Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012729.1 Corchorus olitorius cultivar O-4 contig12762, 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: 83730
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4135 original size:76 final size:76
Alignment explanation
Indices: 3998--4148 Score: 182
Period size: 76 Copynumber: 2.0 Consensus size: 76
3988 ACAAGGACCC
* *
3998 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
4063 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
4074 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
4136 GATGGGCTGTGTC
63 GATGGGCAGTGTC
4149 TTAGCTCATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:9135 original size:25 final size:24
Alignment explanation
Indices: 9107--9163 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
9097 GTCGATTGTA
* *
9107 AAATAAATTGAATAATTAAGATATT
1 AAATAAATTGAAGAATTAA-ACATT
*
9132 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
9156 AAA-AAATT
1 AAATAAATT
9164 CAAGGCTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 7 0.24
25 17 0.59
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:10111 original size:30 final size:30
Alignment explanation
Indices: 10075--10131 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
10065 ATATTCGAAA
*
10075 AATAAGGATATGATAGACGATTCAAAAATT
1 AATAAGGATATAATAGACGATTCAAAAATT
*
10105 AATAAGGATATAATAGGCGATTCAAAA
1 AATAAGGATATAATAGACGATTCAAAA
10132 GTTTTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (30 bp):
AATAAGGATATAATAGACGATTCAAAAATT
Found at i:16844 original size:3 final size:3
Alignment explanation
Indices: 16838--16874 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16828 ATAATAACTC
16838 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16875 ACACTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21565 original size:29 final size:29
Alignment explanation
Indices: 21522--21600 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
21512 GCCTTTTTAA
*
21522 AGAGTTCAGGTGCTTATTTGGCTGCAATT
1 AGAGTTCAGGGGCTTATTTGGCTGCAATT
21551 AGAGTTCAGGGGCTTATTTGGCTGCAATT
1 AGAGTTCAGGGGCTTATTTGGCTGCAATT
*
21580 AGAATTCAGGGGCTTATTTGG
1 AGAGTTCAGGGGCTTATTTGG
21601 TCGTTTTGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (29 bp):
AGAGTTCAGGGGCTTATTTGGCTGCAATT
Found at i:25168 original size:24 final size:26
Alignment explanation
Indices: 25130--25178 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
25120 TTTGCGCCAC
*
25130 CTTCTTCTCCTTGTATGGAGATTTCT
1 CTTCTTCTCCTTGTAAGGAGATTTCT
*
25156 CTTCTT-T-CTTGTAAGGAGTTTTC
1 CTTCTTCTCCTTGTAAGGAGATTTC
25179 CATGAGCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 1 0.05
26 6 0.29
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.51
Consensus pattern (26 bp):
CTTCTTCTCCTTGTAAGGAGATTTCT
Found at i:27431 original size:10 final size:11
Alignment explanation
Indices: 27406--27435 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
27396 TTGTTTTCTG
27406 TTTTTGTTTCA
1 TTTTTGTTTCA
27417 TTTTTGTTTCA
1 TTTTTGTTTCA
27428 TTTTTGTT
1 TTTTTGTT
27436 ACGTTGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.07, G:0.10, T:0.77
Consensus pattern (11 bp):
TTTTTGTTTCA
Found at i:28524 original size:19 final size:18
Alignment explanation
Indices: 28500--28535 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28490 TGAAGACTTA
28500 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
