Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024078.1 Corchorus olitorius cultivar O-4 contig24111, 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: 32746
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:8345 original size:22 final size:22
Alignment explanation
Indices: 8317--8358 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
8307 AGTTCTGAGG
8317 CTACCCGGCCCCGGGTACCCCC
1 CTACCCGGCCCCGGGTACCCCC
*
8339 CTACCCGGCCCTGGGTACCC
1 CTACCCGGCCCCGGGTACCC
8359 TCAGGAATGC
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:0.10, C:0.55, G:0.24, T:0.12
Consensus pattern (22 bp):
CTACCCGGCCCCGGGTACCCCC
Found at i:9304 original size:24 final size:25
Alignment explanation
Indices: 9270--9320 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
9260 ATTGGAGTAT
*
9270 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGTTTATTAATTTTA
*
9295 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTTATTAATTTTA
9319 TT
1 TT
9321 GTTACTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTATTAATTTTA
Found at i:13002 original size:22 final size:22
Alignment explanation
Indices: 12974--13015 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12964 AGTTCTGAGG
12974 CTACCCGGCCCCGGGTACCCCC
1 CTACCCGGCCCCGGGTACCCCC
*
12996 CTACCCGGCCCTGGGTACCC
1 CTACCCGGCCCCGGGTACCC
13016 TCAGGAATGC
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:0.10, C:0.55, G:0.24, T:0.12
Consensus pattern (22 bp):
CTACCCGGCCCCGGGTACCCCC
Found at i:13959 original size:24 final size:25
Alignment explanation
Indices: 13925--13972 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
13915 ATTGGAGTAT
*
13925 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGTTTATTAATTTTA
*
13950 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTTATTAATTTT
13973 GTTGTTACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTATTAATTTTA
Found at i:15863 original size:3 final size:3
Alignment explanation
Indices: 15855--15885 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15845 CCTGCTTCCA
15855 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
15886 TTTTTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16714 original size:16 final size:16
Alignment explanation
Indices: 16693--16727 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
16683 CAGAATTTGG
16693 TGCACCACATTGGAGA
1 TGCACCACATTGGAGA
16709 TGCACCACATTGGAGA
1 TGCACCACATTGGAGA
16725 TGC
1 TGC
16728 CCTTAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (16 bp):
TGCACCACATTGGAGA
Found at i:16784 original size:5 final size:4
Alignment explanation
Indices: 16766--16806 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
16756 TTTTCTTTTC
* *
16766 ATTT ATTT ATTT ATATT ATAT ATTA ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT
16807 CAAAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:17456 original size:116 final size:114
Alignment explanation
Indices: 17252--17482 Score: 408
Period size: 116 Copynumber: 2.0 Consensus size: 114
17242 CCACTTACCT
* *
17252 AGTTAAATGTCCTCTCCATTAGTTAATTTTAATTTTCTAAATCAAATTTTTAATAGTAAAAGTAT
1 AGTTAAATGTACTCTCCATTAGTTAATTTTAATTTTCTAAATCAAATTTTTAATAGTAAAAATAT
* *
17317 ATAACATTTTAAGAAAGATTAATCCATATATATATGCTATATATCTCTTAA
66 ATAACATTTTAAGAAAAATTAATCCATATATATATGC--CATATCTCTTAA
17368 AGTTAAATGTACTCTCCATTAGTTAATTTTAATTTTCTAAATCAAATTTTTAATAGTAAAAATAT
1 AGTTAAATGTACTCTCCATTAGTTAATTTTAATTTTCTAAATCAAATTTTTAATAGTAAAAATAT
17433 ATAACATTTTAAGAAAAATTAATCCATATATATATGCCATATCTCTTAA
66 ATAACATTTTAAGAAAAATTAATCCATATATATATGCCATATCTCTTAA
17482 A
1 A
17483 CCTTCTTTAT
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 12 0.11
116 99 0.89
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (114 bp):
AGTTAAATGTACTCTCCATTAGTTAATTTTAATTTTCTAAATCAAATTTTTAATAGTAAAAATAT
ATAACATTTTAAGAAAAATTAATCCATATATATATGCCATATCTCTTAA
Found at i:17821 original size:29 final size:31
Alignment explanation
Indices: 17785--17851 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
17775 TTTGTCCAAG
* *
17785 GACATTTTGCCCTCTTAACT-TCAAA-TCAA
1 GACATTTTACCCTCTGAACTATCAAATTCAA
* *
17814 GATATTTTACCCTCTGAATTATCAAATTCAA
1 GACATTTTACCCTCTGAACTATCAAATTCAA
17845 GACATTT
1 GACATTT
17852 AGCCTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 16 0.52
30 5 0.16
31 10 0.32
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
GACATTTTACCCTCTGAACTATCAAATTCAA
Found at i:21769 original size:133 final size:133
Alignment explanation
Indices: 21523--21870 Score: 497
Period size: 133 Copynumber: 2.6 Consensus size: 133
21513 TCTTCTAAGG
* * *
21523 TTAGAGTTACTTAA-CTCAAATTTCAAACTTACCAAATTCAATTAATGATGATTAACTTTAATCT
