Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 8 of 185
Found at i:2143894 original size:178 final size:178
Alignment explanation
Indices: 2143595--2143983 Score: 670
Period size: 178 Copynumber: 2.2 Consensus size: 178
2143585 ATCTTTCAAA
* * * *
2143595 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTTTAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
* * *
2143660 TGTTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAA
66 TGTTTCTACTTTTCAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCAGGACACGCTGAA
*
2143725 GTATTTTCAATTTCTGTTCTTTCAATTTCTGTTTTAATTCATGTTTTC
131 GTATTTTCAATTTCTGTTCTTCCAATTTCTGTTTTAATTCATGTTTTC
2143773 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
2143838 TGTTTCTACTTTTCAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCAGGACACGCTGAA
66 TGTTTCTACTTTTCAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCAGGACACGCTGAA
* * *
2143903 GTATTTTGAATTTTTGTTCTTCCAATTTCTGTTTTAATTTATGTTTTC
131 GTATTTTCAATTTCTGTTCTTCCAATTTCTGTTTTAATTCATGTTTTC
*
2143951 AAAAATCAATTCATATTGCGAGAGGTGAGTTGA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
2143984 ACCTTTTAAT
Statistics
Matches: 199, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
178 199 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (178 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
TGTTTCTACTTTTCAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCAGGACACGCTGAA
GTATTTTCAATTTCTGTTCTTCCAATTTCTGTTTTAATTCATGTTTTC
Found at i:2144021 original size:54 final size:53
Alignment explanation
Indices: 2143934--2144037 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 53
2143924 CCAATTTCTG
2143934 TTTTAATTTATGTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACC
1 TTTTAATTTATGTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACC
*
2143987 TTTTAATTTCTGTTTTTCAAAAATCAACTT-ATATTGCGAGAGGTGAGTTGA
1 TTTTAATTTATG-TTTTCAAAAATCAA-TTCATATTGCGAGAGGTGAGTTGA
2144038 GCCTCGGGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
53 11 0.23
54 35 0.73
55 2 0.04
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (53 bp):
TTTTAATTTATGTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACC
Found at i:2144080 original size:14 final size:14
Alignment explanation
Indices: 2144061--2144109 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
2144051 TGCCGAGGTA
*
2144061 TTTTCAGATTCTAT
1 TTTTCAAATTCTAT
*
2144075 TTTTCAAATTCTGT
1 TTTTCAAATTCTAT
* *
2144089 TTTT-AATTTATAT
1 TTTTCAAATTCTAT
2144102 TTTTCAAA
1 TTTTCAAA
2144110 AATCTACTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.59
Consensus pattern (14 bp):
TTTTCAAATTCTAT
Found at i:2144194 original size:14 final size:13
Alignment explanation
Indices: 2144161--2144190 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2144151 CGCTGAGGTA
2144161 TTTTCAATTTCTG
1 TTTTCAATTTCTG
*
2144174 TTTTCAATTTTTG
1 TTTTCAATTTCTG
2144187 TTTT
1 TTTT
2144191 TCAAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:2146087 original size:47 final size:47
Alignment explanation
Indices: 2145980--2146170 Score: 204
Period size: 47 Copynumber: 3.9 Consensus size: 47
2145970 AATGTGATTT
* * * *
2145980 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCATC-G-G---TGTGATATGTGCTA
*
2146032 CCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * *
2146079 CTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
** * *
2146125 CCGTATAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
2146171 ACTATGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
46 27 0.22
47 55 0.45
48 11 0.09
50 1 0.01
51 1 0.01
52 27 0.22
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:2146158 original size:93 final size:97
Alignment explanation
Indices: 2145982--2146188 Score: 235
Period size: 93 Copynumber: 2.1 Consensus size: 97
2145972 TGTGATTTCC
* * *
2145982 GTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTTCCGTATAAGACCATA
1 GTATAAGACCATAGCTGGGATATGGCATC-GAG--ATGTGATATGTGCATCCGTATAAGACCATA
*
2146047 TCCGGGATATGGCATCGG-TGTGATATGTG-CTACT
63 GCCGGGATATGGCATCGGATGTGATATGTGACTA-T
* * *
2146081 GTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATATGTG-ATCCGTATAAGACCATGGCT
1 GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
* *
2146143 GGGCTATGGCCTCGGTATGTGATATGTGACTAT
66 GGGATATGGCATCGG-ATGTGATATGTGACTAT
**
2146176 GTGCAAGACCATA
1 GTATAAGACCATA
2146189 ATTTTACTAT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
93 29 0.31
94 11 0.12
95 23 0.24
96 3 0.03
97 2 0.02
99 26 0.28
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (97 bp):
GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
GGGATATGGCATCGGATGTGATATGTGACTAT
Found at i:2149398 original size:15 final size:15
Alignment explanation
Indices: 2149378--2149446 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
2149368 GTATCTTGGG
2149378 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
2149393 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
2149408 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
2149423 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
2149438 TTTCTTTAT
1 TTTCTTTAT
2149447 TCAGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:2149447 original size:30 final size:30
Alignment explanation
Indices: 2149369--2149448 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
2149359 CATAGTATCG
* * *
2149369 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* *
2149399 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
2149429 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
2149449 AGTTTTCTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:2154800 original size:28 final size:28
Alignment explanation
Indices: 2154755--2154811 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
2154745 CATGTATATA
*
2154755 TAGTATTATCTTTTATTACTTCATTATT
1 TAGTATAATCTTTTATTACTTCATTATT
*
2154783 TAGTATAAT-TTTTAATTACTTTATTATT
1 TAGTATAATCTTTT-ATTACTTCATTATT
2154811 T
1 T
2154812 TTATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (28 bp):
TAGTATAATCTTTTATTACTTCATTATT
Found at i:2156732 original size:30 final size:30
Alignment explanation
Indices: 2156698--2156763 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
2156688 ACTTATTTTA
2156698 TTGTTAATTTTGTTATTAGTTTAAAGACAT
1 TTGTTAATTTTGTTATTAGTTTAAAGACAT
* *
2156728 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTAGTTTAAAGACAT
2156758 TTGTTA
1 TTGTTA
2156764 TTATTTAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTAGTTTAAAGACAT
Found at i:2156894 original size:12 final size:12
Alignment explanation
Indices: 2156861--2156887 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2156851 CATATATTTT
2156861 AAAATTATATAA
1 AAAATTATATAA
2156873 AAAATTATATAA
1 AAAATTATATAA
2156885 AAA
1 AAA
2156888 TTAATATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATTATATAA
Found at i:2161068 original size:45 final size:46
Alignment explanation
Indices: 2161001--2161124 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
2160991 CATATGACCT
*
2161001 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
2161044 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
2161090 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
2161125 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:2161107 original size:46 final size:45
Alignment explanation
Indices: 2161001--2161235 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
2160991 CATATGACCT
*
2161001 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
2161044 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
2161090 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
2161127 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2161164 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2161201 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
