Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020646.1 Corchorus olitorius cultivar O-4 contig20679, 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: 10801
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:6490 original size:14 final size:13
Alignment explanation
Indices: 6468--6514 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
6458 TAAATATGCC
6468 AAAAAAAAAACAA
1 AAAAAAAAAACAA
6481 AAAAACAAAAAC-A
1 AAAAA-AAAAACAA
*
6494 AAAAAGAAAACGAA
1 AAAAAAAAAAC-AA
6508 AAAAAAA
1 AAAAAAA
6515 GTAAAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 5 0.17
13 11 0.38
14 13 0.45
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:6862 original size:5 final size:5
Alignment explanation
Indices: 6843--6881 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
6833 TCCAAGTGCC
6843 AAAA- AAAATG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
6882 AAAGAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:8145 original size:22 final size:23
Alignment explanation
Indices: 8120--8172 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
8110 TCCGGGCACA
*
8120 ATTTCAGAAAT-CTCCGGGTATT
1 ATTTCAGAAATCCTCCGGGTATC
*
8142 ATTTCTGATAAATCCTCCGGGTATC
1 ATTTC--AGAAATCCTCCGGGTATC
8167 ATTTCA
1 ATTTCA
8173 TTTCATCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 1 0.04
24 5 0.19
25 15 0.58
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (23 bp):
ATTTCAGAAATCCTCCGGGTATC
Found at i:8288 original size:140 final size:141
Alignment explanation
Indices: 7740--8439 Score: 963
Period size: 140 Copynumber: 4.9 Consensus size: 141
7730 CATTTTTGGT
* *
7740 AAATTTTTAATCAAAGTTGCATTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTTGAGTTTGCAT
1 AAATTTTTAATCAAAGTTGCGTTTAAATTTC--AA--AAAACCTTGCTCAAGGTTGAGTTTGCAT
* * * *
7805 TTGTAAGTCCTCCGGGCACCATTTCAGAAACCTCCGAGTATTAATTCTGATAAATCCTTCGGGTA
62 TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
**
7870 TCATTTTGTTTCATC
127 TCATTTCATTTCATC
* * * *
7885 AAAATTTTAATCAAAGTCGTGTTTAAGTTTCAAAATCACAACCTTGCTCAAGGTCTCAATTCAGA
1 AAATTTTTAATCAAAGTTGCGTTTAAATTTC-AAA--A-AACCTTGCTCAAGG------TT--GA
*
7950 ATTTGCATTTGTAAGACCTCCGGGCACAATTTTCAGAAACCTCCGGGTATTAATTCTGATAAATC
54 GTTTGCATTTGTAAGACCTCCGGGCACAA-TTTCAGAAACCTCCGGGTATTAATTCTGATAAATC
8015 CTCCGGGTATCATTTCATTTCATC
118 CTCCGGGTATCATTTCATTTCATC
* *
8039 AAGTTTTTAATCAAAGCTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGT
1 AAATTTTTAATCAAAGTTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGT
* *
8104 AAGACCTCCGGGCACAATTTCAGAAATCTCCGGGTATTATTTCTGATAAATCCTCCGGGTATCAT
66 AAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCAT
8169 TTCATTTCATC
131 TTCATTTCATC
* * * *
8180 AAGTTTTTAATCAAAGTTGCGTTTAAATTTC-AAAAACCTTGCTCAATGTTGAATTTGCATTCGT
1 AAATTTTTAATCAAAGTTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGT
8244 AAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCAT
66 AAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCAT
*
8309 CTCATTTCATC
131 TTCATTTCATC
* * **
8320 AAATTTTTAATCAAAGCTGCATTTAAATTTC-AAAAACCTTGCTCAAGGTTGAGTTTGCATCCGT
1 AAATTTTTAATCAAAGTTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGT
* * * *
8384 AAGACCTCCGGGCATAATTTCAGAAATCTCCGGGTATTAATTCTGACAAGTCCTCC
66 AAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCC
8440 AGGCATTCTA
Statistics
Matches: 506, Mismatches: 37, Indels: 29
0.88 0.06 0.05
Matches are distributed among these distances:
140 213 0.42
141 87 0.17
142 31 0.06
144 6 0.01
145 41 0.08
150 14 0.03
151 3 0.01
153 31 0.06
154 80 0.16
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (141 bp):
AAATTTTTAATCAAAGTTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGT
AAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCAT
TTCATTTCATC
Found at i:8650 original size:40 final size:40
Alignment explanation
Indices: 8567--9073 Score: 618
Period size: 40 Copynumber: 12.8 Consensus size: 40
8557 TGAATTTTAG
* * * *
8567 AATCCTGCTCAAGATCATTTCTTTA-CCAATTAATTTCAC
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
8606 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
