Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012351.1 Corchorus capsularis cultivar CVL-1 contig12372, 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: 20445
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Found at i:1046 original size:22 final size:21
Alignment explanation
Indices: 1016--1074 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
1006 AATTCTTGCT
* *
1016 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
1038 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
1057 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
1075 GCACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:1061 original size:11 final size:11
Alignment explanation
Indices: 1044--1074 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1034 ATTGTCTTCA
1044 AATCTTCAAAT
1 AATCTTCAAAT
*
1055 TATCTTCAAAT
1 AATCTTCAAAT
1066 AATCTTCAA
1 AATCTTCAA
1075 GCACGAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:12305 original size:35 final size:35
Alignment explanation
Indices: 12258--12336 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
12248 ATTTTCAGGA
*
12258 ATTCAGATGACTCAGTGTAGTATCTTCAAAATTGG
1 ATTCAGATGACTCAGTGTAGCATCTTCAAAATTGG
* * *
12293 CTTCAGATGACTCAGTGTGGCATCTTCAAGATTGG
1 ATTCAGATGACTCAGTGTAGCATCTTCAAAATTGG
12328 ATTC-GATGA
1 ATTCAGATGA
12337 GCTCGATGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 5 0.13
35 34 0.87
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (35 bp):
ATTCAGATGACTCAGTGTAGCATCTTCAAAATTGG
Found at i:13030 original size:14 final size:14
Alignment explanation
Indices: 13011--13044 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
13001 GCATATTAAC
13011 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
13025 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
13039 ATTAGT
1 TTTAGT
13045 ATCATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:13221 original size:20 final size:20
Alignment explanation
Indices: 13185--13223 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13175 AAATACAAGG
*
13185 CATTTGATTTACGAATTGGA
1 CATTTGATTTACAAATTGGA
*
13205 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
13224 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:15727 original size:14 final size:14
Alignment explanation
Indices: 15705--15736 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
15695 TAATAACATA
15705 ATAACAGATTCATG
1 ATAACAGATTCATG
*
15719 ATAATAGATTCATG
1 ATAACAGATTCATG
15733 ATAA
1 ATAA
15737 ATCAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (14 bp):
ATAACAGATTCATG
Found at i:16418 original size:37 final size:37
Alignment explanation
Indices: 16361--16630 Score: 296
Period size: 37 Copynumber: 7.2 Consensus size: 37
16351 TACCCCAATA
* *
16361 AATTAAGAGTC-AAATAATAGTAACCAGTAATTAAGT
1 AATTAAGAGTCAAAATGATAGTAATCAGTAATTAAGT
*
16397 AATTAAGAGTCAAAATGATAGTAACCAGTAATTAAGT
1 AATTAAGAGTCAAAATGATAGTAATCAGTAATTAAGT
*
