Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_pilon, 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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 43
Found at i:5261489 original size:251 final size:251
Alignment explanation
Indices: 5260791--5262370 Score: 1777
Period size: 251 Copynumber: 6.3 Consensus size: 251
5260781 CAGTTTGTGA
* * * *
5260791 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTGGATATGCCTTTGAGTTGA-GT-GT--A
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA-T-GATGTGCCTTTGAGCTGATGTAGTCGA
** * ** *
5260852 A-TCGAAGGTC-TTGGTTCACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGATG-TC
64 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGAGC
* * * * * * *
5260914 CATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTATCGCCTTGAG
127 C-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAG
* * *
5260979 CTATGCTACAAATGATGTGCCTTGGAGTTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGG
191 CTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGG
* * * * * *
5261040 CAGATAACCCTT-TTAGCCTTGAGTTATGCTACAAAT-AT-TG---TGGAGATGAGTGTAATCAA
1 CAGATAACCCTTCTT-GCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGA-TGTAGTCGA
* * * *
5261099 ACTCGAAAGTCTTTTGTTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGCCT
64 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGAGCCT
* * * *
5261164 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCCAGCCTTGAGTTA
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTA
5261229 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGG
194 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGG
* * *
5261287 CAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGATCGTAGTCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAT-GTAGTCGAA
* *
5261352 CTCGAAGGTCTTTGGTTGACA-ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATTATGAGCCTT
65 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGAGCCTT
* * * * * * * *
5261416 TGAGCAGAGCGTATTCGAACTCGTAGGTTTTTTGTTAGCAAATAGCCCTTCTTGCCTTGAGCTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTAT
** * * * * *
5261481 ATTGCAAATGATGTACCTTAGAACTGAGCGTAATAGAACTCGAAGGTCTTTTGTTGG
195 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGG
* * * *
5261538 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATTGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGA-TGTAGTCGAA
* *
5261603 CTCGAAGGTCTTT--TGGGCAGATAACCCTT-TAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
65 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGAGCCTT
* * * *
5261665 GGAGCTGAGCGTAGTCAAACTCGAAGGTATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTAT
* * *
5261730 GCTGCAAATGATGTGCCTTAGTGTTGAGCGTAATCGAACTCGAA-GTCTTTTGGTGG
195 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGG
* * * * * * *
5261786 CAAATAACCCTTATTTCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGA-TGTAGTCGAA
* * *
5261851 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCATTGAGTTATGCTGTAAATGAT-ATGTCT
65 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGA-GCCT
* * * * * * **
5261915 TTGAGCTGAGTGTAGTCCAACTCGAAAGTCTTTTGGTGGCAAATAACCCTTCTTGTGTTGAGCTA
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTA
* * * * * *
5261980 TGTTGTAAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTAG
194 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGG-TGG
* * * * * *
5262038 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTAAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGA-TGTAGTCGAA
* * * * * * * * *
5262103 CTCGAAGGTCTTTTGTTGGCAAATAATCCTTCTTGTCTTGAGTTATGTTTCAAATGGT-ATGCAT
65 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGA-GCCT
* * *
5262167 TGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTATTGG-AAGATAACCCTTCTAGCCTTGAGTT
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA-ATAACCCTTCTAGCCTTGAGCT
* * * * *
5262231 ATACTGTAAATGATGTGCTTTGGAG-TGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGG
193 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGG
* * * * *
5262289 CAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGTTGTGTCTTTGAGCTGA-GTAATCGAAT
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGATGTAGTCGAAC
*
5262353 TCGAAGGTCTTTTGTTGG
66 TCGAAGGTCTTTGGTTGG
5262371 AATAGGTCTT
Statistics
Matches: 1129, Mismatches: 176, Indels: 52
0.83 0.13 0.04
Matches are distributed among these distances:
242 7 0.01
244 2 0.00
245 3 0.00
246 2 0.00
247 148 0.13
248 95 0.08
249 217 0.19
250 24 0.02
251 412 0.36
252 219 0.19
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (251 bp):
CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGATGTAGTCGAAC
TCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGAGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTATG
CTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGG
Found at i:5262401 original size:15 final size:15
Alignment explanation
Indices: 5262381--5262412 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5262371 AATAGGTCTT
5262381 TTATGCTGCCAATAG
1 TTATGCTGCCAATAG
5262396 TTATGCTGCCAATAG
1 TTATGCTGCCAATAG
5262411 TT
1 TT
5262413 TCTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (15 bp):
TTATGCTGCCAATAG
Found at i:5263743 original size:100 final size:99
Alignment explanation
Indices: 5263526--5263790 Score: 390
Period size: 100 Copynumber: 2.7 Consensus size: 99
5263516 GGCTAGATGG
* * * * * *
5263526 ATCCATAAAGCCAGGGCGTTTAACCCATTTCTCTAGAGGGACAACTCAA--TATCATTGTATAGA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCT-TTATTGTATACA
5263589 TATTATAATCACCTTTATCAGGCTAGCTGAATATT
65 TATTATAATCACCTTTATCAGGCTAGCTGAATATT
*
5263624 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATACAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATACAT
* * *
5263689 ATTATAATCACCTTTATCTGGTTTAGCTGAATCTT
66 ATTATAATCACCTTTATCAGG-CTAGCTGAATATT
* *
5263724 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATACAT
5263789 AT
66 AT
5263791 AATATTATAA
Statistics
Matches: 151, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
98 44 0.29
99 31 0.21
100 76 0.50
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (99 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATACAT
ATTATAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:5266392 original size:22 final size:21
Alignment explanation
Indices: 5266357--5266398 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5266347 ACATAATAAT
*
5266357 GATAATAATATAAAGAAAATA
1 GATAATAAAATAAAGAAAATA
*
5266378 GATAAGTAAAATAAATAAAAT
1 GATAA-TAAAATAAAGAAAAT
5266399 TTAGTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
GATAATAAAATAAAGAAAATA
Found at i:5266862 original size:2 final size:2
Alignment explanation
Indices: 5266855--5266883 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5266845 TGTTCACTTT
5266855 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5266884 TCAATTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5267821 original size:38 final size:36
Alignment explanation
Indices: 5267762--5268013 Score: 206
Period size: 38 Copynumber: 6.8 Consensus size: 36
5267752 ATTATATATA
* * *
5267762 AAAATATTTTCAAAAAC-ATATAATATATAGTTTTCC
1 AAAATGTTTTAAAAAACTATATATTATATA-TTTTCC
* *
5267798 AAAATGTTTTAAAAAAATTATATATTATATATGTTTTC
1 AAAATGTTTT-AAAAAACTATATATTATATAT-TTTCC
**
5267836 AAAA-GTGTTTAAAAAACTATATATTGCATATTTT-C
1 AAAATGT-TTTAAAAAACTATATATTATATATTTTCC
*** * ** **
5267871 AAAATGTTTTTTTTAAACTATATAATATATATAATAT
1 AAAATG-TTTTAAAAAACTATATATTATATATTTTCC
* *
5267908 ATAAATGTTTT-CAAAACTATATATTATATAAGTTTTCA
1 A-AAATGTTTTAAAAAACTATATATTATAT-A-TTTTCC
* *
5267946 AAAATGTTTTCAAAAACTATATATTATATATATTTTCA
1 AAAATGTTTTAAAAAACTATATA-T-TATATATTTTCC
*
5267984 AAAATGTTTTAAAAAATTATATATTATATA
1 AAAATGTTTTAAAAAACTATATATTATATA
5268014 CGTATTTTCA
Statistics
Matches: 176, Mismatches: 27, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
35 5 0.03
36 53 0.30
37 43 0.24
38 68 0.39
39 2 0.01
40 5 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAATGTTTTAAAAAACTATATATTATATATTTTCC
Found at i:5267936 original size:27 final size:25
Alignment explanation
Indices: 5267898--5267948 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
5267888 CTATATAATA
5267898 TATATAATATATAAATGTTTTCAAAAC
1 TATATAATATAT-AA-GTTTTCAAAAC
*
5267925 TATATATTATATAAGTTTTCAAAA
1 TATATAATATATAAGTTTTCAAAA
5267949 ATGTTTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.43
26 2 0.09
27 11 0.48
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (25 bp):
TATATAATATATAAGTTTTCAAAAC
Found at i:5268048 original size:147 final size:146
Alignment explanation
Indices: 5267747--5268060 Score: 350
Period size: 147 Copynumber: 2.1 Consensus size: 146
5267737 AAATAATAAC
* *
5267747 AATATATTATATATAAAAATATTTTCAAAAACATATAATATATAGTTTTCCAAAATGTTTTAAAA
1 AATATA-TATATATATAAATATTTTCAAAAACATATAATATATAGTTTTCAAAAATGTTTTAAAA
* * * * * *
5267812 AAATTATATATTATATATGTTTTCAAAAGTGTTTAAAAAACTATATATTGCATATTTTCAAAATG
65 AAACTATATATTATATATATTTTCAAAAATGTTTAAAAAAATATATATTACATATTTTCAAAATA
* * **
5267877 TTTTTTTTAAAC-TATA
130 CTATTTGCAAACATATA
* *
5267893 TAATATATATAATATATAAATGTTTTC-AAAACTATATATTATATAAGTTTTCAAAAATGTTTT-
1 -AATATATAT-ATATATAAATATTTTCAAAAAC-ATATAATATAT-AGTTTTCAAAAATGTTTTA
* *
5267956 CAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAAAAATTATATATTATATACGTATTT
62 AAAAAACTATATATTATATATATTTTCAAAAATG-TTTAAAAAA--ATATA-TAT-TACATATTT
5268021 TCAAAA-ACTATTTGCAAAC-TATA
122 TCAAAATACTATTTGCAAACATATA
5268044 ATATATATATATATATA
1 A-ATATATATATATATA
5268061 TAAAATATAT
Statistics
Matches: 142, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
146 8 0.06
147 60 0.42
148 26 0.18
150 12 0.08
151 23 0.16
152 13 0.09
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (146 bp):
AATATATATATATATAAATATTTTCAAAAACATATAATATATAGTTTTCAAAAATGTTTTAAAAA
AACTATATATTATATATATTTTCAAAAATGTTTAAAAAAATATATATTACATATTTTCAAAATAC
TATTTGCAAACATATA
Found at i:5270925 original size:19 final size:19
Alignment explanation
Indices: 5270869--5270927 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
5270859 ATCAAGTACT
5270869 ATATCTTTCAATATA-TAA
1 ATATCTTTCAATATATTAA
* *
5270887 ATAT-TATCAAT-TCATCAA
1 ATATCTTTCAATAT-ATTAA
5270905 ATATCTTTCAATATATTAA
1 ATATCTTTCAATATATTAA
5270924 ATAT
1 ATAT
5270928 TACATCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.03
17 7 0.21
18 10 0.30
19 14 0.42
