Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 56 of 310
Found at i:17432366 original size:18 final size:17
Alignment explanation
Indices: 17432331--17432371 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
17432321 ATTTTACTAC
17432331 AATTTAATTAATTTAAA
1 AATTTAATTAATTTAAA
17432348 AATTTCAATT-ATTTAAA
1 AATTT-AATTAATTTAAA
17432365 AATTTAA
1 AATTTAA
17432372 AATTCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTAATTAATTTAAA
Found at i:17432881 original size:31 final size:31
Alignment explanation
Indices: 17432823--17432881 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17432813 AAGAGGTTCA
*
17432823 AAAATTATTATTTTTTAGCTTTGAAGGGCCC
1 AAAATTATTATTTTTTAACTTTGAAGGGCCC
* *
17432854 AAAATT-TTTTTTATTTAACTTTTAAGGG
1 AAAATTATTATTT-TTTAACTTTGAAGGG
17432882 ACCTAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (31 bp):
AAAATTATTATTTTTTAACTTTGAAGGGCCC
Found at i:17437030 original size:20 final size:20
Alignment explanation
Indices: 17436976--17437037 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
17436966 GTAAATCTAA
17436976 ATTTTAAATAGTTAATATATT
1 ATTTTAAATAGTTAATATA-T
* * *
17436997 AATTTAAAT-TTTAAAATAT
1 ATTTTAAATAGTTAATATAT
*
17437016 ATTTTAAGTAGTTAATATAT
1 ATTTTAAATAGTTAATATAT
17437036 AT
1 AT
17437038 AAATATTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 8 0.24
20 17 0.52
21 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTTAAATAGTTAATATAT
Found at i:17437037 original size:22 final size:22
Alignment explanation
Indices: 17436976--17437038 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 22
17436966 GTAAATCTAA
17436976 ATTTTAAATAGTTAATATAT-T
1 ATTTTAAATAGTTAATATATAT
* *
17436997 AATTTAAAT-TTTAA-A-ATAT
1 ATTTTAAATAGTTAATATATAT
*
17437016 ATTTTAAGTAGTTAATATATAT
1 ATTTTAAATAGTTAATATATAT
17437038 A
1 A
17437039 AATATTTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 2 0.06
19 9 0.27
20 8 0.24
21 9 0.27
22 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTTTAAATAGTTAATATATAT
Found at i:17441823 original size:39 final size:40
Alignment explanation
Indices: 17441778--17441962 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
17441768 GCTCCTCGTT
* * *
17441778 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
17441818 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
17441857 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
17441897 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
17441938 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
17441963 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:17441878 original size:40 final size:39
Alignment explanation
Indices: 17441745--17441962 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
17441735 AAATCACGTA
* * **
17441745 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
17441784 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
17441823 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
17441863 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
17441903 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
17441943 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
17441963 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:17449746 original size:40 final size:40
Alignment explanation
Indices: 17449646--17449910 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
17449636 GCTCCTCGTT
* * * *
17449646 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
17449686 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
17449725 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
17449765 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
17449805 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
17449845 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
17449886 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
17449911 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:17449870 original size:80 final size:80
Alignment explanation
Indices: 17449613--17449910 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
17449603 AAATCACGTA
* ** * * *
17449613 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
17449675 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
17449691 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
17449754 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
17449771 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
17449835 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
17449851 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
17449911 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:17449919 original size:41 final size:41
Alignment explanation
Indices: 17449842--17449919 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
17449832 TTTGTATCTC
* * *
17449842 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
17449883 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
17449920 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:17461884 original size:17 final size:17
Alignment explanation
Indices: 17461862--17461895 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17461852 ATCGTTTCTC
*
17461862 TCGTAACACTTGCAAAA
1 TCGTAACACTTACAAAA
17461879 TCGTAACACTTACAAAA
1 TCGTAACACTTACAAAA
17461896 CAACTCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (17 bp):
TCGTAACACTTACAAAA
Found at i:17466854 original size:39 final size:39
Alignment explanation
Indices: 17466811--17466888 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
17466801 TTGAAATTTG
*
17466811 AAACTTAAAAGCCCTTAGGCCATGTGTCTTTCTCTTTTT
1 AAACTTAAAAGCCCTTAGGCCATATGTCTTTCTCTTTTT
17466850 AAACTTAAAAGCCCTTAGGCCATATGTCTTTCTCTTTTT
1 AAACTTAAAAGCCCTTAGGCCATATGTCTTTCTCTTTTT
17466889 CTTTTTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (39 bp):
AAACTTAAAAGCCCTTAGGCCATATGTCTTTCTCTTTTT
Found at i:17470292 original size:7 final size:7
Alignment explanation
Indices: 17470276--17470306 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17470266 GAGGGATAAC
17470276 TGAGGGA
1 TGAGGGA
*
17470283 TGAAGGA
1 TGAGGGA
17470290 TGAGGGA
1 TGAGGGA
17470297 TGAGGGA
1 TGAGGGA
17470304 TGA
1 TGA
17470307 TTAGAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (7 bp):
TGAGGGA
Found at i:17486312 original size:34 final size:34
Alignment explanation
Indices: 17486274--17486341 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
17486264 TCCTAACATG
*
17486274 CAACTATATGAATGAAATAGATTTTAGCAGAACT
1 CAACTATATGAATGAAATAGATTTTAGCAAAACT
17486308 CAACTATATGAATGAAATAGATTTTAGCAAAACT
1 CAACTATATGAATGAAATAGATTTTAGCAAAACT
17486342 AACGCAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (34 bp):
CAACTATATGAATGAAATAGATTTTAGCAAAACT
Found at i:17486764 original size:7 final size:7
Alignment explanation
Indices: 17486752--17486782 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17486742 GATGAATTAG
17486752 TGAGGGA
1 TGAGGGA
17486759 TGAGGGA
1 TGAGGGA
*
17486766 TGATGGA
1 TGAGGGA
17486773 TGAGGGA
1 TGAGGGA
17486780 TGA
1 TGA
17486783 TTAGAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.52, T:0.19
Consensus pattern (7 bp):
TGAGGGA
Found at i:17488507 original size:21 final size:21
Alignment explanation
Indices: 17488483--17488530 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
17488473 GAGAGGGTGA
17488483 TTCAGATACTGGAGGATGTGC
1 TTCAGATACTGGAGGATGTGC
17488504 TTCAGATACTGGAGGATGTGC
1 TTCAGATACTGGAGGATGTGC
17488525 TTCAGA
1 TTCAGA
17488531 GCTGTGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (21 bp):
TTCAGATACTGGAGGATGTGC
Found at i:17495279 original size:18 final size:18
Alignment explanation
Indices: 17495258--17495310 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 18
17495248 TAAAAATTAG
17495258 AAAAAATATAAAAATCGT
1 AAAAAATATAAAAATCGT
*
17495276 AAAAACTATATAAAAAATTGT
1 AAAAA--ATAT-AAAAATCGT
*
17495297 AACAAATTATAAAA
1 AA-AAAATATAAAA
17495311 TATATAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 5 0.17
19 4 0.14
20 7 0.24
21 10 0.34
22 3 0.10
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAAAATATAAAAATCGT
Found at i:17495313 original size:27 final size:29
Alignment explanation
Indices: 17495283--17495339 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
17495273 CGTAAAAACT
* *
17495283 ATATAAAAAATTGT-AACAA-ATTATAAA
1 ATATAAAAAATTATAAAAAATATTATAAA
*
17495310 ATATATAAAATTATAAAAAATATTATAAA
1 ATATAAAAAATTATAAAAAATATTATAAA
17495339 A
1 A
17495340 ATTTATAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.48
28 4 0.16
29 9 0.36
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
ATATAAAAAATTATAAAAAATATTATAAA
Found at i:17495322 original size:17 final size:17
Alignment explanation
Indices: 17495300--17495332 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17495290 AAATTGTAAC
*
17495300 AAATTATAAAATATATA
1 AAATTATAAAAAATATA
17495317 AAATTATAAAAAATAT
1 AAATTATAAAAAATAT
17495333 TATAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTATAAAAAATATA
Found at i:17495329 original size:10 final size:10
Alignment explanation
Indices: 17495238--17495347 Score: 68
Period size: 10 Copynumber: 11.1 Consensus size: 10
17495228 TTCAAATATT
*
17495238 AAAAATGTATT
1 AAAAAT-TATA
*
17495249 AAAAATTAGA
1 AAAAATTATA
17495259 AAAAA-TAT-
1 AAAAATTATA
**
17495267 AAAAATCGTA
1 AAAAATTATA
*
17495277 AAAACTATATA
1 AAAAAT-TATA
*
