Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 43 of 333
Found at i:12211770 original size:25 final size:25
Alignment explanation
Indices: 12211695--12211772 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
12211685 GTTTTTATAA
*
12211695 ACTTCAAATTAGGAATTCTATTAGA
1 ACTTCAAATTAGGAATTCTATTAGG
* * *
12211720 ACTTTAAATTAAGAATTCTATCAGG
1 ACTTCAAATTAGGAATTCTATTAGG
**
12211745 ACTTCAAATTAGGAATTAGATTAGG
1 ACTTCAAATTAGGAATTCTATTAGG
12211770 ACT
1 ACT
12211773 CCCGCTTTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (25 bp):
ACTTCAAATTAGGAATTCTATTAGG
Found at i:12215438 original size:20 final size:21
Alignment explanation
Indices: 12215400--12215452 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
12215390 TTAAATTTAT
12215400 TTAAAA-TAAAAA-TATTAAA
1 TTAAAATTAAAAATTATTAAA
12215419 TTAAAATTAAAAATTA-TAAA
1 TTAAAATTAAAAATTATTAAA
12215439 --AAAATTATAAAATT
1 TTAAAATTA-AAAATT
12215453 TAATATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.23
19 12 0.39
20 10 0.32
21 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TTAAAATTAAAAATTATTAAA
Found at i:12215601 original size:31 final size:28
Alignment explanation
Indices: 12215566--12215630 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
12215556 ATATTATACA
12215566 TTATATTGATTAAAAATATAAATAA-AATTAT
1 TTATATT--TTAAAAA-ATAAA-AATAATTAT
*
12215597 TTATAATTTTAAAAAATAAAAATAATTTT
1 TTAT-ATTTTAAAAAATAAAAATAATTAT
12215626 TTATA
1 TTATA
12215631 AAATTCTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 3 0.10
29 14 0.45
30 7 0.23
31 4 0.13
32 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TTATATTTTAAAAAATAAAAATAATTAT
Found at i:12215623 original size:29 final size:30
Alignment explanation
Indices: 12215575--12215631 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
12215565 ATTATATTGA
12215575 TTAAAAATATAAATAAAATTATTTATAATT
1 TTAAAAATATAAATAAAATTATTTATAATT
*
12215605 TTAAAAA-ATAAA-AATAATTTTTTATAA
1 TTAAAAATATAAATAA-AATTATTTATAA
12215632 AATTCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TTAAAAATATAAATAAAATTATTTATAATT
Found at i:12215641 original size:31 final size:30
Alignment explanation
Indices: 12215576--12215646 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
12215566 TTATATTGAT
*
12215576 TAAAAATATAAATAAAATTATTTATAATTT
1 TAAAAATATAAATAAAATTATTTATAATTC
*
12215606 TAAAAA-ATAAA-AATAATTTTTTATAAAATTC
1 TAAAAATATAAATAA-AATTATTTAT--AATTC
12215637 TAAAATATAT
1 TAAAA-ATAT
12215647 CGTTTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.06
29 14 0.41
30 6 0.18
31 9 0.26
32 1 0.03
33 2 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAAAATATAAATAAAATTATTTATAATTC
Found at i:12215779 original size:23 final size:22
Alignment explanation
Indices: 12215753--12215801 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
12215743 TATAATTATA
12215753 TATTTTAGAATTTTATAAAAAAT
1 TATTTTA-AATTTTATAAAAAAT
* *
12215776 TATTTTTAAATTTTTTTAAAAAT
1 TA-TTTTAAATTTTATAAAAAAT
12215799 TAT
1 TAT
12215802 ATATATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.04
23 17 0.74
24 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTTATAAAAAAT
Found at i:12217514 original size:27 final size:27
Alignment explanation
Indices: 12217466--12217624 Score: 193
Period size: 27 Copynumber: 5.9 Consensus size: 27
12217456 GCGAGGCTGC
* *
12217466 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
12217493 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
12217519 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
12217546 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
12217573 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
12217600 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
12217625 GACGCTTCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.09
27 102 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:12217559 original size:54 final size:54
Alignment explanation
Indices: 12217484--12217624 Score: 248
Period size: 54 Copynumber: 2.6 Consensus size: 54
12217474 GTGACGAAGT
*
12217484 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
12217538 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
12217592 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
12217625 GACGCTTCCT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:12217774 original size:28 final size:28
Alignment explanation
Indices: 12217730--12217805 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
12217720 AAATTAACCC
*
12217730 TAGGGGTATAACGGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTTCCATACA
12217758 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTTCCATACA
* *
12217786 TAGGGGTATTATAGTAATTT
1 TAGGGGTATAACAGTAATTT
12217806 AACTGCTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.36
Consensus pattern (28 bp):
TAGGGGTATAACAGTAATTTTCCATACA
Found at i:12219278 original size:26 final size:26
Alignment explanation
Indices: 12219247--12219354 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
12219237 TGAAATGCCC
*
12219247 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12219273 ATCATGGAACATTTACCCAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
12219299 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
12219325 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12219351 ATCA
1 ATCA
12219355 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12221398 original size:14 final size:14
Alignment explanation
Indices: 12221379--12221417 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
12221369 TAGGAATGTC
12221379 ATAAGAAAATTCTG
1 ATAAGAAAATTCTG
12221393 ATAAGAAAATTCTG
1 ATAAGAAAATTCTG
12221407 ATAAGAAAATT
1 ATAAGAAAATT
12221418 TTATTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (14 bp):
ATAAGAAAATTCTG
Found at i:12225121 original size:26 final size:29
Alignment explanation
Indices: 12225066--12225121 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
12225056 CACTTAAGCT
12225066 ATTGAACTATTCAAAAGCTTTTATTTAAGTC
1 ATTGAACTATT--AAAGCTTTTATTTAAGTC
12225097 ATTGAACTATT-AAG-TTTT-TTTAAGT
1 ATTGAACTATTAAAGCTTTTATTTAAGT
12225122 ATTAGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.28
27 4 0.16
28 3 0.12
31 11 0.44
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (29 bp):
ATTGAACTATTAAAGCTTTTATTTAAGTC
Found at i:12225146 original size:22 final size:21
Alignment explanation
Indices: 12225106--12225149 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
12225096 CATTGAACTA
* *
12225106 TTAAGTTTTTTTAAGTATTAG
1 TTAAATTTTTTTAACTATTAG
12225127 TTAAATTTTATTTAACTATTAG
1 TTAAATTTT-TTTAACTATTAG
12225149 T
1 T
12225150 AAGTTTACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (21 bp):
TTAAATTTTTTTAACTATTAG
Found at i:12226071 original size:93 final size:92
Alignment explanation
Indices: 12225902--12226104 Score: 257
Period size: 93 Copynumber: 2.2 Consensus size: 92
12225892 ATGTACCAAT
* * * *
12225902 AAATTAAGCCCCTATTTTATTTTTTTCACTCATTTGGGTACTTAAACTTTCAAAATCAATCAAAA
1 AAATTAAGCCCCTACTTTATTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATCAATCAAAA
* * *
12225967 AGGCCCTCAAACCTTTTTTTAAAAAACAG
66 AGACCCACAAA-CTTTTTTCAAAAAA-AG
** *
12225996 AAATTAAGTTCCTACTTT-TTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGC-ATCAAA
1 AAATTAAGCCCCTACTTTATTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAAT-CAATCAAA
12226059 AAGACCCACAAACTTTTTTCAAAAAAAG
65 AAGACCCACAAACTTTTTTCAAAAAAAG
* *
12226087 TAATTAAGCCCCTGCTTT
1 AAATTAAGCCCCTACTTT
12226105 TATTAAAAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
91 16 0.17
92 13 0.14
93 49 0.52
94 16 0.17
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.35
Consensus pattern (92 bp):
AAATTAAGCCCCTACTTTATTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATCAATCAAAA
AGACCCACAAACTTTTTTCAAAAAAAG
Found at i:12226180 original size:21 final size:21
Alignment explanation
Indices: 12226156--12226196 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12226146 ATAAAAGCTA
*
12226156 TAAATATTATCAAAT-TTTAAT
1 TAAAAATT-TCAAATATTTAAT
12226177 TAAAAATTTCAAATATTTAA
1 TAAAAATTTCAAATATTTAA
12226197 AATTAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAATTTCAAATATTTAAT
Found at i:12226234 original size:19 final size:20
Alignment explanation
Indices: 12226210--12226275 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
12226200 TAGAAAAAAA
12226210 TATAAAAATCGTAAAAATTTT
1 TATAAAAATCGTAAAAA-TTT
*
12226231 TAAAAAAAGT-GT-AAAATTT
1 TATAAAAA-TCGTAAAAATTT
* *
12226250 TATAAAAATCCTAAAAA-AT
