Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 7 of 106
Found at i:3242713 original size:18 final size:15
Alignment explanation
Indices: 3242652--3242701 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
3242642 ATTAAAAAAT
3242652 TAAA-AAATAAT-AA
1 TAAATAAATAATAAA
3242665 TAAATGAAA-AATAAA
1 TAAAT-AAATAATAAA
3242680 TAAAT-AATAATAAA
1 TAAATAAATAATAAA
3242694 TAATATAA
1 TAA-ATAA
3242702 TTGAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 6 0.19
14 12 0.39
15 12 0.39
16 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
TAAATAAATAATAAA
Found at i:3257617 original size:2 final size:2
Alignment explanation
Indices: 3257612--3257656 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3257602 TCTAAGATAG
* *
3257612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3257654 AT A
1 AT A
3257657 ATGTGTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3262036 original size:15 final size:15
Alignment explanation
Indices: 3262018--3262056 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3262008 CTTTACTTTC
*
3262018 AATCATATTATTTAT
1 AATCATATTATGTAT
3262033 AATCATATTATGTAT
1 AATCATATTATGTAT
3262048 AATCATATT
1 AATCATATT
3262057 GCATTGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (15 bp):
AATCATATTATGTAT
Found at i:3270076 original size:23 final size:23
Alignment explanation
Indices: 3270032--3270076 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3270022 GAATCTCTTA
* *
3270032 TAATTTTATAACAATAATATAAT
1 TAATTTTATAAAAATAAGATAAT
3270055 TAATTTTATTAAAAAT-AGATAA
1 TAATTTTA-TAAAAATAAGATAA
3270077 AAATTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATTTTATAAAAATAAGATAAT
Found at i:3277263 original size:9 final size:9
Alignment explanation
Indices: 3277232--3277290 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
3277222 CTTGTGAGAA
3277232 TGGCAATGG
1 TGGCAATGG
*
3277241 TGGCATTGG
1 TGGCAATGG
*
3277250 AGGCAATGG
1 TGGCAATGG
**
3277259 TGGCAGCGG
1 TGGCAATGG
* *
3277268 AGGCAATAG
1 TGGCAATGG
3277277 TGGCAATGG
1 TGGCAATGG
*
3277286 GGGCA
1 TGGCA
3277291 GCCTGAAAGT
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.24, C:0.14, G:0.46, T:0.17
Consensus pattern (9 bp):
TGGCAATGG
Found at i:3277290 original size:18 final size:18
Alignment explanation
Indices: 3277233--3277290 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
3277223 TTGTGAGAAT
*
3277233 GGCAATGGTGGCATTGGA
1 GGCAATGGTGGCAATGGA
**
3277251 GGCAATGGTGGCAGCGGA
1 GGCAATGGTGGCAATGGA
* *
3277269 GGCAATAGTGGCAATGGG
1 GGCAATGGTGGCAATGGA
3277287 GGCA
1 GGCA
3277291 GCCTGAAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.24, C:0.14, G:0.47, T:0.16
Consensus pattern (18 bp):
GGCAATGGTGGCAATGGA
Found at i:3312860 original size:33 final size:33
Alignment explanation
Indices: 3312818--3312885 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
3312808 GTTTGGAAGT
* *
3312818 GGAGGAAGTGGCTTCTTATAAACTGGAACTGGA
1 GGAGGAAGTGGCTTCGTATAAACCGGAACTGGA
* **
3312851 GGAGGAAGTGGTTTCGTATATTCCGGAACTGGA
1 GGAGGAAGTGGCTTCGTATAAACCGGAACTGGA
3312884 GG
1 GG
3312886 GGGTTTATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.12, G:0.37, T:0.25
Consensus pattern (33 bp):
GGAGGAAGTGGCTTCGTATAAACCGGAACTGGA
Found at i:3312921 original size:57 final size:57
Alignment explanation
Indices: 3312841--3312951 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
3312831 TCTTATAAAC
** *
3312841 TGGAACTGGAGGAGGAAGTGGTTTCGTATATTCCGGAACTGGAGGGGGTTTATAGAT
1 TGGAACTGGAGGAGGAAGTGGTTTCGTATAGACCGGAACTGGAGGGGCTTTATAGAT
* * *
3312898 TGGAACTGGGGGAGGAAGTGGTTTCTTGTAGACCGGAACTGGAGGGGCTTTATA
1 TGGAACTGGAGGAGGAAGTGGTTTCGTATAGACCGGAACTGGAGGGGCTTTATA
3312952 TACTGGAGGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (57 bp):
TGGAACTGGAGGAGGAAGTGGTTTCGTATAGACCGGAACTGGAGGGGCTTTATAGAT
Found at i:3313102 original size:72 final size:72
Alignment explanation
Indices: 3312898--3313104 Score: 292
Period size: 72 Copynumber: 2.9 Consensus size: 72
3312888 GTTTATAGAT
* * * *
3312898 TGGAACTGGGGGAGGAAGTGGTTTCTTGTAGACCGGAACTGGAGG-GGCTTTATATACTGGAGGC
1 TGGAACTGGGGGAGGAAGTGGCTTCTTGTATACCGGAACTGGAGGAGG-TTTATAGACTGGGGGC
3312962 TTGTAAAC
65 TTGTAAAC
* *
3312970 TGGAACTGGGGGAGGAAGTGGCTTCTTGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCT
1 TGGAACTGGGGGAGGAAGTGGCTTCTTGTATACCGGAACTGGAGGAGGTTTATAGACTGGGGGCT
**
3313035 TGTATTC
66 TGTAAAC
* *
3313042 TGGAACTGGAGGG-GGAAGTGGCTTCTCGTATACGGGAACTGGAGGAGGTTTATAGACTGGGGG
1 TGGAACTGG-GGGAGGAAGTGGCTTCTTGTATACCGGAACTGGAGGAGGTTTATAGACTGGGGG
3313105 AGGAAGTGGT
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
72 117 0.96
73 5 0.04
ACGTcount: A:0.22, C:0.12, G:0.40, T:0.26
Consensus pattern (72 bp):
TGGAACTGGGGGAGGAAGTGGCTTCTTGTATACCGGAACTGGAGGAGGTTTATAGACTGGGGGCT
TGTAAAC
Found at i:3313110 original size:51 final size:50
Alignment explanation
Indices: 3313046--3313155 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 50
3313036 GTATTCTGGA
* *
3313046 ACTGGAGGGGGAAGTGGCTTCTCGTATACGGGAACTGGAGGAGGTTTATAG
1 ACTGG-GGGGGAAGTGGCTTCTCGTATACGGGAACCGGAGGAGGGTTATAG
* *
3313097 ACTGGGGGAGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGGTTATAG
1 ACTGGGGG-GGAAGTGGCTTCTCGTATACGGGAACCGGAGGAGGGTTATAG
3313148 ACTGGGGG
1 ACTGGGGG
3313156 CTTGTAAACT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 3 0.06
51 51 0.94
ACGTcount: A:0.23, C:0.12, G:0.43, T:0.23
Consensus pattern (50 bp):
ACTGGGGGGGAAGTGGCTTCTCGTATACGGGAACCGGAGGAGGGTTATAG
Found at i:3313124 original size:123 final size:123
Alignment explanation
Indices: 3312974--3313227 Score: 445
Period size: 123 Copynumber: 2.1 Consensus size: 123
3312964 GTAAACTGGA
* *
3312974 ACTGGGGGAGGAAGTGGCTTCTTGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGTA
1 ACTGGGGGAGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGGTTATAGACTGGGGGCTTGTA
** *
3313039 TTCTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACGGGAACTGGAGGAGGTTTATAG
66 AACTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACGGGAACCGGAGGAGGTTTATAG
*
3313097 ACTGGGGGAGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGGTTATAGACTGGGGGCTTGTA
1 ACTGGGGGAGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGGTTATAGACTGGGGGCTTGTA
*
3313162 AACTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAG
66 AACTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACGGGAACCGGAGGAGGTTTATAG
3313220 ACTGGGGG
1 ACTGGGGG
3313228 CTTGTAAACT
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.24
Consensus pattern (123 bp):
ACTGGGGGAGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGGTTATAGACTGGGGGCTTGTA
AACTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACGGGAACCGGAGGAGGTTTATAG
Found at i:3313173 original size:72 final size:72
Alignment explanation
Indices: 3313097--3313500 Score: 679
Period size: 72 Copynumber: 5.6 Consensus size: 72
3313087 AGGTTTATAG
*
3313097 ACTGG-GGGAGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGGTTATAGACTGGGGGCTTGT
1 ACTGGAGGG-GGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGT
3313161 AAACTGGA
65 AAACTGGA
*
3313169 ACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGTA
1 ACTGGAGGGGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGTA
3313234 AACTGGA
66 AACTGGA
3313241 ACTGG-GGGAGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGT
1 ACTGGAGGG-GGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGT
3313305 AAACTGGA
65 AAACTGGA
*
3313313 ACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGTA
1 ACTGGAGGGGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGTA
*
3313378 CACTGGA
66 AACTGGA
*
3313385 ACTGG-GGGAGGAAGTGGTTTCTCGTATACTGGAACTGGAGGAGGTTTATAGACTGGGGGCTTGT
1 ACTGGAGGG-GGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGT
**
3313449 ATTCTGGA
65 AAACTGGA
* *
3313457 ACTGGAGGGGGAAGTGGTTTCTCGTATACTGGAACTGGGGGAGG
1 ACTGGAGGGGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGG
3313501 AAGTGGCTTC
Statistics
Matches: 317, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
71 6 0.02
72 302 0.95
73 9 0.03
ACGTcount: A:0.23, C:0.13, G:0.40, T:0.25
Consensus pattern (72 bp):
ACTGGAGGGGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGTA
AACTGGA
Found at i:3313173 original size:195 final size:194
Alignment explanation
Indices: 3312836--3313299 Score: 648
Period size: 195 Copynumber: 2.3 Consensus size: 194
3312826 TGGCTTCTTA
* *
3312836 TAAACTGGAACTGGAGGAGGAAGTGGTT-TCGTATATTCCGGAACTGGAGGGGGTTTATAGATTG
1 TAAACTGGAACTGGAGGGGGAAGTGGTTCTCGTATA--CCGGAACTGGAGGAGGTTTAT--A---
* * * *
3312900 GAACTGGGGGAGGAAGTGGTTTCTTGTAGACCGGAACTGGAGGGGCTTTATATACTGGAGGCTTG
59 G-ACTGGGGGAGGAAGTGGTTTCTCGTAGACCGGAACCGGAGGGGCGTTATAGACTGGAGGCTTG
*
3312965 TAAACTGGAACTGG-GGGAGGAAGTGGCTTCTTGTATACTGGAACCGGAGGAGGTTTATAGACTG
123 TAAACTGGAACTGGAGGG-GGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTG
3313029 GGGGCTTG
187 GGGGCTTG
** *
3313037 TATTCTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACGGGAACTGGAGGAGGTTTATAGACTGG
1 TAAACTGGAACTGGAGGGGGAAGTGG-TTCTCGTATACCGGAACTGGAGGAGGTTTATAGACTGG
* * *
3313102 GGGAGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGG-GTTATAGACTGGGGGCTTGTAAACT
65 GGGAGGAAGTGGTTTCTCGTAGACCGGAACCGGAGG-GGCGTTATAGACTGGAGGCTTGTAAACT
3313166 GGAACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTT
129 GGAACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTT
3313231 G
194 G
* *
3313232 TAAACTGGAACTGG-GGGAGGAAGTGGTTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTG
1 TAAACTGGAACTGGAGGG-GGAAGTGG-TTCTCGTATACCGGAACTGGAGGAGGTTTATAGACTG
3313296 GGGG
64 GGGG
3313300 CTTGTAAACT
Statistics
Matches: 240, Mismatches: 18, Indels: 16
0.88 0.07 0.06
Matches are distributed among these distances:
194 3 0.01
195 179 0.75
196 6 0.03
199 1 0.00
201 42 0.17
202 2 0.01
203 7 0.03
ACGTcount: A:0.23, C:0.12, G:0.39, T:0.25
Consensus pattern (194 bp):
TAAACTGGAACTGGAGGGGGAAGTGGTTCTCGTATACCGGAACTGGAGGAGGTTTATAGACTGGG
GGAGGAAGTGGTTTCTCGTAGACCGGAACCGGAGGGGCGTTATAGACTGGAGGCTTGTAAACTGG
AACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTG
Found at i:3313281 original size:105 final size:106
Alignment explanation
Indices: 3313163--3313602 Score: 443
Period size: 105 Copynumber: 4.1 Consensus size: 106
3313153 GGGCTTGTAA
*
3313163 ACTGGAACTGGAGGG-GGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGG
1 ACTGGAACTGGAGGGAGGAAGTGGCTTCTCGTATACTGGAACTGGAGGAGGTTTATAGACTGGGG
*
3313227 GCTTGTAAACTGGAACTGG-GGGAGGAAGTGGTTTCTCGTAT
66 GCTTGTATACTGGAACTGGAGGG-GGAAGTGGTTTCTCGTAT
* *** * * *
3313268 ACTGGAACCGGA-GGAGGTTTATAGACTGGGGGCTTGTAAACTGGAACTGGAGG-GG--GA-AG-
1 ACTGGAACTGGAGGGAGG---A-AG--TGGCTTCTCGTATACTGGAACTGGAGGAGGTTTATAGA
*** * * * *** * *
3313327 -TGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGGCTTGTAC
60 CTGGGGGCTTGTATACTGGAACTGGAGG-GG--GA-AG--TGGTTTCTCGTAT
*
3313379 ACTGGAACTGG-GGGAGGAAGTGGTTTCTCGTATACTGGAACTGGAGGAGGTTTATAGACTGGGG
1 ACTGGAACTGGAGGGAGGAAGTGGCTTCTCGTATACTGGAACTGGAGGAGGTTTATAGACTGGGG
*
3313443 GCTTGTATTCTGGAACTGGAGGGGGAAGTGGTTTCTCGTAT
66 GCTTGTATACTGGAACTGGAGGGGGAAGTGGTTTCTCGTAT
* *
3313484 ACTGGAACTGG-GGGAGGAAGTGGCTTCTTGTATACTGGAACTGGAGGAGGTTTATAGACTGGAG
1 ACTGGAACTGGAGGGAGGAAGTGGCTTCTCGTATACTGGAACTGGAGGAGGTTTATAGACTGGGG
* * *
3313548 GCTTGTAGACTGGAACTGGAGGGGGAAGTGGCTTCTTGTAT
66 GCTTGTATACTGGAACTGGAGGGGGAAGTGGTTTCTCGTAT
3313589 ACTGGAACTGGAGG
1 ACTGGAACTGGAGG
3313603 AAGTTTATAA
Statistics
Matches: 267, Mismatches: 46, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
104 2 0.01
105 170 0.64
106 7 0.03
107 7 0.03
108 6 0.02
109 6 0.02
110 4 0.01
111 65 0.24
ACGTcount: A:0.23, C:0.13, G:0.39, T:0.25
Consensus pattern (106 bp):
ACTGGAACTGGAGGGAGGAAGTGGCTTCTCGTATACTGGAACTGGAGGAGGTTTATAGACTGGGG
GCTTGTATACTGGAACTGGAGGGGGAAGTGGTTTCTCGTAT
Found at i:3313494 original size:177 final size:176
Alignment explanation
Indices: 3313307--3313677 Score: 550
Period size: 177 Copynumber: 2.1 Consensus size: 176
3313297 GGGCTTGTAA
*
3313307 ACTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGGGG
1 ACTGGAACTGG-GGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGAGG
* * *
3313372 CTTGTACACTGGAACTGG-GGGAGGAAGTGGTTTCTCGTATACTGGAACTGGAGGAGGTTTATAG
65 CTTGTACACTGGAACTGGAGGG-GGAAGTGGCTTCTCGTATACTGGAACTGGAGGAAGTTTATAA
** *
3313436 ACTGGG-GGCTTGTATTCTGGAACTGGAGGGGGAAGTGGTTTCTCGTAT
129 AC-GGGAGGCTTGTAAACTGGAACTGGAGGAGGAAGTGGTTTCTCGTAT
* *
3313484 ACTGGAACTGGGGGAGGAAGTGGCTTCTTGTATACTGGAACTGGAGGAGGTTTATAGACTGGAGG
1 ACTGGAACTGGGGG-GGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGAGG
* *
3313549 CTTGTAGACTGGAACTGGAGGGGGAAGTGGCTTCTTGTATACTGGAACTGGAGGAAGTTTATAAA
65 CTTGTACACTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACTGGAGGAAGTTTATAAA
* *
3313614 CGGGAGGCTTGTAAACTGGAACTGGAGGAGGAAGTGGTTTTTTGTAT
130 CGGGAGGCTTGTAAACTGGAACTGGAGGAGGAAGTGGTTTCTCGTAT
3313661 A-TCGGAACTGGTGGGGG
1 ACT-GGAACTGG-GGGGG
3313678 TTTGTATATT
Statistics
Matches: 176, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
176 7 0.04
177 163 0.93
178 6 0.03
ACGTcount: A:0.23, C:0.12, G:0.39, T:0.26
Consensus pattern (176 bp):
ACTGGAACTGGGGGGGAAGTGGCTTCTCGTATACTGGAACCGGAGGAGGTTTATAGACTGGAGGC
TTGTACACTGGAACTGGAGGGGGAAGTGGCTTCTCGTATACTGGAACTGGAGGAAGTTTATAAAC
GGGAGGCTTGTAAACTGGAACTGGAGGAGGAAGTGGTTTCTCGTAT
Found at i:3313528 original size:72 final size:72
Alignment explanation
Indices: 3313477--3313671 Score: 182
Period size: 72 Copynumber: 2.7 Consensus size: 72
3313467 GAAGTGGTTT
* ***
3313477 CTCGTATACTGGAACTGG-GGGAGGAAGTGGCTTCTTGTATACTGGAACTGG-AGGAGGTTTATA
1 CTCGTAGACTGGAACTGGAGGG-GGAAGTGGCTTCTTGTATACTGGAACTGGAAGGAGGGGGATA
3313540 GACTGGAGG
65 GA-TGGAGG
* * *** *
3313549 CTTGTAGACTGGAACTGGAGGGGGAAGTGGCTTCTTGTATACTGGAACTGG-AGGAAGTTTATAA
1 CTCGTAGACTGGAACTGGAGGGGGAAGTGGCTTCTTGTATACTGGAACTGGAAGGAGGGGGATAG
*
3313613 ACGGGAGG
66 A-TGGAGG
* * * * *
3313621 CTTGTAAACTGGAACTGGAGGAGGAAGTGGTTTTTTGTATA-TCGGAACTGG
1 CTCGTAGACTGGAACTGGAGGGGGAAGTGGCTTCTTGTATACT-GGAACTGG
3313672 TGGGGGTTTG
Statistics
Matches: 112, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
71 1 0.01
72 108 0.96
73 3 0.03
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.27
Consensus pattern (72 bp):
CTCGTAGACTGGAACTGGAGGGGGAAGTGGCTTCTTGTATACTGGAACTGGAAGGAGGGGGATAG
ATGGAGG
Found at i:3315910 original size:38 final size:38
Alignment explanation
Indices: 3315865--3315943 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
3315855 TTTCAACATT
3315865 ATAGGTCTTTGTCTGATGAAACACTTGATGGGATTATC
1 ATAGGTCTTTGTCTGATGAAACACTTGATGGGATTATC
3315903 ATAGGTCTTTGTCTGATGAAACACTTGATGGGATTATC
1 ATAGGTCTTTGTCTGATGAAACACTTGATGGGATTATC
3315941 ATA
1 ATA
3315944 TGCTAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (38 bp):
ATAGGTCTTTGTCTGATGAAACACTTGATGGGATTATC
Found at i:3320786 original size:32 final size:32
Alignment explanation
Indices: 3320750--3320812 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
3320740 ATGTGCAGAA
3320750 CTCAAA-CAACAAATAAT-TATAATTATCTTTTT
1 CTCAAATCAA-AAA-AATATATAATTATCTTTTT
* *
3320782 CTCAAATTAAAAAAATATATATTTATCTTTT
1 CTCAAATCAAAAAAATATATAATTATCTTTT
3320813 CTTTTAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 22 0.81
33 2 0.07
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (32 bp):
CTCAAATCAAAAAAATATATAATTATCTTTTT
Found at i:3320820 original size:105 final size:103
Alignment explanation
Indices: 3320665--3320866 Score: 341
Period size: 105 Copynumber: 1.9 Consensus size: 103
3320655 CCGAAAAATG
***
3320665 ATAATTATCTTCTTCTCAAATTTTTAAAAAATATTTATCTTTTCTTTTAAGAAATAAAACAAACC
1 ATAATTATCTTCTTCTCAAATTAAAAAAAAATATTTATCTTTTCTTTTAAGAAATAAAACAAACC
*
3320730 ATATATTATAATGTGCAGAACTCAAACAACAAATAATT
66 ATATATTATAACGTGCAGAACTCAAACAACAAATAATT
*
3320768 ATAATTATCTTTTTCTCAAATTAAAAAAATATATATTTATCTTTTCTTTTAAGAAATAAAACAAA
1 ATAATTATCTTCTTCTCAAATTAAAAAAA-A-ATATTTATCTTTTCTTTTAAGAAATAAAACAAA
3320833 CCATATATTATAACGTGCAGAACTCAAACAACAA
64 CCATATATTATAACGTGCAGAACTCAAACAACAA
3320867 CACGTCCTTG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 25 0.27
104 1 0.01
105 66 0.72
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.37
Consensus pattern (103 bp):
ATAATTATCTTCTTCTCAAATTAAAAAAAAATATTTATCTTTTCTTTTAAGAAATAAAACAAACC
ATATATTATAACGTGCAGAACTCAAACAACAAATAATT
Found at i:3325030 original size:30 final size:30
Alignment explanation
Indices: 3324994--3325051 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3324984 ACTCTTATAC
3324994 TTTTATTTTGAATCAAATAAATATTTATTA
1 TTTTATTTTGAATCAAATAAATATTTATTA
* *
3325024 TTTTATTTTGAGTCAAATAAATTTTTAT
1 TTTTATTTTGAATCAAATAAATATTTAT
3325052 AACTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (30 bp):
TTTTATTTTGAATCAAATAAATATTTATTA
Found at i:3325333 original size:28 final size:28
Alignment explanation
Indices: 3325296--3325365 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
3325286 ATTTGATTAA
*
3325296 AAATAAAATATAAGCGTTTGATTAAATG
1 AAATAAAATATAAACGTTTGATTAAATG
3325324 AAATAAAATATAAACGTTTGATTAAATG
1 AAATAAAATATAAACGTTTGATTAAATG
*
3325352 AAATAAAAAATAAA
1 AAATAAAATATAAA
3325366 TATTTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.29
Consensus pattern (28 bp):
AAATAAAATATAAACGTTTGATTAAATG
Found at i:3325350 original size:23 final size:24
Alignment explanation
Indices: 3325287--3325349 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 24
3325277 TAAATACTTA
*
3325287 TTTGATTAAAAATAAAATATAAGCG
1 TTTGATT-AAAATAAAATATAAACG
3325312 TTTGATTAAATGAAATAAAATATAAACG
1 TTTGATT--A--AAATAAAATATAAACG
3325340 TTTGATTAAA
1 TTTGATTAAA
3325350 TGAAATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 2 0.06
25 7 0.21
26 3 0.09
28 22 0.65
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (24 bp):
TTTGATTAAAATAAAATATAAACG
Found at i:3325376 original size:28 final size:28
Alignment explanation
Indices: 3325296--3325378 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
3325286 ATTTGATTAA
* * *
3325296 AAATAAAATATAAGCGTTTGATTAAATG
1 AAATAAAAAATAAACATTTGATTAAATG
* *
3325324 AAATAAAATATAAACGTTTGATTAAATG
1 AAATAAAAAATAAACATTTGATTAAATG
*
3325352 AAATAAAAAATAAATATTT-ATTTAAAT
1 AAATAAAAAATAAACATTTGA-TTAAAT
3325379 TTTTTAAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 1 0.02
28 49 0.98
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.34
Consensus pattern (28 bp):
AAATAAAAAATAAACATTTGATTAAATG
Found at i:3330334 original size:23 final size:22
Alignment explanation
Indices: 3330307--3330366 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
3330297 CACAGGAGTT
3330307 GGTGGGTNGGGGGGGGGGGGGGG
1 GGTGGGT-GGGGGGGGGGGGGGG
3330330 GGTGGGTGGGGGGGGGGGGGGG
1 GGTGGGTGGGGGGGGGGGGGGG
3330352 GG-GGG-GGGGGGGGGG
1 GGTGGGTGGGGGGGGGG
