Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014700.1 Kokia drynarioides strain JFW-HI SEQ_129739, 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: 333966
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:2873 original size:206 final size:206
Alignment explanation
Indices: 2348--3261 Score: 1216
Period size: 206 Copynumber: 4.5 Consensus size: 206
2338 CCAACTCAGG
* ** * * **
2348 GCTCGATGTGAGCAAATCTTCGAATCTAAGCTTCCT-ATTGAGATATTGAGAAGCAGGGCGAAGC
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGA-TGAGATACTGAGAAGCAGGTCGAAAT
* *
2412 AATAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACAAAATTCGTCTTCCTGATGAG-G
65 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAG
* ** * *
2475 TACAGAGAAGCGCATTGAAACAAGTAAGGCGGTCATATTCCTGATGAGATAC--A-AAGAAGA--
130 -ACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATTTTCCTGATGAGATACTGAGAAGAAGACC
* * * *
2535 ATA-CCAACTCAGG
194 AAATCAAACCCA-C
* * ** **
2548 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGAT-AAATATTGAGAAGCATCTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATA
*
2612 ATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGAGA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAGA
* * *
2677 CAGAGAAGTGGATTGAAACAAACGACGCGGTCATTTTCCTGATGAGATACTGAGAAGAAGACCAA
131 CAGAGAAGCGGATTGAAACAAGCGATGCGGTCATTTTCCTGATGAGATACTGAGAAGAAGACCAA
2742 ATCAAACCCAC
196 ATCAAACCCAC
*
2753 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAATA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATA
* *
2818 TTAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAGA
* *** *
2883 CAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTT-CTGATGAGATAAAAAGAAGAATACCA
131 CAGAGAAGCGGATTGAAACAAGCGATGCGGTCAT-TTTCCTGATGAGATACTGAGAAGAAGACCA
* *
2947 ACTC-AA--GA-
195 AATCAAACCCAC
* * *
2955 -CTCAATGCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAATA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATA
* *
3019 ATAAAATGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAGA
* * *
3084 CAGAGAAGCGGATTGATACAAGCGATGCGGTCATCTTCCTGATGAGGTACTGAGAAGAAGACCAA
131 CAGAGAAGCGGATTGAAACAAGCGATGCGGTCATTTTCCTGATGAGATACTGAGAAGAAGACCAA
3149 ATCAAACCCAC
196 ATCAAACCCAC
* *
3160 GCTCGATGTGAGCAAATCCTCGAA-CCCAGGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAAT
1 GCTCGATGTGAGCAAATCTTCGAACCCCA-GCTTCCTGATGAGATACTGAGAAGCAGGTCGAAAT
3224 AATAAAATGGTTAGCTTCCTGATGAGATA-TAGAGAAGT
65 AATAAAATGGTTAGCTTCCTGATGAGATACT-GAGAAGT
3262 ATACCAACTC
Statistics
Matches: 633, Mismatches: 62, Indels: 32
0.87 0.09 0.04
Matches are distributed among these distances:
199 27 0.04
200 132 0.21
201 181 0.29
202 3 0.00
203 8 0.01
204 1 0.00
205 48 0.08
206 230 0.36
207 3 0.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATA
ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAGA
CAGAGAAGCGGATTGAAACAAGCGATGCGGTCATTTTCCTGATGAGATACTGAGAAGAAGACCAA
ATCAAACCCAC
Found at i:3173 original size:407 final size:405
Alignment explanation
Indices: 2348--3261 Score: 1384
Period size: 407 Copynumber: 2.2 Consensus size: 405
2338 CCAACTCAGG
** * * **
2348 GCTCGATGTGAGCAAATCTTCGAATCTAAGCTTCCT-ATTGAGATATTGAGAAGCAGGGCGAAGC
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGA-TGAGATACTGAGAAGCAGGTCGAAAT
* *
2412 AATAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACAAAATTCGTCTTCCTGATGAGGT
64 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGAT
* * *
2476 ACAGAGAAGCGCATTGAAACAAGTAAGGCGGTCATATTCCTGATGAGATACAAAGAAGAATACCA
129 ACAAAGAAGCGCATTGAAACAAGCAAGGCGGTCATATTCCTGATGAGATAAAAAGAAGAATACCA
* * * * * *
2541 ACTCAGGGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATAAATATTGAGAAGCATCTC
194 ACTCAAGACTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATAAATACTGAGAAGCAGCTC
* *
2606 GAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGAT
259 GAAACAATAAAATGGTTAGCTTCCTAATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGAT
* *
2671 GAGAGACAGAGAAGTGGATTGAAACAAACGACGCGGTCATTTTCCTGATGAGATACTGAGAAGAA
324 GAGAGACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAA
2736 GACCAAATCAAACCCAC
389 GACCAAATCAAACCCAC
*
2753 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAATA
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATA
* *
2818 TTAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
65 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATA
* * * * *
2883 CAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCTGATGAGATAAAAAGAAGAATACCAA
130 CAAAGAAGCGCATTGAAACAAGCAAGGCGGTCATATTCCTGATGAGATAAAAAGAAGAATACCAA
* * *
2948 CTCAAGACTCAATGCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTC
195 CTCAAGACTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGAT-AAATACTGAGAAGCAGCTC
* *
3013 GAAATAATAAAATGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGAT
259 GAAACAATAAAATGGTTAGCTTCCTAATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGAT
* * * * *
3078 GAGATACAGAGAAGCGGATTGATACAAGCGATGCGGTCATCTTCCTGATGAGGTACTGAGAAGAA
324 GAGAGACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAA
3143 GACCAAATCAAACCCAC
389 GACCAAATCAAACCCAC
* *
3160 GCTCGATGTGAGCAAATCCTCGAACCCAGGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAATA
1 GCTCGATGTGAGCAAATCTTCGAACCCA-GCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATA
3225 ATAAAATGGTTAGCTTCCTGATGAGATA-TAGAGAAGT
65 ATAAAATGGTTAGCTTCCTGATGAGATACT-GAGAAGT
3262 ATACCAACTC
Statistics
Matches: 460, Mismatches: 44, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
405 60 0.13
406 158 0.34
407 242 0.53
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (405 bp):
GCTCGATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAA
TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATAC
AAAGAAGCGCATTGAAACAAGCAAGGCGGTCATATTCCTGATGAGATAAAAAGAAGAATACCAAC
TCAAGACTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATAAATACTGAGAAGCAGCTCGA
AACAATAAAATGGTTAGCTTCCTAATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGA
GAGACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA
CCAAATCAAACCCAC
Found at i:3396 original size:116 final size:113
Alignment explanation
Indices: 3069--3443 Score: 333
Period size: 116 Copynumber: 3.2 Consensus size: 113
3059 CCAAATTCGT
* * * * *
3069 CTTCCTGATGAGATACAGAGAAGCGGATTGATACAAGCGATGCGGTCATCTTCCTGATGAGGTAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAG-TAAGAGGTCATCTTCCTGATGAGATAC
* * *
3134 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCC-TCGAACCCAGG
65 --A-AAGAAGA--ATATC-AACTCAGGCTCGATGTGAGCAAA-CCTTCGAACCCA-G
* * * * * * *
3190 CTTCCTGATGAGATACTGAGAAGTAGG-TCGAAATAA-TAAAATGGTTAGCTTCCTGATGAGATA
1 CTTCCTGATGAGATACAGAGAAG-CGGATTGAAACAAGTAAGA-GGTCATCTTCCTGATGAGATA
* * * * *
3253 TAGAGAAGTATACCAACTCAGGGCTCGATGTGATCAAACCTTCGAATCCCAG
64 CAAAGAAGAATATCAACTCA-GGCTCGATGTGAGCAAACCTTCGAA-CCCAG
* * *
3305 CTTCCTGATGAGATACACAGAAGCGGATTGAAACAAGTAAGGAGATCATCTTCCCGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAA-GAGGTCATCTTCCTGATGAGATAC
** *
3370 AAAGAAGAATATCAACTCAGGACTCGATACGAGCAAATCTTCGAACCCCAG
65 AAAGAAGAATATCAACTCAGG-CTCGATGTGAGCAAACCTTCGAA-CCCAG
* *
3421 CTGCCTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
3444 AAGGCCAAGT
Statistics
Matches: 203, Mismatches: 42, Indels: 23
0.76 0.16 0.09
Matches are distributed among these distances:
114 9 0.04
115 54 0.27
116 84 0.41
117 6 0.03
118 1 0.00
119 1 0.00
120 18 0.09
121 28 0.14
122 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (113 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAAGAGGTCATCTTCCTGATGAGATACA
AAGAAGAATATCAACTCAGGCTCGATGTGAGCAAACCTTCGAACCCAG
Found at i:3780 original size:6 final size:6
Alignment explanation
Indices: 3769--3855 Score: 62
Period size: 6 Copynumber: 15.2 Consensus size: 6
3759 GGGCCCAACA
* * *
3769 AAATTT AAATTT -ATTTT AAAATT AAGTTT --ATTT GAAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
*
3815 --ATTT GAATTTT AAATTT --ATTAT AAATTT AAATTT AAATTT A
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT A
3856 TTTAAATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
4 10 0.16
5 5 0.08
6 38 0.60
7 10 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:3798 original size:17 final size:17
Alignment explanation
Indices: 3768--3849 Score: 85
Period size: 17 Copynumber: 4.8 Consensus size: 17
3758 TGGGCCCAAC
*
3768 AAAATTTAAATTTATTTT
1 AAAA-TTAAATTTATTTG
*
3786 AAAATTAAGTTTATTTG
1 AAAATTAAATTTATTTG
*
3803 AAATTTAAATTTATTTG
1 AAAATTAAATTTATTTG
**
3820 AATTTTAAATTTATTAT-
1 AAAATTAAATTTATT-TG
*
3837 AAATTTAAATTTA
1 AAAATTAAATTTA
3850 AATTTATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
17 52 0.91
18 5 0.09
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AAAATTAAATTTATTTG
Found at i:3812 original size:34 final size:34
Alignment explanation
Indices: 3769--3849 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
3759 GGGCCCAACA
* *
3769 AAATTTAAATTTATTTTAAAATTAAGTTTATT-T
1 AAATTTAAATTTATTTGAAAATTAAATTTATTAT
**
3802 GAAATTTAAATTTATTTGAATTTTAAATTTATTAT
1 -AAATTTAAATTTATTTGAAAATTAAATTTATTAT
3837 AAATTTAAATTTA
1 AAATTTAAATTTA
3850 AATTTATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 41 0.98
35 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (34 bp):
AAATTTAAATTTATTTGAAAATTAAATTTATTAT
Found at i:3823 original size:10 final size:10
Alignment explanation
Indices: 3805--3862 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
3795 TTTATTTGAA
3805 ATTTAAATTT
1 ATTTAAATTT
*
3815 ATTTGAA--T
1 ATTTAAATTT
3823 -TTTAAATTT
1 ATTTAAATTT
3832 ATTATAAATTT
1 ATT-TAAATTT
3843 AAATTTAAATTT
1 --ATTTAAATTT
3855 ATTTAAAT
1 ATTTAAAT
3863 AATGTCCCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 1 0.03
9 1 0.03
10 16 0.40
11 7 0.17
12 7 0.17
13 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:3824 original size:23 final size:22
Alignment explanation
Indices: 3798--3855 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
3788 AATTAAGTTT
3798 ATTTGAAATTTAAATTTATTTGAA
1 ATTT-AAATTTAAATTTATTT-AA
* * **
3822 TTTTAAATTTATTATAAATTTAA
1 ATTTAAATTTA-AATTTATTTAA
3845 ATTTAAATTTA
1 ATTTAAATTTA
3856 TTTAAATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (22 bp):
ATTTAAATTTAAATTTATTTAA
Found at i:5801 original size:30 final size:29
Alignment explanation
Indices: 5734--6051 Score: 286
Period size: 30 Copynumber: 10.8 Consensus size: 29
5724 GAAGGTCCCT
* * *
5734 AAACTATCCGAAAATTACATTTTTACCCTC-
1 AAACT-TCCAAAAATTCCATTTTCACCC-CA
* * ***
5764 GAACTTCCATAAATTCCATTTTCGACCTTG
1 AAACTTCCAAAAATTCCATTTTC-ACCCCA
*
5794 AAACTTCCACAAATTCCATTTTCACCCC-
1 AAACTTCCAAAAATTCCATTTTCACCCCA
*
5822 AAACTTCCAAAAATTCCAATTTTTGACCCCA
1 AAACTTCCAAAAATTCC-A-TTTTCACCCCA
*
5853 AAACTTCCAAAAATTCCATTTTCGACCCTA
1 AAACTTCCAAAAATTCCATTTTC-ACCCCA
* *
5883 AAACTTCAAAAAATTCCATTTTCACCCCCG
1 AAACTTCCAAAAATTCCATTTTCA-CCCCA
* *
5913 AAACTTCC-AAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCA-TTTTCACCCCA
*** *
5942 AAACTTCCAAAAATTTTGTTTTCACCCTCG
1 AAACTTCCAAAAATTCCATTTTCACCC-CA
