Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018913.1 Corchorus olitorius cultivar O-4 contig18946, 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: 97992
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:322 original size:6 final size:6
Alignment explanation
Indices: 304--339 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
294 GTTTGGACTT
*
304 ATATAG TATATAG ATATAG ATATAG ATATAT ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATA
340 AAATATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (6 bp):
ATATAG
Found at i:439 original size:25 final size:25
Alignment explanation
Indices: 405--461 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 25
395 TCACACCAAT
405 ACCAGAAAAAAAAAAGTTTGTTCAC
1 ACCAGAAAAAAAAAAGTTTGTTCAC
*
430 ACCAG--AAAAATAAGTTTGTTCAC
1 ACCAGAAAAAAAAAAGTTTGTTCAC
*
453 ACCATAAAA
1 ACCAGAAAA
462 CCCTCTCCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 21 0.75
25 7 0.25
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.21
Consensus pattern (25 bp):
ACCAGAAAAAAAAAAGTTTGTTCAC
Found at i:2902 original size:11 final size:10
Alignment explanation
Indices: 2883--2911 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2873 ATCACCAGCC
2883 AATAAAAAAA
1 AATAAAAAAA
2893 AATAAAAAAA
1 AATAAAAAAA
2903 AATAAAAAA
1 AATAAAAAA
2912 CTCATGCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:8959 original size:299 final size:299
Alignment explanation
Indices: 8421--9019 Score: 1162
Period size: 299 Copynumber: 2.0 Consensus size: 299
8411 TGTCAACCAA
8421 GCGTACACTTTCAAACACTTCACGATCAGGCAATGTATCAAGTCTAGACAAAGCTATCTCTAGTA
1 GCGTACACTTTCAAACACTTCACGATCAGGCAATGTATCAAGTCTAGACAAAGCTATCTCTAGTA
8486 TCTCCATAAAGTTTATTTACATCACAGGCTGGTAACTTAGTATATCAGCCAAGTCAAAACAGACA
66 TCTCCATAAAGTTTATTTACATCACAGGCTGGTAACTTAGTATATCAGCCAAGTCAAAACAGACA
*
8551 AGTTGCTGTTCTCCAGCTCTAAAACTTTAACCAGGCTAGTAAACACCTCAGCTATCTTAAATGGA
131 AGTTGCTGTTCTCCAGCTCTAAAACTTTAACCAGGCTAGCAAACACCTCAGCTATCTTAAATGGA
8616 TATATATCAGCTCTGATATGGTATGGGTCTAAGCATCTGACGCATCTGCTGGGTCAGAGTTTTGG
196 TATATATCAGCTCTGATATGGTATGGGTCTAAGCATCTGACGCATCTGCTGGGTCAGAGTTTTGG
* *
8681 TTTGAAGAGTCAGATATCAAGAGTAGCATACAAACACGG
261 TTTGAAGAGTCAGATATAAAGAGTAGCACACAAACACGG
8720 GCGTACACTTTCAAACACTTCACGATCAGGCAATGTATCAAGTCTAGACAAAGCTATCTCTAGTA
1 GCGTACACTTTCAAACACTTCACGATCAGGCAATGTATCAAGTCTAGACAAAGCTATCTCTAGTA
*
8785 TCTCCATAAGGTTTATTTACATCACAGGCTGGTAACTTAGTATATCAGCCAAGTCAAAACAGACA
66 TCTCCATAAAGTTTATTTACATCACAGGCTGGTAACTTAGTATATCAGCCAAGTCAAAACAGACA
8850 AGTTGCTGTTCTCCAGCTCTAAAACTTTAACCAGGCTAGCAAACACCTCAGCTATCTTAAATGGA
131 AGTTGCTGTTCTCCAGCTCTAAAACTTTAACCAGGCTAGCAAACACCTCAGCTATCTTAAATGGA
8915 TATATATCAGCTCTGATATGGTATGGGTCTAAGCATCTGACGCATCTGCTGGGTCAGAGTTTTGG
196 TATATATCAGCTCTGATATGGTATGGGTCTAAGCATCTGACGCATCTGCTGGGTCAGAGTTTTGG
8980 TTTGAAGAGTCAGATATAAAGAGTAGCACACAAACACGG
261 TTTGAAGAGTCAGATATAAAGAGTAGCACACAAACACGG
9019 G
1 G
9020 AATATTTTTG
Statistics
Matches: 296, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
299 296 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (299 bp):
GCGTACACTTTCAAACACTTCACGATCAGGCAATGTATCAAGTCTAGACAAAGCTATCTCTAGTA
TCTCCATAAAGTTTATTTACATCACAGGCTGGTAACTTAGTATATCAGCCAAGTCAAAACAGACA
AGTTGCTGTTCTCCAGCTCTAAAACTTTAACCAGGCTAGCAAACACCTCAGCTATCTTAAATGGA
TATATATCAGCTCTGATATGGTATGGGTCTAAGCATCTGACGCATCTGCTGGGTCAGAGTTTTGG
TTTGAAGAGTCAGATATAAAGAGTAGCACACAAACACGG
Found at i:17961 original size:24 final size:26
Alignment explanation
Indices: 17906--17965 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 26
17896 CACTTATAAT
17906 ATGAAAAACAGAAATCTGACAAGGAAA
1 ATGAAAAACAGAAATCT-ACAAGGAAA
* *
17933 ATGAAAAACATAAA-CT-CAATGAAA
1 ATGAAAAACAGAAATCTACAAGGAAA
17957 ATGAAAAAC
1 ATGAAAAAC
17966 TAGGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 16 0.52
26 2 0.06
27 13 0.42
ACGTcount: A:0.62, C:0.12, G:0.13, T:0.13
Consensus pattern (26 bp):
ATGAAAAACAGAAATCTACAAGGAAA
Found at i:19720 original size:42 final size:43
Alignment explanation
Indices: 19669--19762 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
19659 AGTGCATTAC
* * *
19669 CTAA-ATTCTA-CTCCGTCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
19710 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
19755 CTAATATT
1 CTAATATT
19763 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:25973 original size:27 final size:27
Alignment explanation
Indices: 25942--25994 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
25932 CAAGACAACC
* *
25942 AAAAACCCATACACCACCTTTTCCAAT
1 AAAAACACATACACCACCTTTGCCAAT
* *
25969 AAAAATACATACGCCACCTTTGCCAA
1 AAAAACACATACACCACCTTTGCCAA
25995 ACTTTTCATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.34, G:0.04, T:0.21
Consensus pattern (27 bp):
AAAAACACATACACCACCTTTGCCAAT
Found at i:28785 original size:5 final size:5
Alignment explanation
Indices: 28775--28805 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
28765 AACTTCCCTC
*
