Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 103 of 163
Found at i:33354166 original size:43 final size:43
Alignment explanation
Indices: 33354113--33354364 Score: 407
Period size: 43 Copynumber: 5.9 Consensus size: 43
33354103 GCATTTTTAG
*
33354113 AAAGCACCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTGTGGGA
33354156 AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTGTGGGA
*
33354199 AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTATGGGA
1 AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTGTGGGA
* * *
33354242 AAAGCGCAGCTAAAGGTCGT-GGTCTTTAGCAGCGTTTGTGTGA
1 AAAGCGCCGCTAAAGGTC-TCGGTCTTTAGCGGCGTTTGTGGGA
* *
33354285 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGA
1 AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTGTGGGA
* *
33354328 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGTGGCGTTT
1 AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTT
33354365 ATTTATAAAA
Statistics
Matches: 198, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
42 1 0.01
43 196 0.99
44 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGTCTCGGTCTTTAGCGGCGTTTGTGGGA
Found at i:33356642 original size:9 final size:9
Alignment explanation
Indices: 33356628--33356658 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33356618 GTTAAACGAA
33356628 TCGAGTTAT
1 TCGAGTTAT
*
33356637 TCGAGTTAA
1 TCGAGTTAT
33356646 TCGAGTTAT
1 TCGAGTTAT
33356655 TCGA
1 TCGA
33356659 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:33358925 original size:17 final size:19
Alignment explanation
Indices: 33358887--33358925 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33358877 ATTATTTATT
33358887 ATTATAAAATATTAGCTTAA
1 ATTATAAAATATTA-CTTAA
33358907 ATTA-AAAATATTA-TTAA
1 ATTATAAAATATTACTTAA
33358924 AT
1 AT
33358926 AAAGTATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
ATTATAAAATATTACTTAA
Found at i:33368911 original size:21 final size:23
Alignment explanation
Indices: 33368887--33368929 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
33368877 TTAATTTTTT
*
33368887 AAAACATATTT-CTTCT-TTTAG
1 AAAACAAATTTGCTTCTGTTTAG
33368908 AAAACAAATTTGCTTCTGTTTA
1 AAAACAAATTTGCTTCTGTTTA
33368930 TAATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (23 bp):
AAAACAAATTTGCTTCTGTTTAG
Found at i:33373739 original size:20 final size:21
Alignment explanation
Indices: 33373714--33373753 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
33373704 TACCTTCAGT
33373714 GGTATCACGATATCC-CCTTG
1 GGTATCACGATATCCACCTTG
*
33373734 GGTATCGCGATATCCACCTT
1 GGTATCACGATATCCACCTT
33373754 TTAAGGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
GGTATCACGATATCCACCTTG
Found at i:33375004 original size:13 final size:13
Alignment explanation
Indices: 33374986--33375010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33374976 TATTTTAATA
33374986 TTATTTTGTGTGT
1 TTATTTTGTGTGT
33374999 TTATTTTGTGTG
1 TTATTTTGTGTG
33375011 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:33375159 original size:75 final size:75
Alignment explanation
Indices: 33375036--33375183 Score: 287
Period size: 75 Copynumber: 2.0 Consensus size: 75
33375026 AAATTTCGTG
33375036 TTTTAATTTCGTCGTTTAAGCGTCCGATTTAATAAAAGGGCTTAATCGCGTAAAATAAAAATTTA
1 TTTTAATTTCGTCGTTTAAGCGTCCGATTTAATAAAAGGGCTTAATCGCGTAAAATAAAAATTTA
33375101 GGGGTTAATT
66 GGGGTTAATT
*
33375111 TTTTAATTTCGTCGTTTAAGCGTCCGATTTAATAAAAGGGCTTAATCGCGTAAAATGAAAATTTA
1 TTTTAATTTCGTCGTTTAAGCGTCCGATTTAATAAAAGGGCTTAATCGCGTAAAATAAAAATTTA
33375176 GGGGTTAA
66 GGGGTTAA
33375184 ATATAAAAGC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (75 bp):
TTTTAATTTCGTCGTTTAAGCGTCCGATTTAATAAAAGGGCTTAATCGCGTAAAATAAAAATTTA
GGGGTTAATT
Found at i:33378081 original size:45 final size:45
Alignment explanation
Indices: 33378010--33378253 Score: 443
Period size: 45 Copynumber: 5.4 Consensus size: 45
33378000 AATGATCTAA
* * *
33378010 ATGAATGAGGATCCCAATAAAAACCTTAAGCGATTTCGAGGGTCT
1 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
33378055 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
1 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
* *
33378100 ATGAATGAGGATCCAAATCAACACCTTAATCGATTTCGAGGGTTT
1 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
33378145 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
1 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
33378190 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
1 ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
33378235 ATGAATGAGGATCCAAATC
1 ATGAATGAGGATCCAAATC
33378254 GAGGGTTTAT
Statistics
Matches: 192, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 192 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (45 bp):
ATGAATGAGGATCCAAATCAACACCTTAAGCGATTTCGAGGGTCT
Found at i:33379335 original size:149 final size:147
Alignment explanation
Indices: 33379041--33379334 Score: 380
Period size: 149 Copynumber: 2.0 Consensus size: 147
33379031 GTGAATTAAG
* *
33379041 AGTAATTAGGTATAAGGACTAAATTGCATAAATGGTGAAAGTTGAGTTATAGATTAAAGAAAAAT
1 AGTAATTAGGTATAAGGACTAAATTACATAAATGGTGAAAGTTGAATTATAGATTAAAGAAAAAT
*** * * * *
33379106 TAAAGGGATTAAAGAAACAATTATGCTATTGTTTCTTTATGAGGCAGCATAAGGTAGATTTTTTT
66 TAAAAAAACTAAAGAAACAATTATGCTATTGTTTCTTTACGAGGCAGCATAAGCTAGA--TTATT
* *
33379171 TGTGAATTTATTATATAAA
129 TATAAATTTATTATATAAA
33379190 AGTAATTAGGTATAAGGACTAAATTACATATAAT-GTGAAAGTTGAATTATAGATTAAAGAAAAA
1 AGTAATTAGGTATAAGGACTAAATTACATA-AATGGTGAAAGTTGAATTATAGATTAAAGAAAAA
* *
33379254 TTAAAAAAACTAAAGAAGCAATTATGCTATTG-TTCTTTAACGAGG-TGACATAAGCTAAGA-TA
65 TTAAAAAAACTAAAGAAACAATTATGCTATTGTTTCTTT-ACGAGGCAG-CATAAGCT-AGATTA
*
33379316 TTTATAAATTTAATATATA
127 TTTATAAATTTATTATATA
33379335 TTATAATAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
147 17 0.13
148 7 0.06
149 97 0.76
150 6 0.05
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (147 bp):
AGTAATTAGGTATAAGGACTAAATTACATAAATGGTGAAAGTTGAATTATAGATTAAAGAAAAAT
TAAAAAAACTAAAGAAACAATTATGCTATTGTTTCTTTACGAGGCAGCATAAGCTAGATTATTTA
TAAATTTATTATATAAA
Found at i:33379378 original size:5 final size:5
Alignment explanation
Indices: 33379368--33379414 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
33379358 AATTATTAAG
33379368 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
33379415 ATGTATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:33379475 original size:17 final size:15
Alignment explanation
Indices: 33379440--33379480 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
33379430 AAAGAATTAA
33379440 AAAAAGAAATAAAGC
1 AAAAAGAAATAAAGC
*
33379455 AAAAACGAAATAGAAGG
1 AAAAA-GAAATA-AAGC
33379472 AAAAAGAAA
1 AAAAAGAAA
33379481 AGGGAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (15 bp):
AAAAAGAAATAAAGC
Found at i:33380451 original size:26 final size:26
Alignment explanation
Indices: 33380421--33380495 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
33380411 GCAACTCTTA
*
33380421 TGAGCGTCCC-ATTATATGGCTCTTCG
1 TGAGCGTCCCGATTA-AAGGCTCTTCG
* *
33380447 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCGTCCCGATTAAAGGCTCTTCG
* * * *
33380473 TGAGCTTCCTGAGTAATGGCTCT
1 TGAGCGTCCCGATTAAAGGCTCT
33380496 CCAGAGCTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 38 0.90
27 4 0.10
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (26 bp):
TGAGCGTCCCGATTAAAGGCTCTTCG
Found at i:33380507 original size:25 final size:24
Alignment explanation
Indices: 33380474--33380615 Score: 83
Period size: 24 Copynumber: 5.9 Consensus size: 24
33380464 GGCTCTTTGT
33380474 GAGCTTCCTGAGTAATGGCTCTCCA
1 GAGCTTCCTGA-TAATGGCTCTCCA
* **
33380499 GAGCTTCCTGAT-ATGGCTCGCTT
1 GAGCTTCCTGATAATGGCTCTCCA
** * * * *
33380522 GAATTTCCCGATTTATGGCTATCCG
1 GAGCTTCCTGA-TAATGGCTCTCCA
* *
33380547 GAGCTTCCTAATAATGGCTCTTCA
1 GAGCTTCCTGATAATGGCTCTCCA
* * * *
33380571 GAGCTACCTGTTATTGGCTC-ACA
1 GAGCTTCCTGATAATGGCTCTCCA
*
33380594 TGAGCTTTCC-GATTATGGCTCT
1 -GAGC-TTCCTGATAATGGCTCT
33380616 TATGAGCTTC
Statistics
Matches: 85, Mismatches: 27, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
23 18 0.21
24 39 0.46
25 28 0.33
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (24 bp):
GAGCTTCCTGATAATGGCTCTCCA
Found at i:33380610 original size:72 final size:73
Alignment explanation
Indices: 33380474--33380613 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 73
33380464 GGCTCTTTGT
* * * *
33380474 GAGCTTCCTGAGTAATGGCTCTCCAGAGCTTCCTGATATGGCTCGCTTGAATTTCCCGATTTATG
1 GAGCTTCCTGAATAATGGCTCTCCAGAGCTACCTGATATGGCTCACATGAATTTCCCGATTTATG
33380539 GCTATCCG
66 GCTATCCG
* * *
33380547 GAGCTTCCT-AATAATGGCTCTTCAGAGCTACCTGTTATTGGCTCACATGAGCTTT-CCGA-TTA
1 GAGCTTCCTGAATAATGGCTCTCCAGAGCTACCTGATA-TGGCTCACATGA-ATTTCCCGATTTA
33380609 TGGCT
64 TGGCT
33380614 CTTATGAGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
72 32 0.55
73 23 0.40
74 3 0.05
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (73 bp):
GAGCTTCCTGAATAATGGCTCTCCAGAGCTACCTGATATGGCTCACATGAATTTCCCGATTTATG
