Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 284 of 284
Found at i:95325521 original size:47 final size:47
Alignment explanation
Indices: 95325468--95325583 Score: 187
Period size: 47 Copynumber: 2.5 Consensus size: 47
95325458 GCACTAATAT
* * *
95325468 AAGGATACCATGTAAGGCCATGTTTGGAATATGGCATTTGGTAAGAC
1 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAAAC
*
95325515 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAAAT
1 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAAAC
*
95325562 AAGGATATCATGTAAGACCATG
1 AAGGATACCATGTAAGACCATG
95325584 CCAAGGCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (47 bp):
AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAAAC
Found at i:95325687 original size:55 final size:54
Alignment explanation
Indices: 95325562--95325758 Score: 202
Period size: 54 Copynumber: 3.6 Consensus size: 54
95325552 TTGGTAAAAT
* * * *
95325562 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATCTCATATAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
** * * * *
95325616 AAGGAAATCATGTAAGACCATGTCAAGACATGACATTAATGAGTTACTATAAGGC
1 AAGGATCTCATATAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * *
95325671 AAAGG-TCTCATATAAGATCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATCTCATATAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* **
95325724 AAGGATAC-CACATAAGACCATGTAAAGACATGGCA
1 AAGGAT-CTCATATAAGACCATGCCAAGACATGGCA
95325759 ATGGTAAGTT
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
52 4 0.03
53 30 0.25
54 41 0.34
55 40 0.34
56 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (54 bp):
AAGGATCTCATATAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:95332261 original size:55 final size:57
Alignment explanation
Indices: 95332201--95332343 Score: 193
Period size: 55 Copynumber: 2.5 Consensus size: 57
95332191 GTTGTTGACG
* * *
95332201 GGATTTAGCCTGGATTGGTAATCCTGTTATAATC-CCTCTAAGCATATGTTAC-AAA
1 GGATTTAGCCTGGACTGGTAATCCTGTTATAAGCTCCTCTAAGCATATATTACAAAA
** * *
95332256 GGATTTAGCCTGGACTGGTAATCCTAAT-TGAGCTCTTCTAAGCATATATTACAAAAA
1 GGATTTAGCCTGGACTGGTAATCCTGTTATAAGCTCCTCTAAGCATATATTAC-AAAA
95332313 GGATTTAGCCTGGACTGGTAATCCTGTTATA
1 GGATTTAGCCTGGACTGGTAATCCTGTTATA
95332344 TGTTATGAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
54 3 0.04
55 41 0.55
57 29 0.39
58 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (57 bp):
GGATTTAGCCTGGACTGGTAATCCTGTTATAAGCTCCTCTAAGCATATATTACAAAA
Found at i:95332953 original size:22 final size:22
Alignment explanation
Indices: 95332928--95332971 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
95332918 AATTATTAAC
*
95332928 ATAATGAATTTTAATTAATTTT
1 ATAATCAATTTTAATTAATTTT
*
95332950 ATAATCAATTTTGATTAATTTT
1 ATAATCAATTTTAATTAATTTT
95332972 GATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
ATAATCAATTTTAATTAATTTT
Found at i:95350654 original size:19 final size:19
Alignment explanation
Indices: 95350608--95350655 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
95350598 GTATATATTT
95350608 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
95350626 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
95350645 TAAGTTTTATT
1 TAAATTTTATT
95350656 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:95356315 original size:13 final size:13
Alignment explanation
Indices: 95356293--95356327 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
95356283 CCAACCATAC
95356293 GCCCGTGTGACCA
1 GCCCGTGTGACCA
*
95356306 GCCTGTGTGACCA
1 GCCCGTGTGACCA
95356319 GCCCGTGTG
1 GCCCGTGTG
95356328 CCCTTTCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.20
Consensus pattern (13 bp):
GCCCGTGTGACCA
Found at i:95363010 original size:44 final size:43
Alignment explanation
Indices: 95362952--95363123 Score: 182
Period size: 44 Copynumber: 3.8 Consensus size: 43
95362942 TATACGTGAT
* *
95362952 GATGCATGTTCCAGACATGTCTTACACTAGCACAACTCTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACAACTC-TAGCC
* *
95362996 GATGCATGTCCCAGACATGTCTTACACTGGCACTCAGCTCTACACC
