Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014310.1 Corchorus capsularis cultivar CVL-1 contig14331, 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: 7601
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1229 original size:26 final size:26
Alignment explanation
Indices: 1213--1279 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
1203 TACTTAGTTT
* *
1213 ATTAGTTTAT-TTTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAATATTTA
1238 ATTAGTTTATGATTAATTAATATTTA
1 ATTAGTTTATGATTAATTAATATTTA
1264 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
1280 AATGAAGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 10 0.26
26 29 0.74
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAATATTTA
Found at i:1255 original size:15 final size:15
Alignment explanation
Indices: 1235--1279 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1225 TAATTAGTAT
1235 TTAATTAGTTTATGA
1 TTAATTAGTTTATGA
*
1250 TTAATTA--ATAT--
1 TTAATTAGTTTATGA
1261 TTAATTAGTTTATGA
1 TTAATTAGTTTATGA
1276 TTAA
1 TTAA
1280 AATGAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
11 7 0.29
13 6 0.25
15 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
TTAATTAGTTTATGA
Found at i:1268 original size:51 final size:47
Alignment explanation
Indices: 1157--1273 Score: 114
Period size: 51 Copynumber: 2.4 Consensus size: 47
1147 TTTAAATTTT
* *
1157 TTAATA-TTAATTAGTTTA-TGATTAGTTTTAATTAGTTAATTAAAA
1 TTAATATTTAATTAGTTTATTAATTAGTTTTAATTAGTTAATGAAAA
* * *
1202 TTACTTAGTTT-ATTAGTTTATTTTAATTAGTATTTAATTAGTTTATGATTAA
1 TTA-ATA-TTTAATTAGTTTA--TTAATTAGT-TTTAATTAGTTAATGA-AAA
1254 TTAATATTTAATTAGTTTAT
1 TTAATATTTAATTAGTTTAT
1274 GATTAAAATG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
45 3 0.05
46 2 0.04
47 9 0.16
48 2 0.04
49 1 0.02
50 10 0.18
51 25 0.44
52 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.56
Consensus pattern (47 bp):
TTAATATTTAATTAGTTTATTAATTAGTTTTAATTAGTTAATGAAAA
Found at i:3207 original size:2 final size:2
Alignment explanation
Indices: 3200--3238 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3190 CAAAAATATA
3200 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3239 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3243 original size:2 final size:2
Alignment explanation
Indices: 3238--3273 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3228 ACACACACAC
3238 AT AT AT 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 AT AT AT
3274 CTTTTTGGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6581 original size:75 final size:75
Alignment explanation
Indices: 6450--6678 Score: 323
Period size: 75 Copynumber: 2.9 Consensus size: 75
6440 AACCAGATTC
6450 AATGGGTAAAATGGGTCGAGATAACGGGTCACTCCATTGAAATATTATCGGGTCAATCCAGAAGC
1 AATGGGTAAAATGGGTCGAGATAACGGG----TCCATTGAAATATTATCGGGTCAATCCAGAAGC
*
6515 AAGAATTTGGGTAA
62 AAGAATTTGGATAA
*
6529 AATGGGTAAAATGGGTCGAGATAACAGGTCCATTGAAATATTATCGGGTCAATCCAGAAGCAAGA
1 AATGGGTAAAATGGGTCGAGATAACGGGTCCATTGAAATATTATCGGGTCAATCCAGAAGCAAGA
*
6594 ATTTGGATTA
66 ATTTGGATAA
* * * *
6604 AATGGGTAAAATAGGTTGAGACAATGGGTCACATCATTGAAATATTATCGGGTCAATCCAGAAGC
1 AATGGGTAAAATGGGTCGAGATAACGGGT--C--CATTGAAATATTATCGGGTCAATCCAGAAGC
6669 AAGAATTTGG
62 AAGAATTTGG
6679 CGCGGAATAA
Statistics
Matches: 138, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
75 69 0.50
77 1 0.01
79 68 0.49
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.25
Consensus pattern (75 bp):
AATGGGTAAAATGGGTCGAGATAACGGGTCCATTGAAATATTATCGGGTCAATCCAGAAGCAAGA
ATTTGGATAA
Found at i:6674 original size:79 final size:78
Alignment explanation
Indices: 6445--6678 Score: 357
Period size: 79 Copynumber: 3.0 Consensus size: 78
6435 GACCGAACCA
*
6445 GATTCAATGGGTAAAATGGGTCGAGATAACGGGTCACTCCATTGAAATATTATCGGGTCAATCCA
1 GATTAAATGGGTAAAATGGGTCGAGATAACGGGTCACT-CATTGAAATATTATCGGGTCAATCCA
6510 GAAGCAAGAATTTG
65 GAAGCAAGAATTTG
* * *
6524 GGTAAAATGGGTAAAATGGGTCGAGATAACAGGT--C-CATTGAAATATTATCGGGTCAATCCAG
1 GATTAAATGGGTAAAATGGGTCGAGATAACGGGTCACTCATTGAAATATTATCGGGTCAATCCAG
6586 AAGCAAGAATTTG
66 AAGCAAGAATTTG
* * * *
6599 GATTAAATGGGTAAAATAGGTTGAGACAATGGGTCACATCATTGAAATATTATCGGGTCAATCCA
1 GATTAAATGGGTAAAATGGGTCGAGATAACGGGTCAC-TCATTGAAATATTATCGGGTCAATCCA
6664 GAAGCAAGAATTTG
65 GAAGCAAGAATTTG
6678 G
1 G
6679 CGCGGAATAA
Statistics
Matches: 140, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
75 67 0.48
77 2 0.01
79 71 0.51
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (78 bp):
GATTAAATGGGTAAAATGGGTCGAGATAACGGGTCACTCATTGAAATATTATCGGGTCAATCCAG
AAGCAAGAATTTG
Done.