28775 TCCTT TCCTT TCCTT TCCTT CCCTT TCCTT T
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT T
28806 AATTACTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (5 bp):
TCCTT
Found at i:32181 original size:2 final size:2
Alignment explanation
Indices: 32174--32240 Score: 68
Period size: 2 Copynumber: 34.5 Consensus size: 2
32164 CGACCGAATA
* *
32174 AT AT AT AT AT AT A- AA AT A- AT AT AT AT TT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
32213 AT CT GAT AT TT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT A
32241 AATAATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
1 3 0.06
2 50 0.93
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33014 original size:70 final size:70
Alignment explanation
Indices: 32940--33100 Score: 313
Period size: 70 Copynumber: 2.3 Consensus size: 70
32930 GTGGCTGACC
32940 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
1 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
33005 GGTTG
66 GGTTG
33010 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
1 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
33075 GGTTG
66 GGTTG
*
33080 AATTTGGTTTCTTATTTTCTT
1 AATTTGTTTTCTTATTTTCTT
33101 CAATTCTCTG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 90 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (70 bp):
AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
GGTTG
Found at i:33653 original size:25 final size:27
Alignment explanation
Indices: 33613--33667 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
33603 AAATGTTAAA
*
33613 TCAATTGTTATATTCTGAATTTCTT-T
1 TCAATTGTAATATTCTGAATTTCTTAT
33639 TCAATTG-AATATTCTGAATTTCTTAT
1 TCAATTGTAATATTCTGAATTTCTTAT
33665 TCA
1 TCA
33668 TTCTGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (27 bp):
TCAATTGTAATATTCTGAATTTCTTAT
Found at i:38493 original size:12 final size:12
Alignment explanation
Indices: 38476--38509 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38466 TAATTAAATA
*
38476 ATAATTATTCTT
1 ATAATTATTATT
38488 ATAATTATTATT
1 ATAATTATTATT
*
38500 ATTATTATTA
1 ATAATTATTA
38510 AGAGGAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:46609 original size:22 final size:22
Alignment explanation
Indices: 46032--46619 Score: 236
Period size: 22 Copynumber: 26.6 Consensus size: 22
46022 TACATAGGAA
*
46032 GGTTATCAAAATTTAATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * *
46054 GGTTACCGAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGTG-T
*
46076 GGTTATCAAAACTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* **
46098 AGTTATCAAAATTTCATAAGAAT
1 GGTTATCAAAATTTCAT-AGTGT
* ****
46121 -GTTACCAAAATTTCATAAAAA
1 GGTTATCAAAATTTCATAGTGT
* * *
46142 GGTTATCAAAATTTCTTAGGGA
1 GGTTATCAAAATTTCATAGTGT
*
46164 GGTTAAC-AAATTTCATACGAT-T
1 GGTTATCAAAATTTCATA-G-TGT
* *
46186 -GTTATCGAAATTTTATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* **
46207 GGTTATCAAAATCTCATAAG-AA
1 GGTTATCAAAATTTCAT-AGTGT
* * * *
46229 GGTTAACAAAATTTCATCGGGA
1 GGTTATCAAAATTTCATAGTGT
46251 GGAAATTTATCAAAA--T--T--TGT
1 GG----TTATCAAAATTTCATAGTGT
* * * * *
46271 GCTTATTAAAATTTCCTAGGGA
1 GGTTATCAAAATTTCATAGTGT
* * * *
46293 CGTTAACAAAATTTCATTGTGA
1 GGTTATCAAAATTTCATAGTGT
* * * *
46315 GGTTATAAAAATTTTA-AGGAGA
1 GGTTATCAAAATTTCATA-GTGT
* * *
46337 GGTTATCAAAATTACATAGAGA
1 GGTTATCAAAATTTCATAGTGT
* * * *
46359 GGATATCACAGTTTCATTCTCATAGAGA
1 GGTTATCA-A----AATT-TCATAGTGT
* *
46387 GGTTATCAAAATTTTATGGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
46409 GATTATCAAAATTTTCATAGTGC
1 GGTTATCAAAA-TTTCATAGTGT
* * *
46432 AGTTA-C-CAATTTTATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * *
46452 GATTATCAAAATTTCATAGAGA
1 GGTTATCAAAATTTCATAGTGT
* ** ** *
46474 GATTATCAAAATTTCGCACCGA
1 GGTTATCAAAATTTCATAGTGT
46496 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
46518 GGTTATCAAAATTTCACAGTAT
1 GGTTATCAAAATTTCATAGTGT
* * *
46540 GGTTATCAAATTTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGT
** * *
46562 GGTTATTGAAATTTCATAATGA
1 GGTTATCAAAATTTCATAGTGT
* *
46584 GGTTATTAAATTTTCACT-GTGT
1 GGTTATCAAAATTTCA-TAGTGT
*
46606 GGTTATCAATATTT
1 GGTTATCAAAATTT
46620 ATACGTTGGA
Statistics
Matches: 422, Mismatches: 111, Indels: 66
0.70 0.19 0.11
Matches are distributed among these distances:
16 8 0.02
18 1 0.00
20 16 0.04
21 25 0.06
22 320 0.76
23 24 0.06
24 1 0.00
26 8 0.02
27 4 0.01
28 15 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:48230 original size:19 final size:19
Alignment explanation
Indices: 48193--48230 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
48183 ATTTCTTTAT
* *
48193 TATTATATTTTTAATCAAA
1 TATTATATTTTAAAACAAA
48212 TATTATATTTTAAAACAAA
1 TATTATATTTTAAAACAAA
48231 CATTTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTATATTTTAAAACAAA
Found at i:52717 original size:32 final size:34
Alignment explanation
Indices: 52679--52886 Score: 114
Period size: 31 Copynumber: 6.3 Consensus size: 34
