Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023730.1 Corchorus olitorius cultivar O-4 contig23763, 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: 29513
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1043 original size:41 final size:41
Alignment explanation
Indices: 955--1049 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
945 TGTTTCCGTG
* *
955 TTCAATATGGTCCCTAATTTAGGATTCTATTTACTATTTGA
1 TTCAATTTGGTCCCTAATTTAGGATTCTAGTTACTATTTGA
** * *
996 CACAATTTAGTCCCTGATTTAGGATTCTAGTTACTATTTGA
1 TTCAATTTGGTCCCTAATTTAGGATTCTAGTTACTATTTGA
1037 TTCAATTTGGTCC
1 TTCAATTTGGTCC
1050 TTATTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (41 bp):
TTCAATTTGGTCCCTAATTTAGGATTCTAGTTACTATTTGA
Found at i:4943 original size:15 final size:16
Alignment explanation
Indices: 4912--4951 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
4902 TTGCTTTGTT
4912 TTGTTTTCTAATTTAA
1 TTGTTTTCTAATTTAA
*
4928 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAATTTAA
4943 TTGTTTTCT
1 TTGTTTTCT
4952 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAATTTAA
Found at i:6178 original size:15 final size:16
Alignment explanation
Indices: 6158--6197 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
6148 AGAGGTTGAG
6158 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
6173 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
6189 AGAAAACAA
1 AGAAAACAA
6198 AACAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:13602 original size:15 final size:15
Alignment explanation
Indices: 13584--13613 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13574 TTTTTTTTTA
13584 GTTTAATTGTTTTCT
1 GTTTAATTGTTTTCT
13599 GTTTAATTGTTTTCT
1 GTTTAATTGTTTTCT
13614 TTCAACCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
GTTTAATTGTTTTCT
Found at i:17862 original size:87 final size:87
Alignment explanation
Indices: 17716--17892 Score: 336
Period size: 87 Copynumber: 2.0 Consensus size: 87
17706 ACATGATCCC
*
17716 TCATGAACCTCCTCCATGATTTTTCTGGCCTCTGTTGAGCATACACATCTGAGCAATGTTTGATC
1 TCATGAACCTCCTCCATGATTTTTCTGGCCTATGTTGAGCATACACATCTGAGCAATGTTTGATC
17781 TCGACTTTTCTTGTACAAGATG
66 TCGACTTTTCTTGTACAAGATG
*
17803 TCATGAACCTCCTCCATGATTTTTCTGGCCTATGTTGAGCATACACATCTGAGCAATGTTTGATT
1 TCATGAACCTCCTCCATGATTTTTCTGGCCTATGTTGAGCATACACATCTGAGCAATGTTTGATC
17868 TCGACTTTTCTTGTACAAGATG
66 TCGACTTTTCTTGTACAAGATG
17890 TCA
1 TCA
17893 CCTTCTAACA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (87 bp):
TCATGAACCTCCTCCATGATTTTTCTGGCCTATGTTGAGCATACACATCTGAGCAATGTTTGATC
TCGACTTTTCTTGTACAAGATG
Found at i:21946 original size:35 final size:35
Alignment explanation
Indices: 21866--22075 Score: 176
Period size: 34 Copynumber: 5.8 Consensus size: 35
21856 AAAATGCTTT
* * *
21866 TTGATGGGAACTTTCCCACTTTTGAAAACTAAAGCTGAAA
1 TTGATGGGAACTTTCCCA-ATTTAAAAACTAAA----AAC
* * *
21906 ATGATGGGAACTTTCCCTAAATTGAAAACT-AAAAC
1 TTGATGGGAACTTTCCC-AATTTAAAAACTAAAAAC
*
21941 TTGATGGGAACTCTCCCAATTTAAAAACTTTGAAAAAC