1 TATAAAAATCGTAAAAATTT
12226269 TATAAAA
1 TATAAAA
12226276 TATATAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 19 0.50
20 8 0.21
21 9 0.24
22 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TATAAAAATCGTAAAAATTT
Found at i:12226267 original size:21 final size:21
Alignment explanation
Indices: 12226210--12226269 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
12226200 TAGAAAAAAA
*
12226210 TATAAAAATCGTAAAAATTTT
1 TATAAAAATCGTAAAAAATTT
*
12226231 TAAAAAAAGT-GT--AAAATTT
1 TATAAAAA-TCGTAAAAAATTT
*
12226250 TATAAAAATCCTAAAAAATT
1 TATAAAAATCGTAAAAAATT
12226270 ATAAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
21 15 0.48
22 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
TATAAAAATCGTAAAAAATTT
Found at i:12226281 original size:28 final size:28
Alignment explanation
Indices: 12226178--12226304 Score: 82
Period size: 28 Copynumber: 4.5 Consensus size: 28
12226168 AATTTTAATT
* * * *
12226178 AAAAATT-TCAAATATTTAAAATTAGAA
1 AAAAATTATAAAATATATAAAAATATAA
* *
12226205 AAAAA-TATAAAA-ATCGTAAAAATTTTTAA
1 AAAAATTATAAAATAT-ATAAAAA--TATAA
* * * *
12226234 AAAAAGTGTAAAATTTTATAAAAATCCT-A
1 AAAAATTATAAAA-TATATAAAAAT-ATAA
*
12226263 AAAAATTATAAAATATATAGAAATATAA
1 AAAAATTATAAAATATATAAAAATATAA
12226291 AAAAATTATAAAAT
1 AAAAATTATAAAAT
12226305 TTTAGAAAGT
Statistics
Matches: 77, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
26 3 0.04
27 15 0.19
28 24 0.31
29 21 0.27
30 7 0.09
31 6 0.08
32 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAAATTATAAAATATATAAAAATATAA
Found at i:12226303 original size:57 final size:58
Alignment explanation
Indices: 12226231--12226350 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 58
12226221 TAAAAATTTT
* *
12226231 TAAAAAAAGTGTAAAATTTTATAAAAATCCTAA-AAAATTAT-AAAATATATAGAAATA
1 TAAAAAAAGTATAAAATTTTA-AAAAATCCTAAGAAAATTATAAAAATATAAAGAAATA
* * * * *
12226288 TAAAAAAATTATAAAATTTTAGAAAGTCGTAAGAAAATTATACAAAATGTAAAGAAATA
1 TAAAAAAAGTATAAAATTTTAAAAAATCCTAAGAAAATTATA-AAAATATAAAGAAATA
12226347 TAAA
1 TAAA
12226351 TTTCATAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 8 0.15
57 27 0.51
59 18 0.34
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.28
Consensus pattern (58 bp):
TAAAAAAAGTATAAAATTTTAAAAAATCCTAAGAAAATTATAAAAATATAAAGAAATA
Found at i:12226597 original size:18 final size:18
Alignment explanation
Indices: 12226576--12226627 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
12226566 AATTCTAATT
*
12226576 TTTATATTTTTATTAGAA
1 TTTATATTTTTATTAAAA
*
12226594 TTTAATAATTTTT-CTAAAA
1 TTT-AT-ATTTTTATTAAAA
12226613 TTTATTATTTTTATT
1 TTTA-TATTTTTATT
12226628 TTTTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTATATTTTTATTAAAA
Found at i:12244889 original size:105 final size:105
Alignment explanation
Indices: 12244634--12244901 Score: 452
Period size: 104 Copynumber: 2.6 Consensus size: 105
12244624 TAACCGTTAT
**
12244634 TGGTGGATC-TCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
12244698 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
12244738 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
12244802 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
* **
12244843 TGGTGGATCAT-GCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
12244902 TTATATACAA
Statistics
Matches: 154, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
104 82 0.53
105 70 0.45
106 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATCATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:12245270 original size:30 final size:30
Alignment explanation
Indices: 12245236--12245293 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
12245226 CCACCCAACT
12245236 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
*** * *
12245266 TTTTGCGTAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
12245294 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:12251933 original size:104 final size:105
Alignment explanation
Indices: 12251753--12252020 Score: 450
Period size: 104 Copynumber: 2.6 Consensus size: 105
12251743 TAACCGTTAT
* **
12251753 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
12251818 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
12251857 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
12251922 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
12251962 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
12252021 TTATATACAA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 82 0.53
105 71 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:12252389 original size:30 final size:30
Alignment explanation
Indices: 12252355--12252412 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
12252345 CCACCCAACT
12252355 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
*** * *
12252385 TTTTGCGTAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
12252413 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:12260541 original size:21 final size:21
Alignment explanation
Indices: 12260515--12260556 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12260505 TTCCTCGGCT
* * *
12260515 TTGCAAGCTTTGTTGACTAAC
1 TTGCAAGATCTGTCGACTAAC
12260536 TTGCAAGATCTGTCGACTAAC
1 TTGCAAGATCTGTCGACTAAC
12260557 ACAACAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
TTGCAAGATCTGTCGACTAAC
Found at i:12260854 original size:22 final size:22
Alignment explanation
Indices: 12260829--12260875 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
12260819 TTTATTTTAG
12260829 CACCACTGATATCAAAGTATTC
1 CACCACTGATATCAAAGTATTC
12260851 CACCACTGATATCAAAGTATTC
1 CACCACTGATATCAAAGTATTC
12260873 CAC
1 CAC
12260876 AAAGTATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.26
Consensus pattern (22 bp):
CACCACTGATATCAAAGTATTC
Found at i:12260880 original size:12 final size:12
Alignment explanation
Indices: 12260863--12260899 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
12260853 CCACTGATAT
12260863 CAAAGTATTCCA
1 CAAAGTATTCCA
12260875 CAAAGTATTCCA
1 CAAAGTATTCCA
12260887 CAAAGTATTCCA
1 CAAAGTATTCCA
12260899 C
1 C
12260900 CACTGATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (12 bp):
CAAAGTATTCCA
Found at i:12261872 original size:12 final size:12
Alignment explanation
Indices: 12261863--12261891 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12261853 CTCGTGTGTC
12261863 AGGCCGTGTGCT
1 AGGCCGTGTGCT
12261875 AGGCCGTGTGCT
1 AGGCCGTGTGCT
12261887 AGGCC
1 AGGCC
12261892 ATGCCAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.28, G:0.41, T:0.21
Consensus pattern (12 bp):
AGGCCGTGTGCT
Found at i:12262838 original size:23 final size:24
Alignment explanation
Indices: 12262786--12262838 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
12262776 ATGCAATTCA
*
12262786 AATTTAATCCAAAACTTAACACAT
1 AATTCAATCCAAAACTTAACACAT
*
12262810 ATATTCAATCCAAGA-TTAA-ACAT
1 A-ATTCAATCCAAAACTTAACACAT
12262833 GAATTC
1 -AATTC
12262839 CACCAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 8 0.32
24 6 0.24
25 11 0.44
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (24 bp):
AATTCAATCCAAAACTTAACACAT
Found at i:12307864 original size:24 final size:24
Alignment explanation
Indices: 12307859--12307952 Score: 152
Period size: 24 Copynumber: 3.9 Consensus size: 24
12307849 TATTGACATT
12307859 CAAATCCGCACACATAGTGCCATA
1 CAAATCCGCACACATAGTGCCATA
**
12307883 CAAATCTACACACATAGTGCCATA
1 CAAATCCGCACACATAGTGCCATA
* *
12307907 CAAATCTGCACACATAGTGCCATT
1 CAAATCCGCACACATAGTGCCATA
12307931 CAAATCCGCACACATAGTGCCA
1 CAAATCCGCACACATAGTGCCA
12307953 AAGTCATTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.19
Consensus pattern (24 bp):
CAAATCCGCACACATAGTGCCATA
Found at i:12307950 original size:48 final size:48
Alignment explanation
Indices: 12307819--12307952 Score: 160
Period size: 48 Copynumber: 2.8 Consensus size: 48
12307809 TGTTAACCCA
* * ** * * * *
12307819 CACACATAGTGTCTTAGTAATCCACACACGTATTGACATTCAAATCCG
1 CACACATAGTGCCATACAAATCCACACACATAGTGCCATACAAATCCG
* *
12307867 CACACATAGTGCCATACAAATCTACACACATAGTGCCATACAAATCTG
1 CACACATAGTGCCATACAAATCCACACACATAGTGCCATACAAATCCG
* *
12307915 CACACATAGTGCCATTCAAATCCGCACACATAGTGCCA
1 CACACATAGTGCCATACAAATCCACACACATAGTGCCA
12307953 AAGTCATTTC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (48 bp):
CACACATAGTGCCATACAAATCCACACACATAGTGCCATACAAATCCG
Found at i:12311025 original size:36 final size:36
Alignment explanation
Indices: 12310978--12311059 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
12310968 GTCAGATCAA
