Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012839.1 Corchorus olitorius cultivar O-4 contig12872, 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: 34300
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:1023 original size:21 final size:20
Alignment explanation
Indices: 982--1030 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
972 GATTATGTAA
**
982 ATGCAAAATGTGAAATTAAT
1 ATGCAAAATGTGAAACAAAT
*
1002 ATGCGAAAATGTGATACAAAT
1 ATGC-AAAATGTGAAACAAAT
1023 ATGCAAAA
1 ATGCAAAA
1031 GAACACAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCAAAATGTGAAACAAAT
Found at i:1188 original size:28 final size:28
Alignment explanation
Indices: 1121--1227 Score: 114
Period size: 27 Copynumber: 3.9 Consensus size: 28
1111 ACTTGAGCAA
* *
1121 TGGA-GTAGAAATGACCATAATGCCCCC
1 TGGATGTAAAAATGACCAAAATGCCCCC
* * * *
1148 T-GAAGCACAAATGACTAAAATGCCCCC
1 TGGATGTAAAAATGACCAAAATGCCCCC
1175 TAGG-TGTAAAAATGACCAAAATG-CCCC
1 T-GGATGTAAAAATGACCAAAATGCCCCC
*
1202 TGGATGTGAAAATGACCAAAATGCCC
1 TGGATGTAAAAATGACCAAAATGCCC
1228 TTAGGTGATC
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
26 4 0.06
27 44 0.67
28 17 0.26
29 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (28 bp):
TGGATGTAAAAATGACCAAAATGCCCCC
Found at i:2578 original size:16 final size:16
Alignment explanation
Indices: 2540--2580 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2530 CAAATAAGTA
2540 AATATACAAGAAAATAT
1 AATAT-CAAGAAAATAT
2557 AA-ATCAAGAAAA-AT
1 AATATCAAGAAAATAT
2571 AGATATCAAG
1 A-ATATCAAG
2581 TGATGGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 9 0.41
16 8 0.36
17 2 0.09
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (16 bp):
AATATCAAGAAAATAT
Found at i:4495 original size:15 final size:12
Alignment explanation
Indices: 4461--4492 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
4451 ATTTATATAT
4461 AAGAAGAAATAC
1 AAGAAGAAATAC
4473 AAGAAGAAATAC
1 AAGAAGAAATAC
4485 AAGAAGAA
1 AAGAAGAA
4493 GAACTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.19, T:0.06
Consensus pattern (12 bp):
AAGAAGAAATAC
Found at i:5200 original size:13 final size:13
Alignment explanation
Indices: 5184--5208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5174 TTTTATTAAA
5184 AGAAAATATTTTG
1 AGAAAATATTTTG
5197 AGAAAATATTTT
1 AGAAAATATTTT
5209 TTCAATCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AGAAAATATTTTG
Found at i:6838 original size:108 final size:108
Alignment explanation
Indices: 6649--6857 Score: 409
Period size: 108 Copynumber: 1.9 Consensus size: 108
6639 GTGATGTTAA
*
6649 TTGGCCACTACTTAGTTAAAATTAGCTAAATTCAGCACAAAAGAAGCAACGAAAGCCTGCTGCAA
1 TTGGCCACTACTTAGTTAAAATTAGCTAAATTCAGCACAAAAGAAGCAACAAAAGCCTGCTGCAA
6714 TGTGATAAGAAGAGGAAGGAATTATCATCAACCACCTAAGAGG
66 TGTGATAAGAAGAGGAAGGAATTATCATCAACCACCTAAGAGG
6757 TTGGCCACTACTTAGTTAAAATTAGCTAAATTCAGCACAAAAGAAGCAACAAAAGCCTGCTGCAA
1 TTGGCCACTACTTAGTTAAAATTAGCTAAATTCAGCACAAAAGAAGCAACAAAAGCCTGCTGCAA
6822 TGTGATAAGAAGAGGAAGGAATTATCATCAACCACC
66 TGTGATAAGAAGAGGAAGGAATTATCATCAACCACC
6858 CAGGAGGCAG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 100 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (108 bp):
TTGGCCACTACTTAGTTAAAATTAGCTAAATTCAGCACAAAAGAAGCAACAAAAGCCTGCTGCAA
TGTGATAAGAAGAGGAAGGAATTATCATCAACCACCTAAGAGG
Found at i:11588 original size:21 final size:21
Alignment explanation
Indices: 11559--11599 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
11549 CTTAGGACGG
11559 AATTCAA-TTTTGGATTTTGA
1 AATTCAATTTTTGGATTTTGA
*
11579 AATTCCAATTTTTGGCTTTTG
1 AATT-CAATTTTTGGATTTTG
11600 CTTTTAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (21 bp):
AATTCAATTTTTGGATTTTGA
Found at i:16583 original size:31 final size:30
Alignment explanation
Indices: 16538--16604 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
16528 CCTTCATTAA
16538 AAATTAAAACAACCCAAGAAAAAGTTCCAT
1 AAATTAAAACAACCCAAGAAAAAGTTCCAT
* * *
16568 AAATTCAAAATAACCCAAGAAAAAGTTCAAC
1 AAATT-AAAACAACCCAAGAAAAAGTTCCAT
16599 AAATTA
1 AAATTA
16605 CATTGCATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (30 bp):
AAATTAAAACAACCCAAGAAAAAGTTCCAT
Found at i:18985 original size:22 final size:22
Alignment explanation
Indices: 18957--18998 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
18947 AAGAGAATCA
18957 TCACAACCATAAATACATTGGC
1 TCACAACCATAAATACATTGGC
18979 TCACAACCATAAATACATTG
1 TCACAACCATAAATACATTG
18999 TCAAGACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (22 bp):
TCACAACCATAAATACATTGGC
Found at i:23501 original size:13 final size:12
Alignment explanation
Indices: 23483--23527 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
23473 ATTTTATTAC
23483 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
23496 TGTTTTATAAAT
1 TGTTTTATAAAT
*
23508 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
23522 TGTTTT
1 TGTTTT
23528 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:28210 original size:22 final size:22
Alignment explanation
Indices: 28182--28226 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28172 GCCCAACAGG
*
28182 AAGAAAA-AAAATGAATGATGAA
1 AAGAAAAGAAAAAGAA-GATGAA
28204 AAGAAAAGAAAAAGAAGATGAA
1 AAGAAAAGAAAAAGAAGATGAA
28226 A
1 A
28227 TGAAGGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (22 bp):
AAGAAAAGAAAAAGAAGATGAA
Found at i:29653 original size:13 final size:12
Alignment explanation
Indices: 29635--29679 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
29625 ATTTTATTAC
29635 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
29648 TGTTTTATAAAT
1 TGTTTTATAAAT
*
29660 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
29674 TGTTTT
1 TGTTTT
29680 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Done.