Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024356.1 Corchorus olitorius cultivar O-4 contig24389, 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: 25379
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:387 original size:39 final size:40
Alignment explanation
Indices: 333--413 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
323 ATACCTAAGA
*
333 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
372 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
412 AT
1 AT
414 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2225 original size:21 final size:21
Alignment explanation
Indices: 2201--2240 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2191 TTCTGTGCAA
2201 ATTA-AAATATTTTGAATTATT
1 ATTAGAAA-ATTTTGAATTATT
*
2222 ATTAGAAACTTTTGAATTA
1 ATTAGAAAATTTTGAATTA
2241 GTGGGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
ATTAGAAAATTTTGAATTATT
Found at i:6616 original size:21 final size:23
Alignment explanation
Indices: 6551--6623 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
6541 GATGACCTAA
6551 CTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
*
6574 TTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
*
6597 CTATGAAATTTT-GT-AACCTTC
1 CTATGAAATTTTAATAAACCTTC
6618 CTATGA
1 CTATGA
6624 TTTTTGATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 13 0.28
22 1 0.02
23 33 0.70
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Found at i:6634 original size:21 final size:22
Alignment explanation
Indices: 6532--6636 Score: 106
Period size: 23 Copynumber: 4.8 Consensus size: 22
6522 CTATGAAATT
* * **
6532 TGAAACTTTGATGACCTAACTA
1 TGAAATTTTGATAACCTTCCTA
* *
6554 TGAAATTTTAATAAACCTTCTTA
1 TGAAATTTTGAT-AACCTTCCTA
*
6577 TGAAATTTTAATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTTCCTA
6600 TGAAATTTTG-TAACCTTCCTA
1 TGAAATTTTGATAACCTTCCTA
*
6621 TG-ATTTTTGATAACCT
1 TGAAATTTTGATAACCT
6637 CTCTGTGAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.08
21 18 0.25
22 11 0.15
23 37 0.51
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCTA
Found at i:8121 original size:22 final size:22
Alignment explanation
Indices: 8087--8130 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8077 TTAGTAAAAT
8087 AATATATTATTATATTATTAAA
1 AATATATTATTATATTATTAAA
* * *
8109 AATATTTTTTTATCTTATTAAA
1 AATATATTATTATATTATTAAA
8131 TGAAAACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTATTATATTATTAAA
Found at i:9087 original size:22 final size:22
Alignment explanation
Indices: 9059--9135 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
9049 TATTTTTATG
*
9059 AAATTTTGATAATCACCCTATT
1 AAATTTTGATAATCACCCTATA
* * *
9081 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATCACCCTATA
*
9103 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATCACCCTATA
*
9124 AAATTGTGATAA
1 AAATTTTGATAA
9136 AATCCATAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 15 0.32
22 32 0.68
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAATCACCCTATA
Found at i:9143 original size:43 final size:44
Alignment explanation
Indices: 9055--9157 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
9045 TGAATATTTT
* * *
9055 TATGAAATTTTGATAATCACCCTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAATCACCCTATAAAATTGTGATAACAACCA
*
9099 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAA-AATCCA
1 TATGAAATTTTGATAATCACCCTATAAAATTGTGATAACAA-CCA
* *
9142 TAAGAAACTTTGATAA
1 TATGAAATTTTGATAA
9158 CCTAACTATG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.02
43 33 0.63
44 18 0.35
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACCCTATAAAATTGTGATAACAACCA
Found at i:12758 original size:34 final size:35
Alignment explanation
Indices: 12708--12790 Score: 116
Period size: 33 Copynumber: 2.4 Consensus size: 35
12698 TCTTTGCGTT
* *
12708 TTTTCATAAAAAAAAAAATTGTTTTGTG-TTTTGCG
1 TTTTC-TAAAAAAAAAAATTATTTTGTGTTTTTACG
*
12743 TTTT-TGAAAAAAAAAATTATTTTGTGTTTTTACG
1 TTTTCTAAAAAAAAAAATTATTTTGTGTTTTTACG
12777 TTTTCTAAAAAAAA
1 TTTTCTAAAAAAAA
12791 GAAAAAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 20 0.48
34 10 0.24
35 12 0.29
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.46
Consensus pattern (35 bp):
TTTTCTAAAAAAAAAAATTATTTTGTGTTTTTACG
Found at i:14475 original size:14 final size:14
Alignment explanation
Indices: 14456--14483 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14446 AGACAAGGAG
14456 ACTGCCGCTGACAA
1 ACTGCCGCTGACAA
14470 ACTGCCGCTGACAA
1 ACTGCCGCTGACAA
14484 GACAGATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.21, T:0.14
Consensus pattern (14 bp):
ACTGCCGCTGACAA
Found at i:16902 original size:17 final size:18
Alignment explanation
Indices: 16860--16896 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16850 AAAGGGTAGT
16860 TAAAAA-AATGTGTTTTCA
1 TAAAAAGAA-GTGTTTTCA
16878 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
16896 T
1 T
16897 GAAAGAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:25198 original size:15 final size:15
Alignment explanation
Indices: 25162--25200 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
25152 TATTATTAAT
*
25162 TTTTTTCAAAAATTA
1 TTTTTTGAAAAATTA
25177 TTTTTTGAAAAATTA
1 TTTTTTGAAAAATTA
25192 TTTTTTGAA
1 TTTTTTGAA
25201 CTTAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTTTTGAAAAATTA
Done.