17495288 AAAAATTGTA
1 AAAAATTATA
*
17495298 ACAAATTAT-
1 AAAAATTATA
17495307 -AAAA-TATA
1 AAAAATTATA
*
17495315 TAAAATTATAA
1 AAAAATTAT-A
17495326 AAAATATTATA
1 AAAA-ATTATA
*
17495337 AAAATTTATA
1 AAAAATTATA
17495347 A
1 A
17495348 CTCATAAGAA
Statistics
Matches: 76, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
7 3 0.04
8 8 0.11
9 7 0.09
10 31 0.41
11 22 0.29
12 5 0.07
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:17495622 original size:38 final size:38
Alignment explanation
Indices: 17495544--17495630 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 38
17495534 CTAGGGGTCA
** *
17495544 TTAATTTTTTTATGATTTTTATAAAATTTTGCAATTTTT
1 TTAA-TTTTTTATGATTTTTATAAAAAATTGCAATATTT
17495583 TTAATTTTTTATGATTTTTATAAAAAAATT-CTAA-ATTT
1 TTAATTTTTTATGATTTTTAT-AAAAAATTGC-AATATTT
17495621 TTATATTTTT
1 TTA-ATTTTT
17495631 ATTAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 24 0.57
39 18 0.43
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (38 bp):
TTAATTTTTTATGATTTTTATAAAAAATTGCAATATTT
Found at i:17498619 original size:30 final size:30
Alignment explanation
Indices: 17498585--17498647 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
17498575 ACTTATTTTA
*
17498585 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTCTAAAGACAT
*
17498615 TTGTTAATTTTGTTATTATTCTAAAGGCAT
1 TTGTTAATTTTGTTATTATTCTAAAGACAT
17498645 TTG
1 TTG
17498648 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTCTAAAGACAT
Found at i:17498790 original size:12 final size:12
Alignment explanation
Indices: 17498769--17498802 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17498759 TATATATATT
*
17498769 AAAATTATATAA
1 AAAATAATATAA
17498781 AAAATAATATAA
1 AAAATAATATAA
*
17498793 AAATTAATAT
1 AAAATAATAT
17498803 GAGTTGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:17500208 original size:57 final size:57
Alignment explanation
Indices: 17500120--17500233 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
17500110 ACTGCCTCGT
* *
17500120 TAAAAATCTTACTAAGAAACCTAGAGGACAAAACCTCGGTTAAGGGAAAAAGTGTAC
1 TAAAAATCTTACTAAGAAACCTAGAGAACAAAACCTCGGTTAAGGGAAAAAGAGTAC
*
17500177 TAAAAATCTTACTAAGAAACCTAGCGAACAAAACCTCGGTTAAGGGAAAAAGAGTAC
1 TAAAAATCTTACTAAGAAACCTAGAGAACAAAACCTCGGTTAAGGGAAAAAGAGTAC
17500234 AACATATATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.18
Consensus pattern (57 bp):
TAAAAATCTTACTAAGAAACCTAGAGAACAAAACCTCGGTTAAGGGAAAAAGAGTAC
Found at i:17503665 original size:27 final size:26
Alignment explanation
Indices: 17503626--17503676 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
17503616 TCTAATATGT
*
17503626 TATATGTTCTGAAAATATGATAAATGA
1 TATACGTTCTGAAAATATGA-AAATGA
*
17503653 TATACGTTTTGAAAATATGAAAAT
1 TATACGTTCTGAAAATATGAAAAT
17503677 TCTGATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (26 bp):
TATACGTTCTGAAAATATGAAAATGA
Found at i:17507465 original size:13 final size:13
Alignment explanation
Indices: 17507449--17507477 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17507439 TTTAAATTAA
17507449 TTAGTTAATTAGT
1 TTAGTTAATTAGT
17507462 TTAGTTAATTAGT
1 TTAGTTAATTAGT
17507475 TTA
1 TTA
17507478 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:17515774 original size:13 final size:13
Alignment explanation
Indices: 17515756--17515784 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17515746 TTTAGTTTAA
17515756 TTAGTTAATTAGT
1 TTAGTTAATTAGT
17515769 TTAGTTAATTAGT
1 TTAGTTAATTAGT
17515782 TTA
1 TTA
17515785 AGAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:17518901 original size:20 final size:21
Alignment explanation
Indices: 17518873--17518912 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17518863 TAATGGTCAG
17518873 TTTGAAAGA-ATGATTCAGAT
1 TTTGAAAGATATGATTCAGAT
* *
17518893 TTTGGAAGATATGCTTCAGA
1 TTTGAAAGATATGATTCAGA
17518913 GCTGTGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (21 bp):
TTTGAAAGATATGATTCAGAT
Found at i:17520121 original size:15 final size:16
Alignment explanation
Indices: 17520103--17520132 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17520093 TTTTTACGTT
17520103 CTTC-TTTTTCTTTTG
1 CTTCTTTTTTCTTTTG
17520118 CTTCTTTTTTCTTTT
1 CTTCTTTTTTCTTTT
17520133 TATGAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (16 bp):
CTTCTTTTTTCTTTTG
Found at i:17526942 original size:30 final size:30
Alignment explanation
Indices: 17526908--17526979 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
17526898 ATGCAGGCTG
*
17526908 ACATTATATTAGGGTTTCTCACACAAGCTA
1 ACATTATATTAGGGTTGCTCACACAAGCTA
* * * *
17526938 ACATTATATCAAGGTTGCTCACAGAAGCTT
1 ACATTATATTAGGGTTGCTCACACAAGCTA
17526968 AC-TTATATTAGG
1 ACATTATATTAGG
17526980 TTACCCATCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 8 0.23
30 27 0.77
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (30 bp):
ACATTATATTAGGGTTGCTCACACAAGCTA
Found at i:17529170 original size:134 final size:134
Alignment explanation
Indices: 17528930--17529179 Score: 315
Period size: 134 Copynumber: 1.9 Consensus size: 134
17528920 ATTTTAAAGC
* * * * *
17528930 TAATGCATTAACTATCACAAATTTTGTTCTTTCAATTATTGATATATTAGCTATTCTAGAGCTTT
1 TAATGCATTAACTATCACAAATTTTGTCCCTTCAAATATTGATAAATTAACTATTCTAGAGCTTT
** * *
17528995 CAACTAATTTTGTAGTACCACATATTAGATTGATATTGGTTTGTTTCAGTATTGAGACCGACTAG
66 CAACTAATTTTGTACAACCAAATATTAGATAGATATTGGTTTGTTTCAGTATTGAGACCGACTAG
17529060 AACA
131 AACA
* * * * * *
17529064 TAATGCATTGATTATCACAAATTTTGTCCCTTCAAATATTGATAAATTAATTCTTTTGGAGCTTT
1 TAATGCATTAACTATCACAAATTTTGTCCCTTCAAATATTGATAAATTAACTATTCTAGAGCTTT
* *
17529129 CACCTAATTTTGTACAACCAAATATT-GCAATAG-TATTGGTTTGTTTTAGTA
66 CAACTAATTTTGTACAACCAAATATTAG--ATAGATATTGGTTTGTTTCAGTA
17529180 CCAAATAAGA
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
133 1 0.01
134 93 0.96
135 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (134 bp):
TAATGCATTAACTATCACAAATTTTGTCCCTTCAAATATTGATAAATTAACTATTCTAGAGCTTT
CAACTAATTTTGTACAACCAAATATTAGATAGATATTGGTTTGTTTCAGTATTGAGACCGACTAG
AACA
Found at i:17531312 original size:24 final size:22
Alignment explanation
Indices: 17531260--17531312 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 22
17531250 GTTTTAATTG
17531260 TTTAATTAGGGTTTAAATTTTA
1 TTTAATTAGGGTTTAAATTTTA
*
17531282 TTAAATTAGGGTTTTAATATTTTA
1 TTTAATTAGGG-TTTAA-ATTTTA
17531306 TTTAATT
1 TTTAATT
17531313 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 10 0.37
23 5 0.19
24 12 0.44
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTAATTAGGGTTTAAATTTTA
Found at i:17531317 original size:42 final size:42
Alignment explanation
Indices: 17531245--17531340 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
17531235 CTGTATTTTT
*
17531245 TTAGGGTTTTAATTGTTTAATTAGGGTTTAAA-TTTTATTAAA
1 TTAGGGTTTTAATTGTTTAATTAAGGTTTAAATTTTTATT-AA
* **
17531287 TTAGGGTTTTAATAT-TTTATTTAATTTTTAAATTTTTATTAA
1 TTAGGGTTTTAAT-TGTTTAATTAAGGTTTAAATTTTTATTAA
*
17531329 TTAGTGTTTTAA
1 TTAGGGTTTTAA
17531341 GGTTTTAGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 39 0.83
43 8 0.17
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (42 bp):
TTAGGGTTTTAATTGTTTAATTAAGGTTTAAATTTTTATTAA
Found at i:17535852 original size:4 final size:5
Alignment explanation
Indices: 17535799--17535854 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
17535789 TTAGAAGCAT
*
17535799 TTTTT TTTTA TTTT- TTTTAA TCTTTAAA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A T-TTT--A TTTTA TTTTA TTTTA TTTTA
17535847 -TTTA TTTT
1 TTTTA TTTT
17535855 TCTATTGTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
4 8 0.18
5 27 0.60
6 1 0.02
7 6 0.13
8 3 0.07
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:17536414 original size:16 final size:15
Alignment explanation
Indices: 17536389--17536430 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
17536379 TTTTTAATAT
*
17536389 AAATTCAACACTTATA
1 AAATTTAACA-TTATA
*
17536405 AAATTTAACAATA-A
1 AAATTTAACATTATA
17536419 AAATTTAACATT
1 AAATTTAACATT
17536431 TATTTTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 2 0.09
16 9 0.39
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTTAACATTATA
Found at i:17537455 original size:30 final size:32
Alignment explanation
Indices: 17537415--17537484 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 32
17537405 AGACTATATC
17537415 TTTATAATTTTTAAAAG-ATTAAA-TAAAATT
1 TTTATAATTTTTAAAAGAATTAAAGTAAAATT
* * *
17537445 TTTATTATTTTTAAGAGAATTAAAGTACAA-T
1 TTTATAATTTTTAAAAGAATTAAAGTAAAATT
17537476 TTTATAATT
1 TTTATAATT
17537485 ACTAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.44
31 15 0.44
32 4 0.12
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (32 bp):
TTTATAATTTTTAAAAGAATTAAAGTAAAATT
Found at i:17549500 original size:6 final size:6
Alignment explanation
Indices: 17549468--17549517 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
17549458 AATAAAAACA
* *
17549468 TAAAA- TAAAAT TAAAA- AAGAAAA TAAAAT TAAAAT TAAAA- TAAAAT
1 TAAAAT TAAAAT TAAAAT TA-AAAT TAAAAT TAAAAT TAAAAT TAAAAT
17549514 TAAA
1 TAAA
17549518 CATCATCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
5 11 0.29
6 26 0.68
7 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (6 bp):
TAAAAT
Found at i:17549501 original size:11 final size:11
Alignment explanation
Indices: 17549468--17549517 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
