Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 106 of 135
Found at i:39179524 original size:73 final size:74
Alignment explanation
Indices: 39179426--39179574 Score: 291
Period size: 73 Copynumber: 2.0 Consensus size: 74
39179416 TTGACATTAA
39179426 TTAATAATATTGAAACAAATTTATTTAAAATTAAATATATAATATTCAAATATGTGAATACTAAA
1 TTAATAATATTGAAACAAATTTATTTAAAATTAAATATATAATATTCAAATATGTGAATACTAAA
39179491 GGAAGGATT
66 GGAAGGATT
39179500 TTAATAATATT-AAACAAATTTATTTAAAATTAAATATATAATATTCAAATATGTGAATACTAAA
1 TTAATAATATTGAAACAAATTTATTTAAAATTAAATATATAATATTCAAATATGTGAATACTAAA
39179564 GGAAGGATT
66 GGAAGGATT
39179573 TT
1 TT
39179575 TTACATAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 64 0.85
74 11 0.15
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (74 bp):
TTAATAATATTGAAACAAATTTATTTAAAATTAAATATATAATATTCAAATATGTGAATACTAAA
GGAAGGATT
Found at i:39180352 original size:32 final size:30
Alignment explanation
Indices: 39180316--39180378 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 30
39180306 TTAGGGTAAA
39180316 TTATATTCATGGTCA-TTAAACTATTAAAAAGT
1 TTATATT-ATGGTCACTT-AA-TATTAAAAAGT
* *
39180348 TTATATTTTGGTCACTTAATTTTAAAAAGT
1 TTATATTATGGTCACTTAATATTAAAAAGT
39180378 T
1 T
39180379 ATAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 11 0.39
31 8 0.29
32 9 0.32
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (30 bp):
TTATATTATGGTCACTTAATATTAAAAAGT
Found at i:39182464 original size:103 final size:106
Alignment explanation
Indices: 39182357--39182562 Score: 278
Period size: 103 Copynumber: 2.0 Consensus size: 106
39182347 TATAATACTG
* * * * *
39182357 ATATACGAAAAGGA-AAAAAAAATTTTGAGTGCTGGCCTGTCAATGGCCGGCA-CCAA-A-CA-G
1 ATATACGAAAA-AATAAAAAAAAATTTGAGTCCTGGCCTGTCAATGGCCGACACCCAATATAATG
39182417 TAAAAAAAAATTACTTTTTTTTTCGTGTCAGAGTCAGATATAA
65 TAAAAAAAAATT-CTTTTTTTTTCGTGTCAGAGTCAGATATAA
* *
39182460 ATATACGAAAAAATAAAAAAAAATTTGGGTCCTGGCCTGTCAATGGCCGACACCCAATATAATTT
1 ATATACGAAAAAATAAAAAAAAATTTGAGTCCTGGCCTGTCAATGGCCGACACCCAATATAA-TG
*
39182525 TTAAAAAAAATTCTTTTTTTTTCGTGTCAGAGTCAGAT
65 TAAAAAAAAATTCTTTTTTTTTCGTGTCAGAGTCAGAT
39182563 CAGGCCAGCA
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
102 1 0.01
103 45 0.51
104 4 0.04
105 1 0.01
106 1 0.01
107 26 0.29
108 11 0.12
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (106 bp):
ATATACGAAAAAATAAAAAAAAATTTGAGTCCTGGCCTGTCAATGGCCGACACCCAATATAATGT
AAAAAAAAATTCTTTTTTTTTCGTGTCAGAGTCAGATATAA
Found at i:39182712 original size:110 final size:110
Alignment explanation
Indices: 39182598--39183311 Score: 792
Period size: 108 Copynumber: 6.5 Consensus size: 110
39182588 AAAAAAAAAA
*
39182598 TTCGTGTCAGAGTCAGATATAAATATACGGAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
1 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
*
39182663 CAATGGCCGGTACCCAGTAC-AA-TTTAAAAAAAAACTTCTTTTTTT
66 CAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAA-TTC-TTTTTT
* * *
39182708 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAATAATTTTAGGTGCTGGCCTGT
1 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
****
39182773 CAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAA---AAAATT
66 CAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTT
* ********* *
39182815 TTCGTGTCAAAGTCAGATANNNNNNNNNNNNNNNNNNNNNNNGAAAAAAA--ATAAAAAAATTTT
1 TTCGTGTCAGAGTCAGATA--------------TAAATATACGAAAAAAATTAAAAAAAAATTTT
* *
39182878 GGGTGCTGGCCTGTCAATGGCCGACACCCAGTACAATTTTTAAAAAAAAAATTC-TTTTT
52 GGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTT-AAAAAAAAATTCTTTTTT
* *
39182937 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAGTT-AAAAAAAATTTT-GGTGCTGGCATGT
1 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
* * * * *
39183000 CAATGGTCGGCAACCATTTCAAATTTTTAAAAAAAATTCTTTTTT
66 CAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTT
* * * *
39183045 TTCGTGTTAGAGTCAGATATAAATATACGAAAAAAATTTTAAAAAAAATTTTGGGTGCCGGTCTG
1 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAA-TTAAAAAAAAATTTTGGGTGCTGGCCTG
****
39183110 TCAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAA---AAAATT
65 TCAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTT
*
39183153 TTCGTGTCAAAGTCAGATATAAATATACGAAAAAAATTAAAAAAAAA-TTTGGGTGCTGGCCTGT
1 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
*
39183217 CAATGGCCGGCACCTAGTACAAA-TTTAAAAAAAAATTCTTTTTT
66 CAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTT
* *
39183261 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAATAATTTT
1 TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTAAAAAAAAATTTT
39183312 NNNNNNNNNN
Statistics
Matches: 499, Mismatches: 75, Indels: 61
0.79 0.12 0.10
Matches are distributed among these distances:
105 12 0.02
106 37 0.07
107 41 0.08
108 161 0.32
109 16 0.03
110 92 0.18
111 43 0.09
112 12 0.02
119 48 0.10
120 9 0.02
121 8 0.02
122 20 0.04
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.29
Consensus pattern (110 bp):
TTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
CAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTT
Found at i:39184763 original size:108 final size:108
Alignment explanation
Indices: 39184577--39185444 Score: 1190
Period size: 108 Copynumber: 8.1 Consensus size: 108
39184567 ACGAAAAGGA
* * *
39184577 AAAAAAAATTTTGAGTGCTGGCCTGTCAATGGCCGGCA-CCA--A-ACA-GTAAAAAAAAATTAC
1 AAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATT-C
*
39184637 TTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTC
64 -TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
* *
39184683 AAAAAAAATTTGGGTGCTGGCCCGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAAATTCTT
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCTT
* *
39184748 TTTTTTCGTGTCAGAGTTAGATATAAATATACGAAAAAAATTA
66 TTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
* *
39184791 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAAAAAAA---A
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TTTAAAAAAAAATTCT
*** * *
39184853 AAATTTTCGGGTCAAAGTCAGATATAAATATACGAAAAAAATTT
65 TTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
* *
39184897 AAAAATAATTTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAA---
1 AAAAA-AAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TTTAAAAAAAAATTC
**** * *
39184959 AAAATTTTCGTGTCAAAGTCAGATATAAATATACGAAAAAAATTA
64 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
*
39185004 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAAATTCTT
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCTT
*
39185069 TTTTTTCGTGTCAGAGTTAGATATAAATATACGAAAAAAATTTT
66 TTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAA-TTT
* * * *
39185113 AAAAAAAATTTTGTGTGCTGGCCTGCCAATGGGCAGCACCCAGTACAAATTT-AAAAAAAATTCT
1 AAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCT
*
39185177 TTTTTTTCGTGTCAGAGTCAGATATAAATATACG-AAAAAAGTT
65 TTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
* * * * *
39185220 AAAAAAAATTTTGGTGCTGGCATGTCAATGGTCGGCACCCATTACAAATTTTTAAAAAAAATTCT
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TTTAAAAAAAAATTCT
*
39185285 TTTTTTTCGTGTTAGAGTCAGATATAAATATACGAAAAAAATTTT
65 TTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAA-TTT
* *
39185330 AAAAAAAATTTTGGGTGCCGGTCTGTCAATGGCCGGCACCCAGTACAAA-TT-AAAAAAAATTCT
1 AAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCT
39185393 TTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
65 TTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
39185437 AAAAAAAA
1 AAAAAAAA
39185445 GTAAATTTTT
Statistics
Matches: 689, Mismatches: 56, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
105 39 0.06
106 125 0.18
107 125 0.18
108 228 0.33
109 78 0.11
110 60 0.09
111 34 0.05
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (108 bp):
AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCTT
TTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATTT
Found at i:39185478 original size:22 final size:21
Alignment explanation
Indices: 39185445--39185488 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
39185435 TTAAAAAAAA
39185445 GTAAATTTTTTTTACTGTTGG
1 GTAAATTTTTTTTACTGTTGG
39185466 GTAAATTTTTTTTACTGTTGG
1 GTAAATTTTTTTTACTGTTGG
39185487 GT
1 GT
39185489 GCTGGCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.05, G:0.20, T:0.57
Consensus pattern (21 bp):
GTAAATTTTTTTTACTGTTGG
Found at i:39187451 original size:47 final size:47
Alignment explanation
Indices: 39187382--39187474 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
39187372 AAGTCGTTAG
39187382 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTAA
1 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTAA
39187429 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTA
1 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTA
39187475 CACACTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (47 bp):
AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTAA
Found at i:39187648 original size:31 final size:31
Alignment explanation
Indices: 39187600--39187658 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
39187590 TTTTTAATTT
* *
39187600 TTTAAAAAATATTTATATTTTTTATTTAATA
1 TTTAAAAAATATTTATATTCTTCATTTAATA
*
39187631 TTTAATAAAT-TTATATATTCTTCATTTA
1 TTTAAAAAATATT-TATATTCTTCATTTA
39187659 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTAAAAAATATTTATATTCTTCATTTAATA
Found at i:39213376 original size:90 final size:90
Alignment explanation
Indices: 39213223--39213555 Score: 576
Period size: 90 Copynumber: 3.7 Consensus size: 90
39213213 CGAGAAGAGT
* * * ****
39213223 ATCTTTATGACAATCATCACCCGGTGAAGCATTGTGTGCATCCATTGAATGTACAACTTCTTGTT
1 ATCTTTATGACAATCTTCAACCGTTGAAGCATTGCACACATCCATTGAATGTACAACTTCTTGTT
39213288 CCTTTGCTTGAGAATTTTCTATGGC
66 CCTTTGCTTGAGAATTTTCTATGGC
39213313 ATCTTTATGACAATCTTCAACCGTTGAAGCATTGCACACATCCATTGAATGTACAACTTCTTGTT
1 ATCTTTATGACAATCTTCAACCGTTGAAGCATTGCACACATCCATTGAATGTACAACTTCTTGTT
39213378 CCTTTGCTTGAGAATTTTCTATGGC
66 CCTTTGCTTGAGAATTTTCTATGGC
39213403 ATCTTTATGACAATCTTCAACCGTTGAAGCATTGCACACATCCATTGAATGTACAACTTCTTGTT
1 ATCTTTATGACAATCTTCAACCGTTGAAGCATTGCACACATCCATTGAATGTACAACTTCTTGTT
39213468 CCTTTGCTTGAGAATTTTCTATGGC
66 CCTTTGCTTGAGAATTTTCTATGGC
* * *
39213493 ATCTCTATGACAACCTTCAACCGTTGAAGCATTGCACACATCCATTGTATGTACAACTTCTTG
1 ATCTTTATGACAATCTTCAACCGTTGAAGCATTGCACACATCCATTGAATGTACAACTTCTTG
39213556 ATCATTTGTT
Statistics
Matches: 233, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 233 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (90 bp):
ATCTTTATGACAATCTTCAACCGTTGAAGCATTGCACACATCCATTGAATGTACAACTTCTTGTT
CCTTTGCTTGAGAATTTTCTATGGC
Found at i:39219333 original size:58 final size:58
Alignment explanation
Indices: 39219246--39219379 Score: 178
Period size: 58 Copynumber: 2.3 Consensus size: 58
39219236 ATATCAAGGA
* * *