*
12310978 CCAAAACACACCAGATGATCACACGAACCAATGCC-T
1 CCAAAACACACCACATGATCACACGAACCAAT-CCTT
* *
12311014 CCAAAACACACCACATGCTCACACGAGCCAATCCTT
1 CCAAAACACACCACATGATCACACGAACCAATCCTT
*
12311050 CTAAAACACA
1 CCAAAACACA
12311060 TCAATGCTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 2 0.05
36 39 0.95
ACGTcount: A:0.41, C:0.38, G:0.09, T:0.12
Consensus pattern (36 bp):
CCAAAACACACCACATGATCACACGAACCAATCCTT
Found at i:12317403 original size:48 final size:48
Alignment explanation
Indices: 12317241--12317407 Score: 200
Period size: 46 Copynumber: 3.6 Consensus size: 48
12317231 TGATATGTGT
* *
12317241 GCTAGTGTAA-AAATGTCTGGGACATGCATCGACCTC-AGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAA
* * * * ** *
12317287 GCCAGTGTAAGACATGTCTGGGACTTGCATCGGCATTGAGA-CGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAA
12317333 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAA
*
12317381 GCTAGTGTAAGACTTG-CATGGGACATG
1 GCTAGTGTAAGACATGTC-TGGGACATG
12317408 GCGTCAGCTT
Statistics
Matches: 99, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
46 47 0.47
47 24 0.24
48 28 0.28
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAA
Found at i:12324649 original size:36 final size:36
Alignment explanation
Indices: 12324600--12324698 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
12324590 GTCAGATCTA
* * *
12324600 CCAAAACACACCAGATGATCACACGAGCCGATCCCT
1 CCAAAACACACCAGATGCTCACAAGAGCCAATCCCT
* * *
12324636 CTAAAACACACCAGATGCTCACATGAACCAATCCCT
1 CCAAAACACACCAGATGCTCACAAGAGCCAATCCCT
12324672 CCAAAACACACCA-ATGCTCACAAGAGC
1 CCAAAACACACCAGATGCTCACAAGAGC
12324699 TAGTCCAACG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 12 0.22
36 43 0.78
ACGTcount: A:0.39, C:0.37, G:0.11, T:0.12
Consensus pattern (36 bp):
CCAAAACACACCAGATGCTCACAAGAGCCAATCCCT
Found at i:12326742 original size:11 final size:11
Alignment explanation
Indices: 12326726--12326756 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12326716 TAAATTCTAA
12326726 CAATTTCATAC
1 CAATTTCATAC
12326737 CAATTTCATAC
1 CAATTTCATAC
12326748 CAATTTCAT
1 CAATTTCAT
12326757 CTAATTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (11 bp):
CAATTTCATAC
Found at i:12330018 original size:27 final size:27
Alignment explanation
Indices: 12329988--12330165 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
12329978 ATATTGAGCC
* *
12329988 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
12330015 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
12330042 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
12330070 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
12330097 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
12330124 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
12330151 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12330166 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:12330100 original size:55 final size:54
Alignment explanation
Indices: 12329988--12330165 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
12329978 ATATTGAGCC
* * * * *
12329988 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
12330042 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
12330097 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
12330151 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12330166 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:12332256 original size:33 final size:32
Alignment explanation
Indices: 12332219--12332297 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
12332209 TGGCCCTACC
* * *
12332219 ATGGTCTTACACTCGTAATTTCATAACCCAGTT
1 ATGGTCTTACACTAG-AATTCCATAACCCAGCT
* * *
12332252 ATGGTCTTATCATTAGGATTCCATAACCTAGCT
1 ATGGTCTTA-CACTAGAATTCCATAACCCAGCT
12332285 ATGGTCTTACACT
1 ATGGTCTTACACT
12332298 TATACATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 3 0.08
33 31 0.82
34 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (32 bp):
ATGGTCTTACACTAGAATTCCATAACCCAGCT
Found at i:12332363 original size:105 final size:102
Alignment explanation
Indices: 12332240--12332434 Score: 248
Period size: 105 Copynumber: 1.9 Consensus size: 102
12332230 CTCGTAATTT
* * *
12332240 CATAACCCAGTTATGGTCTTATCATT-AGGATTCCATAACCTAGCTATGGTCTTACACTTATACA
1 CATAACCCAGTTAAGGTCTTATCATTGA-AATGCCATAACCTAGCTATGGTCTTACACTTA-ACA
* *
12332304 TATACTGACGTGGTTCAACCATGGTCTTACGTTCACGATGC
64 -AT-CTGACATGGTCCAACCATGGTCTTACGTTCACGATGC
* * * *
12332345 CATAACCTAGTTAAGGTCTTTTCATTGAAATGCCATAGCCTAGCTATGGTCTTACATTTAACAAT
1 CATAACCCAGTTAAGGTCTTATCATTGAAATGCCATAACCTAGCTATGGTCTTACACTTAACAAT
* *
12332410 TTGTCATGGTCCAACCATGGTCTTA
66 CTGACATGGTCCAACCATGGTCTTA
12332435 TCCGTCAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
102 21 0.27
103 2 0.03
104 3 0.04
105 51 0.65
106 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (102 bp):
CATAACCCAGTTAAGGTCTTATCATTGAAATGCCATAACCTAGCTATGGTCTTACACTTAACAAT
CTGACATGGTCCAACCATGGTCTTACGTTCACGATGC
Found at i:12334167 original size:46 final size:46
Alignment explanation
Indices: 12334081--12334248 Score: 157
Period size: 46 Copynumber: 3.6 Consensus size: 46
12334071 TATGAGAGCC
* * *
12334081 AGTGTAAGACCATGTCTGGGACATGGTATCGGCATTGAGACG-AGTGTT
1 AGTGTAAGA-CATGTCTGGGACAT-GTATCGGCATCGAGACGTA-AGCT
* *
12334129 AGTGTAAGACACGTCTGGGACATGTATCGGCCTCGAGACGTAAGCT
1 AGTGTAAGACATGTCTGGGACATGTATCGGCATCGAGACGTAAGCT
* * *
12334175 AGTGTAAGACATGTCTGGGACATGCATTGGCTAT-GAGATGT--G-T
1 AGTGTAAGACATGTCTGGGACATGTATCGGC-ATCGAGACGTAAGCT
* *
12334218 CAGTGTAAGACCATGTCTAGGACATGCATCG
1 -AGTGTAAGA-CATGTCTGGGACATGTATCG
12334249 ACTATGAGAT
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.01
44 10 0.10
45 18 0.17
46 51 0.49
47 15 0.14
48 9 0.09
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGTATCGGCATCGAGACGTAAGCT
Found at i:12334241 original size:45 final size:45
Alignment explanation
Indices: 12334175--12334293 Score: 170
Period size: 45 Copynumber: 2.7 Consensus size: 45
12334165 GACGTAAGCT
* * * *
12334175 AGTGTAAGA-CATGTCTGGGACATGCATTGGCTATGAGATGTGTC
1 AGTGTAAGACCATGTCTAGGACATGCATCGACTATGAGATATGTC
12334219 AGTGTAAGACCATGTCTAGGACATGCATCGACTATGAGATATGTC
1 AGTGTAAGACCATGTCTAGGACATGCATCGACTATGAGATATGTC
*
12334264 AGTGTAAGACCATGTCT-GGGCATGGCATCG
1 AGTGTAAGACCATGTCTAGGACAT-GCATCG
12334294 GCACAGATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 14 0.21
45 54 0.79
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (45 bp):
AGTGTAAGACCATGTCTAGGACATGCATCGACTATGAGATATGTC
Found at i:12336457 original size:41 final size:41
Alignment explanation
Indices: 12336411--12336493 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
12336401 ACTCGTTCTG
12336411 ATTGCCCGTCAATCTAAGGATAAAATACTATGCTGAAATTT
1 ATTGCCCGTCAATCTAAGGATAAAATACTATGCTGAAATTT
* * *
12336452 ATTGCCCGTTAATCTAAGGATAAAATACTGTGCTGGAATTT
1 ATTGCCCGTCAATCTAAGGATAAAATACTATGCTGAAATTT
12336493 A
1 A
12336494 GTTTAGTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (41 bp):
ATTGCCCGTCAATCTAAGGATAAAATACTATGCTGAAATTT
Found at i:12341807 original size:33 final size:32
Alignment explanation
Indices: 12341770--12341846 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
12341760 TGCCCCTACC
* *
12341770 ATGGTCTTACACTCGTAATGCCATAA-CTCAGTT
1 ATGGTCTTACACTAG-AATGCCATAACCT-AGCT
* *
12341803 ATGGTCTTATCATTAGGATGCCATAACCTAGCT
1 ATGGTCTTA-CACTAGAATGCCATAACCTAGCT
12341836 ATGGTCTTACA
1 ATGGTCTTACA
12341847 TTTATACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
32 2 0.05
33 30 0.79
34 6 0.16
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (32 bp):
ATGGTCTTACACTAGAATGCCATAACCTAGCT
Found at i:12341898 original size:105 final size:105
Alignment explanation
Indices: 12341767--12341955 Score: 247
Period size: 105 Copynumber: 1.8 Consensus size: 105
12341757 CCATGCCCCT
** * * * *
12341767 ACCATGGTCTTACACTCGTAATGCCATAA-CTCAGTTATGGTCTTATCA-TTAGGATGCCATAAC
1 ACCATGGTCTTACACTCACAATGCCATAACCT-AGTTAAGGTCTTATCACTGA-AATACCATAAC
*
12341830 CTAGCTATGGTCTTACATTTATACATATACTGACATGGTTCA
64 CCAGCTATGGTCTTACATTTATACATATACTGACATGGTTCA
* * * *
12341872 ACCATGGTCTTACATTCACGATGCCATAACCTAGTTAAGGTCTTTTCACTGAAATACCATAGCCC
1 ACCATGGTCTTACACTCACAATGCCATAACCTAGTTAAGGTCTTATCACTGAAATACCATAACCC
12341937 AGCTATGGTCTTACATTTA
66 AGCTATGGTCTTACATTTA
12341956 ACACTTTGCC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
105 67 0.94
106 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (105 bp):
ACCATGGTCTTACACTCACAATGCCATAACCTAGTTAAGGTCTTATCACTGAAATACCATAACCC
AGCTATGGTCTTACATTTATACATATACTGACATGGTTCA