*
5972 AAACTTCCAAAAATTTCATTTTCACCCCTA
1 AAACTTCCAAAAATTCCATTTTCACCCC-A
*
6002 AAACTTCC-AAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCA-TTTTCACCCCA
* * *
6031 AAGC-TCCAAGATTTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
6052 TAACCTCGAA
Statistics
Matches: 239, Mismatches: 36, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
28 23 0.10
29 70 0.29
30 129 0.54
31 17 0.07
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTCACCCCA
Found at i:5844 original size:59 final size:58
Alignment explanation
Indices: 5734--6022 Score: 280
Period size: 59 Copynumber: 4.9 Consensus size: 58
5724 GAAGGTCCCT
* * * * * **
5734 AAACTATCCGAAAATTACATTTTTACCCTCGAACTTCCATAAATTCCATTTTCGA-CCTTG
1 AAACT-TCCAAAAATTCCATTTTCACCC-CAAACTTCCAAAAATTCCATTTTC-ACCCCCG
* * *
5794 AAACTTCCACAAATTCCATTTTCACCCCAAACTTCCAAAAATTCCAATTTTTGA-CCCCA
1 AAACTTCCAAAAATTCCATTTTCACCCCAAACTTCCAAAAATTCC-A-TTTTCACCCCCG
* *
5853 AAACTTCCAAAAATTCCATTTTCGACCCTAAAACTTCAAAAAATTCCATTTTCACCCCCG
1 AAACTTCCAAAAATTCCATTTTC-ACCC-CAAACTTCCAAAAATTCCATTTTCACCCCCG
* * *** *
5913 AAACTTCC-AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTTTGTTTTCACCCTCG
1 AAACTTCCAAAAATTCCA-TTTTCACC-CCAAACTTCCAAAAATTCCATTTTCACCCCCG
*
5972 AAACTTCCAAAAATTTCATTTTCACCCCTAAAACTTCC-AAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTTCACCCC--AAACTTCCAAAAATTCCATTTT
6023 TAACCCCAAA
Statistics
Matches: 192, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
58 17 0.09
59 112 0.58
60 47 0.24
61 16 0.08
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTCACCCCAAACTTCCAAAAATTCCATTTTCACCCCCG
Found at i:5887 original size:89 final size:88
Alignment explanation
Indices: 5734--6051 Score: 376
Period size: 89 Copynumber: 3.6 Consensus size: 88
5724 GAAGGTCCCT
* * * *
5734 AAACTATCCGAAAATTACATTTTT-ACCCTC-GAACTTCCATAAATTCCATTTTCGACCTTGAAA
1 AAACT-TCC-AAAATTCCATTTTTGACCC-CAAAACTTCCAAAAATTCCATTTTCGACCCTGAAA
*
5797 CTTCCACAAATTCCATTTTCACCCC-
63 CTTCCAAAAATTCCATTTTCACCCCA
*
5822 AAACTTCCAAAAATTCCAATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCGACCCTAAAAC
1 AAACTTCC-AAAATTCC-ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCGACCCTGAAAC
* *
5887 TTCAAAAAATTCCATTTTCACCCCCG
64 TTCCAAAAATTCCATTTTCA-CCCCA
* ***
5913 AAACTTCCAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTTTGTTTTC-ACCCTCGAAACT
1 AAACTTCCAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCGACCCT-GAAACT
*
5977 TCCAAAAATTTCATTTTCACCCCTA
65 TCCAAAAATTCCATTTTCACCCC-A
* * * *
6002 AAACTTCCAAAATTCCATTTTTAACCCCAAAGC-TCCAAGATTTCCATTTT
1 AAACTTCCAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTT
6052 TAACCTCGAA
Statistics
Matches: 199, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
87 10 0.05
88 33 0.17
89 136 0.68
90 12 0.06
91 8 0.04
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (88 bp):
AAACTTCCAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCGACCCTGAAACTT
CCAAAAATTCCATTTTCACCCCA
Found at i:6130 original size:30 final size:29
Alignment explanation
Indices: 5760--6130 Score: 229
Period size: 30 Copynumber: 12.6 Consensus size: 29
5750 ACATTTTTAC
*
5760 CCTCG-AACTTCCATAAATTCCATTTTCGA
1 CCTCGAAACTT-CAAAAATTCCATTTTCGA
* *
5789 CCTTGAAACTTCCACAAATTCCATTTTC-A
1 CCTCGAAACTT-CAAAAATTCCATTTTCGA
* *
5818 CC-CCAAACTTCCAAAAATTCCAATTTTTGA
1 CCTCGAAACTT-CAAAAATTCC-ATTTTCGA
* *
5848 CCCCAAAACTTCCAAAAATTCCATTTTCGA
1 CCTCGAAACTT-CAAAAATTCCATTTTCGA
*
5878 CC-CTAAAACTTCAAAAAATTCCATTTTC-A
1 CCTC-GAAACTTC-AAAAATTCCATTTTCGA
* * *
5907 CCCCCGAAACTTCCAAAATTCCATTTTTGA
1 -CCTCGAAACTTCAAAAATTCCATTTTCGA
* ***
5937 CCTCAAAACTTCCAAAAATTTTGTTTTC-A
1 CCTCGAAACTT-CAAAAATTCCATTTTCGA
*
5966 CCCTCGAAACTTCCAAAAATTTCATTTTC-A
1 -CCTCGAAACTT-CAAAAATTCCATTTTCGA
* * * **
5996 CCCCTAAAACTTCCAAAATTCCATTTTTAA
1 CCTC-GAAACTTCAAAAATTCCATTTTCGA
* * * * **
6026 CC-CCAAAGCTCCAAGATTTCCATTTTTAA
1 CCTCGAAA-CTTCAAAAATTCCATTTTCGA
* * *
6055 CCTCGAAACTTTAAAAAATTAGCATTTT-GC
1 CCTCGAAAC-TTCAAAAATT-CCATTTTCGA
** * *
6085 CCTCGAATGTCCAAAAACTCCATTTTCGA
1 CCTCGAAACTTCAAAAATTCCATTTTCGA
6114 CCTCGAAACTCTCAAAA
1 CCTCGAAACT-TCAAAA
6131 TTACCCTTTT
Statistics
Matches: 274, Mismatches: 49, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
28 25 0.09
29 91 0.33
30 133 0.49
31 25 0.09
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (29 bp):
CCTCGAAACTTCAAAAATTCCATTTTCGA
Found at i:10403 original size:13 final size:13
Alignment explanation
Indices: 10375--10414 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
10365 AAAATTTCAG
10375 AATTATGTAT--A
1 AATTATGTATAAA
10386 AATTAT-TAGTAAA
1 AATTATGTA-TAAA
10399 AATTATGTATAAA
1 AATTATGTATAAA
10412 AAT
1 AAT
10415 AATTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.08
11 7 0.28
13 14 0.56
14 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (13 bp):
AATTATGTATAAA
Found at i:10701 original size:163 final size:164
Alignment explanation
Indices: 10412--11087 Score: 945
Period size: 163 Copynumber: 4.1 Consensus size: 164
10402 TATGTATAAA
* * *
10412 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGG-CTTCTATTTCTAATAATTTA
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGAC-CCCATTCCTAATAATTTA
* * * * * * *
10476 TTTGATTGATTACGAATGAATTGTTTCGATAATTAACAAAAGA-CAGTTCATGAAGATTTCATTT
65 TCTGATTGATTACGAATGAGTTGTTTCAATAATTGACAAAAGATGA-TTCGTGAAGATTTCATTC
*
10540 ATCACATTTTAGTGGAAAATGTATAGGTAAAATTTC
129 ATCACATTTGAGTGGAAAATGTATAGGTAAAATTTC
* *
10576 AATAATTTTATATGACATTTTATGATCATAATTGATATGATAGG-CCCCATTCCTAATAATTTAT
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGACCCCATTCCTAATAATTTAT
* *
10640 CTGATTGATTACAAATGAGTTGTTTCAATAATTGACAATAGATGATTCGTGAAGATTTCATTCAT
66 CTGATTGATTACGAATGAGTTGTTTCAATAATTGACAAAAGATGATTCGTGAAGATTTCATTCAT
* *
10705 CATATTTGAGTGGAAAATGTCTAGGTAAAATTTC
131 CACATTTGAGTGGAAAATGTATAGGTAAAATTTC
* * *
10739 AATAATTTTATGTGACAGTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAA--TAT
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGACCCCATTCCTAATAATTTAT
* * * *
10802 CTGATTGATTAGGAAT-AGGTTGTTTCAACAATTGACAAAAGATGGTTTGTGAAGATTTCATTCA
66 CTGATTGATTACGAATGA-GTTGTTTCAATAATTGACAAAAGATGATTCGTGAAGATTTCATTCA
* *
10866 TCACATTTGAGT-GAAAAAGTGTAGGTAAAATTTC
130 TCACATTTGAGTGGAAAATGTATAGGTAAAATTTC
*
10900 AATAATTTTATATGACATTATTTGATCATAATTGACATGATAGGACCCCATTCCTAATAATTTAT
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGACCCCATTCCTAATAATTTAT
* * * * *
10965 CTGATTGATTAGGAATG-GTTTGTTTCAATAATTGACAAAATATGGTTGGTGAAAATTTCATTCA
66 CTGATTGATTACGAATGAG-TTGTTTCAATAATTGACAAAAGATGATTCGTGAAGATTTCATTCA
* *
11029 TCACATTTGTGTGGAAAATGTATAGGTAAAATTTTG
130 TCACATTTGAGTGGAAAATGTATAGGTAAAA-TTTC
11065 AATAATTTTATATGACATTATAT
1 AATAATTTTATATGACATTATAT
11088 AATGGACAGA
Statistics
Matches: 459, Mismatches: 44, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
161 77 0.17
162 71 0.15
163 212 0.46
164 74 0.16
165 25 0.05
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (164 bp):
AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGACCCCATTCCTAATAATTTAT
CTGATTGATTACGAATGAGTTGTTTCAATAATTGACAAAAGATGATTCGTGAAGATTTCATTCAT
CACATTTGAGTGGAAAATGTATAGGTAAAATTTC
Found at i:11025 original size:325 final size:327
Alignment explanation
Indices: 10412--11087 Score: 977
Period size: 325 Copynumber: 2.1 Consensus size: 327
10402 TATGTATAAA
* * * *
10412 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGCTTCTATTTCTAATAATTTAT
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAA-TTAT
* * * *
10477 TTGATTGATTACGAATGAATTGTTTCGATAATTAACAAAAGACAGTTCATGAAGATTTCATTTAT
65 CTGATTGATTACGAATGAATTGTTTCAACAATTAACAAAAGACAGTTCATGAAGATTTCATTCAT
* *
10542 CACATTTTAGTGGAAAATGTATAGGTAAAATTTCAATAATTTTATATGACATTTTATGATCATAA
130 CACATTTGAGTGGAAAAAGTATAGGTAAAATTTCAATAATTTTATATGACATTTTATGATCATAA
*
10607 TTGATATGATAGGCCCCATTCCTAATAATTTATCTGATTGATTACAAATGAGTTGTTTCAATAAT
195 TTGACATGATAGGCCCCATTCCTAATAATTTATCTGATTGATTACAAATGAGTTGTTTCAATAAT
* * * *
10672 TGACAATAGATGATTCGTGAAGATTTCATTCATCATATTTGAGTGGAAAATGTCTAGGTAAAA-T
260 TGACAAAAGATGATTCGTGAAAATTTCATTCATCACATTTGAGTGGAAAATGTATAGGTAAAATT
10736 TTC
325 TTC
* *
10739 AATAATTTTATGTGACAGTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAA-TATC
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAATTATC
* * * ** **
10803 TGATTGATTAGGAAT-AGGTTGTTTCAACAATTGACAAAAGATGGTTTGTGAAGATTTCATTCAT
66 TGATTGATTACGAATGA-ATTGTTTCAACAATTAACAAAAGACAGTTCATGAAGATTTCATTCAT
*
10867 CACATTTGAGT-GAAAAAGTGTAGGTAAAATTTCAATAATTTTATATGACATTATT-TGATCATA
130 CACATTTGAGTGGAAAAAGTATAGGTAAAATTTCAATAATTTTATATGACATT-TTATGATCATA
**
10930 ATTGACATGATAGGACCCCATTCCTAATAATTTATCTGATTGATTAGGAATG-GTTTGTTTCAAT
194 ATTGACATGATAGG-CCCCATTCCTAATAATTTATCTGATTGATTACAAATGAG-TTGTTTCAAT
* * * *
10994 AATTGACAAAATATGGTTGGTGAAAATTTCATTCATCACATTTGTGTGGAAAATGTATAGGTAAA
257 AATTGACAAAAGATGATTCGTGAAAATTTCATTCATCACATTTGAGTGGAAAATGTATAGGTAAA
*
11059 ATTTTG
322 ATTTTC
11065 AATAATTTTATATGACATTATAT
1 AATAATTTTATATGACATTATAT
11088 AATGGACAGA
Statistics
Matches: 310, Mismatches: 34, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
324 62 0.20
325 170 0.55
326 24 0.08
327 54 0.17
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (327 bp):
AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAATTATC
TGATTGATTACGAATGAATTGTTTCAACAATTAACAAAAGACAGTTCATGAAGATTTCATTCATC
ACATTTGAGTGGAAAAAGTATAGGTAAAATTTCAATAATTTTATATGACATTTTATGATCATAAT
TGACATGATAGGCCCCATTCCTAATAATTTATCTGATTGATTACAAATGAGTTGTTTCAATAATT
GACAAAAGATGATTCGTGAAAATTTCATTCATCACATTTGAGTGGAAAATGTATAGGTAAAATTT
TC
Found at i:16418 original size:87 final size:86
Alignment explanation
Indices: 16264--16422 Score: 239
Period size: 87 Copynumber: 1.8 Consensus size: 86
16254 TGCATAAGGA
* *
16264 TGAGTTTTTACTGTTAATGAATTCATATCCAAGATTTTGGGTGATCCTATTGAGACGGACATGAT
1 TGAGTTTTTACTCTTAATGAATTCATATCCAAGATTTTGGGTGATCCTATTGAGACGGACATAAT
16329 GAATTCACTGACTTGACAGGT
66 GAATTCACTGACTTGACAGGT
* * * *
16350 TGAGTTTATTACTCTTAATGAGTTCATATCCCAGATTTTTGGT-AGTCCTATTGAGACGGACTTA
1 TGAGTTT-TTACTCTTAATGAATTCATATCCAAGATTTTGGGTGA-TCCTATTGAGACGGACATA
16414 ATGAATTCA
64 ATGAATTCA
16423 TCGAACTTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
86 8 0.12
87 57 0.88
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (86 bp):
TGAGTTTTTACTCTTAATGAATTCATATCCAAGATTTTGGGTGATCCTATTGAGACGGACATAAT
GAATTCACTGACTTGACAGGT
Found at i:20385 original size:14 final size:14
Alignment explanation
Indices: 20356--20389 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
20346 TTCAAGTAGA
20356 AATATGTTAATTAT
1 AATATGTTAATTAT
20370 AATAT-TTAATTAAT
1 AATATGTTAATT-AT
20384 AATATG
1 AATATG
20390 ATATGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
AATATGTTAATTAT
Found at i:26770 original size:7 final size:7
Alignment explanation
Indices: 26758--26800 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
26748 CATTGTTGTG
26758 ATCCCTC
1 ATCCCTC
26765 ATCCCTC
1 ATCCCTC
26772 ATCCCTC
1 ATCCCTC
26779 ATCCCTC
1 ATCCCTC
26786 ATCCCTC
1 ATCCCTC
26793 ATCCCTC