** * *
8646 AATCCTATTCAGGATCATTGCTTTATCAAGTCAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
8686 AATCCTGCTCAGGATCA-TCCTTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGC-TTTATCAAATTAATTTCAA
* * *
8726 AATCCTGCACATGATCATCT-TTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
*
8766 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
8806 AATCCTGCACAGGATCATCT-TTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* * *
8846 AACCCTGCTCAAGATCATTGCTTTAACAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
8886 AACCCTGCAT-AGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGC-TCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
8926 AATCCTGCACAGGGTCATCT-TTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* *
8966 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * *
9006 AATCCTGCTCAGGATCATTTCTTTA-CCAGTTAA--TCAC
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
9043 AATCCTACTCAGGTTCATTGCTTTCTCAAAT
1 AATCCTGCTCAGGATCATTGCTTTATCAAAT
9074 CCTATTCAGA
Statistics
Matches: 404, Mismatches: 52, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
37 24 0.06
38 3 0.01
39 34 0.08
40 339 0.84
41 3 0.01
42 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (40 bp):
AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
Found at i:9088 original size:28 final size:28
Alignment explanation
Indices: 9038--9099 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
9028 TTACCAGTTA
**
9038 ATCACAATCCTACTCAGGTTCATTGCTTT
1 ATCA-AATCCTACTCAGAATCATTGCTTT
* *
9067 CTCAAATCCTATTCAGAATCATTGCTTT
1 ATCAAATCCTACTCAGAATCATTGCTTT
9095 ATCAA
1 ATCAA
9100 GCCACTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (28 bp):
ATCAAATCCTACTCAGAATCATTGCTTT
Found at i:9164 original size:39 final size:39
Alignment explanation
Indices: 9071--9204 Score: 169
Period size: 39 Copynumber: 3.4 Consensus size: 39
9061 TGCTTTCTCA
* * * *
9071 AATCCTATTCAGAATCATTGCTTTATCAAGCCACTTTTCGG
1 AATCCTATTCAGGATCATTGCTTTATC-AGTCA-ATTTCAG
* *
9112 AATCCTGTTCAGGATCATTTCTTTATCAGTCAATTTCAG
1 AATCCTATTCAGGATCATTGCTTTATCAGTCAATTTCAG
* *
9151 AATCCTATTCAGGATCCTTGCTTTATCAGTCAATTTCAAA
1 AATCCTATTCAGGATCATTGCTTTATCAGTCAATTTC-AG
9191 AATCCTATTCAGGA
1 AATCCTATTCAGGA
9205 CCAGTGGCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 39 0.48
40 19 0.23
41 24 0.29
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (39 bp):
AATCCTATTCAGGATCATTGCTTTATCAGTCAATTTCAG
Found at i:9217 original size:40 final size:39
Alignment explanation
Indices: 9070--9220 Score: 126
Period size: 39 Copynumber: 3.8 Consensus size: 39
9060 TTGCTTTCTC
* * * * * *
9070 AAATCCTATTCAGAATCATTGCTTTATCAAGCCACTTTTCG
1 AAATCCTATTCAGGATCCTGGCTTTATC-AGTCA-ATTTCA
* * * **
9111 GAATCCTGTTCAGGATCATTTCTTTATCAGTCAATTTCA
1 AAATCCTATTCAGGATCCTGGCTTTATCAGTCAATTTCA
* *
9150 GAATCCTATTCAGGATCCTTGCTTTATCAGTCAATTTCAA
1 AAATCCTATTCAGGATCCTGGCTTTATCAGTCAATTTC-A
9190 AAATCCTATTCAGGA-CCAGTGGC-TTATCAGT
1 AAATCCTATTCAGGATCC--TGGCTTTATCAGT
9221 TGATTTCAGC
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 41 0.43
40 27 0.28
41 27 0.28
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (39 bp):
AAATCCTATTCAGGATCCTGGCTTTATCAGTCAATTTCA
Found at i:9649 original size:24 final size:24
Alignment explanation
Indices: 9622--9692 Score: 142
Period size: 24 Copynumber: 3.0 Consensus size: 24
9612 TAATTATTGT
9622 TCTCTTTTTCTTTTAAATAGGATG
1 TCTCTTTTTCTTTTAAATAGGATG
9646 TCTCTTTTTCTTTTAAATAGGATG
1 TCTCTTTTTCTTTTAAATAGGATG
9670 TCTCTTTTTCTTTTAAATAGGAT
1 TCTCTTTTTCTTTTAAATAGGAT
9693 ACAATTTTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (24 bp):
TCTCTTTTTCTTTTAAATAGGATG
Found at i:9824 original size:18 final size:18
Alignment explanation
Indices: 9772--9825 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
9762 TGGGCATTGT
9772 TTCTTGGGCCAATTTTGC
1 TTCTTGGGCCAATTTTGC
9790 TTCAATT-GGCC----TTGC
1 TTC--TTGGGCCAATTTTGC
9805 TTCTTGGGCCAATTTTGC
1 TTCTTGGGCCAATTTTGC
9823 TTC
1 TTC
9826 AATTGGACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
13 2 0.07
14 4 0.14
15 7 0.24
18 10 0.34
19 4 0.14
20 2 0.07
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (18 bp):
TTCTTGGGCCAATTTTGC
Done.