28519 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
28536 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:29138 original size:11 final size:11
Alignment explanation
Indices: 29122--29147 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29112 AGATAATTTC
29122 TTTTCTTCTAG
1 TTTTCTTCTAG
29133 TTTTCTTCTAG
1 TTTTCTTCTAG
29144 TTTT
1 TTTT
29148 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:32435 original size:4 final size:4
Alignment explanation
Indices: 32416--32562 Score: 63
Period size: 4 Copynumber: 37.0 Consensus size: 4
32406 ATATTAAAGC
* * * *
32416 TATT TATC TA-T TATT TATT TA-C TATT CATCT T-TT TATT TATT AATT
1 TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TATT
** * * ** **
32462 TAGC TA-T TATC TATT TATTT TTTT TACC TACC TATT TATCT T-TT TATT
1 TATT TATT TATT TATT TA-TT TATT TATT TATT TATT TAT-T TATT TATT
* * * *
32510 TATC TATT ATTTT TACT TATT T-TT ATATT TATT TATT TATT TATT TATC
1 TATT TATT -TATT TATT TATT TATT -TATT TATT TATT TATT TATT TATT
32559 TATT
1 TATT
32563 ACCTTTTTTT
Statistics
Matches: 105, Mismatches: 27, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
3 12 0.11
4 82 0.78
5 11 0.10
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.66
Consensus pattern (4 bp):
TATT
Found at i:32463 original size:27 final size:27
Alignment explanation
Indices: 32426--32481 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
32416 TATTTATCTA
* *
32426 TTATTTATTTA-CTATTCATCTTTTTAT
1 TTATTAATTTAGCTATT-ATCTATTTAT
32453 TTATTAATTTAGCTATTATCTATTTAT
1 TTATTAATTTAGCTATTATCTATTTAT
32480 TT
1 TT
32482 TTTTTACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATTAATTTAGCTATTATCTATTTAT
Found at i:32562 original size:12 final size:12
Alignment explanation
Indices: 32416--32562 Score: 80
Period size: 12 Copynumber: 13.0 Consensus size: 12
32406 ATATTAAAGC
32416 TATTTATCTA-T
1 TATTTATCTATT
* *
32427 TATTTATTTA-C
1 TATTTATCTATT
* *
32438 TATTCATCTTTT
1 TATTTATCTATT
32450 TATTTAT-TAATT
1 TATTTATCT-ATT
** *
32462 TAGCTAT-TATC
1 TATTTATCTATT
32473 TATTTAT-T-TT
1 TATTTATCTATT
* **
32483 T-TTTACCTACC
1 TATTTATCTATT
*
32494 TATTTATCTTTT
1 TATTTATCTATT
32506 TATTTATCTA-T
1 TATTTATCTATT
*
32517 TATTT-T-TACT
1 TATTTATCTATT
* *
32527 TATTTTTATATT
1 TATTTATCTATT
*
32539 TATTTATTTATT
1 TATTTATCTATT
32551 TATTTATCTATT
1 TATTTATCTATT
32563 ACCTTTTTTT
Statistics
Matches: 102, Mismatches: 26, Indels: 15
0.71 0.18 0.10
Matches are distributed among these distances:
9 6 0.06
10 10 0.10
11 33 0.32
12 53 0.52
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.66
Consensus pattern (12 bp):
TATTTATCTATT
Found at i:36669 original size:21 final size:21
Alignment explanation
Indices: 36645--36695 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
36635 ATCCAACATC
36645 TGAGGCAGGCACAGGAAGAAA
1 TGAGGCAGGCACAGGAAGAAA
* ** * *
36666 TGAGACATTCGCAGGAAGAGA
1 TGAGGCAGGCACAGGAAGAAA
36687 TGAGGCAGG
1 TGAGGCAGG
36696 AAAAAGGTGT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.39, T:0.10
Consensus pattern (21 bp):
TGAGGCAGGCACAGGAAGAAA
Found at i:40243 original size:4 final size:4
Alignment explanation
Indices: 40236--40269 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
40226 TTTCATTCAC
40236 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
