Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010785.1 Corchorus olitorius cultivar O-4 contig10817, 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: 28891
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:19459 original size:21 final size:21
Alignment explanation
Indices: 19433--19497 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
19423 CAAGAAGAAG
19433 AAGAAAAAAGAATTTACTAAA
1 AAGAAAAAAGAATTTACTAAA
19454 AAGAAAAAAGAATTTACTAAA
1 AAGAAAAAAGAATTTACTAAA
19475 AAGAAAAAAGAATTTACTAAA
1 AAGAAAAAAGAATTTACTAAA
19496 AA
1 AA
19498 AACTACAGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.68, C:0.05, G:0.09, T:0.18
Consensus pattern (21 bp):
AAGAAAAAAGAATTTACTAAA
Found at i:22005 original size:36 final size:36
Alignment explanation
Indices: 21958--22027 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
21948 TTCAATAACC
*
21958 TTACATTTTTTGTAATTTTGGTTATCATATTTCTTA
1 TTACATTTTTTGTAATTTTGATTATCATATTTCTTA
21994 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATTTTTTGTAATTTTGATTATCATATTTCT
22028 CCAAAATCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (36 bp):
TTACATTTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:24269 original size:41 final size:39
Alignment explanation
Indices: 24209--24285 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 39
24199 AAATTTTTTA
24209 AATTATTATAAGATAATAATA-ATTAATAATTTACTTCTCAT
1 AATTATTATAAGATAATAATATATT--TAATTTA-TTCTCAT
* * *
24250 AATTATTTTTAGATTATAATATATTTAATTTATTCT
1 AATTATTATAAGATAATAATATATTTAATTTATTCT
24286 TCTTCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.12
40 7 0.22
41 18 0.56
42 3 0.09
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.51
Consensus pattern (39 bp):
AATTATTATAAGATAATAATATATTTAATTTATTCTCAT
Found at i:25304 original size:22 final size:22
Alignment explanation
Indices: 25279--25531 Score: 125
Period size: 22 Copynumber: 11.6 Consensus size: 22
25269 ACAATCAAAC
25279 CAAAATTAT-ATAGGAAGGTTAT
1 CAAAATT-TCATAGGAAGGTTAT
* *
25301 CAAAATTTCATA-CAGAGGTTAC
1 CAAAATTTCATAGGA-AGGTTAT
* * *
25323 CAGAATTTCATAGGGAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
* *
25345 CAAAATTTTATATGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
25367 CGAAATTTTATATTG-TGGTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* * *
25389 CAAAATTTCATAAGAATGTTAA
1 CAAAATTTCATAGGAAGGTTAT
*
25411 CAAAATTTCATAGGGACTGAAGTTAT
1 CAAAATTTCATA-GGA---AGGTTAT
* *
25437 CAAAA-TT--T--G-TGCTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
25453 CAAAATTTCCTATGG-AGGTTAA
1 CAAAATTTCATA-GGAAGGTTAT
*
25475 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
25497 GAAAA-TT-ATATGAAGAGATTAT
1 CAAAATTTCATAGGAAG-G-TTAT
*
25519 CAAAATTACATAG
1 CAAAATTTCATAG
25532 AGAGAATATC
Statistics
Matches: 175, Mismatches: 36, Indels: 38
0.70 0.14 0.15
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
19 1 0.01
20 7 0.04
21 8 0.05
22 127 0.73
23 6 0.03
24 3 0.02
25 2 0.01
26 10 0.06
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:25342 original size:44 final size:44
Alignment explanation
Indices: 25288--25444 Score: 138
Period size: 44 Copynumber: 3.5 Consensus size: 44
25278 CCAAAATTAT
* *
25288 ATAGGAAGGTTATCAAAATTTCATACAG-AGGTTACCAGAATTTC
1 ATAGGGAGGTTATCAAAATTTCATA-AGAAGGTTAACAGAATTTC
* * * * *
25332 ATAGGGAGGTTAACAAAATTTTATATGAAGGTTATC-GAAATTTT
1 ATAGGGAGGTTATCAAAATTTCATAAGAAGGTTAACAG-AATTTC
** * * *
25376 ATATTGTGGTTATCAAAATTTCATAAGAATGTTAACAAAATTTC
1 ATAGGGAGGTTATCAAAATTTCATAAGAAGGTTAACAGAATTTC
25420 ATAGGGACTGAAGTTATCAAAATTT
1 ATAGGGA--G--GTTATCAAAATTT
25445 GTGCTTATCA
Statistics
Matches: 87, Mismatches: 19, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
43 2 0.02
44 71 0.82
46 1 0.01
48 13 0.15
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (44 bp):
ATAGGGAGGTTATCAAAATTTCATAAGAAGGTTAACAGAATTTC
Found at i:25418 original size:66 final size:66
Alignment explanation
Indices: 25279--25424 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
