Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 241 of 292
Found at i:69968113 original size:51 final size:52
Alignment explanation
Indices: 69968002--69968136 Score: 236
Period size: 51 Copynumber: 2.6 Consensus size: 52
69967992 CATGATATTC
* *
69968002 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
*
69968054 TTATCATGGAATATTTACCTAACCTATTATCATG-AACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
69968105 TTATCATGGAACATTTACCTAACCTATTATCA
1 TTATCATGGAACATTTACCTAACCTATTATCA
69968137 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 48 0.61
52 31 0.39
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
Found at i:69972299 original size:25 final size:27
Alignment explanation
Indices: 69972262--69972314 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
69972252 TCAAACATGC
69972262 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
69972288 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
69972314 A
1 A
69972315 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:69973831 original size:26 final size:26
Alignment explanation
Indices: 69973795--69973927 Score: 209
Period size: 26 Copynumber: 5.2 Consensus size: 26
69973785 CATGAAATTC
69973795 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
69973821 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
69973847 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
69973873 TTATCATG-AACATTTACCTAA-CC-
1 TTATCATGAAACATTTACCTAACCCA
* *
69973896 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
69973922 TTATCA
1 TTATCA
69973928 ATTTGTATCA
Statistics
Matches: 100, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
23 8 0.08
24 14 0.14
25 14 0.14
26 64 0.64
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:69973919 original size:49 final size:51
Alignment explanation
Indices: 69973794--69973927 Score: 227
Period size: 49 Copynumber: 2.6 Consensus size: 51
69973784 ACATGAAATT
* *
69973794 CTTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACC
1 CTTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACC
69973845 CATTATCATGGAACATTTACCTAACCTATTATCATG-AACATTTACCTAA-C
1 C-TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACC
69973895 CTTATCATGGAACATTTACCTAACCTATTATCA
1 CTTATCATGGAACATTTACCTAACCTATTATCA
69973928 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
49 32 0.40
50 2 0.03
51 14 0.17
52 32 0.40
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (51 bp):
CTTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACC
Found at i:69974844 original size:25 final size:26
Alignment explanation
Indices: 69974806--69974918 Score: 89
Period size: 25 Copynumber: 4.7 Consensus size: 26
69974796 AAACCCTAAA
* * *
69974806 TCATAATCCCTAAACCCATAATTCA-
1 TCATAAACCTTAAACCCATAATTAAC
* *
69974831 TCATAAATCTTAAA-CCATAGTTAAC
1 TCATAAACCTTAAACCCATAATTAAC
69974856 TCATAAACCTTAAACCC-T-A--AAC
1 TCATAAACCTTAAACCCATAATTAAC
* * *
69974878 T-ATATATCTTAAA-CCATAGTTAAC
1 TCATAAACCTTAAACCCATAATTAAC
*
69974902 TCATAAACCCTAAACCC
1 TCATAAACCTTAAACCC
69974919 TAAACCATAT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
20 2 0.03
21 11 0.16
22 4 0.06
24 12 0.18
25 34 0.51
26 4 0.06
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.28
Consensus pattern (26 bp):
TCATAAACCTTAAACCCATAATTAAC
Found at i:69974887 original size:46 final size:46
Alignment explanation
Indices: 69974832--69974941 Score: 193
Period size: 46 Copynumber: 2.4 Consensus size: 46
69974822 CATAATTCAT
* *
69974832 CATAAATCTTAAACCATAGTTAACTCATAAACCTTAAACCCTAAAC
1 CATATATCTTAAACCATAGTTAACTCATAAACCCTAAACCCTAAAC
*
69974878 TATATATCTTAAACCATAGTTAACTCATAAACCCTAAACCCTAAAC
1 CATATATCTTAAACCATAGTTAACTCATAAACCCTAAACCCTAAAC
69974924 CATATATCTTAAACCATA
1 CATATATCTTAAACCATA
69974942 AACCTTAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (46 bp):
CATATATCTTAAACCATAGTTAACTCATAAACCCTAAACCCTAAAC
Found at i:69974888 original size:21 final size:21
Alignment explanation
Indices: 69974837--69974944 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 21
69974827 TTCATCATAA
*
69974837 ATCTTAAACCATAGTTAACTCATAA
1 ATCTTAAACCATA---AACT-ATAT
* *
69974862 ACCTTAAACCCTAAACTATAT
1 ATCTTAAACCATAAACTATAT
*
69974883 ATCTTAAACCATAGTTAACTCATAA
1 ATCTTAAACCATA---AACT-ATAT
* * * *
69974908 ACCCTAAACCCTAAACCATAT
1 ATCTTAAACCATAAACTATAT
69974929 ATCTTAAACCATAAAC
1 ATCTTAAACCATAAAC
69974945 CTTAAACTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
21 30 0.46
22 7 0.11
24 4 0.06
25 24 0.37
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (21 bp):
ATCTTAAACCATAAACTATAT
Found at i:69974956 original size:14 final size:14
Alignment explanation
Indices: 69974859--69974956 Score: 61
Period size: 14 Copynumber: 6.7 Consensus size: 14
69974849 AGTTAACTCA
* *
69974859 TAAACCTTAAACCC
1 TAAACCATAAACCT
* * *
69974873 TAAACTATATATCT
1 TAAACCATAAACCT
*
69974887 TAAACCATAGTTAACTCA
1 TAAACCATA---AAC-CT
* *
69974905 TAAACCCTAAACCC
1 TAAACCATAAACCT
* *
69974919 TAAACCATATATCT
1 TAAACCATAAACCT
69974933 TAAACCATAAACCT
1 TAAACCATAAACCT
*
69974947 TAAACTATAA
1 TAAACCATAA
69974957 TGACAATTAA
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
14 49 0.79
15 3 0.05
17 1 0.02
18 9 0.15
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.28
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:69975171 original size:41 final size:41
Alignment explanation
Indices: 69975114--69975332 Score: 341
Period size: 41 Copynumber: 5.4 Consensus size: 41
69975104 GTTATATGAC
*
69975114 TTTTAGCTGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
1 TTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
* *
69975155 TTTTAGCGGCGTTTTACTAGAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
69975196 TTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
1 TTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
** * * *
69975237 TTTTAGCGGTATTTTACCAGAAGTGCCGCTAATTCTCTGGT
1 TTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
* *
69975278 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC-TAT
1 TTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
69975318 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
69975333 TTACTAAAAC
Statistics
Matches: 161, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 16 0.10
41 145 0.90
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGT
Found at i:69975364 original size:123 final size:123
Alignment explanation
Indices: 69975125--69975363 Score: 329
Period size: 123 Copynumber: 1.9 Consensus size: 123
69975115 TTTAGCTGCG
* * *
69975125 TTTTACCAGAAGCGCCGCTAATGCTCTTGTTTTTAGCGGCGTTTTACTAGAAGCGCCGCTAATGC
1 TTTTACCAGAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGC
* * * *
69975190 TCTGGTTTTTAGCGGCGTTTTACCAGAAGCGCCGCTAATGCTCTTGTTTTTAGCGGTA
66 TCTGATTTTTAGCGGCGTTTTACCAGAAACGCCACCAATGCTCTTGTTTTTAGCGGTA
* *
69975248 TTTTACCAGAAGTGCCGCTAATTCTCTGGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGC
1 TTTTACCAGAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGC
* * *
69975313 TCT-ATTTTTAGCGGCGTTTTTTACTA-AAACGCCACCATTTCTCTGTGTTTT
66 TCTGATTTTTAGCGGCG--TTTTACCAGAAACGCCACCAATGCTCT-TGTTTT
69975364 ATAATTTTTG
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
122 12 0.12
123 76 0.75
124 13 0.13
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (123 bp):
TTTTACCAGAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGC
TCTGATTTTTAGCGGCGTTTTACCAGAAACGCCACCAATGCTCTTGTTTTTAGCGGTA
Found at i:69975403 original size:12 final size:12
Alignment explanation
Indices: 69975388--69975413 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
69975378 GTTTTTTGAT
69975388 AAAACGCCGCTA
1 AAAACGCCGCTA
69975400 AAAACGCCGCTA
1 AAAACGCCGCTA
69975412 AA
1 AA
69975414 GCCCTATTTT
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:69975587 original size:20 final size:20
Alignment explanation
Indices: 69975564--69975607 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
69975554 TTTTTAATAT
*
69975564 TATATATGTGTATAT-TTTAA
1 TATATATGCGTATATATTT-A
69975584 TATATATGCGTATATATTTA