3330367 TCGGGGGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
20 10 0.27
21 3 0.08
22 17 0.46
23 7 0.19
ACGTcount: A:0.00, C:0.00, G:0.92, T:0.07
Consensus pattern (22 bp):
GGTGGGTGGGGGGGGGGGGGGG
Found at i:3330342 original size:17 final size:16
Alignment explanation
Indices: 3330315--3330373 Score: 86
Period size: 15 Copynumber: 3.8 Consensus size: 16
3330305 TTGGTGGGTN
3330315 GGGGGG-GGGGGGGGG
1 GGGGGGTGGGGGGGGG
*
3330330 GGTGGGTGGGGGGGGG
1 GGGGGGTGGGGGGGGG
3330346 GGGGGG-GGGGGGGGG
1 GGGGGGTGGGGGGGGG
3330361 GGGGGGTCGGGGG
1 GGGGGGT-GGGGG
3330374 AACCAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 20 0.51
16 14 0.36
17 5 0.13
ACGTcount: A:0.00, C:0.02, G:0.93, T:0.05
Consensus pattern (16 bp):
GGGGGGTGGGGGGGGG
Found at i:3330353 original size:31 final size:31
Alignment explanation
Indices: 3330315--3330373 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3330305 TTGGTGGGTN
* *
3330315 GGGGGGGGGGGGGGGGGTGGGTGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGTCGGGGGGGG
3330346 GGGGGGGGGGGGGGGGGGGGGTCGGGGG
1 GGGGGGGGGGGGGGGGGGGGGTCGGGGG
3330374 AACCAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.00, C:0.02, G:0.93, T:0.05
Consensus pattern (31 bp):
GGGGGGGGGGGGGGGGGGGGGTCGGGGGGGG
Found at i:3330373 original size:1 final size:1
Alignment explanation
Indices: 3330315--3330366 Score: 86
Period size: 1 Copynumber: 52.0 Consensus size: 1
3330305 TTGGTGGGTN
* *
3330315 GGGGGGGGGGGGGGGGGTGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3330367 TCGGGGGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.96, T:0.04
Consensus pattern (1 bp):
G
Found at i:3369582 original size:22 final size:22
Alignment explanation
Indices: 3369554--3369600 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3369544 TTTAGATGCC
3369554 TATAGTGTTTACATGCTCAGTT
1 TATAGTGTTTACATGCTCAGTT
3369576 TATAGTGTTTACATGCTCAGTT
1 TATAGTGTTTACATGCTCAGTT
3369598 TAT
1 TAT
3369601 GTATTATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (22 bp):
TATAGTGTTTACATGCTCAGTT
Found at i:3379952 original size:11 final size:12
Alignment explanation
Indices: 3379932--3379964 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3379922 AATTTCAGAA
3379932 TAATATATATTTT
1 TAATA-ATATTTT
3379945 TAA-AATATTTT
1 TAATAATATTTT
3379956 TAATAATAT
1 TAATAATAT
3379965 AATATACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 6 0.32
13 3 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATAATATTTT
Found at i:3384769 original size:2 final size:2
Alignment explanation
Indices: 3384764--3384818 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
3384754 AGCGTGTGTG
* **
3384764 TA TA TA TA TA TA TA TA TA TA TA TA TA CCA CN TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
3384807 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3384819 CACCCCTCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 47 0.98
3 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3384872 original size:2 final size:2
Alignment explanation
Indices: 3384862--3384900 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3384852 ATAGCGTGTG
* * *
3384862 TA TA AA TA TA TA AA TA TA TA TA TA TA TA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3384901 CATTGGCACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3389616 original size:7 final size:7
Alignment explanation
Indices: 3389606--3389632 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3389596 CTGAAGAATG
3389606 TAGAAAC
1 TAGAAAC
3389613 TAGAAAC
1 TAGAAAC
3389620 TAGAAAC
1 TAGAAAC
3389627 TAGAAA
1 TAGAAA
3389633 GTGTGAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (7 bp):
TAGAAAC
Found at i:3390011 original size:22 final size:23
Alignment explanation
Indices: 3389992--3390036 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3389982 TAATAATTTA
3389992 AATTTAAATATTTAAAAATTATAT
1 AATTTAAAT-TTTAAAAATTATAT
* *
3390016 TATTTAAATTTAAAAAATTAT
1 AATTTAAATTTTAAAAATTAT
3390037 TAGATCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTAAATTTTAAAAATTATAT
Found at i:3391363 original size:15 final size:16
Alignment explanation
Indices: 3391343--3391373 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3391333 AGTAAAAGAA
3391343 AGAAGAAGACA-AGTG
1 AGAAGAAGACATAGTG
3391358 AGAAGAAGACATAGTG
1 AGAAGAAGACATAGTG
3391374 GGGTCGTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.06, G:0.32, T:0.10
Consensus pattern (16 bp):
AGAAGAAGACATAGTG
Found at i:3393576 original size:17 final size:17
Alignment explanation
Indices: 3393534--3393576 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3393524 GGCGGTAGTT
*
3393534 TTTTTTTTTTTTTGTGC
1 TTTTTTTTTATTTGTGC
* * *
3393551 GTTTGTTTTATTTGTTC
1 TTTTTTTTTATTTGTGC
3393568 TTTTTTTTT
1 TTTTTTTTT
3393577 TGAGGTTTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.02, C:0.05, G:0.12, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTATTTGTGC
Found at i:3397916 original size:21 final size:21
Alignment explanation
Indices: 3397868--3397908 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3397858 TTGTGCCACT
3397868 AGAAGAAAGTGAAGAAGATGG
1 AGAAGAAAGTGAAGAAGATGG
3397889 AGAAGAAA-TGATAGAAGATG
1 AGAAGAAAGTGA-AGAAGATG
3397909 TGGCAGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.54, C:0.00, G:0.34, T:0.12
Consensus pattern (21 bp):
AGAAGAAAGTGAAGAAGATGG
Found at i:3406244 original size:48 final size:48
Alignment explanation
Indices: 3406049--3406240 Score: 210
Period size: 48 Copynumber: 3.9 Consensus size: 48
3406039 CTAAGACTCT
* *
3406049 ACTTGTATTGATATGTTATGTTGTAGAAGTATTGAATCTTTGTTTATG
1 ACTTGTATTGATATGTTATGTTGTAGAAGTATGGACTCTTTGTTTATG
* * * *
3406097 ACTTGTGTTGATTTGTTATATATGTTGTAGACGTATTGGA-TCTTT-TTTTTCG
1 ACTTGTATTGATATG---T-TATGTTGTAGAAGTA-TGGACTCTTTGTTTAT-G
*
3406149 ACTTGTATTGGTATGTTATGTTGTAGAAGTATGGACTCTTTGTTTATG
1 ACTTGTATTGATATGTTATGTTGTAGAAGTATGGACTCTTTGTTTATG
* * **
3406197 ACTTGTATTGATTTGTTATGTTGT-GGAGTGCGGACTCTTTGTTT
1 ACTTGTATTGATATGTTATGTTGTAGAAGTATGGACTCTTTGTTT
3406241 TATGGTTTGG
Statistics
Matches: 121, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
47 21 0.17
48 55 0.45
49 5 0.04
51 5 0.04
52 32 0.26
53 3 0.02
ACGTcount: A:0.19, C:0.07, G:0.23, T:0.51
Consensus pattern (48 bp):
ACTTGTATTGATATGTTATGTTGTAGAAGTATGGACTCTTTGTTTATG
Found at i:3407408 original size:25 final size:28
Alignment explanation
Indices: 3407380--3407446 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 28
3407370 AATGACATTC
3407380 ATTAAAAATATTT-T-TAA-ATATAAAA
1 ATTAAAAATATTTATCTAATATATAAAA
* *
3407405 ATTAATAATATTTATCTAATGTATAAAA
1 ATTAAAAATATTTATCTAATATATAAAA
3407433 ATTAATAAATATTT
1 ATTAA-AAATATTT
3407447 GCGAATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.34
26 1 0.03
27 3 0.09
28 12 0.34
29 7 0.20
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
ATTAAAAATATTTATCTAATATATAAAA
Found at i:3414966 original size:54 final size:54
Alignment explanation
Indices: 3414908--3415013 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
3414898 TATGTTTATG
* * *
3414908 TTGTACCAGAATTGACTCTTTGTTTATAACTTGTATTGATTTGTTATGTTGTAC
1 TTGTACAAGAATTGACTCGTTGTTTATAACTTGTAGTGATTTGTTATGTTGTAC
* * *
3414962 TTGTACAAGTATTGACTCGTTGTTTGTGACTTGTAGTGATTTGTTATGTTGT
1 TTGTACAAGAATTGACTCGTTGTTTATAACTTGTAGTGATTTGTTATGTTGT
3415014 GGAGTATCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.20, C:0.09, G:0.21, T:0.50
Consensus pattern (54 bp):
TTGTACAAGAATTGACTCGTTGTTTATAACTTGTAGTGATTTGTTATGTTGTAC
Found at i:3419795 original size:53 final size:52
Alignment explanation
Indices: 3419731--3419832 Score: 186
Period size: 53 Copynumber: 1.9 Consensus size: 52
3419721 TCAGTCCCTG
3419731 CCCACGTACCCCAATTTTCCCATCAACCAACACAATCACCACCATGAGCCAA
1 CCCACGTACCCCAATTTTCCCATCAACCAACACAATCACCACCATGAGCCAA
*
3419783 CCCACGCTACCCCAATTTTCCCATCAACCAGCACAATCACCACCATGAGC
1 CCCACG-TACCCCAATTTTCCCATCAACCAACACAATCACCACCATGAGC
3419833 AAGTCCAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 6 0.12
53 42 0.88
ACGTcount: A:0.32, C:0.45, G:0.07, T:0.16
Consensus pattern (52 bp):
CCCACGTACCCCAATTTTCCCATCAACCAACACAATCACCACCATGAGCCAA
Found at i:3421993 original size:13 final size:13
Alignment explanation
Indices: 3421975--3422000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3421965 TAGCCATCCC
3421975 TATAAATTAATTT
1 TATAAATTAATTT
3421988 TATAAATTAATTT
1 TATAAATTAATTT
3422001 CTTCATCGGA
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:0.00, T:0.54
Consensus pattern (13 bp):
TATAAATTAATTT
Found at i:3438140 original size:13 final size:13
Alignment explanation
Indices: 3438122--3438147 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3438112 CACTGAATTT
3438122 ATTTTTTTTATAA
1 ATTTTTTTTATAA
3438135 ATTTTTTTTATAA
1 ATTTTTTTTATAA
3438148 TAGTAATTTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTTTTATAA
Found at i:3439482 original size:11 final size:11
Alignment explanation
Indices: 3439466--3439550 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 11
3439456 GAAAATGAAG
3439466 AAGAAAAAAAA
1 AAGAAAAAAAA
*
3439477 AAGAAAAATAA
1 AAGAAAAAAAA
* **
3439488 GAGAAAAGGAA
1 AAGAAAAAAAA
* *
3439499 AAGGAGAAAAA
1 AAGAAAAAAAA
*
3439510 AGGAAAGAAAGGAA
1 AAGAAA-AAA--AA
*
3439524 AATAAAAAAAA
1 AAGAAAAAAAA
*
3439535 AAGATAAAAAA
1 AAGAAAAAAAA
3439546 AAGAA
1 AAGAA