16434 AATTAAGAGTCAAAATGATAGTAACCAGTAATTAAGT
1 AATTAAGAGTCAAAATGATAGTAATCAGTAATTAAGT
* * *
16471 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGA-T
1 AATTAAGAGTCAAAATGATAGTAATCAGT--AATTAAGT
* *
16509 AATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGA-T
1 AATTAAGAGTCAAAATG--ATAGTAATCAGT-AATTAAGT
* *
16548 AATTAAGAGTCAAAAAGAAATAGTAATCAGTAAAT-AGAT
1 AATTAAGAGTCAAAATG--ATAGTAATCAGTAATTAAG-T
** * * *
16587 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGT
1 AATTAAGAGTCAAAATGATAGTAATCAGTAATTAAGT
16624 AATTAAG
1 AATTAAG
16631 CAAAAAAAAG
Statistics
Matches: 213, Mismatches: 13, Indels: 15
0.88 0.05 0.06
Matches are distributed among these distances:
36 11 0.05
37 112 0.53
38 20 0.09
39 58 0.27
40 12 0.06
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.27
Consensus pattern (37 bp):
AATTAAGAGTCAAAATGATAGTAATCAGTAATTAAGT
Found at i:16524 original size:21 final size:21
Alignment explanation
Indices: 16500--16563 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
16490 AGTAATCAGT
16500 AAAATTGATAATTAAGAGTCA
1 AAAATTGATAATTAAGAGTCA
*
16521 AAAA--GA-AA-T-AGTAATCA
1 AAAATTGATAATTAAG-AGTCA
*
16538 GTAAATTGATAATTAAGAGTCA
1 -AAAATTGATAATTAAGAGTCA
16560 AAAA
1 AAAA
16564 GAAATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 2 0.06
17 5 0.16
18 5 0.16
19 2 0.06
20 2 0.06
21 9 0.28
22 5 0.16
23 2 0.06
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.25
Consensus pattern (21 bp):
AAAATTGATAATTAAGAGTCA
Found at i:16590 original size:153 final size:149
Alignment explanation
Indices: 16361--16675 Score: 363
Period size: 153 Copynumber: 2.1 Consensus size: 149
16351 TACCCCAATA
* *
16361 AATTAAGAGTC--AAATAATAGTAACCAGTAATTAAGTAATTAAGAGTCAAAATGATAGTAACCA
1 AATTAAGAGTCAAAAAAAATAGTAACCAGTAATTAAGTAATTAAGAGTCAAAAAGATAGTAACCA
* * * **
16424 GTAATTAAGTAATTAAGAGTCAAAATGATAGTAACCAGTAATTAAGTAATTAAG-AGTCAAAGTA
66 GTAAATAAGTAATTAAGAGTCAAAATAATAGTAACCAGTAAATAAGTAATTAAGCA---AAAAAA
* *
16488 ATAG-TAATCAGTAAAATTGAT
128 AGAGATAACCAGTAAAATTGAT
* *
16509 AATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGA-TAATTAAGAGTCAAAAAGAAATAGTA
1 AATTAAGAGTCAAAAA-AAATAGTAACCAGT-AATTAAGTAATTAAGAGTCAAAAAG--ATAGTA
* ** * *
16573 ATCAGTAAAT-AGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGCAAAAA
62 ACCAGTAAATAAG-TAATTAAGAGTCAAAATAATAGTAACCAGTAAATAAGTAATTAAGCAAAAA
16637 AAAGAGATTAACCAGTAAAATTGAT
126 AAAGAGA-TAACCAGTAAAATTGAT
16662 AATTAAGAGTCAAA
1 AATTAAGAGTCAAA
16676 GTAATAATAG
Statistics
Matches: 141, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
148 11 0.08
150 3 0.02
151 36 0.26
152 7 0.05
153 83 0.59
154 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.26
Consensus pattern (149 bp):
AATTAAGAGTCAAAAAAAATAGTAACCAGTAATTAAGTAATTAAGAGTCAAAAAGATAGTAACCA
GTAAATAAGTAATTAAGAGTCAAAATAATAGTAACCAGTAAATAAGTAATTAAGCAAAAAAAAGA
GATAACCAGTAAAATTGAT
Found at i:16731 original size:78 final size:72
Alignment explanation
