Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 42
Found at i:1921966 original size:30 final size:30
Alignment explanation
Indices: 1921878--1921980 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
1921868 TTTTTCATTC
* *
1921878 AAGTAT-TAAAGTA-TTTTTTAATCAAAAT
1 AAGTATCTAAAATATTTTTTTAGTCAAAAT
*
1921906 AAGTATCTACAATTATTTTTTTACGT--AAAT
1 AAGTATCTA-AAATATTTTTTTA-GTCAAAAT
*
1921936 AAGTATCTAAAATATTTTTTTTGTCAAAAT
1 AAGTATCTAAAATATTTTTTTAGTCAAAAT
* *
1921966 AGGTACCTAAAATAT
1 AAGTATCTAAAATAT
1921981 ACATATTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
28 8 0.13
29 13 0.21
30 34 0.54
31 7 0.11
32 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (30 bp):
AAGTATCTAAAATATTTTTTTAGTCAAAAT
Found at i:1922821 original size:16 final size:16
Alignment explanation
Indices: 1922800--1922871 Score: 58
Period size: 16 Copynumber: 4.3 Consensus size: 16
1922790 ATTCCCTATC
1922800 TTCTTTTTCTTCACTT
1 TTCTTTTTCTTCACTT
*
1922816 TTCTTTTTCTTTA-TT
1 TTCTTTTTCTTCACTT
1922831 TCTCTTCACGTTTCTTCAC-T
1 T-TCTT----TTTCTTCACTT
* *
1922851 TTCTTTCTCTTCATTT
1 TTCTTTTTCTTCACTT
1922867 TTCTT
1 TTCTT
1922872 CACTTTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
15 10 0.22
16 22 0.49
19 4 0.09
20 9 0.20
ACGTcount: A:0.07, C:0.25, G:0.01, T:0.67
Consensus pattern (16 bp):
TTCTTTTTCTTCACTT
Found at i:1922854 original size:35 final size:36
Alignment explanation
Indices: 1922805--1922882 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 36
1922795 CTATCTTCTT
* *
1922805 TTTCTTCACTTTTCTTTTTCTTTATTTCTCTTCACG
1 TTTCTTCACTTTTCTTTCTCTTCATTTCTCTTCACG
* *
1922841 TTTCTTCAC-TTTCTTTCTCTTCATTTTTCTTCACT
1 TTTCTTCACTTTTCTTTCTCTTCATTTCTCTTCACG
1922876 TTTCTTC
1 TTTCTTC
1922883 TTTCGCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
35 29 0.76
36 9 0.24
ACGTcount: A:0.08, C:0.27, G:0.01, T:0.64
Consensus pattern (36 bp):
TTTCTTCACTTTTCTTTCTCTTCATTTCTCTTCACG
Found at i:1922858 original size:25 final size:25
Alignment explanation
Indices: 1922800--1922877 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
1922790 ATTCCCTATC
* **
1922800 TTCTTTTTCTTCACTTTTCTTTTTCT
1 TTCTTTCTCTTCACTTTTC-TTCACT
* *
1922826 TTATTTCTCTTCACGTTTCTTCACT
1 TTCTTTCTCTTCACTTTTCTTCACT
*
1922851 TTCTTTCTCTTCATTTTTCTTCACT
1 TTCTTTCTCTTCACTTTTCTTCACT
1922876 TT
1 TT
1922878 TCTTCTTTCG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 28 0.64
26 16 0.36
ACGTcount: A:0.08, C:0.26, G:0.01, T:0.65
Consensus pattern (25 bp):
TTCTTTCTCTTCACTTTTCTTCACT
Found at i:1924272 original size:25 final size:26
Alignment explanation
Indices: 1924237--1924311 Score: 116
Period size: 25 Copynumber: 2.9 Consensus size: 26
1924227 TAAATGAACA
*
1924237 ATGAACAAAAGTGAAGAGAAAGAAAG
1 ATGAAGAAAAGTGAAGAGAAAGAAAG
1924263 -TGAAGAAAAGTGAAGAGAAAGAAAG
1 ATGAAGAAAAGTGAAGAGAAAGAAAG
* *
1924288 AAGAAGAAAAGTGAAGAAAAAGAA
1 ATGAAGAAAAGTGAAGAGAAAGAA
1924312 GACGGGGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 24 0.53
26 21 0.47
ACGTcount: A:0.64, C:0.01, G:0.28, T:0.07
Consensus pattern (26 bp):
ATGAAGAAAAGTGAAGAGAAAGAAAG
Found at i:1924300 original size:26 final size:25
Alignment explanation
Indices: 1924243--1924311 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 25
1924233 AACAATGAAC
*
1924243 AAAAGTGAAGAGAAAGAAAGTGAAG
1 AAAAGTGAAGAGAAAGAAAGAGAAG
1924268 AAAAGTGAAGAGAAAGAAAGAAGAAG
1 AAAAGTGAAGAGAAAGAAAG-AGAAG
*
1924294 AAAAGTGAAGAAAAAGAA
1 AAAAGTGAAGAGAAAGAA
1924312 GACGGGGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (25 bp):
AAAAGTGAAGAGAAAGAAAGAGAAG
Found at i:1938243 original size:2 final size:2
Alignment explanation
Indices: 1938204--1938229 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1938194 TTCAAGTGTA
1938204 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
1938230 GATTCATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1942169 original size:41 final size:42
Alignment explanation
Indices: 1942110--1942199 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 42
1942100 CTAATGATAA
* * * *
1942110 GGTTTAGGGTTTAGAGTTTATGTGATAAGG-TTT-ATGTATAG
1 GGTTTAGAGTTTAAAGTTTATATGAT-AGGATTTAAGGTATAG
*
1942151 GGTTTAGAGTTTAAAGTTTATATGATAGGATTTAAGGTTTAG
1 GGTTTAGAGTTTAAAGTTTATATGATAGGATTTAAGGTATAG
1942193 GGTTTAG
1 GGTTTAG
1942200 GTGTTAGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.07
41 26 0.62
42 13 0.31
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (42 bp):
GGTTTAGAGTTTAAAGTTTATATGATAGGATTTAAGGTATAG
Found at i:1942193 original size:14 final size:15
Alignment explanation
Indices: 1942176--1942212 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1942166 GTTTATATGA
*
1942176 TAGGATTTAAGGT-T
1 TAGGGTTTAAGGTGT
1942190 TAGGGTTT-AGGTGT
1 TAGGGTTTAAGGTGT
1942204 TAGGGTTTA
1 TAGGGTTTA
1942213 GAGTTTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (15 bp):
TAGGGTTTAAGGTGT
Found at i:1942200 original size:21 final size:21
Alignment explanation
Indices: 1942176--1942247 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
1942166 GTTTATATGA
1942176 TAGGATTTAAGGTTTAGGGTT
1 TAGGATTTAAGGTTTAGGGTT
* *
1942197 TAGG-TGTTAGGGTTTAGAGTT
1 TAGGAT-TTAAGGTTTAGGGTT
* *
1942218 TATGTGA--TAAGATTTAGGGGT
1 TA-G-GATTTAAGGTTTAGGGTT
1942239 TAGGATTTA
1 TAGGATTTA
1942248 GAGTTTAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 33 0.85
22 1 0.03
23 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (21 bp):
TAGGATTTAAGGTTTAGGGTT
Found at i:1942213 original size:14 final size:13
Alignment explanation
Indices: 1942185--1942219 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
1942175 ATAGGATTTA
1942185 AGGTTTAGGGTTT
1 AGGTTTAGGGTTT
1942198 AGGTGTTAGGGTTT
1 AGGT-TTAGGGTTT
1942212 AGAGTTTA
1 AG-GTTTA
1942220 TGTGATAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 14 0.70
15 2 0.10
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (13 bp):
AGGTTTAGGGTTT
Found at i:1942218 original size:49 final size:49
Alignment explanation
Indices: 1942154--1942248 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
1942144 TGTATAGGGT
* * *
1942154 TTAGAGTTTAAAGTTTATATGATAGGATTTAAGGTTTAGGGTTTAGGTG
1 TTAGAGTTTAAAGTTTATATGATAAGATTTAAGGGTTAGGATTTAGGTG
* * * *
1942203 TTAGGGTTTAGAGTTTATGTGATAAGATTTAGGGGTTAGGATTTAG
1 TTAGAGTTTAAAGTTTATATGATAAGATTTAAGGGTTAGGATTTAG
1942249 AGTTTAAGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (49 bp):
TTAGAGTTTAAAGTTTATATGATAAGATTTAAGGGTTAGGATTTAGGTG
Found at i:1942256 original size:28 final size:28
Alignment explanation
Indices: 1942231--1942285 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1942221 GTGATAAGAT
*
1942231 TTAGGGGTTAGGATTT-AGAGTTTAAGTA
1 TTAGGGGTAAGGATTTAAG-GTTTAAGTA
*
1942259 TTAGGGGTAAGGGTTTAAGGTTTAAGT
1 TTAGGGGTAAGGATTTAAGGTTTAAGT
1942286 TATGCATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (28 bp):
TTAGGGGTAAGGATTTAAGGTTTAAGTA
Found at i:1945147 original size:23 final size:23
Alignment explanation
Indices: 1945121--1945167 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1945111 AGTCGAGTTT
1945121 CACTATTATATTTTAAGTTCAAG
1 CACTATTATATTTTAAGTTCAAG
1945144 CACTATTATATTTTAAGTTCAAG
1 CACTATTATATTTTAAGTTCAAG
1945167 C
1 C
1945168 TGAGCTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (23 bp):
CACTATTATATTTTAAGTTCAAG
Found at i:1950761 original size:44 final size:44
Alignment explanation
Indices: 1950717--1950893 Score: 171
Period size: 44 Copynumber: 4.0 Consensus size: 44
1950707 TTATGAAAAT
* * * * *
1950717 GCCGTAATAGGTCTGGTATTTAGCGATGTTTTTAGGGTACAAAT
1 GCCGTGATAGGTCTGGTATATAGCGACGTTTTTAGGATACAAAC
* * * *
1950761 GTCGCT-ATAGGACTGGAATATAGCGGCGTTTTTAGGATACAAAC
1 GCCG-TGATAGGTCTGGTATATAGCGACGTTTTTAGGATACAAAC
* * * *
1950805 GTCATGATAGGTCAGGTATATAGCGACATTTTTAGGATACAAAC
1 GCCGTGATAGGTCTGGTATATAGCGACGTTTTTAGGATACAAAC
* * *
1950849 GCCGCGATAGGTCTGCTATATAGCGGCGTTTTTTA--ATACAAAC
1 GCCGTGATAGGTCTGGTATATAGCGACG-TTTTTAGGATACAAAC
1950892 GC
1 GC
1950894 TGCAATAGGT
Statistics
Matches: 109, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
43 11 0.10
44 91 0.83
45 7 0.06
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
GCCGTGATAGGTCTGGTATATAGCGACGTTTTTAGGATACAAAC
Found at i:1950902 original size:43 final size:44
Alignment explanation
Indices: 1950778--1950938 Score: 143
Period size: 44 Copynumber: 3.7 Consensus size: 44
1950768 TAGGACTGGA
* *
1950778 ATATAGCGGCG-TTTTTAGGATACAAACG-T-CATGATAGGTCAGGT
1 ATATAGCGGCGTTTTTTA-GATACAAACGCTGCA--ATAGGTCTGAT
* * * * *
1950822 ATATAGCGAC-ATTTTTAGGATACAAACGCCGCGATAGGTCTGCT
1 ATATAGCGGCGTTTTTTA-GATACAAACGCTGCAATAGGTCTGAT
* *
1950866 ATATAGCGGCGTTTTTTA-ATACAAACGCTGCAATAGGTGTTAAT
1 ATATAGCGGCGTTTTTTAGATACAAACGCTGCAATAGGT-CTGAT
* *
1950910 ATTTAGCGGCGTTTTTTATATACAAACGC
1 ATATAGCGGCGTTTTTTAGATACAAACGC
1950939 CACTAAATAT
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
43 18 0.18
44 63 0.64
45 16 0.16
46 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (44 bp):
ATATAGCGGCGTTTTTTAGATACAAACGCTGCAATAGGTCTGAT
Found at i:1958550 original size:82 final size:82
Alignment explanation
Indices: 1958272--1958648 Score: 262
Period size: 82 Copynumber: 4.6 Consensus size: 82
1958262 ATTTTAATAT
* * * * * * **
1958272 AAACGCCACAATAAACAACATATTGTGGCGTTTGTAGGACAAATGTCGCTATATTATTACTCTAT
1 AAACGCCACTATAAACAACATATTGTGGCGTTTGTAGTATAAACGCCGCTAAATTACCACTCTAT
* * * *
1958337 TGTGGCGTTTTTTG-CA
66 TGCGGCATTTGTTGAAA
* * * * * * **
1958353 CAACGCCACTATAAACAATACTATTGCGTCGTTTGT-TTGATAAACGCCGCGAAATTACTTCTCT