17549458 AATAAAAACA
17549468 TAAAATAAAAT
1 TAAAATAAAAT
* *
17549479 TAAAAAAGAAAA
1 TAAAATA-AAAT
17549491 TAAAATTAAAAT
1 TAAAA-TAAAAT
17549503 TAAAATAAAAT
1 TAAAATAAAAT
17549514 TAAA
1 TAAA
17549518 CATCATCATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 16 0.48
12 16 0.48
13 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
TAAAATAAAAT
Found at i:17566298 original size:47 final size:46
Alignment explanation
Indices: 17566236--17566410 Score: 137
Period size: 47 Copynumber: 3.7 Consensus size: 46
17566226 ACAACTCTTA
*
17566236 GCCGATGCATATCCCAGACACGTCTTACACTGGCTATCTCT-GTC-GAG
1 GCCGATGCATGTCCCAGACACGTCTTACACTGGC--TC-CTAGTCAGAG
* * * *
17566283 GCCGATGCATGTCCCAAACATGTCTTACACTAGC-CCTAGTCTAGAT
1 GCCGATGCATGTCCCAGACACGTCTTACACTGGCTCCTAGTC-AGAG
* *
17566329 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-ATG-G
1 GCCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTC-C-TAGTCA-GAG
* * *
17566378 G-CAAAGCATGTCCCAGACATGTCTTACACTGGC
1 GCCGATGCATGTCCCAGACACGTCTTACACTGGC
17566411 ACACGAATCA
Statistics
Matches: 106, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
43 2 0.02
44 4 0.04
46 22 0.21
47 55 0.52
48 15 0.14
49 3 0.03
50 2 0.02
51 3 0.03
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACACGTCTTACACTGGCTCCTAGTCAGAG
Found at i:17566389 original size:94 final size:92
Alignment explanation
Indices: 17566148--17566407 Score: 267
Period size: 94 Copynumber: 2.8 Consensus size: 92
17566138 TATTGTCGAA
* * * * *
17566148 GCCATGTCTCAAACATGGTCTTACATTGGCTCTCATATATGCGTGCTGATGCATGTCCTAGACAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGAG-GC-GATGCATGTCCCAGACAT
*
17566213 GTCTTACACTAGAACAACTCTTAGCCGAT
64 GTCTTACACTAGAACAACTCTGAGCCGAT
* * * * * *
17566242 G-CATATCCCAGACA-CGTCTTACACTGGCTATC-TCTGTCGAGGCCGATGCATGTCCCAAACAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAT-GAGG-CGATGCATGTCCCAGACAT
** * *
17566304 GTCTTACACTAGCCCTAGTCTAGATGCCGAT
64 GTCTTACACTAGAACAACTCT-GA-GCCGAT
* *
17566335 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATG-GGCAAAGCATGTCCCAGACATG
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATATGAGGCGATGCATGTCCCAGACATG
17566399 TCTTACACT
65 TCTTACACT
17566408 GGCACACGAA
Statistics
Matches: 134, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
91 37 0.28
92 19 0.14
93 17 0.13
94 39 0.29
95 18 0.13
96 2 0.01
97 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (92 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGAGGCGATGCATGTCCCAGACATGT
CTTACACTAGAACAACTCTGAGCCGAT
Found at i:17577561 original size:26 final size:26
Alignment explanation
Indices: 17577531--17577716 Score: 345
Period size: 26 Copynumber: 7.2 Consensus size: 26
17577521 TGAAATTCCC
17577531 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
17577557 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
*
17577583 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
*
17577609 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
17577635 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17577661 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17577687 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17577713 ATCA
1 ATCA
17577717 ATTTGTATCA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 158 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:17579189 original size:69 final size:68
Alignment explanation
Indices: 17579111--17579245 Score: 207
Period size: 68 Copynumber: 2.0 Consensus size: 68
17579101 TGATTAAACT
* * * *
17579111 TAATCACTTTAATATTAAATTAATATAATACTTATGAAGTTAAATATTAAATTTAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATAC-TATGAAGATAAATACTAAATTAAATTTAATATT
17579176 AAGA
65 AAGA
* *
17579180 TAATCACTTTAATATTAAATTAATAAAATACTATTAAGATAAGTACTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATGAAGATAAATACTAAATTAAATTTAATATTA
17579245 A
66 A
17579246 ATCTATTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
68 30 0.50
69 30 0.50
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATGAAGATAAATACTAAATTAAATTTAATATTA
AGA
Found at i:17579216 original size:25 final size:25
Alignment explanation
Indices: 17579162--17579216 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
17579152 AAATATTAAA
*
17579162 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
17579187 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
17579211 TATTAA
1 T-TTAA
17579217 GATAAGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:17589204 original size:15 final size:17
Alignment explanation
Indices: 17589184--17589217 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
17589174 TAAAGCTTAG
17589184 TAAACTCG-TATAA-AA
1 TAAACTCGATATAATAA
17589199 TAAACTCGATATAATAA
1 TAAACTCGATATAATAA
17589216 TA
1 TA
17589218 TCCACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 5 0.29
17 4 0.24
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAACTCGATATAATAA
Found at i:17591083 original size:35 final size:35
Alignment explanation
Indices: 17591033--17591105 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
17591023 CAATACATGA
*
17591033 CATGCTATGGCAATTTTATAACATTCACATTCATT
1 CATGCTATGGAAATTTTATAACATTCACATTCATT
17591068 CATGCTATGGAAATTTTATAACATTCACATTCATT
1 CATGCTATGGAAATTTTATAACATTCACATTCATT
17591103 CAT
1 CAT
17591106 TCACAAGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (35 bp):
CATGCTATGGAAATTTTATAACATTCACATTCATT
Found at i:17591984 original size:18 final size:19
Alignment explanation
Indices: 17591943--17591984 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17591933 AATAGTATTT
*
17591943 AAATTAAATTGAAATTACG
1 AAATTAAATTGAAATGACG
17591962 AAATTAAA-T-AAATGACGG
1 AAATTAAATTGAAATGAC-G
17591980 AAATT
1 AAATT
17591985 GAGATGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (19 bp):
AAATTAAATTGAAATGACG
Found at i:17592785 original size:15 final size:15
Alignment explanation
Indices: 17592765--17592794 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17592755 ATAATCTTAA
*
17592765 TAATTATCTTAATAT
1 TAATTATCCTAATAT
17592780 TAATTATCCTAATAT
1 TAATTATCCTAATAT
17592795 AAATAAAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:17593651 original size:14 final size:14
Alignment explanation
Indices: 17593632--17593660 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17593622 TTACTTTAAT
17593632 ATTAAATTAATATA
1 ATTAAATTAATATA
17593646 ATTAAATTAATATA
1 ATTAAATTAATATA
17593660 A
1 A
17593661 ATTCCCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATTAATATA
Found at i:17596622 original size:13 final size:13
Alignment explanation
Indices: 17596604--17596629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17596594 GTGGTGCTTG
17596604 TGTAAAATAAACT
1 TGTAAAATAAACT
17596617 TGTAAAATAAACT
1 TGTAAAATAAACT
17596630 GGTGCTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TGTAAAATAAACT
Found at i:17598519 original size:21 final size:21
Alignment explanation
Indices: 17598495--17598543 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
17598485 TTAAAAAAAT
17598495 AATTGAGGATTGAAAATTGGA
1 AATTGAGGATTGAAAATTGGA
*
17598516 AATTGAGGATTGAAGATTGGA
1 AATTGAGGATTGAAAATTGGA
*
17598537 AGTTGAG
1 AATTGAG
17598544 AATTTAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.29
Consensus pattern (21 bp):
AATTGAGGATTGAAAATTGGA
Found at i:17601917 original size:2 final size:2
Alignment explanation
Indices: 17601910--17601934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17601900 TCTTTTCGAA
17601910 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
17601935 AAAGAGACAT
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:17602441 original size:19 final size:21
Alignment explanation
Indices: 17602391--17602443 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
17602381 ATTTAGTTAA
*
17602391 TAAT-TAATAAGTATATATATT
1 TAATATAATAA-TTTATATATT
*
17602412 TAATTTAATAATTTATAT-TT
1 TAATATAATAATTTATATATT
17602432 TAATAT-ATAATT
1 TAATATAATAATT
17602444 AAAATATTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.21
20 7 0.24
21 10 0.34
22 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TAATATAATAATTTATATATT
Found at i:17603020 original size:116 final size:117
Alignment explanation
Indices: 17602879--17603111 Score: 380
Period size: 117 Copynumber: 2.0 Consensus size: 117
17602869 TAGGTCTACC
*
17602879 CATATTATTTTAAAAATATATATATTAATTTTAAATTAATATCTAAATA-TTTTATTTTTTTATT
1 CATATTATTTTAAAAATATATATATTAATTTTAAATTAATATCTAAATATTTTTATATTTTTATT
* *
17602943 TATAAAAAAGTTTTATTTAGTCATC-TTAACATTTTTTAATGTTTACATTATA
66 TATAAAAAAATTATATTTAGTCATCTTTAACA-TTTTTAATGTTTACATTATA
* * * *
17602995 CATATTATTTTTAAAATATTTATATTAATTTTAATTTAATATCTAACTATTTTTATATTTTTATT
1 CATATTATTTTAAAAATATATATATTAATTTTAAATTAATATCTAAATATTTTTATATTTTTATT
17603060 TATAAAAAAATTATATTTAGTCATCTTTAACATTTTTAATGTTTACATTATA
66 TATAAAAAAATTATATTTAGTCATCTTTAACATTTTTAATGTTTACATTATA
17603112 GTAGTATATA
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
116 45 0.42
117 57 0.53
118 6 0.06
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (117 bp):
CATATTATTTTAAAAATATATATATTAATTTTAAATTAATATCTAAATATTTTTATATTTTTATT
TATAAAAAAATTATATTTAGTCATCTTTAACATTTTTAATGTTTACATTATA
Found at i:17603127 original size:117 final size:116
Alignment explanation
Indices: 17602891--17603143 Score: 350
Period size: 117 Copynumber: 2.2 Consensus size: 116
