Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012076.1 Corchorus olitorius cultivar O-4 contig12109, 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: 20000
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:1150 original size:108 final size:109
Alignment explanation
Indices: 945--1152 Score: 285
Period size: 108 Copynumber: 1.9 Consensus size: 109
935 GAATATTTGC
* * *
945 TAACCACCTACTTACATATATAATAAGAACCGAGAGGAAAAAAAACCTTATAACAAAAATTATAT
1 TAACCACCTACTCACATATATAATAAGAACCGAGAGGAAAAAAAACCTTAAAACAAAAATAATAT
* * * *
1010 GCTAGCCACATATCAAGAATGGTCGACACGCCAGCGCGAACCAA
66 GCTAGCCACAAATCAAGAACGCTCAACACGCCAGCGCGAACCAA
* * * *
1054 TAACTACCTACTCACATATATGATAAGAACCGAGA-GAAAAAAAA-CTCTAAAACTAAAATAATT
1 TAACCACCTACTCACATATATAATAAGAACCGAGAGGAAAAAAAACCT-TAAAACAAAAATAATA
*
1117 TGCTAGCCACAAATCAAGAACGCTCAACGCGCCAGC
65 TGCTAGCCACAAATCAAGAACGCTCAACACGCCAGC
1153 ATGAGCCGAT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
107 2 0.02
108 52 0.60
109 32 0.37
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (109 bp):
TAACCACCTACTCACATATATAATAAGAACCGAGAGGAAAAAAAACCTTAAAACAAAAATAATAT
GCTAGCCACAAATCAAGAACGCTCAACACGCCAGCGCGAACCAA
Found at i:3100 original size:16 final size:16
Alignment explanation
Indices: 3081--3119 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3071 ATCCGCCCGA
3081 ACCCGAACCCAAAATT
1 ACCCGAACCCAAAATT
* *
3097 ACCCGAGCCCAAGATT
1 ACCCGAACCCAAAATT
*
3113 ACTCGAA
1 ACCCGAA
3120 GCCGAGGCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.36, G:0.13, T:0.13
Consensus pattern (16 bp):
ACCCGAACCCAAAATT
Found at i:3344 original size:2 final size:2
Alignment explanation
Indices: 3310--3335 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3300 GTTAAATTAC
3310 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3336 CCTTATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3642 original size:31 final size:31
Alignment explanation
Indices: 3571--3642 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
3561 GTCTATCAGC
*
3571 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
3602 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
3632 GTTTTAATTTG
1 -TTTTAATTTG
3643 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:4138 original size:32 final size:32
Alignment explanation
Indices: 4101--4189 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 32
4091 TATCCAAGAT
* *
4101 CAAACCCGACATAACCCGAGCCTGAAAATACC
1 CAAACCCGACATAACCCGAGCCCGAAAAAACC
* * *
4133 CAAACCCAACTTATCCCGAGCCCGAAAAAACC
1 CAAACCCGACATAACCCGAGCCCGAAAAAACC
* *
4165 CGAACCCGA-AGT-ACCCGAACCCGAA
1 CAAACCCGACA-TAACCCGAGCCCGAA
4190 CCCGTCCGAG
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
31 11 0.24
32 35 0.76
ACGTcount: A:0.39, C:0.39, G:0.13, T:0.08
Consensus pattern (32 bp):
CAAACCCGACATAACCCGAGCCCGAAAAAACC
Found at i:4172 original size:16 final size:16
Alignment explanation
Indices: 4147--4189 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
4137 CCCAACTTAT
*
4147 CCCGAGCCCGAAAAAA
1 CCCGAACCCGAAAAAA
