Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005353.1 Corchorus capsularis cultivar CVL-1 contig05371, 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: 6180
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:4486 original size:15 final size:15
Alignment explanation
Indices: 4455--4581 Score: 74
Period size: 15 Copynumber: 8.5 Consensus size: 15
4445 TATAAAAGTA
*
4455 AATATATATTTATTAT
1 AATATATA-TAATTAT
4471 AATATATATAATTAT
1 AATATATATAATTAT
* *
4486 AATTATAATTTATATAAT
1 AA-TAT-ATATA-ATTAT
4504 AAATATATATAA--AGT
1 -AATATATATAATTA-T
4519 AA-ATATATAATTACT
1 AATATATATAATTA-T
4534 --T-TATAT-ATTAT
1 AATATATATAATTAT
*
4545 -ATATATATAAAGTA-
1 AATATATAT-AATTAT
*
4559 AATACATATAATTAT
1 AATATATATAATTAT
4574 AATATATA
1 AATATATA
4582 ATTTATATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 29
0.70 0.07 0.23
Matches are distributed among these distances:
11 1 0.01
12 5 0.06
13 18 0.20
14 7 0.08
15 28 0.32
16 12 0.14
17 8 0.09
18 7 0.08
19 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:4501 original size:41 final size:41
Alignment explanation
Indices: 4456--4597 Score: 112
Period size: 41 Copynumber: 3.3 Consensus size: 41
4446 ATAAAAGTAA
*
4456 ATATATATTTATTATAATATATATAATTATAATTATAATTT
1 ATATATATATATTATAATATATATAATTATAATTATAATTT
*
4497 ATATAATAAATATATATAAAGTAAATATATAATTACT--TTATATATTAT
1 ATAT-ATATATAT-TAT-AA-T--ATATATAATTA-TAATTATA-ATT-T
* * *
4545 ATATATATAAAGTA-AATACATATAATTATAATATATAATTT
1 ATATATATATATTATAATATATATAATTATAAT-TATAATTT
*
4586 ATATTTAT-TATT
1 ATATATATATATT
4598 TTTTAAAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
40 3 0.04
41 22 0.28
42 10 0.12
43 8 0.10
44 4 0.05
45 1 0.01
46 7 0.09
47 19 0.24
48 6 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (41 bp):
ATATATATATATTATAATATATATAATTATAATTATAATTT
Found at i:4537 original size:39 final size:40
Alignment explanation
Indices: 4494--4572 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
4484 ATAATTATAA
4494 TTTATATAATAAATATATATAAAGTAAAT-ATATAATTAC
1 TTTATATAATAAATATATATAAAGTAAATAATATAATTAC
* *
4533 TTTATATATTATATATATATAAAGTAAATACATATAATTA
1 TTTATATAATAAATATATATAAAGTAAATA-ATATAATTA
4573 TAATATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 27 0.75
41 9 0.25
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (40 bp):
TTTATATAATAAATATATATAAAGTAAATAATATAATTAC
Found at i:4579 original size:39 final size:36
Alignment explanation
Indices: 4449--4589 Score: 118
Period size: 39 Copynumber: 3.9 Consensus size: 36
4439 TAAAGTTATA
4449 AAAGTAAATATAT-ATT-TAT-TA-TA-ATATATAT
1 AAAGTAAATATATAATTATATATATTATATATATAT
* * *
4480 -AATTATAAT-TATAATT-TATATAATAAATATATAT
1 AAAGTA-AATATATAATTATATATATTATATATATAT
4514 AAAGTAAATATATAATTACTTTATATATTATATATATAT
1 AAAGTAAATATATAATTA---TATATATTATATATATAT
* *
4553 AAAGTAAATACATATAATTATAATATATAATTTATAT
1 AAAGTAAAT--ATATAATTAT-ATATATTATATATAT
4590 TTATTATTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
30 7 0.08
31 9 0.10
32 2 0.02
33 2 0.02
34 11 0.12
35 11 0.12
38 1 0.01
39 38 0.42
41 9 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (36 bp):
AAAGTAAATATATAATTATATATATTATATATATAT
Found at i:4589 original size:11 final size:13
Alignment explanation
Indices: 4474--4584 Score: 69
Period size: 13 Copynumber: 8.8 Consensus size: 13
4464 TTATTATAAT
4474 ATATATAATTATA
1 ATATATAATTATA
4487 AT-TATAATT-T-
1 ATATATAATTATA
*
4497 ATATAATAAATAT-
1 ATAT-ATAATTATA
*
4510 ATATA-AAGTA-A
1 ATATATAATTATA
4521 ATATATAATTACT-
1 ATATATAATTA-TA
*
4534 TTATAT-ATTATA
1 ATATATAATTATA
*
4546 TATATATAAAGTA-A
1 -ATATAT-AATTATA
4560 ATACATATAATTATA
1 AT--ATATAATTATA
4575 ATATATAATT
1 ATATATAATT
4585 TATATTTATT
Statistics
Matches: 77, Mismatches: 7, Indels: 28
0.69 0.06 0.25
Matches are distributed among these distances:
10 2 0.03
11 12 0.16
12 21 0.27
13 27 0.35
14 5 0.06
15 10 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:5922 original size:31 final size:30
Alignment explanation
Indices: 5880--5940 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
5870 CTAAATACAC
*
5880 AAACAAATAAATTACAAAGAAAATTCACAT
1 AAACAAATAAATTACAAAGAAAACTCACAT
5910 AAACAAAATAAATTACAAAGAAAACTCACAT
1 AAAC-AAATAAATTACAAAGAAAACTCACAT
5941 TCCATGAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.64, C:0.15, G:0.03, T:0.18
Consensus pattern (30 bp):
AAACAAATAAATTACAAAGAAAACTCACAT
Found at i:6119 original size:2 final size:2
Alignment explanation
Indices: 6112--6141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6102 ATTAACTCTA
6112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6142 GCTTAGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.