Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:2431047 original size:7 final size:8
Alignment explanation
Indices: 2431029--2431067 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
2431019 ATAAAAGTAT
2431029 AAATGCAA
1 AAATGCAA
2431037 AAATG-AA
1 AAATGCAA
2431044 AAATGCAA
1 AAATGCAA
*
2431052 AGATGC-A
1 AAATGCAA
2431059 AAATGCAA
1 AAATGCAA
2431067 A
1 A
2431068 TGTATGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (8 bp):
AAATGCAA
Found at i:2431047 original size:15 final size:15
Alignment explanation
Indices: 2431029--2431067 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2431019 ATAAAAGTAT
2431029 AAATGCAAAAATGAA
1 AAATGCAAAAATGAA
* *
2431044 AAATGCAAAGATGCA
1 AAATGCAAAAATGAA
2431059 AAATGCAAA
1 AAATGCAAA
2431068 TGTATGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (15 bp):
AAATGCAAAAATGAA
Found at i:2433966 original size:31 final size:29
Alignment explanation
Indices: 2433918--2433976 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
2433908 ATTTCAAAAT
2433918 TATAATTATGAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAATAT-TT-ATTTATA
*
2433949 TATATTTAT-AAATAAAATATTTATTTAT
1 TATAATTATGAAA-AAAATATTTATTTAT
2433977 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATGAAAAAAATATTTATTTATA
Found at i:2434071 original size:20 final size:19
Alignment explanation
Indices: 2434032--2434073 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2434022 TTTCTTCGAT
2434032 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
2434051 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
2434071 ATT
1 ATT
2434074 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:2434183 original size:119 final size:120
Alignment explanation
Indices: 2433931--2434174 Score: 309
Period size: 120 Copynumber: 2.0 Consensus size: 120
2433921 AATTATGAAA
2433931 AAAATATATTAATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATG
1 AAAATA-ATTAA--TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATG
* * * *
2433996 ACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATT
63 ACATCCAGGTGCCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATT
**
2434054 AAAATAATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTA-AAATATCAGAAAATGGA
1 AAAATAATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAAT-GA
* ** * *
2434117 CATCCAGTTGTTTTAAGACTG-TCCTTTCTT-AATATTGAAAAATAAATAAAT-ATT
64 CATCCAGGTGCCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATT
2434171 AAAA
1 AAAA
2434175 CATGATTAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
117 7 0.06
118 19 0.18
119 28 0.26
120 43 0.40
122 5 0.05
123 6 0.06
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (120 bp):
AAAATAATTAATATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACA
TCCAGGTGCCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATT
Found at i:2435556 original size:3 final size:3
Alignment explanation
Indices: 2435548--2435616 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
2435538 ATATTTATTA
**
2435548 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT AAT AAT AAT AAT AAT TTT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
2435594 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
2435617 AACGAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 51 0.86
4 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2437687 original size:32 final size:32
Alignment explanation
Indices: 2437646--2437707 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2437636 ACAATATTGA
*
2437646 ATTGATTGATTTGTGATTCGAGTCAATATCAC
1 ATTGATTGATTTGTGAGTCGAGTCAATATCAC
* * * *
2437678 ATTGGTTGATTTTTTAGTCGGGTCAATATC
1 ATTGATTGATTTGTGAGTCGAGTCAATATC
2437708 GAATCATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (32 bp):
ATTGATTGATTTGTGAGTCGAGTCAATATCAC
Found at i:2439471 original size:24 final size:24
Alignment explanation
Indices: 2439439--2439484 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2439429 TCTTCCAGAT
2439439 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
2439463 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
2439485 CATGTCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:2440065 original size:30 final size:30
Alignment explanation
Indices: 2440026--2440091 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
2440016 CATTCACAAC
* * * *
2440026 TTTTCCAAAATTACCGAATTGTTCCCCCAAT
1 TTTTCAAAAATTACAGAA-TGGTCCCCAAAT
2440057 TTTTCAAAAATTACAGAATGGTCCCCAAAT
1 TTTTCAAAAATTACAGAATGGTCCCCAAAT
2440087 TTTTC
1 TTTTC
2440092 TAAGGCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (30 bp):
TTTTCAAAAATTACAGAATGGTCCCCAAAT
Found at i:2440151 original size:20 final size:20
Alignment explanation