2161236 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:2161128 original size:37 final size:37
Alignment explanation
Indices: 2161086--2161262 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
2161076 AGCTGAAGCT
* **
2161086 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
2161123 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
2161160 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
2161197 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
2161234 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
2161263 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:2168766 original size:45 final size:46
Alignment explanation
Indices: 2168699--2168822 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
2168689 CATATGACCT
*
2168699 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
2168742 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
2168788 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
2168823 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:2168805 original size:46 final size:45
Alignment explanation
Indices: 2168699--2168933 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
2168689 CATATGACCT
*
2168699 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
2168742 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
2168788 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
2168825 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2168862 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2168899 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
2168934 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:2168826 original size:37 final size:37
Alignment explanation
Indices: 2168784--2168960 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
2168774 AGCTGAAGCT
* **
2168784 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
2168821 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
2168858 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
2168895 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
2168932 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
2168961 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:2174798 original size:17 final size:17
Alignment explanation
Indices: 2174767--2174813 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
2174757 AAAATTGGGA
*
2174767 TAAATTTTAAAAATTAAT
1 TAAA-TTTAAAATTTAAT
*
2174785 TATATTTCAAAATTTAAT
1 TAAATTT-AAAATTTAAT
2174803 TAAATTTAAAA
1 TAAATTTAAAA
2174814 CACGATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAAATTTAAT
Found at i:2183799 original size:12 final size:12
Alignment explanation
Indices: 2183770--2183804 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2183760 GAATTAGTCC
*
2183770 TATTATTATTAT
1 TATTACTATTAT
2183782 TATTACTATTAT
1 TATTACTATTAT
2183794 TATTACCTATT
1 TATTA-CTATT
2183805 TATTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTACTATTAT
Found at i:2189422 original size:6 final size:6
Alignment explanation
Indices: 2189411--2189435 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2189401 ATTTTTAAAT
2189411 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
2189436 TTATAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:2190322 original size:14 final size:12
Alignment explanation
Indices: 2190289--2190321 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2190279 TTTACATTGT
*
2190289 TTTTAAAATATA
1 TTTTATAATATA
2190301 TTTTATAATATA
1 TTTTATAATATA
2190313 TTTTA-AATA
1 TTTTATAATA
2190322 AGTCGGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTATAATATA
Found at i:2198961 original size:186 final size:186
Alignment explanation
Indices: 2198643--2199009 Score: 524
Period size: 186 Copynumber: 2.0 Consensus size: 186
2198633 CTTTCAGTTT
* *
2198643 TCAACATTAGTAAATTTCTTCTCCCCTGCTCATAGTTTTTTTCTCGAAAGGATTTCCACATAAAA
1 TCAACATTAGTAAATTTCTTCTCCCCTGCTCATAGTTTTTTTCCCGAAAGAATTTCCACATAAAA
* * * * * *
2198708 TTTGTGTGTTTTTTTTATTTTTATTTTTTACTTTACGATCGTTCTACCGTCATTATTGACGTTTA
66 TTTGTGTGTTTTTTTTACTTTTATTTATTACTTTACAATCGTTCTACCATCATTATCGACCTTTA
*
2198773 TTATAACAATTTAGTTATAAACATAATTCCATTAAAAAAAGAAAAAATAGTCATTA
131 TTATAACAATTTAATTATAAACATAATTCCATTAAAAAAAGAAAAAATAGTCATTA
* ** ** * *
2198829 TCAACATTAGTGAATTTCTTCTCCTTTGCTTGTAG-TTTTTTCCCGAAAGAATTTTCACGTAAAA
1 TCAACATTAGTAAATTTCTTCTCCCCTGCTCATAGTTTTTTTCCCGAAAGAATTTCCACATAAAA
* *
2198893 TTTGTGTGCTCTTATTTTT-CTTTT-TTTATTGCTTTGCAATCGTTCTACCATCATTATCGACCT
66 TTTGTGTG-T-TT-TTTTTACTTTTATTTATTACTTTACAATCGTTCTACCATCATTATCGACCT
2198956 TTATTATAACAATTTAATTATAAACATAATTCCATTAAAAAAAGAAAAAATAGT
128 TTATTATAACAATTTAATTATAAACATAATTCCATTAAAAAAAGAAAAAATAGT
2199010 TATAAAGTAA
Statistics
Matches: 160, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
185 33 0.21
186 116 0.73
187 6 0.04
188 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (186 bp):
TCAACATTAGTAAATTTCTTCTCCCCTGCTCATAGTTTTTTTCCCGAAAGAATTTCCACATAAAA
TTTGTGTGTTTTTTTTACTTTTATTTATTACTTTACAATCGTTCTACCATCATTATCGACCTTTA
TTATAACAATTTAATTATAAACATAATTCCATTAAAAAAAGAAAAAATAGTCATTA
Found at i:2202555 original size:15 final size:17
Alignment explanation
Indices: 2202515--2202558 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
2202505 TAGTTTAGGA
*
2202515 TCATTTTAAG-TTGAAC
1 TCATTTTGAGTTTGAAC
2202531 TCATTTTGAGTTTGAAC
1 TCATTTTGAGTTTGAAC
2202548 -CA-TTTGAGTTT
1 TCATTTTGAGTTT
2202559 TCAAATCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 11 0.42
17 6 0.23
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (17 bp):
TCATTTTGAGTTTGAAC
Found at i:2203365 original size:26 final size:26
Alignment explanation
Indices: 2203335--2203386 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2203325 ATATCATTAA
2203335 ATAATTAAAATAA-GACCAT-AAATAAT
1 ATAA-TAAAA-AATGACCATAAAATAAT
*
2203361 ATAATAAAAAATGTCCATAAAATAAT
1 ATAATAAAAAATGACCATAAAATAAT
2203387 TTTTCTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 2 0.09
25 10 0.43
26 11 0.48
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.27
Consensus pattern (26 bp):
ATAATAAAAAATGACCATAAAATAAT
Found at i:2206731 original size:17 final size:17
Alignment explanation
Indices: 2206711--2206744 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2206701 TTTTTTTATT
*
2206711 TTTTTGAATATTTTAAA
1 TTTTTAAATATTTTAAA
2206728 TTTTTAAATATTTTAAA
1 TTTTTAAATATTTTAAA
2206745 AATCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTTAAATATTTTAAA
Found at i:2206732 original size:8 final size:9
Alignment explanation
Indices: 2206712--2206744 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2206702 TTTTTTATTT
*
2206712 TTTTGAATA
1 TTTTAAATA
2206721 TTTTAAAT-
1 TTTTAAATA
2206729 TTTTAAATA
1 TTTTAAATA
2206738 TTTTAAA
1 TTTTAAA
2206745 AATCATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTAAATA
Found at i:2207657 original size:15 final size:15
Alignment explanation
Indices: 2207633--2207664 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2207623 ACCCATATAC
*
2207633 TAACCTAAAGCCCAA
1 TAACCCAAAGCCCAA
2207648 TAACCCAAAGCCCAA
1 TAACCCAAAGCCCAA
2207663 TA
1 TA
2207665 GCCTACTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.34, G:0.06, T:0.12
Consensus pattern (15 bp):
TAACCCAAAGCCCAA
Found at i:2207810 original size:19 final size:19
Alignment explanation
Indices: 2207783--2207827 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
2207773 TTGAAAAGTT
*
2207783 AATAATAATCAAATCTAACTAA
1 AATAATACT-AAAT-TAA-TAA
2207805 AATAATACTAAATTAATAA
1 AATAATACTAAATTAATAA
2207824 AATA
1 AATA
2207828 TGTAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 3 0.14
21 4 0.18
22 8 0.36
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAATACTAAATTAATAA
Found at i:2213422 original size:18 final size:20
Alignment explanation
