Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008162.1 Hibiscus syriacus cultivar Beakdansim tig00110733_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3688897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:3536504 original size:3 final size:3
Alignment explanation
Indices: 3536496--3536530 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3536486 TATATTTATT
*
3536496 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3536531 AAAAAATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3536538 original size:20 final size:20
Alignment explanation
Indices: 3536498--3536538 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3536488 TATTTATTTA
* *
3536498 ATAATAATAATAATAATAAT
1 ATAATAATAATAAAAAAAAT
*
3536518 ATAATATTAATAAAAAAAAT
1 ATAATAATAATAAAAAAAAT
3536538 A
1 A
3536539 AGATCAAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAATAATAATAAAAAAAAT
Found at i:3553044 original size:24 final size:24
Alignment explanation
Indices: 3553017--3553070 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3553007 TGAAAACCGT
**
3553017 AGCCCAATCACCCCTTTTGTTGTG
1 AGCCCAATCACCCCTGCTGTTGTG
*
3553041 AGCCCAGTCACCCCTGCTGTTGTG
1 AGCCCAATCACCCCTGCTGTTGTG
3553065 A-CCCAA
1 AGCCCAA
3553071 ACACTGCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.19, C:0.37, G:0.19, T:0.26
Consensus pattern (24 bp):
AGCCCAATCACCCCTGCTGTTGTG
Found at i:3560968 original size:20 final size:20
Alignment explanation
Indices: 3560943--3560980 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3560933 TTTGGTTCAC
*
3560943 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
3560963 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
3560981 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:3560983 original size:18 final size:19
Alignment explanation
Indices: 3560943--3560986 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3560933 TTTGGTTCAC
*
3560943 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
3560963 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
3560981 GGAATA
1 GGAATA
3560987 GGATTATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:3567063 original size:20 final size:20
Alignment explanation
Indices: 3567038--3567077 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3567028 TTCAGCACAA
3567038 AAAGATTAACAATACATGTT
1 AAAGATTAACAATACATGTT
3567058 AAAGATTAACAATACATGTT
1 AAAGATTAACAATACATGTT
3567078 CCTCTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AAAGATTAACAATACATGTT
Found at i:3567342 original size:19 final size:21
Alignment explanation
Indices: 3567315--3567363 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
3567305 CACTAATTTT
*
3567315 TTATT-TTATTTTTA-AT-TA
1 TTATTATTATTATTATATATA
3567333 TTATTATTATTATTATATATA
1 TTATTATTATTATTATATATA
3567354 TATATTATTA
1 T-TATTATTA
3567364 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.19
19 8 0.31
20 2 0.08
21 3 0.12
22 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTATTATTATTATATATA
Found at i:3569925 original size:158 final size:158
Alignment explanation
Indices: 3569687--3569989 Score: 534
Period size: 158 Copynumber: 1.9 Consensus size: 158
3569677 ATTAATGATT
* * *
3569687 TAAAATAATTTAATTAATATCGTTAAATAATAAAATAATAATTTATCACTTAAATCAACTTCGAA
1 TAAAACAATTTAATTAATATCATTAAATAATAAAATAATAATTTATCACTTAAATCAACTTCAAA
*
3569752 TGTAAGCAACATCTAGGCCGTTTGATGTTGTTTCATAATATTTATAAAATTGCCTAAACACTACT
66 TGTAAGCAACATCTAGGCAGTTTGATGTTGTTTCATAATATTTATAAAATTGCCTAAACACTACT
3569817 CAACTTTTTTATATATATAAAAAACTGC
131 CAACTTTTTTATATATATAAAAAACTGC
*
3569845 TAAAACAATTTAATTAATATCATTAAATAATAAAATAATAATTTATCAGTTAAATCAACTTCAAA
1 TAAAACAATTTAATTAATATCATTAAATAATAAAATAATAATTTATCACTTAAATCAACTTCAAA
* * *
3569910 TTTAAGCAACATCTAGGCAGTTTGATGTTGTTTCATAATATTTATAAAATTGCCTAAACATTATT
66 TGTAAGCAACATCTAGGCAGTTTGATGTTGTTTCATAATATTTATAAAATTGCCTAAACACTACT
3569975 CAACTTTTTTATATA
131 CAACTTTTTTATATA
3569990 AAAACACTGC
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
158 137 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (158 bp):
TAAAACAATTTAATTAATATCATTAAATAATAAAATAATAATTTATCACTTAAATCAACTTCAAA
TGTAAGCAACATCTAGGCAGTTTGATGTTGTTTCATAATATTTATAAAATTGCCTAAACACTACT
CAACTTTTTTATATATATAAAAAACTGC
Found at i:3571711 original size:22 final size:23
Alignment explanation
Indices: 3571685--3571745 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
3571675 CAAACGACCA
3571685 AAAATGTGTCAAAAGACATA-AG
1 AAAATGTGTCAAAAGACATAGAG
*
3571707 AAAATATGT-AATAA-ACATAGAG
1 AAAATGTGTCAA-AAGACATAGAG
3571729 AAAATGTGTCATAAAGA
1 AAAATGTGTCA-AAAGA
3571746 TAGAGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 7 0.22
22 20 0.62
23 3 0.09
24 2 0.06
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (23 bp):
AAAATGTGTCAAAAGACATAGAG
Found at i:3572821 original size:43 final size:43
Alignment explanation
Indices: 3572774--3572940 Score: 165
Period size: 43 Copynumber: 3.9 Consensus size: 43
3572764 TGTTATCGAA
* * *
3572774 AAACGCCGTAATAGCTGTTGATATTTAGCGGCATTTGTCTTAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTGTCTCAC
* * * * *
3572817 AAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTGTCTCAC
** * * * *
3572860 AAACGCCATAGTAGGTGTTGATATTTAGAGGCGCTTT-TATCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGC-ATTTGTCTCAC
* * *
3572903 AAATGCCGCAATAAGTGTTGAGATTTAGCGGCATTTGT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTGT
3572941 AACAAAAAAT
Statistics
Matches: 97, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
42 3 0.03
43 91 0.94
44 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTGTCTCAC
Found at i:3572930 original size:86 final size:86
Alignment explanation
Indices: 3572774--3572934 Score: 200
Period size: 86 Copynumber: 1.9 Consensus size: 86
3572764 TGTTATCGAA
