Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 175 of 189
Found at i:51983315 original size:34 final size:33
Alignment explanation
Indices: 51983255--51983320 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
51983245 TTTATTAGTG
* *
51983255 AGTTTTAAAGAGTTTTTATGATAATAATATTCTT
1 AGTTTTAAAGAGTTTGTATGAGAATAAT-TTCTT
* *
51983289 AGTTTTAAAGAGTTTGTGTGGGAATAATTTCT
1 AGTTTTAAAGAGTTTGTATGAGAATAATTTCT
51983321 ACTCTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (33 bp):
AGTTTTAAAGAGTTTGTATGAGAATAATTTCTT
Found at i:51983429 original size:18 final size:18
Alignment explanation
Indices: 51983408--51983496 Score: 72
Period size: 18 Copynumber: 4.8 Consensus size: 18
51983398 ATTTTAAATT
*
51983408 TTTATAATATTTTTATAA
1 TTTATAATATTTTAATAA
*
51983426 TTTATGATATTTTAATAA
1 TTTATAATATTTTAATAA
* *
51983444 TTTCTTATCATTTTTAATAA
1 TTTATAAT-A-TTTTAATAA
* *
51983464 CTTTAATAA-AATTTAATAT
1 -TTT-ATAATATTTTAATAA
*
51983483 TTTATAAAATTTTA
1 TTTATAATATTTTA
51983497 TTTGAAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
17 4 0.07
18 30 0.53
19 8 0.14
20 10 0.18
21 3 0.05
22 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (18 bp):
TTTATAATATTTTAATAA
Found at i:51986185 original size:6 final size:6
Alignment explanation
Indices: 51986160--51986193 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
51986150 TTGGTGTAGC
* *
51986160 GACAGG GACTGG GGCAGG GACAGG GACAGG GACA
1 GACAGG GACAGG GACAGG GACAGG GACAGG GACA
51986194 AGGCAACATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.50, T:0.03
Consensus pattern (6 bp):
GACAGG
Found at i:51992365 original size:24 final size:24
Alignment explanation
Indices: 51992335--51992381 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
51992325 AAATTTTTTT
51992335 AAAAATGGTC-TATTTGGCCAATTA
1 AAAAATGG-CATATTTGGCCAATTA
*
51992359 AAAAATGGCATATTTGGCTAATT
1 AAAAATGGCATATTTGGCCAATT
51992382 TATTATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (24 bp):
AAAAATGGCATATTTGGCCAATTA
Found at i:51992923 original size:38 final size:37
Alignment explanation
Indices: 51992843--51992922 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
51992833 TATTTAATGC
*
51992843 AATAAATATTTATTATATTTATTTGTGCTTTTAATAT
1 AATAAATATTTATTATATTTATTAGTGCTTTTAATAT
*
51992880 AATAAAATATTTATTATATTTATAGTAGTGTTTTTTAATAT
1 AAT-AAATATTTATTATATTTAT--TAGTG-CTTTTAATAT
51992921 AA
1 AA
51992923 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 3 0.08
38 19 0.51
40 4 0.11
41 11 0.30
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (37 bp):
AATAAATATTTATTATATTTATTAGTGCTTTTAATAT
Found at i:51993372 original size:16 final size:16
Alignment explanation
Indices: 51993335--51993376 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
51993325 TTAATCATAT
*
51993335 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
51993351 TT-AAATATATTATAA
1 TTAAAATATATTATAA
51993366 TTAAAATATAT
1 TTAAAATATAT
51993377 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:51993383 original size:14 final size:15
Alignment explanation
Indices: 51993344--51993385 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
51993334 TTTAAACATA
*
51993344 ATTATTATTAAATAT
1 ATTATAATTAAATAT
51993359 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
51993373 A-TATAATTTAATA
1 ATTATAATTAAATA
51993386 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:51993472 original size:120 final size:121
Alignment explanation
Indices: 51993333--51993630 Score: 501
Period size: 120 Copynumber: 2.5 Consensus size: 121
51993323 ATTTAATCAT
51993333 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
51993398 ATTAATATTCTTATATGAATTTAATCAAATCATAATATATGATACTATAAAAGATA
66 ATTAATATTCTTATATGAATTTAATCAAATCATAATATATGATACTATAAAAGATA
* * *
51993454 ATTT-AACATAATTATTATTAAACATATTCTAAATAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
51993518 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATATTATAAAAGATA
66 ATTAATATTCTTATATGAATTTAATCAAATCATAATATATGATACTATAAAAGATA
* * * *
51993574 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
51993631 TAAAATAATT
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
120 160 0.96
121 6 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTAATCAAATCATAATATATGATACTATAAAAGATA
Found at i:51993507 original size:59 final size:58
Alignment explanation
Indices: 51993341--51993628 Score: 169
Period size: 59 Copynumber: 4.8 Consensus size: 58
51993331 ATATTTAAAC
* * * **
51993341 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT-A
1 ATAATTATTATTAAATATATTCTAAATAAAATATATGATTTAATAAAA--GATAAT--TTAA
* * * * * *
51993402 AT-ATTCTTATATGAATTTAATC-AAATCATAATATATGATACT-ATAAAAGATAATTTAA
1 ATAATTATTAT-TAAATATATTCTAAAT-AAAATATATGAT-TTAATAAAAGATAATTTAA
* * **
51993460 CATAATTATTATTAAACATATTCTAAATAAAATATATAATTTAATAAAATTCTTAATAATT-A
1 -ATAATTATTATTAAATATATTCTAAATAAAATATATGATTTAATAAAA--GATAAT--TTAA
* * * * *
51993522 AT-ATTCTTATATGAATTTACTC-AAATCATAATATATGATATT-ATAAAAGATAATTTGAA
1 ATAATTATTAT-TAAATATATTCTAAAT-AAAATATATGAT-TTAATAAAAGATAATTT-AA
* * *
51993581 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAA
1 ATAATTATTATTAAATATATTCTAAATAAAATATATGATTTAATAAAA
51993629 TTTAAAATAA
Statistics
Matches: 169, Mismatches: 38, Indels: 42
0.68 0.15 0.17
Matches are distributed among these distances:
57 4 0.02
58 4 0.02
59 60 0.36
60 41 0.24
61 54 0.32
62 4 0.02
63 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (58 bp):
ATAATTATTATTAAATATATTCTAAATAAAATATATGATTTAATAAAAGATAATTTAA
Found at i:51993569 original size:61 final size:61
Alignment explanation
Indices: 51993370--51993557 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
51993360 TTATAATTAA
51993370 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTAATCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTAATCAAATCAT
* * ** * * ** *
51993431 AATATATGATACT-ATAAAA--GATAAT--TTAACATAATTATTAT-TAAACATATTCTAAAT-A
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTAATC-AAATCA
*
51993489 A
61 T
*
51993490 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTAATCAAATCAT
51993551 AATATAT
1 AATATAT
51993558 GATATTATAA
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
57 2 0.02
58 2 0.02
59 29 0.31
60 22 0.23
61 36 0.38
62 2 0.02
63 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTAATCAAATCAT
Found at i:51993740 original size:88 final size:90
Alignment explanation
Indices: 51993646--51993850 Score: 306
Period size: 88 Copynumber: 2.3 Consensus size: 90
51993636 TAATTATAAC
* * * * *
51993646 TAATAAATTTTCATATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAAT-A-
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAG
*
51993709 ATATATAATTTCATAAAATTCTTGA
66 ATATATAATTTCATAAAATTCTTAA
*
51993734 TAATAAATTTTCTTATATAAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAA-
51993799 GATATATAATTTCATAAAATTCTTAA
65 GATATATAATTTCATAAAATTCTTAA
*
51993825 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
51993851 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
88 56 0.54
89 1 0.01
91 28 0.27
92 19 0.18
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAG
ATATATAATTTCATAAAATTCTTAA
Found at i:51993810 original size:44 final size:43
Alignment explanation
Indices: 51993671--51993810 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 43
51993661 TATGAATTTG
* *
51993671 TATAATTTAAAATAATTATTATTACATATAATTTAATAATATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
* ** * * * *
51993714 TA-ATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATAAATTTA
1 TATAATT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
51993759 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
51993803 TATAATTT
1 TATAATTT
51993811 CATAAAATTC
Statistics
Matches: 71, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
42 4 0.06
43 9 0.13
44 43 0.61
45 11 0.15
46 4 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:51995589 original size:31 final size:31
Alignment explanation
Indices: 51995554--51995612 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
51995544 GAAAAAGAAA
*
51995554 AGAAACAGA-AGACGCAAATCGGCAGAAACTG
1 AGAAACAGAGAGA-GCAAATCAGCAGAAACTG
*
51995585 AGAAACAGAGGGAGCAAATCAGCAGAAA
1 AGAAACAGAGAGAGCAAATCAGCAGAAA
51995613 ATAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.51, C:0.17, G:0.27, T:0.05
Consensus pattern (31 bp):
AGAAACAGAGAGAGCAAATCAGCAGAAACTG
Found at i:51996962 original size:31 final size:31
Alignment explanation
Indices: 51996925--51996983 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
51996915 AATGATCACT
51996925 AACTATTCAAAAGTTTTCATTTAAGTCATTA
1 AACTATTCAAAAGTTTTCATTTAAGTCATTA
** *
51996956 AACTATTTGAAAGTTTTTATTTAAGTCA
1 AACTATTCAAAAGTTTTCATTTAAGTCA
51996984 CTAGGCTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAGTCATTA
Found at i:52008241 original size:28 final size:29
Alignment explanation
Indices: 52008182--52008243 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
52008172 ATAAGTTATT
*
52008182 TTTTTTTAAAATTTACCGAAATGGGCTGA
1 TTTTTTTAAAATTTACCGAAATGGGCTCA
** * *
52008211 TTTTTTTATTATTTACCGGAAT-GGTTCA
1 TTTTTTTAAAATTTACCGAAATGGGCTCA
52008239 TTTTT
1 TTTTT
52008244 CGTGAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.52
Consensus pattern (29 bp):
TTTTTTTAAAATTTACCGAAATGGGCTCA
Found at i:52008704 original size:124 final size:125
Alignment explanation
Indices: 52008484--52008834 Score: 605
Period size: 124 Copynumber: 2.8 Consensus size: 125
52008474 TTATTTCGAG
* *
52008484 TTGACGTTTCTGATCAAATAGTGTAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
52008549 AAATTGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAT-AATTTTTT
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
52008608 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
52008673 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAAATTTTTT
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
* *
52008733 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
52008798 AAATCGCATCATCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAG
52008835 CAAGTTTGGG
Statistics
Matches: 213, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
124 110 0.52
125 103 0.48
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
Found at i:52010105 original size:30 final size:29
Alignment explanation
Indices: 52010038--52010150 Score: 217
Period size: 29 Copynumber: 3.9 Consensus size: 29
52010028 TAAGGAAAAT
52010038 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
52010067 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
52010096 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
52010126 GGTTAGGGTTTTTAATTAAATTAGG
1 GGTTAGGGTTTTTAATTAAATTAGG
52010151 ATTTTTATTA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
29 54 0.65
30 29 0.35
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:52010236 original size:36 final size:36
Alignment explanation
Indices: 52010196--52010310 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
52010186 ATATCAAATA
*
52010196 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
52010232 ATATC-AAATAAACTTCTATTTTATTAC-AT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
52010267 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
52010303 ACATCAAA
1 ATATCAAA
52010311 TAAACTTCTA