Found at i:12352342 original size:26 final size:28
Alignment explanation
Indices: 12352294--12352350 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 28
12352284 AATCAAAAAG
12352294 TTAAACAGTTCTTTTTTCTTTACCTT-T
1 TTAAACAGTTCTTTTTTCTTTACCTTCT
*
12352321 TTAAACATTTC-TTTTTCTTTACCTTCT
1 TTAAACAGTTCTTTTTTCTTTACCTTCT
12352348 TTA
1 TTA
12352351 TGATTCAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.60
Consensus pattern (28 bp):
TTAAACAGTTCTTTTTTCTTTACCTTCT
Found at i:12356664 original size:27 final size:27
Alignment explanation
Indices: 12356623--12356680 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
12356613 TTTGTAGAAA
* *
12356623 AGAGAAGTAATGAGATTAGAAAATTTT
1 AGAGAAGTAAAGAGATCAGAAAATTTT
12356650 AGAGAAGTAAAGAGATCAGAAAATTTT
1 AGAGAAGTAAAGAGATCAGAAAATTTT
12356677 AGAG
1 AGAG
12356681 TGGGTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.02, G:0.24, T:0.24
Consensus pattern (27 bp):
AGAGAAGTAAAGAGATCAGAAAATTTT
Found at i:12359657 original size:27 final size:27
Alignment explanation
Indices: 12359617--12359681 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
12359607 TTTTATTTTA
* *
12359617 TTTTTAAAAATATTCAAA-ATA-TTATAT
1 TTTTTAATATTATT-AAACATACTTAT-T
12359644 TTTTTAATATTATTAAACATACTTATT
1 TTTTTAATATTATTAAACATACTTATT
12359671 TTATTT-ATATT
1 TT-TTTAATATT
12359682 TAGTCATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 3 0.09
27 23 0.70
28 7 0.21
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTTAATATTATTAAACATACTTATT
Found at i:12359733 original size:13 final size:14
Alignment explanation
Indices: 12359717--12359758 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
12359707 TTTTAATTTT
12359717 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
12359730 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
12359745 ATTTTGAATAATAT
1 ATTTT-AATAATAT
12359759 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:12359810 original size:15 final size:15
Alignment explanation
Indices: 12359776--12359846 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
12359766 ATATTATTGA
12359776 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
12359789 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
12359804 AAATATTTATTATAATTAT
1 AAATA--T-TT-TAATAAT
*
12359823 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
12359838 AAATGTTTT
1 AAATATTTT
12359847 GTAATATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 19 0.42
16 1 0.02
17 2 0.04
18 2 0.04
19 11 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:12359819 original size:19 final size:19
Alignment explanation
Indices: 12359792--12359828 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12359782 TTAATATTAA
*
12359792 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
12359811 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
12359829 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:12360345 original size:15 final size:14
Alignment explanation
Indices: 12360308--12360338 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12360298 ATAAATTATT
12360308 TTTC-AAAAATTAA
1 TTTCTAAAAATTAA
12360321 TTTCTAAAAATTAA
1 TTTCTAAAAATTAA
12360335 TTTC
1 TTTC
12360339 AGTAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTCTAAAAATTAA
Found at i:12361032 original size:22 final size:22
Alignment explanation
Indices: 12361007--12361054 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
12360997 ATTTTTTTTC
12361007 TTTAAAGGGAATAATTT-GATAT
1 TTTAAAGGGAATAATTTAGAT-T
* * *
12361029 TTTACATGGAATTATTTAGATT
1 TTTAAAGGGAATAATTTAGATT
12361051 TTTA
1 TTTA
12361055 TAGAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (22 bp):
TTTAAAGGGAATAATTTAGATT
Found at i:12372531 original size:33 final size:34
Alignment explanation
Indices: 12372489--12372596 Score: 157
Period size: 34 Copynumber: 3.2 Consensus size: 34
12372479 TTTACATTTA
*
12372489 TGATACTATTACCGTAAT-GGCTAAGGCCCACAC
1 TGATACTATTACTGTAATGGGCTAAGGCCCACAC
*
12372522 TGATACTATTACTGTAATGGGCTAAGGCTCACAC
1 TGATACTATTACTGTAATGGGCTAAGGCCCACAC
* *
12372556 CGATACTATTACTGCAATGGGCTAAGG-CCACAC
1 TGATACTATTACTGTAATGGGCTAAGGCCCACAC
*
12372589 TAATACTA
1 TGATACTA
12372597 GACTGTCACT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 28 0.42
34 39 0.58
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (34 bp):
TGATACTATTACTGTAATGGGCTAAGGCCCACAC
Found at i:12378533 original size:186 final size:186
Alignment explanation
Indices: 12378219--12378592 Score: 615
Period size: 186 Copynumber: 2.0 Consensus size: 186
12378209 ATTTATCCCC
*
12378219 TACAAAAGGACTGGCTGGTTCTAATCCAACCAAACCAAAATTGGATTTCAACAATGTCCAATATT
1 TACAAAAGGACAGGCTGGTTCTAATCCAACCAAACCAAAATTGGATTTCAACAATGTCCAATATT
* * *
12378284 GTTTCTAACTTATCTTATTTTTTCCAATAGAGACCATCAGCTTACGGTCTTTTTTAATTTAACCC
66 GTTTCTAACTTATCCTATTTTTTCCAATAAAGACCATCAACTTACGGTCTTTTTTAATTTAACCC
* *
12378349 CTAATGTTCCTAATTTTTCGAGTTTAAAGGAAATCCTGGTATCATAATTTCTGGTG
131 CTAATGTTCCTAATTTTTCGAGTTTAAAGAAAATCCTGGTATAATAATTTCTGGTG
* ** *
12378405 TACAAAAGGACAGGCTGGTTCTAATTCAACTGAACCAAAATTGGATTTCAACATTGTCCAATATT
1 TACAAAAGGACAGGCTGGTTCTAATCCAACCAAACCAAAATTGGATTTCAACAATGTCCAATATT
*
12378470 GTTTCTAACTTTTCCTATTTTTTTCCAATAAAGACCATCAAC-TACGGTCTTTTTTAATTTAACC
66 GTTTCTAACTTATCCTA-TTTTTTCCAATAAAGACCATCAACTTACGGTCTTTTTTAATTTAACC
* *
12378534 CCTAATGTTCCTAATTTTTCGAGTTTAAAGAAAATCTTGGTGTAATAATTTCTGGTG
130 CCTAATGTTCCTAATTTTTCGAGTTTAAAGAAAATCCTGGTATAATAATTTCTGGTG
12378591 TA
1 TA
12378593 TTTACTGCCA
Statistics
Matches: 174, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
186 152 0.87
187 22 0.13
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (186 bp):
TACAAAAGGACAGGCTGGTTCTAATCCAACCAAACCAAAATTGGATTTCAACAATGTCCAATATT
GTTTCTAACTTATCCTATTTTTTCCAATAAAGACCATCAACTTACGGTCTTTTTTAATTTAACCC
CTAATGTTCCTAATTTTTCGAGTTTAAAGAAAATCCTGGTATAATAATTTCTGGTG
Found at i:12381819 original size:67 final size:68
Alignment explanation
Indices: 12381584--12381868 Score: 246
Period size: 67 Copynumber: 4.2 Consensus size: 68
12381574 ATCACTAAGT
* * * * * * * *
12381584 TATGGTTTTACACATCATACCCCATGTTTAAT-TTCCTGGAGGACTCTCTATGTTGTCATAGTC-
1 TATGGTCTTACACATTAAACCTCATGTTTAATGTT-CTAGTGGACTCTTTATGTTGTCATAGCCA
*
12381647 GAGC
65 TAGC
* * * * * *
12381651 TATGATCTTTCACATTATACCTTATATTTAATG-TCTTGGTGGACTCTTTATGTTG-CTATAGCC
1 TATGGTCTTACACATTAAACCTCATGTTTAATGTTC-TAGTGGACTCTTTATGTTGTC-ATAGCC
12381714 A-AGC
64 ATAGC
* *
12381718 TATGGTCTTACGCATTATAACC-CATGTTTGATGTTCTAGTGGACTCTTTATGTTGTCATAG-CA
1 TATGGTCTTACACATTA-AACCTCATGTTTAATGTTCTAGTGGACTCTTTATGTTGTCATAGCCA
12381781 TAGC
65 TAGC
**** * * *
12381785 TATGGTCTTACACATTAAACCTCATGTTTAATGTTCTAACAAACTCTTTATATTGCCATAG--TT
1 TATGGTCTTACACATTAAACCTCATGTTTAATGTTCTAGTGGACTCTTTATGTTGTCATAGCCAT
12381848 GAGC
66 -AGC
12381852 TATGGTCTTACACATTA
1 TATGGTCTTACACATTA
12381869 CCCCATTACA
Statistics
Matches: 181, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
66 9 0.05
67 166 0.92
68 6 0.03
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (68 bp):
TATGGTCTTACACATTAAACCTCATGTTTAATGTTCTAGTGGACTCTTTATGTTGTCATAGCCAT
AGC
Found at i:12384031 original size:3 final size:3
Alignment explanation
Indices: 12384025--12384062 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12384015 CATCATTTAT
12384025 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12384063 TTCACACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12384308 original size:21 final size:21
Alignment explanation
Indices: 12384267--12384316 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
12384257 TATCTTTAAC
*
12384267 TTAATATAAAATAATAATAAT
1 TTAATATAAAACAATAATAAT
12384288 TTAATATAAAACCATACTAATAA-
1 TTAATATAAAA-CA-A-TAATAAT
12384311 TTAATA
1 TTAATA
12384317 ATAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
22 1 0.04
23 7 0.28
24 6 0.24
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAATATAAAACAATAATAAT
Found at i:12389426 original size:76 final size:76
Alignment explanation
Indices: 12389300--12389452 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
12389290 CAAAAATCCC
*
12389300 AACTCAATTTTGACTCAAAAGTGACATGTACTATTAGACTCACTTCCGAGCTCGATTTAGCCTGA
1 AACTCAATTTTGACTCAAAAGTGACATGTACTATTAGACTCACTTCCGAGCTCGATTTAGCCCGA
*
12389365 GAATCGGCTAA
66 GAATCGACTAA
*
12389376 AACTCAATTTTGACTCAAAAGTGGCATGTACTATTAGACTCACTTCCGAGCTCGATTTAGCCCGA
1 AACTCAATTTTGACTCAAAAGTGACATGTACTATTAGACTCACTTCCGAGCTCGATTTAGCCCGA
12389441 GAATCGACTAA
66 GAATCGACTAA
12389452 A
1 A