1 ATCCCTC
26800 A
1 A
26801 AGTAATTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.16, C:0.56, G:0.00, T:0.28
Consensus pattern (7 bp):
ATCCCTC
Found at i:27279 original size:14 final size:13
Alignment explanation
Indices: 27260--27289 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
27250 ATCTAAATAT
27260 TTTTGTAGAAAATG
1 TTTTGTAGAAAA-G
27274 TTTTGTAGAAAAG
1 TTTTGTAGAAAAG
27287 TTT
1 TTT
27290 CATTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (13 bp):
TTTTGTAGAAAAG
Found at i:31952 original size:28 final size:27
Alignment explanation
Indices: 31919--32071 Score: 114
Period size: 28 Copynumber: 5.5 Consensus size: 27
31909 TGAAAAAGTG
*
31919 AGCCTTTGTTGTTGTATCTTTAAAAGGA
1 AGCCTTTGTGGTTG-ATCTTTAAAAGGA
* *
31947 AGCCTTTGTGGTTGATTTTGTTAAAGGA
1 AGCCTTTGTGGTTGATCTT-TAAAAGGA
* * * *
31975 AGCTTTTGTGGCTGGTTCTGTT-AAATGA
1 AGCCTTTGTGG-TTGATCT-TTAAAAGGA
32003 AGCCTTTGTGGTTGAT-TTTATTAAAGGA
1 AGCCTTTGTGGTTGATCTTTA--AAAGGA
* * * *
32031 AGCCTTTATGGCT-AGTTTTGTTAAAGGA
1 AGCCTTTGTGGTTGA-TCTT-TAAAAGGA
32059 AGCCTTTGTGGTT
1 AGCCTTTGTGGTT
32072 AATTCTAGTA
Statistics
Matches: 99, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 8 0.08
28 79 0.80
29 7 0.07
30 2 0.02
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (27 bp):
AGCCTTTGTGGTTGATCTTTAAAAGGA
Found at i:32005 original size:56 final size:56
Alignment explanation
Indices: 31941--32071 Score: 208
Period size: 56 Copynumber: 2.3 Consensus size: 56
31931 TGTATCTTTA
* * * *
31941 AAAGGAAGCCTTTGTGGTTGATTTTGTTAAAGGAAGCTTTTGTGGCTGGTTCTGTT
1 AAAGGAAGCCTTTGTGGTTGATTTTATTAAAGGAAGCCTTTATGGCTAGTTCTGTT
* *
31997 AAATGAAGCCTTTGTGGTTGATTTTATTAAAGGAAGCCTTTATGGCTAGTTTTGTT
1 AAAGGAAGCCTTTGTGGTTGATTTTATTAAAGGAAGCCTTTATGGCTAGTTCTGTT
32053 AAAGGAAGCCTTTGTGGTT
1 AAAGGAAGCCTTTGTGGTT
32072 AATTCTAGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.40
Consensus pattern (56 bp):
AAAGGAAGCCTTTGTGGTTGATTTTATTAAAGGAAGCCTTTATGGCTAGTTCTGTT
Found at i:34526 original size:18 final size:18
Alignment explanation
Indices: 34505--34542 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
34495 TGAATAAATT
34505 TCAA-ATATAAAATATTTA
1 TCAATATATAAAAT-TTTA
34523 TCAATTATATAAAATTTTA
1 TCAA-TATATAAAATTTTA
34542 T
1 T
34543 TAATGAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TCAATATATAAAATTTTA
Found at i:40282 original size:21 final size:20
Alignment explanation
Indices: 40258--40299 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
40248 CTTATTATAA
40258 AAAATAATTGAAG-GAAAATAT
1 AAAATAA-TGAAGAG-AAATAT
*
40279 AAAATTATGAAGAGAAATAT
1 AAAATAATGAAGAGAAATAT
40299 A
1 A
40300 CCTTTTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (20 bp):
AAAATAATGAAGAGAAATAT
Found at i:51154 original size:10 final size:10
Alignment explanation
Indices: 51139--51189 Score: 70
Period size: 10 Copynumber: 5.3 Consensus size: 10
51129 AAAGTTAGAA
51139 ACACACACGC
1 ACACACACGC
*
51149 ACACACACAC
1 ACACACACGC
51159 ACACACACG-
1 ACACACACGC
51168 -CACACACGC
1 ACACACACGC
*
51177 ACGCACACGC
1 ACACACACGC
51187 ACA
1 ACA
51190 TATATATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
8 8 0.23
10 27 0.77
ACGTcount: A:0.41, C:0.49, G:0.10, T:0.00
Consensus pattern (10 bp):
ACACACACGC
Found at i:51155 original size:4 final size:4
Alignment explanation
Indices: 51139--51189 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
51129 AAAGTTAGAA
* * * * *
51139 ACAC ACAC GCAC ACAC ACAC ACAC ACAC GCAC ACAC GCAC GCAC ACGC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
51187 ACA
1 ACA
51190 TATATATATG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.41, C:0.49, G:0.10, T:0.00
Consensus pattern (4 bp):
ACAC
Found at i:51157 original size:6 final size:6
Alignment explanation
Indices: 51139--51189 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
51129 AAAGTTAGAA
* * * * *
51139 ACACAC ACGCAC ACACAC ACACAC ACACGC ACACAC GCACGC ACACGC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
51187 ACA
1 ACA
51190 TATATATATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.41, C:0.49, G:0.10, T:0.00
Consensus pattern (6 bp):
ACACAC
Found at i:59890 original size:37 final size:37
Alignment explanation
Indices: 59830--59903 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
59820 GCTTTCAAAT
*
59830 GAATGACCACCGTTATTCCCGTACCGCGAACTATTTG
1 GAATGACCACCGTTATTCACGTACCGCGAACTATTTG
* *
59867 GAATGACCATCG-TATTTCACGTACCTCGAACTATTTG
1 GAATGACCACCGTTA-TTCACGTACCGCGAACTATTTG
59904 AGTATGGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 2 0.06
37 31 0.94
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (37 bp):
GAATGACCACCGTTATTCACGTACCGCGAACTATTTG
Found at i:65086 original size:22 final size:22
Alignment explanation
Indices: 65042--65086 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
65032 CAACCCGTTA
* *
65042 ACCAACCCGACCCGACCTTTTG
1 ACCAACCCGACCCGAACTATTG
* *
65064 ACCAACTCGACCTGAACTATTG
1 ACCAACCCGACCCGAACTATTG
65086 A
1 A
65087 TTTTGATCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.38, G:0.13, T:0.20
Consensus pattern (22 bp):
ACCAACCCGACCCGAACTATTG
Found at i:65103 original size:23 final size:23
Alignment explanation
Indices: 65077--65120 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
65067 AACTCGACCT
* *
65077 GAACTATTGATTTTGATCGAATC
1 GAACCATTGATTTTGACCGAATC
*
65100 GAACCGTTGATTTTGACCGAA
1 GAACCATTGATTTTGACCGAA
65121 CCGTTGACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (23 bp):
GAACCATTGATTTTGACCGAATC
Found at i:71229 original size:19 final size:20
Alignment explanation
Indices: 71205--71255 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
71195 GATAGTGAAA
71205 AAATTAAAAAAAATTATT-G
1 AAATTAAAAAAAATTATTAG
*
71224 AAATTATAAAAAACTTATTAG
1 AAATTA-AAAAAAATTATTAG
71245 AAA-TAAAAAAA
1 AAATTAAAAAAA
71256 TATTTGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.41
20 13 0.45
21 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
AAATTAAAAAAAATTATTAG
Found at i:71235 original size:21 final size:21
Alignment explanation
Indices: 71209--71274 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 21
71199 GTGAAAAAAT
71209 TAAAAAAAATTATTGAAATTA
1 TAAAAAAAATTATTGAAATTA
*
71230 T-AAAAAACTTATTAGAAA-TA
1 TAAAAAAAATTATT-GAAATTA
*
71250 -AAAAAATA-T-TTGTAAATTA
1 TAAAAAAAATTATTG-AAATTA
71269 TAAAAA
1 TAAAAA
71275 TATATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
17 1 0.03
18 5 0.14
19 3 0.08
20 23 0.62
21 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAAAAAAATTATTGAAATTA
Found at i:71273 original size:19 final size:19
Alignment explanation
Indices: 71263--71303 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
71253 AAATATTTGT
71263 AAATTATAAAAATATATAA
1 AAATTATAAAAATATATAA
71282 AAATTATAAAAA-ATACTAA
1 AAATTATAAAAATATA-TAA
71301 AAA
1 AAA
71304 ACATAAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATTATAAAAATATATAA
Found at i:71280 original size:10 final size:9
Alignment explanation
Indices: 71263--71303 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
71253 AAATATTTGT
71263 AAATTATAA
1 AAATTATAA
71272 AAATATATAA
1 AAAT-TATAA
71282 AAATTATAA
1 AAATTATAA
*
71291 AAAATACTAA
1 AAATTA-TAA
71301 AAA
1 AAA
71304 ACATAAGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATTATAA
Found at i:71293 original size:39 final size:39
Alignment explanation
Indices: 71203--71296 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 39
71193 GTGATAGTGA
71203 AAAAATTAAAAAAA-ATTATTGAAATTATAAAAAACTTATT
1 AAAAATTAAAAAAATA-TATTGAAATTATAAAAAAC-TATT
*
71243 AGAAA-TAAAAAAATAT-TTGTAAATTAT-AAAAA-TATAT
1 AAAAATTAAAAAAATATATTG-AAATTATAAAAAACTAT-T
71280 AAAAATTATAAAAAATA
1 AAAAATTA-AAAAAATA
71297 CTAAAAAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
36 3 0.06
37 5 0.11
38 10 0.21
39 24 0.51
40 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (39 bp):
AAAAATTAAAAAAATATATTGAAATTATAAAAAACTATT
Found at i:71294 original size:21 final size:20
Alignment explanation
Indices: 71203--71294 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 20
71193 GTGATAGTGA
71203 AAAAATTA-AAAAAAATTAT
1 AAAAATTATAAAAAAATTAT
** *
71222 TGAAATTATAAAAAACTTATT
1 AAAAATTATAAAAAAATTA-T
*
71243 AGAAA-TA-AAAAAATATT-T
1 AAAAATTATAAAAAA-ATTAT
** *
71261 GTAAATTATAAAAATA-TAT
1 AAAAATTATAAAAAAATTAT
71280 AAAAATTATAAAAAA
1 AAAAATTATAAAAAA
71295 TACTAAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
18 5 0.09
19 28 0.50
20 18 0.32
21 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (20 bp):
AAAAATTATAAAAAAATTAT
Found at i:71304 original size:10 final size:9
Alignment explanation
Indices: 71267--71309 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
71257 ATTTGTAAAT
71267 TATAAAAATA
1 TATAAAAA-A
*
71277 TATAAAAAT
1 TATAAAAAA
71286 TATAAAAAA
1 TATAAAAAA
71295 TACTAAAAAA
1 TA-TAAAAAA
*
71305 CATAA
1 TATAA
71310 GACATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (9 bp):
TATAAAAAA
Found at i:71309 original size:19 final size:19
Alignment explanation
Indices: 71268--71309 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
71258 TTTGTAAATT
**
71268 ATAAAAATATATAAAAATT
1 ATAAAAATATATAAAAAAC
71287 ATAAAAA-ATACTAAAAAAC
1 ATAAAAATATA-TAAAAAAC
71306 ATAA
1 ATAA
71310 GACATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
ATAAAAATATATAAAAAAC
Found at i:71724 original size:80 final size:81
Alignment explanation
Indices: 71576--71730 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 81
71566 TACGTTAGTA
* * * * * **
71576 AAAATATAATTTTATCATTTTAATAGTTTATATCTTTATAATTTTTAAAAGATTAAATTAAATTT
1 AAAATACAATTTTATCATTTTAATA-TTAAAATCTTTATAAATTATAAAAGATTAAATTAAAAAT
*
71641 TTATTATTTTTGAAGTC
65 TTATCATTTTTGAAGTC
71658 AAAATACAATTTTATCATTATTAAT-TTAAAAT-TTTATAAATTATAAAA-ATTTAAATTAAAAA
1 AAAATACAATTTTATCATT-TTAATATTAAAATCTTTATAAATTATAAAAGA-TTAAATTAAAAA
71720 TTTATCATTTT
64 TTTATCATTTT
71731 AAAAGAGTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
79 1 0.02
80 34 0.54
81 5 0.08
82 18 0.29
83 5 0.08
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (81 bp):
AAAATACAATTTTATCATTTTAATATTAAAATCTTTATAAATTATAAAAGATTAAATTAAAAATT
TATCATTTTTGAAGTC
Found at i:72063 original size:36 final size:37
Alignment explanation
Indices: 71996--72065 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
71986 TTTTATTTTT
*
71996 ATTTTTATAATTTCTAGAATTTTTTTAAAAAATTATG
1 ATTTTTATAATTTATAGAATTTTTTTAAAAAATTATG
* * *
72033 ATTTTTATCATTTATA-ATTTTTTTTTAAAAATT
1 ATTTTTATAATTTATAGAATTTTTTTAAAAAATT
72066 CTAATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 15 0.52
37 14 0.48
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (37 bp):
ATTTTTATAATTTATAGAATTTTTTTAAAAAATTATG
Found at i:72133 original size:20 final size:18
Alignment explanation
Indices: 72090--72191 Score: 59
Period size: 20 Copynumber: 5.5 Consensus size: 18
72080 AAAATTTTGA
72090 AATA-TTTTATATTTTAT
1 AATATTTTTATATTTTAT
* *
72107 AACATTTTTATATTTTTTCT
1 AATATTTTTATA--TTTTAT
* *
