Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023093.1 Corchorus olitorius cultivar O-4 contig23126, 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: 22931
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Found at i:64 original size:15 final size:15
Alignment explanation
Indices: 44--78 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
34 GAATGTTTTT
*
44 TTGCTTTGCTTGATG
1 TTGCTTTGCATGATG
59 TTGCTTTGCATGATG
1 TTGCTTTGCATGATG
74 TTGCT
1 TTGCT
79 GCACTGCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.26, T:0.51
Consensus pattern (15 bp):
TTGCTTTGCATGATG
Found at i:1269 original size:27 final size:27
Alignment explanation
Indices: 1239--1311 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 27
1229 CAGCTTCTTT
1239 GAATTGTCTTCCAATTCAATCTTCTGG
1 GAATTGTCTTCCAATTCAATCTTCTGG
* **
1266 GAATCGTCTTCCGAA-TCAA-CTTCTTT
1 GAATTGTCTTCC-AATTCAATCTTCTGG
*
1292 GAATTGTCTTCCAATCCAAT
1 GAATTGTCTTCCAATTCAAT
1312 ATTAAAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 2 0.05
26 19 0.50
27 15 0.39
28 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (27 bp):
GAATTGTCTTCCAATTCAATCTTCTGG
Found at i:1391 original size:51 final size:51
Alignment explanation
Indices: 1288--1568 Score: 483
Period size: 51 Copynumber: 5.5 Consensus size: 51
1278 GAATCAACTT
* * * *
1288 CTTTGAATTGTCTTCCAATCCAATATT-AAAAGGACCGTCTCCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* *
1338 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCTGCTCATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
*
1389 CTTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1440 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1491 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
*
1542 CTTTGAACTGTCATCCAATTCAATCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT
1569 GAGAAAATCA
Statistics
Matches: 219, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
50 24 0.11
51 195 0.89
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (51 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
Found at i:1929 original size:64 final size:64
Alignment explanation
Indices: 1796--2030 Score: 310
Period size: 64 Copynumber: 3.6 Consensus size: 64
1786 CCGGTGCATC
* * * * * * * * *
1796 TCTTAACAAGATCGTCTTCCGATCAACTTTTGAAAATTTTTGAAAAAAAACATCTTCTAGCGTAC
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAACTCTTG--AGAAACCATCTTCTGGTGTAC
1861 T
64 T
* *
1862 TCTTGACAAGATCATCTTCCGATTAT-TTCTGAAAAACTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTG-AAAACTCTTGAGAAACCATCTTCTGGTGTACT
1926 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * *
1990 TCTTGACAAGATCGTCTTCCGATCAACATCTGAAAATTCTT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAACTCTT
2031 TCTAACAAAC
Statistics
Matches: 151, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
64 112 0.74
65 9 0.06
66 30 0.20
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
Found at i:4094 original size:12 final size:12
Alignment explanation
Indices: 4077--4101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4067 TTTGATTCAC
4077 TTTTGATTTGAA
1 TTTTGATTTGAA
4089 TTTTGATTTGAA
1 TTTTGATTTGAA
4101 T
1 T
4102 CACTTGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TTTTGATTTGAA
Found at i:4417 original size:14 final size:13
Alignment explanation