40270 TCCTTTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:46684 original size:53 final size:53
Alignment explanation
Indices: 46592--46825 Score: 409
Period size: 53 Copynumber: 4.5 Consensus size: 53
46582 TAAAACCTGA
* *
46592 TGGGAACTTTCACAATTT-AAAAAAGAGCTAAATTGAATACTTCGAAGACTGG
1 TGGGAACTTTCCCAATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
*
46644 TGGGAACTTTCCCAATTTGAAAAAAGAGCTAAATTGAATACTTTTAAGACTGG
1 TGGGAACTTTCCCAATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
*
46697 TGGGAACTTTCCCAATTTG-AAAAAGAGCTAGATTGAATACTTTGAAGACTGG
1 TGGGAACTTTCCCAATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
*
46749 TGGGAACTTTCCCAATTTGAAAAAAGAGCTAGATTGAATACTTTGAAGACTGG
1 TGGGAACTTTCCCAATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
46802 TGGGAACTTTCCCAATTTGAAAAA
1 TGGGAACTTTCCCAATTTGAAAAA
46826 CTAAAACTTG
Statistics
Matches: 175, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
52 67 0.38
53 108 0.62
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (53 bp):
TGGGAACTTTCCCAATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
Found at i:46703 original size:105 final size:105
Alignment explanation
Indices: 46592--46825 Score: 414
Period size: 105 Copynumber: 2.2 Consensus size: 105
46582 TAAAACCTGA
* *
46592 TGGGAACTTTCACAATTTAAAAAAGAGCTAAATTGAATACTTCGAAGACTGGTGGGAACTTTCCC
1 TGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTCGAAGACTGGTGGGAACTTTCCC
*
46657 AATTTGAAAAAAGAGCTAAATTGAATACTTTTAAGACTGG
66 AATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
* *
46697 TGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAGACTGGTGGGAACTTTCCC
1 TGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTCGAAGACTGGTGGGAACTTTCCC
*
46762 AATTTGAAAAAAGAGCTAGATTGAATACTTTGAAGACTGG
66 AATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
46802 TGGGAACTTTCCCAATTTGAAAAA
1 TGGGAACTTTCCCAATTTGAAAAA
46826 CTAAAACTTG
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 123 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (105 bp):
TGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTCGAAGACTGGTGGGAACTTTCCC
AATTTGAAAAAAGAGCTAAATTGAATACTTTGAAGACTGG
Found at i:46921 original size:127 final size:128
Alignment explanation
Indices: 46749--46994 Score: 338
Period size: 127 Copynumber: 1.9 Consensus size: 128
46739 TGAAGACTGG
* *
46749 TGGGAACTTTCCCAATTTGAAAAAAGAGCTAGATTGAATACTTTGAAGACTGGTGGGAACTTTCC
1 TGGGAACTTTCCCAATTT-AAAAAAGAGCTAGATTGAATACTTTGAAAACTGATGGGAACTTTCC
46814 CAATTTGAAAAACTAAAACTTGAA-A-ATGACGGGAACTTTCCCTAAATTGAAAACTAAAACCCG
65 CAATTTGAAAAACTAAAA-TTGAATACATGACGGGAACTTTCCC-AAATTGAAAACTAAAACCCG
46877 A
128 A
* * *
46878 TGGGAACTTTCCCAATTT-AAAAAGAGCT-GATTTGAATACTTTGAAAATTGATTGGAACTTTTC
1 TGGGAACTTTCCCAATTTAAAAAAGAGCTAGA-TTGAATACTTTGAAAACTGATGGGAACTTTCC
* * * *
46941 CAATTTGAAAAACTTAAATTGAATACTTTGATGGGAACTTTCCCAATTTGAAAA
65 CAATTTGAAAAACTAAAATTGAATAC-ATGACGGGAACTTTCCCAAATTGAAAA
46995 ACTTGAAGTG
Statistics
Matches: 104, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
126 7 0.07
127 55 0.53
128 9 0.09
129 33 0.32
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (128 bp):
TGGGAACTTTCCCAATTTAAAAAAGAGCTAGATTGAATACTTTGAAAACTGATGGGAACTTTCCC
AATTTGAAAAACTAAAATTGAATACATGACGGGAACTTTCCCAAATTGAAAACTAAAACCCGA
Found at i:50216 original size:33 final size:33
Alignment explanation
Indices: 50174--50286 Score: 97
Period size: 33 Copynumber: 3.3 Consensus size: 33