* * * * * *
3572774 AAACGCCGTAATAGCTGTTGATATTTAGCGGCATTTGTCTTACAAACGCCGCAATAGGTGTTGTT
1 AAACGCCATAATAGCTGTTGATATTTAGAGGCATTTGTATCACAAACGCCGCAATAAGTGTTGTA
3572839 GTTTAGCGGCGTTTTTCCCAC
66 GTTTAGCGGCGTTTTTCCCAC
* * * *
3572860 AAACGCCATAGTAGGTGTTGATATTTAGAGGCGCTTT-TATCACAAATGCCGCAATAAGTGTTG-
1 AAACGCCATAATAGCTGTTGATATTTAGAGGC-ATTTGTATCACAAACGCCGCAATAAGTGTTGT
3572923 AGATTTAGCGGC
65 AG-TTTAGCGGC
3572935 ATTTGTAACA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 1 0.02
86 59 0.94
87 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (86 bp):
AAACGCCATAATAGCTGTTGATATTTAGAGGCATTTGTATCACAAACGCCGCAATAAGTGTTGTA
GTTTAGCGGCGTTTTTCCCAC
Found at i:3573024 original size:44 final size:43
Alignment explanation
Indices: 3572974--3573085 Score: 136
Period size: 44 Copynumber: 2.6 Consensus size: 43
3572964 ATACATTTAA
*
3572974 CGGCGTTTTTAGGATACAAACGCCGCGAAAGGT-TCGGTATATTG
1 CGGCGTTTTTA-GATACAAACGCCGCGAAAGGTCT-GGTATATAG
* * *
3573018 CGGCGTTTTTAGACTACAAATGCCGCTAACGGTCTGGTATATAG
1 CGGCGTTTTTAGA-TACAAACGCCGCGAAAGGTCTGGTATATAG
* *
3573062 CGGCGTTTTTTGTTACAAACGCCG
1 CGGCGTTTTTAGATACAAACGCCG
3573086 AAAAATAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
43 12 0.20
44 46 0.78
45 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (43 bp):
CGGCGTTTTTAGATACAAACGCCGCGAAAGGTCTGGTATATAG
Found at i:3575213 original size:41 final size:40
Alignment explanation
Indices: 3575168--3575316 Score: 140
Period size: 41 Copynumber: 3.6 Consensus size: 40
3575158 AACTACTGCG
* *
3575168 GCGTTTATTAAAAAAAGCCACTAACGAATAAAACAATTGC
1 GCGTTTATTAAAAAACGCCACTAACGAAGAAAACAATTGC
* *
3575208 AGCGTTTATTACGAAAACGCCAC-AACGGAGAAAACAATTGC
1 -GCGTTTATTA-AAAAACGCCACTAACGAAGAAAACAATTGC
* * *
3575249 GACGTTTATTAAGAAAACGCCACTAA-AAGAGAAAATAATTAC
1 G-CGTTTATTAA-AAAACGCCACTAACGA-AGAAAACAATTGC
* *
3575291 GGCATTTATTTAAAAAATGCCACTAA
1 -GCGTTTA-TTAAAAAACGCCACTAA
3575317 ATTACAACTC
Statistics
Matches: 90, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
40 1 0.01
41 45 0.50
42 39 0.43
43 5 0.06
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (40 bp):
GCGTTTATTAAAAAACGCCACTAACGAAGAAAACAATTGC
Found at i:3575299 original size:42 final size:42
Alignment explanation
Indices: 3575212--3575317 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
3575202 AATTGCAGCG
* ** * *
3575212 TTTATTACGAAAACGCCAC-AACGGAGAAAACAATTGCGACG
1 TTTATTAAGAAAACGCCACTAAAAGAGAAAACAATTACGACA
* *
3575253 TTTATTAAGAAAACGCCACTAAAAGAGAAAATAATTACGGCA
1 TTTATTAAGAAAACGCCACTAAAAGAGAAAACAATTACGACA
*
3575295 TTTATTTAA-AAAATGCCACTAAA
1 TTTA-TTAAGAAAACGCCACTAAA
3575318 TTACAACTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 18 0.33
42 33 0.60
43 4 0.07
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (42 bp):
TTTATTAAGAAAACGCCACTAAAAGAGAAAACAATTACGACA
Found at i:3576868 original size:43 final size:40
Alignment explanation
Indices: 3576819--3576909 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
3576809 CATGTTTTTG
*
3576819 CGGCGTTTATACAAAAAAACGCCACTATTGATTAATACTATTA
1 CGGCGTTTAT-C--AAAAACGCCACTATTGATTAACACTATTA
* * *
3576862 TGGCGTTTGTCAAAAATGCCACTATTGATTAACACTATTA
1 CGGCGTTTATCAAAAACGCCACTATTGATTAACACTATTA
3576902 CGGCGTTT
1 CGGCGTTT
3576910 GAGGAATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 34 0.79
42 1 0.02
43 8 0.19
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (40 bp):
CGGCGTTTATCAAAAACGCCACTATTGATTAACACTATTA
Found at i:3576888 original size:40 final size:40
Alignment explanation
Indices: 3576833--3576910 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
3576823 GTTTATACAA
* *
3576833 AAAAACGCCACTATTGATTAATACTATTATGGCGTTTGTC
1 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTC
*
3576873 AAAAATGCCACTATTGATTAACACTATTACGGCGTTTG
1 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTG
3576911 AGGAATAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (40 bp):
AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTC
Found at i:3576981 original size:42 final size:42
Alignment explanation
Indices: 3576903--3576984 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
3576893 ACACTATTAC
* *
3576903 GGCGTTTGAGGAATAAACGCCGCTCTATGTATACTCTATTGT
1 GGCGTTTGAGGAATAAACGCCACTCAATGTATACTCTATTGT
* * *
3576945 GGCGTTTGTGGTATAAACGCCACT-AATTTATCACTCTATT
1 GGCGTTTGAGGAATAAACGCCACTCAATGTAT-ACTCTATT
3576985 CCGGTGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 5 0.15
42 29 0.85
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (42 bp):
GGCGTTTGAGGAATAAACGCCACTCAATGTATACTCTATTGT
Found at i:3579769 original size:29 final size:30
Alignment explanation
Indices: 3579737--3579796 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
3579727 TAATGATGTT
3579737 TGGGATTATTT-TTCTAATAAAATAATAAA
1 TGGGATTATTTATTCTAATAAAATAATAAA
*
3579766 TGGGATTTTTTATTCTAATAAAATAATAAA
1 TGGGATTATTTATTCTAATAAAATAATAAA
3579796 T
1 T
3579797 AGAAAGTCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (30 bp):
TGGGATTATTTATTCTAATAAAATAATAAA
Found at i:3580528 original size:2 final size:2
Alignment explanation
Indices: 3580521--3580554 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3580511 AGAAAAACAA
3580521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3580555 GCCAACATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3586934 original size:21 final size:21
Alignment explanation
Indices: 3586896--3586936 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3586886 TTTTAAAAAT
*
3586896 AATAATATTAATTTTTATATG
1 AATAATATTAATTATTATATG
3586917 AATAATATT-ATCTATTATAT
1 AATAATATTAAT-TATTATAT
3586937 TTTATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AATAATATTAATTATTATATG
Found at i:3588153 original size:17 final size:18
Alignment explanation
Indices: 3588113--3588154 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3588103 GTTATTTTTA