25269 ACAATCAAAC
* * * *
25279 CAAAATTATATAGGAAGGTTATCAAAATTTCATACAGAGGTTACCAGAATTTCATAGGGAGGTTA
1 CAAAATTTTATAGGAAGGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAGAAGGTTA
25344 A
66 A
* * * ** * * *
25345 CAAAATTTTATATGAAGGTTATCGAAATTTTATATTGTGGTTATCAAAATTTCATAAGAATGTTA
1 CAAAATTTTATAGGAAGGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAGAAGGTTA
25410 A
66 A
*
25411 CAAAATTTCATAGG
1 CAAAATTTTATAGG
25425 GACTGAAGTT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (66 bp):
CAAAATTTTATAGGAAGGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAGAAGGTTA
A
Found at i:25535 original size:22 final size:22
Alignment explanation
Indices: 25449--25542 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 22
25439 AAATTTGTGC
* * *
25449 TTATCAAAATTTCCTATG-GAGG
1 TTATCAAAATTACATA-GAGAGA
* * * *
25471 TTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTACATAGAGAGA
* *
25493 TTATGAAAATTATAT-GAAGAGA
1 TTATCAAAATTACATAG-AGAGA
25515 TTATCAAAATTACATAGAGAGA
1 TTATCAAAATTACATAGAGAGA
*
25537 ATATCA
1 TTATCA
25543 CAGCTTCTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 2 0.03
22 55 0.95
23 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.31
Consensus pattern (22 bp):
TTATCAAAATTACATAGAGAGA
Found at i:25663 original size:22 final size:22
Alignment explanation
Indices: 25581--25685 Score: 83
Period size: 22 Copynumber: 4.8 Consensus size: 22
25571 AAATTTCATG
25581 GTGTGATTATCAAAATTTTA-A
1 GTGTGATTATCAAAATTTTACA
* *
25602 GAG-GAGGTTATCAAAATTTTCACG
1 GTGTGA--TTATCAAAATTTT-ACA
* *
25626 GTGTGGTT-TC-CAATTTTACA
1 GTGTGATTATCAAAATTTTACA
*
25646 GTGTGATTATCAAAATTTCACA
1 GTGTGATTATCAAAATTTTACA
* * *
25668 CTGAGGTTATCAAAATTT
1 GTGTGATTATCAAAATTT
25686 CATAATATGG
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
20 11 0.17
21 10 0.15
22 38 0.58
23 3 0.05
24 2 0.03
25 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (22 bp):
GTGTGATTATCAAAATTTTACA
Found at i:25686 original size:22 final size:22
Alignment explanation
Indices: 25652--25743 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 22
25642 TACAGTGTGA
*
25652 TTATCAAAATTTCACACTGA-GG
1 TTATCAAAATTTCACAAT-ATGG
*
25674 TTATCAAAATTTCATAATATGG
1 TTATCAAAATTTCACAATATGG
* * ***
25696 TTATCAAATTTTCATAGGGTGG
1 TTATCAAAATTTCACAATATGG
* * *
25718 TTATCGAAATTTCATAATAAGG
1 TTATCAAAATTTCACAATATGG
25740 TTAT
1 TTAT
25744 TTAATTTTCG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 1 0.02
22 56 0.98
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCACAATATGG
Found at i:25706 original size:65 final size:66
Alignment explanation
Indices: 25581--25731 Score: 155
Period size: 65 Copynumber: 2.3 Consensus size: 66
25571 AAATTTCATG
* ** * *
25581 GTGTGATTATCAAAATTTTAAGAGGAGGTTATCAAAATTTTCACGGTGTGGTTTCCAATTTT-AC
1 GTGTGATTATCAAAATTTCAAGAGGAGGTTATCAAAATTTTCACAATATGGTTTCAAATTTTCAC
25645 A
66 A
** *
25646 GTGTGATTATCAAAATTTCACA-CTGAGGTTATCAAAA-TTTCATAATATGGTTATCAAATTTTC
1 GTGTGATTATCAAAATTTCA-AGAGGAGGTTATCAAAATTTTCACAATATGGTT-TCAAATTTTC
*
25709 ATA
64 ACA
* * *
25712 GGGTGGTTATCGAAATTTCA
1 GTGTGATTATCAAAATTTCA
25732 TAATAAGGTT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
64 11 0.15
65 40 0.56
66 20 0.28
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (66 bp):
GTGTGATTATCAAAATTTCAAGAGGAGGTTATCAAAATTTTCACAATATGGTTTCAAATTTTCAC
A
Found at i:25750 original size:44 final size:44
Alignment explanation
Indices: 25652--25767 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 44
25642 TACAGTGTGA
* ** * *
25652 TTATCAAAATTTCACACTGAGGTTATCAAAATTTCATAATATGG
1 TTATCAAATTTTCACAGGGTGGTTATCAAAATTTCATAATAAGG
* *
25696 TTATCAAATTTTCATAGGGTGGTTATCGAAATTTCATAATAAGG
1 TTATCAAATTTTCACAGGGTGGTTATCAAAATTTCATAATAAGG
** * *
25740 TTATTTAATTTTCGCAGTGTGGTTATCA
1 TTATCAAATTTTCACAGGGTGGTTATCA
25768 CGTTGGAGCA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (44 bp):
TTATCAAATTTTCACAGGGTGGTTATCAAAATTTCATAATAAGG
Done.