Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013934.1 Corchorus capsularis cultivar CVL-1 contig13955, 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: 15502
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:108 original size:39 final size:39
Alignment explanation
Indices: 28--108 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
18 TGAGGAGAGG
* * *
28 CTCTCTCACTTCTCTGGATTGATCCTCTCTGATCACTCT
1 CTCTCTCACTTCTCTCGATTCATCCTCTCTGATCACCCT
* * *
67 CTCTCTGACTTCTCTCGATTCATCTTCTC-GATTGACCCT
1 CTCTCTCACTTCTCTCGATTCATCCTCTCTGA-TCACCCT
106 CTC
1 CTC
109 GGGCTTGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.12, C:0.37, G:0.10, T:0.41
Consensus pattern (39 bp):
CTCTCTCACTTCTCTCGATTCATCCTCTCTGATCACCCT
Found at i:2215 original size:21 final size:21
Alignment explanation
Indices: 2178--2217 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2168 GTAATCAAGA
*
2178 GTTTTCAAGACTTAAACAGTG
1 GTTTTCAAGAATTAAACAGTG
2199 GTTTTCAA-AATTCAAACAG
1 GTTTTCAAGAATT-AAACAG
2218 ACTTAGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
GTTTTCAAGAATTAAACAGTG
Found at i:2940 original size:12 final size:13
Alignment explanation
Indices: 2912--2954 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2902 AACATTGTAA
2912 TTTTCTTTTTAGG
1 TTTTCTTTTTAGG
*
2925 TTTTCTTTTT-GT
1 TTTTCTTTTTAGG
*
2937 TTTTCTTATTAGG
1 TTTTCTTTTTAGG
*
2950 ATTTC
1 TTTTC
2955 AGATTAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.70
Consensus pattern (13 bp):
TTTTCTTTTTAGG
Found at i:5330 original size:10 final size:10
Alignment explanation
Indices: 5317--5341 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5307 TATATTCAGC
5317 CCATATAAGT
1 CCATATAAGT
5327 CCATATAAGT
1 CCATATAAGT
5337 CCATA
1 CCATA
5342 ATTGGAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATAAGT
Found at i:5830 original size:18 final size:17
Alignment explanation
Indices: 5803--5838 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
5793 TTTCTCTTCA
5803 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
5820 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
5838 T
1 T
5839 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:8561 original size:20 final size:20
Alignment explanation
Indices: 8504--8562 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 20
8494 GAGGCTATCA
8504 AGGCTATCAAGAAGCTTTCG
1 AGGCTATCAAGAAGCTTTCG
*
8524 AGGCGTTTTCACCAAGAAGCTTTCG
1 AGGC----T-ATCAAGAAGCTTTCG
8549 AGGCTATCAAGAAG
1 AGGCTATCAAGAAG
8563 TACTTAGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
20 12 0.38
21 1 0.03
24 1 0.03
25 18 0.56
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (20 bp):
AGGCTATCAAGAAGCTTTCG
Found at i:12594 original size:19 final size:18
Alignment explanation
Indices: 12570--12605 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12560 TGAAGATTTC
12570 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
12589 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
12606 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.