Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024370.1 Corchorus olitorius cultivar O-4 contig24403, 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: 16748
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:75 original size:19 final size:18
Alignment explanation
Indices: 51--86 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41 TGAAGATTTA
51 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
70 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
87 ATTAATTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:6812 original size:21 final size:22
Alignment explanation
Indices: 6765--6814 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
6755 TTTTCGGTTG
*
6765 AAGCAAGAGAAGAAGTCGACTT
1 AAGCAAGAGAAGAAGTCGACTA
* *
6787 GAGCAA-AGGAGAAGTCGACTA
1 AAGCAAGAGAAGAAGTCGACTA
6808 AAGCAAG
1 AAGCAAG
6815 TCGATAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.46, C:0.14, G:0.30, T:0.10
Consensus pattern (22 bp):
AAGCAAGAGAAGAAGTCGACTA
Found at i:13516 original size:21 final size:21
Alignment explanation
Indices: 13458--13581 Score: 90
Period size: 22 Copynumber: 5.7 Consensus size: 21
13448 CGTGATATAG
* * *
13458 TATCAAAAAATTATAGGGAGAT
1 TATCAAAATATCATA-GGAGGT
* *
13480 TAACAAAATCTCATAGAGAGGT
1 TATCAAAATATCATAG-GAGGT
13502 TATCAAAA-ATCATAGGAAGGT
1 TATCAAAATATCATAGG-AGGT
*
13523 TA-CAAAATTTCATAGGAAGGTT
1 TATCAAAATATCATAGG-AGG-T
* * *
13545 TATTAAAATTTCATAGTTAGGT
1 TATCAAAATATCATAG-GAGGT
*
13567 TATCAAAATTTCATA
1 TATCAAAATATCATA
13582 TTTCATAGGT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
20 6 0.07
21 24 0.28
22 40 0.47
23 15 0.18
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (21 bp):
TATCAAAATATCATAGGAGGT
Found at i:13556 original size:23 final size:22
Alignment explanation
Indices: 13483--13581 Score: 114
Period size: 22 Copynumber: 4.5 Consensus size: 22
13473 GGGAGATTAA
*
13483 CAAAATCTCATA-GAGAGGTTAT
1 CAAAATTTCATAGGA-AGGTTAT
*
13505 CAAAA-ATCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
13525 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
13548 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
13570 CAAAATTTCATA
1 CAAAATTTCATA
13582 TTTCATAGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.07
21 22 0.33
22 25 0.37
23 15 0.22
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:13585 original size:29 final size:29
Alignment explanation
Indices: 13552--13610 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
13542 GTTTATTAAA
* ** *
13552 ATTTCATAGTTAGGTTATCAAAATTTCAT
1 ATTTCATAGGTAAATTATCAAAATTCCAT
13581 ATTTCATAGGTAAATTATCAAAATTCCAT
1 ATTTCATAGGTAAATTATCAAAATTCCAT
13610 A
1 A
13611 ACGTGCATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (29 bp):
ATTTCATAGGTAAATTATCAAAATTCCAT
Found at i:15450 original size:40 final size:40
Alignment explanation
Indices: 15406--16202 Score: 1184
Period size: 40 Copynumber: 19.9 Consensus size: 40
15396 GAATAGGAAA
* * * ** * *
15406 AACACCTCCCGATGAGGAAGGGCAAACTAAGAATTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* * *
15446 AACACTTTCCGGTAGGGAAAGGCAAACT-GGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* * *
15485 AACTCCTTCCGGTGGAGAAGGGCAAACTAGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
*
15525 AACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
15565 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* * *
15605 AACACCTTCCGGTAGGGAAGGGCAAATTTGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
15645 AACACCTTCTGATGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
15685 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
15725 AACACCTTCCGATGGGGAAGGGCAAATTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
15765 AACACCTTCCGATGGGGAAGGGCAAACTGCGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
*
15805 AACACCTTCCGATGGGGAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
15845 AACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* * *
15885 AATACCTTCCGGTGGGGAAGGGCAAATTGGGTACTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
*
15925 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTA-TTTAAAC
*
15966 AACACCTTCCGGTGGGAAAGGGCAAACTGGGTATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
16006 AACACCTTCCGGTGGGGAAAGGCAAACTGGGGT-TTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACT-GGGTATTTAAAC
* * *
16046 AACACCTTCCGGTGGAGAAGGGCAGACTGGGTATTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
16086 AACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAGAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
*
16126 AACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAAC
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* * *
16166 AACACTTTCCGGTGTGGAAGGGCAGACTGGGTATTTA
1 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
16203 GACTAGACAA
Statistics
Matches: 693, Mismatches: 60, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
39 35 0.05
40 617 0.89
41 41 0.06
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (40 bp):
AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
Done.