Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007813.1 Corchorus capsularis cultivar CVL-1 contig07834, 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: 14408
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:2813 original size:12 final size:12
Alignment explanation
Indices: 2796--2826 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2786 TATTGTCACG
2796 ATTGTTCTCATC
1 ATTGTTCTCATC
2808 ATTGTTCTCATC
1 ATTGTTCTCATC
2820 ATTGTTC
1 ATTGTTC
2827 AGATTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.10, T:0.52
Consensus pattern (12 bp):
ATTGTTCTCATC
Found at i:8629 original size:16 final size:15
Alignment explanation
Indices: 8606--8649 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
8596 ATTTTAAATT
8606 ATTACTTTTATTTTG
1 ATTACTTTTATTTTG
8621 ATATAC-TTTA--TT-
1 AT-TACTTTTATTTTG
8633 ATTACTTTTATTTTG
1 ATTACTTTTATTTTG
8648 AT
1 AT
8650 GTATAATCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 3 0.12
12 6 0.25
13 2 0.08
14 2 0.08
15 8 0.33
16 3 0.12
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTACTTTTATTTTG
Found at i:10315 original size:33 final size:34
Alignment explanation
Indices: 10254--10318 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
10244 ATGCTGGATT
* * *
10254 TTGAGTTTTGAACATGAGATGCAGATTTTGAACA
1 TTGAATTTTGAACATGAAATGCAAATTTTGAACA
10288 TTGAATTTTGAA-ATGAAATGCAAATTTTGAA
1 TTGAATTTTGAACATGAAATGCAAATTTTGAA
10319 TTTTGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (34 bp):
TTGAATTTTGAACATGAAATGCAAATTTTGAACA
Found at i:10434 original size:35 final size:35
Alignment explanation
Indices: 10395--10621 Score: 116
Period size: 35 Copynumber: 6.3 Consensus size: 35
10385 AAATACAGGT
* * * **
10395 TTTGAATTTTGAACCATGAGATGCTGATTTTGAAC
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
*
10430 TTTGATTTTTGAATAATGAAATGCAAATTTTGAAC
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
* * *
10465 TTTGATTTTTGAAGAATAGAATGCTGAAATGCAAGTTTTGAAT
1 TTTGATTTTT---G-A-ACAA---TGAAATGCAAATTTTGAAC
* * * * *** **
10508 TTTGACTTTTGAAGAATGAACCGTG-TAATGCAG-GT
1 TTTGATTTTTGAACAATGAA--ATGCAAATTTTGAAC
* * * ** *
10543 TTTGAATTTTGAACCATGAGATGCTGATTTTGAAT
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
* *
10578 TTTGATTTTTGAATAATGAAATGCAAATTTTGAAT
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
10613 TTTGATTTT
1 TTTGATTTT
10622 CGAAGAATAG
Statistics
Matches: 147, Mismatches: 33, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
33 2 0.01
34 4 0.03
35 99 0.67
36 3 0.02
37 2 0.01
38 5 0.03
39 2 0.01
40 4 0.03
43 26 0.18
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (35 bp):
TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
Found at i:10434 original size:70 final size:70
Alignment explanation
Indices: 10352--10597 Score: 228
Period size: 70 Copynumber: 3.4 Consensus size: 70
10342 GAAATGCAAG
10352 TTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATACAGGTTTTGAATTTTGAACCATGAGAT
1 TTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATACAGGTTTTGAATTTTGAACCATGAGAT
10417 GCTGA
66 GCTGA
* * * * *** ** * **
10422 TTTTGAACTTTGATTTTTGAATAATGAA--ATGCAAATTTTGAACTTTGATTTTTGAAGAAT-AG
1 TTTTGAATTTTGACTTTTGAAGAATGAACCGTG-AAATACAG-GTTTTGAATTTTGAACCATGAG
10484 AATGCTGAAATGCAA
64 -ATGC-----TG--A
* *
10499 GTTTTGAATTTTGACTTTTGAAGAATGAACCGTGTAATGCAGGTTTTGAATTTTGAACCATGAGA
1 -TTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATACAGGTTTTGAATTTTGAACCATGAGA
10564 TGCTGA
65 TGCTGA
* *
10570 TTTTGAATTTTGATTTTTGAATAATGAA
1 TTTTGAATTTTGACTTTTGAAGAATGAA
10598 ATGCAAATTT
Statistics
Matches: 135, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
68 2 0.01
69 7 0.05
70 69 0.51
71 1 0.01
73 2 0.01
75 2 0.01
77 1 0.01
78 43 0.32
79 6 0.04
80 2 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (70 bp):
TTTTGAATTTTGACTTTTGAAGAATGAACCGTGAAATACAGGTTTTGAATTTTGAACCATGAGAT
GCTGA
Found at i:10514 original size:148 final size:148
Alignment explanation
Indices: 10252--10674 Score: 687
