Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012474.1 Corchorus olitorius cultivar O-4 contig12507, 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: 5222
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--54 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1 G
2 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44 TC TC TC TC TC T
1 TC TC TC TC TC T
55 ATATATATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:59 original size:2 final size:2
Alignment explanation
Indices: 54--101 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
44 TCTCTCTCTC
*
54 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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
96 TA TA TA
1 TA TA TA
102 AGGGCCGTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1611 original size:22 final size:21
Alignment explanation
Indices: 1578--1658 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
1568 AAATGAAGGT
*
1578 TTATTAAATTTCATAGTTAAG
1 TTATCAAATTTCATAGTTAAG
**
1599 TTATCAAAGTTTCATA-TGGAG
1 TTATCAAA-TTTCATAGTTAAG
* *
1620 TTTATCACAATTTTATAGTTAAA
1 -TTATCA-AATTTCATAGTTAAG
1643 TTATCAAAATTTCATA
1 TTATC-AAATTTCATA
1659 ACATGGTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
21 10 0.21
22 32 0.68
23 5 0.11
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TTATCAAATTTCATAGTTAAG
Found at i:1632 original size:44 final size:44
Alignment explanation
Indices: 1550--1702 Score: 134
Period size: 44 Copynumber: 3.5 Consensus size: 44
1540 TATAGAGAGA
* *
1550 TTAAGGTTA-CAAAATTTCAAATGAAGGTTTATTAAATTTCATAG
1 TTAA-GTTATCAAAATTTCATATGAAGGTTTATCAAATTTCATAG
* * *
1594 TTAAGTTATCAAAGTTTCATATGGA-GTTTATCACAATTTTATAG
1 TTAAGTTATCAAAATTTCATATGAAGGTTTATCA-AATTTCATAG
* ** * * *
1638 TTAAATTATCAAAATTTCATAACATGG-TTATCAAAACTTAATAG
1 TTAAGTTATCAAAATTTCATATGAAGGTTTATC-AAATTTCATAG
*
1682 -GATAGTTATCAAAATTTCATA
1 TTA-AGTTATCAAAATTTCATA
1703 AAAATATTCA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
43 12 0.13
44 75 0.84
45 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (44 bp):
TTAAGTTATCAAAATTTCATATGAAGGTTTATCAAATTTCATAG
Found at i:1668 original size:22 final size:22
Alignment explanation
Indices: 1643--1703 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
1633 TATAGTTAAA
*
1643 TTATCAAAATTTCATAACATGG
1 TTATCAAAATTTCATAACATAG
* * **
1665 TTATCAAAACTTAATAGGATAG
1 TTATCAAAATTTCATAACATAG
1687 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
1704 AAATATTCAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAACATAG
Found at i:4242 original size:15 final size:15
Alignment explanation
Indices: 4212--4256 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
4202 GATAAAACTG
**
4212 AAAATTAAGTGCTGA
1 AAAATTAAGTATTGA
4227 AAAATTAAGTATTG-
1 AAAATTAAGTATTGA
*
4241 AAAATTTAGTATTGA
1 AAAATTAAGTATTGA
4256 A
1 A
4257 TCTCATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (15 bp):
AAAATTAAGTATTGA
Found at i:4499 original size:17 final size:17
Alignment explanation
Indices: 4477--4516 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4467 ATCACCCCCC
*
4477 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
4494 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
4511 AGATCA
1 AGATCA
4517 ATGGTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:4821 original size:54 final size:54
Alignment explanation
Indices: 4739--4844 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
4729 ATCTACTTCT
*
4739 TTGAACAATTTTCAATTCGAATTAAATTGTTTGATACGTAGGAAATTTCGAAGC
1 TTGAACAATTTTCAATTCGAATTAAATTGTTTGATACGTAAGAAATTTCGAAGC
*
4793 TTGAACAATTTTCTATTCGAATTAAATTGTTTGATACGTAAGAAATTTCGAA
1 TTGAACAATTTTCAATTCGAATTAAATTGTTTGATACGTAAGAAATTTCGAA
4845 AGTACTATGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (54 bp):
TTGAACAATTTTCAATTCGAATTAAATTGTTTGATACGTAAGAAATTTCGAAGC
Done.