Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013987.1 Corchorus olitorius cultivar O-4 contig14020, 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: 7891
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:848 original size:23 final size:23
Alignment explanation
Indices: 810--853 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
800 TCATCCTCCC
* *
810 TTTCATCTTTCTTTTTCTTTTCA
1 TTTCATCATTCATTTTCTTTTCA
*
833 TTTCATCATTCATTTTTTTTT
1 TTTCATCATTCATTTTCTTTT
854 GTTGGGCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTCATCATTCATTTTCTTTTCA
Found at i:950 original size:33 final size:32
Alignment explanation
Indices: 908--1011 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
898 AGCACAGCTA
908 GGCCC-GCGTGCTGCCGAGGTGTGCAGCAGCGC
1 GGCCCAGCGTGCTGCCGAGGTG-GCAGCAGCGC
*
940 GGCCCAGCGTGCTGCCGAGGTGGGCAGCAGTGC
1 GGCCCAGCGTGCTGCCGAGGT-GGCAGCAGCGC
* * * *
973 GGCCTAGCGCGCTGCCCAGCTGGCCAGCAGCGC
1 GGCCCAGCGTGCTGCCGAGGTGG-CAGCAGCGC
1006 GGCCCA
1 GGCCCA
1012 ACGCTGCTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.11
33 54 0.87
34 1 0.02
ACGTcount: A:0.12, C:0.37, G:0.41, T:0.11
Consensus pattern (32 bp):
GGCCCAGCGTGCTGCCGAGGTGGCAGCAGCGC
Found at i:2011 original size:73 final size:73
Alignment explanation
Indices: 1888--2030 Score: 169
Period size: 73 Copynumber: 2.0 Consensus size: 73
1878 GGTAACTAAA
* * ** * * * * *
1888 CAAGCGAGAAAAGACGAAAAGGGGGCGAAACAGTTGTCCCTCATTGAAAGTTAAAAGGAACCTTT
1 CAAGCGAGAAAAGACCAAAACGGAACGAAAAAGTTCTCCCACATTAAAAGTTAAAAGCAACCTTT
1953 AGTAAATT
66 AGTAAATT
* * * *
1961 CAAGCGAGAAAAGACCAAAACGGAACGAAAAAGTTCTCCCACGTTAAAAGTTGATAGCAGCCTTT
1 CAAGCGAGAAAAGACCAAAACGGAACGAAAAAGTTCTCCCACATTAAAAGTTAAAAGCAACCTTT
2026 AGTAA
66 AGTAA
2031 TTTCCAGAGG
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.18
Consensus pattern (73 bp):
CAAGCGAGAAAAGACCAAAACGGAACGAAAAAGTTCTCCCACATTAAAAGTTAAAAGCAACCTTT
AGTAAATT
Found at i:2684 original size:60 final size:59
Alignment explanation
Indices: 2597--2756 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 59
2587 GCTAATTGCT
* *
2597 CAAATAAGGGCCTAACTTTTATC-AAAATGCTCAAATAAGGCTTGATCCTTATAATTTAGC
1 CAAATAAGGGCCTAAC-ATTATCGAAAATGCTCAAATAAGGCCTGAT-CTTATAATTTAGC
* * * * *
2657 CAAACAAGGGCTTAACATTATCGAAAATGCTCAAATAAAAGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAAT-AAGGCCTGATCTTATAATTTAGC
* * *
2717 CAAATAAGTGCCTAGCGTTATCGAAAATGCTCAAATAAGG
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGG
2757 GTCTGTCGTT
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
59 8 0.09
60 69 0.81
61 8 0.09
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (59 bp):
CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGCCTGATCTTATAATTTAGC
Found at i:2845 original size:31 final size:31
Alignment explanation
Indices: 2808--2876 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
2798 CAGACCCTTA
* *
2808 TATTTGAGCATTTTCG-ATAACGTTAGGCCCT
1 TATTTGAACATTTTCGCA-AACGTTAAGCCCT
*
2839 TATTTGAACATTTTGGCAAACGTTAAGCCCT
1 TATTTGAACATTTTCGCAAACGTTAAGCCCT
2870 TATTTGA
1 TATTTGA
2877 TCAAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (31 bp):
TATTTGAACATTTTCGCAAACGTTAAGCCCT
Found at i:5876 original size:25 final size:26
Alignment explanation
Indices: 5848--5901 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