Indices: 16361--16763 Score: 229
Period size: 75 Copynumber: 5.3 Consensus size: 72
16351 TACCCCAATA
* * * * * * * * *
16361 AATTAAGAGTCAAA-TAATAGTAACCAGTAATTAAGTAATTAAGAGTCAAAATGATAGTAACCAG
1 AATTAAGAGTCAAAGTAATAATAATCAGAAAATGA-TAATTAAG-GTCAAAAAGAGATTAATCAG
*
16425 T-AATTAAGT
64 TAAATTGA-T
* * * * * * * *
16434 AATTAAGAGTCAAAATGATAGTAACCAGTAATTAAGTAATTAAGAGTCAAAGTAATAG--TAATC
1 AATTAAGAGTCAAAGTAATAATAATCAGAAAATGA-TAATTAAG-GTCAAA--AAGAGATTAATC
16497 AGTAAAATTGAT
62 AGT-AAATTGAT
* * * *
16509 AATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATTGATAATTAAGAGTCAAAAAGAAATAGTAA
1 AATTAAGAGTC--AAAGTAATAATAATCAG-AAAATGATAATTAAG-GTCAAAAAGAGAT--TAA
*
16574 TCAGTAAATAGAT
60 TCAGTAAATTGAT
* * * * *** *
16587 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGCAAAAAAAAGAGATTAACCAG
1 AATTAAGAGTCAAAGTAATAATAATCAGAAAATGA-TAATTAAG-GTCAAAAAGAGATTAATCAG
16652 TAAAATTGAT
64 T-AAATTGAT
* *
16662 AATTAAGAGTCAAAGTAATAATAGTCGGCAAAAATGATAATTAAGGGTCAAGATAAGAGATTAAT
1 AATTAAGAGTCAAAGTAATAATAATCAG--AAAATGATAATTAA-GGTCAA-A-AAGAGATTAAT
* *
16727 CAGTAAAGTCAGT
61 CAGTAAATTGA-T
* *
16740 AATTAAAGAGTCAAGGTAAAAATA
1 AATT-AAGAGTCAAAGTAATAATA
16764 GTAATCAGTA
Statistics
Matches: 268, Mismatches: 41, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
73 14 0.05
74 49 0.18
75 50 0.19
76 48 0.18
77 40 0.15
78 42 0.16
79 25 0.09
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (72 bp):
AATTAAGAGTCAAAGTAATAATAATCAGAAAATGATAATTAAGGTCAAAAAGAGATTAATCAGTA
AATTGAT
Found at i:16810 original size:153 final size:148
Alignment explanation
Indices: 16396--16820 Score: 407
Period size: 153 Copynumber: 2.8 Consensus size: 148
16386 AGTAATTAAG
* * * ** *
16396 TAATTAAGAGTCAAAATG--ATAGTAACCAGTAATTA-AGTAATTAAGAGTCAAAATGATAGTAA
1 TAATTAAGAGTCAAAAAGAAATA-TAATCAGTAAATAGA-TAATTAAGAGTCAAGGTAATAGTAA
* * * *
16458 CCAGTAATTAAGTAATTAAGAGTCAA-AGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAA
64 TCAGTAAATCAGTAATTAAGAATCAAGAG--AT--TAATCAGTAAAATTGATAATTAAGAGTC-A
* * *
16522 AAAGAAATAGTAATCAGTAAATTGA
124 AAAGAAATAATAATCAGAAAAATGA
16547 TAATTAAGAGTCAAAAAGAAATAGTAATCAGTAAATAGATAATTAAGAGTCAAGGTAATAGTAAT
1 TAATTAAGAGTCAAAAAGAAATA-TAATCAGTAAATAGATAATTAAGAGTCAAGGTAATAGTAAT
** *
16612 CAGTAAATCAGTAATTAAGCAAAAAAAAGAGATTAACCAGTAAAATTGATAATTAAGAGTC-AAA
65 CAGTAAATCAGTAATTAAG---AATCAAGAGATTAATCAGTAAAATTGATAATTAAGAGTCAAAA
* * *
16676 GTAATAATAGTCGGCAAAAATGA
127 GAAATAATAATCAG-AAAAATGA
* *
16699 TAATTAAGGGTCAAGATAAGAGAT-TAATCAGTAAAGTCAG-TAATTAAAGAGTCAAGGTAAAAA
1 TAATTAAGAGTCAA-A-AAGAAATATAATCAGTAAA-T-AGATAATT-AAGAGTCAAGGT---AA
* *
16762 TAGTAATCAGTAAATCAGTAATTAAGAATCAAGGGATTAATCAG-AAAATTGATACTTAA
58 TAGTAATCAGTAAATCAGTAATTAAGAATCAAGAGATTAATCAGTAAAATTGATAATTAA
16821 AGGAGAAAGT
Statistics
Matches: 232, Mismatches: 26, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
151 30 0.13
152 30 0.13
153 102 0.44
154 35 0.15
155 2 0.01
156 3 0.01
157 30 0.13