*
3588113 AAATAAAAGATAAGAATT
1 AAATAAAAGATAACAATT
*
3588131 ATATAAAAGA-AACAATT
1 AAATAAAAGATAACAATT
3588148 AAATAAA
1 AAATAAA
3588155 TAATTTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAACAATT
Found at i:3599406 original size:19 final size:20
Alignment explanation
Indices: 3599362--3599406 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3599352 ATTTGTTTTT
*
3599362 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
3599382 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
3599401 AATAAA
1 AATAAA
3599407 ATATTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:3599435 original size:14 final size:13
Alignment explanation
Indices: 3599407--3599442 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
3599397 TCAAAATAAA
3599407 ATATTAAAATAGT
1 ATATTAAAATAGT
*
3599420 ATATTAATATTAGT
1 ATATTAA-AATAGT
3599434 ATATTAAAA
1 ATATTAAAA
3599443 GATAACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
ATATTAAAATAGT
Found at i:3600857 original size:22 final size:22
Alignment explanation
Indices: 3600798--3600864 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
3600788 AATATCTTAA
*
3600798 AATAATTGAAATAATACATTTTAT
1 AATAATT-AAATAATATATTTT-T
*
3600822 AATAATT---TATTATATTTTT
1 AATAATTAAATAATATATTTTT
3600841 AATAATTAAATAATATATTTTT
1 AATAATTAAATAATATATTTTT
3600863 AA
1 AA
3600865 CATTATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 8 0.22
20 9 0.24
22 13 0.35
24 7 0.19
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
AATAATTAAATAATATATTTTT
Found at i:3600877 original size:22 final size:22
Alignment explanation
Indices: 3600832--3600877 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3600822 AATAATTTAT
*
3600832 TATATTTTTAATAATTAAATAA
1 TATATTTTTAATAATTAAAAAA
*
3600854 TATATTTTTAA-CATTATAAAAA
1 TATATTTTTAATAATTA-AAAAA
3600876 TA
1 TA
3600878 AAAATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTTTTAATAATTAAAAAA
Found at i:3605378 original size:14 final size:15
Alignment explanation
Indices: 3605359--3605387 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3605349 TTCGAGAGAA
3605359 AAGAAAAAG-ACAAG
1 AAGAAAAAGAACAAG
3605373 AAGAAAAAGAACAAG
1 AAGAAAAAGAACAAG
3605388 TTCATGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.07, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAACAAG
Found at i:3610099 original size:35 final size:35
Alignment explanation
Indices: 3610053--3610193 Score: 138
Period size: 36 Copynumber: 3.9 Consensus size: 35
3610043 CCTTAGGTCC
* * **
3610053 ATAAGAAATTACCAGCTGATCATTGTTGAACCTAT
1 ATAAGGAATTACCAGCTGATCAGTACTGAACCTAT
* * *
3610088 ATAAGGAATTACCAGCTTGATTAGAACTGAACCTGT
1 ATAAGGAATTACCAGC-TGATCAGTACTGAACCTAT
* * *
3610124 AATAAGGAATTACCAGATGATCGGTACTGAACCTAG
1 -ATAAGGAATTACCAGCTGATCAGTACTGAACCTAT
* * *
3610160 ATAAGGAATTACAAGCTTGTTCAGAACTGAACCT
1 ATAAGGAATTACCAGC-TGATCAGTACTGAACCT
3610194 GCAGATACTT
Statistics
Matches: 85, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
35 29 0.34
36 41 0.48
37 15 0.18
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (35 bp):
ATAAGGAATTACCAGCTGATCAGTACTGAACCTAT
Found at i:3614230 original size:831 final size:832
Alignment explanation
Indices: 3612608--3614267 Score: 2652
Period size: 831 Copynumber: 2.0 Consensus size: 832
3612598 TTAGTTTCTC
* * * *
3612608 ATATTTTTTTATTTTGGTGTCAAGAGATATTTGTTGTTATGGGAAAATTATAGGGCTAGTCCCTG
1 ATATTTTTTAATTTTGGTGTCAAGAGATATTTATTGTCATGGGAAAATTATAGGGCTAATCCCTG
3612673 AACTTCCTAGATTTCCAAAACTAGCCCAAAAGTTTCACAAATTCATAGTTTAGTCCATAAATCAA
66 AACTTCCTAGATTTCCAAAACTAGCCCAAAAGTTTCACAAATTCATAGTTTAGTCCATAAATCAA
*
3612738 TTAATTAATTCTATAAATTATAAACTAAAAAATTTAGGGTTTGACATTAGTTACAGATCATTTGA
131 TTAATTAATTCTATAAATTATAAACTAAAAAATTTAGGGTTTGACATTAGTTACAGATAATTTGA
* * *
3612803 GTCACATTCTACTTTCTTTAGCCGATTCGCCGCTTCAAGAAGAGTTCTTAGAGGAACATTTGATG
196 GCCACATTCTACTTTCTTTAGCCGATCCGCCGCTTCAAGAAGAGTTATTAGAGGAACATTTGATG
*
3612868 TTAGCACAGAAGATGGTTCCATGGTTAGCTGATATGGTAAATTATCTGGCCACAGATAAATTACC
261 TTAGCACAGAAGATGGTTCCATGGTTAGCGGATATGGTAAATTATCTGGCCACAGATAAATTACC
*
3612933 ATTAGATTTACCTAGATTTGAAATTAATTGGCTGAAATGAGAATACAATATTATATTTGGAATGA
326 ATTAGATTTACCTAGATTTGAAATTAATTGGCTAAAATGAGAATACAATATTATATTTGGAATGA
* *
3612998 TCCCTATTTGTGGAAATAATTCAAGGATCAATAATTACGCGATGCATCGCTGAAGAAGAGGTAAA
391 TCCCTATTTGTGGAAACAATTCAAGGATCAATAATTACGCGATGCATCACTGAAGAAGAGGTAAA
3613063 CTCCATATTAAATTTGTGTCACTCTTATTCGTGGTGGTCACTTTGGACCAAAGCGTACTACCCAT
456 CTCCATATTAAATTTGTGTCACTCTTATTCGTGGTGGTCACTTTGGACCAAAGCGTACTACCCAT
* * * *
3613128 AAATTTTTGGAATGTGGTTTCTTTTGGCCTACTTTATCCTGTGATGCTTACTTATTTTTAAATCA
521 AAAATTTTGGAATGTGGTTTCTTTTGGCCTACTTTATCCCGTGACGCTCACTTATTTTTAAATCA
* * * * * *
3613193 CGTGAGAAGTGCCAACATATAGGAAATTTAAGCCGAATGAATGAATTTCCTCAAAATTTGATTTA
586 CATGAGAAATGCCAACATACAGGAAATTTAAGCCAAAGGAATGAATTTCCTCAAAATTCGATTTA
* * *
3613258 CGATTGTGAGATTTTTTATGTGTGGGGACTCGATTACGTGGGCCCTTTTACTTTTTTATTTGGAA
651 CGATTATGAGATTTTTTATGTGTGGGGACTCGATTACGTAGGCCCTTTTACTTTTTCATTTGGAA
* * *
3613323 ATATTTACATAACACTTGCTGTTGATTACATTTCAAAATGGGTAAAAACTAAGACTACAAAAAAT
716 ATATTTACATAACACTTGCTGTTGACTACATTTCAAAATAGGTAAAAACCAAGACTACAAAAAAT
* * *
3613388 AATGATGCCAAAACCACTATTAACTCCTTGAAAAATTCTATCTTTTTCATAT
781 AATGATGCCAAAACCACTACTAACTCCTTGAAAAATCCAATCTTTTTCATAT
3613440 ATATTTTTTAATTTTGGTGTCAAGAGATATTTATTGTCATGGGAAAATTATAGGGCTAATCCCTG
1 ATATTTTTTAATTTTGGTGTCAAGAGATATTTATTGTCATGGGAAAATTATAGGGCTAATCCCTG
* *
3613505 AATTTCCTAGATTTTC-AAACTAGCCCAAAAGTTTCACAAATTCATAGTTTAGTCCATAAATCAA
66 AACTTCCTAGATTTCCAAAACTAGCCCAAAAGTTTCACAAATTCATAGTTTAGTCCATAAATCAA
* * *
3613569 TTAATTAATTCTATAAATTTTAAACT-AAAAA-TTGGGAGTTTGACA-TAGTTGCAGATAATTTG
131 TTAATTAATTCTATAAATTATAAACTAAAAAATTTAGG-GTTTGACATTAGTTACAGATAATTTG
* *
