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 78 of 292
Found at i:23875781 original size:43 final size:46
Alignment explanation
Indices: 23875732--23875860 Score: 149
Period size: 51 Copynumber: 2.8 Consensus size: 46
23875722 ATGTAGTATC
23875732 CGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG-CCA-G-CA-T
1 CGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGACCATGACATT
* * *
23875774 CTGAGCTCGTTGAGTGGTCCGAGTTCATGATGGATGTGATTCATGTAACATT
1 C-GAGCTCGTTGAGAGGTCCGAGTTCATTATGGA--TGA-CCATG--ACATT
23875826 CGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
1 CGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
23875861 TGTTACATGT
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.01
43 30 0.42
45 2 0.03
47 2 0.03
48 1 0.01
49 2 0.03
51 32 0.44
52 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (46 bp):
CGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGACCATGACATT
Found at i:23884003 original size:131 final size:131
Alignment explanation
Indices: 23883769--23884032 Score: 519
Period size: 131 Copynumber: 2.0 Consensus size: 131
23883759 AGAGGTTTAG
23883769 GAGGAGGTTTGGACATACTTGTACCTAGATTAAGGTAAGTTTGATGTTTTGCCATGAGATTCATG
1 GAGGAGGTTTGGACATACTTGTACCTAGATTAAGGTAAGTTTGATGTTTTGCCATGAGATTCATG
*
23883834 TATGTTTTTCTAGTTAGCTTGAGTTCTAACTAGCCATGGTTCAAATCCTTACTATGTCATGGAGA
66 TATGTTTTTCTAGTTAGCTTGAGTTCTAACTAGCCATGGTTCAAATCCTTACAATGTCATGGAGA
23883899 T
131 T
23883900 GAGGAGGTTTGGACATACTTGTACCTAGATTAAGGTAAGTTTGATGTTTTGCCATGAGATTCATG
1 GAGGAGGTTTGGACATACTTGTACCTAGATTAAGGTAAGTTTGATGTTTTGCCATGAGATTCATG
23883965 TATGTTTTTCTAGTTAGCTTGAGTTCTAACTAGCCATGGTTCAAATCCTTACAATGTCATGGAGA
66 TATGTTTTTCTAGTTAGCTTGAGTTCTAACTAGCCATGGTTCAAATCCTTACAATGTCATGGAGA
23884030 T
131 T
23884031 GA
1 GA
23884033 TATTCGGCTA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (131 bp):
GAGGAGGTTTGGACATACTTGTACCTAGATTAAGGTAAGTTTGATGTTTTGCCATGAGATTCATG
TATGTTTTTCTAGTTAGCTTGAGTTCTAACTAGCCATGGTTCAAATCCTTACAATGTCATGGAGA
T
Found at i:23885191 original size:40 final size:40
Alignment explanation
Indices: 23885136--23885299 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
23885126 TGAATGATAC
* * * *
23885136 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATGT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
23885176 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * ** *
23885216 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
23885256 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
23885296 CCGG
1 CCGG
23885300 TTAAATCCCG
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.03
40 94 0.92
41 5 0.05
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:23893284 original size:40 final size:40
Alignment explanation
Indices: 23893229--23893392 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
23893219 TGAATGATAC
* * *
23893229 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
23893269 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * ** *
23893309 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
23893349 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
23893389 CCGG
1 CCGG
23893393 TTAAATCCCG
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
39 3 0.03
40 95 0.92
41 5 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:23903635 original size:40 final size:40
Alignment explanation
Indices: 23903473--23903636 Score: 170
Period size: 40 Copynumber: 4.1 Consensus size: 40
23903463 TGAATGATAC
* * * *
23903473 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATGT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* *
23903513 CTGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * ** *
23903553 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
23903593 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
23903633 CCGG
1 CCGG
23903637 TTAAATCCCG
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.03
40 92 0.92
41 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:23907343 original size:43 final size:43
Alignment explanation
Indices: 23907247--23907371 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
23907237 AACTAAGAAG
* * * * *
23907247 TCCGAACTCATTGAGTGGTCCGAGTTCGTGA-GGTATG-TAGCA
1 TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGG-ATGCGAGCA
*
23907289 TCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGAGCA
1 TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGCGAGCA
** *
23907332 TCCGAGCTCGTTGAGTTGTCTGAGTTCATGATGGATGCGA
1 TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGCGA
23907372 TTCATGTAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
42 29 0.41
43 42 0.59
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (43 bp):
TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGCGAGCA
Found at i:23908837 original size:13 final size:13
Alignment explanation
Indices: 23908819--23908843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23908809 GATTTGTTTA
23908819 TTAAACTAATTAT
1 TTAAACTAATTAT
23908832 TTAAACTAATTA
1 TTAAACTAATTA
23908844 ACTAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:23911545 original size:40 final size:40
Alignment explanation
Indices: 23911460--23911610 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
23911450 AATTGAATGA
* * *
23911460 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
23911500 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
23911541 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
23911580 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
23911611 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:23911624 original size:40 final size:40
Alignment explanation
Indices: 23911497--23911626 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
23911487 ATGCTGGAAA
* * * *
23911497 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
23911537 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
23911577 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
23911617 TTATATCCGG
1 TTATATCCGG
23911627 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:23919496 original size:40 final size:40
Alignment explanation
Indices: 23919430--23919580 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
23919420 AAATTGAATG
* * *
23919430 ATATCCGGGCTAA-TCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
23919469 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* *
23919509 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
23919549 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
23919581 ACGTGGTTAT
Statistics
Matches: 89, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
39 15 0.17
40 72 0.81
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:23919594 original size:40 final size:40
Alignment explanation
Indices: 23919467--23919596 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
23919457 ATGCTGGAAA
* * *
23919467 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
23919507 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
23919547 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
23919587 TTATATCCGG
1 TTATATCCGG
23919597 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:23922951 original size:17 final size:17
Alignment explanation
Indices: 23922931--23922973 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
23922921 AAATTGAAAT
23922931 GAAAATAAAAATCAA-AA
1 GAAAATAAAAAT-AAGAA
23922948 G-AAATAAAAATAAGAA
1 GAAAATAAAAATAAGAA
*
23922964 TAAAATAAAA
1 GAAAATAAAA
23922974 GGAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (17 bp):
GAAAATAAAAATAAGAA
Found at i:23922957 original size:22 final size:21
Alignment explanation
Indices: 23922926--23923014 Score: 61
Period size: 22 Copynumber: 4.0 Consensus size: 21
23922916 TAAGAAAATT
*
23922926 GAAATGAAAATAAAAATCAAAA
1 GAAATAAAAATAAAAAT-AAAA
*
23922948 GAAATAAAAATAAGAATAAAA
1 GAAATAAAAATAAAAATAAAA
* * *
23922969 TAAAAGGAAATAATAATAATAATAA
1 -GAAA-TAAA-AATAAAAATAA-AA
* * *
23922994 TAAATAATAATAAGAATAAAA
1 GAAATAAAAATAAAAATAAAA
23923015 ATAAAATTGG
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
