Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 170 of 279
Found at i:56500468 original size:39 final size:39
Alignment explanation
Indices: 56500425--56500501 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
56500415 CTGTTCTCAC
*
56500425 CAGATTCGGCAGCAACAGAACTTGAGCCTCTAAATGAAT
1 CAGATTCGGCAGCAACAGAACCTGAGCCTCTAAATGAAT
56500464 CAGATTCGGCAGCAACAGAACCTGAGCCTCTAAATGAA
1 CAGATTCGGCAGCAACAGAACCTGAGCCTCTAAATGAA
56500502 CACTTGGCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (39 bp):
CAGATTCGGCAGCAACAGAACCTGAGCCTCTAAATGAAT
Found at i:56502320 original size:21 final size:21
Alignment explanation
Indices: 56502295--56502343 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
56502285 TAGCGGTGGA
*
56502295 GGTGAGAATAGTTACTGTAGC
1 GGTGAGAATAGATACTGTAGC
* *
56502316 GGTGAGATTGGATACTGTAGC
1 GGTGAGAATAGATACTGTAGC
56502337 GGTGAGA
1 GGTGAGA
56502344 TTAAAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.39, T:0.27
Consensus pattern (21 bp):
GGTGAGAATAGATACTGTAGC
Found at i:56509494 original size:34 final size:32
Alignment explanation
Indices: 56509420--56509494 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 32
56509410 AAAAATTGAA
*
56509420 ATAATT-ATAAATAAATAAATTTAAAATATTT
1 ATAATTAATAAATAAATAAATTTAAAAGATTT
*
56509451 ATCATTTAATATAATAAAT-AATTTAAAACGATTTT
1 AT-AATTAATA-AATAAATAAATTTAAAA-GA-TTT
56509486 ATAATTAAT
1 ATAATTAAT
56509495 TAAAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
31 2 0.06
32 3 0.08
33 12 0.33
34 14 0.39
35 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (32 bp):
ATAATTAATAAATAAATAAATTTAAAAGATTT
Found at i:56516913 original size:5 final size:5
Alignment explanation
Indices: 56516903--56516951 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
56516893 TTATTTTGGT
* * *
56516903 ATCAG ATCAG ATCAA ATCAG ATCAG ATGAG ATGAG ATCAG ATCAG ATCA
1 ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCA
56516952 TTATCTTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (5 bp):
ATCAG
Found at i:56522503 original size:15 final size:15
Alignment explanation
Indices: 56522480--56522510 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56522470 AAATTAGGAT
56522480 AACAACAAGACATAA
1 AACAACAAGACATAA
*
56522495 AACATCAAGACATAA
1 AACAACAAGACATAA
56522510 A
1 A
56522511 GAAACTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.10
Consensus pattern (15 bp):
AACAACAAGACATAA
Found at i:56524613 original size:28 final size:29
Alignment explanation
Indices: 56524584--56524697 Score: 81
Period size: 29 Copynumber: 3.8 Consensus size: 29
56524574 TATTTAAGTT
56524584 AAATTATAATTAAAAATATTTTTATATTA
1 AAATTATAATTAAAAATATTTTTATATTA
* * *
56524613 AAATTTTATTATTAAAAAAATTATATCATATT-
1 AAA--TTATAATTAAAAATATT-T-TTATATTA
* * * *
56524645 AAATAACAA-TAAAAATCGTTATTATATTA
1 AAATTATAATTAAAAAT-ATTTTTATATTA
*
56524674 AAATTATAA-TAAAATTAATTTTTA
1 AAATTATAATTAAAAAT-ATTTTTA
56524698 AAAAAAAATT
Statistics
Matches: 63, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
28 6 0.10
29 27 0.43
30 5 0.08
31 15 0.24
32 4 0.06
33 6 0.10
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
AAATTATAATTAAAAATATTTTTATATTA
Found at i:56524997 original size:26 final size:26
Alignment explanation
Indices: 56524967--56525020 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
56524957 ATTCTTTTAA
56524967 AAATATGATGTGACATATTTTTATTG
1 AAATATGATGTGACATATTTTTATTG
56524993 AAATATGATGTGACATATTTTTATTG
1 AAATATGATGTGACATATTTTTATTG
56525019 AA
1 AA
56525021 TACATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (26 bp):
AAATATGATGTGACATATTTTTATTG
Found at i:56526918 original size:23 final size:23
Alignment explanation
Indices: 56526892--56526943 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
56526882 TTTTATACTT
56526892 TTTCAAATATATATCATATCAAA
1 TTTCAAATATATATCATATCAAA
56526915 TTTCAAATATATATCATATCAAA
1 TTTCAAATATATATCATATCAAA
*
56526938 TCTCAA
1 TTTCAA
56526944 CTAGTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTCAAATATATATCATATCAAA
Found at i:56528479 original size:27 final size:26
Alignment explanation
Indices: 56528419--56528479 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
56528409 AGAAAAAAGG
* *
56528419 TTATAAAATATATACATGTACATATA
1 TTATAAAATATATACATATACATAGA
* * *
56528445 TAAAAAAATTATATACATATATATAGA
1 TTATAAAA-TATATACATATACATAGA
56528472 TTATAAAA
1 TTATAAAA
56528480 AAGATAATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (26 bp):
TTATAAAATATATACATATACATAGA
Found at i:56528479 original size:30 final size:30
Alignment explanation
Indices: 56528443--56528499 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56528433 CATGTACATA
*
56528443 TATAAAAAA-ATTATATACATATATATAGAT
1 TATAAAAAAGATAAT-TACATATATATAGAT
56528473 TATAAAAAAGATAATTACATATATATA
1 TATAAAAAAGATAATTACATATATATA
56528500 AACAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (30 bp):
TATAAAAAAGATAATTACATATATATAGAT
Found at i:56528684 original size:17 final size:17
Alignment explanation
Indices: 56528662--56528705 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
56528652 TAGGAAATAA
56528662 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
56528679 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
56528696 -ATATGTATAT
1 AAAATGTATAT
56528706 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:56528841 original size:3 final size:3
Alignment explanation
Indices: 56528833--56528857 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56528823 ATATATAGTT
56528833 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
56528858 CTTAATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:56528900 original size:7 final size:7
Alignment explanation
Indices: 56528881--56528910 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
56528871 AAATCAAATT
56528881 TAATAAA
1 TAATAAA
56528888 -AATAAA
1 TAATAAA
56528894 TAATAAA
1 TAATAAA
56528901 TAATAAA
1 TAATAAA
56528908 TAA
1 TAA
56528911 AAAAAGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAATAAA
Found at i:56529254 original size:14 final size:12
Alignment explanation
Indices: 56529221--56529246 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56529211 GATTGCATAT
56529221 ATCATATCTAAG
1 ATCATATCTAAG
56529233 ATCATATCTAAG
1 ATCATATCTAAG
56529245 AT
1 AT
56529247 TACATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:56529843 original size:37 final size:37
Alignment explanation
Indices: 56529791--56529863 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
56529781 TTGCTTTCTC
* * *
56529791 AGTCTGCTCCTCTGCAACTTCAGGGAGATAAGACTAG
1 AGTCTGCTCCACTGCAACTTCAGGAAAATAAGACTAG
56529828 AGTCTGCTCCACTGCAACTTCAGGAAAATAAGACTA
1 AGTCTGCTCCACTGCAACTTCAGGAAAATAAGACTA
56529864 TATACGATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (37 bp):
AGTCTGCTCCACTGCAACTTCAGGAAAATAAGACTAG
Found at i:56530387 original size:35 final size:35
Alignment explanation
Indices: 56530338--56530407 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
56530328 ATCTGCTATT
*
56530338 TTCAACCTACTCCACTATTG-CTCAGGGAGATAGGA
1 TTCAACCTACTCCACTACTGAC-CAGGGAGATAGGA
* *
56530373 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA
1 TTCAACCTACTCCACTACTGACCAGGGAGATAGGA
56530408 CCTACAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (35 bp):
TTCAACCTACTCCACTACTGACCAGGGAGATAGGA
Found at i:56530427 original size:44 final size:43
Alignment explanation
Indices: 56530373--56530538 Score: 208
Period size: 44 Copynumber: 3.8 Consensus size: 43
56530363 GGAGATAGGA
56530373 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACCTACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-CTACAATC
* * * *
56530417 TTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCT-CAATT
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA--CTACAATC
* * *
56530461 TTCAACCTATTCCACTGTTGACCAGGGAGATAGGATTCACCATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACT-ACAATC
* *
56530505 TTTAACCTATTCCACTGCTGACCAGGGGGATAGG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGG
56530539 GTTGGGGTCA
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.01
44 101 0.97
45 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTACAATC
Found at i:56530522 original size:88 final size:88
Alignment explanation
Indices: 56530373--56530537 Score: 251
Period size: 88 Copynumber: 1.9 Consensus size: 88
56530363 GGAGATAGGA
* *
56530373 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAACCTATTCCACTGCTGA
56530438 CCAGGGAGATAGAATTCTCAATT
66 CCAGGGAGATAGAATTCTCAATT
* * * *
56530461 TTCAACCTATTCCACTGTTGACCAGGGAGATAGGA-TTCACCATCTTTAACCTATTCCACTGCTG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACCT-ACAATCTTCAACCTATTCCACTGCTG
*
56530525 ACCAGGGGGATAG
65 ACCAGGGAGATAG
56530538 GGTTGGGGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 1 0.01
88 68 0.99
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (88 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAACCTATTCCACTGCTGA
CCAGGGAGATAGAATTCTCAATT
Found at i:56530600 original size:88 final size:88
Alignment explanation
Indices: 56530549--56531113 Score: 896
Period size: 88 Copynumber: 6.4 Consensus size: 88
56530539 GTTGGGGTCA
* *
56530549 TCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
56530614 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
56530637 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGAAAGATCTGCTATTTTTAACCTGCTTCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
56530702 CCAGGGAGGTAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
56530725 TCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
56530790 CCAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
56530813 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCAATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
56530878 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * * *
56530901 TCAATCTGTTTCGCTGTCGGTGCAGAAAAGCAAGATCTGCTTTTTTTAACCTGCTCCACTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* *
56530966 CTAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
56530989 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* * *
56531054 CCAGAGAAGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
56531077 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATC
56531114 CGTTATCTTC
Statistics
Matches: 432, Mismatches: 45, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 432 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:56530626 original size:44 final size:44
Alignment explanation
Indices: 56530571--56531066 Score: 171
Period size: 44 Copynumber: 11.3 Consensus size: 44
56530561 GCTGTCGGTA
*
56530571 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACC
