Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 13 of 131
Found at i:3342011 original size:27 final size:26
Alignment explanation
Indices: 3341979--3342035 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3341969 AATGTTGTCT
* *
3341979 GTAAAATATTTATATTTTTTGAGA-AA
1 GTAAAAAATTTATATTGTTTG-GATAA
*
3342005 GTAAAAAATTTCTATTGTTTGGATAA
1 GTAAAAAATTTATATTGTTTGGATAA
3342031 GTAAA
1 GTAAA
3342036 TGGAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (26 bp):
GTAAAAAATTTATATTGTTTGGATAA
Found at i:3342134 original size:25 final size:24
Alignment explanation
Indices: 3342105--3342163 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 24
3342095 TGATATAATT
3342105 ATTAAAATATTAAAAATTATTTATG
1 ATTAAAATATTAAAAATT-TTTATG
*
3342130 ATTAAAATATATTAAAAATTTTTATT
1 ATT-AAA-ATATTAAAAATTTTTATG
3342156 ATTAAAAT
1 ATTAAAAT
3342164 TTTTTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 2 0.06
25 6 0.19
26 11 0.35
27 12 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTAAAATATTAAAAATTTTTATG
Found at i:3342153 original size:26 final size:27
Alignment explanation
Indices: 3342111--3342163 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
3342101 AATTATTAAA
3342111 ATATTAAAAATTATTTATGATTAAAAT
1 ATATTAAAAATTATTTATGATTAAAAT
*
3342138 ATATTAAAAATT-TTTATTATTAAAAT
1 ATATTAAAAATTATTTATGATTAAAAT
3342164 TTTTTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATTAAAAATTATTTATGATTAAAAT
Found at i:3342160 original size:16 final size:15
Alignment explanation
Indices: 3342137--3342180 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 15
3342127 ATGATTAAAA
3342137 TATATTAAAAATTTT
1 TATATTAAAAATTTT
*
3342152 TATTATTAAAATTTTT
1 TA-TATTAAAAATTTT
3342168 TATATTAAAAATT
1 TATATTAAAAATT
3342181 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTAAAAATTTT
Found at i:3342164 original size:15 final size:15
Alignment explanation
Indices: 3342139--3342210 Score: 58
Period size: 15 Copynumber: 4.6 Consensus size: 15
3342129 GATTAAAATA
3342139 TATTAAAAATTTTTAT
1 TATT-AAAATTTTTAT
3342155 TATTAAAATTTTT-T
1 TATTAAAATTTTTAT
* *
3342169 ATATTAAAAATTATAT
1 -TATTAAAATTTTTAT
*
3342185 T-TTAATAATATATTTAA
1 TATTAA-AAT-T-TTTAT
3342202 TATTAAAAT
1 TATTAAAAT
3342211 ATTATACTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 5 0.11
15 23 0.51
16 6 0.13
17 7 0.16
18 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAAAATTTTTAT
Found at i:3342228 original size:109 final size:109
Alignment explanation
Indices: 3342141--3342393 Score: 345
Period size: 109 Copynumber: 2.4 Consensus size: 109
3342131 TTAAAATATA
* * * *
3342141 TTAAAAATTT-TT-AT-TATTAAAATTTTTTATAT-TAAAAATTATATTTTAATAATATATTTAA
1 TTAAAAATTTATTAATATATTAAAATATTTAAAATAGAAAAATTATATTTTAATAATATATTTAA
*
3342202 TATTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTT
66 TATTAAAATATTATACTAAATATAAAAAATTTAAAACAAAACTT
* ** *
3342246 TTTATTATTTATTAATATTTTAAAATATTTAAAATAGAAAAATTATATTTTAATAATATATTTAA
1 TTAAAAATTTATTAATATATTAAAATATTTAAAATAGAAAAATTATATTTTAATAATATATTTAA
*
3342311 TATTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTAT
66 TATTAAAATATTATACTAAATATAAAAAATTTAAAACAAAACT-T
** *
3342356 TT-ATTATTTATTAATATTTTAAAATATTTAAAATAGAA
1 TTAAAAATTTATTAATATATTAAAATATTTAAAATAGAA
3342394 CTACTATTCT
Statistics
Matches: 135, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
105 7 0.05
106 2 0.01
107 2 0.01
108 14 0.10
109 107 0.79
110 3 0.02
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (109 bp):
TTAAAAATTTATTAATATATTAAAATATTTAAAATAGAAAAATTATATTTTAATAATATATTTAA
TATTAAAATATTATACTAAATATAAAAAATTTAAAACAAAACTT
Found at i:3342263 original size:51 final size:51
Alignment explanation
Indices: 3342208--3342373 Score: 135
Period size: 51 Copynumber: 3.1 Consensus size: 51
3342198 TTAATATTAA
3342208 AATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATT
1 AATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATT
* * ** *
3342259 AATATTTTA--AAATATTTAAAA-TAGAAAA-ATTATA-TTTTAATAATATATTTAATATT
1 AATATTATACTAAATA-TAAAAACTTTAAAACA--AAACTTTT--T-AT-TA-TT--TATT
*
3342315 AAAATATTATACTAAATATAAAAACTTTAAAACAAAACTATTTATTATTTATT
1 --AATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATT
3342368 AATATT
1 AATATT
3342374 TTAAAATATT
Statistics
Matches: 87, Mismatches: 11, Indels: 34
0.66 0.08 0.26
Matches are distributed among these distances:
48 1 0.01
49 14 0.16
50 7 0.08
51 15 0.17
52 2 0.02
53 6 0.07
54 2 0.02
55 2 0.02
56 6 0.07
57 2 0.02
58 9 0.10
59 7 0.08
60 13 0.15
61 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (51 bp):
AATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATT
Found at i:3342270 original size:61 final size:61
Alignment explanation
Indices: 3342204--3342383 Score: 199
Period size: 61 Copynumber: 3.2 Consensus size: 61
3342194 ATATTTAATA
3342204 TTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATTAATATT
1 TTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATTAATATT
* * * * *
3342265 TTAAAATATT-TA--AAATAGAAAAA--TT------ATA-TTTTAATAATATATTTAATA--
1 TTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTA-TTAATATT
*
3342313 TTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTATTTATTATTTATTAATATT
1 TTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATTAATATT
3342374 TTAAAATATT
1 TTAAAATATT
3342384 TAAAATAGAA
Statistics
Matches: 93, Mismatches: 11, Indels: 30
0.69 0.08 0.22
Matches are distributed among these distances:
48 10 0.11
49 12 0.13
50 8 0.09
51 10 0.11
53 2 0.02
56 2 0.02
58 10 0.11
59 8 0.09
60 11 0.12
61 20 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (61 bp):
TTAAAATATTATACTAAATATAAAAACTTTAAAACAAAACTTTTTATTATTTATTAATATT
Found at i:3342751 original size:28 final size:29
Alignment explanation
Indices: 3342705--3342760 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
3342695 ATATGTTATT
*
3342705 TAATATATTATTATTTATTATTAAAATAA
1 TAATATATTACTATTTATTATTAAAATAA
*
3342734 TAATATA-TACTATTTATTATTGAAATA
1 TAATATATTACTATTTATTATTAAAATA
3342761 TTAAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TAATATATTACTATTTATTATTAAAATAA
Found at i:3342751 original size:35 final size:36
Alignment explanation
Indices: 3342672--3342766 Score: 102
Period size: 38 Copynumber: 2.6 Consensus size: 36
3342662 TTAAAATATA
* * *
3342672 ATTTAATATTAATTATTAAAATAATATGTTATTTAAT
1 ATTTATTATTAATTATTAAAATAATA-GATATATAAT
* *
3342709 ATATTATTATTTATTATTAAAATAATA-ATATATACT
1 AT-TTATTATTAATTATTAAAATAATAGATATATAAT
*
3342745 ATTTATTATTGAAATATTAAAA
1 ATTTATTATT-AATTATTAAAA
3342767 ATTTTATGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
35 8 0.16
36 17 0.35
37 2 0.04
38 22 0.45
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (36 bp):
ATTTATTATTAATTATTAAAATAATAGATATATAAT
Found at i:3343260 original size:22 final size:22
Alignment explanation
Indices: 3343219--3343260 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3343209 ATAATTTTAT
* *
3343219 TTTTTGTTGATCAGTAAGTTAA
1 TTTTTATTGATCAATAAGTTAA
*
3343241 TTTTTATTGATCAATTAGTT
1 TTTTTATTGATCAATAAGTT
3343261 TTCTGACTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (22 bp):
TTTTTATTGATCAATAAGTTAA
Found at i:3362426 original size:3 final size:3
Alignment explanation
Indices: 3362418--3362465 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3362408 GCCTCTTGCC
3362418 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3362466 ATACTTTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3368235 original size:298 final size:295
Alignment explanation
Indices: 3367708--3368343 Score: 893
Period size: 298 Copynumber: 2.1 Consensus size: 295
3367698 ATAAACAAGA
* * * * *
3367708 GATGAGCCAATATTATGAATGCAAACACTTGCTTAATTGCCAGCAGGAGGACCATCAATGAAGGG
1 GATGAACCAATATTATGAATGCAAAAACTTGCTTAATTACC-GCAGCAGGACCATCAATGAAGGA
* * * * * * * * * *
3367773 GCCAGCGTTATCATGAAGATTTGGGTCATCATCCACATTCAGCGAGTCTTCAACAAAGCTAGTCC
65 GCCAACGTTACCAGGAAGATTTGGGACATCAACCACATCCAGCAAGTATCCAACAAAGCTAGCCC
3367838 CAACTCCTAAATTAAAAAGAAGAAACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAGACC
130 CAACTCCTAAATTAAAAAGAAGAAACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAGACC
* *
3367903 TTGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACAAGTGAATT
195 TCGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACAAGTAAATT
*
3367968 CTTCGACAATTTGAGAAAAGAATAAGGCA-TAAACAT
260 CTTCAACAATTTGAGAAAAGAATAAGG-AGTAAACAT
* * * *
3368004 GATGAACCAATAATATGAATGCAAAAACTTGCTTAATTACCGTCAGCAGGATCATTAGTGAAGGA
1 GATGAACCAATATTATGAATGCAAAAACTTGCTTAATTACCG-CAGCAGGACCATCAATGAAGGA
* *
3368069 GCCAATGTTACCAGGAAGATTTGGGACATCAACCACATCCAGCAAGTAATCCGA-AAAGCTGACA
65 GCCAACGTTACCAGGAAGATTTGGGACATCAACCACATCCAGCAAGT-ATCCAACAAAGCT---A
*
3368133 GCCCCAACTCCTAAATTAAAAA-AA-AACACAAATCAGGATGAGTGAATTTAGGAAGTTAAGAGA
126 GCCCCAACTCCTAAATTAAAAAGAAGAA-ACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGA
* * * *
3368196 AGTCCTCGTAGTCAAGAGTAAAATTAACCAACTCAAAAGCAGATTTTTAATACCAAGAAACATGT
190 AGACCTCGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACAAGT
*
3368261 AAATTCTTCAACAATTTGAGAAAAGAATAAGGAGTAAACGT
255 AAATTCTTCAACAATTTGAGAAAAGAATAAGGAGTAAACAT
*
3368302 GATGAACCAACATTATGAATGCAAAAACTTGCTTAATTACCG
1 GATGAACCAATATTATGAATGCAAAAACTTGCTTAATTACCG
3368344 GTAGCAGAGT
Statistics
Matches: 301, Mismatches: 32, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
295 1 0.00
296 99 0.33
297 6 0.02
298 173 0.57
299 22 0.07
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (295 bp):
GATGAACCAATATTATGAATGCAAAAACTTGCTTAATTACCGCAGCAGGACCATCAATGAAGGAG
CCAACGTTACCAGGAAGATTTGGGACATCAACCACATCCAGCAAGTATCCAACAAAGCTAGCCCC
AACTCCTAAATTAAAAAGAAGAAACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAGACCT
CGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACAAGTAAATTC
TTCAACAATTTGAGAAAAGAATAAGGAGTAAACAT
Found at i:3368558 original size:302 final size:290
Alignment explanation
Indices: 3367836--3368638 Score: 917
Period size: 298 Copynumber: 2.7 Consensus size: 290
3367826 CAAAGCTAGT
3367836 CCCAACTCCTAAATTAAAAAGAAGAA-ACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAG
1 CCCAACTCCTAAATT-AAAAGAA-AACACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAG
* * *
3367900 ACCTTGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACAAGTGA
64 ACCTTGTAGTCAAGAGTAAAATTAACCAACTCAAAAGCAAATTTTTAATACCAAGAAACATGTAA
* *
3367965 ATTCTTCGACAATTTGAGAAAAGAATAAGGCA-TAAACATGATGAACCAATAATATGAATGCAAA
129 ATTCTTCGACAATTTGAGAAAAGAATAAGG-AGTAAACATGATGAACCAACATTATGAATGCAAA
*
3368029 AACTTGCTTAATTACCGTCAGCAGGATCATTAGTGAAGGAGCCAATGTTACCAGGAAGATTTGGG
193 AACTTGCTTAATTACCGTCAGCAGG-----TAGT--ACGA-CCAATGTTACCAGGAAGATTTGGG
*
3368094 ACATCAACCACATCCAGCAAGTAATCCGAAAAGCTGACAGC
250 ACATCAACCACATCCAGAAAGTAATCCGAAAAGCTGACAGC
* * *
3368135 CCCAACTCCTAAATTAAAAAAAAACACAAATCAGGATGAGTGAATTTAGGAAGTTAAGAGAAGTC
1 CCCAACTCCTAAATTAAAAGAAAACACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAGAC
* *
3368200 CTCGTAGTCAAGAGTAAAATTAACCAACTCAAAAGCAGATTTTTAATACCAAGAAACATGTAAAT
66 CTTGTAGTCAAGAGTAAAATTAACCAACTCAAAAGCAAATTTTTAATACCAAGAAACATGTAAAT
* *
3368265 TCTTCAACAATTTGAGAAAAGAATAAGGAGTAAACGTGATGAACCAACATTATGAATGCAAAAAC
131 TCTTCGACAATTTGAGAAAAGAATAAGGAGTAAACATGATGAACCAACATTATGAATGCAAAAAC
** *
3368330 TTGCTTAATTACCGGT-AGCA-G-AGT-CGA-CAATGTTATTATGACA-ATTTGGGGCAAAGGCA
196 TTGCTTAATTACC-GTCAGCAGGTAGTACGACCAATGTTACCAGGA-AGATTT-GGG---A--CA
* ** * *
3368389 TCCGA-CACAT-TTGAAAAGTTATGATTTGCACCAGAAGAG-TAGCCAGC
253 T-CAACCACATCCAG-AAAG-TA--A--T---CC-GAAAAGCT-GACAGC
* * ** * *
3368436 CCCATCTCCTAAATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAGGAAACTATGAGAGGA
1 CCCAACTCCTAAATTAA-AAGAAAACACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAGA
** * *
3368501 CCTTACAGTCAATAGTAAAATTAACCAACTCAAAAGCAAATTTTTAATACTAAGAAACATGTAAA
65 CCTTGTAGTCAAGAGTAAAATTAACCAACTCAAAAGCAAATTTTTAATACCAAGAAACATGTAAA
* * * *
3368566 TTTTTCGACAATTTGAGAAATGAATAAGGAGTAAACATGATGAACCAACGTTATGAAGGCAAAAA
130 TTCTTCGACAATTTGAGAAAAGAATAAGGAGTAAACATGATGAACCAACATTATGAATGCAAAAA
3368631 CTTGCTTA
195 CTTGCTTA
3368639 GTTGTCAACA
Statistics
Matches: 438, Mismatches: 43, Indels: 43
0.84 0.08 0.08
Matches are distributed among these distances:
286 15 0.03
287 4 0.01
288 2 0.00
290 1 0.00
291 4 0.01
292 11 0.03
293 4 0.01
295 1 0.00
297 5 0.01
298 180 0.41
299 17 0.04
300 3 0.01
301 26 0.06
302 165 0.38
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (290 bp):
CCCAACTCCTAAATTAAAAGAAAACACAAACCAGGATGAGTGAATTTAGGAAGTTAAGAGAAGAC
CTTGTAGTCAAGAGTAAAATTAACCAACTCAAAAGCAAATTTTTAATACCAAGAAACATGTAAAT
TCTTCGACAATTTGAGAAAAGAATAAGGAGTAAACATGATGAACCAACATTATGAATGCAAAAAC
TTGCTTAATTACCGTCAGCAGGTAGTACGACCAATGTTACCAGGAAGATTTGGGACATCAACCAC
ATCCAGAAAGTAATCCGAAAAGCTGACAGC
Found at i:3369086 original size:2 final size:2
Alignment explanation
Indices: 3369079--3369109 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3369069 TATTCCTAAC
