Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017833.1 Corchorus olitorius cultivar O-4 contig17866, 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: 21218
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4277 original size:13 final size:13
Alignment explanation
Indices: 4259--4293 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
4249 TTTTAACCAA
4259 CAAGTGGTTGGTT
1 CAAGTGGTTGGTT
4272 CAAGTGGTTGGTT
1 CAAGTGGTTGGTT
4285 CAAGTGGTT
1 CAAGTGGTT
4294 TGGCACTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (13 bp):
CAAGTGGTTGGTT
Found at i:12055 original size:25 final size:25
Alignment explanation
Indices: 12027--12103 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
12017 TTTAAGATGA
12027 TTGGCTATGTTAATTTATGCTAAAT
1 TTGGCTATGTTAATTTATGCTAAAT
* * * * * *
12052 TTGGGTTTGGGT-ATTTAAGAT-GA-
1 TTGGCTAT-GTTAATTTATGCTAAAT
12075 TTGGCTATGTTAATTTATGCTAAAT
1 TTGGCTATGTTAATTTATGCTAAAT
12100 TTGG
1 TTGG
12104 ATTTGAGTTT
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
22 2 0.06
23 13 0.36
24 2 0.06
25 17 0.47
26 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (25 bp):
TTGGCTATGTTAATTTATGCTAAAT
Found at i:12108 original size:54 final size:48
Alignment explanation
Indices: 12003--12125 Score: 212
Period size: 48 Copynumber: 2.6 Consensus size: 48
11993 AAATAAGAGC
*
12003 TTTGGGTTTGGGTTTTTAAGATGATTGGCTATGTTAATTTATGCTAAA
1 TTTGGGTTTGGGTATTTAAGATGATTGGCTATGTTAATTTATGCTAAA
12051 TTTGGGTTTGGGTATTTAAGATGATTGGCTATGTTAATTTATGCTAAA
1 TTTGGGTTTGGGTATTTAAGATGATTGGCTATGTTAATTTATGCTAAA
* *
12099 TTTGGATTTGAGT-TTTAAGATGATTGG
1 TTTGGGTTTGGGTATTTAAGATGATTGG
12126 GTTATTGTGC
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
47 14 0.19
48 58 0.81
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (48 bp):
TTTGGGTTTGGGTATTTAAGATGATTGGCTATGTTAATTTATGCTAAA
Found at i:14045 original size:32 final size:32
Alignment explanation
Indices: 14009--14072 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
13999 TTGACTCCAT
*
14009 GGGCTTATTTGAGCCAATTTTACAACATTAGG
1 GGGCTAATTTGAGCCAATTTTACAACATTAGG
* *
14041 GGGCTAATTTGAGCCGATTTTACAACGTTAGG
1 GGGCTAATTTGAGCCAATTTTACAACATTAGG
14073 AATTTAATTA
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:0.16, G:0.25, T:0.33
Consensus pattern (32 bp):
GGGCTAATTTGAGCCAATTTTACAACATTAGG
Found at i:15091 original size:15 final size:15
Alignment explanation
Indices: 15071--15101 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15061 ATAATACATT
15071 AACTATCAAATAGAA
1 AACTATCAAATAGAA
*
15086 AACTATCAAATCGAA
1 AACTATCAAATAGAA
15101 A
1 A
15102 CAGATTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:18021 original size:21 final size:21
Alignment explanation
Indices: 17997--18037 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17987 CCAACTAAGC
*
17997 AGCTAACGGTGGAGCTAATGG
1 AGCTAACGGTGGACCTAATGG
18018 AGCTAACGGTGGACCTAATG
1 AGCTAACGGTGGACCTAATG
