Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021151.1 Corchorus olitorius cultivar O-4 contig21184, 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: 4063
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:747 original size:49 final size:47
Alignment explanation
Indices: 646--788 Score: 162
Period size: 49 Copynumber: 3.0 Consensus size: 47
636 GAGCGTGCCA
* * * *
646 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
693 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
742 TTCAATTTTGTAGTAAAAATTGAGAAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAG-AAAAAGTGCAATGAAAAATAAA
789 GGATTACTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
47 12 0.15
48 16 0.20
49 47 0.57
50 7 0.09
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:2083 original size:9 final size:9
Alignment explanation
Indices: 2063--2100 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
2053 TTAATTCATT
2063 TAATTTCC-
1 TAATTTCCA
2071 TAATTTCCA
1 TAATTTCCA
*
2080 TAATTTCCC
1 TAATTTCCA
2089 TAATTTCCA
1 TAATTTCCA
2098 TAA
1 TAA
2101 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:2092 original size:18 final size:17
Alignment explanation
Indices: 2063--2100 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
2053 TTAATTCATT
2063 TAATTTCCTAATTTCCA
1 TAATTTCCTAATTTCCA
2080 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATTTCCA
2098 TAA
1 TAA
2101 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTCCTAATTTCCA
Found at i:3440 original size:15 final size:15
Alignment explanation
Indices: 3420--3611 Score: 151
Period size: 15 Copynumber: 12.7 Consensus size: 15
3410 AACACTTTCA
** *
3420 GTGCCATCAACTTCG
1 GTGCCATCATTTTTG
*
3435 GTGCCATCAGTTTTG
1 GTGCCATCATTTTTG
3450 GTGCCATCATTTTTG
1 GTGCCATCATTTTTG
*
3465 GTGCCATCATTTTCG
1 GTGCCATCATTTTTG
* *
3480 GTGCCGTCGA-TGTTG
1 GTGCCATC-ATTTTTG
*
3495 GTGCCATCAGTTTTG
1 GTGCCATCATTTTTG
*
3510 GTGCCATCATTTTCG
1 GTGCCATCATTTTTG
* *
3525 GTGCCGTCGA-TGTTG
1 GTGCCATC-ATTTTTG
*
3540 GTGCTCAGTCATCTTCT-
1 GTGC-CA-TCAT-TTTTG
* *
3557 GTGCCGTCGA-TGTTG
1 GTGCCATC-ATTTTTG
*
3572 GTGCCATCATCTTTG
1 GTGCCATCATTTTTG
3587 GTGCCATCGA-TTTTG
1 GTGCCATC-ATTTTTG
3602 GTGCCATCAT
1 GTGCCATCAT
3612 CTTCCTCCAT
Statistics
Matches: 140, Mismatches: 25, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
14 5 0.04
15 120 0.86
16 7 0.05
17 6 0.04
18 2 0.01
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (15 bp):
GTGCCATCATTTTTG
Found at i:3456 original size:30 final size:30
Alignment explanation
Indices: 3420--3615 Score: 202
Period size: 30 Copynumber: 6.5 Consensus size: 30
3410 AACACTTTCA
*
3420 GTGCCATCAACTTCGGTGCCATC-AGTTTTG
1 GTGCCATCATCTTCGGTGCCATCGA-TTTTG
* *
3450 GTGCCATCATTTTTGGTGCCATC-ATTTTCG
1 GTGCCATCATCTTCGGTGCCATCGATTTT-G
* *
3480 GTGCCGTCGATGTT-GGTGCCATC-AGTTTTG
1 GTGCCATC-ATCTTCGGTGCCATCGA-TTTTG
* * *
3510 GTGCCATCATTTTCGGTGCCGTCGATGTTG
1 GTGCCATCATCTTCGGTGCCATCGATTTTG
* * *
3540 GTGCTCAGTCATCTTCTGTGCCGTCGATGTTG
1 GTGC-CA-TCATCTTCGGTGCCATCGATTTTG
*
3572 GTGCCATCATCTTTGGTGCCATCGATTTTG
1 GTGCCATCATCTTCGGTGCCATCGATTTTG
3602 GTGCCATCATCTTC
1 GTGCCATCATCTTC
3616 CTCCATGGCA
Statistics
Matches: 143, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
29 8 0.06
30 96 0.67
31 13 0.09
32 26 0.18
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (30 bp):
GTGCCATCATCTTCGGTGCCATCGATTTTG
Found at i:3471 original size:45 final size:45
Alignment explanation
Indices: 3420--3615 Score: 195
Period size: 45 Copynumber: 4.3 Consensus size: 45
3410 AACACTTTCA
* *
3420 GTGCCATCAACTTCGGTGCCATC-AGTTTTGGTGCCATCATTTTTG
1 GTGCCATCATCTTCGGTGCCATCGA-TGTTGGTGCCATCATTTTTG
* * *
3465 GTGCCATCATTTTCGGTGCCGTCGATGTTGGTGCCATCAGTTTTG
1 GTGCCATCATCTTCGGTGCCATCGATGTTGGTGCCATCATTTTTG
* * *
3510 GTGCCATCATTTTCGGTGCCGTCGATGTTGGTGCTCAGTCATCTTCT-
1 GTGCCATCATCTTCGGTGCCATCGATGTTGGTGC-CA-TCAT-TTTTG
* * *
3557 GTGCCGTCGATGTT-GGTGCCATC-ATCTTTGGTGCCATCGA-TTTTG
1 GTGCCATC-ATCTTCGGTGCCATCGAT-GTTGGTGCCATC-ATTTTTG
3602 GTGCCATCATCTTC
1 GTGCCATCATCTTC
3616 CTCCATGGCA
Statistics
Matches: 128, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
44 7 0.05
45 81 0.63
46 8 0.06
47 25 0.20
48 7 0.05
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (45 bp):
GTGCCATCATCTTCGGTGCCATCGATGTTGGTGCCATCATTTTTG
Done.