Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018903.1 Corchorus olitorius cultivar O-4 contig18936, 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: 1851
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:137 original size:21 final size:21
Alignment explanation
Indices: 86--139 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
76 TAATTAAACT
*
86 TTTCAATAACCTCACTAAGCA
1 TTTCAATAATCTCACTAAGCA
107 TTTCAATAATCTCACTAAGCA
1 TTTCAATAATCTCACTAAGCA
128 TTTCAATAATCT
1 TTTCAATAATCT
140 TATATGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (21 bp):
TTTCAATAATCTCACTAAGCA
Found at i:278 original size:21 final size:22
Alignment explanation
Indices: 248--299 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
238 GTTAATAAGC
*
248 TTTTAAGTAA-CCTTACTA-AA
1 TTTTTAGTAACCCTTACTACAA
*
268 TGTTTTAGTAACCCTTATTACAA
1 T-TTTTAGTAACCCTTACTACAA
291 TTTTTAGTA
1 TTTTTAGTA
300 GGCTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 8 0.30
22 15 0.56
23 3 0.11
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (22 bp):
TTTTTAGTAACCCTTACTACAA
Found at i:370 original size:21 final size:21
Alignment explanation
Indices: 346--475 Score: 88
Period size: 21 Copynumber: 6.2 Consensus size: 21
336 TATAATAATC
*
346 TTAAACTCTTTTAGTGA-TTTA
1 TTAAACT-TTTTAGTAACTTTA
367 TTAAACTTTTTAGTAACTTTA
1 TTAAACTTTTTAGTAACTTTA
** *
388 TTAAGTTTTTTAATAAAC-TTA
1 TTAAACTTTTTAGT-AACTTTA
* *
409 TTAAACTTTTTTGTGA-TCTTA
1 TTAAACTTTTTAGTAACT-TTA
** * *
430 TTATGCTTTTTTAGTAACATTG
1 TTAAAC-TTTTTAGTAACTTTA
* *
452 TT-AAGTTTTTAATAACTTTA
1 TTAAACTTTTTAGTAACTTTA
472 TTAA
1 TTAA
476 GACTGCTTTG
Statistics
Matches: 81, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
20 23 0.28
21 43 0.53
22 15 0.19
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (21 bp):
TTAAACTTTTTAGTAACTTTA
Found at i:417 original size:42 final size:43
Alignment explanation
Indices: 364--476 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 43
354 TTTTAGTGAT
364 TTATTAAACTTTTTAGTAACTTTATTAAG-TTTTTTAATAA-A
1 TTATTAAACTTTTTAGTAACTTTATTAAGCTTTTTTAATAACA
* * * *
405 CTTATTAAACTTTTTTGTGA-TCTTATTATGCTTTTTTAGTAACA
1 -TTATTAAACTTTTTAGTAACT-TTATTAAGCTTTTTTAATAACA
* * *
449 TTGTT-AAGTTTTTAATAACTTTATTAAG
1 TTATTAAACTTTTTAGTAACTTTATTAAG
477 ACTGCTTTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.02
42 40 0.70
43 15 0.26
44 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (43 bp):
TTATTAAACTTTTTAGTAACTTTATTAAGCTTTTTTAATAACA
Found at i:440 original size:63 final size:63
Alignment explanation
Indices: 346--490 Score: 170
Period size: 63 Copynumber: 2.3 Consensus size: 63
336 TATAATAATC
*
346 TTAAACTCTTTTAGTGATTTATTAAAC-TTTTTAGTAACTTTATTAAGTTTTTTAATAAAC-TTA
1 TTAAACTCTTTTAGTGATTTATTAAACTTTTTTAGTAACATTATTAAG-TTTTTAAT-AACTTTA
* ** *
409 TTAAACT-TTTTTGTGATCTTATTATGCTTTTTTAGTAACATTGTTAAGTTTTTAATAACTTTA
1 TTAAACTCTTTTAGTGAT-TTATTAAACTTTTTTAGTAACATTATTAAGTTTTTAATAACTTTA
472 TTAAGACTGCTTTGTAGTG
1 TTAA-ACT-CTTT-TAGTG
491 TGTTAAGTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
62 12 0.17
63 29 0.42
64 21 0.30
66 3 0.04
67 4 0.06
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.52
Consensus pattern (63 bp):
TTAAACTCTTTTAGTGATTTATTAAACTTTTTTAGTAACATTATTAAGTTTTTAATAACTTTA
Found at i:645 original size:21 final size:20
Alignment explanation
Indices: 607--656 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
597 TTTCAATATA
607 TAACTTAGTAAGCATTTTAG
1 TAACTTAGTAAGCATTTTAG
* *
627 TAACTTTGTTAAGCTTTTTAG
1 TAACTTAG-TAAGCATTTTAG
648 TAACCTTAG
1 TAA-CTTAG
657 AAAGTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (20 bp):
TAACTTAGTAAGCATTTTAG
Found at i:705 original size:21 final size:21
Alignment explanation
Indices: 607--706 Score: 59
Period size: 21 Copynumber: 4.9 Consensus size: 21
597 TTTCAATATA
* *
607 TAACTTAG-TAAGCATTTTAG
1 TAACTTGGATAAGCTTTTTAG
* *
627 TAACTTTGTTAAGCTTTTTAG
1 TAACTTGGATAAGCTTTTTAG
*
648 TAACCTTAGA-AAG--TTTTA-
1 TAA-CTTGGATAAGCTTTTTAG
* *
666 TATACTCGTG-TAAACTTTTTAG
1 TA-ACTTG-GATAAGCTTTTTAG
*
688 TAACTTGGATAAGTTTTTT
1 TAACTTGGATAAGCTTTTT
707 TTTTATCATC
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
18 4 0.07
19 9 0.15
20 8 0.13
21 34 0.56
22 6 0.10
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (21 bp):
TAACTTGGATAAGCTTTTTAG
Done.