Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010510.1 Corchorus olitorius cultivar O-4 contig10542, 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: 12493
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:1881 original size:22 final size:20
Alignment explanation
Indices: 1853--1924 Score: 56
Period size: 22 Copynumber: 3.4 Consensus size: 20
1843 ACTATGAAAA
1853 TTGATAATCTCATTATGAAATT
1 TTGATAA-CTCA-TATGAAATT
* * *
1875 TTGATAAGCTCCCTACGAAAAT
1 TTGATAA-CT-CATATGAAATT
*
1897 TTGATAAC-CACACTGAAATT
1 TTGATAACTCATA-TGAAATT
1917 TTGATAAC
1 TTGATAAC
1925 CACACAGAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 1 0.03
22 23 0.57
23 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (20 bp):
TTGATAACTCATATGAAATT
Found at i:1936 original size:22 final size:21
Alignment explanation
Indices: 1891--1969 Score: 106
Period size: 22 Copynumber: 3.7 Consensus size: 21
1881 AGCTCCCTAC
*
1891 GAAAATTTGATAACCACAC-T
1 GAAATTTTGATAACCACACGT
*
1911 GAAATTTTGATAACCACACAGA
1 GAAATTTTGATAACCACAC-GT
1933 GAAATTTTGATAACCACACTGT
1 GAAATTTTGATAACCACAC-GT
*
1955 GAAATTTTGAAAACC
1 GAAATTTTGATAACC
1970 TCAGACACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
20 18 0.35
22 34 0.65
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.27
Consensus pattern (21 bp):
GAAATTTTGATAACCACACGT
Found at i:3418 original size:22 final size:22
Alignment explanation
Indices: 3388--3443 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3378 GGAGGTTATA
* * *
3388 AAAAATTCATATTGTGGTTACC
1 AAAATTTCATATTGCGCTTACC
* *
3410 CAAATTTCATAATGCGCTTACC
1 AAAATTTCATATTGCGCTTACC
3432 AAAATTTCATAT
1 AAAATTTCATAT
3444 GAAGGTTATC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
AAAATTTCATATTGCGCTTACC
Found at i:3456 original size:22 final size:22
Alignment explanation
Indices: 3431--3502 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
3421 ATGCGCTTAC
*
3431 CAAAATTTCATATGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
3453 CAAAATTT-ATAGGGATTAGGTTA-
1 CAAAATTTCATA-GGA--AGGTTAT
*
3476 CTAAAATTTCAAAGGAAGGTTAT
1 C-AAAATTTCATAGGAAGGTTAT
3499 CAAA
1 CAAA
3503 TTTTTCTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
21 3 0.07
22 19 0.45
23 2 0.05
24 16 0.38
25 2 0.05
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:3653 original size:22 final size:21
Alignment explanation
Indices: 3628--3678 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
3618 AAAAAAAGAA
*
3628 TCATAGGAAAGTTATTAAAATT
1 TCATAGG-AAGTTATCAAAATT
**
3650 TCATAGTGTGGTTATCAAAATT
1 TCATAG-GAAGTTATCAAAATT
3672 TCATAGG
1 TCATAGG
3679 GAGGCTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (21 bp):
TCATAGGAAGTTATCAAAATT
Found at i:3687 original size:22 final size:22
Alignment explanation
Indices: 3644--3690 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3634 GAAAGTTATT
* * *
3644 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGGGAGGCTATC
3666 AAAATTTCATAGGGAGGCTATC
1 AAAATTTCATAGGGAGGCTATC
3688 AAA
1 AAA
3691 GAGGTTATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGCTATC
Found at i:3741 original size:22 final size:22
Alignment explanation