3613631 AGCCACATTCTACTTTCTTTAGCCGATCCTCCGCTTCGAGAAGAGTTATTAGAGGAACATTTGAT
195 AGCCACATTCTACTTTCTTTAGCCGATCCGCCGCTTCAAGAAGAGTTATTAGAGGAACATTTGAT
* *
3613696 GTTGGCACAGAAGATGGTTCCATGGTTAGCGGATATGGTAAATTATCTGGCCACAGATAAATTAT
260 GTTAGCACAGAAGATGGTTCCATGGTTAGCGGATATGGTAAATTATCTGGCCACAGATAAATTAC
* * * *
3613761 CTTTAGATTTGCCTAGATTTGAAATTAATTGGCTAAAATGGGAATACCAATATTATATTTGGGAT
325 CATTAGATTTACCTAGATTTGAAATTAATTGGCTAAAATGAGAATA-CAATATTATATTTGGAAT
* * * * *
3613826 -ATCCCTATTTGTGGAAGCAATGTC-TGGATCAGGTAATTAGGCGTTGCATCACTGAAGAAGAGG
389 GATCCCTATTTGTGGAAACAAT-TCAAGGATCA-ATAATTACGCGATGCATCACTGAAGAAGAGG
*
3613889 TAAACTCCATATTAAAATTTTTGTCACTCTTATTCGTGGTGGTCACTTTGGACCAAAGCGTACTA
452 TAAACTCCATATT-AAATTTGTGTCACTCTTATTCGTGGTGGTCACTTTGGACCAAAGCGTACTA
3613954 CCCATAAAATTTTGGAATGTGGTTTCTTTTGGCCTACTTTATCCCGTGACGCTCACTTATTTTGT
516 CCCATAAAATTTTGGAATGTGGTTTCTTTTGGCCTACTTTATCCCGTGACGCTCACTTATTTT-T
* *
3614019 AAATCACATGAGAAATGCCAACGTGCA-GAGAATTTAAGCCAAAGGAATGAATTTCCTCAAAATT
580 AAATCACATGAGAAATGCCAACATACAGGA-AATTTAAGCCAAAGGAATGAATTTCCTCAAAATT
* *
3614083 CGATTTACGTTTATGAGATTTTTTATGTGTGGGGACTCGATTATGTAGGCCCTTTTACTTTTTCA
644 CGATTTACGATTATGAGATTTTTTATGTGTGGGGACTCGATTACGTAGGCCCTTTTACTTTTTCA
* * ** *
3614148 TTTGGAAATATTTACATCATACTTGCTGTTGACTAC-TTTTTAAATAGGTAGAAACCAAGACTAC
709 TTTGGAAATATTTACATAACACTTGCTGTTGACTACATTTCAAAATAGGTAAAAACCAAGACTAC
**
3614212 CCAAAATAATGATGCCAAAACCACTACTAACTCCTTGAAAAATCCAATCTTTTTCA
774 AAAAAATAATGATGCCAAAACCACTACTAACTCCTTGAAAAATCCAATCTTTTTCA
3614268 AGTTCGGTAC
Statistics
Matches: 760, Mismatches: 61, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
829 208 0.27
830 72 0.09
831 258 0.34
832 222 0.29
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (832 bp):
ATATTTTTTAATTTTGGTGTCAAGAGATATTTATTGTCATGGGAAAATTATAGGGCTAATCCCTG
AACTTCCTAGATTTCCAAAACTAGCCCAAAAGTTTCACAAATTCATAGTTTAGTCCATAAATCAA
TTAATTAATTCTATAAATTATAAACTAAAAAATTTAGGGTTTGACATTAGTTACAGATAATTTGA
GCCACATTCTACTTTCTTTAGCCGATCCGCCGCTTCAAGAAGAGTTATTAGAGGAACATTTGATG
TTAGCACAGAAGATGGTTCCATGGTTAGCGGATATGGTAAATTATCTGGCCACAGATAAATTACC
ATTAGATTTACCTAGATTTGAAATTAATTGGCTAAAATGAGAATACAATATTATATTTGGAATGA
TCCCTATTTGTGGAAACAATTCAAGGATCAATAATTACGCGATGCATCACTGAAGAAGAGGTAAA
CTCCATATTAAATTTGTGTCACTCTTATTCGTGGTGGTCACTTTGGACCAAAGCGTACTACCCAT
AAAATTTTGGAATGTGGTTTCTTTTGGCCTACTTTATCCCGTGACGCTCACTTATTTTTAAATCA
CATGAGAAATGCCAACATACAGGAAATTTAAGCCAAAGGAATGAATTTCCTCAAAATTCGATTTA
CGATTATGAGATTTTTTATGTGTGGGGACTCGATTACGTAGGCCCTTTTACTTTTTCATTTGGAA
ATATTTACATAACACTTGCTGTTGACTACATTTCAAAATAGGTAAAAACCAAGACTACAAAAAAT
AATGATGCCAAAACCACTACTAACTCCTTGAAAAATCCAATCTTTTTCATAT
Found at i:3615115 original size:6 final size:7
Alignment explanation
Indices: 3615113--3615156 Score: 67
Period size: 6 Copynumber: 6.7 Consensus size: 7
3615103 CTATTTTATT
3615113 TTTTTAA
1 TTTTTAA
3615120 TTTTTAA
1 TTTTTAA
3615127 -TTTTAA
1 TTTTTAA
3615133 -TTTTAA
1 TTTTTAA
3615139 TTTTTAA
1 TTTTTAA
3615146 -TTTTAA
1 TTTTTAA
3615152 TTTTT
1 TTTTT
3615157 TAGGTACCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.51
7 17 0.49
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:3615132 original size:13 final size:13
Alignment explanation
Indices: 3615113--3615156 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
3615103 CTATTTTATT
3615113 TTTTTAATTTTTAA
1 TTTTTAA-TTTTAA
3615127 -TTTTAATTTTAA
1 TTTTTAATTTTAA
3615139 TTTTTAATTTTAA
1 TTTTTAATTTTAA
3615152 TTTTT
1 TTTTT
3615157 TAGGTACCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.21
13 23 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTAATTTTAA
Found at i:3615138 original size:19 final size:19
Alignment explanation
Indices: 3615114--3615155 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
3615104 TATTTTATTT
3615114 TTTTAATTTTTAATTTTAA
1 TTTTAATTTTTAATTTTAA
3615133 TTTTAATTTTTAATTTTAA
1 TTTTAATTTTTAATTTTAA
3615152 TTTT
1 TTTT
3615156 TTAGGTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTAATTTTTAATTTTAA
Found at i:3619031 original size:78 final size:77
Alignment explanation
Indices: 3618902--3619063 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 77
3618892 TTAACTAGTG
* *
3618902 TTTATTTTATGCAACATTTTATGCTTAAATACTCCTTTATTGTTCATTATTATTATTGATTTGGG
1 TTTATTTTATGCAACATTTTACGCTTAAATACTCCTTGATTGTTCATTATTATTA-TGATTTGGG
3618967 CATTTTTACATGA
65 CATTTTTACATGA
*
3618980 TTTATTTTATGCAACATTTTACGCTTAAATATTCCTTGATTGTTCATTATTATTATGATTTGGGC
1 TTTATTTTATGCAACATTTTACGCTTAAATACTCCTTGATTGTTCATTATTATTATGATTTGGGC
3619045 ATTTTTACATGA
66 ATTTTTACATGA
3619057 TTTATTT
1 TTTATTT
3619064 GCAGGACAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 29 0.36
78 52 0.64
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.53
Consensus pattern (77 bp):
TTTATTTTATGCAACATTTTACGCTTAAATACTCCTTGATTGTTCATTATTATTATGATTTGGGC
ATTTTTACATGA
Found at i:3621300 original size:29 final size:29
Alignment explanation
Indices: 3621266--3621324 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3621256 AGTCCCTTAT
* * *
3621266 TCTTTTACTCAATAGTGTTTAACCTTTCA
1 TCTTTTACTCAAAAATGTTTAACCATTCA
3621295 TCTTTTACTCAAAAATGTTTAACCATTCA
1 TCTTTTACTCAAAAATGTTTAACCATTCA
3621324 T
1 T
3621325 TTAACTGGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (29 bp):
TCTTTTACTCAAAAATGTTTAACCATTCA
Found at i:3621383 original size:110 final size:109
Alignment explanation
Indices: 3621262--3621516 Score: 361
Period size: 110 Copynumber: 2.3 Consensus size: 109
3621252 AACTAGTCCC
*
3621262 TTATTCTTTTACTCAATAGTGTTTAACCTTTCATCTTTTACTCAAAAATGTTTAACCATTCATTT
1 TTATTCTTTTACTCAAT-GTGTTTAACCTTTCATCTTTTACTCAAAAATGTTTAACCATTCATCT
* * * *
3621327 AACTGGCAAAATTGACACCTTTCTGCCAATTGCACAGTTAGGCCA
65 AACCGGCAAAATTGACACATTTCTGCCAATTACACAATTAGGCCA
* * *
3621372 TTATTCTTTTACTCAACTGTGATTAACCTTTCATCTTTTACTCAAGAGTGTTTAACCATTCATCT
