Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019861.1 Corchorus olitorius cultivar O-4 contig19894, 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: 4970
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Found at i:2562 original size:28 final size:28
Alignment explanation
Indices: 2530--2584 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2520 CTGCCAAACT
*
2530 GAGCAACCGATGTTCATACTCCAAAATC
1 GAGCAACCAATGTTCATACTCCAAAATC
*
2558 GAGCAACCAATGTTCATACTCCGAAAT
1 GAGCAACCAATGTTCATACTCCAAAAT
2585 TGAGGGCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (28 bp):
GAGCAACCAATGTTCATACTCCAAAATC
Found at i:3743 original size:47 final size:47
Alignment explanation
Indices: 3702--4034 Score: 440
Period size: 47 Copynumber: 7.1 Consensus size: 47
3692 TAAACTGAAC
* *
3702 AGTAAAAGAAGAAGAGA-GTAGTTTAATTCTAGGTAAATAAACT-A--
1 AGTAAAAGAAGAAGA-ATTTAGTTTAATTCTAGGTAATTAAACTAAGT
* * *
3746 AGCAAAAGAGGAAGAATGTAGTTTAATTCTAGGTAATTAAACTAAGT
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGT
*
3793 AGTAAAAGAGGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGT
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGT
* * *
3840 AGAAAAAGGAGAAGAAAATTAGTTTAATTCTAGGTAATTAAACTAAGT
1 AGTAAAAGAAGAAG-AATTTAGTTTAATTCTAGGTAATTAAACTAAGT
* * *
3888 AGTAAAAGAGGAAGAATTTAGTTAAATTCTAGGTAAGTAAACTAAGT
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGT
* *
3935 AGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAAT
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGT
* ** * * *
3982 AGTAAAAGAAGTAGAACCTATTTTAATCCTAGGTAGTTAAACTAAGT
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGT
4029 AGTAAA
1 AGTAAA
4035 GAGTAGTCAA
Statistics
Matches: 257, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
43 1 0.00
44 38 0.15
45 1 0.00
47 174 0.68
48 43 0.17
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28
Consensus pattern (47 bp):
AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGT
Found at i:3892 original size:95 final size:94
Alignment explanation
Indices: 3702--4030 Score: 443
Period size: 95 Copynumber: 3.5 Consensus size: 94
3692 TAAACTGAAC
* * * *
3702 AGTAAAAGAAGAAGAGA-GTAGTTTAATTCTAGGTAAATAAACTAAGCA-AAAGA-G-GAAG-AA
1 AGTAAAAGAAGAAGA-ATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGAAAAAGGAGAAGAAA
3762 TGTAGTTTAATTCTAGGTAATTAAACTAAGT
65 T-TAGTTTAATTCTAGGTAATTAAACTAAGT
*
3793 AGTAAAAGAGGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGAAAAAGGAGAAGAAAA
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGAAAAAGGAGAAG-AAA
3858 TTAGTTTAATTCTAGGTAATTAAACTAAGT
65 TTAGTTTAATTCTAGGTAATTAAACTAAGT
* * * * *
3888 AGTAAAAGAGGAAGAATTTAGTTAAATTCTAGGTAAGTAAACTAAGTAGTAAAAGAAGAAGAAAT
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGAAAAAGGAGAAGAAAT
*
3953 TAGTTTAATTCTAGGTAATTAAACTAAAT
66 TAGTTTAATTCTAGGTAATTAAACTAAGT
* ** * * *
3982 AGTAAAAGAAGTAGAACCTATTTTAATCCTAGGTAGTTAAACTAAGTAG
1 AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGTAG
4031 TAAAGAGTAG
Statistics
Matches: 213, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
90 1 0.00
91 42 0.20
92 4 0.02
93 1 0.00
94 76 0.36
95 86 0.40
96 3 0.01
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28
Consensus pattern (94 bp):
AGTAAAAGAAGAAGAATTTAGTTTAATTCTAGGTAATTAAACTAAGTAGAAAAAGGAGAAGAAAT
TAGTTTAATTCTAGGTAATTAAACTAAGT
Found at i:3919 original size:142 final size:141
Alignment explanation
Indices: 3691--4034 Score: 469
Period size: 142 Copynumber: 2.5 Consensus size: 141
3681 GAAGATAATT
* * * * * * *
3691 TTAAACTGAACAGTAAAAGAAGAAGAGAGTAGTTTAATTCTAGGTAAATAAACT-A--AGCAAAA
1 TTAAACTAAATAGAAAAAGAAGAAGAAACTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAA
* * * *
3753 GAGGAAGAATGTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTA
66 GAGGAAGAATGTAGTTAAATTCTAGGTAAGTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTA
3818 ATTCTAGGTAA
131 ATTCTAGGTAA
* * *
3829 TTAAACTAAGTAGAAAAAGGAGAAGAAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA
1 TTAAACTAAATAGAAAAAGAAGAAG-AAACTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA
*
3894 AGAGGAAGAATTTAGTTAAATTCTAGGTAAGTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTT
65 AGAGGAAGAATGTAGTTAAATTCTAGGTAAGTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTT
3959 AATTCTAGGTAA
130 AATTCTAGGTAA
* * * * * *
3971 TTAAACTAAATAGTAAAAGAAGTAGAACCTATTTTAATCCTAGGTAGTTAAACTAAGTAGTAAA
1 TTAAACTAAATAGAAAAAGAAGAAGAAACTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA
4035 GAGTAGTCAA
Statistics
Matches: 179, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
138 20 0.11
139 26 0.15
140 1 0.01
141 34 0.19
142 98 0.55
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (141 bp):
TTAAACTAAATAGAAAAAGAAGAAGAAACTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAA
GAGGAAGAATGTAGTTAAATTCTAGGTAAGTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTA
ATTCTAGGTAA
Done.