Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 21
Found at i:2440333 original size:11 final size:11
Alignment explanation
Indices: 2440317--2440342 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2440307 AAGCCATATG
2440317 CAGCTCACAAA
1 CAGCTCACAAA
2440328 CAGCTCACAAA
1 CAGCTCACAAA
2440339 CAGC
1 CAGC
2440343 ATGGTAGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.38, G:0.12, T:0.08
Consensus pattern (11 bp):
CAGCTCACAAA
Found at i:2441486 original size:11 final size:11
Alignment explanation
Indices: 2441472--2441496 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2441462 TACAAAAAAA
2441472 GAAGTGCAAGT
1 GAAGTGCAAGT
2441483 GAAGTGCAAGT
1 GAAGTGCAAGT
2441494 GAA
1 GAA
2441497 AGAATCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:2457195 original size:19 final size:18
Alignment explanation
Indices: 2457167--2457213 Score: 85
Period size: 19 Copynumber: 2.6 Consensus size: 18
2457157 GTTCAAAAAC
2457167 AAAAAGAAAAAAATTACA
1 AAAAAGAAAAAAATTACA
2457185 AAAATAGAAAAAAATTACA
1 AAAA-AGAAAAAAATTACA
2457204 AAAAAGAAAA
1 AAAAAGAAAA
2457214 GAAAAGCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAAAAATTACA
Found at i:2464140 original size:45 final size:45
Alignment explanation
Indices: 2464076--2464188 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 45
2464066 ATATCATGCC
* * * *
2464076 TTTATGTTAATAATGCACCCATAAGCAATTCAGTC-ATAATATATT
1 TTTATGTTGATAATGCACCCATAAGCAATTCA-ACAATAACATACT
* * *
2464121 TTTATGTTGATAATGCACCCATATGCATTTCAACAATAGCATACT
1 TTTATGTTGATAATGCACCCATAAGCAATTCAACAATAACATACT
* *
2464166 TTTCTGTTGATAATGTACCCATA
1 TTTATGTTGATAATGCACCCATA
2464189 TACATTTGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 57 0.98
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (45 bp):
TTTATGTTGATAATGCACCCATAAGCAATTCAACAATAACATACT
Found at i:2464247 original size:45 final size:46
Alignment explanation
Indices: 2464120--2464257 Score: 174
Period size: 45 Copynumber: 3.1 Consensus size: 46
2464110 CATAATATAT
* * *
2464120 TTTTATGTTGATAATGCACCCATATGCATTTCAAC-AATAGCATAC
1 TTTTATGTTGATAATGTACCCATATACATTTCAACTAGTAGCATAC
* * *
2464165 TTTTCTGTTGATAATGTACCCATATACATTTGAACTAGT-GCTTAC
1 TTTTATGTTGATAATGTACCCATATACATTTCAACTAGTAGCATAC
* * *
2464210 TTTTATCTAGATAATGTACCCATATACATTTCAACTAG-AGCATCC
1 TTTTATGTTGATAATGTACCCATATACATTTCAACTAGTAGCATAC
2464255 TTT
1 TTT
2464258 CATGCTAATA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
45 77 0.97
46 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (46 bp):
TTTTATGTTGATAATGTACCCATATACATTTCAACTAGTAGCATAC
Found at i:2471001 original size:45 final size:45
Alignment explanation
Indices: 2470937--2471133 Score: 132
Period size: 45 Copynumber: 4.4 Consensus size: 45
2470927 ATATCATGCC
* * * *
2470937 TTTATGTTAATAATGCACCCATAAGCAATTCAGTC-ATAATATATT
1 TTTATGTTGATAATGCACCCATAAGCAATTCA-ACAATAACATACT
* * *
2470982 TTTATGTTGATAATGCACCCATATGCATTTCAACAATAACCTACT
1 TTTATGTTGATAATGCACCCATAAGCAATTCAACAATAACATACT
* * * * * * *
2471027 TTTCTGTTGATAATGTACCCATATA-CATTTGAACTAGT-GCTTACT
1 TTTATGTTGATAATGCACCCATA-AGCAATTCAAC-AATAACATACT
* * * * * *
2471072 TTTATCTTGATAATGTACCCATATA-CATTTCAACTATAGCATCCT
1 TTTATGTTGATAATGCACCCATA-AGCAATTCAACAATAACATACT
* *
2471117 TTCATGCTGATAATGCA
1 TTTATGTTGATAATGCA
2471134 AATGTATGCA
Statistics
Matches: 123, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
44 2 0.02
45 119 0.97
46 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (45 bp):
TTTATGTTGATAATGCACCCATAAGCAATTCAACAATAACATACT
Found at i:2477104 original size:45 final size:45
Alignment explanation
Indices: 2477055--2477243 Score: 211
Period size: 45 Copynumber: 4.2 Consensus size: 45
2477045 TATTTTTATA
* * *
2477055 TTGATAATGCACCCATATGCATTTCAGCAATAGCATACTTTTCTG
1 TTGATAATGTACCCATATACATTTCAACAATAGCATACTTTTCTG
* * * *
2477100 TTGATAATGTACCCATATACATTTCATCTATAGTATACTTTACTG
1 TTGATAATGTACCCATATACATTTCAACAATAGCATACTTTTCTG
* * *
2477145 TTGATACTGTACCCATATACATTTCAACTAGT-GCTTACTTTTCTG
1 TTGATAATGTACCCATATACATTTCAAC-AATAGCATACTTTTCTG
* * * *
2477190 TTGATAATGTACCCAAATACATTTCAACTATATCAT-CATTTCATG
1 TTGATAATGTACCCATATACATTTCAACAATAGCATACTTTTC-TG
*
2477235 CTGATAATG
1 TTGATAATG
2477244 CACTTGTATG
Statistics
Matches: 120, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
44 6 0.05
45 113 0.94
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (45 bp):
TTGATAATGTACCCATATACATTTCAACAATAGCATACTTTTCTG
Found at i:2477186 original size:90 final size:90
Alignment explanation
Indices: 2477055--2477221 Score: 246
Period size: 90 Copynumber: 1.9 Consensus size: 90
2477045 TATTTTTATA
* * *
2477055 TTGATAATGCACCCATATGCATTTCAGCAATAGCATACTTTTCTGTTGATAATGTACCCATATAC
1 TTGATAATGCACCCATATACATTTCAACAATAGCATACTTTTCTGTTGATAATGTACCCAAATAC
*
2477120 ATTTCATCTATAGTATACTTTACTG
66 ATTTCAACTATAGTATACTTTACTG
* * * *
2477145 TTGATACTGTACCCATATACATTTCAACTAGT-GCTTACTTTTCTGTTGATAATGTACCCAAATA
1 TTGATAATGCACCCATATACATTTCAAC-AATAGCATACTTTTCTGTTGATAATGTACCCAAATA
2477209 CATTTCAACTATA
65 CATTTCAACTATA
2477222 TCATCATTTC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
90 66 0.97
91 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (90 bp):
TTGATAATGCACCCATATACATTTCAACAATAGCATACTTTTCTGTTGATAATGTACCCAAATAC
ATTTCAACTATAGTATACTTTACTG
Found at i:2477258 original size:90 final size:90
Alignment explanation
Indices: 2477056--2477246 Score: 237
Period size: 90 Copynumber: 2.1 Consensus size: 90
2477046 ATTTTTATAT
* * * * *
2477056 TGATAATGCACCCATATGCATTTCAGC-AATAGCATACTTTTCTGTTGATAATGTACCCATATAC
1 TGATAATGCACCCATATACATTTCAACTAGT-GCTTACTTTTCTGTTGATAATGTACCCAAATAC
* *
2477120 ATTTCATCTATAGTATACTTTACTGT
65 ATTTCAACTATAGTATACTTTACTGC
* *
2477146 TGATACTGTACCCATATACATTTCAACTAGTGCTTACTTTTCTGTTGATAATGTACCCAAATACA
1 TGATAATGCACCCATATACATTTCAACTAGTGCTTACTTTTCTGTTGATAATGTACCCAAATACA
2477211 TTTCAACTATA-TCAT-CATTT-CATGC
66 TTTCAACTATAGT-ATAC-TTTAC-TGC
2477236 TGATAATGCAC
1 TGATAATGCAC
2477247 TTGTATGCAT
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
89 3 0.03
90 81 0.94
91 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (90 bp):
TGATAATGCACCCATATACATTTCAACTAGTGCTTACTTTTCTGTTGATAATGTACCCAAATACA
TTTCAACTATAGTATACTTTACTGC
Found at i:2478787 original size:24 final size:24
Alignment explanation
Indices: 2478724--2478787 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
2478714 ATTTTTTATT
* * *
2478724 TGAATTTTGTTCTAATACCTGACC
1 TGAATTATGTTATGATACCTGACC
* * *
2478748 TGAATTCTATTATGATATCTGACC
1 TGAATTATGTTATGATACCTGACC
*
2478772 TGAATTATGTTTTGAT
1 TGAATTATGTTATGAT
2478788 TTATGATATC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (24 bp):
TGAATTATGTTATGATACCTGACC
Found at i:2479977 original size:10 final size:10
Alignment explanation
Indices: 2479962--2479987 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2479952 AATATTATTT
2479962 AATTAATTCA
1 AATTAATTCA
2479972 AATTAATTCA
1 AATTAATTCA
2479982 AATTAA
1 AATTAA
2479988 ATATACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTAATTCA
Found at i:2495170 original size:29 final size:29
Alignment explanation
Indices: 2495114--2495170 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2495104 TAATGATTAA
* *
2495114 TAGGGTGACTAAATTAAAATATATTAAAG
1 TAGGGTGACTAAATTAAAATAAAATAAAG
2495143 TAGGGTGACTAAATTGAAAA-AAAATAAA
1 TAGGGTGACTAAATT-AAAATAAAATAAA
2495171 ATTATAGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.26
Consensus pattern (29 bp):
TAGGGTGACTAAATTAAAATAAAATAAAG
Found at i:2495314 original size:19 final size:19
Alignment explanation
Indices: 2495278--2495314 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2495268 ATAATAGGGA
**
2495278 CTAAATATATAATTTTACC
1 CTAAATATATAAACTTACC
2495297 CTAAATATATAAACTTAC
1 CTAAATATATAAACTTAC
2495315 AAATAGAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (19 bp):
CTAAATATATAAACTTACC
Found at i:2496355 original size:24 final size:24
Alignment explanation
Indices: 2496321--2496367 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2496311 GCGGGCTTGC
* *
2496321 TGGAATTGGGCCTGGACTGGTTGT
1 TGGAATAGGGCCTGGACTAGTTGT
2496345 TGGAATAGGGCCTGGACTAGTTG
1 TGGAATAGGGCCTGGACTAGTTG
2496368 CTGAGCGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.13, G:0.40, T:0.30
Consensus pattern (24 bp):
TGGAATAGGGCCTGGACTAGTTGT
Found at i:2496801 original size:89 final size:89
Alignment explanation
Indices: 2496685--2497355 Score: 959
Period size: 89 Copynumber: 7.5 Consensus size: 89
2496675 GATCTTGATC
* * *
2496685 TTGCTTCACTACTCTTCTGTGAAGGCTGAAGATGGC-T-TGAACGAAATCTGTTTAACTACTCTT
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAA-G-AATCTGTTTCACTACTCTT
* ** *
2496748 CCGTGAAGATCGGACTCGAAATTGGA
64 TCGTGAAGATCATACTCAAAATTGGA
* * *
2496774 TTGCTTCACTACTCTTTCGTGAAGGCTGAAGATGACTTGTGAAGAATTTGTTTCACTACTCTTTT
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
*
2496839 GTGAAGATCAGACTCAAAATTGGA
66 GTGAAGATCATACTCAAAATTGGA
** * *
2496863 TTATTTCACTACTCTTCCATGAAGGCTTAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
*
2496928 ATGAAGATCATACTCAAAATTGGA
66 GTGAAGATCATACTCAAAATTGGA
* * * * * *
2496952 TTACTTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAAAAATATGTTTCACTACTCTTTC
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
2497017 GTGAAGATCATACTCAAAATTGGA
66 GTGAAGATCATACTCAAAATTGGA
* * * *
2497041 TTCCTTCACTACTCTTCCGTGAAGGATGAAGATGATTTGTGAAGAATCTGTTTCACTACTCTTTT
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
*
2497106 GTGAAGATCAGACTCAAAATTGGA
66 GTGAAGATCATACTCAAAATTGGA
* *
2497130 TTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
*
2497195 ATGAAGATCATACTCAAAATTGGA
66 GTGAAGATCATACTCAAAATTGGA