GCTATCCG
Found at i:33380612 original size:24 final size:23
Alignment explanation
Indices: 33380571--33380706 Score: 69
Period size: 24 Copynumber: 5.6 Consensus size: 23
33380561 TGGCTCTTCA
* *
33380571 GAGCTACCTGTTATTGGCTCACAT
1 GAGCTTCCCGTTA-TGGCTCACAT
* **
33380595 GAGCTTTCCGATTATGGCTCTTAT
1 GAGCTTCCCG-TTATGGCTCACAT
*
33380619 GAGCTTCCCGTTAT-GCAGCACGGAT
1 GAGCTTCCCGTTATGGC-TCAC--AT
* * * *
33380644 AATCTTCTCGTTAATGGCTCTCCA-
1 GAGCTTCCCGTT-ATGGCTC-ACAT
*
33380668 GAGCTTCCTGTTACATGGCTCACAT
1 GAGCTTCCCGTT--ATGGCTCACAT
*
33380693 GAGCTTCCTGTTAT
1 GAGCTTCCCGTTAT
33380707 ATGGCTCGAA
Statistics
Matches: 83, Mismatches: 20, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
22 2 0.02
23 7 0.08
24 34 0.41
25 34 0.41
26 3 0.04
27 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (23 bp):
GAGCTTCCCGTTATGGCTCACAT
Found at i:33380623 original size:72 final size:72
Alignment explanation
Indices: 33380447--33380626 Score: 175
Period size: 72 Copynumber: 2.5 Consensus size: 72
33380437 TGGCTCTTCG
* * * * *
33380447 TGAGCTTCCCGATTAAAGGCTCTTTGTGAGCTTCCTGAGTAATGGCTCTCCAGAGCTTCCTGATA
1 TGAGCTTTCCGATT-ATGGCTC-TTATGAGCTTCCTGAATAATGGCTCTCCAGAGCTACCTGATA
* *
33380512 TGGCTCGCT
64 TGGCTCACA
* * *** * *
33380521 TGA-ATTTCCCGATTTATGGCTATCCGGAGCTTCCT-AATAATGGCTCTTCAGAGCTACCTGTTA
1 TGAGCTTT-CCGA-TTATGGCTCTTATGAGCTTCCTGAATAATGGCTCTCCAGAGCTACCTGATA
33380584 TTGGCTCACA
64 -TGGCTCACA
33380594 TGAGCTTTCCGATTATGGCTCTTATGAGCTTCC
1 TGAGCTTTCCGATTATGGCTCTTATGAGCTTCC
33380627 CGTTATGCAG
Statistics
Matches: 84, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
72 41 0.49
73 26 0.31
74 15 0.18
75 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (72 bp):
TGAGCTTTCCGATTATGGCTCTTATGAGCTTCCTGAATAATGGCTCTCCAGAGCTACCTGATATG
GCTCACA
Found at i:33386350 original size:44 final size:44
Alignment explanation
Indices: 33386301--33386420 Score: 129
Period size: 44 Copynumber: 2.7 Consensus size: 44
33386291 GCACTAAAAG
* * * *
33386301 AACAGTAGGCACCAAAGTGCAAATC-ACTAAGCATCGAAGTGCAA
1 AACAGTAGGCACCAAACTGCAAAACGA-TAAGCACCAAAGTGCAA
*
33386345 AACAGTAGGCACCAAACTGCAAAACGATAAGCACCAAAGTGCGA
1 AACAGTAGGCACCAAACTGCAAAACGATAAGCACCAAAGTGCAA
* *
33386389 AACAGT-GAGCACTAAAGC-GCAAGACGATAAGC
1 AACAGTAG-GCACCAAA-CTGCAAAACGATAAGC
33386421 GCACTAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
43 1 0.02
44 63 0.95
45 2 0.03
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (44 bp):
AACAGTAGGCACCAAACTGCAAAACGATAAGCACCAAAGTGCAA
Found at i:33386365 original size:22 final size:22
Alignment explanation
Indices: 33386301--33386410 Score: 105
Period size: 22 Copynumber: 5.0 Consensus size: 22
33386291 GCACTAAAAG
*
33386301 AACAGTAGGCACCAAAGTGCAA
1 AACAGTAAGCACCAAAGTGCAA
* * * *
33386323 ATCACTAAGCATCGAAGTGCAA
1 AACAGTAAGCACCAAAGTGCAA
* *
33386345 AACAGTAGGCACCAAACTGCAA
1 AACAGTAAGCACCAAAGTGCAA
*
33386367 AAC-GATAAGCACCAAAGTGCGA
1 AACAG-TAAGCACCAAAGTGCAA
* * *
33386389 AACAGTGAGCACTAAAGCGCAA
1 AACAGTAAGCACCAAAGTGCAA
33386411 GACGATAAGC
Statistics
Matches: 68, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
21 1 0.01
22 66 0.97
23 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.11
Consensus pattern (22 bp):
AACAGTAAGCACCAAAGTGCAA
Found at i:33389319 original size:108 final size:109
Alignment explanation
Indices: 33389207--33389423 Score: 427
Period size: 108 Copynumber: 2.0 Consensus size: 109
33389197 ATGATTTTTG
33389207 GGTTTCGACTCAAAAGTTTAATAAAAATTTTAAAGATTTTTTTGTAATTTTTTTACATATATATT
1 GGTTTCGACTCAAAAGTTTAATAAAAATTTTAAAGATTTTTTTGTAATTTTTTTACATATATATT
33389272 TTGAACTTGTAGAAATTTTTTATTCATAA-TTTTATTTTTAAAA
66 TTGAACTTGTAGAAATTTTTTATTCATAATTTTTATTTTTAAAA
33389315 GGTTTCGACTCAAAAGTTTAATAAAAATTTTAAAGATTTTTTTGTAATTTTTTTACATATATATT
1 GGTTTCGACTCAAAAGTTTAATAAAAATTTTAAAGATTTTTTTGTAATTTTTTTACATATATATT
33389380 TTGAACTTGTAGAAATTTTTTATTCATAATTTTTATTTTTAAAA
66 TTGAACTTGTAGAAATTTTTTATTCATAATTTTTATTTTTAAAA
33389424 ATATTTTTAC
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 94 0.87
109 14 0.13
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (109 bp):
GGTTTCGACTCAAAAGTTTAATAAAAATTTTAAAGATTTTTTTGTAATTTTTTTACATATATATT
TTGAACTTGTAGAAATTTTTTATTCATAATTTTTATTTTTAAAA
Found at i:33389475 original size:12 final size:13
Alignment explanation
Indices: 33389453--33389491 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
33389443 AATAATTCAT
33389453 ATTTATTTTTAAG
1 ATTTATTTTTAAG
33389466 ATTT-TTTTTAAG
1 ATTTATTTTTAAG
* *
33389478 AATTATTGTTAAG
1 ATTTATTTTTAAG
33389491 A
1 A
33389492 AAAATGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (13 bp):
ATTTATTTTTAAG
Found at i:33396228 original size:1 final size:1
Alignment explanation
Indices: 33396195--33396219 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
33396185 AGTGGTTTCT
33396195 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
33396220 TTTCCCCCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:33401824 original size:2 final size:2
Alignment explanation
Indices: 33401817--33401842 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33401807 CTATTTTGCC
33401817 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
33401843 GTCACATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33402011 original size:15 final size:16
Alignment explanation
Indices: 33401993--33402027 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
33401983 AATTAAATTA
*
33401993 AAAAATTAT-GAATAT
1 AAAAATTATGGAAAAT
33402008 AAAAATTATGGAAAAT
1 AAAAATTATGGAAAAT
33402024 AAAA
1 AAAA
33402028 CACCAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
AAAAATTATGGAAAAT
Found at i:33416685 original size:22 final size:22
Alignment explanation
Indices: 33416657--33416699 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
33416647 TACACCAAAA
33416657 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCTTTTAGCGGCGCTTTTT
33416679 TAGGCTTTTAGCGGCGCTTTT
1 TAGGCTTTTAGCGGCGCTTTT
33416700 CTAGAAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
TAGGCTTTTAGCGGCGCTTTTT
Found at i:33421209 original size:19 final size:19
Alignment explanation
Indices: 33421185--33421226 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
33421175 AAATTATAAA
*
33421185 TTTTATTTTTTTATTTCAT
1 TTTTATTTTTGTATTTCAT
*
33421204 TTTTATTTTTGTATTTTAT
1 TTTTATTTTTGTATTTCAT
33421223 TTTT
1 TTTT
33421227 TCTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTGTATTTCAT
Found at i:33421490 original size:8 final size:8
Alignment explanation
Indices: 33421479--33421520 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
33421469 CCCTAAACTG
33421479 CTAACCCT
1 CTAACCCT
33421487 CTAACCC-
1 CTAACCCT
33421494 CTAAACCCT
1 CT-AACCCT
33421503 -TAACCCT
1 CTAACCCT
33421510 CTAACCC-
1 CTAACCCT
33421517 CTAA
1 CTAA
33421521 ACCTTAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 12 0.39
8 19 0.61
ACGTcount: A:0.31, C:0.48, G:0.00, T:0.21
Consensus pattern (8 bp):
CTAACCCT
Found at i:33421492 original size:23 final size:23
Alignment explanation
Indices: 33421465--33421544 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
33421455 CCCTAACGTT
*
33421465 TAACCCCTAAACTGC-TAACCCTC
1 TAACCCCTAAAC-CCTTAACCCTC
33421488 TAACCCCTAAACCCTTAACCCTC
1 TAACCCCTAAACCCTTAACCCTC
**
33421511 TAACCCCTAAA-CCTTAAATCTC
1 TAACCCCTAAACCCTTAACCCTC
*
33421533 -AACCCTTAAACC
1 TAACCCCTAAACC
33421545 ATAATCCCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
21 9 0.18
22 11 0.22
23 31 0.61
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.23
Consensus pattern (23 bp):
TAACCCCTAAACCCTTAACCCTC
Found at i:33421497 original size:15 final size:15
Alignment explanation
Indices: 33421465--33421520 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
33421455 CCCTAACGTT
*
33421465 TAACCCCTAA-ACTGC
1 TAACCCCTAACCCT-C
33421480 TAACCCTCTAACCC-C
1 TAACCC-CTAACCCTC
*
33421495 TAAACCCTTAACCCTC
1 T-AACCCCTAACCCTC
33421511 TAACCCCTAA
1 TAACCCCTAA
33421521 ACCTTAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 22 0.65
16 11 0.32
17 1 0.03
ACGTcount: A:0.32, C:0.45, G:0.02, T:0.21
Consensus pattern (15 bp):
TAACCCCTAACCCTC
Found at i:33421523 original size:8 final size:7
Alignment explanation
Indices: 33421451--33421520 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 7
33421441 CTAACTCTCT
33421451 TAACCCC
1 TAACCCC
***
33421458 TAACGTT
1 TAACCCC
33421465 TAACCCC
1 TAACCCC
**
33421472 TAAACTGC
1 T-AACCCC
33421480 TAACCCTC
1 TAACCC-C
33421488 TAACCCC
1 TAACCCC
*
33421495 TAAACCCT
1 T-AACCCC
33421503 TAACCCTC
1 TAACCC-C
33421511 TAACCCC
1 TAACCCC
33421518 TAA
1 TAA
33421521 ACCTTAAATC
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
7 23 0.49
8 24 0.51
ACGTcount: A:0.31, C:0.43, G:0.03, T:0.23
Consensus pattern (7 bp):
TAACCCC
Found at i:33421561 original size:15 final size:15
Alignment explanation
Indices: 33421539--33421573 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
33421529 TCTCAACCCT