* * * * * ** * * ****
56530615 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCT-ACAACC
* *
56530659 CAGGAAGGAAAGATCTGCTATTTTTAACCTGCTTCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACC
* * * * * * ** * ***
56530703 CAGGGAGGTAAG-GCTGGTGTCTTCGATCTGCTTCGCTATCAGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTA-CAACC
* *
56530747 CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACC
* * * * ** * * * **
56530791 CAGGGAGGCAAG-GCTAG-TGTCTTCGATCTGCTTCGCTGTCGATG
1 CAGGAAGGCAAGATCT-GCTATTTTTAACCTGCTTCGCT-ACAACC
* * *
56530835 CAGGAAGGCAAGATCTGCAATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACC
* * * * * * * * * ****
56530879 CAGGGAGGCAAG-GCTGGTGTCTTCAATCTGTTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCT-ACAACC
* * * * * *
56530923 CAGAAAAGCAAGATCTGCTTTTTTTAACCTGCTCCACTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACC
* * * * * ** * * * **
56530967 TAGGGAGGCAAG-GCTAG-TGTCTTCGATCTGCTTCGCTGTCGATG
1 CAGGAAGGCAAGATCT-GCTATTTTTAACCTGCTTCGCT-ACAACC
* *
56531011 CAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACC
56531055 CAGAGAA-GCAAG
1 CAG-GAAGGCAAG
56531067 GTTGGTGTCT
Statistics
Matches: 294, Mismatches: 143, Indels: 30
0.63 0.31 0.06
Matches are distributed among these distances:
43 81 0.28
44 129 0.44
45 84 0.29
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACC
Found at i:56533307 original size:25 final size:26
Alignment explanation
Indices: 56533256--56533309 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
56533246 AAGAAAATCC
* **
56533256 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
56533282 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
56533307 AAA
1 AAA
56533310 TTGAATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.59, C:0.06, G:0.13, T:0.22
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:56537212 original size:25 final size:23
Alignment explanation
Indices: 56537185--56537235 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
56537175 GGTACAACAT
* *
56537185 ATATACATGTACATATATAAAAA
1 ATATATATATACATATATAAAAA
* *
56537208 ATATATATATACATATATATAGA
1 ATATATATATACATATATAAAAA
56537231 ATATA
1 ATATA
56537236 AAAAAGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATATATATACATATATAAAAA
Found at i:56537240 original size:32 final size:30
Alignment explanation
Indices: 56537199--56537284 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 30
56537189 ACATGTACAT
*
56537199 ATATAAAAAATATATATATACATATATATAGA
1 ATATAAAAAAGATA-AT-TACATATATATAGA
56537231 ATATAAAAAAGATAATTACATATATAT---
1 ATATAAAAAAGATAATTACATATATATAGA
*
56537258 ATATAAACAAATAATAATTACATATAT
1 ATATAAA-AAA-GATAATTACATATAT
56537285 TAAAATTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.14
28 3 0.06
29 14 0.28
30 11 0.22
31 2 0.04
32 13 0.26
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (30 bp):
ATATAAAAAAGATAATTACATATATATAGA
Found at i:56537596 original size:3 final size:3
Alignment explanation
Indices: 56537588--56537629 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
56537578 GTATATATAG
* *
56537588 TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56537630 CTTAATAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:56544149 original size:19 final size:19
Alignment explanation
Indices: 56544122--56544159 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
56544112 AAATATATAT
*
56544122 TTTTTATTTTTAATTTTAA
1 TTTTAATTTTTAATTTTAA
56544141 TTTTAATTTTTAATTTTAA
1 TTTTAATTTTTAATTTTAA
56544160 AATACTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTAATTTTTAATTTTAA
Found at i:56544151 original size:7 final size:7
Alignment explanation
Indices: 56544120--56544157 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
56544110 ATAAATATAT
*
56544120 ATTTTTT
1 ATTTTTA
56544127 ATTTTTA
1 ATTTTTA
56544134 A-TTTTA
1 ATTTTTA
56544140 A-TTTTA
1 ATTTTTA
56544146 ATTTTTA
1 ATTTTTA
56544153 ATTTT
1 ATTTT
56544158 AAAATACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:56544158 original size:13 final size:13
Alignment explanation
Indices: 56544122--56544159 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
56544112 AAATATATAT
*
56544122 TTTTTATTTTTAA
1 TTTTTAATTTTAA
56544135 -TTTTAATTTTAA
1 TTTTTAATTTTAA
56544147 TTTTTAATTTTAA
1 TTTTTAATTTTAA
56544160 AATACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTAATTTTAA
Found at i:56544159 original size:6 final size:6
Alignment explanation
Indices: 56544123--56544159 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
56544113 AATATATATT
*
56544123 TTTTAT TTTTAA TTTTAA TTTTAA TTTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTTTAA
56544160 AATACTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:56544217 original size:26 final size:27
Alignment explanation
Indices: 56544165--56544227 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
56544155 TTTAAAATAC
* *
56544165 TTTTAAAATAAATTTTTCTATTTTTTAT
1 TTTTAAAAT-AATTTTTCTAATGTTTAT
*
56544193 TTTTAAAAT-ATTTTTTTAATGTTTAT
1 TTTTAAAATAATTTTTCTAATGTTTAT
*
56544219 TTTAAAAAT
1 TTTTAAAAT
56544228 GGGCTGGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.71
28 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTAAAATAATTTTTCTAATGTTTAT
Found at i:56545255 original size:9 final size:9
Alignment explanation
Indices: 56545241--56545269 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
56545231 TGAACAATTC
56545241 AATAATATA
1 AATAATATA
56545250 AATAATATA
1 AATAATATA
56545259 AATAATATA
1 AATAATATA
56545268 AA
1 AA
56545270 ATGTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:56545811 original size:9 final size:9
Alignment explanation
Indices: 56545797--56545834 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
56545787 TTATAGTTTG
56545797 TTATTCGAA
1 TTATTCGAA
56545806 TTATTCGAA
1 TTATTCGAA
*
56545815 TTATTCGAG
1 TTATTCGAA
56545824 TTATTCGAA
1 TTATTCGAA
56545833 TT
1 TT
56545835 TGAAAACTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:56551045 original size:35 final size:34
Alignment explanation
Indices: 56550996--56551075 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
56550986 TGTTTAATAA
* *
56550996 TATATAATTAATGATATTTAAA-TATAATTTATAT
1 TATATAATTAATGATAATTAAATTATAA-TGATAT
*
56551030 TATATGAATTTATGATAATTAAATTATAATGATAT
1 TATAT-AATTAATGATAATTAAATTATAATGATAT
*
56551065 TATATTATTAA
1 TATATAATTAA
56551076 ATGAATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
34 9 0.23
35 25 0.64
36 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (34 bp):
TATATAATTAATGATAATTAAATTATAATGATAT
Found at i:56551061 original size:25 final size:23
Alignment explanation
Indices: 56551017--56551077 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
56551007 TGATATTTAA
*
56551017 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
56551041 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
56551066 ATATTATTAAAT
1 ATATAATTAAAT
56551078 GAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:56551446 original size:35 final size:35
Alignment explanation
Indices: 56551402--56551470 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
56551392 TTTGTTTAAT
* *
56551402 AATTAATGATATTTAAA-TATAATTTATATTATATG
1 AATTAATGATAATTAAATTATAA-TGATATTATATG
*
56551437 AATTTATGATAATTAAATTATAATGATATTATAT
1 AATTAATGATAATTAAATTATAATGATATTATAT
56551471 TATTAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (35 bp):
AATTAATGATAATTAAATTATAATGATATTATATG
Found at i:56551462 original size:25 final size:23
Alignment explanation
Indices: 56551418--56551478 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
56551408 TGATATTTAA
*
56551418 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
56551442 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
56551467 ATATTATTAAAT
1 ATATAATTAAAT
56551479 GAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:56552747 original size:39 final size:40
Alignment explanation
Indices: 56552704--56552791 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 40
56552694 TGAATTATAG
* * * *
56552704 AATACTGGATATTGTTTTGAGTACTG-AGTGAATTGTGAA
1 AATACTGAATATAGTTATGAGTAATGCAGTGAATTGTGAA
* * *
56552743 AATACTAAATATAGTTATGTGTAATGCATTGAATTGTGAA
1 AATACTGAATATAGTTATGAGTAATGCAGTGAATTGTGAA
*
56552783 ATTACTGAA
1 AATACTGAA
56552792 GTAATAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
39 20 0.51
40 19 0.49
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (40 bp):
AATACTGAATATAGTTATGAGTAATGCAGTGAATTGTGAA
Found at i:56553066 original size:45 final size:45
Alignment explanation
Indices: 56552998--56553097 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
56552988 GCCGACTACT
* ** *
56552998 GTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTCACC
* *
56553043 GTTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGTCACT
1 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTCACC
*
56553088 GCTACTGTTA
1 GTTACTGTTA
56553098 TTGCTACCGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTCACC
Found at i:56555955 original size:14 final size:14
Alignment explanation
Indices: 56555938--56555966 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56555928 TCAATTCTTT
56555938 CTTCATCAAATATC
1 CTTCATCAAATATC
56555952 CTTCATCAAATATC
1 CTTCATCAAATATC
56555966 C
1 C
56555967 AACAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (14 bp):
CTTCATCAAATATC
Found at i:56563180 original size:16 final size:16
Alignment explanation
Indices: 56563140--56563182 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
56563130 TTAGTATTTT
56563140 AGAAAAAAATATATGAA
1 AGAAAAAAA-ATATGAA
* * *
56563157 ACACAAAAAATGTGAA
1 AGAAAAAAAATATGAA
56563173 AGAAAAAAAA
1 AGAAAAAAAA
56563183 AATGGAAGCA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.12
Consensus pattern (16 bp):
AGAAAAAAAATATGAA
Found at i:56567835 original size:22 final size:22
Alignment explanation
Indices: 56567805--56567847 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56567795 ACACCAAAAC
*
56567805 AGGCTTTTAGCGGCACTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
*
56567827 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCACTTTTT
56567848 AGAGCCACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:56568061 original size:43 final size:43
Alignment explanation
Indices: 56568014--56568152 Score: 183
Period size: 43 Copynumber: 3.2 Consensus size: 43
56568004 AGAGTAATAC
*
56568014 CTTTAGCGGCGTTTTTGGTATAAGCGCCGCTATAGAAT-AGGGT
1 CTTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAG-ATCAGGGT
*
56568057 CTTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAAGGT
1 CTTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGT
* * ***