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.26
Consensus pattern (148 bp):
TAATTAAGAGTCAAAAAGAAATATAATCAGTAAATAGATAATTAAGAGTCAAGGTAATAGTAATC
AGTAAATCAGTAATTAAGAATCAAGAGATTAATCAGTAAAATTGATAATTAAGAGTCAAAAGAAA
TAATAATCAGAAAAATGA
Found at i:16945 original size:18 final size:19
Alignment explanation
Indices: 16922--16962 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
16912 AATCAAATGG
*
16922 TAAGAGT-AGAAAGGGTAT
1 TAAGAGTGAAAAAGGGTAT
*
16940 TAAGAGTGAAAAATGGTAT
1 TAAGAGTGAAAAAGGGTAT
16959 TAAG
1 TAAG
16963 TAAAAAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.24
Consensus pattern (19 bp):
TAAGAGTGAAAAAGGGTAT
Found at i:16973 original size:44 final size:44
Alignment explanation
Indices: 16923--17077 Score: 170
Period size: 44 Copynumber: 3.5 Consensus size: 44
16913 ATCAAATGGT
*
16923 AAGAGTAGAAAGGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
1 AAGAGTAAAAAGGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
* * * *
16967 AAGAGTAAAAATGGTA--AAAAGAGACAAAATGGTATCATAGTAAA
1 AAGAGTAAAAAGGGTATTAAGAGTGA-AAAATGGTATTA-AGTAAA
* * **
17011 AAGAGTAAAAAGGATATTAAGAGTAAAAAAAATGGTATTAAGTATT
1 AAGAGTAAAAAGGGTATTAAGAGT--GAAAAATGGTATTAAGTAAA
*
17057 AAGAGTAAAAATGGTATTAAG
1 AAGAGTAAAAAGGGTATTAAG
17078 TAAAGAGTAA
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
42 6 0.07
43 11 0.12
44 34 0.38
46 27 0.30
47 11 0.12
48 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.23, T:0.23
Consensus pattern (44 bp):
AAGAGTAAAAAGGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
Found at i:16982 original size:25 final size:25
Alignment explanation
Indices: 16941--17099 Score: 110
Period size: 25 Copynumber: 6.6 Consensus size: 25
16931 AAAGGGTATT
16941 AAGAGTGAAAAATGGTATTAAGTAAA
1 AAGAGT-AAAAATGGTATTAAGTAAA
16967 AAGAGTAAAAAT-G------GTAAA
1 AAGAGTAAAAATGGTATTAAGTAAA
*
16985 AAGAG-ACAAAATGGTATCATAGTAAA
1 AAGAGTA-AAAATGGTATTA-AGTAAA
**
17011 AAGAGTAAAAA-GGATATTAAG-AGT
1 AAGAGTAAAAATGG-TATTAAGTAAA
**
17035 AA-A--AAAAATGGTATTAAGTATT
1 AAGAGTAAAAATGGTATTAAGTAAA
17057 AAGAGTAAAAATGGTATTAAGTAAA
1 AAGAGTAAAAATGGTATTAAGTAAA
* *
17082 GAGTAAGAAAAAATGGTA
1 AAG--AGTAAAAATGGTA
17100 ATTAGCAAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 35
0.71 0.05 0.23
Matches are distributed among these distances:
17 1 0.01
18 15 0.14
19 1 0.01
21 12 0.11
22 6 0.06
23 2 0.02
24 4 0.04
25 29 0.27
26 24 0.22
27 13 0.12
ACGTcount: A:0.55, C:0.01, G:0.21, T:0.22
Consensus pattern (25 bp):
AAGAGTAAAAATGGTATTAAGTAAA
Found at i:16985 original size:18 final size:18
Alignment explanation
Indices: 16962--17000 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
16952 ATGGTATTAA
16962 GTAAAAAGAGTA-AAAATG
1 GTAAAAAGAG-ACAAAATG
16980 GTAAAAAGAGACAAAATG
1 GTAAAAAGAGACAAAATG
16998 GTA
1 GTA
17001 TCATAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.59, C:0.03, G:0.23, T:0.15
Consensus pattern (18 bp):
GTAAAAAGAGACAAAATG
Done.