Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012510.1 Corchorus olitorius cultivar O-4 contig12543, 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: 11041
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:5822 original size:25 final size:24
Alignment explanation
Indices: 5794--5896 Score: 59
Period size: 25 Copynumber: 4.2 Consensus size: 24
5784 CTTCAAAATC
5794 AGTTGTAATCAAAGCTTTGATTTCG
1 AGTTGTAATCAAAGCTTTGATTT-G
* * ***
5819 AGTTGTGAGCAAAGGAATGA--TG
1 AGTTGTAATCAAAGCTTTGATTTG
* * ** *
5841 AGTTTTAATCAAAATCTTCAAAATT-
1 AGTTGTAATC-AAAGCTT-TGATTTG
5866 AGTTGTAATCAAAGCTTTGATTTCG
1 AGTTGTAATCAAAGCTTTGATTT-G
5891 AGTTGT
1 AGTTGT
5897 GAGCAAAGGA
Statistics
Matches: 53, Mismatches: 19, Indels: 12
0.63 0.23 0.14
Matches are distributed among these distances:
22 8 0.15
23 7 0.13
24 7 0.13
25 30 0.57
26 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (24 bp):
AGTTGTAATCAAAGCTTTGATTTG
Found at i:5870 original size:72 final size:72
Alignment explanation
Indices: 5752--5945 Score: 298
Period size: 72 Copynumber: 2.6 Consensus size: 72
5742 ATCTGGACTA
* *
5752 TGAGCTAAGGAATGATGACTTTTAATCAAAATCTTCAAAATCAGTTGTAATCAAAGCTTTGATTT
1 TGAGCAAAGGAATGATGAGTTTTAATCAAAATCTTCAAAATCAGTTGTAATCAAAGCTTTGATTT
5817 CGAGTTG
66 CGAGTTG
*
5824 TGAGCAAAGGAATGATGAGTTTTAATCAAAATCTTCAAAATTAGTTGTAATCAAAGCTTTGATTT
1 TGAGCAAAGGAATGATGAGTTTTAATCAAAATCTTCAAAATCAGTTGTAATCAAAGCTTTGATTT
5889 CGAGTTG
66 CGAGTTG
* * *
5896 TGAGCAAAGGAATGACGGTGTTTTAATCAAAAGATGTTTCAAAATCAGTT
1 TGAGCAAAGGAATGA-TGAGTTTTAATC-AAA-AT-CTTCAAAATCAGTT
5946 TTGGTCAAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
72 84 0.76
73 10 0.09
74 3 0.03
75 2 0.02
76 12 0.11
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (72 bp):
TGAGCAAAGGAATGATGAGTTTTAATCAAAATCTTCAAAATCAGTTGTAATCAAAGCTTTGATTT
CGAGTTG
Found at i:6409 original size:9 final size:9
Alignment explanation
Indices: 6360--6400 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
6350 CCAAATAATA
6360 AAAAAAATC
1 AAAAAAATC
*
6369 AAAAAAATG
1 AAAAAAATC
* *
6378 AATAACATC
1 AAAAAAATC
6387 AAAAAAATC
1 AAAAAAATC
6396 AAAAA
1 AAAAA
6401 TGAAAAAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:6794 original size:17 final size:18
Alignment explanation
Indices: 6772--6823 Score: 81
Period size: 17 Copynumber: 2.9 Consensus size: 18
6762 CCACTCCATC
6772 AAGAAATTCAAAAAAAA-
1 AAGAAATTCAAAAAAAAG
6789 AAGAAATT-AAAAAAAAG
1 AAGAAATTCAAAAAAAAG
6806 AGAGAAATTCAAAAAAAA
1 A-AGAAATTCAAAAAAAA
6824 TCAAAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.25
17 9 0.28
18 7 0.22
19 8 0.25
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.12
Consensus pattern (18 bp):
AAGAAATTCAAAAAAAAG
Found at i:6830 original size:17 final size:17
Alignment explanation
Indices: 6773--6838 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 17
6763 CACTCCATCA
*
6773 AGAAATTCAAAAAAAA-A
1 AGAAATT-AAAAAAAATC
**
6790 AGAAATTAAAAAAAAGAG
1 AGAAATTAAAAAAAA-TC
6808 AGAAATTCAAAAAAAATC
1 AGAAATT-AAAAAAAATC
*
6826 A-AAATGAAAAAAA
1 AGAAATTAAAAAAA
6839 TCAAATCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 15 0.36
17 11 0.26
18 8 0.19
19 8 0.19
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (17 bp):
AGAAATTAAAAAAAATC
Found at i:6846 original size:5 final size:5
Alignment explanation
Indices: 6836--6895 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
6826 AAAATGAAAA
**
6836 AAATC AAATC AAAGTC -AAT- AAAAA AAATC AAAAATC AAATC AAATC
1 AAATC AAATC AAA-TC AAATC AAATC AAATC --AAATC AAATC AAATC
6882 AAATC AAAATC AAA
1 AAATC -AAATC AAA
6896 AGAGAATGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 3 0.07
5 31 0.67
6 7 0.15
7 5 0.11
ACGTcount: A:0.67, C:0.15, G:0.02, T:0.17
Consensus pattern (5 bp):
AAATC
Found at i:6859 original size:36 final size:32
Alignment explanation
Indices: 6820--6896 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 32
6810 AAATTCAAAA
6820 AAAATCAAAATGAAAAAAATCAAATCAAAGTCAAT
1 AAAATCAAAAT--AAAAAATCAAATCAAA-TCAAT
*
6855 AAAA--AAAATCAAAAATCAAATCAAATCAAAT
1 AAAATCAAAATAAAAAATCAAATCAAATC-AAT
6886 CAAAATCAAAA
1 -AAAATCAAAA
6897 GAGAATGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
30 2 0.05
31 18 0.49
32 4 0.11
33 5 0.14
34 4 0.11
35 4 0.11
ACGTcount: A:0.69, C:0.13, G:0.03, T:0.16