52669 AAAGGGGGTG
**
52679 ACGCCTCCCACATTGGATTG-AAGGGG-GGCGTA
1 ACGCCTCCCACATTACATTGTAAGGGGAGGCGTA
52711 ACGCCTCCCCACATTACATTGTTAAGGGGAGGCGTA
1 ACGCCT-CCCACATTACATTG-TAAGGGGAGGCGTA
* * *
52747 ACGCCTCCC-CAATTAAATTGTCA--GG-GGCGTG
1 ACGCCTCCCAC-ATTACATTGTAAGGGGAGGCGTA
* * * *
52778 ACGCCTCCC-CAATTAAATTGTTAAGGGGGGGCCTC
1 ACGCCTCCCAC-ATTACATTG-TAAGGGGAGGCGTA
* * * *
52813 ATGCCTCCCA-ATTAAATTGTGA-GGG-GGCGTG
1 ACGCCTCCCACATTACATTGTAAGGGGAGGCGTA
* * * * *
52844 ACACCTCCCCAAATTATATTGTTAGGGG-GGCGTC
1 ACGCCT-CCCACATTACATTGTAAGGGGAGGCGTA
*
52878 ATGCCTCCC
1 ACGCCTCCC
52887 CACTTAAATT
Statistics
Matches: 144, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
31 33 0.23
32 17 0.12
33 27 0.19
34 26 0.18
35 29 0.20
36 12 0.08
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (34 bp):
ACGCCTCCCACATTACATTGTAAGGGGAGGCGTA
Found at i:52776 original size:31 final size:32
Alignment explanation
Indices: 52702--52953 Score: 175
Period size: 34 Copynumber: 7.6 Consensus size: 32
52692 TGGATTGAAG
*
52702 GGGGGCGTAACGCCTCCCCACATTACATTGTTAA
1 GGGGGCGTAACGCCTCCCCA-ATTAAATTG-TAA
*
52736 GGGGAGGCGTAACGCCTCCCCAATTAAATTGTCA
1 -GGG-GGCGTAACGCCTCCCCAATTAAATTGTAA
*
52770 -GGGGCGTGACGCCTCCCCAATTAAATTGTTAA
1 GGGGGCGTAACGCCTCCCCAATTAAATTG-TAA
* * * *
52802 GGGGGGGCCTCATGCCT-CCCAATTAAATTGTGA
1 --GGGGGCGTAACGCCTCCCCAATTAAATTGTAA
* * * *
52835 GGGGGCGTGACACCTCCCCAAATTATATTGTTAG
1 GGGGGCGTAACGCCTCCCC-AATTAAATTG-TAA
* * * **
52869 GGGGGCGTCATGCCTCCCCACTTAAATTGTGT
1 GGGGGCGTAACGCCTCCCCAATTAAATTGTAA
* ** * *
52901 GGGGGCGTGACGTGTCCCCAAATTTGAATGGTTAA
1 GGGGGCGTAACGCCTCCCC-AA-TTAAATTG-TAA
* *
52936 GGGGGCGTCATGCCTCCC
1 GGGGGCGTAACGCCTCCC
52954 AACCCCAATT
Statistics
Matches: 171, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
31 36 0.21
32 23 0.13
33 20 0.12
34 38 0.22
35 37 0.22
36 17 0.10
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGGGCGTAACGCCTCCCCAATTAAATTGTAA
Found at i:52820 original size:66 final size:66
Alignment explanation
Indices: 52703--52953 Score: 285
Period size: 66 Copynumber: 3.8 Consensus size: 66
52693 GGATTGAAGG
* * * * *
52703 GGGGCGTAACGCCTCCCCACATTACATTGTTAAGGGGAGGCGTAACGCCTCCCCAATTAAATTGT
1 GGGGCGTGACGCCTCCCCAAATTAAATTGTTAAGGGG-GGCGTCATGCCTCCCCAATTAAATTGT
52768 CA
65 CA
*
52770 GGGGCGTGACGCCTCCCC-AATTAAATTGTTAAGGGGGGGCCTCATGCCT-CCCAATTAAATTGT
1 GGGGCGTGACGCCTCCCCAAATTAAATTGTTAA-GGGGGGCGTCATGCCTCCCCAATTAAATTGT
*
52833 GA
65 CA
* * *
52835 GGGGGCGTGACACCTCCCCAAATTATATTGTT-AGGGGGGCGTCATGCCTCCCCACTTAAATTGT
1 -GGGGCGTGACGCCTCCCCAAATTAAATTGTTAAGGGGGGCGTCATGCCTCCCCAATTAAATTGT
**
52899 GTG
65 -CA
** * *
52902 GGGGCGTGACGTGTCCCCAAATTTGAATGGTTAA-GGGGGCGTCATGCCTCCC
1 GGGGCGTGACGCCTCCCCAAA-TTAAATTGTTAAGGGGGGCGTCATGCCTCCC
52954 AACCCCAATT
Statistics
Matches: 158, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
65 30 0.19
66 70 0.44
67 57 0.36
68 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (66 bp):
GGGGCGTGACGCCTCCCCAAATTAAATTGTTAAGGGGGGCGTCATGCCTCCCCAATTAAATTGTC
A
Found at i:52885 original size:34 final size:33
Alignment explanation
Indices: 52700--52953 Score: 205
Period size: 35 Copynumber: 7.6 Consensus size: 33
52690 ATTGGATTGA
* *
52700 AGGGGGGCGTAACGCCTCCCCACATTACATTGTT
1 AGGGGGGCGTCACGCCTCCCCA-ATTAAATTGTT
* *
52734 AAGGGGAGGCGTAACGCCTCCCCAATTAAATTGTC
1 -AGGGG-GGCGTCACGCCTCCCCAATTAAATTGTT
*
52769 A--GGGGCGTGACGCCTCCCCAATTAAATTGTT
1 AGGGGGGCGTCACGCCTCCCCAATTAAATTGTT
* * *
52800 AAGGGGGGGCCTCATGCCT-CCCAATTAAATTGTG
1 -A-GGGGGGCGTCACGCCTCCCCAATTAAATTGTT
* * *
52834 A-GGGGGCGTGACACCTCCCCAAATTATATTGTT
1 AGGGGGGCGTCACGCCTCCCC-AATTAAATTGTT
* *
52867 AGGGGGGCGTCATGCCTCCCCACTTAAATTG-T
1 AGGGGGGCGTCACGCCTCCCCAATTAAATTGTT
* ** * *
52899 -GTGGGGGCGTGACGTGTCCCCAAATTTGAATGGTT
1 AG-GGGGGCGTCACGCCTCCCC-AA-TTAAATTGTT
* *
52934 AAGGGGGCGTCATGCCTCCC
1 AGGGGGGCGTCACGCCTCCC
52954 AACCCCAATT
Statistics
Matches: 175, Mismatches: 31, Indels: 26
0.75 0.13 0.11
Matches are distributed among these distances:
31 38 0.22
32 22 0.13
33 21 0.12
34 37 0.21
35 40 0.23
36 17 0.10
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.24
Consensus pattern (33 bp):
AGGGGGGCGTCACGCCTCCCCAATTAAATTGTT
Found at i:53496 original size:19 final size:19
Alignment explanation
Indices: 53457--53495 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53447 TTTTCTATCA
*
53457 TTATTTTATTGTTGTTATT
1 TTATTTTATTGTTATTATT
*
53476 TTATTTTATTTTTATT-TT
1 TTATTTTATTGTTATTATT
53494 TT
1 TT
53496 TTAAGCAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (19 bp):
TTATTTTATTGTTATTATT
Found at i:53561 original size:27 final size:28
Alignment explanation
Indices: 53530--53621 Score: 97
Period size: 27 Copynumber: 3.5 Consensus size: 28
53520 CGCATACCTG
*
53530 GGGGGTCGCCCCCCTTTTGCGCATGGCA
1 GGGGGTCGTCCCCCTTTTGCGCATGGCA
* * *
53558 -GGGGTCATCCCCCTTTT-TGC-TAGCAA
1 GGGGGTCGTCCCCCTTTTGCGCATGGC-A
53584 GGGGGTCG-CCCCC--TTGCGCATGGCA
1 GGGGGTCGTCCCCCTTTTGCGCATGGCA
53609 GGGGGTCGTCCCC