3369079 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3369110 GATGATGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3372832 original size:60 final size:60
Alignment explanation
Indices: 3372756--3372993 Score: 329
Period size: 59 Copynumber: 3.9 Consensus size: 60
3372746 CTCTTTTTTG
* * *
3372756 AAAACTTATTTTTAAGAAAAATGGATACTTTTAACTTTTTCCCAAAAATATTTTTTAGAA
1 AAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAGAA
3372816 AAAACTTA-TTTCTAAGAAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTAGAAA
1 AAAACTTATTTTC-AAGAAAAATTGATACTTTCAACTTTTTCC-CAAAAATA-TTTTTTAG-AA
**
3372878 AAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTAG-A
1 AAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAGAA
* * **
3372937 AAAACTTATTTTCAAGGAAAATTGACACTTTCAACTTTTTCTTAAAAATATATTTTT
1 AAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATAT-TTTTT
3372994 TTGAATTTCA
Statistics
Matches: 164, Mismatches: 7, Indels: 14
0.89 0.04 0.08
Matches are distributed among these distances:
59 59 0.36
60 41 0.25
61 16 0.10
62 39 0.24
63 9 0.05
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.42
Consensus pattern (60 bp):
AAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTAGAA
Found at i:3372844 original size:122 final size:120
Alignment explanation
Indices: 3372706--3372995 Score: 363
Period size: 122 Copynumber: 2.4 Consensus size: 120
3372696 TGCTTTTGTA
* *
3372706 CAAGAAAAATTTATACTTTCAACTTTTCCTAAAAAAAAAACTCTTTTTT-G-AAAACTTATTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCT-AAAAAAAAA-T-TTTTTTAGAAAAACTTATTTTC
*
3372769 AAGAAAAATGGATACTTTTAACTTTTTCCCAAAAATATTTTTTAGAAAAAACTTA-TTT
63 AAGAAAAATGGATACTTTCAACTTTTTCCCAAAAATATTTTTTAG-AAAAACTTATTTT
* *
3372827 CTAAGAAAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTAGAAAAAAACTTATTTTC
1 C-AAGAAAAATTGATACTTTCAACTTTTCCTAAAAAAAAATTTTTTTAG--AAAAACTTATTTTC
* **
3372891 AAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTAGAAAAACTTATTTT
63 AAGAAAAATGGATACTTTCAACTTTTTCCCAAAAATATTTTTTAGAAAAACTTATTTT
* * * * *
3372949 CAAGGAAAATTGACACTTTCAACTTTTTCTTAAAAATATATTTTTTT
1 CAAGAAAAATTGATACTTTCAAC-TTTTCCTAAAAAAAAATTTTTTT
3372996 GAATTTCATT
Statistics
Matches: 148, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
118 6 0.04
119 2 0.01
120 6 0.04
121 30 0.20
122 91 0.61
123 13 0.09
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (120 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAAAAATTTTTTTAGAAAAACTTATTTTCAAG
AAAAATGGATACTTTCAACTTTTTCCCAAAAATATTTTTTAGAAAAACTTATTTT
Found at i:3372969 original size:59 final size:60
Alignment explanation
Indices: 3372706--3372993 Score: 350
Period size: 62 Copynumber: 4.7 Consensus size: 60
3372696 TGCTTTTGTA
* * * * *
3372706 CAAGAAAAATTTATACTTTCAACTTTTCCTAAAAAAAAAACTCTTTTTTG--AAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTTCT--CAAAAATA-T-TTTTTAGAAAAAACTTATTTT
* * * *
3372768 TAAGAAAAATGGATACTTTTAACTTTTTCCCAAAAATATTTTTTAGAAAAAACTTA-TTT
1 CAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAAAACTTATTTT
*
3372827 CTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAAAAACTTATTTT
1 C-AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTAG-AAAAAACTTATTTT
*
3372890 CAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTAG-AAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAAAACTTATTTT
* * *
3372949 CAAGGAAAATTGACACTTTCAACTTTTTCTTAAAAATATATTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTT
3372994 TTGAATTTCA
Statistics
Matches: 201, Mismatches: 18, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
58 6 0.03
59 54 0.27
60 52 0.26
61 16 0.08
62 69 0.34
63 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (60 bp):
CAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAAAACTTATTTT
Found at i:3373956 original size:16 final size:17
Alignment explanation
Indices: 3373937--3374053 Score: 79
Period size: 16 Copynumber: 7.1 Consensus size: 17
3373927 TAAAGATAAT
3373937 ATATTAATAGATAAA-A
1 ATATTAATAGATAAATA
3373953 ATATTAATAGATAAATA
1 ATATTAATAGATAAATA
* *
3373970 ATAATAA-AG-TATAT-
1 ATATTAATAGATAAATA
* *
3373984 ATATCAACAGATAAATA
1 ATATTAATAGATAAATA
*
3374001 ATA--AATA-AAAAATA
1 ATATTAATAGATAAATA
*
3374015 TATATTAATAAATAGTAATA
1 -ATATTAATAGATA--AATA
3374035 ATAATTAAATA-ATAAATA
1 AT-ATT-AATAGATAAATA
3374053 A
1 A
3374054 ATAAGATACA
Statistics
Matches: 81, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
14 11 0.14
15 12 0.15
16 21 0.26
17 14 0.17
18 7 0.09
19 2 0.02
20 10 0.12
21 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
ATATTAATAGATAAATA
Found at i:3374006 original size:7 final size:7
Alignment explanation
Indices: 3373994--3374053 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
3373984 ATATCAACAG
3373994 ATAAATA
1 ATAAATA
3374001 ATAAATA
1 ATAAATA
*
3374008 AAAAAT-
1 ATAAATA
*
3374014 ATATATTA
1 ATA-AATA
3374022 ATAAATA
1 ATAAATA
*
3374029 GTAATAATA
1 AT-A-AATA
3374038 ATTAAATA
1 A-TAAATA
3374046 ATAAATA
1 ATAAATA
3374053 A
1 A
3374054 ATAAGATACA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
6 2 0.05
7 25 0.60
8 9 0.21
9 5 0.12
10 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (7 bp):
ATAAATA
Found at i:3374014 original size:11 final size:11
Alignment explanation
Indices: 3373910--3374057 Score: 68
Period size: 11 Copynumber: 12.5 Consensus size: 11
3373900 AAAAGAAAAA
*
3373910 AAATAAAAAAT
1 AAATAATAAAT
* *
3373921 AAAAAATAAAG
1 AAATAATAAAT
*
3373932 ATAATATATTAAT
1 A-AATA-ATAAAT
*
3373945 AGATAA-AAAT
1 AAATAATAAAT
3373955 ATTAATAGATAAAT
1 A--AATA-ATAAAT
3373969 -AATAATAAAGT
1 AAATAATAAA-T
*
3373980 ATATATATCAACAGAT
1 AAATA-AT--A-A-AT
3373996 AAATAATAAAT
1 AAATAATAAAT
* *
3374007 AAAAAATATAT
1 AAATAATAAAT
*
3374018 -ATTAATAAAT
1 AAATAATAAAT
*
3374028 AGTAATAATAATT
1 A--AATAATAAAT
3374041 AAATAATAAAT
1 AAATAATAAAT
3374052 AAATAA
1 AAATAA
3374058 GATACAAAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
10 16 0.16
11 41 0.40
12 13 0.13
13 18 0.18
14 4 0.04
15 3 0.03
16 6 0.06
17 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:3374325 original size:42 final size:42
Alignment explanation
Indices: 3374271--3374424 Score: 136
Period size: 42 Copynumber: 3.7 Consensus size: 42
3374261 TTTGATCAAG
*
3374271 GCTCATCTAAATAGAAGCTCAACAACTTTAAAAATAAGCAAA
1 GCTCCTCTAAATAGAAGCTCAACAACTTTAAAAATAAGCAAA
* * * * * *
3374313 GCTCCTTTAAATAGAGGCTCGACGACCTTGAAAATAAGCAAA
1 GCTCCTCTAAATAGAAGCTCAACAACTTTAAAAATAAGCAAA
** * *
3374355 GCTCCTCTAAGCA-AAGGCTTAACAACTTTTAAAAATAA--AAG
1 GCTCCTCTAAATAGAA-GCTCAACAAC-TTTAAAAATAAGCAAA
* *
3374396 GCTCCTCT-AATCAGAGGCTCAACGACTTT
1 GCTCCTCTAAAT-AGAAGCTCAACAACTTT
3374425 TGAAAAGTAA
Statistics
Matches: 86, Mismatches: 22, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
40 4 0.05
41 20 0.23
42 53 0.62
43 9 0.10
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (42 bp):
GCTCCTCTAAATAGAAGCTCAACAACTTTAAAAATAAGCAAA
Found at i:3374442 original size:83 final size:82
Alignment explanation
Indices: 3374291--3374447 Score: 185
Period size: 83 Copynumber: 1.9 Consensus size: 82
3374281 ATAGAAGCTC
* *
3374291 AACAACTTTAAAAATAAGCAAAGCTCCTTTAAATAGAGGCTCGACGACCTTGAAAATAAGCAAAG
1 AACAACTTTAAAAATAA-CAAAGCTCCTCTAAATAGAGGCTCAACGACCTTGAAAATAA-CAAAG
3374356 CTCCTCTAAGCAAAGGCTT
64 CTCCTCTAAGCAAAGGCTT
* * *
3374375 AACAACTTTTAAAAATAA-AAGGCTCCTCT-AATCAGAGGCTCAACGACTTTTGAAAAGTAA-AT
1 AACAAC-TTTAAAAATAACAAAGCTCCTCTAAAT-AGAGGCTCAACGAC-CTTGAAAA-TAACAA
*
3374437 TGCTCCTCTAA
62 AGCTCCTCTAA
3374448 TTAGAGGCAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
82 3 0.05
83 33 0.52
84 13 0.21
85 14 0.22
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (82 bp):
AACAACTTTAAAAATAACAAAGCTCCTCTAAATAGAGGCTCAACGACCTTGAAAATAACAAAGCT
CCTCTAAGCAAAGGCTT
Found at i:3374480 original size:41 final size:40
Alignment explanation
Indices: 3374355--3374523 Score: 151
Period size: 41 Copynumber: 4.1 Consensus size: 40
3374345 AATAAGCAAA
* * * * * **
3374355 GCTCCTCTAAGCAAAGGCTTAACAACTTTTAAAAATAAAAG
1 GCTCCTCTAATCAGAGGCATCA-AACTTTGAAAAATAAATT
*
3374396 GCTCCTCTAATCAGAGGC-TCAACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAATCAGAGGCATCAA--AC-TTTGAAAAATAAATT
* *
3374438 GCTCCTCTAATTAGAGGCATCATAACTTTGAAAAATAGATT
1 GCTCCTCTAATCAGAGGCATCA-AACTTTGAAAAATAAATT
* * **
3374479 GCTCCTCTAAACAGAGTCATCACAACTTCAAAAAATAAATT
1 GCTCCTCTAATCAGAGGCATCA-AACTTTGAAAAATAAATT
3374520 GCTC
1 GCTC
3374524 ATTGACAATC
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 69 0.65
42 30 0.28
43 3 0.03
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (40 bp):
GCTCCTCTAATCAGAGGCATCAAACTTTGAAAAATAAATT
Found at i:3375289 original size:25 final size:25
Alignment explanation
Indices: 3375255--3375308 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
3375245 AAACTTAGGC
3375255 CAATGCCCAAAAATGAACAATCAGA
1 CAATGCCCAAAAATGAACAATCAGA
3375280 CAATGCCCAAAAATGAACAATCAGA
1 CAATGCCCAAAAATGAACAATCAGA
3375305 CAAT
1 CAAT
3375309 CATGATAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.11, T:0.13
Consensus pattern (25 bp):
CAATGCCCAAAAATGAACAATCAGA
Found at i:3375557 original size:32 final size:32
Alignment explanation
Indices: 3375519--3375581 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3375509 CCTTGAGTCC
*
3375519 TCTTTTTTC-ATTCATTTTTTTTATTTTTTTT
1 TCTTTTTTCAATTCATTTTTTCTATTTTTTTT
* *
3375550 TCTTTTTTCAATTTATTTTTTCTCTTTTTTTT
1 TCTTTTTTCAATTCATTTTTTCTATTTTTTTT
3375582 CAAGCATAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (32 bp):
TCTTTTTTCAATTCATTTTTTCTATTTTTTTT
Found at i:3375564 original size:23 final size:24
Alignment explanation
Indices: 3375538--3375584 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
3375528 ATTCATTTTT
3375538 TTTATTTTTT-T-TTCTTTTTTCAA
1 TTTATTTTTTCTCTT-TTTTTTCAA
3375561 TTTATTTTTTCTCTTTTTTTTCAA
1 TTTATTTTTTCTCTTTTTTTTCAA
3375585 GCATAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.45
24 10 0.45
25 2 0.09
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTATTTTTTCTCTTTTTTTTCAA
Found at i:3375569 original size:24 final size:23
Alignment explanation
Indices: 3375538--3375584 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3375528 ATTCATTTTT
*
3375538 TTTATTTTT-TTTTCTTTTTTCAA
1 TTTATTTTTCTCTT-TTTTTTCAA
3375561 TTTATTTTTTCTCTTTTTTTTCAA
1 TTTA-TTTTTCTCTTTTTTTTCAA
3375585 GCATAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 14 0.67
25 3 0.14
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTTTTCTCTTTTTTTTCAA
Found at i:3375582 original size:31 final size:31
Alignment explanation
Indices: 3375519--3375582 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3375509 CCTTGAGTCC
* *
3375519 TCTTTTTTCATTCATTTTTTTTATTTTTTTT
1 TCTTTTTTCATTCATTTTTTCTACTTTTTTT
*
3375550 TCTTTTTTCAATTTATTTTTTCT-CTTTTTTT
1 TCTTTTTTC-ATTCATTTTTTCTACTTTTTTT
3375581 TC
1 TC
3375583 AAGCATAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (31 bp):
TCTTTTTTCATTCATTTTTTCTACTTTTTTT
Found at i:3386225 original size:62 final size:60
Alignment explanation
Indices: 3386079--3386317 Score: 347
Period size: 59 Copynumber: 3.9 Consensus size: 60
3386069 CCTTTTTTTG
* **
3386079 AAAACTTATTTTTAAA-GAAAATAGATACTTTCAACTTTTTTTCCAAAAATATTTTTTAGAA
1 AAAACTTA-TTTTAAAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTAGAA
** *
3386140 AAAACTTATTTCCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTTAGAAA
1 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAG-AA
3386202 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAG-A
1 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAA
* *
3386261 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATATTTTT
1 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTT
3386318 TTGAATTTTA
Statistics
Matches: 163, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
59 50 0.31
60 18 0.11
61 46 0.28
62 49 0.30
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (60 bp):
AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAA
Found at i:3386318 original size:62 final size:61
Alignment explanation
Indices: 3386079--3386318 Score: 344
Period size: 61 Copynumber: 3.9 Consensus size: 61
3386069 CCTTTTTTTG
* **
3386079 AAAACTTATTTTTAAA-GAAAATAGATACTTTCAACTTTTTTTCCAAAAATA-TTTTTTAGAA
1 AAAACTTA-TTTTAAAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTAGAA
** *
3386140 AAAACTTATTTCCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTTAGAAA
1 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAG-AA
3386202 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAG-A
1 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAA
* *
3386261 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATATTTTTT
1 AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTT
3386319 TGAATTTTAT
Statistics
Matches: 163, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
59 49 0.30
60 13 0.08
61 52 0.32
62 49 0.30
