Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013485.1 Corchorus capsularis cultivar CVL-1 contig13506, 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: 12017
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:420 original size:31 final size:30
Alignment explanation
Indices: 352--430 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
342 ATTTTTAGCC
*
352 ACCAATTTAAGCCTAAACCTTTCAAAAGTT
1 ACCAATTTGAGCCTAAACCTTTCAAAAGTT
* *
382 GCTCAATTTGAGTCTAAACCTTTCAAAAGTT
1 AC-CAATTTGAGCCTAAACCTTTCAAAAGTT
*
413 AACCAATTTGAACCTAAA
1 -ACCAATTTGAGCCTAAA
431 AACAAAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (30 bp):
ACCAATTTGAGCCTAAACCTTTCAAAAGTT
Found at i:843 original size:15 final size:15
Alignment explanation
Indices: 823--862 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
813 AACCAGTTTG
823 ATTAATGTTAAAAAA
1 ATTAATGTTAAAAAA
838 ATTAATGTT-AAAAA
1 ATTAATGTTAAAAAA
852 ATTAAATGTTA
1 ATT-AATGTTA
863 TTATTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
ATTAATGTTAAAAAA
Found at i:1522 original size:2 final size:2
Alignment explanation
Indices: 1517--1554 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1507 ATTTAGTGTG
1517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1555 ACATAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3767 original size:23 final size:23
Alignment explanation
Indices: 3737--3783 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3727 TGGAGGAAGA
3737 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
*
3760 GGGTTAGTGGTGATTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
3783 G
1 G
3784 CAATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.02, G:0.40, T:0.45
Consensus pattern (23 bp):
GGGTTAGTGGTGACTGTTTTGAT
Found at i:6055 original size:16 final size:16
Alignment explanation
Indices: 6034--6065 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6024 TATAACCTAG
*
6034 TCGTACTTGATGACAA
1 TCGTACTTGATAACAA
6050 TCGTACTTGATAACAA
1 TCGTACTTGATAACAA
6066 GAAAAAGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (16 bp):
TCGTACTTGATAACAA
Found at i:6616 original size:21 final size:21
Alignment explanation
Indices: 6592--6631 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6582 ACAGCTCACC
*
6592 TGGGTGATCAGACAAACCACA
1 TGGGTCATCAGACAAACCACA
*
6613 TGGGTCCTCAGACAAACCA
1 TGGGTCATCAGACAAACCA
6632 TGTGGGCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.15
Consensus pattern (21 bp):
TGGGTCATCAGACAAACCACA
Found at i:8352 original size:11 final size:11
Alignment explanation
Indices: 8321--8374 Score: 53
Period size: 10 Copynumber: 5.3 Consensus size: 11
8311 TCTAACAAAT
8321 ATAATTCACAA
1 ATAATTCACAA
8332 A-AATTCACAA
1 ATAATTCACAA
*
8342 ATAATTAAC-A
1 ATAATTCACAA
* *
8352 ATTA-GCAC-A
1 ATAATTCACAA
8361 ATAATTCACAA
1 ATAATTCACAA
8372 ATA
1 ATA
8375 TAACACCTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 6 0.18
10 17 0.50
11 11 0.32
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.26
Consensus pattern (11 bp):
ATAATTCACAA
Found at i:9119 original size:16 final size:17
Alignment explanation
Indices: 9098--9132 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
9088 TAATAAACAA
9098 TAACATTGTCTC-AAGT
1 TAACATTGTCTCTAAGT
*
9114 TAACATTGTTTCTAAGT
1 TAACATTGTCTCTAAGT
9131 TA
1 TA
9133 GATAACTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
TAACATTGTCTCTAAGT
Found at i:10089 original size:86 final size:85
Alignment explanation
Indices: 9931--10099 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 85
9921 CCCATCATCT
* * * *
9931 CAAAGAAAAATACAGTGAATCAAAGCATTGAACGAAGAAATTAGGCAAATAAACAGCAGATTTAC
1 CAAACAAAAATACAGTAAATCAAAGCATTGAACAAAGAAATTAGGCAAATAAACAGCAGATTAAC
*
9996 TTGATTCGAACCCAAAAATG
66 TTCATTCGAACCCAAAAATG
* * * * *
10016 CAAACAAAAGTACAGTAAATCAAAGCATTTAATCAAAGAATTTGGGCAAATAAACAGCATATTAA
1 CAAACAAAAATACAGTAAATCAAAGCATTGAA-CAAAGAAATTAGGCAAATAAACAGCAGATTAA
10081 CTTCATTCGAACCCAAAAA
65 CTTCATTCGAACCCAAAAA
10100 AAATCAAACT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 28 0.38
86 45 0.62
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.20
Consensus pattern (85 bp):
CAAACAAAAATACAGTAAATCAAAGCATTGAACAAAGAAATTAGGCAAATAAACAGCAGATTAAC
TTCATTCGAACCCAAAAATG
Found at i:10897 original size:12 final size:12
Alignment explanation
Indices: 10882--10936 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
10872 TTTTTTCGTC
10882 ATTTTTCTTTTT
1 ATTTTTCTTTTT
*
10894 ATTTTTC-GTTT
1 ATTTTTCTTTTT
* *
10905 -TGTTTATTTTT
1 ATTTTTCTTTTT
**
10916 CCTTTTCTTTTT
1 ATTTTTCTTTTT
10928 ATTTTTCTT
1 ATTTTTCTT
10937 AGTTACTTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
10 4 0.12
11 6 0.19
12 22 0.69
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (12 bp):
ATTTTTCTTTTT
Found at i:10910 original size:16 final size:16
Alignment explanation
Indices: 10891--10921 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10881 CATTTTTCTT
*
10891 TTTATTTTTCGTTTTG
1 TTTATTTTTCCTTTTG
10907 TTTATTTTTCCTTTT
1 TTTATTTTTCCTTTT
10922 CTTTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTATTTTTCCTTTTG
Found at i:10914 original size:22 final size:21
Alignment explanation
Indices: 10863--10915 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
10853 ATTTCTTATC
10863 TTTATCTTTTTTTTTCGTCATT
1 TTTAT-TTTTTTTTTCGTCATT
* *
10885 TTTCTTTTTATTTTTCGT-TTT
1 TTTATTTTT-TTTTTCGTCATT
10906 GTTTATTTTT
1 -TTTATTTTT
10916 CCTTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.08, C:0.09, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTATTTTTTTTTTCGTCATT
Done.