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 7 0.13
35 17 0.31
36 24 0.44
37 7 0.13
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:52010262 original size:25 final size:25
Alignment explanation
Indices: 52010228--52010338 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
52010218 TTTCTATGCC
*
52010228 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
52010253 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
52010274 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
52010299 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
52010324 TATTACATCAAATAA
1 TATTACATCAAATAA
52010339 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:52010263 original size:71 final size:71
Alignment explanation
Indices: 52010156--52010340 Score: 334
Period size: 71 Copynumber: 2.6 Consensus size: 71
52010146 TTAGGATTTT
*
52010156 TATTACATCAAATAAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAAT-AAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTT
52010221 CTATGCC
65 CTATGCC
*
52010228 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
52010293 TATGCG
66 TATGCC
52010299 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
52010341 AATTTAAATA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
71 97 0.89
72 12 0.11
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:52010769 original size:18 final size:18
Alignment explanation
Indices: 52010742--52010776 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52010732 CGGAAAATGA
* *
52010742 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
52010760 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
52010777 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:52012144 original size:14 final size:14
Alignment explanation
Indices: 52012125--52012164 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52012115 TATAAGTGCA
*
52012125 TATATAATATAAAG
1 TATATAAAATAAAG
*
52012139 TATATAAAAAAAAG
1 TATATAAAATAAAG
*
52012153 TAAATAAAATAA
1 TATATAAAATAA
52012165 GGATATAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (14 bp):
TATATAAAATAAAG
Found at i:52014895 original size:30 final size:30
Alignment explanation
Indices: 52014861--52014925 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
52014851 GCCATTGATG
**
52014861 AAAATATAAAAAATTTA-AAATTATTTTTAA
1 AAAATATAAAAAAAATATAAATTA-TTTTAA
52014891 AAAATATAAAAAAAATATAAATTATTTTAA
1 AAAATATAAAAAAAATATAAATTATTTTAA
52014921 AAAAT
1 AAAAT
52014926 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAATATAAAAAAAATATAAATTATTTTAA
Found at i:52014981 original size:50 final size:51
Alignment explanation
Indices: 52014926--52015039 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 51
52014916 TTTAAAAAAT
* *
52014926 GAAATTGAGGGGAAATTTAAATTAAA-ATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
52014976 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
52015027 GAAATTGAGAGGA
1 GAAATTGAGAGGA
52015040 TTAGAGAGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
50 24 0.40
51 36 0.60
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:52016319 original size:30 final size:30
Alignment explanation
Indices: 52016278--52016340 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
52016268 TCAGTAATTT
*
52016278 AATTGATTGTTTATATT-AGATT-AAAGACTC
1 AATTAATTGTTTATATTCA-ATTAAAAG-CTC
52016308 AATTAATTGTTTATATTCAATTAAAAGCTC
1 AATTAATTGTTTATATTCAATTAAAAGCTC
52016338 AAT
1 AAT
52016341 CAATGATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (30 bp):
AATTAATTGTTTATATTCAATTAAAAGCTC
Found at i:52017166 original size:11 final size:13
Alignment explanation
Indices: 52017142--52017173 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52017132 TAGTTTATTA
52017142 ATATTTTAATATG
1 ATATTTTAATATG
52017155 AT-TTTTAA-ATG
1 ATATTTTAATATG
52017166 ATATTTTA
1 ATATTTTA
52017174 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:52025022 original size:36 final size:38
Alignment explanation
Indices: 52024975--52025049 Score: 127
Period size: 36 Copynumber: 2.0 Consensus size: 38
52024965 ATGTTTCATT
52024975 TTGGCCACCATCATTTTTGGAAAGGCG-T-ATGGTTAG
1 TTGGCCACCATCATTTTTGGAAAGGCGTTGATGGTTAG
*
52025011 TTGGCCACCATCATTTTTGGAAAGGTGTTGATGGTTAG
1 TTGGCCACCATCATTTTTGGAAAGGCGTTGATGGTTAG
52025049 T
1 T
52025050 GCGAATCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 26 0.72
37 1 0.03
38 9 0.25
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (38 bp):
TTGGCCACCATCATTTTTGGAAAGGCGTTGATGGTTAG
Found at i:52027076 original size:50 final size:50
Alignment explanation
Indices: 52027021--52027148 Score: 166
Period size: 50 Copynumber: 2.6 Consensus size: 50
52027011 CATTTAGGTT
* * *
52027021 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATGGGCACCAAG
** * *
52027071 ATGAGAGGTCCCCCGTAAGACCATATCTAGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATGGGCACCAAG
* **
52027121 ATGAAAACTCCCATGTAAGACCATATCT
1 ATGAGAGGTCCCATGTAAGACCATATCT
52027149 GAGATATGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATGGGCACCAAG
Found at i:52040924 original size:33 final size:33
Alignment explanation
Indices: 52040863--52040930 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
52040853 TAATCAATTT
* *
52040863 AATATTAAATTTAATCTAATATTTATCTTGATA
1 AATATTAAATTTAATCTAATATTAATCTTAATA
* *
52040896 AATATTATA-TTAATTTAATATTAAATCTTAATA
1 AATATTAAATTTAATCTAATATT-AATCTTAATA
52040929 AA
1 AA
52040931 ATAATAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (33 bp):
AATATTAAATTTAATCTAATATTAATCTTAATA
Found at i:52041065 original size:19 final size:19
Alignment explanation
Indices: 52041015--52041067 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
52041005 AATAAAATAC
*
52041015 TATTAAGATAGATATTAAAT
1 TATTAAAATA-ATATTAAAT
**
52041035 T-TT-ATTTAATATTAAAT
1 TATTAAAATAATATTAAAT
52041052 TATTAAAATAATATTA
1 TATTAAAATAATATTA
52041068 TTTTTGGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 10 0.37
18 5 0.19
19 11 0.41
20 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATTAAAATAATATTAAAT
Found at i:52049308 original size:14 final size:14
Alignment explanation
Indices: 52049289--52049316 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52049279 GAGCATTAAT
52049289 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
52049303 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
52049317 ATTTTCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TTAAAGAGATTTTA
Found at i:52052349 original size:15 final size:15
Alignment explanation
Indices: 52052329--52052364 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
52052319 GAGTTAAACT
52052329 CACCACCGCC-ACCGC
1 CACCACC-CCAACCGC
52052344 CACCACCCCAACCGC
1 CACCACCCCAACCGC
52052359 CACCAC
1 CACCAC
52052365 TGCCGCCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.25, C:0.67, G:0.08, T:0.00
Consensus pattern (15 bp):
CACCACCCCAACCGC
Found at i:52052582 original size:3 final size:3
Alignment explanation
Indices: 52052574--52052608 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
52052564 GAAATCACTC
*
52052574 TCT TCT TCT TCT TCT TCT TCT TCT TCA TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
52052609 CTCACACCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:52060320 original size:19 final size:20
Alignment explanation
Indices: 52060283--52060337 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
52060273 TTTAATGCAA
**
52060283 GTTATAAAAAGTTATTAAAT
1 GTTATAAAAAAATATTAAAT
*
52060303 TTTATAAAAAAATA-TAAAT
1 GTTATAAAAAAATATTAAAT
*
52060322 GTTAGAAAAAAA-ATTA
1 GTTATAAAAAAATATTA
52060338 TAAAAAACGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.03
19 17 0.59
20 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (20 bp):
GTTATAAAAAAATATTAAAT
Found at i:52060605 original size:11 final size:11
Alignment explanation
Indices: 52060589--52060652 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
52060579 GGTATGATAC
52060589 TTTTTATAATT
1 TTTTTATAATT
**
52060600 TTTTTACGA--
1 TTTTTATAATT
52060609 TTTTTATAATT
1 TTTTTATAATT
*
52060620 TTTTTCTAA--
1 TTTTTATAATT
*
52060629 TTTTTA-AATA
1 TTTTTATAATT
52060639 TTTTTAT-ATT
1 TTTTTATAATT
52060649 TTTT
1 TTTT
52060653 ACTAAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
8 2 0.05
9 12 0.29
10 12 0.29
11 15 0.37
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:52060622 original size:10 final size:10
Alignment explanation
Indices: 52060589--52060672 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
52060579 GGTATGATAC
52060589 TTTTTATAAT
1 TTTTTATAAT
52060599 TTTTT-TACGA-
1 TTTTTATA--AT
52060609 TTTTTATAATT
1 TTTTTATAA-T
*
52060620 TTTTTCTAA-
1 TTTTTATAAT
52060629 TTTTTA-AAT
1 TTTTTATAAT
52060638 ATTTTTAT-AT
1 -TTTTTATAAT
*
52060648 TTTTTACTAAA
1 TTTTTA-TAAT
* *
52060659 ATTTAATAAT
1 TTTTTATAAT
52060669 TTTT
1 TTTT
52060673 AGATTGTAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
8 2 0.04
9 14 0.25
10 25 0.44
11 16 0.28
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:52060632 original size:29 final size:29
Alignment explanation
Indices: 52060589--52060657 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
52060579 GGTATGATAC
* *
52060589 TTTTTA-TAATTTTTTTACGATTTTTATAAT
1 TTTTTACTAA-TTTTTAAAGATTTTTAT-AT
* *
52060619 TTTTTTCTAATTTTTAAATATTTTTATAT
1 TTTTTACTAATTTTTAAAGATTTTTATAT
52060648 TTTTTACTAA
1 TTTTTACTAA
52060658 AATTTAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 11 0.33
30 19 0.58
31 3 0.09
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (29 bp):
TTTTTACTAATTTTTAAAGATTTTTATAT
Found at i:52060642 original size:19 final size:20
Alignment explanation
Indices: 52060589--52060673 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
52060579 GGTATGATAC
* **
52060589 TTTTTATAATTTTTTTACGA
1 TTTTTATAATATTTTTATAA
* *
52060609 TTTTTATAATTTTTTTCTAA
1 TTTTTATAATATTTTTATAA
*
52060629 TTTTTA-AATATTTTTATAT
1 TTTTTATAATATTTTTATAA
* *
52060648 TTTTTACTAA-AATTTAATAA
1 TTTTTA-TAATATTTTTATAA
52060668 TTTTTA
1 TTTTTA
52060674 GATTGTAACA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.30
20 36 0.67
21 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTTTATAATATTTTTATAA
Found at i:52060663 original size:29 final size:30
Alignment explanation
Indices: 52060608--52060673 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
52060598 TTTTTTTACG
* **
52060608 ATTTTTATAATTTTTTTCTAATTTTTAA-A
1 ATTTTTATAATTTTTTACTAAAATTTAATA
52060637 TATTTTTAT-ATTTTTTACTAAAATTTAATA
1 -ATTTTTATAATTTTTTACTAAAATTTAATA
52060667 ATTTTTA
1 ATTTTTA
52060674 GATTGTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTTTATAATTTTTTACTAAAATTTAATA
Found at i:52062698 original size:92 final size:93
Alignment explanation
Indices: 52062556--52062724 Score: 252
Period size: 92 Copynumber: 1.8 Consensus size: 93
52062546 TTTTGTTGCG
* * * * **
52062556 TAGTATGCTTTTCACCTAAAATCGTGATTGTGTTATAAATTGAAATACTAAATGTATTTACAAGT
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
52062621 AATTACACTCAATTTTTTTTTTCTTTCA
66 AATTACACTCAATTTTTTTTTTCTTTCA
*
52062649 TAGTATG-TTTTCACCCAAAATCATGATTGT-TCTATAAATTGAAATACTAAGTGCAATTACAAA
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGT-TATAAATTGAAATACTAAATGCAATTACAAA
52062712 CAATTACACTCAA
65 CAATTACACTCAA
52062725 ATTTAATTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