33421539 TAAA-CCATAATCCC
1 TAAACCCATAATCCC
*
33421553 TAAACCCATACTCCC
1 TAAACCCATAATCCC
33421568 TAAACC
1 TAAACC
33421574 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCATAATCCC
Found at i:33422551 original size:41 final size:41
Alignment explanation
Indices: 33422506--33422852 Score: 404
Period size: 41 Copynumber: 8.9 Consensus size: 41
33422496 TTTTATTATT
* * * *
33422506 ATTAGCGGCGCTTTTTCAAAAATGCTGCTAAAGGCTAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* ** *
33422547 ATTAGCGGCGCTTTTTTGAAAACGCCGCT--------GAGT
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
33422580 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
33422621 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
33422662 ATTAGCGGCGCTTCTTCAAAAA-----C----GGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
33422694 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
** * * *
33422735 ACCAACGACGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* * * *
33422776 ACTAGCGGCGCTTATTGAAAAACCCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
33422817 ATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
33422853 CCAAAAACTC
Statistics
Matches: 263, Mismatches: 26, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
32 31 0.12
33 29 0.11
36 1 0.00
37 1 0.00
41 201 0.76
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:33422694 original size:32 final size:32
Alignment explanation
Indices: 33422653--33422717 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
33422643 CGCCGCTAAA
33422653 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAAC
1 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAAC
33422685 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAAC
1 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAAC
33422717 G
1 G
33422718 CCGCTAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (32 bp):
GGCCAGAGCATTAGCGGCGCTTCTTCAAAAAC
Found at i:33422707 original size:73 final size:73
Alignment explanation
Indices: 33422612--33422840 Score: 287
Period size: 73 Copynumber: 3.0 Consensus size: 73
33422602 CGCCGCTAAA
*
33422612 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCT
1 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGACGCTTCT
33422677 TCAAAAAC
66 TCAAAAAC
* ** *
33422685 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCACCAACGACGCTTCT
1 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGACGCTTCT
33422750 TCAAAAACGCCGC
66 TCAAAAA-----C
* * * * *
33422763 TAAAGGCCCGAGCACTAGCGGCGCTTATTGAAAAACCCCGCTAAAGGCCAGAGCATTAGCGACGC
1 ----GGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGACGC
33422828 TTCTTCAAAAAC
62 TTCTTCAAAAAC
33422840 G
1 G
33422841 CCGCTAAAGG
Statistics
Matches: 133, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
73 68 0.51
77 1 0.01
78 1 0.01
82 63 0.47
ACGTcount: A:0.30, C:0.31, G:0.24, T:0.16
Consensus pattern (73 bp):
GGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGACGCTTCT
TCAAAAAC
Found at i:33422748 original size:114 final size:114
Alignment explanation
Indices: 33422514--33422853 Score: 410
Period size: 114 Copynumber: 2.9 Consensus size: 114
33422504 TTATTAGCGG
* * * * * ** * *
33422514 CGCTTTTTCAAAAATGCTGCTAAAGGCTAGAGCATTAGCGGCGCTTTTTTGAAAACGCCGCTGAG
1 CGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTATTCAAAAACGGC-CAGAG
* * ** * *
33422579 TATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGG
65 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCACCAACGA
*
33422629 CGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGGCCAGAGC
1 CGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTATTCAAAAACGGCCAGAGC
33422694 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCACCAACGA
66 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCACCAACGA
* * *
33422743 CGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCACTAGCGGCGCTTATTGAAAAACCCCGCTAAA
1 CGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTATTCAAAAA-----C----
*
33422808 GGCCAGAGCATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGGCCC
57 GGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
33422854 CAAAAACTCA
Statistics
Matches: 196, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
114 99 0.51
115 51 0.26
119 1 0.01
123 45 0.23
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (114 bp):
CGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTATTCAAAAACGGCCAGAGC
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCACCAACGA
Found at i:33422959 original size:39 final size:40
Alignment explanation
Indices: 33422916--33423022 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
33422906 AGAAAATGCC
* *
33422916 GCTAATGCT-TATTTTTAGAGGCGTTTTCGGAGAAGAGCA
1 GCTAATGCTCTATTTTTAGAGGCGTTTTCAGAAAAGAGCA
** * * * * *
33422955 GCTAATGCTCTACCTTTAGCGGCATTTTTATAAAAGCGCA
1 GCTAATGCTCTATTTTTAGAGGCGTTTTCAGAAAAGAGCA
* *
33422995 GCTAATGCTCGATTTTTAGTGGCGTTTT
1 GCTAATGCTCTATTTTTAGAGGCGTTTT
33423023 TTATCCATGC
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
39 9 0.17
40 44 0.83
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (40 bp):
GCTAATGCTCTATTTTTAGAGGCGTTTTCAGAAAAGAGCA
Found at i:33423153 original size:8 final size:7
Alignment explanation
Indices: 33423130--33423170 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
33423120 GGGTTACAGA
*
33423130 TTTAATT
1 TTTAAAT
*
33423137 TTTATAT
1 TTTAAAT
33423144 TTTAAAAT
1 TTT-AAAT
33423152 TTTAAAT
1 TTTAAAT
33423159 TTTAAAT
1 TTTAAAT
33423166 TTTAA
1 TTTAA
33423171 TCCTAACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTAAAT
Found at i:33430852 original size:17 final size:17
Alignment explanation
Indices: 33430830--33430878 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
33430820 GTGACAAGTT
33430830 TTATTGAAATGAAATTG
1 TTATTGAAATGAAATTG
* *
33430847 TTATTGAAATAGCAAGTG
1 TTATTGAAAT-GAAATTG
*
33430865 ATA-TGAAATGAAAT
1 TTATTGAAATGAAAT
33430879 GTGTACTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 3 0.12
17 16 0.62
18 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (17 bp):
TTATTGAAATGAAATTG
Found at i:33435491 original size:28 final size:28
Alignment explanation
Indices: 33435424--33435491 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
33435414 AGAAGTTTGT
* * * *
33435424 CCTTCAAGGCACGCTTTGTTGTGTATAG
1 CCTTCAAGGCATGCTTCGTTGTATATAA
* *
33435452 CCTTCAAGGCATGCTTCGTTTTATTTAA
1 CCTTCAAGGCATGCTTCGTTGTATATAA
33435480 CCTTCAAGGCAT
1 CCTTCAAGGCAT
33435492 ATTTTATCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.37
Consensus pattern (28 bp):
CCTTCAAGGCATGCTTCGTTGTATATAA
Found at i:33439879 original size:19 final size:19
Alignment explanation
Indices: 33439833--33439879 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
33439823 AGTCCTTTTT
*
33439833 AAAATTAAAAGTAATAATG
1 AAAATTAAAAGTAATAATC
33439852 ATAAGATTAAAGAGTAATAA-C
1 A-AA-ATTAAA-AGTAATAATC
33439873 AAAATTA
1 AAAATTA
33439880 GAGCCCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 7 0.29
22 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.26
Consensus pattern (19 bp):
AAAATTAAAAGTAATAATC
Found at i:33445191 original size:3 final size:3
Alignment explanation
Indices: 33445183--33445214 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33445173 ATTACCCCTT
33445183 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
33445215 TAAGGGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:33445983 original size:31 final size:31
Alignment explanation
Indices: 33445942--33446019 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
33445932 AGACCCACTA
*
33445942 TTAACTTAATTTAATTACATTATATAACATT
1 TTAATTTAATTTAATTACATTATATAACATT
**
33445973 TTAATTTAATTTAATCGCATTATATAACATT
1 TTAATTTAATTTAATTACATTATATAACATT
33446004 TTAATTTAATTTAATT
1 TTAATTTAATTTAATT
33446020 TAATTTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (31 bp):
TTAATTTAATTTAATTACATTATATAACATT
Found at i:33446013 original size:5 final size:5
Alignment explanation
Indices: 33446003--33446033 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
33445993 TATATAACAT
33446003 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
33446034 CACATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:33446056 original size:46 final size:46
Alignment explanation
Indices: 33445972--33446067 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
33445962 TATATAACAT
* * * *
33445972 TTTAATTTAATTTAATCGCATTATATAACATTTTAATTTAATTTAA
1 TTTAATTTAATTTAATCACATTATATAACAGTTCAATTTAAATTAA
* *
33446018 TTTAATTTAATTTAATCACATTATATAATAGTTCAATTTAAATTGA
1 TTTAATTTAATTTAATCACATTATATAACAGTTCAATTTAAATTAA
33446064 TTTA
1 TTTA
33446068 GGAATTAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (46 bp):
TTTAATTTAATTTAATCACATTATATAACAGTTCAATTTAAATTAA
Found at i:33458494 original size:26 final size:25
Alignment explanation
Indices: 33458463--33458526 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
33458453 ATGGCTTTTC