12389453 CCTGATAGCT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (76 bp):
AACTCAATTTTGACTCAAAAGTGACATGTACTATTAGACTCACTTCCGAGCTCGATTTAGCCCGA
GAATCGACTAA
Found at i:12391862 original size:3 final size:3
Alignment explanation
Indices: 12391846--12391910 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
12391836 ATCTTTAACT
* **
12391846 TAA T-A TAA -AA TAA TAA TAA TAA TAA TAA T-T TAA T-A TAA -AA CCA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
12391889 TAC TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA
12391911 AATCTTAGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
2 9 0.18
3 37 0.76
4 3 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12391880 original size:30 final size:31
Alignment explanation
Indices: 12391845--12391905 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
12391835 TATCTTTAAC
*
12391845 TTAATATAAAATAATAATAATAA-TAATAAT
1 TTAATATAAAACAATAATAATAATTAATAAT
* *
12391875 TTAATATAAAACCATACTAATAATTAATAAT
1 TTAATATAAAACAATAATAATAATTAATAAT
12391906 AATAAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (31 bp):
TTAATATAAAACAATAATAATAATTAATAAT
Found at i:12396938 original size:10 final size:11
Alignment explanation
Indices: 12396913--12396941 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12396903 TGTAAATATT
12396913 GTGTATTTTTA
1 GTGTATTTTTA
12396924 GTGTATTTTTA
1 GTGTATTTTTA
12396935 -TGTATTT
1 GTGTATTT
12396942 AGTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (11 bp):
GTGTATTTTTA
Found at i:12399085 original size:20 final size:20
Alignment explanation
Indices: 12399057--12399165 Score: 112
Period size: 20 Copynumber: 5.5 Consensus size: 20
12399047 AGATGCATAA
12399057 CAGGGGCACCGAAGTGCAAT
1 CAGGGGCACCGAAGTGCAAT
* *
12399077 CAGGAGCA-CGAATGTGCGAT
1 CAGGGGCACCGAA-GTGCAAT
12399097 CAGGGGCACCGAAGTGCAAT
1 CAGGGGCACCGAAGTGCAAT
* ** * * *
12399117 CAAGGGCATAGATGTGTATT
1 CAGGGGCACCGAAGTGCAAT
* *
12399137 CAGGTGCACCGAAGTGCAAA
1 CAGGGGCACCGAAGTGCAAT
12399157 CAGGGGCAC
1 CAGGGGCAC
12399166 AGATGTACAT
Statistics
Matches: 68, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
19 4 0.06
20 60 0.88
21 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.34, T:0.14
Consensus pattern (20 bp):
CAGGGGCACCGAAGTGCAAT
Found at i:12399178 original size:40 final size:40
Alignment explanation
Indices: 12399057--12399179 Score: 151
Period size: 40 Copynumber: 3.1 Consensus size: 40
12399047 AGATGCATAA
*
12399057 CAGGGGCACCGAAGTGCAATCAGGAGCAC-GAATGTGCGA-T
1 CAGGGGCACCGAAGTGCAATCAGGGGCACAG-ATGTGC-ATT
* * *
12399097 CAGGGGCACCGAAGTGCAATCAAGGGCATAGATGTGTATT
1 CAGGGGCACCGAAGTGCAATCAGGGGCACAGATGTGCATT
* * *
12399137 CAGGTGCACCGAAGTGCAAACAGGGGCACAGATGTACATT
1 CAGGGGCACCGAAGTGCAATCAGGGGCACAGATGTGCATT
12399177 CAG
1 CAG
12399180 AGGTATCGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 69 0.97
41 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (40 bp):
CAGGGGCACCGAAGTGCAATCAGGGGCACAGATGTGCATT
Found at i:12399190 original size:40 final size:40
Alignment explanation
Indices: 12399057--12399201 Score: 118
Period size: 40 Copynumber: 3.6 Consensus size: 40
12399047 AGATGCATAA
* * *
12399057 CAGGGGCACCGAAGTGCAATC-AGGAGCAC-GAATGTGCGA-T
1 CAGGTGCACCGAAGTGCAAACAAGG-GCACAG-ATGTAC-ATT
* * * **
12399097 CAGGGGCACCGAAGTGCAATCAAGGGCATAGATGTGTATT
1 CAGGTGCACCGAAGTGCAAACAAGGGCACAGATGTACATT
*
12399137 CAGGTGCACCGAAGTGCAAACAGGGGCACAGATGTACATT
1 CAGGTGCACCGAAGTGCAAACAAGGGCACAGATGTACATT
* * *
12399177 CAGAG-GTATCGAAGTACAAACAAGG
1 CAG-GTGCACCGAAGTGCAAACAAGG
12399202 CACTACTTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 83 0.93
41 5 0.06
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (40 bp):
CAGGTGCACCGAAGTGCAAACAAGGGCACAGATGTACATT
Found at i:12403843 original size:13 final size:13
Alignment explanation
Indices: 12403804--12403843 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12403794 GAAGTAATCG
12403804 CACACGGGCGTGT
1 CACACGGGCGTGT
*
12403817 CACACAGGCGTGT
1 CACACGGGCGTGT
* *
12403830 CATACGGGCATGT
1 CACACGGGCGTGT
12403843 C
1 C
12403844 CCTGCCGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:12404421 original size:17 final size:17
Alignment explanation
Indices: 12404399--12404433 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12404389 TATAGATCGA
12404399 GTTAATGCAACCCTAGG
1 GTTAATGCAACCCTAGG
12404416 GTTAATGCAACCCTAGG
1 GTTAATGCAACCCTAGG
12404433 G
1 G
12404434 AGTTAACTAG
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:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (17 bp):
GTTAATGCAACCCTAGG
Found at i:12415474 original size:13 final size:13
Alignment explanation
Indices: 12415456--12415482 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12415446 GCTTGGCAGG
12415456 GACACGCCCGTGT
1 GACACGCCCGTGT
12415469 GACACGCCCGTGT
1 GACACGCCCGTGT
12415482 G
1 G
12415483 CGATTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:12416161 original size:49 final size:50
Alignment explanation
Indices: 12416106--12416234 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 50
12416096 GTTGTGTGTC
*
12416106 AGTGTAAGACCTGTCTGGGACATGACATCGAAAC-CGATAGATGAGAGCT
1 AGTGTAAGACCTGTCTGGGACATGACATCGAAACTCGATAGATGAAAGCT
* * * ** * *
12416155 AGTGTAAGACTTGTCTAGGACACGACATCG-GCCTCGATATATGAAAGTT
1 AGTGTAAGACCTGTCTGGGACATGACATCGAAACTCGATAGATGAAAGCT
* *
12416204 AGTGTAAGAACTGTTTGGGACAT-AGCATCGA
1 AGTGTAAGACCTGTCTGGGACATGA-CATCGA
12416235 CTTTGATGTG
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
48 2 0.03
49 62 0.97
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (50 bp):
AGTGTAAGACCTGTCTGGGACATGACATCGAAACTCGATAGATGAAAGCT
Found at i:12416274 original size:141 final size:138
Alignment explanation
Indices: 12416003--12416271 Score: 315
Period size: 142 Copynumber: 1.9 Consensus size: 138
12415993 ATCGACATTA
* * *
12416003 AGATGAGAGCTAGTGTAAGACATGTCTGGGACATGAATTGGCCTCGAGATATACAAGCTAATGTA
1 AGATGAGAGCTAGTGTAAGACATGTCTAGGACACGAATCGGCCTCGAGATATACAAGCTAATGTA
* * * * *
12416068 AGACCTATTTGGGACATGGCGTCAACTTGTTGTGTGTCAGTGTAAGACCTGTCTGGGACATGACA
66 AGAACTATTTGGGACATAGCATCAACTTGATGTGTGCCAGTGTAAGACCTGTCTGGG--A-GACA
12416133 TCGAAACCGAT
128 TCGAAACCGAT
* * * *
12416144 AGATGAGAGCTAGTGTAAGACTTGTCTAGGACACGACATCGGCCTCGATATATGA-AAGTTAGTG
1 AGATGAGAGCTAGTGTAAGACATGTCTAGGACACGA-ATCGGCCTCGAGATAT-ACAAGCTAATG
* * *
12416208 TAAGAACTGTTTGGGACATAGCATCGACTTTGATGTGCTAGCCAGTGTTAGACCATGTCTGGGA
64 TAAGAACTATTTGGGACATAGCATCAAC-TTGATGTG-T-GCCAGTGTAAGACC-TGTCTGGGA
12416272 CATGACGTCG
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
141 33 0.31
142 44 0.41
143 8 0.07
144 2 0.02
145 12 0.11
146 8 0.07
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27
Consensus pattern (138 bp):
AGATGAGAGCTAGTGTAAGACATGTCTAGGACACGAATCGGCCTCGAGATATACAAGCTAATGTA
AGAACTATTTGGGACATAGCATCAACTTGATGTGTGCCAGTGTAAGACCTGTCTGGGAGACATCG
AAACCGAT
Found at i:12418640 original size:93 final size:93
Alignment explanation
Indices: 12418528--12418698 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
12418518 GCCCATAAGT
* * *
12418528 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA
12418593 CGAGCTCGGATGCCTAGTTACATTTCAC
66 CGAGCTCGGATGCCTAGTTACATTTCAC
* *
12418621 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA
*
12418686 CGAGTTCGGATGC
66 CGAGCTCGGATGC
12418699 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATTTCAC
Found at i:12418695 original size:46 final size:46
Alignment explanation
Indices: 12418520--12418695 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
12418510 TGTAACCCGC
* * *
12418520 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
12418566 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* ** * *
12418612 ACATTTCACGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA-TAAATGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
12418659 CCATAAATGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGA
12418696 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 69 0.64
47 30 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:12423547 original size:20 final size:20
Alignment explanation
Indices: 12423522--12423565 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
12423512 AATCGTCGGC
12423522 ACATCTTGGCCTCTGTAGGA
1 ACATCTTGGCCTCTGTAGGA
12423542 ACATCTTGGCCTCTGTAGGA
1 ACATCTTGGCCTCTGTAGGA
12423562 ACAT
1 ACAT
12423566 ACTCTCTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (20 bp):
ACATCTTGGCCTCTGTAGGA
Found at i:12425717 original size:46 final size:46
Alignment explanation