91 1 0.01
92 60 0.88
93 7 0.10
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (93 bp):
TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
AATTACACTCAATTTTTTTTTTCTTTCA
Found at i:52068035 original size:67 final size:67
Alignment explanation
Indices: 52067927--52068059 Score: 266
Period size: 67 Copynumber: 2.0 Consensus size: 67
52067917 ATGAAAATAG
52067927 TGGTTCTTGGTGTATATGTTCGGGTTTCCTTGATTTTCCTATAAGCAACCCTATCTGGAGCAGTC
1 TGGTTCTTGGTGTATATGTTCGGGTTTCCTTGATTTTCCTATAAGCAACCCTATCTGGAGCAGTC
52067992 AT
66 AT
52067994 TGGTTCTTGGTGTATATGTTCGGGTTTCCTTGATTTTCCTATAAGCAACCCTATCTGGAGCAGTC
1 TGGTTCTTGGTGTATATGTTCGGGTTTCCTTGATTTTCCTATAAGCAACCCTATCTGGAGCAGTC
52068059 A
66 A
52068060 AGTAGCAAGC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (67 bp):
TGGTTCTTGGTGTATATGTTCGGGTTTCCTTGATTTTCCTATAAGCAACCCTATCTGGAGCAGTC
AT
Found at i:52071186 original size:26 final size:27
Alignment explanation
Indices: 52071133--52071187 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
52071123 AAATAAAATA
* * *
52071133 AAAAACTTAAAAATATGTTTGGTAATT
1 AAAAACTTAAAAATATATATGCTAATT
*
52071160 AAAAACTTAAAAATA-ATATGCTTATT
1 AAAAACTTAAAAATATATATGCTAATT
52071186 AA
1 AA
52071188 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (27 bp):
AAAAACTTAAAAATATATATGCTAATT
Found at i:52071210 original size:15 final size:13
Alignment explanation
Indices: 52071182--52071207 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52071172 ATAATATGCT
52071182 TATTAATTAAAAA
1 TATTAATTAAAAA
52071195 TATTAATTAAAAA
1 TATTAATTAAAAA
52071208 AATTTTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:52071211 original size:22 final size:22
Alignment explanation
Indices: 52071186--52071230 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
52071176 TATGCTTATT
*
52071186 AATTAAAAATATTAATTAAAAA
1 AATTAAAAACATTAATTAAAAA
** *
52071208 AATTTTAAACATTCATTAAAAA
1 AATTAAAAACATTAATTAAAAA
52071230 A
1 A
52071231 TAGTTAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTAAAAACATTAATTAAAAA
Found at i:52100208 original size:28 final size:30
Alignment explanation
Indices: 52100154--52100209 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
52100144 TTAAATTACT
*
52100154 TATTATTTAAGTAAATAGATCTTTATTATC
1 TATTATTTAAGTAAATAGATATTTATTATC
52100184 TATT-TTTAAGTAAA-AGATATTTATTA
1 TATTATTTAAGTAAATAGATATTTATTA
52100210 ATTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 10 0.40
30 4 0.16
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (30 bp):
TATTATTTAAGTAAATAGATATTTATTATC
Found at i:52101397 original size:45 final size:44
Alignment explanation
Indices: 52101311--52101398 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 44
52101301 AATAAAATGA
* * * * * * *
52101311 ATAAAATTATGGAAATGTAAAAAGATATATATATGTGTGTATAC
1 ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATAC
52101355 ATAAAATCATAGAAATGTAAAAAAGAAAAATACATATATGTATA
1 ATAAAATCATAGAAATGT-AAAAAGAAAAATACATATATGTATA
52101399 TCTTTTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 16 0.44
45 20 0.56
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (44 bp):
ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATAC
Found at i:52102559 original size:4 final size:4
Alignment explanation
Indices: 52102550--52102577 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
52102540 AATAGACATG
52102550 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
52102578 ATGAGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:52103000 original size:25 final size:25
Alignment explanation
Indices: 52102971--52103021 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
52102961 ATGAAAGGGA
52102971 AATAA-AACTAATAA-AAATTGATAAT
1 AATAATAA-TAATAATAAA-TGATAAT
52102996 AATAATAATAATAATAAATGATAAT
1 AATAATAATAATAATAAATGATAAT
52103021 A
1 A
52103022 CATTTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
AATAATAATAATAATAAATGATAAT
Found at i:52104822 original size:17 final size:17
Alignment explanation
Indices: 52104800--52104863 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
52104790 AATCTTAGAG
52104800 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
52104817 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGC
52104836 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
52104853 TTTTAATTGTA
1 TTCTAATTGTA
52104864 GCCTTTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 4 0.11
17 19 0.50
18 2 0.05
19 9 0.24
20 4 0.11
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:52104833 original size:36 final size:36
Alignment explanation
Indices: 52104792--52104860 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
52104782 GATTATTTAA
52104792 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
52104828 TCTTAGAGTTCTAATTGTATACAGCTTTTAATT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATT
52104861 GTAGCCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:52104841 original size:19 final size:18
Alignment explanation
Indices: 52104792--52104843 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
52104782 GATTATTTAA
52104792 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
52104809 T-ATACAGCTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
52104828 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
52104844 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:52109940 original size:17 final size:17
Alignment explanation
Indices: 52109918--52109981 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
52109908 AATCTTAGAG
52109918 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* * *
52109935 TTCTAATTATGTCTTA-GGA
1 TTCTAA-T-TGT-ATACAGC
52109954 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
52109971 TTTTAATTGTA
1 TTCTAATTGTA
52109982 GCCTTTGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
16 2 0.06
17 20 0.56
18 2 0.06
19 10 0.28
20 2 0.06
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:52109951 original size:36 final size:36
Alignment explanation
Indices: 52109910--52109978 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
52109900 GATTATTTAA
52109910 TCTTA-GAGTTCTAATTGTATACAGCTTCTAATTATG
1 TCTTAGGA-TTCTAATTGTATACAGCTTCTAATTATG
*
52109946 TCTTAGGATTCTAATTGTATACAGCTTTTAATT
1 TCTTAGGATTCTAATTGTATACAGCTTCTAATT
52109979 GTAGCCTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTTAGGATTCTAATTGTATACAGCTTCTAATTATG
Found at i:52112026 original size:131 final size:131
Alignment explanation
Indices: 52111870--52112190 Score: 441
Period size: 131 Copynumber: 2.5 Consensus size: 131
52111860 CATGGTTTTA
* * * * * *
52111870 ATCTGCTCCGCTACTGCTTAGGGAGATAAGATTTACAATCTTTAACCTACTCCACTGCTACTCAG
1 ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTACTCAA
* * * *
52111935 GGAGATAGGACTAGTGACTTAAATCTGCTTCCTACTAT-TTGAGGAAGATAAGATTCGCCGTATT
66 GAAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCG-GGAAGATAAAATTCGCCGTATT
52111999 CG
130 CG
52112001 ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTACTCAA
1 ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTACTCAA
* * * *
52112066 TAAGATAGGACTAGTGGCTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCTCCGTATTT
66 GAAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
52112131 G
131 G
* * *
52112132 ATCTGCTTCACTAT-TGCTTTA-AGAGATAAGATCTGCAATCTTCAACCTATTCCACTGCT
1 ATCTGCTCCACT-TCTGC-TTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCT
52112191 GCTTAAGGAG
Statistics
Matches: 170, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
131 164 0.96
132 6 0.04
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (131 bp):
ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTACTCAA
GAAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
G
Found at i:52118907 original size:30 final size:28
Alignment explanation
Indices: 52118868--52118933 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
52118858 ATGGATTTAA
52118868 ATTAATTATTATTTAAGTAAATAAATATTT
1 ATTAATTATT-TTTAAGTAAA-AAATATTT
* *
52118898 ATTATTTATTTTTAAGTAAAATATATTT
1 ATTAATTATTTTTAAGTAAAAAATATTT
52118926 ATTAATTA
1 ATTAATTA
52118934 AATAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 14 0.42
29 10 0.30
30 9 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTAATTATTTTTAAGTAAAAAATATTT
Found at i:52119775 original size:34 final size:35
Alignment explanation
Indices: 52119717--52119783 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
52119707 CAAACACCAG
52119717 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
52119752 AAAATATTTTCCAG-AAATCATTTTATAGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
52119784 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:52123447 original size:44 final size:45
Alignment explanation
Indices: 52123364--52123454 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 45
52123354 ATAACATTAT
* *
52123364 TAATTTATATGTTTTTTTGTAAATTTTAATTTTATAATTTTT-TA
1 TAATTTATATGTTTTTTTCTAAATTATAATTTTATAATTTTTCTA
*
52123408 TAATTTATATG-TTTTTTCTATATTAT-ATATTTATGAATTTTTCTA
1 TAATTTATATGTTTTTTTCTAAATTATAAT-TTTAT-AATTTTTCTA
52123453 TA
1 TA
52123455 CTTATTTCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.05
43 17 0.41
44 18 0.44
45 4 0.10
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (45 bp):
TAATTTATATGTTTTTTTCTAAATTATAATTTTATAATTTTTCTA
Found at i:52124166 original size:17 final size:16
Alignment explanation
Indices: 52124152--52124184 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
52124142 TATCTTTTCG
52124152 AATTTTTATAGTTTTA
1 AATTTTTATAGTTTTA
52124168 AATTTTATATAGTTTTA
1 AATTTT-TATAGTTTTA
52124185 TACAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
AATTTTTATAGTTTTA
Found at i:52125837 original size:31 final size:32
Alignment explanation
Indices: 52125799--52125861 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
52125789 AGACAAATTA
52125799 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
52125830 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
52125862 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:52131953 original size:31 final size:32
Alignment explanation
Indices: 52131918--52131980 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
52131908 AGGTAAATTA
52131918 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
52131949 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
52131981 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:52138277 original size:58 final size:59
Alignment explanation
Indices: 52138167--52138282 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 59
52138157 GTTAAGTTCA
* * **
52138167 GGTACCAAATTGGACCAAAAAAATATTAAGTATCAACTTAAGAAAATGTGTCAAGTTTG
1 GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTG
*
52138226 GGTACCAAATTAGACC-AAAAAGGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT
1 GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT
52138283 AGATGCCAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
58 37 0.71
59 15 0.29
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (59 bp):
GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTG
Found at i:52138304 original size:58 final size:56
Alignment explanation
Indices: 52138183--52138304 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 56
52138173 AAATTGGACC
* ** * *
52138183 AAAAAAATATTAAGTATCAACTTAAGAAAATGTGTCAAGTTTGGGTACCAAATTAG