Indices: 2440113--2440151 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2440103 GAATATTTCC
*
2440113 TATATTATTTACATCCTTTA
1 TATATTATTTACATACTTTA
* *
2440133 TATATTTTTTCCATACTTT
1 TATATTATTTACATACTTT
2440152 TTCTTACTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTATTTACATACTTTA
Found at i:2441841 original size:10 final size:11
Alignment explanation
Indices: 2441816--2441853 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2441806 GATCAGATGC
2441816 TATCTTGAATT
1 TATCTTGAATT
2441827 TATCTTGAA-T
1 TATCTTGAATT
* *
2441837 TATCTTTACTT
1 TATCTTGAATT
2441848 TATCTT
1 TATCTT
2441854 CAACCGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (11 bp):
TATCTTGAATT
Found at i:2447540 original size:30 final size:30
Alignment explanation
Indices: 2447481--2447549 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
2447471 CAATCATTCA
2447481 CAACTTTTCAAAAATTACCAAATTGGTCCC
1 CAACTTTTCAAAAATTACCAAATTGGTCCC
*
2447511 CTAACTTTTCAAAAATTA-TAGAA-TGGTCCC
1 C-AACTTTTCAAAAATTACCA-AATTGGTCCC
*
2447541 CAAATTTTC
1 CAACTTTTC
2447550 TAAGGCTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.20
30 10 0.29
31 18 0.51
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (30 bp):
CAACTTTTCAAAAATTACCAAATTGGTCCC
Found at i:2451573 original size:21 final size:20
Alignment explanation
Indices: 2451547--2451585 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2451537 ATTAGAACAA
2451547 AAAGAAAAAAGAGAAAAAAAC
1 AAAGAAAAAAG-GAAAAAAAC
2451568 AAAGAAAAAAGGAAAAAA
1 AAAGAAAAAAGGAAAAAA
2451586 GAAAAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAGGAAAAAAAC
Found at i:2451614 original size:7 final size:7
Alignment explanation
Indices: 2451545--2451592 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
2451535 CAATTAGAAC
2451545 AAAAAGA
1 AAAAAGA
2451552 AAAAAGA
1 AAAAAGA
2451559 GAAAAA-A
1 -AAAAAGA
*
2451566 ACAAAGA
1 AAAAAGA
2451573 AAAAAGGA
1 AAAAA-GA
2451581 AAAAAGA
1 AAAAAGA
2451588 AAAAA
1 AAAAA
2451593 AGGAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 4 0.11
7 20 0.56
8 12 0.33
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2451790 original size:69 final size:69
Alignment explanation
Indices: 2451672--2451809 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
2451662 GATTTAAACT
* * *
2451672 ATGAGATTGATCAAGCACAATCATTTTTGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGAACATAGAGCA
2451737 TCAA
66 TCAA
* * *
2451741 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGAATCACTCCACTCGAAGAACATGGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGAACATAGAGCA
2451806 TCAA
66 TCAA
2451810 GAGAGAGACA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGAACATAGAGCA
TCAA
Found at i:2452749 original size:32 final size:32
Alignment explanation
Indices: 2452703--2452782 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
2452693 TGAGGGCATC
2452703 TTTGAAGATTTAACATCAAATGTTGGGACATATT
1 TTTG-AGATTTAACATCAAATGTTGGGACAT-TT
*
2452737 TTT-AGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTTAACATCAAATGTTGGGACATTT
*
2452768 TTTGAGATTCAACAT
1 TTTGAGATTTAACAT
2452783 TGAATATTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 5 0.12
32 35 0.81
34 3 0.07
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (32 bp):
TTTGAGATTTAACATCAAATGTTGGGACATTT
Found at i:2452793 original size:32 final size:32
Alignment explanation
Indices: 2452708--2452794 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
2452698 GCATCTTTGA
* *
2452708 AGATTTAACATCAAATGTTGGGACATATTTTT
1 AGATTCAACATCAAATATTGGGACATATTTTT
* * *
2452740 AGATTTAACATCAAATGTTGGGGCAT-TTTTT
1 AGATTCAACATCAAATATTGGGACATATTTTT
**
2452771 GAGATTCAACATTGAATATTGGGA
1 -AGATTCAACATCAAATATTGGGA
2452795 AATCTTTGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
31 5 0.10
32 43 0.90
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGACATATTTTT
Found at i:2453518 original size:106 final size:106
Alignment explanation
Indices: 2453394--2453667 Score: 422
Period size: 106 Copynumber: 2.6 Consensus size: 106
2453384 ATCGTGCCAA
* * * *
2453394 TCGAGACAACATAAGTTCAACTCCACAACGAAGGGATGGCTGGTTCTCAACAAACAATTTCCAAA
1 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAA
2453459 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
2453500 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAA
1 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAA
*
2453565 TTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
*** * * * * * *
2453606 TCGAGATGGCACAAGTTTAACTTTAGAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCC
1 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
2453668 TAGTTCAATT
Statistics
