Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014100.1 Corchorus capsularis cultivar CVL-1 contig14121, 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: 7864
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Found at i:2136 original size:51 final size:50
Alignment explanation
Indices: 1965--2151 Score: 329
Period size: 50 Copynumber: 3.7 Consensus size: 50
1955 GTCTTTGGCA
*
1965 AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAAAGATTTAAT
1 AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAATGATTTAAT
*
2015 AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCAAATGATTTAAT
1 AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAATGATTTAAT
2065 AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAATGATGTTAAT
1 AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAATGAT-TTAAT
* *
2116 CATAAAAATTAAATCTTTATGTAGTAAGAGTTGAGT
1 AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGT
2152 CCTAGTAATT
Statistics
Matches: 131, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
50 92 0.70
51 39 0.30
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (50 bp):
AATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAATGATTTAAT
Found at i:3005 original size:55 final size:54
Alignment explanation
Indices: 2944--3075 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 54
2934 AAGTAATAGT
*
2944 AATTAAGTGAAAAGAGATTAATCAGAGTCAAGGCAATAGTAATCAGTAAATCAGA
1 AATTAAGT-AAAAGAGATTAATCAGAGTCAAAGCAATAGTAATCAGTAAATCAGA
* * * * *
2999 AATTAAGTAAAAAAGGA-TACATAAGAGTTAAAGTAATAGTAATCAGTAAATCAGT
1 AATTAAGTAAAAGA-GATTA-ATCAGAGTCAAAGCAATAGTAATCAGTAAATCAGA
* *
3054 AATAAAATAAAAG-GATTAATCA
1 AATTAAGTAAAAGAGATTAATCA
3076 AGTAAATTGA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
53 5 0.08
54 9 0.14
55 50 0.78
ACGTcount: A:0.53, C:0.07, G:0.17, T:0.23
Consensus pattern (54 bp):
AATTAAGTAAAAGAGATTAATCAGAGTCAAAGCAATAGTAATCAGTAAATCAGA
Found at i:3112 original size:30 final size:32
Alignment explanation
Indices: 3070--3156 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 32
3060 ATAAAAGGAT
**
3070 TAATCAAGTAAATTGATAATTAAG-GCAG-TAG
1 TAATC-AGTAAATTGATAATTAAGAAAAGATAG
** *
3101 TAATCAGTAAATCAATACTTAAGTAAAAAGATAG
1 TAATCAGTAAATTGATAATTAAG--AAAAGATAG
3135 TAATCAGTAAATTGATAATTAA
1 TAATCAGTAAATTGATAATTAA
3157 AGGGTCAAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
30 15 0.34
31 5 0.11
33 2 0.05
34 22 0.50
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (32 bp):
TAATCAGTAAATTGATAATTAAGAAAAGATAG
Found at i:3156 original size:64 final size:63
Alignment explanation
Indices: 3035--3156 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 63
3025 GTTAAAGTAA
* *
3035 TAGTAATCAGTAAATCAGTAATAAAATAAAAGGATTAATCAAGTAAATTGATAATTAAGGCAG
1 TAGTAATCAGTAAATCAATAATAAAATAAAAAGATTAATCAAGTAAATTGATAATTAAGGCAG
* * *
3098 TAGTAATCAGTAAATCAATACTTAAGTAAAAAGATAGTAATC-AGTAAATTGATAATTAA
1 TAGTAATCAGTAAATCAATAATAAAATAAAAAGAT--TAATCAAGTAAATTGATAATTAA
3157 AGGGTCAAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 30 0.58
64 17 0.33
65 5 0.10
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.29
Consensus pattern (63 bp):
TAGTAATCAGTAAATCAATAATAAAATAAAAAGATTAATCAAGTAAATTGATAATTAAGGCAG
Found at i:3416 original size:14 final size:14
Alignment explanation
Indices: 3396--3490 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
3386 TAATGAAAGG
3396 AAGTAATCAGTAAA
1 AAGTAATCAGTAAA
* *
3410 GAGTAATCGGTAAA
1 AAGTAATCAGTAAA
* * **
3424 AAGTAA-AAATGGCA
1 AAGTAATCAGT-AAA
*
3438 AAG-AGT-AGTAAA
1 AAGTAATCAGTAAA
*
3450 AAGTAATCAGGT-TA
1 AAGTAATCA-GTAAA
*
3464 AAGTAATCAGTAAG
1 AAGTAATCAGTAAA
3478 AAGTAATCAGTAA
1 AAGTAATCAGTAA
3491 GAAGGTCAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
12 4 0.07
13 8 0.14
14 45 0.76
15 2 0.03
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (14 bp):
AAGTAATCAGTAAA
Found at i:3491 original size:14 final size:14
Alignment explanation
Indices: 3444--3494 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
3434 GGCAAAGAGT
*
3444 AGTAAAAAGTAATC
1 AGTAAGAAGTAATC
*
3458 AGGTTA-AAGTAATC
1 A-GTAAGAAGTAATC
3472 AGTAAGAAGTAATC
1 AGTAAGAAGTAATC
3486 AGTAAGAAG
1 AGTAAGAAG
3495 GTCAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 3 0.09
14 27 0.82
15 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.22
Consensus pattern (14 bp):
AGTAAGAAGTAATC
Found at i:3566 original size:43 final size:42
Alignment explanation
Indices: 3486--3616 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 42
3476 AGAAGTAATC
* * *
3486 AGTAAGAAGGTCAAAAATGGTATCAAGTGAAATATGGTATTG
1 AGTAAGAAGGTCAAAAATGGTATCAAGTAAAAAATGGTATTA
*
3528 AGTAAGAAGGTCAAAAAATGGTGT-AGAGTAAAAAATGGTATTA
1 AGTAAGAAGGTC-AAAAATGGTATCA-AGTAAAAAATGGTATTA
* * *
3571 AGTAA-AAGAGT-AAAGAACGGTATTAA--ACAAAAATTGTATTA
1 AGTAAGAAG-GTCAAA-AATGGTATCAAGTA-AAAAATGGTATTA
3612 AGTAA
1 AGTAA
3617 AAGAGTAAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
40 1 0.01
41 20 0.26
42 23 0.30
43 32 0.42
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.24
Consensus pattern (42 bp):
AGTAAGAAGGTCAAAAATGGTATCAAGTAAAAAATGGTATTA
Found at i:3602 original size:25 final size:25
Alignment explanation
Indices: 3552--3602 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3542 AAAATGGTGT
* **
3552 AGAGTAAAAAATGGTATTAAGTAAA
1 AGAGTAAAAAACGGTATTAAACAAA
*
3577 AGAGTAAAGAACGGTATTAAACAAA
1 AGAGTAAAAAACGGTATTAAACAAA
3602 A
1 A
3603 ATTGTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.20
Consensus pattern (25 bp):
AGAGTAAAAAACGGTATTAAACAAA
Found at i:7426 original size:33 final size:32
Alignment explanation
Indices: 7389--7495 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
7379 CGCCTAGCGA
*
7389 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG
*
7422 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
* * *
7455 TGGCCGGTGTTGGCCGGTCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
7488 TGGCCGGT
1 TGGCCGGT
7496 CACTCGCACC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
33 64 0.97
34 2 0.03
ACGTcount: A:0.07, C:0.29, G:0.39, T:0.24
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Done.