1 GATGCATGTCCCAGACATGTCTTACACTGGCA--CAACTCTA-GCC
* * * *
95363042 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGG--CACA-ACTCTAGCC
*
95363090 GATGCATGTCCCAGGCATGTCTTACACTGGCACA
1 GATGCATGTCCCAGACATGTCTTACACTGGCACA
95363124 CAATCACCCA
Statistics
Matches: 108, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
44 33 0.31
45 2 0.02
46 23 0.21
47 27 0.25
48 20 0.19
49 2 0.02
50 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26
Consensus pattern (43 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTAGCC
Found at i:95363092 original size:48 final size:46
Alignment explanation
Indices: 95362850--95363120 Score: 165
Period size: 49 Copynumber: 5.7 Consensus size: 46
95362840 GGGATAAGTT
* * * * * *
95362850 GCCGATGCCATGTCCCAGACTTGGTCTTACACTGCCTATTATCATCGAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAAT-GTG
* * * * *
95362899 GCCAATTCCATGTCCCAGACATGGTCTTGCACTAGCTCTCGTATATACGT-
1 GCCGA-TGCATGTCCCAGACAT-GTCTTACACTGGCTCTC--ATA-ATGTG
** * * * * * *
95362949 GATGATGCATGTTCCAGACATGTCTTACACTAG--CACA-ACTCTTA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAAT-GTG
* ** * *
95362993 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCA-GCTCTAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGT-G
*
95363039 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGTG
*
95363087 GCCGATGCATGTCCCAGGCATGTCTTACACTGGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC
95363121 ACACAATCAC
Statistics
Matches: 173, Mismatches: 37, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
43 2 0.01
44 30 0.17
45 1 0.01
46 26 0.15
47 27 0.16
48 34 0.20
49 46 0.27
50 3 0.02
51 3 0.02
52 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTG
Found at i:95364828 original size:68 final size:67
Alignment explanation
Indices: 95364659--95364828 Score: 243
Period size: 67 Copynumber: 2.5 Consensus size: 67
95364649 CCTAGTAGGA
* * * *
95364659 TTCATATGTTGCCATAACCCGACTATGGTCTTACACATTATGATCCCATGTTTACTGTCCTGGTG
1 TTCATATGTTGCCATAGCCCAACTATGGTCTTACACATTATGATCCCATGTTTACTATCCTGGCG
95364724 GC
66 GC
* ** *
95364726 TTTATATGTTGCCATAGCCCAGTTATGGTCTTACACGA-TATGATCCTATGTTTACTATCCTGGC
1 TTCATATGTTGCCATAGCCCAACTATGGTCTTACAC-ATTATGATCCCATGTTTACTATCCTGGC
95364790 GGAC
65 GG-C
95364794 TTCATATGTTGCCATAGCCCAACTATGGTCTTACA
1 TTCATATGTTGCCATAGCCCAACTATGGTCTTACA
95364829 AGTTTTGGTC
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
67 56 0.62
68 34 0.38
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (67 bp):
TTCATATGTTGCCATAGCCCAACTATGGTCTTACACATTATGATCCCATGTTTACTATCCTGGCG
GC
Found at i:95374970 original size:42 final size:42
Alignment explanation
Indices: 95374923--95375009 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
95374913 TGCTCACTTG
* *
95374923 TGTAACTCACTGAGTTGCCCTACATGCA-T-GTGTGCCAAGCCA
1 TGTAACTCACTGAGTTG-AC-ACATACACTCGTGTGCCAAGCCA
*
95374965 TGTAACTCTCTGAGTTGACACATACACTCGTGTGCCAAGCCA
1 TGTAACTCACTGAGTTGACACATACACTCGTGTGCCAAGCCA
95375007 TGT
1 TGT
95375010 GCTAGGCCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
40 6 0.15
41 2 0.05
42 32 0.80
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (42 bp):
TGTAACTCACTGAGTTGACACATACACTCGTGTGCCAAGCCA
Found at i:95375680 original size:40 final size:40
Alignment explanation
Indices: 95375630--95375951 Score: 392
Period size: 40 Copynumber: 8.1 Consensus size: 40
95375620 TGATTCAAGT
* * * *
95375630 TACCAAAGTACAAAAAGGGGCATGTATGCGCATTCAGGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
*
95375670 TACCGTAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
*
95375710 TACCGGAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
* * * * * *
95375750 TACCTAAGTACAAACAGGGGAACGTATATGCATTTAAGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
* * * * * * *
95375790 TACTGAAGTAAAAACAAGGGTAGGTGTGTGCATTCAGGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
* * * * *
95375830 CATCGAAGTACAAATAGGGGCACGTATATGGATTCAAGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
* *
95375870 TACCGAAGTACAAATAAGGGCACTTATGTGCATTCAGGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