56568100 CTTTAGTGGCGTTTGTGACCGAAA-CGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTG-GTAAAAGCGCCGCTATAGATCAGGGT
56568143 CTTTAGCGGC
1 CTTTAGCGGC
56568153 ACTTTTCCCA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
42 2 0.02
43 80 0.94
44 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGT
Found at i:56568172 original size:43 final size:41
Alignment explanation
Indices: 56568038--56568178 Score: 113
Period size: 43 Copynumber: 3.3 Consensus size: 41
56568028 TTGGTATAAG
* ***
56568038 CGCCGCTATAGAAT-AGGGTCTTTAGCGGCGTTTTTGGTAAAA
1 CGCCGCTATAG-ATCAGGGTCTTTAGCGGC-CTTTTACCAAAA
* * * *
56568080 GCGCCGCTATAGATCAAGGTCTTTAGTGGCGTTTGTGACCGAAA
1 -CGCCGCTATAGATCAGGGTCTTTAGCGGCCTTT-T-ACCAAAA
*
56568124 CGCCGCTATAGATCAGGGTCTTTAGCGGCACTTTTCCCACAAA
1 CGCCGCTATAGATCAGGGTCTTTAGCGGC-CTTTTACCA-AAA
* *
56568167 TGCCGCAATAGA
1 CGCCGCTATAGA
56568179 CCCTGATCTA
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
42 7 0.09
43 66 0.84
44 6 0.08
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (41 bp):
CGCCGCTATAGATCAGGGTCTTTAGCGGCCTTTTACCAAAA
Found at i:56568193 original size:43 final size:43
Alignment explanation
Indices: 56568146--56568262 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
56568136 TCAGGGTCTT
* * *
56568146 TAGCGGCACTTTTCCCACAAATGCCGC-AATAGACCCTGATCTA
1 TAGCGGCGCTTTTACCACAAACGCCGCTAA-AGACCCTGATCTA
**** *
56568189 TAGCGGCGCTTCGGTCACAAACGCCACTAAAGACCCTGATCTA
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATCTA
*
56568232 TAGCGGCGCTTTTACCAAAAACGCCGCTAAA
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAA
56568263 TTTGGCAGAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 58 0.97
44 2 0.03
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.21
Consensus pattern (43 bp):
TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATCTA
Found at i:56568661 original size:21 final size:21
Alignment explanation
Indices: 56568566--56568658 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
56568556 TTTGACGCTG
*
56568566 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
**
56568587 CTCTACTTCCCTCGCTTTAGC
1 CTCTACTTCCCTCGCTGCAGC
*
56568608 CTCTACTTCCCTC-TTAGCAGC
1 CTCTACTTCCCTCGCT-GCAGC
* * *
56568629 CTGTACTTCTCTCGCTGCCGC
1 CTCTACTTCCCTCGCTGCAGC
*
56568650 CTCTGCTTC
1 CTCTACTTC
56568659 TCTTGTTGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.08, C:0.44, G:0.14, T:0.34
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:56568668 original size:21 final size:21
Alignment explanation
Indices: 56568634--56568677 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
56568624 GCAGCCTGTA
*
56568634 CTTCTCTCGCTGCCGCCTCTG
1 CTTCTCTCGCTGCCGCATCTG
* *
56568655 CTTCTCTTGTTGCCGCATCTG
1 CTTCTCTCGCTGCCGCATCTG
56568676 CT
1 CT
56568678 CTAAGCTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.41, G:0.18, T:0.39
Consensus pattern (21 bp):
CTTCTCTCGCTGCCGCATCTG
Found at i:56568739 original size:66 final size:66
Alignment explanation
Indices: 56568649--56568795 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
56568639 CTCGCTGCCG
* * *
56568649 CCTCTGCTTCTCTTGTTGCCGCATCTGCTCTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTG-TAGCTGGAGTTCTTCATATC-TTCGTT
56568712 GAA
64 GAA
* * * *
56568715 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTCTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTCGTTGA
56568780 A
66 A
*
56568781 CATCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
56568796 ATGTTGCCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 69 0.97
67 1 0.01
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTCGTTGA
A
Found at i:56568811 original size:66 final size:66
Alignment explanation
Indices: 56568688--56568818 Score: 192
Period size: 66 Copynumber: 2.0 Consensus size: 66
56568678 CTAAGCTGCT
* * *
56568688 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
56568753 A
66 A
* * *
56568754 GCTGGAGTTCTTCATA-TCTTCTTTGAACATCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTG
1 GCTGGAGTTCTTCATACT-TTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG
56568818 T
65 T
56568819 GTAATTTGCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 1 0.02
66 57 0.98
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:56570179 original size:9 final size:9
Alignment explanation
Indices: 56570143--56570570 Score: 203
Period size: 9 Copynumber: 49.8 Consensus size: 9
56570133 AATTGCACGG
56570143 GTAAGTTAT
1 GTAAGTTAT
*
56570152 GT-A-TTGT
1 GTAAGTTAT
*
56570159 GTAAGCTAT
1 GTAAGTTAT
*
56570168 GTAAGTTGT
1 GTAAGTTAT
56570177 GT-A-TTAT
1 GTAAGTTAT
56570184 GTAAGTTAT
1 GTAAGTTAT
56570193 -T-A-TTAT
1 GTAAGTTAT
56570199 GCTTTAAGTTAT
1 G---TAAGTTAT
*
56570211 GTAAGTAAT
1 GTAAGTTAT
56570220 GT-A-TTAT
1 GTAAGTTAT
*
56570227 GTAAGTTGT
1 GTAAGTTAT
*
56570236 GT-A-TAAT
1 GTAAGTTAT
*
56570243 GTTAGTTAT
1 GTAAGTTAT
56570252 GTAAGTTAT
1 GTAAGTTAT
56570261 GTAAGTTAT
1 GTAAGTTAT
56570270 GT-A---A-
1 GTAAGTTAT
56570274 GTAAGTTAT
1 GTAAGTTAT
56570283 GTAAGTTAT
1 GTAAGTTAT
** *
56570292 CAAAGTAAT
1 GTAAGTTAT
*
56570301 GTATGTTAT
1 GTAAGTTAT
56570310 GTAAG-T-T
1 GTAAGTTAT
56570317 GTAAGTTAT
1 GTAAGTTAT
*
56570326 -TATGTATTAT
1 GTAAG--TTAT
*
56570336 GTAAGTTAA
1 GTAAGTTAT
* *
56570345 G-ATGGATTAC
1 GTA-AG-TTAT
56570355 GTAAGTTAT
1 GTAAGTTAT
56570364 GTAAGTTAAAT
1 GTAAGTT--AT
56570375 GT-A-TTAT
1 GTAAGTTAT
56570382 GTAAG-T-T
1 GTAAGTTAT
56570389 GTAAGTTAGAT
1 GTAAGTT--AT
56570400 GT-A-TTAT
1 GTAAGTTAT
56570407 GTAAG-T-T
1 GTAAGTTAT
56570414 GTAAGTTAGAT
1 GTAAGTT--AT
56570425 GT-A-TTAT
1 GTAAGTTAT
56570432 GTAAG-T-T
1 GTAAGTTAT
56570439 GTAAGTTAT
1 GTAAGTTAT
*
56570448 -TATGTATTAT
1 GTAAG--TTAT
56570458 GTAAGTTAT
1 GTAAGTTAT
56570467 GTAAGTTAAAT
1 GTAAGTT--AT
56570478 GT-A-TTAT
1 GTAAGTTAT
56570485 G-AAGGTTAT
1 GTAA-GTTAT
*
56570494 GTAAGTTGT
1 GTAAGTTAT
**
56570503 GTAAGAGAT
1 GTAAGTTAT
*
56570512 TTAAGTTAT
1 GTAAGTTAT
* *
56570521 GTGAGTTTT
1 GTAAGTTAT
56570530 GT-A-TTAT
1 GTAAGTTAT
56570537 GTAAGTTAT
1 GTAAGTTAT
*
56570546 GTAGGTTAT
1 GTAAGTTAT
* *
56570555 TTAGGTTAT
1 GTAAGTTAT
56570564 GTAAGTT
1 GTAAGTT
56570571 TTGAGTTGTT
Statistics
Matches: 318, Mismatches: 45, Indels: 112
0.67 0.09 0.24
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 4 0.01
7 65 0.20
8 31 0.10
9 167 0.53
10 20 0.06
11 22 0.07
12 5 0.02
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:56570216 original size:43 final size:42
Alignment explanation
Indices: 56570143--56570316 Score: 148
Period size: 43 Copynumber: 4.2 Consensus size: 42
56570133 AATTGCACGG
* *
56570143 GTAAGTTATGTAT--TGTGTAAGCTATGTAAGTTGTGTATTAT
1 GTAAGTTATGTATAATGT-TAAGTTATGTAAGTTATGTATTAT
* *
56570184 GTAAGTTAT-TATTATGCTTTAAGTTATGTAAGTAATGTATTAT
1 GTAAGTTATGTATAATG--TTAAGTTATGTAAGTTATGTATTAT
*
56570227 GTAAGTTGTGTATAATGTT-AGTTATGTAAGTTATGTAAGTTAT
1 GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGT-A-TTAT
* ** *
56570270 GTAAG-TAAGT-T-ATG-TAAGTTATCAAAGTAATGTATGTTAT
1 GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGTA--TTAT
56570310 GTAAGTT
1 GTAAGTT
56570317 GTAAGTTATT
Statistics
Matches: 112, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
39 2 0.02
40 30 0.27
41 27 0.24
42 8 0.07
43 38 0.34
44 7 0.06
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (42 bp):
GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGTATTAT
Found at i:56570236 original size:59 final size:56
Alignment explanation
Indices: 56570159--56570542 Score: 180
Period size: 53 Copynumber: 7.0 Consensus size: 56
56570149 TATGTATTGT
* *
56570159 GTAAGCTATGTAAGTTGTGTATTATGTAAGTTAT-T-A-TTATGCTTTAAGTTATGTAA
1 GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATG---TAAGTTATGTAA
*
56570215 GTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATGTAAGTTATGTAAGTTATGTAA
1 GTAA-G--TTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
* ** * *
56570274 GTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAT-TAT
1 GTAAGTTATGTAAGTTGT-GTA-TAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
* * * *
56570329 GT-A-TTATGTAAGTTAAGATGGATTACGTAAGTTATGTAAGTTA---AA-TGTAT-TAT
1 GTAAGTTATGTAAGTT--G-TGTATAATGTAAGTTATGTAAGTTATGTAAGT-TATGTAA
*
56570382 GTAAG-T-TGTAAGTTAGATGTATTATGTAAG-T-TGTAAGTTAGATGT-A-TTATGTAA
1 GTAAGTTATGTAAGTT-G-TGTATAATGTAAGTTATGTAAGTT--ATGTAAGTTATGTAA
* * * * *
56570436 GT-TG-TAAGTTA-TTATGTATTATGTAAGTTATGTAAGTTAAATGT-A-TTATG-AA
1 GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTT--ATGTAAGTTATGTAA
* * * *
56570488 G---GTTATGTAAGTTGTGTAAGAGATTTAAGTTATGTGAGTTTTGT-A-TTATGTAA
1 GTAAGTTATGTAAGTTGTGT-ATA-ATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
56570541 GT
1 GT
56570543 TATGTAGGTT
Statistics
Matches: 266, Mismatches: 31, Indels: 64
0.74 0.09 0.18
Matches are distributed among these distances:
50 9 0.03
51 19 0.07
52 34 0.13
53 59 0.22
54 43 0.16
55 6 0.02
56 27 0.10
57 3 0.01
58 17 0.06
59 42 0.16
60 1 0.00
61 1 0.00
62 5 0.02
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.45
Consensus pattern (56 bp):
GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
Found at i:56570238 original size:25 final size:26
Alignment explanation
Indices: 56570180--56570570 Score: 274
Period size: 25 Copynumber: 15.1 Consensus size: 26
56570170 AAGTTGTGTA
56570180 TTATGTAAGTT-AT-TATTATGCTTTAAG
1 TTATGTAAGTTAATGTATTATG---TAAG
56570207 TTATGTAAG-TAATGTATTATGTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
*
56570232 TTGTGT-A--TAATGTTAGTTATGTAAG
1 TTATGTAAGTTAATG-TA-TTATGTAAG
56570257 TTATGTAAGTT-ATGTA--A-GTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
* *
56570279 TTATGTAAGTTATCAAAGTA--ATGTATG
1 TTATGTAAG-T-T-AATGTATTATGTAAG
56570306 TTATGTAAGTTGTAA-GTTATTATGT-A-
1 TTATGTAAG-T-TAATG-TATTATGTAAG
* *
56570332 TTATGTAAGTTAAGATGGATTACGTAAG
1 TTATGTAAGTT-A-ATGTATTATGTAAG
56570360 TTATGTAAGTTAAATGTATTATGTAAG
1 TTATGTAAGTT-AATGTATTATGTAAG
56570387 -T-TGTAAGTTAGATGTATTATGTAAG
1 TTATGTAAGTTA-ATGTATTATGTAAG
56570412 -T-TGTAAGTTAGATGTATTATGTAAG
1 TTATGTAAGTTA-ATGTATTATGTAAG
56570437 -T-TGTAAGTTATTATGTATTATGTAAG
1 TTATGTAAGTTA--ATGTATTATGTAAG
56570463 TTATGTAAGTTAAATGTATTATG-AAGG
1 TTATGTAAGTT-AATGTATTATGTAA-G
* ** *
56570490 TTATGTAAGTT-GTGTAAGAGATTTAAG
1 TTATGTAAGTTAATGT-A-TTATGTAAG
* *
56570517 TTATGTGAGTT-TTGTATTATGTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
* *
56570542 TTATGTAGGTT-ATTTAGGTTATGTAAG
1 TTATGTAAGTTAATGTA--TTATGTAAG
56570569 TT
1 TT
56570571 TTGAGTTGTT
Statistics
Matches: 309, Mismatches: 24, Indels: 62
0.78 0.06 0.16
Matches are distributed among these distances:
22 14 0.05
23 7 0.02
24 6 0.02
25 104 0.34
26 48 0.16
27 94 0.30
28 35 0.11
29 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (26 bp):
TTATGTAAGTTAATGTATTATGTAAG
Found at i:56570277 original size:13 final size:13