20 1 0.03
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATCTTTCAATATATTAA
Found at i:5277276 original size:10 final size:11
Alignment explanation
Indices: 5277251--5277287 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5277241 TTTGAGTTAA
*
5277251 TTAAAATATGT
1 TTAAAATGTGT
5277262 TTAAAATGT-T
1 TTAAAATGTGT
5277272 TTAAAATGTGT
1 TTAAAATGTGT
5277283 TTAAA
1 TTAAA
5277288 GCTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (11 bp):
TTAAAATGTGT
Found at i:5277404 original size:20 final size:19
Alignment explanation
Indices: 5277366--5277418 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
5277356 TACTGTTCAT
5277366 AGTTTGGAAACTTTGTAAG
1 AGTTTGGAAACTTTGTAAG
* *
5277385 AGTTTTGAAACTTTATTAAG
1 AGTTTGGAAACTTT-GTAAG
*
5277405 AGTTTCG-AACTTTG
1 AGTTTGGAAACTTTG
5277419 CACCCATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.42
Consensus pattern (19 bp):
AGTTTGGAAACTTTGTAAG
Found at i:5277502 original size:20 final size:20
Alignment explanation
Indices: 5277477--5277577 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 20
5277467 TTAAGTAAAG
5277477 GTTTCGAAACTTTCATCAAA
1 GTTTCGAAACTTTCATCAAA
**
5277497 GTTTCGAAACTTTCAAGAATA
1 GTTTCGAAACTTTCATCAA-A
5277518 GTTT-G----TTT-A--AAA
1 GTTTCGAAACTTTCATCAAA
* *
5277530 GTTTCGATACTTTC-GCAAA
1 GTTTCGAAACTTTCATCAAA
*
5277549 GTTTCGAAACTTTCTTCAAA
1 GTTTCGAAACTTTCATCAAA
*
5277569 GTTTTGAAA
1 GTTTCGAAA
5277578 ATGCATGGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
12 5 0.08
13 3 0.05
15 1 0.02
16 3 0.05
17 3 0.05
19 16 0.24
20 30 0.45
21 5 0.08
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (20 bp):
GTTTCGAAACTTTCATCAAA
Found at i:5277551 original size:19 final size:20
Alignment explanation
Indices: 5277527--5277577 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5277517 AGTTTGTTTA
*
5277527 AAAGTTTCGATACTTTC-GC
1 AAAGTTTCGAAACTTTCTGC
*
5277546 AAAGTTTCGAAACTTTCTTC
1 AAAGTTTCGAAACTTTCTGC
*
5277566 AAAGTTTTGAAA
1 AAAGTTTCGAAA
5277578 ATGCATGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
AAAGTTTCGAAACTTTCTGC
Found at i:5278785 original size:20 final size:19
Alignment explanation
Indices: 5278747--5278800 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
5278737 TACTGTTCAT
*
5278747 AGTTTGGAAACTTTGTAAG
1 AGTTTCGAAACTTTGTAAG
* * *
5278766 TGTTTTGAAACTTTATTAAG
1 AGTTTCGAAACTTT-GTAAG
5278786 AGTTTCGAAACTTTG
1 AGTTTCGAAACTTTG
5278801 CACCCATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (19 bp):
AGTTTCGAAACTTTGTAAG
Found at i:5278883 original size:20 final size:20
Alignment explanation
Indices: 5278858--5278958 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 20
5278848 TTAAGTAAGG
5278858 GTTTCGAAACTTTCATCAAA
1 GTTTCGAAACTTTCATCAAA
**
5278878 GTTTCGAAACTTTCAAGAATA
1 GTTTCGAAACTTTCATCAA-A
5278899 GTTT-G----TTT-A--AAA
1 GTTTCGAAACTTTCATCAAA
* *
5278911 GTTTCGATACTTTC-GCAAA
1 GTTTCGAAACTTTCATCAAA
*
5278930 GTTTCGAAACTTTCTTCAAA
1 GTTTCGAAACTTTCATCAAA
*
5278950 GTTTTGAAA
1 GTTTCGAAA
5278959 ATGCATGTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
12 5 0.08
13 3 0.05
15 1 0.02
16 3 0.05
17 3 0.05
19 16 0.24
20 30 0.45
21 5 0.08
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (20 bp):
GTTTCGAAACTTTCATCAAA
Found at i:5278932 original size:19 final size:20
Alignment explanation
Indices: 5278908--5278958 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5278898 AGTTTGTTTA
*
5278908 AAAGTTTCGATACTTTC-GC
1 AAAGTTTCGAAACTTTCTGC
*
5278927 AAAGTTTCGAAACTTTCTTC
1 AAAGTTTCGAAACTTTCTGC
*
5278947 AAAGTTTTGAAA
1 AAAGTTTCGAAA
5278959 ATGCATGTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
AAAGTTTCGAAACTTTCTGC
Found at i:5280853 original size:45 final size:48
Alignment explanation
Indices: 5280796--5280889 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 48
5280786 AAGTCCAAAA
5280796 TAACTTGAAAATTACGT-TTCTTAATTTC-TT-TATATGTGAAATATT
1 TAACTTGAAAATTACGTGTTCTTAATTTCTTTATATATGTGAAATATT
5280841 TAACTTGAAAATTACGTGTTCTTAATTTCTTTATATATGTGAAATATT
1 TAACTTGAAAATTACGTGTTCTTAATTTCTTTATATATGTGAAATATT
5280889 T
1 T
5280890 TGAGTTAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 17 0.37
46 11 0.24
47 2 0.04
48 16 0.35
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.49
Consensus pattern (48 bp):
TAACTTGAAAATTACGTGTTCTTAATTTCTTTATATATGTGAAATATT
Found at i:5280928 original size:11 final size:11
Alignment explanation
Indices: 5280898--5280933 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5280888 TTTGAGTTAA
5280898 TTAAAATGTGT
1 TTAAAATGTGT
5280909 TT-AAA-GTGT
1 TTAAAATGTGT
5280918 TTAAAATGTGT
1 TTAAAATGTGT
5280929 TTAAA
1 TTAAA
5280934 GCTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.26
10 6 0.26
11 11 0.48
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (11 bp):
TTAAAATGTGT
Found at i:5281041 original size:19 final size:20
Alignment explanation
Indices: 5281013--5281085 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 20
5281003 TAATATTCAT
*
5281013 AGTTTGGAAACTTT-GTAAG
1 AGTTTCGAAACTTTAGTAAG
* *
5281032 AGTTTTGAAACTTTTATTAAG
1 AGTTTCGAAAC-TTTAGTAAG
* *
5281053 AGTTTCGAAACTTTA-CAAA
1 AGTTTCGAAACTTTAGTAAG
*
5281072 AGTTTCAAAACTTT
1 AGTTTCGAAACTTT
5281086 GCACCCAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 25 0.54
20 7 0.15
21 14 0.30
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
AGTTTCGAAACTTTAGTAAG
Found at i:5281219 original size:19 final size:19
Alignment explanation
Indices: 5281195--5281239 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
5281185 AGTGTGTTTA
5281195 AAAGTTTTGATACTTTCAC
1 AAAGTTTTGATACTTTCAC
5281214 AAAGTTTTGATACTTTCAC
1 AAAGTTTTGATACTTTCAC
5281233 AAAGTTT
1 AAAGTTT
5281240 CGAAACTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (19 bp):
AAAGTTTTGATACTTTCAC
Found at i:5281247 original size:19 final size:19
Alignment explanation
Indices: 5281195--5281264 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
5281185 AGTGTGTTTA
* *
5281195 AAAGTTTTGATACTTTCAC
1 AAAGTTTCGAAACTTTCAC
* *
5281214 AAAGTTTTGATACTTTCAC
1 AAAGTTTCGAAACTTTCAC
5281233 AAAGTTTCGAAACTTTTTCA-
1 AAAGTTTCGAAAC--TTTCAC
5281253 AAAGTTTCGAAA
1 AAAGTTTCGAAA
5281265 TTGCATGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 30 0.64
20 12 0.26
21 5 0.11
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
AAAGTTTCGAAACTTTCAC
Found at i:5287015 original size:21 final size:21
Alignment explanation
Indices: 5286956--5287053 Score: 115
Period size: 21 Copynumber: 4.7 Consensus size: 21
5286946 ATTTTTCAGA
*
5286956 AAAAGGATCAATCCATTTCTC
1 AAAAGGATCAATCCCTTTCTC
** * *
5286977 AAAATAATCTATCTCTTTCTC
1 AAAAGGATCAATCCCTTTCTC
** *
5286998 AAAAGGATTGATCCCTTTCTG
1 AAAAGGATCAATCCCTTTCTC
5287019 AAAAGGATCAATCCCTTTCTC
1 AAAAGGATCAATCCCTTTCTC
*
5287040 AAAATGATCAATCC
1 AAAAGGATCAATCC
5287054 ATTCCCTGAA
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (21 bp):
AAAAGGATCAATCCCTTTCTC
Found at i:5290305 original size:18 final size:18
Alignment explanation
Indices: 5290279--5290321 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5290269 GTACGTATCT
* *
5290279 TCATTATCACTACCACTA
1 TCATCATCACCACCACTA
*
5290297 TCATCATCACCATCACTA
1 TCATCATCACCACCACTA
5290315 TCATCAT
1 TCATCAT
5290322 TATCACTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (18 bp):
TCATCATCACCACCACTA
Found at i:5293259 original size:18 final size:19
Alignment explanation
Indices: 5293214--5293261 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
5293204 CCCCTACTGG
*
5293214 GAGTATCGATATTCTACCCTT
1 GAGTATCGATACTCTA--CTT
5293235 G-GTATCGATACTCTA-TT
1 GAGTATCGATACTCTACTT
5293252 GAGTATCGAT
1 GAGTATCGAT
5293262 GCAAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
20 13 0.52
21 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (19 bp):
GAGTATCGATACTCTACTT
Found at i:5294117 original size:39 final size:39
Alignment explanation
Indices: 5294074--5294153 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
5294064 TGGATTTCTC
5294074 TTCTACGCAAAATTTCTATAATAATAAATAAATATAGAA
1 TTCTACGCAAAATTTCTATAATAATAAATAAATATAGAA
5294113 TTCTACGCAAAATTTCTATAATAATAAATAAATATAGAA
1 TTCTACGCAAAATTTCTATAATAATAAATAAATATAGAA
5294152 TT
1 TT
5294154 ATGATACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (39 bp):
TTCTACGCAAAATTTCTATAATAATAAATAAATATAGAA
Found at i:5294271 original size:16 final size:15
Alignment explanation
Indices: 5294225--5294276 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
5294215 AGAGATGATT
*
5294225 TAATTTAAATTAAAA
1 TAATTTAATTTAAAA
5294240 TTAATTTAATCTTAAAA
1 -TAATTTAAT-TTAAAA
5294257 TAATTTAATTGTAAAA
1 TAATTTAATT-TAAAA
5294273 TAAT
1 TAAT
5294277 GTGAATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 1 0.03
16 26 0.79
17 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATTTAATTTAAAA
Found at i:5299144 original size:13 final size:14
Alignment explanation
Indices: 5299126--5299154 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5299116 TCAACCAATA
5299126 TTTAAAGT-TAATT
1 TTTAAAGTCTAATT
5299139 TTTAAAGTCTAATT
1 TTTAAAGTCTAATT
5299153 TT
1 TT
5299155 GTTCATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (14 bp):
TTTAAAGTCTAATT
Found at i:5305943 original size:30 final size:30
Alignment explanation
Indices: 5305903--5305966 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
5305893 TCAAAGCCTC
* * *
5305903 TCCTCTGATTCCAACCCATATACACCCTTG
1 TCCTCCGATTCCAACCCACATACACCCTAG
5305933 TCCTCCGATTCCAACCCACATACACCCTAG
1 TCCTCCGATTCCAACCCACATACACCCTAG
5305963 TCCT
1 TCCT
5305967 TTGTCTTCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.44, G:0.06, T:0.27
Consensus pattern (30 bp):
TCCTCCGATTCCAACCCACATACACCCTAG
Found at i:5311522 original size:18 final size:18
Alignment explanation
Indices: 5311478--5311522 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5311468 TAGATATCTT
* *
5311478 AACTTTTAACTTAGTTAG
1 AACTTTTAGCTTAGCTAG
*
5311496 AACTCTTAGCTTAGCTAG
1 AACTTTTAGCTTAGCTAG
*
5311514 GACTTTTAG
1 AACTTTTAG
5311523 TAATTTCTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (18 bp):
AACTTTTAGCTTAGCTAG
Found at i:5313172 original size:2 final size:2
Alignment explanation
Indices: 5313165--5313201 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5313155 TATTTTGTGA
*
5313165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5313202 AAAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5314718 original size:22 final size:23
