Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 120 of 276
Found at i:38364381 original size:15 final size:15
Alignment explanation
Indices: 38364344--38364372 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38364334 TTTTTCTATC
38364344 TAATAATAATAATTA
1 TAATAATAATAATTA
38364359 TAATAATAATAATT
1 TAATAATAATAATT
38364373 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:38372828 original size:21 final size:22
Alignment explanation
Indices: 38372797--38372842 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
38372787 AAATATCAAA
*
38372797 AAATATATTTTTTATGCCTTTT
1 AAATATATTTTTTATGCATTTT
*
38372819 AAATA-ATTTTTTTTGCATTTT
1 AAATATATTTTTTATGCATTTT
38372840 AAA
1 AAA
38372843 ATTTAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (22 bp):
AAATATATTTTTTATGCATTTT
Found at i:38377027 original size:24 final size:24
Alignment explanation
Indices: 38377000--38377055 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
38376990 TGTACAAATT
*
38377000 CAGATGTAT-TTTCATAATCAGATA
1 CAGATGTATATTT-AGAATCAGATA
* *
38377024 CAGATGCATATTTAGATTCAGATA
1 CAGATGTATATTTAGAATCAGATA
*
38377048 CAAATGTA
1 CAGATGTA
38377056 GACACAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (24 bp):
CAGATGTATATTTAGAATCAGATA
Found at i:38377085 original size:24 final size:24
Alignment explanation
Indices: 38377039--38377085 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38377029 GCATATTTAG
*
38377039 ATTCAGATACAAATGTAGACACAA
1 ATTCAGATACAAATGCAGACACAA
*
38377063 ATTCAGATACAAATGCAGTCACA
1 ATTCAGATACAAATGCAGACACA
38377086 GATCCTACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (24 bp):
ATTCAGATACAAATGCAGACACAA
Found at i:38383044 original size:79 final size:79
Alignment explanation
Indices: 38382952--38383155 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
38382942 TAAATTCTTT
* * *
38382952 TGAACGA-ATGGAATAGAATCCTAAAATAGAATTGTTCAATTGATTTATGTTCCAAAATAGAAAA
1 TGAACGACA-GGAATAAAATCCTGAAATAGAATTGTTCAATTGATTTATGTTCCAAAATAAAAAA
* *
38383016 TCGAAGAAATCCTAT
65 TCGAACAAATCCTAG
* * * * * * * ***
38383031 TGAATGGCCGGAATAAAATCCTGAAACAAAATTGTTCACTTGATTTTTGTTTGGAAATAAAAAAT
1 TGAACGACAGGAATAAAATCCTGAAATAGAATTGTTCAATTGATTTATGTTCCAAAATAAAAAAT
*
38383096 CGAACAAATCCTGG
66 CGAACAAATCCTAG
* *
38383110 TGAACGACAGGAATAAAATTCTGAAATAGAATTGTTCAATCGATTT
1 TGAACGACAGGAATAAAATCCTGAAATAGAATTGTTCAATTGATTT
38383156 CTATTTACAA
Statistics
Matches: 100, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
79 100 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (79 bp):
TGAACGACAGGAATAAAATCCTGAAATAGAATTGTTCAATTGATTTATGTTCCAAAATAAAAAAT
CGAACAAATCCTAG
Found at i:38391583 original size:42 final size:42
Alignment explanation
Indices: 38391521--38391635 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
38391511 AATTTAATGT
* * * *
38391521 TTCTATTACGGTGTGGATAAACCACTCATTGGTGCAGATAGC
1 TTCTAATACGGTGTGAATAAACCACTCAATAGTGCAGATAGC
* *
38391563 TTCTAATATGGTGTGAATAAACCACTCAATAGTGCAGATAAAC
1 TTCTAATACGGTGTGAATAAACCACTCAATAGTGCAGAT-AGC
* * *
38391606 TACTCAA-ACGATGTGGATAAACCACTCAAT
1 TTCT-AATACGGTGTGAATAAACCACTCAAT
38391636 GGTGTTAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 34 0.56
43 25 0.41
44 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (42 bp):
TTCTAATACGGTGTGAATAAACCACTCAATAGTGCAGATAGC
Found at i:38391603 original size:21 final size:23
Alignment explanation
Indices: 38391579--38391635 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
38391569 TATGGTGTGA
38391579 ATAAACCACTCAATA-G-TGCAG
1 ATAAACCACTCAATACGATGCAG
* **
38391600 ATAAACTACTCAA-ACGATGTGG
1 ATAAACCACTCAATACGATGCAG
38391622 ATAAACCACTCAAT
1 ATAAACCACTCAAT
38391636 GGTGTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 13 0.45
22 15 0.52
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (23 bp):
ATAAACCACTCAATACGATGCAG
Found at i:38391846 original size:154 final size:154
Alignment explanation
Indices: 38391649--38391960 Score: 588
Period size: 154 Copynumber: 2.0 Consensus size: 154
38391639 GTTAATAATA
*
38391649 TGTTCATAGTTTCTTCATTCATATCGTCCCACCCCATGCAATGAAACATGATATGCTTACAACAG
1 TGTTCATAATTTCTTCATTCATATCGTCCCACCCCATGCAATGAAACATGATATGCTTACAACAG
38391714 ATCAACATGGTAGCAATAACATGCTTATAGAAAATCAATACAGTAACAATTATCATGCTTATAAC
66 ATCAACATGGTAGCAATAACATGCTTATAGAAAATCAATACAGTAACAATTATCATGCTTATAAC
38391779 GGATCATTACAGTAGCAATAAACT
131 GGATCATTACAGTAGCAATAAACT
38391803 TGTTCATAATTTCTTCATTCATATCGTCCCACCCCATGCAATGAAACATGATATGCTTACAACAG
1 TGTTCATAATTTCTTCATTCATATCGTCCCACCCCATGCAATGAAACATGATATGCTTACAACAG
* * *
38391868 ATCAACATGGTAGTAATAACATGCTTGTAGCAAATCAATACAGTAACAATTATCATGCTTATAAC
66 ATCAACATGGTAGCAATAACATGCTTATAGAAAATCAATACAGTAACAATTATCATGCTTATAAC
38391933 GGATCATTACAGTAGCAATAAACT
131 GGATCATTACAGTAGCAATAAACT
38391957 TGTT
1 TGTT
38391961 TAACATGAGT
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (154 bp):
TGTTCATAATTTCTTCATTCATATCGTCCCACCCCATGCAATGAAACATGATATGCTTACAACAG
ATCAACATGGTAGCAATAACATGCTTATAGAAAATCAATACAGTAACAATTATCATGCTTATAAC
GGATCATTACAGTAGCAATAAACT
Found at i:38405610 original size:16 final size:18
Alignment explanation
Indices: 38405584--38405617 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
38405574 TCTAATTAAA
38405584 TAAATTAATTTTC-CAAT
1 TAAATTAATTTTCTCAAT
38405601 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
38405618 CCAATTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:38408616 original size:44 final size:44
Alignment explanation
Indices: 38408553--38408637 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
38408543 TCAAATAGTA
*
38408553 ATCAAGTCATTTATCACAAAGACAAATGACCTATGGCCACGTTT
1 ATCAAGTCATTTATCACAAAGACAAATGACCTATGACCACGTTT
38408597 ATCAAGTCATTTATCACAAAGACAAATGACCTATGACCACG
1 ATCAAGTCATTTATCACAAAGACAAATGACCTATGACCACG
38408638 CTTACTTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (44 bp):
ATCAAGTCATTTATCACAAAGACAAATGACCTATGACCACGTTT
Found at i:38419263 original size:23 final size:23
Alignment explanation
Indices: 38419233--38419278 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
38419223 TCACAATCTT
38419233 GTAGACAATGAACAACTAACATC
1 GTAGACAATGAACAACTAACATC
38419256 GTAGACAATGAACAACTAACATC
1 GTAGACAATGAACAACTAACATC
38419279 AAAGAGGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (23 bp):
GTAGACAATGAACAACTAACATC
Found at i:38419290 original size:23 final size:23
Alignment explanation
Indices: 38419235--38419283 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
38419225 ACAATCTTGT
**
38419235 AGACAATGAACAACTAACATCGT
1 AGACAATGAACAACTAACATCAA
38419258 AGACAATGAACAACTAACATCAA
1 AGACAATGAACAACTAACATCAA
38419281 AGA
1 AGA
38419284 GGCTGAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.14
Consensus pattern (23 bp):
AGACAATGAACAACTAACATCAA
Found at i:38425180 original size:39 final size:37
Alignment explanation
Indices: 38425137--38425211 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
38425127 TTTTTATCAC
*
38425137 AATTTATTTTATAATATTTAAAATAATAT-ATAATATTTA
1 AATTTATTTT-T-ATATAT-AAATAATATAATAATATTTA
*
38425176 AATTTATTTTTATATATAAATAATTTAATAATATTT
1 AATTTATTTTTATATATAAATAATATAATAATATTT
38425212 GTAAAAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 8 0.24
37 14 0.42
38 1 0.03
39 10 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (37 bp):
AATTTATTTTTATATATAAATAATATAATAATATTTA
Found at i:38429736 original size:17 final size:17
Alignment explanation
Indices: 38429714--38429907 Score: 169
Period size: 17 Copynumber: 11.4 Consensus size: 17
38429704 GCGAGCTATA
*
38429714 TTATATGCTAGCTATGT
1 TTATATGCTAGCTGTGT
38429731 TTATATG-TGAGCTGTGT
1 TTATATGCT-AGCTGTGT
*
38429748 TTATATGCTAGATGTGT
1 TTATATGCTAGCTGTGT
* *
38429765 TTATATGTTAGCTATGT
1 TTATATGCTAGCTGTGT
* * *
38429782 TTATATGCCAGATGTAT
1 TTATATGCTAGCTGTGT
* *
38429799 TTATATTCGAGCTGTGT
1 TTATATGCTAGCTGTGT
* *
38429816 TTATAT-ATGAGCTATGT
1 TTATATGCT-AGCTGTGT
* * *
38429833 TTATGTG-TGAGATGTAT
1 TTATATGCT-AGCTGTGT
* *
38429850 TTATATGCAAGATGTGT
1 TTATATGCTAGCTGTGT
*
38429867 TTATATGCGAGCTGTGT
1 TTATATGCTAGCTGTGT
* *
38429884 TTATATGCAAGTTGTGT
1 TTATATGCTAGCTGTGT
38429901 TTATATG
1 TTATATG
38429908 TGAGTCGTTT
Statistics
Matches: 144, Mismatches: 28, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
16 1 0.01
17 142 0.99
18 1 0.01
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (17 bp):
TTATATGCTAGCTGTGT
Found at i:38429757 original size:34 final size:34
Alignment explanation
Indices: 38429714--38429923 Score: 221
Period size: 34 Copynumber: 6.2 Consensus size: 34
38429704 GCGAGCTATA
* *
38429714 TTATATGCTAGCTATGTTTATATGTGAGCTGTGT
1 TTATATGCTAGATGTGTTTATATGTGAGCTGTGT
* *
38429748 TTATATGCTAGATGTGTTTATATGTTAGCTATGT
1 TTATATGCTAGATGTGTTTATATGTGAGCTGTGT
* *
38429782 TTATATGCCAGATGTATTTATAT-TCGAGCTGTGT
1 TTATATGCTAGATGTGTTTATATGT-GAGCTGTGT
* * * * * *
38429816 TTATAT-ATGAGCTATGTTTATGTGTGAGATGTAT
1 TTATATGCT-AGATGTGTTTATATGTGAGCTGTGT
* *
38429850 TTATATGCAAGATGTGTTTATATGCGAGCTGTGT
1 TTATATGCTAGATGTGTTTATATGTGAGCTGTGT
* *
38429884 TTATATGCAAGTTGTGTTTATATGTGAG-TCGT-T
1 TTATATGCTAGATGTGTTTATATGTGAGCT-GTGT
38429917 TTATATG
1 TTATATG
38429924 TGAATTGTGT
Statistics
Matches: 145, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
33 10 0.07
34 134 0.92
35 1 0.01
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (34 bp):
TTATATGCTAGATGTGTTTATATGTGAGCTGTGT
Found at i:38429777 original size:51 final size:51
Alignment explanation
Indices: 38429714--38429907 Score: 217
Period size: 51 Copynumber: 3.8 Consensus size: 51
38429704 GCGAGCTATA
* * * * *
38429714 TTATATGCTAGCTATGTTTATATGTGAGCTGTGTTTATATGCTAGATGTGT
1 TTATATGCGAGCTATGTTTATATGCGAGATGTATTTATATGCAAGATGTGT
** * * * *
38429765 TTATATGTTAGCTATGTTTATATGCCAGATGTATTTATATTCGAGCTGTGT
1 TTATATGCGAGCTATGTTTATATGCGAGATGTATTTATATGCAAGATGTGT
** * *
38429816 TTATATATGAGCTATGTTTATGTGTGAGATGTATTTATATGCAAGATGTGT
1 TTATATGCGAGCTATGTTTATATGCGAGATGTATTTATATGCAAGATGTGT
* * * *
38429867 TTATATGCGAGCTGTGTTTATATGCAAGTTGTGTTTATATG
1 TTATATGCGAGCTATGTTTATATGCGAGATGTATTTATATG
38429908 TGAGTCGTTT
Statistics