72127 AATATTTTTAGGA-ATTACT
1 AATATTTTTA-TATTTTA-T
*
72146 -AT-TTTTTAAATTTTTAT
1 AATATTTTTATA-TTTTAT
*
72163 AATATTTTTTACATTTTTAT
1 AATA-TTTTTATA-TTTTAT
72183 AATATTTTT
1 AATATTTTT
72192 TTAATTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.02
17 10 0.15
18 16 0.24
19 6 0.09
20 32 0.48
21 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
AATATTTTTATATTTTAT
Found at i:72160 original size:9 final size:9
Alignment explanation
Indices: 72146--72200 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
72136 AGGAATTACT
72146 ATTTTTTAA
1 ATTTTTTAA
72155 ATTTTTATAA
1 ATTTTT-TAA
*
72165 TATTTTTTAC
1 -ATTTTTTAA
72175 ATTTTTATAA
1 ATTTTT-TAA
*
72185 TATTTTTTTA
1 -ATTTTTTAA
72195 ATTTTT
1 ATTTTT
72201 ATGACTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 18 0.46
10 9 0.23
11 12 0.31
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:72192 original size:20 final size:19
Alignment explanation
Indices: 72145--72202 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 19
72135 TAGGAATTAC
72145 TATTTTTTAAATTTTTATAA
1 TATTTTTT-AATTTTTATAA
72165 TATTTTTTACATTTTTATAA
1 TATTTTTTA-ATTTTTATAA
72185 TATTTTTTTAATTTTTAT
1 TA-TTTTTTAATTTTTAT
72203 GACTAAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.78
21 7 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTTAATTTTTATAA
Found at i:81565 original size:17 final size:18
Alignment explanation
Indices: 81540--81573 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
81530 GTGACATGTG
81540 TATAAATAAA-TAATTTT
1 TATAAATAAATTAATTTT
*
81557 TATATATAAATTAATTT
1 TATAAATAAATTAATTT
81574 AATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAATAAATTAATTTT
Found at i:86138 original size:52 final size:51
Alignment explanation
Indices: 86060--86297 Score: 280
Period size: 52 Copynumber: 4.6 Consensus size: 51
86050 ATTTCATTTA
* ** * * * *
86060 ATACTCACGATGATACATAGTCATCGGACCTCACAATCCGTAAAGTACCGAT
1 ATACTCACGATGACATGTAGTCATCGGACCTCATAATCCATAAAGGATC-AT
* *
86112 ATACTCACGATGACATGCAGTCATCGGACCTCATAATCCATAAAGGATTTAT
1 ATACTCACGATGACATGTAGTCATCGGACCTCATAATCCATAAAGGA-TCAT
* *
86164 ATACTCACGATGACATGTAGTCATCAGACCTTATAATCCATAAAGGATTCAT
1 ATACTCACGATGACATGTAGTCATCGGACCTCATAATCCATAAAGGA-TCAT
* * *
86216 ATACTCACGGTGACACGTAGTCATCGGACCTCATAATCCATAAGGGATTCAT
1 ATACTCACGATGACATGTAGTCATCGGACCTCATAATCCATAAAGGA-TCAT
* **
86268 A-ACTCACAATGACACATAGTCATCGGACCT
1 ATACTCACGATGACATGTAGTCATCGGACCT
86298 TTTACATTTA
Statistics
Matches: 164, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
51 26 0.16
52 138 0.84
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (51 bp):
ATACTCACGATGACATGTAGTCATCGGACCTCATAATCCATAAAGGATCAT
Found at i:86240 original size:104 final size:104
Alignment explanation
Indices: 86055--86298 Score: 323
Period size: 104 Copynumber: 2.4 Consensus size: 104
86045 GATTCATTTC
* * * *
86055 ATTTA-ATACTCACGATGATACATAGTCATCGGACCTCACAATCCGTAAAGTACCGATATACTCA
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTTACAATCCATAAAGGACCGATATACTCA
*
86119 CGATGACATGCAGTCATCGGACCTCATAATCCATAAAGG
66 CGATGACACGCAGTCATCGGACCTCATAATCCATAAAGG
** * * *
86158 ATTTATATACTCACGATGACATGTAGTCATCAGACCTTATAATCCATAAAGGATTC-ATATACTC
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTTACAATCCATAAAGGA-CCGATATACTC
* * *
86222 ACGGTGACACGTAGTCATCGGACCTCATAATCCATAAGGG
65 ACGATGACACGCAGTCATCGGACCTCATAATCCATAAAGG
* *
86262 ATTCATA-ACTCACAATGACACATAGTCATCGGACCTT
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTT
86299 TTACATTTAT
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
103 31 0.26
104 89 0.74
105 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (104 bp):
ATTTATATACTCACGATGACACATAGTCATCGGACCTTACAATCCATAAAGGACCGATATACTCA
CGATGACACGCAGTCATCGGACCTCATAATCCATAAAGG
Found at i:91581 original size:11 final size:11
Alignment explanation
Indices: 91565--91635 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 11
91555 GATAGTCACT
91565 TTAATATTAAA
1 TTAATATTAAA
91576 TTAATA--AAA
1 TTAATATTAAA
*
91585 -TACTATTAAAA
1 TTAATATT-AAA
*
91596 TAAATATTAAA
1 TTAATATTAAA
*
91607 TTAA-ATTTAA
1 TTAATATTAAA
*
91617 -TACTATTAAA
1 TTAATATTAAA
*
91627 GTAATATTA
1 TTAATATTA
91636 TTTTTGAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
8 4 0.09
9 5 0.11
10 10 0.22
11 22 0.48
12 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:91602 original size:31 final size:31
Alignment explanation
Indices: 91566--91635 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
91556 ATAGTCACTT
91566 TAATATTAAATT-AATAAAATACTATTAAAA
1 TAATATTAAATTAAATAAAATACTATTAAAA
** *
91596 TAAATATTAAATTAAATTTAATACTATTAAAG
1 T-AATATTAAATTAAATAAAATACTATTAAAA
91628 TAATATTA
1 TAATATTA
91636 TTTTTGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 1 0.03
31 18 0.51
32 16 0.46
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (31 bp):
TAATATTAAATTAAATAAAATACTATTAAAA
Found at i:95473 original size:17 final size:17
Alignment explanation
Indices: 95438--95479 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
95428 GGAAAAAGTA
*
95438 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
95456 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
95473 GTTAAAG
1 GTTAAAG
95480 GTCAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:95479 original size:24 final size:24
Alignment explanation
Indices: 95452--95499 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
95442 CAAGAATATG
* *
95452 AAAGGTTAAAGAAGATGGAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
* *
95476 AAAGGTCAAGGGAGATGAAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
95500 GAACATCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.19
Consensus pattern (24 bp):
AAAGGTCAAAGAAGATGAAAGGTT
Found at i:103747 original size:17 final size:17
Alignment explanation
Indices: 103725--103780 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
103715 GATTCAATAC
103725 TTTAATTCGATTAATTT
1 TTTAATTCGATTAATTT
103742 TTTAATTCGATTAATTT
1 TTTAATTCGATTAATTT
* *
103759 TGGTAATTCGAGTAATTT
1 T-TTAATTCGATTAATTT
103777 TTTA
1 TTTA
103781 TACTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (17 bp):
TTTAATTCGATTAATTT
Found at i:109209 original size:22 final size:21
Alignment explanation
Indices: 109184--109231 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
109174 TTCTTCCGTT
*
109184 TCATCTCAATTCTATTTTCATA
1 TCATCTC-ATTCTAGTTTCATA
* *
109206 TCATTCTCATTTTAGTTTCATT
1 TCA-TCTCATTCTAGTTTCATA
109228 TCAT
1 TCAT
109232 AATCAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 17 0.77
23 4 0.18
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.54
Consensus pattern (21 bp):
TCATCTCATTCTAGTTTCATA
Found at i:110210 original size:3 final size:3
Alignment explanation
Indices: 110202--110230 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
110192 TTTTACTTTT
110202 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
110231 CTTATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:118435 original size:15 final size:15
Alignment explanation
Indices: 118415--118445 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
118405 AATCAATTGT
118415 GCCTCACCCAAATGA
1 GCCTCACCCAAATGA
118430 GCCTCACCCAAATGA
1 GCCTCACCCAAATGA
118445 G
1 G
118446 TTTGAGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.39, G:0.16, T:0.13
Consensus pattern (15 bp):
GCCTCACCCAAATGA
Found at i:121007 original size:180 final size:180
Alignment explanation
Indices: 120702--121065 Score: 692
Period size: 180 Copynumber: 2.0 Consensus size: 180
120692 CCTCAAATGG
* *
120702 TGTAAGCAGCTTCATCCGATTTTGAAGTAGCATATGGTCTATCCCATCAGAGATGTCCTCTTCAC
1 TGTAAGCAGCTTCATCCGATCTCGAAGTAGCATATGGTCTATCCCATCAGAGATGTCCTCTTCAC
120767 ACTTCACTGATACCATGTTACCAAAAGTGCTCCTTTCTGGGTTTTGCAAGTTACTATAATCTAAT
66 ACTTCACTGATACCATGTTACCAAAAGTGCTCCTTTCTGGGTTTTGCAAGTTACTATAATCTAAT
120832 GGTTCAACTTTCACTTTGACAGAAGTATTCAAAGCTGAACTGCATATATT
131 GGTTCAACTTTCACTTTGACAGAAGTATTCAAAGCTGAACTGCATATATT
120882 TGTAAGCAGCTTCATCCGATCTCGAAGTAGCATATGGTCTATCCCATCAGAGATGTCCTCTTCAC
1 TGTAAGCAGCTTCATCCGATCTCGAAGTAGCATATGGTCTATCCCATCAGAGATGTCCTCTTCAC
* *
120947 ACTTTACTGATACCATGTTACCAAAAGTGCTCCTTTCTGGGTTTTGCAAGTTAGTATAATCTAAT
66 ACTTCACTGATACCATGTTACCAAAAGTGCTCCTTTCTGGGTTTTGCAAGTTACTATAATCTAAT
121012 GGTTCAACTTTCACTTTGACAGAAGTATTCAAAGCTGAACTGCATATATT
131 GGTTCAACTTTCACTTTGACAGAAGTATTCAAAGCTGAACTGCATATATT
121062 TGTA
1 TGTA
121066 CTTGCAGGAA
Statistics
Matches: 180, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 180 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (180 bp):
TGTAAGCAGCTTCATCCGATCTCGAAGTAGCATATGGTCTATCCCATCAGAGATGTCCTCTTCAC
ACTTCACTGATACCATGTTACCAAAAGTGCTCCTTTCTGGGTTTTGCAAGTTACTATAATCTAAT
GGTTCAACTTTCACTTTGACAGAAGTATTCAAAGCTGAACTGCATATATT
Found at i:124670 original size:23 final size:23
Alignment explanation
Indices: 124638--124681 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
124628 TTTGATTTAG
*
124638 GACGGATTTGAATGGGTAGGTGC
1 GACGGATTTGAATGGATAGGTGC
* *
124661 GACGGGTTTGGATGGATAGGT
1 GACGGATTTGAATGGATAGGT
124682 AGCACGCGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.07, G:0.45, T:0.27
Consensus pattern (23 bp):
GACGGATTTGAATGGATAGGTGC
Found at i:127896 original size:111 final size:111
Alignment explanation
Indices: 127693--127897 Score: 295
Period size: 111 Copynumber: 1.8 Consensus size: 111
127683 AGAAAATAAA
* *
127693 GGTCAAATTTTGATATTGAACTCTGTAATTTGTGTAAATTATGGATTTAGTATCTTTATTTTAAT
1 GGTCAAATTTTGATATTAAACTCTGTAATTTGTGTAAATTATGGATTTAGTATCTTTACTTTAAT
* * *
127758 TGGGTCATTTTCAGTTTCTATATATTTAGTATCTTTATTTTAATTG
66 TGGATCATTTTCAGTTCCTATACATTTAGTATCTTTATTTTAATTG
* * * *
127804 GGTCAAATTTTGTTATTAAAC-CATGTATTTTGTGTAAATTATGGATTTCGTATTTTTACTTTAA
1 GGTCAAATTTTGATATTAAACTC-TGTAATTTGTGTAAATTATGGATTTAGTATCTTTACTTTAA
* *
127868 TTGGATCATTTTTAGTTCCTGTACATTTAG
65 TTGGATCATTTTCAGTTCCTATACATTTAG
127898 AATTTGAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
110 1 0.01
111 81 0.99
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (111 bp):
GGTCAAATTTTGATATTAAACTCTGTAATTTGTGTAAATTATGGATTTAGTATCTTTACTTTAAT
TGGATCATTTTCAGTTCCTATACATTTAGTATCTTTATTTTAATTG
Found at i:130215 original size:19 final size:20
Alignment explanation
Indices: 130188--130230 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
130178 AATAAATTAC
* *
130188 AATTTAAAATTATATTAA-A
1 AATTCAAAATAATATTAATA
130207 AATTCAAAATAATATTAATA
1 AATTCAAAATAATATTAATA
130227 AATT
1 AATT
130231 ATTTGTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTCAAAATAATATTAATA
Found at i:134054 original size:8 final size:8
Alignment explanation
Indices: 134041--134070 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
134031 ATCTCTAGTC
134041 CAAGGTCT
1 CAAGGTCT
134049 CAAGGTCT
1 CAAGGTCT
134057 CAAGGTCT
1 CAAGGTCT
134065 CAAGGT
1 CAAGGT
134071 ATACAGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (8 bp):
CAAGGTCT
Found at i:137039 original size:21 final size:21
Alignment explanation