Alignment explanation
Indices: 5314690--5314768 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 23
5314680 GATCTTTTAT
*
5314690 TATTATAATGTTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
5314712 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
* * *
5314735 TA-AATATATTTTAAAAATTTTAA
1 TATTATA-ATATTAAAAATATTAA
*
5314758 TAAT-TAATATT
1 TATTATAATATT
5314769 TTGATTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
22 23 0.52
23 21 0.48
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:5314723 original size:30 final size:32
Alignment explanation
Indices: 5314669--5314742 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
5314659 ATTATTAAAA
* * * *
5314669 TAAAAATATAAGATCTTTTATTATTA-TAATGT
1 TAAAAATAT-AGATATTATATTATTAGAAATAT
5314701 TAAAAATATA-ATATTATATTATTAGAAATAT
1 TAAAAATATAGATATTATATTATTAGAAATAT
5314732 TAATAAATATA
1 TAA-AAATATA
5314743 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.33
31 8 0.22
32 16 0.44
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (32 bp):
TAAAAATATAGATATTATATTATTAGAAATAT
Found at i:5314752 original size:23 final size:23
Alignment explanation
Indices: 5314691--5314770 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 23
5314681 ATCTTTTATT
*
5314691 ATTATAATGTTAAAAATA-TAAT-
1 ATTAT-ATTTTAAAAATATTAATA
*
5314713 ATTATATTATTAGAAATATTAATA
1 ATTATATT-TTAAAAATATTAATA
* *
5314737 AATATATTTTAAAAATTTTAATA
1 ATTATATTTTAAAAATATTAATA
5314760 ATTAATATTTT
1 ATT-ATATTTT
5314771 GATTAAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.04
22 13 0.27
23 19 0.40
24 14 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (23 bp):
ATTATATTTTAAAAATATTAATA
Found at i:5316530 original size:37 final size:38
Alignment explanation
Indices: 5316454--5316541 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
5316444 CCCTAAACCC
5316454 AAAA-CCGACCCGACCCGACCCGAATATCACACTTAAA
1 AAAACCCGACCCGACCCGACCCGAATATCACACTTAAA
**
5316491 AAAACCCGACCCGACTTGACCCGAATATCACACTT-AA
1 AAAACCCGACCCGACCCGACCCGAATATCACACTTAAA
5316528 AAAACCCGACCCGA
1 AAAACCCGACCCGA
5316542 ACAAAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 20 0.42
38 28 0.58
ACGTcount: A:0.40, C:0.38, G:0.11, T:0.11
Consensus pattern (38 bp):
AAAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:5316700 original size:258 final size:258
Alignment explanation
Indices: 5316273--5316738 Score: 774
Period size: 258 Copynumber: 1.8 Consensus size: 258
5316263 AAAAAACCCG
* **
5316273 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCTGACCCGAATATATGAATTAGAAATCTGACC
1 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACC
*
5316338 CGACCCGACACGAAATAATAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGA
66 CGACCCGACACGAAATAATAAAAAATATGTTTATTTAATAAAAACAATGACTTAATCCGACCCGA
* **
5316403 CCCGAATTATATATATTTTCAGGTTGGTCCGGTTTTTTTCACCCTAAACCCAAAACCGACCCGAC
131 CCCGAATTATATATATTTTCAGGTCGGTCCGAATTTTTTCACCCTAAACCCAAAACCGACCCGAC
5316468 CCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTTGACCCGAATATCACACTTAAAAA
196 CCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTTGACCCGAATATCACACTTAAAAA
5316531 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACC
1 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACC
* * *
5316596 CGACCCGACCCGAAATAATAAACAATTATGTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
66 CGACCCGACACGAAATAATAAA-AAATATGTTTATTTAATAAAAACAATGACTTAATCCGACCCG
* ** *
5316661 ACCTGAATTATATATATTTTC-GGATCGGTCC-AATTTTTTCACCCTAAACCTGAACCCGACCCG
130 ACCCGAATTATATATATTTTCAGG-TCGGTCCGAATTTTTTCACCCTAAACCCAAAACCGACCCG
5316724 ACCCGACCCGAATAT
194 ACCCGACCCGAATAT
5316739 ATGAATTAGA
Statistics
Matches: 192, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
258 127 0.66
259 65 0.34
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (258 bp):
ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACC
CGACCCGACACGAAATAATAAAAAATATGTTTATTTAATAAAAACAATGACTTAATCCGACCCGA
CCCGAATTATATATATTTTCAGGTCGGTCCGAATTTTTTCACCCTAAACCCAAAACCGACCCGAC
CCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTTGACCCGAATATCACACTTAAAAA
Found at i:5318901 original size:64 final size:64
Alignment explanation
Indices: 5318833--5318992 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
5318823 GAATAAATTG
*** * * * *
5318833 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATC-GATGCACT-TGGGTTTTATTA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCA-CAGATGCACTCAGGCTATT-TTA
5318896 A
64 A
* *
5318897 AACATCGAATGCGTTTCATGCATCGATGCACAAGCAATGCACAGATGCACTCAGGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACAGATGCACTCAGGCTATTTTAA
*
5318961 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
5318993 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 77 0.93
65 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACAGATGCACTCAGGCTATTTTAA
Found at i:5319002 original size:64 final size:62
Alignment explanation
Indices: 5318833--5319012 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 62
5318823 GAATAAATTG
* * * *
5318833 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCA-CGATGCACTAGGCTATTATTAA
* * *
5318897 AACATCGAATGCGTTTCATGCATCGATGCACAAGC-AATGCACAGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCAC-GATGCACT-AGGCTATTATTA
5318960 A
62 A
* *
5318961 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCA-CGATGCACTA
5319013 AGTGTTCCAA
Statistics
Matches: 98, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 87 0.89
65 6 0.06
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (62 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACGATGCACTAGGCTATTATTAA
Found at i:5321700 original size:29 final size:30
Alignment explanation
Indices: 5321631--5321689 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
5321621 AATTTAAGGT
5321631 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
*
5321662 AAAATATTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
5321690 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:5321817 original size:20 final size:20
Alignment explanation
Indices: 5321792--5321858 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
5321782 ACCTGCACTA
*
5321792 ATGCATCGATGTATCCATCC
1 ATGCATCGATGCATCCATCC
5321812 ATGCATCGATGCATCCATCC
1 ATGCATCGATGCATCCATCC
* *
5321832 ATGCATCGATGCATGCATCG
1 ATGCATCGATGCATCCATCC
5321852 ATGCATC
1 ATGCATC
5321859 CTGCCAGGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (20 bp):
ATGCATCGATGCATCCATCC
Found at i:5321851 original size:12 final size:12
Alignment explanation
Indices: 5321820--5321857 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5321810 CCATGCATCG
* *
5321820 ATGCATCCATCC
1 ATGCATCGATGC
5321832 ATGCATCGATGC
1 ATGCATCGATGC
5321844 ATGCATCGATGC
1 ATGCATCGATGC
5321856 AT
1 AT
5321858 CCTGCCAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (12 bp):
ATGCATCGATGC
Found at i:5325200 original size:29 final size:30
Alignment explanation
Indices: 5325130--5325189 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
5325120 CAATTTAAGG
*
5325130 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGAACTTGAATTGAATTTA
*
5325161 CAAAATATTTTTGAACTT-AATTGAATTTA
1 CAAAATGTTTTTGAACTTGAATTGAATTTA
5325190 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGAACTTGAATTGAATTTA
Found at i:5325295 original size:21 final size:21
Alignment explanation
Indices: 5325269--5325324 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
5325259 AGGGTGTCAA
5325269 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCATCCCTAC
*
5325290 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTAC
5325311 AGTGCATCCATGCA
1 AGTGCATCCATGCA
5325325 CTCAAACATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTAC
Found at i:5325376 original size:20 final size:20
Alignment explanation
Indices: 5325347--5325392 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5325337 ATGCACTTAG
*
5325347 TGCATTGATGCATCCAT-CCA
1 TGCATCGATGCATCC-TGCCA
*
5325367 TGCATCGATGTATCCTGCCA
1 TGCATCGATGCATCCTGCCA
5325387 TGCATC
1 TGCATC
5325393 AAGGCTACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Found at i:5331592 original size:21 final size:21
Alignment explanation
Indices: 5331566--5331616 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5331556 ATTTAACAAA
5331566 AAGGGGGAGAAGTGTTATAGT
1 AAGGGGGAGAAGTGTTATAGT
*
5331587 AAGGGGTAGAAGTGTTATAGT
1 AAGGGGGAGAAGTGTTATAGT
5331608 AAGGGGGAG
1 AAGGGGGAG
5331617 TAATAGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.45, T:0.22
Consensus pattern (21 bp):
AAGGGGGAGAAGTGTTATAGT
Found at i:5332157 original size:64 final size:62
Alignment explanation
Indices: 5331988--5332166 Score: 191
Period size: 64 Copynumber: 2.8 Consensus size: 62
5331978 GAATAAATTG
* * * * *
5331988 AACATCGAATGCATTTCATGAATTGATGCACTCTCTATGCATCGATGCACTTGGGTTTTACTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTTGGCTTTTA-TAA
* * *
5332052 AACATCGAATGCATTTCATGCATCGATGAACAAGC-AATGCACCGATGCACTCTGGCTATTT-TC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-TGGCT-TTTATA
5332115 A
62 A
* *
5332116 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACT
5332167 AAGTGTTCCA
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 87 0.90
65 4 0.04
66 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (62 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTTGGCTTTTATAA
Found at i:5333942 original size:15 final size:15
Alignment explanation
Indices: 5333922--5333952 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5333912 TCGATACTGA
5333922 ATGTGCGATATCGAT
1 ATGTGCGATATCGAT
5333937 ATGTGCGATATCGAT
1 ATGTGCGATATCGAT
5333952 A
1 A
5333953 CCATGTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (15 bp):
ATGTGCGATATCGAT
Found at i:5336238 original size:32 final size:32
Alignment explanation
Indices: 5336202--5336282 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
5336192 TTGATGTTCA
5336202 TGTGCATTATCTGAATGCAACGCTAACTCTGT
1 TGTGCATTATCTGAATGCAACGCTAACTCTGT
* * * *
5336234 TGTGCATTATCTAAATACAATGCTAACTTTGT
1 TGTGCATTATCTGAATGCAACGCTAACTCTGT
*
5336266 TTTGCATTATCTGAATG
1 TGTGCATTATCTGAATG
5336283 ATATTGATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTGCATTATCTGAATGCAACGCTAACTCTGT
Found at i:5337585 original size:21 final size:19
Alignment explanation
Indices: 5337538--5337590 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