1 TATATATGCGTATATATTTA
69975604 TATA
1 TATA
69975608 GTATTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (20 bp):
TATATATGCGTATATATTTA
Found at i:69975599 original size:22 final size:23
Alignment explanation
Indices: 69975555--69975602 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
69975545 ATATACATTT
* *
69975555 TTTTAATATTATATATGTGTATA
1 TTTTAATATTATATACGTATATA
*
69975578 TTTTAATA-TATATGCGTATATA
1 TTTTAATATTATATACGTATATA
69975600 TTT
1 TTT
69975603 ATATAGTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTAATATTATATACGTATATA
Found at i:69975667 original size:16 final size:16
Alignment explanation
Indices: 69975646--69975699 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
69975636 GTATGTATAC
69975646 ATTATGTAAATATTAT
1 ATTATGTAAATATTAT
*
69975662 ATTATGTATATATATAT
1 ATTATGTAAATAT-TAT
*
69975679 ATATATTTATATATATTAT
1 AT-TATGTA-A-ATATTAT
69975698 AT
1 AT
69975700 ACATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 12 0.39
17 5 0.16
18 5 0.16
19 5 0.16
20 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (16 bp):
ATTATGTAAATATTAT
Found at i:69975675 original size:2 final size:2
Alignment explanation
Indices: 69975655--69975700 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
69975645 CATTATGTAA
* *
69975655 AT AT -T AT AT -T AT GT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69975695 -T AT AT A
1 AT AT AT A
69975701 CATTTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:69975901 original size:9 final size:9
Alignment explanation
Indices: 69975887--69975922 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
69975877 CTAATATAGG
69975887 TATATATTA
1 TATATATTA
*
69975896 TATATATTT
1 TATATATTA
69975905 TATATA-TA
1 TATATATTA
69975913 TATATATTA
1 TATATATTA
69975922 T
1 T
69975923 GTACTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATATTA
Found at i:69982561 original size:3 final size:3
Alignment explanation
Indices: 69982421--69982540 Score: 114
Period size: 3 Copynumber: 39.7 Consensus size: 3
69982411 AAAAGAAAGA
* * * * *
69982421 AAT AAT AAT AGT AAA AAA AAT AAT AGT AAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
69982469 AGT AAT AAT AAT AGT AAT AAT AGAA AAT AAT AGT AAT AGT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* *
69982515 AAA AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
69982541 ATAAATTAAT
Statistics
Matches: 92, Mismatches: 24, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
3 90 0.98
4 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:69983270 original size:12 final size:12
Alignment explanation
Indices: 69983253--69983287 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
69983243 ATTTAGTCTA
69983253 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
69983265 TTTTCTATTTTC
1 TTTTCTTTTTTC
69983277 -TTTCTTTTTTC
1 TTTTCTTTTTTC
69983288 CTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:69983291 original size:12 final size:12
Alignment explanation
Indices: 69983254--69983291 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
69983244 TTTAGTCTAT
*
69983254 TTTCTTTTTTCT
1 TTTCTTTTTTCC
*
69983266 TTTCTATTTT-C
1 TTTCTTTTTTCC
69983277 TTTCTTTTTTCC
1 TTTCTTTTTTCC
69983289 TTT
1 TTT
69983292 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTTCC
Found at i:69984608 original size:9 final size:9
Alignment explanation
Indices: 69984590--69984625 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
69984580 AGTGAAATAG
*
69984590 AAAAAGGAA
1 AAAAAAGAA
69984599 AAAAAAGAA
1 AAAAAAGAA
*
69984608 AAAAAAAAA
1 AAAAAAGAA
69984617 AAAAAAGAA
1 AAAAAAGAA
69984626 GCAGCAGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:69985364 original size:11 final size:11
Alignment explanation
Indices: 69985339--69985372 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
69985329 AGTACACTCA
69985339 ACTATAT-TAT
1 ACTATATATAT
69985349 A-TATATATAT
1 ACTATATATAT
69985359 ACTATATATAT
1 ACTATATATAT
69985370 ACT
1 ACT
69985373 TAAAGGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 5 0.23
11 12 0.55
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (11 bp):
ACTATATATAT
Found at i:69985364 original size:15 final size:15
Alignment explanation
Indices: 69985341--69985370 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
69985331 TACACTCAAC
*
69985341 TATATTATATATATA
1 TATACTATATATATA
69985356 TATACTATATATATA
1 TATACTATATATATA
69985371 CTTAAAGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATACTATATATATA
Found at i:69994884 original size:5 final size:5
Alignment explanation
Indices: 69994874--69994901 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
69994864 CTGTGTGTTC
69994874 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
69994902 CACAAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:70000516 original size:5 final size:5
Alignment explanation
Indices: 70000506--70000539 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
70000496 CTGTGTGTTC
70000506 TTTAT TTTATT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTT
70000540 CACAACTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:70001408 original size:131 final size:131
Alignment explanation
Indices: 70001166--70001408 Score: 283
Period size: 131 Copynumber: 1.9 Consensus size: 131
70001156 CTTTAAATTG
** * * *
70001166 TTTTATTTTAAAATTTATACTTTGATTTTTAAAAGGATATTCGGTTGTTTAGATCCAACTAGAAA
1 TTTTATTTTAAAATTTATACTTTGAAATTTAAAAGGATATTCGGCTATTTAGATCCAACGAGAAA
* * **
70001231 AAATCGAAACCCCGTAAGTTAGGGGACGACCTTCTCGAATTTCTAAATACGGAATATTGCTTTTA
66 AAATCAAAACCCCGTAAGTTAGGGCACGACCTTCTCGAATCGCTAAATACGGAATATTGCTTTTA
70001296 C
131 C
* * *
70001297 TTTTA-TTTAAAATTTATGTATTTTGAAATTTAAAAGGATATTTGGCTATTTAGATTCAACGAG-
1 TTTTATTTTAAAATTTA--TACTTTGAAATTTAAAAGGATATTCGGCTATTTAGATCCAACGAGA
* * * * ** *
70001360 AGAAATCAAAATCCTGTAAGTTAGTGCACGATTTTCTCGAGTCGCTAAA
64 AAAAATCAAAACCCCGTAAGTTAGGGCACGACCTTCTCGAATCGCTAAA
70001409 ATTCGAAACA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
130 11 0.12
131 43 0.47
132 37 0.41
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (131 bp):
TTTTATTTTAAAATTTATACTTTGAAATTTAAAAGGATATTCGGCTATTTAGATCCAACGAGAAA
AAATCAAAACCCCGTAAGTTAGGGCACGACCTTCTCGAATCGCTAAATACGGAATATTGCTTTTA
C
Found at i:70001960 original size:21 final size:22
Alignment explanation
Indices: 70001934--70001974 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
70001924 ATGAAAAGAT
*
70001934 GATAATAAAATAAT-AATAATG
1 GATAATAAAAAAATCAATAATG
70001955 GATAATAAAAAAATCAATAA
1 GATAATAAAAAAATCAATAA
70001975 AAAGGAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.24
Consensus pattern (22 bp):
GATAATAAAAAAATCAATAATG
Found at i:70006993 original size:18 final size:18
Alignment explanation
Indices: 70006986--70007033 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
70006976 AATAATATTT
70006986 TAAT-AAAAATAAATAAA
1 TAATAAAAAATAAATAAA
70007003 TAATAAAAAATAAA-AAA
1 TAATAAAAAATAAATAAA
*
70007020 T-TTAAAAATATAAA
1 TAATAAAAA-ATAAA
70007034 ATATTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 6 0.21
17 13 0.46
18 9 0.32
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
TAATAAAAAATAAATAAA
Found at i:70007006 original size:17 final size:16
Alignment explanation
Indices: 70006986--70007036 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
70006976 AATAATATTT
70006986 TAATAAAAATAAATAAA
1 TAATAAAAATAAA-AAA
70007003 TAATAAAAAATAAAAAA
1 TAAT-AAAAATAAAAAA
* *
70007020 T-TTAAAAATATAAAA
1 TAATAAAAATAAAAAA
70007035 TA
1 TA
70007037 TTATTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 8 0.27
18 9 0.30
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TAATAAAAATAAAAAA
Found at i:70007061 original size:23 final size:22
Alignment explanation
Indices: 70007035--70007077 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
70007025 AAATATAAAA
*
70007035 TATTATTATTTTTTAATTTTACT
1 TATTATT-TTATTTAATTTTACT
*
70007058 TATTATTTTATTTATTTTTA
1 TATTATTTTATTTAATTTTA
70007078 AAATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTATTTTATTTAATTTTACT
Found at i:70007084 original size:23 final size:23
Alignment explanation
Indices: 70007030--70007091 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
70007020 TTTAAAAATA
*
70007030 TAAAATATTATTATTTTTTAATTT
1 TAAAATATTATT-TTATTTAATTT
** *
70007054 T-ACTTATTATTTTATTTATTTT
1 TAAAATATTATTTTATTTAATTT
*
70007076 TAAAATATTTTTTTAT
1 TAAAATATTATTTTAT
70007092 AGTTGGTGTC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 10 0.33
23 19 0.63
24 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TAAAATATTATTTTATTTAATTT
Found at i:70010730 original size:45 final size:45
Alignment explanation
Indices: 70010675--70010769 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
70010665 ATAATTTAAT
*
70010675 AAAA-ATTATGAAATTTACACATTTAAGAATAATTAGGATGTAAA
1 AAAATATTATGAAATTTACACATTTAAGAATAATTAGGAAGTAAA
*
70010719 AAAATATTATGATATTTACACATTTAAGAATAATTAGGAAGTAAA
1 AAAATATTATGAAATTTACACATTTAAGAATAATTAGGAAGTAAA
70010764 AAAATA
1 AAAATA
70010770 AAAAAATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 4 0.08
45 44 0.92
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (45 bp):
AAAATATTATGAAATTTACACATTTAAGAATAATTAGGAAGTAAA
Found at i:70010779 original size:45 final size:45
Alignment explanation
Indices: 70010687--70010779 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
70010677 AAATTATGAA
* ** **
70010687 ATTTACACATTTAAGAATAATTAGGATGTAAAAAAATATTATGAT
1 ATTTACACATTTAAGAATAATTAGGAAGTAAAAAAATAAAAAAAT
70010732 ATTTACACATTTAAGAATAATTAGGAAGTAAAAAAATAAAAAAAT
1 ATTTACACATTTAAGAATAATTAGGAAGTAAAAAAATAAAAAAAT
70010777 ATT
1 ATT
70010780 GCTAATTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (45 bp):
ATTTACACATTTAAGAATAATTAGGAAGTAAAAAAATAAAAAAAT
Found at i:70017345 original size:71 final size:71
Alignment explanation
Indices: 70017261--70017424 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
70017251 CGATTTGTCT
70017261 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
70017326 CTTTCA
66 CTTTCA
70017332 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
70017397 CTTTCA
66 CTTTCA
70017403 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
70017425 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:70017462 original size:71 final size:70
Alignment explanation
Indices: 70017261--70017458 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
70017251 CGATTTGTCT
* * * *
70017261 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
70017326 CTTTCA
65 CTTTCA
* * * *
70017332 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
70017397 CTTTCA
65 CTTTCA
* *
70017403 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
70017459 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:70035330 original size:2 final size:2
Alignment explanation
Indices: 70035325--70035354 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70035315 ACGTGCACAC
70035325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70035355 GCTAGATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70036451 original size:24 final size:23
Alignment explanation
Indices: 70036414--70036464 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
70036404 TACAATTAAG
* *
70036414 TTTTAAATATAATTTTATTTTTAT
1 TTTTAAATAGAA-TTTATTTATAT
*
70036438 TTTTAATTAGAATTTATTTATAT
1 TTTTAAATAGAATTTATTTATAT
70036461 TTTT
1 TTTT
70036465 TAATGATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTAAATAGAATTTATTTATAT
Found at i:70040868 original size:14 final size:14
Alignment explanation
Indices: 70040830--70040881 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
70040820 TACAATTTAG
* *
70040830 TTTTAAAATAAATT
1 TTTTAAATTATATT
*
70040844 ATTTAATATTATATT
1 TTTTAA-ATTATATT
70040859 TTTTAAATTATATAT
1 TTTTAAATTATAT-T
70040874 TCTTTAAA
1 T-TTTAAA
70040882 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.39
15 13 0.42
16 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATTATATT
Found at i:70041916 original size:24 final size:24
Alignment explanation
Indices: 70041876--70041921 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
70041866 ACAAGCATGT
*
70041876 AAGTGCTAATAATCACGAGCACTG
1 AAGTGCTAAGAATCACGAGCACTG
70041900 AAGTGCTAAGGAA-CACGAGCAC
1 AAGTGCTAA-GAATCACGAGCAC
70041922 ATAGATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (24 bp):
AAGTGCTAAGAATCACGAGCACTG
Found at i:70048316 original size:7 final size:7
Alignment explanation
Indices: 70048304--70048332 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
70048294 CTCATAAGAC
70048304 CCACTTG
1 CCACTTG
70048311 CCACTTG
1 CCACTTG
70048318 CCACTTG
1 CCACTTG
70048325 CCACTTG
1 CCACTTG
70048332 C
1 C
70048333 TTCATTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.45, G:0.14, T:0.28
Consensus pattern (7 bp):
CCACTTG
Found at i:70048615 original size:21 final size:19
Alignment explanation
Indices: 70048589--70048627 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
70048579 AATTAAGTAA
70048589 TTAAAATTATTAAAATTATAT
1 TTAAAATTA--AAAATTATAT
70048610 TTAAAATTAAAAATTATA
1 TTAAAATTAAAAATTATA
70048628 ATATTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAAATTAAAAATTATAT
Found at i:70048617 original size:27 final size:27
Alignment explanation
Indices: 70048587--70048639 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
70048577 TAAATTAAGT
*
70048587 AATT-AAAATTATTAAAATTATATTTAA
1 AATTAAAAATTA-TAAAATTAAATTTAA
*
70048614 AATTAAAAATTATAATATTAAATTTA
1 AATTAAAAATTATAAAATTAAATTTA
70048640 TATATTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTAAAAATTATAAAATTAAATTTAA
Found at i:70048634 original size:21 final size:21
Alignment explanation
Indices: 70048588--70048641 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
70048578 AAATTAAGTA
70048588 ATTAAAATTATTAAAATTATAT
1 ATTAAAATTA-TAAAATTATAT
70048610 -TTAAAATTA-AAAATTATAAT
1 ATTAAAATTATAAAATTAT-AT
*
70048630 ATTAAATTTATA
1 ATTAAAATTATA
70048642 TATTTGTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.29
20 2 0.07
21 17 0.61
22 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAAAATTATAAAATTATAT
Found at i:70052144 original size:12 final size:12
Alignment explanation
Indices: 70052058--70052164 Score: 88
Period size: 12 Copynumber: 8.8 Consensus size: 12
70052048 TTATTATTGC
70052058 TATTATTATCAT
1 TATTATTATCAT
*
70052070 TATTATTATTAT
1 TATTATTATCAT
*
70052082 TATTATTATTAT
1 TATTATTATCAT
* *
70052094 TATTATTATTAC
1 TATTATTATCAT
* **
70052106 TGTTATTATTTT
1 TATTATTATCAT
* * *
70052118 TACTACTACCAT
1 TATTATTATCAT
70052130 TATTATTATCAT
1 TATTATTATCAT
*
70052142 TATAGTATCATCAT
1 TAT--TATTATCAT
*
70052156 CATTATTAT
1 TATTATTAT
70052165 TGTCAAAACT
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
12 66 0.87
14 10 0.13
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (12 bp):
TATTATTATCAT
Found at i:70052165 original size:3 final size:3
Alignment explanation
Indices: 70052017--70052144 Score: 114
Period size: 3 Copynumber: 42.7 Consensus size: 3
70052007 TCCTATCAAC
* * * **
70052017 ATT ATT GTT ATT ATT ACT ATT ATG ATT -TCT ATT ATT ATT GCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
* * *
70052062 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * ** *
70052110 ATT ATT TTT ACT ACT ACC ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
70052145 AGTATCATCA
Statistics
Matches: 99, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
2 1 0.01
3 97 0.98
4 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:70053140 original size:26 final size:24
Alignment explanation
Indices: 70053081--70053239 Score: 105
Period size: 26 Copynumber: 6.5 Consensus size: 24
70053071 AAATAATGAG
* * *
70053081 ACAATTTTAAATAAATACATAAAAA
1 ACAATTTAAAATAGATA-ATATAAA
* *
70053106 ATAAGTTTAAAATAGATATTATAAAA
1 ACAA-TTTAAAATAGATAATAT-AAA
* *
70053132 AGCAATTTAAAGT-GAATAGTATAAA
1 A-CAATTTAAAATAG-ATAATATAAA
70053157 ACAATTTAAAATA-ATTAATATGTAAA
1 ACAATTTAAAATAGA-TAATA--TAAA
70053183 ACAATTTAAAAT--A-AA-ATAAA
1 ACAATTTAAAATAGATAATATAAA
* * * *
70053203 GCAACTTAAAATAAATAATATATA
1 ACAATTTAAAATAGATAATATAAA
70053227 ACAATTTAAAATA