3439551 GAGAAAAAGT
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
11 42 0.78
12 3 0.06
13 3 0.06
14 6 0.11
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:3439489 original size:23 final size:23
Alignment explanation
Indices: 3439447--3439494 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
3439437 AAGGGGAAGG
* *
3439447 AAAAAAGAGGAAAATGAAGAAGAA
1 AAAAAAAAGAAAAATGAAG-AGAA
3439471 AAAAAAAAGAAAAAT-AAGAGAA
1 AAAAAAAAGAAAAATGAAGAGAA
3439493 AA
1 AA
3439495 GGAAAAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 3 0.14
24 13 0.59
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAAAAAGAAAAATGAAGAGAA
Found at i:3439494 original size:16 final size:16
Alignment explanation
Indices: 3439475--3439557 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
3439465 GAAGAAAAAA
*
3439475 AAAAGAAAAATAAGAG
1 AAAAGAAAAAGAAGAG
* * *
3439491 AAAAGGAAAAGGAGAA
1 AAAAGAAAAAGAAGAG
*
3439507 AAAAG-GAAAGAA-AGG
1 AAAAGAAAAAGAAGA-G
* * *
3439522 AAAATAAAAAAAAAAG
1 AAAAGAAAAAGAAGAG
3439538 ATAAA-AAAAAGAAGAG
1 A-AAAGAAAAAGAAGAG
3439554 AAAA
1 AAAA
3439558 AGTTCATCAG
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
14 1 0.02
15 12 0.24
16 34 0.67
17 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAGAAAAAGAAGAG
Found at i:3439500 original size:25 final size:24
Alignment explanation
Indices: 3439443--3439538 Score: 65
Period size: 25 Copynumber: 3.9 Consensus size: 24
3439433 GGAAAAGGGG
*
3439443 AAGGAAAAAAGAGGAAAATGAAGAAGA
1 AAGGAAAAAA-A-GAAAA-AAAGAAGA
3439470 AA--AAAAAAAGAAAAATAAG-AGAA
1 AAGGAAAAAAAGAAAAA-AAGAAG-A
** *
3439493 AAGGAAAAGGAGAAAAAAGGAAAGA
1 AAGGAAAAAAAGAAAAAAAG-AAGA
3439518 AAGGAAAATAAA-AAAAAAAGA
1 AAGGAAAA-AAAGAAAAAAAGA
3439539 TAAAAAAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
22 2 0.04
23 11 0.20
24 4 0.07
25 33 0.60
26 3 0.05
27 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (24 bp):
AAGGAAAAAAAGAAAAAAAGAAGA
Found at i:3439543 original size:13 final size:14
Alignment explanation
Indices: 3439525--3439558 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3439515 AGAAAGGAAA
3439525 ATAAAAAAAA-AAG
1 ATAAAAAAAAGAAG
3439538 ATAAAAAAAAGAAG
1 ATAAAAAAAAGAAG
*
3439552 AGAAAAA
1 ATAAAAA
3439559 GTTCATCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (14 bp):
ATAAAAAAAAGAAG
Found at i:3455978 original size:29 final size:29
Alignment explanation
Indices: 3455944--3456007 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
3455934 TGTAAATTTT
* *
3455944 TTTTTTAAACATGACGTGTAATAATAATA
1 TTTTTTAAACATGACATGTAATAATAACA
* *
3455973 TTTTTTCAACATGATATGTAATAATAACA
1 TTTTTTAAACATGACATGTAATAATAACA
3456002 TTTTTT
1 TTTTTT
3456008 TTAACGTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTTTTAAACATGACATGTAATAATAACA
Found at i:3456039 original size:83 final size:81
Alignment explanation
Indices: 3455945--3456151 Score: 215
Period size: 82 Copynumber: 2.5 Consensus size: 81
3455935 GTAAATTTTT
* * * *
3455945 TTTTTAAACATGACGTGTAATAATAATATTTTTTCAACATGATATGTAATAATAACATTTTTTTT
1 TTTTTATACATGACGTGTAACAATAATATTTTTTCAACATGATACGT-ATAATAAC--CTTTTTT
* *
3456010 AA-CGTGACGTGCAACATG
63 AACCATGACGTGCAACATA
* *
3456028 TTTTTATACATGATGTGTAACAATAATATTTTTTTTTCAACATG--ACGTGTAATAACCTTTTTT
1 TTTTTATACATGACGTGTAACAATAATA---TTTTTTCAACATGATACGTATAATAACCTTTTTT
*
3456091 AACCATGACGTGTAACATA
63 AACCATGACGTGCAACATA
* * * *
3456110 TTTTTATACATGGCATTTAACAATAATA-CTTTTCAACATGAT
1 TTTTTATACATGACGTGTAACAATAATATTTTTTCAACATGAT
3456152 GTATAACATC
Statistics
Matches: 104, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
78 11 0.11
81 8 0.08
82 37 0.36
83 32 0.31
84 3 0.03
86 13 0.12
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (81 bp):
TTTTTATACATGACGTGTAACAATAATATTTTTTCAACATGATACGTATAATAACCTTTTTTAAC
CATGACGTGCAACATA
Found at i:3456049 original size:24 final size:23
Alignment explanation
Indices: 3456005--3456049 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
3455995 AATAACATTT
*
3456005 TTTTTAACGTGACGTGCAACATG
1 TTTTTAACATGACGTGCAACATG
* *
3456028 TTTTTATACATGATGTGTAACA
1 TTTTTA-ACATGACGTGCAACA
3456050 ATAATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
TTTTTAACATGACGTGCAACATG
Found at i:3456081 original size:26 final size:26
Alignment explanation
Indices: 3456051--3456114 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
3456041 TGTGTAACAA
*
3456051 TAATATTTTTTTTTCAA-CATGACGTG
1 TAATATATTTTTTT-AACCATGACGTG
*
3456077 TAATA-ACCTTTTTTAACCATGACGTG
1 TAATATA-TTTTTTTAACCATGACGTG
*
3456103 TAACATATTTTT
1 TAATATATTTTT
3456115 ATACATGGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 2 0.06
26 28 0.90
27 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (26 bp):
TAATATATTTTTTTAACCATGACGTG
Found at i:3456081 original size:29 final size:28
Alignment explanation
Indices: 3455941--3456114 Score: 85
Period size: 30 Copynumber: 6.2 Consensus size: 28
3455931 AAGTGTAAAT
3455941 TTTTTTTTTAAACATGACGTGTAATAATAA
1 TTTTTTTTT-AACATGACGTGTAATAAT-A
* * **
3455971 TATTTTTTCAACATGATATGTAATAATAA
1 TTTTTTTTTAACATGACGTGTAATAAT-A
* * * *
3456000 CATTTTTTTTAACGTGACGTG---CAACA
1 -TTTTTTTTTAACATGACGTGTAATAATA
* * *
3456026 TGTTTTTAT-ACATGATGTGTAACAATAATA
1 TTTTTTTTTAACATGACGTGT---AATAATA
3456056 TTTTTTTTTCAACATGACGTGTAAT-A-A
1 TTTTTTTTT-AACATGACGTGTAATAATA
** *
3456083 -CCTTTTTTAACCATGACGTGTAA-CATA
1 TTTTTTTTTAA-CATGACGTGTAATAATA
3456110 TTTTT
1 TTTTT
3456115 ATACATGGCA
Statistics
Matches: 105, Mismatches: 26, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
24 8 0.08
25 8 0.08
26 20 0.19
27 4 0.04
28 3 0.03
29 21 0.20
30 31 0.30
32 10 0.10
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTTTTTTTAACATGACGTGTAATAATA
Found at i:3469267 original size:35 final size:36
Alignment explanation
Indices: 3469192--3469269 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 36
3469182 GATTTTAATG
* *
3469192 GTTTTTTGCTTTTTTTCGTTTCTTTGTTTTTTGGTT
1 GTTTTTTGCTATTTTTCGTTTCTTTGTTTTTTAGTT
* *
3469228 GTTTTTTGC-ATTTTTGGTTTCTTT-TTTTTTATTT
1 GTTTTTTGCTATTTTTCGTTTCTTTGTTTTTTAGTT
3469262 AGTTTTTT
1 -GTTTTTT
3469270 ATTATGGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 8 0.22
35 20 0.54
36 9 0.24
ACGTcount: A:0.04, C:0.06, G:0.14, T:0.76
Consensus pattern (36 bp):
GTTTTTTGCTATTTTTCGTTTCTTTGTTTTTTAGTT
Found at i:3471822 original size:22 final size:21
Alignment explanation
Indices: 3471797--3471887 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 21
3471787 GTTCTTGCAT
*
3471797 TCAAAATCTTAGAATCGGTTCA
1 TCAAAATC-TAAAATCGGTTCA
*
3471819 TCAAACTCTAAAATCGGTTCA
1 TCAAAATCTAAAATCGGTTCA
* *
3471840 -CACCAAATTCTAAAATTGATT-A
1 TCA--AAA-TCTAAAATCGGTTCA
* * * *
3471862 ACAAAATTTAAAACCGATTCA
1 TCAAAATCTAAAATCGGTTCA
3471883 TCAAA
1 TCAAA
3471888 CCTTAAAACC
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
20 12 0.22
21 20 0.36
22 10 0.18
23 13 0.24
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.29
Consensus pattern (21 bp):
TCAAAATCTAAAATCGGTTCA
Found at i:3472017 original size:21 final size:21
Alignment explanation
Indices: 3471969--3472041 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
3471959 TAAAACTTGA
* *
3471969 TTCACGAAATTCTAAAACCAA-
1 TTCACCAAACTCTAAAA-CAAG
* * *
3471990 TTTACCAGACTTTAAAACAAG
1 TTCACCAAACTCTAAAACAAG
* *
3472011 TTCACCAAACTCTAAAGCCAG
1 TTCACCAAACTCTAAAACAAG
*
3472032 TTCACAAAAC
1 TTCACCAAAC
3472042 CGTATAACCT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.08
21 37 0.93
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (21 bp):
TTCACCAAACTCTAAAACAAG
Found at i:3472071 original size:21 final size:21
Alignment explanation
Indices: 3472047--3472152 Score: 56
Period size: 21 Copynumber: 5.1 Consensus size: 21
3472037 AAAACCGTAT
3472047 AACCTATTCACAAAATTTTAA
1 AACCTATTCACAAAATTTTAA
* * *
3472068 AACCGA-TCACCAAATCTTAA
1 AACCTATTCACAAAATTTTAA
** * * **
3472088 AATGTGTTCACAAGATCCTAA
1 AACCTATTCACAAAATTTTAA
* *
3472109 AA-CTAATTCACAAAACTCTAA
1 AACCT-ATTCACAAAATTTTAA
* *
3472130 AACC-AATCACCAAAACTTTAA
1 AACCTATTCA-CAAAATTTTAA
3472151 AA
1 AA
3472153 TCGATTCATC
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
20 19 0.30
21 44 0.69
22 1 0.02
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.25
Consensus pattern (21 bp):
AACCTATTCACAAAATTTTAA
Found at i:3472097 original size:62 final size:63
Alignment explanation
Indices: 3472031--3472153 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 63
3472021 TCTAAAGCCA
* * * * *
3472031 GTTCACAA-AACCGTATAACCT-ATTCACAAAATTTTAAAACCGATCACCAAATC-TTAAAATGT
1 GTTCACAAGAACC-TA-AAACTAATTCACAAAACTCTAAAACCAATCACCAAAACTTTAAAATGT
*
3472093 GTTCACAAGATCCTAAAACTAATTCACAAAACTCTAAAACCAATCACCAAAACTTTAAAAT
1 GTTCACAAGAACCTAAAACTAATTCACAAAACTCTAAAACCAATCACCAAAACTTTAAAAT
3472154 CGATTCATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
61 4 0.08
62 38 0.73
63 10 0.19
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.25
Consensus pattern (63 bp):
GTTCACAAGAACCTAAAACTAATTCACAAAACTCTAAAACCAATCACCAAAACTTTAAAATGT
Found at i:3472166 original size:21 final size:20
Alignment explanation
Indices: 3472142--3472199 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
3472132 CCAATCACCA
*
3472142 AAACTTTAAAATCGATTCATC
1 AAACTCTAAAATCGATTC-TC
* * *
3472163 AAACCCTAAAATCAATTCTT
1 AAACTCTAAAATCGATTCTC
*
3472183 GAACTCTAAAATCGATT