39219246 CTAACTTGGACAAATAAAAGTTCAAGCCCCAATGTGAAAATAATTGTCAAGTTCAGGGT
1 CTAACTTGGACAAA-AAAAGTTCAAGCCCCAATGTGAAAACAATTGCCAAGTTCAGGGC
* * * * *
39219305 CTAACTTGGGCAAAAAGAGTTCAGGCCCCAATGTGGAAACAATTGCCAAGTTTAGGGC
1 CTAACTTGGACAAAAAAAGTTCAAGCCCCAATGTGAAAACAATTGCCAAGTTCAGGGC
*
39219363 CTAATTTGGACAAAAAA
1 CTAACTTGGACAAAAAA
39219380 CAAGTCCACA
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
58 51 0.80
59 13 0.20
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (58 bp):
CTAACTTGGACAAAAAAAGTTCAAGCCCCAATGTGAAAACAATTGCCAAGTTCAGGGC
Found at i:39222403 original size:16 final size:17
Alignment explanation
Indices: 39222366--39222403 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
39222356 TGGTGTTTTA
39222366 ATATTT-GATCTAAATT
1 ATATTTAGATCTAAATT
39222382 AT-TTTAGATC-AAATT
1 ATATTTAGATCTAAATT
39222397 ATATTTA
1 ATATTTA
39222404 TAATCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (17 bp):
ATATTTAGATCTAAATT
Found at i:39225516 original size:18 final size:17
Alignment explanation
Indices: 39225488--39225522 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39225478 ATTATTAAGA
*
39225488 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39225505 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39225523 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39225768 original size:45 final size:44
Alignment explanation
Indices: 39225668--39225777 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
39225658 TTTTCCATTA
39225668 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
39225707 TACTATTACGCCTCTATTCCATTACATTCAACCAAACATTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
*
39225752 TGCTATTACACCTCTATTCTATTACA
1 TGCTATTACACCTCTATTCCATTACA
39225778 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 24 0.42
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:39225819 original size:16 final size:16
Alignment explanation
Indices: 39225758--39225825 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
39225748 GATTTGCTAT
* * *
39225758 TACACCTCTATTCTAT
1 TACACCTCTAATCCAA
*
39225774 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
39225790 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
39225806 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
39225822 TACA
1 TACA
39225826 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39226896 original size:24 final size:24
Alignment explanation
Indices: 39226864--39226914 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
39226854 ATTGGGATAT
39226864 GTTCAATTTGATACTCCAGTGATG
1 GTTCAATTTGATACTCCAGTGATG
*
39226888 GTTCAATTTGATGCTCCAGTGATG
1 GTTCAATTTGATACTCCAGTGATG
39226912 GTT
1 GTT
39226915 TTTAAAAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (24 bp):
GTTCAATTTGATACTCCAGTGATG
Found at i:39228415 original size:23 final size:23
Alignment explanation
Indices: 39228385--39228430 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
39228375 TTGAAGTAAC
39228385 CTTAATCTAGAATTGCTAAAGAT
1 CTTAATCTAGAATTGCTAAAGAT
39228408 CTTAATCTAGAATTGCTAAAGAT
1 CTTAATCTAGAATTGCTAAAGAT
39228431 AACACAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
CTTAATCTAGAATTGCTAAAGAT
Found at i:39231649 original size:18 final size:19
Alignment explanation
Indices: 39231613--39231661 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
39231603 ATGAATACAT
*
39231613 AAATTATCAA-ATCTATAATT
1 AAATTAT-AATAT-TATAATA
39231633 AAATTA-AATATTATAATA
1 AAATTATAATATTATAATA
39231651 AAATTATAATA
1 AAATTATAATA
39231662 ATGAAGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 14 0.54
19 6 0.23
20 6 0.23
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTATAATATTATAATA
Found at i:39231962 original size:21 final size:22
Alignment explanation
Indices: 39231938--39231987 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
39231928 CCTCTTATAC
39231938 TTATTTTTCTTTTTAT-TTT-TT
1 TTATTTTTCTTTTT-TCTTTCTT
39231959 TTA-TTTTCTTTTTTCTTTCTT
1 TTATTTTTCTTTTTTCTTTCTT
39231980 TT-TTTTTC
1 TTATTTTTC
39231988 CTGGGCCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (22 bp):
TTATTTTTCTTTTTTCTTTCTT
Found at i:39231985 original size:20 final size:19
Alignment explanation
Indices: 39231941--39231987 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
39231931 CTTATACTTA
39231941 TTTTTCTTTTTATTTTTTT
1 TTTTTCTTTTTATTTTTTT
*
39231960 TATTTTCTTTTTTCTTTCTTTT
1 T-TTTTC-TTTTTATTT-TTTT
39231982 TTTTTC
1 TTTTTC
39231988 CTGGGCCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 5 0.21
21 13 0.54
22 5 0.21
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTCTTTTTATTTTTTT
Found at i:39233079 original size:43 final size:48
Alignment explanation
Indices: 39233002--39233191 Score: 132
Period size: 49 Copynumber: 4.1 Consensus size: 48
39232992 AGAAAAAAAG
* ** *
39233002 AAAT-GAAATTGGGAAAAAGAAAGGTCACAGGG-AAAAG-AG-GAG-A
1 AAATGGAAATTGGGAAGAAGAAACATCACAGGGAAAAAGAAGAAAGAA
39233045 AAA-GGAAATTGGGAAGAAGAAACATCACTA-GGAAAAAGAAAGAAAGAA
1 AAATGGAAATTGGGAAGAAGAAACATCAC-AGGGAAAAAG-AAGAAAGAA
** *
39233093 AAATGGAAATAAGGAAGAAGAAACATCACCA-TGAAAAAGAAAGAAA-ACA
1 AAATGGAAATTGGGAAGAAGAAACATCA-CAGGGAAAAAG-AAGAAAGA-A
* * * ** *
39233142 AAAAGGAAATAGGGAA-AGAGAAACATTACCTGGAAAAAGAA-AGAGAA
1 AAATGGAAATTGGGAAGA-AGAAACATCACAGGGAAAAAGAAGAAAGAA
39233189 AAA
1 AAA
39233192 AAAAGAAATA
Statistics
Matches: 121, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
43 26 0.21
44 6 0.05
46 2 0.02
47 8 0.07
48 10 0.08
49 68 0.56
50 1 0.01
ACGTcount: A:0.60, C:0.07, G:0.25, T:0.08
Consensus pattern (48 bp):
AAATGGAAATTGGGAAGAAGAAACATCACAGGGAAAAAGAAGAAAGAA
Found at i:39233088 original size:23 final size:23
Alignment explanation
Indices: 39233061--39233138 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
39233051 AATTGGGAAG
39233061 AAGAAACATCACTAGGAAAAAGA
1 AAGAAACATCACTAGGAAAAAGA
* ** *
39233084 AAGAAAGAAAAAT-GGAAATAAGGAA
1 AAGAAACATCACTAGGAAA-AA-G-A
* *
39233109 GAAGAAACATCACCATGAAAAAGA
1 -AAGAAACATCACTAGGAAAAAGA
39233133 AAGAAA
1 AAGAAA
39233139 ACAAAAAGGA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
22 5 0.12
23 17 0.43
24 2 0.05
25 2 0.05
26 10 0.25
27 4 0.10
ACGTcount: A:0.64, C:0.09, G:0.19, T:0.08
Consensus pattern (23 bp):
AAGAAACATCACTAGGAAAAAGA
Found at i:39233194 original size:49 final size:48
Alignment explanation
Indices: 39233044--39233201 Score: 196
Period size: 49 Copynumber: 3.2 Consensus size: 48
39233034 AAAAGAGGAG
*
39233044 AAAAGGAAATTGGGAAGAAGAAACATCA-CTAGGAAAAAGAAAGAAAGAA
1 AAAAGGAAATAGGGAAGAAGAAACATCACCT-GGAAAAAGAAAGAAA-AA
* *
39233093 AAATGGAAATAAGGAAGAAGAAACATCACCAT-GAAAAAGAAAGAAAACA
1 AAAAGGAAATAGGGAAGAAGAAACATCACC-TGGAAAAAGAAAGAAAA-A
*
39233142 AAAAGGAAATAGGGAA-AGAGAAACATTACCTGGAAAAAGAAAGAGAAAA
1 AAAAGGAAATAGGGAAGA-AGAAACATCACCTGGAAAAAGAAAGA-AAAA
*
39233191 AAAAAGAAATA
1 AAAAGGAAATA
39233202 TTTTTAAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 12
0.83 0.06 0.10
Matches are distributed among these distances:
48 3 0.03
49 88 0.92
50 4 0.04
51 1 0.01
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.08
Consensus pattern (48 bp):
AAAAGGAAATAGGGAAGAAGAAACATCACCTGGAAAAAGAAAGAAAAA
Found at i:39238050 original size:29 final size:27
Alignment explanation
Indices: 39238017--39238079 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 27
39238007 CTAAATTTTA
*
39238017 AAATTTTAAAATTTAAAAAATAAAAA-ATT
1 AAATTTTAAAA--T-AAAAATAAAAATACT
39238046 AAATTCTTTAAAATAAAAATAAAAATACT
1 AAA-T-TTTAAAATAAAAATAAAAATACT
39238075 AAATT
1 AAATT
39238080 CCAAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
27 1 0.03
28 12 0.40
29 9 0.30
30 1 0.03
31 7 0.23
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATTTTAAAATAAAAATAAAAATACT
Found at i:39239426 original size:2 final size:2
Alignment explanation
Indices: 39239419--39239450 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39239409 ATCACTAGTG
39239419 AT AT AT 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 AT AT AT
39239451 TGCTTTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39240862 original size:19 final size:19
Alignment explanation
Indices: 39240840--39240881 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
39240830 TATCAATTTG
39240840 GTCACCAAATTTAAATTAT
1 GTCACCAAATTTAAATTAT
39240859 GTCACCAAATTTAAATTAT
1 GTCACCAAATTTAAATTAT
39240878 GTCA
1 GTCA
39240882 AAATATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (19 bp):
GTCACCAAATTTAAATTAT
Found at i:39241133 original size:18 final size:19
Alignment explanation
Indices: 39241110--39241147 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39241100 ACAAGAAAGG
* *
39241110 ATTAAA-AGTTATGTTTTT
1 ATTAAAGAGTAATGATTTT
39241128 ATTAAAGAGTAATGATTTT
1 ATTAAAGAGTAATGATTTT
39241147 A
1 A
39241148 GCACTGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
ATTAAAGAGTAATGATTTT
Found at i:39241487 original size:27 final size:27
Alignment explanation
Indices: 39241449--39241508 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
39241439 GCCTGATCAG
*
39241449 GCCAATTAAATTGGCGGCACCAAAGGT
1 GCCAAATAAATTGGCGGCACCAAAGGT
* *
39241476 GCCAAATAAATTGGTGGCACCAATGGT
1 GCCAAATAAATTGGCGGCACCAAAGGT
39241503 GCCAAA
1 GCCAAA
39241509 GGAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (27 bp):
GCCAAATAAATTGGCGGCACCAAAGGT
Found at i:39241604 original size:19 final size:19
Alignment explanation
Indices: 39241582--39241651 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
39241572 TTCAACTCAT
*
39241582 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
* *
39241601 TTTTAAGTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
39241619 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
39241638 TTTTAATTTAATAA
1 TTTTAATTTAATAA
39241652 ACTATTAAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:39241631 original size:37 final size:37
Alignment explanation
Indices: 39241587--39241657 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
39241577 CTCATTTTTT
39241587 ATTTAATAACTCTATTTTAAGTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAAGTTAATAAACTATTCTC
*
39241624 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAAGTTAATAAACTATT
39241658 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAAGTTAATAAACTATTCTC
Found at i:39241778 original size:27 final size:27
Alignment explanation
Indices: 39241701--39241786 Score: 106
Period size: 27 Copynumber: 3.2 Consensus size: 27
39241691 TTTTTTTTCC
*
39241701 TTTGGCACCA-TGGTGCCGCCAA-TGA
1 TTTGGCACCATTGGTGCCGCCAATTTA
*
39241726 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACCATTGGTGCCGCCAATTTA
39241754 TTTGGCA-CATTTGGTGCCGCCAATTTA
1 TTTGGCACCA-TTGGTGCCGCCAATTTA
*
39241781 ATTGGC
1 TTTGGC
39241787 CGCTGGTGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
26 12 0.23
27 39 0.74