1 ACAATTTAAAATA
70053240 ACATGTTGAA
Statistics
Matches: 107, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
20 14 0.13
22 2 0.02
23 5 0.05
24 29 0.27
25 11 0.10
26 44 0.41
27 2 0.02
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
ACAATTTAAAATAGATAATATAAA
Found at i:70053166 original size:24 final size:25
Alignment explanation
Indices: 70053153--70053240 Score: 89
Period size: 24 Copynumber: 3.7 Consensus size: 25
70053143 GTGAATAGTA
70053153 TAAAACAATTTAAAATAATTAATATG
1 TAAAACAATTTAAAATAATTAATA-G
70053179 TAAAACAATTTAAAAT-A--AA-A-
1 TAAAACAATTTAAAATAATTAATAG
* * *
70053199 TAAAGCAACTTAAAATAAATAATA-
1 TAAAACAATTTAAAATAATTAATAG
*
70053223 TATAACAATTTAAAATAA
1 TAAAACAATTTAAAATAA
70053241 CATGTTGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
20 14 0.26
21 1 0.02
22 1 0.02
23 4 0.08
24 16 0.30
25 1 0.02
26 16 0.30
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (25 bp):
TAAAACAATTTAAAATAATTAATAG
Found at i:70053222 original size:46 final size:46
Alignment explanation
Indices: 70053152--70053290 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 46
70053142 AGTGAATAGT
* * *
70053152 ATAAAACAATTTAAAATAATTAATATGTAAAACAATTTAAAATAAA
1 ATAAAGCAACTTAAAATAAATAATATGTAAAACAATTTAAAATAAA
* *
70053198 ATAAAGCAACTTAAAATAAATAATA--TATAACAATTTAAAATAAC
1 ATAAAGCAACTTAAAATAAATAATATGTAAAACAATTTAAAATAAA
*** * * * *
70053242 ATGTTGAAAGTCTAGAATAAATAATATGTCAAAAGAAATTTAAAATAAA
1 ATAAAGCAACT-TAAAATAAATAATATGT-AAAA-CAATTTAAAATAAA
70053291 TGACATGTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
44 23 0.31
45 13 0.18
46 22 0.30
47 1 0.01
48 3 0.04
49 12 0.16
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (46 bp):
ATAAAGCAACTTAAAATAAATAATATGTAAAACAATTTAAAATAAA
Found at i:70053337 original size:25 final size:25
Alignment explanation
Indices: 70053309--70053364 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
70053299 AAAAAAAAAC
*
70053309 ATATGAAAAGT-TTAATATAAATAAT
1 ATAT-AAAAGTCTTAAAATAAATAAT
*
70053334 ATATAAAA-TCTTAAAATTAATAAT
1 ATATAAAAGTCTTAAAATAAATAAT
70053358 A-ATAAAA
1 ATATAAAA
70053365 AGGTTTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 17 0.61
25 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (25 bp):
ATATAAAAGTCTTAAAATAAATAAT
Found at i:70053341 original size:24 final size:24
Alignment explanation
Indices: 70053320--70053364 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
70053310 TATGAAAAGT
*
70053320 TTAATATAAATAATATATAAAATC
1 TTAAAATAAATAATATATAAAATC
*
70053344 TTAAAATTAATAATA-ATAAAA
1 TTAAAATAAATAATATATAAAA
70053365 AGGTTTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAAATAAATAATATATAAAATC
Found at i:70053462 original size:2 final size:2
Alignment explanation
Indices: 70053455--70053479 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70053445 AAAATAGATG
70053455 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
70053480 ATAGTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70053696 original size:4 final size:4
Alignment explanation
Indices: 70053687--70053735 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
70053677 AAATAAAAGC
* * ** *
70053687 ATAA ATAA ATAA ATAA ATGA ATGA ATTT ATAA ATAA ATGA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
70053735 A
1 A
70053736 AGAAAACATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:70055455 original size:23 final size:22
Alignment explanation
Indices: 70055425--70055471 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
70055415 TTCACTAGAA
*
70055425 TTTTCTTTGTTATTTCATTTAT
1 TTTTCTTTATTATTTCATTTAT
*
70055447 TTTTCCTTTATTATTTTATTTAT
1 TTTT-CTTTATTATTTCATTTAT
70055470 TT
1 TT
70055472 ATTTCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTTTATTATTTCATTTAT
Found at i:70057389 original size:87 final size:88
Alignment explanation
Indices: 70057245--70057470 Score: 242
Period size: 88 Copynumber: 2.6 Consensus size: 88
70057235 ACTTAATTGC
* * * * * *
70057245 TTTTTTGAAAAATTTTGAGGGTCTTTTT-GATGTATTTTGAAAGTTCAAATACTCAATTGAGTG-
1 TTTTTTGAAAAAATTTAAGGGTATTTTTAGA--AATTTTGAAAGTTTAAGTACTCAATTGAGTGA
* *
70057308 AAAAAAAAGCGGGGGCCTAATTAAT
64 AAAAAAAAGCAGGGACCTAATTAAT
70057333 TTTTTTGAAAAAATTTAAGGGTATTTTTAGAAATTTTGAAAGTTTAAGTA-TCCAATTGAGTGAA
1 TTTTTTGAAAAAATTTAAGGGTATTTTTAGAAATTTTGAAAGTTTAAGTACT-CAATTGAGTGAA
* *
70057397 AAAAAAAGTAGGGACCTAATTACT
65 AAAAAAAGCAGGGACCTAATTAAT
* * * * * * *
70057421 TTTTTTGAAGAAGTTTAAGAGTTTTTTTTATACATTTTAAAAGTTTAAGT
1 TTTTTTGAAAAAATTTAAG-GGTATTTTTAGAAATTTTGAAAGTTTAAGT
70057471 GAAAAAAAAG
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
86 1 0.01
87 26 0.22
88 63 0.54
89 27 0.23
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (88 bp):
TTTTTTGAAAAAATTTAAGGGTATTTTTAGAAATTTTGAAAGTTTAAGTACTCAATTGAGTGAAA
AAAAAAGCAGGGACCTAATTAAT
Found at i:70061370 original size:20 final size:20
Alignment explanation
Indices: 70061341--70061404 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
70061331 TTAATACTTG
* *
70061341 AAAGGCTACTTCAAATATTA
1 AAAGGTTACTTAAAATATTA
* * *
70061361 AAAGGTTACTTGTAAATAATG
1 AAAGGTTACTT-AAAATATTA
*
70061382 AAAGGTTACTTAAAACATTA
1 AAAGGTTACTTAAAATATTA
70061402 AAA
1 AAA
70061405 TAGTTTTTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAGGTTACTTAAAATATTA
Found at i:70061377 original size:21 final size:21
Alignment explanation
Indices: 70061353--70061392 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
70061343 AGGCTACTTC
*
70061353 AAATATTAAAAGGTTACTTGT
1 AAATAATAAAAGGTTACTTGT
*
70061374 AAATAATGAAAGGTTACTT
1 AAATAATAAAAGGTTACTT
70061393 AAAACATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (21 bp):
AAATAATAAAAGGTTACTTGT
Found at i:70084411 original size:19 final size:19
Alignment explanation
Indices: 70084368--70084405 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
70084358 TCCAAACATA
70084368 AGAAAAGTAAATCATTTTC
1 AGAAAAGTAAATCATTTTC
*
70084387 AGAAAAGTAAATTATTTTC
1 AGAAAAGTAAATCATTTTC
70084406 TAAAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (19 bp):
AGAAAAGTAAATCATTTTC
Found at i:70085358 original size:2 final size:2
Alignment explanation
Indices: 70085353--70085384 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
70085343 TTTTAAGTTG
70085353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70085385 TTGTCACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70086408 original size:12 final size:11
Alignment explanation
Indices: 70086389--70086419 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
70086379 TTTATAAAAC
70086389 TTATTTTATTA
1 TTATTTTATTA
70086400 TTAATTTTATTA
1 TT-ATTTTATTA
70086412 TTATTTTA
1 TTATTTTA
70086420 AAGACATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:70086434 original size:30 final size:30
Alignment explanation
Indices: 70086400--70086461 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
70086390 TATTTTATTA
*
70086400 TTAATTTTATTATTATTTTAAAGACATTTG
1 TTAATTTTATTATTAATTTAAAGACATTTG
* *
70086430 TTAATTTTGTTATTAATTTAGAGACATTTG
1 TTAATTTTATTATTAATTTAAAGACATTTG
70086460 TT
1 TT
70086462 TGTTAAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (30 bp):
TTAATTTTATTATTAATTTAAAGACATTTG
Found at i:70086852 original size:29 final size:30
Alignment explanation
Indices: 70086801--70086861 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
70086791 ACTTATTTTC
70086801 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
70086831 TTGTTAATTTT-TTATTATTTTAGAGGGAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
70086860 TT
1 TT
70086862 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:70086980 original size:18 final size:18
Alignment explanation
Indices: 70086945--70086984 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
70086935 GAAATATTTA
*
70086945 TTTTGATGTTTTTAATAT
1 TTTTGATGTTTATAATAT
70086963 TTTTGATGTATTATATATAT
1 TTTTGATGT-TTATA-ATAT
70086983 TT
1 TT
70086985 AAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTGATGTTTATAATAT
Found at i:70095449 original size:36 final size:36
Alignment explanation