**
95375910 TATTGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
1 TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
95375950 TA
1 TA
95375952 ATTATCTATA
Statistics
Matches: 236, Mismatches: 46, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 236 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (40 bp):
TACCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGG
Found at i:95375748 original size:20 final size:20
Alignment explanation
Indices: 95375645--95375749 Score: 65
Period size: 20 Copynumber: 5.2 Consensus size: 20
95375635 AAGTACAAAA
* *
95375645 AGGGGCATGTATGCGCATTC
1 AGGGGCACGTATGTGCATTC
* * *
95375665 AGGGGTACCGTA-GTACAAAT-
1 AGGGGCA-CGTATGTGC-ATTC
95375685 AGGGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
* * * *
95375705 AGGGGTACCGGA-GTACAAAT-
1 AGGGGCA-CGTATGTGC-ATTC
95375725 AGGGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
95375745 AGGGG
1 AGGGG
95375750 TACCTAAGTA
Statistics
Matches: 61, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
19 11 0.18
20 40 0.66
21 10 0.16
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (20 bp):
AGGGGCACGTATGTGCATTC
Found at i:95378208 original size:40 final size:40
Alignment explanation
Indices: 95378094--95378214 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 40
95378084 CGTGTTTTGG
* * * **
95378094 TTGGATTAGCTCTTATAAGCTTCTATCTAGCATGTTTCGG
1 TTGGATTAGCTCTTATGAGCTTCTATCTGGCGTGTTTCAA
* * * *
95378134 TCGGATTAG-TTTTATGAGCTTTTATTTGGCGTGTTTCAA
1 TTGGATTAGCTCTTATGAGCTTCTATCTGGCGTGTTTCAA
* *
95378173 TTGGATTAGCTCTTATGAGCTTCTGTCTGGTGTG-TTCAA
1 TTGGATTAGCTCTTATGAGCTTCTATCTGGCGTGTTTCAA
95378212 TTG
1 TTG
95378215 ATTTGATGAT
Statistics
Matches: 65, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
39 38 0.58
40 27 0.42
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.45
Consensus pattern (40 bp):
TTGGATTAGCTCTTATGAGCTTCTATCTGGCGTGTTTCAA
Found at i:95378816 original size:16 final size:16
Alignment explanation
Indices: 95378797--95378853 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 16
95378787 TGAATTGATG
95378797 ATTATTTTGATGTATA
1 ATTATTTTGATGTATA
*
95378813 ATTATATATTTGAAT-TGATT
1 A-T-TAT-TTTG-ATGT-ATA
95378833 ATTATTTTGATGTATA
1 ATTATTTTGATGTATA
95378849 ATTAT
1 ATTAT
95378854 ATATACTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 10 0.30
17 6 0.18
18 6 0.18
19 6 0.18
20 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (16 bp):
ATTATTTTGATGTATA
Found at i:95378837 original size:36 final size:36
Alignment explanation
Indices: 95378786--95378857 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
95378776 AATTGATGAG
95378786 TTGAATTGATGATTATTTTGATGTATAATTATATAT
1 TTGAATTGATGATTATTTTGATGTATAATTATATAT
*
95378822 TTGAATTGATTATTATTTTGATGTATAATTATATAT
1 TTGAATTGATGATTATTTTGATGTATAATTATATAT
95378858 ACTTGTGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (36 bp):
TTGAATTGATGATTATTTTGATGTATAATTATATAT
Found at i:95382785 original size:37 final size:37
Alignment explanation
Indices: 95382744--95382821 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
95382734 AACCTTTAGT
*
95382744 TCGGGGCTTACCTGGACAAAATCTCCACACGTAGTCA
1 TCGGGGCTTACCCGGACAAAATCTCCACACGTAGTCA
* *
95382781 TCGGGTCTTACCCGGACATAATCTCCACACGTAGTCA
1 TCGGGGCTTACCCGGACAAAATCTCCACACGTAGTCA
95382818 TCGG
1 TCGG
95382822 ACCTTTAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (37 bp):
TCGGGGCTTACCCGGACAAAATCTCCACACGTAGTCA
Found at i:95383015 original size:47 final size:47
Alignment explanation
Indices: 95382944--95383361 Score: 773
Period size: 47 Copynumber: 8.9 Consensus size: 47
95382934 CTCTTCGGGA
* * * * * *
95382944 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
95382991 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95383038 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95383085 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95383132 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95383179 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95383226 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95383273 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
