Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold287
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: 1864789
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 140151 characters in sequence are not A, C, G, or T
File 2 of 7
Found at i:202563 original size:17 final size:17
Alignment explanation
Indices: 202541--202578 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
202531 ATGTAACTCT
202541 CCACTCTATGCCTTTTA
1 CCACTCTATGCCTTTTA
202558 CCACTCTATGCCTTTTA
1 CCACTCTATGCCTTTTA
202575 CCAC
1 CCAC
202579 ATTTGGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.39, G:0.05, T:0.37
Consensus pattern (17 bp):
CCACTCTATGCCTTTTA
Found at i:212843 original size:20 final size:20
Alignment explanation
Indices: 212818--212882 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
212808 AGTTTTTCTG
212818 AAGTTTTATGATAGAATATT
1 AAGTTTTATGATAGAATATT
** *
212838 AAG--TT-TGA-AGTTTTTCT
1 AAGTTTTATGATAGAATAT-T
212855 GAAGTTTTATGATAGAATATT
1 -AAGTTTTATGATAGAATATT
212876 AAGTTTT
1 AAGTTTT
212883 GTTGTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 5 0.15
20 12 0.36
21 4 0.12
22 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.48
Consensus pattern (20 bp):
AAGTTTTATGATAGAATATT
Found at i:212849 original size:38 final size:38
Alignment explanation
Indices: 212801--212881 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
212791 TTCATTGATG
212801 AGTTTGAAGTTTTTCTGAAGTTTTATGATAGAATATTA
1 AGTTTGAAGTTTTTCTGAAGTTTTATGATAGAATATTA
212839 AGTTTGAAGTTTTTCTGAAGTTTTATGATAGAATATTA
1 AGTTTGAAGTTTTTCTGAAGTTTTATGATAGAATATTA
212877 AGTTT
1 AGTTT
212882 TGTTGTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (38 bp):
AGTTTGAAGTTTTTCTGAAGTTTTATGATAGAATATTA
Found at i:215218 original size:42 final size:41
Alignment explanation
Indices: 215138--215220 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
215128 TTAACCCTAA
* * *
215138 TGGGTTTTCGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTT
1 TGGGTTTTCGTTCAGCTCTATTGAGCCTCAGTTCAACCCTT
* *
215179 TGGGTTTTTCGTTTAGCTCCTATT-AGCCTCCGTTCAACCCTT
1 TGGG-TTTTCGTTCAGCT-CTATTGAGCCTCAGTTCAACCCTT
215221 ACGGGTTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.11
42 27 0.77
43 4 0.11
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (41 bp):
TGGGTTTTCGTTCAGCTCTATTGAGCCTCAGTTCAACCCTT
Found at i:223681 original size:40 final size:40
Alignment explanation
Indices: 223459--223673 Score: 340
Period size: 40 Copynumber: 5.3 Consensus size: 40
223449 AACGGCATTT
* * * * * * *
223459 TTAGTGGCGCTTGCATAAAAAACGCCGCTAAAAATTGAGAA
1 TTAGCGGCGCTT-TATATAAAACACCGCTAAAGATCGAGCA
* *
223500 TTAGCTGTGCTTTATATAAAACACCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
223540 TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
223580 TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
223620 TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
223660 TTAGCGGCGCTTTA
1 TTAGCGGCGCTTTA
223674 AGGAAAACGC
Statistics
Matches: 163, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 154 0.94
41 9 0.06
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCGGCGCTTTATATAAAACACCGCTAAAGATCGAGCA
Found at i:223829 original size:42 final size:42
Alignment explanation
Indices: 223729--223933 Score: 351
Period size: 42 Copynumber: 4.9 Consensus size: 42
223719 CCTTTCAGGC
*
223729 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA-GGC
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
* *
223770 CTTTAGCGGCGTTTTTGGAGAAGCGCTGCTAAAGCTCAGGGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
223812 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
* *
223854 CTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCA-AGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
223895 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG
223934 TATCTGTCTA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
41 75 0.49
42 79 0.51
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
Found at i:223897 original size:83 final size:84
Alignment explanation
Indices: 223729--223933 Score: 351
Period size: 83 Copynumber: 2.5 Consensus size: 84
223719 CCTTTCAGGC
*
223729 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA-GGCCTTTAGCGGCGTTTTTGGAGAAG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGCCTTTAGCGGCGTTTTTAGAGAAG
* *
223793 CGCTGCTAAAGCTCAGGGG
66 CGCCGCTAAAGCTCAGAGG
*
223812 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGGCTTTAGCGGCGTTTTTAGAGAAG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGCCTTTAGCGGCGTTTTTAGAGAAG
*
223877 CGCCGCTAATGCTCA-AGG
66 CGCCGCTAAAGCTCAGAGG
223895 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG
223934 TATCTGTCTA
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 79 0.68
84 37 0.32
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.27
Consensus pattern (84 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGCCTTTAGCGGCGTTTTTAGAGAAG
CGCCGCTAAAGCTCAGAGG
Found at i:224035 original size:38 final size:38
Alignment explanation
Indices: 223991--224066 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
223981 TCAATTTATT
*
223991 TTTAATTGAATATTTGTTAAAAATGGATAAATTTGAAA
1 TTTAATTGAATATTTGTTAAAAATAGATAAATTTGAAA
224029 TTTAATTGAATATTTGTTAAAAATAGATAAATTTGAAA
1 TTTAATTGAATATTTGTTAAAAATAGATAAATTTGAAA
224067 CAATGACACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (38 bp):
TTTAATTGAATATTTGTTAAAAATAGATAAATTTGAAA
Found at i:224344 original size:14 final size:14
Alignment explanation
Indices: 224310--224382 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
224300 TAGAGTTTAA
* *
224310 GGTTTATGGATTAT
1 GGTTTAGGGGTTAT
224324 GGGTTTAGGGGTTAT
1 -GGTTTAGGGGTTAT
** *
224339 GGTTTACAGTTTAT
1 GGTTTAGGGGTTAT
* *
224353 GGTTTAAGGTTTA-
1 GGTTTAGGGGTTAT
224366 GGATTTAGGGGTTAT
1 GG-TTTAGGGGTTAT
224381 GG
1 GG
224383 CTTATGGTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
13 2 0.04
14 31 0.66
15 14 0.30
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (14 bp):
GGTTTAGGGGTTAT
Found at i:224388 original size:35 final size:35
Alignment explanation
Indices: 224349--224517 Score: 130
Period size: 35 Copynumber: 4.8 Consensus size: 35
224339 GGTTTACAGT
*
224349 TTATGGTTTAAGGTTTAGGATTTAGGGGTTATGGC
1 TTATGGTTTAAGGTTTAGGAGTTAGGGGTTATGGC
* ** *
224384 TTATGGTTTAAGGTTATA-GA-TTAAGGGTTGGGGT
1 TTATGGTTTAAGGTT-TAGGAGTTAGGGGTTATGGC
* * * * * * *
224418 TTAAGGTTTAGGGGTTAGGGGTAAAGGGTTGA-GGG
1 TTATGGTTTAAGGTTTAGGAGTTAGGGGTT-ATGGC
* * *
224453 TTAAGAG-TTAGGGGTTTAGGATTTAGGGGTTATGGC
1 TTATG-GTTTA-AGGTTTAGGAGTTAGGGGTTATGGC
*
224489 TTATGGTTTAAGGTTTAGGGGTTAGGGGT
1 TTATGGTTTAAGGTTTAGGAGTTAGGGGT
224518 AAGGGGTTGA
Statistics
Matches: 105, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
33 2 0.02
34 23 0.22
35 53 0.50
36 27 0.26
ACGTcount: A:0.21, C:0.01, G:0.40, T:0.38
Consensus pattern (35 bp):
TTATGGTTTAAGGTTTAGGAGTTAGGGGTTATGGC
Found at i:224393 original size:21 final size:21
Alignment explanation
Indices: 224304--224498 Score: 76
Period size: 21 Copynumber: 9.2 Consensus size: 21
224294 ATGGTATAGA
* * *
224304 GTTTAAGGTTTATGGATTATGG
1 GTTTAGGGGTTATGGTTTAT-G
**
224326 GTTTAGGGGTTATGGTTTACA
1 GTTTAGGGGTTATGGTTTATG
* * *
224347 GTTTATGGTTTAAGGTTTA-G
1 GTTTAGGGGTTATGGTTTATG
*
224367 GATTTAGGGGTTATGGCTTATG
1 G-TTTAGGGGTTATGGTTTATG
* * * *
224389 GTTTA-AGGTTATAGATTAAG
1 GTTTAGGGGTTATGGTTTATG
* * *
224409 GGTT-GGGGTTTAAGGTTTAGG
1 GTTTAGGGG-TTATGGTTTATG
* * * *
224430 GGTTAGGGGTAAAGGGTTGA-G
1 GTTTAGGGGT-TATGGTTTATG
* * * *
224451 GGTTAAGAGTTAGGGGTTTA-G
1 GTTTAGGGGTTA-TGGTTTATG
*
224472 GATTTAGGGGTTATGGCTTATG
1 G-TTTAGGGGTTATGGTTTATG
224494 GTTTA
1 GTTTA
224499 AGGTTTAGGG
Statistics
Matches: 129, Mismatches: 35, Indels: 19
0.70 0.19 0.10
Matches are distributed among these distances:
20 18 0.14
21 73 0.57
22 38 0.29
ACGTcount: A:0.22, C:0.02, G:0.37, T:0.40
Consensus pattern (21 bp):
GTTTAGGGGTTATGGTTTATG
Found at i:224530 original size:8 final size:7
Alignment explanation
Indices: 224425--224546 Score: 68
Period size: 7 Copynumber: 17.3 Consensus size: 7
224415 GGTTTAAGGT
224425 TTAGGGG
1 TTAGGGG
224432 TTAGGGG
1 TTAGGGG
* *
224439 TAAAGGG
1 TTAGGGG
224446 TT-GAGGG
1 TTAG-GGG
* *
224453 TTAAGAG
1 TTAGGGG
224460 TTAGGGG
1 TTAGGGG
**
224467 TTTAGGAT
1 -TTAGGGG
224475 TTAGGGG
1 TTAGGGG
* *
224482 TTATGGC
1 TTAGGGG
* *
224489 TTATGGT
1 TTAGGGG
* *
224496 TTAAGGT
1 TTAGGGG
224503 TTAGGGG
1 TTAGGGG
224510 TTAGGGG
1 TTAGGGG
*
224517 TAAGGGG
1 TTAGGGG
224524 TT-GAGGG
1 TTAG-GGG
* *
224531 TTAAGAG
1 TTAGGGG
224538 TTAGGGG
1 TTAGGGG
224545 TT
1 TT
224547 TAGGATTTAG
Statistics
Matches: 86, Mismatches: 24, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
6 1 0.01
7 80 0.93
8 5 0.06
ACGTcount: A:0.21, C:0.01, G:0.45, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:229160 original size:43 final size:42
Alignment explanation
Indices: 229052--229314 Score: 323
Period size: 43 Copynumber: 6.1 Consensus size: 42
229042 AAGATATATT
* *
229052 TTTAGCGGCGTTTGTGTCAAAAGCGTCGCTAAAGGTCTAT--TC
1 TTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCT-TGGTC
*
229094 TATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCTTGGTC
* * *
229137 TTTCGTGGCGTTTTTAGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGGTC
*
229180 TTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
229223 TTTAGCGGCGCTTGTGGGAAAAGCGCCGCTGAAGGTCATGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
229266 TTTAACGGCGTTTGTGGAAAAATCACCGGTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCTTGGTC
229309 TTTAGC
1 TTTAGC
229315 AGCATTTATT
Statistics
Matches: 193, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.01
42 36 0.19