17602881 TATTATTTTA
* * *
17602891 AAAATATATATATTAATTTTAAATTAATATCTAAATATTTTATTTTTTTATTTATAAAAAAGTTT
1 AAAATATATATATTAATTTTAAATTAATATCTAAATATTTTATATTTTTATTTATAAAAAAATTA
* **
17602956 TATTTAGTCATCTTAACATTTTTTAATGTTTACATTATACATATTATTTTT
66 TATTTAGTCATCTTAACATTTTTTAATGTTTACATTATACATAGTATTAAT
* * *
17603007 AAAATATTTATATTAATTTTAATTTAATATCTAACTATTTTTATATTTTTATTTATAAAAAAATT
1 AAAATATATATATTAATTTTAAATTAATATCTAAATA-TTTTATATTTTTATTTATAAAAAAATT
*
17603072 ATATTTAGTCATCTTTAACA-TTTTTAATGTTTACATTATA-GTAGTATATAAT
65 ATATTTAGTCATC-TTAACATTTTTTAATGTTTACATTATACATAGTAT-TAAT
*
17603124 AAAAT-TATAAATTTAATTTT
1 AAAATATATATA-TTAATTTT
17603144 TAAGTGTTAT
Statistics
Matches: 121, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
116 43 0.36
117 72 0.60
118 6 0.05
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (116 bp):
AAAATATATATATTAATTTTAAATTAATATCTAAATATTTTATATTTTTATTTATAAAAAAATTA
TATTTAGTCATCTTAACATTTTTTAATGTTTACATTATACATAGTATTAAT
Found at i:17604668 original size:13 final size:13
Alignment explanation
Indices: 17604650--17604679 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
17604640 ATATTTGGTT
17604650 ATAATTTTAAAAA
1 ATAATTTTAAAAA
17604663 ATAATTTTAAAAA
1 ATAATTTTAAAAA
17604676 ATAA
1 ATAA
17604680 AAATATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATTTTAAAAA
Found at i:17606087 original size:3 final size:3
Alignment explanation
Indices: 17606079--17606104 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17606069 GAAATGCCAT
17606079 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
17606105 TGCCTTAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:17610711 original size:140 final size:140
Alignment explanation
Indices: 17610466--17610738 Score: 320
Period size: 140 Copynumber: 1.9 Consensus size: 140
17610456 TTTTGATGTT
* * * * * *
17610466 AAATCTTTTATGTAACAATAATAATATTGGTTGCCAAATATCATTTTGTAATAGTATTTTAATTG
1 AAATCATTTATATAACAATAATAACATTGATTGCCAAATATCATTTTGCAATAGTATTTTAATCG
* * * * * *
17610531 GTTGTGTATTACATTGCACATCGATAATATGCCATTGTCAAAAATTTATT-TGAACTATCATGAA
66 GATATGTATAACATTGCACATCGATAATATGCCATCGTCAAAAATTTATTCT-AACAATCATAAA
17610595 ATGTAGTTACC
130 ATGTAGTTACC
* *
17610606 AAATCATTTATATAACAATAATACCATTGATTG-CAAATATTATTTTGCAA-AGATATTTTAATC
1 AAATCATTTATATAACAATAATAACATTGATTGCCAAATATCATTTTGCAATAG-TATTTTAATC
** * *
17610669 GGATATGTATAACATTTGCACAAT-GATTTTATGTCATCGTCAAATATTTATTCTAACAATCATA
65 GGATATGTATAACA-TTGCAC-ATCGATAATATGCCATCGTCAAAAATTTATTCTAACAATCATA
17610733 AAATGT
128 AAATGT
17610739 GGTTGCCATG
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
138 2 0.02
139 35 0.32
140 71 0.64
141 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (140 bp):
AAATCATTTATATAACAATAATAACATTGATTGCCAAATATCATTTTGCAATAGTATTTTAATCG
GATATGTATAACATTGCACATCGATAATATGCCATCGTCAAAAATTTATTCTAACAATCATAAAA
TGTAGTTACC
Found at i:17611134 original size:15 final size:15
Alignment explanation
Indices: 17611114--17611143 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17611104 CATTTTATTT
*
17611114 ATATTAGGATAATTA
1 ATATTAAGATAATTA
17611129 ATATTAAGATAATTA
1 ATATTAAGATAATTA
17611144 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:17611187 original size:10 final size:10
Alignment explanation
Indices: 17611172--17611198 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17611162 AGGATTTAAT
17611172 TTTAATTATC
1 TTTAATTATC
17611182 TTTAATTATC
1 TTTAATTATC
17611192 TTTAATT
1 TTTAATT
17611199 GAATGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTAATTATC
Found at i:17612749 original size:231 final size:231
Alignment explanation
Indices: 17612346--17612808 Score: 926
Period size: 231 Copynumber: 2.0 Consensus size: 231
17612336 ACTCAAAGCA
17612346 ACCCACCGCCAGAAATTAGAAACGACGACCAAGTAGAGTCTAGGGTTAACGAAAACCTTACTCAA
1 ACCCACCGCCAGAAATTAGAAACGACGACCAAGTAGAGTCTAGGGTTAACGAAAACCTTACTCAA
17612411 ACTTTTGAAGGCGAAAAAGTAGAAGTCGATTCCCCAGAAGAAGTGCTTAACGCTAGGGTTGACGT
66 ACTTTTGAAGGCGAAAAAGTAGAAGTCGATTCCCCAGAAGAAGTGCTTAACGCTAGGGTTGACGT
17612476 AAACCCTAATTTAGCACCTCAACCTATGGCTCAGATAATTCGGCAATTGGCCGAAGCGCCGACAG
131 AAACCCTAATTTAGCACCTCAACCTATGGCTCAGATAATTCGGCAATTGGCCGAAGCGCCGACAG
17612541 AACAACCGCCACTATGCATCGCGTATCCTACTATGG
196 AACAACCGCCACTATGCATCGCGTATCCTACTATGG
17612577 ACCCACCGCCAGAAATTAGAAACGACGACCAAGTAGAGTCTAGGGTTAACGAAAACCTTACTCAA
1 ACCCACCGCCAGAAATTAGAAACGACGACCAAGTAGAGTCTAGGGTTAACGAAAACCTTACTCAA
17612642 ACTTTTGAAGGCGAAAAAGTAGAAGTCGATTCCCCAGAAGAAGTGCTTAACGCTAGGGTTGACGT
66 ACTTTTGAAGGCGAAAAAGTAGAAGTCGATTCCCCAGAAGAAGTGCTTAACGCTAGGGTTGACGT
17612707 AAACCCTAATTTAGCACCTCAACCTATGGCTCAGATAATTCGGCAATTGGCCGAAGCGCCGACAG
131 AAACCCTAATTTAGCACCTCAACCTATGGCTCAGATAATTCGGCAATTGGCCGAAGCGCCGACAG
17612772 AACAACCGCCACTATGCATCGCGTATCCTACTATGG
196 AACAACCGCCACTATGCATCGCGTATCCTACTATGG
17612808 A
1 A
17612809 TACTGATTTC
Statistics
Matches: 232, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 232 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.20
Consensus pattern (231 bp):
ACCCACCGCCAGAAATTAGAAACGACGACCAAGTAGAGTCTAGGGTTAACGAAAACCTTACTCAA
ACTTTTGAAGGCGAAAAAGTAGAAGTCGATTCCCCAGAAGAAGTGCTTAACGCTAGGGTTGACGT
AAACCCTAATTTAGCACCTCAACCTATGGCTCAGATAATTCGGCAATTGGCCGAAGCGCCGACAG
AACAACCGCCACTATGCATCGCGTATCCTACTATGG
Found at i:17617792 original size:6 final size:5
Alignment explanation
Indices: 17617779--17617861 Score: 71
Period size: 5 Copynumber: 15.6 Consensus size: 5
17617769 TTAATTTTAA
17617779 ATTTT ATTTCT ATTATT ATTATT ATTATT ATTATT ATTTT A--TT ATTTT
1 ATTTT ATTT-T ATT-TT ATT-TT ATT-TT ATT-TT ATTTT ATTTT ATTTT
**
17617827 ATTTCTT ATTTT ATTTT ATTTT AAATT ATTTT ATT
1 A-TT-TT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
17617862 ATTTTAATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.04
5 31 0.46
6 30 0.44
7 4 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:17617797 original size:3 final size:3
Alignment explanation
Indices: 17617789--17617864 Score: 76
Period size: 3 Copynumber: 27.3 Consensus size: 3
17617779 ATTTTATTTC
*
17617789 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT T-T TATT TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
17617833 TAT T-T TAT T-T TAT T-T TA- AAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17617865 TTAATAAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
2 13 0.21
3 46 0.75
4 2 0.03
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:17617797 original size:12 final size:11
Alignment explanation
Indices: 17617779--17617864 Score: 83
Period size: 10 Copynumber: 8.0 Consensus size: 11
17617769 TTAATTTTAA
17617779 ATTTTATT-TCT
1 ATTTTATTAT-T
17617790 ATTATTATTATT
1 ATT-TTATTATT
17617802 ATTATTATTATT
1 ATT-TTATTATT
17617814 ATTTTATTATT
1 ATTTTATTATT
* *
17617825 -TTAT-TTCTT
1 ATTTTATTATT
17617834 ATTTTATT-TT
1 ATTTTATTATT
*
17617844 ATTTTA-AATT
1 ATTTTATTATT
17617854 ATTTTATTATT
1 ATTTTATTATT
17617865 TTAATAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.06
10 22 0.34
11 16 0.25
12 21 0.33
13 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:17617807 original size:15 final size:14
Alignment explanation
Indices: 17617782--17617864 Score: 93
Period size: 15 Copynumber: 5.9 Consensus size: 14
17617772 ATTTTAAATT
17617782 TTATTTCTATTATTA
1 TTATTT-TATTATTA
17617797 TTATTATTATTATTA
1 TTATT-TTATTATTA
17617812 TTATTTTATTATT-
1 TTATTTTATTATTA
*
17617825 TTA-TTTCTTATT-
1 TTATTTTATTATTA
17617837 TTATTTTATT-TTAAA
1 TTATTTTATTATT--A
17617852 TTATTTTATTATT
1 TTATTTTATTATT
17617865 TTAATAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
12 13 0.22
13 8 0.13
14 8 0.13
15 28 0.47
16 3 0.05
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTTATTATTA
Found at i:17625953 original size:43 final size:44
Alignment explanation
Indices: 17625904--17626031 Score: 190
Period size: 43 Copynumber: 3.0 Consensus size: 44
17625894 GATTACCGAG
*
17625904 ATGTGATTACATGTAAGACCATGTCTGAGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
*
17625948 -TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTG-AT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * *
17625990 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTA
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
17626032 CAAGCTATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
42 10 0.13
43 66 0.87
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:17629736 original size:22 final size:22
Alignment explanation
Indices: 17629702--17629746 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
17629692 TGGCATGTAT
*
17629702 ATATTTGGTCTTAAAATGGTTG
1 ATATTTGGTCTTAAAATGCTTG
*
17629724 ATATCTTGG-CTTATAATGCTTG
1 ATAT-TTGGTCTTAAAATGCTTG
17629746 A
1 A
17629747 ATGATTGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (22 bp):
ATATTTGGTCTTAAAATGCTTG
Found at i:17633757 original size:37 final size:37
Alignment explanation
Indices: 17633710--17633793 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
17633700 TAAACATAAG
*
17633710 TTAGCCTATACATATCCAAGATCGGAAAAAATACATA
1 TTAGCCTATACATATCCAAGATAGGAAAAAATACATA
*
17633747 TTAGCCTATACATATCCAAGATAGGACAAAATACATA
1 TTAGCCTATACATATCCAAGATAGGAAAAAATACATA
17633784 TTAGCCTATA
1 TTAGCCTATA
17633794 TATGCCATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (37 bp):
TTAGCCTATACATATCCAAGATAGGAAAAAATACATA
Found at i:17634490 original size:42 final size:41
Alignment explanation