Indices: 2213387--2213428 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
2213377 TTATTTTTAA
2213387 TTTAATAAATAATTATGAAAT
1 TTTAATAAATAA-TATGAAAT
*
2213408 TTTAA-AAATAA-ATGACAT
1 TTTAATAAATAATATGAAAT
2213426 TTT
1 TTT
2213429 TTAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (20 bp):
TTTAATAAATAATATGAAAT
Found at i:2218634 original size:12 final size:12
Alignment explanation
Indices: 2218617--2218643 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2218607 ATGGCATACT
2218617 TATGTATATATA
1 TATGTATATATA
2218629 TATGTATATATA
1 TATGTATATATA
2218641 TAT
1 TAT
2218644 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:2226293 original size:15 final size:15
Alignment explanation
Indices: 2226267--2226303 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2226257 TTTTAAACTT
2226267 AATTTAATATTTTTAA
1 AATTT-ATATTTTTAA
*
2226283 TATTTATATTTTTAA
1 AATTTATATTTTTAA
2226298 AATTTA
1 AATTTA
2226304 AAATTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTATATTTTTAA
Found at i:2226310 original size:15 final size:15
Alignment explanation
Indices: 2226267--2226311 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2226257 TTTTAAACTT
2226267 AATTTAATATTTTTAA
1 AATTTAA-ATTTTTAA
* *
2226283 TATTTATATTTTTAA
1 AATTTAAATTTTTAA
*
2226298 AATTTAAAATTTTA
1 AATTTAAATTTTTA
2226312 TTCTTGATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTAAATTTTTAA
Found at i:2226517 original size:21 final size:22
Alignment explanation
Indices: 2226483--2226532 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2226473 GTCTAACAAG
** *
2226483 ATTAAATTTTTAAAAAT-ATAT
1 ATTAAATTAATAAAAATAAAAT
*
2226504 ATTAAATTAATAAAATTAAAAT
1 ATTAAATTAATAAAAATAAAAT
2226526 ATTAAAT
1 ATTAAAT
2226533 ATTAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAAATTAATAAAAATAAAAT
Found at i:2226523 original size:14 final size:15
Alignment explanation
Indices: 2226497--2226545 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2226487 AATTTTTAAA
*
2226497 AATATATATTAAATT
1 AATAAATATTAAATT
*
2226512 AATAAA-ATTAAAAT
1 AATAAATATTAAATT
*
2226526 ATTAAATATTAAATT
1 AATAAATATTAAATT
*
2226541 CATAA
1 AATAA
2226546 CTTACACATG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAAATATTAAATT
Found at i:2226525 original size:15 final size:15
Alignment explanation
Indices: 2226497--2226538 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2226487 AATTTTTAAA
* *
2226497 AATATATATTAAATT
1 AATAAATATTAAAAT
2226512 AATAAA-ATTAAAAT
1 AATAAATATTAAAAT
*
2226526 ATTAAATATTAAA
1 AATAAATATTAAA
2226539 TTCATAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAAATATTAAAAT
Found at i:2231154 original size:4 final size:4
Alignment explanation
Indices: 2231145--2231180 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
2231135 TACAACTAGT
2231145 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
2231181 AAAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2240031 original size:25 final size:25
Alignment explanation
Indices: 2239997--2240047 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2239987 AGGGTTAAAT
2239997 AACCTTTGGGGTTAATATGAGAACA
1 AACCTTTGGGGTTAATATGAGAACA
2240022 AACCTTTGGGGTTAATATGAGAACA
1 AACCTTTGGGGTTAATATGAGAACA
2240047 A
1 A
2240048 GTGTCAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (25 bp):
AACCTTTGGGGTTAATATGAGAACA
Found at i:2245044 original size:41 final size:41
Alignment explanation
Indices: 2244994--2245076 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
2244984 AGAAATAAAA
*
2244994 AGATCAAATTCTTAAAAATAAATCTACATA-AACTAATTTCC
1 AGATCAAATTCTTAAAAATAAATCTACA-ACAACTAAATTCC
* *
2245035 AGATTAAATTCTTAAAAATAAATTTACAACAACTAAATTCC
1 AGATCAAATTCTTAAAAATAAATCTACAACAACTAAATTCC
2245076 A
1 A
2245077 TTCAAAGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (41 bp):
AGATCAAATTCTTAAAAATAAATCTACAACAACTAAATTCC
Found at i:2256939 original size:19 final size:20
Alignment explanation
Indices: 2256889--2256942 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
2256879 GTGATATTTT
*
2256889 ATAATCTTTTTAAAAAATAG
1 ATAATTTTTTTAAAAAATAG
*
2256909 A-AACTTTATTTTAAAATATA-
1 ATAA-TTT-TTTTAAAAAATAG
2256929 ATAATTTTTTTAAA
1 ATAATTTTTTTAAA
2256943 TGCATTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 9 0.31
20 7 0.24
21 13 0.45
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATTTTTTTAAAAAATAG
Found at i:2258997 original size:20 final size:21
Alignment explanation
Indices: 2258960--2258998 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2258950 AATGTTTGTT
2258960 AGCACAAAAGCTTTGACTCAA
1 AGCACAAAAGCTTTGACTCAA
2258981 AGCA-AAAAG-TTTGGACTC
1 AGCACAAAAGCTTT-GACTC
2258999 TCTCACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
AGCACAAAAGCTTTGACTCAA
Found at i:2259847 original size:19 final size:19
Alignment explanation
Indices: 2259819--2259857 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2259809 ATTTATAAAA
*
2259819 AAAATATATAAAAATCATT
1 AAAATATATAAAAATAATT
*
2259838 AAAATTTATAAAAATAATT
1 AAAATATATAAAAATAATT
2259857 A
1 A
2259858 GAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATATAAAAATAATT
Found at i:2259871 original size:32 final size:32
Alignment explanation
Indices: 2259808--2259873 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
2259798 AAACATAAAG
* *
2259808 AATTTATAAAAAAAATATATAAAAATCATTAA
1 AATTTATAAAAAAAATATAGAAAAATAATTAA
*
2259840 AATTTATAAAAATAAT-TAGAAAAATAAATTAA
1 AATTTATAAAAAAAATATAGAAAAAT-AATTAA
2259872 AA
1 AA
2259874 GCCATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (32 bp):
AATTTATAAAAAAAATATAGAAAAATAATTAA
Found at i:2259882 original size:41 final size:39
Alignment explanation
Indices: 2259818--2259935 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 39
2259808 AATTTATAAA
*
2259818 AAAAAT-ATATAAAAATCATTAAAATTTATAAAAATAATTAG
1 AAAAATAAT-TAAAAACCA-TAAAATTTATAAAAA-AATTAG
* * * *
2259859 AAAAATAAATTAAAAGCCATAAAATTTTTTAAAAAATTTAT
1 AAAAAT-AATTAAAAACCATAAAA-TTTATAAAAAAATTAG
* * *
2259900 AAAAATATTTAAAAACCATAAAAATTAGAAAAAAAT
1 AAAAATAATTAAAAACCATAAAATTTATAAAAAAAT
2259936 CATAAAATTA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
39 9 0.14
40 15 0.24
41 21 0.33
42 16 0.25
43 2 0.03
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.30
Consensus pattern (39 bp):
AAAAATAATTAAAAACCATAAAATTTATAAAAAAATTAG
Found at i:2259933 original size:20 final size:21
Alignment explanation
Indices: 2259910--2259952 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
2259900 AAAAATATTT
2259910 AAAAACCATAAAA-ATTAGAA
1 AAAAACCATAAAATATTAGAA
*
2259930 AAAAATCATAAAATTATTAGAA
1 AAAAACCATAAAA-TATTAGAA
2259952 A
1 A
2259953 TTAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAACCATAAAATATTAGAA
Found at i:2263972 original size:40 final size:40
Alignment explanation
Indices: 2263917--2263997 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2263907 TCGGGGGTAA
2263917 AGTATAAAATTTTAATCAAATGAATTAGTGACATATTTTT
1 AGTATAAAATTTTAATCAAATGAATTAGTGACATATTTTT
*
2263957 AGTATAAAATTTTAATCAAATGAATTAGTGATATATTTTT
1 AGTATAAAATTTTAATCAAATGAATTAGTGACATATTTTT
2263997 A
1 A
2263998 TAATACAACC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (40 bp):
AGTATAAAATTTTAATCAAATGAATTAGTGACATATTTTT
Found at i:2265094 original size:3 final size:3
Alignment explanation
Indices: 2265086--2265126 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2265076 TTTGTATCGG
2265086 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2265127 GTGGGGAGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2269091 original size:17 final size:17
Alignment explanation
Indices: 2269073--2269111 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2269063 AATTCTTTAT
2269073 TTTAATTTTA-AAATTA
1 TTTAATTTTACAAATTA
*
2269089 TTTATTTTTACAAATT-
1 TTTAATTTTACAAATTA
2269105 TTTAATT
1 TTTAATT
2269112 AATTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATTTTACAAATTA
Found at i:2269199 original size:21 final size:21
Alignment explanation
Indices: 2269174--2269247 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
2269164 ATACAATATT
2269174 TATAATATTAATTATTGATAC
1 TATAATATTAATTATTGATAC
* * ** *
2269195 TATAATAATATTTTAATACAATATT
1 TATAATATTA-ATT-AT-TGATA-C
2269220 TATAATATTAATTATTGATAC
1 TATAATATTAATTATTGATAC
*
2269241 TGTAATA
1 TATAATA
2269248 ATATTATAAC
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
21 15 0.39
22 5 0.13
23 4 0.11
24 5 0.13
25 9 0.24
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
TATAATATTAATTATTGATAC
Found at i:2269205 original size:24 final size:24
Alignment explanation
Indices: 2269175--2269253 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
2269165 TACAATATTT
2269175 ATAATATTAATTATTGATACTATA
1 ATAATATTAATTATTGATACTATA
* * * *
2269199 ATAATATT--TTAAT-ACAATATTT
1 ATAATATTAATTATTGATACTA-TA
*
2269221 ATAATATTAATTATTGATACTGTA
1 ATAATATTAATTATTGATACTATA
2269245 ATAATATTA
1 ATAATATTA
2269254 TAACGTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
21 4 0.10
22 13 0.31
24 22 0.52
25 3 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
ATAATATTAATTATTGATACTATA
Found at i:2269227 original size:46 final size:46
Alignment explanation
Indices: 2269160--2269252 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
2269150 GAGTGAACCA
2269160 TTTAATACAATATTTATAATATTAATTATTGATACTATAATAATAT
1 TTTAATACAATATTTATAATATTAATTATTGATACTATAATAATAT
*
2269206 TTTAATACAATATTTATAATATTAATTATTGATACTGTAATAATAT
1 TTTAATACAATATTTATAATATTAATTATTGATACTATAATAATAT
2269252 T
1 T
2269253 ATAACGTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (46 bp):
TTTAATACAATATTTATAATATTAATTATTGATACTATAATAATAT
Found at i:2269235 original size:16 final size:15
Alignment explanation
Indices: 2269170--2269235 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
2269160 TTTAATACAA
2269170 TATTTATAATATTAAT
1 TATTTATAATA-TAAT
* *
2269186 TATTGATACTATAAT
1 TATTTATAATATAAT
*
2269201 AATATTT-TAATACAA-
1 --TATTTATAATATAAT
2269216 TATTTATAATATTAAT
1 TATTTATAATA-TAAT
2269232 TATT
1 TATT
2269236 GATACTGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
13 5 0.13
14 5 0.13
15 6 0.15
16 19 0.49
17 4 0.10
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (15 bp):
TATTTATAATATAAT
Found at i:2272527 original size:120 final size:120
Alignment explanation
Indices: 2272314--2272832 Score: 984
Period size: 120 Copynumber: 4.3 Consensus size: 120
2272304 TTTATGCAGA
*
2272314 ATATAATTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
*
2272379 TATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
66 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
2272434 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
2272499 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
66 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
2272554 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
*
2272619 TATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
66 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
*
2272674 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAATATCATATAT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
* *
2272739 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAAAATTTTATTAAATT
66 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
2272794 ATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTT
2272833 TAAAAATCAT
Statistics
Matches: 392, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 392 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATT
Found at i:2272809 original size:18 final size:17
Alignment explanation
Indices: 2272781--2272815 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2272771 ATTATTAAAA
*
2272781 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2272798 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2272816 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2274759 original size:20 final size:21
Alignment explanation
Indices: 2274716--2274761 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2274706 CGCTTTCTCT
* *
2274716 TTTTTTTTTTTACTTTTTTCC
1 TTTTTTATTTTACTTTTGTCC
2274737 TTTTTTATTTTACTTTTGT-C
1 TTTTTTATTTTACTTTTGTCC
2274757 TTTTT
1 TTTTT
2274762 CTCTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTATTTTACTTTTGTCC
Found at i:2274858 original size:21 final size:23
Alignment explanation
Indices: 2274832--2274888 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
2274822 TTATTAATAT
*
2274832 ATATTTTGAAT-TTACTTTTTTA
1 ATATTTTAAATATTACTTTTTTA
*
2274854 A-ATTTTAAATATTATTTTTTTA
1 ATATTTTAAATATTACTTTTTTA
2274876 ATA-TTTAAATATT
1 ATATTTTAAATATT
2274889 TTAAACTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 8 0.26
22 22 0.71
23 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
ATATTTTAAATATTACTTTTTTA
Found at i:2274971 original size:14 final size:15
Alignment explanation
Indices: 2274946--2274974 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2274936 TTAATTTGTT
2274946 TTATAATATTTTAAA
1 TTATAATATTTTAAA
2274961 TTATAAT-TTTTAAA
1 TTATAATATTTTAAA
2274975 GATATTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATAATATTTTAAA
Found at i:2275496 original size:12 final size:13
Alignment explanation
Indices: 2275442--2275496 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 13
2275432 AAACGTTTGA
2275442 ATATCTTTAAAATT
1 ATAT-TTTAAAATT
2275456 A-ATTTTAAAATT
1 ATATTTTAAAATT
2275468 AATAATTTATAAAAATT
1 -AT-ATTT-T-AAAATT
2275485 ATA-TTTAAAATT
1 ATATTTTAAAATT
2275497 TAAAAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
12 15 0.42
13 4 0.11
14 3 0.08
15 5 0.14
16 3 0.08
17 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTTTAAAATT
Found at i:2275523 original size:13 final size:13
Alignment explanation
Indices: 2275492--2275528 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2275482 ATTATATTTA
2275492 AAATTTAAAA-A-
1 AAATTTAAAATAT
*
2275503 ATATTTAAAATAT
1 AAATTTAAAATAT
2275516 AAATTTAAAATAT
1 AAATTTAAAATAT
2275529 TATAAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 9 0.41
12 1 0.05
13 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTTAAAATAT
Found at i:2275564 original size:116 final size:115
Alignment explanation
Indices: 2275442--2275692 Score: 293
Period size: 115 Copynumber: 2.2 Consensus size: 115
2275432 AAACGTTTGA
**
2275442 ATATCTTTAAAATTAATTTTAAAATT-AATAATTTATAAAA-ATTATATTTAAAATT-TAAAA-A
1 ATATCTTTAAAA-TAATTTTAAAATTAAATAATTTA-AAAACATTAT-TAAAAAATTATAAAACA
*
2275503 ATATTTAAAATATAAATTTAAAATATTATAAAACAAATAATAAAT-TTGAAATGTC
63 A-A-TTAAAATATAAATTTAAAATATTATAAAACAAATAATAAATATGGAAA-GTC
* **
2275558 ATATCTTTAAAAATAA-TAT-ATTTTAAATAATTTAAAAATCATTATTAAAAAATTATAAAACAA
1 ATATCTTT-AAAATAATTTTAAAATTAAATAATTTAAAAA-CATTATTAAAAAATTATAAAACAA
* *
2275621 ATTAAAATATACATTTAAAATATTATAAAACTAATAATAAATATGGAAAGTC
64 ATTAAAATATAAATTTAAAATATTATAAAACAAATAATAAATATGGAAAGTC
*
2275673 ATATATTTAAAAT-ATTTTAA
1 ATATCTTTAAAATAATTTTAA
2275693 TGTTTTATAT
Statistics
Matches: 116, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
113 1 0.01
114 14 0.12
115 68 0.59
116 27 0.23
117 6 0.05
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (115 bp):
ATATCTTTAAAATAATTTTAAAATTAAATAATTTAAAAACATTATTAAAAAATTATAAAACAAAT
TAAAATATAAATTTAAAATATTATAAAACAAATAATAAATATGGAAAGTC
Found at i:2275724 original size:18 final size:21
Alignment explanation
Indices: 2275707--2275745 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2275697 TTATATTATT
2275707 AAAAAT-ATATTTAATATTTC
1 AAAAATAATATTTAATATTTC
2275727 AAAAATAATATTTAA-ATTT
1 AAAAATAATATTTAATATTT
2275746 TTAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAATAATATTTAATATTTC
Found at i:2275731 original size:21 final size:21
Alignment explanation