*
33458463 GGAGCTTCCCGATTAAAGACTCTTTT
1 GGAGCTTCCCGATTAAAGACTC-TCT
* * * *
33458489 TGAGCTTCCTGATTAATGGCTCTCT
1 GGAGCTTCCCGATTAAAGACTCTCT
33458514 GGAGCTTCCCGAT
1 GGAGCTTCCCGAT
33458527 ATGGCTCGCT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (25 bp):
GGAGCTTCCCGATTAAAGACTCTCT
Found at i:33458541 original size:23 final size:23
Alignment explanation
Indices: 33458488--33458551 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
33458478 AAGACTCTTT
* *
33458488 TTGAGCTTCCTGATTAATGGCTCTC
1 TTGAGCTTCCCGA-T-ATGGCTCGC
*
33458513 TGGAGCTTCCCGATATGGCTCGC
1 TTGAGCTTCCCGATATGGCTCGC
*
33458536 TTGAGCTTCTCGATAT
1 TTGAGCTTCCCGATAT
33458552 ATGGCTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 22 0.65
24 1 0.03
25 11 0.32
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (23 bp):
TTGAGCTTCCCGATATGGCTCGC
Found at i:33458568 original size:48 final size:49
Alignment explanation
Indices: 33458488--33458582 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 49
33458478 AAGACTCTTT
* *
33458488 TTGAGCTTCCTGATTAATGGCTCTCTGGAGCTTCCCG-ATATGGCTCGC
1 TTGAGCTTCCTGATTAATGGCTATCTGAAGCTTCCCGAATATGGCTCGC
*
33458536 TTGAGCTT-CTCGA-TATATGGCTATCTGAAGCTTCCTGAATATGGCTC
1 TTGAGCTTCCT-GATTA-ATGGCTATCTGAAGCTTCCCGAATATGGCTC
33458583 TTATGATCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 4 0.10
48 28 0.68
49 9 0.22
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (49 bp):
TTGAGCTTCCTGATTAATGGCTATCTGAAGCTTCCCGAATATGGCTCGC
Found at i:33458651 original size:25 final size:25
Alignment explanation
Indices: 33458590--33458651 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 25
33458580 CTCTTATGAT
* *
33458590 CTTCTCGTTATACAGCCCAGATAAG
1 CTTCCCGTTATACAGCCCAAATAAG
* * * *
33458615 TTTCCCGCTATACAGCTCAAATGAG
1 CTTCCCGTTATACAGCCCAAATAAG
*
33458640 CTTCCTGTTATA
1 CTTCCCGTTATA
33458652 TGGCTCGAGG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (25 bp):
CTTCCCGTTATACAGCCCAAATAAG
Found at i:33461315 original size:20 final size:21
Alignment explanation
Indices: 33461265--33461306 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
33461255 CCTTTCAAAT
33461265 TTTC-TTA-TTTTCATTTGCA
1 TTTCATTACTTTTCATTTGCA
33461284 TTTCATTACTTTTCA-TTGCA
1 TTTCATTACTTTTCATTTGCA
33461304 TTT
1 TTT
33461307 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTCATTACTTTTCATTTGCA
Found at i:33462022 original size:25 final size:25
Alignment explanation
Indices: 33461953--33462022 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
33461943 CTGTGCATGC
* * *
33461953 ATGCTCACACGAGCTGTAAATCAGA
1 ATGCTCACACGAGCTATGAATCAAA
** *
33461978 ATGCTTGCACGAGCTTTGAATCAAA
1 ATGCTCACACGAGCTATGAATCAAA
33462003 ATGCTCACACGAGCTATGAA
1 ATGCTCACACGAGCTATGAA
33462023 AATGGGCCTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (25 bp):
ATGCTCACACGAGCTATGAATCAAA
Found at i:33466940 original size:43 final size:43
Alignment explanation
Indices: 33466880--33467072 Score: 271
Period size: 43 Copynumber: 4.5 Consensus size: 43
33466870 TGTCTTAGAC
* * * *
33466880 ATGGTCTTACAAGGAAATCTCATATCGATTCCAATAGCCCAACT
1 ATGGTCTTAC-ACGAAATCTCAAATCGATGCCAATAGCCCAGCT
* *
33466924 ATTGTCTTACACGAAATCTCAAATCGATGCCAATAGCTCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
* *
33466967 ATGGTCTTACACGAAATCTCAAATCGATACCAATAGCCTAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
** *
33467010 ATGGTCTTACAAAAAATCCCAAATCGATGCCAATAG-CCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
33467052 ATGGTCTTACACGAAATCTCA
1 ATGGTCTTACACGAAATCTCA
33467073 CCTCGGAAGT
Statistics
Matches: 131, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 23 0.18
43 99 0.76
44 9 0.07
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:33474127 original size:40 final size:41
Alignment explanation
Indices: 33474072--33474172 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 41
33474062 AATTGATATA
* * *
33474072 TGATTTGCATGTTAAGCATATTTATTGTACT-A-ATCAAATC
1 TGATTCGCATGTTAAGCATATTGAATGTACTGACAT-AAATC
* *
33474112 TGATTCGCATGTTAAGCATGTTGAATGTATTGACTATAAATC
1 TGATTCGCATGTTAAGCATATTGAATGTACTGAC-ATAAATC
33474154 TGATTCGCATGTTAAGCAT
1 TGATTCGCATGTTAAGCAT
33474173 GCCCACTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
40 26 0.49
41 1 0.02
42 24 0.45
43 2 0.04
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.40
Consensus pattern (41 bp):
TGATTCGCATGTTAAGCATATTGAATGTACTGACATAAATC
Found at i:33474334 original size:24 final size:24
Alignment explanation
Indices: 33474302--33474349 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33474292 TTGTCTGCAA
*
33474302 TATTGAGTGGCTTGGCCACAACGT
1 TATTGAGTGGCTTGACCACAACGT
* * *
33474326 TATTTAGTGGTTTGACCATAACGT
1 TATTGAGTGGCTTGACCACAACGT
33474350 GTAGCTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCACAACGT
Found at i:33474349 original size:63 final size:63
Alignment explanation
Indices: 33474263--33474386 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
33474253 TTTACTACAA
* ** *
33474263 TATTGAGTGGCTTGACCAGAACGTGCAGCTTGTCTGCAATATTGAGTGGCTTGGCCACAACGT
1 TATTGAGTGGCTTGACCAGAACGTGCAGCTTGACTGCAATATACAGTGGCTTGGACACAACGT
* * * *
33474326 TATTTAGTGGTTTGACCATAACGTGTAGCTTGACTGCAATATACAGTGGCTTGGACACAAC
1 TATTGAGTGGCTTGACCAGAACGTGCAGCTTGACTGCAATATACAGTGGCTTGGACACAAC
33474387 ATGGAGTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (63 bp):
TATTGAGTGGCTTGACCAGAACGTGCAGCTTGACTGCAATATACAGTGGCTTGGACACAACGT
Found at i:33478016 original size:10 final size:10
Alignment explanation
Indices: 33477983--33478010 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
33477973 AAATTGGAAA
33477983 TAAAAGATAT
1 TAAAAGATAT
33477993 TAAAAGATAT
1 TAAAAGATAT
33478003 TAAAAGAT
1 TAAAAGAT
33478011 GATAAATGAT
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:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (10 bp):
TAAAAGATAT
Found at i:33478570 original size:11 final size:10
Alignment explanation
Indices: 33478552--33478608 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 10
33478542 GAATTGAATG
33478552 TAAATTATAT
1 TAAATTATAT
*
33478562 TAAATTTATGT
1 TAAA-TTATAT
*
33478573 TAAATTAT-G
1 TAAATTATAT
*
33478582 TAAATTGTAT
1 TAAATTATAT
*
33478592 TAAATTGATGT
1 TAAATT-ATAT
33478603 TAAATT
1 TAAATT
33478609 TACTCGTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 7 0.18
10 14 0.37
11 17 0.45
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (10 bp):
TAAATTATAT
Found at i:33478585 original size:30 final size:30
Alignment explanation
Indices: 33478549--33478608 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
33478539 ATTGAATTGA
*
33478549 ATGTAAATTATATTAAATTTATGTTAAATT
1 ATGTAAATTATATTAAATTGATGTTAAATT
*
33478579 ATGTAAATTGTATTAAATTGATGTTAAATT
1 ATGTAAATTATATTAAATTGATGTTAAATT
33478609 TACTCGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (30 bp):
ATGTAAATTATATTAAATTGATGTTAAATT
Found at i:33491184 original size:25 final size:25
Alignment explanation
Indices: 33491155--33491215 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
33491145 CTCACTTGAA
*
33491155 CTTCCCGTTATATTACTATTCGGTG
1 CTTCCCGTTATATTACTATTCGGAG
* *
33491180 CTTCCCGTTA-ATTGCTCTTCGGAG
1 CTTCCCGTTATATTACTATTCGGAG
*
33491204 CTACCCGTTATA
1 CTTCCCGTTATA
33491216 GGCTCTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.39
Consensus pattern (25 bp):
CTTCCCGTTATATTACTATTCGGAG
Found at i:33495651 original size:43 final size:43
Alignment explanation
Indices: 33495604--33495690 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
33495594 ACAAATCTAA
*
33495604 AATATGAGAAAGAATGATATAGAGGAATGTTTTAAATCCATAG
1 AATATGAGAAAGAATGATATAGAGGAAAGTTTTAAATCCATAG
33495647 AATATGAGAAAGAATGATATAGAGGAAAGTTTTAAATCCATAG
1 AATATGAGAAAGAATGATATAGAGGAAAGTTTTAAATCCATAG
33495690 A
1 A
33495691 GCCATAGACC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (43 bp):
AATATGAGAAAGAATGATATAGAGGAAAGTTTTAAATCCATAG
Found at i:33498003 original size:5 final size:5
Alignment explanation
Indices: 33497995--33498019 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
33497985 AAAAAGATCC
33497995 AGGTT AGGTT AGGTT AGGTT AGGTT
1 AGGTT AGGTT AGGTT AGGTT AGGTT
33498020 GCAGATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
AGGTT
Found at i:33525104 original size:20 final size:20
Alignment explanation
Indices: 33525079--33525132 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
33525069 ACTTTTTCAA
*
33525079 TATAAAAATT-GAAAAAAAT
1 TATAAAAATTACAAAAAAAT
*
33525098 T-TATAAATTACAAAAAAAT
1 TATAAAAATTACAAAAAAAT
*
33525117 TATAAAAATTATAAAA
1 TATAAAAATTACAAAA
33525133 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 7 0.24
19 10 0.34
20 12 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
TATAAAAATTACAAAAAAAT
Found at i:33525132 original size:18 final size:19
Alignment explanation
Indices: 33525079--33525145 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 19
33525069 ACTTTTTCAA
*
33525079 TATAAAAATTGAAAAAAAT
1 TATAAAAATTAAAAAAAAT
*