21 6 0.11
22 28 0.52
23 5 0.09
24 13 0.24
25 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.19
Consensus pattern (21 bp):
GAAATAAAAATAAAAATAAAA
Found at i:23922958 original size:6 final size:6
Alignment explanation
Indices: 23922927--23923020 Score: 57
Period size: 6 Copynumber: 15.3 Consensus size: 6
23922917 AAGAAAATTG
* * * * *
23922927 AAATGA AAATAA AAAT-C AAA-AG AAATAA AAATAA GAATAA AATAAAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA-ATAA
* * * *
23922974 GGAAATAA TAATAA TAATAA TAAATAA TAATAA GAATAA AAATAA AA
1 --AAATAA AAATAA AAATAA -AAATAA AAATAA AAATAA AAATAA AA
23923021 TTGGAGGATT
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
5 6 0.09
6 50 0.72
7 8 0.12
8 3 0.04
9 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:23922978 original size:27 final size:27
Alignment explanation
Indices: 23922938--23922993 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
23922928 AATGAAAATA
23922938 AAAATCAAAAGAAATAAAAATAAGAAT
1 AAAATCAAAAGAAATAAAAATAAGAAT
* *
23922965 AAAAT-AAAAGGAAATAATAATAATAAT
1 AAAATCAAAA-GAAATAAAAATAAGAAT
23922992 AA
1 AA
23922994 TAAATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (27 bp):
AAAATCAAAAGAAATAAAAATAAGAAT
Found at i:23922985 original size:3 final size:3
Alignment explanation
Indices: 23922977--23923018 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
23922967 AATAAAAGGA
* *
23922977 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAG AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
23923019 AATTGGAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:23922998 original size:19 final size:18
Alignment explanation
Indices: 23922976--23923018 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
23922966 AAATAAAAGG
*
23922976 AAATAATAATAATAATAA
1 AAATAATAATAAGAATAA
23922994 TAAATAATAATAAGAATAA
1 -AAATAATAATAAGAATAA
23923013 AAATAA
1 AAATAA
23923019 AATTGGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAATAATAAGAATAA
Found at i:23927823 original size:30 final size:30
Alignment explanation
Indices: 23927789--23927849 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
23927779 TCCTTAACTC
23927789 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
23927819 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
23927849 A
1 A
23927850 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:23931853 original size:13 final size:13
Alignment explanation
Indices: 23931835--23931859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23931825 GATTTGTTTA
23931835 TTAAACTAATTAT
1 TTAAACTAATTAT
23931848 TTAAACTAATTA
1 TTAAACTAATTA
23931860 ACTAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:23934333 original size:45 final size:45
Alignment explanation
Indices: 23934243--23934333 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
23934233 GAACCATGTG
* * *
23934243 ATCTGAACTCATTAAGTTGTGGTTTGAGTTCATGATATATGTGAC
1 ATCTGAACTCATTAAGTTGTAGTCTGAGTTCATGATATATATGAC
* *
23934288 ATCTGATCTCATTGAGTTGTAGTCTGAGTTCATGATGA-ATATGAC
1 ATCTGAACTCATTAAGTTGTAGTCTGAGTTCATGAT-ATATATGAC
23934333 A
1 A
23934334 CATGTTTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 39 0.98
46 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (45 bp):
ATCTGAACTCATTAAGTTGTAGTCTGAGTTCATGATATATATGAC
Found at i:23940991 original size:21 final size:23
Alignment explanation
Indices: 23940965--23941008 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
23940955 TTGGATTATT
23940965 AATTAGA-G-GTCCTTAAATAGC
1 AATTAGATGAGTCCTTAAATAGC
23940986 AATTAGATGAAGTCCTTAAATAG
1 AATTAGATG-AGTCCTTAAATAG
23941009 GAAAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 1 0.05
24 12 0.60
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (23 bp):
AATTAGATGAGTCCTTAAATAGC
Found at i:23942035 original size:45 final size:45
Alignment explanation
Indices: 23941978--23942068 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
23941968 GAACCATGTG
* *
23941978 ATCTGAACTCATTGAGTTGTGGTCTAAGTTCATGATATATGTGAC
1 ATCTGAACTCATTCAGTTGTGGTCTAAGTTCATGATATATATGAC
* * *
23942023 ATCTGAGCTCATTCAGTTGTGGTCTGAGTTCATGATGTATATGAC
1 ATCTGAACTCATTCAGTTGTGGTCTAAGTTCATGATATATATGAC
23942068 A
1 A
23942069 CATGTTTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (45 bp):
ATCTGAACTCATTCAGTTGTGGTCTAAGTTCATGATATATATGAC
Found at i:23942615 original size:39 final size:39
Alignment explanation
Indices: 23942565--23942642 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
23942555 ATTTTTAAAA
23942565 AATGGAGAAAATTTAGATTTTGAAAAATAAAAATATTTT
1 AATGGAGAAAATTTAGATTTTGAAAAATAAAAATATTTT
23942604 AATGGAGAAAATTTAGATTTTGAAAAATAAAAATATTTT
1 AATGGAGAAAATTTAGATTTTGAAAAATAAAAATATTTT
23942643 TTTAAGTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (39 bp):
AATGGAGAAAATTTAGATTTTGAAAAATAAAAATATTTT
Found at i:23943279 original size:25 final size:24
Alignment explanation
Indices: 23943251--23943297 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
23943241 TCACTTGCAT
23943251 TTATACATTATATATTTAATGTTAA
1 TTATACATTATAT-TTTAATGTTAA
* *
23943276 TTATGCATTTTATTTTAATGTT
1 TTATACATTATATTTTAATGTT
23943298 TTATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (24 bp):
TTATACATTATATTTTAATGTTAA
Found at i:23943391 original size:18 final size:21
Alignment explanation
Indices: 23943347--23943392 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
23943337 ATTTTTGTTT
*
23943347 TTATTTATTTTCATGTATATT
1 TTATTTATTTTCATGTATATA
23943368 TATATTTATTTT-AT-TAT-TA
1 T-TATTTATTTTCATGTATATA
23943387 TTATTT
1 TTATTT
23943393 TTACACATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 5 0.22
19 2 0.09
20 3 0.13
21 3 0.13
22 10 0.43
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTTATTTTCATGTATATA
Found at i:23943395 original size:26 final size:26
Alignment explanation
Indices: 23943323--23943395 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
23943313 CTTGTATAAT
* * *
23943323 TTTTATTTATTCTTATTTTTGTTTTTA
1 TTTTA-TTATTATTATTTTTATATTTA
*
23943350 -TTTATT-TTCATGTATATTTATATTTA
1 TTTTATTATT-AT-TATTTTTATATTTA
23943376 TTTTATTATTATTATTTTTA
1 TTTTATTATTATTATTTTTA
23943396 CACATTCCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
24 2 0.05
25 3 0.08
26 22 0.59
27 8 0.22
28 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (26 bp):
TTTTATTATTATTATTTTTATATTTA
Found at i:23945466 original size:17 final size:18
Alignment explanation
Indices: 23945424--23945472 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
23945414 AGTTGAAAAG
23945424 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
23945443 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
23945460 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
23945473 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:23946360 original size:40 final size:40
Alignment explanation
Indices: 23946294--23946460 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
23946284 AAATTGAATG
* * *
23946294 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
23946333 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
23946373 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
23946413 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
23946453 ATATCCGG
1 ATATCCGG
23946461 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:23953474 original size:17 final size:18
Alignment explanation
Indices: 23953432--23953480 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
23953422 AGTTGAAAAG
23953432 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
23953451 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
23953468 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
23953481 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:23954368 original size:40 final size:40
Alignment explanation
Indices: 23954302--23954468 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
23954292 AAATTGAATG
* * *
23954302 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
23954341 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
23954381 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