Matches: 154, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 154 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (106 bp):
TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAA
TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
Found at i:2454945 original size:31 final size:31
Alignment explanation
Indices: 2454908--2454970 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2454898 AATTATCATT
* * *
2454908 AAACCAAGACACCTAACTCTTATCATCTTCC
1 AAACCAAGAAACATAACCCTTATCATCTTCC
2454939 AAACCAAGAAACATAACCCTTATCATCTTCC
1 AAACCAAGAAACATAACCCTTATCATCTTCC
2454970 A
1 A
2454971 TAAGTCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.24
Consensus pattern (31 bp):
AAACCAAGAAACATAACCCTTATCATCTTCC
Found at i:2458170 original size:2 final size:2
Alignment explanation
Indices: 2458163--2458203 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2458153 GCTTATAGTG
2458163 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
2458204 TTGACCCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2458697 original size:21 final size:21
Alignment explanation
Indices: 2458673--2458712 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2458663 TATTTATATT
*
2458673 ATATATATATATATTAATAAA
1 ATATATATATATATAAATAAA
*
2458694 ATATTTATATATATAAATA
1 ATATATATATATATAAATA
2458713 TTACTAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATATATATATATAAATAAA
Found at i:2458848 original size:21 final size:20
Alignment explanation
Indices: 2458802--2458853 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
2458792 TAAGTGTAAA
* * *
2458802 TATAATTTAAATGATATATT
1 TATAATTTACAGGATATATC
*
2458822 TTTAATTTACAGGATAATATC
1 TATAATTTACAGGAT-ATATC
*
2458843 TATAATATACA
1 TATAATTTACA
2458854 TCTTATCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (20 bp):
TATAATTTACAGGATATATC
Found at i:2461106 original size:56 final size:56
Alignment explanation
Indices: 2461020--2461148 Score: 249
Period size: 56 Copynumber: 2.3 Consensus size: 56
2461010 ACACAGTTTA
2461020 TATAGTCTTGTGCACTATATTTGTGATACATTTTTCAAGTGAATAGATGCGTCATG
1 TATAGTCTTGTGCACTATATTTGTGATACATTTTTCAAGTGAATAGATGCGTCATG
2461076 TATAGTCTTGTGCACTATATTTGTGATACATTTTTCAAGTGAATAGATGCGTCATG
1 TATAGTCTTGTGCACTATATTTGTGATACATTTTTCAAGTGAATAGATGCGTCATG
*
2461132 TATAGTCTTGTACACTA
1 TATAGTCTTGTGCACTA
2461149 AATATAATCT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 72 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (56 bp):
TATAGTCTTGTGCACTATATTTGTGATACATTTTTCAAGTGAATAGATGCGTCATG
Found at i:2461577 original size:6 final size:6
Alignment explanation
Indices: 2461566--2461599 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2461556 TCTGATAACT
2461566 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAG
2461600 AAAAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:2467928 original size:13 final size:13
Alignment explanation
Indices: 2467902--2467958 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
2467892 CAATCCAGGC
2467902 GACATACG-GGGT
1 GACATACGAGGGT
2467914 GACATACGAGGGT
1 GACATACGAGGGT
2467927 GACATACGA----
1 GACATACGAGGGT
*
2467936 GCCATACGAGGGT
1 GACATACGAGGGT
2467949 GACATACGAG
1 GACATACGAG
2467959 CCATATACGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.21
12 8 0.21
13 22 0.58
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:2467944 original size:22 final size:22
Alignment explanation
Indices: 2467916--2467963 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
2467906 TACGGGGTGA
2467916 CATACGAGGGTGACATACGAGC
1 CATACGAGGGTGACATACGAGC
2467938 CATACGAGGGTGACATACGAGC
1 CATACGAGGGTGACATACGAGC
2467960 CATA
1 CATA
2467964 TACGAGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.29, T:0.15
Consensus pattern (22 bp):
CATACGAGGGTGACATACGAGC
Found at i:2468164 original size:27 final size:27
Alignment explanation
Indices: 2468132--2468187 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
2468122 CCTACAGCTC
2468132 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
2468159 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
2468186 CC
1 CC
2468188 GTGAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:2468333 original size:23 final size:24
Alignment explanation
Indices: 2468301--2468354 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
2468291 AAAAGAAAGA
2468301 AAGAAA-GGAGAAGAGATTGCAG-
1 AAGAAAGGGAGAAGAGATTGCAGC
2468323 AAGAAAGGGAGAAGAGATTGCAGCC
1 AAGAAAGGGAGAAGAGATTGCAG-C
2468348 AAGAAAG
1 AAGAAAG
2468355 AAAGAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.21
23 16 0.55
25 7 0.24
ACGTcount: A:0.50, C:0.07, G:0.35, T:0.07
Consensus pattern (24 bp):
AAGAAAGGGAGAAGAGATTGCAGC
Found at i:2468376 original size:17 final size:17
Alignment explanation
