Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017783.1 Corchorus olitorius cultivar O-4 contig17816, 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: 40878
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:343 original size:20 final size:20
Alignment explanation
Indices: 315--356 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
305 CACCCACCAA
315 TAGCATAAAAAT-CTAATCTT
1 TAGCATAAAAATCCTAA-CTT
* *
335 TAGCTTAAAGATCCTAACTT
1 TAGCATAAAAATCCTAACTT
355 TA
1 TA
357 AACAATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TAGCATAAAAATCCTAACTT
Found at i:3377 original size:21 final size:20
Alignment explanation
Indices: 3336--3384 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
3326 GATTATGTAA
**
3336 ATGCAAAATGTGAAATTAAT
1 ATGCAAAATGTGAAACGAAT
*
3356 ATGCGAAAATGTGATACGAAT
1 ATGC-AAAATGTGAAACGAAT
3377 ATGCAAAA
1 ATGCAAAA
3385 GAACATAACA
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:0.49, C:0.08, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGCAAAATGTGAAACGAAT
Found at i:3521 original size:28 final size:27
Alignment explanation
Indices: 3481--3552 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
3471 AATGAAGTAG
3481 AAATGACCAAAATGCCCCTGGACATGC-A
1 AAATGACCAAAATGCCCCT-GA-ATGCGA
* * *
3509 AAATGACTAAAATACCCCTGAATGCGC
1 AAATGACCAAAATGCCCCTGAATGCGA
3536 AAATGACCAAAATGCCC
1 AAATGACCAAAATGCCC
3553 TATAGATGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 4 0.11
27 17 0.45
28 17 0.45
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.15
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGCGA
Found at i:3547 original size:27 final size:28
Alignment explanation
Indices: 3481--3548 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
3471 AATGAAGTAG
*
3481 AAATGACCAAAATGCCCCTGGACATGCA
1 AAATGACCAAAATACCCCTGGACATGCA
* *
3509 AAATGACTAAAATACCCCT-GA-ATGCGC
1 AAATGACCAAAATACCCCTGGACATGC-A
3536 AAATGACCAAAAT
1 AAATGACCAAAAT
3549 GCCCTATAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.11
27 14 0.40
28 17 0.49
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.16
Consensus pattern (28 bp):
AAATGACCAAAATACCCCTGGACATGCA
Found at i:9002 original size:49 final size:49
Alignment explanation
Indices: 8940--9038 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
8930 TTTTCGCTAG
* *
8940 ATTCTCATCTTAATTGGTCAAGTCTGTTTAAATTTTGATTAAACCCCAA
1 ATTCCCATCTTAATTGGTCAAGCCTGTTTAAATTTTGATTAAACCCCAA
*
8989 ATTCCCATCTTAATTGGTCAAGCCTGTTTCAATTTTGATTAAACCCCAA
1 ATTCCCATCTTAATTGGTCAAGCCTGTTTAAATTTTGATTAAACCCCAA
9038 A
1 A
9039 CCTTTTGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (49 bp):
ATTCCCATCTTAATTGGTCAAGCCTGTTTAAATTTTGATTAAACCCCAA
Found at i:9105 original size:13 final size:13
Alignment explanation
Indices: 9084--9113 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9074 ACCAAAAGTA
9084 ATTAATATCTTTC
1 ATTAATATCTTTC
*
9097 ATTACTATCTTTC
1 ATTAATATCTTTC
9110 ATTA
1 ATTA
9114 TTTTCCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTAATATCTTTC
Found at i:9138 original size:49 final size:49
Alignment explanation
Indices: 9067--9166 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
9057 TCCTGTTTCC
9067 TTCCTAAACCAAAAGTAATTAATATCTTTCATTACTATCTTTCATTATT
1 TTCCTAAACCAAAAGTAATTAATATCTTTCATTACTATCTTTCATTATT
9116 TTCCTAAACCAAAAGTAATTAATATCTTTCATTACTATCTTTCATTATT
1 TTCCTAAACCAAAAGTAATTAATATCTTTCATTACTATCTTTCATTATT
9165 TT
1 TT
9167 TAGAAGCCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.46
Consensus pattern (49 bp):
TTCCTAAACCAAAAGTAATTAATATCTTTCATTACTATCTTTCATTATT
Found at i:9154 original size:13 final size:13
Alignment explanation
Indices: 9133--9162 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9123 ACCAAAAGTA
