Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010942.1 Corchorus capsularis cultivar CVL-1 contig10963, 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: 15877
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Found at i:13320 original size:16 final size:16
Alignment explanation
Indices: 13301--13361 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 16
13291 CCAGTGAATT
13301 AAGTAATTAAGAGTCA
1 AAGTAATTAAGAGTCA
* *
13317 AAGTAATAGTAACCAGTAA
1 AAGTAAT--TAA-GAGTCA
13336 AATTGATAATTAAGAGTCA
1 AA--G-TAATTAAGAGTCA
13355 AAGTAAT
1 AAGTAAT
13362 GTTAATTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 11 0.31
17 1 0.03
18 3 0.09
19 12 0.34
20 3 0.09
21 1 0.03
22 4 0.11
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (16 bp):
AAGTAATTAAGAGTCA
Found at i:13394 original size:37 final size:38
Alignment explanation
Indices: 13267--13397 Score: 144
Period size: 38 Copynumber: 3.5 Consensus size: 38
13257 TACCCCAATA
* **
13267 AATTAAGAGTC-AAGATAATAGTAACCAGT-GAATTAAGT
1 AATTAAGAGTCAAAG-TAATAGTAACCAGTAAAATCGA-T
*
13305 AATTAAGAGTCAAAGTAATAGTAACCAGTAAAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAACCAGTAAAATCGAT
**
13343 AATTAAGAGTCAAAGTAAT-GTTAATTAGT-AAATCGAT
1 AATTAAGAGTCAAAGTAATAG-TAACCAGTAAAATCGAT
*
13380 GATTAAGAGTCAAAGTAA
1 AATTAAGAGTCAAAGTAA
13398 GAAGATTAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
37 25 0.30
38 51 0.61
39 8 0.10
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (38 bp):
AATTAAGAGTCAAAGTAATAGTAACCAGTAAAATCGAT
Found at i:13551 original size:34 final size:33
Alignment explanation
Indices: 13434--13567 Score: 135
Period size: 34 Copynumber: 3.9 Consensus size: 33
13424 TAAGGAAAAT
* * *
13434 AAAAGTAGTAATCAGTAAATCAGTAATAAACTA
1 AAAAGTAGTAATCAGTAAATCAATAATTAAGTA
* ** *
13467 AAAAG-ATTAATCATGTAAATTGATAATTAAGGGA
1 AAAAGTAGTAATCA-GTAAATCAATAATTAA-GTA
*
13501 GTAAAAGTAGTAATCAGTAAATCAACAATTAAGTA
1 --AAAAGTAGTAATCAGTAAATCAATAATTAAGTA
*
13536 AAAAGATAGTAATCAGTAAATCGATAATTAAG
1 AAAAG-TAGTAATCAGTAAATCAATAATTAAG
13568 AGTCAAGGTA
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
32 7 0.09
33 22 0.27
34 25 0.31
35 2 0.02
36 18 0.22
37 7 0.09
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (33 bp):
AAAAGTAGTAATCAGTAAATCAATAATTAAGTA
Found at i:13587 original size:40 final size:41
Alignment explanation
Indices: 13536--13613 Score: 133
Period size: 40 Copynumber: 1.9 Consensus size: 41
13526 CAATTAAGTA
13536 AAAAGATAGTAATCAGTAAATC-GATAATTAAGAGTCAAGGT
1 AAAAGATAGTAATCAGTAAATCAG-TAATTAAGAGTCAAGGT