Indices: 2275707--2275752 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2275697 TTATATTATT
2275707 AAAAAT-ATATTT-AATATTTC
1 AAAAATAATATTTAAAT-TTTC
*
2275727 AAAAATAATATTTAAATTTTT
1 AAAAATAATATTTAAATTTTC
2275748 AAAAA
1 AAAAA
2275753 ATGATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 3 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATAATATTTAAATTTTC
Found at i:2275759 original size:20 final size:19
Alignment explanation
Indices: 2275705--2275762 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
2275695 TTTTATATTA
2275705 TTAAAAATATATTTAATATTT
1 TTAAAAA-ATATTTAA-ATTT
**
2275726 CAAAAATAATATTTAAATTT
1 TTAAAA-AATATTTAAATTT
2275746 TTAAAAAATGATTTAAA
1 TTAAAAAAT-ATTTAAA
2275763 AATAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 3 0.10
20 15 0.48
21 12 0.39
22 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAAAAAATATTTAAATTT
Found at i:2275764 original size:33 final size:32
Alignment explanation
Indices: 2275722--2275832 Score: 116
Period size: 33 Copynumber: 3.2 Consensus size: 32
2275712 TATATTTAAT
*
2275722 ATTTCAAAAATAATATTTAAATTTTTAAAAAATG
1 ATTT-AAAAATAATATTTAAA-TTTTAAAAAATA
*
2275756 ATTTAAAAATAATATTTAAAATTTAGAAAAATA
1 ATTTAAAAATAATATTTAAATTTTA-AAAAATA
*
2275789 ATTT-CAAATATATATTTAAAATTTTAAAAATATA
1 ATTTAAAAATA-ATATTT-AAATTTTAAAAA-ATA
2275823 TATTATAAAA
1 -ATT-TAAAA
2275833 CATTTCAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
32 9 0.14
33 36 0.55
34 14 0.22
35 3 0.05
36 1 0.02
37 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (32 bp):
ATTTAAAAATAATATTTAAATTTTAAAAAATA
Found at i:2276773 original size:14 final size:15
Alignment explanation
Indices: 2276754--2276782 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2276744 TTTGAATATT
2276754 TTTAAAA-ATTATAA
1 TTTAAAATATTATAA
2276768 TTTAAAATATTATAA
1 TTTAAAATATTATAA
2276783 AACAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAAAATATTATAA
Found at i:2276802 original size:31 final size:34
Alignment explanation
Indices: 2276759--2276849 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 34
2276749 ATATTTTTAA
* *
2276759 AAATTATAATTTAAAATATTATAAAAC-AA-ATT
1 AAATTAAAATTTAAAATATTATAAAACTAATAAT
*
2276791 AAA-TAAAATTTAAATTATTATAAAACTAATAAT
1 AAATTAAAATTTAAAATATTATAAAACTAATAAT
2276824 AAATTTAAAAGTTTAAAATATT-TAAA
1 AAA-TTAAAA-TTTAAAATATTATAAA
2276850 TATTTAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
31 21 0.42
32 5 0.10
33 5 0.10
35 9 0.18
36 10 0.20
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (34 bp):
AAATTAAAATTTAAAATATTATAAAACTAATAAT
Found at i:2276848 original size:17 final size:17
Alignment explanation
Indices: 2276826--2276879 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2276816 CTAATAATAA
2276826 ATTTAAA-AGTTTAAAAT
1 ATTTAAATA-TTTAAAAT
2276843 ATTTAAATATTTAAAA-
1 ATTTAAATATTTAAAAT
*
2276859 A-AT-AATATTTAAAAT
1 ATTTAAATATTTAAAAT
2276874 -TTTAAA
1 ATTTAAA
2276880 AATAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 11 0.35
15 2 0.06
16 3 0.10
17 14 0.45
18 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTAAATATTTAAAAT
Found at i:2276880 original size:21 final size:21
Alignment explanation
Indices: 2276840--2276893 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2276830 AAAAGTTTAA
2276840 AATATTTAAATATTTAAAAAAT
1 AATATTTAAA-ATTTAAAAAAT
*
2276862 AATATTTAAAATTTTAAAAAT
1 AATATTTAAAATTTAAAAAAT
2276883 AA-ATTTAAAAT
1 AATATTTAAAAT
2276894 ATATATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 9 0.29
21 12 0.39
22 10 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATTTAAAATTTAAAAAAT
Found at i:2276921 original size:11 final size:11
Alignment explanation
Indices: 2276857--2276929 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
2276847 AAATATTTAA
2276857 AAAATAATATTT
1 AAAAT-ATATTT
*
2276869 AAAAT-T-TTA
1 AAAATATATTT
*
2276878 AAAATAAATTT
1 AAAATATATTT
2276889 AAAATATATATT
1 AAAATATAT-TT
*
2276901 AATAAAATATTT
1 AA-AATATATTT
*
2276913 CAAATATATTT
1 AAAATATATTT
2276924 CAAAAT
1 -AAAAT
2276930 TTTAAAGTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 7 0.15
10 1 0.02
11 18 0.38
12 16 0.33
13 6 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATATTT
Found at i:2277004 original size:12 final size:11
Alignment explanation
Indices: 2276981--2277012 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2276971 AGAAAAAGAC
2276981 AAAAGTAAAAA
1 AAAAGTAAAAA
2276992 AAAAGTAAAAA
1 AAAAGTAAAAA
2277003 AAAAG-AAAAA
1 AAAAGTAAAAA
2277013 GAAATTGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (11 bp):
AAAAGTAAAAA
Found at i:2277012 original size:6 final size:6
Alignment explanation
Indices: 2276971--2277016 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2276961 TAAAATAAAG
* *
2276971 AGAAAA AGACAAA AGTAAA A-AAAA AGTAAA A-AAAA AGAAAA AGAAA
1 AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
2277017 TTGACTGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 8 0.24
6 20 0.61
7 5 0.15
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (6 bp):
AGAAAA
Found at i:2279397 original size:24 final size:24
Alignment explanation
Indices: 2279370--2279421 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2279360 TTAGTAAGTC
*
2279370 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2279394 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2279418 AAAT
1 AAAT
2279422 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2281367 original size:24 final size:24
Alignment explanation
Indices: 2281340--2281391 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2281330 TTAGTAAGTC
*
2281340 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2281364 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2281388 AAAT
1 AAAT
2281392 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2290753 original size:3 final size:3
Alignment explanation
Indices: 2290740--2290784 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
2290730 ATAGGTAAAG
* *
2290740 ATA ATA A-A ATA AT- ATA ATA GTA ATA ATA ACA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2290785 GTATTGATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2290775 original size:20 final size:19
Alignment explanation
Indices: 2290740--2290784 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2290730 ATAGGTAAAG
*
2290740 ATAATAAAATAATATAATA
1 ATAATAAAACAATATAATA
*
2290759 GTAATAATAACAATATAATA
1 ATAATAA-AACAATATAATA
2290779 ATAATA
1 ATAATA
2290785 GTATTGATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAATAAAACAATATAATA
Found at i:2290959 original size:17 final size:17
Alignment explanation
Indices: 2290937--2290980 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2290927 TATAGTACCT
2290937 AAAATATAGTAATA-ATA
1 AAAATATAG-AATATATA
2290954 AAAATATA-AATATATA
1 AAAATATAGAATATATA
2290970 AGAAATATAGA
1 A-AAATATAGA
2290981 TAGATGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 15 0.62
18 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
AAAATATAGAATATATA
Found at i:2291155 original size:3 final size:3
Alignment explanation
Indices: 2291142--2291356 Score: 77
Period size: 3 Copynumber: 70.3 Consensus size: 3
2291132 ACACTACTAT
* *
2291142 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* ** * * *
2291187 ATG ATA ATA GCA ATA AAA AGTA GAGCA ACTG ATA ATA ATA CATTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA -A-TA A-TA ATA ATA ATA -A-TA ATA
* * * * * *
2291235 AAA ATA ATA AGA AT- ATA TTA GTA ATG ATA AT- ATA ATGGA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT--A ATA ATA
* * * *
2291280 ATG A-A ATGA ATAA ATA GATA A-A AT- ATA GT- GTA ATT ATA ATA ATA
1 ATA ATA AT-A AT-A ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
2291324 TTA TTA ACA A-A ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2291357 CCAAAGCAAT
Statistics
Matches: 157, Mismatches: 38, Indels: 34