Indices: 2468349--2468405 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
2468339 ATTGCAGCCA
2468349 AGAAA-GAAAGAAAGGG
1 AGAAAGGAAAGAAAGGG
2468365 AGAAAGGAAAGAAAGGG
1 AGAAAGGAAAGAAAGGG
* *
2468382 AG-AAGGAAAGTAAAAGA
1 AGAAAGGAAAG-AAAGGG
2468399 AGAAAGG
1 AGAAAGG
2468406 GAGATAAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 13 0.36
17 19 0.53
18 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (17 bp):
AGAAAGGAAAGAAAGGG
Found at i:2468685 original size:45 final size:43
Alignment explanation
Indices: 2468602--2468689 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
2468592 AGTTATTATA
*
2468602 TAAAAAAATAATTATTTAATTAGTTTGTTTTGTTAATAGTAGT
1 TAAAAAAATAATTATTTAATTAGTTTGTTTAGTTAATAGTAGT
2468645 TAAAAAAA-AATTATTTAATTTAGTTTGTGTTAGTTAA-A-TAGT
1 TAAAAAAATAATTATTTAA-TTAGTTTGT-TTAGTTAATAGTAGT
2468687 TAA
1 TAA
2468690 GTTATTTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 17 0.40
43 18 0.43
44 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAAAAAATAATTATTTAATTAGTTTGTTTAGTTAATAGTAGT
Found at i:2470820 original size:17 final size:17
Alignment explanation
Indices: 2470798--2470830 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2470788 CAATGATTTT
*
2470798 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
2470815 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
2470831 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:2470847 original size:24 final size:22
Alignment explanation
Indices: 2470815--2470883 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
2470805 AAATCATTAC
2470815 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
2470837 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
2470862 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
2470884 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:2471102 original size:35 final size:37
Alignment explanation
Indices: 2471021--2471107 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
2471011 TTAGTATTCT
* * *
2471021 ATAATTATTAGT-AATAATTATTAAATTATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATTAATAG-ACTAA
*
2471059 ATCATTATTATAAATAATTACTAAA-TAATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATTAATAGACTAA
2471094 ATAATTATTATAAA
1 ATAATTATTATAAA
2471108 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 5 0.12
38 21 0.49
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATTAATAGACTAA
Found at i:2471128 original size:12 final size:13
Alignment explanation
Indices: 2471037--2471510 Score: 196
Period size: 12 Copynumber: 36.1 Consensus size: 13
2471027 ATTAGTAATA
*
2471037 ATTATTAAATTATT
1 ATTA-TAAATCATT
*
2471051 AGTATTAAATCATT
1 ATTA-TAAATCATT
2471065 ATTATAAAT-A--
1 ATTATAAATCATT
2471075 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
2471086 ATAACTAAATAATT
1 ATTA-TAAATCATT
2471100 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
2471114 ATTAT-AATGATT
1 ATTATAAATCATT
2471126 ATTATCAAATCATT
1 ATTAT-AAATCATT
2471140 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
2471159 AAATATTTAAATCATT
1 --AT-TATAAATCATT
2471175 A-T-TAAATCATT
1 ATTATAAATCATT
* *
2471186 TTTAT-AATGATT
1 ATTATAAATCATT
2471198 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2471212 ATTAT-AATGATT
1 ATTATAAATCATT
2471224 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2471238 ACTAT-AATGATT
1 ATTATAAATCATT
2471250 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2471264 A--CTAAATCATCA
1 ATTATAAATCAT-T
* *
2471276 ATCATTAA--A-T
1 ATTATAAATCATT
2471286 ATT-TAAATCATT
1 ATTATAAATCATT
2471298 A-T-TAAATCATT
1 ATTATAAATCATT
* *
2471309 TTTAT-AATGATT
1 ATTATAAATCATT
2471321 ATTACT-AATCATT
1 ATTA-TAAATCATT
*
2471334 ATTAT-AATGATT
1 ATTATAAATCATT
2471346 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2471360 ACTAT-AATGATT
1 ATTATAAATCATT
2471372 ATTATCAAATCATT
1 ATTAT-AAATCATT
2471386 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
2471405 AAATATTTAAATCATT
1 --AT-TATAAATCATT
2471421 A-T-TAAATCATT
1 ATTATAAATCATT
* *
2471432 TTTAT-AATGATT
1 ATTATAAATCATT
2471444 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2471458 ATTAT-AATGATT
1 ATTATAAATCATT
*
2471470 ATTGTCAAATCATT
1 ATTAT-AAATCATT
* *
2471484 ACTAT-AATGATT
1 ATTATAAATCATT
2471496 ATTATCAAATCATT
1 ATTAT-AAATCATT
2471510 A
1 A
2471511 CTAAATCATC
Statistics
Matches: 361, Mismatches: 49, Indels: 100
0.71 0.10 0.20
Matches are distributed among these distances:
9 3 0.01
10 6 0.02
11 51 0.14
12 113 0.31
13 24 0.07
14 112 0.31
15 2 0.01
16 16 0.04
17 2 0.01
18 6 0.02
19 22 0.06
20 2 0.01
21 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:2471206 original size:26 final size:25
Alignment explanation
Indices: 2471172--2471510 Score: 285