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (61 bp):
AAAACTTATTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAA
Found at i:3386417 original size:4 final size:4
Alignment explanation
Indices: 3386394--3386438 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
3386384 TAATCTAATC
3386394 AATA AAT- AAT- AAT- AAT- AATA AATA AATA AAT- AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
3386437 AA
1 AA
3386439 AAAACTAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 15 0.38
4 24 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:3386427 original size:15 final size:15
Alignment explanation
Indices: 3386394--3386438 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3386384 TAATCTAATC
3386394 AATAAAT-AATAATAAT
1 AATAAATAAAT-A-AAT
3386410 AATAAATAAATAAAT
1 AATAAATAAATAAAT
3386425 AATAAATAAATAAA
1 AATAAATAAATAAA
3386439 AAAACTAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.61
16 8 0.29
17 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAATAAATAAAT
Found at i:3387233 original size:20 final size:20
Alignment explanation
Indices: 3387197--3387251 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3387187 AAAAGAAAGA
*
3387197 AAAAATTAT-AAAA-AATAT
1 AAAAATAATAAAAATAATAT
3387215 AAAAATAATAAAAATAATAT
1 AAAAATAATAAAAATAATAT
**
3387235 ATTAATAGATAAAAATA
1 AAAAATA-ATAAAAATA
3387252 TTAATAGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.26
19 4 0.13
20 10 0.32
21 9 0.29
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATAATAAAAATAATAT
Found at i:3387254 original size:16 final size:17
Alignment explanation
Indices: 3387233--3387268 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
3387223 TAAAAATAAT
3387233 ATATTAATAGATAAA-A
1 ATATTAATAGATAAATA
3387249 ATATTAATAGATAAATA
1 ATATTAATAGATAAATA
3387266 ATA
1 ATA
3387269 ATAAAGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATATTAATAGATAAATA
Found at i:3387266 original size:20 final size:20
Alignment explanation
Indices: 3387204--3387271 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
3387194 AGAAAAAATT
*
3387204 ATAAAAA-ATATAAAAAT-A
1 ATAAAAATATATAATAATAA
* *
3387222 ATAAAAATAATATATTAATAG
1 ATAAAAAT-ATATAATAATAA
3387243 ATAAAAATAT-TAATAGATAA
1 ATAAAAATATATAATA-ATAA
*
3387263 ATAATAATA
1 ATAAAAATA
3387272 AAGTATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 7 0.17
19 4 0.10
20 21 0.52
21 8 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
ATAAAAATATATAATAATAA
Found at i:3387303 original size:7 final size:7
Alignment explanation
Indices: 3387291--3387344 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
3387281 TATCAACAGG
3387291 TAAATAA
1 TAAATAA
3387298 TAAATAA
1 TAAATAA
*
3387305 TATAT-A
1 TAAATAA
*
3387311 T-ATTAA
1 TAAATAA
*
3387317 TAAATAG
1 TAAATAA
3387324 T-AATAA
1 TAAATAA
3387330 TAAATAAA
1 TAAAT-AA
3387338 TAAATAA
1 TAAATAA
3387345 ATAAGATACA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
5 1 0.03
6 9 0.24
7 20 0.54
8 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (7 bp):
TAAATAA
Found at i:3387322 original size:4 final size:4
Alignment explanation
Indices: 3387291--3387397 Score: 57
Period size: 4 Copynumber: 27.0 Consensus size: 4
3387281 TATCAACAGG
* * *
3387291 TAAA T-AA TAAA T-AA TATA TATA TTAA TAAA TAGTAA T-AA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA--AA TAAA TAAA TAAA
* * *
3387338 TAAA TAAA TAAGA TACAA AAAA TAAA -AACA CAAGA TACA -AAA TAAA
1 TAAA TAAA TAA-A TA-AA TAAA TAAA TAA-A TAA-A TAAA TAAA TAAA
3387384 -AAA TAAA -AAA TAAA
1 TAAA TAAA TAAA TAAA
3387398 ATGGATCTAT
Statistics
Matches: 81, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
3 19 0.23
4 49 0.60
5 9 0.11
6 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:3387343 original size:25 final size:26
Alignment explanation
Indices: 3387199--3387348 Score: 82
Period size: 25 Copynumber: 6.0 Consensus size: 26
3387189 AAGAAAGAAA
*
3387199 AAATTATAAA-AAATATAA-AAATAAT
1 AAATAATAAATAAATA-AATAAATAAT
* * *
3387224 AAA-AAT-AATATATTAATAGATAA-
1 AAATAATAAATAAATAAATAAATAAT
* *
3387247 AAAT-ATTAATAGATAAAT-AATAAT
1 AAATAATAAATAAATAAATAAATAAT
* * * **
3387271 AAAGTATATATATCAACAGGTAAATAAT
1 AAA-TA-ATAAATAAATAAATAAATAAT
* * * *
3387299 AAATAATATATATATTAATAAATAGT
1 AAATAATAAATAAATAAATAAATAAT
3387325 -AATAATAAATAAATAAATAAATAA
1 AAATAATAAATAAATAAATAAATAA
3387349 GATACAAAAA
Statistics
Matches: 91, Mismatches: 25, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
23 13 0.14
24 22 0.24
25 24 0.26
26 14 0.15
27 9 0.10
28 9 0.10
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (26 bp):
AAATAATAAATAAATAAATAAATAAT
Found at i:3387347 original size:29 final size:28
Alignment explanation
Indices: 3387293--3387348 Score: 58
Period size: 29 Copynumber: 1.9 Consensus size: 28
3387283 TCAACAGGTA
* * *
3387293 AATAATAAATAATATATATATTAATAAAT
1 AATAAT-AATAATAAATAAATAAATAAAT
*
3387322 AGTAATAATAAATAAATAAATAAATAA
1 AATAATAAT-AATAAATAAATAAATAA
3387349 GATACAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.14
29 19 0.86
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
AATAATAATAATAAATAAATAAATAAAT
Found at i:3387363 original size:22 final size:22
Alignment explanation
Indices: 3387335--3387390 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
3387325 AATAATAAAT
*
3387335 AAATAAATAAATAAGATACAAA
1 AAATAAATAAACAAGATACAAA
3387357 AAATAAA-AACACAAGATACAAA
1 AAATAAATAA-ACAAGATACAAA
*
3387379 ATAAAAAATAAA
1 A-AATAAATAAA
3387391 AAATAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 2 0.07
22 19 0.66
23 6 0.21
24 2 0.07
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (22 bp):
AAATAAATAAACAAGATACAAA
Found at i:3387386 original size:7 final size:7
Alignment explanation
Indices: 3387328--3387398 Score: 54
Period size: 7 Copynumber: 10.0 Consensus size: 7
3387318 AAATAGTAAT
3387328 AATAAATA
1 AATAAA-A
3387336 AATAAATA
1 AATAAA-A
*
3387344 AATAAGA
1 AATAAAA
* *
3387351 TACAAAA
1 AATAAAA
3387358 AAT-AAA
1 AATAAAA
* *
3387364 AACACAA
1 AATAAAA
* *
3387371 GATACAA
1 AATAAAA
3387378 AATAAAA
1 AATAAAA
3387385 AATAAAA
1 AATAAAA
3387392 AATAAAA
1 AATAAAA
3387399 TGGATCTATC
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
6 5 0.10
7 32 0.64
8 13 0.26
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:3391959 original size:31 final size:31
Alignment explanation
Indices: 3391924--3391985 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
3391914 CTTTAGCATA
* *
3391924 TTTAGCAAGTGAACCTCTTTATTTGGTCCAT
1 TTTAGCAAGTGAACCTCTCTATATGGTCCAT
*
3391955 TTTAGCAAGTGAATCTCTCTATATGGTCCAT
1 TTTAGCAAGTGAACCTCTCTATATGGTCCAT
3391986 GGGTTCCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (31 bp):
TTTAGCAAGTGAACCTCTCTATATGGTCCAT
Found at i:3395583 original size:2 final size:2
Alignment explanation
Indices: 3395576--3395600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3395566 TGCTTTTGAG
3395576 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3395601 AATAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3395609 original size:2 final size:2
Alignment explanation
Indices: 3395604--3395644 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3395594 ATATATAAAT
*
3395604 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3395645 AATAAGTGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3396200 original size:2 final size:2
Alignment explanation
Indices: 3396193--3396217 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3396183 AGCATGTTCT
3396193 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 T
3396218 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3398563 original size:2 final size:2
Alignment explanation
Indices: 3398556--3398580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3398546 ATATACAACA
3398556 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3398581 GACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3402779 original size:13 final size:13
Alignment explanation
Indices: 3402745--3402773 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3402735 TATTAATAAG
3402745 TAAAAG-AAAAAA
1 TAAAAGAAAAAAA
3402757 TAAAAGAAAAAAA
1 TAAAAGAAAAAAA
3402770 TAAA
1 TAAA
3402774 CAAAAAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (13 bp):
TAAAAGAAAAAAA
Found at i:3404064 original size:305 final size:296
Alignment explanation
Indices: 3403475--3404188 Score: 863
Period size: 305 Copynumber: 2.4 Consensus size: 296
3403465 TTTCTTGGAT
* * *
3403475 AAAGAGTAAACATGATGAACAACATTATGAATGGAAAAACTTGCTTAATGACCT-GCAGTAGAGT
1 AAAGAGTAAACATGATGAACAACGTTATGAATGCAAAAACTTGCTTAATTA-CTGGCAGTAGAGT
* * * * * *
3403539 CATCAATGAATAGACCAAAGTTATCATGATCTTTCAGGGTATCAAACACATATGGCAAGTCATGA
65 AATCAATGAATAGGCCAATGTTATCATGATCTTT-GGGGCATCAAACACATATAGCAAGTCATGA
* * * *
3403604 TTTGCACCAAAGGAGTAGCCAGACCCAACTCCTAAATTAACAAGAAAACACAAACTAGGATTAGT
129 TTTACACCAAAGGAGTAGCCAGACCCAACTACTAAATTAACAAGAAAACACAAACCAGGATGAGT
* * * * * *
3403669 GAATTTAAGAAGCTATGAGAAGATCTTGTAGTCAAGAGTTAAATTAACCAACACAAAAGCAAATT
194 GAATTTAAGAAGCCATAAGAAGACCTTGTAGTCAAAAGTAAAATTAACCAACACAAAAACAAATT
* * *
3403734 TTTAATATCAAGAAACAAGTAAATTCTTCGACAATTCGAG
259 TTTAATACCAAAAAACAACTAAATTCTTCGACAATT--AG
* ** *
3403774 AAAAAAATGGGTAAACATGATGAACTAGTGTTATGAATGCAAAAACTTGTTTAATTACTGGCAGT
1 ----AAA-GAGTAAACATGATGAAC-AACGTTATGAATGCAAAAACTTGCTTAATTACTGGCAGT
*
3403839 AGAGTTATCAATGAATAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATAGCAAGT
60 AGAGTAATCAATGAATAGGCCAATGTTATCATGATC-TTTGGGGCATCAAACACATATAGCAAGT
* * * * *
3403904 CATGATTTATACCAAAGGGGTAGCCAGCCCCAATTACTAAATTAACAAGAAGACACAAACCAGGA
124 CATGATTTACACCAAAGGAGTAGCCAGACCCAACTACTAAATTAACAAGAAAACACAAACCAGGA
* * * *
3403969 TGAGTGAATTTAGGAAGCCATAAGAATACCTTGTAGTCAAAAGTAAAATTGACCAACATAAAAAC
189 TGAGTGAATTTAAGAAGCCATAAGAAGACCTTGTAGTCAAAAGTAAAATTAACCAACACAAAAAC
* ** *
3404034 AAATTTTTCATACCAAAAAACTTCTAAATTCTTCGACAATTTG
254 AAATTTTTAATACCAAAAAACAACTAAATTCTTCGACAATTAG
* ** * * *
3404077 AAAGAGTAAACATGATCAACCAACGTTACAAATGCAAAAACTTGCTTAGTTATTGGCAGCAGAGT
1 AAAGAGTAAACATGATGAA-CAACGTTATGAATGCAAAAACTTGCTTAATTACTGGCAGTAGAGT
* * *
3404142 AATTAGTGAATAGGCCAATGTTATCATGATCTTTTGAGGCATCAAAC
65 AATCAATGAATAGGCCAATGTTATCATGATC-TTTGGGGCATCAAAC
3404189 CAGAATGAGT
Statistics
Matches: 352, Mismatches: 54, Indels: 15
0.84 0.13 0.04
Matches are distributed among these distances:
298 92 0.26
299 4 0.01
303 4 0.01
304 18 0.05
305 231 0.66
306 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (296 bp):
AAAGAGTAAACATGATGAACAACGTTATGAATGCAAAAACTTGCTTAATTACTGGCAGTAGAGTA
ATCAATGAATAGGCCAATGTTATCATGATCTTTGGGGCATCAAACACATATAGCAAGTCATGATT
TACACCAAAGGAGTAGCCAGACCCAACTACTAAATTAACAAGAAAACACAAACCAGGATGAGTGA
ATTTAAGAAGCCATAAGAAGACCTTGTAGTCAAAAGTAAAATTAACCAACACAAAAACAAATTTT
TAATACCAAAAAACAACTAAATTCTTCGACAATTAG
Found at i:3404754 original size:308 final size:309
Alignment explanation
Indices: 3404184--3405345 Score: 1498
Period size: 308 Copynumber: 3.8 Consensus size: 309
3404174 TTTGAGGCAT
* * * * *
3404184 CAAACCAGAATGAGTGAATTTAGGAAGCTATGAAAAAACCTTATAATCAAAAGTAAAATTAACCA
1 CAAACTAGGATGAGTGAATTTAGGAAGCTATGAAAAGACCTTATAGTCAAGAGTAAAATTAACCA
* ** * **
3404249 ACAGAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTGAC-AAATTGAGAAATTAATA
66 ACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAACGATATTGAGAAAAGAATA
* * * *
3404313 AGGAGTACACATGATGAACCAACGTTATGAATGCAAAAATTTGTTTAATTACCAGTAGTAGAGTC
131 AGGAGTAAACATGATGAACCAACGTTATGAATGCAAAAACTTGCTTAATTACCAGCAGTAGAGTC
* *
3404378 ATCAATGAACAGGCCAATGTTATCATGATCATTTGAGGCATCAAACACATATGACAAGTAATGAT
196 ATCAATGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATGACAAGTCATGAT
3404443 TTGCACCAAAGGAGCAGCCAACCCCAACTCCTAAATTAACAAGAAAACA
261 TTGCACCAAAGGAGCAGCCAACCCCAACTCCTAAATTAACAAGAAAACA
* * * * * *
3404492 CAAACAAAGATTAGTGAATTTTGGAAGCTATGAGAAGACTTTATAGTCAAGAGTAAAATTAACCA
1 CAAACTAGGATGAGTGAATTTAGGAAGCTATGAAAAGACCTTATAGTCAAGAGTAAAATTAACCA
* * * * *
3404557 ACATAAAAACAAATTTTTAATACTAATAAACATGTAAATTTTTCAACGATATT-AGAAAATAATA
66 ACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAACGATATTGAGAAAAGAATA
* * * *
3404621 AGTAGTAAACATGATGAACCAATGCTATGAATGCAAAAACTTGCTTAATTACCAGCAGTAGAGTT
131 AGGAGTAAACATGATGAACCAACGTTATGAATGCAAAAACTTGCTTAATTACCAGCAGTAGAGTC
* * * * * *
3404686 ATCAGTGAACAGGCCAATGTTATCATAATCATTTTGGGCATCAAACACATGTGGCAAGTCGTGAT
196 ATCAATGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATGACAAGTCATGAT
* * * * *
3404751 TTGCACCAAAGAAGTAGCCAGCCCCAAGTCCTAAATCAACAAGAAAACA
261 TTGCACCAAAGGAGCAGCCAACCCCAACTCCTAAATTAACAAGAAAACA
* * ** * *
3404800 GAAACTAGGATGAGTGAATTTAGTAAAATATGAAAAGATCTTGTAGTCAAGAGTAAAATTAACCA
1 CAAACTAGGATGAGTGAATTTAGGAAGCTATGAAAAGACCTTATAGTCAAGAGTAAAATTAACCA
* * * * * *
3404865 ACACAAAAGTAAATTTTTAATACCAAAAAACAAGTAAATTCTTCAATGCT-TTGAGAAAAGAATA
66 ACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAACGATATTGAGAAAAGAATA
* * * ** *
