Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012940.1 Corchorus olitorius cultivar O-4 contig12973, 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: 11300
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:34 original size:15 final size:15
Alignment explanation
Indices: 10--61 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
1 TTTTAAAAA
* *
10 TGAAAAATTACTTTT
1 TGAAACATTATTTTT
25 TGAAACATTATTTTTTT
1 TGAAACATTA--TTTTT
42 TGAAACATTATTTTT
1 TGAAACATTATTTTT
57 TGAAA
1 TGAAA
62 AAGAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 19 0.58
17 14 0.42
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (15 bp):
TGAAACATTATTTTT
Found at i:43 original size:17 final size:17
Alignment explanation
Indices: 21--57 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
11 GAAAAATTAC
21 TTTTTGAAACATTATTT
1 TTTTTGAAACATTATTT
38 TTTTTGAAACATTATTT
1 TTTTTGAAACATTATTT
55 TTT
1 TTT
58 GAAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTTTGAAACATTATTT
Found at i:512 original size:8 final size:8
Alignment explanation
Indices: 499--527 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
489 CTTAGAAATT
499 AAAAAAAG
1 AAAAAAAG
507 AAAAAAAG
1 AAAAAAAG
515 AAAAAAA-
1 AAAAAAAG
522 AAAAAA
1 AAAAAA
528 GAAGAGAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:521 original size:17 final size:17
Alignment explanation
Indices: 499--532 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
489 CTTAGAAATT
*
499 AAAAAAAGAAAAA-AAG
1 AAAAAAAAAAAAAGAAG
515 AAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAGAAG
532 A
1 A
533 GAGCTGGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAG
Found at i:524 original size:14 final size:15
Alignment explanation
Indices: 500--530 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
490 TTAGAAATTA
500 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
515 AAAAAA-AAAAAAAG
1 AAAAAAGAAAAAAAG
529 AA
1 AA
531 GAGAGCTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:3509 original size:26 final size:26
Alignment explanation
Indices: 3467--3519 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3457 TGTGACAGTT
*
3467 CATGTGGCAAGACCCTAGGGAAATAC
1 CATGTGGCAACACCCTAGGGAAATAC
* *
3493 CATGTGGCAACATCCTATGGAAATAC
1 CATGTGGCAACACCCTAGGGAAATAC
3519 C
1 C
3520 TTATGCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (26 bp):
CATGTGGCAACACCCTAGGGAAATAC
Found at i:5416 original size:18 final size:18
Alignment explanation
Indices: 5375--5420 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5365 CACTAGAAAT
*
5375 TTAATAATAATTATTCAA
1 TTAATAATTATTATTCAA
** *
5393 AAAATAATTATTATTTAA
1 TTAATAATTATTATTCAA
5411 TTAATAATTA
1 TTAATAATTA
5421 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATAATTATTATTCAA
Found at i:5745 original size:27 final size:28
Alignment explanation
Indices: 5682--5754 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
5672 CTGACAATAT
* *
5682 ATATCTTATGGCAATTACACTCTTGCCA
1 ATATCTTGTGGCAATTACCCTCTTGCCA
* *
5710 A-ACCATGTGGCAATTACCCTCTTG-CA
1 ATATCTTGTGGCAATTACCCTCTTGCCA
*
5736 ATATCTTGTGCCAATTACC
1 ATATCTTGTGGCAATTACC
5755 TTTTGGCAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.08
27 33 0.89
28 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (28 bp):
ATATCTTGTGGCAATTACCCTCTTGCCA
Found at i:7548 original size:11 final size:11
Alignment explanation
Indices: 7528--7562 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
7518 TTGACAGCGC
7528 AACAAAAACAA
1 AACAAAAACAA
*
7539 AACGAAAACAA
1 AACAAAAACAA
7550 AACAAAAACAA
1 AACAAAAACAA
7561 AA
1 AA
7563 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:10231 original size:2 final size:2
Alignment explanation
Indices: 10226--10250 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10216 ATTGTTTCAC
10226 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10251 ATCATCATCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.