Indices: 4388--4446 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 13
4378 TAAAAGACTC
4388 AAAACCTTTT-TG
1 AAAACCTTTTCTG
4400 AAAACCTATTTCTG
1 AAAACCT-TTTCTG
4414 AAAACCTTTTCTTG
1 AAAACCTTTTC-TG
*
4428 AAAACAATTTTCTTG
1 AAAAC-CTTTTC-TG
4443 AAAA
1 AAAA
4447 ACGTCTCTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
12 7 0.17
13 7 0.17
14 16 0.38
15 12 0.29
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (13 bp):
AAAACCTTTTCTG
Found at i:5677 original size:44 final size:42
Alignment explanation
Indices: 5602--5691 Score: 108
Period size: 44 Copynumber: 2.1 Consensus size: 42
5592 TTACCTATGC
** * *
5602 ATGAACATATATACAAAGGGATGGATAATGCATGATGAATGT
1 ATGAACATATATACAAAGACATGGACAATGCATGAAGAATGT
* *
5644 ATGAACATATATGTACAAAGACATGGACCATGCATGAAGGATGT
1 ATGAACATATA--TACAAAGACATGGACAATGCATGAAGAATGT
5688 ATGA
1 ATGA
5692 CAAATATCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
42 11 0.28
44 29 0.73
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.24
Consensus pattern (42 bp):
ATGAACATATATACAAAGACATGGACAATGCATGAAGAATGT
Found at i:7298 original size:30 final size:33
Alignment explanation
Indices: 7263--7349 Score: 117
Period size: 36 Copynumber: 2.6 Consensus size: 33
7253 ATTTTATTAA
7263 TTTCCAAAATCTTCTTTTGGA-T-TT-CTTTAT
1 TTTCCAAAATCTTCTTTTGGATTATTACTTTAT
*
7293 TTTCCAAAATCTTCTTTTGGAATTAGCTTATTTTAT
1 TTTCCAAAATCTTCTTTTGG-ATTA--TTACTTTAT
7329 TTTCCAAAATCTTCTTTTGGA
1 TTTCCAAAATCTTCTTTTGGA
7350 GTTGCTAAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
30 20 0.40
31 1 0.02
32 1 0.02
35 3 0.06
36 25 0.50
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.53
Consensus pattern (33 bp):
TTTCCAAAATCTTCTTTTGGATTATTACTTTAT
Found at i:7422 original size:24 final size:25
Alignment explanation
Indices: 7394--7442 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
7384 CCTTGAAATC
7394 TCTTTTT-ATTTTCTGAT-TTTTTCT
1 TCTTTTTGATTTT-TGATCTTTTTCT
7418 TCTTTTTGATTTTTGATCTTTTTCT
1 TCTTTTTGATTTTTGATCTTTTTCT
7443 ATCTCTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.08, C:0.12, G:0.06, T:0.73
Consensus pattern (25 bp):
TCTTTTTGATTTTTGATCTTTTTCT
Found at i:8029 original size:41 final size:41
Alignment explanation
Indices: 7979--8349 Score: 399
Period size: 41 Copynumber: 9.1 Consensus size: 41
7969 CTAAAACCAT
* *
7979 GGACCAAATTGAATCAAATAGTAACTAAAATCCTAAATCAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
* * *
8020 GGACTAAATTGCATCAAATAGTAAATAAAACCCTAAATTAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
*
8061 GGACTAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
*
8102 GGACCAAATTGCATTAAATAGTAAATAAAATCCTAAATCAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
* *
8143 GGACCAAATTGCATTAAATAGTAAACAAAATCCTAAATCAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
* * * * ** * *
8184 GGACAAAATTGCATTAATTAATAAAT-TGAT-TTGAAATTAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCT-AAATCAG
*** *
8224 GGACCAAGCCGCAT-AAATTA-AAAATAAAATCCTAAATCAG
1 GGACCAAATTGCATCAAA-TAGTAAATAAAATCCTAAATCAG
* * * * * * *
8264 GGGCGAAATTGAATTAATTAATAAATGAAATCCTAAATCAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
* * * * *
8305 GGACAAAATTGAATCAATTAATAAATGAAATCCTAAATCAG
1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
8346 GGAC
1 GGAC
8350 TAAGGTGAAA
Statistics