Indices: 3691--3750 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3681 GGCTATCAAA
*
3691 GAGGTTATCAAAATTCCATAGC
1 GAGGTTATCAAAATTTCATAGC
* *
3713 GAGGTTATCAGAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGC
*
3735 GTA-GTTACCAAAATTT
1 G-AGGTTATCAAAATTT
3751 TCAGAATTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGC
Found at i:3755 original size:31 final size:31
Alignment explanation
Indices: 3720--3781 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3710 AGCGAGGTTA
3720 TCAGAATTTCATAGTGTAGTTACCAAAATTT
1 TCAGAATTTCATAGTGTAGTTACCAAAATTT
*
3751 TCAGAATTTCATAGTGTGGTTACCAAAATTT
1 TCAGAATTTCATAGTGTAGTTACCAAAATTT
3782 CATAGTAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (31 bp):
TCAGAATTTCATAGTGTAGTTACCAAAATTT
Found at i:3812 original size:28 final size:29
Alignment explanation
Indices: 3776--3830 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
3766 GTGGTTACCA
3776 AAATTTCATA-GTAATGTTAT-AAAATTCT
1 AAATTTCATATG-AATGTTATCAAAATTCT
3804 AAATTTCATATGAATGTTATCAAAATT
1 AAATTTCATATGAATGTTATCAAAATT
3831 TTATAGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (29 bp):
AAATTTCATATGAATGTTATCAAAATTCT
Found at i:3845 original size:50 final size:51
Alignment explanation
Indices: 3646--3852 Score: 152
Period size: 53 Copynumber: 3.9 Consensus size: 51
3636 AAGTTATTAA
* * * * *
3646 AATTTCATAGTGTGGTTATCAAAATTTCATAGGGAGGCTATCAAAGAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAAAATTTCATAGTG-TGTTAT-AAA-A--TTCTCAG
* * * * * *
3702 AATTCCATAGCGAGGTTATCAGAATTTCATAGTGTAGTTACCAAAATTTTCAG
1 AATTTCATAGTGTGGTTATCAAAATTTCATAGTGT-GTTA-TAAAATTCTCAG
* *
3755 AATTTCATAGTGTGGTTACCAAAATTTCATAGTAATGTTATAAAATTCT-A-
1 AATTTCATAGTGTGGTTATCAAAATTTCATAGT-GTGTTATAAAATTCTCAG
*
3805 AATTTCATA-TGAAT-GTTATCAAAATTTTATAGTGTGGTTATCAAAATT
1 AATTTCATAGTG--TGGTTATCAAAATTTCATAGTGT-GTTAT-AAAATT
3853 TCATCAGGAA
Statistics
Matches: 123, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
49 3 0.02
50 31 0.25
51 8 0.07
52 7 0.06
53 37 0.30
54 1 0.01
55 1 0.01
56 35 0.28
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (51 bp):
AATTTCATAGTGTGGTTATCAAAATTTCATAGTGTGTTATAAAATTCTCAG
Found at i:3977 original size:22 final size:22
Alignment explanation
Indices: 3804--4204 Score: 140
Period size: 22 Copynumber: 18.1 Consensus size: 22
3794 ATAAAATTCT
* *
3804 AAATTTCATATGAATGTTATCA
1 AAATTTCATAGGAAGGTTATCA
* *
3826 AAATTTTATAGTG-TGGTTATCA
1 AAATTTCATAG-GAAGGTTATCA
**
3848 AAATTTCATCAGGAA-GCAATCA
1 AAATTTCAT-AGGAAGGTTATCA
* *
3870 AAATCTCATAGAGTA-GTTATCA
1 AAATTTCATAG-GAAGGTTATCA
* ** *
3892 AAAATTCATAGAGATCATATTACCA
1 AAATTTCATAG-GA--AGGTTATCA
*
3917 AAATTGCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
* *
3939 AAA-TTCATAATG-CGGTTATCA
1 AAATTTCAT-AGGAAGGTTATCA
3960 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
* * * * *
3982 GAATATCACAGTG-TGATTA-CTA
1 AAATTTCATAG-GAAGGTTATC-A
* * *
4004 AGATTTCATAGGGAGGTTATAAA
1 AAATTTCATAGGAAGGTTAT-CA
* * *
4027 AAATATCATAGTG-TGCTTA-CGA
1 AAATTTCATAG-GAAGGTTATC-A
* *
4049 ACATTTCACATGGATA--TTATCA
1 AAATTTCATA-GGA-AGGTTATCA
* * * *
4071 AAATTTTATAGTAATGTTTTCA
1 AAATTTCATAGGAAGGTTATCA