43 154 0.80
44 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:229400 original size:12 final size:13
Alignment explanation
Indices: 229385--229413 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
229375 CGACGCTTTT
229385 AAAAGCGCCGC-A
1 AAAAGCGCCGCTA
229397 AAAAGCGCCGCTA
1 AAAAGCGCCGCTA
229410 AAAA
1 AAAA
229414 CCTGTTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.28, G:0.21, T:0.03
Consensus pattern (13 bp):
AAAAGCGCCGCTA
Found at i:231195 original size:21 final size:21
Alignment explanation
Indices: 231150--231189 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
231140 TACTAAACTC
*
231150 TTTTTAAATGTTTTGTTAAAA
1 TTTTTAAAGGTTTTGTTAAAA
*
231171 TTTTTTAAGGTTTTGTTAA
1 TTTTTAAAGGTTTTGTTAA
231190 GTTTTTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (21 bp):
TTTTTAAAGGTTTTGTTAAAA
Found at i:236455 original size:13 final size:13
Alignment explanation
Indices: 236437--236464 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
236427 AACCCATTTC
236437 ATACGTTTTAATT
1 ATACGTTTTAATT
236450 ATACGTTTTAATT
1 ATACGTTTTAATT
236463 AT
1 AT
236465 TCAACACACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (13 bp):
ATACGTTTTAATT
Found at i:241141 original size:443 final size:443
Alignment explanation
Indices: 240315--241195 Score: 1627
Period size: 443 Copynumber: 2.0 Consensus size: 443
240305 ACTTTTATAA
240315 TCCTTCATGGCGTAATCATCCCAACTTTTCTTAAAGTAATAAAGGAAATGGACCCAACAACACCT
1 TCCTTCATGGCGTAATCATCCCAACTTTTCTTAAAGTAATAAAGGAAATGGACCCAACAACACCT
*
240380 ACACGCAACATAGACCAAGTCAACCCCAAGAGTTTAATCAACAAGATTTAAAACGACCATAACCT
66 ACACGCAACATAGACCAAGTCAACCCCAAGAGTTTAATCAACAAGATTTAAAACCACCATAACCT
240445 GAACCATCTAACAGTTTGGAGAATTTGTTGAAGGTGTACATGGTGAAGAATGACACCTTAATCCA
131 GAACCATCTAACAGTTTGGAGAATTTGTTGAAGGTGTACATGGTGAAGAATGACACCTTAATCCA
*
240510 AAGCCAATCAGCAAAACTGAAAATTTTGGAGAACCAAATAGATTAGTTAGCTACGGAGCTTTGTA
196 AAGCCAATCAGCAAAACTGAAAATTTTGGAGAACCAAATAGATTAGTTAGCTACGGAGCTTCGTA
*
240575 ATCGATCGCAAGTAGCCTTGCCAAACGATACAGAAAATCCAAGGCATTTTTGTAAGGAACATTGC
261 ATCGATCGCAAGTAGCCTTGCCAAACGATACAGAAAATCCAAGGCATTTGTGTAAGGAACATTGC
240640 AAGGTAGTTGCTTTACGAAGTGGTAAGAATTTGGAACCCAAGGAAGCTGTGGTTAAAGATGAACC
326 AAGGTAGTTGCTTTACGAAGTGGTAAGAATTTGGAACCCAAGGAAGCTGTGGTTAAAGATGAACC
240705 TACTGAGAAGGAGGAAAGTCAGCCAACAATTGAAATTCCTGCACCATTGAAAT
391 TACTGAGAAGGAGGAAAGTCAGCCAACAATTGAAATTCCTGCACCATTGAAAT
* *
240758 TCCTTCATGGCGTAATCATCCCAACTTTTCTTAGAGTAATAAAGGAAATGGACCCAACAACGCCT
1 TCCTTCATGGCGTAATCATCCCAACTTTTCTTAAAGTAATAAAGGAAATGGACCCAACAACACCT
* * * *
240823 ACATGCAACATAGACCAAGTTAACCCCAAGAGTTTAATCAACAAGTTTTAAAACCACCATAAGCT
66 ACACGCAACATAGACCAAGTCAACCCCAAGAGTTTAATCAACAAGATTTAAAACCACCATAACCT
*
240888 GAACCATCTAACAGTTTGGAGAATTTTTTGAAGGTGTACATGGTGAAGAATGACACCTTAATCCA
131 GAACCATCTAACAGTTTGGAGAATTTGTTGAAGGTGTACATGGTGAAGAATGACACCTTAATCCA
240953 AAGCCAATCAGCAAAACTGAAAATTTTGGAGAACCAAATAGATTAGTTAGCTACGGAGCTTCGTA
196 AAGCCAATCAGCAAAACTGAAAATTTTGGAGAACCAAATAGATTAGTTAGCTACGGAGCTTCGTA
**
241018 ATCGATCGCAAGTAGCCTTGCCAAACGATAGGGAAAATCCAAGGCATTTGTGTAAGGAACATTGC
261 ATCGATCGCAAGTAGCCTTGCCAAACGATACAGAAAATCCAAGGCATTTGTGTAAGGAACATTGC
* *
241083 AAGGTAGTTGGTTTACGAAGTGGTAAGAATTTGGAACCCAAGGAAGTTGTGGTTAAAGATGAACC
326 AAGGTAGTTGCTTTACGAAGTGGTAAGAATTTGGAACCCAAGGAAGCTGTGGTTAAAGATGAACC
*
241148 TACTGAGAAGGAGGAAAGTCAGCCAACAATTGCAATTCCTGCACCATT
391 TACTGAGAAGGAGGAAAGTCAGCCAACAATTGAAATTCCTGCACCATT
241196 AGAGCTAGAA
Statistics
Matches: 423, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
443 423 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (443 bp):
TCCTTCATGGCGTAATCATCCCAACTTTTCTTAAAGTAATAAAGGAAATGGACCCAACAACACCT
ACACGCAACATAGACCAAGTCAACCCCAAGAGTTTAATCAACAAGATTTAAAACCACCATAACCT
GAACCATCTAACAGTTTGGAGAATTTGTTGAAGGTGTACATGGTGAAGAATGACACCTTAATCCA
AAGCCAATCAGCAAAACTGAAAATTTTGGAGAACCAAATAGATTAGTTAGCTACGGAGCTTCGTA
ATCGATCGCAAGTAGCCTTGCCAAACGATACAGAAAATCCAAGGCATTTGTGTAAGGAACATTGC
AAGGTAGTTGCTTTACGAAGTGGTAAGAATTTGGAACCCAAGGAAGCTGTGGTTAAAGATGAACC
TACTGAGAAGGAGGAAAGTCAGCCAACAATTGAAATTCCTGCACCATTGAAAT
Found at i:247339 original size:27 final size:27
Alignment explanation
Indices: 247301--247355 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
247291 AAAAAGTTCA
247301 TGAAAGATTAAGTTGCCATAGAATATT
1 TGAAAGATTAAGTTGCCATAGAATATT
247328 TGAAAGATTAAGTTGCCATAGAATATT
1 TGAAAGATTAAGTTGCCATAGAATATT
247355 T
1 T
247356 TTGGAACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (27 bp):
TGAAAGATTAAGTTGCCATAGAATATT
Found at i:257017 original size:21 final size:20
Alignment explanation
Indices: 256969--257018 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
256959 AACCTATAAA
256969 ATCGATACCAAGATAAAATT
1 ATCGATACCAAGATAAAATT
*
256989 ATCAATACCAA-ATAAAAATGT
1 ATCGATACCAAGAT-AAAAT-T
257010 ATCGATACC
1 ATCGATACC
257019 GGATCGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.58
21 9 0.35
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (20 bp):
ATCGATACCAAGATAAAATT
Found at i:260210 original size:29 final size:30
Alignment explanation
Indices: 260172--260228 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
260162 GGGTTGGGAG
260172 GGGAGAGGAGTAAAAGTTTTGAGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAGT
260202 GGGA-AGGAGTAAAAGTTTTGAGGGAAA
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAA
260229 AGTAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (30 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAGT
Found at i:260362 original size:9 final size:9
Alignment explanation
Indices: 260345--260386 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
260335 TCGAGTTGAT
*
260345 TCGAATAAC
1 TCGATTAAC
260354 TCGATTAAC
1 TCGATTAAC
260363 TCGATTAAC
1 TCGATTAAC
*
260372 TCGAATAAC
1 TCGATTAAC
260381 TCGATT
1 TCGATT
260387 TGTTTAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (9 bp):
TCGATTAAC
Found at i:265218 original size:17 final size:16
Alignment explanation
Indices: 265196--265228 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
265186 TATAGCTCCG
265196 ACGAGCTTCCAACTTGA
1 ACGAGCTTCCAA-TTGA
265213 ACGAGCTTCCAATTGA
1 ACGAGCTTCCAATTGA
265229 CTATAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (16 bp):
ACGAGCTTCCAATTGA
Found at i:265698 original size:25 final size:25
Alignment explanation
Indices: 265662--265755 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
265652 CCTTTACATG
265662 TATGCT-TATACGAGCTGTGAATCGA
1 TATGCTCT-TACGAGCTGTGAATCGA
* *
265687 TATGCTCTTACGAGTTGT-AGATCAA
1 TATGCTCTTACGAGCTGTGA-ATCGA
* * *
265712 TATGCTCTTATGAGCTGTAAATCGG
1 TATGCTCTTACGAGCTGTGAATCGA
**
265737 TATGCTCACACGAGCTGTG
1 TATGCTCTTACGAGCTGTG
265756 GGTCGAACCG
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.02
25 53 0.95
26 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (25 bp):
TATGCTCTTACGAGCTGTGAATCGA
Found at i:266181 original size:21 final size:17
Alignment explanation
Indices: 266132--266172 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
266122 CGGATAAATT
266132 TAACTCAATTTAATATA
1 TAACTCAATTTAATATA
266149 TAACTCAATTTAATATA
1 TAACTCAATTTAATATA
266166 TAACTCA
1 TAACTCA
266173 TTCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACTCAATTTAATATA
Found at i:277358 original size:27 final size:26
Alignment explanation
Indices: 277328--277452 Score: 117
Period size: 28 Copynumber: 4.6 Consensus size: 26
277318 GCCAAAAAAT
277328 GAAAGCCTTTGTGGCAATATATGAAA
1 GAAAGCCTTTGTGGCAATATATGAAA
* *
277354 CGAAAAGCCTTTATGGCAATATATGATAT
1 -G-AAAGCCTTTGTGGCAATATATGA-AA
* * * *
277383 GGAAGCCTTTGTGGCGATCTATGGGAAG
1 GAAAGCCTTTGTGGCAATATAT--GAAA
277411 GAAAGCCTTTGTGGCAA-ATGATGAAA
1 GAAAGCCTTTGTGGCAATAT-ATGAAA
*
277437 GAAACGCCTTCGTGGC
1 GAAA-GCCTTTGTGGC
277453 GTACACAAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
26 7 0.09
27 29 0.36
28 41 0.51
29 3 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (26 bp):
GAAAGCCTTTGTGGCAATATATGAAA
Found at i:277515 original size:27 final size:27
Alignment explanation
Indices: 277485--277559 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
277475 GTGGCAACCA
277485 TCTGAAGGGATAGTATGTATGGCGA-AC
1 TCTGAAGGGATAGTATGTATGGC-ACAC
*
277512 TCTGAAGTGATAGTATGTATGGCACAC
1 TCTGAAGGGATAGTATGTATGGCACAC
* *
277539 TCCGAATGGATAGTATGTATG
1 TCTGAAGGGATAGTATGTATG
277560 ATAAAATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (27 bp):
TCTGAAGGGATAGTATGTATGGCACAC
Found at i:277727 original size:17 final size:17
Alignment explanation
Indices: 277707--277741 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
277697 ACTAGGTGAA
277707 TACAAAGTATGGGCGAG
1 TACAAAGTATGGGCGAG
277724 TACAAAGTATGGGCGAG
1 TACAAAGTATGGGCGAG
277741 T
1 T
277742 TAGACTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.20
Consensus pattern (17 bp):
TACAAAGTATGGGCGAG
Found at i:285259 original size:50 final size:50
Alignment explanation
Indices: 285156--285447 Score: 268
Period size: 50 Copynumber: 5.7 Consensus size: 50
285146 GGTAAAGAGA
* *
285156 TCCCATGTAAGACCATGTCTGGGACATGACGTTGGCGTCATTGAGATTATGAGACG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTT-G-G-CACTGAG---ATGAGACG
* * *
285212 TCTCATGTAAGACCATGTCTGGGACATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGACG
* * *
285262 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGACG
* * * * *
285312 TCACC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC-
1 TC-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAG-ACG
* * * * * * * * *
285362 TCCCATGTAAGACCATATCTAGGATATGACTTTTGCAGTGCA-A-GAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTG-AGATGAGACG
*
285411 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
285448 TGTTATTATC
Statistics