23954421 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
23954461 ATATCCGG
1 ATATCCGG
23954469 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:23958997 original size:28 final size:28
Alignment explanation
Indices: 23958966--23959029 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
23958956 TACATCACGT
*
23958966 AGGGGAAAAACAATCATCTTACCATATA
1 AGGGGAAAAACAATCATCTTACCACATA
* * * *
23958994 A-GGGCAAAATATTCATTTTACCACATA
1 AGGGGAAAAACAATCATCTTACCACATA
*
23959021 AGGGCAAAA
1 AGGGGAAAA
23959030 CGATTATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (28 bp):
AGGGGAAAAACAATCATCTTACCACATA
Found at i:23959038 original size:27 final size:27
Alignment explanation
Indices: 23958979--23959040 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
23958969 GGAAAAACAA
* * *
23958979 TCATCTTACCATATAAGGGCAAAATAT
1 TCATTTTACCACATAAGGGCAAAAGAT
23959006 TCATTTTACCACATAAGGGCAAAACGAT
1 TCATTTTACCACATAAGGGCAAAA-GAT
23959034 T-ATTTTA
1 TCATTTTA
23959041 TCAATTTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (27 bp):
TCATTTTACCACATAAGGGCAAAAGAT
Found at i:23959191 original size:17 final size:18
Alignment explanation
Indices: 23959158--23959191 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23959148 CATAATACGG
*
23959158 GCCCATGTAGGCCCACAC
1 GCCCATGTAGACCCACAC
23959176 GCCCATGT-GACCCACA
1 GCCCATGTAGACCCACA
23959192 TAGCACAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.44, G:0.21, T:0.12
Consensus pattern (18 bp):
GCCCATGTAGACCCACAC
Found at i:23961324 original size:2 final size:2
Alignment explanation
Indices: 23961317--23961347 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23961307 AATAGAATTA
23961317 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
23961348 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23963065 original size:46 final size:46
Alignment explanation
Indices: 23963015--23963190 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
23963005 TGGTTGAGCA
* *
23963015 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
23963061 TCCGAACTCGTTGAGTTGAGTCTGAG-T---TTATGAGATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--ATG
*
23963106 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
23963154 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
23963191 GTGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 5 0.05
43 5 0.05
45 3 0.03
46 59 0.54
47 25 0.23
48 3 0.03
50 6 0.05
51 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:23963171 original size:93 final size:93
Alignment explanation
Indices: 23963012--23963181 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 93
23963002 GGATGGTTGA
* * * *
23963012 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
*
23963077 TGAGTCTGAGTTTATGAGATGTAACTAG
66 TGAGTCCGAGTTTATGAGATGTAACTAG
*
23963105 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
23963170 TGAGTCCGAGTT
66 TGAGTCCGAGTT
23963182 CGCTTATGGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTTATGAGATGTAACTAG
Found at i:23965433 original size:15 final size:15
Alignment explanation
Indices: 23965415--23965444 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23965405 AAAACCATAA
*
23965415 TAATAATAATGATAT
1 TAATAATAATAATAT
23965430 TAATAATAATAATAT
1 TAATAATAATAATAT
23965445 AAAAAAATAA
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:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:23966501 original size:17 final size:18
Alignment explanation
Indices: 23966470--23966509 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
23966460 TTATTTGTTG
23966470 AAAAACAAAAGAGAAAAC
1 AAAAACAAAAGAGAAAAC
*
23966488 AAAAAGAAAA-AGAAAAC
1 AAAAACAAAAGAGAAAAC
23966505 AAAAA
1 AAAAA
23966510 ATAAAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAGAGAAAAC
Found at i:23972282 original size:39 final size:41
Alignment explanation
Indices: 23972181--23972364 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 41
23972171 TCGAATGATG
* * *
23972181 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
*
23972221 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
*
23972261 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
*
23972300 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
23972340 ACCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
23972365 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
39 49 0.39
40 67 0.53
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:23972317 original size:79 final size:80
Alignment explanation
Indices: 23972181--23972362 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 80
23972171 TCGAATGATG
* *
23972181 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
23972245 TGTGCGAGTTACTA-A
65 TGTGCGAGTTACTATA
* * * **
23972260 TTCCGGGCTAAGCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
23972323 TTGTGCGAGTTACTATA
64 TTGTGCGAGTTACTATA
* * *
23972340 ACCGGGCTATGTCCGAAGGCATT
1 TCCGGGCTAAGCCCGAAGGCATT
23972363 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 70 0.79
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:23972371 original size:79 final size:78
Alignment explanation
Indices: 23972234--23972397 Score: 206
Period size: 79 Copynumber: 2.1 Consensus size: 78
23972224 GGACTAAGAT
* **
23972234 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAG-TAGCTA
*
23972298 AATCCGGGTTAAGTC
65 AATCC-GGTTAAATC
* * *
23972313 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAGTAGCTA
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTA
* *
23972377 TATCCGGTTAAATT
65 AATCCGGTTAAATC
23972391 CCGAAGG
1 CCGAAGG
23972398 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 18 0.24
79 56 0.76
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAA
ATCCGGTTAAATC
Found at i:23974973 original size:16 final size:18
Alignment explanation
Indices: 23974942--23974977 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
23974932 CGTACATGAG
23974942 AGAAACAAAAACAAAGAA
1 AGAAACAAAAACAAAGAA
23974960 AGAAA-AAAAA-AAAGAA
1 AGAAACAAAAACAAAGAA
23974976 AG
1 AG
23974978 GAAGAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.81, C:0.06, G:0.14, T:0.00
Consensus pattern (18 bp):
AGAAACAAAAACAAAGAA
Found at i:23974977 original size:20 final size:20
Alignment explanation
Indices: 23974948--23974985 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23974938 TGAGAGAAAC
23974948 AAAAACAAAGAAAGAAAAAA
1 AAAAACAAAGAAAGAAAAAA
* *
23974968 AAAAAGAAAGGAAGAAAA
1 AAAAACAAAGAAAGAAAA
23974986 GTGTTCATCC
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:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAACAAAGAAAGAAAAAA
Found at i:23976273 original size:40 final size:40
Alignment explanation
Indices: 23976214--23976320 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
23976204 CAATTGAATG
* * * *
23976214 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
* * * **
23976254 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
*
23976294 ACATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
23976321 CGTGCAAGTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
Found at i:23976340 original size:40 final size:39
Alignment explanation
Indices: 23976255--23976381 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 39
23976245 CTGGAAATTA
* * *
23976255 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTG-AC
1 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTGTTC
23976293 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
* * *
23976335 TATCCGGGCTAAGACCCGAGGGCATTCGTGCATGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
23976375 TATCCGG
1 TATCCGG
23976382 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 70 0.91
41 1 0.01
42 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGTTC
Found at i:23983565 original size:39 final size:41
Alignment explanation
Indices: 23983465--23983648 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 41
23983455 TCGAATGATG
* * *
23983465 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
*
23983504 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