1 AAACGCCACTATAAACAACA-TATTGTGGCGTTTGTAGT-ATAAACGCCGCTAAATTACCACTCT
* * * *
1958417 ATAGCGTCGTTTGTTGAAC
64 ATTGCGGCATTTGTTGAAA
* * * ** * **
1958436 AAACACCATTATAAACAACACTATCGCAGCGTTTGT-GTAAAAATACCGCTAAATTACCACTCTA
1 AAACGCCACTATAAACAACA-TATTGTGGCGTTTGTAGTATAAACGCCGCTAAATTACCACTCTA
*
1958500 TTGCGACATTTGTTGAAA
65 TTGCGGCATTTGTTGAAA
*
1958518 AAACGCCACTATAAACATCTATATTGTGGCGTTT-TAGCTATAAACGCCGCTAAATTACCACTCT
1 AAACGCCACTATAAACAAC-ATATTGTGGCGTTTGTAG-TATAAACGCCGCTAAATTACCACTCT
* * *
1958582 ATTACGGTATTTGTTTAAA
64 ATTGCGGCATTTGTTGAAA
* * ** * * *
1958601 AAATGCCGCTA-AAGTATCATTTTGTGGCGTTTGGA-TAGTAAACGCCGC
1 AAACGCCACTATAAACAACATATTGTGGCGTTTGTAGTA-TAAACGCCGC
1958649 GGTATGCTTA
Statistics
Matches: 231, Mismatches: 57, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
80 2 0.01
81 41 0.18
82 110 0.48
83 78 0.34
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (82 bp):
AAACGCCACTATAAACAACATATTGTGGCGTTTGTAGTATAAACGCCGCTAAATTACCACTCTAT
TGCGGCATTTGTTGAAA
Found at i:1959434 original size:47 final size:44
Alignment explanation
Indices: 1959365--1959456 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 44
1959355 GAGTGCATGA
*
1959365 TTTTGTAATAGAGGTGAGTATTCGATATACTATGGATATAGTTATGG
1 TTTTGTAATAGAGGTGAGTATTCCATATAC---GGATATAGTTATGG
*
1959412 TTTTGTAATAG-GAGTTAGTATTCCATATACGGATATAGTTATGG
1 TTTTGTAATAGAG-GTGAGTATTCCATATACGGATATAGTTATGG
1959456 T
1 T
1959457 CTAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
44 15 0.36
46 1 0.02
47 26 0.62
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.41
Consensus pattern (44 bp):
TTTTGTAATAGAGGTGAGTATTCCATATACGGATATAGTTATGG
Found at i:1969812 original size:23 final size:23
Alignment explanation
Indices: 1969783--1969839 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1969773 CTCGTATAAA
1969783 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1969806 TGTACCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1969829 TGCACCGAAGT
1 TGCACCGAAGT
1969840 TCCATATAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1974571 original size:18 final size:19
Alignment explanation
Indices: 1974529--1974573 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1974519 TTTGATTCAC
* *
1974529 GGAATGTAAGATTATCAGTG
1 GGAATATAAGATTACCAG-G
1974549 GGAATATAAGATTACCA-G
1 GGAATATAAGATTACCAGG
1974567 GGAATAT
1 GGAATAT
1974574 GATTACTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:1976200 original size:53 final size:54
Alignment explanation
Indices: 1976107--1976210 Score: 158
Period size: 53 Copynumber: 1.9 Consensus size: 54
1976097 TATATTGGTG
* *
1976107 ATTATCTAATTATAGTTTATTTTTATTTTGATCATTATTTTTAAATTCTTATCA
1 ATTATCTAATTATAGTATATTTTTATTTTGATCATCATTTTTAAATTCTTATCA
*
1976161 ATTATCTAATTATAGTAT-TTTTTATTTTGA-CTATCATTTTTGAATTCTTA
1 ATTATCTAATTATAGTATATTTTTATTTTGATC-ATCATTTTTAAATTCTTA
1976211 GGTCACACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 1 0.02
53 28 0.61
54 17 0.37
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.59
Consensus pattern (54 bp):
ATTATCTAATTATAGTATATTTTTATTTTGATCATCATTTTTAAATTCTTATCA
Found at i:1977283 original size:2 final size:2
Alignment explanation
Indices: 1977276--1977321 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1977266 TTTACCCTCT
1977276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1977318 TA TA
1 TA TA
1977322 CGAATTTGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1977383 original size:2 final size:2
Alignment explanation
Indices: 1977378--1977414 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1977368 GGCCCTCATC
1977378 AT 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 AT A
1977415 ATGTTGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1978008 original size:288 final size:288
Alignment explanation
Indices: 1977556--1978124 Score: 888
Period size: 288 Copynumber: 2.0 Consensus size: 288
1977546 CATCGAGAGA
* * * *
1977556 TACCATGTGTCACTATCTAATTGGTAGAAAAATATTTAAATTAAATATAAATTAAATTAAAAACC
1 TACCACGTGTCACTATATAATTGGCAGAAAAATATTTAAAATAAATATAAATTAAATTAAAAACC
**
1977621 CCTCCAATAATATTGTGACATGTGTTGTCATATTATTAGGCAATTAAATATATTAAATTAATTTA
66 CCTCCAATAATATTGTGACACATGTTGTCATATTATTAGGCAATTAAATATATTAAATTAATTTA
* * * *
1977686 AAATTATGACCAATTTGATAGATTCTGTAAGTAATAAGCATTAAATTTATAATTATGCAAATTTT
131 AAATTATGACCAATTTGATAGATTCTGTAAGTAATAAGCACTAAATGTATAATAATACAAATTTT
* *
1977751 ATTAACGATCACGTCAGCACTTCCGTTAAATGTTAACGACAAGTGGCCCGATTGAACGCA-TTAA
196 ATTAACGACCACGTCAGCACTTCCGTTAAATGTTAACGACAAGTGGCCCGATTGAACACATTTAA
* * *
1977815 ATAGTTTAGTGGCCTGATTGAACGTATT
261 ATAATTTAGTGACCCGATTGAACGTATT
* *
1977843 TACCACGTGTCACTATATGATTGGCAGAACAATATTTAAAATAAATATAAATTAAATTAAAAATC
1 TACCACGTGTCACTATATAATTGGCAGAAAAATATTTAAAATAAATATAAATTAAATTAAAAA-C
* *
1977908 CCCTCCAATAATATTGTGACACATGTTGTCATATTATTAGGCGATTAAATATATTGAATTAATTT
65 CCCTCCAATAATATTGTGACACATGTTGTCATATTATTAGGCAATTAAATATATTAAATTAATTT
* * * *
1977973 AAAATTATGACCAATTTTATATATTGTGTAAGTAATAAGGACTAAATGTATAATAATACAAATTT
130 AAAATTATGACCAATTTGATAGATTCTGTAAGTAATAAGCACTAAATGTATAATAATACAAATTT
* *
1978038 TATTAACGACCATGTCAGCACTTCCGTTAAATGTTAACGACAAGTGGCCTGATTGAACACATTTA
195 TATTAACGACCACGTCAGCACTTCCGTTAAATGTTAACGACAAGTGGCCCGATTGAACACATTTA
*
1978103 GATAATTTAGTGACCCGATTGA
260 AATAATTTAGTGACCCGATTGA
1978125 CAAGAATTAA
Statistics
Matches: 254, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
287 57 0.22
288 176 0.69
289 21 0.08
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (288 bp):
TACCACGTGTCACTATATAATTGGCAGAAAAATATTTAAAATAAATATAAATTAAATTAAAAACC
CCTCCAATAATATTGTGACACATGTTGTCATATTATTAGGCAATTAAATATATTAAATTAATTTA
AAATTATGACCAATTTGATAGATTCTGTAAGTAATAAGCACTAAATGTATAATAATACAAATTTT
ATTAACGACCACGTCAGCACTTCCGTTAAATGTTAACGACAAGTGGCCCGATTGAACACATTTAA
ATAATTTAGTGACCCGATTGAACGTATT
Found at i:1980062 original size:18 final size:20
Alignment explanation
Indices: 1980024--1980062 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1980014 ATTTAATAGA
1980024 TTTAATGTTAGAGAGAGTGTT
1 TTTAATGTTA-AGAGAGTGTT
1980045 TTTAATGTT-AGA-AGTGTT
1 TTTAATGTTAAGAGAGTGTT
1980063 GGATTCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
21 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (20 bp):
TTTAATGTTAAGAGAGTGTT
Found at i:1980627 original size:5 final size:5
Alignment explanation
Indices: 1980617--1980737 Score: 228
Period size: 5 Copynumber: 24.6 Consensus size: 5
1980607 AATAAATGTG
1980617 TATAT TATAT TATAT TATA- T-TAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1980665 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1980715 TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TAT
1980738 TCTTTTCCCA
Statistics
Matches: 114, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
3 2 0.02
4 2 0.02
5 110 0.96
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1983695 original size:22 final size:22
Alignment explanation
Indices: 1983665--1983739 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
1983655 GGTCAGAGTT
*
1983665 GACCGTTGATTTTAACCGGTCA
1 GACCATTGATTTTAACCGGTCA
1983687 GACCATTGATTTTAACCGGTCA
1 GACCATTGATTTTAACCGGTCA
1983709 GACCATTGATTTTAACCGGTCA
1 GACCATTGATTTTAACCGGTCA
1983731 GACCATTGA
1 GACCATTGA
1983740 CTTTGACCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (22 bp):
GACCATTGATTTTAACCGGTCA
Found at i:1997072 original size:19 final size:19
Alignment explanation
Indices: 1997048--1997087 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1997038 AAAACATCTC
*
1997048 AAAATAATACACTGAGTTT
1 AAAATAAAACACTGAGTTT
* *
1997067 AAAATAAAATATTGAGTTT
1 AAAATAAAACACTGAGTTT
1997086 AA
1 AA
1997088 TATATGGAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
AAAATAAAACACTGAGTTT
Found at i:1997813 original size:20 final size:21
Alignment explanation
Indices: 1997788--1997836 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1997778 TTGTGGGTAC
*
1997788 CGATACTAAGAATTTAG-TAT
1 CGATACTAAGAATCTAGATAT
*
1997808 CGATACT-AGAATCTGGATAT
1 CGATACTAAGAATCTAGATAT
1997828 CGATACTAA
1 CGATACTAA
1997837 CCTCTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 17 0.68
21 1 0.04
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (21 bp):
CGATACTAAGAATCTAGATAT
Found at i:2001834 original size:9 final size:9
Alignment explanation
Indices: 2001835--2001860 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2001825 GAAAATGAAG
2001835 AGAAGAAAA
1 AGAAGAAAA
2001844 AGAAGAAAA
1 AGAAGAAAA
2001853 AGAAGAAA
1 AGAAGAAA
2001861 GAGGTAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:2008171 original size:24 final size:24
Alignment explanation
Indices: 2008144--2008192 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2008134 TGTAGAATTT
2008144 GTTGATACTTTGCACCAATTAGCG
1 GTTGATACTTTGCACCAATTAGCG
2008168 GTTGATACTTTGCACCAATTAGCG
1 GTTGATACTTTGCACCAATTAGCG
2008192 G
1 G
2008193 ATATCTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
GTTGATACTTTGCACCAATTAGCG
Found at i:2008556 original size:20 final size:20
Alignment explanation
Indices: 2008531--2008568 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2008521 TTTTGGTGCA
*
2008531 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
2008551 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
2008569 TTTGAAGGGG
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:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:2012739 original size:20 final size:22
Alignment explanation
Indices: 2012701--2012740 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2012691 TTTAGTAGAA