Indices: 17634377--17634499 Score: 160
Period size: 41 Copynumber: 3.0 Consensus size: 41
17634367 AGCCTAGTAT
* * * *
17634377 AATACACCGGCA-CAGAGCCTGCTAGGTAATAAACCTGATTT
1 AATACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGA-TA
*
17634418 AATACACCGGCAT-AAAGCCTGCTAGGCAATAAGCTTGATA
1 AATACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATA
*
17634458 ACATACACCGGCATCAAATCCTGCTAGGCAATAAGCCTGATA
1 A-ATACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATA
17634500 TATCACTGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.03
41 45 0.62
42 25 0.35
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (41 bp):
AATACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATA
Found at i:17639545 original size:47 final size:47
Alignment explanation
Indices: 17639494--17639961 Score: 857
Period size: 47 Copynumber: 10.0 Consensus size: 47
17639484 TTAGGATTTT
*
17639494 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
17639541 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
17639588 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
17639635 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
17639682 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
17639729 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
17639776 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
17639823 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
17639870 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** *
17639917 ATGTGATGAATGTGAACATGAATATATGTTG-TAAGGCCGAATGGC
1 ATGTGATGAATGTGAACATGCGTATGTG-TGATAAGGCCGAATGGC
17639962 TAATTCGAAA
Statistics
Matches: 414, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
47 413 1.00
48 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:17656035 original size:16 final size:17
Alignment explanation
Indices: 17656014--17656051 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17656004 AATCCCCAAA
*
17656014 AAAAAGTAA-AGAGAAG
1 AAAAAGTAAGAAAGAAG
17656030 AAAAAGTAAGAAAGAAG
1 AAAAAGTAAGAAAGAAG
17656047 AAAAA
1 AAAAA
17656052 AATAAAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (17 bp):
AAAAAGTAAGAAAGAAG
Found at i:17659867 original size:39 final size:39
Alignment explanation
Indices: 17659825--17660159 Score: 546
Period size: 39 Copynumber: 8.5 Consensus size: 39
17659815 TAATGGAGAA
* *
17659825 TTATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
17659864 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
17659903 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
17659942 TTATATCGGGGCTAAGACCCAAAGGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
17659981 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
17660020 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
17660059 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
17660098 TTATATCCGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
17660137 TTATATTCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
17660160 CATGCTTTGT
Statistics
Matches: 280, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 258 0.92
40 22 0.08
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:17663878 original size:16 final size:15
Alignment explanation
Indices: 17663853--17663886 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17663843 AAAGTTGATA
*
17663853 ATAATCAATATACATT
1 ATAATAAATATA-ATT
17663869 ATAATAAATATAATT
1 ATAATAAATATAATT
17663884 ATA
1 ATA
17663887 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:17675047 original size:26 final size:26
Alignment explanation
Indices: 17675016--17675213 Score: 227
Period size: 26 Copynumber: 7.6 Consensus size: 26
17675006 TGTACTTGAT
*
17675016 TTTAGCAAGCTTTGAGCCAGTGATTA
1 TTTAGCAAGCTTTGAGCCAGTGTTTA
* * *
17675042 GTTAGCAGGCTTTGAGCCGGTGTTTA
1 TTTAGCAAGCTTTGAGCCAGTGTTTA
*
17675068 TTTAGCAAGCTTTGTGCCAGTGTTTA
1 TTTAGCAAGCTTTGAGCCAGTGTTTA
* ** * *
17675094 TTTAGTAAAATTTGTGCCAGTGATTA
1 TTTAGCAAGCTTTGAGCCAGTGTTTA
* *
17675120 TTTAGCAGGCTTTGAGCTAGTGTTTA
1 TTTAGCAAGCTTTGAGCCAGTGTTTA
* * * *
17675146 TATAGCAGGCTTTGAGCCAGTGATTG
1 TTTAGCAAGCTTTGAGCCAGTGTTTA
17675172 TTTAGCAAGCTTTGAGCC-GATGTTTA
1 TTTAGCAAGCTTTGAGCCAG-TGTTTA
*
17675198 TTTAGCAGGCTTTGAG
1 TTTAGCAAGCTTTGAG
17675214 TGGATGAATA
Statistics
Matches: 143, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
25 1 0.01
26 142 0.99
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (26 bp):
TTTAGCAAGCTTTGAGCCAGTGTTTA
Found at i:17675121 original size:52 final size:52
Alignment explanation
Indices: 17675016--17675213 Score: 254
Period size: 52 Copynumber: 3.8 Consensus size: 52
17675006 TGTACTTGAT
* * * *
17675016 TTTAGCAAGCTTTGAGCCAGTGATTAGTTAGCAGGCTTTGAGCCGGTGTTTA
1 TTTAGCAAGCTTTGAGCCAGTGTTTATTTAGCAGGCTTTGAGCCAGTGATTA
* * *** *
17675068 TTTAGCAAGCTTTGTGCCAGTGTTTATTTAGTAAAATTTGTGCCAGTGATTA
1 TTTAGCAAGCTTTGAGCCAGTGTTTATTTAGCAGGCTTTGAGCCAGTGATTA
* * * *
17675120 TTTAGCAGGCTTTGAGCTAGTGTTTATATAGCAGGCTTTGAGCCAGTGATTG
1 TTTAGCAAGCTTTGAGCCAGTGTTTATTTAGCAGGCTTTGAGCCAGTGATTA
17675172 TTTAGCAAGCTTTGAGCC-GATGTTTATTTAGCAGGCTTTGAG
1 TTTAGCAAGCTTTGAGCCAG-TGTTTATTTAGCAGGCTTTGAG
17675214 TGGATGAATA
Statistics
Matches: 122, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
51 1 0.01
52 121 0.99
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (52 bp):
TTTAGCAAGCTTTGAGCCAGTGTTTATTTAGCAGGCTTTGAGCCAGTGATTA
Found at i:17675230 original size:78 final size:78
Alignment explanation
Indices: 17675016--17675232 Score: 267
Period size: 78 Copynumber: 2.8 Consensus size: 78
17675006 TGTACTTGAT
* * *
17675016 TTTAGCAAGCTTTGAGCCAGTGATTAGTTAGCAGGCTTTGAGCCGGTGTTTATTTAGCAAGCTTT
1 TTTAGCAAGCTTTGAGCCAGTGATTATTTAGCAGGCTTTGAGCTGGTGTTTATTTAGCAGGCTTT
* *
17675081 GTGCCAGTGTTTA
66 GAGCCAGTGATTA
* ** * * *
17675094 TTTAGTAAAATTTGTGCCAGTGATTATTTAGCAGGCTTTGAGCTAGTGTTTATATAGCAGGCTTT
1 TTTAGCAAGCTTTGAGCCAGTGATTATTTAGCAGGCTTTGAGCTGGTGTTTATTTAGCAGGCTTT
*
17675159 GAGCCAGTGATTG
66 GAGCCAGTGATTA
* **
17675172 TTTAGCAAGCTTTGAGCC-GATGTTTATTTAGCAGGCTTTGAG-TGGATGAATATTTAGCAGG
1 TTTAGCAAGCTTTGAGCCAG-TGATTATTTAGCAGGCTTTGAGCTGG-TGTTTATTTAGCAGG
17675233 TGCTAAGTAC
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
77 3 0.03
78 113 0.97
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (78 bp):
TTTAGCAAGCTTTGAGCCAGTGATTATTTAGCAGGCTTTGAGCTGGTGTTTATTTAGCAGGCTTT
GAGCCAGTGATTA
Found at i:17678130 original size:42 final size:42
Alignment explanation
Indices: 17678049--17678199 Score: 178
Period size: 42 Copynumber: 3.6 Consensus size: 42
17678039 TTAAGTTTAT
*
17678049 GTGTAAGACCATATCTGGGATATGGCATC-AGCATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGA-TATGAGATTTC
* * * *
17678091 GTGTAAGTCCATATGTGGGATATGGCATCGATATTAGATTTT
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
* * * * *
17678133 GTGTAATACCATAGCTGAGCTATTGGCATCGATATGAGATTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTTC
*
17678176 ATGTAAGACCATATCTGGGATATG
1 GTGTAAGACCATATCTGGGATATG
17678200 ACATTGGTAT
Statistics
Matches: 88, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 53 0.60
43 35 0.40
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
Found at i:17678394 original size:16 final size:16
Alignment explanation
Indices: 17678375--17678418 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 16
17678365 TAAACCCTCG
17678375 GTAAGATTTTGATTGA
1 GTAAGATTTTGATTGA
*
17678391 GTAAG-TTATGATT-A
1 GTAAGATTTTGATTGA
17678405 -TAAGATTTT-ATTGA
1 GTAAGATTTTGATTGA
17678419 TATTCATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
15 7 0.29
16 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (16 bp):
GTAAGATTTTGATTGA
Found at i:17681046 original size:27 final size:27
Alignment explanation
Indices: 17681008--17681065 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
17680998 ACTATCTAAT
**
17681008 TGATAAAATGACTGTTATGCCCCTATA
1 TGATAAAATGACAATTATGCCCCTATA
*
17681035 TGATAAAATGACAATTTTGCCCCTATA
1 TGATAAAATGACAATTATGCCCCTATA
17681062 TGAT
1 TGAT
17681066 GTATGATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (27 bp):
TGATAAAATGACAATTATGCCCCTATA
Found at i:17701461 original size:37 final size:35
Alignment explanation
Indices: 17701391--17701462 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
17701381 TCAGCTAACA
* * *
17701391 TGTTTTGGGCTAAATTGTGATAAATGTATAAGTTT
1 TGTTTTGGGCTAAATTGTAATAAAGGTAAAAGTTT
17701426 TGTTTTAGGGACTAAATTG-AATAAAAGGTAAAAGTTT
1 TGTTTT-GGG-CTAAATTGTAAT-AAAGGTAAAAGTTT
17701463 AGGGTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 6 0.19
36 5 0.16
37 20 0.65
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (35 bp):
TGTTTTGGGCTAAATTGTAATAAAGGTAAAAGTTT
Found at i:17722875 original size:27 final size:26
Alignment explanation
Indices: 17722828--17722878 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
17722818 CGAGGCTGCC
*
17722828 AGATATTGTGACGAAGTCACCAGAAT
1 AGATATTGTGACGAAGCCACCAGAAT
* *
17722854 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
17722879 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAT
Found at i:17725440 original size:46 final size:45
Alignment explanation
Indices: 17725384--17725559 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
17725374 TGTTTGGGCA
17725384 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
17725430 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * *
17725477 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
17725523 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17725560 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 1 0.01
46 67 0.63
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:17725490 original size:93 final size:93
Alignment explanation
Indices: 17725380--17725552 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
17725370 AGGATGTTTG
* * *
17725380 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
17725445 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
17725473 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
17725538 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
17725553 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:17732866 original size:25 final size:25
Alignment explanation
Indices: 17732799--17732877 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
17732789 GGCCCTTCAA
* *
17732799 ATAACTCCCCACAAAGACTTTCTTA-
1 ATAACTCGCCACAAAGGCTTT-TTAG
*
17732824 ATAACAT-GCCACATAGGCTTTTTAG
1 ATAAC-TCGCCACAAAGGCTTTTTAG
* *
17732849 ATAACTCGCCACAAAGGCATTTCAG
1 ATAACTCGCCACAAAGGCTTTTTAG
17732874 ATAA
1 ATAA
17732878 TATGTCACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 4 0.09
25 40 0.89
26 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (25 bp):
ATAACTCGCCACAAAGGCTTTTTAG
Found at i:17732886 original size:25 final size:25
Alignment explanation
Indices: 17732858--17732978 Score: 95
Period size: 25 Copynumber: 4.8 Consensus size: 25
17732848 GATAACTCGC
*
17732858 CACAAAGGCATTTCAGATAATATGT
1 CACAAAGGCCTTTCAGATAATATGT
** * *
17732883 CACATGGGCCTTTCTAAATAATATGC
1 CACAAAGGCCTTTC-AGATAATATGT
* **
17732909 CATATAA-GTTTTTCAGATAACT-TGT
1 CACA-AAGGCCTTTCAGATAA-TATGT
17732934 CACAAA-GCCTTTCTAGATAATATGT
1 CACAAAGGCCTTTC-AGATAATATGT
* *
17732959 CACATAGGCTTTTCAGATAA
1 CACAAAGGCCTTTCAGATAA
17732979 CTCACCATAA
Statistics
Matches: 73, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
24 8 0.11
25 41 0.56
26 24 0.33
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (25 bp):
CACAAAGGCCTTTCAGATAATATGT
Found at i:17732887 original size:50 final size:49
Alignment explanation
Indices: 17732773--17732903 Score: 129
Period size: 50 Copynumber: 2.6 Consensus size: 49
17732763 ACGAATCCCA
17732773 AATAATATGTCACATAGGCCCTTCAAATAACTCCCCACAAAGACTTTCTT
1 AATAATATGTCACATAGGCCCTTCAAATAACTCCCCACAAAGACTTTC-T
* * ** * * * *
17732823 AATAACATGCCACATAGGCTTTTTAGATAACTCGCCACAAAGGCATTTC-
1 AATAATATGTCACATAGGCCCTTCAAATAACTCCCCACAAAGAC-TTTCT
* *
17732872 AGATAATATGTCACATGGGCCTTTCTAAATAA
1 A-ATAATATGTCACATAGGCCCTTC-AAATAA
17732904 TATGCCATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
49 1 0.02
50 54 0.84
51 9 0.14
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (49 bp):
AATAATATGTCACATAGGCCCTTCAAATAACTCCCCACAAAGACTTTCT
Found at i:17732909 original size:76 final size:76
Alignment explanation
Indices: 17732816--17732972 Score: 201
Period size: 76 Copynumber: 2.1 Consensus size: 76
17732806 CCCACAAAGA
* *
17732816 CTTTCTTAATAACATGCCACATAGGCTTTTT-AGATAACTCGCCACAAAGGCATTTC-AGATAAT
1 CTTTCTAAATAACATGCCACATAAG-TTTTTCAGATAACTCGCCACAAA-GCATTTCTAGATAAT
*
17732879 ATGTCACATGGGC
64 ATGTCACATAGGC
* * * * *
17732892 CTTTCTAAATAATATGCCATATAAGTTTTTCAGATAACTTGTCACAAAGCCTTTCTAGATAATAT
1 CTTTCTAAATAACATGCCACATAAGTTTTTCAGATAACTCGCCACAAAGCATTTCTAGATAATAT
17732957 GTCACATAGGC
66 GTCACATAGGC
*
17732968 TTTTC
1 CTTTC
17732973 AGATAACTCA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 11 0.16
76 59 0.84
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (76 bp):
CTTTCTAAATAACATGCCACATAAGTTTTTCAGATAACTCGCCACAAAGCATTTCTAGATAATAT
GTCACATAGGC
Found at i:17732957 original size:50 final size:50
Alignment explanation
Indices: 17732868--17733013 Score: 150
Period size: 50 Copynumber: 2.9 Consensus size: 50
17732858 CACAAAGGCA
** * * *
17732868 TTTCAGATAA-TATGTCACATGGGCCTTTCTAAATAATATGCCATATAAGTT
1 TTTCAGATAACT-TGTCACA-AAGCCTTTCTAGATAATATGCCACATAAGCT
* *
17732919 TTTCAGATAACTTGTCACAAAGCCTTTCTAGATAATATGTCACATAGGCT
1 TTTCAGATAACTTGTCACAAAGCCTTTCTAGATAATATGCCACATAAGCT
*** * **
17732969 TTTCAGATAACTCACCATAAAGGTTTTCTAGATAATATGCCACAT
1 TTTCAGATAACTTGTCACAAAGCCTTTCTAGATAATATGCCACAT
17733014 TGGCTCTGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
50 62 0.77
51 17 0.21
52 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (50 bp):
TTTCAGATAACTTGTCACAAAGCCTTTCTAGATAATATGCCACATAAGCT
Found at i:17735774 original size:40 final size:40
Alignment explanation
Indices: 17735737--17736682 Score: 1720
Period size: 40 Copynumber: 23.6 Consensus size: 40
17735727 GCTACTCGTT
* *
17735737 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
17735777 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17735817 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17735857 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17735897 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17735937 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17735977 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736017 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736057 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736097 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736137 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736177 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736217 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736257 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736297 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736337 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736377 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736417 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736457 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736497 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17736537 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
17736577 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
17736617 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
17736658 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
17736683 CATCATTCAA
Statistics
Matches: 891, Mismatches: 11, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
39 3 0.00
40 874 0.98
41 14 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:17745726 original size:16 final size:16
Alignment explanation
Indices: 17745705--17745763 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
17745695 TTAATCACTT
17745705 TAATATTAAATTAATA
1 TAATATTAAATTAATA
** *
17745721 TAATATTTATCTTGATA
1 TAATA-TTAAATTAATA
* *
17745738 -AATATTATATTAATT
1 TAATATTAAATTAATA
17745753 TAATATTAAAT
1 TAATATTAAAT
17745764 CTTATTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 8 0.24
16 18 0.53
17 8 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:17759776 original size:18 final size:18
Alignment explanation
Indices: 17759753--17759792 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17759743 GGTAAATTTG
*
17759753 TTTTATGAAAACGACGGT
1 TTTTATGAAAACAACGGT
* *
17759771 TTTTATGCAAACAATGGT
1 TTTTATGAAAACAACGGT
17759789 TTTT
1 TTTT
17759793 TCTAAAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (18 bp):
TTTTATGAAAACAACGGT
Found at i:17761448 original size:27 final size:27
Alignment explanation
Indices: 17761383--17761448 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 27
17761373 GTTGGGTCGT
* * *
17761383 TAATACCCCAGT-TTGTAAAATCACTG
1 TAATACCCCTGTACTGTAAAATCACCG
* * * *
17761409 AAATACGCTTGTACTGTAAAATGACCG
1 TAATACCCCTGTACTGTAAAATCACCG
17761436 TAATACCCCTGTA
1 TAATACCCCTGTA
17761449 TGGTAGAATG
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (27 bp):
TAATACCCCTGTACTGTAAAATCACCG
Found at i:17762728 original size:39 final size:39
Alignment explanation
Indices: 17762684--17762761 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
17762674 CTGTAGTTAG
*
17762684 TACTTTCTGAGGCTATACTGAAATAGTTAGGGACTGAAA
1 TACTTTCTGAGGCTATACTAAAATAGTTAGGGACTGAAA
17762723 TACTTTCTGAGGCTATACTAAAATAGTTAGGGACTGAAA
1 TACTTTCTGAGGCTATACTAAAATAGTTAGGGACTGAAA
17762762 CCTCTGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (39 bp):
TACTTTCTGAGGCTATACTAAAATAGTTAGGGACTGAAA
Found at i:17765341 original size:42 final size:42
Alignment explanation
Indices: 17765239--17765347 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
17765229 TCGTTTCAAT
* * * *
17765239 GCCATATCGCC-GATATGGTCTTACATGAAATATCATATCGAC
1 GCCATATC-CCAGATATGATCTTATATGAAATAACATACCGAC
* * * * *
17765281 GCTATGTCCCTGACATGATCTTATATGAAATAACATACCGAG
1 GCCATATCCCAGATATGATCTTATATGAAATAACATACCGAC
*
17765323 GCCATATCTCAGATATGATCTTATA
1 GCCATATCCCAGATATGATCTTATA
17765348 CGGAATCTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 2 0.04
42 51 0.96
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (42 bp):
GCCATATCCCAGATATGATCTTATATGAAATAACATACCGAC
Found at i:17774679 original size:43 final size:43
Alignment explanation
Indices: 17774544--17774664 Score: 188
Period size: 43 Copynumber: 2.8 Consensus size: 43
17774534 ATTTCCGAGA
17774544 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTAT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTAT
* * * * *
17774587 TGTGATTACATGTAAGATCATGTTTGGGAAATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTAT
*
17774630 TGTGATTACGTGTAAGACCATGTCTAGGACATTGG
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGG
17774665 TATCATTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTAT
Found at i:17774689 original size:86 final size:86
Alignment explanation
Indices: 17774543--17774733 Score: 226
Period size: 86 Copynumber: 2.2 Consensus size: 86
17774533 GATTTCCGAG
* *
17774543 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTATTGTGATTACATGTAAGATCAT
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTATTGTGATTACATATAAGACCAT
* *
17774608 GTTTGGGAAATTGGCATTG-T
66 GTTTGGGAAAGTGGCATCGAT
* * ***
17774628 ATTGTGATTACGTGTAAGACCATGTCTAGGACATTGGTA-TCATTATT-TGATTTTTTATAAGAC
1 A-TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTC--TATTGTGATTACATATAAGAC
* *
17774691 CCTGTTTGGGACAGTGGCATCGAT
63 CATGTTTGGGAAAGTGGCATCGAT
*
17774715 ATGTGATAACATGTAAGAC
1 ATGTGATTACATGTAAGAC
17774734 TATATCTGGG
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
85 3 0.03
86 80 0.90
87 6 0.07
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (86 bp):
ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTATTGTGATTACATATAAGACCAT
GTTTGGGAAAGTGGCATCGAT
Found at i:17774732 original size:43 final size:43
Alignment explanation
Indices: 17774543--17774733 Score: 172
Period size: 43 Copynumber: 4.4 Consensus size: 43
17774533 GATTTCCGAG
*
17774543 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTCTAT
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCA-TCGAT
* * * * *
17774587 -TGTGATTACATGTAAGATCATGTTTGGGAAATTGGCATTG-T
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGAT
* *
17774628 ATTGTGATTACGTGTAAGACCATGTCTAGGACATTGGTATC-ATT
1 A-TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGA-T
* *** * * * * *
17774672 ATTTGATTTTTTATAAGACCCTGTTTGGGACAGTGGCATCGAT
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGAT
*
17774715 ATGTGATAACATGTAAGAC
1 ATGTGATTACATGTAAGAC
17774734 TATATCTGGG
Statistics
Matches: 113, Mismatches: 29, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 108 0.96
44 3 0.03
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGAT
Found at i:17786505 original size:46 final size:46
Alignment explanation
Indices: 17786438--17786655 Score: 230
Period size: 46 Copynumber: 4.7 Consensus size: 46
17786428 TGTAACCCGC
** * *
17786438 CCATAAGCAAACTCGGACTCAACTCAATGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCGTTCGCAT
* * * *
17786484 CCATAAGTGAACTCGGACTCAACTTAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GGC--GTTCGCAT
* * * *
17786534 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCGTTCGCAT
*
17786577 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGG-CGTTCGCAT
17786623 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
17786656 TGGATGCTCA
Statistics
Matches: 144, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
42 3 0.02
43 3 0.02
44 2 0.01
45 4 0.03
46 97 0.67
47 24 0.17
48 3 0.02
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCGTTCGCAT
Found at i:17788742 original size:38 final size:38
Alignment explanation
Indices: 17788687--17788761 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
17788677 ACGCTCAATC
* *
17788687 TCTTTCCTTTAGTGTTTGTTTACTCCTTTCACTTCTAG
1 TCTTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTAG
17788725 TCTTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTA
1 TCTTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTA
17788762 TTTTACTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.11, C:0.27, G:0.09, T:0.53
Consensus pattern (38 bp):
TCTTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTAG
Found at i:17795787 original size:42 final size:42
Alignment explanation
Indices: 17795725--17795844 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 42
17795715 TATGTGTTTT
* * *
17795725 CATGTAAGACCACATATGGGACGTTGGCATTGTACTTGATTT
1 CATGTAAGACCACGTCTGGGACGTTGGCATTGTACTTGATTA
* ** *
17795767 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCAATATTTGATTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCAT-TGTACTTGATTA
* *
17795810 CATGTAAGACCACGTCTAGGAAGTTGGCATTGTAC
1 CATGTAAGACCACGTCTGGGACGTTGGCATTGTAC
17795845 GAGCTTTCCG
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
41 1 0.02
42 26 0.43
43 32 0.53
44 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATTGTACTTGATTA
Found at i:17807796 original size:48 final size:48
Alignment explanation
Indices: 17807725--17807939 Score: 224
Period size: 46 Copynumber: 4.6 Consensus size: 48
17807715 AAGCTGACGC
* * * **
17807725 CATGTCCTAGGCAAGTCTTACACTAGCTTGTATATCTCGAGGCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
* * ** * *
17807773 CATGTCCCAGACATATCTTACACTAGC-TCT-CGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
* *
17807819 CATGTCCCAAACATGTCTTACACTGGCTTGTATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
* * * *
17807867 CATGTCCCAGACATGTCTTACACTGGCTCT-CATA-AT-GTGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TGTATATCTCGAGGCCGATG
*
17807913 CATATCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
17807940 ACACATATCA
Statistics
Matches: 139, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
46 68 0.49
47 5 0.04
48 65 0.47
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
Found at i:17807848 original size:94 final size:93
Alignment explanation
Indices: 17807739--17807939 Score: 280
Period size: 94 Copynumber: 2.1 Consensus size: 93
17807729 TCCTAGGCAA
*
17807739 GTCTTACACTAGCTTGTATATCTCGAGGCTAATGCATGTCCCAGACATATCTTACACTAGCTCTC
1 GTCTTACACTAGCTTGTATATCTCGAGGCCAATGCATGTCCCAGACATATCTTACACTAGCTCTC
* *
17807804 GTCTCAA-T-GCCGATGCATGTCCCAAACAT
66 --AT-AAGTGGCCGATGCATATCCCAAACAT
* * * *
17807833 GTCTTACACTGGCTTGTATATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTC
1 GTCTTACACTAGCTTGTATATCTCGAGGCCAATGCATGTCCCAGACATATCTTACACTAGCTCTC
*
17807898 ATAATGTGGCCGATGCATATCCCAGACAT
66 ATAA-GTGGCCGATGCATATCCCAAACAT
17807927 GTCTTACACTAGC
1 GTCTTACACTAGC
17807940 ACACATATCA
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
91 2 0.02
92 1 0.01
93 1 0.01
94 91 0.96
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (93 bp):
GTCTTACACTAGCTTGTATATCTCGAGGCCAATGCATGTCCCAGACATATCTTACACTAGCTCTC
ATAAGTGGCCGATGCATATCCCAAACAT
Found at i:17812602 original size:43 final size:42
Alignment explanation
Indices: 17812542--17812697 Score: 161
Period size: 43 Copynumber: 3.6 Consensus size: 42
17812532 GATTACCGAG
* * *
17812542 ATGTAATTACATGTAAGACCATGTCTGGGACATTGGAATCAT
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAT
* * *
17812584 ATTGTGATTACGTATAAGACCATGTCTAGGACATTGGCATCGT
1 A-TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAT
* * *
17812627 CATATGAGTT-CGTGTAAGACCATGTCCGGGACATTGCCATCGAT
1 -ATGTGA-TTACGTGTAAGACCATGTCTGGGACATTGGCATC-AT
* * *
17812671 ATGTGATAACATGTAAGACCATATCTG
1 ATGTGATTACGTGTAAGACCATGTCTG
17812698 AGATATGGCA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 2 0.02
43 86 0.93
44 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (42 bp):
ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAT
Found at i:17813968 original size:14 final size:14
Alignment explanation
Indices: 17813944--17814009 Score: 66
Period size: 14 Copynumber: 4.6 Consensus size: 14
17813934 CCGTGTGAGG
17813944 CACAC-GGCCTGTT
1 CACACGGGCCTGTT
17813957 CACACGGGCCTGTT
1 CACACGGGCCTGTT
*
17813971 CACACGGGCGTGTGAGGT
1 CACACGGGCCTGT----T
17813989 -ACAC-GGCCTGTT
1 CACACGGGCCTGTT
17814001 CACACGGGC
1 CACACGGGC
17814010 ATGTGAACCC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
12 1 0.02
13 9 0.20
14 23 0.52
16 6 0.14
17 4 0.09
18 1 0.02
ACGTcount: A:0.17, C:0.33, G:0.32, T:0.18
Consensus pattern (14 bp):
CACACGGGCCTGTT
Found at i:17813999 original size:30 final size:31
Alignment explanation
Indices: 17813958--17814015 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
17813948 CGGCCTGTTC
*
17813958 ACACGGGCCTGTTCACACGGGCGTGTGAGGT
1 ACACGGGCCTGTTCACACGGGCATGTGAGGT
17813989 ACAC-GGCCTGTTCACACGGGCATGTGA
1 ACACGGGCCTGTTCACACGGGCATGTGA
17814016 ACCCTGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.19, C:0.28, G:0.34, T:0.19
Consensus pattern (31 bp):
ACACGGGCCTGTTCACACGGGCATGTGAGGT
Found at i:17833433 original size:21 final size:21
Alignment explanation
Indices: 17833408--17833455 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
17833398 GTGACCACAT
*
17833408 GGCGTGCCCCATACCCACACG
1 GGCGTGCCCCATAACCACACG
17833429 GGCGTGCCCCATAACCACACG
1 GGCGTGCCCCATAACCACACG
*
17833450 TGCGTG
1 GGCGTG
17833456 TGAACCCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.42, G:0.27, T:0.12
Consensus pattern (21 bp):
GGCGTGCCCCATAACCACACG
Found at i:17834357 original size:63 final size:63
Alignment explanation
Indices: 17834088--17834359 Score: 246
Period size: 63 Copynumber: 4.3 Consensus size: 63
17834078 CTGGCACACA
* * * * * * * *
17834088 CCGTGTGCCTTACCCGTTTGTCTCAAATATAAACTCAGTGAGTCACA-CAGCCTAGACACACGC
1 CCGTGTGTCTCACCCGTGTGACTCTAATATGAACTCAGTGAGTTACATGA-CCTAGACACACGC
** * * * * * * *
17834151 ATGTATATCTCACCTGTGTGTCTCTAATATGAACTCAGTAAGTT--ATGGCCTGGACACACGC
1 CCGTGTGTCTCACCCGTGTGACTCTAATATGAACTCAGTGAGTTACATGACCTAGACACACGC
* * * * * * *
17834212 CCGTGTGTCTCACCCATGTGACTCTAATATGAAC-CTGGTGAGTTACACGGCTTGGACAGACGC
1 CCGTGTGTCTCACCCGTGTGACTCTAATATGAACTC-AGTGAGTTACATGACCTAGACACACGC