1 AAACTCTAAAATCGATT
3472200 GATAATCCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACTCTAAAATCGATTCTC
Found at i:3472790 original size:33 final size:34
Alignment explanation
Indices: 3472736--3472812 Score: 138
Period size: 33 Copynumber: 2.3 Consensus size: 34
3472726 CTGTTAACAA
*
3472736 ATTATCATATATTTTTTTTTGCAAGGCATTTGTG
1 ATTATCATATATTTTTTTTTGCAAGGCATTCGTG
3472770 ATTATCATATA-TTTTTTTTGCAAGGCATTCGTG
1 ATTATCATATATTTTTTTTTGCAAGGCATTCGTG
3472803 ATTATCATAT
1 ATTATCATAT
3472813 TAAGTAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 31 0.74
34 11 0.26
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (34 bp):
ATTATCATATATTTTTTTTTGCAAGGCATTCGTG
Found at i:3474744 original size:17 final size:18
Alignment explanation
Indices: 3474720--3474765 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
3474710 CTTTATAGCT
3474720 TTTTTTTAAAAAAA-TT-
1 TTTTTTTAAAAAAAGTTA
3474736 TTGTTTTTAAAAAAAGTTA
1 TT-TTTTTAAAAAAAGTTA
3474755 TTTTTTTAAAA
1 TTTTTTTAAAA
3474766 GCTTTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.07
17 12 0.44
18 11 0.41
19 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TTTTTTTAAAAAAAGTTA
Found at i:3474748 original size:18 final size:18
Alignment explanation
Indices: 3474719--3474765 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3474709 TCTTTATAGC
*
3474719 TTTTTTTTAAAAAAATT-
1 TTTTTTTAAAAAAAATTA
*
3474736 TTGTTTTTAAAAAAAGTTA
1 TT-TTTTTAAAAAAAATTA
3474755 TTTTTTTAAAA
1 TTTTTTTAAAA
3474766 GCTTTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TTTTTTTAAAAAAAATTA
Found at i:3489192 original size:20 final size:20
Alignment explanation
Indices: 3489158--3489196 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3489148 CTTTAGGCCC
3489158 ATTATATATTATTAATAAAT
1 ATTATATATTATTAATAAAT
3489178 ATTAT-TATTATTTAATAAA
1 ATTATATATTA-TTAATAAA
3489197 ACACTTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTATATATTATTAATAAAT
Found at i:3503879 original size:31 final size:31
Alignment explanation
Indices: 3503821--3503880 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
3503811 TCTAGAAAAC
* * ***
3503821 AATAACTTTCTGATTTTTTTTTTTGAAAAGT
1 AATAACTTTCTGACTTTGTTGACTGAAAAGT
3503852 AATAACTTTCTGACTTTGTTGACTGAAAA
1 AATAACTTTCTGACTTTGTTGACTGAAAA
3503881 AGCTAAACCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.47
Consensus pattern (31 bp):
AATAACTTTCTGACTTTGTTGACTGAAAAGT
Found at i:3517174 original size:21 final size:21
Alignment explanation
Indices: 3517149--3517191 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3517139 TGGGTCCTGA
*
3517149 GTCGGTCTGTCTTGCCTGAAG
1 GTCGGTCTGTCTTGCCGGAAG
3517170 GTCGGTCTGTCTTGCCGGAAG
1 GTCGGTCTGTCTTGCCGGAAG
3517191 G
1 G
3517192 GCTAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.30
Consensus pattern (21 bp):
GTCGGTCTGTCTTGCCGGAAG
Found at i:3531756 original size:12 final size:12
Alignment explanation
Indices: 3531739--3531763 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3531729 TCTCTTAAGT
3531739 AAGACTAAATTA
1 AAGACTAAATTA
3531751 AAGACTAAATTA
1 AAGACTAAATTA
3531763 A
1 A
3531764 CTTCTATTTT
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAGACTAAATTA
Found at i:3543382 original size:35 final size:35
Alignment explanation
Indices: 3543327--3543403 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
3543317 TATTATATAG
*
3543327 AGAACAACCAGAACAAGTGAAGTGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
* *
3543362 AGAATAACTAGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
3543397 AGAACAA
1 AGAACAA
3543404 GTGAAGCGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (35 bp):
AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
Found at i:3543407 original size:26 final size:26
Alignment explanation
Indices: 3543371--3543445 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
3543361 CAGAATAACT
*
3543371 AGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAAGTGAAGCGCTACTTCACGC
3543397 AGAACAAGTGAAGCGCTACTTCACGC
1 AGAACAAGTGAAGCGCTACTTCACGC
3543423 AGAACAAGTGAAGCGCTACTTCA
1 AGAACAAGTGAAGCGCTACTTCA
3543446 AGTATTACTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (26 bp):
AGAACAAGTGAAGCGCTACTTCACGC
Found at i:3543757 original size:29 final size:28
Alignment explanation
Indices: 3543725--3543794 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
3543715 CTCGTATACT
*
3543725 TATTCATGTACAGCTTATTCTCTTGTACC
1 TATTC-TGTACAGCTTATTCTCTCGTACC
* *
3543754 TATTCTCATACAGCTTCTTCTCTCGTACC
1 TATTCT-GTACAGCTTATTCTCTCGTACC
3543783 TATTCTTGTACA
1 TATTC-TGTACA
3543795 CCTCTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 33 0.94
30 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.44
Consensus pattern (28 bp):
TATTCTGTACAGCTTATTCTCTCGTACC
Found at i:3544032 original size:13 final size:13
Alignment explanation
Indices: 3544014--3544038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3544004 ACTTGAGAGC
3544014 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
3544027 TTCTCTCTCTAA
1 TTCTCTCTCTAA
3544039 TTATCTTGTA
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:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:3552792 original size:18 final size:18
Alignment explanation
Indices: 3552769--3552807 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3552759 ACTTCACATC
3552769 CTCTCTCTCTCTCTGTCT
1 CTCTCTCTCTCTCTGTCT
* *
3552787 CTCTCTTTTTCTCTGTCT
1 CTCTCTCTCTCTCTGTCT
3552805 CTC
1 CTC
3552808 ACTGTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.05, T:0.54
Consensus pattern (18 bp):
CTCTCTCTCTCTCTGTCT
Found at i:3554246 original size:2 final size:2
Alignment explanation
Indices: 3554239--3554265 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3554229 CTTGCATAAA
3554239 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3554266 TCCCACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3561369 original size:3 final size:3
Alignment explanation
Indices: 3561361--3561385 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3561351 CTGATTACAA
3561361 AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT A
3561386 TACCATCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:3562044 original size:2 final size:2
Alignment explanation
Indices: 3562037--3562085 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3562027 TTTGACATAC
3562037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3562079 TA TA TA T
1 TA TA TA T
3562086 CTCTCTGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3590907 original size:12 final size:12
Alignment explanation
Indices: 3590886--3590920 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3590876 AAGAAATACT
*
3590886 CTCTCTCTCTCC
1 CTCTCCCTCTCC
3590898 CTCTCCCTCTCC
1 CTCTCCCTCTCC
3590910 CTCTCCCTCTC
1 CTCTCCCTCTC
3590921 TTCCCTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (12 bp):
CTCTCCCTCTCC
Found at i:3590913 original size:18 final size:18
Alignment explanation
Indices: 3590886--3590920 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3590876 AAGAAATACT
*
3590886 CTCTCTCTCTCCCTCTCC
1 CTCTCCCTCTCCCTCTCC
3590904 CTCTCCCTCTCCCTCTC
1 CTCTCCCTCTCCCTCTC
3590921 TTCCCTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (18 bp):
CTCTCCCTCTCCCTCTCC
Found at i:3591064 original size:6 final size:6
Alignment explanation
Indices: 3591049--3591081 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3591039 AAGAAAATAA
*
3591049 ATTT-C ATTTGC ATTTGC ATTTGG ATTTGC ATTT
1 ATTTGC ATTTGC ATTTGC ATTTGC ATTTGC ATTT
3591082 CAATTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.55
Consensus pattern (6 bp):
ATTTGC
Found at i:3592350 original size:19 final size:20
Alignment explanation
Indices: 3592301--3592354 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
3592291 TATTTATTAT
* *
3592301 CATATTTTATATTAATGTGA
1 CATATTTTATATTTATATGA
3592321 CATAATTTTATATTTATATGA
1 CAT-ATTTTATATTTATATGA
3592342 CAT-TTTTATATTT
1 CATATTTTATATTT
3592355 TACATCAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 10 0.32
20 3 0.10
21 18 0.58
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (20 bp):
CATATTTTATATTTATATGA
Found at i:3592462 original size:18 final size:18
Alignment explanation
Indices: 3592427--3592476 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3592417 TTATTTATTT
*
3592427 AAAATAAAAAATAA-AAA
1 AAAATAAAAATTAATAAA
* * *
3592444 ATAATTAAATTTAATAAA
1 AAAATAAAAATTAATAAA
3592462 AAAATAAAAATTAAT
1 AAAATAAAAATTAAT
3592477 TTAATTTTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAAAATTAATAAA
Found at i:3592476 original size:28 final size:29
Alignment explanation
Indices: 3592423--3592483 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
3592413 TTATTTATTT
3592423 ATTTAAAATAAAAAATAAAAAATAATTAA
1 ATTTAAAATAAAAAATAAAAAATAATTAA
* * *
3592452 ATTTAATA-AAAAAATAAAAATTAATTTA
1 ATTTAAAATAAAAAATAAAAAATAATTAA
3592480 ATTT
1 ATTT
3592484 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
ATTTAAAATAAAAAATAAAAAATAATTAA
Found at i:3592490 original size:27 final size:28
Alignment explanation
Indices: 3592431--3592491 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
3592421 TTATTTAAAA
3592431 TAAAAAATAAAAAATAATTAAATTTAAT
1 TAAAAAATAAAAAATAATTAAATTTAAT
* * * *
3592459 AAAAAAATAAAAATTAATTTAATTT-TT
1 TAAAAAATAAAAAATAATTAAATTTAAT