0.69 0.17 0.15
Matches are distributed among these distances:
2 14 0.09
3 121 0.77
4 15 0.10
5 7 0.04
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2298755 original size:22 final size:23
Alignment explanation
Indices: 2298730--2298773 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2298720 TGGGTATTTT
*
2298730 TAACAGTAGTT-ATTATTAGTGA
1 TAACAGTAATTAATTATTAGTGA
2298752 TAACAGTAATTACATTATTAGT
1 TAACAGTAATTA-ATTATTAGT
2298774 TATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (23 bp):
TAACAGTAATTAATTATTAGTGA
Found at i:2300223 original size:17 final size:17
Alignment explanation
Indices: 2300201--2300236 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2300191 AATTTCTAGA
*
2300201 ATTTACAATATATATAT
1 ATTTACAATAAATATAT
2300218 ATTTACAATAAATATAT
1 ATTTACAATAAATATAT
2300235 AT
1 AT
2300237 ATATGAGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTACAATAAATATAT
Found at i:2301260 original size:16 final size:16
Alignment explanation
Indices: 2301210--2301262 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
2301200 AAGTCACTTG
*
2301210 TTTGAATGATTTCGAA
1 TTTGAATCATTTCGAA
* *
2301226 TTCGAATCATTTAGAA
1 TTTGAATCATTTCGAA
2301242 TTTGAAT-ATTTTCGAA
1 TTTGAATCA-TTTCGAA
2301258 TTTGA
1 TTTGA
2301263 TTCGCAACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (16 bp):
TTTGAATCATTTCGAA
Found at i:2302067 original size:6 final size:6
Alignment explanation
Indices: 2302039--2302080 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
2302029 AGTGTAAAAC
*
2302039 AACAAG AAC-AT AACAATG CAACAAG AACAAG AACAAG AACAA
1 AACAAG AACAAG AACAA-G -AACAAG AACAAG AACAAG AACAA
2302081 AGCCAGCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 4 0.13
6 21 0.68
7 1 0.03
8 5 0.16
ACGTcount: A:0.64, C:0.19, G:0.12, T:0.05
Consensus pattern (6 bp):
AACAAG
Found at i:2314062 original size:29 final size:29
Alignment explanation
Indices: 2314010--2314065 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2314000 ATAGGGACCA
** *
2314010 GATCAAATTAGTCCCTCTATTATTAAATG
1 GATCAAATTAGTCCCTAAACTATTAAATG
*
2314039 GATCAATTTAGTCCCTAAACTATTAAA
1 GATCAAATTAGTCCCTAAACTATTAAA
2314066 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (29 bp):
GATCAAATTAGTCCCTAAACTATTAAATG
Found at i:2317211 original size:14 final size:14
Alignment explanation
Indices: 2317194--2317239 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
2317184 ATTAATTTTT
2317194 ATATATTATAAAAA
1 ATATATTATAAAAA
2317208 ATATAGTTA-AAAAA
1 ATATA-TTATAAAAA
*
2317222 TATATTTTATAAAAA
1 -ATATATTATAAAAA
2317237 ATA
1 ATA
2317240 ACAATTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
ATATATTATAAAAA
Found at i:2321363 original size:16 final size:15
Alignment explanation
Indices: 2321323--2321364 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2321313 TGTGATATAA
*
2321323 TTTAAAATAATTTTT
1 TTTAAAAAAATTTTT
2321338 TTTAAGAAAAATTCTTT
1 TTTAA-AAAAATT-TTT
2321355 TTTAAAAAAA
1 TTTAAAAAAA
2321365 GGATGGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TTTAAAAAAATTTTT
Found at i:2321461 original size:17 final size:18
Alignment explanation
Indices: 2321439--2321477 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2321429 ATTTTTTCTT
2321439 TTTTTTTTTA-ATTTTAC
1 TTTTTTTTTAGATTTTAC
*
2321456 TTTTTTTTTAGTTTTTAC
1 TTTTTTTTTAGATTTTAC
2321474 TTTT
1 TTTT
2321478 AAAATTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTAGATTTTAC
Found at i:2321861 original size:43 final size:43
Alignment explanation
Indices: 2321814--2321896 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
2321804 ATGACTTATC
* * *
2321814 AAAAATGTATTTAGACGACTAATCTATTGATCTAGTTTTACGA
1 AAAAAAGTATTTAGACAACTAATCCATTGATCTAGTTTTACGA
*
2321857 AAAAAAGTATTTAGACAATTAATCCATTGATCTAGTTTTA
1 AAAAAAGTATTTAGACAACTAATCCATTGATCTAGTTTTA
2321897 ATAATATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (43 bp):
AAAAAAGTATTTAGACAACTAATCCATTGATCTAGTTTTACGA
Found at i:2322308 original size:22 final size:22
Alignment explanation
Indices: 2322283--2322327 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2322273 TTATCAACTT
2322283 TTTTGAAATTTGTTG-ATTTTTA
1 TTTT-AAATTTGTTGAATTTTTA
* *
2322305 TTTTTAATTTTTTGAATTTTTA
1 TTTTAAATTTGTTGAATTTTTA
2322327 T
1 T
2322328 GAATAATACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (22 bp):
TTTTAAATTTGTTGAATTTTTA
Found at i:2326888 original size:21 final size:20
Alignment explanation
Indices: 2326834--2326890 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2326824 ATATCTAAAT
*
2326834 AAAGTATCAATACCCTTAAC
1 AAAGTATCAATACCTTTAAC
* * *
2326854 AAAGTATTAGTACCTTTCAC
1 AAAGTATCAATACCTTTAAC
*
2326874 AAAAGTATCGATACCTT
1 -AAAGTATCAATACCTT
2326891 ACTTGGTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (20 bp):
AAAGTATCAATACCTTTAAC
Found at i:2330142 original size:33 final size:33
Alignment explanation
Indices: 2330104--2330166 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2330094 ACCAGGTGTG
*
2330104 GGAGTGGGTTCCGGTAATTTAGCAGGTGATTTA
1 GGAGTGGCTTCCGGTAATTTAGCAGGTGATTTA
**
2330137 GGAGTGGCTTTGGGTAATTTAGCAGGTGAT
1 GGAGTGGCTTCCGGTAATTTAGCAGGTGAT
2330167 CTAGCAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.21, C:0.08, G:0.38, T:0.33
Consensus pattern (33 bp):
GGAGTGGCTTCCGGTAATTTAGCAGGTGATTTA
Found at i:2330265 original size:51 final size:50
Alignment explanation
Indices: 2330209--2330353 Score: 182
Period size: 51 Copynumber: 2.8 Consensus size: 50
2330199 AGTGCATCTT
* *
2330209 CTAGGTGTATGATCCTCTTCTGGTTTCTGCTTTAAACCATTGGCACTTCTC
1 CTAGGTGTATGCTCCTCTCCTGG-TTCTGCTTTAAACCATTGGCACTTCTC
* * *
2330260 TTAGGTGTATGCTGCTCTCCTCGGTTCTGCTTTAAACCATTGGCGCTTCTC
1 CTAGGTGTATGCTCCTCTCCT-GGTTCTGCTTTAAACCATTGGCACTTCTC
* * * *
2330311 CTAGGTGCACGCTTCTCTCCTGGGTTCTTCTTTAAACCATTGG
1 CTAGGTGTATGCTCCTCTCCT-GGTTCTGCTTTAAACCATTGG
2330354 AAACCGAGAC
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 80 0.98
52 2 0.02
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (50 bp):
CTAGGTGTATGCTCCTCTCCTGGTTCTGCTTTAAACCATTGGCACTTCTC
Found at i:2332414 original size:27 final size:27
Alignment explanation
Indices: 2332384--2332762 Score: 677
Period size: 27 Copynumber: 14.0 Consensus size: 27
2332374 GGTCAAATTA
*
2332384 TTGCTCGACTCAGTACCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
*
2332411 TTGCTTGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
* *
2332438 TTGCTTGACTCAGTAGCAGTAGGTTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332465 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
*
2332492 TTGCTCGACTCAGTAGCACTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332519 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332546 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332573 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332600 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332627 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332654 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
*
2332681 TTGCTCAACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332708 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
* **
2332735 TTGCTCGACTCGGTAGCTTTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2332762 T
1 T
2332763 CTTCTGATTT
Statistics
Matches: 340, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 340 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (27 bp):
TTGCTCGACTCAGTAGCAGTAGATTTC
Found at i:2339230 original size:308 final size:303
Alignment explanation
Indices: 2338666--2339284 Score: 802
Period size: 308 Copynumber: 2.0 Consensus size: 303
2338656 ATCTTAAATT
*
2338666 GAAATATTAACACTCATATCTCAATCCATTTAAGATAGAATCAAATCTTAAACATAAAACTTGAA
1 GAAATATTAACACTCATATCTCAATCCATTTAAG--AGAATCAAATCTTAAACACAAAACTTGAA
* *
2338731 ATAAACTTAAAATTTTATACTTTTAAGATAGATTTAAGTATGTTCGATGTCATGATGATGTTTGC