** * * * *
2497219 TTAATTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAAAAATCTGTTTCACTACTCTTTC
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
2497284 GTGAAGATCATACTCAAAATTGGA
66 GTGAAGATCATACTCAAAATTGGA
* * *
2497308 TTGCTTCACTACTCTTCCGTGAAGGATGGAGATGATTTGTGAAGAATC
1 TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATC
2497356 ATCTTGCTCT
Statistics
Matches: 521, Mismatches: 59, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
89 515 0.99
90 2 0.00
91 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (89 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTGAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTC
GTGAAGATCATACTCAAAATTGGA
Found at i:2497163 original size:267 final size:267
Alignment explanation
Indices: 2496688--2497355 Score: 1108
Period size: 267 Copynumber: 2.5 Consensus size: 267
2496678 CTTGATCTTG
** * * * * *
2496688 CTTCACTACTCTTCTGTGAAGGCTGAAGATGGC-T-TGAACGAAATCTGTTTAACTACTCTTCCG
1 CTTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAA--AAATCTGTTTCACTACTCTTTCG
** * * * *
2496751 TGAAGATCGGACTCGAAATTGGATTGCTTCACTACTCTTTCGTGAAGGCTGAAGATGACTTGTGA
64 TGAAGATCATACTCAAAATTGGATTGCTTCACTACTCTTCCGTGAAGGATGAAGATGATTTGTGA
* *
2496816 AGAATTTGTTTCACTACTCTTTTGTGAAGATCAGACTCAAAATTGGATTATTTCACTACTCTTCC
129 AGAATCTGTTTCACTACTCTTTTGTGAAGATCAGACTCAAAATTGGATTACTTCACTACTCTTCC
2496881 ATGAAGGCTTAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTCATGAAGATCATACTCAAA
194 ATGAAGGCTTAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTCATGAAGATCATACTCAAA
2496946 ATTGGATTA
259 ATTGGATTA
*
2496955 CTTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAAAAATATGTTTCACTACTCTTTCGTG
1 CTTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAAAAATCTGTTTCACTACTCTTTCGTG
*
2497020 AAGATCATACTCAAAATTGGATTCCTTCACTACTCTTCCGTGAAGGATGAAGATGATTTGTGAAG
66 AAGATCATACTCAAAATTGGATTGCTTCACTACTCTTCCGTGAAGGATGAAGATGATTTGTGAAG
*
2497085 AATCTGTTTCACTACTCTTTTGTGAAGATCAGACTCAAAATTGGATTGCTTCACTACTCTT-CAG
131 AATCTGTTTCACTACTCTTTTGTGAAGATCAGACTCAAAATTGGATTACTTCACTACTCTTCCA-
2497149 TGAAGGCTTAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTCATGAAGATCATACTCAAAA
195 TGAAGGCTTAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTCATGAAGATCATACTCAAAA
2497214 TTGGATTA
260 TTGGATTA
*
2497222 ATTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAAAAATCTGTTTCACTACTCTTTCGTG
1 CTTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAAAAATCTGTTTCACTACTCTTTCGTG
*
2497287 AAGATCATACTCAAAATTGGATTGCTTCACTACTCTTCCGTGAAGGATGGAGATGATTTGTGAAG
66 AAGATCATACTCAAAATTGGATTGCTTCACTACTCTTCCGTGAAGGATGAAGATGATTTGTGAAG
2497352 AATC
131 AATC
2497356 ATCTTGCTCT
Statistics
Matches: 376, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
266 2 0.01
267 369 0.98
268 1 0.00
269 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (267 bp):
CTTCACTACTCTTCCATGAAGGTTGAAGAAGACTTGTGAAAAATCTGTTTCACTACTCTTTCGTG
AAGATCATACTCAAAATTGGATTGCTTCACTACTCTTCCGTGAAGGATGAAGATGATTTGTGAAG
AATCTGTTTCACTACTCTTTTGTGAAGATCAGACTCAAAATTGGATTACTTCACTACTCTTCCAT
GAAGGCTTAAGATGACTTGTGAAGAATCTGTTTCACTACTCTTTCATGAAGATCATACTCAAAAT
TGGATTA
Found at i:2497417 original size:20 final size:20
Alignment explanation
Indices: 2497394--2497507 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
2497384 CAAAAGATTC
*
2497394 ACAAATTACCCGAAGGCTTT
1 ACAAATGACCCGAAGGCTTT
*
2497414 ACAAATGACCCAAAGG-TTCT
1 ACAAATGACCCGAAGGCTT-T
* * *
2497434 AAAAATTACCC-AGAGGTTTT
1 ACAAATGACCCGA-AGGCTTT
* *
2497454 ACAAATTACCCGGAGGCTTT
1 ACAAATGACCCGAAGGCTTT
2497474 ACAAATGACCCGAAGGCTTT
1 ACAAATGACCCGAAGGCTTT
2497494 ACAAATGACCCGAA
1 ACAAATGACCCGAA
2497508 AAATAATTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
19 3 0.04
20 76 0.94
21 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
ACAAATGACCCGAAGGCTTT
Found at i:2497440 original size:40 final size:40
Alignment explanation
Indices: 2497378--2497504 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
2497368 AGACTAACAG
*
2497378 ATGACCCAAAAGATTC-ACAAATTACCCGAAGGCTTTACAA
1 ATGACCC-AAAGGTTCTACAAATTACCCGAAGGCTTTACAA
* *
2497418 ATGACCCAAAGGTTCTAAAAATTACCC-AGAGGTTTTACAA
1 ATGACCCAAAGGTTCTACAAATTACCCGA-AGGCTTTACAA
* ** *
2497458 ATTACCCGGAGGCTT-TACAAATGACCCGAAGGCTTTACAA
1 ATGACCCAAAGG-TTCTACAAATTACCCGAAGGCTTTACAA
2497498 ATGACCC
1 ATGACCC
2497505 GAAAAATAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
39 8 0.11
40 62 0.85
41 3 0.04
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (40 bp):
ATGACCCAAAGGTTCTACAAATTACCCGAAGGCTTTACAA
Found at i:2504986 original size:26 final size:26
Alignment explanation
Indices: 2504950--2505028 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
2504940 CATCCCACCG
*
2504950 GCGGGATGGTCGGCCACCAGCTGATA
1 GCGGGATGGTCGGCCACCAGCCGATA
2504976 GCGGGATGGTCGGCCACCAGCCGATA
1 GCGGGATGGTCGGCCACCAGCCGATA
* * * * *
2505002 TCAGGATGGCCGACCACCAACCGATA
1 GCGGGATGGTCGGCCACCAGCCGATA
2505028 G
1 G
2505029 TCGTTCGCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.23, C:0.30, G:0.34, T:0.13
Consensus pattern (26 bp):
GCGGGATGGTCGGCCACCAGCCGATA
Found at i:2507600 original size:18 final size:18
Alignment explanation
Indices: 2507562--2507600 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2507552 ACTTATAACA
* *
2507562 TCACAATCCAACCTTACT
1 TCACAATCCAACATTAAT
2507580 TCACAATCCAACATTAAT
1 TCACAATCCAACATTAAT
2507598 TCA
1 TCA
2507601 TTGAATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.28
Consensus pattern (18 bp):
TCACAATCCAACATTAAT
Found at i:2509497 original size:21 final size:21
Alignment explanation
Indices: 2509451--2509499 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2509441 GCACACAAAG
**
2509451 AAGGGATTGATCCTTTTTCAC
1 AAGGGATTGATCCTTTCCCAC
* *
2509472 GAGGGATTGATCCTTTCCCAT
1 AAGGGATTGATCCTTTCCCAC
2509493 AAGGGAT
1 AAGGGAT
2509500 CGATTATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (21 bp):
AAGGGATTGATCCTTTCCCAC
Found at i:2511347 original size:46 final size:46
Alignment explanation
Indices: 2511289--2511401 Score: 163
Period size: 46 Copynumber: 2.5 Consensus size: 46
2511279 GTTAATACAC
* * * *
2511289 CGTTATGTATTTTCATTTGTGGCATCCTTTCATGCCGATTATGCAA
1 CGTTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCAA
*
2511335 CGTTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCAC
1 CGTTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCAA
* *
2511381 CATTATGCATGTTCATTTATG
1 CGTTATGCATTTTCATTTATG
2511402 ACATCATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (46 bp):
CGTTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCAA
Found at i:2511436 original size:47 final size:46
Alignment explanation
Indices: 2511281--2511437 Score: 145
Period size: 46 Copynumber: 3.4 Consensus size: 46
2511271 TTTATGTTGT
* * * * * * * *
2511281 TAATACACCGTTATGTATTTTCATTTGTGGCATCCTTTCATGCCGA
1 TAATGCACCATTATGCATGTTCATTTATGGAATCCTTTCATGACAA
* * * * * *
2511327 TTATGCAACGTTATGCATTTTCATTTATGGAATCCTTTCATGCCGA
1 TAATGCACCATTATGCATGTTCATTTATGGAATCCTTTCATGACAA
* *
2511373 TAATGCACCATTATGCATGTTCATTTAT-GACATCATTTTTATGACAA
1 TAATGCACCATTATGCATGTTCATTTATGGA-ATC-CTTTCATGACAA
2511420 TAATGCACCATTATGCAT
1 TAATGCACCATTATGCAT
2511438 TTAACTTGCA
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
45 2 0.02
46 67 0.71
47 26 0.27
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (46 bp):
TAATGCACCATTATGCATGTTCATTTATGGAATCCTTTCATGACAA
Found at i:2511499 original size:51 final size:51
Alignment explanation
Indices: 2511421--2511544 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 51
2511411 TTATGACAAT
* *
2511421 AATGCACCATTATGCATTTAACTTGCATTAGTGGTAACTTTCTACAAAAAA
1 AATGCACCATTATGCATCTAACTTGCATTAGTGGCAACTTTCTACAAAAAA
* * *
2511472 AATGCCCCA-TATGTCATCTAACTTGCATTAGTGGCACCTTTCTAC--CAAA
1 AATGCACCATTATG-CATCTAACTTGCATTAGTGGCAACTTTCTACAAAAAA
* * *
2511521 AATGCACCGTTAGGCATTTAACTT
1 AATGCACCATTATGCATCTAACTT
2511545 TCGTTTTAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
49 19 0.31
50 7 0.11
51 36 0.58
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (51 bp):
AATGCACCATTATGCATCTAACTTGCATTAGTGGCAACTTTCTACAAAAAA
Found at i:2512050 original size:34 final size:34
Alignment explanation
Indices: 2512006--2512089 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
2511996 CTCCCTTTTA
* * *
2512006 GTATCAATACCATTTCTACATTCTGGAATCCATG
1 GTATCGATACCATTTCTACATTCTAGAATCCACG
2512040 GTATCGATACCATTTCTACATTCTAGAATCCACG
1 GTATCGATACCATTTCTACATTCTAGAATCCACG
2512074 GTATCGATACC-TTTCT
1 GTATCGATACCATTTCT
2512090 CTTAGAATCG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 5 0.11
34 42 0.89
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (34 bp):
GTATCGATACCATTTCTACATTCTAGAATCCACG
Found at i:2515944 original size:46 final size:46
Alignment explanation
Indices: 2515886--2515989 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 46
2515876 GTTAATACAT
* * * *
2515886 TGTTATGTATTTTAATTTATGGCATCATTTCATGCCGATTATGCAAC
1 TGTTATGCATTTTAATTTATGACATCATTTCATGCCAATAATGC-AC
* *
2515933 -GTTATGCATTTTCATTTATGACATCCTTTCATGCCAATAATGCAC
1 TGTTATGCATTTTAATTTATGACATCATTTCATGCCAATAATGCAC
*
2515978 TATTATGCATTT
1 TGTTATGCATTT
2515990 AACTTGCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 2 0.04
46 47 0.96
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.44
Consensus pattern (46 bp):
TGTTATGCATTTTAATTTATGACATCATTTCATGCCAATAATGCAC
Found at i:2516026 original size:49 final size:49
Alignment explanation
Indices: 2515957--2516159 Score: 194
Period size: 49 Copynumber: 4.1 Consensus size: 49
2515947 TTTATGACAT
* * * *
2515957 CCTTTCATGCCAATAATGCACTATTATG-CATTTAACTTGCATTAGTTGCA
1 CCTTTC-TGCCAAAAATGCACCATT-TGTCATCTAACTTGCATTAGTGGCA
* * * **
