Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016281.1 Corchorus capsularis cultivar CVL-1 contig16302, 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: 24071
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:2474 original size:33 final size:33
Alignment explanation
Indices: 2363--2477 Score: 119
Period size: 33 Copynumber: 3.5 Consensus size: 33
2353 GGTTGGTGCG
*
2363 CCAAG-CG-ATGGCCGGT-TGTGGCCGGACATGT
1 CCAAGTCGCATGGCCGGTGT-TGGCCGGACATCT
* * *
2394 CCATGTCGCGTGGCCGGTGTTGGCCGGGCATCT
1 CCAAGTCGCATGGCCGGTGTTGGCCGGACATCT
* * * *
2427 CCGAGTCACGTGGCCGGTGTTGGCCGGACTTCT
1 CCAAGTCGCATGGCCGGTGTTGGCCGGACATCT
*
2460 CTAAGTCGCATGGCCGGT
1 CCAAGTCGCATGGCCGGT
2478 CACTAGTGCT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 4 0.06
32 2 0.03
33 61 0.90
34 1 0.01
ACGTcount: A:0.11, C:0.29, G:0.37, T:0.23
Consensus pattern (33 bp):
CCAAGTCGCATGGCCGGTGTTGGCCGGACATCT
Found at i:5652 original size:17 final size:18
Alignment explanation
Indices: 5626--5660 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5616 TTTTTCTACC
*
5626 TTTCTTTAG-TTTAGGTT
1 TTTCTCTAGTTTTAGGTT
5643 TTTCTCTAGTTTTAGGTT
1 TTTCTCTAGTTTTAGGTT
5661 AAAGGTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (18 bp):
TTTCTCTAGTTTTAGGTT
Found at i:9838 original size:17 final size:18
Alignment explanation
Indices: 9812--9846 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9802 TTTTTCTACC
*
9812 TTTCTTTAG-TTTAGGTT
1 TTTCTCTAGTTTTAGGTT
9829 TTTCTCTAGTTTTAGGTT
1 TTTCTCTAGTTTTAGGTT
9847 AAAGGTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (18 bp):
TTTCTCTAGTTTTAGGTT
Found at i:11549 original size:13 final size:14
Alignment explanation
Indices: 11531--11559 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
11521 ATAATCAGAC
11531 TTTGCATCCAT-CA
1 TTTGCATCCATGCA
11544 TTTGCATCCATGCA
1 TTTGCATCCATGCA
11558 TT
1 TT
11560 AAAGTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (14 bp):
TTTGCATCCATGCA
Found at i:11746 original size:20 final size:21
Alignment explanation
Indices: 11705--11744 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
11695 ATTAAAATTG
11705 TTAATCAAGAGTTTTCAAAAT
1 TTAATCAAGAGTTTTCAAAAT
11726 TTAATC-AGAGGTTTTCAAA
1 TTAATCAAGA-GTTTTCAAA
11745 TTCAAATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
TTAATCAAGAGTTTTCAAAAT
Found at i:11752 original size:21 final size:22
Alignment explanation
Indices: 11707--11755 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
11697 TAAAATTGTT
*
11707 AATCA-AGAGTTTTCAAAATTT
1 AATCAGAGAGTTTTCAAAATTA
11728 AATCAGAG-GTTTTC-AAATTCA
1 AATCAGAGAGTTTTCAAAATT-A
11749 AATCAGA
1 AATCAGA
11756 CTTAGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 18 0.72
22 2 0.08
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
AATCAGAGAGTTTTCAAAATTA
Found at i:17667 original size:10 final size:10
Alignment explanation
Indices: 17652--17681 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17642 GCCCAATCGA
17652 TGGCCGGTTG
1 TGGCCGGTTG
17662 TGGCCGGTTG
1 TGGCCGGTTG
*
17672 TTGCCGGTTG
1 TGGCCGGTTG
17682 GTGCGCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.47, T:0.33
Consensus pattern (10 bp):
TGGCCGGTTG
Found at i:17732 original size:33 final size:32
Alignment explanation
Indices: 17695--17801 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
17685 CGCCAAGCGA
* *
17695 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGGCATCTCCA-GTCGCG
*
17728 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
* *
17761 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
17794 TGGCCGGT
1 TGGCCGGT
17802 CACTAGTGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
33 63 0.97
34 2 0.03
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGGCATCTCCAGTCGCG
Done.