Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021828.1 Corchorus olitorius cultivar O-4 contig21861, 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: 45549
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:1472 original size:144 final size:147
Alignment explanation
Indices: 1202--1491 Score: 469
Period size: 144 Copynumber: 2.0 Consensus size: 147
1192 TTGTTTATCA
* *
1202 TCTTTGTATTCATTAAATAGTGAGATTTATTATTATTATAAAATAATTCTATTATATAGTATATT
1 TCTTTGTATGCATTAAATAGTGAGATTTATTATTACTATAAAATAATTC--TTATATAGTATATT
*
1267 ATTATTAATTGTGTGGTTTATTCAATTGAACATATTAAACAAGTACACATACCAAACAATACAAA
64 ATTATTAATTGTGTGGTTTATTCAATTGAACATATTAAACAAGCACACATACCAAACAATACAAA
1332 ATACAATGAACTATTGAAT
129 ATACAATGAACTATTGAAT
*
1351 TCTTTGTATGCATTAAATAGTGAGTTTTATTATTACTATAAAATAATTC-TAT-TA-TATATTAT
1 TCTTTGTATGCATTAAATAGTGAGATTTATTATTACTATAAAATAATTCTTATATAGTATATTAT
* * *
1413 TATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAAT
66 TATTAATTGTGTGGTTTATTCAATTGAACATATTAAACAAGCACACATACCAAACAATACAAAAT
*
1478 GCAATGAACTATTG
131 ACAATGAACTATTG
1492 GATTTAAATA
Statistics
Matches: 133, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
144 82 0.62
145 2 0.02
146 3 0.02
149 46 0.35
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (147 bp):
TCTTTGTATGCATTAAATAGTGAGATTTATTATTACTATAAAATAATTCTTATATAGTATATTAT
TATTAATTGTGTGGTTTATTCAATTGAACATATTAAACAAGCACACATACCAAACAATACAAAAT
ACAATGAACTATTGAAT
Found at i:1598 original size:109 final size:109
Alignment explanation
Indices: 1407--1624 Score: 382
Period size: 109 Copynumber: 2.0 Consensus size: 109
1397 TTCTATTATA
*
1407 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
* *
1472 CAAAATGCAATGAACTATTGGATTTAAATAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAAAAAAATACAAACACC
* *
1516 TATTATTGTTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
*
1581 CAAAGTGCAATGAACTATTGGATTTAAAAAAAAATACAAACACC
66 CAAAATGCAATGAACTATTGGATTTAAAAAAAAATACAAACACC
1625 AAAATGACTA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAAAAAAATACAAACACC
Found at i:3079 original size:17 final size:17
Alignment explanation
Indices: 3057--3091 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3047 TTATTATTTA
3057 TTAATGCATAATTAATT
1 TTAATGCATAATTAATT
*
3074 TTAATGGATAATTAATT
1 TTAATGCATAATTAATT
3091 T
1 T
3092 CAATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (17 bp):
TTAATGCATAATTAATT
Found at i:7999 original size:15 final size:15
Alignment explanation
Indices: 7979--8007 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7969 GATTATGTTG
7979 GGTATATGGGTTTTA
1 GGTATATGGGTTTTA
7994 GGTATATGGGTTTT
1 GGTATATGGGTTTT
8008 GGTTGTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (15 bp):
GGTATATGGGTTTTA
Found at i:8825 original size:32 final size:32
Alignment explanation
Indices: 8788--8849 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
8778 TATTTTTCTT
*
8788 TGAAAATCAAATCACACAATCCCATTTGAATC
1 TGAAAATCAAATCACACAAACCCATTTGAATC
*
8820 TGAAAATCAAATCACCCAAACCCATTTGAA
1 TGAAAATCAAATCACACAAACCCATTTGAA
8850 CCAAATTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (32 bp):
TGAAAATCAAATCACACAAACCCATTTGAATC
Found at i:13890 original size:16 final size:16
Alignment explanation