Indices: 136992--137054 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
136982 TAGAAGTAAG
* *
136992 ACTTGTTTCGGTAGAA-GAGTC
1 ACTTGTATCGGTAGAACTA-TC
*
137013 AATTGTATCGGTAGAACTATC
1 ACTTGTATCGGTAGAACTATC
*
137034 ACTTGTATTGGTAGAACTATC
1 ACTTGTATCGGTAGAACTATC
137055 TGTAGAAGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACTATC
Found at i:143133 original size:106 final size:107
Alignment explanation
Indices: 142935--143135 Score: 241
Period size: 106 Copynumber: 1.9 Consensus size: 107
142925 AAAAGAAGCA
* * * * *
142935 ATGTTCTTTTATTTTAGGGAATTCGAGAAATTGTGCCCTAATGTATTAGGTATTGTTTTTCTTTG
1 ATGTTCTTTTATTTTAGGGAACTCGAGAAATTGTGCCCAAACGTATGAGGTATTGTTTTTCTTTA
** *
143000 AACCTAAATAATCGAGTATCCTCTTTAAAATTAATAATGTTG
66 AACCTAAATAATCGAACATCCTATTTAAAATTAATAATGTTG
*
143042 ATGTTCTTTTA-TTTAGGGAACTCGA-AGAATTGTGCCCAAACGTACTGA-GTA-TGATTTTTTT
1 ATGTTCTTTTATTTTAGGGAACTCGAGA-AATTGTGCCCAAACGTA-TGAGGTATTG-TTTTTCT
*
143103 TTAAACCTAAATAATGGAACA-CCTTATTTAAAA
63 TTAAACCTAAATAATCGAACATCC-TATTTAAAA
143136 CCAATAAATG
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
105 5 0.06
106 62 0.77
107 13 0.16
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (107 bp):
ATGTTCTTTTATTTTAGGGAACTCGAGAAATTGTGCCCAAACGTATGAGGTATTGTTTTTCTTTA
AACCTAAATAATCGAACATCCTATTTAAAATTAATAATGTTG
Found at i:151631 original size:3 final size:3
Alignment explanation
Indices: 151623--151658 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
151613 TTCACATATT
*
151623 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
151659 ACATGACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:164564 original size:81 final size:80
Alignment explanation
Indices: 164429--164859 Score: 506
Period size: 81 Copynumber: 5.2 Consensus size: 80
164419 AGGCAAAGTT
*
164429 ACCATCCAATCTCTTACCCCGACCATG-GAGCAGATTAAAGTCATCCAATCTTTTACCCTAACCA
1 ACCATCCAATCTCTTA-CCCGACCATGAG-GCAGATTGAAGTCATCCAATCTTTTACCCTAACCA
*
164493 GAGGGCAGATTGGAGAC
64 GAGGGCAGATTGAAGAC
* * * *
164510 ACCATCCAATCTCTTACACCGACCATGAGGCAAATTAAAGTCATCTAATCTTTTACCCTAACCAA
1 ACCATCCAATCTCTTAC-CCGACCATGAGGCAGATTGAAGTCATCCAATCTTTTACCCTAACCAG
* *
164575 AGGGCAAATTAAAGAC
65 AGGGCAGATTGAAGAC
* * *
164591 ACCATCCAATCTCTTACCCTGACCATGAGGCAGATTGAAGTCATCCAATCTTTTACCTTAACTAA
1 ACCATCCAATCTCTTACCC-GACCATGAGGCAGATTGAAGTCATCCAATCTTTTACCCTAACCAG
*
164656 AGGGCATATTGAAGAC
65 AGGGCAGATTGAAGAC
* * * *
164672 ATCATTCAATCTCTTACCTCGACCAT-AGGGCAGATTGAAGCCATCCAATCTTTCACCCTAACCA
1 ACCATCCAATCTCTTACC-CGACCATGA-GGCAGATTGAAGTCATCCAATCTTTTACCCTAACCA
*
164736 GAGGGTAGATTGAAGAC
64 GAGGGCAGATTGAAGAC
* * *
164753 ACCATCTAATCTCTTACCCCGACCATGAGGTAGATTGTAGATTGAAGCCATCCAATCTTTTACCC
1 ACCATCCAATCTCTTA-CCCGACCAT---G-AG---GCAGATTGAAGTCATCCAATCTTTTACCC
* *
164818 TAACTAGAGGGCAGATTAAAGAC
58 TAACCAGAGGGCAGATTGAAGAC
* *
164841 ACAATCCAATCTTTTACCC
1 ACCATCCAATCTCTTACCC
164860 TTAAATCAAA
Statistics
Matches: 303, Mismatches: 33, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
80 4 0.01
81 230 0.76
82 4 0.01
85 1 0.00
86 1 0.00
87 3 0.01
88 60 0.20
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (80 bp):
ACCATCCAATCTCTTACCCGACCATGAGGCAGATTGAAGTCATCCAATCTTTTACCCTAACCAGA
GGGCAGATTGAAGAC
Found at i:164610 original size:42 final size:41
Alignment explanation
Indices: 164429--164860 Score: 219
Period size: 42 Copynumber: 10.5 Consensus size: 41
164419 AGGCAAAGTT
** *
164429 ACCATCCAATCTCTTACCCCGACC-ATGGAGCAGATTAAAG-
1 ACCATCCAATCTCTTACCCTAACCAAAGG-GCAGATTAAAGA
* * * **
164469 -TCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGGAGA
1 ACCATCCAATCTCTTACCCTAACCAAAGGGCAGATTAAAGA
* * *
164509 CACCATCCAATCTCTTACACC-GACC-ATGAGGCAAATTAAAG-
1 -ACCATCCAATCTCTTAC-CCTAACCAAAG-GGCAGATTAAAGA
* * * *
164550 -TCATCTAATCTTTTACCCTAACCAAAGGGCAAATTAAAGA
1 ACCATCCAATCTCTTACCCTAACCAAAGGGCAGATTAAAGA
* * *
164590 CACCATCCAATCTCTTACCCTGACC-ATGAGGCAGATTGAAG-
1 -ACCATCCAATCTCTTACCCTAACCAAAG-GGCAGATTAAAGA
* * * * * *
164631 -TCATCCAATCTTTTACCTTAACTAAAGGGCATATTGAAGA
1 ACCATCCAATCTCTTACCCTAACCAAAGGGCAGATTAAAGA
* * * * *
164671 CATCATTCAATCTCTTA-CCTCGACCATAGGGCAGATTGAAG-
1 -ACCATCCAATCTCTTACCCT-AACCAAAGGGCAGATTAAAGA
* * *
164712 -CCATCCAATCT-TTCACCCTAACCAGAGGGTAGATTGAAGA
1 ACCATCCAATCTCTT-ACCCTAACCAAAGGGCAGATTAAAGA
* ** * * *
164752 CACCATCTAATCTCTTACCCCGACC-ATGAGGTAGATTGTAGATTGA
1 -ACCATCCAATCTCTTACCCTAACCAAAG-GGCAGA-T-TA-A-AGA
* * *
164798 AGCCATCCAATCTTTTACCCTAACTAGAGGGCAGATTAAAGA
1 A-CCATCCAATCTCTTACCCTAACCAAAGGGCAGATTAAAGA
* *
164840 CACAATCCAATCTTTTACCCT
1 -ACCATCCAATCTCTTACCCT
164861 TAAATCAAAA
Statistics
Matches: 297, Mismatches: 64, Indels: 60
0.71 0.15 0.14
Matches are distributed among these distances:
38 4 0.01
39 112 0.38
40 9 0.03
41 6 0.02
42 127 0.43
43 7 0.02
44 3 0.01
45 3 0.01
46 25 0.08
47 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (41 bp):
ACCATCCAATCTCTTACCCTAACCAAAGGGCAGATTAAAGA
Found at i:164667 original size:39 final size:39
Alignment explanation
Indices: 164431--164750 Score: 173
Period size: 39 Copynumber: 8.0 Consensus size: 39
164421 GCAAAGTTAC
* ** * * *
164431 CATCCAATCTCTTACCCCGACC-ATGGAGCAGATTAAAGT
1 CATCCAATCTTTTACCCTAACCAAAGG-GCAAATTGAAGT
* * **
164470 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGGAGACAC
1 CATCCAATCTTTTACCCTAACCAAAGGGCAAATT-GA-A-GT
* * * *
164512 CATCCAATCTCTTACACC-GACC-ATGAGGCAAATTAAAGT
1 CATCCAATCTTTTAC-CCTAACCAAAG-GGCAAATTGAAGT
* * *
164551 CATCTAATCTTTTACCCTAACCAAAGGGCAAATTAAAGACAC
1 CATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAG---T
* * * *
164593 CATCCAATCTCTTACCCTGACC-ATGAGGCAGATTGAAGT
1 CATCCAATCTTTTACCCTAACCAAAG-GGCAAATTGAAGT
* * *
164632 CATCCAATCTTTTACCTTAACTAAAGGGCATATTGAAGACAT
1 CATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAG---T
* * * * * *
164674 CATTCAATCTCTTA-CCTCGACCATAGGGCAGATTGAAGC
1 CATCCAATCTTTTACCCT-AACCAAAGGGCAAATTGAAGT
* * * *
164713 CATCCAATCTTTCACCCTAACCAGAGGGTAGATTGAAG
1 CATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAG
164751 ACACCATCTA
Statistics
Matches: 215, Mismatches: 48, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
38 2 0.01
39 111 0.52
40 11 0.05
41 7 0.03
42 82 0.38
43 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (39 bp):
CATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGT
Found at i:165187 original size:18 final size:19
Alignment explanation
Indices: 165164--165209 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
165154 CTAGCCCGAT
*
165164 AAAAAAATCAAC-AAAAAC
1 AAAAAAATAAACAAAAAAC
*
165182 AAAAAAAAAAACAAAAAAC
1 AAAAAAATAAACAAAAAAC
165201 AAAATAAAT
1 AAAA-AAAT
165210 TTTAAAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.43
19 10 0.43
20 3 0.13
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.07
Consensus pattern (19 bp):
AAAAAAATAAACAAAAAAC
Found at i:165188 original size:19 final size:20
Alignment explanation
Indices: 165164--165209 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
165154 CTAGCCCGAT
*
165164 AAAAAAATCAAC-AAAAACA
1 AAAAAAATAAACAAAAAACA
165183 AAAAAAA-AAACAAAAAACA
1 AAAAAAATAAACAAAAAACA
*
165202 AAATAAAT
1 AAAAAAAT
165210 TTTAAAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.07
Consensus pattern (20 bp):
AAAAAAATAAACAAAAAACA
Found at i:170961 original size:44 final size:43
Alignment explanation
Indices: 170835--170965 Score: 163
Period size: 43 Copynumber: 3.0 Consensus size: 43
170825 ATTTTTATAT
* * * * *
170835 TCATTCGATCACATACTTCCTATATTAGGAAATAGTGTTCCAC
1 TCATTCGATCACATACTTACAATATTAGGAAACAATGTTCCTC
* * * *
170878 ACATTCGATGACATCCTTTCAATATTAGGAAACAATGTTCCTC
1 TCATTCGATCACATACTTACAATATTAGGAAACAATGTTCCTC
*
170921 TCATTCAATCACATACTTACAATATTTAGGAAACAATGTTCCTC
1 TCATTCGATCACATACTTACAATA-TTAGGAAACAATGTTCCTC
170965 T
1 T
170966 AAATGTCATT
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
43 54 0.73
44 20 0.27
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (43 bp):
TCATTCGATCACATACTTACAATATTAGGAAACAATGTTCCTC
Found at i:174819 original size:27 final size:29
Alignment explanation
Indices: 174789--174854 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 29
174779 TTTTTAAAAC
174789 ATATTTATTTTA-TT-TTAATAATTTTAT
1 ATATTTATTTTATTTATTAATAATTTTAT
**
174816 ATA-TT-TTTTATTTATTAATTTTTTTAT
1 ATATTTATTTTATTTATTAATAATTTTAT
*
174843 ATATTCATTTTA
1 ATATTTATTTTA
174855 ATATTATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.16
26 4 0.12
27 17 0.53
28 1 0.03
29 5 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
ATATTTATTTTATTTATTAATAATTTTAT
Found at i:174838 original size:16 final size:16
Alignment explanation
Indices: 174819--174853 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
174809 ATTTTATATA
*
174819 TTTTTTATTTATTAAT
1 TTTTTTATATATTAAT
*
174835 TTTTTTATATATTCAT
1 TTTTTTATATATTAAT
174851 TTT
1 TTT
174854 AATATTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTATATATTAAT
Found at i:179781 original size:229 final size:230
Alignment explanation
Indices: 179361--179823 Score: 856
Period size: 229 Copynumber: 2.0 Consensus size: 230
179351 NNNGGGGGAT
*
179361 GGAAGAGTGGTCTATTTGTTTTTGTACAGAAAGTAAGATGGAGTCGAAGTCTTTGCTAAGAACTT
1 GGAAGAGTGGTCTATTTGTTTTTGTACAAAAAGTAAGATGGAGTCGAAGTCTTTGCTAAGAACTT
* *
179426 CATTTGAAATCCTTATTCTTTTTAAGATTGAATTTGCCATTTGCTGTCAAGCTCTTCTGCATGTT
66 CATTTGAAATCCTTATTCTTTTTAAGATTGAATTTGCCATTTGCTGCCAAGCTCTTCTGCACGTT
*
179491 TATGAAACGTTATTTTTTGCAATGCCTGTCAAAAGTAAAAGTGGAGCAGTCCAAGGACTTGATCC
131 TATGAAACGTTATTTGTTGCAATGCCTGTCAAAAGTAAAAGTGGAGCAGTCCAAGGACTTGATCC
179556 ATTTAAAATGAAACATCATTCATCAAGGTAGTGTA
196 ATTTAAAATGAAACATCATTCATCAAGGTAGTGTA
179591 GGAAGAGTGGTCTATTTGTTTTTGTACAAAAAGTAAGATGGAGTCGAAGTCTTTGCTAAGAACTT
1 GGAAGAGTGGTCTATTTGTTTTTGTACAAAAAGTAAGATGGAGTCGAAGTCTTTGCTAAGAACTT
* *
179656 CATTTGAAATCCTTATTC-TTTTAAGATTGAATTTGCCATTTGCTGCCAAGTTCTTTTGCACGTT
66 CATTTGAAATCCTTATTCTTTTTAAGATTGAATTTGCCATTTGCTGCCAAGCTCTTCTGCACGTT
*
179720 TATGAAACGTTATTTGTTGCGATGCCTGTCAAAAGTAAAAGTGGAGCAGTCCAAGGACTTGATCC
131 TATGAAACGTTATTTGTTGCAATGCCTGTCAAAAGTAAAAGTGGAGCAGTCCAAGGACTTGATCC
179785 ATTTAAAATGAAACATCATTCATCAAGGTAGTGTA
196 ATTTAAAATGAAACATCATTCATCAAGGTAGTGTA
179820 GGAA
1 GGAA
179824 TTTTATTTTG
Statistics
Matches: 226, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
229 144 0.64
230 82 0.36
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (230 bp):
GGAAGAGTGGTCTATTTGTTTTTGTACAAAAAGTAAGATGGAGTCGAAGTCTTTGCTAAGAACTT
CATTTGAAATCCTTATTCTTTTTAAGATTGAATTTGCCATTTGCTGCCAAGCTCTTCTGCACGTT
TATGAAACGTTATTTGTTGCAATGCCTGTCAAAAGTAAAAGTGGAGCAGTCCAAGGACTTGATCC
ATTTAAAATGAAACATCATTCATCAAGGTAGTGTA
Found at i:181850 original size:27 final size:27
Alignment explanation
Indices: 181820--181873 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
181810 TTCATTGAGA
181820 AGAAATGATCAAATCAAACCTCTCTTT
1 AGAAATGATCAAATCAAACCTCTCTTT
181847 AGAAATGATCAAATCAAACCTCTCTTT
1 AGAAATGATCAAATCAAACCTCTCTTT
181874 CTATGCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (27 bp):
AGAAATGATCAAATCAAACCTCTCTTT