18038 TAGTATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.34, T:0.20
Consensus pattern (21 bp):
AGCTAACGGTGGACCTAATGG
Found at i:18468 original size:457 final size:456
Alignment explanation
Indices: 17579--18494 Score: 1376
Period size: 457 Copynumber: 2.0 Consensus size: 456
17569 ATTAAAATGG
*
17579 ATAAACTCTTCCAATTTATGTTTGGATCAACGAAGTTGATCACAAACTTATTGTTTTTCCTTCCC
1 ATAAACCCTTCCAATTTATGTTTGGATCAACGAAGTTGATCACAAACTTATTGTTTTTCCTTCCC
*
17644 CAAATTTTATGGTTTGTCATCCGAAAGAATGAGGGTTTGACTGGAGGTTTAGCTATGGGCTATTT
66 CAAATTCTATGGTTTGTCATCCGAAAGAATGAGGGTTTGACTGGAGGTTTAGCTATGGGCTA---
* * ** * *
17709 TTTTTTTTTTTGTGATAGCGTTAGCAAATTTGGGTTTTATGAAGAAGTTTCCAAAATACTTTGAA
128 ---TTTCTTTGGTGATAGCGTTAGCAAATTTGGGTTTTATGAAGAAG-AACAAAAATACATTGAA
*
17774 ATCAGGGTGTTAACTTATGACATCATTGGAATTCTTCAAAGTGCTTGTTTATTAGCTTGGAAAGA
189 ATCAGGGTGTTAACTTATGACATCATTGGAATTCTTCAAAGTGCTTGTTTATTAGCTTCGAAAGA
*
17839 TGATACCACCCAAGCACAACAACAAACCCTCCTTGTCCTAACCGTGGTGTTTTCTTCTATGCCTT
254 TGATACCACCCAAGCACAACAACAAACCCTCCTTATCCTAACCGTGGTGTTTTCTTCTATGCCTT
17904 GAACTATGTTAACTACATAGTGGACGAAGTCAGGAAATACCACAAAAAAGTAATAGAGAAGGCCA
319 GAACTATGTTAACTACATAGTGGACGAAGTCAGGAAATACCACAAAAAAGTAATAGAGAAGGCCA
17969 AAAGGAAAGCTATTCAAGCCAACTAAGCAGCTAACGGTGGAGCTAATGGAGCTAACGGTGGACCT
384 AAAGGAAAGCTATTCAAGCCAACTAAGCAGCTAACGGTGGAGCTAATGGAGCTAACGGTGGACCT
18034 AATGTAGT
449 AATGTAGT
* *
18042 ATAAACCCTTCCGATTTATGTTTGGATCAACTG-AGTTGATCGCAAACTTATTGTTTTTCCTTCC
1 ATAAACCCTTCCAATTTATGTTTGGATCAAC-GAAGTTGATCACAAACTTATTGTTTTTCCTTCC
* * *
18106 CCAAATTCTCTGGTTTGTC-TCCGAAAGGATGAGGGTTTGACTGTAGGTTTAGCTATGGGCTA-T
65 CCAAATTCTATGGTTTGTCATCCGAAAGAATGAGGGTTTGACTGGAGGTTTAGCTATGGGCTATT
** *
18169 TCTTTGGTGATAGCGTTAGCCCATTTGGGTTTTGTGAAGAA-AACAAAAATACATTGAAATCAGG
130 TCTTTGGTGATAGCGTTAGCAAATTTGGGTTTTATGAAGAAGAACAAAAATACATTGAAATCAGG
* * * * *
18233 GTGTTAACTTATGGCATCATTGGAATTCTTCAAAGTGTTTGTTTCTTGGCTTCGAGAGATGATAC
195 GTGTTAACTTATGACATCATTGGAATTCTTCAAAGTGCTTGTTTATTAGCTTCGAAAGATGATAC
* *
18298 CACCCAAGCACAACAACAAACCCTCCTTATCCTAACCGTGGCGTTTATGTTTTTCTATGCCTTGA
260 CACCCAAGCACAACAACAAACCCTCCTTATCCTAACCGT-G-GTGT-T-TTCTTCTATGCCTTGA
** *** *
18363 ACTATGTTAACTACATAGTGGACGAAGTTGGGAAATACCACATTGAAG-AGATATAGAAGGCCAA
321 ACTATGTTAACTACATAGTGGACGAAGTCAGGAAATACCACAAAAAAGTA-ATAGAGAAGGCCAA
*
18427 AAGGAAAGCTATTCAAGCCAA-TGAAGCAGCTAACGGTGGAGCTAATGGAGCTAACGGTGGAGCT
385 AAGGAAAGCTATTCAAGCCAACT-AAGCAGCTAACGGTGGAGCTAATGGAGCTAACGGTGGACCT
18491 AATG
449 AATG
18495 GAGCTAACGG
Statistics
Matches: 414, Mismatches: 32, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
453 116 0.28
454 1 0.00
455 40 0.10
456 3 0.01
457 136 0.33
462 41 0.10
463 76 0.18
464 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (456 bp):
ATAAACCCTTCCAATTTATGTTTGGATCAACGAAGTTGATCACAAACTTATTGTTTTTCCTTCCC
CAAATTCTATGGTTTGTCATCCGAAAGAATGAGGGTTTGACTGGAGGTTTAGCTATGGGCTATTT
CTTTGGTGATAGCGTTAGCAAATTTGGGTTTTATGAAGAAGAACAAAAATACATTGAAATCAGGG