Consensus pattern (32 bp):
AAAATCAAAATAAAAAATCAAATCAAATCAAT
Found at i:6881 original size:41 final size:39
Alignment explanation
Indices: 6816--6894 Score: 113
Period size: 41 Copynumber: 2.0 Consensus size: 39
6806 AGAGAAATTC
* *
6816 AAAAAAAATCAAAATGAAAAAAATCAAATCAAAGTCAAT
1 AAAAAAAATCAAAATCAAAAAAATCAAATCAAAATCAAT
*
6855 AAAAAAAATCAAAAATCAAATCAAATCAAATCAAAATCAA
1 AAAAAAAATC-AAAATCAAA-AAAATCAAATCAAAATCAA
6895 AAGAGAATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 10 0.29
40 8 0.23
41 17 0.49
ACGTcount: A:0.70, C:0.13, G:0.03, T:0.15
Consensus pattern (39 bp):
AAAAAAAATCAAAATCAAAAAAATCAAATCAAAATCAAT
Found at i:7541 original size:50 final size:50
Alignment explanation
Indices: 7466--7615 Score: 237
Period size: 50 Copynumber: 3.0 Consensus size: 50
7456 AGTTTTAGAA
*
7466 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
7516 TAAAATTGCTTTCCATTTGTTAGTTCAAGATCAAAATTTGCTTTTCAAAT
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
7566 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
7616 GACATTGAAG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:8274 original size:50 final size:50
Alignment explanation
Indices: 8215--8452 Score: 431
Period size: 50 Copynumber: 4.8 Consensus size: 50
8205 CGAATGTTTT
* * *
8215 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
8265 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
8315 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
8365 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
8415 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
8453 TTTCAAACCT
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 183 1.00
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.27
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:8675 original size:50 final size:50
Alignment explanation
Indices: 8509--8664 Score: 285
Period size: 50 Copynumber: 3.1 Consensus size: 50
8499 CATTACCTTT
*
8509 TTTTAAGATTGAATTGGTAGACAGTTCAAACGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
8559 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCAGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
8609 TTTTAAGATTGAATTGGTAGACAGTTCAGAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
8659 TTTTAA
1 TTTTAA
8665 TATTAGATTG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:8687 original size:100 final size:100
Alignment explanation
Indices: 8509--8689 Score: 292
Period size: 100 Copynumber: 1.8 Consensus size: 100
8499 CATTACCTTT
8509 TTTTAAGATTGAATTGGTAGACAGTTCAAACGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
1 TTTTAAGATTGAATTGGTAGACAGTTCAAACGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
* *
8574 GGTAGACAGTTCAAAGGATAAGCAGAAGACGGTCC
66 GGAAGACAATTCAAAGGATAAGCAGAAGACGGTCC
* * *
8609 TTTTAAGATTGAATTGGTAGACAGTTCAGAGGATAAGCGGAAGACGGTCCTTTTAATATT-AGAT
1 TTTTAAGATTGAATTGGTAGACAGTTCAAACGATAAGCGGAAGACGGTCCTTTTAAGATTGA-AT
*
8673 TGGAAGATAATTCAAAG
65 TGGAAGACAATTCAAAG
8690 AAGTTGATCG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
99 1 0.01
100 73 0.99
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (100 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAACGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
GGAAGACAATTCAAAGGATAAGCAGAAGACGGTCC
Found at i:9030 original size:28 final size:27
Alignment explanation
Indices: 8937--9033 Score: 113
Period size: 28 Copynumber: 3.5 Consensus size: 27
8927 ATCTAAGGGA
8937 ATTTTGGGTCATTTTCAAAATCCAGGGGC
1 ATTTT-GGTCATTTTC-AAATCCAGGGGC
* * *
8966 ATTTTGGTCATTTTCATATTCAGGGGT
1 ATTTTGGTCATTTTCAAATCCAGGGGC
* *
8993 ATTTTAGTCATTTTGCACATCCAGGGGC
1 ATTTTGGTCATTTT-CAAATCCAGGGGC
*
9021 ATTGTGGTCATTT
1 ATTTTGGTCATTT
9034 CTACTCCATT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 22 0.38
28 31 0.53
29 5 0.09
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (27 bp):
ATTTTGGTCATTTTCAAATCCAGGGGC
Found at i:9199 original size:25 final size:25
Alignment explanation
Indices: 9171--9222 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
9161 TTAATCTCAC
9171 GTTTGCATTTACATGATCCCAATTA
1 GTTTGCATTTACATGATCCCAATTA
9196 GTTTGCATTTACATGATCCCAATTA
1 GTTTGCATTTACATGATCCCAATTA
9221 GT
1 GT
9223 AATCGAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (25 bp):
GTTTGCATTTACATGATCCCAATTA
Done.