33525098 T-TATAAATTACAAAAAAAT
1 TATAAAAATTA-AAAAAAAT
*
33525117 TATAAAAATT--ATAAAAT
1 TATAAAAATTAAAAAAAAT
33525134 TATTAAAAATTA
1 TA-TAAAAATTA
33525146 TGTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 8 0.20
18 15 0.38
19 10 0.25
20 7 0.17
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
TATAAAAATTAAAAAAAAT
Found at i:33525141 original size:28 final size:27
Alignment explanation
Indices: 33525082--33525146 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
33525072 TTTTCAATAT
*
33525082 AAAAATTGAAAAAAATTTATAAATTACAA
1 AAAAATT-ATAAAAATTTATAAATTAC-A
**
33525111 AAAAATTATAAAAA-TTATAAAATTATT
1 AAAAATTATAAAAATTTAT-AAATTACA
33525138 AAAAATTAT
1 AAAAATTAT
33525147 GTAAAAGAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 13 0.41
28 12 0.38
29 7 0.22
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAATTATAAAAATTTATAAATTACA
Found at i:33525142 original size:10 final size:9
Alignment explanation
Indices: 33525079--33525146 Score: 59
Period size: 10 Copynumber: 7.3 Consensus size: 9
33525069 ACTTTTTCAA
33525079 TATAAAAAT
1 TATAAAAAT
*
33525088 TGAAAAAAAT
1 T-ATAAAAAT
*
33525098 T-TATAAAT
1 TATAAAAAT
*
33525106 TACAAAAAAAT
1 T--ATAAAAAT
33525117 TATAAAAAT
1 TATAAAAAT
33525126 TAT-AAAAT
1 TATAAAAAT
33525134 TATTAAAAAT
1 TA-TAAAAAT
33525144 TAT
1 TAT
33525147 GTAAAAGAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
8 13 0.28
9 13 0.28
10 15 0.32
11 6 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (9 bp):
TATAAAAAT
Found at i:33525347 original size:10 final size:10
Alignment explanation
Indices: 33525334--33525367 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
33525324 ATTTTCATAT
33525334 AATTTTTTAA
1 AATTTTTTAA
*
33525344 AATTTTTTAT
1 AATTTTTTAA
*
33525354 AATTTTCTAA
1 AATTTTTTAA
33525364 AATT
1 AATT
33525368 CTATATTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:33525384 original size:34 final size:36
Alignment explanation
Indices: 33525345--33525429 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 36
33525335 ATTTTTTAAA
33525345 ATTTTTTATAATTTTCTA-AAATTCTATATTTGT-C
1 ATTTTTTATAATTTTCTAGAAATTCTATATTTGTAC
* * * * * *
33525379 ATTTTTAATAATTTTCTAGTATTTTTATATTTTTAT
1 ATTTTTTATAATTTTCTAGAAATTCTATATTTGTAC
33525415 ATTTTTTATAATTTT
1 ATTTTTTATAATTTT
33525430 TGAAAAATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 17 0.40
35 11 0.26
36 14 0.33
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (36 bp):
ATTTTTTATAATTTTCTAGAAATTCTATATTTGTAC
Found at i:33525419 original size:7 final size:8
Alignment explanation
Indices: 33525379--33525430 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 8
33525369 TATATTTGTC
33525379 ATTTTTAAT
1 ATTTTT-AT
33525388 AATTTTCTAGT
1 -ATTTT-TA-T
33525399 ATTTTTAT
1 ATTTTTAT
33525407 ATTTTTAT
1 ATTTTTAT
33525415 ATTTTTTAT
1 A-TTTTTAT
33525424 AATTTTT
1 -ATTTTT
33525431 GAAAAATCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
8 10 0.26
9 14 0.37
10 12 0.32
11 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (8 bp):
ATTTTTAT
Found at i:33525451 original size:25 final size:26
Alignment explanation
Indices: 33525415--33525477 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
33525405 ATATTTTTAT
**
33525415 ATTT-TTTATAATTTTTGAAAAATCT-
1 ATTTATTT-TAATTTTCCAAAAATCTA
* *
33525440 CTTTATTTTAATTTTCCAAAATTCTA
1 ATTTATTTTAATTTTCCAAAAATCTA
33525466 ATTTATTTTAAT
1 ATTTATTTTAAT
33525478 AATTATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTTATTTTAATTTTCCAAAAATCTA
Found at i:33526128 original size:26 final size:27
Alignment explanation
Indices: 33526099--33526168 Score: 70
Period size: 32 Copynumber: 2.4 Consensus size: 27
33526089 TATATTAAAC
33526099 CAAATT-TAAAATATATTAACTTCTAA
1 CAAATTATAAAATATATTAACTTCTAA
*
33526125 CAAATTCAAAAACTAAATATATTAACTTCTAA
1 CAAATT---ATA--AAATATATTAACTTCTAA
*
33526157 CAAATTCTAAAA
1 CAAATTATAAAA
33526169 CTTCAAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
26 6 0.17
27 3 0.09
29 1 0.03
30 1 0.03
32 24 0.69
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (27 bp):
CAAATTATAAAATATATTAACTTCTAA
Found at i:33526148 original size:32 final size:32
Alignment explanation
Indices: 33526107--33526170 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
33526097 ACCAAATTTA
33526107 AAATATATTAACTTCTAACAAATTCAAAAACT
1 AAATATATTAACTTCTAACAAATTCAAAAACT
*
33526139 AAATATATTAACTTCTAACAAATTCTAAAACT
1 AAATATATTAACTTCTAACAAATTCAAAAACT
33526171 TCAAAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.33
Consensus pattern (32 bp):
AAATATATTAACTTCTAACAAATTCAAAAACT
Found at i:33526319 original size:13 final size:12
Alignment explanation
Indices: 33526296--33526329 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
33526286 ATAAAAATTC
33526296 AAAAA-AATTTA
1 AAAAATAATTTA
33526307 AAAAATTAATTTA
1 AAAAA-TAATTTA
33526320 AAAAATAATT
1 AAAAATAATT
33526330 GGTCAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 5 0.24
13 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATAATTTA
Found at i:33532151 original size:25 final size:25
Alignment explanation
Indices: 33532110--33532166 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
33532100 ACAATCCATG
** * *
33532110 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
33532135 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
33532160 TATATCA
1 TAAATCA
33532167 ATTCTTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:33532457 original size:23 final size:24
Alignment explanation
Indices: 33532405--33532462 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 24
33532395 AGCCATGATG
33532405 GGTAAGCTCATTCCGAGCTGATAAAC
1 GGTAAGCTCATT-CGAGCTGA-AAAC
33532431 GGTAAGCTCTATT-GAGCTG-AAAC
1 GGTAAGCTC-ATTCGAGCTGAAAAC
33532454 GGTAAGCTC
1 GGTAAGCTC
33532463 CGTAGAGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 13 0.42
25 6 0.19
26 9 0.29
27 3 0.10
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (24 bp):
GGTAAGCTCATTCGAGCTGAAAAC
Found at i:33532470 original size:23 final size:23
Alignment explanation
Indices: 33532427--33532495 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
33532417 CCGAGCTGAT
* *
33532427 AAACGGTAAGCTCTATTGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
*
33532450 AAACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
* *
33532473 -AATGGTAAGCTTCATACGAGCTG
1 AAACGGTAAGCTCCATA-GAGCTG
33532496 TGGTGAGTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.33
23 26 0.67
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:33536739 original size:9 final size:9
Alignment explanation
Indices: 33536725--33536761 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
33536715 TGATGAACTT
33536725 AAAATTTTA
1 AAAATTTTA
33536734 AAAATTTTA
1 AAAATTTTA
* *
33536743 AAAATCTTC
1 AAAATTTTA
33536752 AAAATTTTA
1 AAAATTTTA
33536761 A
1 A
33536762 TTTTTTTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:33542799 original size:19 final size:19
Alignment explanation
Indices: 33542773--33542814 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
33542763 ATACGTTTAG
*
33542773 TTTTT-TTTAATTT-ATTT
1 TTTTTGTTTTATTTAATTT
33542790 TTTTTGTTTTATTTAATTT
1 TTTTTGTTTTATTTAATTT
33542809 TTTTTG
1 TTTTTG
33542815 AAAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (19 bp):
TTTTTGTTTTATTTAATTT
Found at i:33543051 original size:92 final size:92
Alignment explanation
Indices: 33542876--33543053 Score: 232
Period size: 92 Copynumber: 1.9 Consensus size: 92
33542866 AGTGTTAACA
* *
33542876 ACATGTATAATAATAAAACACATATTGATAGGTCAAGTACCACATTGGACATTTTCAAAGTATAG
1 ACATGTATAATAATAAAACACATATTGATAGGTCAAGTACCACATTAGACATTTTCAAAGTATAA
* * *
33542941 GTATCACACTGAATATTTTATGTAAGT
66 ATATCACACTAAACATTTTATGTAAGT
* * * * *
33542968 ACATGTATCATAATAAAACACATATTGATAGTTCAAGTACCATATTATATATTTTCAAA-TCATA
1 ACATGTATAATAATAAAACACATATTGATAGGTCAAGTACCACATTAGACATTTTCAAAGT-ATA
* *
33543032 AATATCATATTAAACATTTTAT
65 AATATCACACTAAACATTTTAT
33543054 AAAAATACAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
91 1 0.01
92 72 0.99
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (92 bp):
ACATGTATAATAATAAAACACATATTGATAGGTCAAGTACCACATTAGACATTTTCAAAGTATAA
ATATCACACTAAACATTTTATGTAAGT
Found at i:33544282 original size:23 final size:23
Alignment explanation
Indices: 33544229--33544285 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
33544219 TATCGAAAAA
*
33544229 TGAACTTTTAAATATTTTTTATT
1 TGAATTTTTAAATATTTTTTATT
* * *
33544252 TTACTTTTTTAATATTTATTT-TT
1 TGAATTTTTAAATATTT-TTTATT
33544275 TGAATTTTTAA
1 TGAATTTTTAA
33544286 GAATCATGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
TGAATTTTTAAATATTTTTTATT
Found at i:33546016 original size:51 final size:51
Alignment explanation
Indices: 33545951--33546050 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
33545941 TCAATTATTT
33545951 TCTCAATTTCCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTCCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * * *
33546002 TCTCAGTTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTCCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
33546051 TAAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTCCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:33546061 original size:11 final size:11
Alignment explanation
Indices: 33546047--33546071 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33546037 TTAAATCCCT
33546047 ATTTTAAAATA
1 ATTTTAAAATA
33546058 ATTTTAAAATA
1 ATTTTAAAATA
33546069 ATT
1 ATT
33546072 ATTTTTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:33547720 original size:18 final size:18
Alignment explanation
Indices: 33547693--33547732 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33547683 CAGGTGTGTT
* *
33547693 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
33547711 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
33547729 TCCT
1 TCCT
33547733 TTTCTGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:33548281 original size:21 final size:22
Alignment explanation
Indices: 33548245--33548323 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
33548235 TTTAATTGAC
*
33548245 AAACCCTAATCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
33548267 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
33548288 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
33548310 AAACCATAAACCCT
1 AAACCCTAAACCCT
33548324 AAACCCTAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
21 20 0.37
22 34 0.63
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:33548339 original size:35 final size:35
Alignment explanation
Indices: 33548288--33548363 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
33548278 CTTAACTTAA
33548288 AAACCCTAAACCCTTAACTTAAAAACCATAAACCCT
1 AAACCCTAAACCCTTAACTTAAAAACCAT-AACCCT
*
33548324 AAACCCT-AACCCTTAACTTAAAAACCCTAACCCT
1 AAACCCTAAACCCTTAACTTAAAAACCATAACCCT
33548358 -AACCCT
1 AAACCCT
33548364 TGACTGGTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 6 0.15
34 6 0.15
35 20 0.51
36 7 0.18
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (35 bp):
AAACCCTAAACCCTTAACTTAAAAACCATAACCCT
Found at i:33551666 original size:125 final size:125
Alignment explanation
Indices: 33551440--33552006 Score: 895
Period size: 125 Copynumber: 4.5 Consensus size: 125
33551430 CCCAAATATG
* * * *
33551440 CTACTATAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATGT-TTCTGATAAAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAAT-TCTTCTCATAAAGCATCCTG
33551504 CTTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
65 CTTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
* *
33551565 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
33551630 TTGAAGCATTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAAGG-C
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
*
33551689 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAACTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
33551754 TTGAAGCGTTTTTATACTATTTGCTTAGAAACGCCAACTCGAAATTATTTTTTCCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
* * * *
33551814 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATGCTTCTCAGAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
33551879 TTGAAGCGTTTTTTATACCATGTGCTCAGAAATGTCAACTTGAAATTATTTTTTCCAGGAC
66 TTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
* **
33551940 CTACTGTAGCAAAAGAGCGTCCATAAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
33552005 TT
66 TT
33552007 TGATTTTATC
Statistics
Matches: 404, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
124 117 0.29
125 181 0.45
126 106 0.26
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
Found at i:33551813 original size:249 final size:250
Alignment explanation
Indices: 33551440--33552006 Score: 922
Period size: 249 Copynumber: 2.3 Consensus size: 250
33551430 CCCAAATATG
* * * * *
33551440 CTACTATAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATGTTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAAT-CTTCTCATAAAGCATCCTGC
*
33551505 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGACCTACT
65 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGCCAACTCGAAATTATTTTTTCCAGGACCTACT
* * * *
33551570 GTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCATAAAGCATTCTGCTTGAA
130 GTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATGCTTCTCAGAAAGCATCCTACTTGAA
* *
33551635 GC-ATTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAAGG-C
195 GCGATTTTTATACCATGTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAAGGAC
33551689 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAACTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAA-TCTTCTCATAAAGCATCCTGC
*
33551754 TTGAAGCGTTTTTATACTATTTGCTTAGAAACGCCAACTCGAAATTATTTTTTCCAGGACCTACT
65 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGCCAACTCGAAATTATTTTTTCCAGGACCTACT
33551819 GTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATGCTTCTCAGAAAGCATCCTACTTGAA
130 GTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATGCTTCTCAGAAAGCATCCTACTTGAA
* * *
33551884 GCGTTTTTTATACCATGTGCTCAGAAATGTCAACTTGAAATTATTTTTTCCAGGAC
195 GCGATTTTTATACCATGTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAAGGAC
* **
33551940 CTACTGTAGCAAAAGAGCGTCCATAAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAA-TCTTCTCATAAAGCATCCTGC
33552005 TT
65 TT
33552007 TGATTTTATC
Statistics
Matches: 295, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
249 184 0.62
250 47 0.16
251 64 0.22
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (250 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATCTTCTCATAAAGCATCCTGCT
TGAAGCGTTTTTATACTATTTGCTCAGAAACGCCAACTCGAAATTATTTTTTCCAGGACCTACTG
TAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATGCTTCTCAGAAAGCATCCTACTTGAAG
CGATTTTTATACCATGTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAAGGAC
Found at i:33553608 original size:25 final size:25
Alignment explanation
Indices: 33553580--33553664 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 25
33553570 TATTTTTTAG
*
33553580 TTTTATATCAAATTATATTAAAATA
1 TTTTATATTAAATTATATTAAAATA
* *
33553605 TTTTATTTTGAATTATATTTTAAAATTAAATA
1 TTTTATATTAAATTATA--TT---A--AAATA
*
33553637 TTTTGTATTAAATTATATTAAAATA
1 TTTTATATTAAATTATATTAAAATA
33553662 TTT
1 TTT
33553665 CAAATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 22 0.47
27 3 0.06
30 3 0.06
32 19 0.40
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTTATATTAAATTATATTAAAATA
Found at i:33555197 original size:73 final size:71
Alignment explanation
Indices: 33555120--33555342 Score: 231
Period size: 75 Copynumber: 3.1 Consensus size: 71
33555110 TAAAATACGG
* * *
33555120 TAGAATATAATATAAACAATTTTTCATTTTTTTCGTAGATTGTAAATAAGTATATTATT-A-AGA
1 TAGAATACAATACAAACAATTTTTAATTTTTTT-GTAGATTGTAAATAAGTATATTATTGATAGA
33555183 AGACATACAA
65 A-A-ATA-AA
* ** *
33555193 TAGAATACAATACAAGCCTTTTTTAACTTTTTTTATAGATTGTAAATAAGTATATATTATTGATA
1 TAGAATACAATACAAACAATTTTTAA-TTTTTTTGTAGATTGTAAATAAG--TATATTATTGATA
*
33555258 TAAAATAAA
63 GAAAATAAA
*
33555267 TATAATACAATACAAACAATTTTTAAATTTTTTTTGTAGATTGTAAATAAG--TATTATTGAT-G
1 TAGAATACAATACAAACAATTTTT-AA-TTTTTTTGTAGATTGTAAATAAGTATATTATTGATAG
33555329 TAAAATACAA
64 -AAAATA-AA
33555339 TAGA
1 TAGA
33555343 GAAACTTTTT
Statistics
Matches: 126, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
71 16 0.13
72 5 0.04
73 35 0.28
74 29 0.23
75 36 0.29
76 2 0.02
77 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (71 bp):
TAGAATACAATACAAACAATTTTTAATTTTTTTGTAGATTGTAAATAAGTATATTATTGATAGAA
AATAAA
Found at i:33555226 original size:75 final size:72
Alignment explanation
Indices: 33555120--33555342 Score: 233
Period size: 73 Copynumber: 3.1 Consensus size: 72
33555110 TAAAATACGG
* * *
33555120 TAGAATATAATATAAACAATTTTT-CATTTTTTTCGTAGATTGTAAATAAGTATATTATT-A-AG
1 TAGAATACAATACAAACAATTTTTAAATTTTTTT-GTAGATTGTAAATAAGTATATTATTGATAG
33555182 AAGACATACAA
65 AA-A-ATA-AA
* ** * *
33555193 TAGAATACAATACAAGCCTTTTTTAACTTTTTTTATAGATTGTAAATAAGTATATATTATTGATA
1 TAGAATACAATACAAACAATTTTTAAATTTTTTTGTAGATTGTAAATAAG--TATATTATTGATA
*
33555258 TAAAATAAA
64 GAAAATAAA
*
33555267 TATAATACAATACAAACAATTTTTAAATTTTTTTTGTAGATTGTAAATAAG--TATTATTGAT-G
1 TAGAATACAATACAAACAATTTTTAAA-TTTTTTTGTAGATTGTAAATAAGTATATTATTGATAG
33555329 TAAAATACAA
65 -AAAATA-AA
33555339 TAGA
1 TAGA
33555343 GAAACTTTTT
Statistics
Matches: 125, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
71 16 0.13
72 5 0.04
73 34 0.27
74 31 0.25
75 34 0.27
76 2 0.02
77 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (72 bp):
TAGAATACAATACAAACAATTTTTAAATTTTTTTGTAGATTGTAAATAAGTATATTATTGATAGA
AAATAAA
Found at i:33555811 original size:18 final size:19
Alignment explanation
Indices: 33555788--33555829 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
33555778 TATTATTATT
*
33555788 TTTGAA-TAATTGTTTCTA
1 TTTGAAGTAAATGTTTCTA
33555806 TTTGAAGTTAAATGTTTCTA
1 TTTGAAG-TAAATGTTTCTA
33555826 TTTG