1 TTATTCTTTTACTCAA-TGTGTTTAACCTTTCATCTTTTACTCAAAAATGTTTAACCATTCATCT
*
3621437 AACCGGCATAATTGACACATTTCTGCCAATTACACAATTAGGCCA
65 AACCGGCAAAATTGACACATTTCTGCCAATTACACAATTAGGCCA
* *
3621482 TTATT-TTTTACTAAACGGTGTTTAA-CTGTTCATCT
1 TTATTCTTTTACTCAA-TGTGTTTAACCT-TTCATCT
3621517 AACTGGCATA
Statistics
Matches: 131, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
108 2 0.02
109 24 0.18
110 104 0.79
111 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (109 bp):
TTATTCTTTTACTCAATGTGTTTAACCTTTCATCTTTTACTCAAAAATGTTTAACCATTCATCTA
ACCGGCAAAATTGACACATTTCTGCCAATTACACAATTAGGCCA
Found at i:3621426 original size:29 final size:29
Alignment explanation
Indices: 3621376--3621436 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
3621366 AGGCCATTAT
* *
3621376 TCTTTTACTCAACTGTGATTAACCTTTCA
1 TCTTTTACTCAACAGTGATTAACCATTCA
* *
3621405 TCTTTTACTCAAGAGTGTTTAACCATTCA
1 TCTTTTACTCAACAGTGATTAACCATTCA
3621434 TCT
1 TCT
3621437 AACCGGCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGATTAACCATTCA
Found at i:3621540 original size:80 final size:80
Alignment explanation
Indices: 3621407--3621719 Score: 427
Period size: 80 Copynumber: 3.9 Consensus size: 80
3621397 ACCTTTCATC
** * * *
3621407 TTTTACTCAA-GAGTGTTTAACCATTCATCTAACCGGCATAATTGACACATTTCTGCCAATTACA
1 TTTTACTCAACG-GTGTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCA
3621471 CAATTAGGCCATTATT
65 CAATTAGGCCATTATT
* *
3621487 TTTTACTAAACGGTGTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAATTGCAC
1 TTTTACTCAACGGTGTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
* *
3621552 AAATAGGCAATTATT
66 AATTAGGCCATTATT
* *
3621567 CTTTTACTCAACGGTGTTTAACAGTTCATCTAACTGGCATTATTG--ACCTTTCTGCCAATTGCA
1 -TTTTACTCAACGGTGTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCA
*
3621630 CAGTTAGGCCATTATT
65 CAATTAGGCCATTATT
* * *
3621646 ATTTACTCAACGGTGTTTAACCT-TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
1 TTTTACTCAACGGTGTTTAA-CTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCA
*
3621710 CAGTTAGGCC
65 CAATTAGGCC
3621720 TCAAAGGCAC
Statistics
Matches: 207, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
78 39 0.19
79 31 0.15
80 95 0.46
81 42 0.20
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (80 bp):
TTTTACTCAACGGTGTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
AATTAGGCCATTATT
Found at i:3621696 original size:159 final size:161
Alignment explanation
Indices: 3621405--3621699 Score: 474
Period size: 159 Copynumber: 1.8 Consensus size: 161
3621395 TAACCTTTCA
3621405 TCTTTTACTCAAGAGTGTTTAACCATTCATCTAACCGGCATAATTGACACATTTCTGCCAATTAC
1 TCTTTTACTCAAGAGTGTTTAACCATTCATCTAACCGGCATAATTGACACATTTCTGCCAATTAC
*
3621470 ACAATTAGGCCATTATTTTTTACTAAACGGTGTTTAACTGTTCATCTAACTGGCATAATTGACAC
66 ACAATTAGGCCATTATTATTTACTAAACGGTGTTTAACTGTTCATCTAACTGGCATAATTGACAC
3621535 CTTTCTTCCAATTGCACAAATAGGCAATTAT
131 CTTTCTTCCAATTGCACAAATAGGCAATTAT
* *
3621566 TCTTTTACTCAACG-GTGTTTAA-CAGTTCATCTAACTGGCATTATTGAC-C-TTTCTGCCAATT
1 TCTTTTACTCAA-GAGTGTTTAACCA-TTCATCTAACCGGCATAATTGACACATTTCTGCCAATT
* * *
3621627 GCACAGTTAGGCCATTATTATTTACTCAACGGTGTTTAACCT-TTCATCTAACTGGCATAATTGA
64 ACACAATTAGGCCATTATTATTTACTAAACGGTGTTTAA-CTGTTCATCTAACTGGCATAATTGA
3621691 CACCTTTCT
128 CACCTTTCT
3621700 GTCAAATGCA
Statistics
Matches: 125, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
159 78 0.62
160 5 0.04
161 41 0.33
162 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (161 bp):
TCTTTTACTCAAGAGTGTTTAACCATTCATCTAACCGGCATAATTGACACATTTCTGCCAATTAC
ACAATTAGGCCATTATTATTTACTAAACGGTGTTTAACTGTTCATCTAACTGGCATAATTGACAC
CTTTCTTCCAATTGCACAAATAGGCAATTAT
Found at i:3621760 original size:68 final size:68
Alignment explanation
Indices: 3621666--3622187 Score: 789
Period size: 68 Copynumber: 7.7 Consensus size: 68
3621656 CGGTGTTTAA
* *
3621666 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3621731 TAG
66 TAG
* * *
3621734 CCTTTCATCTAACCGGCATAAATGACACATTT-TTTCCAATTGCACAG-TAGGCCTCAAAGGCAC
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGT-CAAATGCACAGTTAGGCCTCAAAGGCAC
3621797 TTAG
65 TTAG
* *
3621801 CCTTTCATCTAACCGACATAAATGACACCTTTCTG-CAAATGCACAGCTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3621865 TAG
66 TAG
* * *
3621868 CCTTTCATCTAACCGACATAAATGACACCTTTCTGTCAAATGCACACTTAGGCCTCAAAGGAACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3621933 TAG
66 TAG
* *
3621936 CCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACACTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3622001 TAG
66 TAG
* * ** * *
3622004 CTTTTCATCAAACCAACATAAATGAGACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3622069 TAG
66 TAG
* * * *
3622072 CCTTTCATCTAACCAGCATAAATGACACTTTTCTGTCAAATTCACAGTTAGGCCCCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3622137 TAG
66 TAG
* *
3622140 CCTTTCATCTAACCGGAATAAATGACACCTTTTTTGTCAAATGCACAG
1 CCTTTCATCTAACCGGCATAAATGACACC-TTTCTGTCAAATGCACAG
3622188 GTAGACCTAT
Statistics
Matches: 415, Mismatches: 34, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
66 10 0.02
67 107 0.26
68 282 0.68
69 16 0.04
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (68 bp):
CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAG
Found at i:3622474 original size:54 final size:54
Alignment explanation
Indices: 3622415--3622552 Score: 147
Period size: 54 Copynumber: 2.5 Consensus size: 54
3622405 ACTACCATAC
* * ** *
3622415 GAAATTCATACACTTGATATAAATTTCTTAG-TTCGCACCCATCGTTCCCATA-A
1 GAAATTCATACACTT-ATATGAATTTCTTAGTTTCGCACACAAAGTGCCCATATA
* *
3622468 GGAAATTCATACACTCAATATGAATTT-TTAGTTTTGCACACAAAGTGCCCATATA
1 -GAAATTCATACACT-TATATGAATTTCTTAGTTTCGCACACAAAGTGCCCATATA
*
3622523 GAAATTAATACACTTAGTATGAATTTCTTA
1 GAAATTCATACACTTA-TATGAATTTCTTA
3622553 AATTCTTGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
53 5 0.07