Matches: 119, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 119 1.00
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (51 bp):
TTATATGCGAGCTATGTTTATATGCGAGATGTATTTATATGCAAGATGTGT
Found at i:38429945 original size:16 final size:16
Alignment explanation
Indices: 38429879--38429949 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
38429869 ATATGCGAGC
* *
38429879 TGTGTTTATATGCAAGT
1 TGTG-TTATATGTAAAT
* *
38429896 TGTGTTTATATGTGAGT
1 TGTG-TTATATGTAAAT
* * *
38429913 CGTTTTATATGTGAAT
1 TGTGTTATATGTAAAT
38429929 TGTGTTATATGTAAAT
1 TGTGTTATATGTAAAT
38429945 TGTGT
1 TGTGT
38429950 CAATGTGTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
16 29 0.63
17 17 0.37
ACGTcount: A:0.23, C:0.03, G:0.24, T:0.51
Consensus pattern (16 bp):
TGTGTTATATGTAAAT
Found at i:38436812 original size:8 final size:8
Alignment explanation
Indices: 38436799--38436823 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38436789 CCTTAATTAT
38436799 TAATTTAC
1 TAATTTAC
38436807 TAATTTAC
1 TAATTTAC
38436815 TAATTTAC
1 TAATTTAC
38436823 T
1 T
38436824 CTTTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (8 bp):
TAATTTAC
Found at i:38438964 original size:21 final size:21
Alignment explanation
Indices: 38438916--38438967 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
38438906 TTTAAGAAGG
**
38438916 GGTATCGATA-TTTCAAAAAA
1 GGTATCGATACTTGAAAAAAA
*
38438936 --TATTGATACTTGAAAAAAA
1 GGTATCGATACTTGAAAAAAA
38438955 GGTATCGATACTT
1 GGTATCGATACTT
38438968 AATAGGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
21 10 0.40
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
GGTATCGATACTTGAAAAAAA
Found at i:38446577 original size:25 final size:26
Alignment explanation
Indices: 38446530--38446589 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
38446520 TTTAATTAAA
* *
38446530 TAAAAATTATTAATGATTCAAT-AAAT
1 TAAAAATTA-TAATAATTAAATAAAAT
38446556 TGAAAAATTA-AATAATTAAATAAAAT
1 T-AAAAATTATAATAATTAAATAAAAT
38446582 TAAAAATT
1 TAAAAATT
38446590 TAGGAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 16 0.53
26 6 0.20
27 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (26 bp):
TAAAAATTATAATAATTAAATAAAAT
Found at i:38447188 original size:17 final size:18
Alignment explanation
Indices: 38447161--38447194 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38447151 AATTAAATAT
38447161 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
*
38447179 ATGC-TATTAATTTATT
1 ATGCATATTAAATTATT
38447195 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:38447342 original size:109 final size:109
Alignment explanation
Indices: 38447198--38447399 Score: 286
Period size: 109 Copynumber: 1.9 Consensus size: 109
38447188 ATTTATTTAA
* *
38447198 AAATAAAATAAACTAATCCTAATTCTATGTTAAATTGATAAAAATTAATATATAAATTATAATAG
1 AAATAAAATAAACTAATCCTAACTCTATGTAAAATTGATAAAAATTAATATAT--ATTATAATAG
38447263 ATACAATTATATATTAA-AGATTATCATCTTATAAAAAAAACTTATC
64 ATACAATTATATATTAATA-ATTATCATCTTATAAAAAAAACTTATC
* * *
38447309 AAAT-AAA-AAACTATTCCTAACTCTA-GATAAAATTGATAATAATTAATATATATTATAATGGA
1 AAATAAAATAAACTAATCCTAACTCTATG-TAAAATTGATAAAAATTAATATATATTATAATAGA
*
38447371 TATAATTATATATTAATAATTATCATCTT
65 TACAATTATATATTAATAATTATCATCTT
38447400 TTTTATAATA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
107 36 0.43
108 2 0.02
109 38 0.46
110 3 0.04
111 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (109 bp):
AAATAAAATAAACTAATCCTAACTCTATGTAAAATTGATAAAAATTAATATATATTATAATAGAT
ACAATTATATATTAATAATTATCATCTTATAAAAAAAACTTATC
Found at i:38454247 original size:15 final size:13
Alignment explanation
Indices: 38454216--38454241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38454206 GACTTGAAAT
38454216 GAGAAAGTGAGAG
1 GAGAAAGTGAGAG
38454229 GAGAAAGTGAGAG
1 GAGAAAGTGAGAG
38454242 AGGAGAGAAG
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:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (13 bp):
GAGAAAGTGAGAG
Found at i:38460334 original size:13 final size:13
Alignment explanation
Indices: 38460317--38460372 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
38460307 GAGCACACGT
*
38460317 AAAACATATCTTT
1 AAAACATATCTTG
*
38460330 AAAACATAGCTTG
1 AAAACATATCTTG
*
38460343 AAAACATAACTTG
1 AAAACATATCTTG
* *
38460356 GAAACATATCCTG
1 AAAACATATCTTG
38460369 AAAA
1 AAAA
38460373 TAGAGTATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (13 bp):
AAAACATATCTTG
Found at i:38461012 original size:27 final size:27
Alignment explanation
Indices: 38460956--38461012 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
38460946 TTTGACTTTG
* *
38460956 ACTGGTGGACCTCTAGTTTGCAACTTA
1 ACTGGTGGACCTCTAGTTTGCAAATAA
*
38460983 ACTGGT-GATCTCTAGTTTGCCAAATAA
1 ACTGGTGGACCTCTAGTTTG-CAAATAA
38461010 ACT
1 ACT
38461013 ATCAAACACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (27 bp):
ACTGGTGGACCTCTAGTTTGCAAATAA
Found at i:38470782 original size:57 final size:58
Alignment explanation
Indices: 38470714--38470836 Score: 185
Period size: 57 Copynumber: 2.1 Consensus size: 58
38470704 TTTTTTAGGT
* *
38470714 CATTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAGTGATTCC-ATTTCTC
1 CATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCTATTTCTC
* * * *
38470771 TATTTTCATTTTTATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTC
1 CATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCTATTTCTC
38470829 CATTTTCA
1 CATTTTCA
38470837 CAATTTCTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 44 0.76
58 14 0.24
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (58 bp):
CATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCTATTTCTC
Found at i:38475842 original size:14 final size:14
Alignment explanation
Indices: 38475825--38475913 Score: 62
Period size: 14 Copynumber: 6.6 Consensus size: 14
38475815 TTTCATAAGA
38475825 CCATTTCCATATAT
1 CCATTTCCATATAT
* *
38475839 CCATAT-CATATTT
1 CCATTTCCATATAT
* * *
38475852 TC-TTTTCA-ATGT
1 CCATTTCCATATAT
*
38475864 CCATTT-CATA-AGA
1 CCATTTCCATATA-T
*
38475877 CCATTTCTATATAT
1 CCATTTCCATATAT
*
38475891 CCATTTCCATATGT
1 CCATTTCCATATAT
38475905 CCATTTCCA
1 CCATTTCCA
38475914 CCTGATAAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
12 8 0.14
13 19 0.33
14 29 0.51
15 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.03, T:0.44
Consensus pattern (14 bp):
CCATTTCCATATAT
Found at i:38478473 original size:253 final size:251
Alignment explanation
Indices: 38478025--38478509 Score: 666
Period size: 253 Copynumber: 1.9 Consensus size: 251
38478015 CCTCTTATAC
* * * *
38478025 AATCTTGGCCTTCTCAACTAGAATCTCAAACACCCTCTCTTGATGTGGTGCAACCTAAACCTTTA
1 AATCTTGACCTTCTCAACTAGAATCTCAAACACCCTCTCCTGATGTGGTACAACCTAAACCATTA
* * * * *
38478090 AATCATACCTCAGCCCATCCTCTAGCTGTACACACTTATTCTACTCAGTAGACACCATATCTGAA
66 AATCATACATCAACCCATCCTCGAGCTGTACACACTTATCCTACTCAGTAGACACCATATCCGAA
* * ** * * *
38478155 GCATAATGGCTCAACCTTAGAAACTTGGCCTCATACTCGACCACTGCCTTAACGCCCTGTTTTAG
131 GCATAATGGCTCAACCTCAAAAACTCAGCCTCATACTCGACCACTGCCTTAACACACTATTTTAG
* *
38478220 CTAAATAAACTCTATTCTACGAGCCTCAACATACCTCTTACTAGAACCTCAACTAG
196 CTAAATAAACTCCATTCTACAAGCCTCAACATACCTCTTACTAGAACCTCAACTAG
* * * * *
38478276 AATCTTGACCTTCTTAACTAGAATCTCAAACATCCTCTCCTGTTGTGGTACAA-ATCGAACCATT
1 AATCTTGACCTTCTCAACTAGAATCTCAAACACCCTCTCCTGATGTGGTACAACCT-AAACCATT
38478340 AAATCATACATCAACCCATCCTCGAGCTGTACACACACTTATCCTACTCAGTAGACACCATATCC
65 AAATCATACATCAACCCATCCTCGAGCTGT--ACACACTTATCCTACTCAGTAGACACCATATCC
* * * *
38478405 GAAGCGTAATGGCTCAACCTCAAAAACTCAGCTTCATACTCGACCACTGTCTTATCACACTATTT
128 GAAGCATAATGGCTCAACCTCAAAAACTCAGCCTCATACTCGACCACTGCCTTAACACACTATTT
* * *
38478470 TAGCTCAATAAACTCCATTCTATAAGGCTCAACATACCTC
193 TAGCTAAATAAACTCCATTCTACAAGCCTCAACATACCTC
38478510 ATACCAATGT
Statistics
Matches: 201, Mismatches: 30, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
250 1 0.00
251 80 0.40
253 120 0.60
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.28
Consensus pattern (251 bp):
AATCTTGACCTTCTCAACTAGAATCTCAAACACCCTCTCCTGATGTGGTACAACCTAAACCATTA
AATCATACATCAACCCATCCTCGAGCTGTACACACTTATCCTACTCAGTAGACACCATATCCGAA
GCATAATGGCTCAACCTCAAAAACTCAGCCTCATACTCGACCACTGCCTTAACACACTATTTTAG
CTAAATAAACTCCATTCTACAAGCCTCAACATACCTCTTACTAGAACCTCAACTAG
Found at i:38484149 original size:10 final size:10
Alignment explanation
Indices: 38484134--38484164 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
38484124 ACCATTTGCT
38484134 TATGAAATGA
1 TATGAAATGA
38484144 TATGAAATGA
1 TATGAAATGA
*
38484154 TATGAACTGA
1 TATGAAATGA
38484164 T
1 T
38484165 CTACGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (10 bp):
TATGAAATGA
Found at i:38485238 original size:11 final size:12
Alignment explanation
Indices: 38485205--38485251 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
38485195 AGTAAGGAAA
* *
38485205 AAAATAAAAGGG
1 AAAAGAAAAGAG
*
38485217 AAAAGAAAAGAT
1 AAAAGAAAAGAG
38485229 AAAA-AAAAGAG
1 AAAAGAAAAGAG
*
38485240 AAAAGAAGAGAG
1 AAAAGAAAAGAG
38485252 GTGTGACGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.04
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:38487532 original size:41 final size:41
Alignment explanation
Indices: 38487469--38487550 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
38487459 ACTTGAACCC
*
38487469 AAGACCTCAAACTACTCCACCACTGAAGCAGATAGCCACTT
1 AAGACCTCAAACTACTCCACCACTGAAGCAGATAGACACTT
* *
38487510 AAGACCTCAAACTCCTCTACCACTGAAGCAGATAGACACTT
1 AAGACCTCAAACTACTCCACCACTGAAGCAGATAGACACTT
38487551 GTGCTAGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.18
Consensus pattern (41 bp):
AAGACCTCAAACTACTCCACCACTGAAGCAGATAGACACTT
Found at i:38495256 original size:21 final size:21
Alignment explanation
Indices: 38495231--38495286 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
38495221 GTGAGGGTCT
*
38495231 CACATGCCCGTGTGCCCACCAA
1 CACATGCCCGTGTGCCCA-AAA
* *
38495253 -ACATGGCCGTGTACCCAAAA
1 CACATGCCCGTGTGCCCAAAA
*
38495273 CACACGCCCGTGTG
1 CACATGCCCGTGTG
38495287 GGATCTTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.25, C:0.39, G:0.21, T:0.14
Consensus pattern (21 bp):
CACATGCCCGTGTGCCCAAAA
Found at i:38514542 original size:71 final size:71