Found at i:182875 original size:28 final size:28
Alignment explanation
Indices: 182824--182892 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
182814 TAGTTTTCTG
*
182824 CTATGAAGTTTTACTCAAGCCAATCTAC
1 CTATGAAGTTTTGCTCAAGCCAATCTAC
* *
182852 CTATGAAGTTTTGCTTAAGTCAATCTAC
1 CTATGAAGTTTTGCTCAAGCCAATCTAC
182880 CTATGAAGTTTTG
1 CTATGAAGTTTTG
182893 GGGTTATGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (28 bp):
CTATGAAGTTTTGCTCAAGCCAATCTAC
Found at i:188102 original size:6 final size:6
Alignment explanation
Indices: 188091--188115 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
188081 CCTTAACATC
188091 TATACA TATACA TATACA TATACA T
1 TATACA TATACA TATACA TATACA T
188116 TCATCAGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:197999 original size:79 final size:79
Alignment explanation
Indices: 197857--198005 Score: 185
Period size: 79 Copynumber: 1.9 Consensus size: 79
197847 GGAATATTAT
* * *
197857 AACTGGCAGTGACACTGTAAACACTGCGATAAATTACTGAACTAGCACTGACACTGTAAAACACT
1 AACTGGCAGTGACACTGTAAACACTACGATAAATTACTAAACTAGAACTGACACTGTAAAACACT
197922 ACAATGCTATCATG
66 ACAATGCTATCATG
* * * * * *
197936 AACTGGC-GTTGACATTGTAAACACTATGATATTATTACTAAACTGGAAGTGACACTGT-GAACA
1 AACTGGCAG-TGACACTGTAAACACTACGATA-AATTACTAAACTAGAACTGACACTGTAAAACA
197999 CTACAAT
64 CTACAAT
198006 ATTAATACCG
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
78 1 0.02
79 37 0.63
80 21 0.36
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (79 bp):
AACTGGCAGTGACACTGTAAACACTACGATAAATTACTAAACTAGAACTGACACTGTAAAACACT
ACAATGCTATCATG
Found at i:198008 original size:40 final size:40
Alignment explanation
Indices: 197857--198038 Score: 145
Period size: 40 Copynumber: 4.6 Consensus size: 40
197847 GGAATATTAT
* * *
197857 AACTGGCAGTGACACTGTAAACACTGCGATA-AATTACTG
1 AACTGGCAGTGACACTGTAAACACTACAATATTATTACTG
* * ** *
197896 AACTAGCACTGACACTGTAAAACACTACAATGCTATCA-TG
1 AACTGGCAGTGACACTGT-AAACACTACAATATTATTACTG
* ** *
197936 AACTGGC-GTTGACATTGTAAACACTATGATATTATTACTA
1 AACTGGCAG-TGACACTGTAAACACTACAATATTATTACTG
* * * *
197976 AACTGGAAGTGACACTGTGAACACTACAATATTAATACCG
1 AACTGGCAGTGACACTGTAAACACTACAATATTATTACTG
* * * *
198016 AGCTAGCTGTGGCACTGTAAACA
1 AACTGGCAGTGACACTGTAAACA
198039 TCGCTAGACT
Statistics
Matches: 108, Mismatches: 30, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
39 30 0.28
40 74 0.69
41 4 0.04
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (40 bp):
AACTGGCAGTGACACTGTAAACACTACAATATTATTACTG
Found at i:201863 original size:16 final size:16
Alignment explanation
Indices: 201824--201866 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
201814 CATATACATA
201824 TATATATTTCTCTTTT
1 TATATATTTCTCTTTT
* *
201840 TTTTTATTAT-TCTTTT
1 TATATATT-TCTCTTTT
201856 TATATATTTCT
1 TATATATTTCT
201867 TGAGATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (16 bp):
TATATATTTCTCTTTT
Found at i:202133 original size:56 final size:56
Alignment explanation
Indices: 202064--202175 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
202054 TTTTGAAGTG
* *
202064 TTCGATTTTTTCCATAATATTTTCAATTCTACAATATGCAAGTTTGATCAAAATAA
1 TTCGATTTTTTCCATAATATTTTCAACTCTACAAAATGCAAGTTTGATCAAAATAA
202120 TTCGATTTTTTCCATAATATTTTCAACTCTACAAAATGCAAGTTTGATCAAAATAA
1 TTCGATTTTTTCCATAATATTTTCAACTCTACAAAATGCAAGTTTGATCAAAATAA
202176 GAAATCATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (56 bp):
TTCGATTTTTTCCATAATATTTTCAACTCTACAAAATGCAAGTTTGATCAAAATAA
Found at i:204126 original size:14 final size:13
Alignment explanation
Indices: 204098--204141 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
204088 GTTTGGGGTA
204098 TTTTTTCTT-TCTT
1 TTTTTTCTTCT-TT
204111 TTTTTTCTTCTATT
1 TTTTTTCTTCT-TT
*
204125 TTTCTTCTTCTTT
1 TTTTTTCTTCTTT
204138 TTTT
1 TTTT
204142 GGATTAGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Found at i:204296 original size:19 final size:17
Alignment explanation
Indices: 204272--204314 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
204262 TTATACTCCC
204272 CCTTTTCTTCCTATTTTTT
1 CCTTTT-TT-CTATTTTTT
*
204291 CCTTTTTTCTCTTTTTT
1 CCTTTTTTCTATTTTTT
204308 CTCTTTT
1 C-CTTTT
204315 GGGCATCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 7 0.32
19 6 0.27
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (17 bp):
CCTTTTTTCTATTTTTT
Found at i:204304 original size:9 final size:9
Alignment explanation
Indices: 204285--204314 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
204275 TTTCTTCCTA
204285 TTTTTTC-C
1 TTTTTTCTC
204293 TTTTTTCTC
1 TTTTTTCTC
204302 TTTTTTCTC
1 TTTTTTCTC
204311 TTTT
1 TTTT
204315 GGGCATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:204792 original size:5 final size:5
Alignment explanation
Indices: 204763--204808 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
204753 ATTTTCATCC
*
204763 TAAAT TAAAAT AAAAT ATAAGAT TAAAT TAAAT TAAAT TAAAT TAA
1 TAAAT T-AAAT TAAAT -TAA-AT TAAAT TAAAT TAAAT TAAAT TAA
204809 TTTGGGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 25 0.69
6 9 0.25
7 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (5 bp):
TAAAT
Found at i:216601 original size:13 final size:14
Alignment explanation
Indices: 216583--216611 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
216573 TGTTAACGCA
216583 ATTAGA-GTTAAAT
1 ATTAGAGGTTAAAT
216596 ATTAGAGGTTAAAT
1 ATTAGAGGTTAAAT
216610 AT
1 AT
216612 GTATTGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (14 bp):
ATTAGAGGTTAAAT
Found at i:222652 original size:17 final size:17
Alignment explanation
Indices: 222617--222650 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
222607 AAACAAATTT
222617 TGAAAAGGAAAGGAAAA
1 TGAAAAGGAAAGGAAAA
*
222634 TGAAATGGAAATGGAAA
1 TGAAAAGGAAA-GGAAA
222651 TGGCTGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (17 bp):
TGAAAAGGAAAGGAAAA
Found at i:224431 original size:21 final size:22
Alignment explanation
Indices: 224407--224448 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
224397 GAGGAGCATC
224407 AATCAAGTTTTGA-G-AAGCTCA
1 AATC-AGTTTTGATGTAAGCTCA
224428 AATCAGTTTTGATGTAAGCTC
1 AATCAGTTTTGATGTAAGCTC
224449 CTGTGCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (22 bp):
AATCAGTTTTGATGTAAGCTCA
Found at i:227805 original size:40 final size:40
Alignment explanation
Indices: 227657--227816 Score: 180
Period size: 40 Copynumber: 4.0 Consensus size: 40
227647 GCGTTATAAT
** *
227657 TGGTAGTGACACTGTAAACACTACGATAACATTACTGAAC
1 TGGTAGTGACACTGTAAACACTACGATATTACTACTGAAC
* * ** * * *
227697 TGGTAGTGACACTGTAAACAGTACAATGCTA-TCAGTAAAT
1 TGGTAGTGACACTGTAAACACTACGATATTACT-ACTGAAC
*
227737 TGACT-GTGACACTGTAAACACTACGATATTACTACTGAAC
1 TG-GTAGTGACACTGTAAACACTACGATATTACTACTGAAC
*
227777 TGGTAGTGACACTGTAAACACTGCGATATTACTACTGAAC
1 TGGTAGTGACACTGTAAACACTACGATATTACTACTGAAC
227817 CAACAGTGAC
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.02
40 94 0.96
41 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (40 bp):
TGGTAGTGACACTGTAAACACTACGATATTACTACTGAAC
Found at i:227825 original size:40 final size:40
Alignment explanation
Indices: 227742--227836 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
227732 TAAATTGACT
****
227742 GTGACACTGTAAACACTACGATATTACTACTGAACTGGTA
1 GTGACACTGTAAACACTACGATATTACTACTGAACCAACA
*
227782 GTGACACTGTAAACACTGCGATATTACTACTGAACCAACA
1 GTGACACTGTAAACACTACGATATTACTACTGAACCAACA
*
227822 GTGACACTGTGAACA
1 GTGACACTGTAAACA
227837 ATACAAATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (40 bp):
GTGACACTGTAAACACTACGATATTACTACTGAACCAACA
Found at i:227826 original size:80 final size:80
Alignment explanation
Indices: 227661--227836 Score: 201
Period size: 80 Copynumber: 2.2 Consensus size: 80
227651 TATAATTGGT
* * *
227661 AGTGACACTGTAAACACTACGATAACATTACTGAACTGGTAGTGACACTGTAAACAGTACAATGC
1 AGTGACACTGTAAACACTACGATAACACTACTGAACTGGTAGTGACACTGTAAACACTACAATAC
* ***
227726 TATCAGTAAATTGAC
66 TATCACTAAACCAAC
* ** * * *
227741 TGTGACACTGTAAACACTACGATATTACTACTGAACTGGTAGTGACACTGTAAACACTGCGATAT
1 AGTGACACTGTAAACACTACGATAACACTACTGAACTGGTAGTGACACTGTAAACACTACAATAC
*
227806 TA-CTACTGAACCAAC
66 TATC-ACTAAACCAAC
*
227821 AGTGACACTGTGAACA
1 AGTGACACTGTAAACA
227837 ATACAAATGC
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
79 1 0.01
80 78 0.99
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (80 bp):
AGTGACACTGTAAACACTACGATAACACTACTGAACTGGTAGTGACACTGTAAACACTACAATAC
TATCACTAAACCAAC
Found at i:231909 original size:15 final size:15
Alignment explanation
Indices: 231889--231917 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
231879 TTAGATATAT
231889 TATTCATTTAACATC
1 TATTCATTTAACATC
231904 TATTCATTTAACAT
1 TATTCATTTAACAT
231918 TCCACATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTCATTTAACATC
Found at i:236850 original size:21 final size:21
Alignment explanation
Indices: 236828--236869 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
236818 ATTGATAGAA
236828 TTGGGAGTTCTATCGATACAAT
1 TTGGG-GTTCTATCGATACAAT
*
236850 TTTGGGTTCTATCGATACAA
1 TTGGGGTTCTATCGATACAA
236870 CCTGGACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (21 bp):
TTGGGGTTCTATCGATACAAT
Found at i:242461 original size:32 final size:32
Alignment explanation
Indices: 242424--242498 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
242414 AATGACCTCA
* *
242424 AAAAAATAATTCTGATTAGTTGGTGACCAAATT
1 AAAAAA-AATTCTAATAAGTTGGTGACCAAATT
* * *
242457 AAAAAAAAATGTAATAATTTGGTGACCAAATT
1 AAAAAAAATTCTAATAAGTTGGTGACCAAATT
242489 AAAAAAAATT
1 AAAAAAAATT
242499 GATAGTTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 30 0.83
33 6 0.17
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (32 bp):
AAAAAAAATTCTAATAAGTTGGTGACCAAATT
Found at i:244292 original size:30 final size:30
Alignment explanation
Indices: 244229--244296 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
244219 TGACTTTATC
*
244229 AAATAAAATATCTTTTTTAAATTTAAATTT
1 AAATAAAATATCTTTTTTAAATTTAAATAT
*
244259 AAATAAAATAT-TTTTTTATAGTTTCAAA-AT
1 AAATAAAATATCTTTTTTA-AATTT-AAATAT
244289 AAATAAAA
1 AAATAAAA
244297 AAATATAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 7 0.21
30 24 0.71
31 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (30 bp):
AAATAAAATATCTTTTTTAAATTTAAATAT
Found at i:248066 original size:63 final size:65
Alignment explanation
Indices: 247994--248122 Score: 208
Period size: 63 Copynumber: 2.0 Consensus size: 65
247984 GGAAACTAAA
* * *
247994 ATCTCCCCCCAAGTAGTTATAATTATTGTCAACAATTAAGT-G-ACAACTTTTTGACTAATGACC
1 ATCTCCCCCCAAATAGTTATAATTATTGTCAAAAATTAAATGGCACAACTTTTTGACTAATGACC
*
248057 ATCTCCCCCCAAATAGTTATAATTATTGTCAAAAATTAAATGGCATAACTTTTTGACTAATGACC
1 ATCTCCCCCCAAATAGTTATAATTATTGTCAAAAATTAAATGGCACAACTTTTTGACTAATGACC
248122 A
1 A
248123 AAAGATTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 38 0.63
64 1 0.02
65 21 0.35
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (65 bp):
ATCTCCCCCCAAATAGTTATAATTATTGTCAAAAATTAAATGGCACAACTTTTTGACTAATGACC
Found at i:248233 original size:39 final size:40