Indices: 70095409--70095481 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
70095399 CATACTTCAA
70095409 GTTAACTTCTTTAGGGCTTTTTAGTAGGAGTCATAC
1 GTTAACTTCTTTAGGGCTTTTTAGTAGGAGTCATAC
70095445 GTTAACTTCTTTAGGGCTTTTTAGTAGGAGTCATAC
1 GTTAACTTCTTTAGGGCTTTTTAGTAGGAGTCATAC
70095481 G
1 G
70095482 CCATCCATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (36 bp):
GTTAACTTCTTTAGGGCTTTTTAGTAGGAGTCATAC
Found at i:70104224 original size:2 final size:2
Alignment explanation
Indices: 70104217--70104252 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
70104207 TATTTCTTAA
*
70104217 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70104253 TATCTCACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:70104695 original size:15 final size:16
Alignment explanation
Indices: 70104667--70104707 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
70104657 TATTAATATA
70104667 TAATTTTT--TTATTT
1 TAATTTTTAATTATTT
70104681 T-ATTTTTAATTATTT
1 TAATTTTTAATTATTT
70104696 TAAATTTTTAAT
1 T-AATTTTTAAT
70104708 ATAACTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 1 0.04
15 7 0.30
17 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TAATTTTTAATTATTT
Found at i:70104787 original size:12 final size:12
Alignment explanation
Indices: 70104772--70104800 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
70104762 GTATTATTTT
70104772 TATTTATTTTAA
1 TATTTATTTTAA
70104784 TATTTATTTTAA
1 TATTTATTTTAA
70104796 TATTT
1 TATTT
70104801 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:70104787 original size:21 final size:20
Alignment explanation
Indices: 70104764--70104843 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 20
70104754 TTGTTTTAGT
70104764 ATTATTTTTATTTATTTTAA
1 ATTATTTTTATTTATTTTAA
* *
70104784 TATTTATTTTAATAT-TTTTAA
1 -A-TTATTTTTATTTATTTTAA
70104805 ATATATTTGATTTATTATATTTTTAA
1 AT-TA-TT--TTTATT-TA-TTTTAA
70104831 ATT-TTTTTATTTA
1 ATTATTTTTATTTA
70104844 ATAAAATAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
19 1 0.02
20 5 0.11
21 15 0.32
22 10 0.21
23 6 0.13
24 1 0.02
25 1 0.02
26 8 0.17
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (20 bp):
ATTATTTTTATTTATTTTAA
Found at i:70104824 original size:26 final size:24
Alignment explanation
Indices: 70104783--70104846 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
70104773 ATTTATTTTA
70104783 ATATTTATTTTAATATTTTTAAAT
1 ATATTTATTTTAATATTTTTAAAT
*
70104807 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TAATATTTTTAAAT
* *
70104833 TTTTTTA-TTTAATA
1 ATATTTATTTTAATA
70104847 AAATAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
25 5 0.15
26 17 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
ATATTTATTTTAATATTTTTAAAT
Found at i:70110636 original size:17 final size:18
Alignment explanation
Indices: 70110616--70110653 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
70110606 TTAGTTAACT
*
70110616 TATAAATATA-ACATGTA
1 TATAAATATACACATGCA
70110633 TAT-AATATACACATGCA
1 TATAAATATACACATGCA
70110650 TATA
1 TATA
70110654 TCATTAAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (18 bp):
TATAAATATACACATGCA
Found at i:70111550 original size:22 final size:22
Alignment explanation
Indices: 70111525--70111567 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
70111515 TAGTTATACA
70111525 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
** *
70111547 ATAATAGTAAAATTGTAGCAA
1 ATAATAACAAAATAGTAGCAA
70111568 AATGGTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:70112794 original size:16 final size:17
Alignment explanation
Indices: 70112773--70112806 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
70112763 ATTTTTTAAA
70112773 ATTAAAAATAT-AAATT
1 ATTAAAAATATGAAATT
*
70112789 ATTAAAATTATGAAATT
1 ATTAAAAATATGAAATT
70112806 A
1 A
70112807 AATTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTAAAAATATGAAATT
Found at i:70114418 original size:22 final size:20
Alignment explanation
Indices: 70114392--70114440 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
70114382 AATATTACAT
*
70114392 ATATATTAATTTTGAAAATATA
1 ATATATT-ATTTTAAAAAT-TA
* *
70114414 ATATAATCTTTTAAAAATTA
1 ATATATTATTTTAAAAATTA
70114434 ATATATT
1 ATATATT
70114441 GTAGGGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 9 0.39
22 6 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATATTATTTTAAAAATTA
Found at i:70116649 original size:22 final size:20
Alignment explanation
Indices: 70116592--70116649 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 20
70116582 TTTTTTTTTC
*
70116592 TTTTTCATTTTTCATGCCTT
1 TTTTTCTTTTTTCATGCCTT
**
70116612 TTTAGCTTTTTGTTCATGCCATT
1 TTTTTC-TTTT-TTCATGCC-TT
70116635 GTTTTTCTTTTTTCA
1 -TTTTTCTTTTTTCA
70116650 GATCTCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.14
21 3 0.10
22 12 0.41
23 6 0.21
24 4 0.14
ACGTcount: A:0.10, C:0.17, G:0.09, T:0.64
Consensus pattern (20 bp):
TTTTTCTTTTTTCATGCCTT
Found at i:70122391 original size:17 final size:16
Alignment explanation
Indices: 70122360--70122398 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
70122350 GGGAGAAGAA
*
70122360 GAGAAAAAATGAAAGG
1 GAGAAAAAATAAAAGG
*
70122376 GAGAAAAAATAAAAAG
1 GAGAAAAAATAAAAGG
70122392 GA-AAAAA
1 GAGAAAAA
70122399 CACATGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (16 bp):
GAGAAAAAATAAAAGG
Found at i:70123417 original size:23 final size:24
Alignment explanation
Indices: 70123391--70123445 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
70123381 TACTTATAAT
*
70123391 TTTTTTTTAA-ATTAGTACCTAAA
1 TTTTTATTAATATTAGTACCTAAA
* * *
70123414 TTTTTATTAATTTTGGTACTTAAA
1 TTTTTATTAATATTAGTACCTAAA
70123438 TTTTTATT
1 TTTTTATT
70123446 TCGTAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (24 bp):
TTTTTATTAATATTAGTACCTAAA
Found at i:70131041 original size:29 final size:29
Alignment explanation
Indices: 70130999--70131058 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
70130989 GTTATAACCA
* * *
70130999 AACCTTTATATGCCATTGTTGACCA-AATT
1 AACCTATACATGCCATT-TTAACCATAATT
70131028 AACCTATACATGCCATTTTAACCATAATT
1 AACCTATACATGCCATTTTAACCATAATT
70131057 AA
1 AA
70131059 TTTACCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.35
Consensus pattern (29 bp):
AACCTATACATGCCATTTTAACCATAATT
Found at i:70132134 original size:43 final size:43
Alignment explanation
Indices: 70132044--70132149 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
70132034 TGAGATCAGG
**
70132044 ATTACCAGTCCAGGCTAAATCCCATCTCTAACATATAATCAGG
1 ATTACCAGTCCAGGCTAAATCCCATCTCTAACATATAATCAAA
* * * *
70132087 ATTACCAATCCAGGCTAAATCCTGATTTC-AACGTA-AGATCAAA
1 ATTACCAGTCCAGGCTAAATCC-CATCTCTAACATATA-ATCAAA
70132130 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
70132150 TCTGTCTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 49 0.91
44 4 0.07
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (43 bp):
ATTACCAGTCCAGGCTAAATCCCATCTCTAACATATAATCAAA
Found at i:70134801 original size:20 final size:20
Alignment explanation
Indices: 70134778--70134816 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
70134768 TCTAAAAATC
*
70134778 TAAGAATTTATCAATATTTT
1 TAAGAATTTATCAAAATTTT
* *
70134798 TAAGACTTTCTCAAAATTT
1 TAAGAATTTATCAAAATTT
70134817 ATCTTTTACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
TAAGAATTTATCAAAATTTT
Found at i:70135273 original size:14 final size:15
Alignment explanation
Indices: 70135248--70135276 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
70135238 ATTAAAAAAA
70135248 TAAAATCAAATAAAT
1 TAAAATCAAATAAAT
70135263 TAAAATC-AATAAAT
1 TAAAATCAAATAAAT
70135277 GCTTTTGGAA
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:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAATCAAATAAAT
Found at i:70152509 original size:20 final size:19
Alignment explanation
Indices: 70152465--70152510 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
70152455 ATATCGATCG
* *
70152465 AGTATCAATATCTTTTGTT
1 AGTATCAATAACTTTTCTT
70152484 AGGTATCAATAACTTTATCTT
1 A-GTATCAATAACTTT-TCTT
70152505 AGTATC
1 AGTATC
70152511 GTTTTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (19 bp):