1 AAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTAGATACCAAATTAG
* * *
52138239 ACCAAAAAGGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTAGATGCCAAGTTAGG
1 A--AAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTAGATACCAAATTA-G
52138298 AAAAAAA
1 AAAAAAA
52138305 ATTTAAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
56 1 0.02
57 5 0.09
58 46 0.85
59 2 0.04
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (56 bp):
AAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTAGATACCAAATTAG
Found at i:52143786 original size:19 final size:19
Alignment explanation
Indices: 52143762--52143798 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
52143752 AAAAATGAAA
52143762 ATTTAGAATTTTTATAAAT
1 ATTTAGAATTTTTATAAAT
*
52143781 ATTTAGAATTTTTTTAAA
1 ATTTAGAATTTTTATAAA
52143799 ATTATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTTAGAATTTTTATAAAT
Found at i:52144152 original size:22 final size:22
Alignment explanation
Indices: 52144127--52144203 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
52144117 AAACTTAATC
52144127 TAATTTTACTATCGTAAAAATA
1 TAATTTTACTATCGTAAAAATA
* * *
52144149 TAATTTTACTAT-TTTAATATA
1 TAATTTTACTATCGTAAAAATA
* *
52144170 TACTTTTGCTATCGTAAAAATA
1 TAATTTTACTATCGTAAAAATA
52144192 TAATTTTACTAT
1 TAATTTTACTAT
52144204 TTTAATATAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 16 0.36
22 28 0.64
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (22 bp):
TAATTTTACTATCGTAAAAATA
Found at i:52144176 original size:21 final size:21
Alignment explanation
Indices: 52144127--52144214 Score: 86
Period size: 22 Copynumber: 4.1 Consensus size: 21
52144117 AAACTTAATC
* * *
52144127 TAATTTTACTATCGTAAAAATA
1 TAATTTTACTAT-TTTAATATA
52144149 TAATTTTACTATTTTAATATA
1 TAATTTTACTATTTTAATATA
* * * * *
52144170 TACTTTTGCTATCGTAAAAATA
1 TAATTTTACTAT-TTTAATATA
52144192 TAATTTTACTATTTTAATATA
1 TAATTTTACTATTTTAATATA
52144213 TA
1 TA
52144215 TTATATACTT
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
21 24 0.46
22 28 0.54
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (21 bp):
TAATTTTACTATTTTAATATA
Found at i:52144182 original size:43 final size:43
Alignment explanation
Indices: 52144130--52144214 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
52144120 CTTAATCTAA
52144130 TTTTACTATCGTAAAAATATAATTTTACTATTTTAATATATAC
1 TTTTACTATCGTAAAAATATAATTTTACTATTTTAATATATAC
*
52144173 TTTTGCTATCGTAAAAATATAATTTTACTATTTTAATATATA
1 TTTTACTATCGTAAAAATATAATTTTACTATTTTAATATATA
52144215 TTATATACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (43 bp):
TTTTACTATCGTAAAAATATAATTTTACTATTTTAATATATAC
Found at i:52145483 original size:18 final size:18
Alignment explanation
Indices: 52145456--52145514 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
52145446 ATCTATATTA
*
52145456 TAATAGTTATATATGTAT
1 TAATAATTATATATGTAT
52145474 TAATAATTATATAT-TA-
1 TAATAATTATATATGTAT
*
52145490 TAAT-ATTATTTTATGTAT
1 TAATAATTA-TATATGTAT
52145508 TAATAAT
1 TAATAAT
52145515 ATACTAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 4 0.11
16 8 0.23
17 4 0.11
18 17 0.49
19 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TAATAATTATATATGTAT
Found at i:52145492 original size:34 final size:34
Alignment explanation
Indices: 52145449--52145514 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
52145439 TATTATAATC
52145449 TATATTATAATAGTTA-TATATGTATTAATAATTA
1 TATATTATAATA-TTATTATATGTATTAATAATTA
*
52145483 TATATTATAATATTATTTTATGTATTAATAAT
1 TATATTATAATATTATTATATGTATTAATAAT
52145515 ATACTAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 3 0.10
34 27 0.90
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (34 bp):
TATATTATAATATTATTATATGTATTAATAATTA
Found at i:52145673 original size:8 final size:8
Alignment explanation
Indices: 52145628--52145677 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
52145618 ATATATTTTA
52145628 ATAATTA-
1 ATAATTAT
52145635 ATAATTAT
1 ATAATTAT
*
52145643 ATATTTATT
1 ATAATTA-T
52145652 ATACA-TATT
1 ATA-ATTA-T
52145661 ATAATTAT
1 ATAATTAT
52145669 ATAATTAT
1 ATAATTAT
52145677 A
1 A
52145678 GTATCAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
7 7 0.19
8 17 0.46
9 13 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (8 bp):
ATAATTAT
Found at i:52146768 original size:18 final size:18
Alignment explanation
Indices: 52146742--52146778 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52146732 CGCGTTTTTT
*
52146742 TAGTTTTGCTTATGCAAG
1 TAGTCTTGCTTATGCAAG
*
52146760 TAGTCTTGCTTTTGCAAG
1 TAGTCTTGCTTATGCAAG
52146778 T
1 T
52146779 GATTTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.46
Consensus pattern (18 bp):
TAGTCTTGCTTATGCAAG
Found at i:52148756 original size:16 final size:16
Alignment explanation
Indices: 52148721--52148758 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
52148711 TTACCATGTG
52148721 TTTTATTTTTTAAATA
1 TTTTATTTTTTAAATA
* *
52148737 -TTTATTTTTTTAGTA
1 TTTTATTTTTTAAATA
52148752 TTTTATT
1 TTTTATT
52148759 ATACATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTTAAATA
Found at i:52149487 original size:9 final size:9
Alignment explanation
Indices: 52149475--52149499 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52149465 AATCAAATTG
52149475 ATAAAATAT
1 ATAAAATAT
52149484 ATAAAATAT
1 ATAAAATAT
52149493 ATAAAAT
1 ATAAAAT
52149500 TTAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAAAATAT
Found at i:52152556 original size:17 final size:19
Alignment explanation
Indices: 52152528--52152564 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
52152518 TTTCAATTAA
52152528 ATAAATTATTAAAAA-ATT
1 ATAAATTATTAAAAATATT
52152546 ATAAA-TATTAAAAATATT
1 ATAAATTATTAAAAATATT
52152564 A
1 A
52152565 AAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAATTATTAAAAATATT
Found at i:52152560 original size:9 final size:9
Alignment explanation
Indices: 52152534--52152568 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
52152524 TTAAATAAAT
52152534 TATTAAAAA
1 TATTAAAAA
*
52152543 -ATTATAAA
1 TATTAAAAA
52152551 TATTAAAAA
1 TATTAAAAA
52152560 TATTAAAAA
1 TATTAAAAA
52152569 ATATAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TATTAAAAA
Found at i:52160865 original size:24 final size:23
Alignment explanation
Indices: 52160821--52160865 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
52160811 GTTTTATGGC
*
52160821 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
52160844 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
52160866 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Found at i:52161026 original size:125 final size:123
Alignment explanation
Indices: 52160882--52161161 Score: 341
Period size: 125 Copynumber: 2.3 Consensus size: 123
52160872 TTTTTTCGAG
* ** ** * * * *
52160882 TTGACGTTTCTG-GTTAAATAGTGGGAAATCGCTTCTACTAGGATGCTATTTAAGAATAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTGTAAAATCGCTGATACCAAGATGCTATATAAGAAGAAATTGT
* *
52160946 GAAATAGTGGCCTCGTGGACGCGATTTCGCTACAG-TGGTCATGT-GAGAAATAAAATTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAG-GAAAT--AATTTTT
* * *
52161006 TTGACGTTTTCTGAGGAAATAGTATAAAATCGCTGATACCAAGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGTAAAATCGCTGATACCAAGATGCTATATAAGAAGAAATTGT
* *
52161071 GAAATCGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTT
*
52161130 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGC
52161162 GCCCTCGTGG
Statistics
Matches: 134, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
123 23 0.17
124 19 0.14
125 76 0.57
126 15 0.11
127 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCAAGATGCTATATAAGAAGAAATTGTG
AAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTT
Found at i:52161211 original size:83 final size:84
Alignment explanation
Indices: 52161072--52161274 Score: 381
Period size: 85 Copynumber: 2.4 Consensus size: 84
52161062 AGAAATTGTG
*
52161072 AAATCGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAA-TTTTTTTGACG
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
52161136 TTTCTGAGCAAATAGTGTC
66 TTTCTGAGCAAATAGTGTC
52161155 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGAC
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAA-TTTTTTTTGAC
52161220 GTTTCTGAGCAAATAGTGTC
65 GTTTCTGAGCAAATAGTGTC
52161240 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
52161275 AGCAAGTTTG
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
83 52 0.44
85 65 0.56
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (84 bp):
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
TTTCTGAGCAAATAGTGTC
Found at i:52164445 original size:23 final size:23
Alignment explanation
Indices: 52164415--52165491 Score: 687
Period size: 23 Copynumber: 44.2 Consensus size: 23
52164405 TACAATTTAA
52164415 TTAGGGTTTTTAATTAAA-TAGGG
1 TTAGGGTTTTTAATTAAATTA-GG
52164438 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
* *
52164461 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
52164484 TTAGGGTTTTTAGTTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52164507 TTAGGGTTTTTAATTTAATTAGGTTAGG
1 TTAGGGTTTTTAA-TTAA--A--TTAGG
52164535 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52164558 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
**** * *
52164581 TTA-GG-TTAGGGTTAAGGTT--T
1 TTAGGGTTTTTAATTAA-ATTAGG
* * *
52164601 TTA----ATTTAAGTAAATTAAG
1 TTAGGGTTTTTAATTAAATTAGG
* *
52164620 TTAGGGTTTTTAATT-TAGTAGGG
1 TTAGGGTTTTTAATTAAATTA-GG
52164643 TTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGG---TT--TTTAATTAAATTAGG
* *
52164671 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52164694 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
52164717 TTAGGATTTTTAATTAAATTAAATTAGG
1 TTAGG--GTTT--TT-AATTAAATTAGG
* *
52164745 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52164768 TTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATT-AA--A--TTAGG
* *
52164796 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52164819 TTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATT-AA--A--TTAGG
52164847 TTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTT-----AATTAAATTAGG
* *
52164875 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52164898 TTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGG---TT--TTTAATTAAATTAGG
* *
52164926 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52164949 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
52164972 TTAGTGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATT-AA--A--TTAGG
52165000 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
52165023 TTAGGGTTTTTGATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
***
52165046 TTA-GG---TT-A--GGGTTAGGG
1 TTAGGGTTTTTAATTAAATTA-GG
*****
52165063 TT-TTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
* *
52165085 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52165108 TTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATT-AA--A--TTAGG
52165136 TTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTT-----AATTAAATTAGG
* *
52165164 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52165187 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
***
52165210 TTA-GG---TT-A--GGGTTAGGG
1 TTAGGGTTTTTAATTAAATTA-GG
*****
52165227 TT-TTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
