Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000906.1 Corchorus olitorius cultivar O-4 contig00906, 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, 748
Length: 1248
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Found at i:479 original size:15 final size:14
Alignment explanation
Indices: 459--511 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
449 ATATATTTCT
459 AAATTTACATTATTA
1 AAATTTA-ATTATTA
474 AAATTT-ATTATTTA
1 AAATTTAATTA-TTA
*
488 AAAATTAATTA-TA
1 AAATTTAATTATTA
501 AAATTTCAATT
1 AAATTT-AATT
512 TAGACCGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 11 0.33
14 12 0.36
15 10 0.30
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTAATTATTA
Found at i:692 original size:22 final size:22
Alignment explanation
Indices: 634--1085 Score: 235
Period size: 22 Copynumber: 20.9 Consensus size: 22
624 AAACTTTTAT
*
634 TATGGA-GTAATCAAAATTTC-
1 TATGGAGGTTATCAAAATTTCA
* *
654 -AGGGAGGATATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
* *
675 TATGAAGGTTTTCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
** *
697 TAGTTTA-GTTTTCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
* ** *
719 TAGGGATATTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
741 TAAT-GAGGTTATCAAAAATTCA
1 T-ATGGAGGTTATCAAAATTTCA
*
763 TAGGGAGGTTATCAAAA--T--
1 TATGGAGGTTATCAAAATTTCA
* *
781 T-TGTA-GTTATCAAGATTTCA
1 TATGGAGGTTATCAAAATTTCA
* * *
801 TAAGGAGGTTATTAAAATTTTA
1 TATGGAGGTTATCAAAATTTCA
* * *
823 TAGGGAGGTTTATTAAAATTTTA
1 TATGGAGG-TTATCAAAATTTCA
*
846 TA-GCGAGGTTATCACAATTTCA
1 TATG-GAGGTTATCAAAATTTCA
* *
868 TAGTGTA-ATTATCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
*
890 AAGTGTGA--TTA-CTAACAA-TTCA
1 TA-TG-GAGGTTATC-AA-AATTTCA
*
912 TATGGAGGTT-TTAAAATTTTCA
1 TATGGAGGTTATCAAAA-TTTCA
** * * *
934 TAACGTGGTTATCAATATATCA
1 TATGGAGGTTATCAAAATTTCA
* *
956 TATGGAGGTTATCAACATCTCA
1 TATGGAGGTTATCAAAATTTCA
**
978 TAGTGTTGGTTATCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
* *
1001 TTTGGAAGTTATC-AAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
1022 TA-GTGAGGTCT-TCAAAATTTCT
1 TATG-GAGGT-TATCAAAATTTCA
** *
1044 TAAAGAGGTTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
* * *
1066 TAAGAAGGTTAACAAAATTT
1 TATGGAGGTTATCAAAATTT
1086 ATAAAAGGGT
Statistics
Matches: 333, Mismatches: 67, Indels: 62
0.72 0.15 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
19 4 0.01
20 19 0.06
21 25 0.08
22 223 0.67
23 48 0.14
24 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATGGAGGTTATCAAAATTTCA
Found at i:801 original size:38 final size:38
Alignment explanation
Indices: 748--820 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
738 TCATAATGAG
*
748 GTTATCAAAAATTCATAGGGAGGTTATCAAAATTTGTA
1 GTTATCAAAAATTCATAAGGAGGTTATCAAAATTTGTA
* * *
786 GTTATCAAGATTTCATAAGGAGGTTATTAAAATTT
1 GTTATCAAAAATTCATAAGGAGGTTATCAAAATTT
821 TATAGGGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (38 bp):
GTTATCAAAAATTCATAAGGAGGTTATCAAAATTTGTA
Found at i:839 original size:23 final size:23
Alignment explanation
Indices: 795--855 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
785 AGTTATCAAG
* *
795 ATTTCATAAGGAGG-TTATTAAA
1 ATTTTATAGGGAGGTTTATTAAA
817 ATTTTATAGGGAGGTTTATTAAA
1 ATTTTATAGGGAGGTTTATTAAA
*
840 ATTTTATAGCGAGGTT
1 ATTTTATAGGGAGGTT
856 ATCACAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 12 0.34
23 23 0.66
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.41
Consensus pattern (23 bp):
ATTTTATAGGGAGGTTTATTAAA
Found at i:1089 original size:21 final size:21
Alignment explanation
Indices: 1034--1093 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
1024 GTGAGGTCTT
*
1034 CAAAATTTCTTAAAGAGGTTAA
1 CAAAATTTCATAAA-AGGTTAA
1056 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAA-AAGGTTAA
1078 CAAAATTT-ATAAAAGG
1 CAAAATTTCATAAAAGG
1094 GTTCTCGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 27 0.75
23 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.28
Consensus pattern (21 bp):
CAAAATTTCATAAAAGGTTAA
Done.