Matches: 200, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
48 2 0.01
49 36 0.18
50 120 0.60
51 4 0.02
53 6 0.03
54 1 0.00
55 1 0.00
56 30 0.15
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGACG
Found at i:291273 original size:17 final size:16
Alignment explanation
Indices: 291240--291271 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
291230 AACTTGAGGG
291240 GCAAAAATGTAATTTT
1 GCAAAAATGTAATTTT
*
291256 GCAAAAATGTGATTTT
1 GCAAAAATGTAATTTT
291272 TGGACTGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (16 bp):
GCAAAAATGTAATTTT
Found at i:303300 original size:55 final size:56
Alignment explanation
Indices: 303215--303325 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 56
303205 CTTTTTGAAA
303215 CTTTTCATTTTTGTCCTCAAATAGTCTTGGGTTATCATAGGAGCTTTCATAAGCTC
1 CTTTTCATTTTTGTCCTCAAATAGTCTTGGGTTATCATAGGAGCTTTCATAAGCTC
303271 CTTTTCA-TTTTGTCCTCAAATAGTCTTGGGTTATCATAGGAGCTTTCATAAGCTC
1 CTTTTCATTTTTGTCCTCAAATAGTCTTGGGTTATCATAGGAGCTTTCATAAGCTC
303326 ATATAACCTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 48 0.87
56 7 0.13
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (56 bp):
CTTTTCATTTTTGTCCTCAAATAGTCTTGGGTTATCATAGGAGCTTTCATAAGCTC
Found at i:304088 original size:3 final size:3
Alignment explanation
Indices: 304080--304106 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
304070 AGAGAAAGTT
304080 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
304107 TTTGGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:304142 original size:10 final size:10
Alignment explanation
Indices: 304129--304232 Score: 58
Period size: 10 Copynumber: 10.4 Consensus size: 10
304119 ATTATTTACA
304129 AATTTTTAAT
1 AATTTTTAAT
304139 AATTATTT-AT
1 AATT-TTTAAT
*
304149 GATTTTTAAT
1 AATTTTTAAT
304159 AA-TTTTAA-
1 AATTTTTAAT
*
304167 AATATTTAAAT
1 AAT-TTTTAAT
*
304178 AAATTTTTTTAT
1 -AA-TTTTTAAT
304190 AA-TTTTAAT
1 AATTTTTAAT
* *
304199 AGCTTTTT-AC
1 A-ATTTTTAAT
*
304209 AA-TTTTAAA
1 AATTTTTAAT
304218 ATATTTTTAAT
1 A-ATTTTTAAT
304229 AATT
1 AATT
304233 ATTGACAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
8 6 0.08
9 18 0.25
10 23 0.32
11 16 0.23
12 7 0.10
13 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:304142 original size:21 final size:20
Alignment explanation
Indices: 304117--304175 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
304107 TTTGGTTTGT
304117 TAATTATTTACAAATTTTTAA
1 TAATTATTTA-AAATTTTTAA
**
304138 TAATTATTTATGATTTTTAA
1 TAATTATTTAAAATTTTTAA
*
304158 TAA-T-TTTAAAATATTTAA
1 TAATTATTTAAAATTTTTAA
304176 ATAAATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 11 0.33
19 1 0.03
20 11 0.33
21 10 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TAATTATTTAAAATTTTTAA
Found at i:304224 original size:19 final size:19
Alignment explanation
Indices: 304178--304226 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
304168 ATATTTAAAT
* *
304178 AAATTTTTTTATAATTTTA
1 AAATATTTTTACAATTTTA
* **
304197 ATAGCTTTTTACAATTTTA
1 AAATATTTTTACAATTTTA
304216 AAATATTTTTA
1 AAATATTTTTA
304227 ATAATTATTG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
AAATATTTTTACAATTTTA
Found at i:304286 original size:29 final size:29
Alignment explanation
Indices: 304257--304333 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 29
304247 AATTTTTTTA
304257 AAATTTTTTTTACAATTTTTA-ATAATTT
1 AAATTTTTTTTACAATTTTTATATAATTT
* * *
304285 AAA-TATTTTCACAATTTTTATATATTTTT
1 AAATTTTTTTTACAATTTTTATATA-ATTT
*
304314 AAATATTTTTTTACGATTTT
1 AAAT-TTTTTTTACAATTTT
304334 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 15 0.38
28 6 0.15
29 6 0.15
31 12 0.31
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (29 bp):
AAATTTTTTTTACAATTTTTATATAATTT
Found at i:304301 original size:27 final size:29
Alignment explanation
Indices: 304263--304322 Score: 88
Period size: 27 Copynumber: 2.1 Consensus size: 29
304253 TTTAAAATTT
*
304263 TTTTTACAATTTTTA-ATA-ATTTAAATA
1 TTTTCACAATTTTTATATATATTTAAATA
*
304290 TTTTCACAATTTTTATATATTTTTAAATA
1 TTTTCACAATTTTTATATATATTTAAATA
304319 TTTT
1 TTTT
304323 TTTACGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 14 0.48
28 3 0.10
29 12 0.41
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTCACAATTTTTATATATATTTAAATA
Found at i:304311 original size:10 final size:10
Alignment explanation
Indices: 304282--304323 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
304272 TTTTTAATAA
304282 TTTAAATATT
1 TTTAAATATT
* *
304292 TTCACA-ATT
1 TTTAAATATT
*
304301 TTTATATATT
1 TTTAAATATT
304311 TTTAAATATT
1 TTTAAATATT
304321 TTT
1 TTT
304324 TTACGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTAAATATT
Found at i:304340 original size:17 final size:17
Alignment explanation
Indices: 304318--304350 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
304308 ATTTTTAAAT
*
304318 ATTTTTTTACGATTTTA
1 ATTTTTTTACAATTTTA
304335 ATTTTTTTACAATTTT
1 ATTTTTTTACAATTTT
304351 TTTTGATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTTTTACAATTTTA
Found at i:304341 original size:29 final size:30
Alignment explanation
Indices: 304244--304354 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 30
304234 TTGACAAAAA
304244 TTTAATTTTTTTAAA-ATTTTTTTTACAATT
1 TTTAATTTTTTTAAATA-TTTTTTTACAATT
** *
304274 TTTAA-TAATTTAAATA--TTTTCACAATT
1 TTTAATTTTTTTAAATATTTTTTTACAATT
* *
304301 TTTATATATTTTTAAATATTTTTTTACGA-T
1 TTTA-ATTTTTTTAAATATTTTTTTACAATT
304331 TTTAATTTTTTTACAAT-TTTTTTT
1 TTTAATTTTTTTA-AATATTTTTTT
304355 GATCAGGTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
27 14 0.21
28 1 0.02
29 30 0.45
30 14 0.21
31 7 0.11
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.64
Consensus pattern (30 bp):
TTTAATTTTTTTAAATATTTTTTTACAATT
Found at i:306467 original size:3 final size:3
Alignment explanation
Indices: 306459--306485 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
306449 AGAGAAAGTT
306459 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
306486 TTTGGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:306521 original size:21 final size:20
Alignment explanation
Indices: 306496--306541 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
306486 TTTGGTTTGT
306496 TAATTATTTACAAATTTTTAA
1 TAATTATTTA-AAATTTTTAA
**
306517 TAATTATTTATGATTTTTAA
1 TAATTATTTAAAATTTTTAA
306537 TAATT
1 TAATT
306542 TTNNNNNNNN
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TAATTATTTAAAATTTTTAA
Found at i:306779 original size:10 final size:10
Alignment explanation
Indices: 306750--306791 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
306740 ATTTTAATAA
306750 TTTAAATATT
1 TTTAAATATT
* *
306760 TTCACA-ATT
1 TTTAAATATT
*
306769 TTTATATATT
1 TTTAAATATT
306779 TTTAAATATT
1 TTTAAATATT
306789 TTT
1 TTT
306792 TTACGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTAAATATT
Found at i:306808 original size:17 final size:17
Alignment explanation
Indices: 306786--306818 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
306776 ATTTTTAAAT
*
306786 ATTTTTTTACGATTTTA
1 ATTTTTTTACAATTTTA
306803 ATTTTTTTACAATTTT
1 ATTTTTTTACAATTTT
306819 TTTTGATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTTTTACAATTTTA
Found at i:310806 original size:22 final size:20
Alignment explanation
Indices: 310760--310814 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
310750 AATTTTAGTT
*
310760 TATATTATTAATTTAATTTA
1 TATATTTTTAATTTAATTTA
310780 -ATATTTTTAATGTTATATTTA
1 TATATTTTTAAT-TTA-ATTTA
310801 TATATTTTTTAATT
1 TATA-TTTTTAATT
310815 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.33
20 3 0.10
21 5 0.17
22 4 0.13
23 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATATTTTTAATTTAATTTA
Found at i:310808 original size:21 final size:19
Alignment explanation
Indices: 310760--310808 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 19
310750 AATTTTAGTT
310760 TATATTATTAATTTAATTTA
1 TATATT-TTAATTTAATTTA
310780 -ATATTTTTAATGTTATATTTA
1 TATA-TTTTAAT-TTA-ATTTA
310801 TATATTTT
1 TATATTTT
310809 TTAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 8 0.32
20 5 0.20
21 9 0.36
22 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATATTTTAATTTAATTTA
Found at i:314589 original size:35 final size:34
Alignment explanation
Indices: 314499--314594 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 34
314489 TACTATCTGT
*
314499 TTGGTGTGTTTCAGAGGGACTAGCTCTTTTGAGCA
1 TTGGTGTGTTT-AGAGGGACTAGCTCTTATGAGCA
* *
314534 TTGGTGTGTTTTGATTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTAGA-GGGACTAGCTCTTATGAGCA
* *
314569 TTGGTGTGTTCTGGAGGGACTGGCTC
1 TTGGTGTGTT-TAGAGGGACTAGCTC
314595 GGGTGAACAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
34 2 0.04
35 48 0.91
36 3 0.06
ACGTcount: A:0.15, C:0.14, G:0.33, T:0.39
Consensus pattern (34 bp):
TTGGTGTGTTTAGAGGGACTAGCTCTTATGAGCA
Found at i:315113 original size:21 final size:21
Alignment explanation
Indices: 315087--315128 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
315077 CCAAGCTATT
315087 GGTTGGATTGTATTATGTTTA
1 GGTTGGATTGTATTATGTTTA
315108 GGTTGGATTGTATTATGTTTA
1 GGTTGGATTGTATTATGTTTA
315129 CTTTTAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (21 bp):
GGTTGGATTGTATTATGTTTA
Found at i:320269 original size:57 final size:57
Alignment explanation
Indices: 320181--320288 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
320171 ACCACCGGTA
* * *
320181 CATAGTACCTGAAAATATATCACTTGCACAGAGTGCTTGGAAACTGTAACATCGTTC
1 CATAGTACCTGAAAATATATCACTGGCACAGAGTGCCTGGAAAATGTAACATCGTTC
* * *
320238 CATAGTACTTGGAAATATATCACTGGCACAGAGTTCCTGGAAAATGTAACA
1 CATAGTACCTGAAAATATATCACTGGCACAGAGTGCCTGGAAAATGTAACA
320289 CCCTAATGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (57 bp):
CATAGTACCTGAAAATATATCACTGGCACAGAGTGCCTGGAAAATGTAACATCGTTC
