Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021193.1 Corchorus olitorius cultivar O-4 contig21226, 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: 27849
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3480 original size:30 final size:30
Alignment explanation
Indices: 3446--4182 Score: 855
Period size: 30 Copynumber: 23.9 Consensus size: 30
3436 ATTTATTCTA
**
3446 CTTACAAAGGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* *
3476 CTTACAAATGACACCATAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
*
3506 CTTACAAATGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* * *
3536 CTTACAAATGGCACCAGAAGTTGTCAATGATCTT
1 CTTACAATTGACACCAGAAGTTGTC-ATG---GT
3570 ACAATTTACAATTGACACCAGAAGTTGTCAATGGT
1 -C---TTACAATTGACACCAGAAGTTGTC-ATGGT
3605 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
3635 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
3665 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
*
3695 CTTACAAATGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* *
3725 CTTACAAATGACACCAGAAGTTGTCATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* *
3755 CTTACAAATGACACCAGAAGTTGTCATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
*
3785 CTTACAATTGACACCAGAAGTTGTCAGTGATCTT
1 CTTACAATTGACACCAGAAGTTGTCA-TG---GT
3819 ACAATTTACAATTGACACCAGAAGTTGTCAATGGT
1 -C---TTACAATTGACACCAGAAGTTGTC-ATGGT
3854 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* *
3884 CTTGCAATTGACACCAGAAGTTGTCAATGAT
1 CTTACAATTGACACCAGAAGTTGTC-ATGGT
* * *
3915 CTTGCAATTGACACCAGAACTTGTCATGCT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* ** * *
3945 CCTGTAATTGACACCAGAACTTGTCATGCT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* * * *
3975 CCTGCAATTGACACCAGAACTTGTCATGCT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* * *
4005 AC-TGCAATTGACACCAGAACTTGTCATGCT
1 -CTTACAATTGACACCAGAAGTTGTCATGGT
* * *
4035 CTTGCAATTGACACCATAAGTTGTCATGTT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* * * *
4065 GTTGCAATTGACACCATAAGTTGTCATGCT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* *
4095 CTTGCAATTGACACCAGAAGTTGTCATGCT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* * * *
4125 CTTGCAATTGACACCCGAAGTTGTTATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
** * *
4155 AATCCAATTGACGCCAGAAGTTGTCATG
1 CTTACAATTGACACCAGAAGTTGTCATG
4183 ATTTTACCTT
Statistics
Matches: 651, Mismatches: 36, Indels: 40
0.90 0.05 0.06
Matches are distributed among these distances:
29 1 0.00
30 507 0.78
31 82 0.13
34 4 0.01
35 4 0.01
38 52 0.08
39 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (30 bp):
CTTACAATTGACACCAGAAGTTGTCATGGT
Found at i:8698 original size:130 final size:129
Alignment explanation
Indices: 8553--8810 Score: 367
Period size: 130 Copynumber: 2.0 Consensus size: 129
8543 GTTTAAACTC
*
8553 TTATAATTTTACTCAACT-AAAACTCTA-TTTTTATTTAATTAAATCTAATATCCTTATAACTAC
1 TTATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTAT-ACAAC
* * * *
8616 TTAATTTTTACCATTTTACTATTTTAAATAAAAAAACTTATATATATTAGTATTTTTAAATATAC
65 TTAATTTTTACCATTTTACTAATTT-AATAAAAAAACTTAGATATATTAGAAATTTTAAA-ATAC
8681 TT
128 TT
* *
8683 TTATATTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATACAATT
1 TTATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATACAACT
* ** * *
8748 TTATTTTTATTATTTTATTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATACT
66 TAATTTTTACCATTTTACTAATTTAATAAAAAAACTTAGATATATTAGAAATTTTAAAATACT
8811 AACATTGTTT
Statistics
Matches: 114, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
129 5 0.04
130 47 0.41
131 32 0.28
132 30 0.26
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (129 bp):
TTATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATACAACT
TAATTTTTACCATTTTACTAATTTAATAAAAAAACTTAGATATATTAGAAATTTTAAAATACTT
Found at i:9457 original size:16 final size:16
Alignment explanation
Indices: 9436--9473 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
9426 CTAAGGCTAC
9436 TCGGGTATTGGGTTAT
1 TCGGGTATTGGGTTAT
* *
9452 TCGGGTTTTGGGTTTT
1 TCGGGTATTGGGTTAT
9468 TCGGGT
1 TCGGGT