Alignment explanation
Indices: 38514425--38514568 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
38514415 ACAAATTAGA
38514425 GCTATGTAGTATAACATAGAAATTGTAATAGAATAATGCAAAGGAACAAATGAAACATAAGATTT
1 GCTATGTAGTATAACATAGAAATTGTAATAGAATAATGCAAAGGAACAAATGAAACATAAGATTT
38514490 GTTAAT
66 GTTAAT
*
38514496 GCTATGTAGTATAACATAGAAATTGTAATAGAATAATGCAATGGAACAAATGAAACATAAGATTT
1 GCTATGTAGTATAACATAGAAATTGTAATAGAATAATGCAAAGGAACAAATGAAACATAAGATTT
38514561 GTTAAT
66 GTTAAT
38514567 GC
1 GC
38514569 AATTTGAATA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (71 bp):
GCTATGTAGTATAACATAGAAATTGTAATAGAATAATGCAAAGGAACAAATGAAACATAAGATTT
GTTAAT
Found at i:38515030 original size:18 final size:16
Alignment explanation
Indices: 38515009--38515062 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 16
38514999 ATTAAATAAA
*
38515009 TTTTATAAATTTTATGTT
1 TTTTA-AAATTTTA-ATT
38515027 TTTTAATAATTTTAATT
1 TTTTAA-AATTTTAATT
38515044 TTTTAAAAATTTTAATT
1 TTTT-AAAATTTTAATT
38515061 TT
1 TT
38515063 AATTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTAAAATTTTAATT
Found at i:38522086 original size:16 final size:15
Alignment explanation
Indices: 38522067--38522100 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
38522057 TTTTTTTATT
38522067 AATTTTAAATTTTGAA
1 AATTTTAAATTTT-AA
38522083 AATTTTAAATTTTAA
1 AATTTTAAATTTTAA
38522098 AAT
1 AAT
38522101 AAATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AATTTTAAATTTTAA
Found at i:38522106 original size:19 final size:19
Alignment explanation
Indices: 38522082--38522120 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38522072 TAAATTTTGA
*
38522082 AAATTTTAAATTTTAAAAT
1 AAATTTTAAATTTCAAAAT
*
38522101 AAATTTTGAATTTCAAAAT
1 AAATTTTAAATTTCAAAAT
38522120 A
1 A
38522121 GAACTCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
AAATTTTAAATTTCAAAAT
Found at i:38523562 original size:28 final size:27
Alignment explanation
Indices: 38523486--38523562 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 27
38523476 TTACAATATT
*
38523486 AGAAGTTAGTTTTATATTTTTATTTTTA
1 AGAATTTAGTTTT-TATTTTTATTTTTA
*
38523514 AGAATTTAATTTCTT-TATTTTATTTTT-
1 AGAATTTAGTTT-TTAT-TTTTATTTTTA
38523541 AGAAATTTAGTCTTTTATTTTT
1 AG-AATTTAGT-TTTTATTTTT
38523563 TAAATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
27 3 0.07
28 34 0.83
29 4 0.10
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (27 bp):
AGAATTTAGTTTTTATTTTTATTTTTA
Found at i:38525551 original size:15 final size:16
Alignment explanation
Indices: 38525525--38525556 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38525515 TCTCGAAACA
38525525 TCTATCCCTTAAAATT
1 TCTATCCCTTAAAATT
38525541 TCTAT-CCTTAAAATT
1 TCTATCCCTTAAAATT
38525556 T
1 T
38525557 TGTTTGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (16 bp):
TCTATCCCTTAAAATT
Found at i:38527169 original size:21 final size:22
Alignment explanation
Indices: 38527127--38527169 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
38527117 TTATTCTCAA
* **
38527127 ATTTCTTCTTTTACTATTTTTG
1 ATTTCTTCTATTACTAAATTTG
38527149 ATTTCTT-TATTACTAAATTTG
1 ATTTCTTCTATTACTAAATTTG
38527170 TTTATTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.63
Consensus pattern (22 bp):
ATTTCTTCTATTACTAAATTTG
Found at i:38528978 original size:38 final size:38
Alignment explanation
Indices: 38528923--38528999 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
38528913 AGCTTGGAGC
38528923 TTTTGCTCATCGACACTAACAAGAAATCATCACCTCTT
1 TTTTGCTCATCGACACTAACAAGAAATCATCACCTCTT
* *
38528961 TTTTGCTCGTCGGCACTAACAAGAAATCATCACCTCTT
1 TTTTGCTCATCGACACTAACAAGAAATCATCACCTCTT
38528999 T
1 T
38529000 CTTCAACTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (38 bp):
TTTTGCTCATCGACACTAACAAGAAATCATCACCTCTT
Found at i:38531626 original size:12 final size:12
Alignment explanation
Indices: 38531611--38531635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38531601 AATCTCAAAA
38531611 ATAAATATTTTT
1 ATAAATATTTTT
38531623 ATAAATATTTTT
1 ATAAATATTTTT
38531635 A
1 A
38531636 AAAAAAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:38537408 original size:14 final size:14
Alignment explanation
Indices: 38537391--38537418 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38537381 AACAATCTTC
38537391 CTAAAATTATCAAA
1 CTAAAATTATCAAA
38537405 CTAAAATTATCAAA
1 CTAAAATTATCAAA
38537419 GTGTAAAATA
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:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (14 bp):
CTAAAATTATCAAA
Found at i:38540564 original size:11 final size:11
Alignment explanation
Indices: 38540550--38540624 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 11
38540540 GATAATCAGT
38540550 TTAATATTAAA
1 TTAATATTAAA
38540561 TTAATA--AAA
1 TTAATATTAAA
38540570 -TAATATTAAA
1 TTAATATTAAA
* *
38540580 ATAAGTATTATA
1 TTAA-TATTAAA
38540592 TTAA-ATTTAATA
1 TTAATA-TTAA-A
38540604 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
38540617 ATAATATT
1 TTAATATT
38540625 CTTTTTGGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
8 5 0.10
9 3 0.06
10 4 0.08
11 16 0.31
12 14 0.27
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:38542979 original size:323 final size:323
Alignment explanation
Indices: 38542386--38543034 Score: 1072
Period size: 323 Copynumber: 2.0 Consensus size: 323
38542376 CAACGCTTTG
* * * *
38542386 AGAAATTAGGCTAGGGATTAGATTTTCGACCTGGATGAACTCCAACTTGAGGTGGTCAAATTTTT
1 AGAAATCAGGCTAGGGATTAAATTTTCAACCTGGATGAACTCCAACTTGAGGTAGTCAAATTTTT
* * *
38542451 TCAGAAAATTTATGGAAAGTTGACGACTCAATGTGGAGATCTACCCTCTAATCCCTTCTCGCATC
66 TCAAAAAATTTATGAAAAGTTGACGACTCAATGTGGAGATCTACCCTCTAATCCCTTCCCGCATC
*
38542516 TTGATCATTGTGATAAGGGATTTTTGAGAAGGGGATTTCGAATGAGAAAATCAAGTGTGCTCTTT
131 TTGATCATTATGATAAGGGATTTTTGAGAAGGGGATTTCGAATGAGAAAATCAAGTGTGCTCTTT
* * * *
38542581 TTGACATGGCATCTCTAAAGGCTCCGTGTCACATCCTAAAAATTAGGTTAGTAGAAATTGGGTTA
196 TTGACATGGCACCTCTAAAGGCTCCGTGTCACATCCTAAAAATCAAGTTAGTAGAAATTGGGATA
38542646 ATGAACCGAGAATGGTCATGTCCAA-TTT-TTTTATGATCTTTTACTCATTTGATAATAAATA
261 ATGAACCGAGAATGGTCATGTCCAATTTTCTTTTATGATCTTTTACTCATTTGATAATAAATA
38542707 AGAAATCAGGCTAGGGATTAAATTTTCAACCTGGATGAACTCCAACTTGAGGTAGTCAAATTTTT
1 AGAAATCAGGCTAGGGATTAAATTTTCAACCTGGATGAACTCCAACTTGAGGTAGTCAAA-TTTT
*
38542772 TTCAAAAAATTTAT-AAAGAGTTG-CTGACTCAATGTGGAGATCTACCTTCTAATCCCTTCCCGC
65 TTCAAAAAATTTATGAAA-AGTTGAC-GACTCAATGTGGAGATCTACCCTCTAATCCCTTCCCGC
*
38542835 ATCTTGATCATTATGATAAGGGATTTTTGGAGAAGGGGATTTCGAATGAGGAAATCAAGTGTGCT
128 ATCTTGATCATTATGATAAGGGATTTTT-GAGAAGGGGATTTCGAATGAGAAAATCAAGTGTGCT
38542900 CTTTTTGACATGGCACCTCTAAAGGCTCCGTGTCACATCCTAAAAATCAAGTTAGTAGAAATTGG
192 CTTTTTGACATGGCACCTCTAAAGGCTCCGTGTCACATCCTAAAAATCAAGTTAGTAGAAATTGG
* * *
38542965 GATAATGAACCGAGAGTGGTCATGTCTAATTTTTCTTTTATGATCTTTTATTCATTTGATAATAA
257 GATAATGAACCGAGAATGGTCATGTCCAA-TTTTCTTTTATGATCTTTTACTCATTTGATAATAA
38543030 ATA
321 ATA
38543033 AG
1 AG
38543035 TATCAATTAT
Statistics
Matches: 304, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
321 59 0.19
322 85 0.28
323 123 0.40
325 3 0.01
326 34 0.11
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (323 bp):
AGAAATCAGGCTAGGGATTAAATTTTCAACCTGGATGAACTCCAACTTGAGGTAGTCAAATTTTT
TCAAAAAATTTATGAAAAGTTGACGACTCAATGTGGAGATCTACCCTCTAATCCCTTCCCGCATC
TTGATCATTATGATAAGGGATTTTTGAGAAGGGGATTTCGAATGAGAAAATCAAGTGTGCTCTTT
TTGACATGGCACCTCTAAAGGCTCCGTGTCACATCCTAAAAATCAAGTTAGTAGAAATTGGGATA
ATGAACCGAGAATGGTCATGTCCAATTTTCTTTTATGATCTTTTACTCATTTGATAATAAATA
Found at i:38543532 original size:19 final size:18
Alignment explanation
Indices: 38543498--38543533 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38543488 TCCACATTCA
*
38543498 TTTTTTTTTATTTTTTCT
1 TTTTTTTTTATCTTTTCT
38543516 TTTTTTTTTCATCTTTTC
1 TTTTTTTTT-ATCTTTTC
38543534 CATTCTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTATCTTTTCT
Found at i:38543897 original size:25 final size:25
Alignment explanation
Indices: 38543865--38543920 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
38543855 TCGAACGACT
38543865 GCCTCCGCCACTATAGCATCGTCAC
1 GCCTCCGCCACTATAGCATCGTCAC
38543890 GCCTCCGCCACTATAGCATCGTCAC
1 GCCTCCGCCACTATAGCATCGTCAC
38543915 GCCTCC
1 GCCTCC
38543921 ACCAGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.18, C:0.46, G:0.16, T:0.20
Consensus pattern (25 bp):
GCCTCCGCCACTATAGCATCGTCAC
Found at i:38548353 original size:45 final size:45
Alignment explanation
Indices: 38548289--38548376 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
38548279 AAGACAAATG
*
38548289 GTTAATGTGTCTAACCTTCCTCTATCAAGTGACTAGATTTTTTTA
1 GTTAATGCGTCTAACCTTCCTCTATCAAGTGACTAGATTTTTTTA
* *
38548334 GTTAATGCGTTTAACCTTCCTCTATCAAGTGACTGGATTTTTT
1 GTTAATGCGTCTAACCTTCCTCTATCAAGTGACTAGATTTTTT
38548377 ACACTCTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (45 bp):
GTTAATGCGTCTAACCTTCCTCTATCAAGTGACTAGATTTTTTTA
Found at i:38548856 original size:5 final size:5
Alignment explanation
Indices: 38548846--38548875 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
38548836 ATTTCTCACC
38548846 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
38548876 CAACTCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:38554854 original size:21 final size:21
Alignment explanation
Indices: 38554829--38554872 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
38554819 AATATCTCTA
38554829 TTTGATTTTATTCAAATTGAT
1 TTTGATTTTATTCAAATTGAT
*
38554850 TTTGATTTTATTCAATTTGAT
1 TTTGATTTTATTCAAATTGAT
38554871 TT
1 TT
38554873 AAAACTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTGATTTTATTCAAATTGAT
Found at i:38556806 original size:20 final size:21
Alignment explanation
Indices: 38556783--38556828 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
38556773 TTGATTCCTT
*
38556783 TTGATTT-TATAAGGACTAAA
1 TTGATTTGTACAAGGACTAAA
*
38556803 TTGATTTGTACAAGGACTAAT
1 TTGATTTGTACAAGGACTAAA
38556824 TTGAT
1 TTGAT
38556829 ACGATCCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (21 bp):
TTGATTTGTACAAGGACTAAA
Found at i:38556997 original size:6 final size:6
Alignment explanation
Indices: 38556986--38557017 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