Found at i:329985 original size:62 final size:62
Alignment explanation
Indices: 329877--330013 Score: 249
Period size: 62 Copynumber: 2.2 Consensus size: 62
329867 CATGACAAGC
329877 AGTATCAACAGTTCCTAGATATATTGAAGAAACTGTAGATCAACATTCCTTTAGTAGACGCTCT
1 AGTA-CAACA-TTCCTAGATATATTGAAGAAACTGTAGATCAACATTCCTTTAGTAGACGCTCT
329941 AGTACAACATTCCTAGATATATTGAAGAAACTGTAGATCAACATTCCTTTAGTAGACGCTCT
1 AGTACAACATTCCTAGATATATTGAAGAAACTGTAGATCAACATTCCTTTAGTAGACGCTCT
330003 AGTACAA-ATTC
1 AGTACAACATTC
330014 TAAGTTATGG
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
61 4 0.05
62 60 0.82
63 5 0.07
64 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (62 bp):
AGTACAACATTCCTAGATATATTGAAGAAACTGTAGATCAACATTCCTTTAGTAGACGCTCT
Found at i:329988 original size:34 final size:34
Alignment explanation
Indices: 329880--329988 Score: 115
Period size: 34 Copynumber: 3.4 Consensus size: 34
329870 GACAAGCAGT
329880 ATCAACAGTTCCTAGATATATTGAAGAAACTGTAG
1 ATCAACA-TTCCTAGATATATTGAAGAAACTGTAG
* ** *
329915 ATCAACATTCCT---T-TA--GTAGACGCTCTAG
1 ATCAACATTCCTAGATATATTGAAGAAACTGTAG
329943 -TACAACATTCCTAGATATATTGAAGAAACTGTAG
1 AT-CAACATTCCTAGATATATTGAAGAAACTGTAG
329977 ATCAACATTCCT
1 ATCAACATTCCT
329989 TTAGTAGACG
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
27 1 0.02
28 19 0.33
30 2 0.03
31 2 0.03
32 2 0.03
34 24 0.41
35 8 0.14
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (34 bp):
ATCAACATTCCTAGATATATTGAAGAAACTGTAG
Found at i:334158 original size:12 final size:12
Alignment explanation
Indices: 334141--334165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
334131 TATTTACGCA
334141 TTTTATTATTAT
1 TTTTATTATTAT
334153 TTTTATTATTAT
1 TTTTATTATTAT
334165 T
1 T
334166 GTCATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:336942 original size:11 final size:13
Alignment explanation
Indices: 336918--336949 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
336908 TAGTTTATTA
336918 ATATTTTAATATG
1 ATATTTTAATATG
336931 AT-TTTTAA-ATG
1 ATATTTTAATATG
336942 ATATTTTA
1 ATATTTTA
336950 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:342606 original size:17 final size:17
Alignment explanation
Indices: 342584--342618 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
342574 GATAGTGTGA
342584 TATAGCTCCAACAAGCT
1 TATAGCTCCAACAAGCT
* *
342601 TATAGCTCGAACGAGCT
1 TATAGCTCCAACAAGCT
342618 T
1 T
342619 CCGATTCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (17 bp):
TATAGCTCCAACAAGCT
Found at i:342892 original size:20 final size:22
Alignment explanation
Indices: 342849--342892 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
342839 CAAATTCTAC
* *
342849 ATACATGTATCATCCATTTCAT
1 ATACATGTATCATCCATGTAAT
342871 ATACATGTAT-A-CCATGTAAT
1 ATACATGTATCATCCATGTAAT
342891 AT
1 AT
342893 CATTTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 1 0.05
22 10 0.50
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (22 bp):
ATACATGTATCATCCATGTAAT
Found at i:343101 original size:25 final size:25
Alignment explanation
Indices: 343072--343169 Score: 96
Period size: 25 Copynumber: 4.0 Consensus size: 25
343062 TACGAGTTAT
*
343072 GAATCAGTATGCTCTCACGAGCT-A
1 GAATCAGTAAGCTCTCACGAGCTGA
* *
343096 GAAATCGGTAACCTCAT-ACGAGCTGA
1 G-AATCAGTAAGCTC-TCACGAGCTGA
*
343122 GAATCAGTAAGCTTTCACGAGCTGA
1 GAATCAGTAAGCTCTCACGAGCTGA
*
343147 G-ATCGGTAAGCTCAT-ACGAGCTG
1 GAATCAGTAAGCTC-TCACGAGCTG
343170 TGGTGTGTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
24 20 0.33
25 38 0.62
26 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (25 bp):
GAATCAGTAAGCTCTCACGAGCTGA
Found at i:343167 original size:49 final size:51
Alignment explanation
Indices: 343057--343169 Score: 160
Period size: 50 Copynumber: 2.3 Consensus size: 51
343047 GTACATGTAT
* *
343057 GCTCATACGAG-TTATGAATCAGTATGCTCTCACGAGCTAGAAATCGGTAA
1 GCTCATACGAGCTGATGAATCAGTAAGCTCTCACGAGCTAGAAATCGGTAA
* * *
343107 CCTCATACGAGCTGA-GAATCAGTAAGCTTTCACGAGCT-GAGATCGGTAA
1 GCTCATACGAGCTGATGAATCAGTAAGCTCTCACGAGCTAGAAATCGGTAA
343156 GCTCATACGAGCTG
1 GCTCATACGAGCTG
343170 TGGTGTGTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 23 0.41
50 31 0.55
51 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (51 bp):
GCTCATACGAGCTGATGAATCAGTAAGCTCTCACGAGCTAGAAATCGGTAA
Found at i:360214 original size:44 final size:44
Alignment explanation
Indices: 360160--360250 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
360150 AGTGTAAGGA
*
360160 AGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGG
1 AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
* * * *
360204 AGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
360248 AGC
1 AGC
360251 GAATTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
Found at i:363171 original size:9 final size:9
Alignment explanation
Indices: 363157--363184 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
363147 NNNNNNNNNA
363157 ACAATTAAT
1 ACAATTAAT
363166 ACAATTAAT
1 ACAATTAAT
363175 ACAATTAAT
1 ACAATTAAT
363184 A
1 A
363185 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:363258 original size:59 final size:59
Alignment explanation
Indices: 363166--363305 Score: 262
Period size: 59 Copynumber: 2.4 Consensus size: 59
363156 AACAATTAAT
*
363166 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGATAGATTTTATTACA
363225 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGATAGATTTTATTACA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGATAGATTTTATTACA
*
363284 ACAATTAATACAATTAACAATT
1 ACAATTAATACAATTAATAATT
363306 AATAATTTGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (59 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGATAGATTTTATTACA
Found at i:363337 original size:16 final size:16
Alignment explanation
Indices: 363316--363357 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
363306 AATAATTTGA
*
363316 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
363332 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
363348 TAGTTTTAAT
1 TAATTTTAAT
363358 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:363341 original size:22 final size:23
Alignment explanation
Indices: 363331--363392 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
363321 TTACTAACAA
* * *
363331 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
363353 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
363376 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
363393 CTGGTCAGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:363346 original size:59 final size:62
Alignment explanation
Indices: 363156--363349 Score: 215
Period size: 59 Copynumber: 3.1 Consensus size: 62
363146 NNNNNNNNNN
363156 AACAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTT-A
1 AACAATTAATACAATT-A-ACAATTAATAATTTGATAAATTTACTAATCAAA--TTAGATTTTAA
363220 T
62 T
* * *
363221 TACAA-CAAT-TAA-T-ACAATTAATAATTTGATAAATTTACTAATCAAATGATAGATTTTATTA
1 AACAATTAATACAATTAACAATTAATAATTTGATAAATTTACTAATCAAAT--TAGATTTTA--A
*
363282 C
62 T
*
363283 AACAATTAATACAATTAACAATTAATAATTTGATAATTTTACTAA-C-AATTA-ATTTTAAT
1 AACAATTAATACAATTAACAATTAATAATTTGATAAATTTACTAATCAAATTAGATTTTAAT
363342 AACAATTA
1 AACAATTA
363350 GTTTTAATTT
Statistics
Matches: 111, Mismatches: 9, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
57 1 0.01
59 50 0.45
61 6 0.05
62 8 0.07
63 5 0.05
64 8 0.07
65 6 0.05
66 27 0.24
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (62 bp):
AACAATTAATACAATTAACAATTAATAATTTGATAAATTTACTAATCAAATTAGATTTTAAT
Found at i:370110 original size:19 final size:18
Alignment explanation
Indices: 370088--370134 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
370078 TAAATTATAA
*
370088 ATTTAAACTTAAAATAATT
1 ATTTAAACTT-AAATAATG
*
370107 ATTTAAAATTAAATAATG
1 ATTTAAACTTAAATAATG
370125 ATGTTAAACT
1 AT-TTAAACT
370135 CACTTGTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTTAAACTTAAATAATG
Found at i:370880 original size:20 final size:19
Alignment explanation
Indices: 370855--370896 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
370845 ATATATATAG
370855 AAAAAATCAAAATAATCTAA
1 AAAAAATCAAAAT-ATCTAA
370875 AAAAAATCAAAATATCTAA
1 AAAAAATCAAAATATCTAA
370894 AAA
1 AAA
370897 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAATCAAAATATCTAA
Found at i:372242 original size:16 final size:16
Alignment explanation
Indices: 372221--372254 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
372211 GACTTAAAAG
372221 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
*
372237 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
372253 TT
1 TT
372255 GAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:375912 original size:15 final size:15
Alignment explanation
Indices: 375892--375924 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
375882 CAACATATTA
*
375892 TAATGTGTTAGAAAT
1 TAATGTGTTACAAAT
375907 TAATGTGTTACAAAT
1 TAATGTGTTACAAAT
375922 TAA
1 TAA
375925 ATCTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (15 bp):
TAATGTGTTACAAAT
Found at i:375985 original size:13 final size:13
Alignment explanation
Indices: 375963--376000 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
375953 TTAAAAGTTC
*
375963 AAACATTATATTA
1 AAACAATATATTA
375976 AAACAATATATTA
1 AAACAATATATTA
375989 AAA-AAGTATATT
1 AAACAA-TATATT
376001 TATAATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 2 0.09
13 21 0.91
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (13 bp):
AAACAATATATTA
Found at i:377774 original size:38 final size:38
Alignment explanation
Indices: 377732--377820 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
377722 AAAAAACACA
* *
377732 ACCATTAACAGCATTAACAGAAAAATCAAAATTAGAGC