13577 AAAA-ATAGTAATCAGTAAATCAGTAATTAAGAGTCAA
1 AAAAGATAGTAATCAGTAAATCAGTAATTAAGAGTCAA
13614 TGGATTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAAGATAGTAATCAGTAAATCAGTAATTAAGAGTCAAGGT
Found at i:13623 original size:74 final size:69
Alignment explanation
Indices: 13391--13669 Score: 265
Period size: 74 Copynumber: 3.9 Consensus size: 69
13381 ATTAAGAGTC
* * * * *
13391 AAAGTAAGAAGATTAATCAAGTGAATTAATAGTTAAGGAAAATAAAAGTAGTAATCAGTAAATCA
1 AAAGTAAAAAGATTAATC-AGTAAATTGATAATTAAGG-AAGTAAAAGTAGTAATCAGTAAATCA
13456 GTAA-T
64 GTAATT
* * *
13461 AAACTAAAAAGATTAATCATGTAAATTGATAATTAAGGGAGTAAAAGTAGTAATCAGTAAATCAA
1 AAAGTAAAAAGATTAATCA-GTAAATTGATAATTAAGGAAGTAAAAGTAGTAATCAGTAAATCAG
*
13526 CAATT
65 TAATT
* *
13531 -AAGTAAAAAGATAGTAATCAGTAAATCGATAATTAAGAGTCAAGGTAAAAATAGTAATCAGTAA
1 AAAGTAAAAAGAT--TAATCAGTAAATTGATAATTAAG-G--AA-GTAAAAGTAGTAATCAGTAA
13595 ATCAGTAATT
60 ATCAGTAATT
* ** * * *
13605 AAGAGTCAATGGATTAATCAGTAAATTGATACTTAAGGGAGAAAGTAAAATTAGTGATCAGTAAA
1 AA-AGTAAAAAGATTAATCAGTAAATTGATAATTAA--G-G-AAGTAAAAGTAGTAATCAGTAAA
13670 GAGAAAAATG
Statistics
Matches: 174, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
69 38 0.22
70 48 0.28
71 7 0.04
73 1 0.01
74 66 0.38
75 3 0.02
76 11 0.06
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (69 bp):
AAAGTAAAAAGATTAATCAGTAAATTGATAATTAAGGAAGTAAAAGTAGTAATCAGTAAATCAGT
AATT
Found at i:13830 original size:28 final size:29
Alignment explanation
Indices: 13798--13927 Score: 120
Period size: 28 Copynumber: 4.3 Consensus size: 29
13788 TGGTAAAAAA
13798 GTAAAAAGCAATCAGT-AAGAGTAAAATG
1 GTAAAAAGCAATCAGTAAAGAGTAAAATG
* * *
13826 GTAAAGAGTAATCAGTAAAAAGTAAAATGG
1 GTAAAAAGCAATCAGTAAAGAGTAAAAT-G
*
13856 TAAAAAAGTAAAAAGCAATCAAT-AAGAGTAAAATG
1 -------GTAAAAAGCAATCAGTAAAGAGTAAAATG
* *
13891 GTAAAGAGCAATCAGTAAACAGTAAAATG
1 GTAAAAAGCAATCAGTAAAGAGTAAAATG
13920 GTAAAAAG
1 GTAAAAAG
13928 TAAAGAGTAA
Statistics
Matches: 81, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
28 28 0.35
29 28 0.35
30 1 0.01
35 1 0.01
36 10 0.12
37 13 0.16
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (29 bp):
GTAAAAAGCAATCAGTAAAGAGTAAAATG
Found at i:13834 original size:15 final size:15
Alignment explanation
Indices: 13814--13931 Score: 55
Period size: 15 Copynumber: 7.6 Consensus size: 15
13804 AGCAATCAGT
13814 AAGAGTAAAATGGTA
1 AAGAGTAAAATGGTA
*
13829 AAGAGT--AATCAGTA
1 AAGAGTAAAAT-GGTA
*
13843 AAAAGTAAAATGGTAA
1 AAGAGTAAAATGGT-A
* * *
13859 AAAAGTAAAAAGCAATCAA
1 AAGAGTAAAATG--GT--A
13878 TAAGAGTAAAATGGTA
1 -AAGAGTAAAATGGTA
