Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013636.1 Corchorus olitorius cultivar O-4 contig13669, 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: 38317
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:10617 original size:89 final size:89
Alignment explanation
Indices: 10452--10624 Score: 276
Period size: 89 Copynumber: 1.9 Consensus size: 89
10442 AAAAAATATG
* * *
10452 ACTGGAGCAAATTCCTTAAATCACATATCCAAGAAACAATTTGAACAAAAAAAAAATCCAAGAAA
1 ACTGAAGCAAATTCCTTAAATCACAAATCCAAGAAACAATCTGAACAAAAAAAAAATCCAAGAAA
* *
10517 CGAAACCAATAATGAAGGGATCTT
66 CAAAACAAATAATGAAGGGATCTT
*
10541 ACTGAAGCAAATTCCTTAAATCACAAATCCAAGAAACAATCTGAAC-AAAACAAAATCCAAGAAA
1 ACTGAAGCAAATTCCTTAAATCACAAATCCAAGAAACAATCTGAACAAAAAAAAAATCCAAGAAA
10605 CAAAAACAAATAATGAAGGG
66 C-AAAACAAATAATGAAGGG
10625 CCACGGTGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 18 0.23
89 59 0.77
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.17
Consensus pattern (89 bp):
ACTGAAGCAAATTCCTTAAATCACAAATCCAAGAAACAATCTGAACAAAAAAAAAATCCAAGAAA
CAAAACAAATAATGAAGGGATCTT
Found at i:11233 original size:13 final size:13
Alignment explanation
Indices: 11215--11249 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
11205 TAATTAATTA
11215 ATCTTACTATCTT
1 ATCTTACTATCTT
11228 ATCTTACTATCTT
1 ATCTTACTATCTT
*
11241 ATTTTACTA
1 ATCTTACTA
11250 CTATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.20, G:0.00, T:0.54
Consensus pattern (13 bp):
ATCTTACTATCTT
Found at i:11978 original size:201 final size:203
Alignment explanation
Indices: 11611--12016 Score: 726
Period size: 201 Copynumber: 2.0 Consensus size: 203
11601 TGTTTTTTAT
11611 AAGGCAAATTATATAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAATGAT
1 AAGGCAAATTATATAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAATGAT
* *
11676 GACATGTGTCCTCTAGATGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACAT
66 GACATGTGTCCTCTAGAGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGAACAT
* * **
11741 GTGTCAACTCCACAACCCGCTTGTGGAATCCAAAATTTACACCGGTGGTGTATCAAATAATTACC
131 GTGTCAACTCCACAACCCGCTTATGAAATCCAAAATTTACACCGACGGTGTATCAAATAATTACC
11806 C-TAACTA
196 CATAACTA
* *
11813 AAGGCAAATTTTATAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAATGGT
1 AAGGCAAATTATATAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAATGAT
11878 GACATGTGTCCTCTAG-GGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGAACAT
66 GACATGTGTCCTCTAGAGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGAACAT
11942 GTGTCAACTCCACAACCCGCTTATGAAATCCAAAATTTACACCGACGGTGTATCAAATAATTACC
131 GTGTCAACTCCACAACCCGCTTATGAAATCCAAAATTTACACCGACGGTGTATCAAATAATTACC
12007 CATAACTA
196 CATAACTA
12015 AA
1 AA
12017 TTTCTTCTAA
Statistics
Matches: 195, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
201 108 0.55
202 87 0.45
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (203 bp):
AAGGCAAATTATATAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAATGAT
GACATGTGTCCTCTAGAGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGAACAT
GTGTCAACTCCACAACCCGCTTATGAAATCCAAAATTTACACCGACGGTGTATCAAATAATTACC
CATAACTA
Found at i:17759 original size:5 final size:5
Alignment explanation
Indices: 17749--17787 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
17739 AATGGGCTTC
*
17749 AATCA AATCA AATCA AATCA AATCA GATCA AATCA AATC
1 AATCA AATCA AATCA AATCA AATCA AATCA AATCA AATC
17788 GTAATTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (5 bp):
AATCA
Found at i:18299 original size:46 final size:46
Alignment explanation
Indices: 18247--18335 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
18237 AGGTACATCA
* *
18247 TGCCTGAATCGTGAGGTCTTTTATGATAGTTTTTTAGTTTAAGATG
1 TGCCTGAACCGTGAGGTCTTTTATGATAATTTTTTAGTTTAAGATG
18293 TGCCTGAACCGTGAGGTCTTTTATGATAATTTTTTAGTTTAAG
1 TGCCTGAACCGTGAGGTCTTTTATGATAATTTTTTAGTTTAAG
18336 TTGATTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.45
Consensus pattern (46 bp):
TGCCTGAACCGTGAGGTCTTTTATGATAATTTTTTAGTTTAAGATG
Found at i:21604 original size:25 final size:25
Alignment explanation
Indices: 21576--21627 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
21566 TCACTTTTGT
21576 ATTGGGTATACTCAATTCAAATTCA
1 ATTGGGTATACTCAATTCAAATTCA
21601 ATTGGGTATACTCAATTCAAATTCA
1 ATTGGGTATACTCAATTCAAATTCA
21626 AT
1 AT
21628 ACAGTATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (25 bp):
ATTGGGTATACTCAATTCAAATTCA
Found at i:21634 original size:25 final size:25
Alignment explanation
Indices: 21581--21634 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
21571 TTTGTATTGG
***
21581 GTATACTCAATTCAAATTCAATTGG
1 GTATACTCAATTCAAATTCAATACA
21606 GTATACTCAATTCAAATTCAATACA
1 GTATACTCAATTCAAATTCAATACA
21631 GTAT
1 GTAT
21635 TCAATATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (25 bp):
GTATACTCAATTCAAATTCAATACA
Found at i:23382 original size:2 final size:2
Alignment explanation
Indices: 23375--23400 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23365 ATATAAATAT
23375 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
23401 TGAGCTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:37214 original size:14 final size:14
Alignment explanation
Indices: 37195--37230 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
37185 CTTGGTAGTT
37195 AATTGTGAATTGAC
1 AATTGTGAATTGAC
*
37209 AATTGTGAATTGAT
1 AATTGTGAATTGAC
37223 AA-TGTGAA
1 AATTGTGAA
37231 GCTTTATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (14 bp):
AATTGTGAATTGAC
Done.