Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015600.1 Corchorus capsularis cultivar CVL-1 contig15621, 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: 9175
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:7036 original size:14 final size:14
Alignment explanation
Indices: 6998--7037 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
6988 TTCAAATAAA
6998 AAAAATAGGTTTTTC
1 AAAAAT-GGTTTTTC
*
7013 AAAAGT-GTTTTTC
1 AAAAATGGTTTTTC
7026 AAAAATGGTTTT
1 AAAAATGGTTTT
7038 CGAAACCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 12 0.55
14 5 0.23
15 5 0.23
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (14 bp):
AAAAATGGTTTTTC
Found at i:7394 original size:12 final size:13
Alignment explanation
Indices: 7338--7394 Score: 84
Period size: 12 Copynumber: 4.6 Consensus size: 13
7328 TAAAACAACA
7338 AAAAAAATCAATC
1 AAAAAAATCAATC
7351 AAAAAAAT-AAT-
1 AAAAAAATCAATC
*
7362 ATAAAAATCAATC
1 AAAAAAATCAATC
7375 AAAAAAATC-ATC
1 AAAAAAATCAATC
7387 AAAAAAAT
1 AAAAAAAT
7395 GAAAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 7 0.17
12 17 0.43
13 16 0.40
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAATCAATC
Found at i:7692 original size:12 final size:13
Alignment explanation
Indices: 7664--7692 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
7654 TGGTCAAAAC
7664 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
7677 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
7690 TTT
1 TTT
7693 CGGGTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (13 bp):
TTTTGAAAAGAGT
Found at i:7735 original size:9 final size:9
Alignment explanation
Indices: 7721--7761 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
7711 CCAAGTGCCG
7721 TGAAAAAAA
1 TGAAAAAAA
7730 TGAAAAAAA
1 TGAAAAAAA
7739 TG-AAAAAA
1 TGAAAAAAA
7747 TG--AAAAA
1 TGAAAAAAA
7754 TGAAAAAA
1 TGAAAAAA
7762 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.23
8 8 0.27
9 15 0.50
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
TGAAAAAAA
Found at i:7737 original size:8 final size:8
Alignment explanation
Indices: 7724--7766 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
7714 AGTGCCGTGA
7724 AAAAAATG
1 AAAAAATG
7732 AAAAAAATG
1 -AAAAAATG
7741 AAAAAATG
1 AAAAAATG
7749 -AAAAATG
1 AAAAAATG
7756 AAAAAA-G
1 AAAAAATG
7763 AAAA
1 AAAA
7767 GAAAAGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 12 0.36
8 13 0.39
9 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:9109 original size:22 final size:22
Alignment explanation
Indices: 9081--9158 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 22
9071 CATTGGTAAG
9081 ACCTCCGGGCACAAATTCAGAA
1 ACCTCCGGGCACAAATTCAGAA
* ** **
9103 ACCTCCGGGTATTAATTTTGATA
1 ACCTCCGGGCACAAATTCAGA-A
9126 AGTCCTCCGGGCACAAATTCAGAA
1 A--CCTCCGGGCACAAATTCAGAA
9150 ACCTCCGGG
1 ACCTCCGGG
9159 TATTAATTCT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
22 24 0.56
23 2 0.05
24 2 0.05
25 15 0.35
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (22 bp):
ACCTCCGGGCACAAATTCAGAA
Found at i:9133 original size:25 final size:25
Alignment explanation
Indices: 9104--9175 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 25
9094 AATTCAGAAA
*
9104 CCTCCGGGTATTAATTTTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* ** *
9129 CCTCCGGGCACAAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
9151 CCTCCGGGTATTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
22 16 0.46
23 2 0.06
24 2 0.06
25 15 0.43
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:9151 original size:47 final size:47
Alignment explanation
Indices: 9077--9175 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
9067 TTTGCATTGG
* *
9077 TAAGACCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTTTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
9124 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
9171 TAAGT
1 TAAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
Found at i:9166 original size:22 final size:22
Alignment explanation
Indices: 9094--9167 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
9084 TCCGGGCACA
9094 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
** * **
9116 AATTTTGATAAGTCCTCCGGGCACA
1 AATTCAGA-AA--CCTCCGGGTATT
9141 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
9163 AATTC
1 AATTC
9168 TGATAAGT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (22 bp):
AATTCAGAAACCTCCGGGTATT
Done.