38556976 ATCAAAACTT
*
38556986 ATCTTG ATCTTG ATCTTG ATCTTA ATCTTG AT
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG AT
38557018 AGACATCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (6 bp):
ATCTTG
Found at i:38572241 original size:5 final size:6
Alignment explanation
Indices: 38572214--38572248 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
38572204 GTTTCTCAAA
38572214 AAATGG AAATGG AAATGG AAAT-G AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG-G AAATG
38572249 ATCCATTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:38581254 original size:89 final size:89
Alignment explanation
Indices: 38581103--38581281 Score: 313
Period size: 89 Copynumber: 2.0 Consensus size: 89
38581093 GATCAATGTT
* *
38581103 ATCGTTATATTAACTTAAATCATGAAAGTACTACTAAGTTTTATCGCTTAATGTATGATTTGTTT
1 ATCGTTATATTAACTGAAATCATGAAAGTACTACTAAGTTTTATCGCTTAACGTATGATTTGTTT
* *
38581168 ATTCCGTGTGTAGGTTTCAGTAGA
66 ATTCCGTATATAGGTTTCAGTAGA
*
38581192 ATCGTTATATTAACTGAAATCATGAAAGTACTACTGAGTTTTATCGCTTAACGTATGATTTGTTT
1 ATCGTTATATTAACTGAAATCATGAAAGTACTACTAAGTTTTATCGCTTAACGTATGATTTGTTT
38581257 ATTCCGTATATAGGTTTCAGTAGA
66 ATTCCGTATATAGGTTTCAGTAGA
38581281 A
1 A
38581282 CTTGAAGACT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (89 bp):
ATCGTTATATTAACTGAAATCATGAAAGTACTACTAAGTTTTATCGCTTAACGTATGATTTGTTT
ATTCCGTATATAGGTTTCAGTAGA
Found at i:38582623 original size:18 final size:19
Alignment explanation
Indices: 38582580--38582628 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
38582570 GATATCAATT
**
38582580 TCACATTTTATTTTTAAAA
1 TCACATTTTATTTAAAAAA
*
38582599 T-AAATTTTA-TTAAAAAA
1 TCACATTTTATTTAAAAAA
38582616 TCACATTTT-TTTA
1 TCACATTTTATTTA
38582629 CATTTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
17 7 0.29
18 16 0.67
19 1 0.04
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (19 bp):
TCACATTTTATTTAAAAAA
Found at i:38583079 original size:18 final size:18
Alignment explanation
Indices: 38583056--38583090 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38583046 CACTCCTAAC
38583056 TTTAATCAAAT-TTTTATT
1 TTTAAT-AAATATTTTATT
38583074 TTTAATAAATATTTTAT
1 TTTAATAAATATTTTAT
38583091 ATTTGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATAAATATTTTATT
Found at i:38591305 original size:19 final size:19
Alignment explanation
Indices: 38591281--38591319 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
38591271 TTTTAAAATG
38591281 ATTCAAAATCAAGTGAGAT
1 ATTCAAAATCAAGTGAGAT
** *
38591300 ATTCAATTTCAAGTGTGAT
1 ATTCAAAATCAAGTGAGAT
38591319 A
1 A
38591320 AGTGGTCATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (19 bp):
ATTCAAAATCAAGTGAGAT
Found at i:38604716 original size:19 final size:20
Alignment explanation
Indices: 38604672--38604716 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
38604662 ATAATGTTCA
38604672 TATTTTTAACATAATTTAAT
1 TATTTTTAACATAATTTAAT
*
38604692 T-GTTTTATA-AT-ATTTAAT
1 TATTTTTA-ACATAATTTAAT
38604710 TATTTTT
1 TATTTTT
38604717 CGACAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 8 0.38
19 11 0.52
20 2 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTAACATAATTTAAT
Found at i:38611511 original size:25 final size:25
Alignment explanation
Indices: 38611483--38611552 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
38611473 CTCTTTTAAT
*
38611483 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
38611508 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
38611533 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
38611553 GCACTTCCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:38611611 original size:10 final size:10
Alignment explanation
Indices: 38611598--38611636 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
38611588 ATATATGAAT
38611598 ATATCATGGC
1 ATATCATGGC
38611608 ATATCATGTGC
1 ATATCATG-GC
*
38611619 AAATCATGGC
1 ATATCATGGC
38611629 ATATCATG
1 ATATCATG
38611637 TATAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
ATATCATGGC
Found at i:38618707 original size:19 final size:20
Alignment explanation
Indices: 38618663--38618707 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
38618653 ATAATGTTCA
38618663 TATTTTTAACATAATTTAAT
1 TATTTTTAACATAATTTAAT
*
38618683 T-GTTTTATA-AT-ATTTAAT
1 TATTTTTA-ACATAATTTAAT
38618701 TATTTTT
1 TATTTTT
38618708 TGACAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 8 0.38
19 11 0.52
20 2 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTAACATAATTTAAT
Found at i:38619079 original size:19 final size:20
Alignment explanation
Indices: 38619035--38619079 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
38619025 ATAATTTTCA
38619035 TATTTTTAACATAATTTAAT
1 TATTTTTAACATAATTTAAT
*
38619055 T-GTTTTATA-AT-ATTTAAT
1 TATTTTTA-ACATAATTTAAT
38619073 TATTTTT
1 TATTTTT
38619080 CGACAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 8 0.38
19 11 0.52
20 2 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTAACATAATTTAAT
Found at i:38623732 original size:40 final size:40
Alignment explanation
Indices: 38623688--38623951 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
38623678 GCTCCTCGTT
* *
38623688 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
38623728 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
38623768 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
38623808 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
38623848 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
38623887 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
38623928 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38623952 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:38635817 original size:17 final size:18
Alignment explanation
Indices: 38635785--38635818 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38635775 ATGTTTGCAT
*
38635785 GATTAATTTAGTAAAAAA
1 GATTAAATTAGTAAAAAA
38635803 GATTAAATT-GTAAAAA
1 GATTAAATTAGTAAAAA
38635819 GTGTAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (18 bp):
GATTAAATTAGTAAAAAA
Found at i:38636609 original size:82 final size:82
Alignment explanation
Indices: 38636485--38636637 Score: 270
Period size: 82 Copynumber: 1.9 Consensus size: 82
38636475 ATGTTTGGGA
**
38636485 TAAATTGGTAATTTTGGATAAATATGAAATATGGATTAAATTGAATACTAGAAATGGTTAATTGA
1 TAAATTGGTAATTTTAAATAAATATGAAATATGGATTAAATTGAATACTAGAAATGGTTAATTGA
38636550 TTAAAAAATATTAGGGG
66 TTAAAAAATATTAGGGG
* *
38636567 TAAATTGGTAATTTTAAATAAATATGAAATGTGGATTAAATTGAATACTAGAAGTGGTTAATTGA
1 TAAATTGGTAATTTTAAATAAATATGAAATATGGATTAAATTGAATACTAGAAATGGTTAATTGA
38636632 TTAAAA
66 TTAAAA
38636638 TTACTTATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.44, C:0.01, G:0.18, T:0.36
Consensus pattern (82 bp):
TAAATTGGTAATTTTAAATAAATATGAAATATGGATTAAATTGAATACTAGAAATGGTTAATTGA
TTAAAAAATATTAGGGG
Found at i:38649356 original size:9 final size:9
Alignment explanation
Indices: 38649338--38649371 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
38649328 AATTTAAATT
38649338 AAAT-TAAA
1 AAATATAAA
38649346 AAATATAAA
1 AAATATAAA
38649355 AAATATAAA
1 AAATATAAA
38649364 AAATATAA
1 AAATATAA
38649372 TAATATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATATAAA
Found at i:38659047 original size:15 final size:15
Alignment explanation
Indices: 38659027--38659055 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38659017 GTCTTATAAC
38659027 AAGTTAAATAACAAT
1 AAGTTAAATAACAAT
38659042 AAGTTAAATAACAA
1 AAGTTAAATAACAA
38659056 GTAAACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (15 bp):
AAGTTAAATAACAAT
Found at i:38659445 original size:19 final size:19
Alignment explanation
Indices: 38659398--38659457 Score: 79
Period size: 17 Copynumber: 3.2 Consensus size: 19
38659388 AATCTTTAAG
*
38659398 GATATGCAATCTTAGGTAT
1 GATATGCAATCTTAGATAT
38659417 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38659434 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
38659455 GAT
1 GAT
38659458 CTTGTAATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 16 0.44
19 11 0.31
21 9 0.25
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:38660278 original size:161 final size:161
Alignment explanation
Indices: 38660098--38660408 Score: 586
Period size: 161 Copynumber: 1.9 Consensus size: 161
38660088 TTCATTAAAT
38660098 GTATGTTCATGTTATTTAGTTTTGTCATAATGATATTATTTATGTTTGTATGGAAATGTTAAAAT
1 GTATGTTCATGTTATTTAGTTTTGTCATAATGATATTATTTATGTTTGTATGGAAATGTTAAAAT
38660163 ATTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCTAAAACGTCATTTAAAATAATAT
66 ATTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCTAAAACGTCATTTAAAATAATAT
38660228 TCCAAGGTTTATTTTAAAAAAAATAAAAGGC
131 TCCAAGGTTTATTTTAAAAAAAATAAAAGGC
* *
38660259 GTATGTTCATGTTATTTAGTTTTGTCTTAATGATATTATTTATGTTTGTATGGAAATGTTAGAAT
1 GTATGTTCATGTTATTTAGTTTTGTCATAATGATATTATTTATGTTTGTATGGAAATGTTAAAAT
*
38660324 ATTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCTAAAACGTCATTTAAAATACTAT
66 ATTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCTAAAACGTCATTTAAAATAATAT
*
38660389 TCCAAGGTTTTTTTTAAAAA
131 TCCAAGGTTTATTTTAAAAA
38660409 TAAAAATAAA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
161 146 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (161 bp):
GTATGTTCATGTTATTTAGTTTTGTCATAATGATATTATTTATGTTTGTATGGAAATGTTAAAAT
ATTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCTAAAACGTCATTTAAAATAATAT
TCCAAGGTTTATTTTAAAAAAAATAAAAGGC
Found at i:38661101 original size:24 final size:24
Alignment explanation
Indices: 38661070--38661144 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
38661060 AAACAAGTTG
*
38661070 CCATGTAGGTTGTGGACAAAGCCA
1 CCATGTAGGTTGTGGACGAAGCCA
* *
38661094 CCATGTAGGTCGTGGAGGAAGCCA
1 CCATGTAGGTTGTGGACGAAGCCA
* *
38661118 TCACGTAGGTTGTGGACGAAGCCA
1 CCATGTAGGTTGTGGACGAAGCCA
38661142 CCA
1 CCA
38661145 ATTCTTCCTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.27, C:0.23, G:0.32, T:0.19
Consensus pattern (24 bp):
CCATGTAGGTTGTGGACGAAGCCA
Found at i:38663012 original size:15 final size:15
Alignment explanation