*
17834275 CCGTGTGTCTCACCCGTGTGACTCTAATATGAACTCAGTGAGTTACATGACCTAGACACATGC
1 CCGTGTGTCTCACCCGTGTGACTCTAATATGAACTCAGTGAGTTACATGACCTAGACACACGC
* * *
17834338 TCGTGTGTCTCATCTGTGTGAC
1 CCGTGTGTCTCACCCGTGTGAC
17834360 CCTTATATCT
Statistics
Matches: 166, Mismatches: 38, Indels: 10
0.78 0.18 0.05
Matches are distributed among these distances:
60 1 0.01
61 46 0.28
63 118 0.71
64 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (63 bp):
CCGTGTGTCTCACCCGTGTGACTCTAATATGAACTCAGTGAGTTACATGACCTAGACACACGC
Found at i:17841351 original size:37 final size:36
Alignment explanation
Indices: 17841292--17841366 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
17841282 TCAATTTCAC
* *
17841292 AATTCTATTGTTCTTAAATATCACAGATTCAACTGAT
1 AATTCTATGGTTCTTAAATATCACAAATTCAA-TGAT
* * *
17841329 AATTTTATGGTTCTTCAGTATCACAAATTCAATGAT
1 AATTCTATGGTTCTTAAATATCACAAATTCAATGAT
17841365 AA
1 AA
17841367 GTAAGGAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (36 bp):
AATTCTATGGTTCTTAAATATCACAAATTCAATGAT
Found at i:17846090 original size:7 final size:7
Alignment explanation
Indices: 17846075--17846113 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
17846065 AATAAAAAGC
17846075 TTTCAGCT
1 TTTC-GCT
17846083 TTTCGCT
1 TTTCGCT
17846090 TTTCGCT
1 TTTCGCT
17846097 TTTCGCT
1 TTTCGCT
17846104 TTTCGCT
1 TTTCGCT
17846111 TTT
1 TTT
17846114 GGTATAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 27 0.87
8 4 0.13
ACGTcount: A:0.03, C:0.26, G:0.13, T:0.59
Consensus pattern (7 bp):
TTTCGCT
Found at i:17847563 original size:20 final size:21
Alignment explanation
Indices: 17847516--17847565 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
17847506 TAGATTTAAC
*
17847516 ATTCATCCTTATTTATCTTTA
1 ATTCATCTTTATTTATCTTTA
17847537 ATT-ATCTTTATTTAT-TTGT-
1 ATTCATCTTTATTTATCTT-TA
17847556 ATTCATCTTT
1 ATTCATCTTT
17847566 TCAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTCATCTTTATTTATCTTTA
Found at i:17849144 original size:43 final size:42
Alignment explanation
Indices: 17849054--17849146 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
17849044 TATTTACGTA
** * * *
17849054 TAAGACCATGTTTGGGACATCGACATCGTATCTGATTTCGTG
1 TAAGACCATGTTTGGGACAGAGACATCATATCTGATTACATG
* * *
17849096 TAAGACCCTGTTTGGGACAGAGGCATCAATATTTGATTACATG
1 TAAGACCATGTTTGGGACAGAGACATC-ATATCTGATTACATG
17849139 TAAGACCA
1 TAAGACCA
17849147 CGTCCGGGAC
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 23 0.56
43 18 0.44
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
TAAGACCATGTTTGGGACAGAGACATCATATCTGATTACATG
Found at i:17855467 original size:29 final size:29
Alignment explanation
Indices: 17855431--17855488 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
17855421 CAAAATTTCA
17855431 ATCAAAACTTTTAATTCTATTTTTATTTT
1 ATCAAAACTTTTAATTCTATTTTTATTTT
17855460 ATCAAAACTTTTAATTCTATTTTTATTTT
1 ATCAAAACTTTTAATTCTATTTTTATTTT
17855489 TTCTTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (29 bp):
ATCAAAACTTTTAATTCTATTTTTATTTT
Found at i:17857050 original size:33 final size:33
Alignment explanation
Indices: 17857013--17857089 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
17857003 GCTAATATGT
* * * * *
17857013 TTGATTTCCAATAGCAGATACAACAAGAAATTG
1 TTGATTTCCAACAGCAAATACAACAACAAACTC
*
17857046 TTGATTTCCAACAGCAAATACTACAACAAACTC
1 TTGATTTCCAACAGCAAATACAACAACAAACTC
17857079 TTGATTTCCAA
1 TTGATTTCCAA
17857090 AAGGAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (33 bp):
TTGATTTCCAACAGCAAATACAACAACAAACTC
Found at i:17858456 original size:5 final size:5
Alignment explanation
Indices: 17858446--17858511 Score: 62
Period size: 5 Copynumber: 12.6 Consensus size: 5
17858436 GCAACCCAAT
*
17858446 TTTTA TTTTA TTTTA TTTTT TTCTTAA TTTTA TTTTTA TTTTA TTATT-
1 TTTTA TTTTA TTTTA TTTTA TT-TT-A TTTTA -TTTTA TTTTA TT-TTA
* *
17858494 TATTA CTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTT
17858512 GGATATTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 2 0.04
5 35 0.70
6 11 0.22
7 2 0.04
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:17858507 original size:31 final size:28
Alignment explanation
Indices: 17858446--17858511 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
17858436 GCAACCCAAT
17858446 TTTTA-TTTTATTTTATTTTTTTCTTAA
1 TTTTATTTTTATTTTATTTTTTTCTTAA
*
17858473 TTTTATTTTTATTTTATTATTTATTACTTTA
1 TTTTATTTTTATTTTATT-TTT-TT-CTTAA
17858504 TTTTATTT
1 TTTTATTT
17858512 GGATATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 5 0.15
28 12 0.35
29 3 0.09
30 2 0.06
31 12 0.35
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTATTTTTATTTTATTTTTTTCTTAA
Found at i:17859830 original size:99 final size:99
Alignment explanation
Indices: 17859650--17859838 Score: 272
Period size: 99 Copynumber: 1.9 Consensus size: 99
17859640 AATAATTTTT
* *
17859650 TTAGGAATATATTGGGCTAAGTAACCGAGGTAGGGTGTTTGGCTGTCATCTCTTTTAACGTCAAA
1 TTAGGAATATATTGGGATAAGTAACCGAGGTAGGGTGCTTGGCTGTCATCTCTTTTAACGTCAAA
* *
17859715 AGGTTCGATATGTTCTTAAGAAAAATATAATAAG
66 AGGTTCAATATATTCTTAAGAAAAATATAATAAG
* * * * * *
17859749 TTAGGAGTATGTTGGGATGAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTT-GCGTCAA
1 TTAGGAATATATTGGGATAAGTAACCGAGGTAGGGTGCTTGGCTGTCATCTCT-TTTAACGTCAA
17859813 AAGGTTCAATATATTCTTAAGAAAAA
65 AAGGTTCAATATATTCTTAAGAAAAA
17859839 AAAACAAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 76 0.96
100 3 0.04
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (99 bp):
TTAGGAATATATTGGGATAAGTAACCGAGGTAGGGTGCTTGGCTGTCATCTCTTTTAACGTCAAA
AGGTTCAATATATTCTTAAGAAAAATATAATAAG
Found at i:17860510 original size:10 final size:10
Alignment explanation
Indices: 17860495--17860544 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
17860485 TGGATTTAAC
17860495 ATTTATCTTT
1 ATTTATCTTT
17860505 ATTTATCTTT
1 ATTTATCTTT
*
17860515 AATTATCTTT
1 ATTTATCTTT
17860525 ATTTAT-TTGT
1 ATTTATCTT-T
*
17860535 ATTCATCTTT
1 ATTTATCTTT
17860545 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:17861550 original size:13 final size:11
Alignment explanation
Indices: 17861514--17861543 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17861504 ATCCAAATTA
17861514 ATTTATATGAT
1 ATTTATATGAT
*
17861525 ATTTATATAAT
1 ATTTATATGAT
17861536 ATTTATAT
1 ATTTATAT
17861544 TGGATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTATATGAT
Found at i:17869227 original size:17 final size:17
Alignment explanation
Indices: 17869205--17869239 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17869195 ATCATAATTT
*
17869205 TAATATTTAAATTCAAG
1 TAATATTCAAATTCAAG
*
17869222 TAATATTCAAATTTAAG
1 TAATATTCAAATTCAAG
17869239 T
1 T
17869240 TTTTTCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (17 bp):
TAATATTCAAATTCAAG
Found at i:17878795 original size:50 final size:50
Alignment explanation
Indices: 17878719--17878960 Score: 225
Period size: 50 Copynumber: 4.8 Consensus size: 50
17878709 ACCGAAGCTC
* * *
17878719 TCTGGTACGCATAGTAGCCTGCACTTAGTATTACACATACGACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* ** * * * * * *
17878769 TCTGGTACACGTAGTAGCCTAAACTTAGTATTACACACGTGATCGAAGCTA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAA-CAA
* * * *
17878820 TCGGGCACGCATAGTATCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* * *
17878870 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-AA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
*** * *
17878919 CCGTCTTAAACACATAGTAGCCTACACATAGTACTACACATG
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATG
17878961 TGCTCTCACA
Statistics
Matches: 151, Mismatches: 37, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
49 2 0.01
50 80 0.53
51 37 0.25
52 32 0.21
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
Found at i:17878863 original size:101 final size:101
Alignment explanation
Indices: 17878711--17878911 Score: 321
Period size: 101 Copynumber: 2.0 Consensus size: 101
17878701 CCCTTGTAAC
* * * *
17878711 CGAAGCTCTCTGGTACGCATAGTAGCCTGCACTTAGTATTACACATACGACCTAACAATCTGGTA
1 CGAAGCTATCGGGCACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTAACAATCTGGTA
*
17878776 CACGTAGTAGCCTAAACTTAGTATTACACACGTGAT
66 CACGTAGTAGCCTAAACTTAGTACTACACACGTGAT
* *
17878812 CGAAGCTATCGGGCACGCATAGTATCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTA
1 CGAAGCTATCGGGCACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTAACAATCTGGTA
**
17878877 CACGTAGTAGCCTGCACTTAGTACTACACACGTGA
66 CACGTAGTAGCCTAAACTTAGTACTACACACGTGA
17878912 CCTAAAACCG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 91 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (101 bp):
CGAAGCTATCGGGCACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTAACAATCTGGTA
CACGTAGTAGCCTAAACTTAGTACTACACACGTGAT
Found at i:17881539 original size:29 final size:32
Alignment explanation
Indices: 17881463--17881539 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 32
17881453 GTTTTTTTTA
*
17881463 TTTTTAATTAATAAAT-ATATTATTTTCAATT
1 TTTTTAATTAATAAATCATACTATTTTCAATT
* *
17881494 TTTTT-ATT-TTAATTCAT-CT-TTTT-AATT
1 TTTTTAATTAATAAATCATACTATTTTCAATT
*
17881521 TTTTTAATTAATAACTCAT
1 TTTTTAATTAATAAATCAT
17881540 TTATATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
27 9 0.24
28 7 0.18
29 12 0.32
30 5 0.13
31 5 0.13
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTAATTAATAAATCATACTATTTTCAATT
Done.