Alignment explanation
Indices: 56570261--56570288 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56570251 TGTAAGTTAT
56570261 GTAAGTTATGTAA
1 GTAAGTTATGTAA
56570274 GTAAGTTATGTAA
1 GTAAGTTATGTAA
56570287 GT
1 GT
56570289 TATCAAAGTA
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:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (13 bp):
GTAAGTTATGTAA
Found at i:56570277 original size:22 final size:22
Alignment explanation
Indices: 56570252--56570341 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 22
56570242 TGTTAGTTAT
56570252 GTAAGTTATGTAAGTTATGTAA
1 GTAAGTTATGTAAGTTATGTAA
56570274 GTAAGTTATGTAAGTTATCAAAGTAA
1 GTAAGTTATGTAAGTTAT----GTAA
*
56570300 TGTATGTTATGTAAG-T-TGTAA
1 -GTAAGTTATGTAAGTTATGTAA
*
56570321 GTTA-TTATGT-A-TTATGTAA
1 GTAAGTTATGTAAGTTATGTAA
56570340 GT
1 GT
56570342 TAAGATGGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
18 2 0.03
19 13 0.22
20 2 0.03
21 4 0.07
22 18 0.31
25 1 0.02
26 5 0.09
27 13 0.22
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.43
Consensus pattern (22 bp):
GTAAGTTATGTAAGTTATGTAA
Found at i:56570338 original size:19 final size:19
Alignment explanation
Indices: 56570316--56570466 Score: 62
Period size: 19 Copynumber: 8.5 Consensus size: 19
56570306 TTATGTAAGT
56570316 TGTAAGTTATTATGTATTA
1 TGTAAGTTATTATGTATTA
** *
56570335 TGTAAGTTAAGATGGATTA
1 TGTAAGTTATTATGTATTA
*
56570354 CGTAAG---TTATGTA--A
1 TGTAAGTTATTATGTATTA
* *
56570368 -GTTAAATGTATTATGTAAGT-
1 TG-TAAGT-TATTATGT-ATTA
*
56570388 TGTAAGTTA-GATGTATTA
1 TGTAAGTTATTATGTATTA
* *
56570406 TGTAAGTT-GTAAG--TTA
1 TGTAAGTTATTATGTATTA
* *
56570422 -G-ATG-TATTATGTAAGT-
1 TGTAAGTTATTATGT-ATTA
56570438 TGTAAGTTATTATGTATTA
1 TGTAAGTTATTATGTATTA
56570457 TGTAAGTTAT
1 TGTAAGTTAT
56570467 GTAAGTTAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 38
0.62 0.13 0.25
Matches are distributed among these distances:
13 2 0.02
14 9 0.10
15 1 0.01
16 7 0.07
17 4 0.04
18 24 0.26
19 42 0.45
20 4 0.04
21 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (19 bp):
TGTAAGTTATTATGTATTA
Found at i:56570537 original size:43 final size:43
Alignment explanation
Indices: 56570490--56570573 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
56570480 ATTATGAAGG
* *
56570490 TTATGTAAGTTGTGTAAGAGATTTAAGTTATGTGAGTTTTGTA
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
* ** *
56570533 TTATGTAAGTTATGTAGGTTATTTAGGTTATGTAAGTTTTG
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTG
56570574 AGTTGTTCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
Found at i:56570720 original size:12 final size:11
Alignment explanation
Indices: 56570693--56570773 Score: 50
Period size: 12 Copynumber: 7.5 Consensus size: 11
56570683 TGTTAAGTAC
56570693 AATTTAATAA-
1 AATTTAATAAT
56570703 AA--TAATATAT
1 AATTTAATA-AT
56570713 AATTTAATAA-
1 AATTTAATAAT
*
56570723 CATTACTAAT-AT
1 AATT--TAATAAT
56570735 AATTATTAATAAT
1 AA-T-TTAATAAT
56570748 -ATTTAATAAT
1 AATTTAATAAT
56570758 AATTTTAAT-AT
1 AA-TTTAATAAT
56570769 AATTT
1 AATTT
56570774 TATTATTAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
8 5 0.09
9 1 0.02
10 18 0.32
11 8 0.14
12 21 0.37
13 3 0.05
14 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:56573108 original size:16 final size:16
Alignment explanation
Indices: 56573087--56573118 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56573077 ATAAAAAACG
56573087 CCACAAATGATTAACT
1 CCACAAATGATTAACT
56573103 CCACAAATGATTAACT
1 CCACAAATGATTAACT
56573119 GAAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
CCACAAATGATTAACT
Found at i:56573395 original size:39 final size:39
Alignment explanation
Indices: 56573331--56573416 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
56573321 AATTCCTAAC
*
56573331 CCAT-AACCCCTAAATCCCCTAAACCCTTAAAGCATAAA
1 CCATAAACCCCTAAATCCCCTAAACCCCTAAAGCATAAA
* *
56573369 CCATAAACCCCTAAATCTCTCT-AACCCCTAAAGCATAAC
1 CCATAAACCCCTAAATC-CCCTAAACCCCTAAAGCATAAA
*
56573408 CCCTAAACC
1 CCATAAACC
56573417 ATTCCAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 4 0.10
39 35 0.83
40 3 0.07
ACGTcount: A:0.40, C:0.40, G:0.02, T:0.19
Consensus pattern (39 bp):
CCATAAACCCCTAAATCCCCTAAACCCCTAAAGCATAAA
Found at i:56574508 original size:7 final size:7
Alignment explanation
Indices: 56574475--56574537 Score: 81
Period size: 7 Copynumber: 8.7 Consensus size: 7
56574465 CTTACCGTTC
56574475 AAACCCT
1 AAACCCT
**
56574482 AAACCAG
1 AAACCCT
*
56574489 AAATCCAT
1 AAA-CCCT
56574497 AAACCCT
1 AAACCCT
56574504 AAACCCT
1 AAACCCT
56574511 AAACCCAT
1 AAACCC-T
56574519 AAACCCT
1 AAACCCT
56574526 AAACCCT
1 AAACCCT
56574533 AAACC
1 AAACC
56574538 TTAACTCTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
7 37 0.74
8 13 0.26
ACGTcount: A:0.48, C:0.38, G:0.02, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:56574508 original size:29 final size:29
Alignment explanation
Indices: 56574475--56574537 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
56574465 CTTACCGTTC
56574475 AAACCCTAAA-CCAGAAATCCATAAACCCT
1 AAACCCTAAACCCAGAAA-CCATAAACCCT
* *
56574504 AAACCCTAAACCCATAAACCCTAAACCCT
1 AAACCCTAAACCCAGAAACCATAAACCCT
56574533 AAACC
1 AAACC
56574538 TTAACTCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.48, C:0.38, G:0.02, T:0.13
Consensus pattern (29 bp):
AAACCCTAAACCCAGAAACCATAAACCCT
Found at i:56574531 original size:22 final size:22
Alignment explanation
Indices: 56574475--56574537 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
56574465 CTTACCGTTC
** *
56574475 AAACCCTAAACCAGAAATCCAT
1 AAACCCTAAACCCTAAACCCAT
56574497 AAACCCTAAACCCTAAACCCAT
1 AAACCCTAAACCCTAAACCCAT
56574519 AAACCCTAAACCCTAAACC
1 AAACCCTAAACCCTAAACC
56574538 TTAACTCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.48, C:0.38, G:0.02, T:0.13
Consensus pattern (22 bp):
AAACCCTAAACCCTAAACCCAT
Found at i:56575024 original size:114 final size:113
Alignment explanation
Indices: 56574820--56575084 Score: 476
Period size: 114 Copynumber: 2.3 Consensus size: 113
56574810 TTTTAAATCC
*
56574820 CTGATCATTAGCGGCGCTTTTATAAAAACGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGAC
1 CTGAACATTAGCGGCGCTTTTATAAAAACGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGAC
56574885 GTTGCGCTTAGTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
66 GTTGCGCTTAGTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
* *
56574933 CTGAACATTAGCGGCGCTTTCTGTAAAAGCGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGA
1 CTGAACATTAGCGGCGCTTT-TATAAAAACGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGA
56574998 CGTTGCGCTTAGTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
65 CGTTGCGCTTAGTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
* *
56575047 CTGAACATTAGCGGCGCTTTAACAAAAACGCCGCTAAA
1 CTGAACATTAGCGGCGCTTTTATAAAAACGCCGCTAAA
56575085 GACTTCAGCA
Statistics
Matches: 144, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 33 0.23
114 111 0.77
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (113 bp):
CTGAACATTAGCGGCGCTTTTATAAAAACGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGAC
GTTGCGCTTAGTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
Found at i:56575062 original size:40 final size:41
Alignment explanation
Indices: 56575017--56575126 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 41
56575007 TAGTTTTTTT
* *
56575017 GCGGCGCTTTCCAAAAAACGCCGCTAAAGAC-TGAACATTA
1 GCGGCGCTTTCAAAAAAACGCCGCTAAAGACTTCAACATTA
*
56575057 GCGGCGCTTT-AACAAAAACGCCGCTAAAGACTTCAGCATTA
1 GCGGCGCTTTCAA-AAAAACGCCGCTAAAGACTTCAACATTA
** *
56575098 GCGGCGCTTTCTGTAAAAGCGCCGCTAAA
1 GCGGCGCTTTC-AAAAAAACGCCGCTAAA
56575127 TCCCTGAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 28 0.47
41 17 0.28
42 14 0.23
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTTCAAAAAAACGCCGCTAAAGACTTCAACATTA
Found at i:56575239 original size:74 final size:74
Alignment explanation
Indices: 56575096--56575239 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 74
56575086 ACTTCAGCAT
* * * *
56575096 TAGCGGCGCTTTCTGTAAAAGCGCCGCTAAATCCCTGAAAGCTCAAGAGACGACGTTCGTTGCGC
1 TAGCGGCGCTTTATG-AAAAGCGCCGCTAAATCCCTGAAAGCTCAAGAAACAACGATCGTTGCGC
56575161 TAGTTTTAAG
65 TAGTTTTAAG
* ** *
56575171 TAGCGGCGCTTTAT-AGAAAGCGCCGCTAAATCCCTGAAATCTCGGGAAACAAC-ATCGTTGGGC
1 TAGCGGCGCTTTATGA-AAAGCGCCGCTAAATCCCTGAAAGCTCAAGAAACAACGATCGTTGCGC
56575234 TTAGTT
65 -TAGTT
56575240 ATTTTTGCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
73 9 0.15
74 37 0.63
75 13 0.22
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (74 bp):
TAGCGGCGCTTTATGAAAAGCGCCGCTAAATCCCTGAAAGCTCAAGAAACAACGATCGTTGCGCT
AGTTTTAAG
Found at i:56590161 original size:24 final size:25
Alignment explanation
Indices: 56590127--56590191 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
56590117 TCATAATTTA
* *
56590127 TTTTTTAAAATTATAAA-A-ACTAT
1 TTTTTTTAAATTATAAATATACGAT
56590150 TTTTTTTGAAATTATAAATATACGAT
1 TTTTTTT-AAATTATAAATATACGAT
*
56590176 TTTTTTTAAATCATAA
1 TTTTTTTAAATTATAA
56590192 TTTTTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 6 0.17
24 10 0.28
25 9 0.25
26 11 0.31
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.51
Consensus pattern (25 bp):
TTTTTTTAAATTATAAATATACGAT
Found at i:56590178 original size:25 final size:24
Alignment explanation
Indices: 56590127--56590185 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
56590117 TCATAATTTA
*
56590127 TTTTTTAAAATTATAAAAACTATT
1 TTTTTTAAAATTATAAAAACGATT
*
56590151 TTTTTTGAAATTATAAATATACGATT
1 TTTTTTAAAATTATAAA-A-ACGATT
56590177 TTTTTTAAA
1 TTTTTTAAA
56590186 TCATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 16 0.53
25 1 0.03
26 13 0.43
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (24 bp):
TTTTTTAAAATTATAAAAACGATT
Found at i:56592808 original size:31 final size:32
Alignment explanation
Indices: 56592773--56592841 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
56592763 GTGGGTGACC
** *
56592773 AAAATGAAAA-TGATTTTTAATGGCAATGCCT
1 AAAATGAAAAGTGAGCTTTAATGGCAATACCT
*
56592804 AAAAT-AAAAGTGGGCTTTAATGGCAATACCT
1 AAAATGAAAAGTGAGCTTTAATGGCAATACCT
56592835 AAAATGA
1 AAAATGA
56592842 TTTTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 4 0.12
31 27 0.84
32 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (32 bp):
AAAATGAAAAGTGAGCTTTAATGGCAATACCT
Found at i:56594887 original size:91 final size:91
Alignment explanation
Indices: 56594748--56594926 Score: 322
Period size: 91 Copynumber: 2.0 Consensus size: 91
56594738 ATAAATATAG
*
56594748 TGATAATTTGATTCTTTGTCGACAGAGTAAATAGGAGAGATTATTTCTTTCTTCGTCTTTACAAA
1 TGATAATTTGATTCTTCGTCGACAGAGTAAATAGGAGAGATTATTTCTTTCTTCGTCTTTACAAA
56594813 AACAAAAAAATATATTTTAAAAGAAA
66 AACAAAAAAATATATTTTAAAAGAAA