95383320 CTTATCACATATATACACTTTCACATTCATCACATCGGCCAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCAT
95383362 GTTCTATTTG
Statistics
Matches: 363, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 363 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:95385875 original size:40 final size:40
Alignment explanation
Indices: 95385818--95385901 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
95385808 TGTTATACTC
* *
95385818 TCTGTTTGGCGTGTTTCGGTTGGATTAGCTCTTATGAGCT
1 TCTGTTTGGCGTATTTCGGTTGAATTAGCTCTTATGAGCT
95385858 TCTGTTTGGCGTATTTCGGTTGAATTAGCTCTTATGAGCT
1 TCTGTTTGGCGTATTTCGGTTGAATTAGCTCTTATGAGCT
95385898 TCTG
1 TCTG
95385902 CCTGGTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.45
Consensus pattern (40 bp):
TCTGTTTGGCGTATTTCGGTTGAATTAGCTCTTATGAGCT
Found at i:95387500 original size:28 final size:29
Alignment explanation
Indices: 95387459--95387521 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
95387449 AGGAAGCGTC
*
95387459 CTGGTGGCTATGCCACAAATTATCTAT-T
1 CTGGTGGCTATGCCACAAAATATCTATAT
*
95387487 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTATAT
95387516 CTGGTG
1 CTGGTG
95387522 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.03
28 23 0.74
29 7 0.23
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTATAT
Found at i:95387532 original size:29 final size:28
Alignment explanation
Indices: 95387469--95387532 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
95387459 CTGGTGGCTA
* *
95387469 TGCCACAAATTATCTATTCTGGTGGCAC
1 TGCCACAAAATATCTATTCTGGTGACAC
* *
95387497 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTAT-TCTGGTGACAC
*
95387526 TGTCACA
1 TGCCACA
95387533 TTTTTTATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTATTCTGGTGACAC
Found at i:95399062 original size:24 final size:24
Alignment explanation
Indices: 95399035--95399088 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
95399025 TGGAAGGTAT
*
95399035 GTATATATGTGTTTATGTGTATAA
1 GTATATATGTGTTCATGTGTATAA
* *
95399059 GTATGTATGTGTTCATGTGTATAT
1 GTATATATGTGTTCATGTGTATAA
95399083 GTATAT
1 GTATAT
95399089 GAAGGTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (24 bp):
GTATATATGTGTTCATGTGTATAA
Found at i:95403261 original size:24 final size:24
Alignment explanation
Indices: 95403199--95403264 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
95403189 GTTATCTATG
**
95403199 ATGCCTTTGTGGCGCATTTGATAA
1 ATGCCTTTGTGGCATATTTGATAA
*
95403223 ATGCCTTTGTGGCATATTTGGTAA
1 ATGCCTTTGTGGCATATTTGATAA
*
95403247 ATGCATTTGTGGCATATT
1 ATGCCTTTGTGGCATATT
95403265 CTATGTTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (24 bp):
ATGCCTTTGTGGCATATTTGATAA
Found at i:95404180 original size:100 final size:100
Alignment explanation
Indices: 95404007--95404206 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
95403997 TGGTTCAAAG
95404007 AGAAAAGAAATATAGATATTGTCTGGTAAGATTTAGAGTCAGGCAAATAGTAAAGTGAGTGTTGA
1 AGAAAAGAAATATAGATATTGTCTGGTAAGATTTAGAGTCAGGCAAATAGTAAAGTGAGTGTTGA
95404072 AACATTAAGTATGGTAGATGACGTATAAGTATATT
66 AACATTAAGTATGGTAGATGACGTATAAGTATATT
95404107 AGAAAAGAAATATAGATATTGTCTGGTAAGATTTAGAGTCAGGCAAATAGTAAAGTGAGTGTTGA
1 AGAAAAGAAATATAGATATTGTCTGGTAAGATTTAGAGTCAGGCAAATAGTAAAGTGAGTGTTGA
95404172 AACATTAAGTATGGTAGATGACGTATAAGTATATT
66 AACATTAAGTATGGTAGATGACGTATAAGTATATT
95404207 TATCCAATAT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (100 bp):
AGAAAAGAAATATAGATATTGTCTGGTAAGATTTAGAGTCAGGCAAATAGTAAAGTGAGTGTTGA
AACATTAAGTATGGTAGATGACGTATAAGTATATT
Found at i:95405145 original size:37 final size:37
Alignment explanation
Indices: 95405085--95405162 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
95405075 TATTATGAAG
* * *
95405085 TCTTACCCAGACATAATCTCCACACGAAGTTATCGGA
1 TCTTACCCAGACAAAATCCCCACACGAAGTCATCGGA
* * *
95405122 TCTTACCCGGACAAAATCCCCACACGTAGTCATCGGG
1 TCTTACCCAGACAAAATCCCCACACGAAGTCATCGGA
