Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012270.1 Corchorus olitorius cultivar O-4 contig12303, 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: 36718
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1652 original size:36 final size:36
Alignment explanation
Indices: 1605--1673 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1595 GAGATTTTGG
*
1605 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
1641 AGAAATATGATAACCAAAATTACAAAAAATGTA
1 AGAAATATGATAACCAAAATTACAAAAAATGTA
1674 TGGTTATTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:9921 original size:38 final size:39
Alignment explanation
Indices: 9849--9927 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 39
9839 ATATAATTAT
*
9849 AATTATCATTATCATAAAATAAAAAAATCATAATTTTAA
1 AATTATAATTATCATAAAATAAAAAAATCATAATTTTAA
9888 AATTATAATTATCATAAAAT-AAAAAATCATAATTTTAA
1 AATTATAATTATCATAAAATAAAAAAATCATAATTTTAA
9926 AA
1 AA
9928 AAATTGTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 20 0.51
39 19 0.49
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (39 bp):
AATTATAATTATCATAAAATAAAAAAATCATAATTTTAA
Found at i:10573 original size:6 final size:6
Alignment explanation
Indices: 10562--10610 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
10552 ATTGTTTCCG
*
10562 GTTTTT GTTTTTT GTTTTT -TTGTT -TTTTT GTTTTT G-TTTT GTTTTT
1 GTTTTT G-TTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
10608 GTT
1 GTT
10611 ATGTTGTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 13 0.34
6 19 0.50
7 6 0.16
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
GTTTTT
Found at i:10573 original size:7 final size:7
Alignment explanation
Indices: 10563--10601 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
10553 TTGTTTCCGG
10563 TTTTTGT
1 TTTTTGT
10570 TTTTTGTT
1 TTTTTG-T
10578 TTTTTGT
1 TTTTTGT
10585 TTTTT-T
1 TTTTTGT
10591 GTTTTTGT
1 -TTTTTGT
10599 TTT
1 TTT
10602 GTTTTTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 20 0.69
8 8 0.28
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTTGT
Found at i:10580 original size:8 final size:8
Alignment explanation
Indices: 10563--10610 Score: 64
Period size: 8 Copynumber: 6.0 Consensus size: 8
10553 TTGTTTCCGG
10563 TTTTTG-T
1 TTTTTGTT
10570 TTTTTGTT
1 TTTTTGTT
10578 TTTTTGTT
1 TTTTTGTT
10586 TTTTTGTT
1 TTTTTGTT
10594 TTTGTT-TT
1 TTT-TTGTT
10602 GTTTTTGTT
1 -TTTTTGTT
10611 ATGTTGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.16
8 24 0.65
9 7 0.19
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (8 bp):
TTTTTGTT
Found at i:10583 original size:15 final size:14
Alignment explanation
Indices: 10562--10601 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
10552 ATTGTTTCCG
10562 GTTTTTGTTTTTTGT
1 GTTTTTGTTTTTT-T
*
10577 TTTTTTGTTTTTTT
1 GTTTTTGTTTTTTT
10591 GTTTTTGTTTT
1 GTTTTTGTTTT
10602 GTTTTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (14 bp):
GTTTTTGTTTTTTT
Found at i:10601 original size:11 final size:11
Alignment explanation
Indices: 10564--10615 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
10554 TGTTTCCGGT
10564 TTTTGTTTTTTG
1 TTTTG-TTTTTG
*
10576 TTTT-TTTGTTT
1 TTTTGTTT-TTG
10587 TTTTGTTTTTG
1 TTTTGTTTTTG
10598 TTTTGTTTTTG
1 TTTTGTTTTTG
*
10609 TTATGTT
1 TTTTGTT
10616 GTCAACTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 3 0.09
11 25 0.71
12 7 0.20
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:11015 original size:27 final size:27
Alignment explanation
Indices: 10983--11063 Score: 135
Period size: 27 Copynumber: 3.0 Consensus size: 27
10973 GCATTAAGGT
10983 CATTCAGGGGCATTTTGGTCATTTTTG
1 CATTCAGGGGCATTTTGGTCATTTTTG
* *
11010 CATTCAGGGGCATTTTGGTCACTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTG
*
11037 CATTCAGGGGCATTTTGGCCATTTTTG
1 CATTCAGGGGCATTTTGGTCATTTTTG
11064 GCTCATCTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTTG
Found at i:12158 original size:16 final size:16
Alignment explanation
Indices: 12133--12166 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12123 TCAGTTGGAG
* *
12133 AAAAAGGGAGGAAAAT
1 AAAAAAGGAGAAAAAT
12149 AAAAAAGGAGAAAAAT
1 AAAAAAGGAGAAAAAT
12165 AA
1 AA
12167 GAAATACAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAAAAGGAGAAAAAT
Found at i:19995 original size:30 final size:30
Alignment explanation
Indices: 19959--20020 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
19949 GTTAATAAGC
19959 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
*
19989 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
20019 CA
1 CA
20021 AGATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGAAAAGT
Found at i:22545 original size:31 final size:31
Alignment explanation
Indices: 22507--22569 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
22497 GCGCGTGCGC
*
22507 TGCAGTCATTTTCTTATTAGGGTTATATTTT
1 TGCAGTCATCTTCTTATTAGGGTTATATTTT
22538 TGCAGTCATCTTCTTATTAGGGTTATATTTT
1 TGCAGTCATCTTCTTATTAGGGTTATATTTT
22569 T
1 T
22570 TGTAGTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.54
Consensus pattern (31 bp):
TGCAGTCATCTTCTTATTAGGGTTATATTTT
Found at i:22829 original size:45 final size:48
Alignment explanation
Indices: 22700--22821 Score: 180