*
56594839 TGATAATTTGATTCTTCGTCGACGGAGTAAATAGGAGAGATTATTTCTTTCTTCGTCTTTACAAA
1 TGATAATTTGATTCTTCGTCGACAGAGTAAATAGGAGAGATTATTTCTTTCTTCGTCTTTACAAA
* *
56594904 AACAAAAATATATATTTTTAAAG
66 AACAAAAAAATATATTTTAAAAG
56594927 TAAAAAAAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (91 bp):
TGATAATTTGATTCTTCGTCGACAGAGTAAATAGGAGAGATTATTTCTTTCTTCGTCTTTACAAA
AACAAAAAAATATATTTTAAAAGAAA
Found at i:56597370 original size:13 final size:13
Alignment explanation
Indices: 56597352--56597376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56597342 GTAAACACAC
56597352 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
56597365 AAAAGAAAAAAA
1 AAAAGAAAAAAA
56597377 ACTGCGTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:56597936 original size:27 final size:27
Alignment explanation
Indices: 56597906--56597958 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
56597896 TTTGGACTGA
56597906 ATTT-ATTTATTATTTTCTTTGTTTTTG
1 ATTTGATTTATT-TTTTCTTTGTTTTTG
* *
56597933 ATTTGATTTCTTTTTTCTTTTTTTTT
1 ATTTGATTTATTTTTTCTTTGTTTTT
56597959 ATTCAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (27 bp):
ATTTGATTTATTTTTTCTTTGTTTTTG
Found at i:56601930 original size:27 final size:24
Alignment explanation
Indices: 56601894--56601945 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 24
56601884 AAAAAATTTA
*
56601894 TATTGTTAATGTACCAAATATTTAGCT
1 TATTGTTAATATA--AAATATTT-GCT
*
56601921 TATTTTTAATATAAAATATTTGCT
1 TATTGTTAATATAAAATATTTGCT
56601945 T
1 T
56601946 TAAATTATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 8 0.35
27 11 0.48
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (24 bp):
TATTGTTAATATAAAATATTTGCT
Found at i:56610876 original size:29 final size:31
Alignment explanation
Indices: 56610808--56610884 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
56610798 TTAACGGCTC
* *
56610808 AGTAACTAAAATGTTACAATACGATAACGTA
1 AGTAACTAAAATGTAACAATACGATAACATA
* * *
56610839 AGTGACTAAAATGTAACATTTC-A-AACATA
1 AGTAACTAAAATGTAACAATACGATAACATA
56610868 AGTAACTAAAATGTAAC
1 AGTAACTAAAATGTAAC
56610885 CTGAGGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 21 0.52
30 1 0.03
31 18 0.45
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (31 bp):
AGTAACTAAAATGTAACAATACGATAACATA
Found at i:56613347 original size:125 final size:125
Alignment explanation
Indices: 56613125--56613375 Score: 448
Period size: 125 Copynumber: 2.0 Consensus size: 125
56613115 AGCCCCCCAC
* * * *
56613125 CTGAAACAAGTCCAATGTTGATAAGCGAAGGAAACCAAAACCTCATTTTAACTATGGGCTTAAGT
1 CTGAAAAAAGTCAAATATTGATAAGCGAAGGAAACCAAAACCTCATTTTAACTATGGGATTAAGT
56613190 TTGGGTTCCGTTGCAAGCTTGTGTTTTGTGATTGCAATATGTAGCTTCTTGTTATACAGG
66 TTGGGTTCCGTTGCAAGCTTGTGTTTTGTGATTGCAATATGTAGCTTCTTGTTATACAGG
*
56613250 CTGAAAAAAGTCAAATATTGATAAGCGAAGGAAACCAAAGCCTCATTTTAACTATGGGATTAAGT
1 CTGAAAAAAGTCAAATATTGATAAGCGAAGGAAACCAAAACCTCATTTTAACTATGGGATTAAGT
*
56613315 TTGGGTTCCGTTGCAAGTTTGTGTTTTGTGATTGCAATATGTAGCTTCTTGTTATACAGG
66 TTGGGTTCCGTTGCAAGCTTGTGTTTTGTGATTGCAATATGTAGCTTCTTGTTATACAGG
56613375 C
1 C
56613376 ATCGAGTCCA
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (125 bp):
CTGAAAAAAGTCAAATATTGATAAGCGAAGGAAACCAAAACCTCATTTTAACTATGGGATTAAGT
TTGGGTTCCGTTGCAAGCTTGTGTTTTGTGATTGCAATATGTAGCTTCTTGTTATACAGG
Found at i:56614806 original size:10 final size:10
Alignment explanation
Indices: 56614791--56614818 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
56614781 TTAGGCCTAC
56614791 TCAATTTAGT
1 TCAATTTAGT
56614801 TCAATTTAGT
1 TCAATTTAGT
56614811 TCAATTTA
1 TCAATTTA
56614819 TTATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (10 bp):
TCAATTTAGT
Found at i:56617273 original size:18 final size:18
Alignment explanation
Indices: 56617252--56617321 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
56617242 GAACAATTTA
56617252 TGGTCAAAATAGAAATGG
1 TGGTCAAAATAGAAATGG
*
56617270 TGGTCAAAATTGGAGTAATGG
1 TGGTCAAAA-T--AGAAATGG
**
56617291 CCAAAGTCAAAATAGAAATGG
1 ---TGGTCAAAATAGAAATGG
56617312 TGGTCAAAAT
1 TGGTCAAAAT
56617322 TGGGGTGCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
18 17 0.43
19 1 0.03
21 14 0.35
23 1 0.03
24 7 0.17
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (18 bp):
TGGTCAAAATAGAAATGG
Found at i:56621850 original size:18 final size:18
Alignment explanation
Indices: 56621829--56621877 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
56621819 ATTATTAAAT
*
56621829 TATTTTTATTTATTTTAA
1 TATTTTTATTTAATTTAA
* *
56621847 TATTATTA-TAAATTTAA
1 TATTTTTATTTAATTTAA
56621864 TATATTTTATTTAA
1 TAT-TTTTATTTAA
56621878 ATATAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 10 0.42
18 11 0.46
19 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTTATTTAATTTAA
Found at i:56622851 original size:15 final size:16
Alignment explanation
Indices: 56622831--56622867 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
56622821 CAAAAAATCA
56622831 ATAAAA-TTACATTAT
1 ATAAAAGTTACATTAT
56622846 ATAAAAGTTACATTAT
1 ATAAAAGTTACATTAT
56622862 ATAAAA
1 ATAAAA
56622868 ATTAAATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (16 bp):
ATAAAAGTTACATTAT
Found at i:56623064 original size:60 final size:60
Alignment explanation
Indices: 56622991--56623108 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
56622981 TAAACTAAAT
* * * * *
56622991 ACAACAATTTATAACTTAATCCTAAATTGCTAATAAATTAAATT-TTAAATAATTACAAAC
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTACAAAC
56623051 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTACAA
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTACAA
56623109 TATTCTTACA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 4 0.08
60 48 0.92
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (60 bp):
ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTACAAAC
Found at i:56623125 original size:19 final size:19
Alignment explanation
Indices: 56623101--56623245 Score: 102
Period size: 19 Copynumber: 7.3 Consensus size: 19
56623091 ATTATAAAAT
*
56623101 AATTACAATATTCTTACAA
1 AATTACAATATTCATACAA
56623120 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* *
56623139 AA-TACTAATCA--AAAACTATA
1 AATTAC-AAT-ATTCATAC-A-A
*
56623159 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
*
56623180 TAATTAAAATATTCATACAA
1 -AATTACAATATTCATACAA
56623200 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
56623221 AATTACAATATTTATACAA
1 AATTACAATATTCATACAA
56623240 AATTAC
1 AATTAC
56623246 CCATTGGCGC
Statistics
Matches: 102, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
18 6 0.06
19 51 0.50
20 13 0.13
21 23 0.23
22 5 0.05
23 4 0.04
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:56623223 original size:21 final size:21
Alignment explanation
Indices: 56623176--56623241 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
56623166 AATTAATTAT
*
56623176 AAAATAATTAAAATATTCATAC
1 AAAA-AATTACAATATTCATAC
56623198 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
56623217 AAAAAATTACAATATTTATAC
1 AAAAAATTACAATATTCATAC
56623238 AAAA
1 AAAA
56623242 TTACCCATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 16 0.40
20 2 0.05
21 22 0.55
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:56623307 original size:27 final size:27
Alignment explanation
Indices: 56623250--56623311 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
56623240 AATTACCCAT
***
56623250 TGGCGCCTCCCTATGAGGCACTTTTAA
1 TGGCGCCTCCCTATGAGGCACAACTAA
* * *
56623277 TGGCGCCTTCTTATGAGGCACAACTAG
1 TGGCGCCTCCCTATGAGGCACAACTAA
56623304 TGGCGCCT
1 TGGCGCCT
56623312 ACCTGATAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.27
Consensus pattern (27 bp):
TGGCGCCTCCCTATGAGGCACAACTAA
Found at i:56623415 original size:27 final size:27
Alignment explanation
Indices: 56623385--56623447 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
56623375 TTTTATTTAA
56623385 ATTTTTTTAAAAA-AATAAAAAAATAAT
1 ATTTTTTTAAAAATAA-AAAAAAATAAT
* *
56623412 ATTTTATTAAAAATAAAAAAAATTAAT
1 ATTTTTTTAAAAATAAAAAAAAATAAT
*
56623439 AATTTTTTA
1 ATTTTTTTA
56623448 TTCATTAGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTTTTTAAAAATAAAAAAAAATAAT
Found at i:56629131 original size:31 final size:31
Alignment explanation
Indices: 56629064--56629129 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
56629054 ATAGTAAAGG
*
56629064 TAAAATTGTAATTTAGTCTTTCTAAAAATGA
1 TAAAATTGTAATTTAATCTTTCTAAAAATGA
* * *
56629095 TAAAATTTTGATTTAATCTTT-TAAAAATTA
1 TAAAATTGTAATTTAATCTTTCTAAAAATGA
56629125 TAAAA
1 TAAAA
56629130 ATATAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (31 bp):
TAAAATTGTAATTTAATCTTTCTAAAAATGA
Found at i:56630308 original size:13 final size:13
Alignment explanation
Indices: 56630290--56630314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56630280 AGATAAGTTG
56630290 AATAAAATATAAT
1 AATAAAATATAAT
56630303 AATAAAATATAA
1 AATAAAATATAA
56630315 GTCTTTAAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAATATAAT
Found at i:56636140 original size:17 final size:16
Alignment explanation
Indices: 56636115--56636148 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
56636105 TCCCATTTTC
*
56636115 GTTATTTTAAATAAAAA
1 GTTAATTTAAA-AAAAA
56636132 GTTAATTTAAAAAAAA
1 GTTAATTTAAAAAAAA
56636148 G
1 G
56636149 GGGGTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
GTTAATTTAAAAAAAA
Found at i:56636597 original size:11 final size:11
Alignment explanation
Indices: 56636581--56636605 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56636571 ATTATGAAGT
56636581 ACTTGACCAAA
1 ACTTGACCAAA
56636592 ACTTGACCAAA
1 ACTTGACCAAA
56636603 ACT
1 ACT
56636606 CTTACGAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (11 bp):
ACTTGACCAAA
Found at i:56640724 original size:10 final size:10
Alignment explanation
Indices: 56640709--56640733 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56640699 CTTAACTACC
56640709 ACTAAGAACA
1 ACTAAGAACA
56640719 ACTAAGAACA
1 ACTAAGAACA
56640729 ACTAA
1 ACTAA
56640734 AATAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.08, T:0.12
Consensus pattern (10 bp):
ACTAAGAACA
Found at i:56642514 original size:32 final size:32
Alignment explanation
Indices: 56642473--56642537 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
56642463 CATGTTTATA
56642473 ATTTGGAGGTTTTATGTTGTAATTTAGCCAAT
1 ATTTGGAGGTTTTATGTTGTAATTTAGCCAAT
*
56642505 ATTTTGAGGTTTTATGTTGTAATTTAGCCAAT
1 ATTTGGAGGTTTTATGTTGTAATTTAGCCAAT
56642537 A
1 A
56642538 GTAAATGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.48
Consensus pattern (32 bp):
ATTTGGAGGTTTTATGTTGTAATTTAGCCAAT
Found at i:56642673 original size:40 final size:38
Alignment explanation
Indices: 56642629--56642747 Score: 130