1 ACCATTAACAGCATTAACAGAAAAATCAAAATCAGAAC
* * *
377770 ACCATTAACAACATTAATAGCAAAATCAAAATCAGAAC
1 ACCATTAACAGCATTAACAGAAAAATCAAAATCAGAAC
377808 ACCATTAACAGCA
1 ACCATTAACAGCA
377821 AAAATCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (38 bp):
ACCATTAACAGCATTAACAGAAAAATCAAAATCAGAAC
Found at i:377813 original size:29 final size:30
Alignment explanation
Indices: 377776--377843 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
377766 GAGCACCATT
*
377776 AACAACATTAATAGC-AAAATCAAAATCAG
1 AACAACATTAACAGCAAAAATCAAAATCAG
* *
377805 AACACCATTAACAGCAAAAATCAAAATCAC
1 AACAACATTAACAGCAAAAATCAAAATCAG
377835 AACCAACAT
1 AA-CAACAT
377844 CAAAAAGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.39
30 15 0.45
31 5 0.15
ACGTcount: A:0.57, C:0.24, G:0.04, T:0.15
Consensus pattern (30 bp):
AACAACATTAACAGCAAAAATCAAAATCAG
Found at i:380049 original size:16 final size:16
Alignment explanation
Indices: 380028--380058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
380018 TTTGGTTCGC
380028 TGTAATGAAATAGAGG
1 TGTAATGAAATAGAGG
*
380044 TGTAATGGAATAGAG
1 TGTAATGAAATAGAG
380059 ACATAATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (16 bp):
TGTAATGAAATAGAGG
Found at i:380320 original size:18 final size:17
Alignment explanation
Indices: 380299--380333 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
380289 TTATTATTAA
*
380299 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
380317 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
380334 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:383639 original size:19 final size:19
Alignment explanation
Indices: 383612--383648 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
383602 AACAAATTAA
*
383612 TTGTTGGTATATGTAAAAT
1 TTGTAGGTATATGTAAAAT
383631 TTGTAGGTATATGTAAAA
1 TTGTAGGTATATGTAAAA
383649 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGTAGGTATATGTAAAAT
Found at i:383935 original size:18 final size:16
Alignment explanation
Indices: 383896--383929 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
383886 AATAAATTGG
383896 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
383912 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
383928 AA
1 AA
383930 AATATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:385271 original size:9 final size:9
Alignment explanation
Indices: 385247--385277 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
385237 ATTATTCCAT
385247 TTCAAATGC
1 TTCAAATGC
385256 TTC-AATGC
1 TTCAAATGC
385264 TTCAAATGC
1 TTCAAATGC
385273 TTCAA
1 TTCAA
385278 CGGTAATCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (9 bp):
TTCAAATGC
Found at i:391052 original size:4 final size:4
Alignment explanation
Indices: 391043--391087 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
391033 CAAACATTTC
* * *
391043 CATA CATA CACA CATA CATA CATG CATA CATA CATA CATA TATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
391088 TTAAGTTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:400758 original size:24 final size:24
Alignment explanation
Indices: 400701--400759 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
400691 TCTCACCACA
*
400701 TTATTTCTCATTCTCTCACATTTC
1 TTATTTCTCCTTCTCTCACATTTC
*
400725 TTATTTCTCCTTCTCTCACTTTTC
1 TTATTTCTCCTTCTCTCACATTTC
400749 TTATTTCTCCT
1 TTATTTCTCCT
400760 ACAATGTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.12, C:0.31, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTTCTCCTTCTCTCACATTTC
Found at i:406245 original size:22 final size:22
Alignment explanation
Indices: 406204--406245 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
406194 TTTGGACCGA
* * *
406204 TGATATTCGGGCTTTGTGCCGG
1 TGATATTCAGGCTCTATGCCGG
406226 TGATATTCAGGCTCTATGCC
1 TGATATTCAGGCTCTATGCC
406246 TAGCAGACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (22 bp):
TGATATTCAGGCTCTATGCCGG
Found at i:406257 original size:38 final size:38
Alignment explanation
Indices: 406215--406379 Score: 136
Period size: 38 Copynumber: 4.3 Consensus size: 38
406205 GATATTCGGG
406215 CTTTGTGCCGGTGATATTCAGGCTCTATGCCTAGCAGA
1 CTTTGTGCCGGTGATATTCAGGCTCTATGCCTAGCAGA
* * *
406253 CTTTGTACCGGTGATATTC-GTGCTCTATACCTATCA-A
1 CTTTGTGCCGGTGATATTCAG-GCTCTATGCCTAGCAGA
* ** * * *
406290 GCTTTATGCCGGTGATATTCAAACTCTGTGCCTAGTAGG
1 -CTTTGTGCCGGTGATATTCAGGCTCTATGCCTAGCAGA
* * * * * * * *
406329 CTTTGTGTCAGAGATTTTCGGGCCCTGTGCCTAGCAGG
1 CTTTGTGCCGGTGATATTCAGGCTCTATGCCTAGCAGA
*
406367 CTTCGTGCCGGTG
1 CTTTGTGCCGGTG
406380 TCTTATATCA
Statistics
Matches: 97, Mismatches: 26, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
37 2 0.02
38 95 0.98
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (38 bp):
CTTTGTGCCGGTGATATTCAGGCTCTATGCCTAGCAGA
Found at i:406268 original size:60 final size:60
Alignment explanation
Indices: 406119--406272 Score: 157
Period size: 60 Copynumber: 2.5 Consensus size: 60
406109 TCGGGTTCTG
* * *
406119 TGCCTAGCAGGCTTTGAGCCGGTGATAATCGGGCTTTATGCCTATCATGATAATCAGGCTTTG
1 TGCCTAGCAGGCTTTGA-CCGGTGATATTCGGGCTTTATGCC--TCATGATAATCAGGCTCTA
* * * * ** *
406182 TACCTAGCAGGTTTTGGACCGATGATATTCGGGCTTTGTGCC-GGTGATATTCAGGCTCTA
1 TGCCTAGCAGGCTTT-GACCGGTGATATTCGGGCTTTATGCCTCATGATAATCAGGCTCTA
*
406242 TGCCTAGCAGACTTTGTACCGGTGATATTCG
1 TGCCTAGCAGGCTTTG-ACCGGTGATATTCG
406273 TGCTCTATAC
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
59 1 0.01
60 38 0.51
63 34 0.45
64 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.32
Consensus pattern (60 bp):
TGCCTAGCAGGCTTTGACCGGTGATATTCGGGCTTTATGCCTCATGATAATCAGGCTCTA
Found at i:409317 original size:19 final size:17
Alignment explanation
Indices: 409293--409328 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
409283 ATCATTCTTA
409293 TGGTTTATTCTATCAAAGG
1 TGGTTTA-TCTAT-AAAGG
409312 TGGTTTATCTATAAAGG
1 TGGTTTATCTATAAAGG
409329 ATATATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (17 bp):
TGGTTTATCTATAAAGG
Found at i:411819 original size:38 final size:38
Alignment explanation
Indices: 411749--411851 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
411739 ACGTTATTCG
* * * * *
411749 AGCTTTGTGCCTAGCAGACTTTATGTCGGTGATAATCA
1 AGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAATCA
* *
411787 GGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATATTCA
1 AGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAATCA
* *
411825 AGCTCTGTGCCTAGCAAGCTTCGTGCC
1 AGCTCTGTGCCTAGCAGGCTTTGTGCC
411852 GGTAGATTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.31
Consensus pattern (38 bp):
AGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGATAATCA
Found at i:417060 original size:25 final size:25
Alignment explanation
Indices: 417026--417141 Score: 103
Period size: 25 Copynumber: 4.6 Consensus size: 25
417016 GTACATGTAT
*
417026 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* *
417051 GCTC-TCACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
*
417076 GCTCATACGAGCTGA-GAATCAGTAA
1 GCTCATACGAGCT-ATGAATCGGTAA
*** *
417101 GCTC-TCACGAGCTGCAAATCGATAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
*
417126 ACTCATACGAGCTATG
1 GCTCATACGAGCTATG
417142 GTGTATCCGC
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
24 2 0.03
25 67 0.94
26 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:417105 original size:50 final size:50
Alignment explanation
Indices: 417026--417141 Score: 171
Period size: 50 Copynumber: 2.3 Consensus size: 50
417016 GTACATGTAT
* * * *
417026 GCTCATACGAGCTATGAATCGGTATGCTCTCACGAGCTGTAAATCGGTAA
1 GCTCATACGAGCTATGAATCAGTAAGCTCTCACGAGCTGCAAATCGATAA
417076 GCTCATACGAGCTGA-GAATCAGTAAGCTCTCACGAGCTGCAAATCGATAA
1 GCTCATACGAGCT-ATGAATCAGTAAGCTCTCACGAGCTGCAAATCGATAA
*
417126 ACTCATACGAGCTATG
1 GCTCATACGAGCTATG
417142 GTGTATCCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
49 1 0.02
50 57 0.97
51 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (50 bp):
GCTCATACGAGCTATGAATCAGTAAGCTCTCACGAGCTGCAAATCGATAA
Found at i:418164 original size:106 final size:107
Alignment explanation
Indices: 418036--418248 Score: 410
Period size: 106 Copynumber: 2.0 Consensus size: 107
418026 TCGAAATATG
418036 GGCCTGATATTTTTCCCAGGCCCGGACCGTGAAAAATATATGAAGCCCGGGCCCGGCCCGGCCCT
1 GGCCTGATATTTTTCCCAGGCCCGGACCGTGAAAAATATATGAAGCCCGGGCCCGGCCCGGCCCT
418101 GCCCGTTTTTTTTTGACTTAAAAGTTAAAACTAATTGTTATT
66 GCCCGTTTTTTTTTGACTTAAAAGTTAAAACTAATTGTTATT
418143 GGCCTGATA-TTTTCCCAGGCCCGGACCGTGAAAAATATATGAAGCCCGGGCCCGGCCCGGCCCT
1 GGCCTGATATTTTTCCCAGGCCCGGACCGTGAAAAATATATGAAGCCCGGGCCCGGCCCGGCCCT
*
418207 GCCCGTTTTTTTTTGACTTAAAAGTTTAAACTAATTGTTATT
66 GCCCGTTTTTTTTTGACTTAAAAGTTAAAACTAATTGTTATT
418249 AAAATTAATT
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 96 0.91
107 9 0.09
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (107 bp):
GGCCTGATATTTTTCCCAGGCCCGGACCGTGAAAAATATATGAAGCCCGGGCCCGGCCCGGCCCT
GCCCGTTTTTTTTTGACTTAAAAGTTAAAACTAATTGTTATT
Found at i:421143 original size:13 final size:13
Alignment explanation
Indices: 421125--421192 Score: 84
Period size: 13 Copynumber: 5.2 Consensus size: 13
421115 ATATTAAAAG
*
421125 TTAAAACATTATA
1 TTAAAACAATATA
421138 TTAAAACAATATA
1 TTAAAACAATATA
* *
421151 TTTATAACAGTATA
1 -TTAAAACAATATA
421165 TTAAAACAATATA
1 TTAAAACAATATA
421178 TTAAAA-AAGTATA
1 TTAAAACAA-TATA
421191 TT
1 TT
421193 TATAATAGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
12 2 0.04
13 35 0.73
14 11 0.23
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (13 bp):
TTAAAACAATATA
Found at i:421164 original size:27 final size:26
Alignment explanation
Indices: 421125--421220 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 26
421115 ATATTAAAAG
*
421125 TTAAAACATTATATTAAAACAATATA
1 TTAAAACAGTATATTAAAACAATATA