Period size: 49 Copynumber: 2.6 Consensus size: 48
22690 AAATTCTATT
22700 CTATCT-TAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCTCCA
1 CTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCTCCA
**
22747 TCTATCTCTAGGTAATTCATCAAAATAAATTTGATATTCTACTCCT-C-
1 -CTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCTCCA
*
22794 C-ATCTCTAGATAATTCATCAAAATAAAG
1 CTATCTCTAGGTAATTCATCAAAATAAAG
22822 GTAATATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
45 25 0.36
46 1 0.01
48 7 0.10
49 36 0.52
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (48 bp):
CTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCTCCA
Found at i:30212 original size:30 final size:30
Alignment explanation
Indices: 30176--30270 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
30166 CAGCCAACTG
30176 TACATCCTGCAGG-AATGGAACATCTGTCTA
1 TACATCCTGC-GGTAATGGAACATCTGTCTA
* *
30206 TACATCCTGCGGTAGA-GGAACAT-TAGTTTG
1 TACATCCTGCGGTA-ATGGAACATCT-GTCTA
* * *
30236 TAAATCCTGCGGTAGTGGAACATCTGCCTA
1 TACATCCTGCGGTAATGGAACATCTGTCTA
30266 TACAT
1 TACAT
30271 TTTGTAGTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
29 3 0.06
30 47 0.90
31 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (30 bp):
TACATCCTGCGGTAATGGAACATCTGTCTA
Found at i:32074 original size:17 final size:17
Alignment explanation
Indices: 32052--32084 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32042 ATACATAGAG
32052 CTATCTAGTGTAACAAA
1 CTATCTAGTGTAACAAA
*
32069 CTATCTGGTGTAACAA
1 CTATCTAGTGTAACAA
32085 CTTTACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (17 bp):
CTATCTAGTGTAACAAA
Found at i:34758 original size:43 final size:43
Alignment explanation
Indices: 34607--34945 Score: 327
Period size: 43 Copynumber: 8.0 Consensus size: 43
34597 TTTTCCCTCC
* *
34607 CCAAAGTCCCCAAACACATTTATAACACAGGGGCAAT-TCTCTTT
1 CCAAAGTCCTCAAACACATTTATAACACAGAGGC-ATCTCTC-TT
* * * *
34651 CTAAAGTCTTCAAACACATTTATAACACAGAGGCATCTAT-AT
1 CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTCTCTT
* * *
34693 -CAAAGTCCCCAAACACAATTATAACACAGGGGCATCTCTCTT
1 CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTCTCTT
** * * *
34735 CCAAAGTTTTCTAACACATTTATAACACAGAGGCATCTAT-AT
1 CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTCTCTT
* * * *
34777 -CAAAGTCCCCAAACATAATTATAACACAGGGGCAAT-TCTC-T
1 CCAAAGTCCTCAAACACATTTATAACACAGAGGC-ATCTCTCTT
* * *
34818 CTAAAAGTCCTCAAACACATTTATAACACAGAGGCATC-C-ATA
1 C-CAAAGTCCTCAAACACATTTATAACACAGAGGCATCTCTCTT
* * * * *
34860 CTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATT
1 CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTCTCTT
* *
34903 TCAAAGTCCTCAAACACATTTATAACACAGAGGCATTTCTCTT
1 CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTCTCTT
34946 TATGTCAAAG
Statistics
Matches: 236, Mismatches: 48, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
41 94 0.40
42 10 0.04
43 100 0.42
44 32 0.14
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (43 bp):
CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTCTCTT
Found at i:34780 original size:84 final size:84
Alignment explanation
Indices: 34608--34938 Score: 479
Period size: 84 Copynumber: 3.9 Consensus size: 84
34598 TTTCCCTCCC
* * *
34608 CAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCTAAAGTCTTCAAACACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTC-TTCCAAAGTCCTCAAACACATTTA
34673 TAACACAGAGGCATCTATAT
65 TAACACAGAGGCATCTATAT
** *
34693 CAAAGTCCCCAAACACAATTATAACACAGGGGC-ATCTCTCTTCCAAAGTTTTCTAACACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAAT-TCTCTTCCAAAGTCCTCAAACACATTTA
34757 TAACACAGAGGCATCTATAT
65 TAACACAGAGGCATCTATAT
* *
34777 CAAAGTCCCCAAACATAATTATAACACAGGGGCAATTCTC-TCTAAAAGTCCTCAAACACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTC-CAAAGTCCTCAAACACATTTA
*
34841 TAACACAGAGGCATCCATA-
65 TAACACAGAGGCATCTATAT
* ** * *
34860 CTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTTCAAAGTCCTCAAACACATTTA
1 C-AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTCCAAAGTCCTCAAACACATTTA
34925 TAACACAGAGGCAT
65 TAACACAGAGGCAT
34939 TTCTCTTTAT
Statistics
Matches: 224, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
83 3 0.01
84 182 0.81
85 39 0.17
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.24
Consensus pattern (84 bp):
CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTCCAAAGTCCTCAAACACATTTAT
AACACAGAGGCATCTATAT
Found at i:34993 original size:2 final size:2
Alignment explanation
Indices: 34986--35017 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
34976 TTGGCTCATA
*
34986 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35018 GGCAAGGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35431 original size:29 final size:29
Alignment explanation
Indices: 35394--35465 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
35384 TTTTACTTCT
* *
35394 CATTGTGGTCATTTTTCATGTCTAGGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGGG
35423 CATTTTGGTCATTTTTCATGTCCAGGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGGG
*
35452 CATTTAGGTCATTT
1 CATTTTGGTCATTT
35466 CAAGTGTACT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.43
Consensus pattern (29 bp):
CATTTTGGTCATTTTTCATGTCCAGGGGG
Done.