2012701 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
2012723 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
2012741 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:2014641 original size:12 final size:12
Alignment explanation
Indices: 2014624--2014661 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2014614 ATATACTTTT
2014624 AATAAAAATATA
1 AATAAAAATATA
2014636 AATAAATAA-ATA
1 AATAAA-AATATA
*
2014648 AATAAAAATTTA
1 AATAAAAATATA
2014660 AA
1 AA
2014662 ATTCTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAATATA
Found at i:2015171 original size:29 final size:28
Alignment explanation
Indices: 2015114--2015190 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
2015104 TATCTCTCCT
* *
2015114 ATTTTACTCACTGAACATTATTTGCTTTC
1 ATTTTACTCACTGAACTTTACTT-CTTTC
2015143 ATTTTACTCACTGAACTTTAAACTT-TTTC
1 ATTTTACTCACTGAACTTT--ACTTCTTTC
* *
2015172 AATTTACTCACTAAACTTT
1 ATTTTACTCACTGAACTTT
2015191 CAAATTACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 39 0.93
31 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.47
Consensus pattern (28 bp):
ATTTTACTCACTGAACTTTACTTCTTTC
Found at i:2017119 original size:11 final size:11
Alignment explanation
Indices: 2017089--2017137 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
2017079 CCCTGGTCTT
2017089 CTTCTT-CTT-
1 CTTCTTCCTTC
2017098 CTTCATT-CTTC
1 CTTC-TTCCTTC
2017109 CTTCTTCCTTC
1 CTTCTTCCTTC
*
2017120 TTTCTTCCTTC
1 CTTCTTCCTTC
*
2017131 TTTCTTC
1 CTTCTTC
2017138 TTATTCTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
9 4 0.11
10 7 0.19
11 25 0.69
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (11 bp):
CTTCTTCCTTC
Found at i:2017153 original size:7 final size:7
Alignment explanation
Indices: 2017085--2017159 Score: 66
Period size: 7 Copynumber: 11.0 Consensus size: 7
2017075 ACTGCCCTGG
2017085 TCTTC-T
1 TCTTCTT
2017091 TCTTC-T
1 TCTTCTT
*
2017097 TCTTCAT
1 TCTTCTT
*
2017104 TCTTCCT
1 TCTTCTT
*
2017111 TCTTCCT
1 TCTTCTT
2017118 TCTTTCTT
1 TC-TTCTT
*
2017126 CCTTCTT
1 TCTTCTT
2017133 TCTTC-T
1 TCTTCTT
*
2017139 TATTCTT
1 TCTTCTT
2017146 TCTTCTT
1 TCTTCTT
*
2017153 TATTCTT
1 TCTTCTT
2017160 CTCTCTCACT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
6 16 0.27
7 38 0.64
8 5 0.08
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (7 bp):
TCTTCTT
Found at i:2017161 original size:3 final size:3
Alignment explanation
Indices: 2017085--2017152 Score: 64
Period size: 3 Copynumber: 20.3 Consensus size: 3
2017075 ACTGCCCTGG
2017085 TCT TCT TCT TCT TCT TCAT TCT TCCT TCT TCCT TCTT TCT TCCT TCTT
1 TCT TCT TCT TCT TCT TC-T TCT T-CT TCT T-CT TC-T TCT T-CT TC-T
*
2017133 TCT TCT TAT TCTT TCT TCT T
1 TCT TCT TCT TC-T TCT TCT T
2017153 TATTCTTCTC
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
3 35 0.62
4 21 0.38
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2017224 original size:37 final size:37
Alignment explanation
Indices: 2017155--2017237 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
2017145 TTCTTCTTTA
* *
2017155 TTCTTC-TCTCTCACTCCCGCGTTAACCTCACTCTTC
1 TTCTTCTTCTCTCACACCCGCGTTAACCCCACTCTTC
*
2017191 TTCTTCTTCTCTCACACCC-CTGTTAGCCCCACTCTTC
1 TTCTTCTTCTCTCACACCCGC-GTTAACCCCACTCTTC
*
2017228 TTCTTATTCT
1 TTCTTCTTCT
2017238 TCTTCTTCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 7 0.17
37 34 0.83
ACGTcount: A:0.11, C:0.42, G:0.05, T:0.42
Consensus pattern (37 bp):
TTCTTCTTCTCTCACACCCGCGTTAACCCCACTCTTC
Found at i:2018474 original size:9 final size:9
Alignment explanation
Indices: 2018451--2018501 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
2018441 TTATGCAAAT
*
2018451 AGAAGAAGA
1 AGAAGAATA
*
2018460 AAAAGAATA
1 AGAAGAATA
2018469 AGAAGAATA
1 AGAAGAATA
2018478 AGAAG-ATA
1 AGAAGAATA
2018486 A-AAG-A-A
1 AGAAGAATA
2018492 AGAAGAATA
1 AGAAGAATA
2018501 A
1 A
2018502 AAATAAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 2 0.06
7 7 0.19
8 5 0.14
9 22 0.61
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.08
Consensus pattern (9 bp):
AGAAGAATA
Found at i:2018509 original size:15 final size:14
Alignment explanation
Indices: 2018474--2018511 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2018464 GAATAAGAAG
2018474 AATAAGAAGATAAA
1 AATAAGAAGATAAA
2018488 AGA-AAGAAGAATAAA
1 A-ATAAGAAG-ATAAA
2018503 AATAAGAAG
1 AATAAGAAG
2018512 CGGGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (14 bp):
AATAAGAAGATAAA
Found at i:2025646 original size:40 final size:39
Alignment explanation
Indices: 2025584--2025662 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 39
2025574 ATAAGGTTAT
2025584 TTATTTTAAAATAATTTATTATAAAATAATTTATTTTAA
1 TTATTTTAAAATAATTTATTATAAAATAATTTATTTTAA
2025623 TTATTTTAAAAATAATTTATTATAAAATAATTTATTTTAA
1 TTATTTT-AAAATAATTTATTATAAAATAATTTATTTTAA
2025663 AATAATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 7 0.18
40 32 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (39 bp):
TTATTTTAAAATAATTTATTATAAAATAATTTATTTTAA
Found at i:2025718 original size:14 final size:15
Alignment explanation
Indices: 2025582--2025724 Score: 138
Period size: 15 Copynumber: 9.5 Consensus size: 15
2025572 TAATAAGGTT
2025582 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2025597 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2025612 ATTTA-TTT----TA
1 ATTTATTTTAAAATA
2025622 A-TTATTTTAAAAATA
1 ATTTATTTT-AAAATA
*
2025637 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2025652 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2025667 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2025682 TGGATTGGTTTATTTTAAAATA
1 ---A----TTTATTTTAAAATA
2025704 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
2025718 ATTTATT
1 ATTTATT
2025725 AGTATGGATT
Statistics
Matches: 108, Mismatches: 6, Indels: 29
0.76 0.04 0.20
Matches are distributed among these distances:
9 3 0.03
10 6 0.06
14 14 0.13
15 64 0.59
16 6 0.06
18 1 0.01
19 1 0.01
22 13 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:2025741 original size:32 final size:32
Alignment explanation
Indices: 2025704--2025801 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 32
2025694 TTTTAAAATA
2025704 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2025736 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2025758 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
2025790 ATTTATTTTAAA
1 ATTTATTTTAAA
2025802 ATATGGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 14 0.25
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 26 0.46
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:2025743 original size:22 final size:22
Alignment explanation
Indices: 2025727--2025769 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2025717 AATTTATTAG
2025727 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2025749 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2025770 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2025751 original size:69 final size:67
Alignment explanation
Indices: 2025582--2025779 Score: 229
Period size: 69 Copynumber: 2.9 Consensus size: 67
2025572 TAATAAGGTT
** * *
2025582 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAATTATTTTAAAAATAATTTATTATA
1 ATTTATTTTAAAATAATTTATTATAAAAT-ATGGA-TTGATTTATTTT-AAAATAATTTATTATA
2025647 AAATA
63 AAATA
* *
2025652 ATTTATTTTAAAATAATTTATTATAAAATATGGATTGGTTTATTTTAAAATAATTTATT-TTAAA
1 ATTTATTTTAAAATAATTTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTATAAAA
2025716 TA
66 TA
** * * *
2025718 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTA
1 ATTTATT--T-TAAAATAATTTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTA
2025780 GTATGGATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
66 13 0.12
67 13 0.12
68 22 0.20
69 35 0.31
70 29 0.26
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTATAAAA
TA
Found at i:2025770 original size:54 final size:53
Alignment explanation
Indices: 2025704--2026242 Score: 330
Period size: 54 Copynumber: 9.8 Consensus size: 53
2025694 TTTTAAAATA
2025704 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATT-GTATGGATTGATTTATTTTAAAATATGGATTG
2025758 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATT-GTATGGATTGATTTATTTTAAAATATGGATTG
* **
2025812 ATTTA--TT--AT--TGTAGTTGTATGGATTGATTTATTTT-AAATAATTTATT-
1 ATTTATTTTAAATAATTTA-TTGTATGGATTGATTTATTTTAAAAT-ATGGATTG
* * * ** * ***
2025859 AGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTATGGATTG
1 A-T-TTATTTTAAATAATTTATTGTATGGATTGATTTATTTT--A-AA---A-TATGGATTG
2025921 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTA-TTGTATGGATTGATTTATTTTAAAATATGGATTG
*
2025975 ATTTA--TT--AT--TGTAGTTGTATGGATTGATTTATTTTTAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTGTATGGATTGATTTA--TTT--TAA---A--A-TATGGATTG
2026033 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTGTATGGATTGATTTA-TTT---TAA---A--A-TATGGATTG
** ** * ** * * *
2026097 ATTTATTTTAAA-ATATGGATTG-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTGTATGGA-TTGATTTATTTTA-AAATATGGATTG
*
2026151 ATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTA-TTGTATGGATTGATTTATTTTAAAATATGGATTG
*
2026205 ATTTA--TT--AT--TGTAGTTGTATGGATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTA-TTGTATGGATTGATTTATTTTAAA
2026243 TAATTTATTA
Statistics
Matches: 394, Mismatches: 48, Indels: 92
0.74 0.09 0.17
Matches are distributed among these distances:
47 5 0.01
48 74 0.19
49 4 0.01