3404929 AGGAGTAAACATAATGAACCAACGTTATGAATGCCAAAACTTGCTAAATTACTGGCAGAAGAGTC
131 AGGAGTAAACATGATGAACCAACGTTATGAATGCAAAAACTTGCTTAATTACCAGCAGTAGAGTC
* * *
3404994 ATCAGTGAATAGGCCAA-GATTATCATGATCATTTGGGGCATCAAACACATACGACAAGTCATGA
196 ATCAATGAACAGGCCAATG-TTATCATGATCATTTGGGGCATCAAACACATATGACAAGTCATGA
* *
3405058 TTTGCACC-AAGGA-CTAGCCAACCCTAACTCCTAAATTAACAAGAAAGCA
260 TTTGCACCAAAGGAGC-AGCCAACCCCAACTCCTAAATTAACAAGAAAACA
* ** *
3405107 CAAACTAGGATGAGTTAATTTAGGAAGCTATGAGCAGACCTTGTAGTCAAGAGTAAAATTAACCA
1 CAAACTAGGATGAGTGAATTTAGGAAGCTATGAAAAGACCTTATAGTCAAGAGTAAAATTAACCA
* *
3405172 ACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAA-AATTTTGAGAAAAGAATA
66 ACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAACGATATTGAGAAAAGAATA
* * * * * *
3405236 AGGATTAAACATGATGAACTAATGTTATGAAGGCAAAAACTTGCTTAATTA-CTG-ATGGCAGAG
131 AGGAGTAAACATGATGAACCAACGTTATGAATGCAAAAACTTGCTTAATTACCAGCA--GTAGAG
* *
3405299 TCATCAACGAACAGGCCAATGTTGTCATG-TCATTTGGGGCATCAAAC
194 TCATCAATGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAAC
3405346 CAGGATGAGT
Statistics
Matches: 732, Mismatches: 114, Indels: 18
0.85 0.13 0.02
Matches are distributed among these distances:
305 1 0.00
306 20 0.03
307 221 0.30
308 486 0.66
309 4 0.01
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (309 bp):
CAAACTAGGATGAGTGAATTTAGGAAGCTATGAAAAGACCTTATAGTCAAGAGTAAAATTAACCA
ACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAACGATATTGAGAAAAGAATA
AGGAGTAAACATGATGAACCAACGTTATGAATGCAAAAACTTGCTTAATTACCAGCAGTAGAGTC
ATCAATGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATGACAAGTCATGAT
TTGCACCAAAGGAGCAGCCAACCCCAACTCCTAAATTAACAAGAAAACA
Found at i:3405547 original size:234 final size:234
Alignment explanation
Indices: 3405107--3405580 Score: 652
Period size: 234 Copynumber: 2.0 Consensus size: 234
3405097 CAAGAAAGCA
* * * * * * *
3405107 CAAACTAGGATGAGTTAATTTAGGAAGCTATGAGCAGACCTTGTAGTCAAGAGTAAAATTAACCA
1 CAAACCAGGATGAGTGAATTCAAGAAGCTATGAGAAGACATTGTAGTCAAGAGTAAAATGAACCA
* * *
3405172 ACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAAAATTTTGAGAAAAGAATAA
66 ACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTCAAAATTTTGAGAAAAAAATAA
* * * * *
3405237 GGATTAAACATGATGAACTAATGTTATGAAGGCAAAAACTTGCTTAATTACTGATGGCAGAGTCA
131 AGAGTAAACATGATGAACCAATGTTATGAAGGCAAAAACTTGCTTAATTACTGA-GACAGAATCA
* * **
3405302 TCAACGAACAGGCCAATGTTGTC-ATGTCATTTGGGGCAT
195 TCAACGAACAGGCCAATGCTATCAAAATCATTTGGGGCAT
3405341 CAAACCAGGATGAGTGAATTCAAGAAGCTATGAGAAGACATTGTAGTCACA-AGTAAAATGAACC
1 CAAACCAGGATGAGTGAATTCAAGAAGCTATGAGAAGACATTGTAGTCA-AGAGTAAAATGAACC
*
3405405 AACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTTTTCAACAA-TTTGAGAAAAAAAT
65 AACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTCAA-AATTTTGAGAAAAAAAT
*
3405469 AAAGAGTAAACATGATGAACCAATGTTATGAATGG-AAATACTTGCTTAATTACCTGCA-ACAGA
129 AAAGAGTAAACATGATGAACCAATGTTATGAA-GGCAAAAACTTGCTTAATTA-CTG-AGACAGA
**
3405532 ATCATCAGTGAACAGGCCAATGCTATCAAAATCATTTGGGGCAT
191 ATCATCAACGAACAGGCCAATGCTATCAAAATCATTTGGGGCAT
3405576 CAAAC
1 CAAAC
3405581 ACATATGGCA
Statistics
Matches: 211, Mismatches: 23, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
234 183 0.87
235 27 0.13
236 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (234 bp):
CAAACCAGGATGAGTGAATTCAAGAAGCTATGAGAAGACATTGTAGTCAAGAGTAAAATGAACCA
ACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTCAAAATTTTGAGAAAAAAATAA
AGAGTAAACATGATGAACCAATGTTATGAAGGCAAAAACTTGCTTAATTACTGAGACAGAATCAT
CAACGAACAGGCCAATGCTATCAAAATCATTTGGGGCAT
Found at i:3405552 original size:849 final size:845
Alignment explanation
Indices: 3404504--3408124 Score: 4366
Period size: 849 Copynumber: 4.3 Consensus size: 845
3404494 AACAAAGATT
* * *
3404504 AGTGAATTTTGGAAGCTATGAGAAGACTTTATAGTCAAGAGTAAAATTAACCAACATAAAAA-CA
1 AGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTCAA-AGTAAAATTAACCAACA-AAAAAGAA
* * * *
3404568 AATTTTTAATACTAATAAACATGTAAATTTTTCAACGATATT-AGAAAATAAT-AAGTAGTAAAC
64 AATTTTTAATACCAAGAAACATGTAAATTTTTCAACAAT-TTGAGAAAAAAATAAAG-AGTAAAC
* * * ** * *
3404631 ATGATGAACCAATGCTATGAATGCAAAAACTTGCTTAATTACCAGCAGTAGAGTTATCAGTGAAC
127 ATGATGAACCAATGTTATGAATGGAAAAACTTGCTTAATTACCTGCAACAGAATCATCAGTGAAC
* * *
3404696 AGGCCAATGTTATCATAATCATTTTGGGCATCAAACACATGTGGCAAGTCGTGATTTGCACCAAA
192 AGGCCAATGTTATCATAATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAAA
* * * * * * *
3404761 GAAGTAGCCAGCCCCAAGTCCTAAATCAACAAGAAAACAGAAACTAGGATGAGTGAATTTAGTAA
257 GAAGTAGCCAACCCCAACTCCTAAATTAACAAGAAAACACAAACCAGGATGAATGAATTTAGGAA
* * *
3404826 AATATGAAAAGATCTTGTAGTCAAGAGTAAAATTAACCAACACAAAAGTAAATTTTTAATACCAA
322 GATATGAGAAGATCTTGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAA
* * *** *
3404891 AAAACAAGTAAATTCTTCAATGCTTTGAGAAAAGAATAAGGAGTAAACATAATGAACCAACGTTA
387 GAAACAAGTAAATTCTTCGACAATTTGAGAAAAGAATAAGGAGTAAACATGATGAACCAACGTTA
3404956 TGAATGCCAAAACTTGCTAAATTACTGGCAGAAGAGTCATCAGTGAATAGGCCAAGATTATCATG
452 TGAATGCCAAAACTTGCTAAATTACTGGCAGAAGAGTCATCAGTGAATAGGCCAAG-TTATCATG
* * * *
3405021 ATCATTTGGGGCATCAAACACATACGACAAGTCATGATTTGCACCAAGGACTAGCCAACCCTAAC
516 ATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAAAGAGTAGCCAACCC-AAC
* * * * *
3405086 TCCTAAATTAACAAGAAAGCACAAACTAGGATGAGTTAATTTAGGAAGCTATGAGCAGACCTTGT
580 TCCTAAATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTGT
* *
3405151 AGTCAAGAGTAAAATTAACCAACATAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTC
645 AGTCAAAAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTC
* * *
3405216 AAAATTTTGAGAAAAGAATAAGGATTAAACATGATGAACTAATGTTATGAAGGCAAAAACTTGCT
710 AAAA-TTTGAGAAAAGAATAAGGATTAAACATGATGAACCAACGTTATGAATGCAAAAACTTGCT
* *
3405281 TAATTACTGATGGCAGAGTCATCAACGAACAGGCCAATGTTGTCATG-TCATTTGGGGCATCAAA
774 TAATTACT-ATAGCAGAGTCATCAACGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAA
3405345 CCAGGATG
838 CCAGGATG
* * * *
3405353 AGTGAATTCAAGAAGCTATGAGAAGACATTGTAGTCACAAGTAAAATGAACCAACAAAAAAGAAA
1 AGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTCA-AAGTAAAATTAACCAACAAAAAAGAAA
3405418 ATTTTTAATACCAAGAAACATGTAAATTTTTCAACAATTTGAGAAAAAAATAAAGAGTAAACATG
65 ATTTTTAATACCAAGAAACATGTAAATTTTTCAACAATTTGAGAAAAAAATAAAGAGTAAACATG
*
3405483 ATGAACCAATGTTATGAATGGAAATACTTGCTTAATTACCTGCAACAGAATCATCAGTGAACAGG
130 ATGAACCAATGTTATGAATGGAAAAACTTGCTTAATTACCTGCAACAGAATCATCAGTGAACAGG
* * * *** *
3405548 CCAATGCTATCAAAATCATTTGGGGCATCAAACACATATGGCAAGTCATGCTTTGCGTTAAAGGA
195 CCAATGTTATCATAATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAAAGAA
* * * *
3405613 GTAGCCAACCCCAACACCTAAATTAACAAGAAAACATAAACCAGGATGAATGAATTTGGGAAGCT
260 GTAGCCAACCCCAACTCCTAAATTAACAAGAAAACACAAACCAGGATGAATGAATTTAGGAAGAT
* * *
3405678 ATGAGAAGACCTTGCAGTCAAGAGTAAAATTAACTAACACAAAAGCAAATTTTTAATATCC-AGA
325 ATGAGAAGATCTTGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATA-CCAAGA
* * *
3405742 AACAAGTAAATTCTTTC-ACGAA-TTAAGAAAAGAATAAGGAGTAAACATGATGAACTAACATTA
389 AACAAGTAAATTC-TTCGAC-AATTTGAGAAAAGAATAAGGAGTAAACATGATGAACCAACGTTA
*
3405805 TGAATGCC-AAACGTTGCTAAATTACTGGCAGAAAAGTCATCAGTGAATA-GCCAAGGTTATCAT
452 TGAATGCCAAAAC-TTGCTAAATTACTGGCAGAAGAGTCATCAGTGAATAGGCCAA-GTTATCAT
* * **
3405868 GATCATTTGGGGCATCAAACACATATGGCAAATCATGATTTGCACTGAAAGAGTAGTTAAACCCA
515 GATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCAC-CAAAGAGTAG-CCAACCCA
* * *
3405933 ACTCCTAAATTAACAAGAAAACACAAACTAGGATGAGTGAATTTAGGAAGCTATAAGAAGACCTT
578 ACTCCTAAATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAGGAAGCTATGAGAAGACCTT
*
3405998 GTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCT
643 GTAGTCAAAAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTC-
* * * * *
3406063 TTGACAGTTTGAGAAAAGAATAAGGATTAAACATGATCAACCAACGTTATGAATGCAAAAACTTA
707 TTCAAAATTTGAGAAAAGAATAAGGATTAAACATGATGAACCAACGTTATGAATGCAAAAACTTG
* *
3406128 CTTAATTACTAGTAGTAGAGTCATCATCGAACAGGCCAATGTTATCATGATCATTTGGGGCATCA
772 CTTAATTACTA-TAGCAGAGTCATCAACGAACAGGCCAATGTTATCATGATCATTTGGGGCATCA
3406193 AACCAGGATG
836 AACCAGGATG
** * * * *
3406203 AGCAAATTTAGGAAGCTATGAGATGAC-CTATAGTCACAAGTAAAATTAACCAACAAAAAATAAA
1 AGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTCA-AAGTAAAATTAACCAACAAAAAAGAAA
* * * *
3406267 ATTTTTAATACCCAGAAACATGTAAATTCTTT-GATAATTCGAGAAAAAAAT--AGAGTAAACAT
65 ATTTTTAATACCAAGAAACATGTAAATT-TTTCAACAATTTGAGAAAAAAATAAAGAGTAAACAT
* * ** * * ** * *
3406329 GATCAGCCAACATTATGAATGGAAAAACCTACTTAATTACCTGCAGTAGAGTCACCAGTGAACAG
129 GATGAACCAATGTTATGAATGGAAAAACTTGCTTAATTACCTGCAACAGAATCATCAGTGAACAG
* * *
3406394 GCCAATGTTATCATAATCATTTCGGGCATCAAACACATATGGCAAGTCATGATTTGCAGCAAAGG
194 GCCAATGTTATCATAATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAAAGA
*** * * *
3406459 AGTAGCCAATTGCAACTCCTAAATTAACAAGAAAACACAAACCAGGATGAGTGAATTTAAGAAGT
259 AGTAGCCAACCCCAACTCCTAAATTAACAAGAAAACACAAACCAGGATGAATGAATTTAGGAAGA
*
3406524 TATGAGAAGA-CTTTGTAGTCAAGAGTAAAATTAACTAACACAAAAGCAAATTTTTAATACCAAG
324 TATGAGAAGATC-TTGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAG
* * * *
3406588 AAACAAGTAAATTCTTTGACAATTTGAGAAGAGAATAAGGAGTAAATATGATGAATCAACGTTAT
388 AAACAAGTAAATTCTTCGACAATTTGAGAAAAGAATAAGGAGTAAACATGATGAACCAACGTTAT
* * * * *
3406653 GAA-GGCAAAAGCTTGCTTAATTA-TCGGCAGCAGAGTCATCAGTGAACAGGCCGATGTTATCAT
453 GAATGCCAAAA-CTTGCTAAATTACT-GGCAGAAGAGTCATCAGTGAATAGGCC-AAGTTATCAT
* ** *
3406716 GATCATTTGGGGCGTCAAACACATATGGCAAGTCATGATTTGCTTCAAAGGAGTAGCCTACCGCA
515 GATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAAA-GAGTAGCCAACC-CA
* **
3406781 ATTCCTAAATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAAAAAGCTATG-GAAAGACCT
578 ACTCCTAAATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAGGAAGCTATGAG-AAGACCT
* * * *
3406845 TGTAGTCAAAAGTAAAATTAACCAATACAAAAGCAAATTTTTAATACTAAGAAGCATGTAACTTC
642 TGTAGTCAAAAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTC
*** * * * * * *
3406910 TTTGGCAATTTGAGAAACGAATATGGAGTATACATGATGAACCAATGTTATGAATGCAAAACCTT
707 -TTCAAAATTTGAGAAAAGAATAAGGATTAAACATGATGAACCAACGTTATGAATGCAAAAACTT
* * ** * * *
3406975 GCTTAATTACTAGCAGCAGAGTCATTATTGAACACGTCATTGTTATCATGATCATTTGGGGCATC
771 GCTTAATTACTA-TAGCAGAGTCATCAACGAACAGGCCAATGTTATCATGATCATTTGGGGCATC
3407040 AAACCAGGATG
835 AAACCAGGATG
* * * * * *
3407051 ACTGAATTTAGGAATCTATGAGAAGACCTTGTAGTCAAGAGTAAGATTAACCAACACCAAATGAA
1 AGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTCAA-AGTAAAATTAACCAACA-AAAAAGAA
* * * * * *
3407116 AATTTTTAGTGCCAAGAAACATGTAAATTGTTT-AACACTTAGAGAAAAGAATAAGGAGTAAACA
64 AATTTTTAATACCAAGAAACATGTAAATT-TTTCAACAATTTGAGAAAAAAATAAAGAGTAAACA
* * *
3407180 TGATGAACCAATGTTATGAATGGAAAAACTTTCTTAATTACCT-AAAGCA-AAGTCATCAGCGAA
128 TGATGAACCAATGTTATGAATGGAAAAACTTGCTTAATTACCTGCAA-CAGAA-TCATCAGTGAA
* *
3407243 TAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAA
191 CAGGCCAATGTTATCATAATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAA
* * * *
3407308 AGAAGTAGCCAGCCCCAACTCTTAAATTAACAAGAAAACACAAACTAGGATAAATGAATTTAGGA
256 AGAAGTAGCCAACCCCAACTCCTAAATTAACAAGAAAACACAAACCAGGATGAATGAATTTAGGA
* * * * *
3407373 AGCA-ATGAGAAG-TCCTTATAGTCAAGTGTAAAATTAACCAACATAAAAGCAAAATTTTAACAC
321 AG-ATATGAGAAGAT-CTTGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATAC
* * * *
3407436 CAAGAAACATGTAAATTCTTTGACAATTTGACAAAAGAATTAAGGAGTAAACATGATGAA-CTAC
384 CAAGAAACAAGTAAATTCTTCGACAATTTGAGAAAAGAA-TAAGGAGTAAACATGATGAACCAAC
* * * * * *
3407500 TGTTATGAATGCAAAAAC-T--T-AATTATTGGCAGTAGAGTTATTAGTGAATAGCCCAATGTTA
448 -GTTATGAATGCCAAAACTTGCTAAATTACTGGCAGAAGAGTCATCAGTGAATAGGCCAA-GTTA
* * * * * *
3407561 TTATGATCATTTAGGGCATCAAACACATATGGTAAGTCATGGTTTACACCAAAAGAGTAGCCAGC
511 TCATGATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACC-AAAGAGTAGCCA-A
*
3407626 CCCAACTCCAAAATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAGGAAAGCTATGAGAAG
574 CCCAACTCCTAAATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAGG-AAGCTATGAGAAG
* *
3407691 ACCTTGTAGTCAAAAGTAAAATTAACCAACATAAAAGTC-AATTTTTGATACCAAGAAACATGTA
638 ACCTTGTAGTCAAAAGTAAAATTAACCAACACAAAAG-CAAATTTTTAATACCAAGAAACATGTA
* * * * * * *
3407755 AAGTCTTCGACAATTT-ACGAAAAGAAT--GCA-TAAACATAACGAACTAACATTATGAATGCAA
702 AATTCTTC-AAAATTTGA-GAAAAGAATAAGGATTAAACATGATGAACCAACGTTATGAATGCAA
* * * * * * *
3407816 AAACTAGTTTAATTACCAATAGTAGAGTCATC-A-GATATATGGCCAATGTTATAATCATCATTT
765 AAACTTGCTTAATTA-CTATAGCAGAGTCATCAACGA-ACA-GGCCAATGTTATCATGATCATTT
* *
3407879 GGGGAATCAAACCTGGATG
827 GGGGCATCAAACCAGGATG
* * * * ** * *
3407898 AGTGAATTTAGGAAGCTAGGAGAATACTTTGTAGTTAGGAGTAAAATTAAGTAGC-ACAAAG-AA
1 AGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTCA-AAGTAAAATTAACCAACAAAAAAGAAA
* * * * * * ** *
3407961 ATTTTCAATACCTAGAAATATGTAAATTCTTCAATAATTTGATAAATGAATAATA-AGCAAACAT
65 ATTTTTAATACCAAGAAACATGTAAATTTTTCAACAATTTGAGAAAAAAATAA-AGAGTAAACAT
* * * * *
3408025 GATAAACCAACGTTATGAATGCAAAAATCTTGCTTAATTACCGGCACCA-AAGTCATCAGTGAAC
129 GATGAACCAATGTTATGAATGGAAAAA-CTTGCTTAATTACCTGCAACAGAA-TCATCAGTGAAC
* *
3408089 AAGCCAATGTTATCATGATCATTTGGGGCATCAAAC
