Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007492.1 Corchorus capsularis cultivar CVL-1 contig07513, 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: 30739
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:1084 original size:13 final size:13
Alignment explanation
Indices: 1066--1095 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1056 GTTTTCACTA
1066 ACAGCAGGTTGAG
1 ACAGCAGGTTGAG
1079 ACAGCAGGTTGAG
1 ACAGCAGGTTGAG
1092 ACAG
1 ACAG
1096 AAAAATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.37, T:0.13
Consensus pattern (13 bp):
ACAGCAGGTTGAG
Found at i:5444 original size:32 final size:31
Alignment explanation
Indices: 5389--5487 Score: 112
Period size: 32 Copynumber: 3.2 Consensus size: 31
5379 TTGAGTTAGA
5389 TCGGGTTAATTTTGGTC-GAGTTGATTTGGGT
1 TCGGGTTAATTTTGGTCAG-GTTGATTTGGGT
* * *
5420 TCGGGTTAAATTTGGATCAGGTTGATTCGGAT
1 TCGGGTTAATTTTGG-TCAGGTTGATTTGGGT
* *
5452 TCGGGTCAATTTTGGGTCAGGTT-AATTGGGT
1 TCGGGTTAATTTT-GGTCAGGTTGATTTGGGT
5483 TCGGG
1 TCGGG
5488 CTTGATAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
31 24 0.42
32 30 0.53
33 3 0.05
ACGTcount: A:0.16, C:0.09, G:0.35, T:0.39
Consensus pattern (31 bp):
TCGGGTTAATTTTGGTCAGGTTGATTTGGGT
Found at i:5695 original size:16 final size:16
Alignment explanation
Indices: 5674--5720 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5664 TTTAAGGTTT
*
5674 GGATTTGGGTTTTTTC
1 GGATTTGAGTTTTTTC
* *
5690 GGATTTCAGATTTTTC
1 GGATTTGAGTTTTTTC
5706 GGATTCTGA-TTTTTT
1 GGATT-TGAGTTTTTT
5721 TAGGGTTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 23 0.92
17 2 0.08
ACGTcount: A:0.13, C:0.09, G:0.23, T:0.55
Consensus pattern (16 bp):
GGATTTGAGTTTTTTC
Found at i:5716 original size:15 final size:16
Alignment explanation
Indices: 5684--5719 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
5674 GGATTTGGGT
5684 TTTTTCGGATTTCAGA
1 TTTTTCGGATTTCAGA
*
5700 TTTTTCGGA-TTCTGA
1 TTTTTCGGATTTCAGA
5715 TTTTT
1 TTTTT
5720 TTAGGGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (16 bp):
TTTTTCGGATTTCAGA
Found at i:11518 original size:20 final size:22
Alignment explanation
Indices: 11480--11522 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
11470 AAGGATGATA
11480 AATACATCTTCCAATCCATGAG
1 AATACATCTTCCAATCCATGAG
11502 AATA-ATCTTCC-ATCCATGAG
1 AATACATCTTCCAATCCATGAG
11522 A
1 A
11523 TTGTTAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (22 bp):
AATACATCTTCCAATCCATGAG
Found at i:16553 original size:31 final size:33
Alignment explanation
Indices: 16495--16568 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 33
16485 AATAATTTCT
*
16495 TATGAAAAGATGCGACCTTCTTTTTTTGAGATA
1 TATGAAAAGATGCGACCTTCTTTTTTTGAGAAA
* *
16528 -ATGAAAAGATGTGA-CTTTTTTTTTTGAGAAA
1 TATGAAAAGATGCGACCTTCTTTTTTTGAGAAA
16559 TATGAAAAGA
1 TATGAAAAGA
16569 AAAGATGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 15 0.41
32 22 0.59
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (33 bp):
TATGAAAAGATGCGACCTTCTTTTTTTGAGAAA
Found at i:24567 original size:28 final size:28
Alignment explanation
Indices: 24535--24591 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
24525 TACAGGGATG
24535 AGCAGAAACCTCACTAATCACAGTGCAA
1 AGCAGAAACCTCACTAATCACAGTGCAA
*
24563 AGCAGAAACCTCACTAATCATAGTGCAA
1 AGCAGAAACCTCACTAATCACAGTGCAA
24591 A
1 A
24592 AACCTTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (28 bp):
AGCAGAAACCTCACTAATCACAGTGCAA
Found at i:29161 original size:50 final size:53
Alignment explanation
Indices: 29064--29166 Score: 149
Period size: 57 Copynumber: 1.9 Consensus size: 53
29054 TCAAAGCCAA
29064 ACATTTCAATTTATTCATAACATAACATAGAGTATATCTAATTAAAATACAATCCCC
1 ACATTTCAATTTATTCATAACATAAC--A-AG-ATATCTAATTAAAATACAATCCCC
29121 ACATTTCAATTTATTCATAACAT-AC-AG-TATCTAATTAAAATACAAT
1 ACATTTCAATTTATTCATAACATAACAAGATATCTAATTAAAATACAAT
29167 ACGTACACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
50 19 0.41
52 2 0.04
56 2 0.04
57 23 0.50
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (53 bp):
ACATTTCAATTTATTCATAACATAACAAGATATCTAATTAAAATACAATCCCC
Found at i:29291 original size:2 final size:2
Alignment explanation
Indices: 29284--29308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29274 ACACAATTAT
29284 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29309 GCCTCGCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30220 original size:21 final size:22
Alignment explanation
Indices: 30194--30236 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
30184 TTTATGTGAA
30194 TTACTAAATACCGCCC-CCTTT
1 TTACTAAATACCGCCCTCCTTT
**
30215 TTACTAGGTACCGCCCTCCTTT
1 TTACTAAATACCGCCCTCCTTT
30237 GGACAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35
Consensus pattern (22 bp):
TTACTAAATACCGCCCTCCTTT
Done.