2516007 CCTTTCTGCCAAAACTGCACTATTTGTCATCTAACTTGCAATAGTGGTG
1 CCTTTCTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGCA
* * * * * *
2516056 TCTTACTAG-CAAAAATGCACCGTTAGGCATTTAACTTGCATTAGTGGCA
1 CCTTTCT-GCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGCA
* * * *
2516105 CCTTTCCGCCAAAAATACACCATTTGTCATCTATCTTGCATTAGTAGCA
1 CCTTTCTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGCA
2516154 CCTTTC
1 CCTTTC
2516160 AACAAAAAAT
Statistics
Matches: 122, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
48 3 0.02
49 112 0.92
50 7 0.06
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (49 bp):
CCTTTCTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGCA
Found at i:2516168 original size:98 final size:98
Alignment explanation
Indices: 2515984--2516195 Score: 264
Period size: 98 Copynumber: 2.2 Consensus size: 98
2515974 GCACTATTAT
* * * * *
2515984 GCATTTAACTTGCATTAGTTGCACCTTTCTGCCAAAACTGCACTATTTGTCATCTAACTTGCAAT
1 GCATTTAACTTGCATTAGTGGCACCTTTCCGCCAAAAATACACCATTTGTCATCTAACTTGCAAT
* *** *
2516049 AGTGGTGTCTTACTAGCAAAAATGCACCGTTAG
66 AGTAGCACCTTACTAACAAAAATGCACCGTTAG
* *
2516082 GCATTTAACTTGCATTAGTGGCACCTTTCCGCCAAAAATACACCATTTGTCATCTATCTTGCATT
1 GCATTTAACTTGCATTAGTGGCACCTTTCCGCCAAAAATACACCATTTGTCATCTAACTTGCAAT
* *
2516147 AGTAGCACCTTTC-AACAAAAAATGCTCCGTTAG
66 AGTAGCACCTTACTAAC-AAAAATGCACCGTTAG
* *
2516180 GAATTTAACTTTCATT
1 GCATTTAACTTGCATT
2516196 TTATAGTAGT
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 2 0.02
98 95 0.98
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (98 bp):
GCATTTAACTTGCATTAGTGGCACCTTTCCGCCAAAAATACACCATTTGTCATCTAACTTGCAAT
AGTAGCACCTTACTAACAAAAATGCACCGTTAG
Found at i:2516568 original size:16 final size:17
Alignment explanation
Indices: 2516549--2516582 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2516539 ATTTTATATT
2516549 CCTA-TTACAATTTCAG
1 CCTACTTACAATTTCAG
2516565 CCTATCTTACAATTTCAG
1 CCTA-CTTACAATTTCAG
2516583 GCTCAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (17 bp):
CCTACTTACAATTTCAG
Found at i:2525577 original size:15 final size:15
Alignment explanation
Indices: 2525557--2525586 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2525547 TTAATTGCTT
2525557 CCTTATCTCTTTTTC
1 CCTTATCTCTTTTTC
*
2525572 CCTTATCTTTTTTTC
1 CCTTATCTCTTTTTC
2525587 TTTCCTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (15 bp):
CCTTATCTCTTTTTC
Found at i:2533822 original size:27 final size:27
Alignment explanation
Indices: 2533784--2533842 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
2533774 ATTTCCCAAG
2533784 TTTATGCTTTAGTTAACTAGCTTTCAA
1 TTTATGCTTTAGTTAACTAGCTTTCAA
2533811 TTTATGCTTTAGTTAACTAGCTTTCAA
1 TTTATGCTTTAGTTAACTAGCTTTCAA
2533838 TTTAT
1 TTTAT
2533843 TCATTTAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTATGCTTTAGTTAACTAGCTTTCAA
Found at i:2540561 original size:18 final size:18
Alignment explanation
Indices: 2540523--2540562 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2540513 TGAGATAACT
* *
2540523 TAAAGGAAATAAAATATC
1 TAAAGGAAATAAAACACC
2540541 TAAAGGAAATAAAACACC
1 TAAAGGAAATAAAACACC
2540559 TAAA
1 TAAA
2540563 AATTATCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (18 bp):
TAAAGGAAATAAAACACC
Found at i:2548507 original size:17 final size:17
Alignment explanation
Indices: 2548485--2548517 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2548475 TTATTTTATT
2548485 CTTTAGTTATTTAGGAC
1 CTTTAGTTATTTAGGAC
2548502 CTTTAGTTATTTAGGA
1 CTTTAGTTATTTAGGA
2548518 TATTTAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (17 bp):
CTTTAGTTATTTAGGAC
Found at i:2548523 original size:17 final size:17
Alignment explanation
Indices: 2548486--2548524 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2548476 TATTTTATTC
*
2548486 TTTAGTTATTTAGGACC
1 TTTAGTTATTTAGGACA
*
2548503 TTTAGTTATTTAGGATA
1 TTTAGTTATTTAGGACA
2548520 TTTAG
1 TTTAG
2548525 AACTCAGTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (17 bp):
TTTAGTTATTTAGGACA
Found at i:2548898 original size:15 final size:15
Alignment explanation
Indices: 2548878--2548913 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2548868 GGTTATCTTA
2548878 CTTTATTTTCAATTT
1 CTTTATTTTCAATTT
2548893 CTTTATTTTCAATTT
1 CTTTATTTTCAATTT
2548908 CTTTAT
1 CTTTAT
2548914 CTTTTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTATTTTCAATTT
Found at i:2552203 original size:24 final size:24
Alignment explanation
Indices: 2552176--2552246 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
2552166 AAACGGAGAT
*
2552176 ATCAGAAATCAAAACAAAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
2552200 ATCA-AATATCATAATAGAATCCAT
1 ATCAGAA-ATCAAAACAGAATTCAG
2552224 ATCAGAAATCAAAACAGAATTCA
1 ATCAGAAATCAAAACAGAATTCA
2552247 AGTCATGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 2 0.05
24 33 0.89
25 2 0.05
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:2552258 original size:48 final size:48
Alignment explanation
Indices: 2552174--2552267 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
2552164 GTAAACGGAG
* *
2552174 ATATCAGAAATCAAAACAAAATTCAGATCAAATATCATAATAGAATCC
1 ATATCAGAAATCAAAACAAAATTCAGATCAAATATCAGAACAGAATCC
* **
2552222 ATATCAGAAATCAAAACAGAATTCA-AGTCATGTATCAGAACAGAAT
1 ATATCAGAAATCAAAACAAAATTCAGA-TCAAATATCAGAACAGAAT
2552268 TCAAGTAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.03
48 39 0.98
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAAAATTCAGATCAAATATCAGAACAGAATCC
Found at i:2552282 original size:24 final size:25
Alignment explanation
Indices: 2552228--2552284 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
2552218 ATCCATATCA
* *
2552228 GAAATCAAAACAGAATTCAAGTCAT
1 GAAATCAGAACAGAATTCAAGTCAG
*
2552253 G-TATCAGAACAGAATTCAAGT-AG
1 GAAATCAGAACAGAATTCAAGTCAG
2552276 GAAATCAGA
1 GAAATCAGA
2552285 TAAAATATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.07
24 24 0.89
25 1 0.04
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (25 bp):
GAAATCAGAACAGAATTCAAGTCAG
Found at i:2556709 original size:18 final size:18
Alignment explanation
Indices: 2556686--2556736 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
2556676 TAGTTTGCCC
2556686 AAAATTTTAAAATAATAA
1 AAAATTTTAAAATAATAA
2556704 AAAATTTTAAAAT-ATAA
1 AAAATTTTAAAATAATAA
* *
2556721 TAAATATCTAAAATAA
1 AAAAT-TTTAAAATAA
2556737 GAAGATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 20 0.69
19 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAATAATAA
Found at i:2557130 original size:17 final size:18
Alignment explanation
Indices: 2557108--2557146 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2557098 TTTTATTAAT
2557108 ATTTATGTATG-TGTGGC
1 ATTTATGTATGATGTGGC
*
2557125 ATTTATGTATGATGTGGT
1 ATTTATGTATGATGTGGC
2557143 ATTT
1 ATTT
2557147 TTCTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:2557377 original size:31 final size:31
Alignment explanation
Indices: 2557342--2557402 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2557332 TAAAGCAGAT
*
2557342 GGAATATTTTTTTAATTT-AATTATAATTTTG
1 GGAATATTTATTTAATTTCAA-TATAATTTTG
* *
2557373 GGAATGTTTATTTGATTTCAATATAATTTT
1 GGAATATTTATTTAATTTCAATATAATTTT
2557403 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (31 bp):
GGAATATTTATTTAATTTCAATATAATTTTG
Found at i:2560126 original size:29 final size:29
Alignment explanation
Indices: 2560089--2560242 Score: 150
Period size: 29 Copynumber: 5.4 Consensus size: 29
2560079 CATTTTACAG
* * *
2560089 AAATGACACCCTTTTTAAAATAATTACCA
1 AAATAACACCCTTTTTAAATTAATTCCCA
* *
2560118 AAATAACACTCTTTTTGAATTAATTCCCA
1 AAATAACACCCTTTTTAAATTAATTCCCA
* *
2560147 AAATAGCA-CCTTTTCAAATTAATTCCCA
1 AAATAACACCCTTTTTAAATTAATTCCCA
* * *
2560175 AAATATCA-CCATTTTGAATTAATTCCCA
1 AAATAACACCCTTTTTAAATTAATTCCCA
* * ** *
2560203 AAATAGCACCCATTTCGAATAAATTCCCA
1 AAATAACACCCTTTTTAAATTAATTCCCA
*
2560232 AAATAGCACCC
1 AAATAACACCC
2560243 GGTCAACGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
28 48 0.44
29 60 0.56
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATAACACCCTTTTTAAATTAATTCCCA
Found at i:2560168 original size:28 final size:28
Alignment explanation
Indices: 2560109--2560241 Score: 169
Period size: 28 Copynumber: 4.7 Consensus size: 28
2560099 CTTTTTAAAA
* * *
2560109 TAATTACCAAAATAACACTCTTTTTGAAT
1 TAATTCCCAAAATAGCAC-CTTTTCGAAT
*
2560138 TAATTCCCAAAATAGCACCTTTTCAAAT
1 TAATTCCCAAAATAGCACCTTTTCGAAT
*
2560166 TAATTCCCAAAATATCACCATTTT-GAAT
1 TAATTCCCAAAATAGCACC-TTTTCGAAT
*
2560194 TAATTCCCAAAATAGCACCCATTTCGAAT
1 TAATTCCCAAAATAGCA-CCTTTTCGAAT
*
2560223 AAATTCCCAAAATAGCACC
1 TAATTCCCAAAATAGCACC
2560242 CGGTCAACGG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
28 50 0.54
29 42 0.46
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.31
Consensus pattern (28 bp):
TAATTCCCAAAATAGCACCTTTTCGAAT
Found at i:2560233 original size:57 final size:56
Alignment explanation
Indices: 2560106--2560241 Score: 184
Period size: 57 Copynumber: 2.4 Consensus size: 56
2560096 ACCCTTTTTA
* * *
2560106 AAAT-AATTACCAAAATAACACTCTTTTTGAATTAATTCCCAAAATAGCACCTTTTC
1 AAATAAATTCCCAAAATAACAC-CATTTTGAATTAATTCCCAAAATAGCACCATTTC
* *
2560162 AAATTAATTCCCAAAATATCACCATTTTGAATTAATTCCCAAAATAGCACCCATTTC
1 AAATAAATTCCCAAAATAACACCATTTTGAATTAATTCCCAAAATAGCA-CCATTTC
* *
2560219 GAATAAATTCCCAAAATAGCACC
1 AAATAAATTCCCAAAATAACACC
2560242 CGGTCAACGG
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
56 30 0.42
57 41 0.58
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.30
Consensus pattern (56 bp):
AAATAAATTCCCAAAATAACACCATTTTGAATTAATTCCCAAAATAGCACCATTTC
Found at i:2560265 original size:17 final size:18
Alignment explanation
Indices: 2560243--2560277 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2560233 AATAGCACCC