192 AGGCCAATGTTATCATAATCATTTGGGGCATCAAAC
3408125 CAGGATGAGT
Statistics
Matches: 2395, Mismatches: 320, Indels: 118
0.85 0.11 0.04
Matches are distributed among these distances:
843 2 0.00
844 73 0.03
845 68 0.03
846 13 0.01
847 457 0.19
848 395 0.16
849 877 0.37
850 208 0.09
851 4 0.00
852 264 0.11
853 29 0.01
854 5 0.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (845 bp):
AGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTCAAAGTAAAATTAACCAACAAAAAAGAAAA
TTTTTAATACCAAGAAACATGTAAATTTTTCAACAATTTGAGAAAAAAATAAAGAGTAAACATGA
TGAACCAATGTTATGAATGGAAAAACTTGCTTAATTACCTGCAACAGAATCATCAGTGAACAGGC
CAATGTTATCATAATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAAAGAAG
TAGCCAACCCCAACTCCTAAATTAACAAGAAAACACAAACCAGGATGAATGAATTTAGGAAGATA
TGAGAAGATCTTGTAGTCAAGAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAA
CAAGTAAATTCTTCGACAATTTGAGAAAAGAATAAGGAGTAAACATGATGAACCAACGTTATGAA
TGCCAAAACTTGCTAAATTACTGGCAGAAGAGTCATCAGTGAATAGGCCAAGTTATCATGATCAT
TTGGGGCATCAAACACATATGGCAAGTCATGATTTGCACCAAAGAGTAGCCAACCCAACTCCTAA
ATTAACAAGAAAACACAAACCAAGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTGTAGTCAA
AAGTAAAATTAACCAACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTCAAAATT
TGAGAAAAGAATAAGGATTAAACATGATGAACCAACGTTATGAATGCAAAAACTTGCTTAATTAC
TATAGCAGAGTCATCAACGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAACCAGGATG
Found at i:3405995 original size:307 final size:305
Alignment explanation
Indices: 3405341--3406195 Score: 1114
Period size: 307 Copynumber: 2.8 Consensus size: 305
3405331 TTTGGGGCAT
* * * *
3405341 CAAACCAGGATGAGTGAATTCAAGAAGCTATGAGAAGACATTGTAGTCACA-AGTAAAATGAACC
1 CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTGTAGTCA-AGAGTAAAATTAACC
* * *
3405405 AACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATT-TTTCAACAATTTGAGAAAAAAAT
65 AACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTC-ACAA-TTGAGAAAAGAAT
* * *
3405469 AAAGAGTAAACATGATGAACCAATGTTATGAATGGAAATACTTGCTTAATTACCTGCA-ACAGAA
128 AAGGAGTAAACATGATGAACCAACGTTATGAATGCAAA-ACTTGCTTAATTA-CTGCAGA-A-AA
* ** *
3405533 -TCATCAGTGAACAGGCCAATGCTATCAAAATCATTTGGGGCATCAAACACATATGGCAAGTCAT
189 GTCATCAGTGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAATCAT
* * * *
3405597 GCTTTGCGTTAAAGGAGTAGCCAACCCCAACACCTAAATTAACAAGAAAACA
254 GATTTGCCTGAAAGGAGTAGCCAAACCCAACACCTAAATTAACAAGAAAACA
* * * * *
3405649 TAAACCAGGATGAATGAATTTGGGAAGCTATGAGAAGACCTTGCAGTCAAGAGTAAAATTAACTA
1 CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
* *
3405714 ACACAAAAGCAAATTTTTAATATCC-AGAAACAAGTAAATTCTTTCACGAATTAAGAAAAGAATA
66 ACACAAAAGCAAATTTTTAATA-CCAAGAAACATGTAAATTCTTTCAC-AATTGAGAAAAGAATA
* * * *
3405778 AGGAGTAAACATGATGAACTAACATTATGAATGCCAAACGTTGCTAAATTACTGGCAGAAAAGTC
129 AGGAGTAAACATGATGAACCAACGTTATGAATGCAAAAC-TTGCTTAATTACT-GCAGAAAAGTC
* *
3405843 ATCAGTGAATA-GCCAAGGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAATCATGAT
192 ATCAGTGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAATCATGAT
** *
3405907 TTGCACTGAAA-GAGTAGTTAAACCCAACTCCTAAATTAACAAGAAAACA
257 TTGC-CTGAAAGGAGTAGCCAAACCCAACACCTAAATTAACAAGAAAACA
* *
3405956 CAAACTAGGATGAGTGAATTTAGGAAGCTATAAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
1 CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
* *
3406021 ACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAGTTTGAGAAAAGAATAA
66 ACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTCACA-ATTGAGAAAAGAATAA
* * * * * *
3406086 GGATTAAACATGATCAACCAACGTTATGAATGCAAAAACTTACTTAATTACTAGTAGTAGAGTCA
130 GGAGTAAACATGATGAACCAACGTTATGAATGC-AAAACTTGCTTAATTACT-GCAGAAAAGTCA
3406151 TCA-TCGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAAC
193 TCAGT-GAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAAC
3406196 CAGGATGAGC
Statistics
Matches: 475, Mismatches: 58, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
306 4 0.01
307 262 0.55
308 200 0.42
309 9 0.02
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (305 bp):
CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
ACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTCACAATTGAGAAAAGAATAAG
GAGTAAACATGATGAACCAACGTTATGAATGCAAAACTTGCTTAATTACTGCAGAAAAGTCATCA
GTGAACAGGCCAATGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAATCATGATTTGC
CTGAAAGGAGTAGCCAAACCCAACACCTAAATTAACAAGAAAACA
Found at i:3406404 original size:232 final size:235
Alignment explanation
Indices: 3405956--3406427 Score: 668
Period size: 232 Copynumber: 2.0 Consensus size: 235
3405946 CAAGAAAACA
* ** *
3405956 CAAACTAGGATGAGTGAATTTAGGAAGCTATAAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
1 CAAACCAGGATGAGCAAATTTAGGAAGCTATAAGAAGACCTTATAGTCAAGAGTAAAATTAACCA
* * * * *
3406021 ACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAGTTTGAGAAAAGAATAA
66 ACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAATTCGAGAAAAAAATAA
* * * *
3406086 GGATTAAACATGATCAACCAACGTTATGAATGCAAAAACTTACTTAATTACTAGTAGTAGAGTCA
131 GGAGTAAACATGATCAACCAACATTATGAATGCAAAAACCTACTTAATTACTAGCAGTAGAGTCA
* * *
3406151 TCATCGAACAGGCCAATGTTATCATGATCATTTGGGGCAT
196 CCATCGAACAGGCCAATGTTATCATAATCATTTCGGGCAT
* *
3406191 CAAACCAGGATGAGCAAATTTAGGAAGCTATGAGATGACC-TATAGTCACA-AGTAAAATTAACC
1 CAAACCAGGATGAGCAAATTTAGGAAGCTATAAGAAGACCTTATAGTCA-AGAGTAAAATTAACC
* * *
3406254 AACAAAAAATAAAATTTTTAATACCCAGAAACATGTAAATTCTTTGATAATTCGAGAAAAAAAT-
65 AACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAATTCGAGAAAAAAATA
* *
3406318 A-GAGTAAACATGATCAGCCAACATTATGAATGGAAAAACCTACTTAATTACCT-GCAGTAGAGT
130 AGGAGTAAACATGATCAACCAACATTATGAATGCAAAAACCTACTTAATTA-CTAGCAGTAGAGT
3406381 CACCAGT-GAACAGGCCAATGTTATCATAATCATTTCGGGCAT
194 CACCA-TCGAACAGGCCAATGTTATCATAATCATTTCGGGCAT
3406423 CAAAC
1 CAAAC
3406428 ACATATGGCA
Statistics
Matches: 211, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
232 95 0.45
233 4 0.02
234 76 0.36
235 36 0.17
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (235 bp):
CAAACCAGGATGAGCAAATTTAGGAAGCTATAAGAAGACCTTATAGTCAAGAGTAAAATTAACCA
ACAAAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAATTCGAGAAAAAAATAA
GGAGTAAACATGATCAACCAACATTATGAATGCAAAAACCTACTTAATTACTAGCAGTAGAGTCA
CCATCGAACAGGCCAATGTTATCATAATCATTTCGGGCAT
Found at i:3406797 original size:308 final size:303
Alignment explanation
Indices: 3406191--3407043 Score: 1057
Period size: 308 Copynumber: 2.8 Consensus size: 303
3406181 TTTGGGGCAT
** * * * *
3406191 CAAACCAGGATGAGCAAATTTAGGAAGCTATGAGATGACCTATAGTCACAAGTAAAATTAACCAA
1 CAAACCAGGATGAGTGAATTTAAGAAGCTATGAGAAGACTTGTAGTCA-AAGTAAAATTAACCAA
* ** * * * *
3406256 CAAAAAATAAAATTTTTAATACCCAGAAACATGTAAATTCTTTGATAATTCGAGAAA-AA-AATA
65 CACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAATTTGAGAAAGAATAA-G
* * * * * * *
3406319 GAGTAAACATGATCAGCCAACATTATGAATGG-AAAAACCTACTTAATTACCTGCAGTAGAGTCA
129 GAGTAAACATGATGAACCAACGTTATGAA-GGCAAAAACTTGCTTAATTA-CAGCAGCAGAGTCA
* * *
3406383 CCAGTGAACAGGCCAATGTTATCATAATCATTTCGGGCATCAAACACATATGGCAAGTCATGATT
192 TCAGTGAACAGGCC-ATGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAGTCATGATT
**
3406448 TGCAGCAAAGGAGTAGCCAATTGCAACTCCTAAATTAACAAGAAAACA
256 TGCAGCAAAGGAGTAGCCAACCGCAACTCCTAAATTAACAAGAAAACA
* *
3406496 CAAACCAGGATGAGTGAATTTAAGAAGTTATGAGAAGACTTTGTAGTCAAGAGTAAAATTAACTA
1 CAAACCAGGATGAGTGAATTTAAGAAGCTATGAGAAGAC-TTGTAGTCAA-AGTAAAATTAACCA
*
3406561 ACACAAAAGCAAATTTTTAATACCAAGAAACAAGTAAATTCTTTGACAATTTGAGAAGAGAATAA
64 ACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAATTTGAGAA-AGAATAA
* * * *
3406626 GGAGTAAATATGATGAATCAACGTTATGAAGGCAAAAGCTTGCTTAATTATCGGCAGCAGAGTCA
128 GGAGTAAACATGATGAACCAACGTTATGAAGGCAAAAACTTGCTTAATTA-CAGCAGCAGAGTCA
*
3406691 TCAGTGAACAGGCCGATGTTATCATGATCATTTGGGGCGTCAAACACATATGGCAAGTCATGATT
192 TCAGTGAACAGGCC-ATGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAGTCATGATT
** * *
3406756 TGCTTCAAAGGAGTAGCCTACCGCAATTCCTAAATTAACAAGAAAACA
256 TGCAGCAAAGGAGTAGCCAACCGCAACTCCTAAATTAACAAGAAAACA
* *
3406804 CAAACCAAGATGAGTGAATTTAAAAAGCTATG-GAAAGACCTTGTAGTCAAAAGTAAAATTAACC
1 CAAACCAGGATGAGTGAATTTAAGAAGCTATGAG-AAGA-CTTGTAGTC-AAAGTAAAATTAACC
* * * * *
3406868 AATACAAAAGCAAATTTTTAATACTAAGAAGCATGTAACTTCTTTGGCAATTTGAGAAACGAATA
63 AACACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAATTTGAGAAA-GAATA
* * * * *
3406933 TGGAGTATACATGATGAACCAATGTTATGAATGCAAAACCTTGCTTAATTACTAGCAGCAGAGTC
127 AGGAGTAAACATGATGAACCAACGTTATGAAGGCAAAAACTTGCTTAATTAC-AGCAGCAGAGTC
* * * *
3406998 ATTATTGAACACGTCATTGTTATCATGATCATTTGGGGCATCAAAC
191 ATCAGTGAACAGGCCA-TGTTATCATGATCATTTGGGGCATCAAAC
3407044 CAGGATGACT
Statistics
Matches: 475, Mismatches: 61, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
305 35 0.07
306 70 0.15
307 7 0.01
308 358 0.75
309 5 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (303 bp):
CAAACCAGGATGAGTGAATTTAAGAAGCTATGAGAAGACTTGTAGTCAAAGTAAAATTAACCAAC
ACAAAAGCAAATTTTTAATACCAAGAAACATGTAAATTCTTTGACAATTTGAGAAAGAATAAGGA
GTAAACATGATGAACCAACGTTATGAAGGCAAAAACTTGCTTAATTACAGCAGCAGAGTCATCAG
TGAACAGGCCATGTTATCATGATCATTTGGGGCATCAAACACATATGGCAAGTCATGATTTGCAG
CAAAGGAGTAGCCAACCGCAACTCCTAAATTAACAAGAAAACA
Found at i:3407218 original size:236 final size:235
Alignment explanation
Indices: 3406804--3407279 Score: 596
Period size: 236 Copynumber: 2.0 Consensus size: 235
3406794 CAAGAAAACA
*
3406804 CAAACCAAGATGAGTGAATTTAAAAAGCTATGGAAAGACCTTGTAGTCAAAAGTAAAATTAACCA
1 CAAACCAAGATGACTGAATTTAAAAAGCTATGGAAAGACCTTGTAGTCAAAAGTAAAATTAACCA
* * * * * ** * * *
3406869 ATACAAAAGCAAATTTTTAATACTAAGAAGCATGTAACTTCTTTGGCAATTTGAGAAACGAATAT
66 ACACAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTTAACAATTAGAGAAAAGAATAA
* * * *
3406934 GGAGTATACATGATGAACCAATGTTATGAATGCAAAACCTTGCTTAATTA-CTAGCAGCAGAGTC
131 GGAGTAAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCTA-AAGCAAAGTC
* ** * *
3406998 ATTATTGAACACGTCATTGTTATCATGATCATTTGGGGCAT
195 ATCAGCGAACACGCCAATGTTATCATGATCATTTGGGGCAT
* ** * * *
3407039 CAAACCAGGATGACTGAATTTAGGAATCTAT-GAGAAGACCTTGTAGTCAAGAGTAAGATTAACC
1 CAAACCAAGATGACTGAATTTAAAAAGCTATGGA-AAGACCTTGTAGTCAAAAGTAAAATTAACC
* * * * *
3407103 AACACCAAATGAAAATTTTTAGTGCCAAGAAACATGTAAATTGTTTAACACTTAGAGAAAAGAAT
65 AACA-CAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTTAACAATTAGAGAAAAGAAT
* *
3407168 AAGGAGTAAACATGATGAACCAATGTTATGAATGGAAAAACTTTCTTAATTACCTAAAGCAAAGT
129 AAGGAGTAAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCTAAAGCAAAGT
* *
3407233 CATCAGCGAATAGGCCAATGTTATCATGATCATTTGGGGCAT
194 CATCAGCGAACACGCCAATGTTATCATGATCATTTGGGGCAT
3407275 CAAAC
1 CAAAC
3407280 ACATATGGCA
Statistics
Matches: 203, Mismatches: 35, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
234 2 0.01
235 57 0.28
236 141 0.69
237 3 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (235 bp):
CAAACCAAGATGACTGAATTTAAAAAGCTATGGAAAGACCTTGTAGTCAAAAGTAAAATTAACCA
ACACAAAAGAAAATTTTTAATACCAAGAAACATGTAAATTCTTTAACAATTAGAGAAAAGAATAA
GGAGTAAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCTAAAGCAAAGTCA
TCAGCGAACACGCCAATGTTATCATGATCATTTGGGGCAT
Found at i:3408112 original size:234 final size:235
Alignment explanation
Indices: 3407653--3408359 Score: 709
Period size: 234 Copynumber: 3.0 Consensus size: 235
3407643 CAAGAAAACA
* * * *
3407653 CAAACCAAGATGAGTGAATTTAGGAAAGCTATGAGAAGACCTTGTAGTCAAAAGTAAAATTAACC
1 CAAACCAGGATGAGTGAATCTAGG-AAGCTAGGAGAAGACCTTGTAGTCAAGAGTAAAATTAACC
* ** * * *
3407718 AACATAAAAGTC-AATTTTTGATACCAAGAAACATGTAAAGTCTTCGACAATTT-ACGAAA-AGA
65 AACAGAAAAG-CAAATTTTCAATAACAAGAAACATGTAAATTCTTCAACAATTTGA--AAATAGA
* * * ** * * * ** *
3407780 AT--GCA-TAAACATAACGAACTAACATTATGAATGCAAAAACTAGTTTAATTACC-AATAGTAG
127 ATAAGAAGCAAACATGATAAACCAACATTATGAATGCAAAAACTTGCTTAATTACCGAA-ACCAA
** * * *
3407841 AGTCATCAGAT-ATA-TGGCCAATGTTATAATCATCATTTGGGGAAT
191 AGTCATCAG-TGA-ACAAGCCAATGTTATCATGATCATTTGGGGCAT
* * * * * * **
3407886 CAAACCTGGATGAGTGAATTTAGGAAGCTAGGAGAATACTTTGTAGTTAGGAGTAAAATTAAGTA
1 CAAACCAGGATGAGTGAATCTAGGAAGCTAGGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
* * * * * *
3407951 GCA-CAAAG-AAATTTTCAATACCTAGAAATATGTAAATTCTTCAATAATTTGATAAAT-GAATA
66 ACAGAAAAGCAAATTTTCAATAACAAGAAACATGTAAATTCTTCAACAATTTGA-AAATAGAATA
* * **
3408013 ATAAGCAAACATGATAAACCAACGTTATGAATGCAAAAATCTTGCTTAATTACCGGCACCAAAGT
130 AGAAGCAAACATGATAAACCAACATTATGAATGCAAAAA-CTTGCTTAATTACCGAAACCAAAGT
3408078 CATCAGTGAACAAGCCAATGTTATCATGATCATTTGGGGCAT
194 CATCAGTGAACAAGCCAATGTTATCATGATCATTTGGGGCAT
*
3408120 CAAACCAGGATGAGTGAATCTAGGAAGCTATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
1 CAAACCAGGATGAGTGAATCTAGGAAGCTAGGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
* ** *
3408185 ACAGAAAAGCAAATTTTTAATAACAAGAAACATGTAAATTCTTTGACAATTTGAGAATAGAATAA
66 ACAGAAAAGCAAATTTTCAATAACAAGAAACATGTAAATTCTTCAACAATTTGAAAATAGAATAA
* * * * * * * *
3408250 GGAGTAAACATGATGAACCAGCATTATGAATGGAAAAACTTGCTTAATTACCTAAAGCAGAGTCA
131 GAAGCAAACATGATAAACCAACATTATGAATGCAAAAACTTGCTTAATTACCGAAACCAAAGTCA
* * *
3408315 TCAGTGAACAGGCCAATGTTATCACGATCATTTGAGGCAT