Period size: 148 Copynumber: 2.9 Consensus size: 148
10242 TAATGCTGGA
* * * *
10252 TTTTGAGTTTTGAA-CATGAGATGCAGATTTTGAACATTGAATTTTG-A-AATGAAATGCAAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
*
10314 TTGAATTTTGATTTTCG-A-AA-GGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
66 TTGAATTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
10376 TGAACCGTGAAATACAGG
131 TGAACCGTGAAATACAGG
10394 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
* *
10459 TTGAACTTTGATTTTTGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
66 TTGAATTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
* *
10524 TGAACCGTGTAATGCAGG
131 TGAACCGTGAAATACAGG
*
10542 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGCAAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
*
10607 TTGAATTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGATTTTTTTGAAG
66 TTGAATTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGA--CTTTTGAAG
10672 AAT
129 AAT
10675 AAACAATAAA
Statistics
Matches: 260, Mismatches: 13, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
142 13 0.05
143 29 0.11
144 1 0.00
145 30 0.12
146 1 0.00
147 2 0.01
148 173 0.67
150 11 0.04
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (148 bp):
TTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCAAATT
TTGAATTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
TGAACCGTGAAATACAGG
Found at i:10550 original size:42 final size:43
Alignment explanation
Indices: 10446--10554 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
10436 TTTTGAATAA
* * * *
10446 TGAAATGCAAATTTTGAACTTTGATTTTTGAAGAATAGAATGC
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATAGAACGC
10489 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAAT-GAAC-C
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATAGAACGC
* *
10530 GTGTAATGCAGGTTTTGAATTTTGA
1 -TGAAATGCAAGTTTTGAATTTTGA
10555 ACCATGAGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 25 0.42
43 33 0.56
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (43 bp):
TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATAGAACGC
Found at i:10686 original size:43 final size:45
Alignment explanation
Indices: 10592--10708 Score: 143
Period size: 43 Copynumber: 2.7 Consensus size: 45
10582 ATTTTTGAAT
* *
10592 AATGAAATGCAAATTTTGAATTTTGA--TTTTCGAAGAATAGAAT
1 AATGAAATGCAAGTTTTGAATTTTGATTTTTTCGAAGAATAGAAC
** *
10635 GCTGAAATGCAAGTTTTGAATTTTGATTTTTTTGAAGAATA-AAC
1 AATGAAATGCAAGTTTTGAATTTTGATTTTTTCGAAGAATAGAAC
* *
10679 AAT-AAATGCATGTTTTGAAATTTGATTTTT
1 AATGAAATGCAAGTTTTGAATTTTGATTTTT
10709 GAGTCAAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 48 0.76
44 3 0.05
45 12 0.19
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (45 bp):
AATGAAATGCAAGTTTTGAATTTTGATTTTTTCGAAGAATAGAAC
Found at i:10732 original size:7 final size:7
Alignment explanation
Indices: 10720--10753 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
10710 AGTCAAGAAA
10720 TTTGAAT
1 TTTGAAT
10727 TTTGAAT
1 TTTGAAT
10734 TTTGAAT
1 TTTGAAT
10741 TTTGAAT
1 TTTGAAT
10748 TTTGAA
1 TTTGAA
10754 GACTTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (7 bp):
TTTGAAT
Found at i:10921 original size:37 final size:37
Alignment explanation
Indices: 10879--11176 Score: 295
Period size: 37 Copynumber: 8.1 Consensus size: 37
10869 TGGTTTTCGA
10879 ACACCTAAACAGGGATCATT-AACAAGATTTTGATGAG
1 ACACCTAAACAGGGATC-TTAAACAAGATTTTGATGAG
* * *
10916 ACACCTAAATAGGGA-CTTTAAACAAGGA-TTTAATAAG
1 ACACCTAAACAGGGATC-TTAAACAA-GATTTTGATGAG
* *
10953 AAACCTAAACAGGAATCTTAAACAAGATTTTGATGAG
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATGAG
* * * *
10990 ACACCTAAACAGGGACCTTAACCAAGGA-TTTAATAAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATGAG
* * *
11027 AAACCTAAACATGAATCTTAAACAAGATTTTGATGAG
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATGAG
* *
11064 ACACCTAAACAGGGA-CTTTAAATAAGGA-TTTGATAAG
1 ACACCTAAACAGGGATC-TTAAACAA-GATTTTGATGAG
* * * * *
11101 AAACCTAAACAGGCATCTTGAACAAGGTTTTGATGAC