Period size: 26 Copynumber: 13.6 Consensus size: 25
2471162 TATTTAAATC
*
2471172 ATTATTAAATCATTTTTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
2471198 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
2471224 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
2471250 ATTATCAAATCATTACTA-AATCATCA
1 ATTAT-AAATCATTATTATAATGAT-T
* *
2471276 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
2471298 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
2471321 ATTACT-AATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
2471346 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
2471372 ATTATCAAATCATTACTA-AATCATCAA
1 ATTAT-AAATCATTATTATAATGAT--T
* *
2471399 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
2471421 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
2471444 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
* *
2471470 ATTGTCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
2471496 ATTATCAAATCATTA
1 ATTAT-AAATCATTA
2471511 CTAAATCATC
Statistics
Matches: 267, Mismatches: 23, Indels: 46
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.04
20 2 0.01
21 2 0.01
22 8 0.03
23 22 0.08
24 12 0.04
25 36 0.13
26 166 0.62
27 8 0.03
28 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (25 bp):
ATTATAAATCATTATTATAATGATT
Found at i:2471261 original size:124 final size:124
Alignment explanation
Indices: 2471053--2471568 Score: 916
Period size: 124 Copynumber: 4.2 Consensus size: 124
2471043 AAATTATTAG
* * * * * * *
2471053 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
2471115 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
2471174 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
2471239 CTATAATGATTATTATCAAATCATTACTAAATCATC-AATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
2471297 TATTAAATCATTTTTATAATGATTATTACT-AATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
2471361 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
2471420 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTGTCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
2471485 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
2471544 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
2471569 ATAAATACAT
Statistics
Matches: 381, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
121 18 0.05
122 70 0.18
123 121 0.32
124 172 0.45
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:2471358 original size:246 final size:247
Alignment explanation
Indices: 2471053--2471568 Score: 914
Period size: 246 Copynumber: 2.1 Consensus size: 247
2471043 AAATTATTAG
* * *
2471053 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTAT
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
2471116 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAA
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAA
2471181 TCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAAT
131 TCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAAT
2471246 GATTATTATCAAATCATTACTAAATCATC-AATCATTAAATATTTAAATCAT
196 GATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* * * * *
2471297 TATTAAATCATTTTTATAATGATTATTACT-AATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
2471361 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAA
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAA
*
2471426 ATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTGTCAAATCATTACTATAA
130 ATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAA
2471491 TGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
195 TGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
2471544 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
2471569 ATAAATACAT
Statistics
Matches: 259, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
244 18 0.07
245 8 0.03
246 186 0.72
247 47 0.18
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (247 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAA
TCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAAT
GATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:2474445 original size:26 final size:24
Alignment explanation
Indices: 2474387--2474445 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
2474377 CTAATAAACC
*
2474387 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
2474411 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
2474439 TAATAAT
1 TAATAAT
2474446 ATATGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:2475289 original size:28 final size:30
Alignment explanation
Indices: 2475249--2475311 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
2475239 ATTTTTTATA
*
2475249 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