*
421151 TTTATAACAGTATATTAAAACAATATA
1 -TTAAAACAGTATATTAAAACAATATA
* * * *
421178 TTAAAAAAGTATATTTATAATAGTATA
1 TTAAAACAGTATA-TTAAAACAATATA
* *
421205 TTAAGATAGTATATTA
1 TTAAAACAGTATATTA
421221 TAAATTTTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
26 14 0.24
27 45 0.76
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (26 bp):
TTAAAACAGTATATTAAAACAATATA
Found at i:421215 original size:13 final size:13
Alignment explanation
Indices: 421134--421258 Score: 78
Period size: 13 Copynumber: 9.5 Consensus size: 13
421124 GTTAAAACAT
* *
421134 TATATTAAAACAA
1 TATATTAAAATAG
* *
421147 TATATTTATAACAG
1 TATA-TTAAAATAG
* *
421161 TATATTAAAACAA
1 TATATTAAAATAG
*
421174 TATATTAAAAAAG
1 TATATTAAAATAG
*
421187 TATATTTATAATAG
1 TATA-TTAAAATAG
*
421201 TATATTAAGATAG
1 TATATTAAAATAG
421214 TATATTATAAAT--
1 TATATTA-AAATAG
*
421226 TTTA-TAACAATA-
1 TATATTAA-AATAG
*
421238 TATTATTAAAACAG
1 TA-TATTAAAATAG
421252 TATATTA
1 TATATTA
421259 CATTTAAAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
10 1 0.01
11 5 0.06
12 4 0.04
13 50 0.56
14 30 0.33
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (13 bp):
TATATTAAAATAG
Found at i:421220 original size:40 final size:40
Alignment explanation
Indices: 421125--421208 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
421115 ATATTAAAAG
*
421125 TTAAAACATTATATTAAAACAATATATTTATAACAGTATA
1 TTAAAACAATATATTAAAACAATATATTTATAACAGTATA
*
421165 TTAAAACAATATATTAAAA-AAGTATATTTATAATAGTATA
1 TTAAAACAATATATTAAAACAA-TATATTTATAACAGTATA
421205 TTAA
1 TTAA
421209 GATAGTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 2 0.05
40 39 0.95
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (40 bp):
TTAAAACAATATATTAAAACAATATATTTATAACAGTATA
Found at i:422934 original size:37 final size:38
Alignment explanation
Indices: 422888--422969 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
422878 ACATTAACAG
* *
422888 AACACCATTAACAGCAAAAATAAAAAACA-CA-ACCATT
1 AACAGCATTAACAGC-AAAATAAAAAACAGAACACCATT
* *
422925 AACAGCATTAACAGCAAAATCAAAATCAGAACACCATT
1 AACAGCATTAACAGCAAAATAAAAAACAGAACACCATT
422963 AACAGCA
1 AACAGCA
422970 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 11 0.28
37 15 0.38
38 13 0.33
ACGTcount: A:0.56, C:0.24, G:0.06, T:0.13
Consensus pattern (38 bp):
AACAGCATTAACAGCAAAATAAAAAACAGAACACCATT
Found at i:426789 original size:17 final size:17
Alignment explanation
Indices: 426764--426871 Score: 60
Period size: 18 Copynumber: 6.1 Consensus size: 17
426754 TCATAAATTG
426764 ATTAAAAAATCATAAAA
1 ATTAAAAAATCATAAAA
*
426781 ATTATAAAAA--AGAAAA
1 ATTA-AAAAATCATAAAA
**
426797 AGAAAAAAATCATCAAAA
1 ATTAAAAAATCAT-AAAA
* *
426815 AATAAAAAAT-ATTAAA
1 ATTAAAAAATCATAAAA
* *
426831 ATTGATATAAACTTATAAAA
1 ATT-A-A-AAAATCATAAAA
426851 ATTATAAAAAAATCATAAAA
1 A-T-T-AAAAAATCATAAAA
426871 A
1 A
426872 CTTGAATTTG
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
15 5 0.07
16 12 0.18
17 8 0.12
18 18 0.26
19 4 0.06
20 17 0.25
21 2 0.03
22 2 0.03
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
ATTAAAAAATCATAAAA
Found at i:426857 original size:9 final size:9
Alignment explanation
Indices: 426764--426860 Score: 53
Period size: 9 Copynumber: 11.1 Consensus size: 9
426754 TCATAAATTG
426764 ATTA-AAAA
1 ATTATAAAA
*
426772 ATCATAAAA
1 ATTATAAAA
426781 ATTATAAAA
1 ATTATAAAA
*
426790 A--AGAAAA
1 ATTATAAAA
* *
426797 A-GAAAAAA
1 ATTATAAAA
*
426805 ATCATCAAAA
1 ATTAT-AAAA
426815 A--ATAAAA
1 ATTATAAAA
* *
426822 AATATTAAA
1 ATTATAAAA
426831 ATTGATATAAA
1 ATT-ATA-AAA
*
426842 CTTATAAAA
1 ATTATAAAA
426851 ATTATAAAA
1 ATTATAAAA
426860 A
1 A
426861 AATCATAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
7 11 0.16
8 11 0.16
9 33 0.47
10 10 0.14
11 5 0.07
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (9 bp):
ATTATAAAA
Found at i:427423 original size:11 final size:9
Alignment explanation
Indices: 427347--427466 Score: 59
Period size: 9 Copynumber: 13.0 Consensus size: 9
427337 ATAAAGTTTA
427347 ATAA-TTTT
1 ATAATTTTT
*
427355 ATTATTTTT
1 ATAATTTTT
*
427364 ATAAAATTTT
1 AT-AATTTTT
427374 A-AATATTTT
1 ATAAT-TTTT
*
427383 ACATATGTTTT
1 ATA-AT-TTTT
427394 ATTAA-TTTT
1 A-TAATTTTT
427403 ATAATTTTT
1 ATAATTTTT
427412 ATAATTTTT
1 ATAATTTTT
* *
427421 TTAGGTTTTT
1 ATA-ATTTTT
*
427431 AT-ATTTTG
1 ATAATTTTT
* *
427439 ATAATATAT
1 ATAATTTTT
*
427448 ATAAGTTTAT
1 ATAA-TTTTT
*
427458 ATCATTTTT
1 ATAATTTTT
427467 TGTCGCATCC
Statistics
Matches: 85, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
8 14 0.16
9 42 0.49
10 20 0.24
11 8 0.09
12 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:432820 original size:42 final size:42
Alignment explanation
Indices: 432737--432826 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
432727 ACGACCTAGC
** ** *
432737 ACACGGCCTGCGACACGGTTGTGTGTTGCAAGTCAGAGAGTT
1 ACACGGCCTGCGACACGGCCGTGTGTACCAACTCAGAGAGTT
*
432779 ACACGGCCTGCGACACGGCCGTGTG-ACCTAACTCAGTGAGTT
1 ACACGGCCTGCGACACGGCCGTGTGTACC-AACTCAGAGAGTT
432821 ACACGG
1 ACACGG
432827 GTTGTGACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 40 0.98
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (42 bp):
ACACGGCCTGCGACACGGCCGTGTGTACCAACTCAGAGAGTT
Found at i:434773 original size:558 final size:554
Alignment explanation
Indices: 433378--435055 Score: 2408
Period size: 561 Copynumber: 3.0 Consensus size: 554
433368 ATCATGCATG
*
433378 GCTAGTTGGCAGATGGCGTATATAAAAGTTTTGTACTTAACTTTTGTTTTTACCTCACAA-TCAT
1 GCTAGTTGGCGGATGGCGTATATAAAAGTTTTGTACTTAACTTTTGTTTTTACCTCACAACT-AT
* *
433442 ATTGTTTTTGTCTTAAAGTGGAACTGCCCCTTATTATGCATGTGTATAC-CAAACTCCCTTAATT
65 ATTGTTTTTGTCTTAAAGTGGAACTGCCCCTTATTATACATGTG--TACGCAAACTCCCTTGATT
*
433506 TGCATATTACAAACTTGCATTTTCTATTAAGTGTATTTGCCATACATGACAATGTATGATTTAAA
128 TGCATATTACAAACTTGC-TTTTCTATTAAGTGTATTTGCCATACATGACAGTGTATGATTTAAA
*
433571 GATTGCCTTTATTAATTCCTATTACTTTCTTCAAGGATACGTTACTAAATGGGCCAAGAATAATG
192 GATTG-CTTTATTAATTCCTATTACTTTCTTCAAGGATACGTTACTAAATGAGCCAAGAATAATG
*
433636 GTCTTTCACTAAAAAGAGAAC-CATTACAACTGATTTCTCAAAGATTTAAATTAAGCCAAAGGAT
256 GTCTTTCACTAAAAGGAGAACTC-TTACAACTGATTTCTCAAAGATTTAAATTAAGCCAAAGGAT
* * * *
433700 TTGAGTCTACCAGTAATGC-CCCGATCCGTTGGGTGGTTTGTTTGGCTAATTGATATATGCCATG
320 TTGAGTCTATCAGTAA--CACCCGATCCGTTGGG-AGTTTGTTTGGCTGATTGATATACGCCATG
* *
433764 TCTCCTGAAGGGCTAAGGGGTGTTACAACAAAACTTCTATTTGAATAAGGTCTAATTCAATAATA
382 TCTCCTGACGGGCTAAGGGGTGTTACAACAAAACATCTATTTGAATAAGGTCTAATTCAATAATA
* ** *
433829 ATATTTAATAAAAAATTACAATATTATAGTAGAACTATAGTACAGGAAACGGTGACA-CCCCCTT
447 ATATTTAATAAAAAA-TACAATATTATAGTAGAACTATAGTATAGGGGACGGTGACACCCCCCAT
* * *
433893 AAAACACTAGGGTTTGTCGCCCCTTACGTGATATAAGGACAAGTTG
511 AAAACATTA-GGTTTGT-GCCCCTTACGTGATATAAGGCCAAGTTA
* * *
433939 GCTAGTTGACGGATGGCATATATAAACGTTTTGTACTTTAA-TTTTGTTTTTA-CTCCACAAAC-
1 GCTAGTTGGCGGATGGCGTATATAAAAGTTTTGTAC-TTAACTTTTGTTTTTACCT-CAC-AACT
434001 ATATTGTTTTTGTCTTAAAGTGGAACTGCCCCTTATTATACATGTGTACGCCAAACTCCCTTGAT
63 ATATTGTTTTTGTCTTAAAGTGGAACTGCCCCTTATTATACATGTGTACG-CAAACTCCCTTGAT
* * * *
434066 TTGCATATTACAAACTTGCCTTTTCTTTTAAGTGTATTCGCCATACACGACAGAGTATGATTTAA
127 TTGCATATTACAAACTTG-CTTTTCTATTAAGTGTATTTGCCATACATGACAGTGTATGATTTAA
434131 AGATTGCATTTATTAATTCCTATTACTTTCTTCAAGGATACGTTACTAAATGAGCCAAGAATAAT
191 AGATTGC-TTTATTAATTCCTATTACTTTCTTCAAGGATACGTTACTAAATGAGCCAAGAATAAT
* *
434196 GGTCTTTCACTAGAAGGAGAACTCTTACAACTGATTTCTCAAATATTTAAATTAAGCCAAAGGAT
255 GGTCTTTCACTAAAAGGAGAACTCTTACAACTGATTTCTCAAAGATTTAAATTAAGCCAAAGGAT
* * * *
434261 TTGAGTCTATCAATAACACATCGATCTGTTGGGCAGTTTGTTTGGCTGGTTGATATACGCCATGT
320 TTGAGTCTATCAGTAACAC-CCGATCCGTTGGG-AGTTTGTTTGGCTGATTGATATACGCCATGT
*
434326 CTCTTGACGGGCTAAGGGGTGTTACAACAAAACATCTATTTGAATAAGGTCTAATTCAATAATAA
383 CTCCTGACGGGCTAAGGGGTGTTACAACAAAACATCTATTTGAATAAGGTCTAATTCAATAATAA
* * *
434391 TATTTAAT-AAAAATGCAATATTATAGTAGAACTATAGTATAGGGGATGGTGACACCCCCCGTAA
448 TATTTAATAAAAAATACAATATTATAGTAGAACTATAGTATAGGGGACGGTGACACCCCCCATAA
*
434455 AACATTAGGATTTGTGCCCCTTACGTGATATAAAGCCAAGTTA
513 AACATTAGG-TTTGTGCCCCTTACGTGATATAAGGCCAAGTTA
* * * * *
434498 TCTAGTTGGCGGATGCCGTATATAAATGTTTTATACTTGACTTTTGTTTTTACCTCACAACTATA
1 GCTAGTTGGCGGATGGCGTATATAAAAGTTTTGTACTTAACTTTTGTTTTTACCTCACAACTATA
* * *
434563 TTGTTTTTGTCATAAAGTAGAACTTCCCCTTATTATACATGTGTACGCAAACTCCCTTGATTTGC
66 TTGTTTTTGTCTTAAAGTGGAACTGCCCCTTATTATACATGTGTACGCAAACTCCCTTGATTTGC
*
434628 ATATTACAAACTTGTCTTTTCTATTAAGTGTATTTGCCATACATGGCAGTGTATGATTTAAAGAT
131 ATATTACAAACTTG-CTTTTCTATTAAGTGTATTTGCCATACATGACAGTGTATGATTTAAAGAT
* * *
434693 TGTCTTTATTAATTCCTATTACTTTCTTCAAAGATACGTTACTAAATGAGCCAATAATAATGATC
195 TG-CTTTATTAATTCCTATTACTTTCTTCAAGGATACGTTACTAAATGAGCCAAGAATAATGGTC
*
434758 TTTCACTAAAAGGAGAA-TCCTTGCAACTGATTTCTCAAAGATTTAAATTAAGCCAAAGG-TTTG
259 TTTCACTAAAAGGAGAACT-CTTACAACTGATTTCTCAAAGATTTAAATTAAGCCAAAGGATTTG
* * * * *
434821 AGTCTATCAGTAACACCCTAGTCCATTGAGAGGTTTATTTGGCTGATTAATATACGCCATGTCTC
323 AGTCTATCAGTAACACCCGA-TCCGTTGGGA-GTTTGTTTGGCTGATTGATATACGCCATGTCTC
* * * * *
434886 CTGGCAGGG-AAAGGGGTGTTACAACATAACATCTATTTGAATAAGGTCTAATTAAATAAAAATA
386 CTGAC-GGGCTAAGGGGTGTTACAACAAAACATCTATTTGAATAAGGTCTAATTCAATAATAATA
* * *
434950 TTTAATAAAAAATACAATATCATAGTAGAACTATAGTATAGGGGACGGTGACACCCTCCACAAAA
450 TTTAATAAAAAATACAATATTATAGTAGAACTATAGTATAGGGGACGGTGACACCCCCCATAAAA
* ** *
435015 CACTAAGGTTTGCCACCCCTTATGTGATATAAGGCCAAGTT
515 CA-TTAGGTTTG-TGCCCCTTACGTGATATAAGGCCAAGTT
435056 GGATCTTTCT
Statistics
Matches: 1008, Mismatches: 85, Indels: 50
0.88 0.07 0.04
Matches are distributed among these distances:
556 3 0.00
557 116 0.12
558 258 0.26
559 187 0.19
560 30 0.03
561 406 0.40
562 8 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (554 bp):
GCTAGTTGGCGGATGGCGTATATAAAAGTTTTGTACTTAACTTTTGTTTTTACCTCACAACTATA