Matches: 284, Mismatches: 40, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
39 7 0.02
40 38 0.13
41 239 0.84
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.24
Consensus pattern (41 bp):
GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
Found at i:12581 original size:15 final size:15
Alignment explanation
Indices: 12561--12595 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12551 GAATGTTTTT
*
12561 TTGCTTTGCTTGATG
1 TTGCTTTGCATGATG
12576 TTGCTTTGCATGATG
1 TTGCTTTGCATGATG
12591 TTGCT
1 TTGCT
12596 GCACTGCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.26, T:0.51
Consensus pattern (15 bp):
TTGCTTTGCATGATG
Found at i:13495 original size:27 final size:26
Alignment explanation
Indices: 13453--13551 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 26
13443 AGTGGACTTA
**
13453 AAATGACCAACGTGCCCCTGAATACAC
1 AAATGACCAAAATGCCCCTGAATA-AC
* * **
13480 AAATGACCAGAATGCCCTTAGTGTAA-
1 AAATGACCAAAATGCCCCT-GAATAAC
* *
13506 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAATA-AC
*
13533 GAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
13552 AGGTGACCCT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
25 2 0.04
26 17 0.30
27 34 0.61
28 3 0.05
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.17
Consensus pattern (26 bp):
AAATGACCAAAATGCCCCTGAATAAC
Found at i:14946 original size:52 final size:52
Alignment explanation
Indices: 14885--14990 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
14875 TATACCTTAT
* *
14885 ATACTATGCAAGGTATATATTATGCATTTTCTCTTTTCATGTCAAGTTCCCA
1 ATACTATGCAAGGTATATACTATGCATTTTCTATTTTCATGTCAAGTTCCCA
14937 ATACTATGCAAGGTATATACTATGCATTTTCTATTTTCATGTCAAGTTCCCA
1 ATACTATGCAAGGTATATACTATGCATTTTCTATTTTCATGTCAAGTTCCCA
14989 AT
1 AT
14991 TCAGTAATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (52 bp):
ATACTATGCAAGGTATATACTATGCATTTTCTATTTTCATGTCAAGTTCCCA
Found at i:18643 original size:60 final size:59
Alignment explanation
Indices: 18559--19044 Score: 405
Period size: 60 Copynumber: 8.1 Consensus size: 59
18549 CATTTTGCCA
* *
18559 ACTCTGTTGTTTTCCTTGGCGCTCTGTATTTTGGCAACGCTGCTCTTGTTCATGTTGCTG
1 ACTCTGTTGTTTTCCTT-GCGCTCTATATTTTGGCGACGCTGCTCTTGTTCATGTTGCTG
* *
18619 ACTCTGTTGTATTTCC-TGCTGCTCTATATTTCGGC-ACCGCTGCTCTTGTTCATGTTGTTG
1 ACTCTGTTGT-TTTCCTTGC-GCTCTATATTTTGGCGA-CGCTGCTCTTGTTCATGTTGCTG
* * *
18679 ACTCT-TCTGCTCTTTTCCCTGACGCTCTATATTCTGGCGACGCTGCTCTTGTTCTTGTTGCTG
1 ACTCTGT-TG---TTTTCCTTG-CGCTCTATATTTTGGCGACGCTGCTCTTGTTCATGTTGCTG
* *** * * * * * *
18742 ACTCTGCTCCATTCCTTGGAGCTCTATAATTCGGTGGTC-CTGCCCTTGTTCATGTTGCTG
1 ACTCTGTTGTTTTCCTT-GCGCTCTATATTTTGG-CGACGCTGCTCTTGTTCATGTTGCTG
* * *
18802 ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGCG--GC-GCTCTTGTTCATGTCGCTG
1 ACTCTGTTGTTTTCCTT-GCGCTCTATATTTTGGCGACGCTGCTCTTGTTCATGTTGCTG
* * * *
18859 ACTCTGTTGTTTTTCATTGCTCTCTACATTAATTCGGCGGTC-CTGCTCTTGTTCATGTTGCTG
1 ACTCTGTTG-TTTTCCTTGCGCTCTATATT--TT-GGC-GACGCTGCTCTTGTTCATGTTGCTG
* * * *
18922 ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGCGGCGCTGCTCTTGTTCATGTCGCTG
1 ACTCTGTTGTTTTCCTT-GCGCTCTATATTTTGGCGACGCTGCTCTTGTTCATGTTGCTG
* * * * * * * *
18982 ACT-TCGTTGTTTTTCATTGCTCTCTACATTTTGGGGGCTCTGCTCTTGTTCATATCGCTG
1 ACTCT-GTTG-TTTTCCTTGCGCTCTATATTTTGGCGACGCTGCTCTTGTTCATGTTGCTG
19042 ACT
1 ACT
19045 TTGCTGATTC
Statistics
Matches: 347, Mismatches: 53, Indels: 52
0.77 0.12 0.12