*
23983544 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
*
23983583 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
23983623 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
23983649 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
39 46 0.36
40 72 0.57
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:23983600 original size:79 final size:80
Alignment explanation
Indices: 23983465--23983646 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 80
23983455 TCGAATGATG
* * *
23983465 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
23983529 GTGCGAGTTACTA-A
66 GTGCGAGTTACTATA
* * * **
23983543 TTCCGGGCTAAGCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
23983606 TTGTGCGAGTTACTATA
64 TTGTGCGAGTTACTATA
* *
23983623 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATT
23983647 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 69 0.78
80 19 0.21
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:23983670 original size:79 final size:79
Alignment explanation
Indices: 23983517--23983681 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
23983507 GGACTAAGAT
* **
23983517 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
23983582 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
23983596 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
23983659 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
23983675 CCGAAGG
1 CCGAAGG
23983682 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:23985760 original size:37 final size:36
Alignment explanation
Indices: 23985708--23985820 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 36
23985698 ATTCCAAAAA
*
23985708 TAATATTATTTTAATAGTTTAATATTAAATTAAATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAAATT
* *
23985744 TAATACTTATCTTAATAGTATT-TTATT-AATTTAATGT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAAAT-T
*
23985781 TAACGTGATTATCTTAATA-TTTAAT-TTAATTTAATATT
1 TAA--T-ATTATCTTAATAGTTTAATATTAAATTAA-ATT
23985819 TA
1 TA
23985821 TCTATATTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
36 12 0.19
37 24 0.39
38 11 0.18
39 14 0.23
40 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAAATT
Found at i:23989910 original size:23 final size:23
Alignment explanation
Indices: 23989884--23989929 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
23989874 AACTAAACCA
23989884 AGTAAAACTCATTCTCCAAATCC
1 AGTAAAACTCATTCTCCAAATCC
23989907 AGTAAAACTCATTCTCCAAATCC
1 AGTAAAACTCATTCTCCAAATCC
23989930 GAGTTGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.26
Consensus pattern (23 bp):
AGTAAAACTCATTCTCCAAATCC
Found at i:23990425 original size:16 final size:16
Alignment explanation
Indices: 23990404--23990444 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
23990394 ATAATATATT
23990404 ATTAATTAATAAAATA
1 ATTAATTAATAAAATA
23990420 ATTAATCT-ATAAAATA
1 ATTAAT-TAATAAAATA
*
23990436 ATGAATTAA
1 ATTAATTAA
23990445 GCCTACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTAATTAATAAAATA
Found at i:23992763 original size:15 final size:15
Alignment explanation
Indices: 23992743--23992777 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
23992733 TTAAATATTA
23992743 TTGAAAAATTAAATG
1 TTGAAAAATTAAATG
*
23992758 TTGAAAAATTAAGTG
1 TTGAAAAATTAAATG
23992773 TTGAA
1 TTGAA
23992778 TTTAAGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
TTGAAAAATTAAATG
Found at i:23994538 original size:21 final size:21
Alignment explanation
Indices: 23994512--23994555 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
23994502 AATCATACAT
23994512 TACATCACATAATACATTACC
1 TACATCACATAATACATTACC
23994533 TACATCACATAATACATTACC
1 TACATCACATAATACATTACC
23994554 TA
1 TA
23994556 AACCCTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (21 bp):
TACATCACATAATACATTACC
Found at i:23999912 original size:18 final size:20
Alignment explanation
Indices: 23999889--23999928 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
23999879 TGTGGGTAGG
23999889 CCGTGTGG-TCA-CACACGC
1 CCGTGTGGCTCAGCACACGC
*
23999907 CCGTGTGGCTCAGGACACGC
1 CCGTGTGGCTCAGCACACGC
23999927 CC
1 CC
23999929 ATGTACTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.15, C:0.40, G:0.30, T:0.15
Consensus pattern (20 bp):
CCGTGTGGCTCAGCACACGC
Found at i:24001455 original size:45 final size:45
Alignment explanation
Indices: 24001400--24001486 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
24001390 CCAAAACATG
* *
24001400 TGTCATATATATCACGAACTCAGACCACAACTTAATGAGTTCGGA
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
*
24001445 TGTCACATATATCATGAACTCAGACCACAACTCAATGAGTTC
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTC
24001487 AGATCACATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
Found at i:24001732 original size:25 final size:25
Alignment explanation
Indices: 24001698--24001746 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
24001688 CATTAATTAT
*
24001698 ATATATTTACCATACATGCAATATA
1 ATATACTTACCATACATGCAATATA
24001723 ATATACTTACCATACATGCAATAT
1 ATATACTTACCATACATGCAATAT
24001747 CAAGTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATACTTACCATACATGCAATATA
Found at i:24003305 original size:41 final size:41
Alignment explanation
Indices: 24003260--24003377 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
24003250 TGAAAGATAA
24003260 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
24003301 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
24003331 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
24003372 ATGTAG
1 ATGTAG
24003378 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:24003309 original size:71 final size:71
Alignment explanation
Indices: 24003228--24003391 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
24003218 GAGATGTATC
24003228 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
24003293 AGGACA
66 AGGACA
24003299 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
24003364 AGGACA
66 AGGACA
24003370 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
24003392 AGACAAATCG
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:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:24008261 original size:40 final size:40
Alignment explanation
Indices: 24008134--24008263 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
24008124 ATGCTGGAAA
* *
24008134 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
24008174 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
24008214 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
24008254 TTATATCCGG
1 TTATATCCGG
24008264 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:24013997 original size:29 final size:29
Alignment explanation
Indices: 24013964--24014095 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
24013954 GTGACGAGAT
24013964 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
24013993 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
24014022 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
24014051 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
24014080 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
24014096 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:24021930 original size:29 final size:29
Alignment explanation
Indices: 24021897--24022028 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
24021887 GTGACGAGAT
24021897 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
24021926 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
24021955 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
24021984 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
24022013 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
24022029 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:24027453 original size:40 final size:40
Alignment explanation
Indices: 24027326--24027455 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
24027316 ATGCTGGAAA
* *
24027326 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
24027366 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
24027406 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