Alignment explanation
Indices: 248179--248265 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 40
248169 GGAGCACTAT
*
248179 AAATATTTAAAAATGTTCCAACAATCTCCCCCCATTTT-G
1 AAATATTTAAAAATGTTCCAACAATCTCCCCCCATTTTCA
* * * *
248218 AAATATTTGAAAATGTTCCGACGATCTTCCCCCATTTTCA
1 AAATATTTAAAAATGTTCCAACAATCTCCCCCCATTTTCA
248258 AAATATTT
1 AAATATTT
248266 TAGATTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 34 0.81
40 8 0.19
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (40 bp):
AAATATTTAAAAATGTTCCAACAATCTCCCCCCATTTTCA
Found at i:250264 original size:185 final size:186
Alignment explanation
Indices: 249856--251149 Score: 1593
Period size: 185 Copynumber: 6.9 Consensus size: 186
249846 TTCACTTTAA
* *
249856 TCCACTGTAACCTCAGGGAGATTAAGATCCGTTACTCATTTTAATTTGATCCACTGCAACTTCAG
1 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
* *
249921 GGATATAGGATTTGGTGCTTCACTCCATTCCACTGTAACCTTAGGGAGATTGAGATATGCTTTTG
66 GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGC---T-
* ** *
249986 TAACTTTAATTCGATCCACTATAATTTTAGGGGTATAGGATTTGGTGTTGTACTTCACT-CATT
127 T---TTTAATTCGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTACTTCACTCCA-T
* * *
250049 TCCACTGTACCCTCAGGGAGATTGAGATTCGTTACTCATTATAATTTGATCCACTACAACTTCAG
1 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
* * * * *
250114 GGATATAGGA-TTGGTGCTTTAGTCTATTCCATTATAACCTCGGGGAGATTGAGATATGCTTTTT
66 GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGCTTTTT
* * * *
250178 AATCCGACCCACTACAACTTTAGGGGTATAAGATTTGGTGTTGTACATCACTCCAT
131 AATTCGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTACTTCACTCCAT
* ** ** *
250234 TCCACTGTAACCTCAGGGAGATTGAGATTCGTTACTCATTTTAATCCGATCCACTGTAACTTTAG
1 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
* * *
250299 GGATATAGGATTTGGTGCTTCACTGCATTCCATTATAACCTCAGGGAGA-TGAGATTTGCTTTTT
66 GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGCTTTTT
* * * *
250363 AATTCAACCCATTGCAACTTTAAGGGTATGGGATTTGGTGTTGTACTTCACTCCAT
131 AATTCGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTACTTCACTCCAT
* * * ** **
250419 TCCACTATAACCTTAAGGAGATTGAGATCCGTTACTCA-TTTAATTTGATCTGCTGTAACTTCAG
1 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
* * * * *
250483 AGATATAGGATTTGGTGTTTCATTCCA-TCCACTGTAACCT-AGGGAGATTGAGATATGCCTTTT
66 GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGCTTTTT
* *
250546 AATTCGACCCACTGCAACTTCAGGGGTATAGGATTTTGTGTTGTACTTCACTCCAT
131 AATTCGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTACTTCACTCCAT
** *
250602 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTT-ACCTGATCCACTACAACTTCAT
1 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
* * * * * * *
250666 GGATATAAGATTTGGTGCTTCAATCCATTCAACTATAA-CTCAAGAAGATTGAGATTTACTTTTT
66 GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGC-TTTT
* * *
250730 TAA-TCTGACCCACTACAACTTTAGGGGTATAGGATTTGGTGCTGTACTTCACTCTAT
130 TAATTC-GACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTACTTCACTCCAT
* * * ** * *
250787 TCTATTGTAACCTCATGGAGATTGAGATCCGTTACTCATTTTAATTCAATCCACTACAACCTCAA
1 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
* * *
250852 GGATATAGGATTTGGTGCTTCACTTCATTCCACTATAACTTTAGGGAGATTGAGATATGCTTTTT
66 GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGCTTTTT
* * *
250917 AATTTGACCCACTGCAATTTTAGGGGTATAGGATTTGGTGTTGTACTTTACTCCAT
131 AATTCGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTACTTCACTCCAT
* * *
250973 TCCACTATAACCTCAGGGAGATTGAGACCCGTTACTCATTTTAATTCGATCC-CTACAACTTCAG
1 TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
* * * * * * *
251037 GGATATAGGATTTGGTGCTTCA-TTCAATCCATTGTAACATCAGAGAGATTGAGAAATGCTTTTG
66 GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGCTTTT-
* *
251101 TAATTTTAATCCGACCCACTGCAACTTTAGAGATATAGGATTTGGTGTT
130 TAA---T--T-CGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTT
251150 TGCTTGGTCC
Statistics
Matches: 951, Mismatches: 132, Indels: 38
0.85 0.12 0.03
Matches are distributed among these distances:
182 7 0.01
183 149 0.16
184 105 0.11
185 340 0.36
186 184 0.19
187 16 0.02
188 2 0.00
189 1 0.00
190 1 0.00
191 34 0.04
192 42 0.04
193 70 0.07
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (186 bp):
TCCACTGTAACCTCAGGGAGATTGAGATCCGTTACTCATTTTAATTTGATCCACTACAACTTCAG
GGATATAGGATTTGGTGCTTCACTCCATTCCACTATAACCTCAGGGAGATTGAGATATGCTTTTT
AATTCGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTACTTCACTCCAT
Found at i:251462 original size:10 final size:10
Alignment explanation
Indices: 251447--251476 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
251437 GAATCTTATA
251447 ATTTAATATT
1 ATTTAATATT
251457 ATTTAATATT
1 ATTTAATATT
251467 A-TTAATATT
1 ATTTAATATT
251476 A
1 A
251477 CTTATTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTAATATT
Found at i:264947 original size:13 final size:13
Alignment explanation
Indices: 264925--264963 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
264915 TGTGAATGAG
264925 GAAAAG-AAAAGA
1 GAAAAGAAAAAGA
*
264937 AAAAGAGAAAAAGA
1 GAAA-AGAAAAAGA
264951 GAAAAGAAAAAGA
1 GAAAAGAAAAAGA
264964 AATATTGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAGA
Found at i:274415 original size:80 final size:80
Alignment explanation
Indices: 274282--274571 Score: 325
Period size: 80 Copynumber: 3.6 Consensus size: 80
274272 CCGATAGTCA
* * * * * **
274282 TGGCACCCAATGCCTAATGGAGAAATCGCAAATGTGAGCCCAACTCTCA-TTGGATTAACTAATG
1 TGGCACCCAGTGCCTAGTGGATAAACCGCAAATGTGAGCCCAGCTCT-AGTTGGATTAACTAACA
*
274346 AATATCTGTCAAATCT
65 AATATCCGTCAAATCT
* * * *
274362 TGGCACCCAGTGCCTAGTGGATAAACCACGAATGTGAGCCTAGCTCTTGTTGGATTAACTAACAA
1 TGGCACCCAGTGCCTAGTGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACTAACAA
* *
274427 ATATCCAT-AAACTCC
66 ATATCCGTCAAA-TCT
* * *
274442 TGGCACTCAGTGCCTAGCT-GATAAACCGCAAATGTCAGCCCAGCTCTAGTTGGATTAACCAACA
1 TGGCACCCAGTGCCTAG-TGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACTAACA
274506 AATATCCGTCAAATCT
65 AATATCCGTCAAATCT
* ** * * *
274522 TGGCACCTAGTGCCTAGCAGTTAAATCGCAAATGTGAGCCTAGCTCTAGT
1 TGGCACCCAGTGCCTAGTGGATAAACCGCAAATGTGAGCCCAGCTCTAGT
274572 CGATTTAACT
Statistics
Matches: 175, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
79 3 0.02
80 168 0.96
81 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (80 bp):
TGGCACCCAGTGCCTAGTGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACTAACAA
ATATCCGTCAAATCT
Found at i:282139 original size:79 final size:80
Alignment explanation
Indices: 281924--282212 Score: 373
Period size: 80 Copynumber: 3.6 Consensus size: 80
281914 CTGATAGTCA
* * * *
281924 TGGCACACAGTGCCTAGTGGATAAATCGCAAATGTGAGCACAACTCTAGTTGGATTAACCAACAA
1 TGGCACACAGTGCCTAGCGGATAAACCGCAAATGTGAGCTCAGCTCTAGTTGGATTAACCAACAA
281989 ATATCCATCAAATCC
66 ATATCCATCAAATCC
* * * * *
282004 TGGCACCCAGTTCCTAGCGGATAAACTGCAAATGTGAGCTTAGTTCTAGTTGGATTAACCAACAA
1 TGGCACACAGTGCCTAGCGGATAAACCGCAAATGTGAGCTCAGCTCTAGTTGGATTAACCAACAA
*
282069 ATATCTATCAAATCC
66 ATATCCATCAAATCC
* * * *
282084 TAGCAC-CAGTGCCTAGTGGATAAACCGCAAATGTGAGCTCAGCTCTAGTTAGATTATCCAACAA
1 TGGCACACAGTGCCTAGCGGATAAACCGCAAATGTGAGCTCAGCTCTAGTTGGATTAACCAACAA
* *
282148 ATATCCGTTAAATCC
66 ATATCCATCAAATCC
* * * * * *
282163 TGGCACACAATACCGAGCGGATAAACCGTAAATGTTAGCCCAGCTCTAGT
1 TGGCACACAGTGCCTAGCGGATAAACCGCAAATGTGAGCTCAGCTCTAGT
282213 CGGTTAAATC
Statistics
Matches: 179, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
79 68 0.38
80 111 0.62
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (80 bp):
TGGCACACAGTGCCTAGCGGATAAACCGCAAATGTGAGCTCAGCTCTAGTTGGATTAACCAACAA
ATATCCATCAAATCC
Found at i:285945 original size:23 final size:23
Alignment explanation
Indices: 285919--285966 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
285909 GCCCAAGCTT
*
285919 GGCCGCCACTCCGATGCCACATC
1 GGCCACCACTCCGATGCCACATC
* * *
285942 GGCCATCATTTCGATGCCACATC
1 GGCCACCACTCCGATGCCACATC
285965 GG
1 GG
285967 TCGTTGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.40, G:0.23, T:0.19
Consensus pattern (23 bp):
GGCCACCACTCCGATGCCACATC
Found at i:288684 original size:29 final size:30
Alignment explanation
Indices: 288637--288693 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
288627 TCATTTGAGA
*
288637 GAAAAAACTAAAGAGAAAAGAAATTTTTTT
1 GAAAAAACTAAAGACAAAAGAAATTTTTTT
**
288667 GAAAAAAC-AAAGACAAAATTAATTTTT
1 GAAAAAACTAAAGACAAAAGAAATTTTT
288694 GTCAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (30 bp):
GAAAAAACTAAAGACAAAAGAAATTTTTTT
Found at i:294091 original size:20 final size:20
Alignment explanation
Indices: 294043--294118 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
294033 ATCCTTGATT
* *
294043 AATGTTTGCTATTTTTTTACC
1 AATGTTTGC-AATTTTTGACC
**
294064 AACATTTGTC-ATTTTTGACC
1 AATGTTTG-CAATTTTTGACC
*
294084 AATGTTTGCAATTTTTGGCC
1 AATGTTTGCAATTTTTGACC
*
294104 ATTGTTT--AATTTTTG
1 AATGTTTGCAATTTTTG
294119 TCATCTTTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
18 8 0.18
19 1 0.02
20 29 0.64
21 6 0.13
22 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (20 bp):
AATGTTTGCAATTTTTGACC
Found at i:294137 original size:47 final size:47
Alignment explanation
Indices: 294068--294164 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
294058 TTTACCAACA
* * *
294068 TTTGTCATTTTTGACCAATGTTTG-CAATTTTTGGCCATTGTTTAAT-T
1 TTTGTCATCTTTGACCAATGTTTGAC-ATTTTT-ACCAATGTTTAATGT
*
294115 TTTGTCATCTTTGACTAATGTTTGACATTTTTACCAATGTTTAATGT
1 TTTGTCATCTTTGACCAATGTTTGACATTTTTACCAATGTTTAATGT
294162 TTT
1 TTT
294165 TAATTCATCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
46 11 0.25
47 32 0.73
48 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.54
Consensus pattern (47 bp):
TTTGTCATCTTTGACCAATGTTTGACATTTTTACCAATGTTTAATGT
Found at i:294865 original size:100 final size:100
Alignment explanation
Indices: 294687--294940 Score: 373
Period size: 100 Copynumber: 2.5 Consensus size: 100
294677 TAAATCAAAC
* * * * *
294687 CCAAATCCTATACCCCTAAAGTTGTAGAAGAGCGGATTAAAACTAATAATAGCAGATCTCAATCT
1 CCAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACTAACAATAGCAAAACTCAATCT
*
294752 CCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACA
66 CCACTGAAGTTGCAGTAGAATGGAGTGAAGCCACA
*
294787 CCAATTCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACTAACAATAGCAAAACTCAATCT
1 CCAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACTAACAATAGCAAAACTCAATCT
* * *
294852 CCACTGAGGTTGCAGTAGAATGGAGTGAAGTCATA
66 CCACTGAAGTTGCAGTAGAATGGAGTGAAGCCACA
* * * * *
294887 CCAAATCTTATACCCCTAAAATTGTAGAGGGGTGAATTAAAACTAACAGTAGCA
1 CCAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACTAACAATAGCA
294941 GATGAATGGA
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 138 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (100 bp):
CCAAATCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACTAACAATAGCAAAACTCAATCT
CCACTGAAGTTGCAGTAGAATGGAGTGAAGCCACA
Found at i:295001 original size:75 final size:75
Alignment explanation
Indices: 294869--295018 Score: 221