Indices: 38662989--38663029 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
38662979 TCGATTCATT
*
38662989 AACCCAATTTCTACA
1 AACCTAATTTCTACA
*
38663004 AACCTAATTTCTACT
1 AACCTAATTTCTACA
38663019 AACCTAGATTT
1 AACCTA-ATTT
38663030 TGGGAAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (15 bp):
AACCTAATTTCTACA
Found at i:38664301 original size:40 final size:40
Alignment explanation
Indices: 38664216--38664485 Score: 174
Period size: 40 Copynumber: 6.8 Consensus size: 40
38664206 TTGGTTTGTT
* * * **
38664216 ATGAAATTATCGAGCTTTA-TGCCTAGTAGGCTTTGTATTG
1 ATGAATTTATCAAGC-TTAGTGCTTAGTAGGCTTTGTACCG
* *
38664256 GTGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTACCT
1 ATGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTACCG
* * * * *
38664296 ATGAATTTATCAAGCTTAATGTTTAGCAAGC-TTGATGCC-
1 ATGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTG-TACCG
* * ** * * * *
38664335 AGTGTAGTTATCGGGTTTTGTGCCTAGTAAGCTTTGTACCG
1 A-TGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTACCG
* * *
38664376 ATGAATTTATCAAGCTTAGTGCTTTGCAGGCTTTGTGCCG
1 ATGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTACCG
* * * ** * *
38664416 GTGTAGTTATCGGGCTTTGTGCCTA-TCAGGCTTTGTACCG
1 ATGAATTTATCAAGCTTAGTGCTTAGT-AGGCTTTGTACCG
* *
38664456 GTGAGTTTATCAA--TTAGTGCTTAGTAGGCT
1 ATGAATTTATCAAGCTTAGTGCTTAGTAGGCT
38664486 AAATTTCAGT
Statistics
Matches: 171, Mismatches: 52, Indels: 16
0.72 0.22 0.07
Matches are distributed among these distances:
38 13 0.08
39 8 0.05
40 146 0.85
41 4 0.02
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (40 bp):
ATGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTACCG
Found at i:38664363 original size:80 final size:80
Alignment explanation
Indices: 38664269--38664468 Score: 262
Period size: 80 Copynumber: 2.5 Consensus size: 80
38664259 AATTTATCAA
* * *
38664269 GCTTAGTGCTTAGTAGGCTTTGTACCTATGAATTTATCAAGCTTAATG-TTTAGCAAGC-TTGAT
1 GCTTTGTGCCTAGTAGGCTTTGTACCGATGAATTTATCAAGCTTAATGCTTT-GCAAGCTTTG-T
38664332 GCCAGTGTAGTTATCGG
64 GCCAGTGTAGTTATCGG
* * * *
38664349 GTTTTGTGCCTAGTAAGCTTTGTACCGATGAATTTATCAAGCTTAGTGCTTTGCAGGCTTTGTGC
1 GCTTTGTGCCTAGTAGGCTTTGTACCGATGAATTTATCAAGCTTAATGCTTTGCAAGCTTTGTGC
*
38664414 CGGTGTAGTTATCGG
66 CAGTGTAGTTATCGG
* *
38664429 GCTTTGTGCCTA-TCAGGCTTTGTACCGGTGAGTTTATCAA
1 GCTTTGTGCCTAGT-AGGCTTTGTACCGATGAATTTATCAA
38664469 TTAGTGCTTA
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
79 1 0.01
80 98 0.93
81 6 0.06
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (80 bp):
GCTTTGTGCCTAGTAGGCTTTGTACCGATGAATTTATCAAGCTTAATGCTTTGCAAGCTTTGTGC
CAGTGTAGTTATCGG
Found at i:38664544 original size:78 final size:79
Alignment explanation
Indices: 38664285--38664544 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 79
38664275 TGCTTAGTAG
* * * * **
38664285 GCTTTGTACCTATGAATTTATCAAGCTTAATGTTTAGCAAGCTTGATGCCAGTGTAGTTATCGGG
1 GCTTTGTACCGATGAATTTATCAA-CTTAGTGCTTAGCAGGCTAAATGCCAGTGTAGTTATCGGG
*
38664350 -TTTTGTGCCTAGTAA
65 CTTTT-TGCCTAGCAA
* *** *
38664365 GCTTTGTACCGATGAATTTATCAAGCTTAGTGCTTTGCAGGCTTTGTGCCGGTGTAGTTATCGGG
1 GCTTTGTACCGATGAATTTATCAA-CTTAGTGCTTAGCAGGCTAAATGCCAGTGTAGTTATCGGG
* * *
38664430 CTTTGTGCCTATCAG
65 CTTTTTGCCTAGCAA
* * * **
38664445 GCTTTGTACCGGTGAGTTTATCAA-TTAGTGCTTAGTAGGCTAAATTTCAGTGT-GATTATCGGG
1 GCTTTGTACCGATGAATTTATCAACTTAGTGCTTAGCAGGCTAAATGCCAGTGTAG-TTATCGGG
38664508 CTTTTTGCCTAGCAA
65 CTTTTTGCCTAGCAA
** *
38664523 GCTTTGTGTCGATGAACTTATC
1 GCTTTGTACCGATGAATTTATC
38664545 GGGCATAGCG
Statistics
Matches: 148, Mismatches: 30, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
77 1 0.01
78 58 0.39
80 86 0.58
81 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (79 bp):
GCTTTGTACCGATGAATTTATCAACTTAGTGCTTAGCAGGCTAAATGCCAGTGTAGTTATCGGGC
TTTTTGCCTAGCAA
Found at i:38668806 original size:13 final size:12
Alignment explanation
Indices: 38668787--38668846 Score: 66
Period size: 13 Copynumber: 4.7 Consensus size: 12
38668777 GCAATGCTTT
*
38668787 TGAAAAGTGTTG
1 TGAAAAGTGTTC
38668799 TGGAAAAGTGCTTC
1 T-GAAAAGTG-TTC
38668813 TGAAAAGTGTTTC
1 TGAAAAGTG-TTC
*
38668826 TGAAAAGTGCTTT
1 TGAAAAGTG-TTC
38668839 TGAAAAGT
1 TGAAAAGT
38668847 TTGGTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
12 1 0.02
13 38 0.90
14 3 0.07
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (12 bp):
TGAAAAGTGTTC
Found at i:38668810 original size:26 final size:26
Alignment explanation
Indices: 38668781--38668846 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 26
38668771 AGTTTAGCAA
38668781 TGCTTTTGAAAAGTGTTGT-GGAAAAG
1 TGCTTTTGAAAAGTGTT-TCGGAAAAG
* *
38668807 TGCTTCTGAAAAGTGTTTCTGAAAAG
1 TGCTTTTGAAAAGTGTTTCGGAAAAG
38668833 TGCTTTTGAAAAGT
1 TGCTTTTGAAAAGT
38668847 TTGGTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGTTTCGGAAAAG
Found at i:38674729 original size:24 final size:24
Alignment explanation
Indices: 38674702--38674776 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
38674692 AGATAAGCTG
*
38674702 CCATGTAGGTTGTGGACAAAGCCA
1 CCATGTAGATTGTGGACAAAGCCA
* * *
38674726 CCATGTAGCTCGTGGAGAAAGCCA
1 CCATGTAGATTGTGGACAAAGCCA
**
38674750 CCATGTAGATTGTGGATGAAGCCA
1 CCATGTAGATTGTGGACAAAGCCA
38674774 CCA
1 CCA
38674777 ATTCCTCCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (24 bp):
CCATGTAGATTGTGGACAAAGCCA
Found at i:38681142 original size:21 final size:21
Alignment explanation
Indices: 38681116--38681161 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
38681106 ATTTTTAAAA
*
38681116 AAAAATAAAATAATAATAACT
1 AAAAATAAAATAAAAATAACT
*
38681137 AAAAATAAAATAAAAATAATT
1 AAAAATAAAATAAAAATAACT
38681158 AAAA
1 AAAA
38681162 CAAACAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAATAAAATAAAAATAACT
Found at i:38681150 original size:11 final size:11
Alignment explanation
Indices: 38681111--38681155 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
38681101 TTTCCATTTT
38681111 TAAAA-AAAAA
1 TAAAATAAAAA
*
38681121 TAAAATAATAA
1 TAAAATAAAAA
*
38681132 T-AACTAAAAA
1 TAAAATAAAAA
38681142 TAAAATAAAAA
1 TAAAATAAAAA
38681153 TAA
1 TAA
38681156 TTAAAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 13 0.45
11 16 0.55
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:38681180 original size:27 final size:26
Alignment explanation
Indices: 38681112--38681187 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
38681102 TTCCATTTTT
*
38681112 AAAAA-AAAATAAAATAA-TAATAACT
1 AAAAATAAAATAAAATAATTAA-AACA
38681137 AAAAATAAAATAAAAATAATTAAAACA
1 AAAAATAAAAT-AAAATAATTAAAACA
*
38681164 AACAAATGAAAAT-AAATATTTAAA
1 AA-AAAT-AAAATAAAATAATTAAA
38681188 CTTTTAAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 5 0.11
26 5 0.11
27 22 0.50
28 7 0.16
29 5 0.11
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (26 bp):
AAAAATAAAATAAAATAATTAAAACA
Found at i:38694707 original size:729 final size:729
Alignment explanation
Indices: 38692818--38696426 Score: 6563
Period size: 729 Copynumber: 5.0 Consensus size: 729
38692808 AAAACTCAAG
38692818 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
1 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
*
38692883 TGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
66 CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
* *
38692948 AAAATTACATGTAACAGCCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCTGA
131 AAAATTACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCCGA
*
38693013 GTTAAAAATAAAAAT-AAAA--A--TTATTTTATTTTATTTTATGGTTGGCATCATGATAAGAAG
196 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
38693073 GTCACAT-AAAATTTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAA
261 GTCACATGAAAA-TTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAA
38693137 TTGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAAC
325 TTGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAAC
38693202 TTAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCC
390 TTAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCC
38693267 ATGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTC
455 ATGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTC
*
38693332 CCAAAATTTATATGGAAACCCTAGGAGAGACGTAGACAACTTACCAAGCTTGAAAAGGTATGAAA
520 CCAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAA
*
38693397 TCAAGTCCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGG
585 TCAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGG
38693462 GGATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGA
650 GGATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGA
38693527 TATTTATGGTAGAAA
715 TATTTATGGTAGAAA
38693542 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGC-AAAAAAAAA
1 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
*
38693606 GGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
66 CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
* *
38693671 AAAATAACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTGGTTTCGGGACCACAAATCCGA
131 AAAATTACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCCGA
38693736 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
196 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
38693801 GTCACATGAAAATTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAAT
261 GTCACATGAAAATTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAAT
* *
38693866 TGCATAAAATGCAAAAGTTGGATTATAGTAGCTATGGGTATCAAATAGCTATAAAATTCAAAACT
326 TGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAACT
*
38693931 TAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATCTTAATGACTCATCCA
391 TAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCCA
38693996 TGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTCC
456 TGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTCC
38694061 CAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAAT
521 CAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAAT
38694126 CAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGGG
586 CAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGGG
38694191 GATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGAT
651 GATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGAT
38694256 ATTTATGGTAGAAA
716 ATTTATGGTAGAAA
38694270 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
1 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
*
38694335 TGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
66 CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
* *
38694400 AAAATTACATGTAACAGCCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCTGA
131 AAAATTACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCCGA
38694465 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
196 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
38694530 GTCACAT-AAAATTTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAA
261 GTCACATGAAAA-TTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAA
38694594 TTGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAAC
325 TTGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAAC
38694659 TTAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCC
390 TTAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCC
38694724 ATGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTC
455 ATGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTC
38694789 CCAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAA
520 CCAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAA
38694854 TCAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGG
585 TCAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGG
38694919 GGATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGA
650 GGATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGA
38694984 TATTTATGGTAGAAA
715 TATTTATGGTAGAAA
*
38694999 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCACAAAAAAAA
1 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
38695064 CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
66 CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
*
38695129 AAAATTACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTGGTTTCGGGACCACAAATCCGA
131 AAAATTACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCCGA
38695194 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
196 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
38695259 GTCACATGAAAATTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAAT
261 GTCACATGAAAATTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAAT
38695324 TGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAACT
326 TGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAACT
38695389 TAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCCA
391 TAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCCA
38695454 TGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTCC
456 TGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTCC
38695519 CAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAAT
521 CAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAAT
38695584 CAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGGG
586 CAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGGG
38695649 GATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGAT
651 GATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGAT
38695714 ATTTATGGTAGAAA
716 ATTTATGGTAGAAA
38695728 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGC-AAAAAAAAA
1 GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
38695792 CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAA--T--C-
66 CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
38695852 -----T--A-G---CAA---AA-----AT-A-----G--T-G--GTTTCGGGACCACAAATCCGA
131 AAAATTACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCCGA
38695887 GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATA
196 GTTAAAAATAAAAAT-AAAA--A--TTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATA
38695952 GGAAGGTCACATGAAAATTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGAC
256 GGAAGGTCACATGAAAATTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGAC
*
38696017 TACATTGCATAAAATGA-AAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTC
321 TAAATTGCATAAAAT-ACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTC
* *
38696081 AAAACTTAAGGTCCTTATGTGGTAATTAGGCCATTGAATTGTAGCTAGTACATATTTTAATGACT
385 AAAACTTAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACT
* *
38696146 CATCCATGGAAAAATTAGAAAAGGCAAGTGACTAAATTAGAAATCACTAAAATTAAAAGAATCTT
450 CATCCATGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCAT
* *
38696211 CTTTCCCAAAATTTCTATGGAAACCCTAGGAGAGAGGTAGA-AACCTTACCAAGCTTGAAAAGAT
515 CTTTCCCAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAA-CTTACCAAGCTTGAAAAGGT
* *
38696275 GTGAAATCAAGTCCCGTTTTTAATGATTTTTATATTTTTTTAAACTAGGATAATCTAATCTCTCT
579 ATGAAATCAAGTTCCGTTTTTAATGATTTTTATA-TTTTTTAAACTAGGATAATCTAATCTCTCT
*
38696340 ATTTAGGGGATTAATTTGAAAAGTTATCAAGGTATGAAATTTGGGTCATGGATGAATATGCTGAA
643 ATTTAGGGGATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAA
38696405 AATTTGATATTTATGGTAGAAA
708 AATTTGATATTTATGGTAGAAA
38696427 ATGAAAAGTT
Statistics
Matches: 2833, Mismatches: 35, Indels: 59
0.97 0.01 0.02
Matches are distributed among these distances:
693 36 0.01
694 4 0.00
695 1 0.00
696 2 0.00
697 2 0.00
698 384 0.14
699 117 0.04
703 1 0.00
704 2 0.00
709 2 0.00
712 3 0.00
715 1 0.00
716 1 0.00
718 1 0.00
723 149 0.05
724 60 0.02
726 2 0.00
728 623 0.22
729 1438 0.51
730 4 0.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (729 bp):
GACTTTGGAACGTTTTTAATGGAGTGGGTTAAAATTAATAAGGGGCTATGTAAGCAAAAAAAAAA
CGGAAGAGTTGAATTCAAGATTAAGTTGGTTAAATAATGAAGACCTTGATGAAGAAAATCTAGCA
AAAATTACATGTAACAACCCAATTTTGATGAGGTCGGAATAGTAGTTTCGGGACCACAAATCCGA
GTTAAAAATAAAAATAAAAATTATTTTATTTTATTTTATTTTATGGTTGGCATCATGATAGGAAG
GTCACATGAAAATTTTGATACGAAAATTTTATCGATTGTGTGGTTAATTAGGTAAAGGACTAAAT
TGCATAAAATACAAAAGTTGGATTATAGTAGCTATAGGTATCAAATAGCTATAAAATTCAAAACT
TAAGGTCCTTATATGGTAATTAGACCATTGAATTGTAGCTAGTACATATTTTAATGACTCATCCA
TGGAAAAATTAGAAAAGGCAAGTGACTAAATTGGAAATCACTAAAATTAAAAGAATCATCTTTCC
CAAAATTTATATGGAAACCCTAGGAGAGAGGTAGACAACTTACCAAGCTTGAAAAGGTATGAAAT
CAAGTTCCGTTTTTAATGATTTTTATATTTTTTAAACTAGGATAATCTAATCTCTCTATTTAGGG
GATTAATTTGAAAAGTTATCAAGGTATGAAATTTGCGTCATGGATGAATATGCTGAAAATTTGAT
ATTTATGGTAGAAA
Found at i:38695915 original size:5 final size:5
Alignment explanation
Indices: 38695907--38695935 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
38695897 AAAATAAAAA
38695907 TTATT TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTAT
38695936 GGTTGGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:38719581 original size:13 final size:13
Alignment explanation
Indices: 38719563--38719587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38719553 CTAAAAGTAC
38719563 AAAAATCATCAAG
1 AAAAATCATCAAG
38719576 AAAAATCATCAA
1 AAAAATCATCAA
38719588 AATCACTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:38722461 original size:23 final size:22
Alignment explanation
Indices: 38722434--38722485 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
38722424 AATTAAATAA
*
38722434 ATTATAATTACAAATTATATAATT
1 ATTATAATTA-AAAATAT-TAATT
*
38722458 -TTATATTTAAAAATATTAATT
1 ATTATAATTAAAAATATTAATT
38722479 ATTATAA
1 ATTATAA
38722486 AATTTATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 5 0.21
22 11 0.46
23 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTATAATTAAAAATATTAATT
Found at i:38729479 original size:38 final size:38
Alignment explanation
Indices: 38729429--38729524 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 38
38729419 CCAACTCCGT
* * *
38729429 CCAACCCAGCACACCATGTGGGGATAAAATCGACCCAC
1 CCAACCCTGCACACCATATGGGGATAAAATCAACCCAC
* *
38729467 CCATCCCTGCACACCATATATGGGGATAAAATCAACCCAT
1 CCAACCCTGCACACC--ATATGGGGATAAAATCAACCCAC
*
38729507 CCAACCCTACACACCATA
1 CCAACCCTGCACACCATA
38729525 AAGTACTGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
38 16 0.33
40 33 0.67
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (38 bp):
CCAACCCTGCACACCATATGGGGATAAAATCAACCCAC
Found at i:38732139 original size:46 final size:44
Alignment explanation
Indices: 38732088--38732264 Score: 183
Period size: 46 Copynumber: 3.9 Consensus size: 44
38732078 ATGGTTGAGC
*
38732088 ATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
*** * * *
38732132 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTGGGC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TGCGA
* * *
38732181 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* *
38732225 CCACCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 --ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38732265 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 68 0.63
47 31 0.29
48 1 0.01
49 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:38732245 original size:93 final size:93
Alignment explanation
Indices: 38732086--38732256 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
38732076 GGATGGTTGA
***
38732086 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
38732151 TGAGTCCGAGTTCGAGAGATGTAACTGG
66 TGAGTCCGAGTTCGAGAGATGTAACTGG
* * * *
38732179 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGC-AACCACCCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAA-CACCCGAACTCGTTGAG
38732243 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
38732257 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTGG
Found at i:38747039 original size:43 final size:44
Alignment explanation
Indices: 38746976--38747141 Score: 139
Period size: 43 Copynumber: 3.9 Consensus size: 44
38746966 GATTACCGAG
** * *
38746976 ATGTGATTACATG-AAGACCATGTATGGGACATTGGCATTGTAT
1 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * *
38747019 -TGTGATTATGTGTAAGACCATGTTTAGGATATTGGCATCGTTAT
1 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCG-TAT
* *
38747063 AT-T-ATT-TCGTGTAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 ATGTGATTAT-GTGTAAGACCATGTCTGGGACATTGGCATCGTAT
* ** * *
38747104 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCAT
38747142 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
41 4 0.04
42 18 0.18
43 72 0.73
44 4 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (44 bp):
ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:38752141 original size:29 final size:29
Alignment explanation
Indices: 38752108--38752167 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
38752098 ATAATGATAT
38752108 GTGCAAATGTGCGTAGGTATTCATGTGTG
1 GTGCAAATGTGCGTAGGTATTCATGTGTG
38752137 GTGCAAATGTGCGTAGGTATTCATGTGTG
1 GTGCAAATGTGCGTAGGTATTCATGTGTG
38752166 GT
1 GT
38752168 ATGGTTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (29 bp):
GTGCAAATGTGCGTAGGTATTCATGTGTG
Found at i:38754062 original size:15 final size:15
Alignment explanation
Indices: 38754042--38754073 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38754032 GTCAGTCCAA
*
38754042 TCAGTCACGTTTATG
1 TCAGTCACATTTATG
38754057 TCAGTCACATTTATG
1 TCAGTCACATTTATG
38754072 TC
1 TC
38754074 TCTATCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (15 bp):
TCAGTCACATTTATG
Found at i:38755322 original size:57 final size:57
Alignment explanation
Indices: 38755234--38755348 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
38755224 TGTGATCGAT
38755234 ATCTCTGACTTCTTTTGGTCCTTAAGCTAGATAGGCGACACTATAAGAAAATGAAAA
1 ATCTCTGACTTCTTTTGGTCCTTAAGCTAGATAGGCGACACTATAAGAAAATGAAAA
* * *
38755291 ATCTCTGACTTCTTTTGGTCTTTGAGCTAGATAGGCGGCACTATAAGAAAATGAAAA
1 ATCTCTGACTTCTTTTGGTCCTTAAGCTAGATAGGCGACACTATAAGAAAATGAAAA
38755348 A
1 A
38755349 GGAGAGGGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (57 bp):
ATCTCTGACTTCTTTTGGTCCTTAAGCTAGATAGGCGACACTATAAGAAAATGAAAA
Found at i:38756015 original size:49 final size:49
Alignment explanation
Indices: 38755962--38756056 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
38755952 CTCATAACAT
38755962 GACCCATGTGTTGATTTTTGAGTTGTGTTGCAAGAAACCTTTGGTTGTG
1 GACCCATGTGTTGATTTTTGAGTTGTGTTGCAAGAAACCTTTGGTTGTG
*
38756011 GACCCATGTGTTGATTTTTGAGTTGTGTTGCAAGAAACTTTTGGTT
1 GACCCATGTGTTGATTTTTGAGTTGTGTTGCAAGAAACCTTTGGTT
38756057 ATGCTCTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (49 bp):
GACCCATGTGTTGATTTTTGAGTTGTGTTGCAAGAAACCTTTGGTTGTG
Found at i:38757233 original size:27 final size:27
Alignment explanation
Indices: 38757200--38757378 Score: 241
Period size: 27 Copynumber: 6.6 Consensus size: 27
38757190 TAAATTGTGC
38757200 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
38757227 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
38757254 AGCACTAAGTGTGCGAGTTTGACTATAT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
*
38757282 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
38757309 AGCACTAAGTGTGCGAGTTTGATTATGC
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
38757337 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
38757364 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
38757379 GACTTAATAT
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
27 89 0.65
28 48 0.35
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:38757288 original size:55 final size:55
Alignment explanation
Indices: 38757200--38757378 Score: 270
Period size: 55 Copynumber: 3.3 Consensus size: 55
38757190 TAAATTGTGC
* *
38757200 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
* *
38757254 AGCACTAAGTGTGCGAGTTTGACTATATAGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
* * * *
38757309 AGCACTAAGTGTGCGAGTTTGATTATGCAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
*
38757364 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
38757379 GACTTAATAT
Statistics
Matches: 114, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 16 0.14
55 98 0.86
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
Found at i:38757363 original size:82 final size:82
Alignment explanation
Indices: 38757200--38757378 Score: 288
Period size: 82 Copynumber: 2.2 Consensus size: 82
38757190 TAAATTGTGC
*
38757200 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGAATATGCAGCACTAAGTG
38757265 TGCGAGTTTGACTATAT
66 TGCGAGTTTGACTATAT
* * *
38757282 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGCAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGA-ATTGAATATGCAGCACTAAGT
*
38757347 GTGCGAG-TTGATTATAT
65 GTGCGAGTTTGACTATAT
*
38757364 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
38757379 GACTTAATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 65 0.72
83 25 0.28
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGAATATGCAGCACTAAGTG
TGCGAGTTTGACTATAT
Found at i:38760222 original size:20 final size:17
Alignment explanation
Indices: 38760186--38760225 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
38760176 TTTTTAATTA
38760186 TTTTTATTTTTTCCTTT
1 TTTTTATTTTTTCCTTT
38760203 TTTTTATTTGTTAGTCCTTT
1 TTTTTATTT-TT--TCCTTT
38760223 TTT
1 TTT
38760226 CGTTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
20 9 0.45
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTTCCTTT
Found at i:38766146 original size:62 final size:62
Alignment explanation
Indices: 38766065--38766194 Score: 172
Period size: 62 Copynumber: 2.1 Consensus size: 62
38766055 GTGTGAACGA
*
38766065 CCGTATAACACACTGTTCATTATATAAAACCACACGGACAAGGACACAGG-CGTGTACCCAGG
1 CCGTGTAACACACTGTTCATTATATAAAACCACACGGACAAGGACA-AGGACGTGTACCCAGG
* * * * * *
38766127 CCGTGTAACTCACTGTTCATTGTATAAAACCACACGGCCAGGGACATGGACGTGTGCCCAGG
1 CCGTGTAACACACTGTTCATTATATAAAACCACACGGACAAGGACAAGGACGTGTACCCAGG
*
38766189 CAGTGT
1 CCGTGT
38766195 GGCTTACTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 2 0.03
62 57 0.97
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (62 bp):
CCGTGTAACACACTGTTCATTATATAAAACCACACGGACAAGGACAAGGACGTGTACCCAGG
Found at i:38772408 original size:25 final size:22
Alignment explanation
Indices: 38772351--38772415 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 22
38772341 TTCTATTATT
38772351 TTTTTCTTTTTCCTTCTTTTTC
1 TTTTTCTTTTTCCTTCTTTTTC
*
38772373 TTTCTCCCTTTCTTCCTTCTTTATTC
1 TTT-T-TCTTT-TTCCTTCTTT-TTC
38772399 TATTTTCTTTTTACCTT
1 T-TTTTCTTTTT-CCTT
38772416 TTCCCTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 3 0.09
23 1 0.03
24 6 0.17
25 18 0.51
26 5 0.14
27 2 0.06
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTCTTTTTCCTTCTTTTTC
Found at i:38773241 original size:62 final size:62
Alignment explanation
Indices: 38772975--38773228 Score: 328
Period size: 62 Copynumber: 4.1 Consensus size: 62
38772965 CCATGTGAAC
* * * * * *
38772975 GGCCATGTAACTCACAATTTATTGTATAAAACCACACGGCCAGGGACACGGGCATGTGTCCA
1 GGCCGTGTAACTCACTATTCATTGTATAAAACCACACGGCCAGGGACATGGGCATATGCCCA
* * *
38773037 GGCCGTGTAACTCACTATTCATTGTATAAAACCTCGCGGCCAGGGACATGGGCGTATGCCCA
1 GGCCGTGTAACTCACTATTCATTGTATAAAACCACACGGCCAGGGACATGGGCATATGCCCA
* * *
38773099 GGCCGTGTAACTCACTATTCATTGTATAAAACCAAACGGCCAGGGATATGAGCATATGCCCA
1 GGCCGTGTAACTCACTATTCATTGTATAAAACCACACGGCCAGGGACATGGGCATATGCCCA
* * * ** ** *
38773161 AGCCGTGTAACTCACTGTTCATAGTATAAAACCACATAGCCAGGGACATGGGTGTGTGCCCA
1 GGCCGTGTAACTCACTATTCATTGTATAAAACCACACGGCCAGGGACATGGGCATATGCCCA
38773223 GGCCGT
1 GGCCGT
38773229 ATGATTTACT
Statistics
Matches: 165, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 165 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (62 bp):
GGCCGTGTAACTCACTATTCATTGTATAAAACCACACGGCCAGGGACATGGGCATATGCCCA
Found at i:38777493 original size:23 final size:19
Alignment explanation
Indices: 38777447--38777522 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 19
38777437 TTTTGATATC
* *
38777447 TACATAATTTAAA-AAAAA
1 TACATAAATTAAATATAAA
38777465 TACATAAATTAAATATAAA
1 TACATAAATTAAATATAAA
*
38777484 TATCTGCATAATTTAAA-A-AAA
1 TA----CATAAATTAAATATAAA
38777505 TACATAAATTAAATATAA
1 TACATAAATTAAATATAA
38777523 TTAATTTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
17 10 0.21
18 13 0.28
19 8 0.17
21 5 0.11
22 1 0.02
23 10 0.21
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.32
Consensus pattern (19 bp):
TACATAAATTAAATATAAA
Found at i:38777513 original size:40 final size:41
Alignment explanation
Indices: 38777442--38777522 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 41
38777432 AGACATTTTG
38777442 ATATCTACATAATTTAAAAAAAATACATAAATTAAATATAA
1 ATATCTACATAATTTAAAAAAAATACATAAATTAAATATAA
*
38777483 ATATCTGCATAATTT-AAAAAAATACATAAATTAAATATAA
1 ATATCTACATAATTTAAAAAAAATACATAAATTAAATATAA
38777523 TTAATTTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 25 0.64
41 14 0.36
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.32
Consensus pattern (41 bp):
ATATCTACATAATTTAAAAAAAATACATAAATTAAATATAA
Found at i:38778279 original size:14 final size:14
Alignment explanation
Indices: 38778262--38778305 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
38778252 TTATAAAACA
38778262 AATAGTAAACAAAT
1 AATAGTAAACAAAT
*
38778276 AATAATAAACAAAT
1 AATAGTAAACAAAT
*
38778290 AA-AGAAAAACAAAT
1 AATAG-TAAACAAAT
38778304 AA
1 AA
38778306 ATAAAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 1 0.04
14 25 0.96
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.16
Consensus pattern (14 bp):
AATAGTAAACAAAT
Found at i:38778306 original size:14 final size:14
Alignment explanation
Indices: 38778268--38778339 Score: 65
Period size: 14 Copynumber: 4.8 Consensus size: 14
38778258 AACAAATAGT
*
38778268 AAACAAATAATA-AT
1 AAACAAATAA-AGAA
38778282 AAACAAATAAAGAA
1 AAACAAATAAAGAA
38778296 AAACAAATAAATAAAGAA
1 AAAC----AAATAAAGAA
*
38778314 AAAGGAAATAAAGAA
1 AAA-CAAATAAAGAA
38778329 AAACAAATAAA
1 AAACAAATAAA
38778340 AATAGAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
13 1 0.02
14 22 0.45
15 13 0.27
18 13 0.27
ACGTcount: A:0.76, C:0.06, G:0.07, T:0.11
Consensus pattern (14 bp):
AAACAAATAAAGAA
Found at i:38778321 original size:25 final size:25
Alignment explanation
Indices: 38778268--38778417 Score: 92
Period size: 26 Copynumber: 5.7 Consensus size: 25
38778258 AACAAATAGT
38778268 AAACAAATAATAATAAACAAATAAA-GAA
1 AAACAAAT-A-AATAAA-AAA-AAAGGAA
*
38778296 AAACAAATAAATAAAGAAAAAGGAA
1 AAACAAATAAATAAAAAAAAAGGAA
* *
38778321 ATAA-AGAA-AAACAAATAAAAATAGAAA
1 A-AACA-AATAAATAAA-AAAAA-AGGAA
* *
38778348 AAGGACAAACAAATAAAAAAAAAGAAA
1 AA--ACAAATAAATAAAAAAAAAGGAA
* *
38778375 AATACAAACAAATAAAAAAACA-GAA
1 AA-ACAAATAAATAAAAAAAAAGGAA
*
38778400 AAAGGAAATAAATAAAAA
