Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022932.1 Corchorus olitorius cultivar O-4 contig22965, 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: 12546
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1639 original size:137 final size:134
Alignment explanation
Indices: 1497--1773 Score: 392
Period size: 134 Copynumber: 2.0 Consensus size: 134
1487 AAAAATAAGA
* *
1497 AATAAAGTTGAAGGAGTAAATTGTATGAAATTAAATATTTGAGAGACTAAGTTGCATAAAATGAA
1 AATAAAGTTGAAGGACTAAATTGTATAAAATTAAA-ATTTGAGAGACTAAGTTGCATAAAATGAA
* * * *
1562 AATGTCTAAGGGATTTTATGTAAATAAAAATAAAGTTGAATGGCTAAATCTTGAAAAAGAAATAA
65 AATATCTAA-GGATTTTATATAAAT-AAAACAAAGTTGAAGGGCTAAATCTTGAAAAAGAAATAA
1627 TAAAAAG
128 TAAAAAG
* *
1634 AATAAAGTTGAAGGACTAAATTGTATAAAATTAAAATTTGAGGGACTAAGTTGCATAAAATTAAA
1 AATAAAGTTGAAGGACTAAATTGTATAAAATTAAAATTTGAGAGACTAAGTTGCATAAAATGAAA
* * * ***
1699 ATATCTAAGGCTTTTATATGAATAAAACAAAGTTGAAGGGCTAAATCTTGGAAAATCTATAATAA
66 ATATCTAAGGATTTTATATAAATAAAACAAAGTTGAAGGGCTAAATCTTGAAAAAGAAATAATAA
1764 AAAG
131 AAAG
*
1768 ACTAAA
1 AATAAA
1774 TAAAATAAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
134 45 0.36
135 12 0.10
136 35 0.28
137 33 0.26
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (134 bp):
AATAAAGTTGAAGGACTAAATTGTATAAAATTAAAATTTGAGAGACTAAGTTGCATAAAATGAAA
ATATCTAAGGATTTTATATAAATAAAACAAAGTTGAAGGGCTAAATCTTGAAAAAGAAATAATAA
AAAG
Found at i:1681 original size:30 final size:30
Alignment explanation
Indices: 1641--1700 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1631 AAGAATAAAG
*
1641 TTGAAGGACTAAATTGTATAAAATTAAAAT
1 TTGAAGGACTAAATTGCATAAAATTAAAAT
* *
1671 TTGAGGGACTAAGTTGCATAAAATTAAAAT
1 TTGAAGGACTAAATTGCATAAAATTAAAAT
1701 ATCTAAGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.32
Consensus pattern (30 bp):
TTGAAGGACTAAATTGCATAAAATTAAAAT
Found at i:1781 original size:5 final size:5
Alignment explanation
Indices: 1771--1798 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1761 TAAAAAGACT
1771 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
1799 ATGATCGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:4079 original size:2 final size:2
Alignment explanation
Indices: 4072--4123 Score: 67
Period size: 2 Copynumber: 27.5 Consensus size: 2
4062 TTAATACACC
4072 TA TA TA TA TA TA -A TA TA -A TA -A TA TA TA TA -A 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
4110 TA TA TA TA CTA TA T
1 TA TA TA TA -TA TA T
4124 TAGGAGGAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.09
2 39 0.87
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4123 original size:17 final size:17
Alignment explanation
Indices: 4072--4123 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
4062 TTAATACACC
4072 TATATATATATAATATA
1 TATATATATATAATATA
4089 -ATAATATATATAATATA
1 TAT-ATATATATAATATA
*
4106 TATATATATATACTATA
1 TATATATATATAATATA
4123 T
1 T
4124 TAGGAGGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 2 0.06
17 28 0.88
18 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATATATATAATATA
Found at i:4123 original size:19 final size:18
Alignment explanation
Indices: 4072--4123 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 18
4062 TTAATACACC
4072 TATATATATATA-ATATA
1 TATATATATATATATATA
4089 -ATA-ATATATATA-ATA
1 TATATATATATATATATA
4104 TATATATATATATACTATA
1 TATATATATATATA-TATA
4123 T
1 T
4124 TAGGAGGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 10 0.33
16 7 0.23
17 9 0.30
19 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATATATATATATATA
Found at i:5167 original size:14 final size:14
Alignment explanation
Indices: 5148--5176 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5138 ACATGTTTAA
5148 TATATTTAGTTACC
1 TATATTTAGTTACC
5162 TATATTTAGTTACC
1 TATATTTAGTTACC
5176 T
1 T
5177 GTTTAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATTTAGTTACC
Found at i:12422 original size:26 final size:26
Alignment explanation
Indices: 12393--12444 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12383 TAGCTCCAAG
12393 GTCTTCTAATCAATCTCCCAAAGTGC
1 GTCTTCTAATCAATCTCCCAAAGTGC
12419 GTCTTCTAATCAATCTCCCAAAGTGC
1 GTCTTCTAATCAATCTCCCAAAGTGC
12445 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (26 bp):
GTCTTCTAATCAATCTCCCAAAGTGC
Done.