TTGTTTTTGTCTTAAAGTGGAACTGCCCCTTATTATACATGTGTACGCAAACTCCCTTGATTTGC
ATATTACAAACTTGCTTTTCTATTAAGTGTATTTGCCATACATGACAGTGTATGATTTAAAGATT
GCTTTATTAATTCCTATTACTTTCTTCAAGGATACGTTACTAAATGAGCCAAGAATAATGGTCTT
TCACTAAAAGGAGAACTCTTACAACTGATTTCTCAAAGATTTAAATTAAGCCAAAGGATTTGAGT
CTATCAGTAACACCCGATCCGTTGGGAGTTTGTTTGGCTGATTGATATACGCCATGTCTCCTGAC
GGGCTAAGGGGTGTTACAACAAAACATCTATTTGAATAAGGTCTAATTCAATAATAATATTTAAT
AAAAAATACAATATTATAGTAGAACTATAGTATAGGGGACGGTGACACCCCCCATAAAACATTAG
GTTTGTGCCCCTTACGTGATATAAGGCCAAGTTA
Found at i:441337 original size:16 final size:16
Alignment explanation
Indices: 441316--441348 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
441306 TTGATTTGCT
441316 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
441332 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
441348 A
1 A
441349 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:457213 original size:45 final size:44
Alignment explanation
Indices: 457147--457237 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
457137 AGATTAGAGG
* *
457147 TGTAATGGAATAGAAGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGAAATAGAAGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
457192 TGTAATGAAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGAAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
457236 TG
1 TG
457238 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGAAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:468764 original size:19 final size:20
Alignment explanation
Indices: 468734--468795 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 20
468724 TTTTTGTAAA
*
468734 ATTTTCAATTTTAATATATT
1 ATTTTCAATTTTTATATATT
*
468754 ATTTT-AATTTTTATAAATT
1 ATTTTCAATTTTTATATATT
* *
468773 CTTTTGAATTATTTATATATT
1 ATTTTCAATT-TTTATATATT
468794 AT
1 AT
468796 ATTTTTTTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 16 0.46
20 9 0.26
21 10 0.29
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTCAATTTTTATATATT
Found at i:470323 original size:83 final size:84
Alignment explanation
Indices: 470183--470344 Score: 317
Period size: 83 Copynumber: 1.9 Consensus size: 84
470173 TAGAGCTCTA
470183 GACGTTCGGAAAGAAACTTAGATTTTTGACACAACCTAAAACACAATCAAATCCAAGTTAGATAA
1 GACGTTCGGAAAGAAACTTAGATTTTTGACACAACCTAAAACACAATCAAATCCAAGTTAGATAA
470248 AACAATTAAAATAAGTAAC
66 AACAATTAAAATAAGTAAC
470267 GACGTTCGG-AAGAAACTTAGATTTTTGACACAACCTAAAACACAATCAAATCCAAGTTAGATAA
1 GACGTTCGGAAAGAAACTTAGATTTTTGACACAACCTAAAACACAATCAAATCCAAGTTAGATAA
470331 AACAATTAAAATAA
66 AACAATTAAAATAA
470345 ATAATTAATA
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 69 0.88
84 9 0.12
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (84 bp):
GACGTTCGGAAAGAAACTTAGATTTTTGACACAACCTAAAACACAATCAAATCCAAGTTAGATAA
AACAATTAAAATAAGTAAC
Found at i:474022 original size:27 final size:27
Alignment explanation
Indices: 473992--474050 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
473982 AATGAACAAT
* *
473992 AAAAAGAAAAAAATGAAAACCTAAAGC
1 AAAAACAAAAAAATGAAAACCAAAAGC
*
474019 AAAAACAAACAAATGAAAACCAAAAGC
1 AAAAACAAAAAAATGAAAACCAAAAGC
474046 AAAAA
1 AAAAA
474051 ATTCGGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.73, C:0.14, G:0.08, T:0.05
Consensus pattern (27 bp):
AAAAACAAAAAAATGAAAACCAAAAGC
Found at i:474760 original size:326 final size:326
Alignment explanation
Indices: 474167--474819 Score: 1306
Period size: 326 Copynumber: 2.0 Consensus size: 326
474157 ATTTAGGAGT
474167 TTTATGTCAATAAGAAAATTTAGTTTAAAACTACTTCTTGTTTAGATTAATTAGAGTTCTAGTAT
1 TTTATGTCAATAAGAAAATTTAGTTTAAAACTACTTCTTGTTTAGATTAATTAGAGTTCTAGTAT
474232 ACTTAAGAGTTTTATTTAGATTTATTTAGCTAGCCTATATATAGGCCTTTGCATTGTACACAAAT
66 ACTTAAGAGTTTTATTTAGATTTATTTAGCTAGCCTATATATAGGCCTTTGCATTGTACACAAAT
474297 CATTCAATTTATTATTATTCAACTTATATTTTGAGTTTATATCCTACATTTTCTTCTTATATATT
131 CATTCAATTTATTATTATTCAACTTATATTTTGAGTTTATATCCTACATTTTCTTCTTATATATT
474362 CTAATATTGTTTTTGTTTATGAGATTTTTCTAATTGAAATCTGGACGCATGTCTGAAATGATATC
196 CTAATATTGTTTTTGTTTATGAGATTTTTCTAATTGAAATCTGGACGCATGTCTGAAATGATATC
474427 TGCTGATTTATTTATATGTTATACACTGAGCTTAGAAGCTCATTCTCTGTTTGTTTGATCTTCAG
261 TGCTGATTTATTTATATGTTATACACTGAGCTTAGAAGCTCATTCTCTGTTTGTTTGATCTTCAG
474492 G
326 G
474493 TTTATGTCAATAAGAAAATTTAGTTTAAAACTACTTCTTGTTTAGATTAATTAGAGTTCTAGTAT
1 TTTATGTCAATAAGAAAATTTAGTTTAAAACTACTTCTTGTTTAGATTAATTAGAGTTCTAGTAT
474558 ACTTAAGAGTTTTATTTAGATTTATTTAGCTAGCCTATATATAGGCCTTTGCATTGTACACAAAT
66 ACTTAAGAGTTTTATTTAGATTTATTTAGCTAGCCTATATATAGGCCTTTGCATTGTACACAAAT
474623 CATTCAATTTATTATTATTCAACTTATATTTTGAGTTTATATCCTACATTTTCTTCTTATATATT
131 CATTCAATTTATTATTATTCAACTTATATTTTGAGTTTATATCCTACATTTTCTTCTTATATATT
474688 CTAATATTGTTTTTGTTTATGAGATTTTTCTAATTGAAATCTGGACGCATGTCTGAAATGATATC
196 CTAATATTGTTTTTGTTTATGAGATTTTTCTAATTGAAATCTGGACGCATGTCTGAAATGATATC
474753 TGCTGATTTATTTATATGTTATACACTGAGCTTAGAAGCTCATTCTCTGTTTGTTTGATCTTCAG
261 TGCTGATTTATTTATATGTTATACACTGAGCTTAGAAGCTCATTCTCTGTTTGTTTGATCTTCAG
474818 G
326 G
474819 T
1 T
474820 AATCCTCAGA
Statistics
Matches: 327, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
326 327 1.00
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (326 bp):
TTTATGTCAATAAGAAAATTTAGTTTAAAACTACTTCTTGTTTAGATTAATTAGAGTTCTAGTAT
ACTTAAGAGTTTTATTTAGATTTATTTAGCTAGCCTATATATAGGCCTTTGCATTGTACACAAAT
CATTCAATTTATTATTATTCAACTTATATTTTGAGTTTATATCCTACATTTTCTTCTTATATATT
CTAATATTGTTTTTGTTTATGAGATTTTTCTAATTGAAATCTGGACGCATGTCTGAAATGATATC
TGCTGATTTATTTATATGTTATACACTGAGCTTAGAAGCTCATTCTCTGTTTGTTTGATCTTCAG
G
Found at i:477567 original size:78 final size:79
Alignment explanation
Indices: 477468--477624 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 79
477458 TAAAAAAAAA
477468 ACAATTTCAACCAACTTCAATATTTCCAACCAATAACAATTATATATATATTCAGACATAATTTA
1 ACAATTTCAACCAACTTCAATATTTCCAACCAATAACAATTATATATATATTCAGACATAATTTA
477533 TCCATTAATAAACT
66 TCCATTAATAAACT
477547 ACAATTTCAA-CAACTTCAATATTTCCAACCAATAACAATTATATATATATTCAGACATAATTTA
1 ACAATTTCAACCAACTTCAATATTTCCAACCAATAACAATTATATATATATTCAGACATAATTTA
477611 TCCATTAATAAACT
66 TCCATTAATAAACT
477625 CCAACATATT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 68 0.87
79 10 0.13
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.34
Consensus pattern (79 bp):
ACAATTTCAACCAACTTCAATATTTCCAACCAATAACAATTATATATATATTCAGACATAATTTA
TCCATTAATAAACT
Found at i:485359 original size:50 final size:50
Alignment explanation
Indices: 485255--485582 Score: 235
Period size: 51 Copynumber: 6.5 Consensus size: 50
485245 CCCGAGTTGA
* *
485255 AGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAATTTACATAGT
1 AGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGATTCACATAGT
* * *
485304 AGCCTTCACATAGTACTACACACGTGAACAAGTTTTACGACTCACGTAGT
1 AGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGATTCACATAGT
*
485354 AGCCTTCAC-TCAGTACTACACACGTGTTCAAGCTTCTTA-G-TTCACATAGT
1 AGCCTTCACAT-AGTACTACACACGTGATCAAG-TT-TTACGATTCACATAGT
* ** * * * ** *
485404 AGCCTTCACTTAGTACTACACATATAACCGTAG-TTTACCGAGACACGT-GAT
1 AGCCTTCACATAGTACTACACACGTGATC-AAGTTTTA-CGATTCACATAG-T
* * * * *
485455 AGCATTCACACAGTACTACACACGTGCTCAAAGCTTCTT--GGTGCACATAGT
1 AGCCTTCACATAGTACTACACACGTGATC-AAG-TT-TTACGATTCACATAGT
* * * * * *
485506 AGCCTTCACTTAGTACCACACATGTGA-CCA-TTACTTATCGATACACGTAGT
1 AGCCTTCACATAGTACTACACACGTGATCAAGTT--TTA-CGATTCACATAGT
*
485557 AGCCTTCACACAGTACTACACACGTG
1 AGCCTTCACATAGTACTACACACGTG
485583 TTCATCGATA
Statistics
Matches: 215, Mismatches: 46, Indels: 34
0.73 0.16 0.12
Matches are distributed among these distances:
47 2 0.01
48 6 0.03
49 31 0.14
50 77 0.36
51 92 0.43
52 4 0.02
53 1 0.00
54 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (50 bp):
AGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGATTCACATAGT
Found at i:485519 original size:102 final size:99
Alignment explanation
Indices: 485255--485582 Score: 335
Period size: 102 Copynumber: 3.3 Consensus size: 99
485245 CCCGAGTTGA
* * * ** *
485255 AGCCTTCACATAGTACTACACACGTGATC-AG-TT-TTACAATTTACATAGTAGCCTTCACATAG
1 AGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTT--AGTGCACATAGTAGCCTTCACTTAG
* * *
485317 TACTACACACGTGAA-CAAGTTTTACGACTCACGTAGT
64 TACTACACATGT-AACCTAG-TTTACGACACACGTAGT
* * *
485354 AGCCTTCACTCAGTACTACACACGTGTTCAAGCTTCTTAGTTCACATAGTAGCCTTCACTTAGTA
1 AGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAGCCTTCACTTAGTA
* *
485419 CTACACATATAACCGTAGTTTACCGAGACACGT-GAT
66 CTACACATGTAACC-TAGTTTA-CGACACACGTAG-T
* *
485455 AGCATTCACACAGTACTACACACGTGCTCAAAGCTTCTTGGTGCACATAGTAGCCTTCACTTAGT
1 AGCCTTCACACAGTACTACACACGTGCTC-AAGCTTCTTAGTGCACATAGTAGCCTTCACTTAGT
* * * *
485520 ACCACACATGTGACCATTA-CTTATCGATACACGTAGT
65 ACTACACATGTAACC--TAGTTTA-CGACACACGTAGT
485557 AGCCTTCACACAGTACTACACACGTG
1 AGCCTTCACACAGTACTACACACGTG
485583 TTCATCGATA
Statistics
Matches: 195, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
99 28 0.14
100 40 0.21
101 39 0.20
102 85 0.44
103 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (99 bp):
AGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAGCCTTCACTTAGTA
CTACACATGTAACCTAGTTTACGACACACGTAGT
Found at i:498924 original size:21 final size:21
Alignment explanation
Indices: 498900--498947 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
498890 TTTGAAATGT
498900 GATAAGTATAAAATGTAATAC
1 GATAAGTATAAAATGTAATAC
* * ** *
498921 GATATGTATGATCTGTAATAT
1 GATAAGTATAAAATGTAATAC
498942 GATAAG
1 GATAAG
498948 CATGATCTGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (21 bp):
GATAAGTATAAAATGTAATAC
Found at i:498952 original size:21 final size:21
Alignment explanation
Indices: 498913--498958 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
498903 AAGTATAAAA
* *
498913 TGTAATACGATATGTATGATC