50 9 0.02
51 1 0.00
52 9 0.02
53 1 0.00
54 130 0.33
55 18 0.05
56 3 0.01
57 2 0.01
58 18 0.05
59 3 0.01
60 13 0.03
61 25 0.06
62 9 0.02
63 13 0.03
64 57 0.14
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (53 bp):
ATTTATTTTAAATAATTTATTGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2025844 original size:80 final size:80
Alignment explanation
Indices: 2025749--2026044 Score: 504
Period size: 80 Copynumber: 3.7 Consensus size: 80
2025739 TATTTTAAAA
2025749 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2025814 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
2025829 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* *
2025894 TTATT-TTAAATAATTTAG
66 TTATTATT--GT-AGTT-G
*
2025912 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2025977 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
2025992 TATGGATTGATTTATTTTTAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
2026045 TAATTTATTT
Statistics
Matches: 202, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
79 2 0.01
80 121 0.60
81 4 0.02
82 4 0.02
83 69 0.34
84 2 0.01
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:2025870 original size:32 final size:30
Alignment explanation
Indices: 2025828--2026194 Score: 270
Period size: 32 Copynumber: 12.7 Consensus size: 30
2025818 TATTGTAGTT
2025828 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAA--TATTA
*
2025860 GTATGAATTGATTTA-TTT---TAA-A--A
1 GTATGGATTGATTTATTTTAAATAATATTA
2025883 -TATGGATTGATTTATTTTAAATAAT-TTA
1 GTATGGATTGATTTATTTTAAATAATATTA
*
2025911 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAA--TATTA
2025943 GTATGGATTGATTTATTTT-AA-AATA-T-
1 GTATGGATTGATTTATTTTAAATAATATTA
* * * * * **
2025969 GGATTGATTTA-TTATTGT-AGTTGTA-T-
1 GTATGGATTGATTTATTTTAAATAATATTA
* * *
2025995 GGATTGATTTA-TT-TT-T-AATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAA--TATTA
*
2026023 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAA--TATTA
2026055 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAA--TATTA
2026087 GTATGGATTGATTTA-TTT---TAA-A--A
1 GTATGGATTGATTTATTTTAAATAATATTA
2026110 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAA--TATTA
*
2026141 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAA--TATTA
*
2026173 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2026195 ATATGGATTG
Statistics
Matches: 285, Mismatches: 20, Indels: 60
0.78 0.05 0.16
Matches are distributed among these distances:
22 27 0.09
23 8 0.03
24 3 0.01
25 11 0.04
26 32 0.11
27 2 0.01
28 17 0.06
29 27 0.09
30 4 0.01
31 11 0.04
32 143 0.50
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (30 bp):
GTATGGATTGATTTATTTTAAATAATATTA
Found at i:2025886 original size:22 final size:22
Alignment explanation
Indices: 2025861--2025903 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2025851 AATTTATTAG
2025861 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
2025883 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
2025904 TAATTTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2025932 original size:163 final size:169
Alignment explanation
Indices: 2025749--2026108 Score: 588
Period size: 163 Copynumber: 2.1 Consensus size: 169
2025739 TATTTTAAAA
2025749 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2025814 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
2025879 -A-AA-A-TATGGATTGATTTATTTTAAATAA-T-TTAG
131 AATAATATTATGGATTGATTTATTTTAAATAATTATTAG
*
2025912 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* *
2025977 TTATTATTGTAGTTGTATGGATTGATTTATTTTTAATAATTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
2026042 AAATAATTTATTTGTATGGATTGATTTATTTTAAATAATTTATTAG
131 -AATAA--TA--T-TATGGATTGATTTATTTTAAATAA-TTATTAG
2026088 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2026109 ATATGGATTG
Statistics
Matches: 181, Mismatches: 3, Indels: 13
0.92 0.02 0.07
Matches are distributed among these distances:
163 127 0.70
165 1 0.01
166 2 0.01
169 1 0.01
173 24 0.13
175 1 0.01
176 25 0.14
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (169 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AATAATATTATGGATTGATTTATTTTAAATAATTATTAG
Found at i:2026046 original size:112 final size:112
Alignment explanation
Indices: 2025883--2026274 Score: 612
Period size: 112 Copynumber: 3.5 Consensus size: 112
2025873 TATTTTAAAA
2025883 TATGGATTGATTTATTTTAAATAA--T-TTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
2025945 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
66 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
*
2025992 TATGGATTGATTTATTTTTAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
* * * * ***
2026057 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
66 ATGGATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTA-TTATTGTAGTTG
2026110 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
*
2026175 ATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
66 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
2026222 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
2026275 ATATGGATTG
Statistics
Matches: 255, Mismatches: 17, Indels: 19
0.88 0.06 0.07
Matches are distributed among these distances:
109 23 0.09
111 8 0.03
112 115 0.45
113 3 0.01
114 4 0.02
116 4 0.02
117 3 0.01
118 88 0.35
119 7 0.03
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (112 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
Found at i:2026052 original size:14 final size:14
Alignment explanation
Indices: 2026033--2026085 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
2026023 GTATGGATTG
2026033 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
2026047 ATTTATTTGTATGGATTG
1 ATTTATTT-TA---AATA
2026065 ATTTATTTTAAATA
1 ATTTATTTTAAATA
2026079 ATTTATT
1 ATTTATT
2026086 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 2 0.06
17 2 0.06
18 10 0.32
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:2026113 original size:22 final size:22
Alignment explanation
Indices: 2026088--2026130 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2026078 AATTTATTAG
2026088 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2026110 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2026131 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2026125 original size:86 final size:86
Alignment explanation
Indices: 2026024--2026305 Score: 477
Period size: 86 Copynumber: 3.3 Consensus size: 86
2026014 AATTTATTAG
2026024 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATAATTTATTAGT
2026089 ATGGATTGATTTATTTTAAAA
66 ATGGATTGATTTATTTTAAAA
* *
2026110 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATAATTTATTAGT
*
2026175 ATAGATTGATTTATTTTAAAA
66 ATGGATTGATTTATTTTAAAA
* *
2026196 TATGGATTGATTTA--TT--AT--TGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATAATTTATTAGT
2026255 ATGGATTGATTTATTTTAAAA
66 ATGGATTGATTTATTTTAAAA
2026276 TATGGATTGATTTATTTTAAATAATTTATT
1 TATGGATTGATTTATTTTAAATAATTTATT
2026306 ATTATAGTTG
Statistics
Matches: 180, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
80 71 0.39
82 4 0.02
84 4 0.02
86 101 0.56
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (86 bp):
TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATAATTTATTAGT
ATGGATTGATTTATTTTAAAA
Found at i:2026279 original size:22 final size:22
Alignment explanation
Indices: 2026254--2026296 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2026244 AATTTATTAG
2026254 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2026276 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2026297 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2026293 original size:54 final size:54
Alignment explanation
Indices: 2026056--2026306 Score: 305
Period size: 54 Copynumber: 4.6 Consensus size: 54
2026046 AATTTATTTG
2026056 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
2026110 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * ***
2026163 TA---ATTTATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
2026222 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
2026276 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
2026307 TTATAGTTGT
Statistics
Matches: 165, Mismatches: 18, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
49 3 0.02
50 14 0.08
52 2 0.01
53 5 0.03
54 96 0.58
55 3 0.02
56 4 0.02
57 2 0.01
58 15 0.09
59 2 0.01
60 2 0.01
62 14 0.08
63 3 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:2029482 original size:20 final size:20
Alignment explanation
Indices: 2029459--2029507 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
2029449 CACGGAATGT
2029459 AAGATTACCTGTGGGAATAA
1 AAGATTACCTGTGGGAATAA
2029479 AAGATTACCTGTGGGAATAA
1 AAGATTACCTGTGGGAATAA
2029499 AAGATTACC
1 AAGATTACC
2029508 AGGGAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (20 bp):
AAGATTACCTGTGGGAATAA
Found at i:2029514 original size:18 final size:19
Alignment explanation
Indices: 2029459--2029515 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2029449 CACGGAATGT
*
2029459 AAGATTACCTGTGGGAATAA
1 AAGATTACC-GAGGGAATAA
*
2029479 AAGATTACCTGTGGGAATAA
1 AAGATTACC-GAGGGAATAA
2029499 AAGATTACC-AGGGAATA
1 AAGATTACCGAGGGAATA
2029516 TGATTACTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 7 0.19
20 29 0.81
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (19 bp):
AAGATTACCGAGGGAATAA
Found at i:2029581 original size:35 final size:35
Alignment explanation