2560243 GGTCAAC-GGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
2560260 GGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
2560278 AACCGGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:2561564 original size:4 final size:4
Alignment explanation
Indices: 2561550--2561600 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
2561540 ATTTAAATTG
*
2561550 TTTA CTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2561598 TTT
1 TTT
2561601 TTTGCTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:2561825 original size:57 final size:57
Alignment explanation
Indices: 2561763--2561871 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
2561753 AGGGTGCAAC
* * *
2561763 TGCTTTTACATTTACTGTTTTTTCATTAATTATCATGAATTTCAACAAGCATGTTAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTATCATAAATTGCAACAAGCATGTTAT
* * *
2561820 TGCTTTTACATTTACTGCTTTTTGATTAATTTTCATAAATTGCAGCAAGCAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTATCATAAATTGCAACAAGCAT
2561872 ATAAATGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.48
Consensus pattern (57 bp):
TGCTTTTACATTTACTGCTTTTTCATTAATTATCATAAATTGCAACAAGCATGTTAT
Found at i:2562624 original size:25 final size:25
Alignment explanation
Indices: 2562582--2562632 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2562572 AATCGCATAG
2562582 AATTTGTCTCGAAGGACCACGTAGA
1 AATTTGTCTCGAAGGACCACGTAGA
* *
2562607 AATTTGTC-CTGAATGACCGCGTAGA
1 AATTTGTCTC-GAAGGACCACGTAGA
2562632 A
1 A
2562633 CCCTCGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
AATTTGTCTCGAAGGACCACGTAGA
Found at i:2562813 original size:15 final size:15
Alignment explanation
Indices: 2562737--2562813 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
2562727 GTCTTTTATC
2562737 CACATAGAACACTTT
1 CACATAGAACACTTT
** * *
2562752 TGCATAGAGCATTTT
1 CACATAGAACACTTT
* **
2562767 CACGTAGAACACAGT
1 CACATAGAACACTTT
2562782 CACATA-AAGCACTTT
1 CACATAGAA-CACTTT
*
2562797 CACATAGAACACATT
1 CACATAGAACACTTT
2562812 CA
1 CA
2562814 TATATTAATA
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:2564575 original size:24 final size:24
Alignment explanation
Indices: 2564499--2564607 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
2564489 AAACGGAGAT
*
2564499 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
2564523 ATCAGATATCATAATAGAA-TCTAG
1 ATCAGAAATCAGAACAGAATTC-AG
*
2564547 ATCATAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
2564571 GTCATG-TATCAGAACATAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
2564594 AGTAAGAAATCAGA
1 A-TCAGAAATCAGA
2564608 TAAAATATTC
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
23 3 0.05
24 61 0.92
25 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:2569391 original size:17 final size:18
Alignment explanation
Indices: 2569369--2569407 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2569359 TTTTATTAAT
2569369 ATTTATGTATG-TGTGGC
1 ATTTATGTATGATGTGGC
*
2569386 ATTTATGTATGATGTGGT
1 ATTTATGTATGATGTGGC
2569404 ATTT
1 ATTT
2569408 TTCTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:2569639 original size:31 final size:31
Alignment explanation
Indices: 2569604--2569664 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2569594 TAAAGCAGAT
* *
2569604 GGAATATTTGTTTTATTT-AATTATAATTTTG
1 GGAATATTTATTTGATTTCAA-TATAATTTTG
*
2569635 GGAATGTTTATTTGATTTCAATATAATTTT
1 GGAATATTTATTTGATTTCAATATAATTTT
2569665 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.56
Consensus pattern (31 bp):
GGAATATTTATTTGATTTCAATATAATTTTG
Found at i:2572398 original size:29 final size:29
Alignment explanation
Indices: 2572361--2572514 Score: 177
Period size: 29 Copynumber: 5.3 Consensus size: 29
2572351 CATTTTACAG
* * * *
2572361 AAATGGCACCATTTTTAAAATAATTACCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* *
2572390 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
2572419 AAATAGCACCATTTTTGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* *
2572448 CAATATCACCA-TTTTGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* * *
2572476 AAATAGCACC-TATTTCGAATAAATTACCA
1 AAATAGCACCAT-TTTTGAATTAATTCCCA
*
2572505 AAATACCACC
1 AAATAGCACC
2572515 CGGTCAACGA
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
28 25 0.23
29 82 0.77
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCATTTTTGAATTAATTCCCA
Found at i:2573797 original size:4 final size:4
Alignment explanation
Indices: 2573783--2573820 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
2573773 ATTTAAATTG
*
2573783 TTTA CTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2573821 TTTGCTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2574045 original size:57 final size:57
Alignment explanation
Indices: 2573983--2574091 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
2573973 GGGGTGCAAC
*
2573983 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATGAATTTCAGCAAGCATGTTAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
*
2574040 TGCTTTTACATTTACTGCTTTTTGATTAATTTTCATAAATTTCAGCAAGCAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCAT
2574092 ATAAATGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.49
Consensus pattern (57 bp):
TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
Found at i:2574843 original size:25 final size:25
Alignment explanation
Indices: 2574801--2574851 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2574791 AACCGCACAG
2574801 AATTTGTCTCGAAGGACCACGTAGA
1 AATTTGTCTCGAAGGACCACGTAGA
* *
2574826 AATTTGTC-CTGAATGACCGCGTAGA
1 AATTTGTCTC-GAAGGACCACGTAGA
2574851 A
1 A
2574852 CCCTCGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
AATTTGTCTCGAAGGACCACGTAGA
Found at i:2575032 original size:15 final size:15
Alignment explanation
Indices: 2574956--2575032 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
2574946 TTCTTTTATC
2574956 CACATAGAACACTTT
1 CACATAGAACACTTT
** * *
2574971 TGCATAGAGCATTTT
1 CACATAGAACACTTT
* **
2574986 CACGTAGAACACAGT
1 CACATAGAACACTTT
2575001 CACATA-AAGCACTTT
1 CACATAGAA-CACTTT
*
2575016 CACATAGAACACATT
1 CACATAGAACACTTT
2575031 CA
1 CA
2575033 TATATTAACA
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:2576746 original size:24 final size:25
Alignment explanation
Indices: 2576719--2576788 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 25
2576709 AAACGGAGAT
2576719 ATCAGAAATCAAAACAGAATTCT-G
1 ATCAGAAATCAAAACAGAATTCTAG
* * *
2576743 ATCAGATATCATAATAGAA-TCTAG
1 ATCAGAAATCAAAACAGAATTCTAG
* * *
2576767 ATCATAAATCAGAACATAATTC
1 ATCAGAAATCAAAACAGAATTC
2576789 AGGTCATGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 3 0.08
24 31 0.86
25 2 0.06
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.26
Consensus pattern (25 bp):
ATCAGAAATCAAAACAGAATTCTAG
Found at i:2576795 original size:24 final size:24
Alignment explanation
Indices: 2576768--2576827 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2576758 AGAATCTAGA
*
2576768 TCATAAATCAGAACATAATTCAGG
1 TCATAAATCAGAACATAATTCAAG
** *
2576792 TCATGTATCATAACATAATTCAAG
1 TCATAAATCAGAACATAATTCAAG
*
2576816 TCAGAAATCAGA
1 TCATAAATCAGA
2576828 TAAAATATTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (24 bp):
TCATAAATCAGAACATAATTCAAG
Found at i:2576824 original size:48 final size:48
Alignment explanation
Indices: 2576719--2576827 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
2576709 AAACGGAGAT
* * * *
2576719 ATCAGAAATCAAAACAGAATTCTGATCAGATATCATAATAGAATCTAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCATAACAGAATCAAG
* * * *
2576767 ATCATAAATCAGAACATAATTCAGGTCATG-TATCATAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATCA-GATATCATAACAGAA-TCAAG
2576816 -TCAGAAATCAGA
1 ATCAGAAATCAGA
2576828 TAAAATATTC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCATAACAGAATCAAG
Found at i:2581241 original size:18 final size:18
Alignment explanation
Indices: 2581218--2581268 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
2581208 TAGTTTGCCC
2581218 AAAATTTTAAAATAATAA
1 AAAATTTTAAAATAATAA
2581236 AAAATTTTAAAAT-ATAA
1 AAAATTTTAAAATAATAA
* *
2581253 TAAATATCTAAAATAA
1 AAAAT-TTTAAAATAA
2581269 GAAGATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 20 0.69
19 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAATAATAA
Found at i:2581661 original size:17 final size:18
Alignment explanation
Indices: 2581639--2581677 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2581629 TTTTATTAAT
2581639 ATTTATGTATG-TGTGGC
1 ATTTATGTATGATGTGGC
*
2581656 ATTTATGTATGATGTGGT
1 ATTTATGTATGATGTGGC
2581674 ATTT
1 ATTT
2581678 TTTCTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:2581904 original size:31 final size:31
Alignment explanation
Indices: 2581869--2581929 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2581859 TAAAGCAGAT
* *
2581869 GGAATATTTTTTTTATTT-AATTATAATTTTG
1 GGAATATTTATTTGATTTCAA-TATAATTTTG
*
2581900 GGAATGTTTATTTGATTTCAATATAATTTT
1 GGAATATTTATTTGATTTCAATATAATTTT
2581930 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (31 bp):
GGAATATTTATTTGATTTCAATATAATTTTG
Found at i:2584650 original size:29 final size:29
Alignment explanation
Indices: 2584613--2584767 Score: 186
Period size: 29 Copynumber: 5.4 Consensus size: 29
2584603 CATTTTACAG
* * * *
2584613 AAATGGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
2584642 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
2584671 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* *
2584700 AAATATCA-CCATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* ** * *
2584728 AAATAGCACCCATTTCAAATAAATTCTCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
2584757 AAATAGCACCC
1 AAATAGCACCC