TGTTAACTTATGACATCATTGGAATTCTTCAAAGTGCTTGTTTATTAGCTTCGAAAGATGATACC
ACCCAAGCACAACAACAAACCCTCCTTATCCTAACCGTGGTGTTTTCTTCTATGCCTTGAACTAT
GTTAACTACATAGTGGACGAAGTCAGGAAATACCACAAAAAAGTAATAGAGAAGGCCAAAAGGAA
AGCTATTCAAGCCAACTAAGCAGCTAACGGTGGAGCTAATGGAGCTAACGGTGGACCTAATGTAG
T
Found at i:18471 original size:12 final size:12
Alignment explanation
Indices: 18454--18513 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
18444 CCAATGAAGC
18454 AGCTAACGGTGG
1 AGCTAACGGTGG
18466 AGCTAA---TGG
1 AGCTAACGGTGG
18475 AGCTAACGGTGG
1 AGCTAACGGTGG
18487 AGCTAA---TGG
1 AGCTAACGGTGG
18496 AGCTAACGGTGG
1 AGCTAACGGTGG
*
18508 ACCTAA
1 AGCTAA
18514 TGTAGTAGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
9 18 0.44
12 23 0.56
ACGTcount: A:0.30, C:0.17, G:0.35, T:0.18
Consensus pattern (12 bp):
AGCTAACGGTGG
Found at i:18477 original size:9 final size:9
Alignment explanation
Indices: 18463--18501 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
18453 CAGCTAACGG
18463 TGGAGCTAA
1 TGGAGCTAA
18472 TGGAGCTAA
1 TGGAGCTAA
18481 CGGTGGAGCTAA
1 ---TGGAGCTAA
18493 TGGAGCTAA
1 TGGAGCTAA
18502 CGGTGGACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 18 0.67
12 9 0.33
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.21
Consensus pattern (9 bp):
TGGAGCTAA
Found at i:18478 original size:21 final size:21
Alignment explanation
Indices: 18454--18538 Score: 116
Period size: 21 Copynumber: 3.9 Consensus size: 21
18444 CCAATGAAGC
18454 AGCTAACGGTGGAGCTAATGG
1 AGCTAACGGTGGAGCTAATGG
18475 AGCTAACGGTGGAGCTAATGG
1 AGCTAACGGTGGAGCTAATGG
*
18496 AGCTAACGGTGGACCTAATGTAG
1 AGCTAACGGTGGAGCTAATG--G
**
18519 TAGCTAATTGTGGAGCTAAT
1 -AGCTAACGGTGGAGCTAAT
18539 AGAGTTGGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
21 40 0.70
23 1 0.02
24 16 0.28
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (21 bp):
AGCTAACGGTGGAGCTAATGG
Found at i:18538 original size:12 final size:11
Alignment explanation
Indices: 18454--18537 Score: 59
Period size: 12 Copynumber: 7.5 Consensus size: 11
18444 CCAATGAAGC
18454 AGCTAACGGTGG
1 AGCTAA-GGTGG
18466 AGCTAA--TGG
1 AGCTAAGGTGG
18475 AGCTAACGGTGG
1 AGCTAA-GGTGG
18487 AGCTAA--TGG
1 AGCTAAGGTGG
18496 AGCTAACGGTGG
1 AGCTAA-GGTGG
* * *
18508 ACCTAATGTAGT
1 AGCTAAGGT-GG
*
18520 AGCTAATTGTGG
1 AGCTAA-GGTGG
18532 AGCTAA
1 AGCTAA
18538 TAGAGTTGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
9 18 0.31
11 2 0.03
12 36 0.61
13 3 0.05
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (11 bp):
AGCTAAGGTGG
Found at i:19601 original size:24 final size:24
Alignment explanation
Indices: 19574--19634 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
19564 GTAACTATTG
19574 GAGCTAACGGTGGTGGAGCTAATA
1 GAGCTAACGGTGGTGGAGCTAATA
** *
19598 GAGCTAACGGTGGTGGTTCTAATG
1 GAGCTAACGGTGGTGGAGCTAATA
19622 GAGCTAACGGTGG
1 GAGCTAACGGTGG
19635 ACCTATTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.39, T:0.23
Consensus pattern (24 bp):
GAGCTAACGGTGGTGGAGCTAATA
Done.