24027446 TTATATCCGG
1 TTATATCCGG
24027456 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:24034161 original size:68 final size:70
Alignment explanation
Indices: 24034089--24034286 Score: 285
Period size: 71 Copynumber: 2.8 Consensus size: 70
24034079 ACACCTTGTA
* * * *
24034089 GTAGCTAGGTCACATGTGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCACATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
24034151 ATAAAT
65 ATAAAT
* *
24034157 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCACATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
24034222 ATAAAT
65 ATAAAT
*
24034228 GTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCACATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
24034287 AGACAAATCG
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
68 23 0.19
69 3 0.03
70 1 0.01
71 92 0.77
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (70 bp):
GTAGCTAGGTCACATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:24034211 original size:71 final size:71
Alignment explanation
Indices: 24034123--24034286 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
24034113 GAGATGTATC
*
24034123 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
24034188 AGGACA
66 AGGACA
24034194 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
24034259 AGGACA
66 AGGACA
24034265 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
24034287 AGACAAATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
AGGACA
Found at i:24036588 original size:29 final size:29
Alignment explanation
Indices: 24036548--24036607 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
24036538 TTTATTTCAT
*
24036548 AATTTAACCCCTCAATTTACACTTTT-CTC
1 AATTTAACCCCT-AATATACACTTTTACTC
* *
24036577 AATTTAATCCCTAATATACATTTTTACTC
1 AATTTAACCCCTAATATACACTTTTACTC
24036606 AA
1 AA
24036608 AGTCACTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTTAACCCCTAATATACACTTTTACTC
Found at i:24042714 original size:29 final size:30
Alignment explanation
Indices: 24042642--24042715 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
24042632 TTTTTAGTGA
* * *
24042642 AAATGTAAAATAGGGATTAAATTGAGAAAT
1 AAATGAAAAATATGGATTAAAATGAGAAAT
* * *
24042672 -ATTGAAAATTTATGG-TTAAAATGTGAAAT
1 AAATGAAAA-ATATGGATTAAAATGAGAAAT
24042701 AAATGAAAAATATGG
1 AAATGAAAAATATGG
24042716 GCTCCTAGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (30 bp):
AAATGAAAAATATGGATTAAAATGAGAAAT
Found at i:24051307 original size:51 final size:51
Alignment explanation
Indices: 24051227--24051393 Score: 271
Period size: 51 Copynumber: 3.3 Consensus size: 51
24051217 CTTCTTATCT
* * *
24051227 GTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTAATCAGTGACAA
1 GTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
* **
24051278 GTGACAAATGATAAGTGGTAAATTTAGCTACACTTATCTGATCAGTGACAA
1 GTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
*
24051329 GTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
1 GTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
24051380 GTGACAAGTGATAA
1 GTGACAAGTGATAA
24051394 ATGTGATCAG
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 105 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (51 bp):
GTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
Found at i:24055368 original size:12 final size:12
Alignment explanation
Indices: 24055351--24055377 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24055341 TCAAGCCCGA
24055351 ATTCTTCTTTCT
1 ATTCTTCTTTCT
24055363 ATTCTTCTTTCT
1 ATTCTTCTTTCT
24055375 ATT
1 ATT
24055378 TCCGTCTCTT
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:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTCTTCTTTCT
Found at i:24060760 original size:40 final size:40
Alignment explanation
Indices: 24060701--24060868 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
24060691 CATTTGAATG
* *
24060701 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGATT
* *
24060741 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTAG-GAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-AT-GCTAG-TGATT
* * * **
24060781 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGATT
* * * * *
24060821 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGATT
24060861 ATATCCGG
1 ATATCCGG
24060869 TTAAATCCCG
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
39 4 0.04
40 95 0.90
41 6 0.06
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGATT
Found at i:24064328 original size:30 final size:30
Alignment explanation
Indices: 24064289--24064353 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
24064279 TTTCTAATCC
* *
24064289 TTAAAATTAATCGTCAGATAGATTTA-AAT
1 TTAAAATTAATCGTCAAATAAATTTAGAAT
24064318 TTAAACATTAATCGTCAAATAAATTTAGAAT
1 TTAAA-ATTAATCGTCAAATAAATTTAGAAT
24064349 TTAAA
1 TTAAA
24064354 TTATGTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 5 0.16
30 19 0.59
31 8 0.25
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (30 bp):
TTAAAATTAATCGTCAAATAAATTTAGAAT
Found at i:24064452 original size:31 final size:31
Alignment explanation
Indices: 24064414--24064475 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24064404 ACTAATCAAT
24064414 TTTTTAAAAAAATTAATAATCTAAATAAAAA
1 TTTTTAAAAAAATTAATAATCTAAATAAAAA
* * * *
24064445 TTTTTAAATAATTTAATTATTTAAATAAAAA
1 TTTTTAAAAAAATTAATAATCTAAATAAAAA
24064476 CTTTCAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTTAAAAAAATTAATAATCTAAATAAAAA
Found at i:24064454 original size:14 final size:14
Alignment explanation
Indices: 24064435--24064493 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
24064425 ATTAATAATC
24064435 TAAATAAAAATTTT
1 TAAATAAAAATTTT
*
24064449 TAAATAATTTAATTATT
1 TAAATAA--AAATT-TT
*
24064466 TAAATAAAAACTTT
1 TAAATAAAAATTTT
* *
24064480 CAAATAATAATTTT
1 TAAATAAAAATTTT
24064494 AGTATGCTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 20 0.56
15 3 0.08
16 4 0.11
17 9 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAATAAAAATTTT
Found at i:24064485 original size:31 final size:31
Alignment explanation
Indices: 24064426--24064487 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24064416 TTTAAAAAAA
* *
24064426 TTAATAATCTAAATAAAAATTTTTAAATAAT
1 TTAATAATCTAAATAAAAACTTTCAAATAAT
* *
24064457 TTAATTATTTAAATAAAAACTTTCAAATAAT
1 TTAATAATCTAAATAAAAACTTTCAAATAAT
24064488 AATTTTAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAATAATCTAAATAAAAACTTTCAAATAAT
Found at i:24067765 original size:30 final size:30
Alignment explanation
Indices: 24067726--24067782 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
24067716 TTTTATAAAT
24067726 AATTAATA-TTTATTGC-TTAAAAATATTTAA
1 AATTAATATTTTATT-CATT-AAAATATTTAA
*
24067756 AATTTATATTTTATTCATTAAAATATT
1 AATTAATATTTTATTCATTAAAATATT
24067783 AACAAGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (30 bp):
AATTAATATTTTATTCATTAAAATATTTAA
Found at i:24067991 original size:35 final size:35
Alignment explanation
Indices: 24067951--24068023 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
24067941 AATTTTAAAC
* *
24067951 TAAACTTTTGAAAAGCACTTTCTAAAAGTATTTTT
1 TAAACTTTTCAAAAGCACTTTCTAAAAGTACTTTT
*
24067986 TAAACTTTTCAAAAGCACTTTTTAAAAGTACTTTT
1 TAAACTTTTCAAAAGCACTTTCTAAAAGTACTTTT
24068021 TAA
1 TAA
24068024 CAGTACTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (35 bp):
TAAACTTTTCAAAAGCACTTTCTAAAAGTACTTTT
Found at i:24068021 original size:13 final size:13
Alignment explanation
Indices: 24067954--24068030 Score: 63
Period size: 13 Copynumber: 6.2 Consensus size: 13
24067944 TTTAAACTAA
* *
24067954 ACTTTTGAAAAGC
1 ACTTTTTAAAAGT
*
24067967 ACTTTCTAAAAGT
1 ACTTTTTAAAAGT
*
24067980 A-TTTTT-TAA--
1 ACTTTTTAAAAGT
* *
24067989 ACTTTTCAAAAGC
1 ACTTTTTAAAAGT
24068002 ACTTTTTAAAAGT
1 ACTTTTTAAAAGT
*
24068015 ACTTTTTAACAGT
1 ACTTTTTAAAAGT
24068028 ACT
1 ACT
24068031 CTTCAAAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
9 1 0.02
10 4 0.08
11 4 0.08
12 4 0.08
13 37 0.74
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (13 bp):
ACTTTTTAAAAGT
Found at i:24069499 original size:29 final size:30