AGTATCAATAACTTTTCTT
Found at i:70155443 original size:2 final size:2
Alignment explanation
Indices: 70155436--70155468 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70155426 CCCACTTAAC
70155436 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 A
70155469 CCAACTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70162992 original size:8 final size:8
Alignment explanation
Indices: 70162979--70163007 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
70162969 TTATGTTTAG
70162979 TATATTAT
1 TATATTAT
70162987 TATATTAT
1 TATATTAT
70162995 TATATTAT
1 TATATTAT
70163003 TATAT
1 TATAT
70163008 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:70163040 original size:5 final size:5
Alignment explanation
Indices: 70163030--70163065 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
70163020 TTATGTTTTA
70163030 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
70163066 AAACTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:70164350 original size:15 final size:15
Alignment explanation
Indices: 70164330--70164386 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
70164320 CGATGAATTT
70164330 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
70164345 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
70164360 ATTGAATTTATATTG
1 ATTGAATTTATATTG
70164375 ATTGAA-TTATAT
1 ATTGAATTTATAT
70164387 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:70165975 original size:44 final size:45
Alignment explanation
Indices: 70165880--70165993 Score: 140
Period size: 44 Copynumber: 2.5 Consensus size: 45
70165870 ACAGGACAGA
* * *
70165880 ACAGAAATGAGCCATGTAAGCCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
70165926 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* **
70165970 ACAGGAATAATTCATGTAAGTCCA
1 ACAGGAATGAGCCATGTAAGTCCA
70165994 CGTCAAAGAC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 34 0.58
46 25 0.42
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:70172997 original size:16 final size:17
Alignment explanation
Indices: 70172966--70172998 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
70172956 TTAATAAGTA
70172966 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
70172983 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
70172999 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:70173344 original size:46 final size:46
Alignment explanation
Indices: 70173279--70173552 Score: 354
Period size: 46 Copynumber: 6.0 Consensus size: 46
70173269 TTATCTTTGA
* * * * *
70173279 CATGATGCCATAGTGTCTTTCAACTATAGTCTTACTT-ATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA-TTCA-TTTCATGT
70173325 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* **
70173371 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * *
70173417 CATGTTGCCATGGTATCTTTTAACCACGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* ** *
70173463 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* **
70173509 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
70173553 ATCAGAGAGC
Statistics
Matches: 206, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
45 6 0.03
46 200 0.97
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:70177652 original size:18 final size:18
Alignment explanation
Indices: 70177631--70177913 Score: 151
Period size: 18 Copynumber: 15.3 Consensus size: 18
70177621 GAACAATTAT
70177631 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * * *
70177649 TTATTCGGTAACAATAAA
1 TTATTCAGTAACAGTCAG
* * **
70177667 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
70177685 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
70177711 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
70177729 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * * *
70177746 ATATTCAGTAATAATTAAG
1 TTATTCAGTAA-CAGTCAG
*
70177765 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
70177782 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
70177801 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
70177819 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
70177837 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
70177855 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
70177873 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
70177891 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
70177909 TTATT
1 TTATT
70177914 TTATACCTTT
Statistics
Matches: 199, Mismatches: 50, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
17 17 0.09
18 149 0.75
19 17 0.09
21 2 0.01
22 1 0.01
23 2 0.01
26 11 0.06
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:70177846 original size:72 final size:71
Alignment explanation
Indices: 70177712--70177913 Score: 228
Period size: 72 Copynumber: 2.8 Consensus size: 71
70177702 ATTGATCGGT
* * *
70177712 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTCAGTAATAATTAAGTTATTCAGTAG
1 TATCCAGTAACAATCAATTATTCAGTAAAATCA-ATTATTCAGTAAT-ATTCAGTTATTCAGTAA
*
70177776 CAGTC-AT
64 CAGTCTAA
* * * *
70177783 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
70177848 CAGTCTAA
64 CAGTCTAA
* * * * *
70177856 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
70177914 TTATACCTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
71 1 0.01
72 91 0.83
73 17 0.16
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:70179501 original size:2 final size:2
Alignment explanation
Indices: 70179494--70179521 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70179484 ATGTAAGCCC
70179494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70179522 GGCATTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70188657 original size:21 final size:19
Alignment explanation
Indices: 70188620--70188661 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
70188610 AAACTTTCAA
70188620 TTTTCCCTTTCTTCTTTCT
1 TTTTCCCTTTCTTCTTTCT
70188639 TTTTCTCCTTTCTTTCTTTCT
1 TTTTC-CCTTTC-TTCTTTCT
70188660 TT
1 TT
70188662 CCCTGCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 6 0.29
21 10 0.48
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCCCTTTCTTCTTTCT
Found at i:70188670 original size:21 final size:20
Alignment explanation
Indices: 70188625--70188670 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
70188615 TTCAATTTTC
**
70188625 CCTTTCTTCTTTCTTTTTCT
1 CCTTTCTTCTTTCTTTCCCT
70188645 CCTTTCTTTCTTTCTTTCCCT
1 CCTTTC-TTCTTTCTTTCCCT
*
70188666 GCTTT
1 CCTTT
70188671 TCGTTTTGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (20 bp):
CCTTTCTTCTTTCTTTCCCT
Found at i:70190461 original size:12 final size:12
Alignment explanation
Indices: 70190418--70190453 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
70190408 AAAACATATA
*
70190418 AAAGAAATAGAAT
1 AAAGAAA-AGAAC
70190431 AAAGAAAAGAAC
1 AAAGAAAAGAAC
70190443 AAAGAAAAGAA
1 AAAGAAAAGAA
70190454 AACAGAAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (12 bp):
AAAGAAAAGAAC
Found at i:70192000 original size:53 final size:53
Alignment explanation
Indices: 70191864--70192009 Score: 213
Period size: 53 Copynumber: 2.7 Consensus size: 53
70191854 TGCGCTCGTT
**
70191864 TAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACTCCGTA
1 TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACTCCGTA
*
70191917 TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATTCCGTA
1 TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACTCCGTA
* *
70191970 TAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 TAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
70192010 ACCGTGTAAG
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 77 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (53 bp):
TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACTCCGTA
Found at i:70193405 original size:16 final size:17
Alignment explanation
Indices: 70193381--70193414 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
70193371 GTATTGATAT
*
70193381 TTGAGTTGAATGG-GAA
1 TTGAATTGAATGGTGAA
70193397 TTGAATTGAATGGTGAA
1 TTGAATTGAATGGTGAA
70193414 T
1 T
