Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012197.1 Corchorus capsularis cultivar CVL-1 contig12218, 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: 22694
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:6007 original size:3 final size:3
Alignment explanation
Indices: 5993--6023 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5983 ATTATATTAA
*
5993 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
6024 GAAAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:8143 original size:33 final size:33
Alignment explanation
Indices: 8101--8167 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
8091 ACTGATATCA
8101 TGTGAATGTTTCAGAAGGCATGTTCGATGTCTT
1 TGTGAATGTTTCAGAAGGCATGTTCGATGTCTT
**
8134 TGTGAATGTTTCATTAGGCATGTTCGATGTCTT
1 TGTGAATGTTTCAGAAGGCATGTTCGATGTCTT
8167 T
1 T
8168 TAAGGTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (33 bp):
TGTGAATGTTTCAGAAGGCATGTTCGATGTCTT
Found at i:20456 original size:17 final size:14
Alignment explanation
Indices: 20419--20449 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20409 TTTAAGGTCG
20419 TTTTTTTAGTATTC
1 TTTTTTTAGTATTC
20433 TTTTTTTAGTATTC
1 TTTTTTTAGTATTC
20447 TTT
1 TTT
20450 CGTTTTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTTTTAGTATTC
Found at i:20637 original size:32 final size:32
Alignment explanation
Indices: 20595--20697 Score: 154
Period size: 32 Copynumber: 3.2 Consensus size: 32
20585 TTGAGTCAGG
20595 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
* *
20627 TCGGATTAAATTTGAGTCAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
* *
20659 TCGGGTTAATTTTGGGTCAGGTTAATTCGCGG-
1 TCGGGTTAAATTTGGGTCAGGTTGATTCG-GGT
20691 TCGGGTT
1 TCGGGTT
20698 CGGGCTGGGT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 62 0.97
33 2 0.03
ACGTcount: A:0.17, C:0.11, G:0.35, T:0.38
Consensus pattern (32 bp):
TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
Found at i:20684 original size:16 final size:15
Alignment explanation
Indices: 20593--20685 Score: 62
Period size: 16 Copynumber: 5.9 Consensus size: 15
20583 GCTTGAGTCA
*
20593 GGTCGGGTTAAATTTG
1 GGTCAGGTT-AATTTG
* *
20609 GGTCAGGTTGATTCG
1 GGTCAGGTTAATTTG
20624 GGTTC-GGATTAAATTTG
1 GG-TCAGG-TT-AATTTG
* * *
20641 AGTCAGGTTGATTCG
1 GGTCAGGTTAATTTG
*
20656 GGTTCGGGTTAATTTTG
1 GG-TCAGGTTAA-TTTG
20673 GGTCAGGTTAATT
1 GGTCAGGTTAATT
20686 CGCGGTCGGG
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
15 15 0.26
16 31 0.53
17 12 0.21
ACGTcount: A:0.18, C:0.09, G:0.34, T:0.39
Consensus pattern (15 bp):
GGTCAGGTTAATTTG
Found at i:20692 original size:16 final size:15
Alignment explanation
Indices: 20593--20697 Score: 59
Period size: 16 Copynumber: 6.6 Consensus size: 15
20583 GCTTGAGTCA
* *
20593 GGTCGGGTTAAATTTG
1 GGTCAGGTT-AATTCG
*
20609 GGTCAGGTTGATTCG
1 GGTCAGGTTAATTCG
*
20624 GGTTC-GGATTAAATTTG
1 GG-TCAGG-TT-AATTCG
* *
20641 AGTCAGGTTGATTCG
1 GGTCAGGTTAATTCG
* *
20656 GGTTCGGGTTAATTTTG
1 GG-TCAGGTTAA-TTCG
20673 GGTCAGGTTAATTCG
1 GGTCAGGTTAATTCG
*
20688 CGGTCGGGTT
1 -GGTCAGGTT
20698 CGGGCTGGGT
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
15 16 0.24
16 39 0.58
17 12 0.18
ACGTcount: A:0.16, C:0.10, G:0.36, T:0.37
Consensus pattern (15 bp):
GGTCAGGTTAATTCG
Found at i:20937 original size:15 final size:15
Alignment explanation
Indices: 20893--20949 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
20883 GTTTCTTCAA
*
20893 GTTCAGGTTTTATCGG
1 GTTCTGGTTTT-TCGG
* *
20909 GTTTTAGATTTTTCGG
1 GTTCT-GGTTTTTCGG
20925 GTTCTGGTTTTTCGG
1 GTTCTGGTTTTTCGG
*
20940 GTTCGGGTTT
1 GTTCTGGTTT
20950 AGGAGGGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 18 0.53
16 11 0.32
17 5 0.15
ACGTcount: A:0.07, C:0.11, G:0.32, T:0.51
Consensus pattern (15 bp):
GTTCTGGTTTTTCGG
Done.