Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005364.1 Corchorus capsularis cultivar CVL-1 contig05382, 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: 10775
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:8740 original size:13 final size:13
Alignment explanation
Indices: 8718--8753 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
8708 AGAGTCATGG
8718 TTTTCAAAAATGTT
1 TTTTCAAAAATG-T
8732 TTTTCAAAAATGT
1 TTTTCAAAAATGT
8745 TTTTCAAAA
1 TTTTCAAAA
8754 GAGAATCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (13 bp):
TTTTCAAAAATGT
Found at i:8788 original size:14 final size:15
Alignment explanation
Indices: 8718--8794 Score: 59
Period size: 14 Copynumber: 5.1 Consensus size: 15
8708 AGAGTCATGG
8718 TTTTCAAAAATG-TT
1 TTTTCAAAAATGTTT
8732 TTTTCAAAAATGTTT
1 TTTTCAAAAATGTTT
*** * **
8747 TTCAAAAGAGAATCATGG
1 TTTTCAA-A-AAT-GTTT
8765 TTTTCAAAAATGTTT
1 TTTTCAAAAATGTTT
8780 TTTTC-AAAATGTTT
1 TTTTCAAAAATGTTT
8794 T
1 T
8795 CTTAAAAAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 22 0.47
15 12 0.26
16 4 0.09
17 4 0.09
18 5 0.11
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (15 bp):
TTTTCAAAAATGTTT
Found at i:8816 original size:47 final size:46
Alignment explanation
Indices: 8714--8820 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 46
8704 TTAGAGAGTC
* * *
8714 ATGGTTTTCAAAAATGTTTTTTCAAAAATGTTTTTCAAAAGAGAAT
1 ATGGTTTTCAAAAATGTTTTTTCAAAAATGTTTTTAAAAAAAAAAT
8760 CATGGTTTTCAAAAATGTTTTTTTC-AAAATGTTTTCTTAAAAAAAAAAT
1 -ATGGTTTTCAAAAATG-TTTTTTCAAAAATG-TTT-TTAAAAAAAAAAT
*
8809 -TGTTTTTCAAAA
1 ATGGTTTTCAAAA
8821 GAGAGTCATG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
47 33 0.62
48 10 0.19
49 10 0.19
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (46 bp):
ATGGTTTTCAAAAATGTTTTTTCAAAAATGTTTTTAAAAAAAAAAT
Found at i:8872 original size:67 final size:64
Alignment explanation
Indices: 8718--8877 Score: 168
Period size: 67 Copynumber: 2.4 Consensus size: 64
8708 AGAGTCATGG
*
8718 TTTTCAAAAATGTTTTTTC--AAAAA-TGTTTTTCAAAAGAGAATCATGGTTTTCAAAAATGTTT
1 TTTTC-AAAATGTTTTTTCAAAAAAATTGTTTTTCAAAAGAGAATCATGGTTTTCAAAAAAGTTT
* *
8780 TTTTCAAAATGTTTTCTTAAAAAAAAAATTGTTTTTCAAAAGAGAGTCATGGTTTTCAAAAAAAA
1 TTTTCAAAATGTTTT-TT--CAAAAAAATTGTTTTTCAAAAGAGAATCATGGTTTTC----AAAA
8845 AAG-TT
59 AAGTTT
8850 TTTTCAAAGATG-TTTTTCAAAAATAATT
1 TTTTCAAA-ATGTTTTTTCAAAAA-AATT
8878 TTTGAAACTT
Statistics
Matches: 82, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
61 10 0.12
62 7 0.09
66 5 0.06
67 32 0.39
68 4 0.05
69 2 0.02
70 13 0.16
71 9 0.11
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (64 bp):
TTTTCAAAATGTTTTTTCAAAAAAATTGTTTTTCAAAAGAGAATCATGGTTTTCAAAAAAGTTT
Found at i:9198 original size:13 final size:12
Alignment explanation
Indices: 9175--9240 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 12
9165 ATAAAGTTGC
9175 AAAAA-AAATGA
1 AAAAAGAAATGA
9186 AAAAATGAAATGA
1 AAAAA-GAAATGA
*
9199 AAATAAAAAGATGAAA
1 AAA-AAGAA-ATG--A
9215 AAAAAGAAA-GA
1 AAAAAGAAATGA
*
9226 AAAAAGAAGTGA
1 AAAAAGAAATGA
9238 AAA
1 AAA
9241 GAAATTGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
11 14 0.31
12 5 0.11
13 12 0.27
14 6 0.13
15 4 0.09
16 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (12 bp):
AAAAAGAAATGA
Found at i:9227 original size:27 final size:27
Alignment explanation
Indices: 9175--9240 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
9165 ATAAAGTTGC
*
9175 AAAAAAA-ATG-AAAAAATGAAATGAA
1 AAAAAAAGATGAAAAAAAAGAAATGAA
9200 AATAAAAAGATGAAAAAAAAGAAA-GAA
1 AA-AAAAAGATGAAAAAAAAGAAATGAA
*
9227 AAAAGAAG-TGAAAA
1 AAAAAAAGATGAAAA
9241 GAAATTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 8 0.22
26 10 0.28
27 8 0.22
28 10 0.28
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (27 bp):
AAAAAAAGATGAAAAAAAAGAAATGAA
Found at i:9550 original size:6 final size:6
Alignment explanation
Indices: 9539--9588 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
9529 TGCAATAAGA
* * *
9539 AAAAAG AAAAAG --AAAG AAAAAG AAAACG -AAACG AAAACG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
9584 AAAAA
1 AAAAA
9589 CAGCTCTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 4 0.10
5 5 0.13
6 30 0.77
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9560 original size:16 final size:17
Alignment explanation
Indices: 9539--9586 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
9529 TGCAATAAGA
9539 AAAAAGAAAAAGAAA-G
1 AAAAAGAAAAAGAAACG
*
9555 AAAAAGAAAACGAAACG
1 AAAAAGAAAAAGAAACG
*
9572 AAAACGAAAAAGAAA
1 AAAAAGAAAAAGAAA
9587 AACAGCTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAACG
Done.