5838 ATTTAATAAA
5848 TTAATAATGGCAATTT-AAATATATT
1 TTAATAATGGCAATTTAAAATATATT
5873 TTAATAATGGCAATTTAGAAATATATT
1 TTAATAATGGCAATTTA-AAATATATT
5900 TT
1 TT
5902 TAAAAGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 16 0.59
27 11 0.41
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (26 bp):
TTAATAATGGCAATTTAAAATATATT
Found at i:6434 original size:211 final size:213
Alignment explanation
Indices: 6063--6471 Score: 660
Period size: 211 Copynumber: 1.9 Consensus size: 213
6053 GTAGAATTAA
6063 GGGTAATTATTTGATACACCGACGGTGTAAATTTTGGACTCCACAACCACAAACGGGTTGTGGAG
1 GGGTAATTATTTGATACACCGACGGTGTAAATTTTGGACT-----ACCACAAACGGGTTGTGGAG
6128 TTGACACATGTCCATTTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGAC
61 TTGACACATGTCCATTTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGAC
* * * *
6193 ACATGTCACCCTTTAGTACCCACTTGTGTAGTCTGTTAAACTCCACCGCCGGTGTATTGTATAAT
126 ACATGTCACCCTTCAGGACCCACTTGTGTAGTCTGCTAAACTCCACCGCCGATGTATTGTATAAT
6258 TTGTCGTAGAACTAATTAAAAAT
191 TTGTCGTAGAACTAATTAAAAAT
* * *
6281 GGGTAATTATTTGATACATCGGCGGTGTAAATTTTGGACT-CCACAAGCGGGTTGTGGAGTTGAC
1 GGGTAATTATTTGATACACCGACGGTGTAAATTTTGGACTACCACAAACGGGTTGTGGAGTTGAC
* *
6345 ACATGTTCA-TTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACATATG
66 ACATGTCCATTTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATG
* *
6409 TCACCCTTCAGGATCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGATGTATTGTATAATTTG
131 TCACCCTTCAGGACCCACTTGTGTAGTCTGCTAAACTCCACCGCCGATGTATTGTATAATTTG
6472 CCATTAAAAA
Statistics
Matches: 180, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
211 111 0.62
212 31 0.17
218 38 0.21
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (213 bp):
GGGTAATTATTTGATACACCGACGGTGTAAATTTTGGACTACCACAAACGGGTTGTGGAGTTGAC
ACATGTCCATTTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATG
TCACCCTTCAGGACCCACTTGTGTAGTCTGCTAAACTCCACCGCCGATGTATTGTATAATTTGTC
GTAGAACTAATTAAAAAT
Found at i:6953 original size:11 final size:11
Alignment explanation
Indices: 6929--6963 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6919 TTGACAGCAC
6929 AATAAAAACAA
1 AATAAAAACAA
* *
6940 AATGAAAACGA
1 AATAAAAACAA
6951 AATAAAAACAA
1 AATAAAAACAA
6962 AA
1 AA
6964 AACAAAAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.09, G:0.06, T:0.09
Consensus pattern (11 bp):
AATAAAAACAA
Found at i:7052 original size:42 final size:42
Alignment explanation
Indices: 7006--7090 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
6996 TGATTCACAT
*
7006 TTCACACTACTTGATTATTTATTTCTTATTATTATGTGAGAA
1 TTCACACTACTTGATTATTTATTTCTTATTATTAAGTGAGAA
*
7048 TTCACACTACTTGATTCTTTATTTCTTATTATTAAGTGAGAA
1 TTCACACTACTTGATTATTTATTTCTTATTATTAAGTGAGAA
7090 T
1 T
7091 CCGTATGCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (42 bp):
TTCACACTACTTGATTATTTATTTCTTATTATTAAGTGAGAA
Found at i:7726 original size:28 final size:30
Alignment explanation
Indices: 7672--7745 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 30
7662 GCTAAATACC
* *
7672 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGATTT-CTTTTGGGA
7703 CAAAATAATCCCTTAT-ATTT-TTTTGGGA
1 CAAAATAATCCCTTATGATTTCTTTTGGGA
*
7731 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
7746 CGTTTCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATGATTTCTTTTGGGA
Done.