1 GGGGGTCGTCCCC
53622 GCGCTTAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
24 2 0.04
25 14 0.27
26 15 0.29
27 21 0.40
ACGTcount: A:0.09, C:0.35, G:0.35, T:0.22
Consensus pattern (28 bp):
GGGGGTCGTCCCCCTTTTGCGCATGGCA
Found at i:53613 original size:26 final size:26
Alignment explanation
Indices: 53505--53621 Score: 87
Period size: 27 Copynumber: 4.4 Consensus size: 26
53495 TTTAAGCAAA
* * *
53505 GGGTTGCCCCCTTTGCGCATACCTGGG
1 GGGTCGCCCCCTTTGCGCATAGC-AGG
*
53532 GGGTCGCCCCCCTTTTGCGCATGGCA-G
1 GGGTCG-CCCCC-TTTGCGCATAGCAGG
* **
53559 GGGTCATCCCCCTTTTTGC-TAGCAAGG
1 GGGTC-GCCCCCTTTGCGCATAGC-AGG
*
53586 GGGTCGCCCCC-TTGCGCATGGCAGG
1 GGGTCGCCCCCTTTGCGCATAGCAGG
*
53611 GGGTCGTCCCC
1 GGGTCGCCCCC
53622 GCGCTTAGTG
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
25 20 0.28
26 14 0.20
27 22 0.31
28 5 0.07
29 10 0.14
ACGTcount: A:0.09, C:0.35, G:0.33, T:0.23
Consensus pattern (26 bp):
GGGTCGCCCCCTTTGCGCATAGCAGG
Found at i:55379 original size:25 final size:24
Alignment explanation
Indices: 55331--55399 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 24
55321 TTTGGTGGGT
*
55331 GTGTTTATGGTATACCTTTGATGG
1 GTGTTTACGGTATACCTTTGATGG
*
55355 GTTTTTACGGTATACCCTTTGATGG
1 GTGTTTACGGTATA-CCTTTGATGG
*
55380 GTGTTTACAGTATACCTTTG
1 GTGTTTACGGTATACCTTTG
55400 GTTGGTCCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 18 0.45
25 22 0.55
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (24 bp):
GTGTTTACGGTATACCTTTGATGG
Found at i:57203 original size:419 final size:425
Alignment explanation
Indices: 56545--57388 Score: 1339
Period size: 420 Copynumber: 2.0 Consensus size: 425
56535 CAACAAACCC
*
56545 AATAAATGTCAACATATATATATATATATATATATAATCATACAACGTAAATGGATAAATTCAAA
1 AATAAATGTCAACATATATATATATATATATACATAATCATACAACGTAAATGGATAAATTCAAA
*
56610 AGGTTTTTTTTTTAAAAAAAATTAATCCTTTTGCTATTATATATTATATATATATGTAATCTACA
66 AGGTTTTTTTTTTAAAAAAAATCAATCCTTTTGCTATTATATATTATATATATATGTAATCTACA
* * * ** *
56675 CGTATAACCAGAGCCATTATTTGTTTTATCTATCATTTATAGTTTTAGCTAAATCTTTTTTTATA
131 CGCATAACCAGAGCCATTATTTGATTTATCTATCATTTATAGATAGAGCTAAATCTGTTTTTATA
56740 AAAATACTATGTTCATTATCCACTCAATTCAAATTTAAGGATATTTAAATATTTG-TTAAGTTGG
196 AAAATACTATGTTCATTATCCACTCAATTCAAATTTAAGGATATTTAAATATTTGATTAAGTTGG
* * *
56804 TGATTTTTAAAATCAAGTTTCATTAGATGGTAACTTTCATTCAAAATGGTGAGGGAAAATTCATT
261 CGATTTGTAAAATCAAGTTTCATTAGATGGTAACTTTCATTCAAAATGATGAGGGAAAATTCATT
*
56869 CAATAATGGGTAATGAAACGATTTTGTAAATATTTATATAT-GTTTTTTTGTTATTTTCTCATAT
326 CAATAATGGGTAATGAAACGATTTTGCAAATATTTATATATGGTTTTTTTGTTATTTTCTCATAT
*
56933 ATATCGGTACTTGCTAAACATTCCAATTTTACACA
391 ATATCGGTACTTGCTAAACATTCCAATATTACACA
* * *
56968 AATAAATGTCAACATATATAT-T-T-T-TATACATATTCATACAATG-AAATTGATAAATTCAAA
1 AATAAATGTCAACATATATATATATATATATACATAATCATACAACGTAAATGGATAAATTCAAA
* * ** *
57028 AGTTTTTTTTTTTTAAAATTATCAATCTTTTTGCTATTATATATTATATATATATATATGTAATC
66 AGGTTTTTTTTTTAAAAAAAATCAATCCTTTTGCTA-T-TATA-TAT-TATATATATATGTAATC
57093 TACACGCATAACCAGAGCCATTATTTGATTTATCTATCATTTATA-ATAGAGCT-AAT-TGTTTT
127 TACACGCATAACCAGAGCCATTATTTGATTTATCTATCATTTATAGATAGAGCTAAATCTGTTTT
* *
57155 TATAAGAATACTATGTTCATTATCCACTTAATTCAAATTTAAGGATATTTAAATATTTGATTAAG
192 TATAAAAATACTATGTTCATTATCCACTCAATTCAAATTTAAGGATATTTAAATATTTGATTAAG
*
57220 TTGGCGATTTGTAAAATCAAGTTTCATTAGATGGTAACTTTCATTCAAAATGATGAGGGACAATT
257 TTGGCGATTTGTAAAATCAAGTTTCATTAGATGGTAACTTTCATTCAAAATGATGAGGGAAAATT
* * *
57285 CATTCAATATTGGGTAATTAAACGATTTTGCAAATATTTATATATGGTTTTTTTTTTATTTTCTC
322 CATTCAATAATGGGTAATGAAACGATTTTGCAAATATTTATATATGGTTTTTTTGTTATTTTCTC
57350 ATATATATCGGTACTTGCTAAACATTCCAATATTACACA
387 ATATATATCGGTACTTGCTAAACATTCCAATATTACACA
57389 GACTTCAAAA
Statistics
Matches: 388, Mismatches: 27, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
418 46 0.12
419 79 0.20
420 116 0.30
421 65 0.17
422 61 0.16
423 21 0.05
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (425 bp):
AATAAATGTCAACATATATATATATATATATACATAATCATACAACGTAAATGGATAAATTCAAA
AGGTTTTTTTTTTAAAAAAAATCAATCCTTTTGCTATTATATATTATATATATATGTAATCTACA
CGCATAACCAGAGCCATTATTTGATTTATCTATCATTTATAGATAGAGCTAAATCTGTTTTTATA
AAAATACTATGTTCATTATCCACTCAATTCAAATTTAAGGATATTTAAATATTTGATTAAGTTGG
CGATTTGTAAAATCAAGTTTCATTAGATGGTAACTTTCATTCAAAATGATGAGGGAAAATTCATT
CAATAATGGGTAATGAAACGATTTTGCAAATATTTATATATGGTTTTTTTGTTATTTTCTCATAT
ATATCGGTACTTGCTAAACATTCCAATATTACACA
Found at i:59376 original size:23 final size:23
Alignment explanation
Indices: 59326--59378 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
59316 ACTTTCATTT
* *
59326 TTTTTC-TCTTTTCTCTTTTCCG
1 TTTTTCTTTTTTTCTCTTCTCCG
59348 TTTTTCTTTTTTTCTCTTCTCC-
1 TTTTTCTTTTTTTCTCTTCTCCG
59370 TTCTTTCTT
1 TT-TTTCTT
59379 AACACGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTCTTTTTTTCTCTTCTCCG
Found at i:60430 original size:14 final size:14
Alignment explanation
Indices: 60389--60421 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
60379 ATATTTTGTC
60389 TGATTTTGATATTG