1 TTAG-GTTACTTAACCT-AAATTTCAAATTTATCAAATTCACTTAATGA--A-TAACTTTAATCT
* *
21587 TTAATGAATTATGAAAGTTTTTACCAAAGTTTATTAACTAAAGGTTATAATTACTTAATTAAAAA
61 TAAATGAATTATGAAGGTTTTTACCAAAGTTTATTAACTAAAGGTTATAATTACTTAATTAAAAA
*
21652 CTAAAGTT
126 CAAAAGTT
* *
21660 TTAGGTTACTTAACCTTAATTCCAAATTTATCAAATTCACTTAATGAATAACTTTAATCTTAAAT
1 TTAGGTTACTTAACCTAAATTTCAAATTTATCAAATTCACTTAATGAATAACTTTAATCTTAAAT
* *
21725 GAATTATGAAGGCTTTTT-CCAAAGTTTATTGACTAAAGGTTATAATTACTTAATTAAAACCAAA
66 GAATTATGAAGG-TTTTTACCAAAGTTTATTAACTAAAGGTTATAATTACTTAATTAAAAACAAA
21789 AGTT
130 AGTT
*
21793 TTAGGTTACTTAACCTCAATTTCAAATTTATCAAATTCACTTAATG-ATCAAC-TTAATCTTAAA
1 TTAGGTTACTTAACCTAAATTTCAAATTTATCAAATTCACTTAATGAAT-AACTTTAATCTTAAA
*
21856 AGAATTATGAAGGTT
65 TGAATTATGAAGGTT
21871 CCAAAAAAAA
Statistics
Matches: 195, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
131 2 0.01
132 25 0.13
133 121 0.62
134 6 0.03
136 35 0.18
137 6 0.03
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (133 bp):
TTAGGTTACTTAACCTAAATTTCAAATTTATCAAATTCACTTAATGAATAACTTTAATCTTAAAT
GAATTATGAAGGTTTTTACCAAAGTTTATTAACTAAAGGTTATAATTACTTAATTAAAAACAAAA
GTT
Found at i:21918 original size:133 final size:133
Alignment explanation
Indices: 21523--21916 Score: 361
Period size: 133 Copynumber: 2.9 Consensus size: 133
21513 TCTTCTAAGG
* * * *
21523 TTAGAGTTACTTAA-CTCAAATTTCAAACTTACCAAATTCAATTAATGATGATTAACTTTAATCT
1 TTAG-GTTACTTAACCTC-AATTCCAAATTTATCAAATTCACTTAATGA--A-TAACTTTAATCT
* * * * ** ** * * * * *
21587 TTAATGAATTATGAAAGTTTTTACCAAAGTTTATTAACTAAAGGTTATAATTACTTAATTAAAAA
61 TAAAAGAATTATGAAGGCTTAAAAAAAAGATTATTGACTAAAGGCTATAATGACTTAATTAAAAC
*
21652 CTAAAGTT
126 CAAAAGTT
* *
21660 TTAGGTTACTTAACCTTAATTCCAAATTTATCAAATTCACTTAATGAATAACTTTAATCTTAAAT
1 TTAGGTTACTTAACCTCAATTCCAAATTTATCAAATTCACTTAATGAATAACTTTAATCTTAAAA
***** * * *
21725 GAATTATGAAGGCTTTTTCCAAAGTTTATTGACTAAAGGTTATAATTACTTAATTAAAACCAAAA
66 GAATTATGAAGGCTTAAAAAAAAGATTATTGACTAAAGGCTATAATGACTTAATTAAAACCAAAA
21790 GTT
131 GTT
*
21793 TTAGGTTACTTAACCTCAATTTCAAATTTATCAAATTCACTTAATG-ATCAAC-TTAATCTTAAA
1 TTAGGTTACTTAACCTCAATTCCAAATTTATCAAATTCACTTAATGAAT-AACTTTAATCTTAAA
*
21856 AGAATTATGAAGG-TTCCAAAAAAAAAGATTACT--CTTCAAAGGCT-TAATCGACTTAATTAAA
65 AGAATTATGAAGGCTT---AAAAAAAAGATTATTGAC-T-AAAGGCTATAAT-GACTTAATTAAA
21917 CCTAACAAGG
Statistics
Matches: 225, Mismatches: 24, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
131 2 0.01
132 26 0.12
133 130 0.58
134 26 0.12
136 35 0.16
137 6 0.03
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38
Consensus pattern (133 bp):
TTAGGTTACTTAACCTCAATTCCAAATTTATCAAATTCACTTAATGAATAACTTTAATCTTAAAA
GAATTATGAAGGCTTAAAAAAAAGATTATTGACTAAAGGCTATAATGACTTAATTAAAACCAAAA
GTT
Found at i:29127 original size:19 final size:18
Alignment explanation
Indices: 29094--29129 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29084 TTGAAATAAT
29094 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
29112 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
29130 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:29549 original size:2 final size:2
Alignment explanation
Indices: 29544--29583 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
29534 ACACACACAG
29544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
29584 CTACATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29856 original size:57 final size:56
Alignment explanation
Indices: 29768--29882 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 56
29758 TATCTGTTTC
* *
29768 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCCTATCTCTATTTAATTTTT
1 CTTTCACACAATAAATATTATAATAAATCCTAT-CCCCCTATCTCTACTTAATTATT
*
29825 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
29881 CT
1 CT
29883 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 23 0.42
57 32 0.58
ACGTcount: A:0.33, C:0.25, G:0.01, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:30007 original size:42 final size:42
Alignment explanation
Indices: 29948--30028 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
29938 CAAGGATCAG
29948 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
29990 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
30029 AAGACTTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:32507 original size:21 final size:21
Alignment explanation
Indices: 32459--32509 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
32449 GTAGAGGATA
*
32459 GCGCGGATGGCCGGGCATGTG
1 GCGCAGATGGCCGGGCATGTG
*
32480 GCTCAGATGGCCGGGCATG-G
1 GCGCAGATGGCCGGGCATGTG
32500 TGCGCAGATG
1 -GCGCAGATG
32510 AGTCAGGGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.14, C:0.24, G:0.47, T:0.16
Consensus pattern (21 bp):
GCGCAGATGGCCGGGCATGTG
Done.