3592486 TAAAAA
1 TAAAAA
3592492 TAATTGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAAAAATAAAAAATAATTAAATTTAAT
Found at i:3594423 original size:23 final size:22
Alignment explanation
Indices: 3594394--3594463 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
3594384 TCAAAATAAC
3594394 TTTTATTATAATTTAATAATAT
1 TTTTATTATAATTTAATAATAT
* **
3594416 TTTGTATTAAAAGATAATTAA-AT
1 TTT-TATTATAATTTAA-TAATAT
* *
3594439 TTTTCATTCTAATTAAATAATAT
1 TTTT-ATTATAATTTAATAATAT
3594462 TT
1 TT
3594464 AATATTAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
22 7 0.19
23 26 0.72
24 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (22 bp):
TTTTATTATAATTTAATAATAT
Found at i:3594585 original size:11 final size:11
Alignment explanation
Indices: 3594503--3594586 Score: 54
Period size: 11 Copynumber: 8.0 Consensus size: 11
3594493 TACATTTATT
3594503 ATATTTAAATA
1 ATATTTAAATA
*
3594514 ATAATATTAAGTA
1 AT-AT-TTAAATA
**
3594527 ATATTTTTATA
1 ATATTTAAATA
*
3594538 ATATTT--ATT
1 ATATTTAAATA
* *
3594547 ATAGTGAAATA
1 ATATTTAAATA
3594558 ATA-TT-AAT-
1 ATATTTAAATA
3594566 ATA-TTAAATA
1 ATATTTAAATA
3594576 ATATTTAAATA
1 ATATTTAAATA
3594587 TTTTCATTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
8 5 0.09
9 12 0.21
10 4 0.07
11 24 0.42
12 4 0.07
13 8 0.14
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (11 bp):
ATATTTAAATA
Found at i:3595136 original size:19 final size:19
Alignment explanation
Indices: 3595099--3595137 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3595089 ATATCAAAAG
*
3595099 TGTAATTTTTATTAGTATA
1 TGTAATTTTTATAAGTATA
*
3595118 TGTAATTTTTATAATTATA
1 TGTAATTTTTATAAGTATA
3595137 T
1 T
3595138 CTTATTCATA
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:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TGTAATTTTTATAAGTATA
Found at i:3610567 original size:34 final size:34
Alignment explanation
Indices: 3610529--3610594 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
3610519 TATGGTAAGG
*
3610529 TCAAAG-TTTCAACACCAAATGTTACATGTCAAGC
1 TCAAAGCTTT-AACACCAAATATTACATGTCAAGC
* *
3610563 TCAAAGCTTTAGCATCAAATATTACATGTCAA
1 TCAAAGCTTTAACACCAAATATTACATGTCAA
3610595 AACTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (34 bp):
TCAAAGCTTTAACACCAAATATTACATGTCAAGC
Found at i:3614045 original size:17 final size:18
Alignment explanation
Indices: 3614023--3614067 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3614013 ATATGATTTA
*
3614023 TAACATGCTT-ATACGAT
1 TAACATGATTGATACGAT
* *
3614040 TAACATAATTGATGCGAT
1 TAACATGATTGATACGAT
3614058 TAACATGATT
1 TAACATGATT
3614068 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (18 bp):
TAACATGATTGATACGAT
Found at i:3614151 original size:26 final size:24
Alignment explanation
Indices: 3614122--3614177 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
3614112 TTACTACAAA
3614122 AAATT-ATAAATATTGTAATATTAAT
1 AAATTAATAAAT-TT-TAATATTAAT
3614147 CAAATATAATAAATTTTAATATTAAT
1 -AAAT-TAATAAATTTTAATATTAAT
3614173 AAATT
1 AAATT
3614178 TTAATTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 1 0.04
25 4 0.14
26 14 0.50
27 3 0.11
28 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATTAATAAATTTTAATATTAAT
Found at i:3614191 original size:16 final size:16
Alignment explanation
Indices: 3614149--3614182 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3614139 ATATTAATCA
3614149 AATA-TAATAAATTTT
1 AATATTAATAAATTTT
3614164 AATATTAATAAATTTT
1 AATATTAATAAATTTT
3614180 AAT
1 AAT
3614183 TATCATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTAATAAATTTT
Found at i:3616990 original size:2 final size:2
Alignment explanation
Indices: 3616983--3617019 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3616973 AAATGAAGTT
3616983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3617020 TATTTGTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3655558 original size:17 final size:17
Alignment explanation
Indices: 3655518--3655561 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3655508 CTTGATTTTG
* *
3655518 ATATATTTTATAAAATT
1 ATATATTTAATAAAAAT
*
3655535 CTCATATTTAATAAAAAT
1 AT-ATATTTAATAAAAAT
3655553 ATATATTTA
1 ATATATTTA
3655562 TTCTGATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATTTAATAAAAAT
Found at i:3657006 original size:2 final size:2
Alignment explanation
Indices: 3656999--3657023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3656989 TCATCGTCGT
3656999 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3657024 GCTTGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3665497 original size:125 final size:125
Alignment explanation
Indices: 3665272--3665525 Score: 463
Period size: 125 Copynumber: 2.0 Consensus size: 125
3665262 TTCATCGAAC
* * *
3665272 AAAATATACTTGCTTCAGGTGCATAACATAGAACAACTATGATGCTTTCACTCAGCTAACATTGA
1 AAAATATACTTGCTTCAGGTGCATAACATAGAACAACTATGATGCTTTCACTCAACAAACAATGA
3665337 ATTTTACACATCAGACAACCGTATAAGCTAACCAGGTTTTATGGTTAGGTATACAACCAG
66 ATTTTACACATCAGACAACCGTATAAGCTAACCAGGTTTTATGGTTAGGTATACAACCAG
3665397 AAAATATACTTGCTTCAGGTGCATAACATAGAACAACTATGATGCTTTCACTCAACAAACAATGA
1 AAAATATACTTGCTTCAGGTGCATAACATAGAACAACTATGATGCTTTCACTCAACAAACAATGA
* *
3665462 ATTTTACACATCAGACAACCGTATAAGCTATCCAGGTTTTATGGTTAGGTATACTACCAG
66 ATTTTACACATCAGACAACCGTATAAGCTAACCAGGTTTTATGGTTAGGTATACAACCAG
3665522 AAAA
1 AAAA
3665526 AAAAAAATTG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (125 bp):
AAAATATACTTGCTTCAGGTGCATAACATAGAACAACTATGATGCTTTCACTCAACAAACAATGA
ATTTTACACATCAGACAACCGTATAAGCTAACCAGGTTTTATGGTTAGGTATACAACCAG
Found at i:3682208 original size:90 final size:90
Alignment explanation
Indices: 3682100--3682273 Score: 260
Period size: 90 Copynumber: 1.9 Consensus size: 90
3682090 GGATAAAGAG
* *
3682100 GTGGCTGGCGTGGCGGAGGAAAGAGGG-ATTGCTGAGGCAGCAGAGGTGGATGGTGTGACAGAGC
1 GTGGCTGACGTGGCGGAGGAAAG-GGGAATTGCTAAGGCAGCAGAGGTGGATGGTGTGACAGAGC
*
3682164 AAATTGTGGTTATGGAGGAAACATGC
65 AAATTGGGGTTATGGAGGAAACATGC
* * * * *
3682190 GTGGCTGACGTGGTGGAGGAAAGGGGAATTGCTAAGGCGGCAGAGGTGGGTGTTGTGACGGAGCA
1 GTGGCTGACGTGGCGGAGGAAAGGGGAATTGCTAAGGCAGCAGAGGTGGATGGTGTGACAGAGCA
3682255 AATTGGGGTTATGGAGGAA
66 AATTGGGGTTATGGAGGAA
3682274 GCGGGCCTGG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 3 0.04
90 72 0.96
ACGTcount: A:0.25, C:0.10, G:0.46, T:0.20
Consensus pattern (90 bp):
GTGGCTGACGTGGCGGAGGAAAGGGGAATTGCTAAGGCAGCAGAGGTGGATGGTGTGACAGAGCA
AATTGGGGTTATGGAGGAAACATGC
Found at i:3682285 original size:90 final size:90
Alignment explanation
Indices: 3682101--3682297 Score: 252
Period size: 90 Copynumber: 2.2 Consensus size: 90
3682091 GATAAAGAGG
* *
3682101 TGGCTGGCGTGGCGGAGGAAAGAGGGATTGCTGAGGCAGCAGAGGTGGATGGTGTGACAGAGCAA
1 TGGCTGACGTGGCGGAGGAAAGAGGGATTGCTAAGGCAGCAGAGGTGGATGGTGTGACAGAGCAA
* * *
3682166 ATTGTGGTTATGGAGGAAACATGCG
66 ATTGGGGTTATGGAGGAAACAGGCC
* * * * *
3682191 TGGCTGACGTGGTGGAGGAAAG-GGGAATTGCTAAGGCGGCAGAGGTGGGTGTTGTGACGGAGCA
1 TGGCTGACGTGGCGGAGGAAAGAGGG-ATTGCTAAGGCAGCAGAGGTGGATGGTGTGACAGAGCA
* *
3682255 AATTGGGGTTATGGAGGAAGCGGGCC
65 AATTGGGGTTATGGAGGAAACAGGCC
* *
3682281 TGGCTGACATGACGGAG
1 TGGCTGACGTGGCGGAG
3682298 AGAACAGGAA
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 3 0.03
90 88 0.97
ACGTcount: A:0.24, C:0.12, G:0.46, T:0.19
Consensus pattern (90 bp):
TGGCTGACGTGGCGGAGGAAAGAGGGATTGCTAAGGCAGCAGAGGTGGATGGTGTGACAGAGCAA
ATTGGGGTTATGGAGGAAACAGGCC
Found at i:3686101 original size:323 final size:322
Alignment explanation
Indices: 3685525--3686105 Score: 803
Period size: 323 Copynumber: 1.8 Consensus size: 322
3685515 ATTTCCATAG
* * * * *
3685525 TTTTAATTGATAGTTGGAAGCTGATGTTTGAAACTATTTCTCCACTTTTCTCGATTGCTCTGCTT
1 TTTTAATCGATAGTTGGAAGCTGATATTTGAAACCAGTTCTCCACTTTTCTCGATTGCTCTGCTG
*
3685590 TAGCTATTCTGTTCGAAGTTTTAGTTTCTCTTGATACTATTTTGGCTAATAGGCTTATGATTGTG
66 TAGCTATTCTGTTCGAAGTTTTAGTTTCTCTGGATACTATTTTGGCTAATAGGCTTATGATTGTG
* * ** * *
3685655 TGGAAAGTTGTAAATATGTAACTTGGCAATTCATAGCCTCATCTTTCTTCTTTCACATAATGTCA
131 TGGAAAGTTGTAAATAAGTAACTCGGCAATTCATAAACTCACCTTTCTTCCTTCACATAATGTCA
* * *
3685720 AAATTATAAATATCATTTTTGAGATCATTTTTGTCCTCTCTGGGTGGTTGGTGGGGTGTGGGGTG
196 AAATTATAAATATCATTCTCGAGATCATTTTTGTCCTCTCTGGGTAGTTGGTGGGGTGTGGGGTG
3685785 CTGTGCATTAAGTATGTTCAACTTCTTGTGTTGTCTTCTTCATTTGCAGTATACTTCCGTGA
261 CTGTGCATTAAGTATGTTCAACTTCTTGTGTTGTCTTCTTCATTTGCAGTATACTTCCGTGA
* * * *
3685847 TTTTAATCGATAGTTGGAAGTTGATATTTGAAACCAGTTCTGCACTTTTCTTGATTGTTCTTGCT
1 TTTTAATCGATAGTTGGAAGCTGATATTTGAAACCAGTTCTCCACTTTTCTCGATTGCTC-TGCT
* *
3685912 GTAGCTATTCTGTTTGAAGTTTTAGTTTCTCTGGATAGT-TTTTGGGCTAATAGGCTTATGATTG
65 GTAGCTATTCTGTTCGAAGTTTTAGTTTCTCTGGATACTATTTT-GGCTAATAGGCTTATGATTG
* * * * **
3685976 TTTGGTAAGTTGTAAATAAGTAA-TACGGCAATTTATAAAGTTGCCTTTCTTCCTTCACATAATG
129 TGTGGAAAGTTGTAAATAAGTAACT-CGGCAATTCATAAACTCACCTTTCTTCCTTCACATAATG
* * *
3686040 TCAAAGTTATAAATATCATTCTCGAGCTC-TCTCTTT-T-CTCTCTGGGTATTTGGTGGGGGTGT
193 TCAAAATTATAAATATCATTCTCGAGATCAT-T-TTTGTCCTCTCTGGGTAGTTGGT-GGGGTGT
3686102 GGGG
255 GGGG
3686106 GTTTGTTGCA
Statistics
Matches: 223, Mismatches: 30, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
322 73 0.33
323 147 0.66
324 3 0.01
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (322 bp):
TTTTAATCGATAGTTGGAAGCTGATATTTGAAACCAGTTCTCCACTTTTCTCGATTGCTCTGCTG
TAGCTATTCTGTTCGAAGTTTTAGTTTCTCTGGATACTATTTTGGCTAATAGGCTTATGATTGTG