1 TGATTTTGATATTG
60403 TGATTTTGATATTG
1 TGATTTTGATATTG
60417 TGATT
1 TGATT
60422 GTTTAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (14 bp):
TGATTTTGATATTG
Found at i:61019 original size:22 final size:22
Alignment explanation
Indices: 60969--61020 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
60959 AAATGAAATA
*
60969 TTCA-TATCAAATTATGATAAC
1 TTCACTATTAAATTATGATAAC
*
60990 TTCCCTATTAAATTATGATAA-
1 TTCACTATTAAATTATGATAAC
61011 TTACACTATT
1 TT-CACTATT
61021 TTTGATAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (22 bp):
TTCACTATTAAATTATGATAAC
Found at i:61065 original size:23 final size:23
Alignment explanation
Indices: 61039--61096 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
61029 CGTCGCTATG
61039 AAATTTTGATAAACCTTC-TTATA
1 AAATTTTGATAAACC-TCATTATA
*
61062 AAATTTTGATAAACCTCATTATG
1 AAATTTTGATAAACCTCATTATA
*
61085 AAATCTTGATAA
1 AAATTTTGATAA
61097 CTACAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 2 0.06
23 30 0.94
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAAACCTCATTATA
Found at i:61262 original size:22 final size:21
Alignment explanation
Indices: 61020--61291 Score: 112
Period size: 22 Copynumber: 12.6 Consensus size: 21
61010 ATTACACTAT
* *
61020 TTTTGATAACGTCGCTATGAAA
1 TTTTGATAACCTC-ATATGAAA
* *
61042 TTTTGATAAACCTTCTTATAAAA
1 TTTTGAT-AACC-TCATATGAAA
61065 TTTTGATAAACCTCATTATGAAA
1 TTTTGAT-AACCTCA-TATGAAA
* *
61088 TCTTGATAA---C-TA-CAAA
1 TTTTGATAACCTCATATGAAA
* * **
61104 TTTTGATAATCTGCCTATGATT
1 TTTTGATAACCT-CATATGAAA
*
61126 TTTTAATAACCTCATTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
61148 TTTTG-TTACTCTCCCTATGAAA
1 TTTTGATAAC-CT-CATATGAAA
* *
61170 TTTTGATCTACAT-ACTATGAAA
1 TTTTGAT-AACCTCA-TATGAAA
*
61192 TATTT-ATAACCCTCTTATGAAA
1 T-TTTGATAA-CCTCATATGAAA
* * *
61214 TTTTGA-AAACTAAACTATGAGA
1 TTTTGATAACCT-CA-TATGAAA
61236 TTTTGATAACCATCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* * *
61258 TTTTGATCACTTCATAATAAAA
1 TTTTGATAACCTCAT-ATGAAA
* *
61280 GTTTAATAACCT
1 TTTTGATAACCT
61292 TCCTAATTTG
Statistics
Matches: 188, Mismatches: 38, Indels: 48
0.69 0.14 0.18
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
19 1 0.01
20 3 0.02
21 16 0.09
22 106 0.56
23 43 0.23
24 6 0.03
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:61398 original size:21 final size:21
Alignment explanation
Indices: 61372--61597 Score: 93
Period size: 22 Copynumber: 10.3 Consensus size: 21
61362 TCACATTTTG
* *
61372 GAAATTTGGTAACCTCTTTAT
1 GAAATTTGATAACCTCTCTAT
61393 GAAATTTTGATAACCTCTCTAT
1 GAAA-TTTGATAACCTCTCTAT
* * * *
61415 AAAATTTTGTTGACCCCTCTAT
1 GAAA-TTTGATAACCTCTCTAT
* *
61437 GAAATTTTGATAATCACAT-TAT
1 GAAA-TTTGATAACCTC-TCTAT
* *
61459 GTAATTTTGATAACCT-TGCTTT
1 G-AAATTTGATAACCTCT-CTAT
*** *
61481 GAAATTTTGATAAAAACACTAT
1 GAAA-TTTGATAACCTCTCTAT
*
61503 GAAATTTTGATAATCT-TCCTAT
1 GAAA-TTTGATAACCTCT-CTAT
*
61525 -AAATTTTGATAATCCGATTTCTAT
1 GAAA-TTTGATAA-CC--TCTCTAT
** * *
61549 GATTTTTCGATAATCACTCTAT
1 GAAATTT-GATAACCTCTCTAT
*
61571 GAGATTTGATAACCT-TCTAT
1 GAAATTTGATAACCTCTCTAT
*
61591 CAAATTT
1 GAAATTT
61598 TGGTACTCCT
Statistics
Matches: 154, Mismatches: 37, Indels: 29
0.70 0.17 0.13
Matches are distributed among these distances:
20 11 0.07
21 24 0.16
22 100 0.65
23 3 0.02
24 9 0.06
25 7 0.05
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
GAAATTTGATAACCTCTCTAT
Found at i:61401 original size:22 final size:22
Alignment explanation
Indices: 61372--61536 Score: 108
Period size: 22 Copynumber: 7.6 Consensus size: 22
61362 TCACATTTTG
*
61372 GAAA-TTTGGTAACCTCTTTAT
1 GAAATTTTGATAACCTCTTTAT
*
61393 GAAATTTTGATAACCTCTCTAT
1 GAAATTTTGATAACCTCTTTAT
* * * * *
61415 AAAATTTTGTTGACCCCTCTAT
1 GAAATTTTGATAACCTCTTTAT
* * *
61437 GAAATTTTGATAATCACATTAT
1 GAAATTTTGATAACCTCTTTAT
*
61459 GTAATTTTGATAACCT-TGCTT-T
1 GAAATTTTGATAACCTCT--TTAT
*** **
61481 GAAATTTTGATAAAAACACTAT
1 GAAATTTTGATAACCTCTTTAT
61503 GAAATTTTGATAA--TCTTCCTAT
1 GAAATTTTGATAACCTCTT--TAT
61525 -AAATTTTGATAA
1 GAAATTTTGATAA
61537 TCCGATTTCT
Statistics
Matches: 111, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.01
21 17 0.15
22 91 0.82
23 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTTTAT
Found at i:61465 original size:44 final size:43
Alignment explanation
Indices: 61348--61538 Score: 136
Period size: 44 Copynumber: 4.4 Consensus size: 43
61338 AATACCACTT
* * * * *
61348 TGAAATTTTGGTAATCACATTTTGGAAA-TTTGGTAACCTCTTTA
1 TGAAATTTTGATAATCACATTAT-GAAATTTTGAT-ACCCCTCTA
* * * *
61392 TGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCACAT-TATGAAATTTTGAT-ACCCCTCTA
* * * *
61436 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTTGCTT
1 TGAAATTTTGATAATCACATTATGAAATTTTGATACCCCT-CTA
** * ** *
61480 TGAAATTTTGATAAAAACACTATGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAATCACATTATGAAATTTTGATACCCCT-CTA
61524 T-AAATTTTGATAATC
1 TGAAATTTTGATAATC
61539 CGATTTCTAT
Statistics