1 TTGATGGGAACTTTCCCAATTTAAAAAC--T-AAAAAC
* * *
21979 TAG-TGGGAAC-CTCCCAATTTTAAAACTTAAAAAC
1 TTGATGGGAACTTTCCCAATTTAAAAAC-TAAAAAC
*
22013 TTGTTGGGAACTTTCCCAATTTAAAAACT-AAAAC
1 TTGATGGGAACTTTCCCAATTTAAAAACTAAAAAC
* * *
22047 CTGGTGGGAACTTTCCCAATTTGAAAACT
1 TTGATGGGAACTTTCCCAATTTAAAAACT
22076 TCAAAGCCTG
Statistics
Matches: 147, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
34 48 0.33
35 27 0.18
36 30 0.20
37 7 0.05
38 7 0.05
39 2 0.01
40 25 0.17
41 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (35 bp):
TTGATGGGAACTTTCCCAATTTAAAAACTAAAAAC
Found at i:26454 original size:36 final size:36
Alignment explanation
Indices: 26415--27001 Score: 238
Period size: 36 Copynumber: 16.5 Consensus size: 36
26405 ACTGAAGAAT
**
26415 TGAAAAAAGACCACCCTGGATCATTCTGAAATAAGT
1 TGAAAAAAGACCACCCTGGATCATTCTGAAATAAAC
** * *
26451 TGAAGCAAGACCACCCTGGGTCACT-TGAAATAAAC
1 TGAAAAAAGACCACCCTGGATCATTCTGAAATAAAC
* * * * *
26486 TGAAAAAATGATCACCCTCGATCATTCCGACACAAAC
1 TGAAAAAA-GACCACCCTGGATCATTCTGAAATAAAC
* *
26523 T-AAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
1 TGAAA-AAAGACCACCCTGGATCATTCTGAAATAAAC
* * * * **
26558 T-AAAGAACGACCACCCTCGATCATTCCGAACTGGAC
1 TGAAA-AAAGACCACCCTGGATCATTCTGAAATAAAC
* * * * *
26594 TGAGGAACA-ACCACCCTCGATCATT-TCGACACAAAC
1 TGA-AAAAAGACCACCCTGGATCATTCT-GAAATAAAC
* * *
26630 TGAAGAAAGACCACCCTGGGTCGA-T-TGAACTAAAC
1 TGAAAAAAGACCACCCTGGATC-ATTCTGAAATAAAC
* *
26665 TGAAGAAAAGACAACCCTGGGTCGA--CT-AACATAAAC
1 TGAA-AAAAGACCACCCTGGATC-ATTCTGAA-ATAAAC
* * * ** *
26701 TGAAGAAACGACCACCTTGGGTCGA--CTGTCATAGAC
1 TGAA-AAAAGACCACCCTGGATC-ATTCTGAAATAAAC
* * * * * *
26737 TGAAGAAAAAACCGCTCTGGGT--TGACTAAAATAAAC
1 TGAA-AAAAGACCACCCTGGATCAT-TCTGAAATAAAC
* * *
26773 TGAAGAAAGACCACCCTGGGTCGA-T-TGAAATTAAC
1 TGAAAAAAGACCACCCTGGATC-ATTCTGAAATAAAC
* * *
26808 TGAAGAAAGACCGCCCTGGGTCGA--CTGAAATAAAC
1 TGAAAAAAGACCACCCTGGATC-ATTCTGAAATAAAC
* * * * **
26843 TGAAGAACGACCACCCTGGGTCA-ACTGACTTAAAC
1 TGAAAAAAGACCACCCTGGATCATTCTGAAATAAAC
*
26878 TGAAGAAGAGACCACCCT-GAGTCGA-T-TGAAATAAAC
1 TGAA-AAAAGACCACCCTGGA-TC-ATTCTGAAATAAAC
* * * *
26914 T-AAAGAACGACCATCCTGGGTC--GCTGAAATAAAC
1 TGAAA-AAAGACCACCCTGGATCATTCTGAAATAAAC
* * * *
26948 TGAAGAAAGACCGCCCTGGGTCA-ACTGAAATAAAC
1 TGAAAAAAGACCACCCTGGATCATTCTGAAATAAAC
* *
26983 TGAAGAAAGACCGCCCTGG
1 TGAAAAAAGACCACCCTGG
27002 GTCAACTAAA
Statistics
Matches: 427, Mismatches: 95, Indels: 59
0.73 0.16 0.10
Matches are distributed among these distances:
34 27 0.06
35 188 0.44
36 196 0.46
37 15 0.04
38 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (36 bp):
TGAAAAAAGACCACCCTGGATCATTCTGAAATAAAC
Found at i:26559 original size:35 final size:35
Alignment explanation
Indices: 26415--27153 Score: 554
Period size: 35 Copynumber: 20.9 Consensus size: 35
26405 ACTGAAGAAT
* * * **
26415 TGAAAAAAGACCACCCTGGATCATTCTGAAATAAGT
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
*
26451 TGAAGCAAGACCACCCTGGGTC-ACTTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