TGGAAAGTTGTAAATAAGTAACTCGGCAATTCATAAACTCACCTTTCTTCCTTCACATAATGTCA
AAATTATAAATATCATTCTCGAGATCATTTTTGTCCTCTCTGGGTAGTTGGTGGGGTGTGGGGTG
CTGTGCATTAAGTATGTTCAACTTCTTGTGTTGTCTTCTTCATTTGCAGTATACTTCCGTGA
Found at i:3693482 original size:96 final size:93
Alignment explanation
Indices: 3693355--3693548 Score: 327
Period size: 93 Copynumber: 2.1 Consensus size: 93
3693345 AAATTATGTT
*
3693355 TAAAATTTTATTTTTTTTTAAAAAAAATTTTAAAGATTTTTTAAAATTTATGTTTAATTTAATTT
1 TAAAATTTTATTTTTTTTAAAAAAAAATTTTAAAGA-TTTTTAAAATTTA-GTTTAATTTAA-TT
3693420 TTTTTTAAAGATAGATAAGTTGAAAAAAAAA
63 TTTTTTAAAGATAGATAAGTTGAAAAAAAAA
3693451 NTAAAA-TTTATTTTTTTTAAAAAAAAATTTTAAAGATTTTTAAAATTTAGTTTAATTTAATTTT
1 -TAAAATTTTATTTTTTTTAAAAAAAAATTTTAAAGATTTTTAAAATTTAGTTTAATTTAATTTT
3693515 TTTTAAAGATAGATAAGTTGAAAAAAAAA
65 TTTTAAAGATAGATAAGTTGAAAAAAAAA
*
3693544 AAAAA
1 TAAAA
3693549 AATCAAACAA
Statistics
Matches: 95, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
92 4 0.04
93 33 0.35
94 11 0.12
95 13 0.14
96 29 0.31
97 5 0.05
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.46
Consensus pattern (93 bp):
TAAAATTTTATTTTTTTTAAAAAAAAATTTTAAAGATTTTTAAAATTTAGTTTAATTTAATTTTT
TTTAAAGATAGATAAGTTGAAAAAAAAA
Found at i:3701620 original size:2 final size:2
Alignment explanation
Indices: 3701613--3701638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3701603 ACTCATCAAC
3701613 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3701639 TTCAATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3702131 original size:96 final size:98
Alignment explanation
Indices: 3701959--3702154 Score: 333
Period size: 97 Copynumber: 2.0 Consensus size: 98
3701949 TAACATCAGT
* * * *
3701959 TTAATTAATCTTGAATATATATTTGATTTAAAATAAAAAATAAAAAATTTATTTAAATTTTGATA
1 TTAATTAATCGTGAAGATATATTTAATTTAAAATAAAAAATAAAAAATTTATTTAAATTTTCATA
*
3702024 AAATATTTCCTTTAATAT-ATGTCAATGATTTG
66 AAATATTTCCTTTAATATGATGTCAATGACTTG
3702056 TTAATTAATCGTGAAGATATATTTAATTTAAAATAAAAAAT-AAAAATTTATTTAAATTTTCATA
1 TTAATTAATCGTGAAGATATATTTAATTTAAAATAAAAAATAAAAAATTTATTTAAATTTTCATA
3702120 AAATATTTCCTTTAATATGATGTCAATGACTTG
66 AAATATTTCCTTTAATATGATGTCAATGACTTG
3702153 TT
1 TT
3702155 GATTTTTGTA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 40 0.43
97 53 0.57
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (98 bp):
TTAATTAATCGTGAAGATATATTTAATTTAAAATAAAAAATAAAAAATTTATTTAAATTTTCATA
AAATATTTCCTTTAATATGATGTCAATGACTTG
Found at i:3705170 original size:9 final size:9
Alignment explanation
Indices: 3705149--3705189 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
3705139 AAAAAAATTA
3705149 AAATTAAATT
1 AAATTAAA-T
3705159 AAATTAAAT
1 AAATTAAAT
*
3705168 AAAATAAAT
1 AAATTAAAT
*
3705177 AAATAAAAT
1 AAATTAAAT
3705186 AAAT
1 AAAT
3705190 AATAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAATTAAAT
Found at i:3734643 original size:20 final size:20
Alignment explanation
Indices: 3734615--3734656 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3734605 AAAAAAAGAA
*
3734615 AATAATGAAAATTTGTAATG
1 AATAATGAAAATTTGAAATG
* *
3734635 AATATTGAAAGTTTGAAATG
1 AATAATGAAAATTTGAAATG
3734655 AA
1 AA
3734657 ATTTCAGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (20 bp):
AATAATGAAAATTTGAAATG
Found at i:3736072 original size:18 final size:17
Alignment explanation
Indices: 3736049--3736082 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3736039 TAAAGGGTAT
3736049 TTAATAAAGAACTTTCTA
1 TTAATAAAGAA-TTTCTA
*
3736067 TTAATAACGAATTTCT
1 TTAATAAAGAATTTCT
3736083 TTGTTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
TTAATAAAGAATTTCTA
Found at i:3737960 original size:26 final size:25
Alignment explanation
Indices: 3737920--3737972 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
3737910 TTTTAAATAA
* * *
3737920 CAAATTACCCGTCAAGTCTCGATATT
1 CAAATAACCCATCAAGTCACGA-ATT
3737946 CAAATAACCCATCAAGTCACGAATT
1 CAAATAACCCATCAAGTCACGAATT
3737971 CA
1 CA
3737973 CTTAAAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.25
Consensus pattern (25 bp):
CAAATAACCCATCAAGTCACGAATT
Found at i:3756803 original size:13 final size:13
Alignment explanation
Indices: 3756749--3756804 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
3756739 ATTTTATTTT
3756749 AAACATTATATAA
1 AAACATTATATAA
** *
3756762 AAACAGCATATAGT
1 AAACATTATATA-A
*
3756776 AAGCATTATAT--
1 AAACATTATATAA
3756787 AAACATTATATAA
1 AAACATTATATAA
3756800 AAACA
1 AAACA
3756805 ACATATAGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
11 10 0.30
13 15 0.45
14 8 0.24
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (13 bp):
AAACATTATATAA
Found at i:3757741 original size:23 final size:23
Alignment explanation
Indices: 3757715--3757763 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
3757705 ATAACATTCT
3757715 TTACTAACAAGTCACGCAATGCC
1 TTACTAACAAGTCACGCAATGCC
3757738 TTACTAACAAGTCACGCAATGCC
1 TTACTAACAAGTCACGCAATGCC
3757761 TTA
1 TTA
3757764 TCAGAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (23 bp):
TTACTAACAAGTCACGCAATGCC
Found at i:3757784 original size:26 final size:26
Alignment explanation
Indices: 3757724--3758044 Score: 316
Period size: 26 Copynumber: 13.0 Consensus size: 26
3757714 TTTACTAACA
* *
3757724 AGTCACGCAATGCCTTA-C--TAACA
1 AGTCACGCAATGCCTTATCAGAAACT
3757747 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAGAAACT
* *
3757773 AGTCACGTAATGCCTTATCAGAAATT
1 AGTCACGCAATGCCTTATCAGAAACT
* *
3757799 AGTCACGCAA----TTCTC--AAAGT
1 AGTCACGCAATGCCTTATCAGAAACT
3757819 CAGTCACGCAATGCCTTATCAGAAACT
1 -AGTCACGCAATGCCTTATCAGAAACT
* * *
3757846 AGTCACACAATGCCTTATTAAAAACT
1 AGTCACGCAATGCCTTATCAGAAACT
3757872 AGTCACGCAATGCC-TATC---AACT
1 AGTCACGCAATGCCTTATCAGAAACT
*
3757894 AGTCACGCAATGCTTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAGAAACT
* *
3757920 AGTCACGTAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAGAAACT
3757946 AGTCACGCAATGCC-TATC---AACT
1 AGTCACGCAATGCCTTATCAGAAACT
* * *
3757968 AGTTACGCAATACTTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAGAAACT
* *** *
3757994 AATCACGCAATAATTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAGAAACT
* *
3758020 AGTCACGCAATACCTTATCAAAAAC
1 AGTCACGCAATGCCTTATCAGAAAC
3758045 CAAGCACAAA
Statistics
Matches: 251, Mismatches: 29, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.02
21 10 0.04
22 36 0.14
23 25 0.10
24 1 0.00
25 11 0.04
26 160 0.64
27 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (26 bp):
AGTCACGCAATGCCTTATCAGAAACT
Found at i:3757924 original size:74 final size:74
Alignment explanation
Indices: 3757724--3758040 Score: 399
Period size: 74 Copynumber: 4.3 Consensus size: 74
3757714 TTTACTAACA
* *
3757724 AGTCACGCAATGCCT-TACTAACAAGTCACGCAATGCCTTATCAGAAACTAGTCACGTAATGCCT
1 AGTCACGCAATGCCTAT-C-AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCT
* *
3757788 TATCAGAAATT
64 TATCAAAAACT
* * *
3757799 AGTCACGCAAT---TCTCAAAGTCAGTCACGCAATGCCTTATCAGAAACTAGTCACACAATGCCT
1 AGTCACGCAATGCCTATC-AACT-AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCT
*
3757861 TATTAAAAACT
64 TATCAAAAACT
* *
3757872 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCTTTATCAGAAACTAGTCACGTAATGCCTTA
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTTA
3757937 TCAAAAACT
66 TCAAAAACT
* * * * ***
3757946 AGTCACGCAATGCCTATCAACTAGTTACGCAATACTTTATCAGAAACTAATCACGCAATAATTTA
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTTA
3758011 TCAAAAACT
66 TCAAAAACT
*
3758020 AGTCACGCAATACCTTATCAA
1 AGTCACGCAATGCC-TATCAA
3758041 AAACCAAGCA
Statistics
Matches: 214, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
72 4 0.02
73 59 0.28
74 128 0.60
75 20 0.09
76 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (74 bp):
AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTTA
TCAAAAACT
Found at i:3757951 original size:100 final size:98
Alignment explanation
Indices: 3757820--3758044 Score: 274
Period size: 100 Copynumber: 2.3 Consensus size: 98
3757810 TCTCAAAGTC
* *
3757820 AGTCACGCAATGCCTTATCAGAAACTAGTCACACAATGCCTTATTAAAAACTAGTCACGCAATGC
1 AGTCACGCAATGCCTTATCAAAAACTAGTCACACAATGCC-TA-T--AAACTAGTCACGCAATAC
* ** *
3757885 -CTATC-AACTAGTCACGCAATGCTTTATCAGAAACT
62 TCTATCAAACTAATCACGCAATAATTTATCAAAAACT
* * * * *
3757920 AGTCACGTAATGCCTTATCAAAAACTAGTCACGCAATGCCTATCAACTAGTTACGCAATACTTTA
1 AGTCACGCAATGCCTTATCAAAAACTAGTCACACAATGCCTATAAACTAGTCACGCAATACTCTA
3757985 TCAGAAACTAATCACGCAATAATTTATCAAAAACT
66 TC--AAACTAATCACGCAATAATTTATCAAAAACT
*
3758020 AGTCACGCAATACCTTATCAAAAAC
1 AGTCACGCAATGCCTTATCAAAAAC
3758045 CAAGCACAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
96 15 0.14
97 4 0.04
98 1 0.01
99 2 0.02
100 86 0.80
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (98 bp):
AGTCACGCAATGCCTTATCAAAAACTAGTCACACAATGCCTATAAACTAGTCACGCAATACTCTA
TCAAACTAATCACGCAATAATTTATCAAAAACT
Found at i:3757968 original size:48 final size:49
Alignment explanation
Indices: 3757724--3758044 Score: 268
Period size: 48 Copynumber: 6.5 Consensus size: 49
3757714 TTTACTAACA
* *
3757724 AGTCACGCAATGCCTTA-C--TAACAAGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCC-TATC--AAACT
* * * *
3757773 AGTCACGTAATGCCTTATCAGAAATTAGTCACGCAAT---TCTCAAAGT
1 AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTATCAAACT
* *
3757819 CAGTCACGCAATGCCTTATCAGAAACTAGTCACACAATGCCTTATTAAAAACT