Indices: 2029542--2029621 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
2029532 TACATTATTG
*
2029542 TGTTTGGTTGGTTTGGCAGGAATGTAATATTACAA
1 TGTTTGGTTGGTTTGACAGGAATGTAATATTACAA
2029577 TGTTTGGTTGGTTTGACAGGAATGTAATATTACAA
1 TGTTTGGTTGGTTTGACAGGAATGTAATATTACAA
*
2029612 TATTTGGTTG
1 TGTTTGGTTG
2029622 AAGGAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (35 bp):
TGTTTGGTTGGTTTGACAGGAATGTAATATTACAA
Found at i:2029745 original size:27 final size:27
Alignment explanation
Indices: 2029715--2029772 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
2029705 AAATAAAAAT
*
2029715 TATTTATATAAAAATTCATCGATAATA
1 TATTTAAATAAAAATTCATCGATAATA
*
2029742 TATTTAAATAAAAATTCATCGATGATA
1 TATTTAAATAAAAATTCATCGATAATA
2029769 TATT
1 TATT
2029773 ATTTTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (27 bp):
TATTTAAATAAAAATTCATCGATAATA
Found at i:2041346 original size:20 final size:19
Alignment explanation
Indices: 2041318--2041357 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2041308 CGCTACGTGG
2041318 TCAAATGAAAAATACTTGGA
1 TCAAATG-AAAATACTTGGA
* *
2041338 TCAACTGAAGATACTTGGA
1 TCAAATGAAAATACTTGGA
2041357 T
1 T
2041358 ACATTACGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (19 bp):
TCAAATGAAAATACTTGGA
Found at i:2042716 original size:42 final size:42
Alignment explanation
Indices: 2042650--2042746 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
2042640 TCCCTTTACA
* **
2042650 AAAAGAATCGATCCCTTGAGGAAAATGATAGATAC-CTTCACC-
1 AAAAGGATCGATCCCTCAAGGAAAATGATAGAT-CTCTTC-CCT
* *
2042692 AAAAGGATCGATCCCTCAATGAAAATGATCGATCTCTTCCCT
1 AAAAGGATCGATCCCTCAAGGAAAATGATAGATCTCTTCCCT
*
2042734 AAAAGGATTGATC
1 AAAAGGATCGATC
2042747 AATTTCTTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.06
42 44 0.94
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (42 bp):
AAAAGGATCGATCCCTCAAGGAAAATGATAGATCTCTTCCCT
Found at i:2043257 original size:15 final size:15
Alignment explanation
Indices: 2043237--2043272 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2043227 ATCCTTAGTA
2043237 TGGATGCTAAGGTAG
1 TGGATGCTAAGGTAG
2043252 TGGATGCTAAGGTAG
1 TGGATGCTAAGGTAG
2043267 TGGATG
1 TGGATG
2043273 TAGACTTCGG
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:0.25, C:0.06, G:0.42, T:0.28
Consensus pattern (15 bp):
TGGATGCTAAGGTAG
Found at i:2046895 original size:22 final size:24
Alignment explanation
Indices: 2046865--2046923 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
2046855 AGACTAGTCA
2046865 GCATGTCAGACATTTCAT-AATCAT
1 GCAT-TCAGACATTTCATGAATCAT
*
2046889 GC-TTCAGACATTTCATGCATCAT
1 GCATTCAGACATTTCATGAATCAT
*
2046912 GCATTTAGACAT
1 GCATTCAGACAT
2046924 CTTTTGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 13 0.42
23 8 0.26
24 10 0.32
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (24 bp):
GCATTCAGACATTTCATGAATCAT
Found at i:2050808 original size:65 final size:66
Alignment explanation
Indices: 2050718--2050961 Score: 206
Period size: 65 Copynumber: 3.6 Consensus size: 66
2050708 TCTTGAGACA
* * * *
2050718 TTTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
1 TTTTCTCTTAAAACAAATTTCGTCTCCCCTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
2050783 G
66 G
* * ** * * * **
2050784 TTTTC-CTTAAAGCAAATTTCGTCTCCCCTGAGAAAGTTTCTTTTGGAACTAAGT-TTTGTCTCT
1 TTTTCTCTTAAAACAAATTTCGTCTCCCCTGAGACAGTTTCCCTTGAAACAAAATCTTTG--AAT
2050847 CTTTAG
64 C--T-G
* * * * * *
2050853 ACATTTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACATTTTCCCTTGAAACAAAATCTTTTAA
1 ---TTTTCTCTTAAAACAAATTTCGTCTCCCCTGAGACAGTTTCCCTTGAAACAAAATCTTTGAA
*
2050918 TTTG
63 TCTG
*
2050922 TTTTC-CTTAAAACAAATTTCTTCTCCCCTGAGACAGTTTC
1 TTTTCTCTTAAAACAAATTTCGTCTCCCCTGAGACAGTTTC
2050962 TTTTGGAACT
Statistics
Matches: 133, Mismatches: 35, Indels: 21
0.70 0.19 0.11
Matches are distributed among these distances:
64 4 0.03
65 67 0.50
66 12 0.09
68 1 0.01
69 2 0.02
70 1 0.01
72 6 0.05
73 37 0.28
74 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (66 bp):
TTTTCTCTTAAAACAAATTTCGTCTCCCCTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
G
Found at i:2050872 original size:138 final size:138
Alignment explanation
Indices: 2050654--2051046 Score: 581
Period size: 138 Copynumber: 2.8 Consensus size: 138
2050644 TAATTTATTC
* * * * * ** * *
2050654 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACA
1 AAAACAAA-TTTCGTCTCCCCTGAGAAAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACA
*
2050718 TTTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
65 TTTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATCT
2050783 GTTTTCCTT
130 GTTTTCCTT
*
2050792 AAAGCAAATTTCGTCTCCCCTGAGAAAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACAT
1 AAAACAAATTTCGTCTCCCCTGAGAAAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACAT
* * *
2050857 TTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACATTTTCCCTTGAAACAAAATCTTTTAATTTG
66 TTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATCTG
2050922 TTTTCCTT
131 TTTTCCTT
* * *
2050930 AAAACAAATTTCTTCTCCCCTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACAG
1 AAAACAAATTTCGTCTCCCCTGAGAAAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACAT
* * * *
2050995 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAATTTCCCTTGAATCAAA
66 TTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
2051047 TTTTGTCTCT
Statistics
Matches: 232, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
137 26 0.11
138 206 0.89
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (138 bp):
AAAACAAATTTCGTCTCCCCTGAGAAAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACAT
TTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATCTG
TTTTCCTT
Found at i:2051022 original size:174 final size:174
Alignment explanation
Indices: 2050812--2051234 Score: 616
Period size: 174 Copynumber: 2.4 Consensus size: 174
2050802 TCGTCTCCCC
* * * * * * * *
2050812 TGAGAAAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACATTTTCTCTTAAAACAATTTTT
1 TGAGACAGTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTT
* *
2050877 GTCTCTCTTGAGACATTTTCCCTTGAAACAAAATCTTTTAATTTGTTTTCCTTAAAACAAATTTC
65 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTTAATATGTTTTCCTTAAAACAAATTT-
*
2050942 T-TCTCCCCTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
129 TGTCTCCCCTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
* * * *
2050987 TTAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAATTTCCCTTGAATCAAATTTTG
1 TGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTG
* *
2051052 TCTCT-TGTGAGACAGTTTCCCTTGAAACAAAATCTTTTAATATGTTTTCCTTTAAACGAATTTT
66 TCTCTCT-TGAGACAGTTTCCCTTGAAACAAAATCTTTTAATATGTTTTCCTTAAAACAAATTTT
* *
2051116 GTCTCCCTTGAGACAATTTCTTTTGGAACTATGTTTTGTCTCTCT
130 GTCTCCCCTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
*
2051161 TGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTT
1 TGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA-TTTT
2051226 GTCTCTCTT
65 GTCTCTCTT
2051235 AGGATAGTTT
Statistics
Matches: 220, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
173 2 0.01
174 189 0.86
175 28 0.13
176 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.44
Consensus pattern (174 bp):
TGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTG
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTTAATATGTTTTCCTTAAAACAAATTTTG
TCTCCCCTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
Found at i:2051171 original size:102 final size:102
Alignment explanation
Indices: 2050995--2051183 Score: 249
Period size: 102 Copynumber: 1.9 Consensus size: 102
2050985 CTTTAGACAG
*
2050995 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAATTTCCCTTGAATCAAATTTTGTCTCTTGT
1 TTTCTCTTGAAACAAATTTTATCTCCCTTGAGACAATTTCCCTTGAATCAAATTTTGTCTCTTGT
2051060 GAGACAGTTTCCCTTGAAACAAAATCTTTTAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATCTTTTAATATGT
* * * ** **
2051097 TTTC-CTTTAAACGAATTTTGTCTCCCTTGAGACAATTTCTTTTGGAA-CTATGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTTATCTCCCTTGAGACAATTTCCCTT-GAATC-AAATTTTGTCTCT-
*
2051160 T-TGAGACAGTTTCTCTTGAAACAA
63 TGTGAGACAGTTTCCCTTGAAACAA
2051184 GTTTTGTCTC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
101 34 0.45
102 40 0.53
103 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTTATCTCCCTTGAGACAATTTCCCTTGAATCAAATTTTGTCTCTTGT
GAGACAGTTTCCCTTGAAACAAAATCTTTTAATATGT
Found at i:2051231 original size:73 final size:73
Alignment explanation
Indices: 2051112--2051249 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 73
2051102 TTTAAACGAA
** * * *
2051112 TTTTGTCTCCCTTGAGACAATTTCTTTTGGAACTATGTTTTGTCTCTCTT-GAGACAGTTTCTCT
1 TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTAG-GACAGTTTCTCT
2051176 TGAAACAAG
65 TGAAACAAG
* * *
2051185 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTAGGATAGTTTCTCTT
1 TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTAGGACAGTTTCTCTT
2051250 AAAATACCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 55 0.98
74 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (73 bp):
TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTAGGACAGTTTCTCTT
GAAACAAG
Found at i:2053028 original size:12 final size:12
Alignment explanation
Indices: 2053007--2053044 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2052997 TTTCATTCAT
*
2053007 TTCATGTTATTA
1 TTCATATTATTA
2053019 TTCATATTATTA
1 TTCATATTATTA
2053031 TT-ATTATTATTA
1 TTCA-TATTATTA
2053043 TT
1 TT