Alignment explanation
Indices: 24069444--24069502 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
24069434 ATCTCAAAAT
* *
24069444 TATACATGAACTTTGATTTAATGTGCAATTG
1 TATACATGAACTTTAATTT-AGGTGCAATTG
24069475 TATACATGAACTTTAATTT-GGTGCAATT
1 TATACATGAACTTTAATTTAGGTGCAATT
24069503 ATTCAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAGGTGCAATTG
Found at i:24073107 original size:14 final size:14
Alignment explanation
Indices: 24073090--24073136 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
24073080 ATTTAATTCA
24073090 TATTATATTTTAAT
1 TATTATATTTTAAT
* *
24073104 TATTTATATTTAAAA
1 TA-TTATATTTTAAT
*
24073119 TATTATATTTTAGT
1 TATTATATTTTAAT
24073133 TATT
1 TATT
24073137 TACATTATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TATTATATTTTAAT
Found at i:24073112 original size:15 final size:15
Alignment explanation
Indices: 24073081--24073138 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
24073071 ATCATTTTTA
24073081 TTTAATTCATATTATAT
1 TTTAATT-AT-TTATAT
24073098 TTTAATTATTTATAT
1 TTTAATTATTTATAT
* *
24073113 TTAAAATA-TTATAT
1 TTTAATTATTTATAT
*
24073127 TTTAGTTATTTA
1 TTTAATTATTTA
24073139 CATTATCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 11 0.31
15 15 0.43
16 2 0.06
17 7 0.20
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTAATTATTTATAT
Found at i:24075902 original size:40 final size:40
Alignment explanation
Indices: 24075733--24075903 Score: 175
Period size: 40 Copynumber: 4.3 Consensus size: 40
24075723 GAGCATTTGA
* * * *
24075733 ATTATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTG
* *
24075773 ATTATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TG
* * *
24075814 -TTATATCTGGGCTAAGACCCGAAGGCAATTGTGCAAGTT
1 ATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTG
** * * *
24075853 ACCAAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTG
*
24075893 GTTATATCCGG
1 ATTATATCCGG
24075904 TTAAATCCCG
Statistics
Matches: 105, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.03
40 97 0.92
41 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTG
Found at i:24079464 original size:13 final size:13
Alignment explanation
Indices: 24079443--24079473 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24079433 TGTGGTGCAG
*
24079443 AGGCTTAGAAAAA
1 AGGCCTAGAAAAA
24079456 AGGCCTAGAAAAA
1 AGGCCTAGAAAAA
24079469 AGGCC
1 AGGCC
24079474 AGAGTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.16, G:0.26, T:0.10
Consensus pattern (13 bp):
AGGCCTAGAAAAA
Found at i:24084191 original size:18 final size:17
Alignment explanation
Indices: 24084156--24084209 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 17
24084146 CAATTTAGGC
* *
24084156 CGTGTGGGCCACACGGG
1 CGTGTAGGCCACATGGG
24084173 CGTGTAGGCCCACATGGG
1 CGTGTAGG-CCACATGGG
24084191 C----AGGCCACATGGG
1 CGTGTAGGCCACATGGG
24084204 CGTGTA
1 CGTGTA
24084210 AGCCTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 10 0.33
14 3 0.10
17 8 0.27
18 9 0.30
ACGTcount: A:0.17, C:0.28, G:0.41, T:0.15
Consensus pattern (17 bp):
CGTGTAGGCCACATGGG
Found at i:24086862 original size:19 final size:20
Alignment explanation
Indices: 24086829--24086867 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
24086819 ATTTGAAATT
24086829 TTTTTCGAATCAAG-TAAAA
1 TTTTTCGAATCAAGTTAAAA
* *
24086848 TTTTTCGAGTTAAGTTAAAA
1 TTTTTCGAATCAAGTTAAAA
24086868 AAAATTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
TTTTTCGAATCAAGTTAAAA
Found at i:24087089 original size:18 final size:19
Alignment explanation
Indices: 24087066--24087103 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
24087056 TTAAAAAAAA
24087066 TTATAAAT-TTTGTAATTT
1 TTATAAATATTTGTAATTT
*
24087084 TTATAAATATTTTTAATTT
1 TTATAAATATTTGTAATTT
24087103 T
1 T
24087104 AAAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTATAAATATTTGTAATTT
Found at i:24087104 original size:18 final size:18
Alignment explanation
Indices: 24087066--24087120 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
24087056 TTAAAAAAAA
*
24087066 TTATAAAT-TTTGTAATTT
1 TTATAAATATTTTTAA-TT
24087084 TTATAAATATTTTTAATT
1 TTATAAATATTTTTAATT
* *
24087102 TTAAAAATTATTTTGAATT
1 TTATAAA-TATTTTTAATT
24087121 ATTTGTTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TTATAAATATTTTTAATT
Found at i:24087113 original size:19 final size:18
Alignment explanation
Indices: 24087072--24087120 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
24087062 AAAATTATAA
*
24087072 ATTTTGTAATTTTTATAAAT
1 ATTTT-TAA-TTTTAAAAAT
24087092 ATTTTTAATTTTAAAAATT
1 ATTTTTAATTTTAAAAA-T
*
24087111 ATTTTGAATT
1 ATTTTTAATT
24087121 ATTTGTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 13 0.50
20 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
ATTTTTAATTTTAAAAAT
Found at i:24088563 original size:62 final size:61
Alignment explanation
Indices: 24088486--24088601 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 61
24088476 TTAATTTGTA
* * *
24088486 TTAAATATTATAATTATTTAAA-TTTATTTTTTACCTAATTAATATTTA-AATACTATTTATAC
1 TTAAATATTACAATTA-TTAAACTTTA--CTTTACCAAATTAATATTTAGAATACTATTTATAC
* *
24088548 TTAAATATTGCAATTATTAAACTTTACTTTATCAAATTAATATTTAGAATACTA
1 TTAAATATTACAATTATTAAACTTTACTTTACCAAATTAATATTTAGAATACTA
24088602 CCTTGTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
60 17 0.36
61 12 0.26
62 18 0.38
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (61 bp):
TTAAATATTACAATTATTAAACTTTACTTTACCAAATTAATATTTAGAATACTATTTATAC
Found at i:24090330 original size:10 final size:10
Alignment explanation
Indices: 24090317--24090341 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24090307 GTAAATTTTA
24090317 TTTTTATAAT
1 TTTTTATAAT
24090327 TTTTTATAAT
1 TTTTTATAAT
24090337 TTTTT
1 TTTTT
24090342 TTCTAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:24092078 original size:3 final size:3
Alignment explanation
Indices: 24092070--24092130 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
24092060 AACAAATCAA
24092070 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24092118 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
24092131 TCCAACCAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24095348 original size:49 final size:49
Alignment explanation
Indices: 24095288--24095459 Score: 147
Period size: 49 Copynumber: 3.5 Consensus size: 49
24095278 GTTGTGTGTT
* **
24095288 AGTGTAAGACCTGTCTGAGACATGGCATCAACAC-TGATGGATGGGAGCC
1 AGTGTAAGACCTGTCTGAGACATGGCATCAAC-CTTGATAGATGAAAGCC
* * * * *
24095337 AGTGTAAGACCTGTTTGAGAC-TCGTCATCAGCCTTGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGAGACAT-GGCATCAACCTTGATAGATGAAAGCC
* * * *
24095386 AGTGTAAGACCTGTCT-AGGACATGGCATCGACTTTGAT-G-TGCAAGCT
1 AGTGTAAGACCTGTCTGA-GACATGGCATCAACCTTGATAGATGAAAGCC
* *
24095433 AGTGTAATACCATGTCTGGGACATGGC
1 AGTGTAAGACC-TGTCTGAGACATGGC
24095460 GTCGATATTG
Statistics
Matches: 98, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
47 15 0.15
48 16 0.16
49 66 0.67
50 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGAGACATGGCATCAACCTTGATAGATGAAAGCC
Found at i:24096968 original size:27 final size:28
Alignment explanation
Indices: 24096934--24097002 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
24096924 TACTCGATCA
* *
24096934 CGCACACTTAGTGCCATATATTC-AGCT
1 CGCACACTTAGTGCCATATAATCAAACT
*
24096961 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCCATATAATCAAACT
24096989 CGCACACTTAGTGC
1 CGCACACTTAGTGC
24097003 TGTACAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATAATCAAACT
Found at i:24098370 original size:18 final size:18
Alignment explanation
Indices: 24098338--24098375 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
24098328 ATCCACCCCA
24098338 TTTTTTTTCATCATTATCTT
1 TTTTTTTTCA-CATT-TCTT
24098358 TTTTTTTTC-CATTTCTT
1 TTTTTTTTCACATTTCTT
24098375 T
1 T
24098376 ATTCTCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
20 9 0.50
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTTCACATTTCTT
Found at i:24104957 original size:27 final size:28
Alignment explanation
Indices: 24104923--24104991 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