95405159 TCTT
1 TCTT
95405163 TAGAGCTCGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.24
Consensus pattern (37 bp):
TCTTACCCAGACAAAATCCCCACACGAAGTCATCGGA
Found at i:95405407 original size:49 final size:48
Alignment explanation
Indices: 95405281--95405421 Score: 214
Period size: 47 Copynumber: 3.0 Consensus size: 48
95405271 CCCTTCGGGA
* * * *
95405281 CTTATCACATT-TATACACTTTCACATCCATCACGTTGGCTATTAGGC
1 CTTATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
95405328 CTTATCAC-GTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGC
95405375 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAG
1 CTTATCACAT-TATATACACTTTCACATTCATCACATCGGCCATTAG
95405422 TGTGACAGCC
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
46 1 0.01
47 48 0.56
49 36 0.42
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (48 bp):
CTTATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:95407025 original size:29 final size:28
Alignment explanation
Indices: 95406989--95407066 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
95406979 TCATGAGATT
95406989 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
95407019 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
95407046 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
95407067 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:95407219 original size:29 final size:29
Alignment explanation
Indices: 95407168--95407235 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
95407158 GCGGAAAAGG
95407168 TAAGTGTGCGAATTTGAAATGCATGGCAC
1 TAAGTGTGCGAATTTGAAATGCATGGCAC
* *
95407197 TAAGTGTGTGAGTTT-AAAGTGCATGGCAC
1 TAAGTGTGCGAATTTGAAA-TGCATGGCAC
95407226 TAAGTGTGCG
1 TAAGTGTGCG
95407236 TGGTTGATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 3 0.09
29 32 0.91
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.29
Consensus pattern (29 bp):
TAAGTGTGCGAATTTGAAATGCATGGCAC
Found at i:95407284 original size:174 final size:174
Alignment explanation
Indices: 95407019--95407346 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
95407009 AAATTGTACA
95407019 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
* * *
95407084 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
95407149 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAATTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAATTTGAAATGCATG
* *
95407193 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
*
95407258 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
95407323 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
95407347 ACCTTGAGTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAATTTGAAATGCATG
Found at i:95409187 original size:237 final size:237
Alignment explanation
Indices: 95408772--95409228 Score: 905
Period size: 237 Copynumber: 1.9 Consensus size: 237
95408762 GTTACAACAC
*
95408772 ATATACACTTTCACATTCATCACGTCGGCTATTAGGCCTTATCACACATATACACTCTCTTGGCT
1 ATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTCTCTTGGCT
95408837 GAATCTACATCTATCATTTTCCAATATCACAATTTAGAATTCACGTATGGGTTTAATCGATAGCT
66 GAATCTACATCTATCATTTTCCAATATCACAATTTAGAATTCACGTATGGGTTTAATCGATAGCT
95408902 TATGAGCAACTAGAACAAGTTTATCAAGGTTTACAACACAATCTCAAATTCAGCACAAGCTGTTT
131 TATGAGCAACTAGAACAAGTTTATCAAGGTTTACAACACAATCTCAAATTCAGCACAAGCTGTTT
95408967 TTCCTCAGCAATAGTCACTAAATAAGTTAGGCCTTATTACAT
196 TTCCTCAGCAATAGTCACTAAATAAGTTAGGCCTTATTACAT
95409009 ATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTCTCTTGGCT
1 ATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTCTCTTGGCT
95409074 GAATCTACATCTATCATTTTCCAATATCACAATTTAGAATTCACGTATGGGTTTAATCGATAGCT
66 GAATCTACATCTATCATTTTCCAATATCACAATTTAGAATTCACGTATGGGTTTAATCGATAGCT
95409139 TATGAGCAACTAGAACAAGTTTATCAAGGTTTACAACACAATCTCAAATTCAGCACAAGCTGTTT
131 TATGAGCAACTAGAACAAGTTTATCAAGGTTTACAACACAATCTCAAATTCAGCACAAGCTGTTT
95409204 TTCCTCAGCAATAGTCACTAAATAA
196 TTCCTCAGCAATAGTCACTAAATAA
95409229 TTTATAACTG
Statistics
Matches: 219, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 219 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (237 bp):
ATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTCTCTTGGCT
GAATCTACATCTATCATTTTCCAATATCACAATTTAGAATTCACGTATGGGTTTAATCGATAGCT
TATGAGCAACTAGAACAAGTTTATCAAGGTTTACAACACAATCTCAAATTCAGCACAAGCTGTTT
TTCCTCAGCAATAGTCACTAAATAAGTTAGGCCTTATTACAT
Found at i:95409482 original size:68 final size:68
Alignment explanation
Indices: 95409371--95409506 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
95409361 TTCCCCTGTT
* * *
95409371 CCACTGTTTGACTAATCTGACCACTCTTCAGTACGAATAAAATTTCTCATTTTACAGGATTCAAA
1 CCACTATTTGACTAATCTGACCACTCTTCACTACGAATAAAATTTCTCATTTTACAGAATTCAAA
95409436 ATG
66 ATG
* *
95409439 CCACTATTTGACTACTCTGACCACTCTTCACTACGAATCAAATTTCTCATTTTACAGAATTCAAA
1 CCACTATTTGACTAATCTGACCACTCTTCACTACGAATAAAATTTCTCATTTTACAGAATTCAAA
95409504 ATG
66 ATG
95409507 TGTTGTATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (68 bp):
CCACTATTTGACTAATCTGACCACTCTTCACTACGAATAAAATTTCTCATTTTACAGAATTCAAA
ATG
Found at i:95412910 original size:42 final size:42
Alignment explanation
Indices: 95412852--95412963 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
95412842 AGGAAACTCG
* * *
95412852 CACACTCAGTGCCAAATAAATAGCCGAAGTTGTATCAATCTCA
1 CACACTAAGTG-CAAATAAATAGCCGAAGCTATATCAATCTCA
* * * * * *
95412895 CACATTGAGTGCAAATATATAGCTGAAGCTATCTCGATCTCA
1 CACACTAAGTGCAAATAAATAGCCGAAGCTATATCAATCTCA
* *
95412937 CACACTAAGTGCACATAATTAGCCGAA
1 CACACTAAGTGCAAATAAATAGCCGAA
95412964 TCATCGTCGA
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
42 46 0.84
43 9 0.16
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (42 bp):
CACACTAAGTGCAAATAAATAGCCGAAGCTATATCAATCTCA
Found at i:95414665 original size:16 final size:18
Alignment explanation
Indices: 95414644--95414676 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
95414634 CATACTAGCT
95414644 CCAAAAT-ATAG-TAGTA
1 CCAAAATGATAGATAGTA
95414660 CCAAAATGATAGATAGT
1 CCAAAATGATAGATAGT
95414677 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (18 bp):
CCAAAATGATAGATAGTA
Found at i:95415234 original size:41 final size:43
Alignment explanation
Indices: 95415160--95415311 Score: 136
Period size: 41 Copynumber: 3.6 Consensus size: 43
95415150 TTTATCAAAT
* * * *
95415160 CACCGGCATTTAGCCTACTAGGTTTTAAACCCGAAT-TCA-TC
1 CACCGGCATTTAGCCTGCTAGGCTTGAAGCCCGAATATCATTC
* * *
95415201 CACCGGCATTTCGCCTGCTAGGCTCGAAGCCCG-ATATCATTT
1 CACCGGCATTTAGCCTGCTAGGCTTGAAGCCCGAATATCATTC
*
95415243 CACTGGCATTATAGCCTGCTAGGCTTGAAGGCCCGAATAGT-A-TC
1 CACCGGCATT-TAGCCTGCTAGGCTTGAA-GCCCGAATA-TCATTC
*
95415287 TCACC-GCATTATAGCCTGGTAGGCT
1 -CACCGGCATT-TAGCCTGCTAGGCT
95415312 CAAAGGCCCA
Statistics
Matches: 91, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.02
41 30 0.33
42 10 0.11
43 16 0.18
44 25 0.27
45 7 0.08
46 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (43 bp):
CACCGGCATTTAGCCTGCTAGGCTTGAAGCCCGAATATCATTC
Found at i:95415361 original size:45 final size:45
Alignment explanation
Indices: 95415201--95415373 Score: 212
Period size: 44 Copynumber: 3.9 Consensus size: 45
95415191 CGAATTCATC
* * *
95415201 CACCGGCATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATTT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCT
* **
95415243 CACTGGCATTATAGCCTGCTAGGCTTGAAGGCCCGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
* *
95415288 CACC-GCATTATAGCCTGGTAGGCTCAAAGGCCCAAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
* *
95415332 CACCGGCATCATAGCCTACTAGGCTCAAAGGCCCGAATAGTA
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
95415374 CCATACGATA
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
42 9 0.08
43 16 0.14
44 45 0.40
45 42 0.37
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (45 bp):
CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
Found at i:95425103 original size:15 final size:15
Alignment explanation
Indices: 95425083--95425113 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
95425073 ATTTATTACA
95425083 AATTTACTCTTTCAC
1 AATTTACTCTTTCAC
95425098 AATTTACTCTTTCAC
1 AATTTACTCTTTCAC
95425113 A
1 A