54 61 0.87
55 4 0.06
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (54 bp):
GAAATTCATACACTTATATGAATTTCTTAGTTTCGCACACAAAGTGCCCATATA
Found at i:3623090 original size:94 final size:95
Alignment explanation
Indices: 3622932--3623120 Score: 281
Period size: 94 Copynumber: 2.0 Consensus size: 95
3622922 CGATACTTCT
* *
3622932 ATACTATGGTACCGATACCCCATTCCGGTATCGATACCAATATTAGGTTCAATGTTGCATGGTAT
1 ATACTATGGTACCGATACCCCATTCCAGTATCGATACCAATATTAGATTCAATGTTGCATGGTAT
*
3622997 CGATACCCTTACCATGGAATCAATACTACC
66 CGAAACCCTTACCATGGAATCAATACTACC
* * * *
3623027 ATACTATGGTACTGATACCCC-TTCTATTATCGATACCAATATTAGATTCAATGTTGCTTGGTAT
1 ATACTATGGTACCGATACCCCATTCCAGTATCGATACCAATATTAGATTCAATGTTGCATGGTAT
* * *
3623091 CGAAACCTTTACCATGGTATCGATACTACC
66 CGAAACCCTTACCATGGAATCAATACTACC
3623121 TCGTCAGTAT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
94 64 0.76
95 20 0.24
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (95 bp):
ATACTATGGTACCGATACCCCATTCCAGTATCGATACCAATATTAGATTCAATGTTGCATGGTAT
CGAAACCCTTACCATGGAATCAATACTACC
Found at i:3625603 original size:29 final size:29
Alignment explanation
Indices: 3625557--3625617 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
3625547 AGGCCATTAT
* * *
3625557 TCTTTTACTCAACGGTGTTTAACCTTTCA
1 TCTTATACTCAACAGTGTTTAACCATTCA
3625586 TCTTATACTCAACAGTGTTTAACCATTCA
1 TCTTATACTCAACAGTGTTTAACCATTCA
3625615 TCT
1 TCT
3625618 AACTGGCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.43
Consensus pattern (29 bp):
TCTTATACTCAACAGTGTTTAACCATTCA
Found at i:3625687 original size:109 final size:103
Alignment explanation
Indices: 3625477--3625697 Score: 300
Period size: 109 Copynumber: 2.1 Consensus size: 103
3625467 AATCACCTTG
* *
3625477 TTTCATCTTTACTCAACAGTGCCATTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCA
1 TTTCATCTTTACTCAACAGTGCCATTCATCTAACTGACATAATTGACACATCTCTGCCAATTACA
3625542 TAGTTAGGCCATTATTCTTTTACTCAACGGTGTTTAACC
66 TA-TTAGGCCATTATTCTTTTACTCAACGGTGTTTAACC
* * *
3625581 TTTCATCTTATACTCAACAGTGTTTAACCATTCATCTAACTGGCATAATTGACACCTCTCTTCCA
1 TTTCATCTT-TACTCAACAGTG-----CCATTCATCTAACTGACATAATTGACACATCTCTGCCA
*
3625646 ATTTACAT-TTAGGCCATTATTCTTTTACTCAATGGTGTTTAACC
60 A-TTACATATTAGGCCATTATTCTTTTACTCAACGGTGTTTAACC
*
3625690 GTTCATCT
1 TTTCATCT
3625698 AACTGGCATA
Statistics
Matches: 103, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
104 9 0.09
105 12 0.12
109 42 0.41
110 35 0.34
111 5 0.05
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.39
Consensus pattern (103 bp):
TTTCATCTTTACTCAACAGTGCCATTCATCTAACTGACATAATTGACACATCTCTGCCAATTACA
TATTAGGCCATTATTCTTTTACTCAACGGTGTTTAACC
Found at i:3625768 original size:81 final size:81
Alignment explanation
Indices: 3625586--3625903 Score: 413
Period size: 81 Copynumber: 3.9 Consensus size: 81
3625576 TAACCTTTCA
* * * * * *
3625586 TCTTATACTCAACAGTGTTTAACCATTCATCTAACTGGCATAATTGACACCTCTCTTCCAATT-T
1 TCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGC
*
3625650 ACATTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* * *
3625666 TCTTTTACTCAATGGTGTTTAACCGTTCATCTAACTGGCATAATTGATACCTTTCTACTAATTGC
1 TCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGC
* *
3625731 GCAGTTAGGTCATTAT
66 ACAGTTAGGCCATTAT
* * ** *
3625747 TCTTTTACTCAACGGTGTTTAACTGTTCATCTAACTGGTATTGTTGACACCTTTCTGCCAATTGC
1 TCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGC
*
3625812 ACAGTTAGGCCATTCT
66 ACAGTTAGGCCATTAT
* * * * *
3625828 TCTTTTACTCAACGGTGTTTAACCTTTCATCTAACTAGTATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGC
*
3625893 ACAATTAGGCC
66 ACAGTTAGGCC
3625904 TCAAAGGCAC
Statistics
Matches: 207, Mismatches: 30, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
80 55 0.27
81 152 0.73
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (81 bp):
TCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGC
ACAGTTAGGCCATTAT
Found at i:3626046 original size:68 final size:68
Alignment explanation
Indices: 3625850--3626241 Score: 520
Period size: 68 Copynumber: 5.8 Consensus size: 68
3625840 CGGTGTTTAA
** * * * *
3625850 CCTTTCATCTAACTAGTATAATTGACACCTTTCTGCCAAATGCACAATTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
*
3625915 TAA
66 TAG
* * ** *
3625918 CCTTTTATCTAACCGACAT-AATGA-TTC-TTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3625980 TAG
66 TAG
* * *
3625983 CCTTTCATCTAACCGGCATAAATAACACCTTTTTGTCAAATGCATAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3626048 TAG
66 TAG
* * * * * * *
3626051 ACTTTCATATAACCGGCATAAATGACACATTTTTGTCAAATGTACAGTTAGGCTTCAAAGACACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3626116 TAG
66 TAG
* * * * *
3626119 CCTTTCATCTAACCGACATAAATGACATCTTTCTGTCAAATGCAGAATTAGGCTTCAAAGGCACT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
3626184 TAG
66 TAG
3626187 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
1 CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
3626242 ATTAATCTTT
Statistics
Matches: 279, Mismatches: 42, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
65 51 0.18
66 5 0.02
67 5 0.02
68 218 0.78
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (68 bp):
CCTTTCATCTAACCGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAG
Found at i:3626516 original size:54 final size:55
Alignment explanation
Indices: 3626450--3626592 Score: 175
Period size: 55 Copynumber: 2.6 Consensus size: 55
3626440 ACATATATTT
* * * * *
3626450 CCCATAAGGAAATTCATACACTT-GATATGAATTTCTTTG-TTAGCACCCATAGTA-
1 CCCATACGGAAATTCATACACTTAG-TATGAATTTCGTAGTTTAGCACACAAAG-AG
* *
3626504 CCCATACGGAAATTCATACACTCAGTATGAATTTCGTAGTTTTGCACACAAAGAG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCGTAGTTTAGCACACAAAGAG
*
3626559 CCCATACAGAAATTCATACACTTAGTATGAATTT
1 CCCATACGGAAATTCATACACTTAGTATGAATTT
3626593 ATTAAATTCT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