64 ATAAACTTAAAATTTTATACTTTTAAGATAGATTTAAGTATCTTCGATGTCATGATGATATTTGC
* *
2338796 ACTAAATCTAGTTTTAGTAATGTTTGATAGAAATATGATCAATGATTTTGATACCCATAGATATA
129 ACTAAATCTAGTCTTAGTAATGTTTGATAGAAATATGATCAATGAATTTGATACCCATAGATATA
* * **
2338861 AGATTTAACCCTAGTTATTATAAATTAAATTTTGTATGTTGACACGAGGTATAGGATTTGATCTG
194 AGATTTAACCCTAGTTACTATAAATTAAATTTTGTATGTTGACAC-AAGTATACAATTTGATCTG
* * * *
2338926 ATGTAATTTGCTTTTTCTTTTATTGTTGAAGGAGTTGGACAATTCA
258 ATGTAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGACAATTCA
* ** *
2338972 GAAATATTAACACTCATTTCTCAATCCATTT-AG-G-ATGGAATCTTAAATACAAAACTTGAAAT
1 GAAATATTAACACTCATATCTCAATCCATTTAAGAGAATCAAATCTTAAACACAAAACTTGAAAT
* * * *
2339034 AAACTTGAGATTTTATACTTTTAAGGATAGATTTAAGTGTCTTCTATGTCATGATCATGTGGATT
66 AAACTTAAAATTTTATACTTTTAA-GATAGATTTAAGTATCTTCGATGTCATG---A--T-GA--
* * * *
2339099 TAATTTGCTCTTAATCTAGTCTTGGTAATG-TTGATAGAAATATGATTAAT-AATTT-ATACCCA
122 T-ATTTGCACTAAATCTAGTCTTAGTAATGTTTGATAGAAATATGATCAATGAATTTGATACCCA
* * *
2339161 TAGATATTAGATTTAACCCTAGTTACTATAAATTAATTTTTGTATGTTAGTATA-AAGTATACAA
186 TAGATATAAGATTTAACCCTAGTTACTATAAATTAAATTTTGTATGTT-G-ACACAAGTATACAA
2339225 TTTGATCTGATGTAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGACAATTCA
249 TTTGATCTGATGTAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGACAATTCA
2339280 GAAAT
1 GAAAT
2339285 TTATTGAGAT
Statistics
Matches: 273, Mismatches: 28, Indels: 22
0.85 0.09 0.07
Matches are distributed among these distances:
301 46 0.17
302 26 0.10
305 3 0.01
306 30 0.11
307 1 0.00
308 117 0.43
309 5 0.02
310 22 0.08
311 23 0.08
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (303 bp):
GAAATATTAACACTCATATCTCAATCCATTTAAGAGAATCAAATCTTAAACACAAAACTTGAAAT
AAACTTAAAATTTTATACTTTTAAGATAGATTTAAGTATCTTCGATGTCATGATGATATTTGCAC
TAAATCTAGTCTTAGTAATGTTTGATAGAAATATGATCAATGAATTTGATACCCATAGATATAAG
ATTTAACCCTAGTTACTATAAATTAAATTTTGTATGTTGACACAAGTATACAATTTGATCTGATG
TAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGACAATTCA
Found at i:2340204 original size:17 final size:17
Alignment explanation
Indices: 2340178--2340213 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2340168 AGACAGCTGA
* *
2340178 AAAGATTTGATTGTAAC
1 AAAGACTTGATTGAAAC
2340195 AAAGACTTGATTGAAAC
1 AAAGACTTGATTGAAAC
2340212 AA
1 AA
2340214 TACATTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (17 bp):
AAAGACTTGATTGAAAC
Found at i:2342705 original size:22 final size:22
Alignment explanation
Indices: 2342680--2342727 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2342670 TTTAGGTACC
*
2342680 AAATT-ATATTAAAAATTAAAGA
1 AAATTAAT-TTAAAAATTAAACA
*
2342702 AAATTAATTTCAAAATTAAACA
1 AAATTAATTTAAAAATTAAACA
2342724 AAAT
1 AAAT
2342728 ATAGAGTCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTAATTTAAAAATTAAACA
Found at i:2344491 original size:15 final size:15
Alignment explanation
Indices: 2344467--2344497 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2344457 TTAGAGTATA
*
2344467 TTTTAGTTTATAAAT
1 TTTTACTTTATAAAT
2344482 TTTTACTTTATAAAT
1 TTTTACTTTATAAAT
2344497 T
1 T
2344498 GATAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTTACTTTATAAAT
Found at i:2344789 original size:17 final size:17
Alignment explanation
Indices: 2344767--2344801 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2344757 TAATTTTTTA
2344767 TATTATTGATATATAAT
1 TATTATTGATATATAAT
2344784 TATTATTGATATATAAT
1 TATTATTGATATATAAT
2344801 T
1 T
2344802 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TATTATTGATATATAAT
Found at i:2344838 original size:20 final size:20
Alignment explanation
Indices: 2344813--2344850 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2344803 TTTTAATTTC
2344813 AATCTCAAACTCTAAACTTG
1 AATCTCAAACTCTAAACTTG
* *
2344833 AATCTCGAACTTTAAACT
1 AATCTCAAACTCTAAACT
2344851 CAAAACTATA
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:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (20 bp):
AATCTCAAACTCTAAACTTG
Found at i:2357564 original size:11 final size:12
Alignment explanation
Indices: 2357550--2357587 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
2357540 AAGAAAAAAA
2357550 GAAGAGAG-AGG
1 GAAGAGAGAAGG
2357561 GAAGAGAGAAGG
1 GAAGAGAGAAGG
2357573 G-AGAGAGAAGG
1 GAAGAGAGAAGG
2357584 GAAG
1 GAAG
2357588 GGGAAGGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:2357577 original size:22 final size:22
Alignment explanation
Indices: 2357552--2357595 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2357542 GAAAAAAAGA
2357552 AGAGAG-AGGGAAGAGAGAAGGG
1 AGAGAGAAGGGAAG-GAGAAGGG
*
2357574 AGAGAGAAGGGAAGGGGAAGGG
1 AGAGAGAAGGGAAGGAGAAGGG
2357596 GAATCCGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (22 bp):
AGAGAGAAGGGAAGGAGAAGGG
Found at i:2357698 original size:13 final size:12
Alignment explanation
Indices: 2357680--2357732 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
2357670 GTAAAAAATA
2357680 TTTTTTTATTATT
1 TTTTTTTATT-TT
2357693 TTTTTTTATTTT
1 TTTTTTTATTTT
**
2357705 TTTATGTTTATACT
1 TTT-T-TTTATTTT
*
2357719 TTTTTGTATTTT
1 TTTTTTTATTTT
2357731 TT
1 TT
2357733 ATATATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
12 12 0.36
13 12 0.36
14 9 0.27
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (12 bp):
TTTTTTTATTTT
Found at i:2357707 original size:10 final size:11
Alignment explanation
Indices: 2357678--2357709 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
2357668 AGGTAAAAAA
2357678 TATTTTTTTAT
1 TATTTTTTTAT
2357689 TATTTTTTT-T
1 TATTTTTTTAT
2357699 TATTTTTTTAT
1 TATTTTTTTAT
2357710 GTTTATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TATTTTTTTAT
Found at i:2358149 original size:35 final size:35
Alignment explanation
Indices: 2358110--2358176 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
2358100 GTGTGTGATG
2358110 GTGCTGGTGGCAGACAGCATGGGAGAGTGGGAGTA
1 GTGCTGGTGGCAGACAGCATGGGAGAGTGGGAGTA
2358145 GTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 GTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
2358177 AGAGGCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.22, C:0.12, G:0.49, T:0.16
Consensus pattern (35 bp):
GTGCTGGTGGCAGACAGCATGGGAGAGTGGGAGTA
Found at i:2363440 original size:25 final size:24
Alignment explanation
Indices: 2363399--2363453 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2363389 ATAAAAATTT
* *
2363399 AATATAATCTTTCAAAAATTATAAA
1 AATATAAACTTTC-AAAATGATAAA
2363424 AATATAAACTATT-AAAATGATAAA
1 AATATAAACT-TTCAAAATGATAAA
*
2363448 ATTATA
1 AATATA
2363454 TTTTTACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 15 0.58
25 9 0.35
26 2 0.08
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (24 bp):
AATATAAACTTTCAAAATGATAAA
Found at i:2363671 original size:20 final size:20
Alignment explanation
Indices: 2363646--2363685 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2363636 ATATTTTTTT
*
2363646 TAGAGAA-AGGAAGTTGGTAA
1 TAGAGAATAGAAAG-TGGTAA
2363666 TAGAGAATAGAAAGTGGTAA
1 TAGAGAATAGAAAGTGGTAA
2363686 GGATTTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (20 bp):
TAGAGAATAGAAAGTGGTAA
Found at i:2364329 original size:30 final size:30
Alignment explanation
Indices: 2364295--2364356 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2364285 TAGTAATAGT
2364295 AAAATTACACTTT-ACCCTTTAAAAATGATA
1 AAAATTACA-TTTAACCCTTTAAAAATGATA
** * *
2364325 AAAATTTGATTTAATCCTTTAAAAATTATA
1 AAAATTACATTTAACCCTTTAAAAATGATA
2364355 AA
1 AA
2364357 TATATATGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTAACCCTTTAAAAATGATA
Found at i:2369467 original size:20 final size:22
Alignment explanation
Indices: 2369439--2369483 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2369429 TATACTTTTT
*
2369439 AATA-ATTTTA-ATTTTTTAAA
1 AATATATTTTATAGTTTTTAAA
*
2369459 AATATTTTTTATAGTTTTTAAA
1 AATATATTTTATAGTTTTTAAA