* * * * * * * *
26486 TGAAAAAATGATCACCCTCGATCATTCCGACACAAAC
1 TGAAGAAA-GACCACCCTGGGTCA-ACTGAAATAAAC
*
26523 TAAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * * * * **
26558 TAAAGAACGACCACCCTCGATCATTCCGAACTGGAC
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
* * * ** * *
26594 TGAGGAACA-ACCACCCTCGATCATTTCGACACAAAC
1 TGAAGAA-AGACCACCCTGGGTCAACT-GAAATAAAC
* * *
26630 TGAAGAAAGACCACCCTGGGTCGATTGAACTAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
26665 TGAAGAAAAGACAACCCTGGGTCGACT-AACATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAA-ATAAAC
* * ** *
26701 TGAAGAAACGACCACCTTGGGTCGACTGTCATAGAC
1 TGAAGAAA-GACCACCCTGGGTCAACTGAAATAAAC
* * * ** *
26737 TGAAGAAAAAACCGCTCTGGGTTGACTAAAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
26773 TGAAGAAAGACCACCCTGGGTCGATTGAAATTAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
26808 TGAAGAAAGACCGCCCTGGGTCGACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* **
26843 TGAAGAACGACCACCCTGGGTCAACTGACTTAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
26878 TGAAGAAGAGACCACCCTGAGTCGATTGAAATAAAC
1 TGAAGAA-AGACCACCCTGGGTCAACTGAAATAAAC
* * * *
26914 TAAAGAACGACCATCCTGGGTC-GCTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
*
26948 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
26983 TGAAGAAAGACCGCCCTGGGTCAACT-AAATTAAAT
1 TGAAGAAAGACCACCCTGGGTCAACTGAAA-TAAAC
* * * *
27018 TGAAGAAAGACCGCCCTAGGTCAACTAAAATAGAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * * *
27053 TGAAGAATGATCGCCCTGGATCAACTTAAAAACAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATA-AAC
* * * **
27089 TGAATAAAGACCGCCCTGGGTCTACTGAAATTTAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
27124 TAAATG-GAGACCGCCCTGGGTCAACTGAAA
1 TGAA-GAAAGACCACCCTGGGTCAACTGAAA
27154 CTTTGAACAT
Statistics
Matches: 561, Mismatches: 123, Indels: 39
0.78 0.17 0.05
Matches are distributed among these distances:
34 32 0.06
35 286 0.51
36 226 0.40
37 16 0.03
38 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.18
Consensus pattern (35 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
Found at i:28506 original size:7 final size:7
Alignment explanation
Indices: 28463--28505 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
28453 TCTTATACCT
28463 TTTTCAA
1 TTTTCAA
28470 TTTTCAA
1 TTTTCAA
28477 TTTTC-A
1 TTTTCAA
28483 TTTTC-A
1 TTTTCAA
*
28489 CTTTCAA
1 TTTTCAA
28496 TTTTC-A
1 TTTTCAA
28502 TTTT
1 TTTT
28506 TTTTTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 16 0.48
7 17 0.52
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63
Consensus pattern (7 bp):
TTTTCAA
Found at i:28835 original size:14 final size:14
Alignment explanation
Indices: 28813--28845 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28803 TGAAAACAAA
28813 TTTTG-GAAACCAT
1 TTTTGAGAAACCAT
*
28826 TTTTGAGAAATCAT
1 TTTTGAGAAACCAT
28840 TTTTGA
1 TTTTGA
28846 AAAATCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (14 bp):
TTTTGAGAAACCAT
Done.