54 34 0.44
55 43 0.56
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (55 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCGTAGTTTAGCACACAAAGAG
Found at i:3627060 original size:20 final size:20
Alignment explanation
Indices: 3627035--3627092 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
3627025 TTTGATGTTG
*
3627035 CATGGTATCAATACCCTTAC
1 CATGGTATCAATACCCATAC
*
3627055 CATGGTATCGATACTACCATAC
1 CATGGTATCAATAC--CCATAC
* *
3627077 TATGGTACCAATACCC
1 CATGGTATCAATACCC
3627093 CTTTCAGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 15 0.48
22 16 0.52
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (20 bp):
CATGGTATCAATACCCATAC
Found at i:3627143 original size:94 final size:95
Alignment explanation
Indices: 3626978--3627166 Score: 308
Period size: 94 Copynumber: 2.0 Consensus size: 95
3626968 CAATACTTCT
* * **
3626978 ATACTATGGTACCGATACCCCATTCCAGTATCGATACCAATATTAGGTTTGATGTTGCATGGTAT
1 ATACTATGGTACCAATACCCCATTCCAGTATCGATACCAATATTAGATTCAATGTTGCATGGTAT
3627043 CAATACCCTTACCATGGTATCGATACTACC
66 CAATACCCTTACCATGGTATCGATACTACC
* *
3627073 ATACTATGGTACCAATACCCC-TTTCAGTATCGATACCAATATTAGATTCAATGTTGCTTGGTAT
1 ATACTATGGTACCAATACCCCATTCCAGTATCGATACCAATATTAGATTCAATGTTGCATGGTAT
*
3627137 CGATACCCTTACCATGGTATCGATACTACC
66 CAATACCCTTACCATGGTATCGATACTACC
3627167 TCATCAGTAT
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 67 0.77
95 20 0.23
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (95 bp):
ATACTATGGTACCAATACCCCATTCCAGTATCGATACCAATATTAGATTCAATGTTGCATGGTAT
CAATACCCTTACCATGGTATCGATACTACC
Found at i:3627195 original size:21 final size:21
Alignment explanation
Indices: 3627169--3627223 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3627159 ATACTACCTC
3627169 ATCAGTATCGATACTTATTGA
1 ATCAGTATCGATACTTATTGA
*
3627190 ATCAGTAACGATACTTATTGA
1 ATCAGTATCGATACTTATTGA
3627211 ATCAGTATCGATA
1 ATCAGTATCGATA
3627224 GTACCCAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
ATCAGTATCGATACTTATTGA
Found at i:3631451 original size:16 final size:16
Alignment explanation
Indices: 3631432--3631476 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
3631422 TTATTTTCTT
3631432 AGTTTGAGAGTTT-CAA
1 AGTTTGAGAGTTTAC-A
*
3631448 AGTTTGAAAGTTTACA
1 AGTTTGAGAGTTTACA
3631464 AGTTTGAGAGTTT
1 AGTTTGAGAGTTT
3631477 GATATTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.40
Consensus pattern (16 bp):
AGTTTGAGAGTTTACA
Found at i:3631475 original size:8 final size:8
Alignment explanation
Indices: 3631432--3631478 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
3631422 TTATTTTCTT
*
3631432 AGTTTGAG
1 AGTTTGAA
*
3631440 AGTTTCAA
1 AGTTTGAA
3631448 AGTTTGAA
1 AGTTTGAA
3631456 AGTTT-ACA
1 AGTTTGA-A
*
3631464 AGTTTGAG
1 AGTTTGAA
3631472 AGTTTGA
1 AGTTTGA
3631479 TATTTCAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 1 0.03
8 31 0.94
9 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (8 bp):
AGTTTGAA
Found at i:3631666 original size:68 final size:68
Alignment explanation
Indices: 3631557--3631726 Score: 261
Period size: 68 Copynumber: 2.5 Consensus size: 68
3631547 ATTATGTAAA
* *
3631557 ATGGCAGAGATTTT-TGAATAATAATGGAACATGCTCTTTCATTTCGAATGGGATGGAACAATAT
1 ATGGCAGAGATTTTCTGAATAATAATGGAACATGCGCGTTCATTTCGAATGGGATGGAACAATAT
3631621 GAC
66 GAC
* * * *
3631624 ATGGCAAAGATTTTCTTAATAATAATGGAACATGCGCGTTCATTTCGGATGGGATGGAACACTAT
1 ATGGCAGAGATTTTCTGAATAATAATGGAACATGCGCGTTCATTTCGAATGGGATGGAACAATAT
3631689 GAC
66 GAC
* *
3631692 ATGGCAGAGATTATCTGAATAATAATGGAAAATGC
1 ATGGCAGAGATTTTCTGAATAATAATGGAACATGC
3631727 TTCCCCTATA
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
67 13 0.14
68 79 0.86
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (68 bp):
ATGGCAGAGATTTTCTGAATAATAATGGAACATGCGCGTTCATTTCGAATGGGATGGAACAATAT
GAC
Found at i:3631796 original size:83 final size:83
Alignment explanation
Indices: 3631662--3631959 Score: 431
Period size: 83 Copynumber: 3.6 Consensus size: 83
3631652 AACATGCGCG
* * *
3631662 TTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTATCTGAATAATAATGGAAAATGC
1 TTCATTTCGGATGGGATGAAACACTATGACATGGCAAAGATTCTCTGAATAATAATGGAAAATGC
** *
3631727 TTCCCCTATAACGCGTCT
66 TTCCCCTGGAACGCGCCT
3631745 TTCATTTCGGATGGGATGAAACACTATGACATGGCAAAGATTCTCTGAATAATAATGGAAAATGC
1 TTCATTTCGGATGGGATGAAACACTATGACATGGCAAAGATTCTCTGAATAATAATGGAAAATGC
3631810 TTCCCCTGGAACGCGCCT
66 TTCCCCTGGAACGCGCCT
* * * * *
3631828 TTCTTTTCGGATTGGATGAAACACCATGACATGGCAGAGATTCTCTGAATAATAATAGAAAATG-
1 TTCATTTCGGATGGGATGAAACACTATGACATGGCAAAGATTCTCTGAATAATAATGGAAAATGC
*
3631892 TCTCCCCTGGAATGCGCCT
66 T-TCCCCTGGAACGCGCCT
*
3631911 TTCATTAT-GGATGGGATGGAACACTATGACATGG-AAGAGATTCTCTGAA
1 TTCATT-TCGGATGGGATGAAACACTATGACATGGCAA-AGATTCTCTGAA
3631960 AATGGGGAAA
Statistics
Matches: 195, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
82 2 0.01
83 192 0.98
84 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (83 bp):
TTCATTTCGGATGGGATGAAACACTATGACATGGCAAAGATTCTCTGAATAATAATGGAAAATGC
TTCCCCTGGAACGCGCCT
Found at i:3632954 original size:32 final size:32
Alignment explanation
Indices: 3632918--3632978 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
3632908 CCTTAACCAA
3632918 TAAATAAAAGCATACACATACACCTAAAATAG
1 TAAATAAAAGCATACACATACACCTAAAATAG
3632950 TAAATAAAAGCATACACATACACCTAAAA
1 TAAATAAAAGCATACACATACACCTAAAA
3632979 CATACTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.18
Consensus pattern (32 bp):
TAAATAAAAGCATACACATACACCTAAAATAG
Found at i:3643026 original size:7 final size:7
Alignment explanation
Indices: 3643016--3643052 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
3643006 TAGTTTATTT
3643016 TTTAGGG
1 TTTAGGG
3643023 TTTAGGG
1 TTTAGGG
*
3643030 TTTAAGG
1 TTTAGGG
3643037 TTTAGGG
1 TTTAGGG
3643044 TTTAGGG