1 -AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCC-TA-T-CAAACT
*
3757872 AGTCACGCAATGCC-TATC---AACTAGTCACGCAATGCTTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGC-CTATC--AAACT
* *
3757920 AGTCACGTAATGCCTTATCAAAAACTAGTCACGCAATGCCTATC-AACT
1 AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTATCAAACT
* * * * ***
3757968 AGTTACGCAATACTTTATCAGAAACTAATCACGCAATAATTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAAT-GCCTATC--AAACT
* *
3758020 AGTCACGCAATACCTTATCAAAAAC
1 AGTCACGCAATGCCTTATCAGAAAC
3758045 CAAGCACAAA
Statistics
Matches: 222, Mismatches: 29, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
46 4 0.02
47 35 0.16
48 74 0.33
49 24 0.11
50 1 0.00
51 9 0.04
52 71 0.32
53 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (49 bp):
AGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTATCAAACT
Found at i:3758147 original size:17 final size:17
Alignment explanation
Indices: 3758125--3758157 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3758115 CTTTCAAAAT
*
3758125 TTCTAATTGGATAGAAG
1 TTCTAACTGGATAGAAG
3758142 TTCTAACTGGATAGAA
1 TTCTAACTGGATAGAA
3758158 CTTGAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.33
Consensus pattern (17 bp):
TTCTAACTGGATAGAAG
Found at i:3758505 original size:22 final size:22
Alignment explanation
Indices: 3758477--3758524 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
3758467 GCTAGAAGAA
3758477 GGAGGAACGACTTTAGCAAAAT
1 GGAGGAACGACTTTAGCAAAAT
3758499 GGAGGAACGACTTTAGCAAAAT
1 GGAGGAACGACTTTAGCAAAAT
3758521 GGAG
1 GGAG
3758525 AAGAAACAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.31, T:0.17
Consensus pattern (22 bp):
GGAGGAACGACTTTAGCAAAAT
Found at i:3773433 original size:31 final size:31
Alignment explanation
Indices: 3773398--3773463 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
3773388 TAATACTTTA
3773398 TTAAAAT-TAATTAATTATTT-TAAATATAATT
1 TTAAAATCTAATTAATT-TTTATAAAT-TAATT
* * *
3773429 TTAAACTCTAATTTATTTTTATGAATTAATT
1 TTAAAATCTAATTAATTTTTATAAATTAATT
3773460 TTAA
1 TTAA
3773464 TTTATTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (31 bp):
TTAAAATCTAATTAATTTTTATAAATTAATT
Found at i:3773479 original size:14 final size:14
Alignment explanation
Indices: 3773453--3773480 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3773443 ATTTTTATGA
3773453 ATTAATTTTAATTT
1 ATTAATTTTAATTT
3773467 ATTAATTTTAATTT
1 ATTAATTTTAATTT
3773481 TTATTAATAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTAATTTTAATTT
Found at i:3779884 original size:22 final size:22
Alignment explanation
Indices: 3779859--3779911 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
3779849 ATTTTATAGA
3779859 GGCTTAATCCAATTAAGTATTG
1 GGCTTAATCCAATTAAGTATTG
3779881 GGCTTAATCCAATTAAGTATTG
1 GGCTTAATCCAATTAAGTATTG
*
3779903 GGCTAAATC
1 GGCTTAATC
3779912 AAATATGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (22 bp):
GGCTTAATCCAATTAAGTATTG
Found at i:3780547 original size:28 final size:27
Alignment explanation
Indices: 3780519--3780582 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
3780509 ATGATTATTT
3780519 ATTT-TATTT-TTT-AAAATAGTAATA
1 ATTTATATTTATTTCAAAATAGTAATA
*
3780543 ATTTATAATTTATTTCAAAATATTAATA
1 ATTTAT-ATTTATTTCAAAATAGTAATA
*
3780571 ATTGATAATTTA
1 ATTTAT-ATTTA
3780583 AATATTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 4 0.12
25 1 0.03
26 4 0.12
27 3 0.09
28 22 0.65
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTATATTTATTTCAAAATAGTAATA
Found at i:3780787 original size:157 final size:156
Alignment explanation
Indices: 3780515--3780916 Score: 541
Period size: 150 Copynumber: 2.6 Consensus size: 156
3780505 ATTTATGATT
* *
3780515 ATTTATTTTATT-TTTTAAAATAGTAATAATTTATAATTTATTTCAAAATATTAATAATTGATAA
1 ATTTATTTTTTTATTTTAAAATATTAATAATTTATAATTTA-TTCAAAATATTAATAATTGATAA
* * **
3780579 TTTAAATATTAATATTTTATTTATAATTTAATTATTAACATTATAATATATTTTTATTTTA-TTA
65 TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATATTAATATTTTATTTA
* * *
3780643 TAATTTAAATGTTATTATGATTATTTTG
130 TAATTTAAATGATATCATG-GTATTTTG
* *
3780671 ATTTATTTGTTTTATTTTAAAATATTAATAATTTATAATTTATTCAAAACATTAATAATAGATAA
1 ATTTATTT-TTTTATTTTAAAATATTAATAATTTATAATTTATTCAAAATATTAATAATTGATAA
* ** * * *
3780736 TTTAAATGTTAATATTTTATTTATGTTTTAATCATTAACGTTTTAAAATATTAATATTTTATTTG
65 TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATATTAATATTTTATTTA
3780801 TAATTTAAATGATATCATGGT-TTTT-
130 TAATTTAAATGATATCATGGTATTTTG
* * *
3780826 -TTTA---TTTTATTTTGAAATATTAATCATTTATAATTTATTTAAAATATTAATAATTGATAAT
1 ATTTATTTTTTTATTTTAAAATATTAATAATTTATAATTTATTCAAAATATTAATAATTGATAAT
3780887 TTAAATATTAATATTTTATTTATAATTTAA
66 TTAAATATTAATATTTTATTTATAATTTAA
3780917 ATGTTATTAT
Statistics
Matches: 218, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
150 79 0.36
154 4 0.02
156 12 0.06
157 77 0.35
158 46 0.21
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (156 bp):
ATTTATTTTTTTATTTTAAAATATTAATAATTTATAATTTATTCAAAATATTAATAATTGATAAT
TTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATATTAATATTTTATTTAT
AATTTAAATGATATCATGGTATTTTG
Found at i:3780873 original size:27 final size:28
Alignment explanation
Indices: 3780831--3780889 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
3780821 TTTTTTTTAT
* * *
3780831 TTTATTTTGAAATATTAATCATTTATAA
1 TTTATTTTAAAATATTAATAATTGATAA
3780859 TTTA-TTTAAAATATTAATAATTGATAA
1 TTTATTTTAAAATATTAATAATTGATAA
3780886 TTTA
1 TTTA
3780890 AATATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTATTTTAAAATATTAATAATTGATAA
Found at i:3780898 original size:108 final size:114
Alignment explanation
Indices: 3780781--3781032 Score: 345
Period size: 118 Copynumber: 2.2 Consensus size: 114
3780771 TAACGTTTTA
*
3780781 AAATATTAATATTTTATTTGTAATTTAAATGATATCATG-GT-TTT-TTTTATTTTA-T-TTTG-
1 AAATATTAATATTTTATTTATAATTTAAATGATATCATGAGTATTTATTTTATTTTATTATTTGT
* *
3780840 AAATATTAATCATTTATAATTTATTTAAAATATTAATAATTGATAATTT
66 AAACATTAATCATTTATAATTTATTTAAAATATCAATAATTGATAATTT
* * *
3780889 AAATATTAATATTTTATTTATAATTTAAATGTTATTATGATTATTTACTTTTATTTTAGTTTATT
1 AAATATTAATATTTTATTTATAATTTAAATGATATCATGAGTATTTA-TTTTATTTTA--TTATT
* *
3780954 TGTTATACATTAATCATTTATAATTTATTTAAAATATCAATAATTGATCATTT
63 TG-TAAACATTAATCATTTATAATTTATTTAAAATATCAATAATTGATAATTT
*
3781007 ATATATTAATATTTTATTTATAATTT
1 AAATATTAATATTTTATTTATAATTT
3781033 TTAATTACTC
Statistics
Matches: 125, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
108 36 0.29
109 1 0.01
110 3 0.02
112 10 0.08
115 1 0.01
116 4 0.03
118 70 0.56
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (114 bp):
AAATATTAATATTTTATTTATAATTTAAATGATATCATGAGTATTTATTTTATTTTATTATTTGT
AAACATTAATCATTTATAATTTATTTAAAATATCAATAATTGATAATTT
Found at i:3781053 original size:34 final size:34
Alignment explanation
Indices: 3781013--3781104 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 34
3781003 ATTTATATAT
* ** *
3781013 TAATATTTTATTTATAATTTTTAATTACTCATTAA
1 TAATATTTTATTTATAATTTAT-ATTACAAAATAA
*
3781048 -AATATTTATAATTTAATAATTAATATTACAAAATAA
1 TAATATTT-T-ATTT-ATAATTTATATTACAAAATAA
3781084 TAATATTTTATTTATAATTTA
1 TAATATTTTATTTATAATTTA
3781105 AATGTTATTG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
34 14 0.30
35 5 0.11
36 14 0.30
37 14 0.30
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (34 bp):
TAATATTTTATTTATAATTTATATTACAAAATAA
Found at i:3781153 original size:28 final size:28
Alignment explanation
Indices: 3781122--3781208 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
3781112 TTGTGATTAT
3781122 TTTATTTTTAAATATTAATAATTAATAA
1 TTTATTTTTAAATATTAATAATTAATAA
* *
3781150 TTTATTTTTAAATATGAATAATTTATAA
1 TTTATTTTTAAATATTAATAATTAATAA
* * *
3781178 TTTA-TTTAAAATATTAATAATTGATCA
1 TTTATTTTTAAATATTAATAATTAATAA
3781205 TTTA
1 TTTA
3781209 AATATTAGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.43
28 30 0.57
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTATTTTTAAATATTAATAATTAATAA
Found at i:3781341 original size:72 final size:72
Alignment explanation
Indices: 3781205--3781363 Score: 194
Period size: 72 Copynumber: 2.2 Consensus size: 72
3781195 TAATTGATCA
* * * * *
3781205 TTTAAATATTAGTATTCTATTTATAATTTAATCATTACTATTTTAAAATATTATTATGATTATTT
1 TTTAAATATTAGTATTCTATTTATAATTTAATCATTAATATGTTAAAATACTAATATGAATATTT
3781270 TTTTATT
66 TTTTATT
* * *
3781277 TTTAGATATTATTAATT-TATTTATAATTTAATCATTAATATGTTAAAATACTAATATTAATATT
1 TTTAAATATTAGT-ATTCTATTTATAATTTAATCATTAATATGTTAAAATACTAATATGAATATT
3781341 TATATTTATAT
65 T-T-TTTAT-T
3781352 TTATAAATATTA
1 TT-TAAATATTA
3781364 ATGGGACTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
72 53 0.73
73 4 0.05
74 5 0.07
75 3 0.04
76 8 0.11
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (72 bp):
TTTAAATATTAGTATTCTATTTATAATTTAATCATTAATATGTTAAAATACTAATATGAATATTT
TTTTATT
Found at i:3782420 original size:25 final size:25
Alignment explanation
Indices: 3782391--3782458 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
3782381 TTAATCATAA
3782391 TAATATTAAATTATAAATAAAATAT
1 TAATATTAAATTATAAATAAAATAT
*
3782416 TAATAATTAAATTAT-ACTAAAATAT
1 TAAT-ATTAAATTATAAATAAAATAT
3782441 TAATATTTAAATTATAAA
1 TAATA-TTAAATTATAAA
3782459 ATTATTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 1 0.03
25 26 0.68
26 11 0.29
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATATTAAATTATAAATAAAATAT
Done.