Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012378.1 Corchorus capsularis cultivar CVL-1 contig12399, 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: 42842
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:617 original size:2 final size:2
Alignment explanation
Indices: 610--639 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
600 TTATTAATTA
*
610 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
640 GTACAGCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1399 original size:17 final size:17
Alignment explanation
Indices: 1377--1434 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
1367 TATCAAGATA
1377 TATATATCTATACTAAT
1 TATATATCTATACTAAT
*
1394 TATATATCTA-ACCATATTAG
1 TATATATCTATA-C-TA--AT
1414 TATATATCTATACTAAT
1 TATATATCTATACTAAT
1431 TATA
1 TATA
1435 ATGTCAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 1 0.03
17 16 0.47
18 2 0.06
19 2 0.06
20 12 0.35
21 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (17 bp):
TATATATCTATACTAAT
Found at i:1615 original size:2 final size:2
Alignment explanation
Indices: 1610--1639 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1600 TGTGTGTGTG
1610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1640 ATACATGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2073 original size:11 final size:11
Alignment explanation
Indices: 2030--2067 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2020 TTCCTATATA
*
2030 AAATAAATTAT
1 AAATTAATTAT
2041 CAAA-TAATTAT
1 -AAATTAATTAT
2052 AAATTAATTAT
1 AAATTAATTAT
2063 AAATT
1 AAATT
2068 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:4941 original size:2 final size:2
Alignment explanation
Indices: 4934--5020 Score: 71
Period size: 2 Copynumber: 45.5 Consensus size: 2
4924 ATTTCCCCTT
*
4934 TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA -A TA -A T- TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* *
4973 TA GTA TA TG TA TA T- TC T- TCA T- TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
5014 TA TA TA T
1 TA TA TA T
5021 TGATATTTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
1 7 0.10
2 60 0.85
3 4 0.06
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12551 original size:8 final size:8
Alignment explanation
Indices: 12538--12570 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
12528 AACATATATC
12538 TTCTTTTT
1 TTCTTTTT
12546 TTC-TTTT
1 TTCTTTTT
12553 TTCTTTTT
1 TTCTTTTT
*
12561 TCCTTTTT
1 TTCTTTTT
12569 TT
1 TT
12571 TTCCCTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTCTTTTT
Found at i:12558 original size:15 final size:15
Alignment explanation
Indices: 12538--12569 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12528 AACATATATC
*
12538 TTCTTTTTTTCTTTT
1 TTCTTTTTTCCTTTT
12553 TTCTTTTTTCCTTTT
1 TTCTTTTTTCCTTTT
12568 TT
1 TT
12570 TTTCCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTTTCCTTTT
Found at i:15478 original size:3 final size:3
Alignment explanation
Indices: 15470--15500 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15460 TACATTTTAG
15470 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
15501 ATAAAACCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:16595 original size:21 final size:21
Alignment explanation
Indices: 16560--16620 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
16550 TTCGGTGAGA
* *
16560 ATAAAATTGGTTACTGTACGT
1 ATAAAATTTGTTACTGTACGG
* *
16581 ATTAGATTTGTTACTGTACGG
1 ATAAAATTTGTTACTGTACGG
16602 ATAAAATTTGTTACTGTAC
1 ATAAAATTTGTTACTGTAC
16621 AAATGAGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (21 bp):
ATAAAATTTGTTACTGTACGG
Found at i:28415 original size:1 final size:1
Alignment explanation
Indices: 28411--28440 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
28401 TATCTGTCAG
28411 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28441 CCGCTTTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:30954 original size:31 final size:31
Alignment explanation
Indices: 30886--31047 Score: 126
Period size: 31 Copynumber: 5.5 Consensus size: 31
30876 GCGGCATCCG
* * **
30886 ACGTGGCATGCCACGTGCCATTTTTTGAAAC
1 ACGTGGCATGCCACGTGTCACTTTTTGGTAC
*
30917 ATGTGGCATGCCACGTGTCACTTTTTGGTAC
1 ACGTGGCATGCCACGTGTCACTTTTTGGTAC
* * *
30948 ACGTGGCGTGACATGTGTCACTTTTTGGTAC
1 ACGTGGCATGCCACGTGTCACTTTTTGGTAC
*
30979 A--T-GTA-G-CAC--G--ACTTTTTGGTAC
1 ACGTGGCATGCCACGTGTCACTTTTTGGTAC
** * * *
31001 ATATGGCGTGCCACATGTCACTTTTTTGTAC
1 ACGTGGCATGCCACGTGTCACTTTTTGGTAC
*
31032 ACGTGGCGTGCCACGT
1 ACGTGGCATGCCACGT
31048 CAGACACCGT
Statistics
Matches: 104, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
25 1 0.01
26 3 0.03
27 4 0.04
28 1 0.01
29 2 0.02
31 78 0.75
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTCACTTTTTGGTAC
Found at i:34668 original size:13 final size:13
Alignment explanation
Indices: 34650--34676 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34640 TACTTTTGTT
34650 ATAAATTAAGTTA
1 ATAAATTAAGTTA
34663 ATAAATTAAGTTA
1 ATAAATTAAGTTA
34676 A
1 A
34677 CCAACAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATAAATTAAGTTA
Done.