Indices: 13869--13904 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
13859 ACTCTACCGA
13869 TAGTCACGTGATCTGT
1 TAGTCACGTGATCTGT
13885 TAGTCACGTGATCTGT
1 TAGTCACGTGATCTGT
13901 TAGT
1 TAGT
13905 AGAGTGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (16 bp):
TAGTCACGTGATCTGT
Found at i:38671 original size:111 final size:110
Alignment explanation
Indices: 38456--38708 Score: 357
Period size: 111 Copynumber: 2.3 Consensus size: 110
38446 TATCTCTTAC
* * * * *
38456 AAATCTCACCTAACAAATGTTTTTGTTTGCTTTACAAGGAGGGAGAGGGATGATGAGCAACTTGA
1 AAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGGGAGAGGGA-GATGAGCAACTCGA
* * *
38521 ACTCATACTCTTACATGACTTTCCTTTAACTCGGACCTAGACAGGT
65 ACCCACACTCTTACATGACTTTCCTTTAACCCGGACCTAGACAGGT
*
38567 AAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGTGAG-GGG-GATGAGCAACTCGAA
1 AAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGGGAGAGGGAGATGAGCAACTCGAA
* *
38630 CCCACACTCTTACATGACTTTCCTTTAAGCCCCTGGTCCTAGAGAGGT
66 CCCACACTCTTACATGACTTTCCTTTAA--CCC-GGACCTAGACAGGT
38678 AAATCCCACCTAACAAATGCTTTCGTTTGGT
1 AAATCCCACCTAACAAATGCTTTCGTTTGGT
38709 ACTCGGACCT
Statistics
Matches: 128, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
108 40 0.31
110 5 0.04
111 83 0.65
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (110 bp):
AAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGGGAGAGGGAGATGAGCAACTCGAA
CCCACACTCTTACATGACTTTCCTTTAACCCGGACCTAGACAGGT
Found at i:38813 original size:160 final size:160
Alignment explanation
Indices: 38549--38868 Score: 631
Period size: 160 Copynumber: 2.0 Consensus size: 160
38539 CTTTCCTTTA
38549 ACTCGGACCTAGACAGGTAAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGTGAGGG
1 ACTCGGACCTAGACAGGTAAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGTGAGGG
38614 GGATGAGCAACTCGAACCCACACTCTTACATGACTTTCCTTTAAGCCCCTGGTCCTAGAGAGGTA
66 GGATGAGCAACTCGAACCCACACTCTTACATGACTTTCCTTTAAGCCCCTGGTCCTAGAGAGGTA
38679 AATCCCACCTAACAAATGCTTTCGTTTGGT
131 AATCCCACCTAACAAATGCTTTCGTTTGGT
38709 ACTCGGACCTAGACAGGTAAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGTGAGGG
1 ACTCGGACCTAGACAGGTAAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGTGAGGG
*
38774 GGATGAGCAACTCGAACTCACACTCTTACATGACTTTCCTTTAAGCCCCTGGTCCTAGAGAGGTA
66 GGATGAGCAACTCGAACCCACACTCTTACATGACTTTCCTTTAAGCCCCTGGTCCTAGAGAGGTA
38839 AATCCCACCTAACAAATGCTTTCGTTTGGT
131 AATCCCACCTAACAAATGCTTTCGTTTGGT
38869 GTATAAGGAG
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 159 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (160 bp):
ACTCGGACCTAGACAGGTAAATCCCACCTAACAAATGCTTTCGTTTGGTTTACAAGGAGTGAGGG
GGATGAGCAACTCGAACCCACACTCTTACATGACTTTCCTTTAAGCCCCTGGTCCTAGAGAGGTA
AATCCCACCTAACAAATGCTTTCGTTTGGT
Found at i:39075 original size:49 final size:47
Alignment explanation
Indices: 38981--39110 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 47
38971 GAGCGTGCCA
* ** *
38981 ATCAATTTTGTCAAAAAATTGATTAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
39028 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* *
39077 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCA
39111 GAAAAGTCAA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
47 12 0.16
48 19 0.26
49 42 0.58
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Done.