70193415 GTGTATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (17 bp):
TTGAATTGAATGGTGAA
Found at i:70203063 original size:7 final size:7
Alignment explanation
Indices: 70203051--70203078 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
70203041 TCGGGGCTTC
70203051 TTTGGCA
1 TTTGGCA
70203058 TTTGGCA
1 TTTGGCA
70203065 TTTGGCA
1 TTTGGCA
70203072 TTTGGCA
1 TTTGGCA
70203079 ATCAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (7 bp):
TTTGGCA
Found at i:70205537 original size:25 final size:26
Alignment explanation
Indices: 70205509--70205557 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
70205499 TCTCTTTTCT
*
70205509 TTTTA-TATATTAATTAAAAATTTAA
1 TTTTATTATAGTAATTAAAAATTTAA
* *
70205534 TTTTATTATAGTATTTATAAATTT
1 TTTTATTATAGTAATTAAAAATTT
70205558 TTACGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTTATTATAGTAATTAAAAATTTAA
Found at i:70207322 original size:91 final size:91
Alignment explanation
Indices: 70207157--70207326 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
70207147 TAACTTGTTA
* *
70207157 AGTTTTGAAGGATGCTAATGTTATGAAAGTATAAAAGCCAATATCAATTCATTTGAAACAATTTG
1 AGTTTTGAAGGATGCTAATATTATGAAAGTATAAAAGCCAATATCAATTCATTTGAAACAATTTA
*
70207222 TCTTGAAGATTAGAACAAAATCTTTG
66 TCTTAAAGATTAGAACAAAATCTTTG
* * * *
70207248 AGTTTTGAAGGATGCTAATATTGTGCAAGTATAAAAGTCAATATCAATTCATTTTAAACAATTTA
1 AGTTTTGAAGGATGCTAATATTATGAAAGTATAAAAGCCAATATCAATTCATTTGAAACAATTTA
70207313 TCTTAAAGATTAGA
66 TCTTAAAGATTAGA
70207327 TTAGATCGCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.35
Consensus pattern (91 bp):
AGTTTTGAAGGATGCTAATATTATGAAAGTATAAAAGCCAATATCAATTCATTTGAAACAATTTA
TCTTAAAGATTAGAACAAAATCTTTG
Found at i:70208284 original size:14 final size:14
Alignment explanation
Indices: 70208265--70208293 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
70208255 TTGGTTAAAC
70208265 AAATTCGCGACAAG
1 AAATTCGCGACAAG
70208279 AAATTCGCGACAAG
1 AAATTCGCGACAAG
70208293 A
1 A
70208294 GAGCAGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
AAATTCGCGACAAG
Found at i:70211096 original size:27 final size:26
Alignment explanation
Indices: 70211034--70211175 Score: 158
Period size: 27 Copynumber: 5.3 Consensus size: 26
70211024 AGCATGGCTG
* *
70211034 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
70211060 CCAAATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
70211088 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
70211115 CCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
** * *
70211142 CCAGGTCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
70211169 CCAGAAC
1 CCAGAAC
70211176 GCTTCCTCCA
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
26 4 0.04
27 83 0.81
28 16 0.16
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:70211172 original size:54 final size:55
Alignment explanation
Indices: 70211034--70211173 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 55
70211024 AGCATGGCTG
* * *
70211034 CCAGAACAGATA-ATGTGACAGAGTCACCAAATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* *
70211088 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
** * *
70211142 CCAGGTCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGA
70211174 ACGCTTCCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 59 0.78
55 17 0.22
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (55 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:70216350 original size:28 final size:28
Alignment explanation
Indices: 70216310--70216365 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
70216300 ACTTGTTGAT
70216310 GTCGTATACATGTAGATTGTCATGTGAA
1 GTCGTATACATGTAGATTGTCATGTGAA
*
70216338 GTCGTATATATGTAGATTGTCATGTGAA
1 GTCGTATACATGTAGATTGTCATGTGAA
70216366 CGTTACATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.38
Consensus pattern (28 bp):
GTCGTATACATGTAGATTGTCATGTGAA
Found at i:70223882 original size:47 final size:47
Alignment explanation
Indices: 70223772--70223884 Score: 199
Period size: 47 Copynumber: 2.4 Consensus size: 47
70223762 TCCGACCTTG
* * *
70223772 TTGAGTTGAGTCCGAGCTCGTGAGATGTAACTAGGCATCCGAACTCG
1 TTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCAAACTCA
70223819 TTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCAAACTCA
1 TTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCAAACTCA
70223866 TTGAGTTGAGTCCGAGTTC
1 TTGAGTTGAGTCCGAGTTC
70223885 ACTTATGGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (47 bp):
TTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCAAACTCA
Found at i:70226394 original size:14 final size:14
Alignment explanation
Indices: 70226375--70226405 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
70226365 TACAAAAAGG
*
70226375 ATATCTAATCTAGA
1 ATATCTAATCTAAA
70226389 ATATCTAATCTAAA
1 ATATCTAATCTAAA
70226403 ATA
1 ATA
70226406 ATAATATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (14 bp):
ATATCTAATCTAAA
Found at i:70232713 original size:39 final size:40
Alignment explanation
Indices: 70232654--70232738 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
70232644 AAATGAATTG
* * * *
70232654 TGCTGAGATTGTATCCGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
* *
70232693 TGCTGGGATTGTATCTGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
70232733 TGCTGG
1 TGCTGG
70232739 TGAATTAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 17 0.44
40 22 0.56
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.31
Consensus pattern (40 bp):
TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:70233392 original size:2 final size:2
Alignment explanation
Indices: 70233385--70233409 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70233375 AATTAAGTTT
70233385 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 T
70233410 CATGTATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70234738 original size:45 final size:44
Alignment explanation
Indices: 70234639--70234772 Score: 177
Period size: 45 Copynumber: 3.0 Consensus size: 44
70234629 TTTTCTCAAA
* *
70234639 TCACCGGCATT-TTGCCTGCTAGGCTCG-AGGCCCG-ATATCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCCGAATAT-ATT
70234681 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCCGAATAGTATT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCCGAATA-TATT
*
70234726 TCACCGACATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAATATT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAAT-ATATT
70234771 TC
1 TC
70234773 CCCATTCATT
Statistics
Matches: 83, Mismatches: 3, Indels: 9
0.87 0.03 0.09
Matches are distributed among these distances:
42 11 0.13
43 15 0.18
44 9 0.11
45 46 0.55
46 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (44 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCCGAATATATT
Found at i:70234994 original size:43 final size:43
Alignment explanation
Indices: 70234933--70235177 Score: 366
Period size: 43 Copynumber: 5.7 Consensus size: 43
70234923 CAACAAACTT
* * * * *
70234933 GCACACTTAGTGCTAATTAATTAACCTAAGTTATAATGGTTTC
1 GCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATC
70234976 GCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATC
1 GCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATC
*
70235019 GCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATC
1 GCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATC
* * *
70235062 GCACACTTAGTGCCAATTAATTAGCCAAAGCTATAATTATATC
1 GCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATC
* *
70235105 GCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTATATC
1 GCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATC
70235148 GCACACTTAGTGCC-ATTACATTAAACCGAA
1 GCACACTTAGTGCCAATTA-ATT-AACCGAA
70235178 CTTATCTCTG
Statistics
Matches: 190, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
42 4 0.02
43 180 0.95
44 6 0.03
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (43 bp):
GCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATC
Found at i:70240374 original size:108 final size:108
Alignment explanation
Indices: 70240180--70240416 Score: 435
Period size: 108 Copynumber: 2.2 Consensus size: 108