Period size: 40 Copynumber: 3.0 Consensus size: 38
56642619 AGAAAAAATC
*
56642629 GAGCATTAGCGGCGTTTTTAAGAAAACACCGCTAAAATA
1 GAGCATTAGCGGCGTTTTTAATAAAACACCGCTAAAA-A
* * * *
56642668 GGAGCATTAGCGGCATTTTAAATAACACGCCGCTAAAAA
1 -GAGCATTAGCGGCGTTTTTAATAAAACACCGCTAAAAA
* * *
56642707 GAGCCATTAGCGGCGGTTTTAATAAAAACGCCGCAAAAAA
1 GAG-CATTAGCGGCGTTTTTAAT-AAAACACCGCTAAAAA
56642747 G
1 G
56642748 CCAAAGCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
38 3 0.04
39 17 0.25
40 47 0.70
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (38 bp):
GAGCATTAGCGGCGTTTTTAATAAAACACCGCTAAAAA
Found at i:56642872 original size:41 final size:42
Alignment explanation
Indices: 56642784--56642940 Score: 169
Period size: 41 Copynumber: 3.8 Consensus size: 42
56642774 ACTTTCGGGT
* *
56642784 CTTTAGCGGCGTTTT-T-TAATAAGTGCCGCTAATTCTATGGGC
1 CTTTAGCGGCGTTTTCTGTAA-AAGCGCCGCTAATGCT-TGGGC
* * *
56642826 TTTTAGCGGCGTTTT-TGTAAAAGCACCGCTAATGCTTTGGC
1 CTTTAGCGGCGTTTTCTGTAAAAGCGCCGCTAATGCTTGGGC
* * * * *
56642867 CTTTAGCGGCGTTTTGTGAAAAAACGCCGCTAATG-ATGGGT
1 CTTTAGCGGCGTTTTCTGTAAAAGCGCCGCTAATGCTTGGGC
*
56642908 CTTTAGCGGCGTTTTCTGGAAAAGCGCCGCTAA
1 CTTTAGCGGCGTTTTCTGTAAAAGCGCCGCTAA
56642941 GGACATTTTA
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 51 0.52
42 44 0.45
43 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTCTGTAAAAGCGCCGCTAATGCTTGGGC
Found at i:56642931 original size:83 final size:83
Alignment explanation
Indices: 56642784--56642940 Score: 203
Period size: 83 Copynumber: 1.9 Consensus size: 83
56642774 ACTTTCGGGT
* * ** * *
56642784 CTTTAGCGGCGTTTTTTAATAAGTGCCGCTAATTCTATGGGCTTTTAGCGGCGTTTTTGTAAAAG
1 CTTTAGCGGCGTTTTTGAAAAAACGCCGCTAATTCGATGGGCTTTTAGCGGCGTTTTTGGAAAAG
56642849 CACCGCTAATGCTTTGGC
66 CACCGCTAATGCTTTGGC
56642867 CTTTAGCGGCGTTTTGTGAAAAAACGCCGCTAA-T-GATGGG-TCTTTAGCGGCGTTTTCTGGAA
1 CTTTAGCGGCGTTTT-TGAAAAAACGCCGCTAATTCGATGGGCT-TTTAGCGGCGTTTT-TGGAA
*
56642929 AAGCGCCGCTAA
63 AAGCACCGCTAA
56642941 GGACATTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
81 1 0.02
82 19 0.30
83 31 0.48
84 13 0.20
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (83 bp):
CTTTAGCGGCGTTTTTGAAAAAACGCCGCTAATTCGATGGGCTTTTAGCGGCGTTTTTGGAAAAG
CACCGCTAATGCTTTGGC
Found at i:56643587 original size:15 final size:15
Alignment explanation
Indices: 56643564--56643598 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56643554 TAGGGATTAT
56643564 GGTTT-AAGGGTTGG
1 GGTTTAAAGGGTTGG
*
56643578 GGTTTAAAGGTTTGG
1 GGTTTAAAGGGTTGG
56643593 GGTTTA
1 GGTTTA
56643599 GGGATAGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (15 bp):
GGTTTAAAGGGTTGG
Found at i:56645044 original size:82 final size:81
Alignment explanation
Indices: 56644789--56645089 Score: 221
Period size: 82 Copynumber: 3.7 Consensus size: 81
56644779 AATTTAATTT
* * * * * * **
56644789 GTGGCGTTTTTTGGGAAAACGCCGTAAATATGTGTTATAGTTTCTCAGAACGGCACCGTTTC-AG
1 GTGGCGTTTTTTCGGAAAACGCCGCAAATATGTATTAAAGTTTCTTAAAACGGCACCGTTTCTTT
* *
56644853 AAGAGGAGTGTAATCTATTA
66 CAGA--AGT-TAAT-TTTTA
* * ** * * *
56644873 GTGGCGTTTATGCTAAAAACGCCGCAATTATGTATTAATGTTT-TTCAAAACGTCACCGTTTCTC
1 GTGGCGTTTTTTCGGAAAACGCCGCAAATATGTATTAAAGTTTCTT-AAAACGGCACCGTTTCT-
* * *
56644937 TTCAGGACTTGAAATTTTA
64 TTCAGAAGTT-AATTTTTA
* * *
56644956 GT-GCGTTTTTTCGGAAAACGCCGGAAATATGAATTAAAGTTTCTTAAAACGGCACTGTTTCTTT
1 GTGGCGTTTTTTCGGAAAACGCCGCAAATATGTATTAAAGTTTCTTAAAACGGCACCGTTTCTTT
56645020 CAGTAAGTTAATTTTTA
66 CAG-AAGTTAATTTTTA
**** * ** * *
56645037 GTGGCGTTTTTGATAAAAACGCCGCAACTATACATTGAAGGTTCTTAAAACGG
1 GTGGCGTTTTTTCGGAAAACGCCGCAAATATGTATTAAAGTTTCTTAAAACGG
56645090 TGCTGTTTCA
Statistics
Matches: 167, Mismatches: 43, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
81 14 0.08
82 90 0.54
83 10 0.06
84 51 0.31
86 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (81 bp):
GTGGCGTTTTTTCGGAAAACGCCGCAAATATGTATTAAAGTTTCTTAAAACGGCACCGTTTCTTT
CAGAAGTTAATTTTTA
Found at i:56645151 original size:448 final size:449
Alignment explanation
Indices: 56644234--56645568 Score: 2111
Period size: 448 Copynumber: 3.0 Consensus size: 449
56644224 TTGGATATAT
* ** **
56644234 AGGACCACATTATAAGAAATAAAAAACATTAGCAGCGTTTGGGTAGAAACGCCGCAACTATGTAC
1 AGGACCACATTATAAGGAA-AAAAAACATTAGTGGCGTTTGCATAGAAACGCCGCAACTATGTAC
* * *
56644299 CCATTTTTTTCAAAACGGCGTCGTAT-CCATTTAGAAATTTAATTTAATTTGTGGCATTTTATGG
65 CCATTTTTTTCAAAACGACGTCGT-TCCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGG
* * * * * * * ** * *
56644363 GAAAATGCCATAAATATGTATTTTAATTTATCAAAACGGCGTCGTTTCAGAAGAGTACTGTAATC
129 GAAAACGCCGTAAATATGTGTTATAGTTTCTCAGAACGGCACCGTTTCAGAAGAGGAGTGTAATC
* * * * *
56644428 TATCAGTGGTGTTTATGCTAGAAACGCTGC-A--ATG-A-T-A----TTTCAAAATGTCACCGTT
194 TATTAGTGGCGTTTATGCTAAAAACGCCGCAATTATGTATTAATGTTTTTCAAAACGTCACCGTT
* * * *
56644483 TCACTTCAGGACTTGACATTTTAGTGGCGTTTTTCCGGAAAACGCTGGAAATATGAATTAAAGTT
259 TCTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTTCGGAAAACGCCGGAAATATGAATTAAAGTT
56644548 TCTTAAAACGGCACTGTTTCTTTTCAGTAAGTTAATTTTTAGTGGCGTTTTTGATAAAAACGCCG
324 TCTTAAAACGGCACTGTTTC-TTTCAGTAAGTTAATTTTTAGTGGCGTTTTTGATAAAAACGCCG
* * *
56644613 AAACTATACATTGAAGGTTCTTAAAACAGTGCTATTTCAGAATTTAATTTTGGCAATTACGC
388 CAACTATACATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTACGC
*
56644675 AGGACGACATTATAAGGAAAAAAAACATTAGTGGCGTTTGCATAGAAACGCCGCAACTATGTACC
1 AGGACCACATTATAAGGAAAAAAAACATTAGTGGCGTTTGCATAGAAACGCCGCAACTATGTACC
56644740 CATTTTTTTCAAAACGACGTCGTTCCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGGA
66 CATTTTTTTCAAAACGACGTCGTTCCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGGA
56644805 AAACGCCGTAAATATGTGTTATAGTTTCTCAGAACGGCACCGTTTCAGAAGAGGAGTGTAATCTA
131 AAACGCCGTAAATATGTGTTATAGTTTCTCAGAACGGCACCGTTTCAGAAGAGGAGTGTAATCTA
56644870 TTAGTGGCGTTTATGCTAAAAACGCCGCAATTATGTATTAATGTTTTTCAAAACGTCACCGTTTC
196 TTAGTGGCGTTTATGCTAAAAACGCCGCAATTATGTATTAATGTTTTTCAAAACGTCACCGTTTC
56644935 TCTTCAGGACTTGAAATTTTAGT-GCGTTTTTTCGGAAAACGCCGGAAATATGAATTAAAGTTTC
261 TCTTCAGGACTTGAAATTTTAGTGGCGTTTTTTCGGAAAACGCCGGAAATATGAATTAAAGTTTC
56644999 TTAAAACGGCACTGTTTCTTTCAGTAAGTTAATTTTTAGTGGCGTTTTTGATAAAAACGCCGCAA
326 TTAAAACGGCACTGTTTCTTTCAGTAAGTTAATTTTTAGTGGCGTTTTTGATAAAAACGCCGCAA
56645064 CTATACATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTACGC
391 CTATACATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTACGC
*
56645123 AGGACCACATTATAAGGGAAAAAAACATTAGTGGCGTTTGCATAGAAACGCCGCAACTATGTACC
1 AGGACCACATTATAAGGAAAAAAAACATTAGTGGCGTTTGCATAGAAACGCCGCAACTATGTACC
56645188 CATTTTTTTCAAAACGACGTCGTTCCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGGA
66 CATTTTTTTCAAAACGACGTCGTTCCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGGA
*
56645253 AAACGTCGTAAATATGTGTTATAGTTTCTCAGAACGGCACCGTTTCAGAAGAGGAGTGTAATCTA
131 AAACGCCGTAAATATGTGTTATAGTTTCTCAGAACGGCACCGTTTCAGAAGAGGAGTGTAATCTA
*
56645318 TTAGTGGCGTTTATGCTAAAAACGCCACAATTATGTATTAATGTTTTTCAAAACGTCACCGTTTC
196 TTAGTGGCGTTTATGCTAAAAACGCCGCAATTATGTATTAATGTTTTTCAAAACGTCACCGTTTC
* * * *
56645383 TCTTCAGGACTTGAAATTTTAGTGGCGTTTTTT-GGGAAACGCCAGAACTATGGATTAAAGTTTC
261 TCTTCAGGACTTGAAATTTTAGTGGCGTTTTTTCGGAAAACGCCGGAAATATGAATTAAAGTTTC
* * * *
56645447 TTAAAACGGCACCGTTTCTATTCAGTAAGGTAATTTTTAGTGGCGTTTTTGCTAAAAACGCCACA
326 TTAAAACGGCACTGTTTCT-TTCAGTAAGTTAATTTTTAGTGGCGTTTTTGATAAAAACGCCGCA
* * * * *
56645512 AATATATATTTAAGGTTCTTAAAACGGTGCTGTTTCGGAATTTAATTTTGGAAATTA
390 ACTATACATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTA
56645569 TGGAAGCAAT
Statistics
Matches: 832, Mismatches: 49, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
439 1 0.00
440 180 0.22
441 18 0.02
443 3 0.00
444 1 0.00
445 1 0.00
446 1 0.00
448 427 0.51
449 160 0.19
450 40 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (449 bp):
AGGACCACATTATAAGGAAAAAAAACATTAGTGGCGTTTGCATAGAAACGCCGCAACTATGTACC
CATTTTTTTCAAAACGACGTCGTTCCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGGA
AAACGCCGTAAATATGTGTTATAGTTTCTCAGAACGGCACCGTTTCAGAAGAGGAGTGTAATCTA
TTAGTGGCGTTTATGCTAAAAACGCCGCAATTATGTATTAATGTTTTTCAAAACGTCACCGTTTC
TCTTCAGGACTTGAAATTTTAGTGGCGTTTTTTCGGAAAACGCCGGAAATATGAATTAAAGTTTC
TTAAAACGGCACTGTTTCTTTCAGTAAGTTAATTTTTAGTGGCGTTTTTGATAAAAACGCCGCAA
CTATACATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTACGC
Found at i:56645485 original size:82 final size:82
Alignment explanation
Indices: 56645337--56645496 Score: 198
Period size: 82 Copynumber: 2.0 Consensus size: 82
56645327 TTTATGCTAA
* * * * * * *
56645337 AAACGCCACAATTATGTATTAATGTTTTTCAAAACGTCACCGTTTCTCTTCAGGACTTGAAATTT
1 AAACGCCACAACTATGGATTAAAGTTTTTCAAAACGGCACCGTTTCTATTCAGAACGTGAAATTT
56645402 TAGTGGCGTTTTTTGGG
66 TAGTGGCGTTTTTTGGG
* * *
56645419 AAACGCCAGAACTATGGATTAAAGTTTCTT-AAAACGGCACCGTTTCTATTCAGTAAGGT-AATT
1 AAACGCCACAACTATGGATTAAAGTTT-TTCAAAACGGCACCGTTTCTATTCAG-AACGTGAAAT
56645482 TTTAGTGGCGTTTTT
64 TTTAGTGGCGTTTTT
56645497 GCTAAAAACG
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
82 62 0.94
83 4 0.06
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (82 bp):
AAACGCCACAACTATGGATTAAAGTTTTTCAAAACGGCACCGTTTCTATTCAGAACGTGAAATTT
TAGTGGCGTTTTTTGGG
Found at i:56645547 original size:83 final size:83
Alignment explanation
Indices: 56645318--56645539 Score: 211
Period size: 83 Copynumber: 2.7 Consensus size: 83
56645308 GTGTAATCTA
* * * *
56645318 TTAGTGGCGTTTATGCTAAAAACGCCACAATTATGTA-TTAATGTTTTTCAAAAC-GTCACCGTT
1 TTAGTGGCGTTTTTGCTAAAAACGCCACAAATATGTATTTAAGGTTCTT-AAAACGGT-ACCGTT
* * *
56645381 TCTCTTCAGGACTTGAAATT
64 TCTATTCAGAACGTGAAATT
** * * * * * *
56645401 TTAGTGGCGTTTTT--TGGGAAACGCCAGAACTATGGATTAAAGTTTCTTAAAACGGCACCGTTT
1 TTAGTGGCGTTTTTGCT-AAAAACGCCACAAATATGTATTTAAGGTTCTTAAAACGGTACCGTTT
* *
56645464 CTATTCAGTAAGGT-AATTT
65 CTATTCAG-AACGTGAAATT
*
56645483 TTAGTGGCGTTTTTGCTAAAAACGCCACAAATATATATTTAAGGTTCTTAAAACGGT
1 TTAGTGGCGTTTTTGCTAAAAACGCCACAAATATGTATTTAAGGTTCTTAAAACGGT
56645540 GCTGTTTCGG
Statistics
Matches: 108, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
81 1 0.01
82 52 0.48
83 54 0.50
84 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (83 bp):
TTAGTGGCGTTTTTGCTAAAAACGCCACAAATATGTATTTAAGGTTCTTAAAACGGTACCGTTTC
TATTCAGAACGTGAAATT
Found at i:56645781 original size:14 final size:14
Alignment explanation
Indices: 56645743--56645781 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
56645733 ATCGAAAGGA
*
56645743 AAAGAAAAAAATAG
1 AAAGAAAAAAATAC
**
56645757 AAAGACCAAAATAC
1 AAAGAAAAAAATAC
56645771 AAAGAAAAAAA
1 AAAGAAAAAAA
56645782 ATCAGAGGAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.77, C:0.08, G:0.10, T:0.05
Consensus pattern (14 bp):
AAAGAAAAAAATAC
Found at i:56646124 original size:16 final size:16
Alignment explanation
Indices: 56646103--56646163 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