50164 GGTAAGTACC
50174 TAAGTAATGATCAAGAGGAAAAAGGATTTAATT
1 TAAGTAATGATCAAGAGGAAAAAGGATTTAATT
* *** * *
50207 TAAGTAATGATTAATGAGGGCTCAAGG--GTAAGTACC
1 TAAGTAATGATCAA-GA-GGAAAAAGGATTTAA-T--T
50243 TAAGTAATGATCAAGAGGAAAAAGGATTTGAA-T
1 TAAGTAATGATCAAGAGGAAAAAGGATTT-AATT
50276 TAAGTAATGAT
1 TAAGTAATGAT
50287 TAATGACCCA
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
33 27 0.45
34 9 0.15
35 8 0.13
36 14 0.23
37 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.24, T:0.27
Consensus pattern (33 bp):
TAAGTAATGATCAAGAGGAAAAAGGATTTAATT
Found at i:50246 original size:69 final size:68
Alignment explanation
Indices: 50156--50292 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 68
50146 AAATAAACAT
*
50156 GGGCTTAAGGTAAGTACCTAAGTAATGATCAAGAGGAAAAAGGATTT-AATTTAAGTAATGATTA
1 GGGCTCAAGGTAAGTACCTAAGTAATGATCAAGAGGAAAAAGGATTTGAA-TTAAGTAATGATTA
50220 ATGA
65 ATGA
50224 GGGCTCAAGGGTAAGTACCTAAGTAATGATCAAGAGGAAAAAGGATTTGAATTAAGTAATGATTA
1 GGGCTCAA-GGTAAGTACCTAAGTAATGATCAAGAGGAAAAAGGATTTGAATTAAGTAATGATTA
50289 ATGA
65 ATGA
50293 CCCAGAGGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
68 7 0.11
69 57 0.86
70 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (68 bp):
GGGCTCAAGGTAAGTACCTAAGTAATGATCAAGAGGAAAAAGGATTTGAATTAAGTAATGATTAA
TGA
Found at i:52231 original size:21 final size:22
Alignment explanation
Indices: 52207--52247 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52197 AACAAAAGAG
*
52207 AAAAATAATTTTTTT-TATCGC
1 AAAAACAATTTTTTTATATCGC
*
52228 AAAACCAATTTTTTTATATC
1 AAAAACAATTTTTTTATATC
52248 AATTTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAAACAATTTTTTTATATCGC
Found at i:53194 original size:31 final size:31
Alignment explanation
Indices: 53158--53219 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
53148 CACCAAAGGA
53158 TTAGAAGTATTAAGAATTTAGCTACTCATGG
1 TTAGAAGTATTAAGAATTTAGCTACTCATGG
53189 TTAGAAGTATTAAGAATTTAGCTACTCATGG
1 TTAGAAGTATTAAGAATTTAGCTACTCATGG
53220 ATTTAGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (31 bp):
TTAGAAGTATTAAGAATTTAGCTACTCATGG
Found at i:57558 original size:54 final size:54
Alignment explanation
Indices: 57475--57892 Score: 404
Period size: 54 Copynumber: 7.7 Consensus size: 54
57465 TTTTGTAGAA
* * *
57475 AGTTCATCATCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAA
1 AGTTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAG
* * * *
57529 AGTTGATCCTCAGATGATCTAGTGAGGTCAGTCCAAGAAGTTTACAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAG
* * * * * *
57583 AGTTGATCCTTAGATAATCTAATGCAGTCATTCCAAGATGTTTTCAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAG
* * * *
57637 AGTTGATCCTCAGATGATCTAGTGCGGTCATTCCGAGAAGTTTCCGAA-GTTCAG
1 AGTTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AATGATCAG
* * * **
57691 AGTTGAT-GTCCAGACGATCCAGTGCGGTCCTTCTGAGAAGTTTTCGAA-GATCAG
1 AGTTGATCCT-CAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AATGATCAG
* * **
57745 AGTTGAT-CTCCAGATGATCC-GATGCGATCCTTTGAAGAAGTTTTCGAA-GATCAG
1 AGTTGATCCT-CAGATGATCCAG-TGCGGTCATTCCAAGAAGTTTTC-AATGATCAG
* **
57799 AGTTGATTCC-CAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTTGATGATCAG
1 AGTTGA-TCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAG
* *
57853 AGTTGAT-CTCCA-ATTTGATCCAATGTGGTCATTCCAAGAA
1 AGTTGATCCT-CAGA--TGATCCAGTGCGGTCATTCCAAGAA
57893 AAGTTTGCGT
Statistics
