Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021387.1 Corchorus olitorius cultivar O-4 contig21420, 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: 11828
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--45 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 TAC
4 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46 CCTTTTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:761 original size:152 final size:153
Alignment explanation
Indices: 553--862 Score: 570
Period size: 152 Copynumber: 2.0 Consensus size: 153
543 CAAAAAAAAA
553 AAAAAAAGTCACCCAAAAACAATGAATGGAATAGGATTGACCAAAATTGGAGAATTGAAGATTTG
1 AAAAAAAGTCACCCAAAAACAATGAATGGAATAGGATTGACCAAAATTGGAGAATTGAAGATTTG
618 GGAGACGATGGGAGGGAGAGAGTTATAGTAGGAATATTATCTCTTTTTTTGTTAATATGATATTA
66 GGAGACGATGGGAGGGAGAGAGTTATAGTAGGAATATTATCTC-TTTTTTGTTAATATGATATTA
683 TTAAAAGTTATTGATATTTATTTT
130 TTAAAAGTTATTGATATTTATTTT
*
707 AAAAAAATTCACCCAAAAACAATGAATGG-A-AGGATTGACCAAAATTGGAGAATTGAAGATTTG
1 AAAAAAAGTCACCCAAAAACAATGAATGGAATAGGATTGACCAAAATTGGAGAATTGAAGATTTG
770 GGAGACGATGGGAGGGAGAGAGTTATAGTAGGAATATTATCTCTTTTTTGTTAATATGATATTAT
66 GGAGACGATGGGAGGGAGAGAGTTATAGTAGGAATATTATCTCTTTTTTGTTAATATGATATTAT
*
835 TAAAAGTTATTTATATTTATTTT
131 TAAAAGTTATTGATATTTATTTT
*
858 TAAAA
1 AAAAA
863 TAATAAAAAT
Statistics
Matches: 153, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
151 48 0.31
152 76 0.50
153 1 0.01
154 28 0.18
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (153 bp):
AAAAAAAGTCACCCAAAAACAATGAATGGAATAGGATTGACCAAAATTGGAGAATTGAAGATTTG
GGAGACGATGGGAGGGAGAGAGTTATAGTAGGAATATTATCTCTTTTTTGTTAATATGATATTAT
TAAAAGTTATTGATATTTATTTT
Found at i:1881 original size:2 final size:2
Alignment explanation
Indices: 1868--1898 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1858 CTCAAACTAT
*
1868 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1899 TTCTAACTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2285 original size:1 final size:1
Alignment explanation
Indices: 2279--2331 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
2269 ATTAGATTGC
* * * * * *
2279 AAAAAAAAAAAAAACAAAACAAAACAAAAAAAAACAAAACAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2332 GTGTAACTTA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2287 original size:5 final size:5
Alignment explanation
Indices: 2278--2331 Score: 74
Period size: 5 Copynumber: 11.0 Consensus size: 5
2268 GATTAGATTG
* * *
2278 CAAAA AAAAA AAAAA CAAAA CAAAA CAAAA AAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
2328 -AAAA
1 CAAAA
2332 GTGTAACTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:2306 original size:25 final size:25
Alignment explanation
Indices: 2278--2331 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
2268 GATTAGATTG
2278 CAAAAAAAAAAAAAACAAAACAAAA
1 CAAAAAAAAAAAAAACAAAACAAAA
*
2303 CAAAAAAAAACAAAACAAAACAAAA
1 CAAAAAAAAAAAAAACAAAACAAAA
2328 -AAAA
1 CAAAA
2332 GTGTAACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (25 bp):
CAAAAAAAAAAAAAACAAAACAAAA
Found at i:2307 original size:20 final size:20
Alignment explanation
Indices: 2278--2331 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2268 GATTAGATTG
*
2278 CAAAAAAAAAAAAAACAAAA
1 CAAAACAAAAAAAAACAAAA
2298 CAAAACAAAAAAAAACAAAA
1 CAAAACAAAAAAAAACAAAA
2318 CAAAACAAAAAAAA
1 CAAAACAAAAAAAA
2332 GTGTAACTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (20 bp):
CAAAACAAAAAAAAACAAAA
Found at i:3799 original size:43 final size:44
Alignment explanation
Indices: 3752--3840 Score: 119
Period size: 43 Copynumber: 2.0 Consensus size: 44
3742 CACAGTTTTT
* *
3752 TATGG-AGTTTATCACAATTTTATAGG-TAATTATCAAAATTTCA
1 TATGGTAG-TTATCAAAATTTAATAGGATAATTATCAAAATTTCA
* *
3795 TATGGTAGTTATCAAAATTTAATAGGATGATTATCGAAATTTCA
1 TATGGTAGTTATCAAAATTTAATAGGATAATTATCAAAATTTCA
3839 TA
1 TA
3841 AAACTATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 21 0.52
44 19 0.47
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (44 bp):
TATGGTAGTTATCAAAATTTAATAGGATAATTATCAAAATTTCA
Found at i:3806 original size:22 final size:21
Alignment explanation
Indices: 3647--3840 Score: 92
Period size: 22 Copynumber: 9.0 Consensus size: 21
3637 AAAATTGTAG
* *
3647 GGAGATTAACAAAATCTCATA
1 GGAGATTATCAAAATTTCATA
* *
3668 GAGAGATTATAAAAAATT-ATA
1 G-GAGATTATCAAAATTTCATA
*
3689 GGAAGGTTA-CAAAA-TTCATA
1 GG-AGATTATCAAAATTTCATA
* * *
3709 GGAAAGTTTATTAAATTTTCATA
1 GG--AGATTATCAAAATTTCATA
* * * * **
3732 GTTAGGTTATCACAGTTTTTTA
1 G-GAGATTATCAAAATTTCATA
* * *
3754 TGGAGTTTATCACAATTTTATA
1 -GGAGATTATCAAAATTTCATA
3776 GGTA-ATTATCAAAATTTCATA
1 GG-AGATTATCAAAATTTCATA
*
3797 TGGTAG-TTATCAAAATTTAATA
1 -GG-AGATTATCAAAATTTCATA
*
3819 GGATGATTATCGAAATTTCATA
1 GGA-GATTATCAAAATTTCATA
3841 AAACTATTCA
Statistics
Matches: 134, Mismatches: 26, Indels: 25
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.01
20 11 0.08
21 35 0.26
22 78 0.58
23 8 0.06
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (21 bp):
GGAGATTATCAAAATTTCATA
Found at i:3922 original size:2 final size:2
Alignment explanation
Indices: 3899--3946 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
3889 GTAAAACTAG
* *
3899 TA TA TA -A TA TA AA TA TA AA 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 TA TA TA TA TA TA
3940 TA TA TA T
1 TA TA TA T
3947 TCTGAGTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4825 original size:15 final size:16
Alignment explanation
Indices: 4800--4829 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4790 AGTATGCCTG
4800 ACATGAGAGAAAGAAC
1 ACATGAGAGAAAGAAC
4816 ACAT-AGAGAAAGAA
1 ACATGAGAGAAAGAA
4830 GCAGCAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.10, G:0.23, T:0.07
Consensus pattern (16 bp):
ACATGAGAGAAAGAAC
Done.