196 TCAGTGAACAAGCCAATGTTATCATGATCATTTGGGGCAT
3408355 CAAAC
1 CAAAC
3408360 ACATATGGCA
Statistics
Matches: 387, Mismatches: 74, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
230 41 0.11
231 5 0.01
232 36 0.09
233 52 0.13
234 108 0.28
235 71 0.18
236 74 0.19
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (235 bp):
CAAACCAGGATGAGTGAATCTAGGAAGCTAGGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
ACAGAAAAGCAAATTTTCAATAACAAGAAACATGTAAATTCTTCAACAATTTGAAAATAGAATAA
GAAGCAAACATGATAAACCAACATTATGAATGCAAAAACTTGCTTAATTACCGAAACCAAAGTCA
TCAGTGAACAAGCCAATGTTATCATGATCATTTGGGGCAT
Found at i:3408797 original size:309 final size:307
Alignment explanation
Indices: 3408120--3408976 Score: 1164
Period size: 309 Copynumber: 2.8 Consensus size: 307
3408110 TTTGGGGCAT
* * *
3408120 CAAACCAGGATGAGTGAATCTAGGAAGCTATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCA
1 CAAACCAAGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTATAGTCAAGAGTAAAATTAACCA
* ** *
3408185 ACAGAAAAGCAAATTTTTAATAACAAGAAACATGTAAATTCTTTGACAATTTGAGAATAGAATAA
66 ACACAAAAGCAAATTTTTAATGCCAAGAAACATGTAAATTCTTTGACAATTTGAGAA-AAAATAA
*** * *
3408250 GGAGTAAACATGATGAACCAGCATTATGAATGGAAAAACTTGCTTAATTACCTAAAGCAGAGTCA
130 GGAGTAAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCGAAAGCAGAGTCA
3408315 TCAGTGAACAGGCCAATGTTATCACGATCATTTGAGGCATCAAACACATATGGCAAGCCATGATT
195 TCAGTGAACAGGCCAATGTTATCACGATCATTTGAGGCATCAAACACATATGGCAAGCCATGATT
3408380 TGCACCAAAAGAGTAGCCAGCCTCAACTCCTAAATTAACAAAAAAACA
260 TGCACCAAAAGAGTAGCCAGCCTCAACTCCTAAATTAACAAAAAAACA
* * * * * *
3408428 CAAACCAAGATAAGTAAATTTAGGAAGCTATGAGAAGTCCTAATAGTCAAGGGTAAAATTAATCA
1 CAAACCAAGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTATAGTCAAGAGTAAAATTAACCA
* *
3408493 ACACAAAAGAAAATTTTTAATGCCAAGAAACATGTAAATTCTTTGAAAATTTGAGAAAAAATTAA
66 ACACAAAAGCAAATTTTTAATGCCAAGAAACATGTAAATTCTTTGACAATTTGAGAAAAAA-TAA
* * * * *
3408558 GGAGTAAACATGATGAGCCAATGTTGTGAATGCAAAAACTTGCTTAATTATCGACA-CTAGTGTC
130 GGAGTAAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCGAAAGC-AGAGTC
* ** * * *
3408622 ATCAGTGAACAGGCCAATGTTATCATGATTTTTTTGGGGCATCAAACACATATGGTAAGTCATGA
194 ATCAGTGAACAGGCCAATGTTATCACGA-TCATTTGAGGCATCAAACACATATGGCAAGCCATGA
* * *
3408687 TTTGCACCAAAGGAGTAGCCAGCC-CTAACTCCTAAATTAATAAGAAAACA
258 TTTGCACCAAAAGAGTAGCCAGCCTC-AACTCCTAAATTAACAAAAAAACA
* *
3408737 CAAACCAAGATGAGTGAATTTAGGAATCTATGAGAAGACCTTATAGTCAAGTGTAAAATTAACCA
1 CAAACCAAGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTATAGTCAAGAGTAAAATTAACCA
* * * *
3408802 ACACAAAAGCAAATTTTTAATGCCAAAAAACAAGAAAATTCTTTGACAATTTGAGAAAAGAATCA
66 ACACAAAAGCAAATTTTTAATGCCAAGAAACATGTAAATTCTTTGACAATTTGAGAAAA-AATAA
* * *
3408867 GGAGTTAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACC-AGCAGCAAAGTC
130 GGAGTAAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCGA-AAGCAGAGTC
* * * ** * *
3408931 ATCAATTAA-ATGACCAATGTTATCATAATCATTTGGGGAATCAAAC
194 ATCAGTGAACA-GGCCAATGTTATCACGATCATTTGAGGCATCAAAC
3408977 CTGGATGAGT
Statistics
Matches: 481, Mismatches: 60, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
307 4 0.01
308 208 0.43
309 266 0.55
310 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.25
Consensus pattern (307 bp):
CAAACCAAGATGAGTGAATTTAGGAAGCTATGAGAAGACCTTATAGTCAAGAGTAAAATTAACCA
ACACAAAAGCAAATTTTTAATGCCAAGAAACATGTAAATTCTTTGACAATTTGAGAAAAAATAAG
GAGTAAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCGAAAGCAGAGTCAT
CAGTGAACAGGCCAATGTTATCACGATCATTTGAGGCATCAAACACATATGGCAAGCCATGATTT
GCACCAAAAGAGTAGCCAGCCTCAACTCCTAAATTAACAAAAAAACA
Found at i:3409156 original size:235 final size:232
Alignment explanation
Indices: 3408737--3409445 Score: 854
Period size: 235 Copynumber: 3.0 Consensus size: 232
3408727 TAAGAAAACA
* * * * *
3408737 CAAACCAAGATGAGTGAATTTAGGAATCTATGAGAAGACCTTATAGTCAAGTGTAAAATTAACCA
1 CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGT-AGGTGTAAAATTAACCA
* * * * *
3408802 ACACAAAAGCAAATTTTTAATGCCAAAAAACAAGAAAATTCTTTGACAATTTGAGAAAAGAATCA
65 ACACAAAAGCAAATTTTTAATGCTAAGAAACATGTAAATTCTTCGACAATTTGAGAAAAGAAT-A
* * * *
3408867 GGAGTTAACATGATGAACCAATGTTATGAATGCAAAAACTTGCTTAATTACCAGCAGCAAAGTCA
129 -GAGTAAACATGATGAACCAATATTATGAATACAAAAGCTTGCTTAATTACCAGCAGCAAAGTCA
*
3408932 TCAATTAA-ATGACCAATGTTATCATAATCATTTGGGGAAT
193 TCAATGAACATG-CCAATGTTATCATAATCATTTGGGGAAT
* * * **
3408972 CAAACCTGGATGAGTGAATTTAGGAAGCTATGAGAATACTTTGTAAGTAGGAGTAAAATTAAGTA
1 CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACTTTGT-AGTAGGTGTAAAATTAACCA
* * *
3409037 GCACAAAAGCAAATTTCTAATGCTAAGAAACATGTAAATTCTTCGATAATTTGAGAAAAGAATAA
65 ACACAAAAGCAAATTTTTAATGCTAAGAAACATGTAAATTCTTCGACAATTTGAGAAAAGAAT-A
* * *
3409102 GAAGTAAACATGATAAACCAACATTATGAATACAAAAGCTTG-TTAAATTACCAGCAGCAGAGTC
129 G-AGTAAACATGATGAACCAATATTATGAATACAAAAGCTTGCTT-AATTACCAGCAGCAAAGTC
* *
3409166 ATCAATGAACATGCCAATGCTATCATGATCATTT-GGGAAT
192 ATCAATGAACATGCCAATGTTATCATAATCATTTGGGGAAT
* * * * *
3409206 CAAATCAGGATGAGTAAATTTAGGAAGTTATGAGAAGACTTTGTGGTCGAGTGTAAAATTAACCA
1 CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTAG-GTGTAAAATTAACCA
* * *
3409271 ACATAGAAA-CAAATTTTTAAT-ATAAAGAAACATGTAAATTCTTCGACAATTTGAGGAAAGAAT
65 ACACA-AAAGCAAATTTTTAATGCT-AAGAAACATGTAAATTCTTCGACAATTTGAGAAAAGAAT
* * * *
3409334 -GAGTAAACATGATGAACCAATGGTATTATGAGTACAAAAGTTTGCTTAATTATCGGCAGCAAAG
128 AGAGTAAACATGATGAACCAA---TATTATGAATACAAAAGCTTGCTTAATTACCAGCAGCAAAG
* * * *
3409398 TCATCAGTGAACAAGCCAATATTATCATAATCATTTGGGGTAT
190 TCATCAATGAACATGCCAATGTTATCATAATCATTTGGGGAAT
3409441 CAAAC
1 CAAAC
3409446 ACATATGGCA
Statistics
Matches: 403, Mismatches: 59, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
231 18 0.04
232 1 0.00
233 4 0.01
234 174 0.43
235 200 0.50
236 6 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (232 bp):
CAAACCAGGATGAGTGAATTTAGGAAGCTATGAGAAGACTTTGTAGTAGGTGTAAAATTAACCAA
CACAAAAGCAAATTTTTAATGCTAAGAAACATGTAAATTCTTCGACAATTTGAGAAAAGAATAGA
GTAAACATGATGAACCAATATTATGAATACAAAAGCTTGCTTAATTACCAGCAGCAAAGTCATCA
ATGAACATGCCAATGTTATCATAATCATTTGGGGAAT
Found at i:3409803 original size:307 final size:305
Alignment explanation
Indices: 3409214--3409888 Score: 824
Period size: 307 Copynumber: 2.2 Consensus size: 305
3409204 ATCAAATCAG
* * * * * *
3409214 GATGAGTAAATTTAGGAAGTTATGAGAAGACTTTGTGGTCGAGTGTAAAATTAACCAACATAGAA
1 GATGAGTAAATTTA-GAAGATATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCAACACAGAA
* * * *
3409279 ACAAATTTTTAATATAAAGAAACATGTAAATTCTTCGACAATTTGAGGAAAGAATGAGTAAACAT
65 ACAAATTTTTAATACAAAGAAACATGTAAATTCTTCGACAATTTAAGAAAAAAATGAGTAAACAT
* * ** * * *
3409344 GATGAACCAATGGTATTATGAGTACAAAAGTTTGCTTAATTATCGGCAGCAAAGTCATCAGTGAA
130 GATGAACCAA--GCATTATGAATACAAAAACTTGCTTAATTACCAGCAACAAAGTCATCAGTGAA
* * * **
3409409 CAAGCCAATATTATCATAATCATTTGGGGTATCAAACACATATGGCAAGTCATGATTTGTACCAA
193 CAAGCCAATATTATCATAATCATTTAGGGCATCAAACACATATGGCAAGCCATGATTTACACCAA
* *
3409474 AGGAGTAGTCAGCCCTAACTCCTAAATTAACAAGAAAACACAAACCAA
258 AAGAGTAGCCAGCCCTAACTCCTAAATTAACAAGAAAACACAAACCAA
* * * * *
3409522 GATGAGTGAATGTATGAAGCTATGAGAAGACCTTGTATTCAAGAGTAAAATAAACCAACACA-AA
1 GATGAGTAAATTTA-GAAGATATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCAACACAGAA
* *
3409586 AGCAAATTTTTAATACCAAGAAACAAT-TAAATTTTTC-ACTAATTTAAGAAAAAAAATCGAGTA
65 A-CAAATTTTTAATACAAAGAAAC-ATGTAAATTCTTCGAC-AATTTAAG-AAAAAAAT-GAGTA
* * * *
3409649 AACATGATGAACCAA-CATTATGAATGCAAAAACTTGCTTACTTACCAGCAACAGAGTCATTAGT
125 AACATGATGAACCAAGCATTATGAATACAAAAACTTGCTTAATTACCAGCAACAAAGTCATCAGT
* * * *
3409713 GAAGAGGCCAATGTTATCATTA-CTATTTAGGGCATCAAACACATATGGCAAGCCATGATTTACA
190 GAACAAGCCAATATTATCATAATC-ATTTAGGGCATCAAACACATATGGCAAGCCATGATTTACA
*
3409777 CCAAAAGAGTAGCCAGCACC-AACTCCTAAATTAACAAGAAAACACAAACCAG
254 CCAAAAGAGTAGCCAGC-CCTAACTCCTAAATTAACAAGAAAACACAAACCAA
3409829 GATGAGTAAATTTAGAAAGATATGAGACA-ACCTTGTAGTCAAGAGTAAAATTAACCAACA
1 GATGAGTAAATTTAG-AAGATATGAGA-AGACCTTGTAGTCAAGAGTAAAATTAACCAACA
3409889 TTATAAATAA
Statistics
Matches: 313, Mismatches: 45, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
306 2 0.01
307 193 0.62
308 90 0.29
309 8 0.03
310 20 0.06
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (305 bp):
GATGAGTAAATTTAGAAGATATGAGAAGACCTTGTAGTCAAGAGTAAAATTAACCAACACAGAAA
CAAATTTTTAATACAAAGAAACATGTAAATTCTTCGACAATTTAAGAAAAAAATGAGTAAACATG
ATGAACCAAGCATTATGAATACAAAAACTTGCTTAATTACCAGCAACAAAGTCATCAGTGAACAA
GCCAATATTATCATAATCATTTAGGGCATCAAACACATATGGCAAGCCATGATTTACACCAAAAG
AGTAGCCAGCCCTAACTCCTAAATTAACAAGAAAACACAAACCAA
Found at i:3410098 original size:255 final size:256
Alignment explanation
Indices: 3409644--3410137 Score: 703
Period size: 255 Copynumber: 1.9 Consensus size: 256
3409634 AAAAAAAATC
* *
3409644 GAGTAAACATGATGAACCAACATTATGAATGCAAAAACTTGCTTACTTACCAGCAACAGAGTCAT
1 GAGTAAACATGATAAACCAACATTATGAATGCAAAAACTTGCTTAATTACCAGCAACAGAGTCAT
* * * *
3409709 TAGTGAAGAGGCCAATGTTATCATTACTATTTAGGGCATCAAACACATATGGCAAGCCATGATTT
66 TAGAGAACAAGCCAATGTTATCATGACTATTTAGGGCATCAAACACATATGGCAAGCCATGATTT
* *
3409774 ACACCAAAAGAGTAGCCAGCACCAACTCCTAAATTAACAAGAAAACACAAACCAGGATGAGTAAA
131 ACACCAAAAAAGTAGCCAGCACCAACTCCTAAATTAACAAGAAAACACAAACCAGGATAAGTAAA
* * *
3409839 TTTAGAAAGATATGAGACA-ACCTTGTAGTCAAGAGTAAAATTAACCAACATTATAAATAAG
196 TTTAGAAAGATATAAGA-AGACCTTGCAGTCAAGAATAAAATTAACCAACATTATAAATAAG
*
3409900 GAGTAAACATGATAAACCAACATTATGAATGCAAAAACTTGCTTAATTACC-GACGACAGAGTCA
1 GAGTAAACATGATAAACCAACATTATGAATGCAAAAACTTGCTTAATTACCAG-CAACAGAGTCA
* *
3409964 TTAGAGAACAAGCCAATGTTATCATGA-TCATTTGGGGTATC-AACACATATGGCAA-CTCATGA
65 TTAGAGAACAAGCCAATGTTATCATGACT-ATTTAGGGCATCAAACACATATGGCAAGC-CATGA
* * * * *
3410026 TTTACACCAAAAAAGTTGCTAGC-CTTAACTCCTAAATTAATAAGAAAACATAAACCAGGATAAG
128 TTTACACCAAAAAAGTAGCCAGCAC-CAACTCCTAAATTAACAAGAAAACACAAACCAGGATAAG
* * *
3410090 TGAATTTAGGAAGCTATAAGAAGACCTTGCAGTCAAGAATAAAATTAA
192 TAAATTTAGAAAGATATAAGAAGACCTTGCAGTCAAGAATAAAATTAA
3410138 ACAAGACAAA
Statistics
Matches: 211, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
254 3 0.01
255 116 0.55
256 92 0.44
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (256 bp):
GAGTAAACATGATAAACCAACATTATGAATGCAAAAACTTGCTTAATTACCAGCAACAGAGTCAT
TAGAGAACAAGCCAATGTTATCATGACTATTTAGGGCATCAAACACATATGGCAAGCCATGATTT
ACACCAAAAAAGTAGCCAGCACCAACTCCTAAATTAACAAGAAAACACAAACCAGGATAAGTAAA
TTTAGAAAGATATAAGAAGACCTTGCAGTCAAGAATAAAATTAACCAACATTATAAATAAG
Found at i:3415460 original size:2 final size:2
Alignment explanation
Indices: 3415453--3415500 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3415443 GGAGCACCCA
3415453 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3415495 TC TC TC
1 TC TC TC
3415501 GTACTAGTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3417076 original size:3 final size:3
Alignment explanation
Indices: 3417068--3417097 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3417058 GAGTTTCTAG
3417068 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3417098 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3417104 original size:3 final size:3
Alignment explanation
Indices: 3417098--3417133 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3417088 AATAATAATA
3417098 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3417134 TATTGAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3417419 original size:10 final size:10
Alignment explanation
Indices: 3417394--3417431 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
3417384 TGGTTTAACA
*
3417394 TTCTTTTACAC
1 TTCTTTT-CCC
3417405 TTCTTTTCCC
1 TTCTTTTCCC
3417415 TTCTTTTCCC
1 TTCTTTTCCC
3417425 TTCTTTT
1 TTCTTTT
3417432 GAGTTACATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (10 bp):
TTCTTTTCCC
Found at i:3417773 original size:2 final size:2
Alignment explanation
Indices: 3417766--3417792 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3417756 TATGCTTTTG
3417766 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3417793 GGGTGTAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3426826 original size:14 final size:15
Alignment explanation
Indices: 3426794--3426833 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
3426784 TTAACAAAAT
*
3426794 AATATTAAATATATGA
1 AATA-TAAATATATAA
3426810 AATATAAA-ATATAA
1 AATATAAATATATAA
3426824 AATATAAATA
1 AATATAAATA
3426834 AAAACGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 13 0.59
15 5 0.23
16 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATATAAATATATAA
Found at i:3435514 original size:18 final size:20
Alignment explanation
Indices: 3435486--3435523 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3435476 GGTACAATAA
3435486 AAAATTTTA-TTTTATTAAT
1 AAAATTTTATTTTTATTAAT
3435505 AAAA-TTTATTTTTATTAAT
1 AAAATTTTATTTTTATTAAT
3435524 TTTAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTTTATTTTTATTAAT
Found at i:3435854 original size:10 final size:10
Alignment explanation
Indices: 3435841--3435870 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3435831 ATTGAGCTTT