95425114 CATCTTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTACTCTTTCAC
Found at i:95425701 original size:26 final size:26
Alignment explanation
Indices: 95425672--95425731 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
95425662 TCCCTTTGAA
* * *
95425672 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
95425698 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
95425726 CCATTC
1 TCATTC
95425732 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:95425717 original size:28 final size:28
Alignment explanation
Indices: 95425686--95425748 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
95425676 TCGATATTTT
*
95425686 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
95425714 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
95425742 GTACACT
1 GCACACT
95425749 GAGTACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:95430166 original size:30 final size:31
Alignment explanation
Indices: 95430142--95430199 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
95430132 AGCTCCTATC
*
95430142 AGCTCACTTGAGTTTATTTT-AGCTCATACG
1 AGCTCAATTGAGTTTATTTTCAGCTCATACG
* *
95430172 AGCTCAATTTAGTTTCTTTTCAGCTCAT
1 AGCTCAATTGAGTTTATTTTCAGCTCAT
95430200 TTCTTTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (31 bp):
AGCTCAATTGAGTTTATTTTCAGCTCATACG
Found at i:95439620 original size:30 final size:28
Alignment explanation
Indices: 95439569--95439627 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 28
95439559 TAAAAGCTAC
95439569 ATGAATGCATGAAACATATAAAAATCAAA
1 ATGAATGCATGAAACATATAAAAAT-AAA
95439598 ATGAATGATCATGAAA-ATATAAAAATAAA
1 ATGAATG--CATGAAACATATAAAAATAAA
95439627 A
1 A
95439628 GGTTGGAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (28 bp):
ATGAATGCATGAAACATATAAAAATAAA
Found at i:95445056 original size:24 final size:24
Alignment explanation
Indices: 95445010--95445058 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
95445000 CCACAAGGCT
**
95445010 TCATCCAACCTCACTGATCAATCC
1 TCATCCAACCTCACTGAAAAATCC
95445034 TCATCCAACCTCACTGAAAAATCC
1 TCATCCAACCTCACTGAAAAATCC
95445058 T
1 T
95445059 TATAGTTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.39, G:0.04, T:0.24
Consensus pattern (24 bp):
TCATCCAACCTCACTGAAAAATCC
Found at i:95449366 original size:20 final size:17
Alignment explanation
Indices: 95449327--95449361 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
95449317 GTAAGTCATT
95449327 TTTGACTCGGTTTTTAA
1 TTTGACTCGGTTTTTAA
95449344 TTTGACTCGGTTTTTAA
1 TTTGACTCGGTTTTTAA
95449361 T
1 T
95449362 AATTTCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTGACTCGGTTTTTAA
Found at i:95451674 original size:16 final size:16
Alignment explanation
Indices: 95451653--95451684 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
95451643 ATTGTAACGC
95451653 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
95451669 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
95451685 TCATGAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.38, G:0.06, T:0.06
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:95452408 original size:63 final size:63
Alignment explanation
Indices: 95452341--95452468 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
95452331 TGATCCATTG
*
95452341 TTAGTTAGCCGACTTCTTCTTGATTCCCTTGGTGCCAGATAAACCTTGTTCATCATACTAAGT
1 TTAGTTAGCCGACTTCTTCTTGATTCCATTGGTGCCAGATAAACCTTGTTCATCATACTAAGT
*
95452404 TTAGTTAGCCGATTTCTTCTTGATTCCATTGGTGCCAGATAAACCTTGTTCATCATACTAAGT
1 TTAGTTAGCCGACTTCTTCTTGATTCCATTGGTGCCAGATAAACCTTGTTCATCATACTAAGT
95452467 TT
1 TT
95452469 GGAAACCGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (63 bp):
TTAGTTAGCCGACTTCTTCTTGATTCCATTGGTGCCAGATAAACCTTGTTCATCATACTAAGT
Found at i:95453632 original size:53 final size:52
Alignment explanation
Indices: 95453552--95453657 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 52
95453542 GCGTGTCCCT
95453552 GCCGAGCCCAAGTTGAGTCCAATTTGGAAAAAGGCTAATTTTGAGGGCTCTTA
1 GCCGAGCCCAAGTTGAGTCCAATTTGG-AAAAGGCTAATTTTGAGGGCTCTTA
95453605 GCCGAGCCCAAGTTGAGTCCAATTTGGAAAAGGCTAATTTTGAGGGCTCTTA