2584768 GGTCAACAGT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 25 0.22
29 87 0.78
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (29 bp):
AAATAGCACCCTTTTTGAATTAATTCCCA
Found at i:2584737 original size:57 final size:58
Alignment explanation
Indices: 2584613--2584766 Score: 211
Period size: 57 Copynumber: 2.7 Consensus size: 58
2584603 CATTTTACAG
* * * * *
2584613 AAATGGCACCCTTTTTAAAATAATTACCAAAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAATTAATTCCCAAAATAGCACCATTTTCGAATTAATTCCCA
* *
2584671 AAATAGCACCCTTTTCGAATTAATTCCCAAAATATCACCATTTT-GAATTAATTCCCA
1 AAATAGCACCCTTTTCAAATTAATTCCCAAAATAGCACCATTTTCGAATTAATTCCCA
* * *
2584728 AAATAGCACCCATTTCAAATAAATTCTCAAAATAGCACC
1 AAATAGCACCCTTTTCAAATTAATTCCCAAAATAGCACC
2584767 CGGTCAACAG
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
57 47 0.56
58 37 0.44
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.30
Consensus pattern (58 bp):
AAATAGCACCCTTTTCAAATTAATTCCCAAAATAGCACCATTTTCGAATTAATTCCCA
Found at i:2586324 original size:57 final size:57
Alignment explanation
Indices: 2586262--2586370 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
2586252 AGGGTGCAAC
*
2586262 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATGAATTTCAGCAAGCATGTTAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
* *
2586319 TGCTTTTACATTTATTGCTTTTTGATTAATTTTCATAAATTTCAGCAAGCAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCAT
2586371 ATAAATGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.50
Consensus pattern (57 bp):
TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
Found at i:2587122 original size:25 final size:25
Alignment explanation
Indices: 2587080--2587130 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2587070 AACCGCACAG
2587080 AATTTGTCTCGAAGGACCACGTAGA
1 AATTTGTCTCGAAGGACCACGTAGA
* *
2587105 AATTTGTCAT-GAATGACCGCGTAGA
1 AATTTGTC-TCGAAGGACCACGTAGA
2587130 A
1 A
2587131 CCCTCGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (25 bp):
AATTTGTCTCGAAGGACCACGTAGA
Found at i:2587311 original size:15 final size:15
Alignment explanation
Indices: 2587235--2587311 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
2587225 GTCTTTTATC
2587235 CACATAGAACACTTT
1 CACATAGAACACTTT
** * *
2587250 TGCATAGAGCATTTT
1 CACATAGAACACTTT
* **
2587265 CACGTAGAACACAGT
1 CACATAGAACACTTT
2587280 CACATA-AAGCACTTT
1 CACATAGAA-CACTTT
*
2587295 CACATAGAACACATT
1 CACATAGAACACTTT
2587310 CA
1 CA
2587312 TATATTAACA
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:2589074 original size:24 final size:24
Alignment explanation
Indices: 2589001--2589069 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
2588991 CGGAGATATT
* *
2589001 AGAAATCAAAACAGAATTCATATC
1 AGAAATCAGAACAGAATTCAGATC
* * *
2589025 AGATATCATAATAGAA-TCTAGATC
1 AGAAATCAGAACAGAATTC-AGATC
*
2589049 ATAAATCAGAACAGAATTCAG
1 AGAAATCAGAACAGAATTCAG
2589070 GTCATGTATC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.06
24 31 0.89
25 2 0.06
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (24 bp):
AGAAATCAGAACAGAATTCAGATC
Found at i:2589103 original size:48 final size:48
Alignment explanation
Indices: 2589001--2589106 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
2588991 CGGAGATATT
* * *
2589001 AGAAATCAAAACAGAATTCATATCAGATATCATAATAGAATCTAGATC
1 AGAAATCAGAACAGAATTCAGATCAGATATCATAACAGAATCTAGATC
* * * *
2589049 ATAAATCAGAACAGAATTCAGGTCATG-TATCATAACATAATTTA-AGTC
1 AGAAATCAGAACAGAATTCAGATCA-GATATCATAACAGAATCTAGA-TC
2589097 AGAAATCAGA
1 AGAAATCAGA
2589107 TAAAATATTC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
47 1 0.02
48 46 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.25
Consensus pattern (48 bp):
AGAAATCAGAACAGAATTCAGATCAGATATCATAACAGAATCTAGATC
Found at i:2591413 original size:27 final size:28
Alignment explanation
Indices: 2591378--2591462 Score: 99
Period size: 27 Copynumber: 3.2 Consensus size: 28
2591368 TTTGGGTCAA
*
2591378 CAAATCGGGTCT-GGTCAACGGGTTGGGT
1 CAAA-CGGGTCTGGGTCAACGAGTTGGGT
2591406 CAAACGGGT-TGGGTCAACGAGTTGGGT
1 CAAACGGGTCTGGGTCAACGAGTTGGGT
* *
2591433 CAAACGGGTC-GGGCCAA--AATTGGGT
1 CAAACGGGTCTGGGTCAACGAGTTGGGT
2591458 CAAAC
1 CAAAC
2591463 TGCCCTAACA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 12 0.23
26 1 0.02
27 35 0.67
28 4 0.08
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.20
Consensus pattern (28 bp):
CAAACGGGTCTGGGTCAACGAGTTGGGT
Found at i:2591450 original size:14 final size:14
Alignment explanation
Indices: 2591390--2591441 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
2591380 AATCGGGTCT
2591390 GGTC-AACGGGTTG
1 GGTCAAACGGGTTG
2591403 GGTCAAACGGGTTG
1 GGTCAAACGGGTTG
*
2591417 GGTC-AACGAGTTG
1 GGTCAAACGGGTTG
2591430 GGTCAAACGGGT
1 GGTCAAACGGGT
2591442 CGGGCCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
13 16 0.46
14 19 0.54
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.21
Consensus pattern (14 bp):
GGTCAAACGGGTTG
Found at i:2593894 original size:17 final size:18
Alignment explanation
Indices: 2593872--2593910 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2593862 TTTTATTAAT
2593872 ATTTATGTATG-TGTGGC
1 ATTTATGTATGATGTGGC
*
2593889 ATTTATGTATGATGTGGT
1 ATTTATGTATGATGTGGC
2593907 ATTT
1 ATTT
2593911 TTCTCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:2594143 original size:31 final size:31
Alignment explanation
Indices: 2594108--2594168 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2594098 TAAAGCAGAT
*
2594108 GGAATATTTTTTTAATTT-AATTATAATTTTG
1 GGAATATTTATTTAATTTCAA-TATAATTTTG
* *
2594139 GGAATGTTTATTTGATTTCAATATAATTTT
1 GGAATATTTATTTAATTTCAATATAATTTT
2594169 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (31 bp):
GGAATATTTATTTAATTTCAATATAATTTTG
Found at i:2595743 original size:26 final size:26
Alignment explanation
Indices: 2595712--2595766 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
2595702 TTAAAACAAT
2595712 TATAAT-ATATATATATATATAAACTA
1 TATAATAATATA-ATATATATAAACTA
2595738 TATAATAATATAATATATATAAACTA
1 TATAATAATATAATATATATAAACTA
2595764 TAT
1 TAT
2595767 GGTTTATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
TATAATAATATAATATATATAAACTA
Found at i:2595759 original size:17 final size:18
Alignment explanation
Indices: 2595712--2595759 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
2595702 TTAAAACAAT
2595712 TATAATATATAT-ATATA
1 TATAATATATATAATATA
2595729 TATAA-ACTATATAATA-A
1 TATAATA-TATATAATATA
2595746 TATAATATATATAA
1 TATAATATATATAA
2595760 ACTATATGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 23 0.82
18 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAATATATATAATATA
Found at i:2595779 original size:20 final size:20
Alignment explanation
Indices: 2595762--2595808 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2595752 ATATATAAAC
*
2595762 TATATGGTTTATACATAATA
1 TATATAGTTTATACATAATA
*
2595782 TATATAGTTTATACATAGTA
1 TATATAGTTTATACATAATA
2595802 GTATATA
1 -TATATA
2595809 AGTATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (20 bp):
TATATAGTTTATACATAATA
Found at i:2595895 original size:13 final size:13
Alignment explanation
Indices: 2595851--2595976 Score: 52
Period size: 13 Copynumber: 10.0 Consensus size: 13
2595841 AATAATAAAC
*
2595851 TATATATGAACTA
1 TATATATAAACTA
* **
2595864 TATATAGAATAGAA
1 TATATATAA-ACTA
2595878 TTATATATAAACTA
1 -TATATATAAACTA
* *
2595892 TATAGTTTACAC-A
1 TATA-TATAAACTA
* *
2595905 AATATATATAC--
1 TATATATAAACTA
* *
2595916 TATGTATAAATTA
1 TATATATAAACTA
*
2595929 TATAGT-TTAA-TA
1 TATA-TATAAACTA
2595941 -ATATA-A-ACTA
1 TATATATAAACTA
*
2595951 TATATATAAATTA
1 TATATATAAACTA
2595964 TATATATAAACTA
1 TATATATAAACTA
2595977 AATAAATTAT
Statistics
Matches: 81, Mismatches: 21, Indels: 22
0.65 0.17 0.18
Matches are distributed among these distances:
9 1 0.01
10 3 0.04
11 15 0.19
12 8 0.10
13 36 0.44
14 10 0.12
15 8 0.10
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2595966 original size:22 final size:22
Alignment explanation
Indices: 2595941--2596024 Score: 57
Period size: 22 Copynumber: 3.7 Consensus size: 22
2595931 TAGTTTAATA
2595941 ATATAAACTATATATATAAATT
1 ATATAAACTATATATATAAATT
* * *
2595963 ATATATA-TAAACTAAATAAATT
1 ATATAAACTATA-TATATAAATT
*
2595985 ATATAATTTACTA-ATATA-AACAAT
1 ATATAA---ACTATATATATAA-ATT
*
2596009 ATATAAACCATATATA
1 ATATAAACTATATATA
2596025 CTATATGTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
21 6 0.12
22 25 0.52
23 2 0.04
24 11 0.23
25 2 0.04
26 2 0.04
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATAAACTATATATATAAATT
Found at i:2595982 original size:35 final size:35
Alignment explanation
Indices: 2595879--2595989 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 35
2595869 AGAATAGAAT
* *
2595879 TATATATAAACTATATAGTTTACACA-AATATATA-TA
1 TATATATAAATTATATAG-TTA-A-ATAATATAAACTA
* *
2595915 CTATGTATAAATTATATAGTTTAATAATATAAACTA
1 -TATATATAAATTATATAGTTAAATAATATAAACTA
*
2595951 TATATATAAATTATATA-TATAAACTAA-ATAAATTA
1 TATATATAAATTATATAGT-TAAA-TAATATAAACTA
2595986 TATA
1 TATA
2595990 ATTTACTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
34 2 0.03
35 38 0.60
36 7 0.11
37 16 0.25
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (35 bp):
TATATATAAATTATATAGTTAAATAATATAAACTA
Found at i:2596023 original size:57 final size:58
Alignment explanation
Indices: 2595921--2596029 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
2595911 TATACTATGT
* *
2595921 ATAAATTATATAGTTTAATAATATAAACTATATATATAAATTATATA-TATAAACTAA
1 ATAAATTATATAATTTAATAATATAAACTATATATATAAAATATATACTATAAACTAA
*
2595978 ATAAATTATATAATTTACTAATATAAAC-A-ATATATAAACCATATATACTATA
1 ATAAATTATATAATTTAATAATATAAACTATATATATAAA--ATATATACTATA