24104913 TACTCGATCA
* *
24104923 CGCACACTTAGTGCCATATATTC-AGCT
1 CGCACACTTAGTGCCATATAATCAAACT
*
24104950 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCCATATAATCAAACT
24104978 CGCACACTTAGTGC
1 CGCACACTTAGTGC
24104992 TGTACAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATAATCAAACT
Found at i:24106358 original size:18 final size:18
Alignment explanation
Indices: 24106326--24106363 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
24106316 ATCCACCCCA
24106326 TTTTTTTTCATCATTATCTT
1 TTTTTTTTCA-CATT-TCTT
24106346 TTTTTTTTC-CATTTCTT
1 TTTTTTTTCACATTTCTT
24106363 T
1 T
24106364 ATTCTCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
20 9 0.50
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTTCACATTTCTT
Found at i:24112370 original size:27 final size:28
Alignment explanation
Indices: 24112340--24112396 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
24112330 ATTTTTGATG
24112340 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
24112367 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
24112396 A
1 A
24112397 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:24114912 original size:37 final size:37
Alignment explanation
Indices: 24114858--24114929 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
24114848 TAGCTTATGT
*
24114858 GTTAGACTCGAAAGTGAATGATAAGAAAGTTGAATTA
1 GTTAGACCCGAAAGTGAATGATAAGAAAGTTGAATTA
*
24114895 GTTAGACCCGAATGTGAATGATAAGAAAGTTGAAT
1 GTTAGACCCGAAAGTGAATGATAAGAAAGTTGAAT
24114930 CAGTGCCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (37 bp):
GTTAGACCCGAAAGTGAATGATAAGAAAGTTGAATTA
Found at i:24117448 original size:156 final size:156
Alignment explanation
Indices: 24117152--24117444 Score: 543
Period size: 156 Copynumber: 1.9 Consensus size: 156
24117142 GGTACGAATT
*
24117152 TTCAAAGCCCATATCTGAATTTCTATTTCTGTTAAAGATTTCATGAAATGCCATTGTTGATATCA
1 TTCAAAGCCCATATCTGAATTTCTATTTCTATTAAAGATTTCATGAAATGCCATTGTTGATATCA
*
24117217 TGAGTTTTGTGATGTTTTTGGATGAATTATGAAGGCTTGTTAGTTGAGTTATATGTTTTGTTCTT
66 TGAGTTTTGTGATGTTTTTGGATGAATTATGAAGGCTTGTTAGTTGAGTTATATGTTTTGTTCTA
24117282 GATATTTTGATCATTGCTTCGTGTTC
131 GATATTTTGATCATTGCTTCGTGTTC
*
24117308 TTCAAAGCCCATATCTGAATTTCTGTTTCTATTAAAGATTTCATGAAATGCCATTGTTGATATCA
1 TTCAAAGCCCATATCTGAATTTCTATTTCTATTAAAGATTTCATGAAATGCCATTGTTGATATCA
*
24117373 TGAGTTTTGTGATGTTTTTGGATGAATTATGAAGGCTTGTTAGTTTAGTTATATGTTTTGTTCTA
66 TGAGTTTTGTGATGTTTTTGGATGAATTATGAAGGCTTGTTAGTTGAGTTATATGTTTTGTTCTA
24117438 GA-ATTTT
131 GATATTTT
24117445 TGATGAAATG
Statistics
Matches: 133, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
155 5 0.04
156 128 0.96
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (156 bp):
TTCAAAGCCCATATCTGAATTTCTATTTCTATTAAAGATTTCATGAAATGCCATTGTTGATATCA
TGAGTTTTGTGATGTTTTTGGATGAATTATGAAGGCTTGTTAGTTGAGTTATATGTTTTGTTCTA
GATATTTTGATCATTGCTTCGTGTTC
Found at i:24118548 original size:12 final size:13
Alignment explanation
Indices: 24118531--24118562 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
24118521 GCAAATGTTA
24118531 AGTTTTG-TGCAT
1 AGTTTTGATGCAT
24118543 AGTTTTGATGCAT
1 AGTTTTGATGCAT
24118556 -GTTTTGA
1 AGTTTTGA
24118563 ATTATGCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (13 bp):
AGTTTTGATGCAT
Found at i:24123284 original size:29 final size:29
Alignment explanation
Indices: 24123249--24123322 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
24123239 GTTGTGAGAT
* *
24123249 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
24123278 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
24123307 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
24123323 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:24131080 original size:29 final size:29
Alignment explanation
Indices: 24131045--24131118 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
24131035 GTTGTGAGAT
* *
24131045 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
24131074 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
24131103 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
24131119 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:24133333 original size:11 final size:11
Alignment explanation
Indices: 24133302--24133358 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
24133292 ATGATTAAAG
24133302 ACTTTTATTTATT
1 ACTTTTA-TT-TT
*
24133315 ATTTTTATTTT
1 ACTTTTATTTT
24133326 ACTTTTATTTT
1 ACTTTTATTTT
24133337 ACTTTTTATTTT
1 AC-TTTTATTTT
*
24133349 A-ATTTATTTT
1 ACTTTTATTTT
24133359 TAGTTCATCC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
10 8 0.20
11 14 0.35
12 12 0.30
13 6 0.15
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (11 bp):
ACTTTTATTTT
Found at i:24133359 original size:23 final size:22
Alignment explanation
Indices: 24133305--24133360 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
24133295 ATTAAAGACT
*
24133305 TTTATTTATTATTTTTATTTTAC
1 TTTATTT-TTATTTTTATTTTAA
24133328 TTT-TATTTTACTTTTTATTTTAA
1 TTTAT-TTTTA-TTTTTATTTTAA
24133351 TTTATTTTTA
1 TTTATTTTTA
24133361 GTTCATCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 24 0.83
24 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTTTATTTTTATTTTAA
Found at i:24133360 original size:6 final size:6
Alignment explanation
Indices: 24133304--24133353 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
24133294 GATTAAAGAC
* *
24133304 TTTTAT TTATTAT TTTTA- TTTTAC TTTTA- TTTTACT TTTTAT TTTAAT
1 TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT
24133352 TT
1 TT
24133354 ATTTTTAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 18 0.46
7 11 0.28
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:24140516 original size:32 final size:32
Alignment explanation
Indices: 24140475--24140538 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
24140465 TTTCAGAGTT
24140475 TGTCTCGAGATGTTTAATTTGTCAACAAGTAA
1 TGTCTCGAGATGTTTAATTTGTCAACAAGTAA
24140507 TGTCTCGAGATGTTTAATTTGTCAACAAGTAA
1 TGTCTCGAGATGTTTAATTTGTCAACAAGTAA
24140539 AAGCCAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (32 bp):
TGTCTCGAGATGTTTAATTTGTCAACAAGTAA
Found at i:24145342 original size:24 final size:24
Alignment explanation
Indices: 24145310--24145396 Score: 165
Period size: 24 Copynumber: 3.6 Consensus size: 24
24145300 AATCTCAAAT
24145310 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
24145334 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
24145358 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
24145382 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
24145397 ACATAATGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:24145407 original size:22 final size:22
Alignment explanation
Indices: 24145310--24145416 Score: 119
Period size: 24 Copynumber: 4.6 Consensus size: 22
24145300 AATCTCAAAT
24145310 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGA--TACTATG
*
24145334 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGA--TACTATG
24145358 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGA--TACTATG
24145382 GCACTATGTGTGCGA-ACATAAT-
1 GCACTATGTGTGCGATAC-T-ATG
24145404 GCACTATGTGTGC
1 GCACTATGTGTGC
24145417 AACGTTTGGT
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
21 2 0.03
22 14 0.18
23 2 0.03
24 61 0.77
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (22 bp):
GCACTATGTGTGCGATACTATG
Found at i:24153186 original size:24 final size:24
Alignment explanation
Indices: 24153154--24153238 Score: 161
Period size: 24 Copynumber: 3.5 Consensus size: 24
24153144 AATCTCAAAT
24153154 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
24153178 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
24153202 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
24153226 GCACTATGTGTGC
1 GCACTATGTGTGC
24153239 AACGTTTGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:24156580 original size:41 final size:41
Alignment explanation
Indices: 24156523--24156600 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
24156513 GCAAGACCTG
24156523 GATGTCAAACACAAAGGAACTAAAAGTACTAGTATTAACTT