3435841 TATATTTTAA
1 TATATTTTAA
3435851 TATATTTTAA
1 TATATTTTAA
3435861 T-TATTTTAA
1 TATATTTTAA
3435870 T
1 T
3435871 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:3435867 original size:9 final size:9
Alignment explanation
Indices: 3435843--3435872 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3435833 TGAGCTTTTA
3435843 TATTTTAAT
1 TATTTTAAT
3435852 ATATTTTAAT
1 -TATTTTAAT
3435862 TATTTTAAT
1 TATTTTAAT
3435871 TA
1 TA
3435873 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:3436183 original size:2 final size:2
Alignment explanation
Indices: 3436178--3436225 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
3436168 TGTGTGTGTG
* *
3436178 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T- TA CA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3436218 TA TA TA TA
1 TA TA TA TA
3436226 GACGGTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3436373 original size:21 final size:20
Alignment explanation
Indices: 3436349--3436399 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3436339 TTTAAATATG
* *
3436349 AATTTTATCTTTTTAATAAAT
1 AATTTTAT-TATTTAACAAAT
*
3436370 AATTTTAGTTATTTACCAAAT
1 AATTTTA-TTATTTAACAAAT
3436391 AATTTTATT
1 AATTTTATT
3436400 TAAATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (20 bp):
AATTTTATTATTTAACAAAT
Found at i:3445885 original size:31 final size:30
Alignment explanation
Indices: 3445817--3445889 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
3445807 GAAACTTAAG
* *
3445817 TAAAA-AAATTTTTATATAAAGAGAATAAA
1 TAAAATAATTTTTTATATAAAAAGAATAAA
3445846 TAAAATAATTTTTTATATAAAAAGAATAAA
1 TAAAATAATTTTTTATATAAAAAGAATAAA
3445876 TGAAAATAATTTTT
1 T-AAAATAATTTTT
3445890 GAACTTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 5 0.12
30 23 0.57
31 12 0.30
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (30 bp):
TAAAATAATTTTTTATATAAAAAGAATAAA
Found at i:3447617 original size:18 final size:18
Alignment explanation
Indices: 3447596--3447637 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3447586 TCGTATATTT
3447596 ATATAATATTTTATATAA
1 ATATAATATTTTATATAA
* * *
3447614 ATATTATATTTTTTATTA
1 ATATAATATTTTATATAA
3447632 ATATAA
1 ATATAA
3447638 AATATATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATAATATTTTATATAA
Found at i:3447660 original size:22 final size:25
Alignment explanation
Indices: 3447602--3447665 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 25
3447592 ATTTATATAA
3447602 TATTTTATATAAATATTATATTTTT
1 TATTTTATATAAATATTATATTTTT
*
3447627 TA-TTAATATAAA-A-TATATTTTT
1 TATTTTATATAAATATTATATTTTT
3447649 TATTTTAT-TAAAT-TTAT
1 TATTTTATATAAATATTAT
3447666 TTATAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 15 0.44
23 8 0.24
24 9 0.26
25 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTTTATATAAATATTATATTTTT
Found at i:3447661 original size:21 final size:21
Alignment explanation
Indices: 3447609--3447676 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
3447599 TAATATTTTA
*
3447609 TATAAATATTATATTTTTTATTAA
1 TATAAA-A-TATATTTTTTATT-T
3447633 TATAAAATATATTTTTTATTT
1 TATAAAATATATTTTTTATTT
* * * *
3447654 TATTAAATTTATTTATAATTT
1 TATAAAATATATTTTTTATTT
3447675 TA
1 TA
3447677 AATAAAGTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 19 0.49
22 13 0.33
23 1 0.03
24 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATAAAATATATTTTTTATTT
Found at i:3450664 original size:29 final size:30
Alignment explanation
Indices: 3450619--3450693 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
3450609 ATTGATAATT
* *
3450619 TATATATATATTATTTTATC-T-AAAAATAA
1 TATATATA-ATTTTTTTAACATAAAAAATAA
3450648 TATATCATAATTTTTTTAACATAAAAAATAA
1 TATAT-ATAATTTTTTTAACATAAAAAATAA
*
3450679 -AAATATAATTTTTTT
1 TATATATAATTTTTTT
3450694 TATTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 25 0.62
30 7 0.17
31 8 0.20
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (30 bp):
TATATATAATTTTTTTAACATAAAAAATAA
Found at i:3467885 original size:24 final size:25
Alignment explanation
Indices: 3467844--3467903 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
3467834 AGTTAAAAAT
* *
3467844 AATAATAATAATTATTATTA-TTATG
1 AATAA-AAAAATTATTATAAGTTATG
*
3467869 ATTAAAAAAATTATTATAAGTTATG
1 AATAAAAAAATTATTATAAGTTATG
3467894 AATAAAAAAA
1 AATAAAAAAA
3467904 ATTTCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
AATAAAAAAATTATTATAAGTTATG
Found at i:3467912 original size:25 final size:25
Alignment explanation
Indices: 3467864--3467912 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
3467854 ATTATTATTA
* *
3467864 TTATGATTAAAAAAATTATTATAAG
1 TTATGATAAAAAAAATTATCATAAG
3467889 TTATGAATAAAAAAAATT-TCATAA
1 TTATG-ATAAAAAAAATTATCATAA
3467913 AAATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
TTATGATAAAAAAAATTATCATAAG
Found at i:3467943 original size:15 final size:15
Alignment explanation
Indices: 3467910--3467941 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3467900 AAAAATTTCA
3467910 TAAA-AATTTTATAT
1 TAAATAATTTTATAT
3467924 TAAATAATTTT-TAT
1 TAAATAATTTTATAT
3467938 TAAA
1 TAAA
3467942 ATTGACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATAATTTTATAT
Found at i:3470156 original size:28 final size:28
Alignment explanation
Indices: 3470099--3470156 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3470089 TAATTGTAAG
* * *
3470099 TTTTATTATTATATATTTTACATCTATT
1 TTTTATTATTATAAATTTGACATATATT
3470127 TTTTATTATTAATAAATTTG--ATATATT
1 TTTTATTATT-ATAAATTTGACATATATT
3470154 TTT
1 TTT
3470157 AAAACATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 9 0.35
28 10 0.38
29 7 0.27
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATTATTATAAATTTGACATATATT
Found at i:3470245 original size:112 final size:112
Alignment explanation
Indices: 3470106--3470324 Score: 298
Period size: 112 Copynumber: 1.9 Consensus size: 112
3470096 AAGTTTTATT
* *
3470106 ATTATATATTTTACATCTATTTTTTATTATTAATAAATTTGATATATTTTTAAAACATTATTATA
1 ATTATATATTTTA-ATCTATTTTTTATTATTAATAAATTTAATATAATTTTAAAACATTATTATA
* *
3470171 AAATATTACTTTGA-TCCTTTCAAAATTAAACATCAAGATCTATCATTA
65 AAATATTACTTTAACCCCTTT-AAAATTAAACATCAAGATCTATCATTA
* * * **
3470219 ATTATATATTTGT-ATTTATTTTTTATTATTAATTATTTTAATATAATTTTAAAATTTTATTATA
1 ATTATATATTT-TAATCTATTTTTTATTATTAATAAATTTAATATAATTTTAAAACATTATTATA
* *
3470283 AAATATTACTTTAACCCCTTTAAAGTTAAACATCGAGATCTA
65 AAATATTACTTTAACCCCTTTAAAATTAAACATCAAGATCTA
3470325 CCACCGCTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
112 76 0.82
113 16 0.17
114 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (112 bp):
ATTATATATTTTAATCTATTTTTTATTATTAATAAATTTAATATAATTTTAAAACATTATTATAA
AATATTACTTTAACCCCTTTAAAATTAAACATCAAGATCTATCATTA
Found at i:3471203 original size:28 final size:29
Alignment explanation
Indices: 3471163--3471220 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3471153 TAAATGAATG
*
3471163 ATAAAATTGATTCTAA-TAAAATTAAAAA
1 ATAAAATTGATTCTAACCAAAATTAAAAA
*
3471191 ATAATAATT-ATTCTAACCATAATTAAAAA
1 ATAA-AATTGATTCTAACCAAAATTAAAAA
3471220 A
1 A
3471221 ATTAGTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (29 bp):
ATAAAATTGATTCTAACCAAAATTAAAAA
Found at i:3474275 original size:15 final size:15
Alignment explanation
Indices: 3474239--3474281 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3474229 TATATTTTCA
3474239 TTTAAATTTAATAAT
1 TTTAAATTTAATAAT
** *
3474254 TCAAAATTTAATTAT
1 TTTAAATTTAATAAT
*
3474269 TTTAAATTGAATA
1 TTTAAATTTAATA
3474282 TACAATTTAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTAAATTTAATAAT
Found at i:3481092 original size:30 final size:30
Alignment explanation
Indices: 3481056--3481115 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3481046 GTCTCCTATA
*
3481056 GTCCACTCATAAATAAATATACATACCTAG
1 GTCCACTCATAAATAAATATACACACCTAG
3481086 GTCCACTCATAAATAAATATACACACCTAG
1 GTCCACTCATAAATAAATATACACACCTAG
3481116 AGCCCCATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (30 bp):
GTCCACTCATAAATAAATATACACACCTAG
Found at i:3482320 original size:52 final size:52
Alignment explanation
Indices: 3482249--3482395 Score: 170
Period size: 52 Copynumber: 2.8 Consensus size: 52
3482239 TATAATCATA
* *
3482249 CAAACTTGCCCATTAAGAATCCTTTTCCTCTTAAAATTCTTCTCCTATAAGT
1 CAAACTTGCCTATTAAGAATCCTTTTCCTCTTAAAATTCTTCTCCTACAAGT
* * * ** *
3482301 CAAACTTGCCTATTAAGAATCCATTTCCTTTTAAAATTTTTCTGTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCTTTTCCTCTTAAAATTCTTCTCCTACAAGT
** * *
3482353 CAAACTTAACTATTAAGAAT-CTTCTTTCTCTTAGAATTCTTCT
1 CAAACTTGCCTATTAAGAATCCTT-TTCCTCTTAAAATTCTTCT
3482396 TTTGCAAGAT
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
51 2 0.03
52 77 0.97
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCTTTTCCTCTTAAAATTCTTCTCCTACAAGT
Found at i:3483032 original size:52 final size:52
Alignment explanation
Indices: 3482964--3483076 Score: 172
Period size: 52 Copynumber: 2.2 Consensus size: 52
3482954 AAACGTGCCC
* ** *
3482964 ATTAAGAATCCCTTTCCTCTTAGAATTTTTCTCTTGTAAGTCAAACTTACCT
1 ATTAAGAATCCATTTCCTCTTAGAATTTTTCTCTTACAAGTCAAACTTAACT
* *
3483016 ATTAAGAATCCATTTCCTTTTAGAATTTTTCTGTTACAAGTCAAACTTAACT
1 ATTAAGAATCCATTTCCTCTTAGAATTTTTCTCTTACAAGTCAAACTTAACT
3483068 ATTAAGAAT
1 ATTAAGAAT
3483077 TGTCCGCTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (52 bp):
ATTAAGAATCCATTTCCTCTTAGAATTTTTCTCTTACAAGTCAAACTTAACT
Found at i:3494311 original size:15 final size:15
Alignment explanation
Indices: 3494291--3494328 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3494281 AGTTTCATTT
3494291 TTATATATTTAAATA
1 TTATATATTTAAATA
*
3494306 TTATATATTTAATTA
1 TTATATATTTAAATA
3494321 TT-TATATT
1 TTATATATT
3494329 CAGTCCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATATTTAAATA
Found at i:3517612 original size:31 final size:31
Alignment explanation
Indices: 3517577--3517640 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3517567 TATACGTAGG
3517577 TATGTTTTTAATTTTGAAAGAACCTTACATC
1 TATGTTTTTAATTTTGAAAGAACCTTACATC
3517608 TATGTTTTTAATTTTGAAAGAACCTTACATC
1 TATGTTTTTAATTTTGAAAGAACCTTACATC
3517639 TA
1 TA
3517641 AGAACTCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (31 bp):
TATGTTTTTAATTTTGAAAGAACCTTACATC
Found at i:3538137 original size:15 final size:15
Alignment explanation
Indices: 3538117--3538147 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3538107 ATAATTCAAT
*
3538117 TAATTTAATTTTAAA
1 TAATTTAATTTAAAA
3538132 TAATTTAATTTAAAA
1 TAATTTAATTTAAAA
3538147 T
1 T
3538148 TTATTGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTTAATTTAAAA
Found at i:3553909 original size:31 final size:32
Alignment explanation
Indices: 3553871--3553936 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
3553861 TGAATATGTG
*
3553871 TATATATATAAATT-ATTT-TTTTTCAAAATTA
1 TATATATACAAATTAATTTCTTTTT-AAAATTA
3553902 TATATATACAAATTAATTTCTTTTTAAAATTA
1 TATATATACAAATTAATTTCTTTTTAAAATTA
3553934 TAT
1 TAT
3553937 TCAAATCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 13 0.41
32 14 0.44
33 5 0.16
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATATACAAATTAATTTCTTTTTAAAATTA
Found at i:3555077 original size:2 final size:2
Alignment explanation
Indices: 3555070--3555123 Score: 56
Period size: 2 Copynumber: 26.0 Consensus size: 2
3555060 TATATTGTTA
* *
3555070 AT AT AT AT AT AT AT AT AT AT AC AT AT -T AG AT AT GAT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT
3555113 AT AT AT GAT AT
1 AT AT AT -AT AT
3555124 CTTATTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 1 0.02
2 37 0.84
3 6 0.14
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3555216 original size:32 final size:32
Alignment explanation
Indices: 3555168--3555243 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
3555158 TTGTCACATT
* * *
3555168 AATAT-TAAAAGA-AATATTTTAAAAATTTTAA
1 AATATATAAAATATAATATTTTTAAAA-ATTAA
3555199 AA-ATATAAAATATAATATTTTTAAAAATTAA
1 AATATATAAAATATAATATTTTTAAAAATTAA
3555230 AATATATAAAATAT
1 AATATATAAAATAT
3555244 TTTTAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.05
31 14 0.36
32 23 0.59
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
AATATATAAAATATAATATTTTTAAAAATTAA
Found at i:3555218 original size:23 final size:23
Alignment explanation
Indices: 3555193--3555258 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 23
3555183 ATTTTAAAAA
3555193 TTTTAAAAATATAAAATATAATAT
1 TTTTAAAAAT-TAAAATATAATAT
3555217 TTTTAAAAATTAAAATATATAAAATAT
1 TTTTAAAAATT-AAA-ATAT--AATAT
3555244 TTTTAAAAATTAAAA
1 TTTTAAAAATTAAAA
3555259 AAGTATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.03
24 13 0.34
25 5 0.13
26 3 0.08
27 16 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTTAAAAATTAAAATATAATAT
Found at i:3555340 original size:37 final size:38
Alignment explanation
Indices: 3555274--3555362 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 38
3555264 TGAAAACTTA