70240170 GTTAAATTGG
*
70240180 CATGAATTTAGATATGATTTGAATGAAGTAATATTGTTTAAATTTTGATAAAAATATGTAAAGTA
1 CATGTATTTAGATATGATTTGAATGAAGTAATATTGTTTAAATTTTGATAAAAATATGTAAAGTA
70240245 CCTATGTTGGTATGTTGGTTAGATCATTAGATTAATTATTTGA
66 CCTATGTTGGTATGTTGGTTAGATCATTAGATTAATTATTTGA
70240288 CATGTATTTAGATATGATTTGAATGAAGTAATATTGTTTAAATTTTGATAAAAATATGTAAAGTA
1 CATGTATTTAGATATGATTTGAATGAAGTAATATTGTTTAAATTTTGATAAAAATATGTAAAGTA
70240353 CCTATGTTGGTATGTTGGTTAGATCATTAGATTAATTATTTGA
66 CCTATGTTGGTATGTTGGTTAGATCATTAGATTAATTATTTGA
70240396 CATGT-TTTA-A-ATGTATTTGAA
1 CATGTATTTAGATATG-ATTTGAA
70240417 CGTGTTTTGG
Statistics
Matches: 127, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
105 3 0.02
106 8 0.06
107 4 0.03
108 112 0.88
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (108 bp):
CATGTATTTAGATATGATTTGAATGAAGTAATATTGTTTAAATTTTGATAAAAATATGTAAAGTA
CCTATGTTGGTATGTTGGTTAGATCATTAGATTAATTATTTGA
Found at i:70249154 original size:21 final size:21
Alignment explanation
Indices: 70249128--70249172 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
70249118 GGAATAGGGT
70249128 TACGAGGTATTACCAGACTTA
1 TACGAGGTATTACCAGACTTA
* *
70249149 TACGAGGTATTATCGGACTTA
1 TACGAGGTATTACCAGACTTA
70249170 TAC
1 TAC
70249173 ACTAACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (21 bp):
TACGAGGTATTACCAGACTTA
Found at i:70250454 original size:6 final size:6
Alignment explanation
Indices: 70250443--70250469 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
70250433 GGAATACACC
70250443 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
70250470 GCGGTACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:70251368 original size:18 final size:20
Alignment explanation
Indices: 70251345--70251389 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
70251335 AAAGCGCTAA
70251345 TTTTCCCTTTT-C-TCTTTC
1 TTTTCCCTTTTCCTTCTTTC
70251363 TTTTCCCTTTTCCTTCTTTC
1 TTTTCCCTTTTCCTTCTTTC
70251383 -TTTCCCT
1 TTTTCCCT
70251390 CAATTTTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.44
19 8 0.32
20 6 0.24
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTCCCTTTTCCTTCTTTC
Found at i:70255121 original size:39 final size:39
Alignment explanation
Indices: 70255037--70255271 Score: 296
Period size: 39 Copynumber: 6.0 Consensus size: 39
70255027 CAAATCCAAT
* * *
70255037 CACCACCAC-AAAGCATGCGGGACTTTAAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGAC-TT-AGCCCGGATATAA
* * *
70255077 TACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAG
1 CACCAGCACGAAAGCCTTCGGGAC-TTAGCCCGGATATAA
70255116 CACCAGCAC-AAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAA-GCCTTCGGGACTTAGCCCGGATATAA
* *
70255155 CACCAGCACGAATGCCTTCGGGACTTAGCCCGAATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
* *
70255194 TACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
* * *
70255233 CACCAGCACGAATGCCTTCGGGACTTAGCTCAGATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
70255272 TTCTCCATTA
Statistics
Matches: 179, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 144 0.80
40 35 0.20
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (39 bp):
CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
Found at i:70255270 original size:117 final size:119
Alignment explanation
Indices: 70255054--70255271 Score: 343
Period size: 117 Copynumber: 1.8 Consensus size: 119
70255044 ACAAAGCATG
* *
70255054 CGGGACTTTAAGCCCGGATATAATACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAGCAC
1 CGGGACTTTAAGCCCGAATATAATACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACAC
*
70255119 CAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
66 CAGCACAAATGCCTTCGGGACTTAGCCCAGATATAACACCAGCACGAATGCCTT
* *
70255173 CGGGAC-TT-AGCCCGAATATAATACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACA
1 CGGGACTTTAAGCCCGAATATAATACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAACA
* *
70255235 CCAGCACGAATGCCTTCGGGACTTAGCTCAGATATAA
65 CCAGCACAAATGCCTTCGGGACTTAGCCCAGATATAA
70255272 TTCTCCATTA
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
117 71 0.78
118 14 0.15
119 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.19
Consensus pattern (119 bp):
CGGGACTTTAAGCCCGAATATAATACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACAC
CAGCACAAATGCCTTCGGGACTTAGCCCAGATATAACACCAGCACGAATGCCTT
Found at i:70274998 original size:18 final size:20
Alignment explanation
Indices: 70274965--70275001 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
70274955 TATTATGAGT
70274965 TTTTTATAATTTTTTAAATA
1 TTTTTATAATTTTTTAAATA
70274985 TTTTTAT-A-TTTTTAAAT
1 TTTTTATAATTTTTTAAAT
70275002 TACTTATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATAATTTTTTAAATA
Found at i:70275522 original size:11 final size:11
Alignment explanation
Indices: 70275500--70275538 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
70275490 AAAAACTTAT
*
70275500 AAAATTTATAA
1 AAAATATATAA
*
70275511 AAAATATTTAA
1 AAAATATATAA
*
70275522 AAAATATAAAA
1 AAAATATATAA
70275533 AAAATA
1 AAAATA
70275539 AAAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAATATATAA
Found at i:70275709 original size:22 final size:22
Alignment explanation
Indices: 70275662--70275709 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
70275652 CAATGACTTT
*
70275662 TTATAATTTTTTAAAAAATAAT
1 TTATAATTTTTTAAAAAATAAC
* * *
70275684 TTATATTTTTTTATAACATAAC
1 TTATAATTTTTTAAAAAATAAC
70275706 TTAT
1 TTAT
70275710 GAAATATAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATAATTTTTTAAAAAATAAC
Found at i:70285606 original size:39 final size:39
Alignment explanation
Indices: 70285507--70285606 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
70285497 TGTGGTATTT
* * * *
70285507 AAAATATATATAT-ATATATGTATATATAATAGTATTTA
1 AAAATATATACATAATATATATATATATAATAGCATTAA
* * * *
70285545 AGAATATATACATAAGAAATATATA-ACTAATGGCATTAA
1 AAAATATATACATAATATATATATATA-TAATAGCATTAA
70285584 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
70285607 AAATACCTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
38 12 0.24
39 37 0.76
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATATATACATAATATATATATATATAATAGCATTAA
Found at i:70286116 original size:28 final size:29
Alignment explanation
Indices: 70286084--70286147 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
70286074 GTGGCTAGGG
70286084 TTTCTTGGTTTTTTTT-GGGGGTTAGGTT
1 TTTCTTGGTTTTTTTTGGGGGGTTAGGTT
70286112 TTTCTT--TTTTTTTTGGAGGGGGTTAGGTT
1 TTTCTTGGTTTTTTTT-G-GGGGGTTAGGTT
70286141 TTT-TTGG
1 TTTCTTGG
70286148 GGGGCTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 8 0.26
28 8 0.26
29 15 0.48
ACGTcount: A:0.05, C:0.03, G:0.31, T:0.61
Consensus pattern (29 bp):
TTTCTTGGTTTTTTTTGGGGGGTTAGGTT
Found at i:70287006 original size:30 final size:30
Alignment explanation
Indices: 70286970--70287030 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
70286960 TTTGAAAAAT
70286970 AGAAATT-AAAAGACTCAACTCAACTCTCGC
1 AGAAATTAAAAAG-CTCAACTCAACTCTCGC
*
70287000 AGAAATTAAAAAGCTCAACTCACCTCTCGC
1 AGAAATTAAAAAGCTCAACTCAACTCTCGC
70287030 A
1 A
70287031 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.20
Consensus pattern (30 bp):
AGAAATTAAAAAGCTCAACTCAACTCTCGC
Found at i:70287148 original size:88 final size:87
Alignment explanation
Indices: 70287054--70287215 Score: 218
Period size: 88 Copynumber: 1.8 Consensus size: 87
70287044 TTTTTTGAAA
* * *
70287054 AAAAACAGAAATTGAAAATAGCTCAGCACA-TGAGCCAAGGCTCAACTCACTTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTC-G-ACAGTGACCCAAGGCTCAACTCACATCTCGCAATATGA
70287118 GTTGATTTTTGAAAACAAAATTTG
64 GTTGATTTTTGAAAACAAAATTTG
** * * *
70287142 AAAAACAGATTTTGAAAATACCTCGACATGTGACCCGATGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGAAATTGAAAATACCTCGACA-GTGACCCAAGGCTCAACTCACATCTCGCAATATGAG
70287207 TTGATTTTT
65 TTGATTTTT
70287216 TTGAAAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 3 0.05
87 1 0.02
88 60 0.94
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCGACAGTGACCCAAGGCTCAACTCACATCTCGCAATATGAGT
TGATTTTTGAAAACAAAATTTG
Done.