2053045 ATTATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 1 0.04
12 23 0.96
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (12 bp):
TTCATATTATTA
Found at i:2053029 original size:3 final size:3
Alignment explanation
Indices: 2053013--2053049 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
2053003 TCATTTCATG
2053013 TTA TTA TTCA -TA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2053050 ATATATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2053095 original size:2 final size:2
Alignment explanation
Indices: 2053088--2053128 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2053078 ATTATTTGAT
2053088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2053129 TAAATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2053253 original size:21 final size:21
Alignment explanation
Indices: 2053229--2053268 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2053219 TATTTTAGTT
*
2053229 ATTTGCTTTATTAATTTATGC
1 ATTTACTTTATTAATTTATGC
* *
2053250 ATTTACTTTTTTTATTTAT
1 ATTTACTTTATTAATTTAT
2053269 TTTATATACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (21 bp):
ATTTACTTTATTAATTTATGC
Found at i:2053399 original size:44 final size:42
Alignment explanation
Indices: 2053313--2053399 Score: 95
Period size: 44 Copynumber: 2.0 Consensus size: 42
2053303 TATTATTTTG
* *
2053313 TTTATTTGTTTTATTTATATTTTTCCTTCTTTTCCTTTATTT
1 TTTATTTGTTTTACTTATATTTTTCCTTCTTTTCCTTCATTT
* * *
2053355 TTTATTATTTTTTACTTACTATTTTATCTTTGTTTT-CTTCATTT
1 TTTATT-TGTTTTACTTA-TATTTT-TCCTTCTTTTCCTTCATTT
2053399 T
1 T
2053400 ATCGTTTTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
42 6 0.16
43 9 0.24
44 14 0.38
45 8 0.22
ACGTcount: A:0.14, C:0.11, G:0.02, T:0.72
Consensus pattern (42 bp):
TTTATTTGTTTTACTTATATTTTTCCTTCTTTTCCTTCATTT
Found at i:2054002 original size:15 final size:17
Alignment explanation
Indices: 2053982--2054019 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
2053972 ATTATTTTAA
*
2053982 ATATTTTA-AACAAT-T
1 ATATTTTATAAAAATAT
2053997 ATATTTTATAAAAATAT
1 ATATTTTATAAAAATAT
2054014 ATATTT
1 ATATTT
2054020 AAAAACTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 5 0.25
17 7 0.35
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTTATAAAAATAT
Found at i:2054016 original size:17 final size:15
Alignment explanation
Indices: 2053982--2054024 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
2053972 ATTATTTTAA
*
2053982 ATATTTTAAACAATT
1 ATATTTTAAAAAATT
2053997 ATATTTTATAAAAA-T
1 ATATTTTA-AAAAATT
2054012 ATATATTTAAAAA
1 ATAT-TTTAAAAA
2054025 CTACTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATTTTAAAAAATT
Found at i:2056176 original size:2 final size:2
Alignment explanation
Indices: 2056164--2056195 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2056154 AAATTTAAAC
*
2056164 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2056196 AATTCTCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2075752 original size:19 final size:19
Alignment explanation
Indices: 2075728--2075777 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2075718 GAACACTTAG
2075728 TGCATCGGTGCACTAAGGA
1 TGCATCGGTGCACTAAGGA
*
2075747 TGCATCGGTGCACTAAGGG
1 TGCATCGGTGCACTAAGGA
*
2075766 TGCATCGATGCA
1 TGCATCGGTGCA
2075778 TAAACTGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (19 bp):
TGCATCGGTGCACTAAGGA
Found at i:2075818 original size:46 final size:46
Alignment explanation
Indices: 2075765--2075885 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 46
2075755 TGCACTAAGG
* *
2075765 GTGCATCGATGCATAAACTGCATTCGATGTTT-CA-AACAAGCCTGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGCAT-GA
*
2075811 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAATCATGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCATGA
* *
2075857 GTGTATCGATGCATGAAAGTGCA-TCGATG
1 GTGCATCGATGCAT-AAAATGCATTCGATG
2075886 CATAAAATGC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 52 0.78
47 13 0.19
48 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCATGA
Found at i:2075882 original size:18 final size:17
Alignment explanation
Indices: 2075856--2075897 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2075846 TAAAATCATG
*
2075856 AGTGTATCGATGCATGAA
1 AGTGCATCGATGCAT-AA
2075874 AGTGCATCGATGCATAA
1 AGTGCATCGATGCATAA
*
2075891 AATGCAT
1 AGTGCAT
2075898 TCGAAATGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (17 bp):
AGTGCATCGATGCATAA
Found at i:2075901 original size:18 final size:18
Alignment explanation
Indices: 2075861--2075897 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2075851 TCATGAGTGT
*
2075861 ATCGATGCATGAAAGTGC
1 ATCGATGCATGAAAATGC
2075879 ATCGATGCAT-AAAATGC
1 ATCGATGCATGAAAATGC
2075896 AT
1 AT
2075898 TCGAAATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (18 bp):
ATCGATGCATGAAAATGC
Found at i:2076280 original size:53 final size:53
Alignment explanation
Indices: 2076212--2076318 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
2076202 TTTTTGATAT
2076212 AACAAAACATTTGAGTAATTTTAAGATTTTTAAGAAAATCATTTTGAAATCAA
1 AACAAAACATTTGAGTAATTTTAAGATTTTTAAGAAAATCATTTTGAAATCAA
**
2076265 AACAAAACATTTGAGTAATTTTAAGATTTTTAAGAAAATTGTTTTGAAATCAA
1 AACAAAACATTTGAGTAATTTTAAGATTTTTAAGAAAATCATTTTGAAATCAA
2076318 A
1 A
2076319 TTTGAAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (53 bp):
AACAAAACATTTGAGTAATTTTAAGATTTTTAAGAAAATCATTTTGAAATCAA
Found at i:2076584 original size:27 final size:27
Alignment explanation
Indices: 2076554--2076611 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2076544 CTAAATGATG
* * *
2076554 CAAAAATCTAATAAACCAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
* *
2076581 CAAAAACCAAATATATAAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
2076608 CAAA
1 CAAA
2076612 CATTCAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (27 bp):
CAAAAACCAAATAAACAAATATAAGTT
Found at i:2078635 original size:23 final size:23
Alignment explanation
Indices: 2078598--2078680 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
2078588 ATACACTATT
*
2078598 GAGTGCATCAATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* * *
2078621 GAGTGCATCGGTGCACCTTC-AT
1 GAGTGCATCGATGCACATTCAAG
*
2078643 G-GTGTATCGATGCACATTCATAG
1 GAGTGCATCGATGCACATTCA-AG
*
2078666 G-GATGCATTGATGCA
1 GAG-TGCATCGATGCA
2078681 TCTTCATAGT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 20 0.43
24 10 0.21
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:2078656 original size:21 final size:21
Alignment explanation
Indices: 2078627--2078701 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
2078617 CAAGGAGTGC
*
2078627 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCATGGTGT
* *
2078648 ATCGATGCACATTCATAGGGATGC
1 ATCGATGCACCTTCAT--GG-TGT
* * *
2078672 ATTGATGCATCTTCATAGTGT
1 ATCGATGCACCTTCATGGTGT
2078693 ATCGATGCA
1 ATCGATGCA
2078702 TTATGCACAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
21 24 0.57
22 1 0.02
23 2 0.05
24 15 0.36
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (21 bp):
ATCGATGCACCTTCATGGTGT
Found at i:2078687 original size:45 final size:44
Alignment explanation
Indices: 2078599--2078701 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
2078589 TACACTATTG
* * *
2078599 AGTGCATCAATGCACATTCAAGGAGTGCATCGGTGCACCTTCAT
1 AGTGTATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCAT
* * *
2078643 GGTGTATCGATGCACATTCATAGG-GATGCATTGATGCATCTTCAT
1 AGTGTATCGATGCACATTCA-AGGAG-TGCATCGATGCACCTTCAT
2078688 AGTGTATCGATGCA
1 AGTGTATCGATGCA
2078702 TTATGCACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 18 0.36
45 32 0.64
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCAT
Found at i:2082303 original size:22 final size:21
Alignment explanation
Indices: 2082262--2082301 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2082252 GAGATTATTT
*
2082262 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
2082283 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2082302 ATTATAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:2093100 original size:9 final size:9
Alignment explanation
Indices: 2093081--2093122 Score: 75
Period size: 9 Copynumber: 4.6 Consensus size: 9
2093071 TATTTCCTCA
2093081 TTTATGTTTG
1 TTTA-GTTTG
2093091 TTTAGTTTG
1 TTTAGTTTG
2093100 TTTAGTTTG
1 TTTAGTTTG
2093109 TTTAGTTTG
1 TTTAGTTTG
2093118 TTTAG
1 TTTAG
2093123 ACTTGTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 28 0.88
10 4 0.12
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (9 bp):
TTTAGTTTG
Found at i:2099288 original size:10 final size:10
Alignment explanation
Indices: 2099249--2099298 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
2099239 TTCATCACAC
2099249 CAAATTCTCT
1 CAAATTCTCT
*
2099259 CAATTTCTCT
1 CAAATTCTCT
*
2099269 CAACTTCTCT
1 CAAATTCTCT
*
2099279 CAAATACTCT
1 CAAATTCTCT
* *
2099289 TATATTCTCT
1 CAAATTCTCT
2099299 ATTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2099362 original size:23 final size:22
Alignment explanation
Indices: 2099323--2099367 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2099313 TTATTATATT
*
2099323 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
2099346 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
2099368 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:2099374 original size:17 final size:18
Alignment explanation
Indices: 2099337--2099375 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2099327 ATATTTTGTA
