Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01005247.1 Corchorus olitorius cultivar O-4 contig05270, 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, 652
Length: 1087
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Found at i:33 original size:24 final size:24
Alignment explanation
Indices: 1--158 Score: 203
Period size: 24 Copynumber: 6.6 Consensus size: 24
*
1 TTCATCTAAATCATTATAATAACT
1 TTCATCTAAATCATTATAAGAACT
*
25 TTCATCTAAATCATTATCAGAACT
1 TTCATCTAAATCATTATAAGAACT
* * *
49 TT-TTGATAAATCATTATCAGAACT
1 TTCAT-CTAAATCATTATAAGAACT
*
73 TTCATCTAAATCATTATAATAACT
1 TTCATCTAAATCATTATAAGAACT
*
97 TTCATCTAAATCATTATAATAACT
1 TTCATCTAAATCATTATAAGAACT
* *
121 TTC-TGATAAATCATTATCAGAACT
1 TTCAT-CTAAATCATTATAAGAACT
145 TTCATCTAAATCAT
1 TTCATCTAAATCAT
159 AACCACTTGT
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
23 2 0.02
24 114 0.97
25 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (24 bp):
TTCATCTAAATCATTATAAGAACT
Found at i:121 original size:72 final size:72
Alignment explanation
Indices: 1--158 Score: 289
Period size: 72 Copynumber: 2.2 Consensus size: 72
* *
1 TTCATCTAAATCATTATAATAACTTTCATCTAAATCATTATCAGAACTTTTTGATAAATCATTAT
1 TTCATCTAAATCATTATAATAACTTTCATCTAAATCATTATAAGAACTTTCTGATAAATCATTAT
66 CAGAACT
66 CAGAACT
*
73 TTCATCTAAATCATTATAATAACTTTCATCTAAATCATTATAATAACTTTCTGATAAATCATTAT
1 TTCATCTAAATCATTATAATAACTTTCATCTAAATCATTATAAGAACTTTCTGATAAATCATTAT
138 CAGAACT
66 CAGAACT
145 TTCATCTAAATCAT
1 TTCATCTAAATCAT
159 AACCACTTGT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 83 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (72 bp):
TTCATCTAAATCATTATAATAACTTTCATCTAAATCATTATAAGAACTTTCTGATAAATCATTAT
CAGAACT
Found at i:495 original size:15 final size:15
Alignment explanation
Indices: 475--505 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
465 AATTACAATG
475 ATCATAGTTAATGTT
1 ATCATAGTTAATGTT
490 ATCATAGTTAATGTT
1 ATCATAGTTAATGTT
505 A
1 A
506 ATGTTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ATCATAGTTAATGTT
Found at i:898 original size:18 final size:18
Alignment explanation
Indices: 866--910 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
856 AGTGTTTTAA
*
866 ATTTCTTAAATTTCTTTTC
1 ATTTC-TAAACTTCTTTTC
885 ATTTCTAAACTTCTTTTC
1 ATTTCTAAACTTCTTTTC
903 ATTTCTAA
1 ATTTCTAA
911 GTGTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTCTAAACTTCTTTTC
Found at i:920 original size:27 final size:27
Alignment explanation
Indices: 847--926 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
837 CTTATCCGTC
847 TCATTTCTAAGTGTTTTAAATTTC-TT
1 TCATTTCTAAGTGTTTTAAATTTCTTT
** ** * *
873 AAATTTCT-TTTCATTTCTAAACTTCTTT
1 TCATTTCTAAGT-GTTT-TAAATTTCTTT
901 TCATTTCTAAGTGTTTTAAATTTCTT
1 TCATTTCTAAGTGTTTTAAATTTCTT
927 AAATTTATTT
Statistics
Matches: 38, Mismatches: 12, Indels: 7
0.67 0.21 0.12
Matches are distributed among these distances:
25 1 0.03
26 9 0.24
27 16 0.42
28 11 0.29
29 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57
Consensus pattern (27 bp):
TCATTTCTAAGTGTTTTAAATTTCTTT
Done.