* *
52165249 TTAGGGTTTTTAATT-TAGTAGGG
1 TTAGGGTTTTTAATTAAATTA-GG
*
52165272 TTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGG---TT--TTTAATTAAATTAGG
* *
52165300 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52165323 TTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATT-AA--A--TTAGG
52165351 TTAGGGTTTTTAATTTAAGTAGGTTAGG
1 TTAGGGTTTTTAA-TTAA--A--TTAGG
* *
52165379 TTAGGGTTTTTAATTTAATTAAAATAATG
1 TTAGGG---TT--TTTAATT-AAATTAGG
*
52165408 TTAAGGTTTTTAATTTAATTAGGTTAGG
1 TTAGGGTTTTTAA-TTAA--A--TTAGG
52165436 TTAGGGTTTTTAATTTAAGTAGGTTAGG
1 TTAGGGTTTTTAA-TTAA--A--TTAGG
52165464 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52165487 TTAGG
1 TTAGG
52165492 TTAGGGTTTT
Statistics
Matches: 848, Mismatches: 104, Indels: 204
0.73 0.09 0.18
Matches are distributed among these distances:
16 6 0.01
17 10 0.01
18 6 0.01
19 7 0.01
20 7 0.01
21 8 0.01
22 22 0.03
23 414 0.49
24 21 0.02
25 15 0.02
26 18 0.02
27 13 0.02
28 260 0.31
29 15 0.02
30 2 0.00
31 3 0.00
32 6 0.01
33 15 0.02
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:52164477 original size:28 final size:28
Alignment explanation
Indices: 52164446--52165577 Score: 918
Period size: 28 Copynumber: 42.5 Consensus size: 28
52164436 GGTTAGGGTT
52164446 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164474 --T--TT-AAGTAGGTTAGGGTTTTT-A
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164496 ---G-TTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
**
52164520 TTTAATTAGGTTAGGTTAGGG---TT--
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
52164543 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* * *
52164571 TTAAATTAGGTTAGGTTAGGGTTAAGGTTTTTAA
1 TTTAATTA----A-ATTA-GGTTAGGGTTTTTAA
* *
52164605 TTTAAGTAAATTAAGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
52164633 TTT-AGT--A--GGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
52164656 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164684 --T--TT-AAGTAGGTTAGGGTTTTT-A
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164706 ---A-TTAAATTAGGTTAGGATTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164730 TTAAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164758 --T--TT-AAGTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52164781 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164809 --T--TT-AAGTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52164832 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
52164860 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164888 --T--TT-AAGTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
52164911 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164939 --T--TT-AAGTAGGTTAGGGTTTTT-A
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52164961 ---A-TTAAATTAGGTTAGTGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52164985 TTAAATTAGGTTAGGTTAGGG---TT--
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52165008 TTTAATTAAATTAGGTTAGGGTTTTTGA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
52165036 TTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTA----A-ATTA-GGTTAGGGTTTTTAA
52165070 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52165098 --T--TT-AAGTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52165121 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
52165149 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52165177 --T--TT-AAGTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
52165200 TTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTA----A-ATTA-GGTTAGGGTTTTTAA
52165234 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
52165262 TTT-AGT--A--GGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52165285 TTTAATTAAATAAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52165313 --T--TT-AAGTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52165336 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52165364 TTTAAGTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* * *
52165392 TTTAATTAAAATAATGTTAAGGTTTTTAA
1 TTTAATT-AAATTAGGTTAGGGTTTTTAA
**
52165421 TTTAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52165449 TTTAAGTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
52165477 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
52165505 TTTAATTAAATTAGGTTAGGGTTAGGGTT--
1 TTTAATTAAATTAGGTTAGGGTT---TTTAA
*
52165534 TTTAATT-AAGTAGGGTTTAGGGTTTTTAA
1 TTTAATTAAATTA-GG-TTAGGGTTTTTAA
52165563 TTTAATTAAATTAGG
1 TTTAATTAAATTAGG
52165578 GTTTTTAATT
Statistics
Matches: 903, Mismatches: 103, Indels: 195
0.75 0.09 0.16
Matches are distributed among these distances:
22 9 0.01
23 283 0.31
24 25 0.03
25 7 0.01
26 13 0.01
27 21 0.02
28 404 0.45
29 50 0.06
30 15 0.02
31 2 0.00
32 3 0.00
33 8 0.01
34 63 0.07
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (28 bp):
TTTAATTAAATTAGGTTAGGGTTTTTAA
Found at i:52164511 original size:51 final size:51
Alignment explanation
Indices: 52164415--52165614 Score: 840
Period size: 51 Copynumber: 22.8 Consensus size: 51
52164405 TACAATTTAA
*
52164415 TTAGGGTTTTTAA-TTAAATAGGGTTAGGGTTTTTAATT--A--AA-TTAGG
1 TTAGGGTTTTTAATTTAAGTA-GGTTAGGGTTTTTAATTAAATTAAGTTAGG
*
52164461 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAGTT--A--AA-TTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
52164507 TTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTAATT--A--AA-TTAGG
1 TTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
* * * * *
52164558 TTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAAGGTTTTTAATTTAAGTAAATTAAG
1 TTAGGGTTTTTAA-T---TTA----A-G-TA-GGTTAGGGTTTTTAATTAAATTAAGTTAGG
* *
52164620 TTAGGGTTTTTAATTT-AGTAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAATTTAAGTA-GGTTAGGGTTTTTAATTAAATTAAGTTAGG
*
52164671 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
* *
52164722 ATT----TTTAATTAAATTAAATTAGGTTAGGGTTTTTAA-T---TTAAG-TAGG
1 -TTAGGGTTT--TT-AATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
*
52164768 TTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAA-T---TTAAG-TAGG
1 TTAGGGTTTTTAA-T---TTAAG-TAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
* * *
52164819 TTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAA-T---TTAAG-TAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
* *
52164875 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
*
52164926 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGTG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAG-G
* * *
52164978 TT----TTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTT--TTAATTTAAG-TAGGTTAGGGTTTTTAATTAAATTAAGTTA-GG
** * * ** * * *
52165029 TTTTTGATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 -TTAGGGTT--TTTAATTTAAG-TA-GGTTAGGGTTTTTAATTAAATTAAGTTAGG
*
52165085 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
*
52165136 TTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAA-T---TTAAG-TAGG
1 TTAGGGTTTTTAA--T--TT-AAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
* *
52165187 TTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAA-T---TTA----A-G-TA-GGTTAGGGTTTTTAATTAAATTAAGTTAGG
* * *
52165249 TTAGGGTTTTTAATTT-AGTAGGGTTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGGTTTTTAATTTAAGTA-GGTTAGGGTTTTTAATTAAATTAAGTTAGG
*
52165300 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
* * * *
52165351 TTAGGGTTTTTAATTTAAGTAGGTTAGGTTAGGGTTTTTAATTTAATTAAAATAATG
1 TTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAAATT-AAGTTAGG
* * * *
52165408 TTAAGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGG
1 TTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
* *
52165464 TTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAA-T---TTAAG-TAGGTTAGGG---TT--TTTAATTAAATTAAGTTA-GG
*
52165526 TTAGGGTTTTTAA-TTAAGTAGGGTTTAGGGTTTTTAATTTAATTAA---A--
1 TTAGGGTTTTTAATTTAAGTA-GG-TTAGGGTTTTTAATTAAATTAAGTTAGG
* *
52165573 TTAGGGTTTTTAA-TTAAGTAGGGTTAGGGATTTTAATCAAAT
1 TTAGGGTTTTTAATTTAAGTA-GGTTAGGGTTTTTAATTAAAT
52165615 AATGTCAAAA
Statistics
Matches: 996, Mismatches: 71, Indels: 174
0.80 0.06 0.14
Matches are distributed among these distances:
45 2 0.00
46 75 0.08
47 37 0.04
48 6 0.01
49 4 0.00
50 18 0.02
51 464 0.47
52 31 0.03
53 22 0.02
54 3 0.00
55 18 0.02
56 114 0.11
57 112 0.11
58 11 0.01
59 4 0.00
60 2 0.00
61 24 0.02
62 49 0.05
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.47
Consensus pattern (51 bp):
TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
Found at i:52164623 original size:34 final size:34
Alignment explanation
Indices: 52164546--52164627 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
52164536 TAGGGTTTTT
* * *
52164546 AATTAAATTA-GGTTAGGGTTTTTAATTAAATTA
1 AATTAAGTTAGGGTTAAGGTTTTTAATTAAAGTA
** * *
52164579 GGTTAGGTTAGGGTTAAGGTTTTTAATTTAAGTA
1 AATTAAGTTAGGGTTAAGGTTTTTAATTAAAGTA
52164613 AATTAAGTTAGGGTT
1 AATTAAGTTAGGGTT
52164628 TTTAATTTAG
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 6 0.16
34 32 0.84
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (34 bp):
AATTAAGTTAGGGTTAAGGTTTTTAATTAAAGTA
Found at i:52165060 original size:34 final size:34
Alignment explanation
Indices: 52165021--52165092 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
52165011 AATTAAATTA
* **
52165021 GGTTAGGGTTTTTGATTAAATTAGGTTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
*
52165055 GGTTAGGGTTTTTAATTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
52165089 GGTT
1 GGTT
52165093 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (34 bp):
GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
Found at i:52165228 original size:34 final size:34
Alignment explanation
Indices: 52165185--52165256 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
52165175 AATTTAAGTA
**
52165185 GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
*
52165219 GGTTAGGGTTTTTAATTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
52165253 GGTT
1 GGTT
52165257 TTTAATTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (34 bp):
GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
Found at i:52165538 original size:85 final size:83
Alignment explanation
Indices: 52164446--52165577 Score: 933
Period size: 79 Copynumber: 14.2 Consensus size: 83
52164436 GGTTAGGGTT
* *
52164446 TTTAATTAAATTAGGTTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAGTTAA--A--
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTATTTAAGTAGG
52164502 TTAGGTTAGGGTTTTTAA
66 TTAGGTTAGGGTTTTTAA
* *
52164520 TTTAATTAGGTTAGGTTAGGGTTTTTAA-TTAA--A--TTAGGTTAGGGTTTTTAATTAAATTAG
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-A-T---TTAA
*
52164580 GTTAGGTTAGGGTTAAGGTTTTTAA
61 G-TAGGTTA-GGTTAGGGTTTTTAA
* * * * * *
52164605 TTTAAGTAAATTAAGTTAGGGTTTTTAATTT-AGTA-G---GGTTAGGGTTTTTAATTTAATTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTAG
*
52164665 ATTAGGTTAGGGTTTTTAA
65 GTTAGGTTAGGGTTTTTAA
* * * *
52164684 --T--TTAAG-TAGGTTAGGGTTTTTAA-TTAA--A--TTAGGTTAGGATTTTTAATTAAATTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTAG
*
52164739 ATTAGGTTAGGGTTTTTAA
65 GTTAGGTTAGGGTTTTTAA
*
52164758 --T--TTAAG-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTT-A--A-
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTAG
52164814 G-TAGGTTAGGGTTTTTAA
65 GTTAGGTTAGGGTTTTTAA
* * **
52164832 TTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTT-A--A-
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTAG
52164893 G-TAGGTTAGGGTTTTTAA
65 GTTAGGTTAGGGTTTTTAA
* *
52164911 TTTAATTAAATTAGGTTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAA--A--
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTATTTAAGTAGG
*
52164967 TTAGGTTAGTGTTTTTAA
66 TTAGGTTAGGGTTTTTAA
* * * *** * * * *
52164985 TTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTG-ATTAAATTAGGTTA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTA-GGTTAGGGTTTTTATTTAAG-TA
52165049 GGTTAGGGTTAGGGTTTTTAA
64 GGTTA-GGTTAGGGTTTTTAA
* * *
52165070 TTTAATTAAATTAGGTTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAAATTAG
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTAG
52165130 GTTAGGTTAGGGTTTTTAA
65 GTTAGGTTAGGGTTTTTAA
* *
52165149 TTTAATTAAATTAGGTTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAAATTAG
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-A-T---TTAA
52165209 GTTAGGTTAGGGTTAGGGTTTTTAA
61 G-TAGGTTA-GGTTAGGGTTTTTAA
* * * *
52165234 TTTAATTAAATTAGGTTAGGGTTTTTAATTT-AGTA-G---GGTTAGGGTTTTTAATTTAATTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTAG
* *
52165294 ATAAGGTTAGGGTTTTTAA
65 GTTAGGTTAGGGTTTTTAA
*
52165313 --T--TTAAG-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAAGTAG
1 TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTAG
52165373 GTTAGGTTAGGGTTTTTAA
65 GTTAGGTTAGGGTTTTTAA
* * * *
52165392 TTTAATTAAAATAATGTTAAGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTAATTTAAGTA
1 TTTAATT-AAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTT-ATTTAAGTA
52165457 GGTTAGGTTAGGGTTTTTAA
64 GGTTAGGTTAGGGTTTTTAA
* * *
52165477 TTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA--T--TT-AATTAGGTTA-GGTTAGGGTTTTTATTTA
*
52165542 AGTAGG---GTTTAGGGTTTTTAA
60 AGTAGGTTAGGTTAGGGTTTTTAA
*
52165563 TTTAATTAAATTAGG
1 TTTAATTAAGTTAGG
52165578 GTTTTTAATT
Statistics
Matches: 897, Mismatches: 89, Indels: 132
0.80 0.08 0.12
Matches are distributed among these distances:
72 1 0.00
73 7 0.01
74 220 0.25
75 15 0.02
76 3 0.00
77 4 0.00
78 7 0.01
79 263 0.29
80 26 0.03
81 11 0.01
82 3 0.00
83 4 0.00
84 34 0.04
85 232 0.26
86 29 0.03
87 3 0.00
88 2 0.00
89 20 0.02
90 13 0.01
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (83 bp):
TTTAATTAAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTATTTAAGTAGG
TTAGGTTAGGGTTTTTAA
Found at i:52165590 original size:136 final size:136
Alignment explanation
Indices: 52165106--52165614 Score: 555
Period size: 136 Copynumber: 3.7 Consensus size: 136
52165096 AATTTAAGTA
*
52165106 GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAA-ATTAGGTTAGGG
1 GGTTAGGGTTTTTAATTAAAGTA-G---GGTTAGGGTTTTTAATTTAATTAATA-TA-GTTAGGG
*
52165170 TTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTT--TTTA
60 TTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTT---TTTAATTTA
* **
52165233 ATTTAATTAAATTA-
122 ATTAAATTAGGTTAG
*
52165247 GGTTAGGGTTTTTAATT-TAGTAGGGTTAGGGTTTTTAATTTAATTAA-ATAAGGTTAGGGTTTT
1 GGTTAGGGTTTTTAATTAAAGTAGGGTTAGGGTTTTTAATTTAATTAATAT-A-GTTAGGGTTTT
* **
52165310 TAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAAGTAGGT
64 TAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAAT
52165375 TAGGTTAG
129 TAGGTTAG
* * ** * *
52165383 GGTT---TTTAATTTAATTAAAATAATGTTAAGGTTTTTAATTTAATTAGGT-TAGGTTAGGGTT
1 GGTTAGGGTT--TTTAATTAAAGTAGGGTTAGGGTTTTTAATTTAATTA-ATATA-GTTAGGGTT
52165444 TTTAATTTAAGTAGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTA
62 TTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTA
52165509 ATTAAATTAGGTTAG
122 ATTAAATTAGGTTAG
52165524 GGTTAGGGTTTTTAATT-AAGTAGGGTTTAGGGTTTTTAATTTAATT-A-A-A-TTAGGGTTTTT
1 GGTTAGGGTTTTTAATTAAAGTAGGG-TTAGGGTTTTTAATTTAATTAATATAGTTAGGGTTTTT
* *
52165584 AA-TTAAGTAGGGTTAGGGATTTTAATCAAAT
65 AATTTAAGTA-GGTTAGGGTTTTTAATTAAAT
52165615 AATGTCAAAA
Statistics
Matches: 321, Mismatches: 27, Indels: 49
0.81 0.07 0.12
Matches are distributed among these distances:
131 2 0.01
132 20 0.06
133 5 0.02
135 21 0.07
136 136 0.42
137 15 0.05
139 3 0.01
140 4 0.01
141 87 0.27
142 26 0.08
144 2 0.01
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (136 bp):
GGTTAGGGTTTTTAATTAAAGTAGGGTTAGGGTTTTTAATTTAATTAATATAGTTAGGGTTTTTA
ATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAATTA
GGTTAG
Found at i:52165596 original size:17 final size:18
Alignment explanation
Indices: 52165563--52165597 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52165553 GGGTTTTTAA
*
52165563 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
52165581 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
52165598 AGGGATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Found at i:52167942 original size:27 final size:28
Alignment explanation
Indices: 52167880--52167933 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
52167870 TGAAAATATT
52167880 AAAAATTTTAAAATTATTTAAAAAAATA
1 AAAAATTTTAAAATTATTTAAAAAAATA
52167908 AAAAATTTTAAAATT-TTCTAAAAAAA
1 AAAAATTTTAAAATTATT-TAAAAAAA
52167934 ATGAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAAATTTTAAAATTATTTAAAAAAATA
Found at i:52168007 original size:22 final size:22
Alignment explanation
Indices: 52167977--52168018 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52167967 ATTTGGAGAT
*
52167977 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
52167999 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
52168019 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:52168045 original size:22 final size:23
Alignment explanation
Indices: 52168020--52168111 Score: 104
Period size: 22 Copynumber: 4.2 Consensus size: 23
52168010 ATTTGAGAGT
52168020 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
52168042 TTGATG-GAAATTTT-GAAGGGAA
1 TTGA-GAGAAATTTTGGAAGGAAA
*
52168064 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
52168086 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
52168108 TTGA
1 TTGA
52168112 TATTGAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
21 10 0.17
22 39 0.65
23 11 0.18
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:52168060 original size:52 final size:51
Alignment explanation
Indices: 52167968--52168070 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
52167958 TTAATATGGA
* * *
52167968 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAA-TTGAGAG
52168019 TTTGAGAGAATTTTGGAAGGAAATTGATG-GAAATTTT-GAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGA-GAG-AATTTTGGAAGGGAATTGAGAG
52168071 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
51 4 0.09
52 31 0.69
53 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
Found at i:52168068 original size:44 final size:44
Alignment explanation
Indices: 52168020--52168111 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
52168010 ATTTGAGAGT
* * *
52168020 TTGAGAG-AATTTTGGAAGGAAATTGATG-GAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGA-GAGAAATTTTGAAAGAAA
*
52168064 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
52168108 TTGA
1 TTGA
52168112 TATTGAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 30 0.71
45 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:52173079 original size:19 final size:20
Alignment explanation
Indices: 52173055--52173092 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52173045 AACTTAACTT
*
52173055 AAAATGAAT-TTTTAAAAAA
1 AAAATGAATATTGTAAAAAA
52173074 AAAATGAATATTGTAAAAA
1 AAAATGAATATTGTAAAAA
52173093 TGCATGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAATGAATATTGTAAAAAA
Found at i:52185991 original size:25 final size:23
Alignment explanation
Indices: 52185954--52186017 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
52185944 TAATGCTGAG
52185954 AATAGTTTATTAAATAAAAATAAAAT
1 AATA-TTT-TTAAAT-AAAATAAAAT
*
52185980 AATACTTTTTAAAGTAGAATAAAAT
1 AATA-TTTTTAAA-TAAAATAAAAT
*
52186005 AATATTTTAAAAT
1 AATATTTTTAAAT
52186018 TTCTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.03
24 7 0.21
25 18 0.53
26 8 0.24
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (23 bp):
AATATTTTTAAATAAAATAAAAT
Found at i:52186665 original size:37 final size:38
Alignment explanation
Indices: 52186619--52186692 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
52186609 TACAATCACA
*
52186619 ACCACTTATAATCAATATTAGATAAAATTATCATAGAT
1 ACCACTTATAATCAAAATTAGATAAAATTATCATAGAT
*
52186657 ACCA-TTATAATCAAAATTAGATAAAATTATTATAGA
1 ACCACTTATAATCAAAATTAGATAAAATTATCATAGA
52186693 AGGTCTCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 30 0.88
38 4 0.12
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (38 bp):
ACCACTTATAATCAAAATTAGATAAAATTATCATAGAT
Found at i:52191575 original size:18 final size:18
Alignment explanation
Indices: 52191552--52191587 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
52191542 ATAGTTTGAC
52191552 ATTCGAATTATTTGAATT
1 ATTCGAATTATTTGAATT
*
52191570 ATTCGAGTTATTTGAATT
1 ATTCGAATTATTTGAATT
52191588 CAAAAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (18 bp):
ATTCGAATTATTTGAATT
Found at i:52191657 original size:9 final size:9
Alignment explanation
Indices: 52191640--52191670 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52191630 TCGAGTTGAT
52191640 TCGAATAAC
1 TCGAATAAC
*
52191649 TCGATTAAC
1 TCGAATAAC
52191658 TCGAATAAC
1 TCGAATAAC
52191667 TCGA
1 TCGA
52191671 TTCGTTTAAC
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:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:52192964 original size:57 final size:57
Alignment explanation
Indices: 52192889--52192996 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 57
52192879 TTAATAAACT
* * * * *
52192889 ATTTGGTACTTGAATTTGGTTTCAATGTTCAATTTAGTATTTGAATTTTTTGTCCGA
1 ATTTGGTACGTGAATTTGGCTTCAATATTCAAATTAGTACTTGAATTTTTTGTCCGA
* * *
52192946 ATTTGGTACGTGAGTTTGGCTTCAATATTCAAATTGGTACTTGAGTTTTTT
1 ATTTGGTACGTGAATTTGGCTTCAATATTCAAATTAGTACTTGAATTTTTT
52192997 CAATTTGATA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.49
Consensus pattern (57 bp):
ATTTGGTACGTGAATTTGGCTTCAATATTCAAATTAGTACTTGAATTTTTTGTCCGA
Found at i:52203945 original size:25 final size:27
Alignment explanation
Indices: 52203912--52203961 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
52203902 AAATAACATA
*
52203912 GAAAGCAATTTAAA-TAGGTAATATAT
1 GAAAGCAATTTAAAGTAGCTAATATAT
52203938 GAAA-CAATTTAAAGTAGCTAATAT
1 GAAAGCAATTTAAAGTAGCTAATAT
52203962 CAAACATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (27 bp):
GAAAGCAATTTAAAGTAGCTAATATAT
Found at i:52203966 original size:24 final size:25
Alignment explanation
Indices: 52203917--52203973 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
52203907 ACATAGAAAG
* *
52203917 CAATTTAAATAGGTAATATATGAAA
1 CAATTTAAATAGCTAATATATCAAA
52203942 CAATTTAAAGTAGCT-A-ATATCAAA
1 CAATTTAAA-TAGCTAATATATCAAA
*
52203966 CATTTTAA
1 CAATTTAA
52203974 TATGAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 10 0.36
26 4 0.14
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (25 bp):
CAATTTAAATAGCTAATATATCAAA
Found at i:52205932 original size:129 final size:129
Alignment explanation
Indices: 52205727--52206022 Score: 425
Period size: 129 Copynumber: 2.3 Consensus size: 129