5337528 TATTACCTTG
**
5337538 AGTATCGATACTGTCCTGC
1 AGTATCGATACTCACCTGC
*
5337557 AATATCGATACTCACCTTGGC
1 AGTATCGATACTCACC-T-GC
5337578 AGTATCGATACTC
1 AGTATCGATACTC
5337591 CTGTCTGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
21 14 0.50
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (19 bp):
AGTATCGATACTCACCTGC
Found at i:5340466 original size:2 final size:2
Alignment explanation
Indices: 5340450--5340483 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5340440 ACTTTTCTTG
5340450 AT AT -T AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5340484 TCAGAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5344269 original size:21 final size:20
Alignment explanation
Indices: 5344232--5344287 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5344222 AAATTACCCT
*
5344232 AGTATCTATACTCCTA-CTTGG
1 AGTATCGATACT-CTACCTT-G
5344253 AGTATCGATACCTCTACCTTG
1 AGTATCGATA-CTCTACCTTG
5344274 -GTATCGATACTCTA
1 AGTATCGATACTCTA
5344288 TGTGAGTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.16
20 9 0.28
21 13 0.41
22 5 0.16
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTCTACCTTG
Found at i:5345552 original size:10 final size:11
Alignment explanation
Indices: 5345512--5345568 Score: 57
Period size: 12 Copynumber: 5.2 Consensus size: 11
5345502 GTAAAACGGT
5345512 CGACTGTTGAC
1 CGACTGTTGAC
5345523 CTGACTGTTGAC
1 C-GACTGTTGAC
*
5345535 CGGC-GTTGAC
1 CGACTGTTGAC
5345545 C-ACTGTTGAC
1 CGACTGTTGAC
5345555 CAGAACT-TTGAC
1 C-G-ACTGTTGAC
5345567 CG
1 CG
5345569 GCATTGAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 1 0.03
10 14 0.36
11 4 0.10
12 17 0.44
13 3 0.08
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (11 bp):
CGACTGTTGAC
Found at i:5345555 original size:32 final size:32
Alignment explanation
Indices: 5345514--5345575 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
5345504 AAAACGGTCG
* *
5345514 ACTGTTGACCTG-ACTGTTGACCGGCGTTGACC
1 ACTGTTGACCAGAACT-TTGACCGGCATTGACC
5345546 ACTGTTGACCAGAACTTTGACCGGCATTGA
1 ACTGTTGACCAGAACTTTGACCGGCATTGA
5345576 ACGACCTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (32 bp):
ACTGTTGACCAGAACTTTGACCGGCATTGACC
Found at i:5347955 original size:24 final size:24
Alignment explanation
Indices: 5347928--5347992 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
5347918 TCCGATTTGA
*
5347928 ATTCTGTTATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
5347952 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
5347976 ATTTTGATATGATACTT
1 ATTCTGATATGATACTT
5347993 AACCTGAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:5356796 original size:3 final size:3
Alignment explanation
Indices: 5356788--5356833 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5356778 TTTAGTCCCG
5356788 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5356834 CTACTACTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5356907 original size:23 final size:22
Alignment explanation
Indices: 5356880--5356927 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
5356870 TTATTACAGA
*
5356880 CCCAATTACAAGCAAACCCGAAG
1 CCCAATTACAAACAAACCC-AAG
5356903 CCCAATTACAAACAAACCCAAG
1 CCCAATTACAAACAAACCCAAG
5356925 CCC
1 CCC
5356928 GATACATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.44, C:0.40, G:0.08, T:0.08
Consensus pattern (22 bp):
CCCAATTACAAACAAACCCAAG
Found at i:5358759 original size:65 final size:63
Alignment explanation
Indices: 5358637--5358846 Score: 226
Period size: 65 Copynumber: 3.3 Consensus size: 63
5358627 TTTTTCAGAG
* * * * **
5358637 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCAT
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTAAGGA-TATTTTGAAACATCGAATGCAT
5358701 T
63 T
* *
5358702 TCATACATCGATGCACATACCATGCATCGATGCACTAAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTAAGGATATTT-TG-AAACATCGAATGCAT
5358766 T
63 T
* ** * *
5358767 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCATT
5358831 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
5358847 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 51 0.41
65 63 0.51
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCATT
Found at i:5367505 original size:17 final size:19
Alignment explanation
Indices: 5367477--5367525 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5367467 TATTTTGAAA
5367477 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
5367495 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
5367514 CACCGATGCACT
1 CATCGATGCACT
5367526 AAGGGTCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:5376041 original size:41 final size:41
Alignment explanation
Indices: 5375935--5376041 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
5375925 ACCAAATTGG
* * * *
5375935 TAAGTTCTTCGGGCCATCAC-TAAGTCTTTCGAGCATGATTA
1 TAAGTCCTTCGGGTCATC-CGTAAGTCTTTCGAGCAAGATGA
* * * *
5375976 TAAAATCCTTTGGGTTATCTGTAAGTCTTTCGAGCAAGATGA
1 T-AAGTCCTTCGGGTCATCCGTAAGTCTTTCGAGCAAGATGA
5376018 TAAGTCCTTCGGGTCATCCGTAAG
1 TAAGTCCTTCGGGTCATCCGTAAG
5376042 ACCTTTGGGT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (41 bp):
TAAGTCCTTCGGGTCATCCGTAAGTCTTTCGAGCAAGATGA
Found at i:5376199 original size:248 final size:248
Alignment explanation
Indices: 5375578--5377437 Score: 2507
Period size: 248 Copynumber: 7.5 Consensus size: 248
5375568 TGTTTCGAAA
* * * *
5375578 AATGAAAAAGTGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAAT-AAATTTTTTGAAAAGT
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAA-TTTTTGAAAAGT
* * * ***
5375642 AATAAAGCAAGTT-CTAAAGTTTCTTACCCAGTAAACTATTTTTGAAATTGGTAAGTCCTTCGGG
65 AAGAAAGCGA-TTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGG
* * * * * *
5375706 CCATCAATAAGTCTTTCCAGCATGATGATTAAATCATTCGGATCATCTGTAAGTCTTTCGACCAA
129 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAA
* * *
5375771 GATGATAAGTCGTTTGGGCCATCCGT---ACCTTCAGGTAGGATGTTTTCACATG
194 GATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
* ** * ****
5375823 AATGAGAAAACGAAGTCCAAAGTTTCTCATTTAATGTTTTCAG---ATTTTTTTTTTGAAAAGTA
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
* * * *
5375885 AGAAAGCGATTACCAAAGTTTCTTACCGAGTAAATTATTTACCAAATTGGTAAGTTCTTCGGGCC
66 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCC
* * * * * *
5375950 ATCACTAAGTCTTTCGAGCATGATTATAAAATCCTTTGGGTTATCTGTAAGTCTTTCGAGCAAGA
131 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
* * *
5376015 TGATAAGTCCTTCGGGTCATCCGTAAGACCTTTGGGTAGAAT-TTTTCACATG
196 TGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
* * *
5376067 AACGAGAAAGTGATGTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTTGAAAAGT
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAA-TTTTTGAAAAGT
* * * *
5376132 AAGAAAGCGATTACAAAAGTTTCTTACCCAATAAACTATTTCCCAAATTAGTAAGTCATTCGGGC
65 AAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGC
* *
5376197 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATTTATAAGTCTTTCGAGCAAG
130 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
* * * *
5376262 ATGATAAGTCATTCGGTCCATTCGTAAGACCTTCGGGTAGGATGTTTTCACATT
195 ATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
*
5376316 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTA
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
* * * *
5376381 A-AAAGTGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAATCATTCGAGCC
66 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCC
* *
5376445 ATCAGTAAGTCTTTCGAGCATGATGATTAAATTCTTTGGGTCATCTATAAGTCTTTCGAGCAAGA
131 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
5376510 TGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
196 TGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
**
5376563 AATGAGAAAGAAATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
* * *
5376628 AGAAAGCGATTACAAAAGTTTCTTACCTAGTAAACTATGTCCCAAATTGGTAAGTCCTTCGGGCC
66 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCC
* ** *
5376693 ATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTCATCTGTAAGTCTTTCGAGCAAGA
131 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
* *
5376758 TGATATGTCCTTCGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTTCACATG
196 TGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
* * * *
5376811 AATGTGAAAGCGATTTCCAAAGTTTCTTGTTTAATGTTTTCAAAAAATGAAATTTTTCAAAAGTA
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
* * * *
5376876 AGAAAGCGATTACCAAAGTTTCTTACACAGTAAATTATTTCTCGAATTGGTAAGTCCTTCGAGCC
66 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCC-T------
* * *
5376941 ATCAATAAGTCTTGGCCATCGGTAAGTCTTTCGAACATGATGATTAAATCATTCGGGTCATCTAT
124 -TC-----G----GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTAT
* * * *
5377006 AAGTGTTTCGAGCAAGATGATATGTCCTTCGGGCCATCCGTAAGTCCTTCGGCTAGGATGTTTTC
179 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTC
5377071 ACATG
244 ACATG
* * * *
5377076 AATGAGAAAGCAATTTCTAAAGTTTCTCGTTTAATGTTTTCAAAAAATGAAAATTTTGAAAAGTA
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
* * *
5377141 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTTCGAAATTGGTAAGTCCTTTGGGCC
66 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCC
* * *
5377206 ATCAGTAAGTCTTTCGAACATGAAGATTAAATCCTTCGGGTCATCTATAAGTATTTCGAGCAAGA
131 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
* * * *
5377271 TGATAAGTCCTTTGGGTCATCCGTAAGACCTCCGGGTAGGATATTTTCACATG
196 TGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
* * *
5377324 AATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATGTTTTTAGAAAATGAAATTTTTGAAAAGTA
1 AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
* * * *
5377389 AGAAAGCGATTTCAAAAGTTTCTTATCCAGTAAACTATTTCCAAAATTG
66 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG
5377438 ATCTAACTAC
Statistics
Matches: 1430, Mismatches: 157, Indels: 53
0.87 0.10 0.03
Matches are distributed among these distances:
241 2 0.00
242 145 0.10
244 48 0.03
245 49 0.03
247 232 0.16
248 669 0.47
249 58 0.04
252 1 0.00
256 2 0.00
257 1 0.00
261 1 0.00
264 1 0.00
265 221 0.15
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (248 bp):
AATGAGAAAGCGATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCC
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
TGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATG
Found at i:5376621 original size:495 final size:496
Alignment explanation
Indices: 5375590--5377437 Score: 2509
Period size: 513 Copynumber: 3.7 Consensus size: 496