28 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATTTA
Found at i:39241876 original size:24 final size:23
Alignment explanation
Indices: 39241825--39241869 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
39241815 GTTTTTTTTG
39241825 ATATATTTTGGTAAATAAAAAAT
1 ATATATTTTGGTAAATAAAAAAT
39241848 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
39241870 AGTTATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (23 bp):
ATATATTTTGGTAAATAAAAAAT
Found at i:39244368 original size:13 final size:13
Alignment explanation
Indices: 39244350--39244374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39244340 AGTATTTATC
39244350 TAATAAATATATA
1 TAATAAATATATA
39244363 TAATAAATATAT
1 TAATAAATATAT
39244375 TTTTTATTAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAAATATATA
Found at i:39247806 original size:42 final size:43
Alignment explanation
Indices: 39247747--39247835 Score: 135
Period size: 44 Copynumber: 2.1 Consensus size: 43
39247737 TGTTGAATGT
* * *
39247747 TAATTTCTCTCT-CTCTCTCATGGAGGCTCATTCTCTTGTTTA
1 TAATTTCTCTATACTCTCTCATGGAGGCTCATCCTCTTATTTA
39247789 TAATTTCTCTATATCTCTCTCATGGAGGCTCATCCTCTTATTTA
1 TAATTTCTCTATA-CTCTCTCATGGAGGCTCATCCTCTTATTTA
39247833 TAA
1 TAA
39247836 GGCACGGTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 11 0.26
44 31 0.74
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (43 bp):
TAATTTCTCTATACTCTCTCATGGAGGCTCATCCTCTTATTTA
Found at i:39250220 original size:10 final size:10
Alignment explanation
Indices: 39250180--39250220 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
39250170 AAATATGCAG
39250180 ATGTATATAT
1 ATGTATATAT
39250190 AT-TATA-AT
1 ATGTATATAT
*
39250198 ATATATATAT
1 ATGTATATAT
*
39250208 ATGTATACAT
1 ATGTATATAT
39250218 ATG
1 ATG
39250221 GTTACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 4 0.15
9 8 0.30
10 15 0.56
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (10 bp):
ATGTATATAT
Found at i:39254686 original size:20 final size:20
Alignment explanation
Indices: 39254661--39254701 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
39254651 TAATGATTGA
39254661 TATCAAGAT-TTTGGCAAGAT
1 TATCAA-ATATTTGGCAAGAT
39254681 TATCAAATATTTGGCAAGAT
1 TATCAAATATTTGGCAAGAT
39254701 T
1 T
39254702 TTGTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (20 bp):
TATCAAATATTTGGCAAGAT
Found at i:39257074 original size:57 final size:57
Alignment explanation
Indices: 39256981--39257107 Score: 209
Period size: 57 Copynumber: 2.2 Consensus size: 57
39256971 GAAAGAATGA
* *
39256981 TGCAAGAAAAGACAAGTGAACAGGAAATATTTTCTGGCGAAAACAGTAAATATTCCC
1 TGCAAGAAAAGACAAGTGAACAAGAAATATTCTCTGGCGAAAACAGTAAATATTCCC
*
39257038 TGCAAGAAAAGACAAGTGAACAAGAAATATTCTCTGGCGAAAACAGTAAATATTCCT
1 TGCAAGAAAAGACAAGTGAACAAGAAATATTCTCTGGCGAAAACAGTAAATATTCCC
**
39257095 TATAAGAAAAGAC
1 TGCAAGAAAAGAC
39257108 GTATGAATAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.20
Consensus pattern (57 bp):
TGCAAGAAAAGACAAGTGAACAAGAAATATTCTCTGGCGAAAACAGTAAATATTCCC
Found at i:39258703 original size:37 final size:37
Alignment explanation
Indices: 39258625--39258712 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
39258615 CCGAATGCAC
* *
39258625 ATATACACTTATGTCCACCTATGCCGAATGCATAAAA
1 ATATACATTTATATCCACCTATGCCGAATGCATAAAA
* * *
39258662 ATATATATTTATATCCACCTATGCCGAATGCATACAT
1 ATATACATTTATATCCACCTATGCCGAATGCATAAAA
*
39258699 ATATACATATATAT
1 ATATACATTTATAT
39258713 ACATCCAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (37 bp):
ATATACATTTATATCCACCTATGCCGAATGCATAAAA
Found at i:39260622 original size:13 final size:13
Alignment explanation
Indices: 39260604--39260628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39260594 CAATCAAATG
39260604 CACACAAAATAAA
1 CACACAAAATAAA
39260617 CACACAAAATAA
1 CACACAAAATAA
39260629 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:39262099 original size:16 final size:16
Alignment explanation
Indices: 39262080--39262119 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
39262070 TTGAAAAGAA
39262080 AAATAATTTAAAACTT
1 AAATAATTTAAAACTT
**
39262096 AAATTTTTTAAAACTT
1 AAATAATTTAAAACTT
39262112 AAA-AATTT
1 AAATAATTT
39262120 GGAGAAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAATTTAAAACTT
Found at i:39262392 original size:57 final size:57
Alignment explanation
Indices: 39262329--39262535 Score: 236
Period size: 57 Copynumber: 3.6 Consensus size: 57
39262319 TTACAAACTA
* * *
39262329 CAGAGAATATTTACTATTCA-TGCGTCTTTTCTTGTAGGGAATATTTACTGTTTTCAC
1 CAGAGAATATTTCCTATTCACT-CGTCTTTTCTTGCAGGGAATATTTACTGTTTTCGC
* * * * * * *
39262386 CAGAGAATATTTTCTGTCCACTTGTCTTTTCTTGCGGGGAATATTTACTATTTTTGC
1 CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCAGGGAATATTTACTGTTTTCGC
* * * * *
39262443 TAGAGAATATTTCCTGTTCATTCGTCTTTTCTTGCAAGAAATATTTACTGTTTTCGC
1 CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCAGGGAATATTTACTGTTTTCGC
* * *
39262500 TAGAGAGTATTTCCTATTCACTTGTCTTTTCTTGCA
1 CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCA
39262536 TTATTTTTTC
Statistics
Matches: 126, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
57 125 0.99
58 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.45
Consensus pattern (57 bp):
CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCAGGGAATATTTACTGTTTTCGC
Found at i:39268988 original size:9 final size:9
Alignment explanation
Indices: 39268974--39269004 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39268964 GTTAAACGAA
39268974 TCGAGTTAT
1 TCGAGTTAT
*
39268983 TCGAGTTAA
1 TCGAGTTAT
39268992 TCGAGTTAT
1 TCGAGTTAT
39269001 TCGA
1 TCGA
39269005 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:39269047 original size:14 final size:14
Alignment explanation
Indices: 39269022--39269055 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39269012 CGAATTTTTT
*
39269022 TTCGAA-TTTCGAG
1 TTCGAATTTTCGAA
39269035 TTCGAATTTTCGAA
1 TTCGAATTTTCGAA
39269049 TTCGAAT
1 TTCGAAT
39269056 AATTCGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (14 bp):
TTCGAATTTTCGAA
Found at i:39273674 original size:25 final size:26
Alignment explanation
Indices: 39273612--39273675 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 26
39273602 ACATTATATG
39273612 AAAAACTAAATAAAAATTAAATTAAAT
1 AAAAA-TAAATAAAAATTAAATTAAAT
* * *
39273639 TAAAA-ACATAAACA-TATAATT-AAT
1 AAAAATAAATAAAAATTA-AATTAAAT
39273663 AAAAATAAATAAA
1 AAAAATAAATAAA
39273676 TACTAAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
24 9 0.30
25 17 0.57
27 4 0.13
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAATAAATAAAAATTAAATTAAAT
Found at i:39274807 original size:13 final size:14
Alignment explanation
Indices: 39274774--39274807 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39274764 ACATCCCAAA
39274774 AATCGAGTTAGTAG
1 AATCGAGTTAGTAG
*
39274788 AATCGAGTTTGTAG
1 AATCGAGTTAGTAG
39274802 -ATCGAG
1 AATCGAG
39274808 AGTGGTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (14 bp):
AATCGAGTTAGTAG
Found at i:39282172 original size:30 final size:30
Alignment explanation
Indices: 39282138--39282200 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
39282128 CATATCAAAC
39282138 ATACATTAAATATGATAAAACCACATATAT
1 ATACATTAAATATGATAAAACCACATATAT
**
39282168 ATACATTAAATATGATAAGGCCACATATAT
1 ATACATTAAATATGATAAAACCACATATAT
39282198 ATA
1 ATA
39282201 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (30 bp):
ATACATTAAATATGATAAAACCACATATAT
Found at i:39282199 original size:2 final size:2
Alignment explanation
Indices: 39282192--39282224 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39282182 ATAAGGCCAC
39282192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39282225 CACAAATACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39282661 original size:30 final size:30
Alignment explanation
Indices: 39282607--39282667 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
39282597 ACTAAGCAAA
39282607 TTTCATATACATGTATCATCCATTT-CATG
1 TTTCATATACATGTATCATCCATTTCCATG
39282636 TTTCAATATATCATGTAAT-AT-CATTTCCATG
1 TTTC-ATATA-CATGT-ATCATCCATTTCCATG
39282667 T
1 T
39282668 ATTTCATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 4 0.14
30 10 0.36
31 12 0.43
32 2 0.07
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTCATATACATGTATCATCCATTTCCATG
Found at i:39282887 original size:25 final size:26
Alignment explanation
Indices: 39282859--39282932 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
39282849 CATGAGTTGT
39282859 GAATTGGTAAGCTCAAACGAGCT-AA
1 GAATTGGTAAGCTCAAACGAGCTGAA
* ** *
39282884 GAATCGGTAAGCTCTCACGAGCTGCA
1 GAATTGGTAAGCTCAAACGAGCTGAA
* *
39282910 -AATTGGTAAGCCCATACGAGCTG
1 GAATTGGTAAGCTCAAACGAGCTG
39282933 TGGTGTGTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 39 0.98
26 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (26 bp):
GAATTGGTAAGCTCAAACGAGCTGAA
Found at i:39282898 original size:50 final size:50
Alignment explanation
Indices: 39282819--39282931 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
39282809 GTACATGTAT
* * * * **
39282819 GCTCATAA-GAGCTATGAATCGGTATGCTCTCATGAGTTGTGAATTGGTAA
1 GCTCA-AACGAGCTAAGAATCGGTAAGCTCTCACGAGCTGCAAATTGGTAA
39282869 GCTCAAACGAGCTAAGAATCGGTAAGCTCTCACGAGCTGCAAATTGGTAA
1 GCTCAAACGAGCTAAGAATCGGTAAGCTCTCACGAGCTGCAAATTGGTAA
* *
39282919 GCCCATACGAGCT
1 GCTCAAACGAGCT
39282932 GTGGTGTGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
49 2 0.04
50 52 0.96
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (50 bp):
GCTCAAACGAGCTAAGAATCGGTAAGCTCTCACGAGCTGCAAATTGGTAA
Found at i:39286302 original size:23 final size:24
Alignment explanation
Indices: 39286276--39286321 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
39286266 TGATTATATC
39286276 CAGACATGGAGTGTAG-GGTTGGA
1 CAGACATGGAGTGTAGAGGTTGGA
**
39286299 CAGAGTTGGAGTGTAGAGGTTGG
1 CAGACATGGAGTGTAGAGGTTGG
39286322 CTGGGTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.24, C:0.07, G:0.46, T:0.24
Consensus pattern (24 bp):
CAGACATGGAGTGTAGAGGTTGGA
Found at i:39292953 original size:74 final size:75
Alignment explanation
Indices: 39292873--39293011 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 75
39292863 TTTTTTTAAT
* * *
39292873 AACGCCACTAAAACTAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATA-TTTGCGGCG
1 AACGCCACTAAAACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGCG
39292937 TTTTATCGTA
66 TTTTATCGTA
*** * *
39292947 AACGCCACTAATTTTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
1 AACGCCACTAAAACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGCG
39293012 CTTACAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
74 47 0.84
75 9 0.16
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (75 bp):
AACGCCACTAAAACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGCG
TTTTATCGTA