Indices: 12425650--12425824 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
12425640 TGTAACCCGC
12425650 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
12425696 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * * * *
12425746 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
12425789 CCATAAATGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
12425825 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 63 0.59
47 26 0.24
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:12425770 original size:93 final size:93
Alignment explanation
Indices: 12425658--12425828 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
12425648 GCCCATAAGT
* * * *
12425658 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
12425723 CGAGCTCGGATGCCTAGTTACATTTCAC
66 CGAGCTCGGATGCCTAGTTACATTTCAC
*
12425751 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
12425816 CGAGTTCGGATGC
66 CGAGCTCGGATGC
12425829 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATTTCAC
Found at i:12430296 original size:17 final size:17
Alignment explanation
Indices: 12430274--12430307 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12430264 ATAGCTGAAG
12430274 CCACATGAGAAAAACTA
1 CCACATGAGAAAAACTA
*
12430291 CCACATGAGAGAAACTA
1 CCACATGAGAAAAACTA
12430308 ACCAACGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.12
Consensus pattern (17 bp):
CCACATGAGAAAAACTA
Found at i:12430648 original size:22 final size:22
Alignment explanation
Indices: 12430623--12430664 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12430613 AGATGACTCT
12430623 GAACAAGACAGATTGTGAATCA
1 GAACAAGACAGATTGTGAATCA
12430645 GAACAAGACAGATTGTGAAT
1 GAACAAGACAGATTGTGAAT
12430665 TAGACTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (22 bp):
GAACAAGACAGATTGTGAATCA
Found at i:12431893 original size:30 final size:30
Alignment explanation
Indices: 12431858--12431938 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
12431848 TTTACGAGCC
*
12431858 TAGGGGCAAAAATGTAATTTTGACAAAGTT
1 TAGGGGCAAAATTGTAATTTTGACAAAGTT
12431888 TAGGGGCAAAATTGTAATTTTGACAAAGTT
1 TAGGGGCAAAATTGTAATTTTGACAAAGTT
*
12431918 TAGGGGCAAAATTATAATTTT
1 TAGGGGCAAAATTGTAATTTT
12431939 CCAAAATATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.33
Consensus pattern (30 bp):
TAGGGGCAAAATTGTAATTTTGACAAAGTT
Found at i:12432271 original size:27 final size:27
Alignment explanation
Indices: 12432241--12432294 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12432231 TGTCATGTGA
* *
12432241 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
12432268 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
12432295 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:12432652 original size:51 final size:49
Alignment explanation
Indices: 12432543--12432786 Score: 281
Period size: 49 Copynumber: 4.9 Consensus size: 49
12432533 TATTTTGAGG
* *
12432543 TCACGTGTATAGTACGAAGTGCAGGCTACTACGTGTACCGGATAATTGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGA
* * * * * *
12432592 TCACATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGATTACTTCGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGA-TAATT-GA
* * ** *
12432643 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCGGATGGTTAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GA
* *
12432693 TCACGTGTGTAGTACTAAGTGCAGTCTACTACGTGTACCGGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGA
* * * * *
12432742 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA
12432787 CCTTGTCTAC
Statistics
Matches: 165, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
49 76 0.46
50 50 0.30
51 39 0.24
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGA
Found at i:12436575 original size:46 final size:48
Alignment explanation
Indices: 12436522--12436641 Score: 158
Period size: 46 Copynumber: 2.6 Consensus size: 48
12436512 TATGTGTGCT
***
12436522 AGTGTAAGACATGTCTGGAACATGCATCGG-C-C-ACATATTGTGAGCC
1 AGTGTAAGACATGTCTGGAACATGCATCGGCCTCGACATA-TACCAGCC
* *
12436568 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATATACCAGTC
1 AGTGTAAGACATGTCTGGAACATGCATCGGCCTCGACATATACCAGCC
12436616 AGTGTAA-ACATGTCTGGAACATGCAT
1 AGTGTAAGACATGTCTGGAACATGCAT
12436642 TAGTATTGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
46 29 0.45
47 19 0.29
48 12 0.18
49 5 0.08
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGAACATGCATCGGCCTCGACATATACCAGCC
Found at i:12436812 original size:49 final size:50
Alignment explanation
Indices: 12436753--12436878 Score: 141
Period size: 49 Copynumber: 2.6 Consensus size: 50
12436743 GTTATGTGTT
* * *
12436753 AGTGTAAGACCTATCTGGGACATGGCATTGA-CAC-CAATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATTCAGC-CTCAATAGATGAAAGCC
* * * * * *
12436802 AGTGTAAGACCTGTCTGGAACACGACA-TCAGCCTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATTCAGCCTCAATAGATGAAAGCC
12436851 AGTGTAAGACCTGTCTGGGACATGGCAT
1 AGTGTAAGACCTGTCTGGGACATGGCAT
12436879 CGACTTTGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
48 3 0.05
49 59 0.95
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (50 bp):
AGTGTAAGACCTGTCTGGGACATGGCATTCAGCCTCAATAGATGAAAGCC
Found at i:12443668 original size:16 final size:16
Alignment explanation
Indices: 12443640--12443673 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12443630 AGATTTGAGG
12443640 GATATTGGGAGTCATT
1 GATATTGGGAGTCATT
12443656 GATA-TGGGAAGTCATT
1 GATATTGGG-AGTCATT
12443672 GA
1 GA
12443674 AATTATCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (16 bp):
GATATTGGGAGTCATT
Found at i:12452426 original size:12 final size:13
Alignment explanation
Indices: 12452390--12452426 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
12452380 CTATTTGAAA
12452390 AAAAAGTAAAAA-T
1 AAAAA-TAAAAACT
12452403 AAAAATAAAAACT
1 AAAAATAAAAACT
12452416 AAAAA-AAAAAC
1 AAAAATAAAAAC
12452427 GATTGTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.81, C:0.05, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAACT
Found at i:12458218 original size:30 final size:30
Alignment explanation
Indices: 12458178--12458252 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
12458168 TATGAAATAA
12458178 GGACTAAATTGTAAAAATGTGAAAGTTTAG
1 GGACTAAATTGTAAAAATGTGAAAGTTTAG
*
12458208 GGACTGAATTGTAAAAATGTGAAAGTTTAG
1 GGACTAAATTGTAAAAATGTGAAAGTTTAG
12458238 GGA--AAATGTGTAAAA
1 GGACTAAAT-TGTAAAA
12458253 TAACCCTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
28 3 0.07
29 7 0.17
30 32 0.76
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (30 bp):
GGACTAAATTGTAAAAATGTGAAAGTTTAG
Found at i:12459720 original size:12 final size:12
Alignment explanation
Indices: 12459703--12459743 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
12459693 ATAGGATTAG
*
12459703 CACGGTTTAGCA
1 CACGGTTTGGCA
12459715 CACGGTTTGGCA
1 CACGGTTTGGCA
12459727 CACGGTTTGGCA
1 CACGGTTTGGCA
12459739 CACGG
1 CACGG
12459744 GCATGTGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.22
Consensus pattern (12 bp):
CACGGTTTGGCA
Found at i:12464130 original size:14 final size:13
Alignment explanation
Indices: 12464106--12464143 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
12464096 TTCCCATATA
12464106 AAAAT-CCAATTC
1 AAAATACCAATTC
12464118 AAACATACCAATTC
1 AAA-ATACCAATTC
*
12464132 AAAATACAAATT
1 AAAATACCAATT
12464144 TTATATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 10 0.43
14 10 0.43
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATACCAATTC
Found at i:12465902 original size:49 final size:49
Alignment explanation
Indices: 12465843--12465973 Score: 174
Period size: 51 Copynumber: 2.6 Consensus size: 49
12465833 GGAATGCATG
* *
12465843 GTAGCCTGCACTTAGTACTACACATGTGACCAACAG-TCTGGTACACGTA
1 GTAGCCTGCACTTAGTACTACACATGTGACC-ACAGTTCGGGTACACATA
* * *
12465892 GTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCATA
1 GTAGCCTGCACTTAGTACTACACATGTGACCACAG--TTCGGGTACACATA
*
12465943 GTAGCCTGCACTTAGTACTACACATGCGACC
1 GTAGCCTGCACTTAGTACTACACATGTGACC
12465974 TCACAATAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
48 4 0.06
49 29 0.41
51 38 0.54
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (49 bp):
GTAGCCTGCACTTAGTACTACACATGTGACCACAGTTCGGGTACACATA
Found at i:12467934 original size:42 final size:43
Alignment explanation
Indices: 12467852--12467952 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 43
12467842 TCCAAAACGT
* *
12467852 GGTCTTACATGCAATCAAATATCGATGCCACTGTCCCAGACAG
1 GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGACAG
* * *
12467895 GGTCTTACACGAAATCAAATA-CGATGTCGA-TGTTCCAGACAT
1 GGTCTTACACGAAATCAAATATCGATG-CCACTGTCCCAGACAG
*
12467937 GGTCTTACACGTAATC
1 GGTCTTACACGAAATC
12467953 TCAAATTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 30 0.59
43 21 0.41
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGACAG
Found at i:12475211 original size:26 final size:27
Alignment explanation
Indices: 12475157--12475211 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
12475147 ATTTGGTAAG
* * *
12475157 GTATGGCATAAAAAGCCTTCTGGTCTA
1 GTATGACAAAAAAAGCCTGCTGGTCTA
*
12475184 GTATGACAAAAAAAGCCTGC-GGTTTA
1 GTATGACAAAAAAAGCCTGCTGGTCTA
12475210 GT
1 GT
12475212 GGATAATGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (27 bp):
GTATGACAAAAAAAGCCTGCTGGTCTA
Found at i:12477379 original size:39 final size:39
Alignment explanation
Indices: 12477325--12477403 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
12477315 GAAGACACTA
12477325 GAAATGTATCCGAGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGAGCTAAAGTCCCGCAGGCTTCGTGCTG
*
12477364 GAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTGCTG
1 GAAATGTATCCGAGCTAAAGTCCCGCAGGCTTCGTGCTG
12477403 G
1 G
12477404 TAATATAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
GAAATGTATCCGAGCTAAAGTCCCGCAGGCTTCGTGCTG
Found at i:12480655 original size:27 final size:27
Alignment explanation
Indices: 12480625--12480686 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
12480615 GGAGGAAGTG
12480625 TACTGTTACTGGTGGCTTTGCCACATA
1 TACTGTTACTGGTGGCTTTGCCACATA
*
12480652 TACTATTACTGGTGGCTTTGCCACATA
1 TACTGTTACTGGTGGCTTTGCCACATA
12480679 TACTGTTA
1 TACTGTTA
12480687 TTGGCAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTTGCCACATA
Found at i:12480697 original size:27 final size:27
Alignment explanation
Indices: 12480640--12480699 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
12480630 TTACTGGTGG
***
12480640 CTTTGCCACATATACTATTACTGGTGG
1 CTTTGCCACATATACTATTACTGGCAA
* *
12480667 CTTTGCCACATATACTGTTATTGGCAA
1 CTTTGCCACATATACTATTACTGGCAA
12480694 CTTTGC
1 CTTTGC
12480700 TATGATACTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (27 bp):
CTTTGCCACATATACTATTACTGGCAA
Found at i:12482266 original size:19 final size:20
Alignment explanation
Indices: 12482234--12482276 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
12482224 ATGGAGTTGG
*
12482234 TAAT-TACATGTGTA-AAAA
1 TAATATACATATGTATAAAA
12482252 TAATATACATATGTATAAAA
1 TAATATACATATGTATAAAA
12482272 TAATA
1 TAATA
12482277 AATTATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 9 0.41
20 9 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
TAATATACATATGTATAAAA
Found at i:12482409 original size:22 final size:22
Alignment explanation
Indices: 12482356--12482401 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12482346 AAATAAAAAG
12482356 AATAAAAATAGAAACAAAGTTA
1 AATAAAAATAGAAACAAAGTTA
12482378 AATAAAAATAGAAACAAAGTTA
1 AATAAAAATAGAAACAAAGTTA
12482400 AA
1 AA
12482402 ACGAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (22 bp):
AATAAAAATAGAAACAAAGTTA
Found at i:12482440 original size:17 final size:16
Alignment explanation
Indices: 12482416--12482447 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12482406 AATATAGAAG
12482416 AAAAAGAAAGAAAAGA
1 AAAAAGAAAGAAAAGA
12482432 AAAAGAGAAAGAAAAG
1 AAAA-AGAAAGAAAAG
12482448 GAGAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAGA
Found at i:12487465 original size:49 final size:49
Alignment explanation
Indices: 12487344--12487473 Score: 174
Period size: 49 Copynumber: 2.6 Consensus size: 49
12487334 GAAATGTGTC
*
12487344 AGTGTAAGACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATTGCCACGGATA-GTGAGAGCT
* * * *
12487394 AGTGTAAGACCATGTCTAGGACATGGCATTAGCCTCGG-T-GATGATAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATT-GCCACGGATAG-TGAGAGCT
12487443 AGTGTAAGACCATGTCTGGGACATGGCATTG
1 AGTGTAAGACCATGTCTGGGACATGGCATTG
12487474 GCAACTTGTC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
48 2 0.03
49 35 0.49
50 30 0.42
51 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATTGCCACGGATAGTGAGAGCT
Found at i:12490374 original size:16 final size:16
Alignment explanation
Indices: 12490353--12490386 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12490343 TGAAGTCTAG
12490353 GTGGATTTGTCCTTAA
1 GTGGATTTGTCCTTAA
12490369 GTGGATTTGTCCTTAA
1 GTGGATTTGTCCTTAA
12490385 GT
1 GT
12490387 ATTGTCTCAA
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:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (16 bp):
GTGGATTTGTCCTTAA
Found at i:12493823 original size:55 final size:53
Alignment explanation
Indices: 12493704--12493832 Score: 134
Period size: 55 Copynumber: 2.4 Consensus size: 53
12493694 TGCGACATGG
* * *
12493704 CCGTGGGTGAACCTGCCAAAACAACACGGGCATTCGACACGCCCGTGCCTCGAAA
1 CCGTGGGTGAACCTGTC-AAACAACACGGGCATGCGACACACCCGTGCCTC-AAA
* * * * *
12493759 CCATAGGTGAACCTGTCAAACTAGCACGGGTATGCGACACACCCGTGCC-CATCAT
1 CCGTGGGTGAACCTGTCAAAC-AACACGGGCATGCGACACACCCGTGCCTCA--AA
12493814 CCGTGGGTGAACCTGTCAA
1 CCGTGGGTGAACCTGTCAA
12493833 GTTAACACGG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
53 1 0.02
54 5 0.08
55 55 0.90
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (53 bp):
CCGTGGGTGAACCTGTCAAACAACACGGGCATGCGACACACCCGTGCCTCAAA
Found at i:12500905 original size:16 final size:16
Alignment explanation
Indices: 12500884--12500919 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
12500874 ATGATATGAG
*
12500884 AAGATTATTTGAGAAT
1 AAGATTATTTGAGAAA
12500900 AAGATTATTTGAGAAA
1 AAGATTATTTGAGAAA
12500916 AAGA
1 AAGA
12500920 CAAAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (16 bp):
AAGATTATTTGAGAAA
Found at i:12501436 original size:25 final size:26
Alignment explanation
Indices: 12501387--12501444 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
12501377 ATGAAACCTA
*
12501387 AAAATGAAATAGTATTAAATGAAGAT
1 AAAATGAAAAAGTATTAAATGAAGAT
12501413 AAAAT-AAAAAGTACTTAAAT-AAGAT
1 AAAATGAAAAAGTA-TTAAATGAAGAT
12501438 -AAATGAA
1 AAAATGAA
12501445 GATAAAAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.14
25 14 0.48
26 11 0.38
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (26 bp):
AAAATGAAAAAGTATTAAATGAAGAT
Found at i:12512276 original size:46 final size:46
Alignment explanation
Indices: 12512099--12512280 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
12512089 TTTGACATGA
* * * * * * *
12512099 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
** * *
12512145 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
12512191 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
12512237 TGCCATGGTATCTTTCAACCATTGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
12512281 AGAGCACACT
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 120 0.97
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:12514236 original size:20 final size:20
Alignment explanation
Indices: 12514208--12514247 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12514198 ACACCTTTGA
12514208 TTTTCCTTTTTC-TTCTTTC
1 TTTTCCTTTTTCTTTCTTTC
12514227 TTTTCTCTTTTTCTTTCTTTC
1 TTTTC-CTTTTTCTTTCTTTC
12514248 CTTCCCCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCCTTTTTCTTTCTTTC
Found at i:12514302 original size:29 final size:30
Alignment explanation
Indices: 12514269--12514330 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
12514259 TTCTGTTTCG
12514269 TTTGCTTTGTTTCTTTATTTC-TCTCCTTT
1 TTTGCTTTGTTTCTTTATTTCTTCTCCTTT
* * *
12514298 TTTGCTTTTTTTCTTTTTTTCTTTTCCTTT
1 TTTGCTTTGTTTCTTTATTTCTTCTCCTTT
12514328 TTT
1 TTT
12514331 TATATATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.76
Consensus pattern (30 bp):
TTTGCTTTGTTTCTTTATTTCTTCTCCTTT
Found at i:12516808 original size:46 final size:44
Alignment explanation
Indices: 12516755--12516923 Score: 173
Period size: 46 Copynumber: 3.7 Consensus size: 44
12516745 ATTGTGGGCT
* *
12516755 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCAT-TGA-GAGAGCC
*
12516801 AGTGTAAGACCATGTCTAGGACATGGCATCGG-CATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCATTGAGA-GA--GCC
*
12516849 AGTGTAAGACATGTCT-GTGACATGCATCGGCC-TTGGGACGTAAGCC
1 AGTGTAAGACATGTCTAG-GACATGCATCGGCCATTGAGA-G--AGCC
*
12516895 AGTGTAAGACATGTCTAGGACATGTATCG
1 AGTGTAAGACATGTCTAGGACATGCATCG
12516924 ACTACGAAAT
Statistics
Matches: 107, Mismatches: 6, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
45 2 0.02
46 56 0.52
47 30 0.28
48 19 0.18