* *
13894 AAGAG--CAATCAGTA
1 AAGAGTAAAAT-GGTA
*
13908 AACAGTAAAATGGTA
1 AAGAGTAAAATGGTA
*
13923 AAAAGTAAA
1 AAGAGTAAA
13932 GAGTAATCAA
Statistics
Matches: 78, Mismatches: 14, Indels: 22
0.68 0.12 0.19
Matches are distributed among these distances:
13 6 0.08
14 15 0.19
15 24 0.31
16 19 0.24
18 2 0.03
19 2 0.03
20 10 0.13
ACGTcount: A:0.58, C:0.05, G:0.19, T:0.18
Consensus pattern (15 bp):
AAGAGTAAAATGGTA
Found at i:13856 original size:65 final size:65
Alignment explanation
Indices: 13785--13945 Score: 261
Period size: 65 Copynumber: 2.5 Consensus size: 65
13775 GTAATCAGTG
*
13785 AAATGGTAAAAAAGTAAAAAGCAATCAGTAAGAGTAAAATGGTAAAGAGTAATCAGTAAAAAGTA
1 AAATGGTAAAAAAGTAAAAAGCAATCAGTAAGAGTAAAATGGTAAAGAGCAATCAGTAAAAAGTA
* *
13850 AAATGGTAAAAAAGTAAAAAGCAATCAATAAGAGTAAAATGGTAAAGAGCAATCAGTAAACAGTA
1 AAATGGTAAAAAAGTAAAAAGCAATCAGTAAGAGTAAAATGGTAAAGAGCAATCAGTAAAAAGTA
* *
13915 AAATGGT-AAAAAGTAAAGAGTAATCAAGTAA
1 AAATGGTAAAAAAGTAAAAAGCAATC-AGTAA
13946 AATGATAGGG
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 16 0.18
65 73 0.82
ACGTcount: A:0.57, C:0.06, G:0.19, T:0.18
Consensus pattern (65 bp):
AAATGGTAAAAAAGTAAAAAGCAATCAGTAAGAGTAAAATGGTAAAGAGCAATCAGTAAAAAGTA
Found at i:13923 original size:29 final size:28
Alignment explanation
Indices: 13863--13927 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 28
13853 TGGTAAAAAA
*
13863 GTAAAAAGCAATCAATAAGAGTAAAATG
1 GTAAAAAGCAATCAATAACAGTAAAATG
* *
13891 GTAAAGAGCAATCAGTAAACAGTAAAATG
1 GTAAAAAGCAATCAAT-AACAGTAAAATG
13920 GTAAAAAG
1 GTAAAAAG
13928 TAAAGAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.55, C:0.08, G:0.20, T:0.17
Consensus pattern (28 bp):
GTAAAAAGCAATCAATAACAGTAAAATG
Found at i:13936 original size:29 final size:30
Alignment explanation
Indices: 13882--13949 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
13872 AATCAATAAG
* *
13882 AGTAAAATGGTAAAGAGCAATCAGTAAAC-
1 AGTAAAATGGTAAAAAGCAAACAGTAAACA
* * *
13911 AGTAAAATGGTAAAAAGTAAAGAGTAATCA
1 AGTAAAATGGTAAAAAGCAAACAGTAAACA
13941 AGTAAAATG
1 AGTAAAATG
13950 ATAGGGAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 24 0.73
30 9 0.27
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (30 bp):
AGTAAAATGGTAAAAAGCAAACAGTAAACA
Found at i:13960 original size:94 final size:93
Alignment explanation
Indices: 13798--13988 Score: 224
Period size: 94 Copynumber: 2.0 Consensus size: 93
13788 TGGTAAAAAA
* * * *
13798 GTAAAAAGCAATCAGTAAGAGTAAAATGGTAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAA
1 GTAAAAAGCAATCAGTAACAGTAAAATGGTAAAAAGTAAACAGTAAAAAGTAAAATGATAAAAAA
13863 GTAAAAAGCAATCAATAAGAGT-AAAATG
66 GTAAAAAGCAATCAATAA-AGTGAAAATG
* * * **
13891 GTAAAGAGCAATCAGTAAACAGTAAAATGGTAAAAAGTAAAGAGTAATCAAGTAAAATGAT-AGG
1 GTAAAAAGCAATCAGT-AACAGTAAAATGGTAAAAAGTAAACAGTAA-AAAGTAAAATGATAAAA
* * * *
13955 GAGTAAATAGTAATCAGTAAAGTGAAAATG
64 AAGTAAAAAGCAATCAATAAAGTGAAAATG
13985 GTAA
1 GTAA
13989 TCAGTAAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
93 18 0.22
94 53 0.65
95 11 0.13
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.19
Consensus pattern (93 bp):
GTAAAAAGCAATCAGTAACAGTAAAATGGTAAAAAGTAAACAGTAAAAAGTAAAATGATAAAAAA
GTAAAAAGCAATCAATAAAGTGAAAATG
Found at i:13983 original size:65 final size:63
Alignment explanation
Indices: 13785--13998 Score: 225
Period size: 65 Copynumber: 3.3 Consensus size: 63
13775 GTAATCAGTG
* * *
13785 AAATGGTAAAAAAGTAAAAAGCAATCAGTAAGAGTAAAATGGTAAAGAGTAATCAGTAAAAAGTA
1 AAATGGT-AAAAAGTAAAAAGCAATCAATAAAAGTAAAAGGGTAAAGAGTAATCAGT-AAAAGTA
* * *
13850 AAATGGTAAAAAAGTAAAAAGCAATCAATAAGAGTAAAATGGTAAAGAGCAATCAGTAAACAGTA
1 AAATGGT-AAAAAGTAAAAAGCAATCAATAAAAGTAAAAGGGTAAAGAGTAATCAGTAAA-AGTA
* * * * *
13915 AAATGGTAAAAAGTAAAGAGTAATCAAGTAAAA-TGATAGGGAGTAAATAGTAATCAGT-AAAGT
1 AAATGGTAAAAAGTAAAAAGCAATCAA-TAAAAGT-AAAAGG-GTAAAGAGTAATCAGTAAAAGT
13978 GA
63 -A
**
13980 AAATGGTAATCAGTAAAAA
1 AAATGGTAAAAAGTAAAAA
13999 AGAATAAAAA
Statistics
Matches: 131, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
64 25 0.19
65 92 0.70
66 14 0.11
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.19
Consensus pattern (63 bp):
AAATGGTAAAAAGTAAAAAGCAATCAATAAAAGTAAAAGGGTAAAGAGTAATCAGTAAAAGTA
Found at i:14027 original size:19 final size:20
Alignment explanation
Indices: 13992--14033 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13982 ATGGTAATCA
*
13992 GTAAAAAAGAATAAAAAATG
1 GTAAAAAAAAATAAAAAATG
14012 GTAAAAAAAAAT-AAAAATG
1 GTAAAAAAAAATAAAAAATG
14031 GTA
1 GTA
14034 TTCAGTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (20 bp):
GTAAAAAAAAATAAAAAATG
Found at i:14066 original size:33 final size:31
Alignment explanation
Indices: 14012--14075 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
14002 ATAAAAAATG
* *
14012 GTAAAAAAAAATAAAAATGGTATTCAGTAAA
1 GTAAAAAAAAATAAAAATGGTAATCAATAAA
*
14043 GTAAAAAAAGAGTAAAAAGTGGTAATCAATAAA
1 GTAAAAAAA-AATAAAAA-TGGTAATCAATAAA
14076 AGAGAGTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.32
32 7 0.25
33 12 0.43
ACGTcount: A:0.61, C:0.03, G:0.16, T:0.20
Consensus pattern (31 bp):
GTAAAAAAAAATAAAAATGGTAATCAATAAA
Done.