Matches: 117, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
43 20 0.17
44 96 0.82
45 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (43 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGATACCCCTCTA
Found at i:61486 original size:66 final size:66
Alignment explanation
Indices: 61389--61517 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
61379 GGTAACCTCT
* * *** *
61389 TTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATGAAATTTTGATAATCAC
1 TTATGAAATTTTGATAACCTCTCTATAAAATTTTGATAAAAACACTATGAAATTTTGATAATCAC
61454 A
66 A
* * *
61455 TTATGTAATTTTGATAACCT-TGCTTTGAAATTTTGATAAAAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTCT-CTATAAAATTTTGATAAAAACACTATGAAATTTTGATAATC
61518 TTCCTATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCTCTATAAAATTTTGATAAAAACACTATGAAATTTTGATAATCAC
A
Found at i:61508 original size:88 final size:88
Alignment explanation
Indices: 61348--61511 Score: 206
Period size: 88 Copynumber: 1.9 Consensus size: 88
61338 AATACCACTT
* * * *** *
61348 TGAAATTTTGGTAATCACATTTTGGAAATTTGGTAACCTCTTTATGAAATTTTGATAACCTCTCT
1 TGAAATTTTGATAATCACATTATGGAAATTTGATAACCTCTTTATGAAATTTTGATAAAAACACT
61413 ATAAAATTTTGTTGACCCCTCTA
66 ATAAAATTTTGTTGACCCCTCTA
* *
61436 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCT-TGCTT-TGAAATTTTGATAAAAACA
1 TGAAATTTTGATAATCACATTATGGAAATTTGATAACCTCT--TTATGAAATTTTGATAAAAACA
*
61499 CTATGAAATTTTG
64 CTATAAAATTTTG
61512 ATAATCTTCC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
87 1 0.02
88 61 0.95
89 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (88 bp):
TGAAATTTTGATAATCACATTATGGAAATTTGATAACCTCTTTATGAAATTTTGATAAAAACACT
ATAAAATTTTGTTGACCCCTCTA
Found at i:61749 original size:22 final size:22
Alignment explanation
Indices: 61636--61752 Score: 91
Period size: 22 Copynumber: 5.3 Consensus size: 22
61626 ATAACCTTCA
*
61636 TATGAAAATTTGATAATCACAC
1 TATGAAAATTTGATAACCACAC
*
61658 TA-AAAAATTTTGATAACCACAC
1 TATGAAAA-TTTGATAACCACAC
* * *
61680 TAAGAAATTTTGATAACCTCTAC
1 TATGAAAATTTGATAACCAC-AC
*
61703 -AT-AAAATATT-AGTAACCTC-C
1 TATGAAAAT-TTGA-TAACCACAC
*
61723 TTATGAAAATTTGTTAACCACAC
1 -TATGAAAATTTGATAACCACAC
61746 TATGAAA
1 TATGAAA
61753 TTCTTATAAC
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.01
21 9 0.12
22 55 0.72
23 11 0.14
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (22 bp):
TATGAAAATTTGATAACCACAC
Found at i:61763 original size:44 final size:41
Alignment explanation
Indices: 61622--61770 Score: 111
Period size: 44 Copynumber: 3.4 Consensus size: 41
61612 AAATTTAGAC
* * *
61622 TTTTATAACCTTCATATGAAAATTTGATAATCACACTAAAAAA
1 TTTTATAACC-TCCTATGAAAATTTGATAACCACACT-ATAAA
* * * *
61665 TTTTGATAACCACACTAAGAAATTTTGATAACCTCTAC-ATAAAA
1 TTTT-ATAACCTC-CTATGAAAATTTGATAACCAC-ACTAT-AAA
* *
61709 TATTAGTAACCTCCTTATGAAAATTTGTTAACCACACTATGAAA
1 TTTTA-TAACCTCC-TATGAAAATTTGATAACCACACTAT-AAA
61753 TTCTTATAACCTCGCTAT
1 TT-TTATAACCTC-CTAT
61771 TACATTTTGA
Statistics
Matches: 82, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
43 10 0.12
44 66 0.80
45 6 0.07
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (41 bp):
TTTTATAACCTCCTATGAAAATTTGATAACCACACTATAAA
Found at i:61900 original size:22 final size:22
Alignment explanation
Indices: 61801--61976 Score: 110
Period size: 22 Copynumber: 7.9 Consensus size: 22
61791 GATAACTTTT
* *
61801 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
* ** *
61823 TTATGAAATTTCAATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* *
61845 CTAAGAAATTTTAATAACCTGATC-
1 CTATGAAATTTTGATAACC--A-CA
*
61869 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
61891 CTATGGAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
61913 CCATGAAATTTTTGATAACTTC-CA
1 CTATGAAA-TTTTGATAAC--CACA
*
61937 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
61958 CTATGGAATTTTAATAACC
1 CTATGAAATTTTGATAACC
61977 TCCTCATGAA
Statistics
Matches: 119, Mismatches: 24, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 78 0.66
23 19 0.16
24 17 0.14
25 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:61921 original size:68 final size:66
Alignment explanation
Indices: 61792--62021 Score: 232
Period size: 68 Copynumber: 3.5 Consensus size: 66
61782 AATCTCTTTG
* * * * * * * * * *
61792 ATAACTTTTCTATAAAATTGTGATAACCACATTATGAAATTTCAATAACCTTCCTAAGAAATTTT
1 ATAACCTTCCTATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCCCATGAAATTTT
61857 A
66 A
*
61858 ATAACCTGATCCTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT--TCCTATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCCCATGAAA-T
*
61923 TTTG
63 TTTA
61927 ATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTAATAACC-TCCTCATG-AATT
1 ATAACCTTCC-TATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCC-CATGAAATT
*
61989 ATA
64 TTA
* * ** *
61992 ATAACCATCTTACAAAATTTTGATAACCAC
1 ATAACCTTCCTATGAAATTTTGGTAACCAC
62022 GTAGAGGCAA
Statistics
Matches: 138, Mismatches: 20, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