Matches are distributed among these distances:
57 35 0.10
58 7 0.02
59 10 0.03
60 185 0.53
61 17 0.05
62 12 0.03
63 79 0.23
64 2 0.01
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (59 bp):
ACTCTGTTGTTTTCCTTGCGCTCTATATTTTGGCGACGCTGCTCTTGTTCATGTTGCTG
Found at i:18892 original size:120 final size:119
Alignment explanation
Indices: 18559--19044 Score: 491
Period size: 123 Copynumber: 4.0 Consensus size: 119
18549 CATTTTGCCA
* * * * *
18559 ACTCTGTTGTTTTCCTTGGCGCTCTGTATTTTGGCAACGCTGCTCTTGTTCATGTTGCTGACTCT
1 ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGCAGCGCTGCTCTTGTTCATGTCGCTGACTCT
* * * *** *
18624 GTTGTATTTC-CTGCTGCTCTATATTTCGGCACCGCTGCTCTTGTTCATGTTGTTG
66 GTTGTTTTTCATTGCT-CTCTATAATTCGGGGTC-CTGCTCTTGTTCATGTTGCTG
* * * * * * *
18679 ACTCTTCTGCTCTTTTCCCTGACGCTCTATATTCTGGC-GACGCTGCTCTTGTTCTTGTTGCTGA
1 ACTCTT-T--TGTTGTCCTTGGCGCTCTATATTTTGGCAG-CGCTGCTCTTGTTCATGTCGCTGA
* *** * ** *
18743 CTCTGCT-CCATTCCTTGGAGCTCTATAATTCGGTGGTCCTGCCCTTGTTCATGTTGCTG
62 CTCTGTTGTTTTTCATT-GCTCTCTATAATTCGG-GGTCCTGCTCTTGTTCATGTTGCTG
18802 ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGC-G-GC-GCTCTTGTTCATGTCGCTGACTCT
1 ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGCAGCGCTGCTCTTGTTCATGTCGCTGACTCT
18864 GTTGTTTTTCATTGCTCTCTACATTAATTCGGCGGTCCTGCTCTTGTTCATGTTGCTG
66 GTTGTTTTTCATTGCTCTCT--A-TAATTCGG-GGTCCTGCTCTTGTTCATGTTGCTG
*
18922 ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGCGGCGCTGCTCTTGTTCATGTCGCTGACT-T
1 ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGCAGCGCTGCTCTTGTTCATGTCGCTGACTCT
* * * * * *
18986 CGTTGTTTTTCATTGCTCTCTACATTTTGGGGGCTCTGCTCTTGTTCATATCGCTG
66 -GTTGTTTTTCATTGCTCTCTATAATTCGGGGTC-CTGCTCTTGTTCATGTTGCTG
19042 ACT
1 ACT
19045 TTGCTGATTC
Statistics
Matches: 307, Mismatches: 43, Indels: 32
0.80 0.11 0.08
Matches are distributed among these distances:
117 29 0.09
118 7 0.02
119 4 0.01
120 123 0.40
121 3 0.01
122 7 0.02
123 132 0.43
124 2 0.01
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (119 bp):
ACTCTTTTGTTGTCCTTGGCGCTCTATATTTTGGCAGCGCTGCTCTTGTTCATGTCGCTGACTCT
GTTGTTTTTCATTGCTCTCTATAATTCGGGGTCCTGCTCTTGTTCATGTTGCTG
Found at i:20015 original size:45 final size:45
Alignment explanation
Indices: 19966--20078 Score: 217
Period size: 45 Copynumber: 2.5 Consensus size: 45
19956 TGCAGTGTTA
*
19966 ATCCCTTGGCCGCCAGAGGTTTGCTTTGCTTGGACACCGGTATTG
1 ATCCCTTGGCCGCCTGAGGTTTGCTTTGCTTGGACACCGGTATTG
20011 ATCCCTTGGCCGCCTGAGGTTTGCTTTGCTTGGACACCGGTATTG
1 ATCCCTTGGCCGCCTGAGGTTTGCTTTGCTTGGACACCGGTATTG
20056 ATCCCTTGGCCGCCTGAGGTTTG
1 ATCCCTTGGCCGCCTGAGGTTTG
20079 GACCTTTTCT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.12, C:0.27, G:0.29, T:0.32
Consensus pattern (45 bp):
ATCCCTTGGCCGCCTGAGGTTTGCTTTGCTTGGACACCGGTATTG
Found at i:20019 original size:21 final size:21
Alignment explanation
Indices: 19994--20064 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
19984 GTTTGCTTTG
19994 CTTGGACACCGGTATTGATCC
1 CTTGGACACCGGTATTGATCC
* * * **
20015 CTTGGCCGCCTGAGGT-TTGCTTTG
1 CTTGGACACC---GGTATTG-ATCC
20039 CTTGGACACCGGTATTGATCC
1 CTTGGACACCGGTATTGATCC
20060 CTTGG
1 CTTGG
20065 CCGCCTGAGG
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 17 0.49
22 3 0.09
23 3 0.09
24 12 0.34
ACGTcount: A:0.13, C:0.27, G:0.28, T:0.32
Consensus pattern (21 bp):
CTTGGACACCGGTATTGATCC
Done.