1 TGTAATACGATAAGCATGATC
*
498934 TGTAATATGATAAGCATGATC
1 TGTAATACGATAAGCATGATC
498955 TGTA
1 TGTA
498959 TCTGTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (21 bp):
TGTAATACGATAAGCATGATC
Found at i:503219 original size:14 final size:16
Alignment explanation
Indices: 503200--503231 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
503190 GGCCAAGCCC
503200 AAAACAAA-AAA-ACA
1 AAAACAAACAAAGACA
503214 AAAACAAACAAAGACA
1 AAAACAAACAAAGACA
503230 AA
1 AA
503232 TCCAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAACAAACAAAGACA
Found at i:508972 original size:11 final size:11
Alignment explanation
Indices: 508935--509018 Score: 91
Period size: 11 Copynumber: 7.6 Consensus size: 11
508925 ACCTAAATCC
508935 TTTCTCTC-AA
1 TTTCTCTCAAA
*
508945 TTTCTCTCCAA
1 TTTCTCTCAAA
508956 TATTCTCTCAAA
1 T-TTCTCTCAAA
508968 TTTCTCTCAAA
1 TTTCTCTCAAA
*
508979 TTCCTCTCAAA
1 TTTCTCTCAAA
* *
508990 TTCCTTTC-AA
1 TTTCTCTCAAA
509000 TTTCCTCTCAAA
1 TTT-CTCTCAAA
*
509012 TTCCTCT
1 TTTCTCT
509019 TAAAAAAGCT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
10 12 0.19
11 38 0.59
12 14 0.22
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:510781 original size:18 final size:18
Alignment explanation
Indices: 510758--510795 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
510748 TGCTAGGTGC
* *
510758 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
510776 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
510794 GT
1 GT
510796 TTCCCTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:511087 original size:21 final size:21
Alignment explanation
Indices: 511063--511102 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
511053 TTACCGAATG
* *
511063 AACCAGAATCCCCGCCGGAGC
1 AACCACAACCCCCGCCGGAGC
*
511084 AACCACAACCCCCGGCGGA
1 AACCACAACCCCCGCCGGA
511103 AGCTGGACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.45, G:0.23, T:0.03
Consensus pattern (21 bp):
AACCACAACCCCCGCCGGAGC
Found at i:511254 original size:32 final size:33
Alignment explanation
Indices: 511218--511287 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
511208 CATTTTGAAT
*
511218 ATTTT-GATATTATTTGATGTAATAAAATAGAA
1 ATTTTCGATATTATTTCATGTAATAAAATAGAA
* * *
511250 ATTTTTCTATATTATTTCATGTTATAAAATTGAA
1 A-TTTTCGATATTATTTCATGTAATAAAATAGAA
511284 ATTT
1 ATTT
511288 ACTTTTACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 1 0.03
33 7 0.22
34 24 0.75
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.50
Consensus pattern (33 bp):
ATTTTCGATATTATTTCATGTAATAAAATAGAA
Found at i:511397 original size:116 final size:116
Alignment explanation
Indices: 511277--511487 Score: 318
Period size: 116 Copynumber: 1.8 Consensus size: 116
511267 CATGTTATAA
* * *
511277 AATTGAAATTTACTTTTACATTTTTAATATAATAGAA-ATTCTTTTAAATAACA-CAATATTTTG
1 AATTGAAATTTACTTTAACATTTTTAATAAAATA-AATATTCTTTTAAATAA-AGCAATATTCTG
*
511340 AATATTTCTATATTATTTCATTTAATAAAATAAAACGCTGTTTTGAATAAAGT
64 AATATTTCCATATTATTTCATTTAATAAAATAAAACGCTGTTTTGAATAAAGT
* * *
511393 AATTGTAATTTACTTTAATATTTTTAATAAAATAAATTTTCTTTTAAATAAAGCAATATTCTGAA
1 AATTGAAATTTACTTTAACATTTTTAATAAAATAAATATTCTTTTAAATAAAGCAATATTCTGAA
*
511458 TATTTCCATATTATTTGATTTAATAAAATA
66 TATTTCCATATTATTTCATTTAATAAAATA
511488 CAAATAATGT
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
115 3 0.04
116 82 0.96
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (116 bp):
AATTGAAATTTACTTTAACATTTTTAATAAAATAAATATTCTTTTAAATAAAGCAATATTCTGAA
TATTTCCATATTATTTCATTTAATAAAATAAAACGCTGTTTTGAATAAAGT
Found at i:514598 original size:126 final size:126
Alignment explanation
Indices: 514293--514706 Score: 652
Period size: 126 Copynumber: 3.3 Consensus size: 126
514283 TCAGGCCAAA
* * * *
514293 CAGGAGCTACTGTAGCAAAAACGCGTCCACGTGAGAGCTTCTTTCAATACTTTTGCTGTCAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
*
514358 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTTAGAAACGTCTACTCGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* *
514419 -AGGAGCTATTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGG
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * *
514483 GTCCTGCTTAAAGCATTTTTTG-CACTATTTTCTCAGAAACGTCTACTCGAAATTATTTTTT
66 ATCCTGCTTAAAGC-GTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
*
514544 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTAGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * *
514609 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTTTTCTCAAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* * *
514670 CAAGAGCTACTGTAGCAAAAGAGTGTCCACGTGGGAG
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAG
514707 TTTTTTTAAA
Statistics
Matches: 262, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
125 114 0.44
126 148 0.56
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
Found at i:515825 original size:25 final size:26
Alignment explanation
Indices: 515788--515837 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
515778 TTCTAAAACC
* * *
515788 AAAAAAGATAAAAACCAAATCAAAGT
1 AAAAAAGAAAAAAAACAAAGCAAAGT
515814 AAAAAA-AAAAAAAACAAAGCAAAG
1 AAAAAAGAAAAAAAACAAAGCAAAG
515838 CCACAACATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.76, C:0.10, G:0.08, T:0.06
Consensus pattern (26 bp):
AAAAAAGAAAAAAAACAAAGCAAAGT
Found at i:519039 original size:33 final size:33
Alignment explanation
Indices: 519001--519066 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
518991 GCCATCAGAA
519001 TTATCAGTATATCATTCACGCACACATATATAT
1 TTATCAGTATATCATTCACGCACACATATATAT
519034 TTATCAGTATATCATTCACGCACACATATATAT
1 TTATCAGTATATCATTCACGCACACATATATAT
519067 CACATACCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (33 bp):
TTATCAGTATATCATTCACGCACACATATATAT
Found at i:520523 original size:31 final size:31
Alignment explanation
Indices: 520488--520547 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
520478 TTGGTCATTG
520488 AACTATTCAAAAGTTTTCATTTAAGTCACCA
1 AACTATTCAAAAGTTTTCATTTAAGTCACCA
* * *
520519 AACTATTTAGAAGTTTTTATTTAAGTCAC
1 AACTATTCAAAAGTTTTCATTTAAGTCAC
520548 TGGGTTGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAGTCACCA
Found at i:521505 original size:22 final size:25
Alignment explanation
Indices: 521463--521507 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
521453 GTACCATAAT
521463 TATTTAACAAATTATGTAATTTATA
1 TATTTAACAAATTATGTAATTTATA
521488 TATTT-ACAAA-T-TGTAATTTA
1 TATTTAACAAATTATGTAATTTA
521508 CATTTGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 5 0.25
25 5 0.25
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
TATTTAACAAATTATGTAATTTATA
Found at i:521882 original size:30 final size:32
Alignment explanation
Indices: 521814--521884 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
521804 TTATTTGACC
* *
521814 AATTTTAGTCATTTTACTTTTCGAATTGGTCA
1 AATTTTAGTCATTATACTTTTCAAATTGGTCA
* *
521846 AA-TTTAGTCA-TATACTTTTCAAATT-TTGA
1 AATTTTAGTCATTATACTTTTCAAATTGGTCA
521875 AATTTTAGTC
1 AATTTTAGTC
521885 TTGACCTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 4 0.12
30 20 0.59
31 8 0.24
32 2 0.06
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (32 bp):
AATTTTAGTCATTATACTTTTCAAATTGGTCA
Found at i:522944 original size:86 final size:86
Alignment explanation
Indices: 522842--523025 Score: 228
Period size: 86 Copynumber: 2.1 Consensus size: 86
522832 TGTTATAGAC
* ** * *
522842 AACGCCGCTACAGAACATAACCTTTAGCGGTGCTTTTATAAAAAATGCCGCT-AAATAAAATAAC
1 AACGCCGCTAAAGAACATAACCTTTAGCGACGCTTTTATAAAAAACGCCACTAAAAT-AAATAAC
* *
522906 CTTTAGCAACGC-TTTATCCACA
65 CTTTAACAACACTTTTAT-CACA
* * ** *
522928 AACGCCGCTAAAGAACATAACCTTTAGCGACGCTTTTATCACAAACGCCACTAAAATTCATGACC
1 AACGCCGCTAAAGAACATAACCTTTAGCGACGCTTTTATAAAAAACGCCACTAAAATAAATAACC
522993 TTTAACAACACTTTTATCACA
66 TTTAACAACACTTTTATCACA
523014 AACGCCGCTAAA
1 AACGCCGCTAAA
523026 AGTACAATTC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 75 0.89
87 9 0.11
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (86 bp):
AACGCCGCTAAAGAACATAACCTTTAGCGACGCTTTTATAAAAAACGCCACTAAAATAAATAACC
TTTAACAACACTTTTATCACA
Found at i:523026 original size:43 final size:42
Alignment explanation
Indices: 522842--523026 Score: 192
Period size: 43 Copynumber: 4.3 Consensus size: 42
522832 TGTTATAGAC
* *** * *
522842 AACGCCGCTACAGAACATAACCTTTAGCGGTGCTTTTATAAAA
1 AACGCCGCTA-AAAACATAACCTTTAGCAACGCTTTTATCACA
* *
522885 AATGCCGCTAAATAAAATAACCTTTAGCAACGC-TTTATCCACA
1 AACGCCGCTAAA-AACATAACCTTTAGCAACGCTTTTAT-CACA
*
522928 AACGCCGCTAAAGAACATAACCTTTAGCGACGCTTTTATCACA
1 AACGCCGCTAAA-AACATAACCTTTAGCAACGCTTTTATCACA
* * * * *
522971 AACGCCACTAAAATTCATGACCTTTAACAACACTTTTATCACA
1 AACGCCGCTAAAA-ACATAACCTTTAGCAACGCTTTTATCACA
523014 AACGCCGCTAAAA
1 AACGCCGCTAAAA
523027 GTACAATTCT
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 7 0.06
43 107 0.90
44 5 0.04
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.24
Consensus pattern (42 bp):
AACGCCGCTAAAAACATAACCTTTAGCAACGCTTTTATCACA
Found at i:523039 original size:43 final size:43
Alignment explanation
Indices: 522905--523044 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 43
522895 AATAAAATAA
* * *
522905 CCTTTAGCAACGC-TTTATCCACAAACGCCGCT-AAAGAACATAA
1 CCTTTAGCAACACTTTTAT-CACAAACGCCGCTAAAAGTACA-AT
* * * *
522948 CCTTTAGCGACGCTTTTATCACAAACGCCACTAAAA-TTC-AT
1 CCTTTAGCAACACTTTTATCACAAACGCCGCTAAAAGTACAAT
*
522989 GACCTTTAACAACACTTTTATCACAAACGCCGCTAAAAGTACAAT
1 --CCTTTAGCAACACTTTTATCACAAACGCCGCTAAAAGTACAAT
*
523034 TCTTTAGCAAC
1 CCTTTAGCAAC
523045 GTTTATGAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
43 66 0.84
44 10 0.13
45 2 0.03
ACGTcount: A:0.36, C:0.29, G:0.10, T:0.26
Consensus pattern (43 bp):
CCTTTAGCAACACTTTTATCACAAACGCCGCTAAAAGTACAAT
Done.