52205717 AGATTCATTG
* * *
52205727 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGAATTGGTTTTTTCTGTCTACTCCACTGCAA
1 TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
* * * *
52205792 CTTTAGGGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAGAAG-TAAGATCTGTGT
66 CTTCAGAGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGA-AAGAGAAGATCTGTAT
**
52205856 TTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
1 TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
* * * *
52205921 CTTCAGAGAGATAAGACTGGATGCGATCTGCTCTACTGTAACTTTAGAAAGAGAAGATTTGTAT
66 CTTCAGAGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAAAGAGAAGATCTGTAT
* *
52205985 TTTTAATCTGCACCACTGCAACTTTA-GAGAGATAGGAT
1 TTTTAATCTGCTCCACTGCAACTTCAGGA-AGATAGGAT
52206023 CTGTGTTTTT
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
128 5 0.03
129 143 0.97
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (129 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
CTTCAGAGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAAAGAGAAGATCTGTAT
Found at i:52206005 original size:173 final size:173
Alignment explanation
Indices: 52205826--52206317 Score: 599
Period size: 173 Copynumber: 2.8 Consensus size: 173
52205816 GATATGCTCT
* * * *
52205826 ACTGCAACTTCAGAGA-AGTAAGATCTGTGTTTTTAATCCACTCCACTGCAACTTCAGGAAGATA
1 ACTGCAACTTTAGAGAGA-TAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
* * *
52205890 GGATTGGTTTCTTCTGTCTACTCCACTGCAACTTCAGAGAGATAAGACTGGATGCGATCTGCTCT
65 GGATTGGTTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCT
* * * *
52205955 ACTGTAACTTTAGAAAGAGAAGATTTGTATTTTTAATCTGCACC
130 ACTGCAACTTCAGAAAGAGAAGATCTGTATTTTTAATCCGCACC
* **
52205999 ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCTGCTCCACTATAACTTCAGGGAGATAG
1 ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
* * * *
52206064 GATTGGTTTTTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGTGATCTGTTCTA
66 GATTGGTTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTA
* * * * **
52206129 TTGCAACTTCAGATAGATAAGATCTGTGTTTTTAATCCGTTCC
131 CTGCAACTTCAGAAAGAGAAGATCTGTATTTTTAATCCGCACC
* * * * *
52206172 ACTACAACTTTAGGGAGATAGGATCTGTGTTTTAAATTCGCTCAACTGCAACTTCAGGGAGATAG
1 ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
* ** * * * * * *
52206237 GATTAGTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCT
66 GATTGGTTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG-A--TGCGATCTGCT
52206302 CTACTGCAACTTCAGA
128 CTACTGCAACTTCAGA
52206318 TAGATAAGGT
Statistics
Matches: 269, Mismatches: 46, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
173 246 0.91
174 2 0.01
176 21 0.08
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (173 bp):
ACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
GATTGGTTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTA
CTGCAACTTCAGAAAGAGAAGATCTGTATTTTTAATCCGCACC
Found at i:52206043 original size:129 final size:127
Alignment explanation
Indices: 52205727--52206062 Score: 424
Period size: 129 Copynumber: 2.6 Consensus size: 127
52205717 AGATTCATTG
*
52205727 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGAATTGGTTTTTTCTGTCTACTCCACTGCAA
1 TTTTAATCTGCTCCACTGCAACTTCA-GGAGATAGGATTGG-TTTTTCTGTCTACTCCACTGCAA
* * *
52205792 CTTTAGGGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAGAAGTAAGATCTGTGT
64 CTTCAGGGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAGAAGGAAGATCTGTAT
**
52205856 TTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTGTCTACTCCACTGCAA
1 TTTTAATCTGCTCCACTGCAACTTCAGG-AGATAGGATTGGTTT-TTCTGTCTACTCCACTGCAA
* * * * *
52205921 CTTCAGAGAGATAAGACTGGATGCGATCTGCTCTACTGTAACTTTAGA-AAGAGAAGATTTGTAT
64 CTTCAGGGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAGAAG-GAAGATCTGTAT
* * ** * **
52205985 TTTTAATCTGCACCACTGCAACTTTAGAGAGATAGGATCTGTGTTTTT-AATCTGCTCCACTATA
1 TTTTAATCTGCTCCACTGCAACTTCAG-GAGATAGGAT-TG-GTTTTTCTGTCTACTCCACTGCA
52206049 ACTTCAGGGAGATA
63 ACTTCAGGGAGATA
52206063 GGATTGGTTT
Statistics
Matches: 180, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
128 8 0.04
129 163 0.91
130 5 0.03
131 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (127 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGAGATAGGATTGGTTTTTCTGTCTACTCCACTGCAACT
TCAGGGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAGAAGGAAGATCTGTAT
Found at i:52206123 original size:129 final size:129
Alignment explanation
Indices: 52205990--52206235 Score: 316
Period size: 129 Copynumber: 1.9 Consensus size: 129
52205980 TGTATTTTTA
* * * *
52205990 ATCTGCACCACTGCAACTTTAGAGAGATAGGATCTGTGTTTTTAATCTGCTCCACTATAACTTCA
1 ATCTGCACCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTTAATCCGCTCCACTACAACTTCA
*** * *
52206055 GGGAGATAGGAT-TG-GTTTTTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGT
66 GGGAGATAGGATCTGTGTTTTAAAT-TC-GCTCAACTGCAACTTCAGGGAGATAAGACTGGATGT
52206118 G
129 G
** * * * * *
52206119 ATCTGTTCTATTGCAACTTCAGATAGATAAGATCTGTGTTTTTAATCCGTTCCACTACAACTTTA
1 ATCTGCACCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTTAATCCGCTCCACTACAACTTCA
52206184 GGGAGATAGGATCTGTGTTTTAAATTCGCTCAACTGCAACTTCAGGGAGATA
66 GGGAGATAGGATCTGTGTTTTAAATTCGCTCAACTGCAACTTCAGGGAGATA
52206236 GGATTAGTAG
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
129 89 0.90
130 4 0.04
131 6 0.06
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (129 bp):
ATCTGCACCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTTAATCCGCTCCACTACAACTTCA
GGGAGATAGGATCTGTGTTTTAAATTCGCTCAACTGCAACTTCAGGGAGATAAGACTGGATGTG
Found at i:52206406 original size:44 final size:45
Alignment explanation
Indices: 52205551--52206472 Score: 341
Period size: 44 Copynumber: 21.0 Consensus size: 45
52205541 TTGGTTTTAG
* * * **
52205551 TCTGCTCCACTGCAACTTTATGAAGATAAGACTT-GTCGCTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATCTTCAAC
** * * * *
52205596 -CTGCTCCACTGTGACTTCAGGGAGATAGGATTAGTAGCTTTAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * ** *
52205639 TATGCTCCACTGCAACTTCAGGAAGATAAGACTTGTTATGATAGATTTAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG----G-TATCTTCAAC
* * * * ** * *
52205689 TCCGAC-CTACTGTAACTTCAGAGG-TATAAGATTCAT-TGTTTTAA-
1 TCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTGGTAT-CTTCAAC
* * **
52205733 TCTGCTCCACTGCAACTTCAGGGAGAT-AGAATTGGTTTTTTC-TG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG-ATTGGTATCTTCAAC
* * * * *
52205777 TCTACTCCACTGCAACTTTAGGGAGATAAGACTGG-A--TGCGA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * *
52205818 TATGCTCTACTGCAACTTCAGAGA-AGTAAGATCTGTGT-T-TTTAA-
1 TCTGCTCCACTGCAACTTCAGGGAGA-TAAGAT-TG-GTATCTTCAAC
** * * * **
52205862 TCCACTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTC-TG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * * *
52205906 TCTACTCCACTGCAACTTCAGAGAGATAAGACTGG-A--TGCGA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * ** * * * *
52205947 TCTGCTCTACTGTAACTTTAGAAAGAGAAGATTTGTATTTTTAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * * *
52205991 TCTGCACCACTGCAACTTTAGAGAGATAGGATCTGTGT-T-TTTAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTATCTTCAAC
** * * * *
52206035 TCTGCTCCACTATAACTTCAGGGAGATAGGATTGGTTTTTTCTA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * *
52206079 TCTGCTCCACTGCAACTTTAGGGAGATAAGACTGG-AT-GT-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* * * ** *
52206120 TCTGTTCTATTGCAACTTCAGATAGATAAGATCTGTGT-T-TTTAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTATCTTCAAC
* * * * * * *
52206164 TCCGTTCCACTACAACTTTAGGGAGATAGGATCTGTGT-T-TTAAAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTATCTTCAAC
* * * *
52206209 TC-GCTCAACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
*
52206252 TCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
* ** * * *
52206297 -CTGCTCTACTGCAACTTCAGATAGATAAGGTTGGTTACCTTC-AG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TATCTTCAAC
*
52206341 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTATTTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATCTTCAAC
* * * * * *
52206386 T-TGCCCCATTGCAACTTCAGGGGGATAAGGTTTGTCAT-TTTAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT-ATCTTCAAC
* * * * *
52206429 TCCGCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAA
52206473 TCTATTTAAT
Statistics
Matches: 668, Mismatches: 157, Indels: 105
0.72 0.17 0.11
Matches are distributed among these distances:
40 1 0.00
41 81 0.12
42 12 0.02
43 25 0.04
44 464 0.69
45 47 0.07
46 4 0.01
49 3 0.00
50 29 0.04
51 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAAC
Found at i:52206456 original size:133 final size:127
Alignment explanation
Indices: 52206001--52206461 Score: 355
Period size: 133 Copynumber: 3.5 Consensus size: 127
52205991 TCTGCACCAC
* * * * *
52206001 TGCAACTTTAGAGAGATAGGATCTGTGT-TTTTAATCTGCTCCACTATAACTTCAGGGAGATAGG
1 TGCAACTTCAGGGAGATAAGAT-T-TGTATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGG
* * * * * * *
52206065 ATTGGTTTTTTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGAC-TGGATGTGATC-TGTTCT
64 ATTGG--TTTTC-ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATTTCAACTTGCTCC
52206128 AT
126 AT
** * *
52206130 TGCAACTTCAGATAGATAAGATCTGTGT-TTTTAATCCGTTCCACTACAACTTTAGGGAGATAGG
1 TGCAACTTCAGGGAGATAAGAT-T-TGTATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGG
* * * *
52206194 ATCTGTGTTTTAAAT-TCGCTCAACTGCAACTTCAGGGAGATAGGA-TTAGTAGCTTCAA-TCTG
64 AT-TG-GTTTT-CATCT-GCTCCACTGCAACTTCAGGGAGATAAGACTT-GTA-TTTCAACT-TG
**
52206256 CTCCGC
122 CTCCAT
* * * * **
52206262 TGCAACTTCAGGGAGATAAGATTGGTATCTTCAA-CCTGCTCTACTGCAACTTCAGATAGATAAG
1 TGCAACTTCAGGGAGATAAGATTTGTAT-TTTAATCC-GCTCCACTACAACTTCAGGGAGAT-AG
52206326 G-TTGGTTACCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATTTTCAACTTGC
63 GATTGGTT---TTCA-TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTA-TTTCAACTTGC
*
52206390 CCCAT
123 TCCAT
* * * *
52206395 TGCAACTTCAGGGGGATAAGGTTTGTCATTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGA
1 TGCAACTTCAGGGAGATAAGATTTGT-ATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGA
52206460 TT
65 TT
52206462 AGTAGCTTCA
Statistics
Matches: 263, Mismatches: 46, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
128 1 0.00
129 91 0.35
130 9 0.03
131 9 0.03
132 51 0.19
133 94 0.36
134 8 0.03
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (127 bp):
TGCAACTTCAGGGAGATAAGATTTGTATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGAT
TGGTTTTCATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATTTCAACTTGCTCCAT
Found at i:52206521 original size:50 final size:50
Alignment explanation
Indices: 52206463--52207480 Score: 696
Period size: 50 Copynumber: 20.4 Consensus size: 50
52206453 GATAGGATTA
* * * *
52206463 GTAGCTTCAATCTATTTAATTGCAATGTCGGGGAAGGAAGATTCGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * ** * **
52206513 GTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTTGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* *
52206563 GTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * *
52206613 GTAGCTTCAATCTATTCCACTGCACCA-CT-AGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCA--ATGTCAGGGAAGTAAGATTCACCGTT
* *
52206663 GTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCATT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * ** * ** * ** *
