Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021468.1 Corchorus olitorius cultivar O-4 contig21501, 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: 5442
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Found at i:234 original size:22 final size:22
Alignment explanation
Indices: 164--461 Score: 100
Period size: 22 Copynumber: 13.3 Consensus size: 22
154 TCAATCAAAC
*
164 CAAAATTACATA-GGAAGGTTAT
1 CAAAATTTCATATGG-AGGTTAT
* * *
186 CAAATTTTCATA-GTGTGTTTAGT
1 CAAAATTTCATATG-GAGGTTA-T
209 -AAAATTTCATATGGAGGTTAT
1 CAAAATTTCATATGGAGGTTAT
** *
230 CAAAACATCATAGTGTA-GTTAT
1 CAAAATTTCATA-TGGAGGTTAT
* ** *
252 CAAAATTCCATACAGACGTTA-
1 CAAAATTTCATATGGAGGTTAT
* ***
273 CAAAAATTTTATAAAAAGGTTAT
1 C-AAAATTTCATATGGAGGTTAT
* * *
296 CAAAATTTCTTA-GAGTGTCGTTAA
1 CAAAATTTCATATG-GAG--GTTAT
* * *
320 CAAAATTTTATACGAAGGTTAT
1 CAAAATTTCATATGGAGGTTAT
342 CAAAATTT-ATAGTGTGA--TTAT
1 CAAAATTTCATA-TG-GAGGTTAT
*
363 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCAT----ATGGAGGTTAT
* * * *
389 CAAAGTTTCCTAGGGAGGTTAA
1 CAAAATTTCATATGGAGGTTAT
*
411 CAAAATTTCAT-TGGAAGGTT-G
1 CAAAATTTCATATGG-AGGTTAT
432 CAAAAATTT--TATGGAGATGTTAT
1 C-AAAATTTCATATGGAG--GTTAT
455 CAAAATT
1 CAAAATT
462 AAATAAAGAG
Statistics
Matches: 206, Mismatches: 43, Indels: 54
0.68 0.14 0.18
Matches are distributed among these distances:
20 3 0.01
21 24 0.12
22 137 0.67
23 9 0.04
24 17 0.08
25 2 0.01
26 14 0.07
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATATGGAGGTTAT
Found at i:599 original size:22 final size:22
Alignment explanation
Indices: 568--643 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
558 TGCGGTTACC
*
568 AATTTTATAGTGTGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* *
590 AATTTCATAGTTTGGTTATCAA
1 AATTTCATAGTGTGATTATCAA
* * *
612 AATTTCACAATGTGTTTAT-AA
1 AATTTCATAGTGTGATTATCAA
633 AATTTTCATAG
1 AA-TTTCATAG
644 GTTATCGAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 4 0.09
22 40 0.91
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.45
Consensus pattern (22 bp):
AATTTCATAGTGTGATTATCAA
Found at i:1638 original size:21 final size:21
Alignment explanation
Indices: 1609--1677 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
1599 TTGATACATA
*
1609 TATAACTTTTTTCATAACCGT
1 TATAGCTTTTTTCATAACCGT
* *
1630 TATAGC-TTTTTGAGGAA---T
1 TATAGCTTTTTTCA-TAACCGT
1648 TA-A-CTTTTTTCATAACCGT
1 TATAGCTTTTTTCATAACCGT
1667 TATAGCTTTTT
1 TATAGCTTTTT
1678 GAGTAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
16 3 0.08
17 7 0.19
18 3 0.08
19 3 0.08
20 7 0.19
21 13 0.36
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.49
Consensus pattern (21 bp):
TATAGCTTTTTTCATAACCGT
Found at i:1661 original size:37 final size:37
Alignment explanation
Indices: 1611--1687 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
1601 GATACATATA
1611 TAACTTTTTTCATAACCGTTATAGCTTTTTGAGGAAT
1 TAACTTTTTTCATAACCGTTATAGCTTTTTGAGGAAT
*
1648 TAACTTTTTTCATAACCGTTATAGCTTTTTGAGTAAT
1 TAACTTTTTTCATAACCGTTATAGCTTTTTGAGGAAT
1685 TAA
1 TAA
1688 GTATTGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.47
Consensus pattern (37 bp):
TAACTTTTTTCATAACCGTTATAGCTTTTTGAGGAAT
Found at i:2994 original size:12 final size:12
Alignment explanation
Indices: 2979--3035 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
2969 GAGATGGATA
*
2979 TTTATATTCCGT
1 TTTAAATTCCGT
2991 TTTAAATTCCGTT
1 TTTAAATTCCG-T
3004 TTTAAACTTTCCGT
1 TTTAAA--TTCCGT
*
3018 TTGAAATTCCGT
1 TTTAAATTCCGT
3030 TTTAAA
1 TTTAAA
3036 CTCAGATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
12 21 0.54
13 7 0.18
14 6 0.15
15 5 0.13
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51
Consensus pattern (12 bp):
TTTAAATTCCGT
Found at i:3018 original size:27 final size:26
Alignment explanation
Indices: 2985--3037 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
2975 GATATTTATA
*
2985 TTCCGTTTTAAATTCCGTTTTTAAACT
1 TTCCGTTTGAAATTCCG-TTTTAAACT
3012 TTCCGTTTGAAATTCCGTTTTAAACT
1 TTCCGTTTGAAATTCCGTTTTAAACT
3038 CAGATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (26 bp):
TTCCGTTTGAAATTCCGTTTTAAACT
Done.