Period size: 75 Copynumber: 2.0 Consensus size: 75
294859 GGTTGCAGTA
* * * **
294869 GAATGGAGTGAAGTCATACCAAATCTTATACCCCTAAAATTGTAGAGGGGTGAATTAAAACTAAC
1 GAATGGAGTGAAGCCACACCAAATCCTATACCCCTAAAATTGTAGAGGGCAGAATTAAAACTAAC
294934 AGTAGCAGAT
66 AGTAGCAGAT
* *
294944 GAATGGAGTGAAGCCACACCAAATCCTATACCCCTACAGTTGTAGAAGGGCAG-ATTAAAACTAA
1 GAATGGAGTGAAGCCACACCAAATCCTATACCCCTAAAATTGTAG-AGGGCAGAATTAAAACTAA
295008 CAGTAGCAGAT
65 CAGTAGCAGAT
295019 CTCAATCTCC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 62 0.93
76 5 0.07
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (75 bp):
GAATGGAGTGAAGCCACACCAAATCCTATACCCCTAAAATTGTAGAGGGCAGAATTAAAACTAAC
AGTAGCAGAT
Found at i:295076 original size:175 final size:174
Alignment explanation
Indices: 294769--295112 Score: 508
Period size: 175 Copynumber: 2.0 Consensus size: 174
294759 AGTTGCAGTG
* * *
294769 GAATGGAGTGAAGCCACACCAATTCCTATACCCCTAAAGTTGTAGAGGGGCGGATTAAAACTAAC
1 GAATGGAGTGAAGCCACACCAAATCCTATACCCCTAAAGTTGTAGAAGGGCAGATTAAAACTAAC
* * * * * *
294834 AATAGCAAAACTCAATCTCCACTGAGGTTGCAGTAGAATGGAGTGAAGTCATACCAAATCTTATA
66 AATAGCAAAACTCAATCTCCACTAAAGTTGCAGTAGAATAGAGTGAAGCCACACCAAATCCTATA
294899 CCCCTAAAATTGTAGAGGGGTGAATTAAAACTAACAGTAGCAGAT
131 CCCCTAAAATTGTAGA-GGGTGAATTAAAACTAACAGTAGCAGAT
*
294944 GAATGGAGTGAAGCCACACCAAATCCTATACCCCTACAGTTGTAGAAGGGCAGATTAAAACTAAC
1 GAATGGAGTGAAGCCACACCAAATCCTATACCCCTAAAGTTGTAGAAGGGCAGATTAAAACTAAC
* * * * * *
295009 AGTAGCAGATCTCAATCTCCACTAAAGTTGTAGTGGAATAGAGTGAAGCCACATCAAATCCTATA
66 AATAGCAAAACTCAATCTCCACTAAAGTTGCAGTAGAATAGAGTGAAGCCACACCAAATCCTATA
* * *
295074 CCCTTAAAGTTGTAGAGGGTGGATTAAAACTAACAGTAG
131 CCCCTAAAATTGTAGAGGGTGAATTAAAACTAACAGTAG
295113 AAAATCTCAA
Statistics
Matches: 150, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
174 22 0.15
175 128 0.85
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (174 bp):
GAATGGAGTGAAGCCACACCAAATCCTATACCCCTAAAGTTGTAGAAGGGCAGATTAAAACTAAC
AATAGCAAAACTCAATCTCCACTAAAGTTGCAGTAGAATAGAGTGAAGCCACACCAAATCCTATA
CCCCTAAAATTGTAGAGGGTGAATTAAAACTAACAGTAGCAGAT
Found at i:295133 original size:99 final size:98
Alignment explanation
Indices: 294944--295254 Score: 394
Period size: 99 Copynumber: 3.1 Consensus size: 98
294934 AGTAGCAGAT
* * *
294944 GAATGGAGTGAAGCCACACCAAATCCTATACCCCTACAGTTGTAGAAGGGCAGATTAAAACTAAC
1 GAATAGAGTGAAGCCACACCAAATCCTATA-CCCTAAAGTTGTAG-AGGGCGGATTAAAACTAAC
*
295009 AGTAGCAGATCTCAATCTCCACTAAAGTTGTAGTG
64 AGTAGCAGATCTCAATCTCCACTAAAGTTGCAGTG
* *
295044 GAATAGAGTGAAGCCACATCAAATCCTATACCCTTAAAGTTGTAGAGGGTGGATTAAAACTAACA
1 GAATAGAGTGAAGCCACACCAAATCCTATACCC-TAAAGTTGTAGAGGGCGGATTAAAACTAACA
* * *
295109 GTAGAAAATCTCAATCTCCACTAAAGGTGCAGTG
65 GTAGCAGATCTCAATCTCCACTAAAGTTGCAGTG
* * *
295143 GAA-AGGACTAAAGCCACACCAAATCCTATACACCTAAAGTTGCAGAGGGGCGGATTAAAACTAA
1 GAATA-GAGTGAAGCCACACCAAATCCTATAC-CCTAAAGTTGTAGA-GGGCGGATTAAAACTAA
* * *
295207 TC-TTAGCGGATCTCAATCTCC-CTGAAGTTGCAGTG
63 -CAGTAGCAGATCTCAATCTCCACTAAAGTTGCAGTG
*
295242 GAATGGAGTGAAG
1 GAATAGAGTGAAG
295255 TTACAAACCC
Statistics
Matches: 182, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
98 1 0.01
99 109 0.60
100 71 0.39
101 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (98 bp):
GAATAGAGTGAAGCCACACCAAATCCTATACCCTAAAGTTGTAGAGGGCGGATTAAAACTAACAG
TAGCAGATCTCAATCTCCACTAAAGTTGCAGTG
Found at i:297155 original size:33 final size:32
Alignment explanation
Indices: 297112--297199 Score: 81
Period size: 34 Copynumber: 2.7 Consensus size: 32
297102 GACTTTACTG
* *
297112 TTTTTGTTTTTATTTAATTTAGCCT-TTTTATTT
1 TTTTTATTTTTATTTAATTTAG--TATTTAATTT
*
297145 TTTTTATTTTTTCATTTATTTTAGTATTTAATTT
1 TTTTTA-TTTTT-ATTTAATTTAGTATTTAATTT
*
297179 TTATTTATTGTTATTT-ATTTA
1 TT-TTTATTTTTATTTAATTTA
297200 TTTATTTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
32 4 0.09
33 10 0.22
34 18 0.39
35 14 0.30
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (32 bp):
TTTTTATTTTTATTTAATTTAGTATTTAATTT
Found at i:297156 original size:17 final size:17
Alignment explanation
Indices: 297136--297198 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
297126 TAATTTAGCC
297136 TTTTTATTTTTTTTATT
1 TTTTTATTTTTTTTATT
* * *
297153 TTTTCATTTATTTTAGT
1 TTTTTATTTTTTTTATT
* *
297170 ATTTAATTTTTATTTATT
1 TTTTTATTTTT-TTTATT
297188 GTTATTTATTT
1 -TT-TTTATTT
297199 ATTTATTTGT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
17 22 0.65
18 5 0.15
19 1 0.03
20 6 0.18
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTTTTATT
Found at i:297206 original size:12 final size:11
Alignment explanation
Indices: 297138--297206 Score: 63
Period size: 12 Copynumber: 6.3 Consensus size: 11
297128 ATTTAGCCTT
297138 TTTA-TTTTT-
1 TTTATTTTTTA
297147 TTTATTTTTTCA
1 TTTATTTTTT-A
*
297159 TTTATTTTAGTA
1 TTTATTTT-TTA
*
297171 TTTAATTTTTA
1 TTTATTTTTTA
*
297182 TTTA-TTGTTA
1 TTTATTTTTTA
297192 TTTATTTATTTA
1 TTTATTT-TTTA
297204 TTT
1 TTT
297207 GTAATTCATT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 4 0.08
10 14 0.29
11 8 0.16
12 22 0.45
13 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.75
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:297206 original size:33 final size:28
Alignment explanation
Indices: 297136--297206 Score: 70
Period size: 33 Copynumber: 2.3 Consensus size: 28
297126 TAATTTAGCC
297136 TTTTTATTTTTTTTATTTTTTCATTTAT
1 TTTTTATTTTTTTTATTTTTTCATTTAT
* *
297164 TTTAGTATTTAATTTTTATTTATTGTTATTTAT
1 TTT-TTATTT--TTTTTATTT-TT-TCATTTAT
297197 TTATTTATTT
1 TT-TTTATTT
297207 GTAATTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.09
29 5 0.15
31 9 0.26
32 2 0.06
33 14 0.41
34 1 0.03
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (28 bp):
TTTTTATTTTTTTTATTTTTTCATTTAT
Found at i:297220 original size:40 final size:39
Alignment explanation
Indices: 297136--297222 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
297126 TAATTTAGCC
* *
297136 TTTTTATTTTTTTTATTTTTTCATTTATTTTAGTATTTAA
1 TTTTTATTTTTGTTATTTTTTCATTTATTTTAG-ATTCAA
*
297176 TTTTTATTTATTGTTATTTATTT-ATTTATTTGTA-ATTCAT
1 TTTTTATTT-TTGTTATTT-TTTCATTTATTT-TAGATTCAA
297216 TTTTTAT
1 TTTTTAT
297223 GCTATTCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 20 0.49
41 16 0.39
42 5 0.12
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (39 bp):
TTTTTATTTTTGTTATTTTTTCATTTATTTTAGATTCAA
Found at i:297221 original size:18 final size:19
Alignment explanation
Indices: 297178--297222 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
297168 GTATTTAATT
* *
297178 TTTATTTA-TTGTTATTTA
1 TTTATTTATTTGTAATTCA
297196 TTTATTTATTTGTAATTCA
1 TTTATTTATTTGTAATTCA
297215 TTT-TTTAT
1 TTTATTTAT
297223 GCTATTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTATTTATTTGTAATTCA
Found at i:297290 original size:11 final size:10
Alignment explanation
Indices: 297241--297308 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 10
297231 TACTCTTGCC
297241 TTTTATTTAAT
1 TTTTATTT-AT
*
297252 TTTTAATTAT
1 TTTTATTTAT
* *
297262 TCATTGTTT-T
1 T-TTTATTTAT
297272 TTTT-TTTAT
1 TTTTATTTAT
297281 ATTTTATTTAT
1 -TTTTATTTAT
*
297292 TTGTTATCTAT
1 TT-TTATTTAT
297303 TTTTAT
1 TTTTAT
297309 GCCATTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 15 0.33
11 25 0.54
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:300228 original size:15 final size:15
Alignment explanation
Indices: 300210--300258 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
300200 TCATAGTGCC
*
300210 CATCTTCATAGATAT
1 CATCATCATAGATAT
* *
300225 CATCATCAAAGATGT
1 CATCATCATAGATAT
*
300240 CATCATCATAAATAT
1 CATCATCATAGATAT
300255 CATC
1 CATC
300259 TGGACAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (15 bp):
CATCATCATAGATAT
Found at i:302733 original size:6 final size:6
Alignment explanation
Indices: 302709--302802 Score: 62
Period size: 6 Copynumber: 14.3 Consensus size: 6
302699 TACCAACTCG
* *
302709 TTGACT TTGACCT GATGACT TTGACTT GTTGACCT GTTGACT TTGACCA
1 TTGACT TTGA-CT -TTGACT TTGAC-T -TTGA-CT -TTGACT TTGA-CT
* * * *
302758 TTGACT TTGACT TTGACCA TTAACT TTGACC TTGACC TTGACT TT
1 TTGACT TTGACT TTGA-CT TTGACT TTGACT TTGACT TTGACT TT
302803 TCTTTGACAA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
6 41 0.58
7 16 0.23
8 13 0.18
9 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (6 bp):
TTGACT
Found at i:302741 original size:14 final size:14
Alignment explanation
Indices: 302708--302751 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
302698 TTACCAACTC
*
302708 GTTGACTTTGACCT
1 GTTGACTTTGACTT
*
302722 GATGACTTTGACTT
1 GTTGACTTTGACTT
302736 GTTGACCTGTTGACTT
1 GTTGA-CT-TTGACTT
302752 TGACCATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 16 0.64
15 2 0.08
16 7 0.28
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (14 bp):
GTTGACTTTGACTT
Found at i:302769 original size:19 final size:19
Alignment explanation
Indices: 302745--302802 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
302735 TGTTGACCTG
302745 TTGACTTTGACCATTGACT
1 TTGACTTTGACCATTGACT
*
302764 TTGACTTTGACCATTAACT
1 TTGACTTTGACCATTGACT
*
302783 TTGACCTTGACC-TTGACT
1 TTGACTTTGACCATTGACT
302801 TT
1 TT
302803 TCTTTGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
18 7 0.19
19 29 0.81
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (19 bp):
TTGACTTTGACCATTGACT
Found at i:308089 original size:15 final size:15
Alignment explanation
Indices: 308071--308100 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
308061 AATTTAAAAC
*
308071 GAAACAATTAAAAGA
1 GAAACAAATAAAAGA
308086 GAAACAAATAAAAGA
1 GAAACAAATAAAAGA
308101 AAATGTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (15 bp):
GAAACAAATAAAAGA
Found at i:318158 original size:73 final size:73
Alignment explanation
Indices: 318039--318178 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 73
318029 CCGAAAATAA
* * * *
318039 CAGTTCCAAGTGACCATATTGTCTGTGGTCAAAGGTTAGATAGGATCGAGGTG-GAAATGTAATC
1 CAGTTCAAAGTGACCATATTATCTGTGGTCAAAGGCTAGATAGGATCAAGG-GAGAAATGTAATC
318103 CATAAAGAG
65 CATAAAGAG
*
318112 CAGTTCAAAGTGACCATATTATCTTTGGTCAAAGGCTAGATAGGATCAAGGGAGAAATGTAATCC
1 CAGTTCAAAGTGACCATATTATCTGTGGTCAAAGGCTAGATAGGATCAAGGGAGAAATGTAATCC
318177 AT
66 AT
318179 GAGGGCAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 1 0.02
73 60 0.98
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (73 bp):
CAGTTCAAAGTGACCATATTATCTGTGGTCAAAGGCTAGATAGGATCAAGGGAGAAATGTAATCC
ATAAAGAG
Found at i:330896 original size:42 final size:40
Alignment explanation
Indices: 330806--330898 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 40
330796 TGTCTATGTT
* *
330806 ACAACAAACCCCCTTCGTCATGGCATAGAATATCTATGTT
1 ACAACAAACCCCCTTCGTCATGGCATAGAATATCTACGTC
* * *
330846 ACAACAAACCCCTTTCGTCATGAGACATAGCATGTCTACGTC
1 ACAACAAACCCCCTTCGTCATG-G-CATAGAATATCTACGTC
**
330888 ATGACAAACCC
1 ACAACAAACCC
330899 TTGAAAATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 21 0.48
41 1 0.02
42 22 0.50
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (40 bp):
ACAACAAACCCCCTTCGTCATGGCATAGAATATCTACGTC
Done.