2475279 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
2475307 TAATA
1 TAATA
2475312 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:2475318 original size:28 final size:28
Alignment explanation
Indices: 2475253--2475318 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
2475243 TTTATATAAT
*
2475253 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
2475281 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
2475309 ATAATTTATA
1 ATAATATATA
2475319 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:2475321 original size:21 final size:21
Alignment explanation
Indices: 2475288--2475336 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2475278 CTAATATAAT
2475288 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2475309 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2475330 ATTAACT
1 A-TAACT
2475337 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2477426 original size:30 final size:30
Alignment explanation
Indices: 2477390--2477459 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
2477380 TTGGTTATAG
*
2477390 ATTACTTAAAAACTATTTTACATAAAATGA
1 ATTACTTAAAAACTATTTTACATAAAATCA
* * **
2477420 ATTACTTAAAAATTGTTTTATGTAAAATCA
1 ATTACTTAAAAACTATTTTACATAAAATCA
*
2477450 ATTACCTAAA
1 ATTACTTAAA
2477460 CCTGTTTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (30 bp):
ATTACTTAAAAACTATTTTACATAAAATCA
Found at i:2477940 original size:19 final size:19
Alignment explanation
Indices: 2477916--2477961 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
2477906 GAGTATATAT
2477916 TAATATAATATTAAAAATA
1 TAATATAATATTAAAAATA
*
2477935 TAATAT--TATTAAAATTA
1 TAATATAATATTAAAAATA
*
2477952 TATTATAATA
1 TAATATAATA
2477962 ATATTACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATATAATATTAAAAATA
Found at i:2479134 original size:38 final size:36
Alignment explanation
Indices: 2479063--2479139 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 36
2479053 ACTCAACTCA
*
2479063 ACTTGAAAATTATACATTTCACTCGATTCGAATTCG
1 ACTTGAAAAATATACATTTCACTCGATTCGAATTCG
* *
2479099 ACTTGAAAAATATATATCTTACACTCGACTT-GAATTTG
1 ACTTGAAAAATATACAT-TT-CACTCGA-TTCGAATTCG
2479137 ACT
1 ACT
2479140 CGTTTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 15 0.43
37 2 0.06
38 16 0.46
39 2 0.06
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (36 bp):
ACTTGAAAAATATACATTTCACTCGATTCGAATTCG
Found at i:2479799 original size:16 final size:16
Alignment explanation
Indices: 2479775--2479809 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2479765 CGGGATAGTA
*
2479775 TATAGTATATATTTTG
1 TATAGTATATATTATG
*
2479791 TATATTATATATTATG
1 TATAGTATATATTATG
2479807 TAT
1 TAT
2479810 TAGATATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (16 bp):
TATAGTATATATTATG
Found at i:2479810 original size:14 final size:14
Alignment explanation
Indices: 2479793--2479878 Score: 52
Period size: 14 Copynumber: 6.1 Consensus size: 14
2479783 ATATTTTGTA
2479793 TATTATATATTATG
1 TATTATATATTATG
*
2479807 TATTAGATATTA-G
1 TATTATATATTATG
*
2479820 ATATTATAATAGTAT-
1 -TATTAT-ATATTATG
* * *
2479835 AAATATATATT-TA
1 TATTATATATTATG
* *
2479848 TAATATATATTATA
1 TATTATATATTATG
2479862 TATTATAGTATATATG
1 TATTATA-TAT-TATG
2479878 T
1 T
2479879 TATAGTGTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
12 1 0.02
13 15 0.27
14 28 0.50
15 8 0.14
16 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATTATATATTATG
Found at i:2479849 original size:22 final size:20
Alignment explanation
Indices: 2479823--2479875 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2479813 ATATTAGATA
2479823 TTATAATAGTATAAATATATAT
1 TTATAATA-TAT-AATATATAT
*
2479845 TTATAATATATATTATATA-
1 TTATAATATATAATATATAT
*
2479864 TTATAGTATATA
1 TTATAATATATA
2479876 TGTTATAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.38
20 7 0.24
21 3 0.10
22 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TTATAATATATAATATATAT
Found at i:2479854 original size:13 final size:14
Alignment explanation
Indices: 2479781--2479868 Score: 63
Period size: 14 Copynumber: 6.4 Consensus size: 14
2479771 AGTATATAGT
* *
2479781 ATATATTTTGTATA
1 ATATATATTATATA
* *
2479795 TTATATATTATGTA
1 ATATATATTATATA
* * *
2479809 TTAGATATTAGATA
1 ATATATATTATATA
* *
2479823 TTATAATAGTATA-A
1 ATAT-ATATTATATA
2479837 ATATATATT-TATA
1 ATATATATTATATA
2479850 ATATATATTATATA
1 ATATATATTATATA
*
2479864 TTATA
1 ATATA
2479869 GTATATATGT
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
12 2 0.03
13 14 0.24
14 36 0.62
15 6 0.10
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
ATATATATTATATA
Found at i:2479910 original size:5 final size:5
Alignment explanation
Indices: 2479894--2480016 Score: 58
Period size: 5 Copynumber: 23.8 Consensus size: 5
