 28
187 AAGTGAACTT
* * *
197 AAAATGACCAAAATACCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGGATATGC
*
225 -AAATGACCAAAATGCCCCTGGATGTGC
1 AAAATGACCAAAATGCCCCTGGATATGC
* * *
252 AGAAATGACCAAAATGCCCATAGATTTTTG-
1 A-AAATGACCAAAATGCCCCTGGA--TATGC
282 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
302 AGGTGATCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 23 0.35
29 38 0.58
30 1 0.02
31 3 0.05
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGATATGC
Found at i:680 original size:50 final size:50
Alignment explanation
Indices: 597--1086 Score: 784
Period size: 50 Copynumber: 9.8 Consensus size: 50
587 AAAGTAAGGC
* * * * * *
597 TTGACTCATATGGAAGCCG-GTTTGACTTATGGAAAAGTCTATGTTGAAAA
1 TTGACTCGTATGGAA-ACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* *
647 TTGACTCGTATAGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* *
697 TTGACTCGTATGGAAACGAGTCTGGCTTGTGGAAAAGCCCATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* * *
747 TTGACTTGTATGGAAACGAGTTTGGCTTATGGAAAAGGCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
*
797 TTGACTCGTAATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAA
1 TTGACTCGT-ATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
848 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
*
898 TTGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
948 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* *
998 TTGACTCGTATTGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* *
1048 TTGATTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1087 AAAGCATTCG
Statistics
Matches: 410, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
49 2 0.00
50 361 0.88
51 47 0.11
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (50 bp):
TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
Found at i:971 original size:201 final size:200
Alignment explanation
Indices: 597--1086 Score: 786
Period size: 201 Copynumber: 2.4 Consensus size: 200
587 AAAGTAAGGC
* * * * * * *
597 TTGACTCATATGGAAGCCG-GTTTGACTTATGGAAAAGTCTATGTTGAAAATTGACTCGTATAGA
1 TTGACTCGTATGGAA-ACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGA
661 AACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCTGGCTTG
65 AACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCTGGCTTG
* *
726 TGGAAAAGCCCATGTTGATAATTGACTTGTATGGAAACGAGTTTGGCTTATGGAAAAGGCTATGT
130 TGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCCTATGT
791 TGATAA
195 TGATAA
*
797 TTGACTCGTAATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCGTATGGA
1 TTGACTCGT-ATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGA
*
862 AACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT-TCGGCTT
65 AACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCT-GGCTT
* *
926 GTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
129 GTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCCTATG
991 TTGATAA
194 TTGATAA
* * *
998 TTGACTCGTATTGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAATTGATTCGTATGGAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAA
*
1063 ACGAGTTTGGCTTATGGAAAAGCC
66 ACGAGTTTGGCTTGTGGAAAAGCC
1087 AAAGCATTCG
Statistics
Matches: 269, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
200 86 0.32
201 183 0.68
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (200 bp):
TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAA
ACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCTGGCTTGT
GGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCCTATGTT
GATAA
Found at i:1042 original size:251 final size:250
Alignment explanation
Indices: 597--1086 Score: 793
Period size: 251 Copynumber: 2.0 Consensus size: 250
587 AAAGTAAGGC
* *
597 TTGACTCATATGGAAGCCGGTTTGACTTATGGAAAAGTCTATGTTGAAAATTGACTCGTATAGAA
1 TTGACTCATATGGAAGACGGTTTGACTTATGGAAAAGCCTATGTTGAAAATTGACTCGTATAGAA
*
662 ACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCTGGCTTGT
66 ACGAGTTCGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCTGGCTTGT
* * *
727 GGAAAAGCCCATGTTGATAATTGACTTGTATGGAAACGAGTTTGGCTTATGGAAAAGGCTATGTT
131 GGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTATGGAAAAGCCTATGTT
*
792 GATAATTGACTCGTAATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAA
196 GATAATTGACTCGT-ATGGAAACGAGTTTGGCTTATGGAAAAGCCTGTGTTGATAA
* * * * *
848 TTGACTCGTATGGAA-ACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGA
1 TTGACTCATATGGAAGACG-GTTTGACTTATGGAAAAGCCTATGTTGAAAATTGACTCGTATAGA
* *
912 AACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTG
65 AACGAGTTCGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCTGGCTTG
* * *
977 TGGAAAAGCCTATGTTGATAATTGACTCGTATTGAAACGAGTTCGGCTTGTGGAAAAGCCTATGT
130 TGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTATGGAAAAGCCTATGT
*
1042 TGATAATTGATTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
195 TGATAATTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
1087 AAAGCATTCG
Statistics
Matches: 220, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
250 31 0.14
251 189 0.86
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (250 bp):
TTGACTCATATGGAAGACGGTTTGACTTATGGAAAAGCCTATGTTGAAAATTGACTCGTATAGAA
ACGAGTTCGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTCTGGCTTGT
GGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTATGGAAAAGCCTATGTT
GATAATTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCCTGTGTTGATAA
Found at i:1328 original size:91 final size:91
Alignment explanation
Indices: 1163--1366 Score: 336
Period size: 91 Copynumber: 2.2 Consensus size: 91
1153 AAGAAAATAC
* * * *
1163 CTTGGAAAATAACTCTGAATTTGATGTTGTAACTGAAAAGTACTTGATTGATGATGAAAAAGGAC
1 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTACTTGATTGATGATGAAAAAGGAC
1228 CAATGTGCAGTCAACTTGAAAAACAA
66 CAATGTGCAGTCAACTTGAAAAACAA
* *
1254 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGAC
1 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTACTTGATTGATGATGAAAAAGGAC
* *
1319 CAATTTGCAGTCAACTTGACAAACAA
66 CAATGTGCAGTCAACTTGAAAAACAA
1345 CTTGAAAAATAACTCTGAGTCT
1 CTTGAAAAATAACTCTGAGTCT
1367 AACGTTATGA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 105 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (91 bp):
CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTACTTGATTGATGATGAAAAAGGAC
CAATGTGCAGTCAACTTGAAAAACAA
Found at i:2546 original size:14 final size:13
Alignment explanation
Indices: 2527--2581 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
2517 TCTCTTTTGA
2527 TTTTGATTTGATTT
1 TTTTGATTTGA-TT
2541 TTTTGA-TTGA--
1 TTTTGATTTGATT
*
2551 CTTTGATTTGATT
1 TTTTGATTTGATT
2564 TTTTGATTTTGATT
1 TTTTGA-TTTGATT
2578 TTTT
1 TTTT
2582 TTTTGAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
13 9 0.26
14 17 0.49
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.69
Consensus pattern (13 bp):
TTTTGATTTGATT
Found at i:2555 original size:24 final size:23
Alignment explanation
Indices: 2523--2571 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
2513 CAATTCTCTT
*
2523 TTGATTTTGATTTGATTTTTTTGA
1 TTGACTTTGATTTGA-TTTTTTGA
2547 TTGACTTTGATTTGATTTTTTGA
1 TTGACTTTGATTTGATTTTTTGA
2570 TT
1 TT
2572 TTGATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.65
Consensus pattern (23 bp):
TTGACTTTGATTTGATTTTTTGA
Found at i:2591 original size:19 final size:18
Alignment explanation
Indices: 2527--2587 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
2517 TCTCTTTTGA
2527 TTTTGA-TTTGATTTTTT
1 TTTTGATTTTGATTTTTT
* * *
2544 TGATTGACTTTGATTTGATT
1 T-TTTGATTTTGATTT-TTT
2564 TTTTGATTTTGATTTTTT
1 TTTTGATTTTGATTTTTT
2582 TTTTGA
1 TTTTGA
2588 ATTTCTTGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 12 0.33
19 20 0.56
20 3 0.08
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.69
Consensus pattern (18 bp):
TTTTGATTTTGATTTTTT
Done.