9133 ATTAATATCTTTC
1 ATTAATATCTTTC
*
9146 ATTACTATCTTTC
1 ATTAATATCTTTC
9159 ATTA
1 ATTA
9163 TTTTTAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTAATATCTTTC
Found at i:13623 original size:30 final size:30
Alignment explanation
Indices: 13587--13648 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
13577 GCTAATAAGC
**
13587 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTAAAGGGTATAAGAGAAAAGT
*
13617 CATTAAAATTAAAGGGTATAAGAGGAAAGT
1 CATTAAAATTAAAGGGTATAAGAGAAAAGT
13647 CA
1 CA
13649 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.23, T:0.24
Consensus pattern (30 bp):
CATTAAAATTAAAGGGTATAAGAGAAAAGT
Found at i:13860 original size:38 final size:40
Alignment explanation
Indices: 13818--13911 Score: 122
Period size: 41 Copynumber: 2.4 Consensus size: 40
13808 CGCAATCTTA
*
13818 GGGAAAGATCCCATCTAGGT-TTTTT-AA-TGTTCAATTTC
1 GGGAAAGATCCCATCTA-GTCTTTTTAAAGTGTTCAATTAC
* *
13856 GGGAAAGATCCCATCTAGTCTTTTTCAAAGTTTTCAATTAG
1 GGGAAAGATCCCATCTAGTCTTTTT-AAAGTGTTCAATTAC
13897 GGGAAAGATCCCATC
1 GGGAAAGATCCCATC
13912 AAATTTTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
37 2 0.04
38 22 0.45
40 2 0.04
41 23 0.47
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (40 bp):
GGGAAAGATCCCATCTAGTCTTTTTAAAGTGTTCAATTAC
Found at i:16867 original size:3 final size:3
Alignment explanation
Indices: 16859--16946 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
16849 CTTCTAAATT
16859 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16907 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16947 ATATATATAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17569 original size:17 final size:17
Alignment explanation
Indices: 17524--17565 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
17514 TATATCACTA
17524 GTGATCTAAGATCACCAG
1 GTGATC-AAGATCACCAG
17542 G-GATGCAAGATCACC-G
1 GTGAT-CAAGATCACCAG
17558 GTGATCAA
1 GTGATCAA
17566 AGATTACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 2 0.09
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (17 bp):
GTGATCAAGATCACCAG
Found at i:20778 original size:18 final size:19
Alignment explanation
Indices: 20755--20794 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
20745 TCCATGAAAT
20755 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
20773 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
20792 AAT
1 AAT
20795 CACGAACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:21236 original size:21 final size:21
Alignment explanation
Indices: 21211--21262 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21201 TTTGTAATCA
* *
21211 TCATTTCTGTATCTTTCTCTT
1 TCATTTCTGTATCTATCTCTG
*
21232 TCATTTC-GAAATCTATCTCTG
1 TCATTTCTG-TATCTATCTCTG
21253 TCATTTCTGT
1 TCATTTCTGT
21263 GTATGTCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (21 bp):
TCATTTCTGTATCTATCTCTG
Found at i:29513 original size:17 final size:17
Alignment explanation
Indices: 29491--29531 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
29481 GTATTTGTGA
29491 AATGGATTTTGTCAGTG
1 AATGGATTTTGTCAGTG
29508 AATGGATTTTGTCAGTG
1 AATGGATTTTGTCAGTG
29525 AATGGAT
1 AATGGAT
29532 CTATACATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.39
Consensus pattern (17 bp):
AATGGATTTTGTCAGTG
Found at i:35272 original size:19 final size:21
Alignment explanation
Indices: 35245--35296 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
35235 ACTCATCAAC
35245 ATTTGGTGTAAT-GT-TCACT
1 ATTTGGTGTAATGGTATCACT
* *
35264 ATTTAGTGTAATGGTATCATT
1 ATTTGGTGTAATGGTATCACT
35285 ATTTGGTGTAAT
1 ATTTGGTGTAAT
35297 AAAATGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
21 15 0.54
ACGTcount: A:0.25, C:0.06, G:0.21, T:0.48
Consensus pattern (21 bp):
ATTTGGTGTAATGGTATCACT
Done.