Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015586.1 Corchorus capsularis cultivar CVL-1 contig15607, 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: 12083
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:4255 original size:19 final size:19
Alignment explanation
Indices: 4231--4267 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4221 AAGGGTAGTT
4231 AAAAAAAATCTTTTTCATA
1 AAAAAAAATCTTTTTCATA
* *
4250 AAAAAAAGTGTTTTTCAT
1 AAAAAAAATCTTTTTCAT
4268 GCAAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAAAAATCTTTTTCATA
Found at i:5136 original size:18 final size:18
Alignment explanation
Indices: 5113--5147 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5103 AATTTCGTGA
*
5113 TTGAAGATATTTGAAGAT
1 TTGAAGATAATTGAAGAT
5131 TTGAAGATAATTGAAGA
1 TTGAAGATAATTGAAGA
5148 ATTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:10108 original size:49 final size:49
Alignment explanation
Indices: 10055--10429 Score: 356
Period size: 49 Copynumber: 7.5 Consensus size: 49
10045 AAAAAGTGCA
* * * *
10055 TTTTAAGAAAAAGCGAGTAAACATTAACGCCTTCCGTCCGGGAAGGGCG
1 TTTTAGGAAAAAGCAAGTAAAAATTAGCGCCTTCCGTCCGGGAAGGGCG
* *
10104 TTTTAGGAAAAAGAAAGTAAAAAAATAGCGCCTTCCGTCCGGGAAGGGCG
1 TTTTAGGAAAAAGCAAGT-AAAAATTAGCGCCTTCCGTCCGGGAAGGGCG
* * *
10154 TTTTAGGAAAAAACAAGTAAAAATTAGTGTCTTCCGTCCGGGAAGGGCG
1 TTTTAGGAAAAAGCAAGTAAAAATTAGCGCCTTCCGTCCGGGAAGGGCG
* * * * * *
10203 TTTTGGGAAAAAGCAAGTAAAAATTAGTGTCTTCCATTCGGGAAGGGCA
1 TTTTAGGAAAAAGCAAGTAAAAATTAGCGCCTTCCGTCCGGGAAGGGCG
* * * ***
10252 TTTTAGGAAAAAGCGAGTAAAAATTAAATATCGCCTTCCGTCCGAGAAGGTTA
1 TTTTAGGAAAAAGCAAGTAAAAA-T---TAGCGCCTTCCGTCCGGGAAGGGCG
* * * * *
10305 TTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCG
1 TTTTAGGAAAAAGCAAGTAAAAATTAGCGCCTTCCGTCCGGGAAGGGCG
* * * *
10354 TTTTGGGGAAAAA-CGAGTAAAAAGTAAATAGCGCCTTCCGTCCAGGAAGGGCA
1 TTTT-AGGAAAAAGCAAGTAAAAA-T---TAGCGCCTTCCGTCCGGGAAGGGCG
* **
10407 TTTTGGGAAATGGCAAGTAAAAA
1 TTTTAGGAAAAAGCAAGTAAAAA
10430 CTGAAAAATG
Statistics
Matches: 268, Mismatches: 47, Indels: 18
0.80 0.14 0.05
Matches are distributed among these distances:
49 138 0.51
50 53 0.20
52 7 0.03
53 70 0.26
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (49 bp):
TTTTAGGAAAAAGCAAGTAAAAATTAGCGCCTTCCGTCCGGGAAGGGCG
Found at i:10331 original size:102 final size:99
Alignment explanation
Indices: 10052--10429 Score: 404
Period size: 102 Copynumber: 3.8 Consensus size: 99
10042 TCCAAAAAGT
* * * * *
10052 GCATTTTAAGAAAAAGCGAGTAAACATTAA-CGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAA
1 GCATTTTAGGAAAAAGCGAGTAAAAATTAATCGCCTTCCGTCCGAGAAGGGCATTTTGGGAAAAA
* * * *
10116 GAAAGTAAAAAAATAGCGCCTTCCGTCCGGGAAGG
66 GCAAGT-AAAAATTAGTGCCTTCCATCCGGGAAGG
* * * * * * *
10151 GCGTTTTAGGAAAAAACAAGTAAAAATTAGT-GTCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA
1 GCATTTTAGGAAAAAGCGAGTAAAAATTAATCGCCTTCCGTCCGAGAAGGGCATTTTGGGAAAAA
* *
10215 GCAAGTAAAAATTAGTGTCTTCCATTCGGGAAGG
66 GCAAGTAAAAATTAGTGCCTTCCATCCGGGAAGG
**
10249 GCATTTTAGGAAAAAGCGAGTAAAAATTAAATATCGCCTTCCGTCCGAGAAGGTTATTTTGGGAA
1 GCATTTTAGGAAAAAGCGAGTAAAAATT--A-ATCGCCTTCCGTCCGAGAAGGGCATTTTGGGAA
* *
10314 ATAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGG
63 AAAGCAAGTAAAAATTAGTGCCTTCCATCCGGGAAGG
* * *
10351 GCGTTTTGGGGAAAAA-CGAGTAAAAAGTAAATAGCGCCTTCCGTCC-AGGAAGGGCATTTTGGG
1 GCATTTT-AGGAAAAAGCGAGTAAAAA-TTAAT--CGCCTTCCGTCCGA-GAAGGGCATTTTGGG
**
10414 AAATGGCAAGTAAAAA
61 AAAAAGCAAGTAAAAA
10430 CTGAAAAATG
Statistics
Matches: 235, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
98 48 0.20
99 60 0.26
100 3 0.01
101 3 0.01
102 113 0.48
103 8 0.03
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (99 bp):