2479884 TGTTATAGTG
* * * * *
2479894 TTATA TTTATA TTATA TAAATG TTATA TTATA TCATA GTATA -TACA TTTATA
1 TTATA -TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA -TTATA
* *
2479946 TGGTATA TTATA -TACTA TTATA -TATA TTTTA TT-TA TTGTA TTATA
1 T--TATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA
*
2479991 TTATTA GTATCTA TT-TA TTATA TTAT
1 TTA-TA -T-TATA TTATA TTATA TTAT
2480017 TTTTGGTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
4 17 0.18
5 50 0.54
6 16 0.17
7 8 0.09
8 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:2479917 original size:22 final size:22
Alignment explanation
Indices: 2479892--2479959 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 22
2479882 AGTGTTATAG
2479892 TGTTATATTTATATTATATAAA
1 TGTTATATTTATATTATATAAA
*
2479914 TGTTATATTATATCATAGTATATACA
1 TGTTATATT-TAT-AT--TATATAAA
*
2479940 T-TTATATGGTATATTATATA
1 TGTTATAT-TTATATTATATA
2479960 CTATTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 15 0.38
23 3 0.08
24 4 0.10
25 9 0.23
26 8 0.21
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.51
Consensus pattern (22 bp):
TGTTATATTTATATTATATAAA
Found at i:2481370 original size:8 final size:9
Alignment explanation
Indices: 2481357--2481394 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2481347 TCTCATTTTT
2481357 TTAATA-TA
1 TTAATATTA
2481365 TTAATATTA
1 TTAATATTA
*
2481374 TTATTATTA
1 TTAATATTA
*
2481383 TTATTATTA
1 TTAATATTA
2481392 TTA
1 TTA
2481395 TTAATTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTAATATTA
Found at i:2481375 original size:3 final size:3
Alignment explanation
Indices: 2481363--2481397 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2481353 TTTTTTAATA
*
2481363 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2481398 ATTTACATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2496725 original size:127 final size:128
Alignment explanation
Indices: 2496496--2497014 Score: 432
Period size: 128 Copynumber: 4.1 Consensus size: 128
2496486 TATGCTCTGA
* * * * * *
2496496 TACTCTTTATGGAGATCAGATCTAGAAATTTTGATTCATTTTATTTCTCTTT-AGGTAAAATGGA
1 TACTCTTTAAGGAGATCAGAT-TGGAAATTTTGATTCATTTCACTACTCTTTAAGG-AAAATTGA
** * * *
2496560 ATCATGGTTGATTTGCTT-ACTACT-CTTTAAGAATATCAAATTTAGAAAAGAGATCTACTCCAC
64 ATCATGGTTGATTTGCTTCACTTTTACTTCAAGAAGATCAAATTTAGAAAAGAGATCTACTCTAC
* * * * *
2496623 CACTCTTTAAGGATATCAGATATGGAAATTTTGATTCA-TTCATTGCTCTTCAAGGAAAATTGAA
1 TACTCTTTAAGGAGATCAGAT-TGGAAATTTTGATTCATTTCACTACTCTTTAAGGAAAATTGAA
* * ** *
2496687 TCATGGTTGATTTGCTTTA-TTTTACTTCAAGAAGATCAAATATGTA-AAAAG-GATATGTTTTA
65 TCATGGTTGATTTGCTTCACTTTTACTTCAAGAAGATCAAAT-T-TAGAAAAGAGATCTACTCTA
2496749 C
128 C
* * * * * *
2496750 TACTCTTTAATGAGATCAGATTTGAAATTTTTTATTCTTTTCACTACCCTTTATGGAAAATTGAA
1 TACTCTTTAAGGAGATCAGATTGGAAA-TTTTGATTCATTTCACTACTCTTTAAGGAAAATTGAA
* ** * * * *
2496815 TCGTGGATT-ATTTGCTTCACTAAT-CTTCAAGAATATCAAATTT-GTAAAAGAGATTTGCTCTG
65 TCATGG-TTGATTTGCTTCACTTTTACTTCAAGAAGATCAAATTTAG-AAAAGAGATCTACTCTA
2496877 C
128 C
* * *
2496878 TACTCTTT-AGAGAGGTCAAATTTGAAAATTTTGATTCATTTCACTACTCTTTAAGGAAAATTGA
1 TACTCTTTAAG-GAGATCAGA-TTGGAAATTTTGATTCATTTCACTACTCTTTAAGGAAAATTGA
** * * * * * * * * *
2496942 ATTTTAGTTGATTTGCTTCACCTTTA-TTCAGGAAGATCAAATCTATAAAAGGGATCTATTTTGC
64 ATCATGGTTGATTTGCTTCACTTTTACTTCAAGAAGATCAAATTTAGAAAAGAGATCTACTCTAC
2497006 TACTCTTTA
1 TACTCTTTA
2497015 GGAAAGACTA
Statistics
Matches: 312, Mismatches: 62, Indels: 34
0.76 0.15 0.08
Matches are distributed among these distances:
126 43 0.14
127 94 0.30
128 164 0.53
129 11 0.04
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (128 bp):
TACTCTTTAAGGAGATCAGATTGGAAATTTTGATTCATTTCACTACTCTTTAAGGAAAATTGAAT
CATGGTTGATTTGCTTCACTTTTACTTCAAGAAGATCAAATTTAGAAAAGAGATCTACTCTAC
Found at i:2496885 original size:255 final size:256
Alignment explanation
Indices: 2496496--2497014 Score: 590
Period size: 256 Copynumber: 2.0 Consensus size: 256
2496486 TATGCTCTGA
* * *
2496496 TACTCTTT-ATGGAGATCAGATCTAGAAATTTTGATTCATTTTATTTCTCTTTAGGTAAAATGGA
1 TACTCTTTAATGGAGATCAGATCTAGAAATTTTGATTCATTTTACTACCCTTTAGGTAAAATGGA
* *
2496560 ATCATGGTTGATTTGCTTACTACTCTTTAAGAATATCAAATTTAGAAAAGAGATCTACTCCACCA
66 ATCATGGTTGATTTGCTTACTAATCTTCAAGAATATCAAATTTAGAAAAGAGATCTACTCCACCA
* * * * *
2496625 CTCTTTA-AGGATATCAGATATGGAAATTTTGATTCA-TTCATTGCTCTTCAAGGAAAATTGAAT
131 CTCTTTAGA-GAGATCAAATATGAAAATTTTGATTCATTTCACTACTCTTCAAGGAAAATTGAAT
* * * * *
2496688 CATGGTTGATTTGCTTTA-TTTTACTTCAAGAAGATCAAATATGTAAAAAGGATATGTTTTAC
195 CATAGTTGATTTGCTTCACCTTTA-TTCAAGAAGATCAAATATATAAAAAGGATATATTTTAC
* *
2496750 TACTCTTTAAT-GAGATCAGAT-TTGAAATTTTTTATTC-TTTTCACTACCCTTTATGG-AAAAT
1 TACTCTTTAATGGAGATCAGATCTAGAAA-TTTTGATTCATTTT-ACTACCCTTTA-GGTAAAAT