2596030 TGTGAATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
55 9 0.20
56 1 0.02
57 32 0.70
58 4 0.09
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (58 bp):
ATAAATTATATAATTTAATAATATAAACTATATATATAAAATATATACTATAAACTAA
Found at i:2596075 original size:9 final size:9
Alignment explanation
Indices: 2596058--2596144 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
2596048 TACAATTTAC
*
2596058 ATATGAACT
1 ATATAAACT
2596067 ATATAAACT
1 ATATAAACT
2596076 ATATAAACT
1 ATATAAACT
**
2596085 ATACTTTA-T
1 ATA-TAAACT
*
2596094 AAATAAACT
1 ATATAAACT
**
2596103 ATAGTCTA-T
1 ATA-TAAACT
2596112 ATATAAACT
1 ATATAAACT
**
2596121 ATAGTCTA-T
1 ATA-TAAACT
2596130 ATATAAACT
1 ATATAAACT
2596139 ATATAA
1 ATATAA
2596145 TTTATACATA
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
8 6 0.11
9 45 0.79
10 6 0.11
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (9 bp):
ATATAAACT
Found at i:2596150 original size:18 final size:18
Alignment explanation
Indices: 2596075--2596141 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
2596065 CTATATAAAC
* *
2596075 TATATAAACTATACTTTA
1 TATATAAACTATAGTATA
* *
2596093 TAAATAAACTATAGTCTA
1 TATATAAACTATAGTATA
*
2596111 TATATAAACTATAGTCTA
1 TATATAAACTATAGTATA
2596129 TATATAAACTATA
1 TATATAAACTATA
2596142 TAATTTATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (18 bp):
TATATAAACTATAGTATA
Found at i:2596211 original size:33 final size:33
Alignment explanation
Indices: 2596120--2596231 Score: 95
Period size: 33 Copynumber: 3.4 Consensus size: 33
2596110 ATATATAAAC
* * *
2596120 TATAGTCTATA-T-ATAAACTATATAATTTATA
1 TATAGTATATATTAATAAAATATATAACTTATA
* **
2596151 CATAGTAGTATA-TAAGTATAAATTATATGGCTTATA
1 TATAGTA-TATATTAA-TA-AAA-TATATAACTTATA
* *
2596187 TATAGTTTATATTAATAAAATATATAATTTATA
1 TATAGTATATATTAATAAAATATATAACTTATA
2596220 TATAGTATATAT
1 TATAGTATATAT
2596232 ATTTATAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
31 5 0.08
32 5 0.08
33 22 0.35
34 5 0.08
35 8 0.13
36 18 0.29
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (33 bp):
TATAGTATATATTAATAAAATATATAACTTATA
Found at i:2596221 original size:2 final size:2
Alignment explanation
Indices: 2596206--2596978 Score: 129
Period size: 2 Copynumber: 389.5 Consensus size: 2
2596196 TATTAATAAA
* * *
2596206 AT AT AT A- AT TT AT AT AT AGT AT AT AT AT TT AT A- AT -T AT AC
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * *
2596246 AT AGT AT AT AT AT AA AT AT AA AT -T AT AT AGT TT AT AT AT AT AGT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
* * * *
2596290 AT AT AT AGT TT AT AT TT AT AT -T AT AT TT AT AT AT AT ACT AT GT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
2596333 AT AA AT -T AT AT AGT TT AT -T A- AT AT AA ACT AT AT AT ACT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT A-T AT
* * * *
2596373 AT AGT TT AT ACT -T AT AT ACT ACT AT GT AT AA ACT AT AT AT AA AT
1 AT A-T AT AT A-T AT AT AT A-T A-T AT AT AT AT A-T AT AT AT AT AT
* * * *
2596417 CAT AT AT ACT AT AT AT AA AT -T AT AT AT AT AA ACT AA AT AA AT
1 -AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
2596459 -T AT AT AGT TT AC AT AT GA- ACT AT AT AT AT AA ACT A- AT AG ACT
1 AT AT AT A-T AT AT AT AT -AT A-T AT AT AT AT AT A-T AT AT AT A-T
* * * * *
2596501 AT AG AA AT -T AT AT AT AA AT AT TT AT AA ACT AT AT AGT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* *
2596543 TT AT AT AT ACT AT AT AT A- AT -T AT A- AT -T AT AT AT AT AT GT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2596582 AT AA AT -T AT AT AGT -T AT -T A- AT AT AA ACT AT AT AT AA ACC
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT A-T
* * * * *
2596621 AT AT AT ACT AT AT GT AA ACT AT AT AGT TT AC AT AT GA- AC A- AT
1 AT AT AT A-T AT AT AT AT A-T AT AT A-T AT AT AT AT -AT AT AT AT
* * * *
2596663 AT AT AT AA AT -T AT A- AA ACT AT AT ACT AT AGT TT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT A-T AT AT AT AT AT
* * *
2596704 AT AT AG AT AT AT AT AT -T AT AT AT -T AT AT AT -T AT AGT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * * *
2596744 GT TT AT AT A- AT AT AT AC AT AT A- AA AT AT A- AGT AT AC AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
2596783 AT ACT -T AT AT A- AGT AT AT A- AT A- AGT GT AT A- AGT AT AT AT
1 AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT A-T AT AT AT
* * * * * * *
2596822 -T TT AA AT GT AT AT AT AT -T GT AT AT AT GT GT AA ACT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
2596862 AA AC A- AT AC AT -T AT A- AGT AT AT A- AGT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT
* * * *
2596902 AA AA AT AT AT AT A- AA AGC AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
2596943 -T AT AG A- AGT AT AT A- AT AT AT AT AC AT AT AT A- AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2596979 AGTATACATT
Statistics
Matches: 553, Mismatches: 121, Indels: 194
0.64 0.14 0.22
Matches are distributed among these distances:
1 52 0.09
2 444 0.80
3 57 0.10
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2596309 original size:22 final size:21
Alignment explanation
Indices: 2596183--2596315 Score: 96
Period size: 22 Copynumber: 6.3 Consensus size: 21
2596173 TTATATGGCT
*
2596183 TATATATAGTTTATATTAATAA
1 TATATATAGTTTATATTTAT-A
* *
2596205 AATATATAATTTATA--TATA
1 TATATATAGTTTATATTTATA
*
2596224 GTATATATA-TTTATAATTATA
1 -TATATATAGTTTATATTTATA
* * **
2596245 CATAGTATA-TATATAAATATA
1 TATA-TATAGTTTATATTTATA
* *
2596266 AATTATATAGTTTATATATATA
1 TA-TATATAGTTTATATTTATA
2596288 GTATATATAGTTTATATTTATA
1 -TATATATAGTTTATATTTATA
2596310 T-TATAT
1 TATATAT
2596316 TTATATATAT
Statistics
Matches: 92, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.08
20 17 0.18
21 24 0.26
22 43 0.47
23 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.50
Consensus pattern (21 bp):
TATATATAGTTTATATTTATA
Found at i:2596313 original size:11 final size:11
Alignment explanation
Indices: 2596206--2596446 Score: 89
Period size: 11 Copynumber: 21.8 Consensus size: 11
2596196 TATTAATAAA
2596206 ATATATA-ATT
1 ATATATATATT
*
2596216 -TATATATAGT
1 ATATATATATT
2596226 ATATATAT-TT
1 ATATATATATT
*
2596236 ATA-AT-TATAC
1 ATATATATAT-T
2596246 ATAGTATATATAT
1 ATA-TATATAT-T
* *
2596259 AAATATAAATT
1 ATATATATATT
*
2596270 ATATA-GT-TT
1 ATATATATATT
*
2596279 ATATATATAGT
1 ATATATATATT
2596290 ATATATAGT-TT
1 ATATATA-TATT
2596301 ATAT-T-TA-T
1 ATATATATATT
2596309 AT-TATAT-TT
1 ATATATATATT
*
2596318 ATATATATACT
1 ATATATATATT
* *
2596329 ATGTATAAATT
1 ATATATATATT
*
2596340 ATATAGTTTATT
1 ATATA-TATATT
* *
2596352 A-ATATAAACT
1 ATATATATATT
2596362 ATATATACTA-T
1 ATATATA-TATT
*
2596373 ATAGTTTATACTT
1 ATA-TATATA-TT
2596386 ATATACTACTATGT
1 ATATA-TA-TAT-T
*
2596400 ATAAACTATATATAA
1 AT--A-TATATAT-T
*
2596415 ATCATATATACT
1 AT-ATATATATT
*
2596427 ATATATAAATT
1 ATATATATATT
2596438 ATATATATA
1 ATATATATA
2596447 AACTAAATAA
Statistics
Matches: 170, Mismatches: 33, Indels: 55
0.66 0.13 0.21
Matches are distributed among these distances:
7 1 0.01
8 6 0.04
9 20 0.12
10 20 0.12
11 67 0.39
12 21 0.12
13 19 0.11
14 6 0.04
15 5 0.03
16 3 0.02
17 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (11 bp):
ATATATATATT
Found at i:2596357 original size:31 final size:32
Alignment explanation
Indices: 2596311--2596442 Score: 112
Period size: 31 Copynumber: 4.1 Consensus size: 32
2596301 ATATTTATAT
*
2596311 TATA-TTTA-TATATATACTATGTATAAATTA
1 TATAGTTTATTATATATACTATGTATAAACTA
* *
2596341 TATAGTTTATTAATATAAACTA--TATATACTA
1 TATAGTTTATT-ATATATACTATGTATAAACTA
2596372 TATAGTTTATACTTATATACTACTATGTATAAACTA
1 TATAG-TT-TA-TTATATA-TACTATGTATAAACTA
** * * *
2596408 TATA-TAAATCATATATACTATATATAAATTA
1 TATAGTTTATTATATATACTATGTATAAACTA
2596439 TATA
1 TATA
2596443 TATAAACTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
30 4 0.05
31 34 0.41
32 9 0.11
33 17 0.20
34 7 0.08
36 12 0.14
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (32 bp):
TATAGTTTATTATATATACTATGTATAAACTA
Found at i:2596492 original size:13 final size:13
Alignment explanation
Indices: 2596426--2596535 Score: 57
Period size: 13 Copynumber: 8.3 Consensus size: 13
2596416 TCATATATAC
*
2596426 TATATATAAATTA
1 TATATATAAACTA
2596439 TATATATAAACTAAA
1 TATATATAAACT--A
* * * *
2596454 TAAATTATATAGTT
1 TATA-TATAAACTA
* *
2596468 TACATATGAACTA
1 TATATATAAACTA
2596481 TATATATAAACTAA
1 TATATATAAACT-A
* *
2596495 TAGACTATAGAAAT-
1 TATA-TATA-AACTA
2596509 TATATATAAA-TA
1 TATATATAAACTA
2596521 T-T-TATAAACTA
1 TATATATAAACTA
2596532 TATA
1 TATA
2596536 GTTATATTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
10 6 0.08
11 5 0.07
12 4 0.06
13 30 0.42
14 10 0.14
15 8 0.11
16 9 0.12
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2596535 original size:21 final size:23
Alignment explanation
Indices: 2596509--2596587 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 23
2596499 CTATAGAAAT
2596509 TATATATAAATATTTATA-A-AC
1 TATATATAAATATTTATATATAC
*
2596530 TATATAGT-TATATTTATATATAC
1 TATATA-TAAATATTTATATATAC
*
2596553 TATATATAATTATAATTATATATA-
1 TATATATAA--ATATTTATATATAC
*
2596577 TATGTATAAAT
1 TATATATAAAT
2596588 TATATAGTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
21 15 0.31
22 5 0.10
23 8 0.17
24 8 0.17
25 12 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (23 bp):
TATATATAAATATTTATATATAC
Found at i:2596585 original size:58 final size:55
Alignment explanation
Indices: 2596506--2596650 Score: 154
Period size: 56 Copynumber: 2.6 Consensus size: 55
2596496 AGACTATAGA
* * * *
2596506 AATTATATATAAATATTTATAAACTATATAGTTATATTTATATATACTATATATAATTAT
1 AATTATATAT--ATATGTATAAACTATATAGTT-TATTAATATAAACTATATATAA--AC
*
2596566 AATTATATATATATGTATAAATTATATAG-TTATTAATATAAACTATATATAAAC