9474 CTAGGACTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.05, C:0.08, G:0.39, T:0.47
Consensus pattern (16 bp):
TCGGGTATTGGGTTAT
Found at i:9742 original size:41 final size:42
Alignment explanation
Indices: 9692--9779 Score: 169
Period size: 41 Copynumber: 2.1 Consensus size: 42
9682 AAATTTATTC
9692 ATTATGTAAAAAAACAAATTACTAATTATAAATTTATCATGA
1 ATTATGTAAAAAAACAAATTACTAATTATAAATTTATCATGA
9734 ATTA-GTAAAAAAACAAATTACTAATTATAAATTTATCATGA
1 ATTATGTAAAAAAACAAATTACTAATTATAAATTTATCATGA
9775 ATTAT
1 ATTAT
9780 TCATATAACT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (42 bp):
ATTATGTAAAAAAACAAATTACTAATTATAAATTTATCATGA
Found at i:22353 original size:17 final size:17
Alignment explanation
Indices: 22331--22364 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22321 CTTCGTTGCA
22331 GCACTTTTTATCAGACT
1 GCACTTTTTATCAGACT
22348 GCACTTTTTATCAGACT
1 GCACTTTTTATCAGACT
22365 ATAAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
GCACTTTTTATCAGACT
Found at i:23438 original size:107 final size:109
Alignment explanation
Indices: 23283--23535 Score: 368
Period size: 107 Copynumber: 2.3 Consensus size: 109
23273 TCACTCTTTT
*
23283 AAAAAATAAAACA-ACTTTATAATTGGGGGCTAAACCTTATTTATAAGTGTTCAAACTTATTTTT
1 AAAAAATAAAACATA-TTTATAATT-GGGGCTAAACCTTATTTAAAAGTGTTCAAACTTATTTTT
* * * ** *
23347 CTAAAACCCTAAGATAGTGGATTTTATCATTTTAGATTTACCCTTA
64 CTAAAACCCTAAAATAATGGATCTTAAAATTTAAGATTTACCCTTA
* *
23393 AAAAAATAAAACATA-TT-TAGTTGGGGCTAAATCTTATTTAAAAGTGTTCAAACTTATTTTTCT
1 AAAAAATAAAACATATTTATAATTGGGGCTAAACCTTATTTAAAAGTGTTCAAACTTATTTTTCT
* *
23456 AAAACCCTAAAATAATGGGTCTTAAAATTTAAGATTTACCCTTT
66 AAAACCCTAAAATAATGGATCTTAAAATTTAAGATTTACCCTTA
23500 AAAAAATAAAACATATTTATAATTGGGGCTAAACCT
1 AAAAAATAAAACATATTTATAATTGGGGCTAAACCT
23536 GAATTATTGT
Statistics
Matches: 127, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
107 90 0.71
108 6 0.05
109 17 0.13
110 13 0.10
111 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (109 bp):
AAAAAATAAAACATATTTATAATTGGGGCTAAACCTTATTTAAAAGTGTTCAAACTTATTTTTCT
AAAACCCTAAAATAATGGATCTTAAAATTTAAGATTTACCCTTA
Found at i:23872 original size:32 final size:32
Alignment explanation
Indices: 23831--23893 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
23821 TAAAATTGAA
*
23831 GGACCAAATCGTA-TAGAATAGAAATGTCTAAT
1 GGACCAAATCGCATTA-AATAGAAATGTCTAAT
*
23863 GGACTAAATCGCATTAAATAGAAATGTCTAA
1 GGACCAAATCGCATTAAATAGAAATGTCTAA
23894 GGGTATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (32 bp):
GGACCAAATCGCATTAAATAGAAATGTCTAAT
Found at i:24020 original size:32 final size:32
Alignment explanation
Indices: 23979--24041 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
23969 TGAAATTGAA
*
23979 GGACCAAATCGTA-TAGAATAGAAATGTCTAAT
1 GGACCAAATCGCATTA-AATAGAAATGTCTAAT
*
24011 GGACTAAATCGCATTAAATAGAAATGTCTAA
1 GGACCAAATCGCATTAAATAGAAATGTCTAA
24042 GGGTATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (32 bp):
GGACCAAATCGCATTAAATAGAAATGTCTAAT
Found at i:24091 original size:148 final size:148
Alignment explanation
Indices: 23823--24122 Score: 591
Period size: 148 Copynumber: 2.0 Consensus size: 148
23813 TAAAAAAATA
23823 AAATTGAAGGACCAAATCGTATAGAATAGAAATGTCTAATGGACTAAATCGCATTAAATAGAAAT
1 AAATTGAAGGACCAAATCGTATAGAATAGAAATGTCTAATGGACTAAATCGCATTAAATAGAAAT
23888 GTCTAAGGGTATTCTTGTAAAATAAGTAAAGCTGAAGAACTGAATCTAATAAAATAAAAATTATT
66 GTCTAAGGGTATTCTTGTAAAATAAGTAAAGCTGAAGAACTGAATCTAATAAAATAAAAATTATT
23953 GAGGGACTAAATCGCATG
131 GAGGGACTAAATCGCATG
23971 AAATTGAAGGACCAAATCGTATAGAATAGAAATGTCTAATGGACTAAATCGCATTAAATAGAAAT
1 AAATTGAAGGACCAAATCGTATAGAATAGAAATGTCTAATGGACTAAATCGCATTAAATAGAAAT
*
24036 GTCTAAGGGTATTCTTGTAAAATAAGTAAAGCTGAAGAACTGAATCTAATAAAATAAAAATTTTT
66 GTCTAAGGGTATTCTTGTAAAATAAGTAAAGCTGAAGAACTGAATCTAATAAAATAAAAATTATT
24101 GAGGGACTAAATCGCATG
131 GAGGGACTAAATCGCATG
24119 AAAT
1 AAAT
24123 AAAATTTATG
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 151 1.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (148 bp):
AAATTGAAGGACCAAATCGTATAGAATAGAAATGTCTAATGGACTAAATCGCATTAAATAGAAAT
GTCTAAGGGTATTCTTGTAAAATAAGTAAAGCTGAAGAACTGAATCTAATAAAATAAAAATTATT
GAGGGACTAAATCGCATG
Done.