1 TTTAGGG
3643051 TT
1 TT
3643053 ACTGAGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:3646218 original size:2 final size:2
Alignment explanation
Indices: 3646206--3646257 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
3646196 CACTTATTTA
3646206 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3646247 AT AT AT AT AT A
1 AT AT AT AT AT A
3646258 AAAATATAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3647060 original size:14 final size:14
Alignment explanation
Indices: 3647043--3647073 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3647033 CAAAATTATT
3647043 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
3647057 TAAATAAATTCTAA
1 TAAATAAATTCAAA
3647071 TAA
1 TAA
3647074 TTTAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:3659145 original size:11 final size:13
Alignment explanation
Indices: 3659113--3659142 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3659103 TGGCCAAAGA
3659113 TGAAAAGGTATGT
1 TGAAAAGGTATGT
3659126 TGAAAAGGTATG-
1 TGAAAAGGTATGT
3659138 TGAAA
1 TGAAA
3659143 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:3670673 original size:2 final size:2
Alignment explanation
Indices: 3670668--3670692 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3670658 ATACAGTAAT
3670668 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3670693 TATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3674986 original size:14 final size:15
Alignment explanation
Indices: 3674958--3674989 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3674948 ATAGAAAATA
3674958 TAATTATATTATTTT
1 TAATTATATTATTTT
3674973 TAATTATA-TATTTT
1 TAATTATATTATTTT
3674987 TAA
1 TAA
3674990 AATATGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTATATTATTTT
Found at i:3675023 original size:2 final size:2
Alignment explanation
Indices: 3675011--3675052 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
3675001 AAATAAGTTA
* *
3675011 AT AT A- AT AT AT AT A- AT AT AT AT AT AG AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3675051 AT
1 AT
3675053 GTTTTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3675044 original size:16 final size:15
Alignment explanation
Indices: 3675009--3675051 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
3674999 ACAAATAAGT
*
3675009 TAATATA-ATATATA
1 TAATATATATATAGA
3675023 TAATATATATATAGA
1 TAATATATATATAGA
3675038 TAGATATATATATA
1 TA-ATATATATATA
3675052 TGTTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 7 0.27
15 8 0.31
16 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
TAATATATATATAGA
Found at i:3682480 original size:41 final size:41
Alignment explanation
Indices: 3682435--3682565 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
3682425 ACAAACGCTT
3682435 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
1 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
* ** * * * *
3682476 CAATATAGTGGTAAA-CTGGCAGC-ATTTTTA-CCACAAACGCCA
1 CAATAGA-TTATAAATTTTGCGGCGA--TTTAGCCA-AAACGCCG
* * *
3682518 CAATAGAGTATAAATTTTGCGGCGATTGAGTCAAAACGCCG
1 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
3682559 CAATAGA
1 CAATAGA
3682566 GCGGTAAATT
Statistics
Matches: 66, Mismatches: 17, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
40 1 0.02
41 35 0.53
42 29 0.44
43 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (41 bp):
CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
Found at i:3682522 original size:83 final size:83
Alignment explanation
Indices: 3682424--3682578 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 83
3682414 GCGTTTATAT
** * * * *
3682424 CACAAACGCTTCAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTA
1 CACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGCGGTA
3682489 AACTGGCAGCATTTTTAC
66 AACTGGCAGCATTTTTAC
*
3682507 CACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGTCAAAACGCCGCAATAGAGCGGTA
1 CACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGCGGTA
*
3682572 AATTGGC
66 AACTGGC
3682579 GGCGTTTTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 64 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (83 bp):
CACAAACGCCACAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGCGGTA
AACTGGCAGCATTTTTAC
Found at i:3682581 original size:41 final size:40
Alignment explanation
Indices: 3682453--3682582 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 40
3682443 TATAAATTTT
* *
3682453 GCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTAAACTG
1 GCGGCGATTTAGCCAAAACGCCGCAATAGAG-GGTAAATTG
* * ** *
3682494 GCAGC-ATTTTTA-CCACAAACGCCACAATAGAGTATAAATTTT
1 GCGGCGA--TTTAGCCA-AAACGCCGCAATAGAGGGTAAA-TTG
* *
3682536 GCGGCGATTGAGTCAAAACGCCGCAATAGAGCGGTAAATTG
1 GCGGCGATTTAGCCAAAACGCCGCAATAGAG-GGTAAATTG
3682577 GCGGCG
1 GCGGCG
3682583 TTTTGACAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
40 1 0.01
41 37 0.54
42 29 0.43
43 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (40 bp):
GCGGCGATTTAGCCAAAACGCCGCAATAGAGGGTAAATTG
Found at i:3682597 original size:83 final size:83
Alignment explanation
Indices: 3682435--3682599 Score: 231
Period size: 83 Copynumber: 2.0 Consensus size: 83
3682425 ACAAACGCTT
* * * *
3682435 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTAAACTGGCAGCA
1 CAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGCGGTAAACTGGCAGCA
* * *
3682500 TTTTTACCACAAACGCCA
66 TTTTGACAAAAAACGCCA
* * * *
3682518 CAATAGAGTATAAATTTTGCGGCGATTGAGTCAAAACGCCGCAATAGAGCGGTAAATTGGCGGCG
1 CAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGCGGTAAACTGGCAGCA
3682583 TTTTGACAAAAAACGCC
66 TTTTGACAAAAAACGCC
3682600 GCAAATATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (83 bp):
CAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGCGGTAAACTGGCAGCA
TTTTGACAAAAAACGCCA
Done.