Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022335.1 Corchorus olitorius cultivar O-4 contig22368, 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: 31667
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1484 original size:19 final size:18
Alignment explanation
Indices: 1451--1486 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1441 TGGAAATAAT
1451 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1469 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1487 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2299 original size:15 final size:16
Alignment explanation
Indices: 2279--2320 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2269 AGGAATAGGC
2279 AATCAATC-AAGCAAT
1 AATCAATCAAAGCAAT
2294 AATCAATCAAAGCAA-
1 AATCAATCAAAGCAAT
2309 AA-CAATGCAAAG
1 AATCAAT-CAAAG
2321 AAAAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.57, C:0.19, G:0.10, T:0.14
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:5507 original size:19 final size:18
Alignment explanation
Indices: 5483--5518 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5473 TGAAGACTTA
5483 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
5502 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
5519 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:6934 original size:17 final size:17
Alignment explanation
Indices: 6912--6959 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
6902 GATCACCCCC
*
6912 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
6929 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
*
6946 AGATCACCGGTGAT
1 AGATCACCAGTGAT
6960 CAAATATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 27 0.96
18 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:11093 original size:19 final size:18
Alignment explanation
Indices: 11071--11106 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11061 AGGGTAATTA
*
11071 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
11089 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
11107 GATAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:13806 original size:6 final size:7
Alignment explanation
Indices: 13758--13804 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
13748 AAGTTAGAAG
13758 TTAAAAA
1 TTAAAAA
13765 -TAAAAA
1 TTAAAAA
13771 TTTAAAAA
1 -TTAAAAA
13779 TTAAAAA
1 TTAAAAA
*
13786 TTGAAAA
1 TTAAAAA
13793 TT-AAAA
1 TTAAAAA
13799 TTAAAA
1 TTAAAA
13805 TTGGGTTGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 12 0.33
7 18 0.50
8 6 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:20542 original size:11 final size:11
Alignment explanation
Indices: 20528--20561 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
20518 TAAAGGAAAA
20528 AGCTAGGAAGG
1 AGCTAGGAAGG
20539 AGCTAGGAAGG
1 AGCTAGGAAGG
*
20550 AGTTAGGAAGG
1 AGCTAGGAAGG
20561 A
1 A
20562 CCCTACTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.44, T:0.12
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:24162 original size:56 final size:56
Alignment explanation
Indices: 24076--24189 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
24066 TATCTGTTTC
* *
24076 CTTTCACATAATAAATGTTATAATAAATCATATCCCCCTATCTCTATTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
24132 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
24188 CT
1 CT
24190 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:29807 original size:21 final size:21
Alignment explanation
Indices: 29783--29916 Score: 200
Period size: 21 Copynumber: 6.4 Consensus size: 21
29773 CTTAGGCAAT
*
29783 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
29804 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
29825 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
29846 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
29867 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
29888 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
29909 TCCAATGA
1 TCCAATGA
29917 ACTTCTAGCA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 105 0.97
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.