56646093 ACCTGTTTTC
56646103 TTATTTTGGTATCTAA
1 TTATTTTGGTATCTAA
* **
56646119 TTATTTTGGTATAATTC
1 TTATTTTGGTAT-CTAA
56646136 TTATTTTGGTATCTAA
1 TTATTTTGGTATCTAA
56646152 TTATTTTGGTAT
1 TTATTTTGGTAT
56646164 ACTCAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 25 0.66
17 13 0.34
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.59
Consensus pattern (16 bp):
TTATTTTGGTATCTAA
Found at i:56646137 original size:33 final size:33
Alignment explanation
Indices: 56646100--56646164 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
56646090 TATACCTGTT
56646100 TTCTTATTTTGGTATCTAATTATTTTGGTATAA
1 TTCTTATTTTGGTATCTAATTATTTTGGTATAA
56646133 TTCTTATTTTGGTATCTAATTATTTTGGTATA
1 TTCTTATTTTGGTATCTAATTATTTTGGTATA
56646165 CTCAAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.58
Consensus pattern (33 bp):
TTCTTATTTTGGTATCTAATTATTTTGGTATAA
Found at i:56646593 original size:12 final size:12
Alignment explanation
Indices: 56646578--56646609 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
56646568 ATTCTTGGGT
56646578 TTTGTTTTCTAG
1 TTTGTTTTCTAG
56646590 TTTGTTTTCTAG
1 TTTGTTTTCTAG
*
56646602 TCTGTTTT
1 TTTGTTTT
56646610 GCGAGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.09, G:0.16, T:0.69
Consensus pattern (12 bp):
TTTGTTTTCTAG
Found at i:56647618 original size:29 final size:30
Alignment explanation
Indices: 56647577--56647636 Score: 68
Period size: 33 Copynumber: 1.9 Consensus size: 30
56647567 GATTAGTTTA
*
56647577 TTCGGTTTAATG-TGAATAAATTATCGATT
1 TTCGATTTAATGATGAATAAATTATCGATT
*
56647606 TTCGATTTTATGTCAATGAATAAATTATCGA
1 TTCGATTTAATG---ATGAATAAATTATCGA
56647637 CGTTAGATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 10 0.40
33 15 0.60
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (30 bp):
TTCGATTTAATGATGAATAAATTATCGATT
Found at i:56647682 original size:11 final size:11
Alignment explanation
Indices: 56647662--56647694 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
56647652 ATTGATTGAC
*
56647662 TGTCAGTGAAT
1 TGTCAATGAAT
56647673 TGTCAATGAA-
1 TGTCAATGAAT
56647683 TGTCAATGAAT
1 TGTCAATGAAT
56647694 T
1 T
56647695 ATTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (11 bp):
TGTCAATGAAT
Found at i:56647775 original size:13 final size:13
Alignment explanation
Indices: 56647729--56647855 Score: 62
Period size: 13 Copynumber: 9.4 Consensus size: 13
56647719 TATAACTTAC
*
56647729 ATTACGTAAATAT
1 ATTACTTAAATAT
* *
56647742 ATTAATTACTAAAAT
1 ATTACTTA--AATAT
56647757 -TTACTTAAATAT
1 ATTACTTAAATAT
*
56647769 ATTACTTAAATAC
1 ATTACTTAAATAT
* *
56647782 ATTACTT-ACTAA
1 ATTACTTAAATAT
* * *
56647794 AGTTAAAGTATATATTAC
1 A-TT--ACT-TA-AATAT
*
56647812 ATTACTTACAT-T
1 ATTACTTAAATAT
*
56647824 ACTTACTAAAATAT
1 A-TTACTTAAATAT
56647838 ATTACTTAAATAT
1 ATTACTTAAATAT
56647851 ATTAC
1 ATTAC
56647856 ATTACTTAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
12 9 0.11
13 51 0.60
14 10 0.12
15 8 0.09
16 1 0.01
17 2 0.02
18 4 0.05
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:56647822 original size:9 final size:9
Alignment explanation
Indices: 56647808--56647883 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
56647798 AAAGTATATA
56647808 TTACATTAC
1 TTACATTAC
56647817 TTACATTAC
1 TTACATTAC
* *
56647826 TTAC-TAAA
1 TTACATTAC
* *
56647834 ATATATTAC
1 TTACATTAC
*
56647843 TTAAATATA-
1 TTACAT-TAC
56647852 TTACATTAC
1 TTACATTAC
*
56647861 TTAAAATTA-
1 TT-ACATTAC
56647870 TTACATTAC
1 TTACATTAC
56647879 TTACA
1 TTACA
56647884 AAAATTTTTA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
8 11 0.22
9 33 0.65
10 7 0.14
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.43
Consensus pattern (9 bp):
TTACATTAC
Found at i:56647861 original size:18 final size:18
Alignment explanation
Indices: 56647838--56647927 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
56647828 ACTAAAATAT
56647838 ATTACTTAAATATATTAC
1 ATTACTTAAATATATTAC
56647856 ATTACTTAAA-ATTATTAC
1 ATTACTTAAATA-TATTAC
*
56647874 ATTACTTACAAAAATTTTTAACTTAC
1 ATTACTT----AAA--TAT-A-TTAC
56647900 ATTACTTAAATATATTAC
1 ATTACTTAAATATATTAC
56647918 ATTACTTAAA
1 ATTACTTAAA
56647928 ATTTATATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
17 1 0.02
18 37 0.62
19 1 0.02
20 2 0.03
22 6 0.10
24 1 0.02
25 1 0.02
26 11 0.18
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTACTTAAATATATTAC
Found at i:56648215 original size:9 final size:9
Alignment explanation
Indices: 56648197--56648413 Score: 146
Period size: 9 Copynumber: 25.8 Consensus size: 9
56648187 CTTATATATA
*
56648197 AACTTGCAT
1 AACTTACAT
56648206 AACTTACAT
1 AACTTACAT
*
56648215 AA-TAACATAAT
1 AACTTAC---AT
56648226 AACTTACAT
1 AACTTACAT
*
56648235 TA--TACAT
1 AACTTACAT
*
56648242 AACCTACAT
1 AACTTACAT
56648251 AACTTACAT
1 AACTTACAT
*
56648260 AA--TACAC
1 AACTTACAT
56648267 AACTTACAT
1 AACTTACAT
*
56648276 AACTTAAAT
1 AACTTACAT
56648285 AACTTACAT
1 AACTTACAT
*
56648294 -AC-T--GT
1 AACTTACAT
**
56648299 AACTTTGAT
1 AACTTACAT
*
56648308 AACTAACAT
1 AACTTACAT
* *
56648317 TA--TACAC
1 AACTTACAT
56648324 AACTTACAT
1 AACTTACAT
56648333 AA--TACAT
1 AACTTACAT
*
56648340 TACTTACAT
1 AACTTACAT
56648349 AACTTACAT
1 AACTTACAT
56648358 AA--TA-AT
1 AACTTACAT
56648364 AACTTACAT
1 AACTTACAT
*
56648373 AA--TACAC
1 AACTTACAT
56648380 AACTTACAT
1 AACTTACAT
*
56648389 AACTTAAAT
1 AACTTACAT
56648398 AACTTACAT
1 AACTTACAT
56648407 AACTTAC
1 AACTTAC
56648414 CCGTGCAATT
Statistics
Matches: 161, Mismatches: 26, Indels: 42
0.70 0.11 0.18
Matches are distributed among these distances:
5 1 0.01
6 6 0.04
7 32 0.20
8 7 0.04
9 108 0.67
11 4 0.02
12 3 0.02
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:56648255 original size:25 final size:25
Alignment explanation
Indices: 56648216--56648408 Score: 125
Period size: 25 Copynumber: 7.9 Consensus size: 25
56648206 AACTTACATA
*
56648216 ATAACATA-ATAACTTACATTATAC
1 ATAACATACATAACTTACATAATAC
*
56648240 ATAACCTACATAACTTACATAATAC
1 ATAACATACATAACTTACATAATAC
* * *
56648265 ACAACTTACATAACTTAAAT-A-AC
1 ATAACATACATAACTTACATAATAC
* * **
56648288 -TTACATACTGTAACTTTGATAACTAAC
1 ATAACATAC-ATAACTTACATAA-T-AC
* *
56648315 AT--TATACACAACTTACATAATAC
1 ATAACATACATAACTTACATAATAC
* *
56648338 ATTACTTACATAACTTACATAATA-
1 ATAACATACATAACTTACATAATAC
* *
56648362 ATAACTTACATAA--TACACAACTTAC
1 ATAACATACATAACTTACATAA--TAC
* *
56648387 ATAACTTAAATAACTTACATAA
1 ATAACATACATAACTTACATAA
56648409 CTTACCCGTG
Statistics
Matches: 132, Mismatches: 23, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
22 11 0.08
23 14 0.11
24 24 0.18
25 70 0.53
26 4 0.03
27 8 0.06
28 1 0.01
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.32
Consensus pattern (25 bp):
ATAACATACATAACTTACATAATAC
Found at i:56648372 original size:40 final size:41
Alignment explanation
Indices: 56648197--56648413 Score: 142
Period size: 41 Copynumber: 5.2 Consensus size: 41
56648187 CTTATATATA
* * *
56648197 AACTTGCATAACTTACATAATAACATAATAACTTACATTATACAT
1 AACTTACATAAC-TACATAATTAC---ATAACTTACATAATACAT
* * *
56648242 AACCTACATAACTTACATAA-TACACAACTTACATAACTTAAAT
1 AACTTACATAAC-TACATAATTACATAACTTACATAA--TACAT
* ** * * *
56648285 AACTTACAT-ACT--GTAACTTTGATAACTAACATTATACAC
1 AACTTACATAACTACATAA-TTACATAACTTACATAATACAT
*
56648324 AACTTACATAA-TACATTACTTACATAACTTACATAATA-AT
1 AACTTACATAACTACA-TAATTACATAACTTACATAATACAT
* *
56648364 AACTTACATAA-TACACAACTTACATAACTTAAATAACTTACAT
1 AACTTACATAACTACATAA-TTACATAACTTACATAA--TACAT
56648407 AACTTAC
1 AACTTAC
56648414 CCGTGCAATT
Statistics
Matches: 135, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
39 17 0.13
40 33 0.24
41 38 0.28
42 6 0.04
43 21 0.16
44 2 0.01
45 18 0.13
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (41 bp):
AACTTACATAACTACATAATTACATAACTTACATAATACAT
Found at i:56648387 original size:31 final size:33
Alignment explanation
Indices: 56648344--56648408 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 33
56648334 ATACATTACT
*
56648344 TACATAACTTACATAA-T-AATAACTTACATAA
1 TACACAACTTACATAACTAAATAACTTACATAA
56648375 TACACAACTTACATAACTTAAATAACTTACATAA
1 TACACAACTTACATAAC-TAAATAACTTACATAA
56648409 CTTACCCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 15 0.50
33 1 0.03
34 14 0.47
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (33 bp):
TACACAACTTACATAACTAAATAACTTACATAA
Found at i:56653920 original size:66 final size:66
Alignment explanation
Indices: 56653814--56653983 Score: 243
Period size: 66 Copynumber: 2.6 Consensus size: 66
56653804 AGCAAATTAC
* * * *
56653814 ACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTC-AAAAAAGATATGAAGAACTCCAG
1 ACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGGTTCAAAAAAAG-TATGAAGAACTCCAG
*
56653878 CT
65 CA
*
56653880 ACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCCGAGGTTCAAAAAAAGTATGAAGAACTCCAGC
1 ACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGGTTCAAAAAAAGTATGAAGAACTCCAGC
56653945 A
66 A
* * *
56653946 ACAGCTTAAAGCAGATGCGGCAGCGAGAGAAGCAGAGG
1 ACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGG
56653984 CTGCAACGAG
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
66 87 0.93
67 7 0.07
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (66 bp):
ACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGGTTCAAAAAAAGTATGAAGAACTCCAGC
A
Found at i:56653978 original size:21 final size:21
Alignment explanation
Indices: 56653954--56654045 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 21
56653944 CAACAGCTTA
* *
56653954 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAACGAGAG
* *
56653975 AAGCAGAGGCTGCAACGAGGG
1 AAGCAGAGGCGGCAACGAGAG
** *
56653996 AAGCAGAGGC-TAAAGCGAGGG
1 AAGCAGAGGCGGCAA-CGAGAG
* * * *
56654017 AAGTAGAAGCTGCAACGAGGG
1 AAGCAGAGGCGGCAACGAGAG
56654038 AAGCAGAG
1 AAGCAGAG
56654046 CAGCGTAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.41, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:56654428 original size:43 final size:43
Alignment explanation
Indices: 56654381--56654602 Score: 261
Period size: 43 Copynumber: 5.1 Consensus size: 43
56654371 AAAAATGCCA
* *
56654381 CTAAAGAGAAGGGTCTTTAGCGGCGTTTGTGTAGAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGAAGAAAGCGCCG
* * *
56654424 CTAAAGATAAAGGTCATTTA-CGGCGTTTTTGGAGAAAGCGCCG
1 CTAAAGATAAGGGTC-TTTAGCGGCGTTTGTGAAGAAAGCGCCG
* * *
56654467 CTAAAGA-AAGGGGTCTTTTTGCGGCGTTTCTGGAGAAAGCGCCG
1 CTAAAGATAA-GGGTC-TTTAGCGGCGTTTGTGAAGAAAGCGCCG
* *
56654511 CTAAAGACT-AGGTTCTTTAGCGGCGTTTGTGAAAAAAGCGCCG
1 CTAAAGA-TAAGGGTCTTTAGCGGCGTTTGTGAAGAAAGCGCCG
* * * *
56654554 CTAAAGATCAGGTTCTTTATCGGCGTTTGTGAAAAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGAAGAAAGCGCCG
56654597 CTAAAG
1 CTAAAG
56654603 GTCCTCGTCT
Statistics