2099337 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
2099355 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
2099372 TTTA
1 TTTA
2099376 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:2101262 original size:12 final size:12
Alignment explanation
Indices: 2101245--2101270 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2101235 TCAGGAGGAC
2101245 GACGACGACGAT
1 GACGACGACGAT
2101257 GACGACGACGAT
1 GACGACGACGAT
2101269 GA
1 GA
2101271 TGGTGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.35, T:0.08
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:2101546 original size:35 final size:35
Alignment explanation
Indices: 2101507--2101584 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
2101497 GTATTTCAGT
2101507 TAATTTTGTT-T-A-TTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATCATTTACCATTTAATA-C--TTATTG
*
2101542 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTATCATTTACCATTTAATACTTATTG
2101577 TAAGTTTT
1 TAA-TTTT
2101585 TTTGTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 18 0.49
36 4 0.11
37 2 0.05
38 13 0.35
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (35 bp):
TAATTTTGTTATCATTTACCATTTAATACTTATTG
Found at i:2101594 original size:35 final size:36
Alignment explanation
Indices: 2101507--2101594 Score: 85
Period size: 35 Copynumber: 2.5 Consensus size: 36
2101497 GTATTTCAGT
*
2101507 TAATTTTGTT-TA-TTACCATTTAATATCAGTTATTG
1 TAATTTTTTTGTATTTACCATTTAATATCA-TTATTG
** *
2101542 TAATTTGGTTATCATTTACCATTTAATA-C-TTATTG
1 TAATTTTTTTGT-ATTTACCATTTAATATCATTATTG
2101577 TAAGTTTTTTTGTATTTA
1 TAA-TTTTTTTGTATTTA
2101595 AAATTATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
35 23 0.51
36 7 0.16
37 2 0.04
38 13 0.29
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.56
Consensus pattern (36 bp):
TAATTTTTTTGTATTTACCATTTAATATCATTATTG
Found at i:2107484 original size:20 final size:20
Alignment explanation
Indices: 2107436--2107485 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2107426 CTGATAGTGT
*
2107436 CAACAGTGACAGCCACAGAC
1 CAACAGTGGCAGCCACAGAC
2107456 CAACAGTGGCAGCCACAGAC
1 CAACAGTGGCAGCCACAGAC
2107476 CAACAGTGGC
1 CAACAGTGGC
2107486 CAATCGATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.34, G:0.24, T:0.06
Consensus pattern (20 bp):
CAACAGTGGCAGCCACAGAC
Found at i:2108942 original size:43 final size:43
Alignment explanation
Indices: 2108856--2108956 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 43
2108846 CGTTCAAAGA
* * *
2108856 ATCTCTCGACGTCTTTAACACAAAAATTTACATGCATTATTGG
1 ATCTCTCGACGTCTTCAACACAAAAATTTACATACAATATTGG
* *
2108899 ATCTCTCGACGTCTTCATTCA-AAAAATTTCCATACAA-ATTTGG
1 ATCTCTCGACGTCTTCA-ACACAAAAATTTACATACAATA-TTGG
*
2108942 AT-TACTCGGCGTCTT
1 ATCT-CTCGACGTCTT
2108957 TTATGCAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
42 2 0.04
43 45 0.92
44 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (43 bp):
ATCTCTCGACGTCTTCAACACAAAAATTTACATACAATATTGG
Found at i:2111363 original size:38 final size:37
Alignment explanation
Indices: 2111328--2111406 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 37
2111318 ATTTGGTATT
2111328 TAAAAACAACAAACTTACAATAA-GA-ATTAAATGGTAAA
1 TAAAAAC--CAAA-TTACAATAACGATATTAAATGGTAAA
*
2111366 TAATAACCAAATTACAATAACTGATATTAAATGGT-AA
1 TAAAAACCAAATTACAATAAC-GATATTAAATGGTAAA
2111403 TAAA
1 TAAA
2111407 CAAAATTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
35 9 0.25
36 4 0.11
37 7 0.19
38 16 0.44
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.25
Consensus pattern (37 bp):
TAAAAACCAAATTACAATAACGATATTAAATGGTAAA
Found at i:2111413 original size:35 final size:35
Alignment explanation
Indices: 2111335--2111414 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
2111325 ATTTAAAAAC
*
2111335 AACAAACTTACAATAAGAATTAAATGGTAAATAAT
1 AACAAAATTACAATAAGAATTAAATGGTAAATAAT
*
2111370 AACCAAATTACAATAACTGATATTAAATGGT-AAT-A-
1 AACAAAATTACAATAA--GA-ATTAAATGGTAAATAAT
2111405 AACAAAATTA
1 AACAAAATTA
2111415 ACTGAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
35 23 0.59
36 1 0.03
37 5 0.13
38 10 0.26
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (35 bp):
AACAAAATTACAATAAGAATTAAATGGTAAATAAT
Found at i:2113634 original size:111 final size:111
Alignment explanation
Indices: 2113496--2113828 Score: 621
Period size: 111 Copynumber: 3.0 Consensus size: 111
2113486 ATTACAAAAA
* *
2113496 TTAATTCTTACTCTAATAATCATGCATTAAATAAATTAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
2113561 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
2113607 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
2113672 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
*
2113718 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
2113783 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
2113829 GTGATTTCCA
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 217 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:2116864 original size:2 final size:2
Alignment explanation
Indices: 2116857--2116885 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2116847 AGCAATATTA
2116857 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 A
2116886 ACACTCTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2117274 original size:27 final size:27
Alignment explanation
Indices: 2117165--2117257 Score: 141
Period size: 27 Copynumber: 3.4 Consensus size: 27
2117155 CCGCCATCAC
2117165 CACTTTGAACTTAAAACTCTATAACAT
1 CACTTTGAACTTAAAACTCTATAACAT
**
2117192 CACTTTGAACTTAAAACTCTATAGTAT
1 CACTTTGAACTTAAAACTCTATAACAT
* * *
2117219 TACTTTGAACTTGAAACTCTGTAACAT
1 CACTTTGAACTTAAAACTCTATAACAT
2117246 CACTTTGAACTT
1 CACTTTGAACTT
2117258 GAAAGTCCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (27 bp):
CACTTTGAACTTAAAACTCTATAACAT
Found at i:2117610 original size:23 final size:22
Alignment explanation
Indices: 2117580--2117631 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
2117570 TTTTCCAGAA
*
2117580 TGCTACAGGGGGTATCGATACCC-
1 TGCTACA--GGGTACCGATACCCT
*
2117603 TGCTACAGTGTACCGATACCCT
1 TGCTACAGGGTACCGATACCCT
2117625 TGCTACA
1 TGCTACA
2117632 ATAATTTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 12 0.46
22 7 0.27
23 7 0.27
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCTACAGGGTACCGATACCCT
Found at i:2118388 original size:32 final size:32
Alignment explanation
Indices: 2118269--2118393 Score: 121
Period size: 31 Copynumber: 4.0 Consensus size: 32
2118259 AACCTCGACA
* * *
2118269 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCGTAGAACATAGGTAAT
* * * *
2118300 ACTGTCCATATGTTCCTTAGAACACAGAT-AT
1 ACTGTCCATATGTCCCGTAGAACATAGGTAAT
* *
2118331 ACTATCCATATGTCCCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTCCCGTAGA-ACATAGGTAAT
* *
2118363 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTCCCGTAGAACATAGGTAA
2118394 ATCCTCGACG
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
30 3 0.04
31 42 0.58
32 26 0.36
33 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (32 bp):
ACTGTCCATATGTCCCGTAGAACATAGGTAAT
Found at i:2120790 original size:13 final size:13
Alignment explanation
Indices: 2120772--2120796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2120762 ATATTATTTT
2120772 TTCTTCATTTATA
1 TTCTTCATTTATA
2120785 TTCTTCATTTAT
1 TTCTTCATTTAT
2120797 TATTATACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (13 bp):
TTCTTCATTTATA
Found at i:2121794 original size:28 final size:28
Alignment explanation
Indices: 2121734--2121788 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2121724 CAATAACCAT
*
2121734 ATATTTAACTAAAATAAAACTCATACAA
1 ATATTAAACTAAAATAAAACTCATACAA
* * *
2121762 ATATTAAACTAAACTCAAATTCATACA
1 ATATTAAACTAAAATAAAACTCATACA
2121789 TGTATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (28 bp):
ATATTAAACTAAAATAAAACTCATACAA
Found at i:2124707 original size:21 final size:20
Alignment explanation
Indices: 2124683--2124723 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
2124673 ATATTAGATA
2124683 GAGGGTTTTAAAACCAGCTAT
1 GAGGGTTTTAAAACCA-CTAT
2124704 GAGGGTTTTAAAACCACTAT
1 GAGGGTTTTAAAACCACTAT
2124724 TGCATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (20 bp):
GAGGGTTTTAAAACCACTAT
Found at i:2129525 original size:20 final size:19
Alignment explanation
Indices: 2129500--2129553 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2129490 GCGAAATAAA
2129500 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
2129520 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
2129540 AATCGCAACGCGAT
1 AATCGCAACGCGAT
2129554 TATATAAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:2129625 original size:20 final size:20
Alignment explanation
Indices: 2129581--2129811 Score: 266
Period size: 20 Copynumber: 11.4 Consensus size: 20
2129571 GATTTTGACT
* *
2129581 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGAATCCGT-AA
*
2129602 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATCCGTAA
*
2129622 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGAATCCGT-AA
*
2129643 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATCCGTAA
* *
2129663 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGAATCCGTAA
* *
2129683 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGAATCCGTAA
* *
2129703 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGAATCCGTAA
*
2129723 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATCCGTAA
* *
2129743 ATCGCAATGCGAATACGTAA
1 ATCGCAACGCGAATCCGTAA