* * *
4093 AAATTTTATAGGGAGGTTAACA
1 AAATTTCATAGGAAGGTTATCA
* * * **
4115 AAATTTCATAGGGATGTTCTTG
1 AAATTTCATAGGAAGGTTATCA
* * * *
4137 AAATTTGATAGGAATGTTTTCG
1 AAATTTCATAGGAAGGTTATCA
* * ***
4159 AAATTGCATAGTATCATTATCA
1 AAATTTCATAGGAAGGTTATCA
* *
4181 AAATTTCATAGAAATGTTATCA
1 AAATTTCATAGGAAGGTTATCA
4203 AA
1 AA
4205 GGTTTATAAG
Statistics
Matches: 275, Mismatches: 81, Indels: 46
0.68 0.20 0.11
Matches are distributed among these distances:
20 1 0.00
21 23 0.08
22 213 0.77
23 20 0.07
24 4 0.01
25 14 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
AAATTTCATAGGAAGGTTATCA
Found at i:4022 original size:44 final size:45
Alignment explanation
Indices: 3962--4056 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
3952 GGTTATCAAA
* * * *
3962 ATTTCATAGGAAGGTTAT-CAGAATATCACAGTGTGATTACTAAG
1 ATTTCATAGGAAGGTTATAAAAAATATCACAGTGTGATTACGAAC
* * *
4006 ATTTCATAGGGAGGTTATAAAAAATATCATAGTGTGCTTACGAAC
1 ATTTCATAGGAAGGTTATAAAAAATATCACAGTGTGATTACGAAC
4051 ATTTCA
1 ATTTCA
4057 CATGGATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 17 0.40
45 26 0.60
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (45 bp):
ATTTCATAGGAAGGTTATAAAAAATATCACAGTGTGATTACGAAC
Found at i:9409 original size:40 final size:41
Alignment explanation
Indices: 9327--9410 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
9317 GATTTTTAAG
** * * *
9327 AAACCTTATAACGTTACTAAAAAAATCTTATATGATTTCTA
1 AAACCTTATAAAATTAATAAAAAAATCTTATAAGATTACTA
*
9368 AAACCTTATAAAATTAATAAAAAAA-CTTTTAAGATTACTA
1 AAACCTTATAAAATTAATAAAAAAATCTTATAAGATTACTA
9408 AAA
1 AAA
9411 GAGTTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 15 0.41
41 22 0.59
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (41 bp):
AAACCTTATAAAATTAATAAAAAAATCTTATAAGATTACTA
Found at i:9789 original size:21 final size:21
Alignment explanation
Indices: 9733--9795 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
9723 TCAAAACTTC
* * *
9733 AAAAAAACTTATTAAGTTACT
1 AAAAAATCTTACTAAGTTATT
9754 AAAAAATC-TACTAAGCTTATT
1 AAAAAATCTTACTAAG-TTATT
*
9775 AAAAGATCTTA-TAAGATTATT
1 AAAAAATCTTACTAAG-TTATT
9796 TTTAAAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.17
21 27 0.77
22 2 0.06
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAAAATCTTACTAAGTTATT
Found at i:9856 original size:23 final size:23
Alignment explanation
Indices: 9823--9869 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
9813 AAAAGGTGTT
*
9823 AAAAAATTTATAAGATTATTAAA
1 AAAAAACTTATAAGATTATTAAA
*
9846 AAAAAACTTATAAGGTTATTAAA
1 AAAAAACTTATAAGATTATTAAA
9869 A
1 A
9870 GTGCTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (23 bp):
AAAAAACTTATAAGATTATTAAA
Found at i:12453 original size:37 final size:37
Alignment explanation
Indices: 12412--12482 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
12402 GTTAGTTATA
* *
12412 CCCCGTGCTTAGTAGTCAGCTACTCATTTATGTATTC
1 CCCCGTGCTTAGTAGTCACCTACTCAATTATGTATTC
12449 CCCCGTGCTTAGTAGTCACCTACTCAATTATGTA
1 CCCCGTGCTTAGTAGTCACCTACTCAATTATGTA
12483 CCCCCCCCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.35
Consensus pattern (37 bp):
CCCCGTGCTTAGTAGTCACCTACTCAATTATGTATTC
Done.