Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007758.1 Corchorus capsularis cultivar CVL-1 contig07779, 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: 17335
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:365 original size:3 final size:3
Alignment explanation
Indices: 354--395 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
344 TACTGCTAAT
*
354 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
396 GATGTATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:483 original size:15 final size:15
Alignment explanation
Indices: 463--492 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
453 TTACAGTAAA
463 GTAAGTCTTGATTCG
1 GTAAGTCTTGATTCG
478 GTAAGTCTTGATTCG
1 GTAAGTCTTGATTCG
493 TGAAATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (15 bp):
GTAAGTCTTGATTCG
Found at i:4750 original size:14 final size:15
Alignment explanation
Indices: 4715--4754 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
4705 TGATTGACAC
*
4715 TAAAGTAAA-ATATA
1 TAAAGTAAATAAATA
4729 TAAA-TAAATAAATA
1 TAAAGTAAATAAATA
4743 -AAAGTAAATAAA
1 TAAAGTAAATAAA
4755 ATTCATCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
TAAAGTAAATAAATA
Found at i:4973 original size:16 final size:16
Alignment explanation
Indices: 4952--5021 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
4942 GTTCGGGTGC
4952 TTCGGGTATTTTCGGG
1 TTCGGGTATTTTCGGG
4968 TTCGGGTATTTTCGGG
1 TTCGGGTATTTTCGGG
*
4984 TGCGGGT-TCTTTCGGG
1 TTCGGGTAT-TTTCGGG
5000 TTCGGGTATTTTCGGG
1 TTCGGGTATTTTCGGG
5016 TTCGGG
1 TTCGGG
5022 CTCGGATCGG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.02
16 48 0.96
17 1 0.02
ACGTcount: A:0.04, C:0.14, G:0.40, T:0.41
Consensus pattern (16 bp):
TTCGGGTATTTTCGGG
Found at i:5033 original size:17 final size:17
Alignment explanation
Indices: 5011--5055 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
5001 TCGGGTATTT
*
5011 TCGGGTTCGGGCTCGGA
1 TCGGGTTCGGGCCCGGA
*
5028 TCGGGTTCGGGCCCGGG
1 TCGGGTTCGGGCCCGGA
5045 TCGGGTTCGGG
1 TCGGGTTCGGG
5056 TTCACTTACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.02, C:0.24, G:0.51, T:0.22
Consensus pattern (17 bp):
TCGGGTTCGGGCCCGGA
Found at i:7823 original size:20 final size:21
Alignment explanation
Indices: 7798--7845 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
7788 TAAAGAGATT
* * *
7798 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAACAAAGTA
7818 AATTAAAAACAAAACAAAGTA
1 AATTAAAAACAAAACAAAGTA
7839 AATTAAA
1 AATTAAA
7846 TCTAAATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAACAAAGTA
Found at i:8613 original size:16 final size:17
Alignment explanation
Indices: 8569--8613 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
8559 ACCCTAACCC
8569 TAAAACT-AGAGAAAAA
1 TAAAACTAAGAGAAAAA
*
8585 TAAAACTAA-AGAAAGA
1 TAAAACTAAGAGAAAAA
*
8601 TAGAA-TAAGAGAA
1 TAAAACTAAGAGAA
8614 TTATGAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.12
16 21 0.84
17 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.16, T:0.13
Consensus pattern (17 bp):
TAAAACTAAGAGAAAAA
Found at i:10120 original size:22 final size:23
Alignment explanation
Indices: 10093--10142 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
10083 CTCCCCTCCC
* *
10093 TTTTTCTTTTTTTCTT-TATTGT
1 TTTTTCTCTTCTTCTTGTATTGT
*
10115 TTTTTCTCTTCTTCTTGTATTTT
1 TTTTTCTCTTCTTCTTGTATTGT
10138 TTTTT
1 TTTTT
10143 TAAATATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTTCTCTTCTTCTTGTATTGT
Found at i:16359 original size:2 final size:2
Alignment explanation
Indices: 16354--16391 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
16344 AAGAATTTTA
*
16354 AT AT AT A- AT AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16392 TGTATAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16947 original size:21 final size:22
Alignment explanation
Indices: 16923--16970 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
16913 ACTATGTTGA
16923 AATTTTGACAA-C-TGCCTATAT
1 AATTTTGACAACCAT-CCTATAT
* *
16944 AATTATGATAACCATCCTATAT
1 AATTTTGACAACCATCCTATAT
16966 AATTT
1 AATTT
16971 CGATAACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 9 0.41
22 12 0.55
23 1 0.05
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (22 bp):
AATTTTGACAACCATCCTATAT
Found at i:17105 original size:22 final size:22
Alignment explanation
Indices: 17077--17130 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
17067 ACATCGGTTA
*
17077 AATTTTGATAAACGCCCTATAT
1 AATTTTGATAAACGCCATATAT
* *
17099 AATTTTGATAATCGCCATATCT
1 AATTTTGATAAACGCCATATAT
*
17121 TATTTTGATA
1 AATTTTGATA
17131 TGATTCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (22 bp):
AATTTTGATAAACGCCATATAT
Done.