* *
2129763 ATCGCAATGCGAATCTGTAA
1 ATCGCAACGCGAATCCGTAA
* *
2129783 ATCGCAATGCGAATCTGTAA
1 ATCGCAACGCGAATCCGTAA
2129803 ATCGCAACG
1 ATCGCAACG
2129812 AGATTCTGAC
Statistics
Matches: 182, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
20 148 0.81
21 34 0.19
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATCCGTAA
Found at i:2129696 original size:40 final size:40
Alignment explanation
Indices: 2129581--2129811 Score: 329
Period size: 40 Copynumber: 5.7 Consensus size: 40
2129571 GATTTTGACT
* *
2129581 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
*
2129622 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
*
2129663 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
2129703 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* * * * *
2129743 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
2129783 ATCGCAATGCGAAT-CTGTAAATCGCAACG
1 ATCGCAACGAGAATAC-GTAAATCGCAACG
2129812 AGATTCTGAC
Statistics
Matches: 177, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 121 0.68
41 55 0.31
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
Found at i:2129819 original size:20 final size:20
Alignment explanation
Indices: 2129540--2129819 Score: 184
Period size: 20 Copynumber: 13.9 Consensus size: 20
2129530 CAGTTCCCAG
* *
2129540 AATCGCAACGCGATTATATA
1 AATCGCAACGCGATTCTGTA
*
2129560 AATCGCAACGCGATTTTG-A
1 AATCGCAACGCGATTCTGTA
* * *
2129579 CTATCGCAACGAG-TATCCGTAA
1 -AATCGCAACGCGAT-TCTGT-A
*
2129601 AATCGCAACGCG-TATCCGTA
1 AATCGCAACGCGAT-TCTGTA
* *
2129621 AATCGCAACGACAATAC-GTAA
1 AATCGCAACG-CGATTCTGT-A
*
2129642 AATCGCAACGCG-TATCCGTA
1 AATCGCAACGCGAT-TCTGTA
* *
2129662 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCG-ATTCTGTA
2129682 AATCGCAACGCG-TATCTGTA
1 AATCGCAACGCGAT-TCTGTA
* *
2129702 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCG-ATTCTGTA
*
2129722 AATCGCAACGCG-TATCCGTA
1 AATCGCAACGCGAT-TCTGTA
* *
2129742 AATCGCAATGCGAATAC-GTA
1 AATCGCAACGCG-ATTCTGTA
* *
2129762 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGATTCTGTA
* *
2129782 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGATTCTGTA
*
2129802 AATCGCAACGAGATTCTG
1 AATCGCAACGCGATTCTG
2129820 ACTATCGCAA
Statistics
Matches: 213, Mismatches: 27, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.01
19 7 0.03
20 164 0.77
21 35 0.16
22 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTCTGTA
Found at i:2130719 original size:24 final size:24
Alignment explanation
Indices: 2130668--2130721 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2130658 GTATTCGAAA
* *
2130668 TTTGATCTTGGTCAATACCCTGAC
1 TTTGATCTTGGTAAATACCCGGAC
* *
2130692 TTTGATCTTGGTAAATACTCGGAT
1 TTTGATCTTGGTAAATACCCGGAC
2130716 TTTGAT
1 TTTGAT
2130722 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCGGAC
Found at i:2133180 original size:20 final size:20
Alignment explanation
Indices: 2133134--2133187 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2133124 GACATTCATT
* * *
2133134 TGACTACCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
2133154 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
2133174 TGACTATCACAACG
1 TGACTATCGCAACG
2133188 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:2133209 original size:33 final size:33
Alignment explanation
Indices: 2133159--2133356 Score: 227
Period size: 33 Copynumber: 5.8 Consensus size: 33
2133149 GGAATTGACT
* ** *
2133159 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
2133193 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGA
* *
2133231 ATCGCAATGCGAAATGAAAATTGCAACGACTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
*
2133264 ATCGCAATGCGAAAATGAAAATCGCAACGCGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
*
2133298 ATCGCAATGCGAAATGAAAATCGCAACGCGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2133331 ATCGTAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2133357 TATGAAATGA
Statistics
Matches: 145, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
33 73 0.50
34 39 0.27
35 2 0.01
36 2 0.01
37 1 0.01
38 28 0.19
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2133216 original size:19 final size:19
Alignment explanation
Indices: 2133192--2133417 Score: 204
Period size: 19 Copynumber: 12.8 Consensus size: 19
2133182 ACAACGAGAG
2133192 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2133211 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2133230 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
2133249 AATTGCAA--CG-ACT--A
1 AATCGCAATGCGAAATGAA
2133263 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2133283 AATCGCAACGCG--A-G--
1 AATCGCAATGCGAAATGAA
2133297 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2133316 AATCGCAACGCG--A-G--
1 AATCGCAATGCGAAATGAA
*
2133330 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
2133349 AATCGCAATATGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
2133368 AATCTCAA-G-G--A-GTA
1 AATCGCAATGCGAAATGAA
2133382 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2133402 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
2133418 TTCGCATTGC
Statistics
Matches: 167, Mismatches: 18, Indels: 44
0.73 0.08 0.19
Matches are distributed among these distances:
14 38 0.23
15 2 0.01
16 9 0.05
17 7 0.04
18 2 0.01
19 84 0.50
20 25 0.15
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2133310 original size:86 final size:82
Alignment explanation
Indices: 2133210--2133417 Score: 242
Period size: 86 Copynumber: 2.4 Consensus size: 82
2133200 TGCGAAATGA
* *
2133210 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT-GAAAATTGC-AACGACTAAATCGCAATG
1 AAATCGCAATGCGAAATGAAAATCGCAACGCGAAATCG-AAA-TGCAAACGA--AAATCGCAATA
2133273 CGAAAATGAAAATCGCAACGCGAG
62 CG-AAATGAAAATCGCAA-G-GAG
* * *
2133297 -AATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGTAATGCGAAATGAAAATCGCAATATG
1 AAATCGCAATGCGAAATGAAAATCGCAACGCGA-AATCGAAATGC-AAACGAAAATCGCAATACG
*
2133361 AAATGAAAATCTCAAGGAG
64 AAATGAAAATCGCAAGGAG
2133380 TAAATCGCAATGCGAAAATGAAAATCGCAACGCGAAAT
1 -AAATCGCAATGCG-AAATGAAAATCGCAACGCGAAAT
2133418 TTCGCATTGC
Statistics
Matches: 108, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
83 3 0.03
84 1 0.01
85 29 0.27
86 65 0.60
87 5 0.05
88 5 0.05
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (82 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGCGAAATCGAAATGCAAACGAAAATCGCAATACGAA
ATGAAAATCGCAAGGAG
Found at i:2133318 original size:67 final size:69
Alignment explanation
Indices: 2133159--2133356 Score: 242
Period size: 67 Copynumber: 2.9 Consensus size: 69
2133149 GGAATTGACT
* ** * * *
2133159 ATCGCAACGCGGAAATGACTATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAACGCG-
2133224 AATGAAA
64 AATG-AA
* *
2133231 ATCGCAATGCGAAATGAAAATTGCAACGACTA-AATCGCAATGCGAAAATGAAAATCGCAACGCG
1 ATCGCAATGCGAAATGAAAATCGCAACG-CGAGAATCGCAATGCG-AAATGAAAATCGCAACGCG
2133295 -A-G-A
64 AATGAA
*
2133298 ATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGTAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAA
2133357 TATGAAATGA
Statistics
Matches: 112, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
66 17 0.15
67 39 0.35
69 1 0.01
70 1 0.01
71 26 0.23
72 28 0.25
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (69 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAA
TGAA
Found at i:2133357 original size:52 final size:52
Alignment explanation
Indices: 2133297--2133417 Score: 156
Period size: 52 Copynumber: 2.3 Consensus size: 52
2133287 GCAACGCGAG
*
2133297 AATCGCAATGCGAAATGAAAATCGCAACGCGAG-AATCGTAATGCG-AAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-G-GAGAAATCGCAATGCGAAAATGAA
** *
2133349 AATCGCAATATGAAATGAAAATCTCAAGGAGTAAATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGGAG-AAATCGCAATGCGAAAATGAA
*
2133402 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
2133418 TTCGCATTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 3 0.05
51 1 0.02
52 35 0.59
53 20 0.34
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAAGGAGAAATCGCAATGCGAAAATGAA
Found at i:2133371 original size:105 final size:103
Alignment explanation
Indices: 2133159--2133356 Score: 267
Period size: 105 Copynumber: 1.9 Consensus size: 103
2133149 GGAATTGACT
* ** *
2133159 ATCGCAACGCGGAAATGACTATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 ATCGCAACGCGAAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCG-
* *
2133224 AATGAAAATCGCAATGCGAAATGAAAATTGCAACGACTAA
65 AATG-AAATCGCAATGCGAAATGAAAATCGCAACGAATAA
* * *
2133264 ATCGCAATGCGAAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAACGCG-
1 ATCGCAACGCGAAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGA
*
2133328 A-G-AATCGTAATGCGAAATGAAAATCGCAA
66 ATGAAATCGCAATGCGAAATGAAAATCGCAA
2133357 TATGAAATGA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
100 25 0.30
102 1 0.01
103 1 0.01
105 57 0.68
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (103 bp):
ATCGCAACGCGAAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGA
ATGAAATCGCAATGCGAAATGAAAATCGCAACGAATAA
Found at i:2133482 original size:20 final size:19
Alignment explanation
Indices: 2133436--2133483 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
2133426 GCGATTCACT
2133436 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2133455 CATTGCGATTTTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
2133475 CGTTGCGAT
1 CGTTGCGAT
2133484 AGTTTGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Done.