**
4163 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAAAA
4178 CCCGAACCCGAA
1 CCCGAACCCGAA
4190 CCCGTCCGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.37, C:0.42, G:0.19, T:0.02
Consensus pattern (16 bp):
CCCGAACCCGAAAAAA
Found at i:5748 original size:22 final size:22
Alignment explanation
Indices: 5723--5764 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5713 CGGAATCCTC
*
5723 TGAAATTACATACGAATAAAGA
1 TGAAATTACATACAAATAAAGA
5745 TGAAATTACATACAAATAAA
1 TGAAATTACATACAAATAAA
5765 CACGAAAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (22 bp):
TGAAATTACATACAAATAAAGA
Found at i:5771 original size:22 final size:22
Alignment explanation
Indices: 5724--5771 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5714 GGAATCCTCT
* * *
5724 GAAATTACATACGAATAAAGAT
1 GAAATTACATACAAATAAACAC
5746 GAAATTACATACAAATAAACAC
1 GAAATTACATACAAATAAACAC
5768 GAAA
1 GAAA
5772 GACAGAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.19
Consensus pattern (22 bp):
GAAATTACATACAAATAAACAC
Found at i:6177 original size:3 final size:3
Alignment explanation
Indices: 6169--6228 Score: 95
Period size: 3 Copynumber: 20.3 Consensus size: 3
6159 TTAGTAAATA
* *
6169 ATT ATT ATT -TC AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6216 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
6229 AGTTTATGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 1 0.02
3 51 0.98
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:11733 original size:661 final size:660
Alignment explanation
Indices: 9376--12007 Score: 4449
Period size: 659 Copynumber: 4.0 Consensus size: 660
9366 GAAGAAGATT
*
9376 TTGTGCGCCTGGCAAACAATGGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
1 TTGTGCGCCTGGCACACAATGGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
* * * * *
9441 GAGACTTCTTTGTGATGTCTAGCAATGTGGGAAGATATGAAACCTTGTTGCACGAAGATCATGAA
66 GAGACTTCTTTGAGATGTCTACCAAGGTGGGAAGATATGAAGCCTTGTTGCACGAAGATCACGAA
* *
9506 CGACAGAGTTTATCGTATGGCACTTATTATCAAGAGCCAAACTTTGAACTTGGCATAGCTGAAGT
131 CGGCAGAGTTCATCGTATGGCACTTATTATCAAGAGCCAAACTTTGAACTTGGCATAGCTGAAGT
*
9571 CAAGGCTAACCGACCTTTTGAATGCCCATCATTGGTTAAAGCTAGAATAGGTCACCCACAGACAC
196 CAAGGCTAACCGACCTGTTGAATGCCCATCATTGGTTAAAGCTAGAATAGGTCACCCACAGACAC
*
9636 AAGAACTCATAACTATGCAACATCAACGTTAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
261 AAGAACTCATAACTATGCAACATCAACGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
* *
9701 ACTCATTTGACGTGTCAAAGACTAACGGAGTTTTCGATTTCTTATTTAAGTCT-AGCATGATTAA
326 ACTCATTTGACGTGTCAAAGACTAACAGAGTTTTCGATTTCTTATTTAAGTCTGA-TATGATTAA
* *
9765 GCTCCCTCTAGGTCATATTATTCCTTCGTTAGAAGACCTCAAGGGCAAAGAGTATTGCAAGTAGC
390 GCTCCCTCCAGGTCATATTATTCCTTCGTTAGAAAACCTCAAGGGCAAAGAGTATTGCAAGTAGC
9830 ACGACTCATGGAGACATACGACCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAAGATT
455 ACGACTCATGGAGACATACGACCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAAGATT
9895 GATCATGGCA-ACTTAAGTTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCATT
520 GATCATGGCATACTTAAGTTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCATT
9959 TCCTGCGCCTGTACACATGGTGGTAGTCAACTTCCCCAAAGATGGTTGACTGACAAGGAGGAAAA
585 TCCTGCGCCTGTACACATGGTGGTAGTCAACTTCCCCAAAGATGGTTGACTGACAAGGAGGAAAA
*
10024 GGCTAAAGCTG
650 GGCTAAAGGTG
* * *
10035 TTGTGCGCCCGGCACACAATGGTCTAGACATGGAACTCAGAAATAATTCGAAGGAGTCGACCTCA
1 TTGTGCGCCTGGCACACAATGGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
* *
10100 GAGACTTCTTTGAGATGTCTACCAAGGTGGGAAGATATGAAGCCTTGTTTCACGAAGAACACGAA
66 GAGACTTCTTTGAGATGTCTACCAAGGTGGGAAGATATGAAGCCTTGTTGCACGAAGATCACGAA
*
10165 CGGCAGAGTTCATCGTATGGCACTTATTATCAAGAGCCAAACTTTGAACTTGGCATAGCTGAAAT
131 CGGCAGAGTTCATCGTATGGCACTTATTATCAAGAGCCAAACTTTGAACTTGGCATAGCTGAAGT
* * * *
10230 CAAGGTTAACCGACTTGTTGAATGTCCATCATTGGTTAAAGCTAGATTAGGTCACCCACAGACAC
196 CAAGGCTAACCGACCTGTTGAATGCCCATCATTGGTTAAAGCTAGAATAGGTCACCCACAGACAC
*
10295 AAGAACTCATAATTATGCAACATCAACGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
261 AAGAACTCATAACTATGCAACATCAACGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
* *
10360 ACTCATTTGACGTGTCAAAGACTAACAGAGTTTTCGATTTCTTATTTATGTCTGGTATGATTAAG
326 ACTCATTTGACGTGTCAAAGACTAACAGAGTTTTCGATTTCTTATTTAAGTCTGATATGATTAAG
* * *
10425 CTCCCCCCAAGTCATATTATTCTTTCGTTAGAAAACCTCAAGGGCAAAGAGTATTGCAAGTAGCA
391 CTCCCTCCAGGTCATATTATTCCTTCGTTAGAAAACCTCAAGGGCAAAGAGTATTGCAAGTAGCA
10490 CGACTCATGGAGACATACGACCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAAGATTG
456 CGACTCATGGAGACATACGACCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAAGATTG
*
10555 ATCATGGCATACTTAAATTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCATTT
521 ATCATGGCATACTTAAGTTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCATTT
* *
10620 CCTGCGCCTGTACACATGGTGGTAGTCAACTTCACCAAAGCTGGTTGACTGACAAGGAGGAAAAG
586 CCTGCGCCTGTACACATGGTGGTAGTCAACTTCCCCAAAGATGGTTGACTGACAAGGAGGAAAAG
10685 GCTAAAGGTG
651 GCTAAAGGTG
* * *
10695 TTGTGCGCTTTGCACACAATTGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
1 TTGTGCGCCTGGCACACAATGGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
*
10760 GAGACTTCTTTGAGATGTCTACCAAGGTGGGAAGATATGAAGCCTTGTTGCACGAAGATCACAAA
66 GAGACTTCTTTGAGATGTCTACCAAGGTGGGAAGATATGAAGCCTTGTTGCACGAAGATCACGAA
* *
10825 CGGCGGAG-T--TCG--T----CTTATTATAAAGAGCCAAACTTTGAACTTGGCATAGCTGAAGT
131 CGGCAGAGTTCATCGTATGGCACTTATTATCAAGAGCCAAACTTTGAACTTGGCATAGCTGAAGT
*
10881 CAAGGCTAACCGACCTGTTGAATGCCCATCATTGGTTAAAGTTAGAATAGGTCACCCACAGACAC
196 CAAGGCTAACCGACCTGTTGAATGCCCATCATTGGTTAAAGCTAGAATAGGTCACCCACAGACAC
*
10946 AAGAACTCATAGCTATGCAACATCAACGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
261 AAGAACTCATAACTATGCAACATCAACGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
* ** *
11011 ACTCATTTGACGTGTTAAAGACTAATGGAGTTTTCGATTTCTTATTTAAGTCTGGTATGATTAAG
326 ACTCATTTGACGTGTCAAAGACTAACAGAGTTTTCGATTTCTTATTTAAGTCTGATATGATTAAG
* * * *
11076 CTTCCTCCAGGTCATATTATTCTTTCATTAGAAAACCTCAAGGGCAAAAAGTATTGCAAGTAGCA
391 CTCCCTCCAGGTCATATTATTCCTTCGTTAGAAAACCTCAAGGGCAAAGAGTATTGCAAGTAGCA
* *
11141 CGACTCATGGAGACATACGTCCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAACATTG
456 CGACTCATGGAGACATACGACCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAAGATTG
* *
11206 ATCATGGTATACTTAAGTTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGATAAAGATCCATTT
521 ATCATGGCATACTTAAGTTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCATTT
* *
11271 CCTGCGCCTGTACACATGTTGGTAGTCAACTTCCCCAAAGATGGCTGACTGACCAAGGAGGAAAA
586 CCTGCGCCTGTACACATGGTGGTAGTCAACTTCCCCAAAGATGGTTGACTGA-CAAGGAGGAAAA
11336 GGCTAAAGGTG
650 GGCTAAAGGTG
*
11347 TTGTGCGCCTGACACACAATGGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
1 TTGTGCGCCTGGCACACAATGGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
* * *
11412 AAGACTTCTTTGAGATGTCTACCAAGATGGGAAGATATGAAGCCTTGTTGCACGAAGATCATGAA
66 GAGACTTCTTTGAGATGTCTACCAAGGTGGGAAGATATGAAGCCTTGTTGCACGAAGATCACGAA
* * *
11477 CGGCGGAGTTCATCGTATGACACTTATTATCAAGAGCCAAAATTTGAACTTGGCATAGCTGAAGT
131 CGGCAGAGTTCATCGTATGGCACTTATTATCAAGAGCCAAACTTTGAACTTGGCATAGCTGAAGT
* *
11542 CAAGGCTAACCGACCTGTTGAATGCCCATCATTGGTTAAAGCGAGAATAGGTCACCCAGAGACAC
196 CAAGGCTAACCGACCTGTTGAATGCCCATCATTGGTTAAAGCTAGAATAGGTCACCCACAGACAC
* *
11607 AAGAACTCATAGCTATGCAACATCAATGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
261 AAGAACTCATAACTATGCAACATCAACGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
* * *
11672 AGTCATTTGACGTGTCAAAGACTAGCAGAGTTTTCGATTTCTTATTTAAGTTTGATATGATTAAG
326 ACTCATTTGACGTGTCAAAGACTAACAGAGTTTTCGATTTCTTATTTAAGTCTGATATGATTAAG
* * *
11737 CTTCCTCCAGGTCATATTATTCCTTCGTTAGAAGACCTCAAGGGCAAAGATTATTGCAAGTAGCA
391 CTCCCTCCAGGTCATATTATTCCTTCGTTAGAAAACCTCAAGGGCAAAGAGTATTGCAAGTAGCA
* *
11802 CGACTGATGGAGACATACGACCAACAACTACATCGTGTTCAAGAACATAGTGCAAGAAAAGATTG
456 CGACTCATGGAGACATACGACCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAAGATTG
* * *
11867 ATCATGGCATACCTAAGTTCCCTAAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCACTT
521 ATCATGGCATACTTAAGTTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCATTT
*
11932 CCTGCGCCTGTACACATGGTGGTAGTCAACTTCCCCAAAGATGGTTGATTGACCAAGGAGGAAAA
586 CCTGCGCCTGTACACATGGTGGTAGTCAACTTCCCCAAAGATGGTTGACTGA-CAAGGAGGAAAA
11997 GGCTAAAGGTG
650 GGCTAAAGGTG
12008 CAATGGAAGT
Statistics
Matches: 1852, Mismatches: 109, Indels: 22
0.93 0.05 0.01
Matches are distributed among these distances:
651 458 0.25
652 153 0.08
653 1 0.00
655 4 0.00
657 4 0.00
659 499 0.27
660 254 0.14
661 479 0.26
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (660 bp):
TTGTGCGCCTGGCACACAATGGTCTAGACATGGAACTCAGAAAAAATTCGAAGGAGTCGACTTCA
GAGACTTCTTTGAGATGTCTACCAAGGTGGGAAGATATGAAGCCTTGTTGCACGAAGATCACGAA
CGGCAGAGTTCATCGTATGGCACTTATTATCAAGAGCCAAACTTTGAACTTGGCATAGCTGAAGT
CAAGGCTAACCGACCTGTTGAATGCCCATCATTGGTTAAAGCTAGAATAGGTCACCCACAGACAC
AAGAACTCATAACTATGCAACATCAACGTCAGGCACAAAGGAAACACATGATGGGAGTAGAACAT
ACTCATTTGACGTGTCAAAGACTAACAGAGTTTTCGATTTCTTATTTAAGTCTGATATGATTAAG
CTCCCTCCAGGTCATATTATTCCTTCGTTAGAAAACCTCAAGGGCAAAGAGTATTGCAAGTAGCA
CGACTCATGGAGACATACGACCAACAACTGCATCGTGTTCAAGAACATAGTGCAAGAAAAGATTG
ATCATGGCATACTTAAGTTCCCTGAACCTCTTAAGAAGGACATGGGAGTCGACAAAGATCCATTT
CCTGCGCCTGTACACATGGTGGTAGTCAACTTCCCCAAAGATGGTTGACTGACAAGGAGGAAAAG
GCTAAAGGTG
Done.