GCATTTTAGGAAAAAGCGAGTAAAAATTAATCGCCTTCCGTCCGAGAAGGGCATTTTGGGAAAAA
GCAAGTAAAAATTAGTGCCTTCCATCCGGGAAGG
Found at i:10345 original size:151 final size:149
Alignment explanation
Indices: 10061--10416 Score: 410
Period size: 151 Copynumber: 2.4 Consensus size: 149
10051 TGCATTTTAA
* * *
10061 GAAAAAGCGAGTAAACATTAACGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGAAAGTAAAA
1 GAAAAAGCGAGTAAAAATTAACGCCTTCCATCCGGGAAGGGCATTTTAGGAAAAAGAAAGTAAAA
* * * *
10126 AAATAGCGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAACAAGTAAAAATTAGTGTCTTCCGT
66 AAATAGCGCCTTCCGTCCGAGAAGGGCATTTTAGGAAAAAACAAGTAAAAATTAGTGCCTTCCAT
10191 CCGGGAAGGGCGTTTT-GG
131 CCGGGAAGGGCGTTTTGGG
* ** * * **
10209 GAAAAAGCAAGTAAAAATTAGTGTCTTCCATTCGGGAAGGGCATTTTAGGAAAAAGCGAGTAAAA
1 GAAAAAGCGAGTAAAAATTAACGCCTTCCATCCGGGAAGGGCATTTTAGGAAAAAGAAAGT-AAA
* ** * * * *
10274 ATTAAATATCGCCTTCCGTCCGAGAAGGTTATTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTC
65 A--AAATAGCGCCTTCCGTCCGAGAAGGGCATTTTAGGAAAAAACAAGTAAAAATTAGTGCCTTC
10339 CATCCGGGAAGGGCGTTTTGGG
128 CATCCGGGAAGGGCGTTTTGGG
* * * *
10361 GAAAAA-CGAGTAAAAAGTAAATAGCGCCTTCCGTCCAGGAAGGGCATTTTGGGAAA
1 GAAAAAGCGAGTAAAAA-T---TAACGCCTTCCATCCGGGAAGGGCATTTTAGGAAA
10417 TGGCAAGTAA
Statistics
Matches: 172, Mismatches: 28, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
148 51 0.30
149 4 0.02
151 79 0.46
152 9 0.05
155 29 0.17
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (149 bp):
GAAAAAGCGAGTAAAAATTAACGCCTTCCATCCGGGAAGGGCATTTTAGGAAAAAGAAAGTAAAA
AAATAGCGCCTTCCGTCCGAGAAGGGCATTTTAGGAAAAAACAAGTAAAAATTAGTGCCTTCCAT
CCGGGAAGGGCGTTTTGGG
Found at i:10531 original size:21 final size:20
Alignment explanation
Indices: 10501--10539 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
10491 AAGAAGCCCC
*
10501 TTTTTCTTTTTAAGTTTTCT
1 TTTTTCTTTTTAACTTTTCT
10521 TTTTTCTTTTTTAACTTTT
1 TTTTTC-TTTTTAACTTTT
10540 TTTGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTTCTTTTTAACTTTTCT
Found at i:11551 original size:28 final size:28
Alignment explanation
Indices: 11489--11576 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
11479 TACTTTTATC
11489 ATTT-TTACTCTTTTCTTACTCT-TTTT
1 ATTTATTACTCTTTTCTTACTCTCTTTT
***
11515 ACCAATTACTCTTTTCTTACTCTCTTTT
1 ATTTATTACTCTTTTCTTACTCTCTTTT
*
11543 ATTTATTAC-CACTTT-TTACTCTCCTTTT
1 ATTTATTACTC-TTTTCTTACTCT-CTTTT
*
11571 TTTTAT
1 ATTTAT
11577 ACTGACTACC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 26 0.52
28 23 0.46
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTATTACTCTTTTCTTACTCTCTTTT
Found at i:11703 original size:15 final size:14
Alignment explanation
Indices: 11671--11718 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
11661 TGTTTTACTC
11671 TTACTGATTATCTT
1 TTACTGATTATCTT
*
11685 TTACTGATTACTATT
1 TTACTGATTA-TCTT
11700 TTACTGATTATCTT
1 TTACTGATTATCTT
11714 TTACT
1 TTACT
11719 TTTTACTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.23, C:0.15, G:0.06, T:0.56
Consensus pattern (14 bp):
TTACTGATTATCTT
Found at i:11723 original size:21 final size:22
Alignment explanation
Indices: 11692--11771 Score: 80
Period size: 21 Copynumber: 3.8 Consensus size: 22
11682 CTTTTACTGA
*
11692 TTACTATTTTACTGATTATCTT
1 TTACTATTTTACTGATTACCTT
11714 TTACT-TTTTACTGATTACCATT
1 TTACTATTTTACTGATTACC-TT
*
11736 TTACTCTTTTA--GA-TACCTT
1 TTACTATTTTACTGATTACCTT
*
11755 TACACT-TTTTACTGATT
1 T-TACTATTTTACTGATT
11772 GCATGCTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
19 8 0.16
20 7 0.14
21 17 0.34
22 13 0.26
23 5 0.10
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.55
Consensus pattern (22 bp):
TTACTATTTTACTGATTACCTT
Done.