Found at i:39293348 original size:74 final size:75
Alignment explanation
Indices: 39293268--39293407 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 75
39293258 GTTTTTTTAA
* * *
39293268 AAACGCCACTAACACTAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATA-TTTGCGGC
1 AAACGCCACTAACACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
39293332 GTTTTATCGT
66 GTTTTATCGT
** * * * *
39293342 AAACGCCACTAATTCTAATATACCTCAAAACCAAGCGCTGTGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACTAACACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
39293407 G
66 G
39293408 CNNNNNNNNN
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
74 47 0.84
75 9 0.16
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (75 bp):
AAACGCCACTAACACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
GTTTTATCGT
Found at i:39295742 original size:10 final size:10
Alignment explanation
Indices: 39295727--39295753 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
39295717 ATCTTAACAC
39295727 AAATACAGAT
1 AAATACAGAT
39295737 AAATACAGAT
1 AAATACAGAT
39295747 AAATACA
1 AAATACA
39295754 TAAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.07, T:0.19
Consensus pattern (10 bp):
AAATACAGAT
Found at i:39307091 original size:44 final size:44
Alignment explanation
Indices: 39307007--39307668 Score: 603
Period size: 44 Copynumber: 14.9 Consensus size: 44
39306997 ATCAGACTTG
* * *
39307007 TATCTTCGATCTACTTCGCCACCAATATGA-GAAGACAAGATCTGC
1 TATCTTCGATCTACTTC-ACGCCAATA-CATGAAGACAAGATCTGC
* * *
39307052 TATCTTTGATCTACTTCAAGCCAATACATGAAGATAAGATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * ***
39307096 TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
* *
39307141 TATCTTCGATTTACTTCACGCCAATACATGAAGATAAGATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * ***
39307185 TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
*
39307230 TATCTTCGATTTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* *
39307274 TATCTTCGATTTACTTCACGCCAATACATGAAGACAATATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* *
39307318 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGAT-T-C
1 TATCTTC-GATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * *** * *
39307360 ATTACCTTCGATCTACTTCTCCACCAGTATGGGAAGACGAGATCTTC
1 --TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
* *
39307407 TATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATCTGC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * *** *
39307451 TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTTC
1 TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
* * *
39307496 TATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATCTAC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * *
39307540 TTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTAC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * *** * *
39307584 TTTCTTCGATCTACTTCGCCACCAGTATGGGAGGACAAGATCTGT
1 TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
* * * * *
39307629 TGTCTTTGGTCTGCTTCATGCCAATACATGAAGACAAGAT
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
39307669 TTGTTATATT
Statistics
Matches: 491, Mismatches: 114, Indels: 25
0.78 0.18 0.04
Matches are distributed among these distances:
42 1 0.00
43 4 0.01
44 304 0.62
45 180 0.37
46 1 0.00
47 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (44 bp):
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
Found at i:39307118 original size:89 final size:89
Alignment explanation
Indices: 39307009--39307556 Score: 805
Period size: 89 Copynumber: 6.2 Consensus size: 89
39306999 CAGACTTGTA
* * *
39307009 TCTTCGATCTACTTCGCCACCAATATGAGAAGACAAGATCTGCTATCTTTGATCTACTTCAAGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
39307074 AATACATGAAGATAAGATCTGCTT
66 AATACATGAAGATAAGATCTGCTT
* *
39307098 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATTTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
39307163 AATACATGAAGATAAGATCTGCTT
66 AATACATGAAGATAAGATCTGCTT
* *
39307187 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATTTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
* *
39307252 AATACATGAAGACAAGATCTGCTA
66 AATACATGAAGATAAGATCTGCTT
* * * * *** * * * *
39307276 TCTTCGATTTACTTC-ACGCCAATACATGAAGACAATATCTGCTATCTCTGATCTACTTCATGTC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
*
39307340 AATACATGAAGACAAGAT-T-CATT
66 AATACATGAAGATAAGATCTGC-TT
* * * *
39307363 ACCTTCGATCTACTTCTCCACCAGTATGGGAAGACGAGATCTTCTATCTTTGATCTACTTCACGC
1 -TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGC
39307428 CAATACATGAAGATAAGATCTGCTT
65 CAATACATGAAGATAAGATCTGCTT
*
39307453 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTTCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
*
39307518 AATACATGAAGATAAGATCTACTT
66 AATACATGAAGATAAGATCTGCTT
*
39307542 TCTTTGATCTACTTC
1 TCTTCGATCTACTTC
39307557 ATGCCAATAC
Statistics
Matches: 413, Mismatches: 41, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
86 1 0.00
87 2 0.00
88 68 0.16
89 338 0.82
90 3 0.01
91 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (89 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
AATACATGAAGATAAGATCTGCTT
Found at i:39307430 original size:266 final size:265
Alignment explanation
Indices: 39307007--39307600 Score: 888
Period size: 266 Copynumber: 2.2 Consensus size: 265
39306997 ATCAGACTTG
* * *
39307007 TATCTTCGATCTACTTCGCCACCAATATGA-GAAGACAAGATCTGCTATCTTTGATCTACTTCAA
1 TATCTTCGATCTACTTC-ACGCCAATA-CATGAAGACAAGATCTGCTATC-TTGATCTACTTCAA
* *
39307071 GCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
63 GCCAATACATGAAGACAAGATCTGCTTCCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
*
39307136 TCTGCTATCTTCGATTTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTT
128 TCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTT
*
39307201 CGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATTTACTTCACGCCAATACATGAAGACA
193 CGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACA
*
39307266 AGATCTGC
258 AGATCTAC
* * * *
39307274 TATCTTCGATTTACTTCACGCCAATACATGAAGACAATATCTGCTATCTCTGATCTACTTCATGT
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCT-TGATCTACTTCAAGC
* *
39307339 CAATACATGAAGACAAGAT-T-CATTACCTTCGATCTACTTCTCCACCAGTATGGGAAGACGAGA
65 CAATACATGAAGACAAGATCTGC-TT-CCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
* *
39307402 TCTTCTATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTT
128 TCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTT
* * *
39307467 CGCCACCAGTATGGGAAGACAAGATCTTCTATCTTTGATCTACTTCACGCCAATACATGAAGATA
193 CGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACA
39307532 AGATCTAC
258 AGATCTAC
* * * * *
39307540 TTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTC
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTT-GATCTACTTC
39307601 GCCACCAGTA
Statistics
Matches: 296, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
264 1 0.00
265 6 0.02
266 273 0.92
267 16 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (265 bp):
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTGATCTACTTCAAGCC
AATACATGAAGACAAGATCTGCTTCCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT
GCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGC
CACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGA
TCTAC
Found at i:39307601 original size:133 final size:132
Alignment explanation
Indices: 39307007--39307668 Score: 667
Period size: 133 Copynumber: 5.0 Consensus size: 132
39306997 ATCAGACTTG
* * * * *
39307007 TATCTTCGATCTACTTCGCCACCAATATGA-GAAGACAAGATCTGCTATCTTTGATCTACTTCAA
1 TATCTTCGATCTACTTC-ACGCCAATA-CATGAAGACAAGATCTGCTTTCTTCGATCTACTTC--
*** * * * * ***
39307071 GCCA--A-TACATGAAGATAAGATCTGCTT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGAC
62 GCCACCAGTATGGGAAGACAAGATCT--TTATCTTCGATCTACTTC-ACGCCAATACATGAAGAC
39307132 AAGATCTGC
124 AAGATCTGC
* *
39307141 TATCTTCGATTTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
* *
39307206 CCAGTATGGGAAGACAAGATCTGCTATCTTCGATTTACTTCACGCCAATACATGAAGACAAGATC
66 CCAGTATGGGAAGACAAGATCT-TTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
39307271 TGC
130 TGC
* * *
39307274 TATCTTCGATTTACTTCACGCCAATACATGAAGACAATATCTGCTATC-TCTGATCTACTTCATG
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC-GATCTACTTC--G
* *** * * * * * *** *
39307338 TCA--A-TACATGAAGACAAGATTCATTACCTTCGATCTACTTCTCCACCAGTATGGGAAGACGA
63 CCACCAGTATGGGAAGACAAGA-TCTTTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAA
*
39307400 GATCTTC
126 GATCTGC
* *
39307407 TATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
* *
39307472 CCAGTATGGGAAGACAAGATCTTCTATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATC
66 CCAGTATGGGAAGACAAGATCTT-TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
*
39307537 TAC
130 TGC
* * * *
39307540 TTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
* * * * * *
39307605 CCAGTATGGGAGGACAAGATCTGTTGTCTTTGGTCTGCTTCATGCCAATACATGAAGACAAGAT
66 CCAGTATGGGAAGACAAGATCT-TTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
39307669 TTGTTATATT
Statistics
Matches: 442, Mismatches: 70, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
131 7 0.02
132 30 0.07
133 328 0.74
134 74 0.17
135 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (132 bp):
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
CCAGTATGGGAAGACAAGATCTTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
GC
Found at i:39307711 original size:222 final size:221
Alignment explanation
Indices: 39307009--39307668 Score: 593
Period size: 222 Copynumber: 3.0 Consensus size: 221
39306999 CAGACTTGTA
* * * * * *
39307009 TCTTCGATCTACTTCGCCACCAATATGAGAAGACAAGATCTGCTATCTTTGATCTACTTCAAGCC
1 TCTTCGAAC-ACTGCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
* * * ***
39307074 AATACATGAAGATAAGATCTGCTTTCT-TCGATCTACTTC--GCCACCAGTATGGGAAGACAAGA
65 AATACATGAAGACAAGATCTACTATCTCT-GATCTACTTCATGCCA--A-TACATGAAGACAAGA
* * * * * *** * * * *
39307136 -TC-TGCTATCTTCGATTTACTTC-ACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTA
126 TTCAT--TACCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTTCTATCTTTGATCTA
* * * *** *
39307198 CTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
189 CTTC-ACGCCAATACATGAAGACAAGATCTGCTT
** * * * * *** *
39307232 TCTTCGATTTACTTC-ACGCCAATACATGAAGACAAGATCTGCTATCTTCGATTTACTTCACGCC
1 TCTTCGA-ACACTGCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
* * *
39307296 AATACATGAAGACAATATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATTCA
65 AATACATGAAGACAAGATCTACTATCTCTGATCTACTTCATGCCAATACATGAAGACAAGATTCA
* *
39307361 TTACCTTCGATCTACTTCTCCACCAGTATGGGAAGACGAGATCTTCTATCTTTGATCTACTTCAC
130 TTACCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTTCTATCTTTGATCTACTTCAC
*