1 AAA-CAAATAAATAAAAA
38778418 TAAATAAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
24 4 0.04
25 29 0.28
26 33 0.32
27 13 0.13
28 16 0.16
29 7 0.07
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.09
Consensus pattern (25 bp):
AAACAAATAAATAAAAAAAAAGGAA
Found at i:38778322 original size:19 final size:18
Alignment explanation
Indices: 38778286--38778349 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
38778276 AATAATAAAC
38778286 AAATAAAGAAAAACAAAT
1 AAATAAAGAAAAACAAAT
**
38778304 AAATAAAG--AAA-AAGG
1 AAATAAAGAAAAACAAAT
38778319 AAATAAAGAAAAACAAAT
1 AAATAAAGAAAAACAAAT
38778337 AAA-AATAGAAAAA
1 AAATAA-AGAAAAA
38778350 GGACAAACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 10 0.26
16 3 0.08
17 5 0.13
18 20 0.53
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.09
Consensus pattern (18 bp):
AAATAAAGAAAAACAAAT
Found at i:38778324 original size:33 final size:33
Alignment explanation
Indices: 38778286--38778352 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
38778276 AATAATAAAC
38778286 AAATAAAGAAAAACAAATAAATAA-AGAAAAAGG
1 AAATAAAGAAAAACAAATAAA-AATAGAAAAAGG
38778319 AAATAAAGAAAAACAAATAAAAATAGAAAAAGG
1 AAATAAAGAAAAACAAATAAAAATAGAAAAAGG
38778352 A
1 A
38778353 CAAACAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (33 bp):
AAATAAAGAAAAACAAATAAAAATAGAAAAAGG
Found at i:38778384 original size:51 final size:50
Alignment explanation
Indices: 38778329--38778427 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 50
38778319 AAATAAAGAA
*
38778329 AAACAAAT-AAAAATAGAAAAAGGACAAACAAATAAAAAAAAAGAAAAATAC
1 AAACAAATAAAAAACAGAAAAAGG--AAACAAATAAAAAAAAAGAAAAATAC
* * *
38778380 AAACAAATAAAAAAACAGAAAAAGGAAATAAATAAAAATAAATAAAAA
1 AAACAAAT-AAAAAACAGAAAAAGGAAACAAATAAAAAAAAAGAAAAA
38778428 AACATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 28 0.67
53 14 0.33
ACGTcount: A:0.78, C:0.06, G:0.07, T:0.09
Consensus pattern (50 bp):
AAACAAATAAAAAACAGAAAAAGGAAACAAATAAAAAAAAAGAAAAATAC
Found at i:38778402 original size:35 final size:35
Alignment explanation
Indices: 38778362--38778438 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
38778352 ACAAACAAAT
* *
38778362 AAAAAAAAAGAAAAATACAAACAAATAAAAAAACAG
1 AAAAAGAAA-AAAAATAAAAACAAATAAAAAAACAG
* * * *
38778398 AAAAAGGAAATAAATAAAAATAAATAAAAAAACAT
1 AAAAAGAAAAAAAATAAAAACAAATAAAAAAACAG
38778433 AAAAAG
1 AAAAAG
38778439 GACAATAGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 28 0.80
36 7 0.20
ACGTcount: A:0.79, C:0.05, G:0.06, T:0.09
Consensus pattern (35 bp):
AAAAAGAAAAAAAATAAAAACAAATAAAAAAACAG
Found at i:38778418 original size:10 final size:10
Alignment explanation
Indices: 38778358--38778437 Score: 51
Period size: 10 Copynumber: 7.9 Consensus size: 10
38778348 AAGGACAAAC
*
38778358 AAATAAAAAA
1 AAATAAAAAT
*
38778368 AAAGAAAAAT
1 AAATAAAAAT
*
38778378 ACAA-ACAAAT
1 A-AATAAAAAT
*
38778388 AAA-AAAACAG
1 AAATAAAA-AT
38778398 AAA-AAGGAAAT
1 AAATAA--AAAT
38778409 AAATAAAAAT
1 AAATAAAAAT
38778419 AAATAAAAA-
1 AAATAAAAAT
38778428 AACATAAAAA
1 AA-ATAAAAA
38778438 GGACAATAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 7 0.12
10 41 0.71
11 6 0.10
12 4 0.07
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:38778439 original size:35 final size:36
Alignment explanation
Indices: 38778374--38778445 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
38778364 AAAAAAAGAA
*
38778374 AAATACAAACAAATAAAAAAACAGAAAAAGGA-AAT
1 AAATAAAAACAAATAAAAAAACAGAAAAAGGACAAT
* *
38778409 AAATAAAAATAAATAAAAAAACATAAAAAGGACAAT
1 AAATAAAAACAAATAAAAAAACAGAAAAAGGACAAT
38778445 A
1 A
38778446 GGCAATAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.11
Consensus pattern (36 bp):
AAATAAAAACAAATAAAAAAACAGAAAAAGGACAAT
Found at i:38780438 original size:46 final size:46
Alignment explanation
Indices: 38780342--38780461 Score: 129
Period size: 46 Copynumber: 2.6 Consensus size: 46
38780332 CGAGGGCTAG
* *
38780342 TGTAAGACATGTCTGGGAGATGCATCAGCCTCGAGACGTAAGTCAG
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGTCAA
* *
38780388 TGTAAGACATGTCTGGGACATGCATCCG-CTAC-AGGATG-ATAGTCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCT-CGA-GACGTA-AGTCAA
*
38780434 TGTAAGACCATGTCTTGGACATGGCATC
1 TGTAAGA-CATGTCTGGGACAT-GCATC
38780462 GACTTGAGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
45 4 0.06
46 42 0.66
47 13 0.20
48 5 0.08
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGTCAA
Found at i:38780485 original size:47 final size:47
Alignment explanation
Indices: 38780292--38780509 Score: 130
Period size: 47 Copynumber: 4.7 Consensus size: 47
38780282 TATGAGAACT
* * * *
38780292 AGTGTAAGACCATGT-TTGGGACATGGCATCGAAATTGAGACGA-GGGCT
1 AGTGTAAGACCATGTCTT-GGACATGGCATCG-ACTTGAGA-TATGAGCC
* * * * ** * *
38780340 AGTGTAAGA-CATGTCTGGGAGAT-GCATCAGCCTCGAGACGTAAGTC
1 AGTGTAAGACCATGTCTTGGACATGGCATC-GACTTGAGATATGAGCC
* ** *
38780386 AGTGTAAGA-CATGTCTGGGACAT-GCATCCG-CTACAGGATGAT-AGTC
1 AGTGTAAGACCATGTCTTGGACATGGCAT-CGACTTGA-GAT-ATGAGCC
*
38780432 AATGTAAGACCATGTCTTGGACATGGCATCGACTTGAGATATGAGCC
1 AGTGTAAGACCATGTCTTGGACATGGCATCGACTTGAGATATGAGCC
* *
38780479 AGTGTAAGACCATG-CCTGCGATATGGCATCG
1 AGTGTAAGACCATGTCTTG-GACATGGCATCG
38780510 GCACCTTACC
Statistics
Matches: 135, Mismatches: 24, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
45 3 0.02
46 57 0.42
47 58 0.43
48 17 0.13
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTTGGACATGGCATCGACTTGAGATATGAGCC
Found at i:38787423 original size:21 final size:22
Alignment explanation
Indices: 38787399--38787446 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
38787389 GAAGTTGTTA
38787399 TAAGAGT-AAAAATAGTTTAGC
1 TAAGAGTAAAAAATAGTTTAGC
**
38787420 TAAGCTTAAAAAAATAGTTTAGC
1 TAAGAGT-AAAAAATAGTTTAGC
38787443 TAAG
1 TAAG
38787447 CTTAAGAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
23 18 0.78
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (22 bp):
TAAGAGTAAAAAATAGTTTAGC
Found at i:38787436 original size:23 final size:23
Alignment explanation
Indices: 38787406--38787451 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
38787396 TTATAAGAGT
38787406 AAAAATAGTTTAGCTAAGCTTAA
1 AAAAATAGTTTAGCTAAGCTTAA
38787429 AAAAATAGTTTAGCTAAGCTTAA
1 AAAAATAGTTTAGCTAAGCTTAA
38787452 GAGGAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (23 bp):
AAAAATAGTTTAGCTAAGCTTAA
Found at i:38787942 original size:46 final size:46
Alignment explanation
Indices: 38787891--38788056 Score: 176
Period size: 46 Copynumber: 3.6 Consensus size: 46
38787881 TGTGAGCTAG
* *
38787891 TGTAAGACATGTCTGGGACATGCATCTGCCTT-ATTATGAGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCTGCCTTGA-GATGAGAGCCAA
* * * * * * *
38787937 TGTAAGACCATGTTTTGGACATGGCATCGGCATTGAGACGAGGGCTAA
1 TGTAAGA-CATGTCTGGGACAT-GCATCTGCCTTGAGATGAGAGCCAA
*
38787985 TGTAAGACATGTCTGGGACATGCAT-TGGCCTTGAGATGTA-AGTCAA
1 TGTAAGACATGTCTGGGACATGCATCT-GCCTTGAGATG-AGAGCCAA
38788031 TGTAAGACATGTCTGGGACATGCATC
1 TGTAAGACATGTCTGGGACATGCATC
38788057 CGCTACGGGA
Statistics
Matches: 97, Mismatches: 17, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
46 48 0.49
47 25 0.26
48 23 0.24
49 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCTGCCTTGAGATGAGAGCCAA
Found at i:38788075 original size:46 final size:46
Alignment explanation
Indices: 38787891--38788104 Score: 141
Period size: 46 Copynumber: 4.6 Consensus size: 46
38787881 TGTGAGCTAG
* * * * *
38787891 TGTAAGACATGTCTGGGACATGCATCTGCCT-TATTATG-AGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCCGCCTCGA-GATGTA-AGTCAA
* * * * * * * *
38787937 TGTAAGACCATGTTTTGGACATGGCATCGGCATTGAGACG-AGGGCTAA
1 TGTAAGA-CATGTCTGGGACAT-GCATCCGCCTCGAGATGTAAGTC-AA
** *
38787985 TGTAAGACATGTCTGGGACATGCATTGGCCTTGAGATGTAAGTCAA
1 TGTAAGACATGTCTGGGACATGCATCCGCCTCGAGATGTAAGTCAA
* *
38788031 TGTAAGACATGTCTGGGACATGCATCCG-CTACGGGATG-ATAGTCAG
1 TGTAAGACATGTCTGGGACATGCATCCGCCT-CGAGATGTA-AGTCAA
*
38788077 TGTAAGGCCATGTCTGGGACATGGCATC
1 TGTAA-GACATGTCTGGGACAT-GCATC
38788105 AAATTAAGAT
Statistics
Matches: 136, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
45 3 0.02
46 64 0.47
47 44 0.32
48 24 0.18
49 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCCGCCTCGAGATGTAAGTCAA
Found at i:38796015 original size:26 final size:24
Alignment explanation
Indices: 38795984--38796033 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
38795974 AAATAAAAAA
*
38795984 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
38796010 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
38796034 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:38796053 original size:21 final size:21
Alignment explanation
Indices: 38796004--38796062 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
38795994 ATAATAAATC
*
38796004 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
38796024 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
38796046 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
38796063 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:38796144 original size:21 final size:22
Alignment explanation
Indices: 38796093--38796146 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
38796083 TTAACAATAT
* **
38796093 AATAAAAAATAGTTATATTAAA
1 AATAAAAAATAATTATAAAAAA
**
38796115 AATTTAAAATAATT-TAAAAAA
1 AATAAAAAATAATTATAAAAAA
38796136 AATAAAAAATA
1 AATAAAAAATA
38796147 TATATTAATA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAAAAATAATTATAAAAAA
Found at i:38798825 original size:13 final size:13
Alignment explanation
Indices: 38798807--38798831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38798797 GTTCTTTATT
38798807 TTTTTTATTTTTA
1 TTTTTTATTTTTA
38798820 TTTTTTATTTTT
1 TTTTTTATTTTT
38798832 TGCAGTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:38801195 original size:10 final size:10
Alignment explanation
Indices: 38801180--38801204 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38801170 AGAAAGTGGG
38801180 GAGGGGAAGA
1 GAGGGGAAGA
38801190 GAGGGGAAGA
1 GAGGGGAAGA
38801200 GAGGG
1 GAGGG
38801205 CAAAGGTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (10 bp):
GAGGGGAAGA
Done.