Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018821.1 Corchorus olitorius cultivar O-4 contig18854, 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: 59299
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:4790 original size:33 final size:32
Alignment explanation
Indices: 4744--4805 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
4734 AAATTTTAGT
4744 AATTTCAAAAAAGAACATCTTAAGACTATCAA
1 AATTTCAAAAAAGAACATCTTAAGACTATCAA
*
4776 AATTTTAAACAAAGAACATCTTAAGACTAT
1 AATTTCAAA-AAAGAACATCTTAAGACTAT
4806 AAATACTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (32 bp):
AATTTCAAAAAAGAACATCTTAAGACTATCAA
Found at i:6280 original size:45 final size:44
Alignment explanation
Indices: 6212--6315 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 44
6202 AGCTTTTTTG
** **
6212 GTTGTAATTGTTGCCATAAGAAATTGATTAAGAGGCTGAATAAT
1 GTTGTAATTCCTGCCATAAGAAATAAATTAAGAGGCTGAATAAT
* * *
6256 AGTTGTAATTCCTGCCGTAGGAAATAAATTAAGTGGCTGAATAAT
1 -GTTGTAATTCCTGCCATAAGAAATAAATTAAGAGGCTGAATAAT
*
6301 GATTCTAATTCCTGC
1 G-TTGTAATTCCTGC
6316 TACAAAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (44 bp):
GTTGTAATTCCTGCCATAAGAAATAAATTAAGAGGCTGAATAAT
Found at i:16266 original size:35 final size:35
Alignment explanation
Indices: 16220--16291 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
16210 ATCACATTAG
*
16220 ATTTCAATTAATTCGGGGTTAGCATTGGATCTCAA
1 ATTTCAATTAATTCGGGGTTAGCATTGGACCTCAA
16255 ATTTCAATTAATTCGGGGTTAGCATTGGACCTCAA
1 ATTTCAATTAATTCGGGGTTAGCATTGGACCTCAA
16290 AT
1 AT
16292 GAGAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (35 bp):
ATTTCAATTAATTCGGGGTTAGCATTGGACCTCAA
Found at i:20561 original size:49 final size:49
Alignment explanation
Indices: 20444--20574 Score: 126
Period size: 50 Copynumber: 2.7 Consensus size: 49
20434 TTACATCTCA
* * * * *
20444 TGCACCTTTTTCTCAATTTTTACAACAAAATTGAATCTTTAATTTTTCT
1 TGCACTTTTTTATCAATTTTTACAAAAAAATTGAATATTTAACTTTTCT
* * *
20493 TGCACCTTTTTAAT-GATTTTTATGAAAAAAATTGAATATTT-ACTTTTCAT
1 TGCA-CTTTTTTATCAATTTTTA-CAAAAAAATTGAATATTTAACTTTTC-T
*
20543 TGCA-TTTTTTATCAATTTTTA-AACAAAATTGA
1 TGCACTTTTTTATCAATTTTTACAAAAAAATTGA
20575 TTGGCACGCT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
47 10 0.15
48 7 0.10
49 24 0.36
50 26 0.39
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (49 bp):
TGCACTTTTTTATCAATTTTTACAAAAAAATTGAATATTTAACTTTTCT
Found at i:29689 original size:19 final size:19
Alignment explanation
Indices: 29665--29703 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29655 GTATTCTCGG
29665 ATGCTGGCTGCTGTTCATA
1 ATGCTGGCTGCTGTTCATA
29684 ATGCTGGCTGCTGTTCATA
1 ATGCTGGCTGCTGTTCATA
29703 A
1 A
29704 GTCGGCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (19 bp):
ATGCTGGCTGCTGTTCATA
Found at i:32468 original size:31 final size:31
Alignment explanation
Indices: 32430--32490 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
32420 GATTATTATC
32430 AAAAAAGATTGAAAGAAAATCCACGTATGCA
1 AAAAAAGATTGAAAGAAAATCCACGTATGCA
32461 AAAAAAGATTGAAAGAAAATCCACGTATGC
1 AAAAAAGATTGAAAGAAAATCCACGTATGC
32491 GGAAGATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.54, C:0.13, G:0.16, T:0.16
Consensus pattern (31 bp):
AAAAAAGATTGAAAGAAAATCCACGTATGCA
Found at i:32527 original size:44 final size:44
Alignment explanation
Indices: 32465--32557 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
32455 TATGCAAAAA
* *
32465 AAGATTGAAAGAAAATCCACGTATGCGGA-AGATTATTATCAAAG
1 AAGATTGAAAGAAAATCCAAGTATACGGAGA-ATTATTATCAAAG
*
32509 AAGATTGAAA-AAAGATCCAAGTATATGGAGAATTATTATCAAAG
1 AAGATTGAAAGAAA-ATCCAAGTATACGGAGAATTATTATCAAAG
32553 AAGAT
1 AAGAT
32558 CCAAGGAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 3 0.07
44 40 0.91
45 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (44 bp):
AAGATTGAAAGAAAATCCAAGTATACGGAGAATTATTATCAAAG
Found at i:36916 original size:38 final size:38
Alignment explanation
Indices: 36865--36943 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
36855 ACTTGTAAAG
36865 ATGTCGCCAAATTGTATTACTTTACCCATACCAACACC
1 ATGTCGCCAAATTGTATTACTTTACCCATACCAACACC
36903 ATGTCGCCAAATTGTATTACTTTACCCATACCAACACC
1 ATGTCGCCAAATTGTATTACTTTACCCATACCAACACC
36941 ATG
1 ATG
36944 GTGGTACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.29
Consensus pattern (38 bp):
ATGTCGCCAAATTGTATTACTTTACCCATACCAACACC
Found at i:42556 original size:1 final size:1
Alignment explanation
Indices: 42550--42574 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
42540 ACCATTAATC
42550 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
42575 ACGTAACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.