52206713 GTAGATTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTTGCCGCT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * ** *
52206763 GTGGCTTCAATCTTTTTAATTGAAATATCTTGGAAGTAAGATTTACCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * * * **
52206813 GTAACTTCAAT-TTGTTCCATTACACTGCCAGGGAAGTAAGATTCACTATT
1 GTAGCTTCAATCTT-TTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * *
52206863 GTGGCTTCAATCTTTTTAATTGTAATGTCAGAGAAGCAAGATTCACTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * **** * * *
52206913 GTAGCTTCAATCTGTTCCACTGCACCACCAGGGAAGTAAAATTCGCTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * *
52206963 GTGGCTTCAATC-TTTTAATTGCCATGTCGGGGAAGCAAGATTCACTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * ** * * *
52207012 GTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * * *
52207062 GTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCGCTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * * ** * *
52207112 GTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGGTTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * * * *
52207162 GTGGCTTCAATCTTTTTAATTTCAATTTCGGGGAAGCAAGATTCGCTGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * ** * * * *
52207212 GTAGCTTCAATATGTTCCACTGTACTGCCAGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * *
52207262 GTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGTGAGATTCACCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * ** * * ** **
52207312 GTAACTTCAATCTGTTCCACTACACCGTCAGGGAAGTAAGATTTTCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* * * * ** **
52207362 ATGGCTTCAATCGTTTTAATTACAATGTCAGGGAAACAAGATTTGCCGTT
1 GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* ** * * ** * * *
52207412 GTAGTTTCAAT-TTGTTCCACTACACCGCCAAGGAAGTAAGATTCGCCGTT
1 GTAGCTTCAATCTT-TTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
* *
52207462 GTGGTTTCAATCTTTTTAA
1 GTAGCTTCAATCTTTTTAA
52207481 CTGTAACCTA
Statistics
Matches: 719, Mismatches: 240, Indels: 18
0.74 0.25 0.02
Matches are distributed among these distances:
48 1 0.00
49 39 0.05
50 673 0.94
51 5 0.01
52 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (50 bp):
GTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCGTT
Found at i:52206604 original size:100 final size:100
Alignment explanation
Indices: 52206466--52207480 Score: 1348
Period size: 100 Copynumber: 10.2 Consensus size: 100
52206456 AGGATTAGTA
* * *
52206466 GCTTCAATCTATTTAATTGCAATGTCGGGGAAGGAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
*
52206531 ACTGCACCGCCAGGGAAGTAAGATTTGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* *
52206566 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * *
52206631 ACTGCACCACTAGGGAAGTAAGATTCACCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * * * *
52206666 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACCATTGTAGATTCAATCTATTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* *
52206731 ACTGCACCGCCAGGGAAGTAAGATTTGCCGCTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * ** * * * *
52206766 GCTTCAATCTTTTTAATTGAAATATCTTGGAAGTAAGATTTACCGTTGTAACTTCAATTTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * * **
52206831 ATTACACTGCCAGGGAAGTAAGATTCACTATTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * * *
52206866 GCTTCAATCTTTTTAATTGTAATGTCAGAGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * *
52206931 ACTGCACCACCAGGGAAGTAAAATTCGCTGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * *
52206966 GCTTCAATC-TTTTAATTGCCATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTATTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
*
52207030 ACTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * *
52207065 GCTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * *
52207130 ACTACACCGCCAGGGAAGTAAGGTTCACCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * * * *
52207165 GCTTCAATCTTTTTAATTTCAATTTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATATGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * *
52207230 ACTGTACTGCCAGGGAAGTAAGATTCACCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* ** *
52207265 GCTTCAATCTTTTTAATTGCAATATCGGGGAAGTGAGATTCACCGTTGTAACTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * ** *
52207330 ACTACACCGTCAGGGAAGTAAGATTTTCCGTTATG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
* * * * ** * *
52207365 GCTTCAATCGTTTTAATTACAATGTCAGGGAAACAAGATTTGCCGTTGTAGTTTCAATTTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* *
52207430 ACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
*
52207465 GTTTCAATCTTTTTAA
1 GCTTCAATCTTTTTAA
52207481 CTGTAACCTA
Statistics
Matches: 807, Mismatches: 107, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
99 92 0.11
100 715 0.89
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (100 bp):
GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTG
Found at i:52208075 original size:45 final size:45
Alignment explanation
Indices: 52207989--52208075 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
52207979 AGCTCGAAAT
* * *
52207989 GAATGAATTAATCAAGATAGTAAATTTTGCTAGAATACAAAATGA
1 GAATAAATTAATCAAGATAGTAAATTTTGCCAAAATACAAAATGA
* ** *
52208034 GAATAAATTAATCAAGATGGTGTATTTTGCCAAAATCCAAAA
1 GAATAAATTAATCAAGATAGTAAATTTTGCCAAAATACAAAA
52208076 ATGAATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (45 bp):
GAATAAATTAATCAAGATAGTAAATTTTGCCAAAATACAAAATGA
Found at i:52212075 original size:25 final size:27
Alignment explanation
Indices: 52212041--52212091 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
52212031 AAAATAACAT
*
52212041 TGAAAGCAATTTAAA-TAGGTAATATA
1 TGAAAGCAATTTAAAGTAGCTAATATA
52212067 TGAAA-CAATTTAAAGTAGCTAATAT
1 TGAAAGCAATTTAAAGTAGCTAATAT
52212092 CAAACATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (27 bp):
TGAAAGCAATTTAAAGTAGCTAATATA
Found at i:52212096 original size:24 final size:25
Alignment explanation
Indices: 52212047--52212103 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
52212037 ACATTGAAAG
* *
52212047 CAATTTAAATAGGTAATATATGAAA
1 CAATTTAAATAGCTAATATATCAAA
52212072 CAATTTAAAGTAGCT-A-ATATCAAA
1 CAATTTAAA-TAGCTAATATATCAAA
*
52212096 CATTTTAA
1 CAATTTAA
52212104 TATGAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 10 0.36
26 4 0.14
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (25 bp):
CAATTTAAATAGCTAATATATCAAA
Found at i:52212952 original size:17 final size:17
Alignment explanation
Indices: 52212932--52212972 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
52212922 AGATTTTTGT
**
52212932 AAAAAAGTTGATAAATA
1 AAAAAAGTAAATAAATA
*
52212949 AAAAAAGTAAATAATTA
1 AAAAAAGTAAATAAATA
52212966 AAAAAAG
1 AAAAAAG
52212973 AATTAGAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (17 bp):
AAAAAAGTAAATAAATA
Found at i:52216190 original size:24 final size:23
Alignment explanation
Indices: 52216145--52216195 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
52216135 CTTTTTACTA
**
52216145 AAAATATTTAAAAATATCTATAAT
1 AAAATATTTAAAAATAAATAT-AT
52216169 AAAATATTTAAAAATAAATATAT
1 AAAATATTTAAAAATAAATATAT
52216192 AAAA
1 AAAA
52216196 AATGAAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATATTTAAAAATAAATATAT
Found at i:52222173 original size:24 final size:24
Alignment explanation
Indices: 52222152--52222203 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
52222142 AATTAATGTC
*
52222152 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
52222176 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
52222200 AAAT
1 AAAT
52222204 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:52224068 original size:100 final size:100
Alignment explanation
Indices: 52223887--52224082 Score: 257
Period size: 100 Copynumber: 2.0 Consensus size: 100
52223877 GCTTCAAAAA
* * * * * * *
52223887 AAGTAGATGTTTCTTGATTTGCATCTATATCTTCATCCACGTTTAAACCATAAATAGCTAGATCA
1 AAGTAAATGTTTCTTAATTTACATATATATCTTAATCCACGTTTAAACCATAAACAACTAGATCA
* *
52223952 GCCTCAGCATATCTCTTTAAAGGTTTAATTTGAAT
66 ACCTCAGCATACCTCTTTAAAGGTTTAATTTGAAT
* *
52223987 AAGTAAATGTTTCTTAATTTACATATATATCTTAATCCACGTTTAAAGCATAAGCAACTAGATCA
1 AAGTAAATGTTTCTTAATTTACATATATATCTTAATCCACGTTTAAACCATAAACAACTAGATCA
* * **
52224052 ACCTCGGCGTACCTCTTTGGAGGTTTAATTT
66 ACCTCAGCATACCTCTTTAAAGGTTTAATTT
52224083 CTTTTTTATG
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (100 bp):
AAGTAAATGTTTCTTAATTTACATATATATCTTAATCCACGTTTAAACCATAAACAACTAGATCA
ACCTCAGCATACCTCTTTAAAGGTTTAATTTGAAT
Found at i:52224568 original size:14 final size:14
Alignment explanation
Indices: 52224557--52224587 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52224547 GATAAACAAG
52224557 CATTCGACAACATA
1 CATTCGACAACATA
*
52224571 CATTTGACAACATA
1 CATTCGACAACATA
52224585 CAT
1 CAT
52224588 CAAACTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (14 bp):
CATTCGACAACATA
Found at i:52226672 original size:24 final size:24
Alignment explanation
Indices: 52226626--52226690 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 24
52226616 TAATAAATAT
*
52226626 TAATAAATATTAAATCTTAATATTATGC
1 TAATAAATATT-AA--TT-ATATTATAC
*
52226654 TAATAAATCTTAATTATATTATAC
1 TAATAAATATTAATTATATTATAC
52226678 TAATAAATATTAA
1 TAATAAATATTAA
52226691 ATCTTCTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 20 0.59
25 2 0.06
27 2 0.06
28 10 0.29
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAATATTAATTATATTATAC
Found at i:52240749 original size:8 final size:8
Alignment explanation
Indices: 52240732--52240780 Score: 71
Period size: 8 Copynumber: 6.1 Consensus size: 8
52240722 TATATTTTAT
*
52240732 ATTACTAA
1 ATTACAAA
52240740 ATTACAAA
1 ATTACAAA
52240748 ATTACAAA
1 ATTACAAA
52240756 ATTACAAA
1 ATTACAAA
*
52240764 ATTAAAAA
1 ATTACAAA
*
52240772 ATTATAAA
1 ATTACAAA
52240780 A
1 A
52240781 AATATAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (8 bp):
ATTACAAA
Found at i:52240986 original size:18 final size:19
Alignment explanation
Indices: 52240954--52240991 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
52240944 AAAATTTATG
52240954 ATAATTATACATTTA-AAA
1 ATAATTATACATTTATAAA
52240972 ATAATTATA-ATTTTATAAA
1 ATAATTATACA-TTTATAAA
52240991 A
1 A
52240992 AATGTGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 13 0.72
19 4 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATTATACATTTATAAA
Found at i:52241256 original size:17 final size:19
Alignment explanation
Indices: 52241223--52241258 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
52241213 AGTGTTAATT
52241223 TTATTAATGTAAAATAGAA
1 TTATTAATGTAAAATAGAA
52241242 TTATTAAT-T-AAATAGAA
1 TTATTAATGTAAAATAGAA
52241259 CTCTAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (19 bp):
TTATTAATGTAAAATAGAA
Found at i:52243373 original size:38 final size:38
Alignment explanation
Indices: 52243330--52243424 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 38
52243320 TGTAATAGAA
* *
52243330 CAATTCAACACTAGCAGTACTCATGCTTAACATGTATT
1 CAATTCAACACTAGCAATAATCATGCTTAACATGTATT
* *
52243368 TAATTCAACACTAGTAATAATCATGCTTAACATGTATT
1 CAATTCAACACTAGCAATAATCATGCTTAACATGTATT
*
52243406 CAATTCAATACTAGCAATA
1 CAATTCAACACTAGCAATA
52243425 GACATGTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (38 bp):
CAATTCAACACTAGCAATAATCATGCTTAACATGTATT
Done.