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCATTGAGAGAGCC
Found at i:12517001 original size:50 final size:49
Alignment explanation
Indices: 12516939--12517068 Score: 147
Period size: 49 Copynumber: 2.6 Consensus size: 49
12516929 GAAATGTGTC
* * * *
12516939 AGTGTAAGACCATGCCTAGGACATGGCGTTGG-CACGGAT-ATGTGAGAGCT
1 AGTGTAAAACCATGTCTAGGACATGGCATCGGCCACGG-TGA--TGAGAGCT
* * *
12516989 AGTGTAAAACCATGTCTGGGACATGGCATCGGCCTCGGTGATGATAGCT
1 AGTGTAAAACCATGTCTAGGACATGGCATCGGCCACGGTGATGAGAGCT
*
12517038 AGTGTAAAACCATGTCTAAGACATGGCATCG
1 AGTGTAAAACCATGTCTAGGACATGGCATCG
12517069 ACAACTTGCC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
49 36 0.52
50 28 0.41
51 5 0.07
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (49 bp):
AGTGTAAAACCATGTCTAGGACATGGCATCGGCCACGGTGATGAGAGCT
Found at i:12525740 original size:9 final size:9
Alignment explanation
Indices: 12525726--12525767 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
12525716 ATAATAAAAG
12525726 AAGAAAGCA
1 AAGAAAGCA
*
12525735 AAGAAAGTA
1 AAGAAAGCA
* *
12525744 AAAAAAACA
1 AAGAAAGCA
12525753 AAGAAA-CA
1 AAGAAAGCA
12525761 AAGAAAG
1 AAGAAAG
12525768 AACAAGCAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.74, C:0.07, G:0.17, T:0.02
Consensus pattern (9 bp):
AAGAAAGCA
Found at i:12529987 original size:30 final size:30
Alignment explanation
Indices: 12529953--12530013 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12529943 TCCTTAACTC
12529953 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
12529983 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
12530013 A
1 A
12530014 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:12533057 original size:20 final size:20
Alignment explanation
Indices: 12533032--12533077 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12533022 ATAACCGATT
12533032 ATATATATATGTACATGAAC
1 ATATATATATGTACATGAAC
* *
12533052 ATATATATATGTTCATGTAC
1 ATATATATATGTACATGAAC
12533072 ATATAT
1 ATATAT
12533078 TTGTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
ATATATATATGTACATGAAC
Found at i:12533075 original size:18 final size:19
Alignment explanation
Indices: 12533034--12533082 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
12533024 AACCGATTAT
*
12533034 ATATATATGTACATGAACA
1 ATATATATGTTCATGAACA
*
12533053 TATATATATGTTCATGTAC-
1 -ATATATATGTTCATGAACA
*
12533072 ATATATTTGTT
1 ATATATATGTT
12533083 TTTATCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (19 bp):
ATATATATGTTCATGAACA
Found at i:12533381 original size:56 final size:55
Alignment explanation
Indices: 12533321--12533472 Score: 232
Period size: 56 Copynumber: 2.7 Consensus size: 55
12533311 CAGACAGGGT
* *
12533321 CTTACTTACACACATATATCAGAATCACATATCGATGCCAACGTATGAAACGTGGA
1 CTTACTTGCACACATATATC-GAATCACATATCGATGCCAACGTATGAAACATGGA
* *
12533377 CTTACTCGCACACATATATCGATATCACATATCGATGCCAATGTATGAAACATGGA
1 CTTACTTGCACACATATATCGA-ATCACATATCGATGCCAACGTATGAAACATGGA
*
12533433 CTCACTTGCACACATATATCGGAATCACATATCGATGCCA
1 CTTACTTGCACACATATATC-GAATCACATATCGATGCCA
12533473 CATATACTTC
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
55 2 0.02
56 84 0.95
57 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (55 bp):
CTTACTTGCACACATATATCGAATCACATATCGATGCCAACGTATGAAACATGGA
Found at i:12535111 original size:20 final size:19
Alignment explanation
Indices: 12535069--12535142 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
12535059 TGTTACACGG
*
12535069 ATGAATTACT-GTTATATGA
1 ATGAATTACTATTTATA-GA
*
12535088 ATGAAATACTATTTATAGA
1 ATGAATTACTATTTATAGA
* *
12535107 GATGAGTTACTA-TTATCGA
1 -ATGAATTACTATTTATAGA
*
12535126 ATGAATTACTGTTTATA
1 ATGAATTACTATTTATA
12535143 TGATTGAGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
18 9 0.20
19 21 0.48
20 14 0.32
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (19 bp):
ATGAATTACTATTTATAGA
Found at i:12535141 original size:38 final size:39
Alignment explanation
Indices: 12535068--12535142 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
12535058 GTGTTACACG
* *
12535068 GATGAATTACTGTTATATGAATGAAATACTATTTATAGA
1 GATGAATTACTATTATACGAATGAAATACTATTTATAGA
* * *
12535107 GATGAGTTACTATTAT-CGAATGAATTACTGTTTATA
1 GATGAATTACTATTATACGAATGAAATACTATTTATA
12535143 TGATTGAGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 17 0.55
39 14 0.45
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (39 bp):
GATGAATTACTATTATACGAATGAAATACTATTTATAGA
Found at i:12537608 original size:26 final size:25
Alignment explanation
Indices: 12537571--12537644 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 25
12537561 TGAATGTCTG
12537571 TAAAT-AT-TATGAATAAAATAATAA
1 TAAATGATATATG-ATAAAATAATAA
12537595 TAAATGATATATGATAAAAT-A-AA
1 TAAATGATATATGATAAAATAATAA
* *
12537618 TAATTGATA-AT-ATAAAATAATAG
1 TAAATGATATATGATAAAATAATAA
12537641 TAAA
1 TAAA
12537645 ATTAATTACA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
21 7 0.16
22 3 0.07
23 14 0.33
24 6 0.14
25 9 0.21
26 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (25 bp):
TAAATGATATATGATAAAATAATAA
Found at i:12537627 original size:16 final size:17
Alignment explanation
Indices: 12537606--12537638 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12537596 AAATGATATA
12537606 TGATAAAAT-AAATAAT
1 TGATAAAATAAAATAAT
*
12537622 TGATAATATAAAATAAT
1 TGATAAAATAAAATAAT
12537639 AGTAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
TGATAAAATAAAATAAT
Found at i:12540057 original size:12 final size:12
Alignment explanation
Indices: 12540040--12540064 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12540030 AGATGTGTGT
12540040 TGAGAATGTGCC
1 TGAGAATGTGCC
12540052 TGAGAATGTGCC
1 TGAGAATGTGCC
12540064 T
1 T
12540065 TAGACTTGCT
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:0.16, G:0.32, T:0.28
Consensus pattern (12 bp):
TGAGAATGTGCC
Found at i:12542252 original size:11 final size:11
Alignment explanation
Indices: 12542236--12542262 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12542226 CAAAATGCTC
12542236 AAATTAGGCTA
1 AAATTAGGCTA
12542247 AAATTAGGCTA
1 AAATTAGGCTA
12542258 AAATT
1 AAATT
12542263 TGTTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (11 bp):
AAATTAGGCTA
Found at i:12542734 original size:18 final size:18
Alignment explanation
Indices: 12542707--12542749 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
12542697 AATTTTCATT
*
12542707 TAAAATATTTAAAAATAA
1 TAAAAAATTTAAAAATAA
* * *
12542725 TAAAAAATTTTAAACTTA
1 TAAAAAATTTAAAAATAA
12542743 TAAAAAA
1 TAAAAAA
12542750 ATAGAATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAATTTAAAAATAA
Found at i:12542781 original size:17 final size:17
Alignment explanation
Indices: 12542743--12542782 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
12542733 TTTAAACTTA
12542743 TAAAAAAATAGAATTTC
1 TAAAAAAATAGAATTTC
* *
12542760 AAAAAAAATAGAATTTT
1 TAAAAAAATAGAATTTC
12542777 TAAAAA
1 TAAAAA
12542783 TATATGGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (17 bp):
TAAAAAAATAGAATTTC
Found at i:12542894 original size:19 final size:19
Alignment explanation
Indices: 12542872--12542981 Score: 52
Period size: 18 Copynumber: 5.7 Consensus size: 19
12542862 ATAAAAAGGA
12542872 AAAATTATAAAAATATATT
1 AAAATTATAAAAATATATT
* *
12542891 AAAATTTATTTAAAATAATATA
1 AAAA-TTA-TAAAAAT-ATATT
* *
12542913 AAAATGTA-AAAACT-TATA
1 AAAAT-TATAAAAATATATT
** *
12542931 AAAATTGCAAACA-ATATT
1 AAAATTATAAAAATATATT
12542949 AAAA--ATAGAAAAT-TATT
1 AAAATTATA-AAAATATATT
12542966 AAAAATTATATAAAAT
1 -AAAATTATA-AAAAT
12542982 TATGAAAAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
16 1 0.01
17 8 0.12
18 23 0.34
19 4 0.06
20 15 0.22
21 7 0.10
22 10 0.15
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAAATATATT
Found at i:12542982 original size:20 final size:19
Alignment explanation
Indices: 12542871--12542990 Score: 79
Period size: 20 Copynumber: 6.3 Consensus size: 19
12542861 TATAAAAAGG
12542871 AAAAATTATAAAAATATATT
1 AAAAATTATAAAAAT-TATT
* * *
12542891 AAAATTTATTTAAAATAATAT
1 AAAAATTA-TAAAAATTAT-T
*
12542912 AAAAATGTA-AAAACTTA-T
1 AAAAAT-TATAAAAATTATT
**
12542930 AAAAATTGCAAACAA-TATT
1 AAAAATTATAAA-AATTATT
*
12542949 AAAAA-TA-GAAAATTATT
1 AAAAATTATAAAAATTATT
*
12542966 AAAAATTATATAAAATTATG
1 AAAAATTATA-AAAATTATT
12542986 AAAAA
1 AAAAA
12542991 GAATCAGCAT
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
16 2 0.03
17 12 0.16
18 15 0.19
19 7 0.09
20 27 0.35
21 12 0.16
22 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATTATAAAAATTATT
Done.