1 GATGTCAAACACAAAGGAACTAAAAGTACTAGTATTAACTT
* * *
24156564 GATGTCGAACCCAAAGGAACTAAAAGTACTATTATTA
1 GATGTCAAACACAAAGGAACTAAAAGTACTAGTATTA
24156601 GCTTTCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (41 bp):
GATGTCAAACACAAAGGAACTAAAAGTACTAGTATTAACTT
Found at i:24164468 original size:27 final size:27
Alignment explanation
Indices: 24164434--24164602 Score: 161
Period size: 27 Copynumber: 6.3 Consensus size: 27
24164424 GGGTCTTCAG
24164434 TAATTTTACAAACGAGGGGTATTTCGA
1 TAATTTTACAAACGAGGGGTATTTCGA
*
24164461 TAATTTTACAAATTG-GGGGTATTTC-A
1 TAATTTTACAAA-CGAGGGGTATTTCGA
** *
24164487 GTAATTTTACAAGTTGA-GGGTATTTCGG
1 -TAATTTTACAA-ACGAGGGGTATTTCGA
* *
24164515 TAATTTTACAAAC-CGGGGTATTTTGA
1 TAATTTTACAAACGAGGGGTATTTCGA
* *
24164541 TAACTTTACAAATCGA-GGGCATTTCGA
1 TAATTTTACAAA-CGAGGGGTATTTCGA
**
24164568 TAATTTTACAAATTAGGGGTATTTC-A
1 TAATTTTACAAACGAGGGGTATTTCGA
24164594 GTAATTTTA
1 -TAATTTTA
24164603 AATAGTTTGG
Statistics
Matches: 116, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
26 23 0.20
27 92 0.79
28 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.38
Consensus pattern (27 bp):
TAATTTTACAAACGAGGGGTATTTCGA
Found at i:24164494 original size:54 final size:53
Alignment explanation
Indices: 24164429--24164602 Score: 217
Period size: 54 Copynumber: 3.2 Consensus size: 53
24164419 TACAGGGGTC
*
24164429 TTCAGTAATTTTACAAACGAGGGGTATTTCGATAATTTTACAAATTGGGGGTAT
1 TTCAGTAATTTTACAAACGA-GGGTATTTCGATAATTTTACAAATTAGGGGTAT
** * **
24164483 TTCAGTAATTTTACAAGTTGAGGGTATTTCGGTAATTTTACAAA-CCGGGGTAT
1 TTCAGTAATTTTACAA-ACGAGGGTATTTCGATAATTTTACAAATTAGGGGTAT
* * *
24164536 TT-TGATAACTTTACAAATCGAGGGCATTTCGATAATTTTACAAATTAGGGGTAT
1 TTCAG-TAATTTTACAAA-CGAGGGTATTTCGATAATTTTACAAATTAGGGGTAT
24164590 TTCAGTAATTTTA
1 TTCAGTAATTTTA
24164603 AATAGTTTGG
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
52 1 0.01
53 42 0.42
54 54 0.54
55 3 0.03
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (53 bp):
TTCAGTAATTTTACAAACGAGGGTATTTCGATAATTTTACAAATTAGGGGTAT
Found at i:24164535 original size:80 final size:81
Alignment explanation
Indices: 24164429--24164602 Score: 237
Period size: 80 Copynumber: 2.2 Consensus size: 81
24164419 TACAGGGGTC
* * * *
24164429 TTCAGTAATTTTACAAACGAGGGGTATTTCGATAATTTTACAAATTGGGGGTATTTC-AGTAATT
1 TTCAGTAATTTTACAAACGAGGGGTATTTCGATAACTTTACAAATCGAGGGCATTTCGA-TAATT
*
24164493 TTACAAGTT-GAGGGTAT
65 TTACAAATTAG-GGGTAT
* * *
24164510 TTCGGTAATTTTACAAAC-CGGGGTATTTTGATAACTTTACAAATCGAGGGCATTTCGATAATTT
1 TTCAGTAATTTTACAAACGAGGGGTATTTCGATAACTTTACAAATCGAGGGCATTTCGATAATTT
24164574 TACAAATTAGGGGTAT
66 TACAAATTAGGGGTAT
24164590 TTCAGTAATTTTA
1 TTCAGTAATTTTA
24164603 AATAGTTTGG
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
80 63 0.77
81 19 0.23
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (81 bp):
TTCAGTAATTTTACAAACGAGGGGTATTTCGATAACTTTACAAATCGAGGGCATTTCGATAATTT
TACAAATTAGGGGTAT
Found at i:24168842 original size:42 final size:43
Alignment explanation
Indices: 24168739--24168844 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
24168729 CAATGCCAAC
* * *
24168739 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACATGAAATCAAATATCGATACCACT
* *
24168782 ATCCCAGACAGGGTCTTACATGAAATCAAATA-CGATACCGA-T
1 GTCCCAGACATGGTCTTACATGAAATCAAATATCGATACC-ACT
24168824 GTCCCAGACATGGTCTTACAT
1 GTCCCAGACATGGTCTTACAT
24168845 ATAAATCATA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
42 26 0.47
43 29 0.53
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGAAATCAAATATCGATACCACT
Found at i:24181452 original size:40 final size:40
Alignment explanation
Indices: 24181382--24181519 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
24181372 AACCCAAGTA
* *
24181382 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
24181421 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAGAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
24181461 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
24181501 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
24181520 TTATCATCCG
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
39 14 0.15
40 79 0.85
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:24189361 original size:39 final size:40
Alignment explanation
Indices: 24189307--24189442 Score: 177
Period size: 40 Copynumber: 3.4 Consensus size: 40
24189297 AACCCAAGTA
* * * *
24189307 CCTTCAGGATTTAG-CCGGATATACCT-ACTCGCTCAAATT
1 CCTTCAGGACTTAGCCCGGATATA-GTAACTCGCACAAATG
* *
24189346 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
24189386 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
24189426 CCTACAGGACTTAGCCC
1 CCTTCAGGACTTAGCCC
24189443 AGTTATCATC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 13 0.15
40 73 0.85
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (40 bp):
CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:24202352 original size:40 final size:40
Alignment explanation
Indices: 24202258--24202437 Score: 206
Period size: 40 Copynumber: 4.5 Consensus size: 40
24202248 TACTCGAATG
*
24202258 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACT
* * *
24202299 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGACT
* *
24202339 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * **
24202379 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
24202418 ATATCC-GGCTAA-ACCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
24202438 ATGCTTGATT
Statistics
Matches: 121, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
37 8 0.07
38 6 0.05
39 16 0.13
40 62 0.51
41 28 0.23
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:24210376 original size:40 final size:40
Alignment explanation
Indices: 24210282--24210426 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
24210272 TACTCGAATG
*
24210282 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
24210323 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
24210363 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
*
24210403 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
24210427 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 63 0.68
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:24216284 original size:20 final size:20
Alignment explanation
Indices: 24216259--24216298 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
24216249 TATTATTCTG
24216259 ATGTTTTCATGGTTTATAAA
1 ATGTTTTCATGGTTTATAAA
*
24216279 ATGTTTTCATGGTTTCTAAA
1 ATGTTTTCATGGTTTATAAA
24216299 CTTATAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (20 bp):
ATGTTTTCATGGTTTATAAA
Found at i:24220957 original size:40 final size:39
Alignment explanation
Indices: 24220830--24220959 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
24220820 ATGCTGGAAA
* *
24220830 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG
* * *
24220870 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG
*
24220910 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG
24220950 TTATATCCGG
1 TTATATCCGG
24220960 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG
Found at i:24222637 original size:24 final size:24
Alignment explanation
Indices: 24222586--24222681 Score: 131
Period size: 24 Copynumber: 4.0 Consensus size: 24
24222576 GCTTTATCAT
*
24222586 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
24222611 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
*
24222635 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
24222659 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
24222682 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
24 52 0.81
25 12 0.19
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:24222756 original size:20 final size:20
Alignment explanation
Indices: 24222731--24222791 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
24222721 TTATGATTAC
24222731 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
24222751 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* * *
24222771 GTCATTTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
24222791 A
1 A
24222792 CCATATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Done.