1 TTTG
33555830 TATTGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (19 bp):
TTTGAAGTAAATGTTTCTA
Found at i:33556763 original size:6 final size:6
Alignment explanation
Indices: 33556749--33556782 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
33556739 TAAGTTTCTA
* *
33556749 GAAAAG GAAATG GAAATG GAAATG AAAATG GAAA
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAA
33556783 CTTATAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (6 bp):
GAAATG
Found at i:33556959 original size:26 final size:26
Alignment explanation
Indices: 33556930--33557003 Score: 123
Period size: 26 Copynumber: 2.9 Consensus size: 26
33556920 AATTTTCATG
33556930 AAATTTTACCGAGGGTAAAATTGTCA
1 AAATTTTACCGAGGGTAAAATTGTCA
*
33556956 AAATTTTACCGAGAGTAAAATTGTCA
1 AAATTTTACCGAGGGTAAAATTGTCA
*
33556982 AAATTTTACTG-GGGTAAAATTG
1 AAATTTTACCGAGGGTAAAATTG
33557004 GGGTGAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
25 10 0.22
26 35 0.78
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (26 bp):
AAATTTTACCGAGGGTAAAATTGTCA
Found at i:33559964 original size:40 final size:37
Alignment explanation
Indices: 33559906--33559989 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
33559896 CACTCAATGC
** *
33559906 CTCATCGGATAATTCGAAGTAATAATTTGATACCCAGTGT
1 CTCATCGGATAAACCGAAGT-A-AA-TTGACACCCAGTGT
*
33559946 CTCATCGGCTAAACCGAAGTAAATTGACACCCAGTGT
1 CTCATCGGATAAACCGAAGTAAATTGACACCCAGTGT
33559983 CTCATCG
1 CTCATCG
33559990 ACTCGAAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 20 0.50
38 2 0.05
39 1 0.03
40 17 0.43
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (37 bp):
CTCATCGGATAAACCGAAGTAAATTGACACCCAGTGT
Found at i:33563228 original size:26 final size:25
Alignment explanation
Indices: 33563182--33563230 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
33563172 ATAGACATAG
* *
33563182 ATAATTTAAAAACCACCATATTTAA
1 ATAATTTAAAAAACACAATATTTAA
*
33563207 ATAATTTTAAAAAATACAATATTT
1 ATAA-TTTAAAAAACACAATATTT
33563231 TTACAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATTTAAAAAACACAATATTTAA
Found at i:33564411 original size:23 final size:23
Alignment explanation
Indices: 33564348--33564425 Score: 95
Period size: 23 Copynumber: 3.2 Consensus size: 23
33564338 ACTAGTACAA
33564348 AAAAATATAATTTGATACAATTTTAAT
1 AAAAATATAATTT--T--AATTTTAAT
*
33564375 AACAAT-TAATTTTAATTTTAAT
1 AAAAATATAATTTTAATTTTAAT
33564397 AAAAATATAATTTTAATTTTAATT
1 AAAAATATAATTTTAATTTTAA-T
33564421 AAAAA
1 AAAAA
33564426 ACGGGCCGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.30
23 15 0.32
24 7 0.15
26 6 0.13
27 5 0.11
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (23 bp):
AAAAATATAATTTTAATTTTAAT
Found at i:33564640 original size:13 final size:13
Alignment explanation
Indices: 33564605--33564641 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
33564595 GATATATTTG
*
33564605 TAATTTGAAAGCT
1 TAATTTGAAAACT
33564618 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
33564632 TAATTTGAAA
1 TAATTTGAAA
33564642 TTTTGGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:33564944 original size:35 final size:35
Alignment explanation
Indices: 33564900--33565012 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 35
33564890 TTCACTTGTC
* * *
33564900 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
33564935 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
33564970 -TTTATTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
33565004 TTTTGTTGC
1 TTTTGTTGC
33565013 NNNNNNNNNN
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
34 31 0.46
35 37 0.54
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:33564983 original size:34 final size:34
Alignment explanation
Indices: 33564905--33565006 Score: 150
Period size: 34 Copynumber: 3.0 Consensus size: 34
33564895 TTGTCTTTTC
* * *
33564905 TTGCAGGGAATATTTCCTGTTCACGCATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTA
* *
33564940 TTGCAGGGAATCTCTCCTGTTCACACATCATTTA
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTA
33564974 TTGCAGGGAATCTCTCCTGTTCACGCATTATTT
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTT
33565007 TGTTGCNNNN
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
34 34 0.57
35 26 0.43
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (34 bp):
TTGCAGGGAATCTCTCCTGTTCACGCATTATTTA
Found at i:33573228 original size:27 final size:28
Alignment explanation
Indices: 33573180--33573234 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
33573170 CTTATTTTCC
* *
33573180 TCTCTTTTTTTTCTTTA-ATTTTTCATT
1 TCTCTTTTTCTTCTTCATATTTTTCATT
* *
33573207 TCTCTTTTTCTTCTTCCTTTTTTTCATT
1 TCTCTTTTTCTTCTTCATATTTTTCATT
33573235 ATTGTTACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (28 bp):
TCTCTTTTTCTTCTTCATATTTTTCATT
Found at i:33574364 original size:9 final size:9
Alignment explanation
Indices: 33574353--33574437 Score: 125
Period size: 9 Copynumber: 9.4 Consensus size: 9
33574343 TTTGGTTAAA
*
33574353 AATTAACCA
1 AATTAACCG
33574362 AATTAACCG
1 AATTAACCG
33574371 AATTAACCG
1 AATTAACCG
*
33574380 AATTACCCG
1 AATTAACCG
33574389 AATTAACCG
1 AATTAACCG
*
33574398 AATTACCCG
1 AATTAACCG
*
33574407 AATTACCCG
1 AATTAACCG
33574416 AATTAACCG
1 AATTAACCG
*
33574425 AATTAACCA
1 AATTAACCG
33574434 AATT
1 AATT
33574438 GAATCACTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 70 1.00
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:33584092 original size:24 final size:25
Alignment explanation
Indices: 33584065--33584111 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
33584055 ATTAATTTGT
*
33584065 AAGTTGAAT-TATTATTCTGTATTA
1 AAGTTAAATGTATTATTCTGTATTA
* *
33584089 AAGTTAAATGTTTTATTTTGTAT
1 AAGTTAAATGTATTATTCTGTAT
33584112 CGTAACACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (25 bp):
AAGTTAAATGTATTATTCTGTATTA
Found at i:33594436 original size:20 final size:20
Alignment explanation
Indices: 33594411--33594455 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
33594401 TGTAAAGAAA
*
33594411 GGTGCCACTGATTGCACTCC
1 GGTGCCACTAATTGCACTCC
*
33594431 GGTGCCTCTAATTGCACTCC
1 GGTGCCACTAATTGCACTCC
33594451 GGTGC
1 GGTGC
33594456 TCTTATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.27, T:0.27
Consensus pattern (20 bp):
GGTGCCACTAATTGCACTCC
Found at i:33605015 original size:25 final size:25
Alignment explanation
Indices: 33604987--33605153 Score: 68
Period size: 25 Copynumber: 6.6 Consensus size: 25
33604977 CTTATGAGCG
33604987 TCCCGATATATGGCTCTTCGAAGCT
1 TCCCGATATATGGCTCTTCGAAGCT
*
33605012 TCCCGAT-TAAAGGCTCTTTC-ATGAGCT
1 TCCCGATAT-ATGGCTC-TTCGA--AGCT
** *
33605039 TCCTAAT-TAATTGGCTCTCCAGAA-CT
1 TCCCGATAT-A-TGGCTCTTC-GAAGCT
*
33605065 TCCCGATAT-TGGCTCGCTT-GAACCT
1 TCCCGATATATGGCT--CTTCGAAGCT
33605090 TCCCGATAT-TGGCTCGTAT-GAA-CT
1 TCCCGATATATGGCTC-T-TCGAAGCT
* *
33605114 TCCCGTTA-ATGGCTC-TCAAAAGCT
1 TCCCGATATATGGCTCTTC-GAAGCT
* *
33605138 TCCCGTTACATGGCTC
1 TCCCGATATATGGCTC
33605154 ACATGAGCTT
Statistics
Matches: 114, Mismatches: 10, Indels: 36
0.71 0.06 0.22
Matches are distributed among these distances:
21 1 0.01
23 3 0.03
24 35 0.31
25 41 0.36
26 12 0.11
27 16 0.14
28 5 0.04
29 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (25 bp):
TCCCGATATATGGCTCTTCGAAGCT
Found at i:33605076 original size:24 final size:23
Alignment explanation
Indices: 33605048--33605142 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 23
33605038 TTCCTAATTA
33605048 ATTGGCTCTCCAGAACTTCCCGAT
1 ATTGGCTCT-CAGAACTTCCCGAT
* *
33605072 ATTGGCTCGCTTGAACCTTCCCGAT
1 ATTGGCTCTC-AGAA-CTTCCCGAT
*
33605097 ATTGGCTCGT-ATGAACTTCCCGTT
1 ATTGGCTC-TCA-GAACTTCCCGAT
* *
33605121 AATGGCTCTCAAAAGCTTCCCG
1 ATTGGCTCTCAGAA-CTTCCCG
33605143 TTACATGGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
23 4 0.07
24 34 0.59
25 20 0.34
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.31
Consensus pattern (23 bp):
ATTGGCTCTCAGAACTTCCCGAT
Found at i:33605162 original size:25 final size:24
Alignment explanation
Indices: 33605088--33605193 Score: 77
Period size: 24 Copynumber: 4.3 Consensus size: 24
33605078 TCGCTTGAAC
* * ** *
33605088 CTTCCCGATATTGGCTCGTATGAA
1 CTTCCCGTTAATGGCTCACATGAG
* **
33605112 CTTCCCGTTAATGGCTCTCAAAAG
1 CTTCCCGTTAATGGCTCACATGAG
33605136 CTTCCCGTTACATGGCTCACATGAG
1 CTTCCCGTTA-ATGGCTCACATGAG
* * **
33605161 CTTTCCGTTTATGTGCTCTTATGAG
1 CTTCCCGTTAATG-GCTCACATGAG
33605186 CATTCCCG
1 C-TTCCCG
33605194 AATATGAATT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 30 0.47
25 29 0.45
26 5 0.08
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (24 bp):
CTTCCCGTTAATGGCTCACATGAG
Found at i:33605299 original size:13 final size:13
Alignment explanation
Indices: 33605281--33605306 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33605271 CGATATTATG
33605281 AAAGATTCAACGA
1 AAAGATTCAACGA
33605294 AAAGATTCAACGA
1 AAAGATTCAACGA
33605307 GCAATGTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAGATTCAACGA
Found at i:33613197 original size:12 final size:12
Alignment explanation
Indices: 33613180--33613204 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33613170 GGTGTTCATT
33613180 CGGTTAACCGAC
1 CGGTTAACCGAC
33613192 CGGTTAACCGAC
1 CGGTTAACCGAC
33613204 C
1 C
33613205 CAAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:33613379 original size:9 final size:9
Alignment explanation
Indices: 33613365--33613428 Score: 57
Period size: 9 Copynumber: 7.4 Consensus size: 9
33613355 TTTGGTTAAA
33613365 AATTACCCG
1 AATTACCCG
33613374 AATTACCCG
1 AATTACCCG
*
33613383 AATTAACCG
1 AATTACCCG
33613392 -A--A-CCG
1 AATTACCCG
33613397 AATTA-CCG
1 AATTACCCG
*
33613405 AAAAATACCCG
1 --AATTACCCG
33613416 AATTACCCG
1 AATTACCCG
33613425 AATT
1 AATT
33613429 TTGTTTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
5 3 0.07
6 2 0.04
8 5 0.11
9 29 0.63
10 4 0.09
11 3 0.07
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (9 bp):
AATTACCCG
Found at i:33613589 original size:13 final size:13
Alignment explanation
Indices: 33613567--33613596 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33613557 TTTTAGTTTT
33613567 ATTGGATTGGGTA
1 ATTGGATTGGGTA
*
33613580 ATTGGGTTGGGTA
1 ATTGGATTGGGTA
33613593 ATTG
1 ATTG
33613597 AGTTTGGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (13 bp):
ATTGGATTGGGTA
Found at i:33614219 original size:7 final size:7
Alignment explanation
Indices: 33614207--33614260 Score: 99
Period size: 7 Copynumber: 7.7 Consensus size: 7
33614197 CGTGATCCTC
33614207 TCCCCTT
1 TCCCCTT
33614214 TCCCCTT
1 TCCCCTT
33614221 TCCCCTT
1 TCCCCTT
33614228 TCCCCTT
1 TCCCCTT
*
33614235 TTCCCTT
1 TCCCCTT
33614242 TCCCCTT
1 TCCCCTT
33614249 TCCCCTT
1 TCCCCTT
33614256 TCCCC
1 TCCCC
33614261 CTTACTTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (7 bp):
TCCCCTT
Found at i:33626007 original size:27 final size:27
Alignment explanation
Indices: 33625969--33626022 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
33625959 CTATCCTATC
33625969 CACGGTGCCTCGACTTGACCCTTTCAT
1 CACGGTGCCTCGACTTGACCCTTTCAT
33625996 CACGGTGCCTCGACTTGACCCTTTCAT
1 CACGGTGCCTCGACTTGACCCTTTCAT
33626023 TTTCTCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.37, G:0.19, T:0.30
Consensus pattern (27 bp):
CACGGTGCCTCGACTTGACCCTTTCAT
Found at i:33633737 original size:9 final size:9
Alignment explanation
Indices: 33633718--33633762 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
33633708 TTTTTTCTCC
*
33633718 AAAACCTTA
1 AAAACCCTA
*
33633727 AAAATCCTA
1 AAAACCCTA
33633736 AAAACCCT-
1 AAAACCCTA
33633744 AAAACCCT-
1 AAAACCCTA
33633752 -AAACCCTA
1 AAAACCCTA
33633760 AAA
1 AAA
33633763 TCCAAAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 7 0.23
8 8 0.26
9 16 0.52
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAACCCTA
Found at i:33634225 original size:9 final size:9
Alignment explanation
Indices: 33634209--33634264 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
33634199 AAAAATACAT
33634209 AAAA-TATA
1 AAAATTATA
*
33634217 GAAATTATA
1 AAAATTATA
*
33634226 AATAAATATA
1 AA-AATTATA
*
33634236 ACAATATATA
1 AAAAT-TATA
33634246 AAATATTATA
1 AAA-ATTATA
33634256 AAAATTATA
1 AAAATTATA
33634265 GGAACTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
8 3 0.08
9 13 0.34
10 20 0.53
11 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:33634244 original size:10 final size:9
Alignment explanation
Indices: 33634200--33634258 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
33634190 AAAAAATAAA
*
33634200 AAAATACAT
1 AAAATATAT
33634209 AAAATATA-
1 AAAATATAT
*
33634217 GAAAT-TAT
1 AAAATATAT
*
33634225 AAATAAATAT
1 AAA-ATATAT
33634235 AACAATATAT
1 AA-AATATAT
33634245 AAAATATTAT
1 AAAATA-TAT
33634255 AAAA
1 AAAA
33634259 ATTATAGGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
7 2 0.05
8 6 0.15
9 12 0.30
10 19 0.47
11 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATATAT
Found at i:33634251 original size:17 final size:16
Alignment explanation
Indices: 33634200--33634251 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
33634190 AAAAAATAAA
*
33634200 AAAATACATAAAATAT
1 AAAATATATAAAATAT
*
33634216 AGAAATTATAAATAAATAT
1 A-AAA-TATATA-AAATAT
33634235 AACAATATATAAAATAT
1 AA-AATATATAAAATAT
33634252 TATAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.03
17 9 0.31
18 10 0.34
19 9 0.31
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (16 bp):
AAAATATATAAAATAT
Found at i:33636826 original size:39 final size:38
Alignment explanation
Indices: 33636776--33636916 Score: 153
Period size: 39 Copynumber: 3.6 Consensus size: 38
33636766 ATTTAGTTAA
*
33636776 ATTAATTTAAGTCTTTAATTATGTCATAATTTGAACATC
1 ATTAATATAAGT-TTTAATTATGTCATAATTTGAACATC
*
33636815 ATTAATATAAGTTTTAATTATGTCATAATCTGAACATC
1 ATTAATATAAGTTTTAATTATGTCATAATTTGAACATC
* * *
33636853 TTTAATA-AGGGTTTTTAATTATGTCATAATTTAGGACATC
1 ATTAATATA-AG-TTTTAATTATGTCATAATTT-GAACATC
*
33636893 -TTAAATATATA-TTTTAAATATGTC
1 ATT-AATATA-AGTTTTAATTATGTC
33636917 CTAGTTTAGA
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
37 1 0.01
38 32 0.36
39 44 0.50
40 10 0.11
41 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (38 bp):
ATTAATATAAGTTTTAATTATGTCATAATTTGAACATC
Found at i:33640730 original size:38 final size:38
Alignment explanation
Indices: 33640688--33640836 Score: 147
Period size: 38 Copynumber: 3.9 Consensus size: 38
33640678 AGTTTAAGTA
*
33640688 TTTAATTATGTCATAATTTAAACATCATTAATATGAGT
1 TTTAATTATGTCATAATTTAAACATCTTTAATATGAGT
* * * * *
33640726 TTTAATTATATCATAATCTGAACATCTTTAATAAGGGTT
1 TTTAATTATGTCATAATTTAAACATCTTTAATATGAG-T
* * * *
33640765 TTTAATTATGTCATAGTTTAGGACATCTTAAATAT-ATAT
1 TTTAATTATGTCATAATTTA-AACATCTTTAATATGA-GT
* * *
33640804 TTTAAATATGTCCTAGTTTAAACATCTTTAATA
1 TTTAATTATGTCATAATTTAAACATCTTTAATA
33640837 CATGTCTTTA
Statistics
Matches: 89, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
38 42 0.47
39 36 0.40
40 11 0.12
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (38 bp):
TTTAATTATGTCATAATTTAAACATCTTTAATATGAGT
Found at i:33640807 original size:78 final size:77
Alignment explanation
Indices: 33640688--33640836 Score: 176
Period size: 78 Copynumber: 1.9 Consensus size: 77
33640678 AGTTTAAGTA
* * *
33640688 TTTAATTATGTCATAATTTAAACATCATTAATATGAGTTTTAATTATATCATAATCTGAACATCT
1 TTTAATTATGTCATAATTTAAACATCATTAATATGAATTTTAAATATATCATAATCTAAACATCT
33640753 TTAATAAGGGTT
66 TTAATAAGGGTT
* * * * * *
33640765 TTTAATTATGTCATAGTTTAGGACATC-TTAAATAT-ATATTTTAAATATGTCCTAGTTTAAACA
1 TTTAATTATGTCATAATTTA-AACATCATT-AATATGA-ATTTTAAATATATCATAATCTAAACA
33640828 TCTTTAATA
63 TCTTTAATA
33640837 CATGTCTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
77 22 0.37
78 38 0.63
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (77 bp):
TTTAATTATGTCATAATTTAAACATCATTAATATGAATTTTAAATATATCATAATCTAAACATCT
TTAATAAGGGTT
Found at i:33646782 original size:39 final size:39
Alignment explanation
Indices: 33646728--33646821 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 39
33646718 AAAAATTAGG
* **
33646728 AAAAAGTATAAAAAATTGTAAA-ATTTTATAAAGTT-GTAA
1 AAAAATTAT-AAAAATTGTAAATA-AATATAAAGTTGGTAA
* *
33646767 GAAAATTATACAAAA-TGTAAATAAATATAAATTTGGTAA
1 AAAAATTATA-AAAATTGTAAATAAATATAAAGTTGGTAA
33646806 AAAAATTATAAAAATT
1 AAAAATTATAAAAATT
33646822 ATCACACCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
38 19 0.42
39 26 0.58
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.32
Consensus pattern (39 bp):
AAAAATTATAAAAATTGTAAATAAATATAAAGTTGGTAA
Found at i:33646817 original size:20 final size:19
Alignment explanation
Indices: 33646739--33646818 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
33646729 AAAAGTATAA
**
33646739 AAAATTGT-AAAATTTTAT
1 AAAATTGTAAAAAAATTAT
* *
33646757 AAAGTTGTAAGAAAATTAT
1 AAAATTGTAAAAAAATTAT
* *
33646776 ACAAAATGTAAATAAA-TAT
1 A-AAATTGTAAAAAAATTAT
*
33646795 AAATTTGGTAAAAAAATTAT
1 AAAATT-GTAAAAAAATTAT
33646815 AAAA
1 AAAA
33646819 ATTATCACAC
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
18 10 0.22
19 20 0.43
20 16 0.35
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.33
Consensus pattern (19 bp):
AAAATTGTAAAAAAATTAT
Found at i:33646982 original size:21 final size:21
Alignment explanation
Indices: 33646956--33647000 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33646946 GGGTCGTTAA
* * *
33646956 TTTTTTATGATTTTTATAATT
1 TTTTTTATAATTTTAATAAAT
*
33646977 TTTTTTCTAATTTTAATAAAT
1 TTTTTTATAATTTTAATAAAT
33646998 TTT
1 TTT
33647001 AAATTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTATAATTTTAATAAAT
Found at i:33647036 original size:19 final size:18
Alignment explanation
Indices: 33647014--33647049 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33647004 TTTTTTTTAT
33647014 TAAAATTCAATAATTTTTC
1 TAAAATT-AATAATTTTTC
*
33647033 TAAAATTTATAATTTTT
1 TAAAATTAATAATTTTT
33647050 TTATCTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAATTAATAATTTTTC
Done.