39307426 GCCAATACATGAAGATAAGATCTGCTT
195 GCCAATACATGAAGACAAGATCTGCTT
* * * *
39307453 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTTCTATCTTTGATCTACTTCACGCC
1 TCTTCGAAC-ACTGCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
* * *
39307518 AATACATGAAGATAAGATCTACTTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGA-TCT
65 AATACATGAAGACAAGATCTACTATCTCTGATCTACTTCATGCCAATACATGAAGACAAGATTC-
* * * * *
39307582 ACTT-TCTTCGATCTACTTCGCCACCAGTATGGGAGGACAAGATCTGT-TGTCTTTGGTCTGCTT
129 A-TTACCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-TCTATCTTTGATCTACTT
*
39307645 CATGCCAATACATGAAGACAAGAT
192 CACGCCAATACATGAAGACAAGAT
39307669 TTGTTATATT
Statistics
Matches: 363, Mismatches: 62, Indels: 25
0.81 0.14 0.06
Matches are distributed among these distances:
220 1 0.00
221 62 0.17
222 279 0.77
223 17 0.05
224 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (221 bp):
TCTTCGAACACTGCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
ATACATGAAGACAAGATCTACTATCTCTGATCTACTTCATGCCAATACATGAAGACAAGATTCAT
TACCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTTCTATCTTTGATCTACTTCACG
CCAATACATGAAGACAAGATCTGCTT
Found at i:39309936 original size:20 final size:20
Alignment explanation
Indices: 39309911--39309951 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39309901 GGTTCGGCAG
39309911 AAAAAATCCAAAAGAATGAA
1 AAAAAATCCAAAAGAATGAA
**
39309931 AAAAAATCGTAAAGAATGAA
1 AAAAAATCCAAAAGAATGAA
39309951 A
1 A
39309952 GAACATTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAAATCCAAAAGAATGAA
Found at i:39312326 original size:17 final size:17
Alignment explanation
Indices: 39312291--39312326 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39312281 TTCTATGATG
*
39312291 AAATGTCATGCAGTAAA
1 AAATGTCATGCAGCAAA
39312308 AAATGTCATGCAGCCAAA
1 AAATGTCATGCAG-CAAA
39312326 A
1 A
39312327 CAAAACACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (17 bp):
AAATGTCATGCAGCAAA
Found at i:39313862 original size:2 final size:2
Alignment explanation
Indices: 39313855--39313885 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39313845 ATAAGGGTAC
39313855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39313886 GAAATTAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39320826 original size:19 final size:17
Alignment explanation
Indices: 39320792--39320824 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39320782 CCTTGAGAGC
*
39320792 GTGTTTTCACTTGAAGA
1 GTGTTTACACTTGAAGA
39320809 GTGTTTACACTT-AAGA
1 GTGTTTACACTTGAAGA
39320825 AGCGAATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39
Consensus pattern (17 bp):
GTGTTTACACTTGAAGA
Found at i:39321452 original size:77 final size:79
Alignment explanation
Indices: 39321307--39321465 Score: 259
Period size: 77 Copynumber: 2.0 Consensus size: 79
39321297 AACCTTAATA
* *
39321307 TCAAGAATAGCCAAAACACATTGATTGCCGATCGAAAGCAGTAATGAATCGAGTCAAATGGCGCT
1 TCAAGAATAGCCAAAACACATTGATTGCCGATCGAAAGCAGTAACGAATCGAGTCAAATGACGCT
* *
39321372 CTCAAGTAATTTCG
66 CTCAAATAATTCCG
*
39321386 TCAA-AATAGCCAAAACACATTGATTGCCGAT-GAAAGCAGTAACGAATCGAGTCAAATGACGTT
1 TCAAGAATAGCCAAAACACATTGATTGCCGATCGAAAGCAGTAACGAATCGAGTCAAATGACGCT
39321449 CTCAAATAATTCCG
66 CTCAAATAATTCCG
39321463 TCA
1 TCA
39321466 CATTTGGTGG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
77 44 0.59
78 27 0.36
79 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (79 bp):
TCAAGAATAGCCAAAACACATTGATTGCCGATCGAAAGCAGTAACGAATCGAGTCAAATGACGCT
CTCAAATAATTCCG
Found at i:39324804 original size:90 final size:90
Alignment explanation
Indices: 39324640--39324831 Score: 287
Period size: 90 Copynumber: 2.1 Consensus size: 90
39324630 ACACACCGTG
* * * *
39324640 TTGTGGATGAACCACCAGAGTTGCAGGTTATTACGCTGCCAGAATGTTGTGAATACACAATGATT
1 TTGTGGATGAACCACCAAAGTTGCAGGTTATTACGCTGCCAGAAGGTTGTGAATACACAACGAAT
* * *
39324705 TTGTAGATAAGAGTTGCC-AAAATAT
66 TTGCAGATAAGAGCTACCTAAAA-AT
*
39324730 TTGTGGATGAACCACCAAAGTTGCAGGTTATTACGCTGCCAGAAGGTTGTGAATGCACAACGAAT
1 TTGTGGATGAACCACCAAAGTTGCAGGTTATTACGCTGCCAGAAGGTTGTGAATACACAACGAAT
*
39324795 TTGCCGATAAGAGCTACCTAAAAAT
66 TTGCAGATAAGAGCTACCTAAAAAT
39324820 TTGTGGATGAAC
1 TTGTGGATGAAC
39324832 TACCTGTCAC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 88 0.96
91 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (90 bp):
TTGTGGATGAACCACCAAAGTTGCAGGTTATTACGCTGCCAGAAGGTTGTGAATACACAACGAAT
TTGCAGATAAGAGCTACCTAAAAAT
Found at i:39326130 original size:17 final size:18
Alignment explanation
Indices: 39326108--39326143 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39326098 CCAGGAAGGT
*
39326108 CGTGTGAAA-CATACGGG
1 CGTGTGAAATCACACGGG
39326125 CGTGTGAAATCACACGGG
1 CGTGTGAAATCACACGGG
39326143 C
1 C
39326144 AGGATAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.17
Consensus pattern (18 bp):
CGTGTGAAATCACACGGG
Found at i:39334466 original size:22 final size:22
Alignment explanation
Indices: 39334438--39334498 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
39334428 CAATGGAGAA
39334438 GGAAAATAGAGAAAGGGAAAAT
1 GGAAAATAGAGAAAGGGAAAAT
39334460 GGAAAATAGAGAAAGGGAAAAT
1 GGAAAATAGAGAAAGGGAAAAT
* * *
39334482 GAAAAATACAAAAAGGG
1 GGAAAATAGAGAAAGGG
39334499 GCCCAACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.61, C:0.02, G:0.30, T:0.08
Consensus pattern (22 bp):
GGAAAATAGAGAAAGGGAAAAT
Found at i:39339028 original size:21 final size:22
Alignment explanation
Indices: 39339004--39339063 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
39338994 TTTAGAATTG
*
39339004 AATTAAATTATGAATT-TTTTA
1 AATTAAATTATGAATTATATTA
*
39339025 AATTAAAATAT-AATTATATTA
1 AATTAAATTATGAATTATATTA
* *
39339046 TATTAATTTATG-ATTATA
1 AATTAAATTATGAATTATA
39339064 CAATTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
AATTAAATTATGAATTATATTA
Found at i:39357321 original size:26 final size:27
Alignment explanation
Indices: 39357274--39357324 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
39357264 GCTATTTTAA
39357274 AATATTTATAGAAAAAAAGCTAATTTT
1 AATATTTATAGAAAAAAAGCTAATTTT
*
39357301 AATATTTATA-AAAAATAGCTAATT
1 AATATTTATAGAAAAAAAGCTAATT
39357325 ATTGCAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
AATATTTATAGAAAAAAAGCTAATTTT
Found at i:39362564 original size:13 final size:13
Alignment explanation
Indices: 39362546--39362572 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39362536 GCTTTATATT
39362546 GCCTCACATTGAA
1 GCCTCACATTGAA
39362559 GCCTCACATTGAA
1 GCCTCACATTGAA
39362572 G
1 G
39362573 TCACGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (13 bp):
GCCTCACATTGAA
Found at i:39364796 original size:18 final size:17
Alignment explanation
Indices: 39364755--39364787 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39364745 AAATAAATAT
39364755 AAATTAAATAAAATCCTA
1 AAATTAAAT-AAATCCTA
39364773 AAATTAAAT-AATCCT
1 AAATTAAATAAATCCT
39364788 TAATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTAAATAAATCCTA
Found at i:39364811 original size:15 final size:14
Alignment explanation
Indices: 39364790--39364825 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
39364780 ATAATCCTTA
*
39364790 ATAATTATCTTAAT
1 ATAATTATCCTAAT
39364804 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
39364819 ATAATTA
1 ATAATTA
39364826 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:39366541 original size:22 final size:22
Alignment explanation
Indices: 39366516--39366564 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
39366506 GAATTTAATT
39366516 TTTATATT-TTTATTTTTAAAAA
1 TTTA-ATTGTTTATTTTTAAAAA
*
39366538 TTTAATTGTTTATTTTTAAAAG
1 TTTAATTGTTTATTTTTAAAAA
39366560 TTTAA
1 TTTAA
39366565 AATTCGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTAATTGTTTATTTTTAAAAA
Found at i:39368095 original size:43 final size:43
Alignment explanation
Indices: 39368043--39368153 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
39368033 TCTTTAATGG
39368043 CGCTTTTATCACAAACGCCGCTAAAGATA-ATGACCTTTAGCGA
1 CGCTTTTATCACAAACGCCGCTAAAGA-ACATGACCTTTAGCGA
* * * *
39368086 CGCTTTTATCACAAACGCCACTATAGAACATGATCTTTAGCGG
1 CGCTTTTATCACAAACGCCGCTAAAGAACATGACCTTTAGCGA
39368129 CGCTTTTATCACAAACGCCGCTAAA
1 CGCTTTTATCACAAACGCCGCTAAA
39368154 AGTACCGTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (43 bp):
CGCTTTTATCACAAACGCCGCTAAAGAACATGACCTTTAGCGA
Found at i:39368166 original size:43 final size:42
Alignment explanation
Indices: 39368030--39368170 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 42
39368020 CTTTTGGGCA
** *
39368030 TGATCTTTAATGGCGCTTTTATCACAAACGCCGCTAAAGATAA
1 TGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG-TAC
* * * * *
39368073 TGACCTTTAGCGACGCTTTTATCACAAACGCCACTATAGAAC
1 TGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGTAC
39368115 ATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAAGTAC
1 -TGATCTTTAGCGGCGCTTTTATCACAAACGCCGCT-AAAGTAC
* *
39368159 CGTTCTTTAGCG
1 TGATCTTTAGCG
39368171 ACGTTTATGA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.01
43 75 0.93
44 5 0.06
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
TGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGTAC
Found at i:39369617 original size:7 final size:7
Alignment explanation
Indices: 39369605--39369656 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
39369595 ACTAGTTAAT
39369605 CTAAACC
1 CTAAACC
39369612 CTAAACC
1 CTAAACC
* *
39369619 ATAAA-T
1 CTAAACC
39369625 CTAAACC
1 CTAAACC
39369632 CTAAAACC
1 CT-AAACC
39369640 CTAAAACC
1 CT-AAACC
*
39369648 TTAAACC
1 CTAAACC
39369655 CT
1 CT
39369657 TAACACATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 4 0.11
7 19 0.51
8 14 0.38
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:39369653 original size:15 final size:15
Alignment explanation
Indices: 39369606--39369656 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
39369596 CTAGTTAATC
*
39369606 TAAACCCT-AAACCA
1 TAAACCCTAAAACCT
* *
39369620 TAAA-TCTAAACCCT
1 TAAACCCTAAAACCT
*
39369634 AAAACCCTAAAACCT
1 TAAACCCTAAAACCT
39369649 TAAACCCT
1 TAAACCCT
39369657 TAACACATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCTAAAACCT
Found at i:39369735 original size:15 final size:14
Alignment explanation
Indices: 39369695--39369738 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
39369685 CAGCCTTTAT
* *
39369695 ACCATAAACCATAA
1 ACCATAACCCTTAA
39369709 ACCATAACCCTTAA
1 ACCATAACCCTTAA
*
39369723 ACCTATAATCCTTAA
1 ACC-ATAACCCTTAA
39369738 A
1 A
39369739 TCTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
ACCATAACCCTTAA
Found at i:39370170 original size:41 final size:41
Alignment explanation
Indices: 39370111--39370266 Score: 204
Period size: 41 Copynumber: 3.8 Consensus size: 41
39370101 AATGTTTTTT
** *
39370111 GCGGCGCTTTTTCAAAAACGCTGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAAGCATTA
** *
39370152 GCGGCGCTTTTTGGAAAACGCCACTAAAGCCCTAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAAGCATTA
* * * *
39370193 GCGGCACTTTTTCAAAACCGCCACTAAAGCACTAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAAGCATTA
**
39370234 GCGGCGCTTTTTCAAAAACGCTGCTAAAGCCCC
1 GCGGCGCTTTTTCAAAAACGCCACTAAAGCCCC
39370267 GAAAGTCAGA
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 98 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAAGCATTA
Found at i:39370354 original size:40 final size:40
Alignment explanation
Indices: 39370327--39370435 Score: 157
Period size: 40 Copynumber: 2.8 Consensus size: 40
39370317 AGAAAAACAT
*
39370327 CGCTAATGCTC-ATTTTTAGCGGCATTTTCCAAAAAGCGC
1 CGCTAATGCTCGATTTTTAGCGGCATTTTTCAAAAAGCGC
* * * *
39370366 CGCAAATGCTCGATCTTTAGCGGCGTTTTTCATAAAGCGC
1 CGCTAATGCTCGATTTTTAGCGGCATTTTTCAAAAAGCGC
*
39370406 CGCTAGTGCTCGATTTTTAGCGGCATTTTT
1 CGCTAATGCTCGATTTTTAGCGGCATTTTT
39370436 TTATCCAAAC
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 10 0.17
40 50 0.83
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (40 bp):
CGCTAATGCTCGATTTTTAGCGGCATTTTTCAAAAAGCGC
Found at i:39372404 original size:4 final size:4
Alignment explanation
Indices: 39372397--39372421 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39372387 TATTTGAACG
39372397 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
39372422 GTTAACTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:39372462 original size:15 final size:15
Alignment explanation
Indices: 39372442--39372473 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39372432 CATTTCACTA
*
39372442 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
39372457 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
39372472 TT
1 TT
39372474 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:39374253 original size:14 final size:15
Alignment explanation
Indices: 39374234--39374265 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39374224 TTTGTAATAA
39374234 AAATTTT-AAAACTT
1 AAATTTTGAAAACTT
39374248 AAATTTTGAAAACTT
1 AAATTTTGAAAACTT
39374263 AAA
1 AAA
39374266 AATTCGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATTTTGAAAACTT
Found at i:39374280 original size:18 final size:19
Alignment explanation
Indices: 39374257--39374297 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39374247 TAAATTTTGA
39374257 AAAC-TTAAAAATTCGGAG
1 AAACTTTAAAAATTCGGAG
* *
39374275 AAACTTTAAAACTTTGGAG
1 AAACTTTAAAAATTCGGAG
39374294 AAAC
1 AAAC
39374298 GAGTTTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (19 bp):
AAACTTTAAAAATTCGGAG
Found at i:39377993 original size:16 final size:16
Alignment explanation
Indices: 39377959--39377997 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
39377949 ATTTGTAATA
39377959 AAAATTTT-AAAACTT
1 AAAATTTTGAAAACTT
39377974 -AAATTTTGAAAACTT
1 AAAATTTTGAAAACTT
39377989 AAAATTTTG
1 AAAATTTTG
39377998 GAGAAGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 7 0.32
16 8 0.36
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (16 bp):
AAAATTTTGAAAACTT
Found at i:39379716 original size:91 final size:88
Alignment explanation
Indices: 39379598--39379777 Score: 288
Period size: 91 Copynumber: 2.0 Consensus size: 88
39379588 TTGTATTTTT
*
39379598 GGAGGATTTTGATGATGATGATGATTTCTCATTTTGTTCTTCATGACAAATTTCATACCATGACT
1 GGAGGATTTTGATGATGATGATGATTTCTCATTTTCTTCTTCATGACAAATTTCATACCATGACT
39379663 TAATTGGTTTTGAAGAAATTTGG
66 TAATTGGTTTTGAAGAAATTTGG
* * *
39379686 GGAGGATTTTGATGATGATAATGATGATTTCTCATTTTCTTCTTCATGGCAAATTTTATACCCTG
1 GGAGGATTTTGATGATG---ATGATGATTTCTCATTTTCTTCTTCATGACAAATTTCATACCATG
*
39379751 AGTTAATTGGTTTTGAAGAAATTTGG
63 ACTTAATTGGTTTTGAAGAAATTTGG
39379777 G
1 G
39379778 TTTTGGATGA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
88 17 0.20
91 67 0.80
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (88 bp):
GGAGGATTTTGATGATGATGATGATTTCTCATTTTCTTCTTCATGACAAATTTCATACCATGACT
TAATTGGTTTTGAAGAAATTTGG
Found at i:39380289 original size:181 final size:184
Alignment explanation
Indices: 39379981--39380346 Score: 621
Period size: 181 Copynumber: 2.0 Consensus size: 184
39379971 TTTTGTAAAA
*
39379981 CTTCTTTTGCTGATTTGCAATCGATTCGTAAAAGAAATTTTTGATTTAATAAATCACTTTGGAAT
1 CTTCTTTTGCTGATTTGCAATCGATTCGTAAAAGAAATATTTGATTTAATAAATCACTTTGGAAT
*
39380046 TTTGTAATGCACAAAACAATTGATAAAATTTCTTTTTTAATAGTACTATAATTTTGCTGAGTAGA
66 TTTGTAATACACAAAACAATTGA-AAAATTTCTTTTTTAATAGTACTATAATTTTGCTGAGTAGA
39380111 ATTCCAGTGTCTAGAAGTAAACTGGACTATTTGCTCTTTTCCTCCTTTAACTTGT
130 ATTCCAGTGTCTAGAAGTAAACTGGACTATTTGCTCTTTTCCTCCTTTAACTTGT
* *
39380166 CTTCTTTTTCTGATTTGCAATTGATTCGTAAAAGAAA-ATTTGATTTAATAAATCACTTTGG-AT
1 CTTCTTTTGCTGATTTGCAATCGATTCGTAAAAGAAATATTTGATTTAATAAATCACTTTGGAAT
* * *
39380229 TTTGTAATACACAAAACAATTG-ACATTTTCTTTTTTAATAGTACTATAATTTTGCTGAGTAGGA
66 TTTGTAATACACAAAACAATTGAAAAATTTCTTTTTTAATAGTACTATAATTTTGCTGAGTAGAA
* *
39380293 TTCCAGTGTCTGGAAGTAAACTGGACTATTTGCTTTTTTCCTCCTTTAACTTGT
131 TTCCAGTGTCTAGAAGTAAACTGGACTATTTGCTCTTTTCCTCCTTTAACTTGT
39380347 TTTAGGATCC
Statistics
Matches: 172, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
181 91 0.53
183 23 0.13
184 23 0.13
185 35 0.20
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (184 bp):
CTTCTTTTGCTGATTTGCAATCGATTCGTAAAAGAAATATTTGATTTAATAAATCACTTTGGAAT
TTTGTAATACACAAAACAATTGAAAAATTTCTTTTTTAATAGTACTATAATTTTGCTGAGTAGAA
TTCCAGTGTCTAGAAGTAAACTGGACTATTTGCTCTTTTCCTCCTTTAACTTGT
Found at i:39382913 original size:40 final size:40
Alignment explanation
Indices: 39382823--39382913 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
39382813 TTTTGCAGCA
* *
39382823 TTTTTCAAAAAGCGTCGCTAATGCTCAATCAATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCAATCAATAGCGACG
* * *
39382863 TTTCTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGACG
1 TTTTTCAAAAAGCGCCGCTAATGCTCAATCAATAGCGACG
*
39382903 TTTTTAAAAAA
1 TTTTTCAAAAA
39382914 ACACCACTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCAATCAATAGCGACG
Found at i:39382924 original size:40 final size:40
Alignment explanation
Indices: 39382840--39382926 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
39382830 AAAAGCGTCG
* * * * *
39382840 CTAATGCTCAATCAATAGCGGCGTTTCTCAAAAAGCGCCG
1 CTAATGCTCAATCAATAGCGACGTTTCTAAAAAAACACCA
* * *
39382880 CTAATGCTCGATCTATAGCGACGTTTTTAAAAAAACACCA
1 CTAATGCTCAATCAATAGCGACGTTTCTAAAAAAACACCA
39382920 CTAATGC
1 CTAATGC
39382927 CACTAACGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
CTAATGCTCAATCAATAGCGACGTTTCTAAAAAAACACCA
Found at i:39383014 original size:40 final size:39
Alignment explanation
Indices: 39382957--39383103 Score: 179
Period size: 40 Copynumber: 3.7 Consensus size: 39
39382947 ATATTTTGCG
* *
39382957 GCGTTTTTCAAAAAGCGCAGCTAATGGTCGATCTATAGT
1 GCGTTTTTAAAAAAGCGCAGCTAATGCTCGATCTATAGT
* *
39382996 AGTGTTTTTAAAAAAGCGCCGCTAATGCTCGATCTATAGT
1 -GCGTTTTTAAAAAAGCGCAGCTAATGCTCGATCTATAGT
* *
39383036 GACATTTTTAAAAAAGCACCA-CTAATGCTCGATCTATAGT
1 G-CGTTTTTAAAAAAGC-GCAGCTAATGCTCGATCTATAGT
* *
39383076 GGCGTTTTTCAAAAAGCGCCGCTAATGC
1 -GCGTTTTTAAAAAAGCGCAGCTAATGC
39383104 CACTAAAGCT
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 87 0.96
41 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (39 bp):
GCGTTTTTAAAAAAGCGCAGCTAATGCTCGATCTATAGT
Found at i:39383059 original size:137 final size:137
Alignment explanation
Indices: 39382813--39383063 Score: 369
Period size: 137 Copynumber: 1.8 Consensus size: 137
39382803 TTATTGAATT
* *
39382813 TTTTGCAGCATTTTTCAAAAAGCGTCGCTAATGCTCAATCAATAGCGGCGTTTCTCAAAAAGCGC
1 TTTTGCAGCATTTTTCAAAAAGCGTCGCTAATGCTCAATCAATAGCAGCGTTTCTAAAAAAGCGC
*
39382878 CGCTAATGCTCGATCTATAGCGACGTTTTTAAAAAAACACCACTAATGCCACTAACGGTGTTATG
66 CGCTAATGCTCGATCTATAGCGACATTTTTAAAAAAACACCACTAATGCCACTAACGGTGTTATG
39382943 CTTAATA
131 CTTAATA
* * * * * * * *
39382950 TTTTGCGGCGTTTTTCAAAAAGCG-CAGCTAATGGTCGATCTATAGTAGTGTTTTTAAAAAAGCG
1 TTTTGCAGCATTTTTCAAAAAGCGTC-GCTAATGCTCAATCAATAGCAGCGTTTCTAAAAAAGCG
* *
39383014 CCGCTAATGCTCGATCTATAGTGACATTTTTAAAAAAGCACCACTAATGC
65 CCGCTAATGCTCGATCTATAGCGACATTTTTAAAAAAACACCACTAATGC
39383064 TCGATCTATA
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
136 1 0.01
137 99 0.99
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (137 bp):
TTTTGCAGCATTTTTCAAAAAGCGTCGCTAATGCTCAATCAATAGCAGCGTTTCTAAAAAAGCGC
CGCTAATGCTCGATCTATAGCGACATTTTTAAAAAAACACCACTAATGCCACTAACGGTGTTATG
CTTAATA
Found at i:39384149 original size:75 final size:73
Alignment explanation
Indices: 39384020--39384164 Score: 202
Period size: 75 Copynumber: 2.0 Consensus size: 73
39384010 TGGACTTTAT
* **
39384020 TTTTAGTCAATATTGTATTTTTTTTCGAAACAATACACAAATTTGAGTG-TTTTTTCGTTTATAC
1 TTTTAGTCAATATTGTATTTTTTTTCGAAACAACACACAAATTTGAACGCTTTTTTCGTTTATAC
39384084 GAGCATAA
66 GAGCATAA
* * *
39384092 TTTTAGTCAGTATTGTATTTTTTATTTTCGAAACAACACACAAATTTTAACGCTTTTTTGGTTTA
1 TTTTAGTCAATATTGTA--TTTT-TTTTCGAAACAACACACAAATTTGAACGCTTTTTTCGTTTA
39384157 TACGAGCA
63 TACGAGCA
39384165 AATGGCATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
72 16 0.25
74 4 0.06
75 24 0.38
76 19 0.30
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (73 bp):
TTTTAGTCAATATTGTATTTTTTTTCGAAACAACACACAAATTTGAACGCTTTTTTCGTTTATAC
GAGCATAA
Found at i:39385661 original size:29 final size:30
Alignment explanation
Indices: 39385613--39385669 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
39385603 AAGTTGGATC
39385613 AAATCAAAATTCCATGTATAAAATTGCATA
1 AAATCAAAATTCCATGTATAAAATTGCATA
* *
39385643 AAATCAAAGTT-CATGTATATAATTGCA
1 AAATCAAAATTCCATGTATAAAATTGCA
39385670 CATCAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTCCATGTATAAAATTGCATA
Found at i:39391691 original size:16 final size:16
Alignment explanation
Indices: 39391644--39391692 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
39391634 AATAATAATA
39391644 AAAATACATATATATAT
1 AAAA-ACATATATATAT
* *
39391661 AAAAACGTATGTATAT
1 AAAAACATATATATAT
* *
39391677 ATAAGCATATATATAT
1 AAAAACATATATATAT
39391693 GAATGTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
AAAAACATATATATAT
Found at i:39393146 original size:87 final size:89
Alignment explanation
Indices: 39392981--39393196 Score: 289
Period size: 87 Copynumber: 2.5 Consensus size: 89
39392971 TTAAGGATAT
* * *
39392981 AAAAA-GCCCTCAAACTTTTTCAAAAAAGGTAATTAAGCCCTTCTTTTTTTTTTGCACTTAATTG
1 AAAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCC-TCTTATTTTTTTGCACTTAATTG
*
39393045 AGCACTTAAACTTTCAAAATGTATC
65 AGCACTTAAACTTTCAAAATGCATC
*
39393070 AAAAAGGCCCTCAAACTTGTTCAAAAAAAAGCAATTAAGCCC-C-TATTTTTTT-CACTTAATTG
1 AAAAAGGCCCTCAAACTTTTTC-AAAAAAAGCAATTAAGCCCTCTTATTTTTTTGCACTTAATTG
* *
39393132 GGTACTTAAACTTTCAAAATGCATC
65 AGCACTTAAACTTTCAAAATGCATC
* * *
39393157 AAAAAGACCCTCAAAATTTTTC-AAAAAATCAATTAAGCCC
1 AAAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCC
39393197 ATGCTTTTAT
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
85 17 0.15
87 51 0.45
88 8 0.07
89 6 0.05
90 15 0.13
91 17 0.15
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (89 bp):
AAAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCTCTTATTTTTTTGCACTTAATTGA
GCACTTAAACTTTCAAAATGCATC
Found at i:39393683 original size:9 final size:10
Alignment explanation
Indices: 39393663--39393699 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
39393653 TTCCTTTTTG
39393663 TTTT-TAATT
1 TTTTATAATT
39393672 TTTTATAATT
1 TTTTATAATT
39393682 TTTTATAATT
1 TTTTATAATT
*
39393692 TTTAATAA
1 TTTTATAA
39393700 AAATAGGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:39393850 original size:89 final size:90
Alignment explanation
Indices: 39393698--39393903 Score: 301
Period size: 89 Copynumber: 2.3 Consensus size: 90
39393688 AATTTTTAAT
* **
39393698 AAAAA-TAGGGGATTAATTGCTTTTTTCTAAAAAAGTTTGAGGGTTTTTTTGATGCATTTTGAAA
1 AAAAAGTAGGGGCTTAATTGCTTTTTT-TAAAAAAGTTTGAGGGCATTTTTGATGCATTTTGAAA
* *
39393762 GTTCAAGTACCCAATTGAGTGCAAAC
65 GTTCAACTACCCAATTGAGTGCAAAA
* *
39393788 AAAAAGTAGGGGCTTAATTG-TTTTTTTGAAAAGGTTTGAGGGCATTTTTGATGCATTTTGAAAG
1 AAAAAGTAGGGGCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGCATTTTTGATGCATTTTGAAAG
* *
39393852 TTCAACTGCTCAATTGAGTGCAAAA
66 TTCAACTACCCAATTGAGTGCAAAA
39393877 AAAAAG-AGGGGCTTAATTGCTTTTTTT
1 AAAAAGTAGGGGCTTAATTGCTTTTTTT
39393904 TTTTTTTAAG
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
88 13 0.12
89 68 0.65
90 11 0.10
91 13 0.12
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (90 bp):
AAAAAGTAGGGGCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGCATTTTTGATGCATTTTGAAAG
TTCAACTACCCAATTGAGTGCAAAA
Found at i:39419611 original size:22 final size:22
Alignment explanation
Indices: 39419569--39419611 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39419559 TTACATAACA
*
39419569 GAGCATATCATATAACTTATCG
1 GAGCATATCATATAACATATCG
* *
39419591 GAGCTTATCATATATCATATC
1 GAGCATATCATATAACATATC
39419612 AAAATGTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (22 bp):
GAGCATATCATATAACATATCG
Found at i:39420765 original size:32 final size:31
Alignment explanation
Indices: 39420698--39420766 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
39420688 ATTTTGGGCC
* * *
39420698 CACACGACCCAAATAGACAGCTTGTGTGGCT
1 CACACGACCCAAAAAGACAGCTTGTGTGCCA
*
39420729 CACACGACCCAAAAAGCCCAGAC-TGTGTGCCA
1 CACACGACCCAAAAAG-ACAG-CTTGTGTGCCA
39420761 CACACG
1 CACACG
39420767 GTCCACTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 15 0.47
32 16 0.50
33 1 0.03
ACGTcount: A:0.32, C:0.35, G:0.20, T:0.13
Consensus pattern (31 bp):
CACACGACCCAAAAAGACAGCTTGTGTGCCA
Found at i:39422401 original size:38 final size:38
Alignment explanation
Indices: 39422327--39422401 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
39422317 TAGAAATAGG
* * *
39422327 CATGTTTAACATGTATTAAGTTCACCAGTAATAGTAGA
1 CATGTTTAACATGTATTAAGTTCAACAATAACAGTAGA
* * *
39422365 CATGTTTAGCATGTATTCAGTTCAACAATGACAGTAG
1 CATGTTTAACATGTATTAAGTTCAACAATAACAGTAG
39422402 GCATTCAACC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (38 bp):
CATGTTTAACATGTATTAAGTTCAACAATAACAGTAGA
Found at i:39424925 original size:15 final size:16
Alignment explanation
Indices: 39424902--39424934 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
39424892 TTTGGTTTAA
39424902 ATTTATATATATTATT
1 ATTTATATATATTATT
39424918 ATTT-TATATATTATT
1 ATTTATATATATTATT
39424933 AT
1 AT
39424935 CTATGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATATATATTATT
Found at i:39430027 original size:16 final size:16
Alignment explanation
Indices: 39430006--39430039 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
39429996 GTAAAAAAAA
39430006 AAATCTCTGCCGTGGC
1 AAATCTCTGCCGTGGC
39430022 AAATCTCTGCCGTGGC
1 AAATCTCTGCCGTGGC
39430038 AA
1 AA
39430040 CATATTGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (16 bp):
AAATCTCTGCCGTGGC
Found at i:39431545 original size:128 final size:128
Alignment explanation
Indices: 39431317--39432347 Score: 1569
Period size: 128 Copynumber: 8.0 Consensus size: 128
39431307 TACAGATCAG
* * *
39431317 TAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAATCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
* * *
39431382 AAACAGTAGTGGAGCAGACAGAAGGAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGAT
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
* *
39431445 TAAAACCACAAATCTTATCTTTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
** * *
39431510 AAAAAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTGGAGCAGAT
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
*
39431573 TAAAACCACAGATCTTATCTCTCTGAAGTTATAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
** * *
39431638 AAAAAGTAGTGGAGCAGACAGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
* * *
39431701 TAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAAATCGCATCAAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
* *
39431766 AAGCAGTAGTGGAGAAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGAT
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
* * * *
39431829 TAAAACCATAGATCTTATCTCTTTGAAGTTACAGTAGAGCAAATCGCATCTAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
* * * * * *
39431894 GAAGTTA-CAGTGGAGCAGACAGAAGAAACCAAACCTATCTCCCTAAATTTACAGTGGAGCGGAT
66 -AAG-CAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
* *
39431958 TAAAACCACAGATCGTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
*
39432023 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGAT
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
* *
39432086 TAAATCCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATTAAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
* *
39432151 AAGCAGTAGTGGAGCAGACAGAAGAAATCAATCATATCTCCCTGAAGTTGCAGTGGAGCGGAT
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
* * * *
39432214 TAAAACCACAGATTTTATCTCTCTAAAGTTGCAGTAGAGCAGATCGCATCGAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
** * * ** * *
39432279 GAAGTTGCAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGAT
66 -AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
39432343 TAAAA
1 TAAAA
39432348 TGATGAATCC
Statistics
Matches: 827, Mismatches: 72, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
127 1 0.00
128 653 0.79
129 172 0.21
130 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (128 bp):
TAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
Found at i:39431778 original size:84 final size:86
Alignment explanation
Indices: 39431416--39432297 Score: 279
Period size: 84 Copynumber: 10.3 Consensus size: 86
39431406 GAACCAATCC
* * * * * * * *
39431416 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCTTTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
*
39431481 GAGCAG-ATCGCATCAAGTCT
66 GAGCAGAATCGAATCAAGTCT
** ** * * *
39431501 TATCTCCCT-AAAAAGTAGTGGAGCAGACAGAAGAAAC-CA-ATCCTATCTCTCTGAAGTTGCAG
1 TATCTCCCTGAAGTAGTAGTGGAGCAGA-TTAA-AACCACAGATCTTATCTCTCTAAAGTTGCAG
* * ** *
39431563 TGGAGCAGATTAAAACCACAGATCT
64 TAGAGCAGAATCGAATCA-AG-TCT
* * *** * *
39431588 TATCTCTCTGAAGTTA-TAGTAGAGCAGA-TCGCATCA-AG-TCTTATCTCCCTAAAAAGTAGTG
1 TATCTCCCTGAAG-TAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCT--AAAGT--TG
* * * *
39431649 GAGCAGA-CAGAA--GAAACTAA-TCC
61 CAGTAGAGCAGAATCGAATC-AAGTCT
* *
39431672 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
*
39431737 GAGCA-AATCGCATCAAGTCT
66 GAGCAGAATCGAATCAAGTCT
* * ** * * *
39431757 TATCTCCCT-AAGCAGTAGTGGAGAAGACAGAAGAAAC-CA-ATCCTATCTCCCTAAAGTTGCAG
1 TATCTCCCTGAAGTAGTAGTGGAGCAGA-TTAA-AACCACAGATCTTATCTCTCTAAAGTTGCAG
* * * ** *
39431819 TGGAGCGGATTAAAACCATAGATCT
64 TAGAGCAGAATCGAATCA-AG-TCT
** * * * *** * * * * *
39431844 TATCTCTTTGAAGTTA-CAGTAGAGCA-AATCGCATC-TAG-TCTTATCTCCCTGAAGTTACAGT
1 TATCTCCCTGAAG-TAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGT
* ** * * *
39431905 GGAGCAGACAGAAGAAACCAA-ACC
65 AGAGCAGA-A-TCG-AATCAAGTCT
* * * * * * *
39431929 TATCTCCCTAAATTTA-CAGTGGAGCGGATTAAAACCACAGATCGTATCTCTCTGAAGTTACAGT
1 TATCTCCCTGAA-GTAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGT
* *
39431993 AGAGTAG-ATCGCATCAAGTCT
65 AGAGCAGAATCGAATCAAGTCT
* ** * * * *
39432014 TATCTCCCT-AAGCAGTAGTGGAGCAGACAGAAGAAAC-CA-ATCCTATCTCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTAGTAGTGGAGCAGA-TTAA-AACCACAGATCTTATCTCTCTAAAGTTGCAG
* * **
39432076 TGGAG-AGGATTAAATCCACAGATCT
64 TAGAGCAGAATCGAAT-CA-AG-TCT
* * * *** ** *
39432101 TATCTCTCTGAAGTTA-CAGTAGAGCAGA-TCGCATTA-AG-TCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTGAAG-TAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAA--AGT--TG
* * *
39432162 GAGCAGA-CAGAA--GAAATCAA-TCA
61 CAGTAGAGCAGAATCG-AATCAAGTCT
* * * *
39432185 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATTTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
* *
39432250 GAGCAG-ATCGCATCGAGTCT
66 GAGCAGAATCGAATCAAGTCT
* *
39432270 TATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TATCTCCCTGAAGTAGTAGTGGAGCAGA
39432298 CTGAAGCTAC
Statistics
Matches: 576, Mismatches: 158, Indels: 126
0.67 0.18 0.15
Matches are distributed among these distances:
83 22 0.04
84 183 0.32
85 179 0.31
86 30 0.05
87 70 0.12
88 74 0.13
89 18 0.03
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (86 bp):
TATCTCCCTGAAGTAGTAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
GAGCAGAATCGAATCAAGTCT
Found at i:39432099 original size:385 final size:384
Alignment explanation
Indices: 39431317--39432347 Score: 1620
Period size: 385 Copynumber: 2.7 Consensus size: 384
39431307 TACAGATCAG
* *
39431317 TAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAATCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
* *
39431382 AAACAGTAGTGGAGCAGACAGAAGGAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTA
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTA
*
39431447 AAACCACAAATCTTATCT-TTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTA
131 AAACCACAGATCTTATCTCTT-TGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT-
* * *
39431511 AAAAG-T-AGTGGAGCAGACAGAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATT
194 -GAAGTTCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT
* *
39431574 AAAACCACAGATCTTATCTCTCTGAAGTTATAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTA
258 AAAACCACAGATCGTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTA
*
39431639 AAAAGTAGTGGAGCAGACAGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
323 AAAAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* *
39431701 TAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAAATCGCATCAAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
*
39431766 AAGCAGTAGTGGAGAAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTA
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTA
* * *
39431831 AAACCATAGATCTTATCTCTTTGAAGTTACAGTAGAGCAAATCGCATCTAGTCTTATCTCCCTGA
131 AAACCACAGATCTTATCTCTTTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGA
* * * *
39431896 AGTTACAGTGGAGCAGACAGAAGAAACCAAACCTATCTCCCTAAATTTACAGTGGAGCGGATTAA
196 AGTT-CAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
* *
39431961 AACCACAGATCGTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTAAG
260 AACCACAGATCGTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAA
*
39432026 CAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGAT
325 AAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCA-GAT
* * *
39432086 TAAATCCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATTAAGTCTTATCTCCCT
1 TAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
* * *
39432151 AAGCAGTAGTGGAGCAGACAGAAGAAATCAATCATATCTCCCTGAAGTTGCAGTGGAGCGGATTA
66 AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTA
* * * * *
39432216 AAACCACAGATTTTATCTCTCTAAAGTTGCAGTAGAGCAGATCGCATCGAGTCTTATCTCCCTGA
131 AAACCACAGATCTTATCTCTTTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGA
* ** * *
39432281 AGTTGCAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAA
196 AGTT-CAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
39432346 AA
260 AA
39432348 TGATGAATCC
Statistics
Matches: 592, Mismatches: 50, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
382 3 0.01
383 1 0.00
384 180 0.30
385 408 0.69
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (384 bp):
TAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT
AAGCAGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTA
AAACCACAGATCTTATCTCTTTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGA
AGTTCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
ACCACAGATCGTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAAA
AGTAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
Found at i:39432357 original size:44 final size:43
Alignment explanation
Indices: 39432270--39432390 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 43
39432260 CATCGAGTCT
* * * **
39432270 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTAATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCGGA-TTAAAATACTAATCC
39432314 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATGA-TGAATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAAT-ACT-AATCC
* *
39432358 TATAC-CTTTGAAGTTGCAGAGG-GTCGGATTAAA
1 TAT-CTCCTTGAAGTTGCAGTGGAG-CGGATTAAA
39432391 TTTGAGGTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.09
44 59 0.89
45 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATACTAATCC
Found at i:39433116 original size:8 final size:8
Alignment explanation
Indices: 39433094--39433127 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
39433084 TTCCAAAACC
39433094 TTTTT-TT
1 TTTTTATT
*
39433101 TGTTTATT
1 TTTTTATT
39433109 TTTTTATT
1 TTTTTATT
39433117 TTTTTATT
1 TTTTTATT
39433125 TTT
1 TTT
39433128 ACTTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:39433122 original size:16 final size:15
Alignment explanation
Indices: 39433094--39433137 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
39433084 TTCCAAAACC
39433094 TTTTTTTTGTTTATT
1 TTTTTTTTGTTTATT
*
39433109 TTTTTATTTTTTTATT
1 TTTTT-TTTGTTTATT
*
39433125 TTTACTTTTGTTT
1 TTT-TTTTTGTTT
39433138 TTTCTAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 18 0.75
17 1 0.04
ACGTcount: A:0.09, C:0.02, G:0.05, T:0.84
Consensus pattern (15 bp):
TTTTTTTTGTTTATT
Found at i:39433820 original size:15 final size:16
Alignment explanation
Indices: 39433797--39433829 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
39433787 TTTGGTTTAA
39433797 ATTTATATATATTATT
1 ATTTATATATATTATT
39433813 ATTT-TATATATTATT
1 ATTTATATATATTATT
39433828 AT
1 AT
39433830 CTATGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATATATATTATT
Found at i:39453812 original size:43 final size:43
Alignment explanation
Indices: 39453755--39453868 Score: 167
Period size: 43 Copynumber: 2.7 Consensus size: 43
39453745 AATGCCACTG
* *
39453755 TCCCAGACAG-GGTCTTACACAAAAACACAAGTCGATTCCAACA
1 TCCCAGAC-GTGGTCTTACACGAAAACACAAGTCGATACCAACA
* * *
39453798 TCCTAGACGTGGTCTTACACGAAAACACAAGTCGATACTAACG
1 TCCCAGACGTGGTCTTACACGAAAACACAAGTCGATACCAACA
39453841 TCCCAGACGTGGTCTTACACGAAAACAC
1 TCCCAGACGTGGTCTTACACGAAAACAC
39453869 TTATCAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.18
Consensus pattern (43 bp):
TCCCAGACGTGGTCTTACACGAAAACACAAGTCGATACCAACA
Found at i:39464654 original size:83 final size:84
Alignment explanation
Indices: 39464550--39464721 Score: 330
Period size: 83 Copynumber: 2.1 Consensus size: 84
39464540 GTGGCATATG
39464550 CAAATTTGAAGGTGGTAGGCAGGGTCTTGTTGTTTTAATAATGAACTTTTTTTAATTCAATCCTT
1 CAAATTTGAAGGTGGTAGGCAGGGTCTTGTTGTTTTAATAATGAACTTTTTTTAATTCAATCCTT
39464615 CTATAAAT-GAAAATTTAT
66 CTATAAATAGAAAATTTAT
39464633 CAAATTTGAAGGTGGTAGGCAGGGTCTTGTTGTTTTAATAATGAACTTTTTTTAATTCAATCCTT
1 CAAATTTGAAGGTGGTAGGCAGGGTCTTGTTGTTTTAATAATGAACTTTTTTTAATTCAATCCTT
39464698 CTATAAATAGAAAATTTAT
66 CTATAAATAGAAAATTTAT
39464717 -AAATT
1 CAAATT
39464722 AATATATGGT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
83 78 0.89
84 10 0.11
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (84 bp):
CAAATTTGAAGGTGGTAGGCAGGGTCTTGTTGTTTTAATAATGAACTTTTTTTAATTCAATCCTT
CTATAAATAGAAAATTTAT
Found at i:39468001 original size:40 final size:40
Alignment explanation
Indices: 39467946--39468041 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
39467936 TGCCAAACGG
* * *
39467946 AGGCACCGTAGTGCAAATAGAGGCATC-AATGTGCAATCAA
1 AGGCACCGAAGTGCAAACAGAGGCA-CAAATGCGCAATCAA
* * * *
39467986 AGGCACCAAAGTGCAAACAGGGGTACAAATGCGCAATCAG
1 AGGCACCGAAGTGCAAACAGAGGCACAAATGCGCAATCAA
39468026 AGGCACCGAAGTGCAA
1 AGGCACCGAAGTGCAA
39468042 TCTCGTACAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (40 bp):
AGGCACCGAAGTGCAAACAGAGGCACAAATGCGCAATCAA
Found at i:39468043 original size:20 final size:20
Alignment explanation
Indices: 39467945--39468043 Score: 76
Period size: 20 Copynumber: 5.0 Consensus size: 20
39467935 ATGCCAAACG
**
39467945 GAGGCACCGTAGTGCAAAT-A
1 GAGGCACCAAAGTGC-AATCA
* *
39467965 GAGGCATCAATGTGCAATCA
1 GAGGCACCAAAGTGCAATCA
* *
39467985 AAGGCACCAAAGTGCAAACA
1 GAGGCACCAAAGTGCAATCA
* * *
39468005 GGGGTA-CAAATGCGCAATCA
1 GAGGCACCAAA-GTGCAATCA
*
39468025 GAGGCACCGAAGTGCAATC
1 GAGGCACCAAAGTGCAATC
39468044 TCGTACAAGC
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
19 7 0.12
20 49 0.83
21 3 0.05
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.13
Consensus pattern (20 bp):
GAGGCACCAAAGTGCAATCA
Found at i:39473561 original size:56 final size:56
Alignment explanation
Indices: 39473470--39473582 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
39473460 GGCAGAGTTG
39473470 TACGGAGGACAGGAGGTGGAGTGGAGAAAGTTGACAAATGAAAAAGTGATGTGATA
1 TACGGAGGACAGGAGGTGGAGTGGAGAAAGTTGACAAATGAAAAAGTGATGTGATA
* *
39473526 TACGTAGGACAGGAGGTGGAGTGGAGAAAGTTGACAAATGAAAAGGTGATGTGATA
1 TACGGAGGACAGGAGGTGGAGTGGAGAAAGTTGACAAATGAAAAAGTGATGTGATA
39473582 T
1 T
39473583 GAGCAATTGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.38, C:0.05, G:0.37, T:0.19
Consensus pattern (56 bp):
TACGGAGGACAGGAGGTGGAGTGGAGAAAGTTGACAAATGAAAAAGTGATGTGATA
Found at i:39487684 original size:30 final size:30
Alignment explanation
Indices: 39487638--39487726 Score: 125
Period size: 25 Copynumber: 3.1 Consensus size: 30
39487628 ATTTCTTATG
*
39487638 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
39487669 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
39487698 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
39487724 CCA
1 CCA
39487727 TAAATATTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
25 23 0.43
26 2 0.04
29 2 0.04
30 19 0.36
31 7 0.13
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:39487693 original size:15 final size:15
Alignment explanation
Indices: 39487648--39487694 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
39487638 CCAATATCTC
39487648 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
39487663 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
39487678 GATACCCATATCTTT
1 GATACCCATATCTTT
39487693 GA
1 GA
39487695 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:39489776 original size:6 final size:6
Alignment explanation
Indices: 39489765--39489802 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
39489755 ATTACTCAGT
39489765 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CT
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CT
39489803 TCATTTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCA
Found at i:39502986 original size:30 final size:30
Alignment explanation
Indices: 39502952--39503010 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39502942 AACAAACATT
39502952 CTCTGCGTA-GCTCTGTTCAGTTTTGCTCTA
1 CTCTG-GTATGCTCTGTTCAGTTTTGCTCTA
* * *
39502982 CTCTGTTATGTTCTGTTCTGTTTTGCTCT
1 CTCTGGTATGCTCTGTTCAGTTTTGCTCT
39503011 GTTCTATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.07, C:0.24, G:0.19, T:0.51
Consensus pattern (30 bp):
CTCTGGTATGCTCTGTTCAGTTTTGCTCTA
Found at i:39502993 original size:5 final size:5
Alignment explanation
Indices: 39502983--39503051 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
39502973 TTTGCTCTAC
* * * * ** *
39502983 TCTGT TATGT TCTGT TCTGT TTTGC TCTGT TCTAT TCTAC TCTGC TCTGT
1 TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT
*
39503033 TCTAT TCTG- TCATGT TCTG
1 TCTGT TCTGT TC-TGT TCTG
39503052 GTGGGTTTGT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
4 2 0.04
5 46 0.92
6 2 0.04
ACGTcount: A:0.07, C:0.22, G:0.16, T:0.55
Consensus pattern (5 bp):
TCTGT
Found at i:39503003 original size:15 final size:15
Alignment explanation
Indices: 39502961--39503015 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
39502951 TCTCTGCGTA
* *
39502961 GCTCTGTTCAGTTTT
1 GCTCTGTTCTGTTAT
**
39502976 GCTCTACTCTGTTAT
1 GCTCTGTTCTGTTAT
* *
39502991 GTTCTGTTCTGTTTT
1 GCTCTGTTCTGTTAT
39503006 GCTCTGTTCT
1 GCTCTGTTCT
39503016 ATTCTACTCT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.05, C:0.22, G:0.18, T:0.55
Consensus pattern (15 bp):
GCTCTGTTCTGTTAT
Found at i:39503015 original size:20 final size:20
Alignment explanation
Indices: 39502990--39503042 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
39502980 TACTCTGTTA
* *
39502990 TGTTCTGTTCTGTTTTGCTC
1 TGTTCTATTCTGTTCTGCTC
**
39503010 TGTTCTATTCTACTCTGCTC
1 TGTTCTATTCTGTTCTGCTC
39503030 TGTTCTATTCTGT
1 TGTTCTATTCTGT
39503043 CATGTTCTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.06, C:0.23, G:0.15, T:0.57
Consensus pattern (20 bp):
TGTTCTATTCTGTTCTGCTC
Done.