5375580 TGAAAAAGTG
* * * *
5375590 ATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAAT-AAATTTTTTGAAAAGTAATAAAGCAAGT
1 ATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTTGAAAAGTAAGAAAGCGA-T
* *** *
5375654 T-CTAAAGTTTCTTACCCAGTAAACTATTTTTGAAATTGGTAAGTCCTTCGGGCCATCAATAAGT
65 TACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCCATCAGTAAGT
* * * *
5375718 CTTTCCAGCATGATGATTAAATCATTC-GGATCATCTGTAAGTCTTTCGACCAAGATGATAAGTC
130 CTTTCGAGCATGATGATTAAATCCTTCAGG-TCATCTATAAGTCTTTCGAGCAAGATGATAAGTC
* * * * **
5375782 GTTTGGGCCATCCGT---ACCTTCAGGTAGGATGTTTTCACATGAATGAGAAAACGAAGTCCAAA
194 ATTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGCGATTTCCAAA
****
5375844 GTTTCTCATTTAATGTTTTCAG---ATTTTTTTTTTGAAAAGTAAGAAAGCGATTACCAAAGTTT
259 GTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTACCAAAGTTT
* * * * * *
5375906 CTTACCGAGTAAATTATTTACCAAATTGGTAAGTTCTTCGGGCCATCACTAAGTCTTTCGAGCAT
324 CTTACCCAGTAAACTATTTCCCAAATTGGTAA-ATCTTCGAGCCATCAGTAAGTCTTTCGAGCAT
* * * * * *
5375971 GATTATAAAATCCTTTGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATC
388 GATGATTAAATTCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* * * **
5376036 CGTAAGACCTTTGGGTAGAAT-TTTTCACATGAACGAGAAAGTG
453 CGTAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGAA
*
5376079 ATGTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTTGAAAAGTAAGAAAGCGATT
1 ATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTTGAAAAGTAAGAAAGCGATT
* * *
5376144 ACAAAAGTTTCTTACCCAATAAACTATTTCCCAAATTAGTAAGTCATTCGGGCCATCAGTAAGTC
66 ACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC
*
5376209 TTTCGAGCATGATGATTAAATCCTTCAGGTCATTTATAAGTCTTTCGAGCAAGATGATAAGTCAT
131 TTTCGAGCATGATGATTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCAT
* * *
5376274 TCGGTCCATTCGTAAGACCTTCGGGTAGGATGTTTTCACATTAATGAGAAAGCGATTTCCAAAGT
196 TCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGCGATTTCCAAAGT
* * *
5376339 TTCTCGTTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAA-AAAGTGATTACCAAAGTTTCT
261 TTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTACCAAAGTTTCT
5376403 TACCCAGTAAACTATTTCCCAAATTGGTAAATCATTCGAGCCATCAGTAAGTCTTTCGAGCATGA
326 TACCCAGTAAACTATTTCCCAAATTGGTAAATC-TTCGAGCCATCAGTAAGTCTTTCGAGCATGA
5376468 TGATTAAATTCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCG
390 TGATTAAATTCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCG
5376533 TAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGAA
455 TAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGAA
5376575 ATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAA-TTTTTGAAAAGTAAGAAAGCGATT
1 ATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTTGAAAAGTAAGAAAGCGATT
* * *
5376639 ACAAAAGTTTCTTACCTAGTAAACTATGTCCCAAATTGGTAAGTCCTTCGGGCCATTAGTAAGTC
66 ACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC
* * * *
5376704 TTTCGAGCATGATGATTAAATCCTTTAGGTCATCTGTAAGTCTTTCGAGCAAGATGATATGTCCT
131 TTTCGAGCATGATGATTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCAT
* *
5376769 TCGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTTCACATGAATGTGAAAGCGATTTCCAAAGT
196 TCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGCGATTTCCAAAGT
** * *
5376834 TTCTTGTTTAATGTTTTCAAAAAATGAAATTTTTCAAAAGTAAGAAAGCGATTACCAAAGTTTCT
261 TTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTACCAAAGTTTCT
* * * * *
5376899 TACACAGTAAATTATTTCTCGAATTGGTAAGTCCTTCGAGCCATCAATAAGTCTTGGCCATCGGT
326 TACCCAGTAAACTATTTCCCAAATTGGTAAAT-CTTCGAG-C--C----A----T---CA---GT
* * *
5376964 AAGTCTTTCGAACATGATGATTAAA-TCATTCGGGTCATCTATAAGTGTTTCGAGCAAGATGATA
373 AAGTCTTTCGAGCATGATGATTAAATTC-TTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATA
* * * *
5377028 TGTCCTTCGGGCCATCCGTAAGTCCTTCGGCTAGGATGTTTTCACATGAATGAGAAAGCA
437 AGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGAA
* * *
5377088 ATTTCTAAAGTTTCTCGTTTAATGTTTTCAAAAAATGAAA-ATTTTGAAAAGTAAGAAAGCGATT
1 ATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTTGAAAAGTAAGAAAGCGATT
* * * *
5377152 ACCAAAGTTTCTTACCCAGTAAACTATTTTCGAAATTGGTAAGTCCTTTGGGCCATCAGTAAGTC
66 ACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC
* * * * *
5377217 TTTCGAACATGAAGATTAAATCCTTCGGGTCATCTATAAGTATTTCGAGCAAGATGATAAGTCCT
131 TTTCGAGCATGATGATTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCAT
* * * * *
5377282 TTGGGTCATCCGTAAGACCTCCGGGTAGGATATTTTCACATGAATGAGAAAGCAATTTCCAAAGT
196 TCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGCGATTTCCAAAGT
* * *
5377347 TTCTCATTTAATGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCAAAAGTTTCT
261 TTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTACCAAAGTTTCT
* *
5377412 TATCCAGTAAACTATTTCCAAAATTG
326 TACCCAGTAAACTATTTCCCAAATTG
5377438 ATCTAACTAC
Statistics
Matches: 1206, Mismatches: 122, Indels: 38
0.88 0.09 0.03
Matches are distributed among these distances:
489 35 0.03
490 146 0.12
491 2 0.00
493 62 0.05
494 2 0.00
495 394 0.33
496 127 0.11
497 2 0.00
499 1 0.00
503 1 0.00
507 1 0.00
510 2 0.00
512 2 0.00
513 429 0.36
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (496 bp):
ATTTCCAAAGTTTCTCGTTTAATGTTTTCAGAAAATGAAATTTTTTGAAAAGTAAGAAAGCGATT
ACAAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC
TTTCGAGCATGATGATTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCAT
TCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGCGATTTCCAAAGT
TTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTACCAAAGTTTCT
TACCCAGTAAACTATTTCCCAAATTGGTAAATCTTCGAGCCATCAGTAAGTCTTTCGAGCATGAT
GATTAAATTCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGT
AAGACCTTCGGGTAGGATGTTTTCACATGAATGAGAAAGAA
Found at i:5376784 original size:41 final size:42
Alignment explanation
Indices: 5376678--5376784 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
5376668 CCCAAATTGG
* *
5376678 TAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGAT
* ** * *
5376720 TAAATCCTTTAGGTCATCTGTAAGTCTTTCGAGCAAGATGA-
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGAT
* *
5376761 TATGTCCTTCGGGCCATCCGTAAG
1 TAAGTCCTTCGGGCCATCAGTAAG
5376785 ACCTTTGGGT
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGAT
Found at i:5377050 original size:41 final size:42
Alignment explanation
Indices: 5376954--5377056 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 42
5376944 AATAAGTCTT
* *
5376954 GGCCATCGGTAAGTCTTTCGAACATGATGATTAAATCATTCG
1 GGCCATCCGTAAGTCTTTCGAACAAGATGATTAAATCATTCG
* ** * * ** *
5376996 GGTCATCTATAAGTGTTTCGAGCAAGATGA-TATGTCCTTCG
1 GGCCATCCGTAAGTCTTTCGAACAAGATGATTAAATCATTCG
*
5377037 GGCCATCCGTAAGTCCTTCG
1 GGCCATCCGTAAGTCTTTCG
5377057 GCTAGGATGT
Statistics
Matches: 47, Mismatches: 14, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
41 23 0.49
42 24 0.51
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
GGCCATCCGTAAGTCTTTCGAACAAGATGATTAAATCATTCG
Found at i:5377289 original size:41 final size:42
Alignment explanation
Indices: 5377191--5377297 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
5377181 TCGAAATTGG
* * *
5377191 TAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAACATGAAGAT
1 TAAGTCCTTTGGGTCATCAGTAAGTATTTCGAACAAGAAGAT
* * * *
5377233 TAAATCCTTCGGGTCATCTA-TAAGTATTTCGAGCAAGATGA-
1 TAAGTCCTTTGGGTCATC-AGTAAGTATTTCGAACAAGAAGAT
*
5377274 TAAGTCCTTTGGGTCATCCGTAAG
1 TAAGTCCTTTGGGTCATCAGTAAG
5377298 ACCTCCGGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAGTCCTTTGGGTCATCAGTAAGTATTTCGAACAAGAAGAT
Found at i:5377629 original size:3 final size:3
Alignment explanation
Indices: 5377621--5377686 Score: 100
Period size: 3 Copynumber: 22.3 Consensus size: 3
5377611 TTTCGTCCCG
5377621 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
*
5377667 ATT A-T AAT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
5377687 CAGAACCAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5382064 original size:57 final size:54
Alignment explanation
Indices: 5381984--5382101 Score: 148
Period size: 57 Copynumber: 2.1 Consensus size: 54
5381974 AATCTAAATA
* *
5381984 TATTAATATTTTAAAATAATTAAAATAATATATTTTATAATAATATGTTTATAAATTTT
1 TATT-ATATTTTAAAATAATTAAAATAATATATTTGACAATAAT-T-TTTAT--ATTTT
**
5382043 TATTATATTTT-AAATGGTTAAAATAATATATTTGACAATAATTTTTATATTTT
1 TATTATATTTTAAAATAATTAAAATAATATATTTGACAATAATTTTTATATTTT
5382096 TATTAT
1 TATTAT
5382102 TAAATAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
53 11 0.20
55 5 0.09
56 1 0.02
57 27 0.49
58 7 0.13
59 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (54 bp):
TATTATATTTTAAAATAATTAAAATAATATATTTGACAATAATTTTTATATTTT
Found at i:5384238 original size:2 final size:2
Alignment explanation
Indices: 5384231--5384349 Score: 238
Period size: 2 Copynumber: 59.5 Consensus size: 2
5384221 ATTTATAGAA
5384231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5384273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5384315 AT AT AT AT 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 AT AT AT AT A
5384350 GGTTGTTAAA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 117 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5387174 original size:24 final size:24
Alignment explanation
Indices: 5387125--5387197 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
5387115 AGCAATTTAA
5387125 TTTAATTTTTG-ATATTTTTATA-
1 TTTAATTTTTGAATATTTTTATAT
5387147 TTTAATTTTTGAATATTTTTATAT
1 TTTAATTTTTGAATATTTTTATAT
** * *
5387171 TTTAAACTATAAATATTTTTATAT
1 TTTAATTTTTGAATATTTTTATAT
5387195 TTT
1 TTT
5387198 TTTCTAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.24
23 11 0.24
24 23 0.51
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (24 bp):
TTTAATTTTTGAATATTTTTATAT
Found at i:5387711 original size:21 final size:22
Alignment explanation
Indices: 5387667--5387711 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5387657 TATTATCACC
5387667 AAATAATGTTTAGTTGACAATTT
1 AAATAATGTTTAGTTGA-AATTT
* *
5387690 AAATAATTTTTATTTG-AATTT
1 AAATAATGTTTAGTTGAAATTT
5387711 A
1 A
5387712 TAGATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
23 14 0.70
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
AAATAATGTTTAGTTGAAATTT
Found at i:5387840 original size:19 final size:19
Alignment explanation
Indices: 5387816--5387852 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5387806 TTCTAATGGA
5387816 TTTTAATACTTAAAAGTTT
1 TTTTAATACTTAAAAGTTT
5387835 TTTTAATACTTAAAAGTT
1 TTTTAATACTTAAAAGTT
