Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024626.1 Corchorus olitorius cultivar O-4 contig24659, 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: 16306
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:452 original size:55 final size:54
Alignment explanation
Indices: 391--494 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 54
381 GATGGGGGTC
* *
391 ACTTGAGTTGAAAACCCGAAAAGGGACGGCTCAAGTGAATGATGGAAAAGGAGAA
1 ACTTGAGTTGAAAACCCGAAAAGGG-CGGCTCAAGCGAAAGATGGAAAAGGAGAA
* *
446 ACTTGAGTTGAAAACCCGCAAAGGGCGGCTCAAGCGAAAGTTGGAAAAG
1 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGCGAAAGATGGAAAAG
495 ACATAGTCCG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 21 0.47
55 24 0.53
ACGTcount: A:0.39, C:0.15, G:0.31, T:0.14
Consensus pattern (54 bp):
ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGCGAAAGATGGAAAAGGAGAA
Found at i:1518 original size:58 final size:58
Alignment explanation
Indices: 1428--1798 Score: 566
Period size: 58 Copynumber: 6.4 Consensus size: 58
1418 TTCATCAGAA
1428 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
1 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
*
1486 ATGGATCTAAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
1 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
1544 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
1 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
* * *
1602 ATGGATCTGAAGACAGTTCATAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCACAG
1 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
* *
1660 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGACTGAAGACAGCTCACAA
1 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
* * ** * * * * *
1718 ATGGATTTGAAGACAATTCCT-AAACCTTTTAAGAATGGGTA-TGAAGACAACCCACAA
1 ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAG-ACTGAAGACAGCTCACAG
* *
1775 ATGGATTTGAAGACAATTCCTAAA
1 ATGGATCTGAAGACAGTTCCTAAA
1799 CTTTTTAAGA
Statistics
Matches: 294, Mismatches: 17, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
57 48 0.16
58 246 0.84
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (58 bp):
ATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCACAG
Found at i:4078 original size:34 final size:34
Alignment explanation
Indices: 4035--4118 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
4025 TTTTAAATTT
4035 AGGGAAAGATCCCATCCAGTCTTCAAGGTTTTTA
1 AGGGAAAGATCCCATCCAGTCTTCAAGGTTTTTA
*
4069 AGGGAAAGATCCCATCCAGTCTTCAAGGTTTTTT
1 AGGGAAAGATCCCATCCAGTCTTCAAGGTTTTTA
4103 AGGGAAAGATCCCATC
1 AGGGAAAGATCCCATC
4119 AAGTTTTTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (34 bp):
AGGGAAAGATCCCATCCAGTCTTCAAGGTTTTTA
Found at i:4147 original size:39 final size:34
Alignment explanation
Indices: 4032--4158 Score: 155
Period size: 34 Copynumber: 3.6 Consensus size: 34
4022 TTTTTTTAAA
*
4032 TTTAGGGAAAGATCCCATCCAGTCTTCAAGGTTT
1 TTTAGGGAAAGATCCCATCAAGTCTTCAAGGTTT
* *
4066 TTAAGGGAAAGATCCCATCCAGTCTTCAAGGTTT
1 TTTAGGGAAAGATCCCATCAAGTCTTCAAGGTTT
* *
4100 TTTAGGGAAAGATCCCATCAAGTTTTTCAGAAGTTTT
1 TTTAGGGAAAGATCCCATCAAG-TCTTC--AAGGTTT
*
4137 AATTTAGGGAAAGATTCCATCA
1 --TTTAGGGAAAGATCCCATCA
4159 TCCAGTAGTT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
34 53 0.65
35 4 0.05
37 6 0.07
39 19 0.23
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (34 bp):
TTTAGGGAAAGATCCCATCAAGTCTTCAAGGTTT
Found at i:5512 original size:18 final size:19
Alignment explanation
Indices: 5491--5532 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
5481 CATGACTGCC
5491 AGCAGAAGACG-TTTTCTT
1 AGCAGAAGACGTTTTTCTT
*
5509 AGCAGAAGGCGTTTTTCTT
1 AGCAGAAGACGTTTTTCTT
5528 AGCAG
1 AGCAG
5533 GATTAAGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (19 bp):
AGCAGAAGACGTTTTTCTT
Found at i:10947 original size:27 final size:27
Alignment explanation
Indices: 10908--10969 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
10898 AAGTATTGTC
*
10908 CCTCTAAAAAAAAAAGAGTGTTAGTAA
1 CCTCTAAAAAAAAAAGAGAGTTAGTAA
*
10935 CCTC-AAAAGAAAAAAGGGAGTTAGTAA
1 CCTCTAAAA-AAAAAAGAGAGTTAGTAA
*
10962 CCCCTAAA
1 CCTCTAAA
10970 TCATGAACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 23 0.77
28 3 0.10
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (27 bp):
CCTCTAAAAAAAAAAGAGAGTTAGTAA
Found at i:13325 original size:11 final size:11
Alignment explanation
Indices: 13311--13336 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13301 TAAAAATCCC
13311 CTTTGGTAAGA
1 CTTTGGTAAGA
13322 CTTTGGTAAGA
1 CTTTGGTAAGA
13333 CTTT
1 CTTT
13337 CTTTAGTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (11 bp):
CTTTGGTAAGA
Found at i:14189 original size:22 final size:21
Alignment explanation
Indices: 14137--14190 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
14127 TGCTTCTTAA
14137 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
14158 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
14177 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
14191 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:15062 original size:17 final size:18
Alignment explanation
Indices: 15027--15062 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15017 CTCCTCTATC
*
15027 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
15045 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
15062 A
1 A
15063 ATTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Done.