1 AATTATATATATATGTATAAACTATATAGTTTATTAATATAAACTATATATAAAC
*
2596620 CA-TATATACTATATG--TAAACTATATAGTTTA
1 AATTATATA-TATATGTATAAACTATATAGTTTA
2596651 CATATGAACA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
52 11 0.14
53 9 0.12
54 8 0.11
56 20 0.26
57 1 0.01
58 17 0.22
60 10 0.13
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (55 bp):
AATTATATATATATGTATAAACTATATAGTTTATTAATATAAACTATATATAAAC
Found at i:2596588 original size:25 final size:25
Alignment explanation
Indices: 2596530--2596591 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
2596520 ATTTATAAAC
* *
2596530 TATATAGTTATATTTATATATACTA
1 TATATAATTATAATTATATATACTA
2596555 TATATAATTATAATTATATATA-TA
1 TATATAATTATAATTATATATACTA
*
2596579 TGTATAAATTATA
1 TATAT-AATTATA
2596592 TAGTTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 6 0.18
25 27 0.82
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (25 bp):
TATATAATTATAATTATATATACTA
Found at i:2596619 original size:11 final size:11
Alignment explanation
Indices: 2596601--2596645 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
2596591 ATAGTTATTA
2596601 ATATAAACTAT
1 ATATAAACTAT
*
2596612 ATATAAACCAT
1 ATATAAACTAT
2596623 ATAT--ACTAT
1 ATATAAACTAT
*
2596632 ATGTAAACTAT
1 ATATAAACTAT
2596643 ATA
1 ATA
2596646 GTTTACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.25
11 21 0.75
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (11 bp):
ATATAAACTAT
Found at i:2596689 original size:7 final size:7
Alignment explanation
Indices: 2596681--2596737 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
2596671 ATTATAAAAC
*
2596681 TATATAC
1 TATATAT
2596688 TATAGT-T
1 TATA-TAT
2596695 TATAT-T
1 TATATAT
2596701 TATATA-
1 TATATAT
*
2596707 TAGATA-
1 TATATAT
2596713 TATATAT
1 TATATAT
2596720 TATATAT
1 TATATAT
2596727 TATATAT
1 TATATAT
2596734 TATA
1 TATA
2596738 GTTTTTGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
6 17 0.39
7 26 0.59
8 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:2596886 original size:8 final size:7
Alignment explanation
Indices: 2596873--2597031 Score: 51
Period size: 8 Copynumber: 21.3 Consensus size: 7
2596863 AACAATACAT
2596873 TATAAGTA
1 TATAA-TA
2596881 TATAAGTA
1 TATAA-TA
*
2596889 TAT-ATC
1 TATAATA
2596895 TAT-ATA
1 TATAATA
*
2596901 TA-AAAA
1 TATAATA
2596907 TAT-ATA
1 TATAATA
* *
2596913 TAAAAGCA
1 TATAA-TA
2596921 TATATATA
1 TATA-ATA
2596929 TATATATA
1 TATA-ATA
2596937 TATAATTA
1 TATAA-TA
*
2596945 TAGAAGTA
1 TATAA-TA
2596953 TATAATATA
1 TAT-A-ATA
2596962 TATACATA
1 TATA-ATA
2596970 TATAATA
1 TATAATA
2596977 TA-AGTATA
1 TATA--ATA
* *
2596985 CATTATA
1 TATAATA
2596992 CGTATAAGTA
1 --TATAA-TA
*
2597002 TA-AGTA
1 TATAATA
2597008 TATAATA
1 TATAATA
*
2597015 TAAAATA
1 TATAATA
2597022 TATAAGTA
1 TATAA-TA
2597030 TA
1 TA
2597032 AAGTACATAT
Statistics
Matches: 115, Mismatches: 20, Indels: 32
0.69 0.12 0.19
Matches are distributed among these distances:
6 21 0.18
7 25 0.22
8 56 0.49
9 10 0.09
10 3 0.03
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (7 bp):
TATAATA
Found at i:2596984 original size:19 final size:19
Alignment explanation
Indices: 2596923--2597017 Score: 81
Period size: 19 Copynumber: 4.9 Consensus size: 19
2596913 TAAAAGCATA
* *
2596923 TATATATATATATATATAAT
1 TATACATATATA-ATATAAG
*
2596943 TATAGAAGTATATAATAT-A-
1 TATA-CA-TATATAATATAAG
2596962 TATACATATATAATATAAG
1 TATACATATATAATATAAG
*
2596981 TATACAT-TATACGTATAAG
1 TATACATATATA-ATATAAG
2597000 TATA-AGTATATAATATAA
1 TATACA-TATATAATATAA
2597018 AATATATAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
17 10 0.16
18 7 0.11
19 27 0.42
20 9 0.14
21 5 0.08
22 6 0.09
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (19 bp):
TATACATATATAATATAAG
Found at i:2597016 original size:25 final size:24
Alignment explanation
Indices: 2596970--2597016 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2596960 TATATACATA
*
2596970 TATAATATAAGTATACATTATACG
1 TATAATATAAGTATACAATATACG
*
2596994 TATAAGTATAAGTATATAATATA
1 TATAA-TATAAGTATACAATATA
2597017 AAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (24 bp):
TATAATATAAGTATACAATATACG
Found at i:2597084 original size:18 final size:18
Alignment explanation
Indices: 2597054--2597095 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
2597044 ATAGGAATAA
2597054 ATTAAATATGTATAAAAT
1 ATTAAATATGTATAAAAT
2597072 ATATAAA-ATGTATAAAAT
1 AT-TAAATATGTATAAAAT
2597090 ATTAAA
1 ATTAAA
2597096 GTATAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
ATTAAATATGTATAAAAT
Found at i:2597139 original size:2 final size:2
Alignment explanation
Indices: 2597134--2597236 Score: 206
Period size: 2 Copynumber: 51.5 Consensus size: 2
2597124 TATATATGTC
2597134 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2597176 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2597218 TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
2597237 AAGATATATA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 101 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2598071 original size:182 final size:182
Alignment explanation
Indices: 2597827--2598212 Score: 607
Period size: 185 Copynumber: 2.1 Consensus size: 182
2597817 TTTTCTAACT
* * *
2597827 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAATATTCTAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAATTCTAATTAATTTAAATAATATATAAT
* *
2597891 TTTAAAATAAAAATTTTATAT-TTTTTTAATTAATTAATATTGATTTATGTTTAAAAGTTATTGG
66 TATAAAATAAAAATTTTATATATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGG
* *
2597955 ATCTTAAATTATTAATTGAGTTTTAAACGGTTTGGGCTGAGTCCATATGTTA
131 ATCTTAAATTATTAATTGAGTTTTAAACGGTTTAGGCTGAGCCCATATGTTA
2598007 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAATTAC-AATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAA-AATT-CTAATTAATTTAAATAATATATA
2598071 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
64 ATTATAAAATAAAAATTTTATAT--ATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* ** *
2598136 TTGGATCTTAAATTATTAATTGGGTTTTAAGTGGTTTAGGTTGAGCCCATATGTTA
127 TTGGATCTTAAATTATTAATTGAGTTTTAAACGGTTTAGGCTGAGCCCATATGTTA
*
2598192 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
2598213 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
180 7 0.04
181 26 0.14
182 46 0.24
183 1 0.01
185 108 0.57
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (182 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAATTCTAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTTATATATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGG
ATCTTAAATTATTAATTGAGTTTTAAACGGTTTAGGCTGAGCCCATATGTTA
Found at i:2598440 original size:50 final size:51
Alignment explanation
Indices: 2598383--2598546 Score: 228
Period size: 50 Copynumber: 3.3 Consensus size: 51
2598373 TGAACACCCC
*
2598383 TAGATCTAACCCAAAAAATCATTGTTCATCCGGAAAAAAATCTCA-CTTTT
1 TAGATCTAACCCAAAAAATCATTGTTCATCCGGAAAAAAATCTCATTTTTT
*
2598433 TAGATCTAACCCAAAAAATTATTGTTCATCC--AAAAAAATCTCATTTTTT
1 TAGATCTAACCCAAAAAATCATTGTTCATCCGGAAAAAAATCTCATTTTTT
* * * *
2598482 TATATCTAACCCAGAAAATCACTGTTCATCCGG-AAAATATCTCATATTTTTT
1 TAGATCTAACCCAAAAAATCATTGTTCATCCGGAAAAAAATCTC--ATTTTTT
2598534 TAGATCTAACCCA
1 TAGATCTAACCCA
2598547 GGAATAGCAC
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
48 12 0.12
49 31 0.31
50 39 0.39
52 19 0.19
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (51 bp):
TAGATCTAACCCAAAAAATCATTGTTCATCCGGAAAAAAATCTCATTTTTT
Found at i:2598914 original size:26 final size:25
Alignment explanation
Indices: 2598851--2598915 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
2598841 AAAATATGTG
*
2598851 TTTTATAATTTTATTTTATTTTCCT
1 TTTTATAATTTTTTTTTATTTTCCT
*
2598876 TTTTAT-ATGTTTTTTTCTTTTTTCCT
1 TTTTATAAT-TTTTTTT-TATTTTCCT
2598902 TTTTATAATTTTTT
1 TTTTATAATTTTTT
2598916 ATATTATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 2 0.06
25 12 0.34
26 19 0.54
27 2 0.06
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTATAATTTTTTTTTATTTTCCT
Found at i:2598959 original size:21 final size:20
Alignment explanation
Indices: 2598929--2598967 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2598919 TTATGTTTTG
*
2598929 TATTTGTTTTTTATTATTAA
1 TATTTGTTTTGTATTATTAA
2598949 TATTGTGTTTTGTATTATT
1 TATT-TGTTTTGTATTATT
2598968 TTTTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (20 bp):
TATTTGTTTTGTATTATTAA
Found at i:2598960 original size:26 final size:25
Alignment explanation
Indices: 2598910--2598961 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
2598900 CTTTTTATAA
* *
2598910 TTTTTTATATTATGTTTTGTATTTG
1 TTTTTTATATTATATTGTGTATTTG
2598935 TTTTTTATTATTAATATTGTGT-TTTG
1 TTTTTTA-TATT-ATATTGTGTATTTG
2598961 T
1 T
2598962 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 7 0.30
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (25 bp):
TTTTTTATATTATATTGTGTATTTG
Found at i:2599039 original size:21 final size:21
Alignment explanation
Indices: 2599013--2599125 Score: 65
Period size: 20 Copynumber: 5.1 Consensus size: 21
2599003 TGTTTTGTTT
2599013 TTTGTTATATGTTATTTATTA
1 TTTGTTATATGTTATTTATTA
2599034 TTTGTTGTGTATATGTTA-TTATT-
1 --T-TTGT-TATATGTTATTTATTA
**
2599057 TTTCGTTACCTGTT-TTTATT-
1 TTT-GTTATATGTTATTTATTA
* *
2599077 TTT-TTGTTATGTTTTTTATTTA
1 TTTGTT-ATATGTTATTTA-TTA
2599099 TATAGTGTTATATGTTATTTATTA
1 T-T--TGTTATATGTTATTTATTA
2599123 TTT
1 TTT
2599126 TTTGTATATG
Statistics
Matches: 71, Mismatches: 7, Indels: 26
0.68 0.07 0.25
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 20 0.28
21 6 0.08
22 1 0.01
23 3 0.04
24 13 0.18
25 20 0.28
26 2 0.03
ACGTcount: A:0.19, C:0.03, G:0.12, T:0.67
Consensus pattern (21 bp):
TTTGTTATATGTTATTTATTA