* ***
3555274 AAAAATTCAAAAAACTCAAAATTTTAATAAAATTT-TT
1 AAAAATTCAAAAAACTAAAAATAAAAATAAAATTTCTT
3555311 GAAAAATTCAAAAAA-TAAAAATAAAAATAAAATTTCTT
1 -AAAAATTCAAAAAACTAAAAATAAAAATAAAATTTCTT
* *
3555349 AAAATTTTAAAAAA
1 AAAAATTCAAAAAA
3555363 ATTCACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 28 0.64
38 16 0.36
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (38 bp):
AAAAATTCAAAAAACTAAAAATAAAAATAAAATTTCTT
Found at i:3555554 original size:8 final size:9
Alignment explanation
Indices: 3555482--3555612 Score: 61
Period size: 10 Copynumber: 13.9 Consensus size: 9
3555472 ATTCATAACC
3555482 ATTTAAAAAA
1 ATTT-AAAAA
*
3555492 ATTCAAAAA
1 ATTTAAAAA
*
3555501 A-ATAAAAA
1 ATTTAAAAA
*
3555509 ATTTTCAAAA
1 A-TTTAAAAA
* *
3555519 ATCTGAAATA
1 AT-TTAAAAA
*
3555529 TTCTTAAAAA
1 AT-TTAAAAA
3555539 ATTATAAAAA
1 ATT-TAAAAA
*
3555549 ATTAAAAAA
1 ATTTAAAAA
*
3555558 GATTCTGAAAA
1 -ATT-TAAAAA
*
3555569 A-TAAAAAA
1 ATTTAAAAA
*
3555577 ACTT-AAAA
1 ATTTAAAAA
3555585 ATTTAATAATA
1 ATTTAA-AA-A
*
3555596 ATCTAAAAA
1 ATTTAAAAA
3555605 ATTTAAAA
1 ATTTAAAA
3555613 TTGTATGATT
Statistics
Matches: 90, Mismatches: 21, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
8 18 0.20
9 24 0.27
10 38 0.42
11 10 0.11
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:3555605 original size:67 final size:64
Alignment explanation
Indices: 3555484--3555612 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 64
3555474 TCATAACCAT
** * *
3555484 TTAAAAAAATTCAAAAAAATAAAAAATTTTCAAAAATCTGAAATATTCTTAAAAAATTATAAAAA
1 TTAAAAAAATTCAAAAAAATAAAAAAACTTCAAAAATCTAAAATAATC-TAAAAAATT-TAAAAA
3555549 A
64 A
** *
3555550 TTAAAAAAGATTCTGAAAAATAAAAAAACTT-AAAAATTTAATAATAATCTAAAAAATTTAAAA
1 TTAAAAAA-ATTCAAAAAAATAAAAAAACTTCAAAAATCTAA-AATAATCTAAAAAATTTAAAA
3555613 TTGTATGATT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
65 5 0.09
66 25 0.46
67 24 0.44
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (64 bp):
TTAAAAAAATTCAAAAAAATAAAAAAACTTCAAAAATCTAAAATAATCTAAAAAATTTAAAAAA
Found at i:3555795 original size:20 final size:21
Alignment explanation
Indices: 3555750--3555800 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3555740 AAATTTTAAG
*
3555750 AAAATTTTAAGAATTTTTATT
1 AAAATTTTAAGAATTTTTATA
*
3555771 TAAATTTTAAG-ATTTTT-TGA
1 AAAATTTTAAGAATTTTTAT-A
3555791 AAAATTTTAA
1 AAAATTTTAA
3555801 ATTATCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 15 0.58
21 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
AAAATTTTAAGAATTTTTATA
Found at i:3556051 original size:6 final size:6
Alignment explanation
Indices: 3556019--3556062 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
3556009 TAACATTAAC
*
3556019 ATCAAA TATCAAA AT-AAA CAACAAA ATCAAA ATCAAA ATCAAA A
1 ATCAAA -ATCAAA ATCAAA -ATCAAA ATCAAA ATCAAA ATCAAA A
3556063 CCATAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 3 0.09
6 21 0.64
7 9 0.27
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ATCAAA
Found at i:3556061 original size:18 final size:18
Alignment explanation
Indices: 3556016--3556062 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3556006 AAATAACATT
3556016 AACATCAAATATCAAAATA
1 AACATCAAA-ATCAAAATA
*
3556035 AACAACAAAATCAAAATCA
1 AACATCAAAATCAAAAT-A
3556054 AA-ATCAAAA
1 AACATCAAAA
3556063 CCATAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.68, C:0.17, G:0.00, T:0.15
Consensus pattern (18 bp):
AACATCAAAATCAAAATA
Found at i:3559146 original size:45 final size:45
Alignment explanation
Indices: 3559082--3559173 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
3559072 ACATTAAACT
3559082 TTGACTCTCAGCATCAGCAGATTCTTTTACTAAAAGAAAAGAAAA
1 TTGACTCTCAGCATCAGCAGATTCTTTTACTAAAAGAAAAGAAAA
*
3559127 TTGACTCTCAGCATCAGCAGATTGTTTTACTAAAAGAAAAGAAAA
1 TTGACTCTCAGCATCAGCAGATTCTTTTACTAAAAGAAAAGAAAA
3559172 TT
1 TT
3559174 ATCAAATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.28
Consensus pattern (45 bp):
TTGACTCTCAGCATCAGCAGATTCTTTTACTAAAAGAAAAGAAAA
Found at i:3565056 original size:36 final size:38
Alignment explanation
Indices: 3565003--3565083 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
3564993 TTAAACAAAC
*
3565003 TTTATTTGAATAGTTATA-TTTT-TCTGTTCAGACATA
1 TTTATTTGAATAGTTATATTTTTCTCTGTTCAAACATA
* *
3565039 TTTATTTGGACTA-TTATATTTTTCTCTGTTCAAACATG
1 TTTATTT-GAATAGTTATATTTTTCTCTGTTCAAACATA
3565077 TTTATTT
1 TTTATTT
3565084 AAAATTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
36 12 0.31
37 8 0.21
38 19 0.49
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (38 bp):
TTTATTTGAATAGTTATATTTTTCTCTGTTCAAACATA
Found at i:3569438 original size:11 final size:11
Alignment explanation
Indices: 3569424--3569456 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
3569414 TAATTAAAAA
3569424 TTATTTAATTT
1 TTATTTAATTT
3569435 TTATTTAATTT
1 TTATTTAATTT
3569446 TTATTGTAATT
1 TTATT-TAATT
3569457 AATCAACTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
TTATTTAATTT
Found at i:3570665 original size:5 final size:5
Alignment explanation
Indices: 3570655--3570679 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3570645 GATCCAAACC
3570655 AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA
3570680 GGGAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:3571647 original size:23 final size:22
Alignment explanation
Indices: 3571616--3571663 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3571606 CTTATAAATT
* * *
3571616 AAAAATAATTTTTTTACTTTAA
1 AAAAATAATTATCTTACATTAA
3571638 AAAAATTAATTATCTTACATTAA
1 AAAAA-TAATTATCTTACATTAA
3571661 AAA
1 AAA
3571664 GACGATGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATAATTATCTTACATTAA
Found at i:3580134 original size:7 final size:7
Alignment explanation
Indices: 3580122--3580149 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3580112 GTCGTTATAA
3580122 AATATTT
1 AATATTT
3580129 AATATTT
1 AATATTT
3580136 AATATTT
1 AATATTT
3580143 AATATTT
1 AATATTT
3580150 CATTTAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:3585662 original size:3 final size:3
Alignment explanation
Indices: 3585654--3585682 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3585644 CATGAACTAT
3585654 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3585683 CTTATGGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3590452 original size:30 final size:30
Alignment explanation
Indices: 3590395--3590472 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
3590385 AGAAAAGTCG
*
3590395 TTAAATTTTATCATTT-TATTTAAATAAAATT-
1 TTAAATTTTA--ATTTGTATTCAAAT-AAATTC
3590426 TTAAATTTTAATTTGTATTCAAATAAATTC
1 TTAAATTTTAATTTGTATTCAAATAAATTC
* *
3590456 ATAATTTTTAATTTGTA
1 TTAAATTTTAATTTGTA
3590473 AATGAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.21
30 23 0.55
31 10 0.24
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.54
Consensus pattern (30 bp):
TTAAATTTTAATTTGTATTCAAATAAATTC
Found at i:3590579 original size:29 final size:29
Alignment explanation
Indices: 3590512--3590582 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
3590502 TTTATTTAAA
*
3590512 ATAAAAATTTAGTTAAATACAAATAAAAT
1 ATAAAAATTTATTTAAATACAAATAAAAT
* *
3590541 ATTAATAATTTATTTAGATAC-AATAAAAAT
1 A-TAAAAATTTATTTAAATACAAAT-AAAAT
3590571 ATAAAAATTTAT
1 ATAAAAATTTAT
3590583 CAAAATAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
ATAAAAATTTATTTAAATACAAATAAAAT
Found at i:3593465 original size:30 final size:31
Alignment explanation
Indices: 3593398--3593465 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
3593388 CAATCAAGGG
*
3593398 TTTAATT-GAGTAAAAATAGATATATAAAGA
1 TTTAATTGGAGTAAAAATAAATATATAAAGA
* *
3593428 TTCAATTGGA-TAAAAATAAATAT-TTAAGAA
1 TTTAATTGGAGTAAAAATAAATATATAAAG-A
3593458 TTTAATTG
1 TTTAATTG
3593466 ATTTGAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.12
30 26 0.81
31 2 0.06
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (31 bp):
TTTAATTGGAGTAAAAATAAATATATAAAGA
Found at i:3595348 original size:9 final size:9
Alignment explanation
Indices: 3595334--3595362 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3595324 ATAGTTTAAA
3595334 AAAAAAAAG
1 AAAAAAAAG
3595343 -AAAAAAAG
1 AAAAAAAAG
3595351 AAAAAAAAG
1 AAAAAAAAG
3595360 AAA
1 AAA
3595363 GAGATTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3596630 original size:18 final size:19
Alignment explanation
Indices: 3596607--3596643 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3596597 ATGATTATCT
3596607 AAAATATTT-TTATGTAAG
1 AAAATATTTCTTATGTAAG
*
3596625 AAAATATTTCTTATTTAAG
1 AAAATATTTCTTATGTAAG
3596644 TCCAAGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
AAAATATTTCTTATGTAAG
Found at i:3598889 original size:13 final size:14
Alignment explanation
Indices: 3598847--3598895 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
3598837 AAATGGCAAA
3598847 TTTTCT-AAGAAA-
1 TTTTCTAAAGAAAT
3598859 TTTT-TAAGAGAAAT
1 TTTTCTAA-AGAAAT
*
3598873 TTTTCTAAATAAAT
1 TTTTCTAAAGAAAT
3598887 TTTTCTAAA
1 TTTTCTAAA
3598896 TTTTTCCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 1 0.03
12 5 0.16
13 5 0.16
14 18 0.56
15 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (14 bp):
TTTTCTAAAGAAAT
Found at i:3603302 original size:16 final size:16
Alignment explanation
Indices: 3603277--3603310 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3603267 ATGTGCCATT
*
3603277 TTCTAGGGATGGGAAA
1 TTCTAGGGATGGAAAA
*
3603293 TTCTATGGATGGAAAA
1 TTCTAGGGATGGAAAA
3603309 TT
1 TT
3603311 TGATAATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (16 bp):
TTCTAGGGATGGAAAA
Found at i:3607690 original size:17 final size:16
Alignment explanation
Indices: 3607643--3607690 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
3607633 AAACATGAAG
*
3607643 AAAAAAGAGAAAAGAA
1 AAAAAAGAGGAAAGAA
*
3607659 AAAAAATGAAAGAAAGAA
1 AAAAAA-G-AGGAAAGAA
3607677 AAAAAAGATGGAAA
1 AAAAAAGA-GGAAA
3607691 TGTAAAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 7 0.27
17 6 0.23
18 13 0.50
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAAAAGAGGAAAGAA
Found at i:3609185 original size:22 final size:21
Alignment explanation
Indices: 3609098--3609187 Score: 72
Period size: 22 Copynumber: 4.1 Consensus size: 21
3609088 ATAAGAAATG
**
3609098 ATTTATAAGACCTTCGGGCATA
1 ATTT-TAAGACCTTCAAGCATA
*
3609120 ATTTGTAAGACCTCCAAGCATA
1 ATTT-TAAGACCTTCAAGCATA
* * * *
3609142 ATCTTCAATAACTTCAATCATA
1 AT-TTTAAGACCTTCAAGCATA
*
3609164 ATATTTAAGACCTTTAAGCATA
1 AT-TTTAAGACCTTCAAGCATA
3609186 AT
1 AT
3609188 CTCAAAAAAA
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 50 0.96
23 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
ATTTTAAGACCTTCAAGCATA
Found at i:3609227 original size:20 final size:19
Alignment explanation
Indices: 3609191--3609230 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3609181 GCATAATCTC
*
3609191 AAAAAAATAAAAGTTTTAA
1 AAAAAAATAAAAATTTTAA
3609210 AAAAAAATAAAACATTTTAA
1 AAAAAAATAAAA-ATTTTAA
3609230 A
1 A
3609231 GAGATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAAAATAAAAATTTTAA
Found at i:3609676 original size:22 final size:22
Alignment explanation
Indices: 3609621--3609680 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3609611 TTTAAGTGTT
* *
3609621 AAGATTTGTAAGACTTCTAGGC
1 AAGATTTGTAAGTCTTCCAGGC
* *
3609643 ATA-ATCTCTAAGTCTTCCAGGC
1 A-AGATTTGTAAGTCTTCCAGGC
3609665 AAGATTTGTAAGTCTT
1 AAGATTTGTAAGTCTT
3609681 ATGAGCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (22 bp):
AAGATTTGTAAGTCTTCCAGGC
Found at i:3609889 original size:42 final size:44
Alignment explanation
Indices: 3609797--3609900 Score: 131
Period size: 42 Copynumber: 2.4 Consensus size: 44
3609787 AGTAAGAATA
*
3609797 TTTTTCTATTTTTCAAAAGTTATTGAGCCTCTATTAAGATAAGC
1 TTTTTATATTTTTCAAAAGTTATTGAGCCTCTATTAAGATAAGC
* * * * *
3609841 TTTTTATATTTTT-AAAAGTTGTTGA-CCTTTGTTTAGATGAGC
1 TTTTTATATTTTTCAAAAGTTATTGAGCCTCTATTAAGATAAGC
*
3609883 TTTTTATATTGTTCAAAA
1 TTTTTATATTTTTCAAAA
3609901 AGTTTGAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 25 0.48
43 15 0.29
44 12 0.23
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (44 bp):
TTTTTATATTTTTCAAAAGTTATTGAGCCTCTATTAAGATAAGC
Found at i:3610877 original size:60 final size:59
Alignment explanation
Indices: 3610787--3610921 Score: 155
Period size: 60 Copynumber: 2.3 Consensus size: 59
3610777 TAAATTAAAT
* * * ** *
3610787 TAAGAATTAAAATCAATTGAGAAAGATTTAATCTATTAAA-AGTAAATTTAATTAATTTGG
1 TAAGAA-TCAAATCAATTGAGAAAAATTTAAGCTATTAAATA-TAAATGCAATTAATTTGA
* * *
3610847 TTAGAATCAAATTAATTGAGAGAAAATTTAAGCTATTAAATATTAATGCAATTAATTTGA
1 TAAGAATCAAATCAATTGAGA-AAAATTTAAGCTATTAAATATAAATGCAATTAATTTGA
3610907 TAAGAATCAAATCAA
1 TAAGAATCAAATCAA
3610922 ATTAACTCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 13 0.21
60 48 0.77
61 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (59 bp):
TAAGAATCAAATCAATTGAGAAAAATTTAAGCTATTAAATATAAATGCAATTAATTTGA
Done.