2369481 AAT
1 AAT
2369484 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATATATTTTATAGTTTTTAAA
Found at i:2369616 original size:15 final size:16
Alignment explanation
Indices: 2369589--2369622 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2369579 TACATAAATT
*
2369589 TAAAAATTAAAATATA
1 TAAAAATTAAAATAAA
2369605 TAAAAATT-AAATAAA
1 TAAAAATTAAAATAAA
2369620 TAA
1 TAA
2369623 CTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATTAAAATAAA
Found at i:2372783 original size:73 final size:73
Alignment explanation
Indices: 2372675--2372822 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 73
2372665 TAGAGTAAAA
* *
2372675 AAAATCTTGCCGTCGTGCCCGATAGTAGACGAGAGAGGTTTACGTCTCCAACGACGGTCTGCTTA
1 AAAATCTTGCCGTCGTGCCCGATAGTAGACGAGAGAGGTTCACGTCTCCAACGACGGTCTACTTA
2372740 GACAAAGC
66 GACAAAGC
*
2372748 AAAATCTTGCCGTCGTGCCCGATAGTAGACGAGAGAGGTTCACGTCTCCAACGACGGTCTACTTG
1 AAAATCTTGCCGTCGTGCCCGATAGTAGACGAGAGAGGTTCACGTCTCCAACGACGGTCTACTTA
2372813 GACAAAGC
66 GACAAAGC
2372821 AA
1 AA
2372823 CACATCCAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (73 bp):
AAAATCTTGCCGTCGTGCCCGATAGTAGACGAGAGAGGTTCACGTCTCCAACGACGGTCTACTTA
GACAAAGC
Found at i:2384026 original size:18 final size:18
Alignment explanation
Indices: 2384003--2384038 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2383993 AAATTAAAAG
2384003 ATTGGAGTTGAGAGCAAA
1 ATTGGAGTTGAGAGCAAA
2384021 ATTGGAGTTGAGAGCAAA
1 ATTGGAGTTGAGAGCAAA
2384039 CTCGATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (18 bp):
ATTGGAGTTGAGAGCAAA
Found at i:2385396 original size:29 final size:29
Alignment explanation
Indices: 2385354--2385415 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
2385344 ATCATGTATA
2385354 CAAACGTCAATTTTGTTAGAATATGGATG
1 CAAACGTCAATTTTGTTAGAATATGGATG
2385383 CAAACGTCAATTTTGTTAGAATATGGATG
1 CAAACGTCAATTTTGTTAGAATATGGATG
2385412 CAAA
1 CAAA
2385416 ATTCTTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (29 bp):
CAAACGTCAATTTTGTTAGAATATGGATG
Found at i:2387654 original size:24 final size:24
Alignment explanation
Indices: 2387627--2387675 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2387617 AAGATTACTA
2387627 TAAAAATTAATAACTAAGAAAATT
1 TAAAAATTAATAACTAAGAAAATT
*
2387651 TAAAAATTGATAACTAAGAAAATT
1 TAAAAATTAATAACTAAGAAAATT
2387675 T
1 T
2387676 CATAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (24 bp):
TAAAAATTAATAACTAAGAAAATT
Found at i:2388408 original size:15 final size:17
Alignment explanation
Indices: 2388384--2388418 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2388374 TTATTTTTTA
2388384 TTTATGTTATTC-GGAT
1 TTTATGTTATTCAGGAT
2388400 TTTAT-TTATTCAGGAT
1 TTTATGTTATTCAGGAT
2388416 TTT
1 TTT
2388419 TCTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (17 bp):
TTTATGTTATTCAGGAT
Found at i:2395574 original size:32 final size:32
Alignment explanation
Indices: 2395525--2395599 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
2395515 GTTTACTATT
*
2395525 TTCAATTAAGTATTTAATTGATTATTTATTTTTA
1 TTCAATT-A-TATTTAATTGATTATTTATTTGTA
2395559 TTCAATTATATTTAATTGATTATTTATTTGTA
1 TTCAATTATATTTAATTGATTATTTATTTGTA
*
2395591 TCCAATTAT
1 TTCAATTAT
2395600 GGTATAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
32 31 0.79
33 1 0.03
34 7 0.18
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (32 bp):
TTCAATTATATTTAATTGATTATTTATTTGTA
Found at i:2401189 original size:131 final size:131
Alignment explanation
Indices: 2400997--2401246 Score: 374
Period size: 131 Copynumber: 1.9 Consensus size: 131
2400987 TTTAAATAAA
* * * *
2400997 TGAAAATTTGAAGGGATACTCGATTATTTTGAGTAAATGCGAAATTGCAACCCAACACGTTAGGG
1 TGAAAATTTGAAGGGATACTCGATTATTTCGAGCAAACGCGAAATTCCAACCCAACACGTTAGGG
* * * *
2401062 TACGATTCCGCGAATTACTAAATATCGAATCTCGTCTTCGTTTTGAAGAATTTTAAAAGACATGA
66 CACGATTCCGCGAATTACCAAACATCGAATCTCGCCTTCGTTTTGAAGAATTTTAAAAGACATGA
2401127 G
131 G
* * *
2401128 TGAAATTTTGAAGTGATATTCGATTATTTCGAGCAAACGCGAAATTCCAACCCAACACGTTAGGG
1 TGAAAATTTGAAGGGATACTCGATTATTTCGAGCAAACGCGAAATTCCAACCCAACACGTTAGGG
* * *
2401193 CACGATTCCGCGAATTGCCAACCATCGAATCTCGCCTTCGTTTTGAAGGATTTT
66 CACGATTCCGCGAATTACCAAACATCGAATCTCGCCTTCGTTTTGAAGAATTTT
2401247 TGAATTAATA
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 105 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (131 bp):
TGAAAATTTGAAGGGATACTCGATTATTTCGAGCAAACGCGAAATTCCAACCCAACACGTTAGGG
CACGATTCCGCGAATTACCAAACATCGAATCTCGCCTTCGTTTTGAAGAATTTTAAAAGACATGA
G
Found at i:2424999 original size:20 final size:19
Alignment explanation
Indices: 2424958--2425005 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2424948 TTTTTATAAA
2424958 TATTTTAAAAATTTAAAAT
1 TATTTTAAAAATTTAAAAT
* *
2424977 TATTTTGAAAATTTGAAATT
1 TATTTTAAAAATTT-AAAAT
2424997 TATTTTAAA
1 TATTTTAAA
2425006 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
TATTTTAAAAATTTAAAAT
Found at i:2433662 original size:18 final size:19
Alignment explanation
Indices: 2433625--2433666 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
2433615 ACATATGCAT
2433625 ATCTGCTTTTGTAATCTGA
1 ATCTGCTTTTGTAATCTGA
* *
2433644 ATCTGGTTTTG-ATTCTGA
1 ATCTGCTTTTGTAATCTGA
2433662 ATCTG
1 ATCTG
2433667 AAACTGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (19 bp):
ATCTGCTTTTGTAATCTGA
Found at i:2439128 original size:46 final size:46
Alignment explanation
Indices: 2439078--2439252 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
2439068 TGGTTGAGCA
2439078 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
2439124 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
2439170 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2439216 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2439253 GCGGGTTACA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2441566 original size:19 final size:21
Alignment explanation
Indices: 2441522--2441589 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2441512 AAAACTTCCA
2441522 TGAATGTCACGACATTGGAAT
1 TGAATGTCACGACATTGGAAT
*
2441543 TGAATGTCACGACATT-G-CT
1 TGAATGTCACGACATTGGAAT
** * *
2441562 TGAATGTTGCAACATTGGATT
1 TGAATGTCACGACATTGGAAT
2441583 TGAATGT
1 TGAATGT
2441590 TGAGACATCG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 14 0.35
20 2 0.05
21 24 0.60
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (21 bp):
TGAATGTCACGACATTGGAAT
Found at i:2441597 original size:21 final size:21
Alignment explanation
Indices: 2441532--2441597 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
2441522 TGAATGTCAC
*
2441532 GACATTGGAATTGAATG-TCA
1 GACATTGGAATTGAATGTTGA
*
2441552 CGACATT-G-CTTGAATGTTGCA
1 -GACATTGGAATTGAATGTTG-A
*
2441573 -ACATTGGATTTGAATGTTGA
1 GACATTGGAATTGAATGTTGA
2441593 GACAT
1 GACAT
2441598 CGTTTTTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
19 12 0.32
20 4 0.11
21 21 0.57
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (21 bp):
GACATTGGAATTGAATGTTGA
Found at i:2449933 original size:43 final size:43
Alignment explanation
Indices: 2449830--2449937 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
2449820 TAGCCCAACT
* *
2449830 ATGGTCTTACACGA-AATCAAATAACGATGCCAATGTCCTAGAC
1 ATGGTCTTACAC-ATAATCACATAACGATGCCAATGTCCCAGAC
* ** *
2449873 ATGGTTTTACATGTAATCACATAATGATGCCAATGTCCCAGAC
1 ATGGTCTTACACATAATCACATAACGATGCCAATGTCCCAGAC
*
2449916 ATGGTGTTACACATAATCACAT
1 ATGGTCTTACACATAATCACAT
2449938 CTCGTTAGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACATAATCACATAACGATGCCAATGTCCCAGAC
Found at i:2452598 original size:18 final size:19
Alignment explanation
Indices: 2452565--2452600 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2452555 TTTTTTACTA
2452565 TAAACATTATTTATATATG
1 TAAACATTATTTATATATG
*
2452584 TAAAGATTA-TTATATAT
1 TAAACATTATTTATATAT
2452601 TATATCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (19 bp):
TAAACATTATTTATATATG
Done.