Matches: 309, Mismatches: 44, Indels: 21
0.83 0.12 0.06
Matches are distributed among these distances:
52 1 0.00
53 5 0.02
54 276 0.89
55 26 0.08
56 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (54 bp):
AGTTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAG
Found at i:59823 original size:27 final size:27
Alignment explanation
Indices: 59786--59842 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
59776 TATTTATCTA
* **
59786 TTATTTATTTA-CTATTTATCTTTTTAT
1 TTATTAATTTAGCTA-TTATCTGCTTAT
59813 TTATTAATTTAGCTATTATCTGCTTAT
1 TTATTAATTTAGCTATTATCTGCTTAT
59840 TTA
1 TTA
59843 CTATTATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.25, C:0.09, G:0.04, T:0.63
Consensus pattern (27 bp):
TTATTAATTTAGCTATTATCTGCTTAT
Found at i:59848 original size:18 final size:19
Alignment explanation
Indices: 59819--59859 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
59809 TTATTTATTA
*
59819 ATTTAGCTATTATCTGCTT
1 ATTTAGCTATTATCTACTT
59838 ATTTA-CTATTATCTACTT
1 ATTTAGCTATTATCTACTT
59856 ATTT
1 ATTT
59860 TTTTTACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTTAGCTATTATCTACTT
Found at i:59945 original size:12 final size:12
Alignment explanation
Indices: 59896--59957 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
59886 TCTATATACC
* *
59896 TATTTGTCTTTT
1 TATTTTTCTATT
*
59908 TATTTATCTA-T
1 TATTTTTCTATT
*
59919 TA-TTTT-TACT
1 TATTTTTCTATT
59929 TATTTTTCTATT
1 TATTTTTCTATT
59941 TATTTATT-TATT
1 TATTT-TTCTATT
59953 TATTT
1 TATTT
59958 ATTTATCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 2 0.05
10 6 0.14
11 7 0.17
12 25 0.60
13 2 0.05
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (12 bp):
TATTTTTCTATT
Found at i:59946 original size:4 final size:4
Alignment explanation
Indices: 59906--59968 Score: 65
Period size: 4 Copynumber: 15.5 Consensus size: 4
59896 TATTTGTCTT
* * *
59906 TTTA TTTA TCTA TTATT TTTA CTTA TTT- TTCTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA
*
59955 TTTA TTTA TCTA TT
1 TTTA TTTA TTTA TT
59969 ACATTTTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 2 0.04
4 41 0.85
5 5 0.10
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:64527 original size:19 final size:18
Alignment explanation
Indices: 64503--64538 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
64493 TGAAGACCAT
64503 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
64522 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
64539 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:67725 original size:19 final size:17
Alignment explanation
Indices: 67693--67729 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
67683 TTGAAATAAT
67693 TCTTCAAAATCTTCAAA
1 TCTTCAAAATCTTCAAA
67710 TCTTCAAATTATCTTCAAA
1 TCTTCAAA--ATCTTCAAA
67729 T
1 T
67730 GAGTCTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCTTCAAAATCTTCAAA
Found at i:70962 original size:22 final size:23
Alignment explanation
Indices: 70937--70984 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
70927 CGGCCTGGCG
70937 CGGGGC-ATGGCC-GAGTCATGAC
1 CGGGGCTATGGCCTG-GTCATGAC
*
70959 C-GGGCTGTGGCCTGGTCATGAC
1 CGGGGCTATGGCCTGGTCATGAC
70981 CGGG
1 CGGG
70985 TGCCACCGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 4 0.18
22 15 0.68
23 3 0.14
ACGTcount: A:0.12, C:0.27, G:0.44, T:0.17
Consensus pattern (23 bp):
CGGGGCTATGGCCTGGTCATGAC
Done.