5387853 GAATGTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTTAATACTTAAAAGTTT
Found at i:5388500 original size:23 final size:23
Alignment explanation
Indices: 5388467--5388511 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5388457 CACAAACGAA
* *
5388467 CAAACATAATAAATGAACATAAG
1 CAAACACAATAAACGAACATAAG
5388490 CAAACACAATAAACGAACATAA
1 CAAACACAATAAACGAACATAA
5388512 ATTTACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.18, G:0.07, T:0.13
Consensus pattern (23 bp):
CAAACACAATAAACGAACATAAG
Found at i:5391231 original size:76 final size:76
Alignment explanation
Indices: 5391105--5391252 Score: 242
Period size: 76 Copynumber: 1.9 Consensus size: 76
5391095 AGTGAAAGCA
* * *
5391105 GCATCTCCATATGAATTCAGAAAATATCAATGTTGAGGTAAATTCATTGTGATTAGTTGAAAGAT
1 GCATCTCCATATGAATTCAGAAAATATCAATATTGAGGTAAATTCATTGTGATTAATTGAAAGAG
5391170 TTATGTAAGTG
66 TTATGTAAGTG
* * *
5391181 GCATCTCTATATGAATTCAGAAAATATGAATATTGAGGTACATTCATTGTGATTAATTGAAAGAG
1 GCATCTCCATATGAATTCAGAAAATATCAATATTGAGGTAAATTCATTGTGATTAATTGAAAGAG
5391246 TTATGTA
66 TTATGTA
5391253 TGTTTAGTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (76 bp):
GCATCTCCATATGAATTCAGAAAATATCAATATTGAGGTAAATTCATTGTGATTAATTGAAAGAG
TTATGTAAGTG
Found at i:5392060 original size:19 final size:19
Alignment explanation
Indices: 5392036--5392097 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
5392026 AAATATCAAG
5392036 TTAAAATTTA-GCATCAAAA
1 TTAAAATTTACG-ATCAAAA
* * *
5392055 TTAAAATTAATGATCAATA
1 TTAAAATTTACGATCAAAA
5392074 TTAAAATTTACGTATCAAAA
1 TTAAAATTTACG-ATCAAAA
5392094 TTAA
1 TTAA
5392098 TATTATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 25 0.69
20 11 0.31
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (19 bp):
TTAAAATTTACGATCAAAA
Found at i:5392988 original size:19 final size:18
Alignment explanation
Indices: 5392929--5392988 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
5392919 AACAAATTAA
5392929 ATTATTTAA-ATTAAATAGT
1 ATTATTTAATA-TAAATA-T
* *
5392948 ATT-TTTAATAAAAAAAT
1 ATTATTTAATATAAATAT
5392965 CATTATTTAATTATAAATAT
1 -ATTATTTAA-TATAAATAT
5392985 ATTA
1 ATTA
5392989 AAAGTAGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 1 0.03
18 12 0.36
19 13 0.39
20 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTATTTAATATAAATAT
Found at i:5393719 original size:28 final size:27
Alignment explanation
Indices: 5393662--5393722 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
5393652 AAATATGATA
*
5393662 AAAATATAAGAGTTTGTTTAGTTTTAG
1 AAAATATAAGAGTTTATTTAGTTTTAG
* *
5393689 AAAATATAAGCTATTTTATTTA-TTTTTG
1 AAAATATAAG--AGTTTATTTAGTTTTAG
5393717 AAAATA
1 AAAATA
5393723 AAAATGTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 10 0.34
28 11 0.38
29 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (27 bp):
AAAATATAAGAGTTTATTTAGTTTTAG
Found at i:5400256 original size:15 final size:15
Alignment explanation
Indices: 5400236--5400270 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5400226 TATTGGTACT
*
5400236 ATACTCACAGTATTG
1 ATACTCACAGTATCG
5400251 ATACTCACAGTATCG
1 ATACTCACAGTATCG
5400266 ATACT
1 ATACT
5400271 GTAAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (15 bp):
ATACTCACAGTATCG
Found at i:5400823 original size:21 final size:21
Alignment explanation
Indices: 5400799--5400851 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5400789 ATTCAGACTA
*
5400799 TCGCATTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
5400820 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
5400841 TCGCAATGCGA
1 TCGCATTGCGA
5400852 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:5400870 original size:20 final size:20
Alignment explanation
Indices: 5400841--5400973 Score: 194
Period size: 20 Copynumber: 6.7 Consensus size: 20
5400831 TTTTCCTAAT
5400841 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
5400861 TCGCATTGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
5400881 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
5400901 TTGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
5400921 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
5400941 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
5400961 TCGTAACGCGAAT
1 TCGCAATGCGAAT
5400974 CTGACTATCG
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 100 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:5400991 original size:20 final size:20
Alignment explanation
Indices: 5400841--5400991 Score: 160
Period size: 20 Copynumber: 7.5 Consensus size: 20
5400831 TTTTCCTAAT
*
5400841 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATATGTAAA
* *
5400861 TCGCATTGCGAATACGTAAA
1 TCGCAATGCGAATATGTAAA
* *
5400881 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATATGTAAA
* * *
5400901 TTGCAATACGAATACGTAAA
1 TCGCAATGCGAATATGTAAA
* *
5400921 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATATGTAAA
5400941 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
* * * *
5400961 TCGTAACGCGAATCTG-ACTA
1 TCGCAATGCGAATATGTA-AA
5400981 TCGCAATGCGA
1 TCGCAATGCGA
5400992 TTTACATAGC
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
19 1 0.01
20 112 0.99
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:5401158 original size:21 final size:21
Alignment explanation
Indices: 5401092--5401170 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 21
5401082 CAGTATATCC
5401092 CGTTCAAGAGGCCCCTATCAT
1 CGTTCAAGAGGCCCCTATCAT
** * ** *
5401113 CCCTCAAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCAT
* *
5401134 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCCCTATCAT
* *
5401155 CGTTGAAGAGGTCCCT
1 CGTTCAAGAGGCCCCT
5401171 CCCAACATTC
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTATCAT
Found at i:5401164 original size:42 final size:42
Alignment explanation
Indices: 5401091--5401174 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
5401081 ACAGTATATC
*
5401091 CCGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCA
1 CCGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCA
* ** *
5401133 CCGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CCGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
5401175 ACATTCTAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.21, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CCGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
Found at i:5402251 original size:14 final size:14
Alignment explanation
Indices: 5402232--5402285 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
5402222 GGAAATGACT
5402232 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
5402246 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
5402265 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
5402279 ATCGCAA
1 ATCGCAA
5402286 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:5402300 original size:34 final size:33
Alignment explanation
Indices: 5402223--5402307 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
5402213 TCGTAACGCG
**
5402223 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
5402256 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
5402289 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
5402308 CGAAACTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 32 0.65
34 17 0.35
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:5402303 original size:20 final size:19
Alignment explanation
Indices: 5402245--5402312 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
5402235 GCAACGAGAG
5402245 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5402264 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5402278 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
5402298 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
5402313 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5402383 original size:33 final size:34
Alignment explanation
Indices: 5402322--5402397 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
5402312 ACTAAATTCG
*
5402322 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
*
5402356 CGTTGCGATTTTTATTTT-GCATTGCGATTATCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
5402389 CGTTGCGAT
1 CGTTGCGAT
5402398 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 23 0.57
34 17 0.43
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
Found at i:5402414 original size:20 final size:20
Alignment explanation
Indices: 5402389--5402482 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
5402379 GCGATTATCT
5402389 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
5402409 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
5402429 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
5402449 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
5402469 CGTTGTGATAGTCA
1 CGTTGCGATAGTCA
5402483 AATGAATGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
20 66 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:5404931 original size:24 final size:24
Alignment explanation
Indices: 5404897--5404950 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5404887 CTGAAAAATC
5404897 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
5404921 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
5404945 ATCAAA
1 ATCAAA
5404951 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5405817 original size:20 final size:20
Alignment explanation
Indices: 5405792--5405858 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
5405782 AAATTCAGTA
5405792 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
**
5405812 TTGCGATAGTTGGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
5405832 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
5405852 TTGCGAT
1 TTGCGAT
5405859 TTACATATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:5405868 original size:20 final size:20
Alignment explanation
Indices: 5405845--5405975 Score: 235
Period size: 20 Copynumber: 6.5 Consensus size: 20
5405835 CGATAGTCAG
* *
5405845 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
5405865 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5405885 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5405905 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
5405925 ATGCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5405945 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5405965 ATTCGCATTGC
1 ATTCGCATTGC