Found at i:2599140 original size:21 final size:21
Alignment explanation
Indices: 2599010--2599151 Score: 73
Period size: 21 Copynumber: 6.3 Consensus size: 21
2599000 GTATGTTTTG
2599010 TTTTTTGTTATATGTTATTTATTA
1 TTTTTTG-TATATG-T-TTTATTA
2599034 TTTGTTGTGTATATG--TTATTA
1 TTT-TT-TGTATATGTTTTATTA
*
2599055 TTTTTCGT-TACCTG-TTT-TTA
1 TTTTTTGTATA--TGTTTTATTA
2599075 TTTTTTTGT-TATGTTTT-TTA
1 -TTTTTTGTATATGTTTTATTA
2599095 TTTATATAGTGTTATATGTTATTTATTA
1 TTT-T-T--TG-TATATG-T-TTTATTA
2599123 TTTTTTGTATATGTTTTATATA
1 TTTTTTGTATATGTTTTAT-TA
2599145 TTATTTT
1 TT-TTTT
2599152 TCGTTATCTG
Statistics
Matches: 98, Mismatches: 2, Indels: 37
0.72 0.01 0.27
Matches are distributed among these distances:
18 2 0.02
19 7 0.07
20 14 0.14
21 26 0.27
22 5 0.05
23 12 0.12
24 6 0.06
25 12 0.12
26 4 0.04
27 4 0.04
28 6 0.06
ACGTcount: A:0.19, C:0.02, G:0.11, T:0.68
Consensus pattern (21 bp):
TTTTTTGTATATGTTTTATTA
Found at i:2599163 original size:93 final size:92
Alignment explanation
Indices: 2599015--2599190 Score: 245
Period size: 93 Copynumber: 1.9 Consensus size: 92
2599005 TTTTGTTTTT
2599015 TGTTATATGTTATTTATTATTTGTTGTGTATATGTTATTATTTTTCGTTACCTGTTTTTAT-TT-
1 TGTTATATGTTATTTATTATTTGTTGTGTATATGTTATTATTTTTCGTTACCTGTTTTTATATTA
2599078 T-TTTGTTATGTTTTTTATTTATATAG
66 TGTTTGTTATGTTTTTTATTTATATAG
*
2599104 TGTTATATGTTATTTATTATTT-TT-TGTATATGTTTTATATATTATTTTTCGTTATCTGTTTTT
1 TGTTATATGTTATTTATTATTTGTTGTGTATATG-----T-TATTATTTTTCGTTACCTGTTTTT
*
2599167 ATATTATGTTTGTTTTGTTTTTTA
60 ATATTATGTTTGTTATGTTTTTTA
2599191 GTAGTATGTT
Statistics
Matches: 76, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
87 8 0.11
88 2 0.03
89 22 0.29
92 1 0.01
93 25 0.33
94 2 0.03
95 1 0.01
96 15 0.20
ACGTcount: A:0.18, C:0.03, G:0.11, T:0.68
Consensus pattern (92 bp):
TGTTATATGTTATTTATTATTTGTTGTGTATATGTTATTATTTTTCGTTACCTGTTTTTATATTA
TGTTTGTTATGTTTTTTATTTATATAG
Found at i:2599168 original size:48 final size:46
Alignment explanation
Indices: 2599050--2599187 Score: 138
Period size: 48 Copynumber: 2.9 Consensus size: 46
2599040 GTGTATATGT
* *
2599050 TATTATTTTTCGTTACCTGTTTTTA-TTTTTTTGTTATGTTTTTTA
1 TATTATTTTTCGTTATCTGTTTTTATTTTTTTTGTTATGTTTTATA
** *
2599095 T-TTATATAGT-GTTATATGTTATTTATTATTTTTTGTATATGTTTTATA
1 TATTAT-TTTTCGTTATCTGTT-TTTATT-TTTTTTGT-TATGTTTTATA
* *
2599143 TATTATTTTTCGTTATCTGTTTTTATATTATGTTTGTTTTGTTTT
1 TATTATTTTTCGTTATCTGTTTTTAT-TT-TTTTTGTTATGTTTT
2599188 TTAGTAGTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
44 12 0.16
45 7 0.09
46 1 0.01
47 8 0.11
48 26 0.35
49 20 0.27
ACGTcount: A:0.17, C:0.04, G:0.10, T:0.69
Consensus pattern (46 bp):
TATTATTTTTCGTTATCTGTTTTTATTTTTTTTGTTATGTTTTATA
Found at i:2599169 original size:25 final size:24
Alignment explanation
Indices: 2599011--2599188 Score: 107
Period size: 23 Copynumber: 7.8 Consensus size: 24
2599001 TATGTTTTGT
*
2599011 TTTTTGTTATATGTTATT-TATTA
1 TTTTTGTTATATGTTTTTATATTA
2599034 TTTGTTGTGTATATG----T-TATTA
1 TTT-TTGT-TATATGTTTTTATATTA
**
2599055 TTTTTCGTTACCTG-TTTT-TATT-
1 TTTTT-GTTATATGTTTTTATATTA
*
2599077 TTTTTGTTATGT-TTTTTAT-TTA
1 TTTTTGTTATATGTTTTTATATTA
** *
2599099 TATAGTGTTATATGTTATT-TATTA
1 T-TTTTGTTATATGTTTTTATATTA
2599123 TTTTT-TGTATATGTTTTATATATTA
1 TTTTTGT-TATATGTTTT-TATATTA
*
2599148 TTTTTCGTTATCTGTTTTTATATTA
1 TTTTT-GTTATATGTTTTTATATTA
*
2599173 TGTTTGTT-T-TGTTTTT
1 TTTTTGTTATATGTTTTT
2599189 TAGTAGTATG
Statistics
Matches: 125, Mismatches: 13, Indels: 35
0.72 0.08 0.20
Matches are distributed among these distances:
20 6 0.05
21 22 0.18
22 15 0.12
23 29 0.23
24 16 0.13
25 27 0.22
26 9 0.07
27 1 0.01
ACGTcount: A:0.17, C:0.03, G:0.11, T:0.69
Consensus pattern (24 bp):
TTTTTGTTATATGTTTTTATATTA
Found at i:2599202 original size:15 final size:15
Alignment explanation
Indices: 2599182--2599211 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2599172 ATGTTTGTTT
2599182 TGTTTTTTAGTAGTA
1 TGTTTTTTAGTAGTA
*
2599197 TGTTTTTTATTAGTA
1 TGTTTTTTAGTAGTA
2599212 ATTCTAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (15 bp):
TGTTTTTTAGTAGTA
Found at i:2600097 original size:14 final size:14
Alignment explanation
Indices: 2600078--2600104 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2600068 TTTTTATAAT
2600078 TTTAATTATTTTAA
1 TTTAATTATTTTAA
2600092 TTTAATTATTTTA
1 TTTAATTATTTTA
2600105 TTTTCACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTATTTTAA
Found at i:2600567 original size:4 final size:4
Alignment explanation
Indices: 2600558--2600596 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
2600548 ATTTAAATTG
2600558 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2600597 TTTGCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2600821 original size:57 final size:57
Alignment explanation
Indices: 2600759--2600867 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
2600749 AGGGTGCAAC
*
2600759 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATGAATTTCAGCAAGCATGTTAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
*
2600816 TGCTTTTACATTTACTGCTTTTTGATTAATTTTCATAAATTTCAGCAAGCAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCAT
2600868 ATAAATGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.49
Consensus pattern (57 bp):
TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
Found at i:2608536 original size:24 final size:24
Alignment explanation
Indices: 2608499--2608572 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
2608489 TGCCACATAG
* *
2608499 ATTTGTCCAAAAGGATCGCGTAGA
1 ATTTGTCCAGAAGGACCGCGTAGA
* *
2608523 ATTTGTCCTGAAGGACCACGTAGAA
1 ATTTGTCCAGAAGGACCGCGTAG-A
* * *
2608548 ATTTTTCCCGAATGACCGCGTAGA
1 ATTTGTCCAGAAGGACCGCGTAGA
2608572 A
1 A
2608573 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (24 bp):
ATTTGTCCAGAAGGACCGCGTAGA
Found at i:2608564 original size:25 final size:25
Alignment explanation
Indices: 2608475--2608572 Score: 69
Period size: 25 Copynumber: 4.0 Consensus size: 25
2608465 CTACTCATAT
* *
2608475 AATTTGTACCGAAGTG-CCACATAG-
1 AATTTGTCCCGAAG-GACCACGTAGA
** * *
2608499 -ATTTGTCCAAAAGGATCGCGTAG-
1 AATTTGTCCCGAAGGACCACGTAGA
*
2608522 AATTTGTCCTGAAGGACCACGTAGA
1 AATTTGTCCCGAAGGACCACGTAGA
* * *
2608547 AATTTTTCCCGAATGACCGCGTAGA
1 AATTTGTCCCGAAGGACCACGTAGA
2608572 A
1 A
2608573 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.02
23 15 0.26
24 19 0.33
25 22 0.39
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (25 bp):
AATTTGTCCCGAAGGACCACGTAGA
Found at i:2610233 original size:28 final size:28
Alignment explanation
Indices: 2610200--2610264 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
2610190 TTGTCTTGTA
2610200 AATTGTTGTTATTGGTCTGATAGAACTC
1 AATTGTTGTTATTGGTCTGATAGAACTC
2610228 AATTGTTGTTATTGGTCTGATAGAACTC
1 AATTGTTGTTATTGGTCTGATAGAACTC
2610256 AATTGTTGT
1 AATTGTTGT
2610265 AAATTCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.45
Consensus pattern (28 bp):
AATTGTTGTTATTGGTCTGATAGAACTC
Found at i:2611642 original size:29 final size:30
Alignment explanation
Indices: 2611599--2611668 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
2611589 TTTGTATCTT
*
2611599 TTATACCACTAAACTTTTAATTT-TTTCAA
1 TTATACCACTAAACTTTGAATTTGTTTCAA
* * *
2611628 TTATAACACTGAACTTTGATTTTGTTTCAA
1 TTATACCACTAAACTTTGAATTTGTTTCAA
2611658 TTATACCACTA
1 TTATACCACTA
2611669 GGCCGTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (30 bp):
TTATACCACTAAACTTTGAATTTGTTTCAA
Found at i:2613743 original size:15 final size:15
Alignment explanation
Indices: 2613725--2613759 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2613715 TAAAAGTATA
2613725 AAATTTAAATTACTG
1 AAATTTAAATTACTG
*
2613740 AAATTTAGATTACTG
1 AAATTTAAATTACTG
2613755 AAATT
1 AAATT
2613760 ATGACTAAAT
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:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (15 bp):
AAATTTAAATTACTG
Found at i:2614383 original size:20 final size:20
Alignment explanation
Indices: 2614347--2614387 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
2614337 CAACTTAGCC
2614347 ATAATAGAAAACCTTTTTGT
1 ATAATAGAAAACCTTTTTGT
2614367 ATAA-AGAAAACCTTTTTGT
1 ATAATAGAAAACCTTTTTGT
2614386 AT
1 AT
2614388 TTGGCTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (20 bp):
ATAATAGAAAACCTTTTTGT
Found at i:2621770 original size:181 final size:181
Alignment explanation
Indices: 2621468--2621829 Score: 658
Period size: 181 Copynumber: 2.0 Consensus size: 181
2621458 AATCTTTTTA
2621468 TAAAGGGTGAAGAGCAAAGAAATGGATGTGCTTTCAAATGAAGTTTTGTCAAGGCTTTAGTAAGC
1 TAAAGGGTGAAGAGCAAAGAAATGGATGTGCTTTCAAATGAAGTTTTGTCAAGGCTTTAGTAAGC
*
2621533 AGGGCAGAACAGTGAGTAGTTAATATCCTTTTTGTAAACATGGCGGATGTTTATATTTCTCAGAT
66 AGGGCAGAACAGTGAGTAGTTAATATCCTTTTAGTAAACATGGCGGATGTTTATATTTCTCAGAT
2621598 TTTTCTCTCAAC-A-TATCATGATATTACCAGTGCATCCTTGTGTCCGAAC
131 TTTTCTCTCAACAATTATCATGATATTACCAGTGCATCCTTGTGTCCGAAC
2621647 TAAAGGGTGAAGAGCAAAGAAACTGGATGTGCTTTCAAATGAAGTTTTTGTCAAGGC-TTAGTAA
1 TAAAGGGTGAAGAGCAAAGAAA-TGGATGTGCTTTCAAATGAAG-TTTTGTCAAGGCTTTAGTAA
2621711 GCAGTGGCAGAACAGTGAGTAGTTAATATCCTTTTAGTAAACATGGCGGATGTTTATATTTCTCA
64 GCAG-GGCAGAACAGTGAGTAGTTAATATCCTTTTAGTAAACATGGCGGATGTTTATATTTCTCA
2621776 GATTTTTCTCTCAACATATTATCATGATATTACCAGTGCATCCTTGTGTCCGAA
128 GATTTTTCTCTCAACA-ATTATCATGATATTACCAGTGCATCCTTGTGTCCGAA
2621830 GATGAAGAGA
Statistics
Matches: 176, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
179 22 0.12
180 32 0.18
181 86 0.49
183 1 0.01
184 35 0.20
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (181 bp):
TAAAGGGTGAAGAGCAAAGAAATGGATGTGCTTTCAAATGAAGTTTTGTCAAGGCTTTAGTAAGC
AGGGCAGAACAGTGAGTAGTTAATATCCTTTTAGTAAACATGGCGGATGTTTATATTTCTCAGAT
TTTTCTCTCAACAATTATCATGATATTACCAGTGCATCCTTGTGTCCGAAC
Done.