Matches: 159, Mismatches: 14, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
42 3 0.02
43 118 0.74
44 37 0.23
45 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (43 bp):
CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGAAGAAAGCGCCG
Found at i:56654514 original size:87 final size:87
Alignment explanation
Indices: 56654354--56654602 Score: 258
Period size: 87 Copynumber: 2.9 Consensus size: 87
56654344 TCTGCCAAAA
* * * ** * * *
56654354 TTAGTGGCGTTTTTTAAAAAAATGCCACTAAAGAGAAGGGTC-TTTAGCGGCGTTTGTGTAGAAA
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGAGAAGGGTCTTTTTGCGGCGTTTGTGAAGAAA
56654418 GCGCCGCTAAAGA-TAAAGG-TCAT
66 GCGCCGCTAAAGACT--AGGTTC-T
* * * * *
56654441 TTA-CGGCGTTTTTGGAGAAAGCGCCGCTAAAGA-AAGGGGTCTTTTTGCGGCGTTTCTGGAGAA
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGAGAA-GGGTCTTTTTGCGGCGTTTGTGAAGAA
56654504 AGCGCCGCTAAAGACTAGGTTCT
65 AGCGCCGCTAAAGACTAGGTTCT
** * * *
56654527 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCAGGTTCTTTAT-CGGCGTTTGTGAAAAAA
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGAGAAGGGTCTTTTTGCGGCGTTTGTGAAGAAA
56654591 GCGCCGCTAAAG
66 GCGCCGCTAAAG
56654603 GTCCTCGTCT
Statistics
Matches: 137, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
85 2 0.01
86 61 0.45
87 72 0.53
88 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.27
Consensus pattern (87 bp):
TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGAGAAGGGTCTTTTTGCGGCGTTTGTGAAGAAA
GCGCCGCTAAAGACTAGGTTCT
Found at i:56654614 original size:43 final size:43
Alignment explanation
Indices: 56654394--56654673 Score: 210
Period size: 43 Copynumber: 6.3 Consensus size: 43
56654384 AAGAGAAGGG
* * * * *
56654394 TCTTTAGCGGCGTTTGTGTAGAAAGCGCCGCTAAAGATAAAGG
1 TCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCACGT
* * * * * *
56654437 TCATTTA-CGGCGTTTTTGGAGAAAGCGCCGCTAAAGA-AAGGGG
1 TC-TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCA-CGT
* * * * *
56654480 TCTTTTTGCGGCGTTTCTGGAGAAAGCGCCGCTAAAGA-CTAGGT
1 TC-TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATC-ACGT
*
56654524 TCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCAGGT
1 TCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCACGT
* * *
56654567 TCTTTATCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTCG-
1 TCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGAT-CACGT
* * *
56654610 TCTTTAGCGGCATTTTTAGTAAAAAA-CGCCGCTAAAGTTAGCGACGCCT
1 TCTTTAGCGGCGTTTGT-G-AAAAAAGCGCCGCTAAAG--ATC-ACG--T
56654659 TCTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTT
56654674 TTCCTGGCGC
Statistics
Matches: 200, Mismatches: 23, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
42 2 0.01
43 122 0.61
44 52 0.26
45 8 0.04
46 2 0.01
49 14 0.07
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCACGT
Found at i:56654640 original size:130 final size:130
Alignment explanation
Indices: 56654370--56654646 Score: 299
Period size: 130 Copynumber: 2.1 Consensus size: 130
56654360 GCGTTTTTTA
* * * * *
56654370 AAAAAATGCCACTAAAGAGAAGGGTCTTTAGCGGCGTTTGTGTAGAAAGCGCCGCTAAAGATAAA
1 AAAAAACGCCGCTAAAGACAAGGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATAAA
* * * * * * *
56654435 GGTCATTTACGGCGTTTTTGGAGAAAGCGCCGCTAAAGAAAGGGGTCTTTTTGCGGCGTTTCTGG
66 GGTCATTTACGGCGTTTGTGAAAAAAGCGCCGCTAAAGAAACGCGTCTTTTAGCGGCATTTCTGG
* * * * *
56654500 AGAAAGCGCCGCTAAAGACTAGGTTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGAT-CA
1 AAAAAACGCCGCTAAAGACAAGGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATAAA
*** * *
56654564 GGTTC-TTTATCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTCGTC-TTTAGCGGCATTTTT
66 GG-TCATTTA-CGGCGTTTGTGAAAAAAGCGCCGCTAAAGAAACGCGTCTTTTAGCGGCATTTCT
*
56654627 AGT
129 -GG
56654630 AAAAAACGCCGCTAAAG
1 AAAAAACGCCGCTAAAG
56654647 TTAGCGACGC
Statistics
Matches: 119, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
129 19 0.16
130 100 0.84
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (130 bp):
AAAAAACGCCGCTAAAGACAAGGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATAAA
GGTCATTTACGGCGTTTGTGAAAAAAGCGCCGCTAAAGAAACGCGTCTTTTAGCGGCATTTCTGG
Found at i:56654641 original size:87 final size:84
Alignment explanation
Indices: 56654354--56654646 Score: 268
Period size: 86 Copynumber: 3.4 Consensus size: 84
56654344 TCTGCCAAAA
* * * * * *
56654354 TTAGTGGCGTTTTTTAAAAAAATGCCACTAAAGAGAAGGGTCTTTAGCGGCGTTTGTGTAGAAAG
1 TTAGCGGCG-TTTTTGAAAAAACGCCGCTAAAGA-AAGGGTCTTTATCGGCGTTTGTGAAGAAAG
* **
56654419 CGCCGCTAAAGATAAAGGTCAT
64 CGCCGCTAAAGGTACTGGTC-T
* * * * *
56654441 TTA-CGGCGTTTTTGGAGAAAGCGCCGCTAAAGAAAGGGGTCTTTTTGCGGCGTTTCTGGAGAAA
1 TTAGCGGCGTTTTT-GAAAAAACGCCGCTAAAGAAA-GGGTCTTTAT-CGGCGTTTGTGAAGAAA
56654505 GCGCCGCTAAA-G-ACTAGGTTCT
63 GCGCCGCTAAAGGTACT-GG-TCT
* * * *
56654527 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCAGGTTCTTTATCGGCGTTTGTGAAAAAAG
1 TTAGCGGCGTTTTTGAAAAAA-CGCCGCTAAAGA-AAGGGTCTTTATCGGCGTTTGTGAAGAAAG
* *
56654592 CGCCGCTAAAGGTCCTCGTCT
64 CGCCGCTAAAGGTACTGGTCT
*
56654613 TTAGCGGCATTTTTAGTAAAAAACGCCGCTAAAG
1 TTAGCGGCGTTTTT-G-AAAAAACGCCGCTAAAG
56654647 TTAGCGACGC
Statistics
Matches: 168, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
85 8 0.05
86 77 0.46
87 74 0.44
88 9 0.05
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (84 bp):
TTAGCGGCGTTTTTGAAAAAACGCCGCTAAAGAAAGGGTCTTTATCGGCGTTTGTGAAGAAAGCG
CCGCTAAAGGTACTGGTCT
Found at i:56655699 original size:28 final size:28
Alignment explanation
Indices: 56655659--56655784 Score: 180
Period size: 28 Copynumber: 4.5 Consensus size: 28
56655649 TGACTTCCGA
*
56655659 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
56655687 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
56655715 CACTAAGTGTACGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
56655743 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
56655771 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
56655785 ACTTATTAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 87 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:56656592 original size:70 final size:70
Alignment explanation
Indices: 56656495--56657063 Score: 754
Period size: 70 Copynumber: 8.1 Consensus size: 70
56656485 ATGTTCATGT
* * *
56656495 AATTTTTATGCTTAAATGCT-ATCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGCT-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATG
56656559 CTGTCC
65 CTGTCC
* * * * *
56656565 AATCTTGATG-TAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGCATATATG
1 AATTTTTATGCT-AAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATG
56656629 CTGTCC
65 CTGTCC
* * *
56656635 AATTTTTATGCTTAAATGCTG-TCCAATTTGTTGTATTTATGCTGCCCAAATTGGTGCATATTTG
1 AATTTTTATGCTAAAATGCTGCT-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATG
* *
56656699 CTCTCA
65 CTGTCC
*
56656705 AATTTTTATGCTAAAATGATG-TCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATG
1 AATTTTTATGCTAAAATGCTGCT-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATG
56656769 CTGTCC
65 CTGTCC
* *
56656775 AATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
1 AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
56656840 TGTCC
66 TGTCC
* * * *
56656845 AATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTACCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
56656910 TGTCC
66 TGTCC
* * * * * * *
56656915 AATTTTGATG-TAAAAATGCTGTTAAATTTGGTATATATATAGGCTGCCCAAATTGTTGTATATA
1 AATTTTTATGCT-AAAATGCTGCTCAATTT-GT-TGTATTTATGCTGCCCAAATTGTTGCATATA
56656979 TGCTGTCC
63 TGCTGTCC
* * *
56656987 AATTTTTATGCTAAAATGCTGCTCAATTTGATTG-ATATATGTTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGCTCAATTTG-TTGTATTTATGCTGCCCAAATTGTTGCATATATG
56657051 CTGTCC
65 CTGTCC
56657057 AATTTTT
1 AATTTTT
56657064 GGTGTGAAAA
Statistics
Matches: 445, Mismatches: 44, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
69 3 0.01
70 375 0.84
71 6 0.01
72 60 0.13
73 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (70 bp):
AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
TGTCC
Found at i:56656857 original size:210 final size:210
Alignment explanation
Indices: 56656495--56657063 Score: 838
Period size: 210 Copynumber: 2.7 Consensus size: 210
56656485 ATGTTCATGT
* *
56656495 AATTTTTATGCTTAAATGCTATCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
* * * *
56656560 TGTCCAATCTTGATG-TAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGCAT
66 TGTCCAATTTTTATGCT-AAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGCAT
* *
56656624 ATATGCTGTCCAATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGG
130 ATATGCTGTCCAATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTACCCAAATTGG
*
56656689 TGCATATTTGCTCTCA
195 TGCATATATGCTCTCA
* *
56656705 AATTTTTATGCTAAAATGATGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
* * *
56656770 TGTCCAATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATA
66 TGTCCAATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGCATA
*
56656835 TATGCTGTCCAATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTACCCAAATTGTT
131 TATGCTGTCCAATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTACCCAAATTGGT
* * *
56656900 GTATATATGCTGTCC
196 GCATATATGCTCTCA
* ** * * *
56656915 AATTTTGATG-TAAAAATGCTGTTAAATTTGGTATATATATAGGCTGCCCAAATTGTTGTATATA
1 AATTTTTATGCT-AAAATGCTGTCCAATTT-GT-TGTATTTATGCTGCCCAAATTGTTGTATATA
*
56656979 TGCTGTCCAATTTTTATGCTAAAATGCTGCTCAATTTGATTG-ATATATGTTGCCCAAATTGTTG
63 TGCTGTCCAATTTTTATGCTAAAATGCTGCTCAATTTG-TTGTATATATGCTGCCCAAATTGTTG
*
56657043 TATATATGCTGTCCAATTTTT
127 CATATATGCTGTCCAATTTTT
56657064 GGTGTGAAAA
Statistics
Matches: 323, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
209 1 0.00
210 213 0.66
211 3 0.01
212 103 0.32
213 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (210 bp):
AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
TGTCCAATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGCATA
TATGCTGTCCAATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTACCCAAATTGGT
GCATATATGCTCTCA
Found at i:56657373 original size:72 final size:72
Alignment explanation
Indices: 56657284--56657424 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
56657274 TTAAATTTTC
56657284 ATTAGGTAAATGATAATGATATGGTTGAATTTTTGAAACATGGTTAGTATATGAAATTTGATTAA
1 ATTAGGTAAATGATAATGATATGGTTGAATTTTTGAAACATGGTTAGTATATGAAATTTGATTAA
56657349 TGATTTG
66 TGATTTG
*
56657356 ATTATGTAAATGATAATGATATGGTTGAATTTTTGAAACATGGTTAGTATATGAAATTTGATTAA
1 ATTAGGTAAATGATAATGATATGGTTGAATTTTTGAAACATGGTTAGTATATGAAATTTGATTAA
56657421 TGAT
66 TGAT
56657425 GCATGTTGAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (72 bp):
ATTAGGTAAATGATAATGATATGGTTGAATTTTTGAAACATGGTTAGTATATGAAATTTGATTAA
TGATTTG
Done.