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATGAG
* *
11138 ACACCTAAACAGGGACCTTAAACAAGGA-TTTGACGAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATGAG
11175 AC
1 AC
11177 TGAATTTTTC
Statistics
Matches: 209, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
36 9 0.04
37 191 0.91
38 9 0.04
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (37 bp):
ACACCTAAACAGGGATCTTAAACAAGATTTTGATGAG
Found at i:11170 original size:74 final size:74
Alignment explanation
Indices: 10881--11168 Score: 452
Period size: 74 Copynumber: 3.9 Consensus size: 74
10871 GTTTTCGAAC
* * *
10881 ACCTAAACAGGGATCATT-AACAAGATTTTGATGAGACACCTAAATAGGGACTTTAAACAAGGAT
1 ACCTAAACAGGAATC-TTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGAT
10945 TTAATAAGAA
65 TTAATAAGAA
*
10955 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAACCAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
11020 TAATAAGAA
66 TAATAAGAA
* * *
11029 ACCTAAACATGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACTTTAAATAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
11094 TGATAAGAA
66 TAATAAGAA
* * * *
11103 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGACACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
11168 T
66 T
11169 GACGAGACTG
Statistics
Matches: 197, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
73 2 0.01
74 195 0.99
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
TAATAAGAA
Found at i:11940 original size:87 final size:87
Alignment explanation
Indices: 11790--11957 Score: 230
Period size: 87 Copynumber: 1.9 Consensus size: 87
11780 TGATTGATGC
* * * * * *
11790 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCTAACTCAATTGATGTTTCTAGATCAG
1 CCCAAACCTTCCTCCAATTTGATAATGCATTGATATTCCCAACTCAATTGATATTTCTAGATCAG
11855 CTTCTCACCTCAAGAATTATTT
66 CTTCTCACCTCAAGAATTATTT
*
11877 CCCAAATCTTCCTCCAATTTGATAATGCATTGATATTCCCAACTCAATTGATATTTC-AGGATCA
1 CCCAAACCTTCCTCCAATTTGATAATGCATTGATATTCCCAACTCAATTGATATTTCTA-GATCA
* * *
11941 GTTTCTCATCTTAAGAA
65 GCTTCTCACCTCAAGAA
11958 ACTTTCAAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
86 1 0.01
87 69 0.99
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (87 bp):
CCCAAACCTTCCTCCAATTTGATAATGCATTGATATTCCCAACTCAATTGATATTTCTAGATCAG
CTTCTCACCTCAAGAATTATTT
Found at i:12105 original size:17 final size:17
Alignment explanation
Indices: 12085--12117 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12075 AACCTTTTGA
12085 TTTTTCTTTCTTTTTTC
1 TTTTTCTTTCTTTTTTC
*
12102 TTTTTCTTTGTTTTTT
1 TTTTTCTTTCTTTTTT
12118 TTTAGATTGC
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:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTCTTTCTTTTTTC
Found at i:12793 original size:14 final size:14
Alignment explanation
Indices: 12766--12805 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
12756 TTTTGAAAAC
12766 TGAAAAC-C-TTTT
1 TGAAAACTCATTTT
12778 TGAAAACTCATTTT
1 TGAAAACTCATTTT
*
12792 TG-AAAGTCATTTT
1 TGAAAACTCATTTT
12805 T
1 T
12806 TTGAAAGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 6 0.24
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (14 bp):
TGAAAACTCATTTT
Found at i:12806 original size:14 final size:14
Alignment explanation
Indices: 12774--12825 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
12764 ACTGAAAACC
*
12774 TTTTTGAAAACTCA-
1 TTTTTG-AAAGTCAT
12788 TTTTTGAAAGTCATT
1 TTTTTGAAAGTCA-T
12803 TTTTTGAAAG-CAT
1 TTTTTGAAAGTCAT
12816 TTTCTTGAAA
1 TTT-TTGAAA
12826 TTTTTTCGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 10 0.29
14 14 0.41
15 10 0.29
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAGTCAT
Found at i:12806 original size:15 final size:14
Alignment explanation
Indices: 12788--12825 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
12778 TGAAAACTCA
12788 TTTTTGAAAGTCATT
1 TTTTTGAAAG-CATT
12803 TTTTTGAAAGCATT
1 TTTTTGAAAGCATT
*
12817 TTCTTGAAA
1 TTTTTGAAA
12826 TTTTTTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTTTGAAAGCATT
Done.