5405976 AAATTAGGAA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 107 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:5406001 original size:21 final size:21
Alignment explanation
Indices: 5405977--5406019 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5405967 TCGCATTGCA
5405977 AATTAGGAAAATCGCAACGCG
1 AATTAGGAAAATCGCAACGCG
* *
5405998 AATTTGGAAAATCGCAATGCG
1 AATTAGGAAAATCGCAACGCG
5406019 A
1 A
5406020 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (21 bp):
AATTAGGAAAATCGCAACGCG
Found at i:5408440 original size:185 final size:182
Alignment explanation
Indices: 5408160--5408547 Score: 570
Period size: 185 Copynumber: 2.1 Consensus size: 182
5408150 ATTAAATTTT
*
5408160 AAATATTAAATATATTATATAACATATGAGCTCAGACCAAACTATTTAAAACTCAATTAATAATT
1 AAATATTAAATATATTATATAACATATGAGCTCAGACCAAACCATTTAAAACTCAATTAATAATT
*
5408225 TAAGATCTAATAACTTCTAAACCTAAATCAATATTAATTAATTAAAAATTTTATAT-AAATTTTT
66 TAAGATCTAATAACTTCTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATGAAA-TTTT
*
5408289 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTGCTTTTTT-AATTAAA
130 TATTTTATAATTATATATTATTTAAATTAATTATAAACT--TTTTTTGAATTAAA
* * *
5408343 AAATATTATATATATTATATATAATATATGAGCTCAGCCCAAACCATTTAAAAC-CTAATTAATA
1 AAATATTAAATATA-T-TATATAACATATGAGCTCAGACCAAACCATTTAAAACTC-AATTAATA
* * *
5408407 ATTTAAGAT-TAAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTGAAAT
63 ATTTAAGATCT-AATAACTTCTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATGAAAT
5408471 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
127 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* * *
5408527 AAACATTTAAT-TCTTATATAA
1 AAATATTAAATATATTATATAA
5408548 ATTAGAAAAT
Statistics
Matches: 186, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
181 7 0.04
182 1 0.01
183 20 0.11
184 18 0.10
185 137 0.74
186 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (182 bp):
AAATATTAAATATATTATATAACATATGAGCTCAGACCAAACCATTTAAAACTCAATTAATAATT
TAAGATCTAATAACTTCTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATGAAATTTTT
ATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:5422692 original size:13 final size:12
Alignment explanation
Indices: 5422676--5422722 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5422666 GAAAAAATAG
5422676 ATTGAAACAAGAA
1 ATTGAAACAA-AA
*
5422689 ATTGAAATAAAA
1 ATTGAAACAAAA
* *
5422701 ATCGAATCAAAA
1 ATTGAAACAAAA
5422713 ATT-AAACAAA
1 ATTGAAACAAA
5422723 GTCCATACAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 6 0.21
12 13 0.46
13 9 0.32
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.19
Consensus pattern (12 bp):
ATTGAAACAAAA
Found at i:5428087 original size:23 final size:23
Alignment explanation
Indices: 5428050--5428097 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5428040 CTATTTATTA
*
5428050 AAAATGTATAAATTTCATATGAT
1 AAAATGTATAAATTTAATATGAT
*
5428073 AAAAT-TATAATATTTAATGTGAT
1 AAAATGTATAA-ATTTAATATGAT
5428096 AA
1 AA
5428098 TGATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (23 bp):
AAAATGTATAAATTTAATATGAT
Found at i:5428580 original size:31 final size:31
Alignment explanation
Indices: 5428529--5428602 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
5428519 GGTATGTCTA
* * *
5428529 ATTTAAGTCCCTAACTTTATCAGTCCGTTCG
1 ATTTTAGTCCCTAACGTTATCAGTCCATTCG
* *
5428560 ATTTTAGTCTCTAACGTTATCGGTCCATTCG
1 ATTTTAGTCCCTAACGTTATCAGTCCATTCG
5428591 ATTTTAGTCCCT
1 ATTTTAGTCCCT
5428603 CAACCATGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (31 bp):
ATTTTAGTCCCTAACGTTATCAGTCCATTCG
Found at i:5437806 original size:31 final size:32
Alignment explanation
Indices: 5437768--5437828 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
5437758 TACAACAAAC
5437768 TTACAAT-A-AGTATTAAATGGTAAATAAAAAA
1 TTACAATAACAGTATTAAATGGT-AATAAAAAA
5437799 TTACAATAACTAGTATTAAATGGTAATAAA
1 TTACAATAAC-AGTATTAAATGGTAATAAA
5437829 CAAAGTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 7 0.26
32 1 0.04
33 6 0.22
34 13 0.48
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (32 bp):
TTACAATAACAGTATTAAATGGTAATAAAAAA
Found at i:5437922 original size:12 final size:13
Alignment explanation
Indices: 5437901--5437944 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5437891 AATGATAAAT
*
5437901 AATAAAAAAATAC
1 AATAAAAAAGTAC
*
5437914 AATAAAAAAGTCC
1 AATAAAAAAGTAC
*
5437927 AATAAACAAGTA-
1 AATAAAAAAGTAC
5437939 AATAAA
1 AATAAA
5437945 GATATTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (13 bp):
AATAAAAAAGTAC
Found at i:5440205 original size:20 final size:20
Alignment explanation
Indices: 5440180--5440219 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5440170 AATATACCTT
* *
5440180 AAGTTGGGAGGATTTGAGAG
1 AAGTTGAGAGGATTTAAGAG
*
5440200 AAGTTGAGATGATTTAAGAG
1 AAGTTGAGAGGATTTAAGAG
5440220 GATTTGGTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.28
Consensus pattern (20 bp):
AAGTTGAGAGGATTTAAGAG
Found at i:5448550 original size:268 final size:268
Alignment explanation
Indices: 5448068--5448609 Score: 1057
Period size: 268 Copynumber: 2.0 Consensus size: 268
5448058 CCGGGTCCTC
*
5448068 AGTTATCTTATCCCCATGAAGTCTAACATTGTAATGCAAAATTATTGGTGGATCAGGCTCCCCTG
1 AGTTTTCTTATCCCCATGAAGTCTAACATTGTAATGCAAAATTATTGGTGGATCAGGCTCCCCTG
*
5448133 GAAGTGTTTCCCCTGTTAAATCAATGTGAAAATCACCAAGAACACCATTTGTAACGCCAATGATT
66 GAAGTGTTTCCCCTGTTAAATCAATGCGAAAATCACCAAGAACACCATTTGTAACGCCAATGATT
5448198 GTAATGGAAGAACCTTGAGTGAGACCACAGGGAACTCTCAACTTGTAGTGACTCTCAGGTTCTGT
131 GTAATGGAAGAACCTTGAGTGAGACCACAGGGAACTCTCAACTTGTAGTGACTCTCAGGTTCTGT
*
5448263 AGCATTCATTTTATTAATAAACTGCGAACTCTGCTCTTTTGATCTTCCAGATGAATTATCATTCC
196 AGCATTCATTTTATTAATAAACTGCGAACACTGCTCTTTTGATCTTCCAGATGAATTATCATTCC
5448328 GATAACCA
261 GATAACCA
5448336 AGTTTTCTTATCCCCATGAAGTCTAACATTGTAATGCAAAATTATTGGTGGATCAGGCTCCCCTG
1 AGTTTTCTTATCCCCATGAAGTCTAACATTGTAATGCAAAATTATTGGTGGATCAGGCTCCCCTG
5448401 GAAGTGTTTCCCCTGTTAAATCAATGCGAAAATCACCAAGAACACCATTTGTAACGCCAATGATT
66 GAAGTGTTTCCCCTGTTAAATCAATGCGAAAATCACCAAGAACACCATTTGTAACGCCAATGATT
5448466 GTAATGGAAGAACCTTGAGTGAGACCACAGGGAACTCTCAACTTGTAGTGACTCTCAGGTTCTGT
131 GTAATGGAAGAACCTTGAGTGAGACCACAGGGAACTCTCAACTTGTAGTGACTCTCAGGTTCTGT
5448531 AGCATTCATTTTATTAATAAACTGCGAACACTGCTCTTTTGATCTTCCAGATGAATTATCATTCC
196 AGCATTCATTTTATTAATAAACTGCGAACACTGCTCTTTTGATCTTCCAGATGAATTATCATTCC
5448596 GATAACCA
261 GATAACCA
5448604 AGTTTT
1 AGTTTT
5448610 TCCTCTTCGA
Statistics
Matches: 271, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
268 271 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (268 bp):
AGTTTTCTTATCCCCATGAAGTCTAACATTGTAATGCAAAATTATTGGTGGATCAGGCTCCCCTG
GAAGTGTTTCCCCTGTTAAATCAATGCGAAAATCACCAAGAACACCATTTGTAACGCCAATGATT
GTAATGGAAGAACCTTGAGTGAGACCACAGGGAACTCTCAACTTGTAGTGACTCTCAGGTTCTGT
AGCATTCATTTTATTAATAAACTGCGAACACTGCTCTTTTGATCTTCCAGATGAATTATCATTCC
GATAACCA
Found at i:5455035 original size:16 final size:17
Alignment explanation
Indices: 5455010--5455043 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5455000 TCGAGGTGTC
5455010 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
5455026 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
5455043 A
1 A
5455044 GAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:5455419 original size:2 final size:2
Alignment explanation
Indices: 5455412--5455478 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
5455402 TCATATAGCC
5455412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5455454 AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5455479 GCATATTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5455832 original size:21 final size:21
Alignment explanation
Indices: 5455800--5455882 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
5455790 ATAGAATTTG
*
5455800 TCCCAAAGGACCACATATATA
1 TCCCAAATGACCACATATATA
* * *
5455821 TCCCGAATGACCACATAGAAA
1 TCCCAAATGACCACATATATA
* *
5455842 TCTCCTTAAGGACCACATATATA
1 TC-CC-AAATGACCACATATATA
* *
5455865 TTCCAAATGACCAAATAT
1 TCCCAAATGACCACATAT
5455883 GTGTCTCGAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 30 0.62
22 4 0.08
23 14 0.29
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.23
Consensus pattern (21 bp):
TCCCAAATGACCACATATATA
Found at i:5456474 original size:22 final size:22
Alignment explanation
Indices: 5456446--5456487 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5456436 CCACATACTC
*
5456446 ATATTCAAGTACTCATGCACTT
1 ATATTCAAGTACTCAGGCACTT
5456468 ATATTCAAGTACTCAGGCAC
1 ATATTCAAGTACTCAGGCAC
5456488 ACATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (22 bp):
ATATTCAAGTACTCAGGCACTT
Found at i:5456863 original size:20 final size:22
Alignment explanation
Indices: 5456824--5456865 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5456814 TCTTACTATA
5456824 GTATCGATACTATCCTCTTATG
1 GTATCGATACTATCCTCTTATG
5456846 GTATCGATACT-T-CTCTTATG
1 GTATCGATACTATCCTCTTATG
5456866 TACCAATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (22 bp):
GTATCGATACTATCCTCTTATG
Found at i:5466247 original size:2 final size:2
Alignment explanation
Indices: 5466240--5466267 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5466230 ATTATCACAA
5466240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5466268 CAGTATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5467620 original size:219 final size:218
Alignment explanation
Indices: 5467240--5467678 Score: 835
Period size: 219 Copynumber: 2.0 Consensus size: 218
5467230 ACTTAGGTTA
5467240 GTTTATTACAGAGAAGAGCTCGACTTTAGAGTTTCAGCTTAGAGAAGTACGGTTATAGTCTAGGG
1 GTTTATTACAGAGAAGAGCTCGACTTTAGAGTTTCAGCTTAGAGAAGTACGGTTATAG-CTAGGG
5467305 GCATGTACTAACGAGACATCCTATGACATTCAATCGGTCGGTCTACCCAAAAAACTTGACTCAAC
65 GCATGTACTAACGAGACATCCTATGACATTCAATCGGTCGGTCTACCCAAAAAACTTGACTCAAC
*
5467370 CTAAGCTCTGATACCACTAAATGTAACACCTACATACCGATGCGGGTGACCCGATCCGATCTGAG
130 CTAAGCTCTGATACCACTAAATGTAACACCTACATACCGATGCGGGTGACCCGATCCGATCCGAG
5467435 GTGTCTATATTAGGGCTACCAGAGC
195 GTGTC-ATATTAGGGCTACCAGAGC
5467460 GTTTATTACAGAGAAGAGCTCGACTTTAGAGTTTCAGCTTAGAGAAGTACGGTTATAG-TAGGGG
1 GTTTATTACAGAGAAGAGCTCGACTTTAGAGTTTCAGCTTAGAGAAGTACGGTTATAGCTAGGGG
5467524 CATGTACTAACGAGACATCCTATGACATTCAAATCGGTCGGTCTACCCAAAAAACTTGACTCAAC
66 CATGTACTAACGAGACATCCTATGACATTC-AATCGGTCGGTCTACCCAAAAAACTTGACTCAAC
5467589 CTAAGCTCTGATACCACTAAATGTAACACCTACATACCGATGCGGGTGACCCGATCCGATCCGAG
130 CTAAGCTCTGATACCACTAAATGTAACACCTACATACCGATGCGGGTGACCCGATCCGATCCGAG
5467654 GTGTCATATTAGGGCTACCAGAGC
195 GTGTCATATTAGGGCTACCAGAGC