65 24 0.17
66 17 0.12
67 43 0.31
68 46 0.33
69 8 0.06
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (66 bp):
ATAACCTTCCTATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCCCATGAAATTTT
A
Found at i:61929 original size:23 final size:23
Alignment explanation
Indices: 61899--61947 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
61889 CACTATGGAA
61899 TTTTGATAACCTTCC-CATGAAAT
1 TTTTGATAA-CTTCCACATGAAAT
*
61922 TTTTGATAACTTCCATATGAAAT
1 TTTTGATAACTTCCACATGAAAT
61945 TTT
1 TTT
61948 GGTAACCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (23 bp):
TTTTGATAACTTCCACATGAAAT
Found at i:61948 original size:45 final size:45
Alignment explanation
Indices: 61825--61954 Score: 115
Period size: 46 Copynumber: 2.9 Consensus size: 45
61815 TAACCACATT
** * * *
61825 ATGAAATTTCAATAACCTTCC-TAAGAAATTTTAATAACCTGATCCT
1 ATGAAATTTTGATAA-CTTCCATATGAAATTTTGATAACCT-ATCCC
* *
61871 ATGAAATTTTGGTAAC--CACACTATGGAATTTTGATAACCT-TCCC
1 ATGAAATTTTGATAACTTC-CA-TATGAAATTTTGATAACCTATCCC
*
61915 ATGAAATTTTTGATAACTTCCATATGAAATTTTGGTAACC
1 ATGAAA-TTTTGATAACTTCCATATGAAATTTTGATAACC
61955 ACACTATGGA
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
43 1 0.01
44 10 0.15
45 26 0.38
46 30 0.44
47 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (45 bp):
ATGAAATTTTGATAACTTCCATATGAAATTTTGATAACCTATCCC
Found at i:61959 original size:67 final size:65
Alignment explanation
Indices: 61788--61986 Score: 229
Period size: 67 Copynumber: 3.0 Consensus size: 65
61778 TGATAATCTC
* * * * * * * * *
61788 TTTGATAACTTTTCTATAAAATTGTGATAACCACATTATGAAATTTCAATAACCTTCCTAAGAAA
1 TTTGATAAC-TTCCTATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCCCATGAAA
61853 T
65 T
* *
61854 TTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTTCCCATGA
1 TTTGATAA-CT--TCCTATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCCCATGA
61919 AATT
63 AA-T
61923 TTTGATAACTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTAATAACC-TCCTCATGAA
1 TTTGATAACTTCC-TATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCC-CATGAA
61987 TTATAATAAC
Statistics
Matches: 114, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
66 14 0.12
67 46 0.40
68 46 0.40
69 8 0.07
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (65 bp):
TTTGATAACTTCCTATGAAATTTTGGTAACCACACTATGGAATTTTAATAACCTTCCCATGAAAT
Found at i:66777 original size:16 final size:15
Alignment explanation
Indices: 66758--66791 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
66748 TTTCCCTGTT
*
66758 TTTTTTTCCTTTTTCC
1 TTTTCTTCC-TTTTCC
66774 TTTTCTTCCTTTTCC
1 TTTTCTTCCTTTTCC
66789 TTT
1 TTT
66792 GTCCTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTCCTTTTCC
Found at i:66787 original size:22 final size:22
Alignment explanation
Indices: 66761--66802 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
66751 CCCTGTTTTT
*
66761 TTTTCCTTTTTCCTTTTCTTCC
1 TTTTCCTTTGTCCTTTTCTTCC
66783 TTTTCCTTTGTCCTTTTCTT
1 TTTTCCTTTGTCCTTTTCTT
66803 TTTCGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTCCTTTGTCCTTTTCTTCC
Found at i:66895 original size:20 final size:20
Alignment explanation
Indices: 66870--66932 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
66860 CGCAGGCCAA
66870 GGCCATGCGCTGGCCTGCTG
1 GGCCATGCGCTGGCCTGCTG
*
66890 GGCCATGCG--GG-C--C-A
1 GGCCATGCGCTGGCCTGCTG
*
66904 GGCCATGTGCTGGCCTGCTG
1 GGCCATGCGCTGGCCTGCTG
66924 GGCCATGCG
1 GGCCATGCG
66933 GGCCAGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
14 8 0.24
15 1 0.03
16 2 0.06
17 2 0.06
18 2 0.06
19 1 0.03
20 17 0.52
ACGTcount: A:0.08, C:0.33, G:0.41, T:0.17
Consensus pattern (20 bp):
GGCCATGCGCTGGCCTGCTG
Found at i:66916 original size:34 final size:34
Alignment explanation
Indices: 66855--66996 Score: 160
Period size: 34 Copynumber: 4.1 Consensus size: 34
66845 CCAAGCAGTA
* *
66855 GGCCACGCAGGCCAAGGCCATGCGCTGGCCTGCTG
1 GGCCATGCGGGCC-AGGCCATGCGCTGGCCTGCTG
*
66890 GGCCATGCGGGCCAGGCCATGTGCTGGCCTGCTG
1 GGCCATGCGGGCCAGGCCATGCGCTGGCCTGCTG
***
66924 GGCCATGCGGGCCAGGCCATGCGCTGGCCAATTG
1 GGCCATGCGGGCCAGGCCATGCGCTGGCCTGCTG
** * *
66958 GGCCGCGCGGGTCAGGCCCCA-GCGCTTGCCTGCTG
1 GGCCATGCGGGCCAGG--CCATGCGCTGGCCTGCTG
66993 GGCC
1 GGCC
66997 GTGCAAGCCA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
34 63 0.69
35 25 0.27
36 3 0.03
ACGTcount: A:0.11, C:0.36, G:0.39, T:0.14
Consensus pattern (34 bp):
GGCCATGCGGGCCAGGCCATGCGCTGGCCTGCTG
Found at i:67218 original size:12 final size:12
Alignment explanation
Indices: 67201--67256 Score: 94
Period size: 12 Copynumber: 4.7 Consensus size: 12
67191 ACCTGGCAAT
67201 TCGTGTTTCGTG
1 TCGTGTTTCGTG
*
67213 TCGTGTTTTGTG
1 TCGTGTTTCGTG
67225 TCGTGTTTCGTG
1 TCGTGTTTCGTG
*
67237 TCGTGTTTCATG
1 TCGTGTTTCGTG
67249 TCGTGTTT
1 TCGTGTTT
67257 ACATAGGGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.02, C:0.14, G:0.30, T:0.54
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:67772 original size:5 final size:5