1 GCCGAGCCCAAGTTGAGTCCAATTTGGAAAAGGCTAATTTTGAGGGCTCTTA
95453657 G
1 G
95453658 GCATTCCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 26 0.49
53 27 0.51
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (52 bp):
GCCGAGCCCAAGTTGAGTCCAATTTGGAAAAGGCTAATTTTGAGGGCTCTTA
Found at i:95469698 original size:49 final size:49
Alignment explanation
Indices: 95469605--95469703 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
95469595 TAGAGGTAGG
* *
95469605 TATTGAGATAGCTTCAGCTACATATATATTGGCACTTCGGGTGCAAGAT
1 TATTGAGATAGCTTCAGCTACATATATATTGGAACTTAGGGTGCAAGAT
* * * * **
95469654 TATTGAGATAGCTTCGGCTATATTTTTATTGGAACTTATTGTGCAAGAT
1 TATTGAGATAGCTTCAGCTACATATATATTGGAACTTAGGGTGCAAGAT
95469703 T
1 T
95469704 CCCAGGTGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (49 bp):
TATTGAGATAGCTTCAGCTACATATATATTGGAACTTAGGGTGCAAGAT
Found at i:95475036 original size:6 final size:6
Alignment explanation
Indices: 95474995--95475035 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
95474985 GTTAAGGTGA
* *
95474995 GGTTTC GGTTTC GGTTTC GGTTTC GGTTTT GGTTTT GGTTT
1 GGTTTC GGTTTC GGTTTC GGTTTC GGTTTC GGTTTC GGTTT
95475036 TTGGGTAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.10, G:0.34, T:0.56
Consensus pattern (6 bp):
GGTTTC
Found at i:95475364 original size:19 final size:18
Alignment explanation
Indices: 95475340--95475384 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
95475330 ATTTGGCCAT
95475340 ATGGGCCACAATGGGCTAA
1 ATGGGCC-CAATGGGCTAA
*
95475359 ATGGGCCCGATGGGCT-A
1 ATGGGCCCAATGGGCTAA
*
95475376 TTGGGCCCA
1 ATGGGCCCA
95475385 TAATAGGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.22, C:0.24, G:0.36, T:0.18
Consensus pattern (18 bp):
ATGGGCCCAATGGGCTAA
Found at i:95475373 original size:18 final size:19
Alignment explanation
Indices: 95475340--95475375 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
95475330 ATTTGGCCAT
95475340 ATGGGCCACAATGGGCTAA
1 ATGGGCCACAATGGGCTAA
*
95475359 ATGGGCC-CGATGGGCTA
1 ATGGGCCACAATGGGCTA
95475376 TTGGGCCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.25, C:0.22, G:0.36, T:0.17
Consensus pattern (19 bp):
ATGGGCCACAATGGGCTAA
Found at i:95475496 original size:29 final size:28
Alignment explanation
Indices: 95475442--95475502 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
95475432 GTGAGCATGA
*
95475442 ATATGAATGTGACTGGGCCTAATGGGCC
1 ATATAAATGTGACTGGGCCTAATGGGCC
* * *
95475470 ATATAAATGTGATTTGGGCCTAGTGGGTC
1 ATATAAATGTGA-CTGGGCCTAATGGGCC
95475499 ATAT
1 ATAT
95475503 TCAAGTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (28 bp):
ATATAAATGTGACTGGGCCTAATGGGCC
Found at i:95475513 original size:29 final size:29
Alignment explanation
Indices: 95475455--95475530 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
95475445 TGAATGTGAC
*
95475455 TGGGCCTAATGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTCATT
* * *
95475484 TGGGCCTAGTGGGTCATATTCAA-GTCATT
1 TGGGCCTAATGGGCCATA-TAAATGTCATT
* *
95475513 TGAGCGTAATGGGCCATA
1 TGGGCCTAATGGGCCATA
95475531 CGAATATGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 35 0.92
30 3 0.08
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTCATT
Found at i:95478406 original size:27 final size:27
Alignment explanation
Indices: 95478358--95478413 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
95478348 AATACTTGAA
*
95478358 ATCATTTCAAGTTTCACATCTCATTTC
1 ATCATTTCAAGTTTCACATCTCATCTC
* **
95478385 ATCATTTCATGTTTCATTTCTCATCTC
1 ATCATTTCAAGTTTCACATCTCATCTC
95478412 AT
1 AT
95478414 ATCCATTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.04, T:0.48
Consensus pattern (27 bp):
ATCATTTCAAGTTTCACATCTCATCTC
Found at i:95479576 original size:13 final size:13
Alignment explanation
Indices: 95479558--95479582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95479548 CTTCTTCTCA
95479558 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
95479571 TTTTCTTTCTTT
1 TTTTCTTTCTTT
95479583 AATGTTTGCA
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Done.