5467678 G
1 G
5467679 ACCCACAGTA
Statistics
Matches: 217, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
218 56 0.26
219 103 0.47
220 58 0.27
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (218 bp):
GTTTATTACAGAGAAGAGCTCGACTTTAGAGTTTCAGCTTAGAGAAGTACGGTTATAGCTAGGGG
CATGTACTAACGAGACATCCTATGACATTCAATCGGTCGGTCTACCCAAAAAACTTGACTCAACC
TAAGCTCTGATACCACTAAATGTAACACCTACATACCGATGCGGGTGACCCGATCCGATCCGAGG
TGTCATATTAGGGCTACCAGAGC
Found at i:5470342 original size:22 final size:22
Alignment explanation
Indices: 5470314--5470362 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5470304 GACTTTTTTT
* * *
5470314 GTCAAAGTTAATGGTTAGACCG
1 GTCAAAGTCAACGGTCAGACCG
5470336 GTCAAAGTCAACGGTCAGACCG
1 GTCAAAGTCAACGGTCAGACCG
*
5470358 ATCAA
1 GTCAA
5470363 GGGTCGGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCAGACCG
Found at i:5472654 original size:103 final size:103
Alignment explanation
Indices: 5472429--5472646 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
5472419 GTAGAGGGTC
*
5472429 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
*
5472494 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
5472532 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATATGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
*
5472597 TTGATCCTTGGCATATGTATATGATTTTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
5472635 TATGTGGTCCTT
1 TATGTGGTCCTT
5472647 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:5472700 original size:23 final size:23
Alignment explanation
Indices: 5472663--5472725 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
5472653 ATTATTATAT
*
5472663 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
5472686 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
**
5472709 GGCACTTAGGTGCAATT
1 GGCACTCCGGTGCAATT
5472726 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:5478685 original size:20 final size:20
Alignment explanation
Indices: 5478660--5478697 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5478650 GAATGCTAGA
*
5478660 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
5478680 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
5478698 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:5479352 original size:101 final size:101
Alignment explanation
Indices: 5479172--5479395 Score: 389
Period size: 101 Copynumber: 2.2 Consensus size: 101
5479162 GTAGAGGGTC
5479172 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAAGTGTGAGGTCTGGTGAGACACATACTT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAAGTGTGAGGTCTGGTGAGACACATACTT
*
5479237 GATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
5479273 TATGTGGTCCTTCGGGACATATATGTA-T-TTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAA-A-GTGTGAGGTCTGGTGAGACACATAC
5479336 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
64 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
**
5479374 TATGTGGTCCTTATGGACATAT
1 TATGTGGTCCTTCGGGACATAT
5479396 TATATGGCAC
Statistics
Matches: 118, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
99 7 0.06
100 2 0.02
101 109 0.92
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAAGTGTGAGGTCTGGTGAGACACATACTT
GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:5479434 original size:23 final size:23
Alignment explanation
Indices: 5479401--5479463 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
5479391 CATATTATAT
5479401 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
5479424 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
5479447 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
5479464 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:5483798 original size:31 final size:31
Alignment explanation
Indices: 5483749--5483841 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 31
5483739 AAACCCGACT
* *
5483749 CGACCCGAATTTCACACTTAAAAAACTCAACC
1 CGACTCGAATATCACACTTAAAAAACTC-ACC
5483781 CGACTC-AATATCACACTTAAAAAACT----
1 CGACTCGAATATCACACTTAAAAAACTCACC
*
5483807 -GACTCGAATATCACACTTAAAAAACCCGACC
1 CGACTCGAATATCACACTTAAAAAACTC-ACC
5483838 CGAC
1 CGAC
5483842 CTGAACCCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
25 5 0.10
26 19 0.37
31 19 0.37
32 8 0.16
ACGTcount: A:0.42, C:0.32, G:0.08, T:0.18
Consensus pattern (31 bp):
CGACTCGAATATCACACTTAAAAAACTCACC
Found at i:5483943 original size:27 final size:27
Alignment explanation
Indices: 5483905--5483956 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5483895 AAAACATGAC
* *
5483905 CGACCCGAATATCACACTTAAAAAAAT
1 CGACCCAAATATCAAACTTAAAAAAAT
5483932 CGACCCAAATATCAAACTTAAAAAA
1 CGACCCAAATATCAAACTTAAAAAA
5483957 CCCGACTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.52, C:0.25, G:0.06, T:0.17
Consensus pattern (27 bp):
CGACCCAAATATCAAACTTAAAAAAAT
Found at i:5483962 original size:27 final size:27
Alignment explanation
Indices: 5483903--5483967 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
5483893 AAAAAACATG
* *
5483903 ACCGACCCGAATATCACACTTAAAAAA
1 ACCGACCCAAATATCAAACTTAAAAAA
*
5483930 ATCGACCCAAATATCAAACTTAAAAAA
1 ACCGACCCAAATATCAAACTTAAAAAA
* *
5483957 CCCGACTCAAA
1 ACCGACCCAAA
5483968 CCGAATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.15
Consensus pattern (27 bp):
ACCGACCCAAATATCAAACTTAAAAAA
Found at i:5489108 original size:288 final size:290
Alignment explanation
Indices: 5488590--5489170 Score: 1091
Period size: 288 Copynumber: 2.0 Consensus size: 290
5488580 AAATCTAAAA
5488590 TAGAGGAGAATTTAAAAAAATTTAGGGAGTGATTGACTCCACCCGCCCTCTTCGGTTCATCCTTG
1 TAGAGGAGAATTTAAAAAAATTTAGGGAGTGATTGACTCCACCCGCCCTCTTCGGTTCATCCTTG
5488655 ATTATACGTACATCTGTTTGGTGTATAAATTTTTTTCTTATTATGACAGCACACATACACTCTAC
66 ATTATACGTACATCTGTTTGGTGTATAAATTTTTTTCTTATTATGACAG-ACACATACACTCTAC
5488720 AAACGCAATTACTATGAGTACATAATCGTCATTCCTTTTTTTTTAAGAAATACTAATTGTATGTA
130 AAACGCAATTACTATGAGTACATAATCGTCATTCCTTTTTTTTTAAGAAATACTAATTGTATGTA
5488785 ATAAAAATTTTGGATTATATTGAATTTGAACAGCGGGTTTCGCAGTTTATATTTAA-TTGATTGT
195 ATAAAAATTTTGGATTATATTGAATTTGAACAGCGGGTTTCGCAGTTTATATTTAATTTGATTGT
5488849 CTTGGATTTATGGTTGGCAGAGAGTTCAATT
260 CTTGGATTTATGGTTGGCAGAGAGTTCAATT
5488880 TAGAGGAGAATTTAAAAAAATTTAGGGAGTGATTGACT-C-CCCGCCCTCTTCGGTTCATCCTTG
1 TAGAGGAGAATTTAAAAAAATTTAGGGAGTGATTGACTCCACCCGCCCTCTTCGGTTCATCCTTG
5488943 ATTATACGTACATCTGTTTGGTGTATAAATTTTTTTCTTAATTATTGACAG-CACATACACTCTA
66 ATTATACGTACATCTGTTTGGTGTATAAATTTTTTTCTT-ATTA-TGACAGACACATACACTCTA
5489007 CAAACGCAATTACTATGAGTACATAATCGTCATTCC-TTTTTTTTAAGAAAATACTAATTGTATG
129 CAAACGCAATTACTATGAGTACATAATCGTCATTCCTTTTTTTTTAAG-AAATACTAATTGTATG
5489071 TAATAAAAATTTTGGATTATATTGAATTTGAACAGCGGGTTTCGCAGTTTATATTTAATTTGATT
193 TAATAAAAATTTTGGATTATATTGAATTTGAACAGCGGGTTTCGCAGTTTATATTTAATTTGATT
5489136 GTCTTGGATTTATGGTTGGCAGAGAGTTCAATT
258 GTCTTGGATTTATGGTTGGCAGAGAGTTCAATT
5489169 TA
1 TA
5489171 ACCGAATTTA
Statistics
Matches: 287, Mismatches: 0, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
287 11 0.04
288 186 0.65
289 46 0.16
290 44 0.15
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (290 bp):
TAGAGGAGAATTTAAAAAAATTTAGGGAGTGATTGACTCCACCCGCCCTCTTCGGTTCATCCTTG
ATTATACGTACATCTGTTTGGTGTATAAATTTTTTTCTTATTATGACAGACACATACACTCTACA
AACGCAATTACTATGAGTACATAATCGTCATTCCTTTTTTTTTAAGAAATACTAATTGTATGTAA
TAAAAATTTTGGATTATATTGAATTTGAACAGCGGGTTTCGCAGTTTATATTTAATTTGATTGTC
TTGGATTTATGGTTGGCAGAGAGTTCAATT
Found at i:5493319 original size:33 final size:34
Alignment explanation
Indices: 5493250--5493335 Score: 120
Period size: 33 Copynumber: 2.5 Consensus size: 34
5493240 ATTTCGTAGT
5493250 TTATATCGATCATCAAACTAAGAGAGATTTAATGG
1 TTATATCGATCATCAAACT-AGAGAGATTTAATGG
* *
5493285 TTATATCGATCATCAAACT-TAGAGATTTAGTGG
1 TTATATCGATCATCAAACTAGAGAGATTTAATGG
* *
5493318 TTATGTCAATCATCAAAC
1 TTATATCGATCATCAAAC
5493336 GGAATTGTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 28 0.60
35 19 0.40
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (34 bp):
TTATATCGATCATCAAACTAGAGAGATTTAATGG
Found at i:5493687 original size:18 final size:18
Alignment explanation
Indices: 5493666--5493701 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5493656 TTAGAACTTG
5493666 AATTAATCTCAAATTTTA
1 AATTAATCTCAAATTTTA
*
5493684 AATTAATTTCAAATTTTA
1 AATTAATCTCAAATTTTA
5493702 CCAACCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTAATCTCAAATTTTA
Found at i:5494045 original size:15 final size:15
Alignment explanation
Indices: 5494027--5494082 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
5494017 TAACCGGTTT
5494027 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
5494042 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
5494059 C-GTTATAAAAAAAAC
1 CGGTT-TTAAAAAAAC
*
5494074 CGATTTTAA
1 CGGTTTTAA
5494083 TATTTCAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
14 2 0.06
15 15 0.47
16 3 0.09
17 12 0.38
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:5494274 original size:21 final size:21
Alignment explanation
Indices: 5494250--5494302 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5494240 ACACTTAGGG
5494250 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
5494271 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
5494292 TACCGATTCCC
1 AACCGATTCCC
5494303 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:5494516 original size:13 final size:13
Alignment explanation
Indices: 5494495--5494546 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
5494485 AGTTTCGATA
*
5494495 AATTCAAATACTT
1 AATTGAAATACTT
5494508 AATTGAAATACTT
1 AATTGAAATACTT
* *
5494521 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
5494535 AATTGAAATACT
1 AATTGAAATACT
5494547 AAATACTTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 3 0.10
13 18 0.58
14 7 0.23
15 3 0.10
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:5494590 original size:33 final size:33
Alignment explanation
Indices: 5494535--5494632 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
5494525 AACTCAACAT
* *
5494535 AATTGAAATAC-TAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
5494567 AATTCAAATACTTAAAAACTTCCAA-TTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTT-GATA
5494600 AATTCAAATACTTAAAAACTT-CAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
5494632 A
1 A
5494633 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
32 21 0.34
33 40 0.66
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTTGATA
Done.