Alignment explanation
Indices: 67762--67787 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
67752 TATTTCGTTC
67762 CGTGT CGTGT CGTGT CGTGT CGTGT C
1 CGTGT CGTGT CGTGT CGTGT CGTGT C
67788 AAGACCCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.38, T:0.38
Consensus pattern (5 bp):
CGTGT
Found at i:69546 original size:13 final size:13
Alignment explanation
Indices: 69516--69558 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
69506 ATTTGACTGT
*
69516 TTTGGTTAATTA-
1 TTTGGTTTATTAC
69528 TCTTGGTTTATTAC
1 T-TTGGTTTATTAC
*
69542 TTTGGTTTATAAC
1 TTTGGTTTATTAC
69555 TTTG
1 TTTG
69559 ATTATGATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 1 0.04
13 25 0.93
14 1 0.04
ACGTcount: A:0.19, C:0.07, G:0.16, T:0.58
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:71990 original size:10 final size:10
Alignment explanation
Indices: 71975--72004 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
71965 AAAATATCCA
71975 ATTCCCGCTT
1 ATTCCCGCTT
71985 ATTCCCGCTT
1 ATTCCCGCTT
71995 ATTCCCGCTT
1 ATTCCCGCTT
72005 CTAGTCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.40, G:0.10, T:0.40
Consensus pattern (10 bp):
ATTCCCGCTT
Found at i:80096 original size:21 final size:21
Alignment explanation
Indices: 80054--80096 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
80044 CAATTTAGGC
*
80054 TTAGATTTAAGTTTCTTGTTT
1 TTAGATTTAAGTTTATTGTTT
80075 TTAGATTTAAGATTTATT-TTT
1 TTAGATTTAAG-TTTATTGTTT
80096 T
1 T
80097 ATGCATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (21 bp):
TTAGATTTAAGTTTATTGTTT
Found at i:80416 original size:21 final size:21
Alignment explanation
Indices: 80390--80433 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
80380 ATAGGTTTGT
80390 TGTTTGAATAATTGAGTCATA
1 TGTTTGAATAATTGAGTCATA
80411 TGTTTGAATAATTGAGTCATA
1 TGTTTGAATAATTGAGTCATA
80432 TG
1 TG
80434 CTAGTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
TGTTTGAATAATTGAGTCATA
Found at i:80951 original size:22 final size:22
Alignment explanation
Indices: 80924--80980 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
80914 TTCTGTGCTT
80924 ATATATATATATATTATTAATTAC
1 ATATAT-TA-ATATTATTAATTAC
80948 ATATATTAATATTATTAATTAC
1 ATATATTAATATTATTAATTAC
80970 ATATATTAATA
1 ATATATTAATA
80981 GTGAGAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 25 0.76
23 2 0.06
24 6 0.18
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATTAATATTATTAATTAC
Found at i:80956 original size:13 final size:13
Alignment explanation
Indices: 80938--80979 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
80928 ATATATATAT
80938 TATTAATTACATA
1 TATTAATTACATA
80951 TATTAA-T--AT-
1 TATTAATTACATA
80960 TATTAATTACATA
1 TATTAATTACATA
80973 TATTAAT
1 TATTAAT
80980 AGTGAGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 6 0.24
10 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTAATTACATA
Found at i:93533 original size:15 final size:15
Alignment explanation
Indices: 93503--93544 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
93493 TTACTTTGCT
93503 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
93519 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
93534 TTGCTTTCTGT
1 TTGTTTTCTGT
93545 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:93899 original size:30 final size:30
Alignment explanation
Indices: 93865--93959 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
93855 TTGAGTCTGC
*
93865 GTTTTTTCTAAAAAAAAAAATTTGTTTTGT
1 GTTTTTTCTATAAAAAAAAATTTGTTTTGT
** *
93895 GTTTTTTGCGTCATAAAAAAAAA-GGGTTTTGC
1 GTTTTTT-C-T-ATAAAAAAAAATTTGTTTTGT
** * *
93927 GTTTTTGATTTAAAAAAGAATTTGTTTTGT
1 GTTTTTTCTATAAAAAAAAATTTGTTTTGT
93957 GTT
1 GTT
93960 GCGTTTTTGA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
29 9 0.18
30 17 0.34
31 1 0.02
32 13 0.26
33 10 0.20
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (30 bp):
GTTTTTTCTATAAAAAAAAATTTGTTTTGT
Found at i:93913 original size:32 final size:30
Alignment explanation
Indices: 93877--93959 Score: 78
Period size: 32 Copynumber: 2.7 Consensus size: 30
93867 TTTTTCTAAA
*
93877 AAAAAAAATTTGTTTTGTGTTTTTTGCGTCAT
1 AAAAAAAATTTGTTTTGTGTTTTTTG-AT-AT
*** * *
93909 AAAAAAAAAGGGTTTTGCG-TTTTTGATTT
1 AAAAAAAATTTGTTTTGTGTTTTTTGATAT
93938 AAAAAAGAATTTGTTTTGTGTT
1 AAAAAA-AATTTGTTTTGTGTT
93960 GCGTTTTTGA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
29 7 0.18
30 10 0.26
31 7 0.18
32 15 0.38
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.46
Consensus pattern (30 bp):
AAAAAAAATTTGTTTTGTGTTTTTTGATAT
Found at i:96986 original size:22 final size:22
Alignment explanation
Indices: 96943--96986 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
96933 TCATCCTTAA
* *
96943 AACTATTTTATTTTTACCATTT
1 AACTATTTTACTTTTACAATTT
*
96965 AACTATTTTACTTTTATAATTT
1 AACTATTTTACTTTTACAATTT
96987 TAATCAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (22 bp):
AACTATTTTACTTTTACAATTT
Done.