Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014619.1 Corchorus olitorius cultivar O-4 contig14652, 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: 81507
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6354 original size:1 final size:1
Alignment explanation
Indices: 6348--6376 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
6338 AGCAAATAGT
6348 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6377 CAACGTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17183 original size:42 final size:42
Alignment explanation
Indices: 17124--17214 Score: 164
Period size: 42 Copynumber: 2.1 Consensus size: 42
17114 AGCAGCCTGG
*
17124 TTCTTCTCAAGTTGTTGGCGACATGAAACTGAGACCATGCAA
1 TTCTTCACAAGTTGTTGGCGACATGAAACTGAGACCATGCAA
17166 TTCTTCACAAGTTGTTGGCGACATGAAACTGAGACCATGCAA
1 TTCTTCACAAGTTGTTGGCGACATGAAACTGAGACCATGCAA
17208 TATCTTC
1 T-TCTTC
17215 CTTTTGAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 42 0.89
43 5 0.11
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (42 bp):
TTCTTCACAAGTTGTTGGCGACATGAAACTGAGACCATGCAA
Found at i:19688 original size:9 final size:9
Alignment explanation
Indices: 19665--19696 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
19655 ATTGATTCCT
19665 TTTTATTTAA
1 TTTTATTT-A
19675 TTTTATTTA
1 TTTTATTTA
19684 TTTTATTTA
1 TTTTATTTA
19693 TTTT
1 TTTT
19697 TGGTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:20152 original size:16 final size:17
Alignment explanation
Indices: 20109--20154 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
20099 ATATATTTCG
20109 TAATGCTTCTATACGAT
1 TAATGCTTCTATACGAT
* *
20126 TAATG-TACTATA-TAT
1 TAATGCTTCTATACGAT
*
20141 TCATGCTTCTATAC
1 TAATGCTTCTATAC
20155 TAGCTTCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (17 bp):
TAATGCTTCTATACGAT
Found at i:22828 original size:50 final size:51
Alignment explanation
Indices: 22745--22845 Score: 141
Period size: 50 Copynumber: 2.0 Consensus size: 51
22735 TCGGGAATGG
* *
22745 GCAAAACCAAAGAGAAGAGGAAGAAATCCATTGAGAAAGAG-CATGCCTTT
1 GCAAAACCAAACAGAAGAGGAAGAAATCCATTGAGAAAGAGCCAGGCCTTT
* * * *
22795 GCAAAACCGAACAGAAGAGGAAGAGATCGATTGAGAGAGAGCCAGGCCTTT
1 GCAAAACCAAACAGAAGAGGAAGAAATCCATTGAGAAAGAGCCAGGCCTTT
22846 TGTTTTAGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 36 0.82
51 8 0.18
ACGTcount: A:0.43, C:0.17, G:0.28, T:0.13
Consensus pattern (51 bp):
GCAAAACCAAACAGAAGAGGAAGAAATCCATTGAGAAAGAGCCAGGCCTTT
Found at i:23497 original size:31 final size:31
Alignment explanation
Indices: 23425--23514 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 31
23415 AAAAATGACA
* * * *
23425 CATGGCATGTGTC-CTTTTT-GTGCACGAGG
1 CATGTCATGTGTCACTTTTTGGTACATGTGG
*
23454 CATGTCACGTGTCACTTTTTGGTACATGTGG
1 CATGTCATGTGTCACTTTTTGGTACATGTGG
*
23485 CGTGTCATGTGTCACTTTTTGGTACATGTG
1 CATGTCATGTGTCACTTTTTGGTACATGTG
23515 TGCCACGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
29 11 0.21
30 6 0.12
31 35 0.67
ACGTcount: A:0.14, C:0.19, G:0.28, T:0.39
Consensus pattern (31 bp):
CATGTCATGTGTCACTTTTTGGTACATGTGG
Found at i:23581 original size:31 final size:31
Alignment explanation
Indices: 23494--23582 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 31
23484 GCGTGTCATG
* *
23494 TGTCACTTTTTGGT--ACAT-GTGTGCCACG
1 TGTCGCTTTTTGGTACACATGGTGTGCCACA
* * * *
23522 TGTCGCTTTTTTGAACACGTGGCGTGCCACA
1 TGTCGCTTTTTGGTACACATGGTGTGCCACA
*
23553 TGTCGCTTTTTGGTACACATGGTATGCCAC
1 TGTCGCTTTTTGGTACACATGGTGTGCCAC
23583 GTCGAACATC
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 11 0.23
30 3 0.06
31 33 0.70
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.36
Consensus pattern (31 bp):
TGTCGCTTTTTGGTACACATGGTGTGCCACA
Found at i:29840 original size:48 final size:48
Alignment explanation
Indices: 29782--29876 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
29772 TGAATCAGTA
29782 TGAAAAACAACCAGACAACTTCATGGAAAGGACCA-TTTTCAACAAATC
1 TGAAAAACAACCAGACAACTTCATGGAAAGGA-CAGTTTTCAACAAATC
* * *
29830 TGAAATACAACCAGACAACTTCCTGGAAAGGACAGTTTTCAATAAAT
1 TGAAAAACAACCAGACAACTTCATGGAAAGGACAGTTTTCAACAAAT
29877 GAATCTCATG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 2 0.05
48 41 0.95
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (48 bp):
TGAAAAACAACCAGACAACTTCATGGAAAGGACAGTTTTCAACAAATC
Found at i:30404 original size:1 final size:1
Alignment explanation
Indices: 30398--30432 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
30388 TGCAAGAAGG
30398 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30433 TAAATAACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32286 original size:16 final size:17
Alignment explanation
Indices: 32265--32296 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
32255 GAAACCATGT
32265 ATTTTTCTT-TTCTTCC
1 ATTTTTCTTCTTCTTCC
32281 ATTTTTCTTCTTCTTC
1 ATTTTTCTTCTTCTTC
32297 TTCTTCCGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTCTTCTTCTTCC
Found at i:43544 original size:36 final size:36
Alignment explanation
Indices: 43503--43581 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
43493 GATGCCTAAG
43503 TTCTTCTAGTTAGGACACTCGGTAATAGATCAACAA
1 TTCTTCTAGTTAGGACACTCGGTAATAGATCAACAA
43539 TTCTTCTAGTTAGGACACTCGGTAATAGATCAACAA
1 TTCTTCTAGTTAGGACACTCGGTAATAGATCAACAA
43575 TTCTTCT
1 TTCTTCT
43582 GCTAGAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (36 bp):
TTCTTCTAGTTAGGACACTCGGTAATAGATCAACAA
Found at i:73489 original size:29 final size:28
Alignment explanation
Indices: 73444--73498 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
73434 TCCAATTTTC
73444 AAGTTTAAGGGGCAAAACATCCAAAATTA
1 AAGTTTAAGGGGCAAAACAT-CAAAATTA
* *
73473 AAGTTT-AGAGGGTAAAACGTCAAAAT
1 AAGTTTAAG-GGGCAAAACATCAAAAT
73499 CGTACGAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (28 bp):
AAGTTTAAGGGGCAAAACATCAAAATTA
Found at i:78995 original size:3 final size:3
Alignment explanation
Indices: 78987--79022 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
78977 TTTCATGCCC
78987 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
79023 AAAGAACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Done.