* * * *
2496811 TGAATCGTGGATT-ATTTGCTTCACTAATCTTCAAGAATATCAAATTT-GTAAAAGAGATTTGCT
63 GGAATCATGG-TTGATTTGCTT-ACTAATCTTCAAGAATATCAAATTTAG-AAAAGAGATCTACT
** * * * *
2496874 CTGCTACTCTTTAGAGAGGTCAAATTTGAAAATTTTGATTCATTTCACTACTCTTTAAGGAAAAT
125 CCACCACTCTTTAGAGAGATCAAATATGAAAATTTTGATTCATTTCACTACTCTTCAAGGAAAAT
** * * * *
2496939 TGAATTTTAGTTGATTTGCTTCACCTTTATTCAGGAAGATCAAATCTATAAAAGGGATCTATTTT
190 TGAATCATAGTTGATTTGCTTCACCTTTATTCAAGAAGATCAAATATATAAAAAGGATATATTTT
*
2497004 GC
255 AC
2497006 TACTCTTTA
1 TACTCTTTA
2497015 GGAAAGACTA
Statistics
Matches: 221, Mismatches: 34, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
253 9 0.04
254 56 0.25
255 73 0.33
256 79 0.36
257 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (256 bp):
TACTCTTTAATGGAGATCAGATCTAGAAATTTTGATTCATTTTACTACCCTTTAGGTAAAATGGA
ATCATGGTTGATTTGCTTACTAATCTTCAAGAATATCAAATTTAGAAAAGAGATCTACTCCACCA
CTCTTTAGAGAGATCAAATATGAAAATTTTGATTCATTTCACTACTCTTCAAGGAAAATTGAATC
ATAGTTGATTTGCTTCACCTTTATTCAAGAAGATCAAATATATAAAAAGGATATATTTTAC
Found at i:2502080 original size:12 final size:12
Alignment explanation
Indices: 2502059--2502107 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
2502049 ACATGATAAA
* *
2502059 GAATGGAAGAAG
1 GAATGAAAGAAT
2502071 GAATGAAAGAAT
1 GAATGAAAGAAT
*
2502083 GAATGGAAGAAT
1 GAATGAAAGAAT
2502095 GAATGAAAGAAT
1 GAATGAAAGAAT
2502107 G
1 G
2502108 TTTGCCAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.14
Consensus pattern (12 bp):
GAATGAAAGAAT
Found at i:2502086 original size:24 final size:24
Alignment explanation
Indices: 2502059--2502107 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2502049 ACATGATAAA
2502059 GAATGGAAGAAGGAATGAAAGAAT
1 GAATGGAAGAAGGAATGAAAGAAT
*
2502083 GAATGGAAGAATGAATGAAAGAAT
1 GAATGGAAGAAGGAATGAAAGAAT
2502107 G
1 G
2502108 TTTGCCAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.14
Consensus pattern (24 bp):
GAATGGAAGAAGGAATGAAAGAAT
Found at i:2505549 original size:23 final size:23
Alignment explanation
Indices: 2505481--2505541 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2505471 CATTATTATA
*
2505481 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
2505504 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
2505527 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
2505542 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:2518622 original size:18 final size:18
Alignment explanation
Indices: 2518582--2518631 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
2518572 ACTGACTTGG
*
2518582 TTGAAACTGTTAGGGTGG
1 TTGAAACTGTTAGGGTGA
* * *
2518600 CTGAAATTGTTAGGGTTA
1 TTGAAACTGTTAGGGTGA
2518618 TTGAAACTGTTAGG
1 TTGAAACTGTTAGG
2518632 ATTGTTGGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.36
Consensus pattern (18 bp):
TTGAAACTGTTAGGGTGA
Found at i:2518643 original size:18 final size:18
Alignment explanation
Indices: 2518582--2518644 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
2518572 ACTGACTTGG
* **
2518582 TTGAAACTGTTAGGGTGG
1 TTGAAACTGTTAGGATTA
* * *
2518600 CTGAAATTGTTAGGGTTA
1 TTGAAACTGTTAGGATTA
*
2518618 TTGAAACTGTTAGGATTG
1 TTGAAACTGTTAGGATTA
*
2518636 TTGGAACTG
1 TTGAAACTG
2518645 ATAGAATTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.25, C:0.06, G:0.32, T:0.37
Consensus pattern (18 bp):
TTGAAACTGTTAGGATTA
Found at i:2525900 original size:6 final size:6
Alignment explanation
Indices: 2525895--2525966 Score: 108
Period size: 6 Copynumber: 12.0 Consensus size: 6
2525885 TATCCAATAC
* * * *
2525895 ATATAC ATATAC ATATAC ATATAC ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
2525943 ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT
2525967 GTATTTGTAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:2528867 original size:170 final size:169
Alignment explanation
Indices: 2528586--2528924 Score: 669
Period size: 170 Copynumber: 2.0 Consensus size: 169
2528576 ACCATTCTCC
2528586 AAAGCATTGAAGGATCCACTCAACTGACAATGAAATCACGCACATCGTTCCCATTACGCAGTCTG
1 AAAGCATTGAAGGATCCACTCAACTGACAATGAAATCACGCACATCGTTCCCATTACGCAGTCTG
2528651 GGGGGCACAAATGTATGAGCACGAAAATCATCGAGACATGAGTCTACACAAGCTCCCACCGCAAC
66 GGGGGCACAAATGTATGAGCACGAAAATCATCGAGACATGAGTCTACACAAGCTCCCACCGCAAC
2528716 TGGAAACAACGAACCACCTTCAGCATTCGAAACATCGGG
131 TGGAAACAACGAACCACCTTCAGCATTCGAAACATCGGG
2528755 AAAGCATTGAAGGATCCACTCAACTGACAAATGAAATCACGCACATCGTTCCCATTACGCAGTCT
1 AAAGCATTGAAGGATCCACTCAACTGAC-AATGAAATCACGCACATCGTTCCCATTACGCAGTCT
2528820 GGGGGGCACAAATGTATGAGCACGAAAATCATCGAGACATGAGTCTACACAAGCTCCCACCGCAA
65 GGGGGGCACAAATGTATGAGCACGAAAATCATCGAGACATGAGTCTACACAAGCTCCCACCGCAA
2528885 CTGGAAACAACGAACCACCTTCAGCATTCGAAACATCGGG
130 CTGGAAACAACGAACCACCTTCAGCATTCGAAACATCGGG
2528925 GACAGCATGC
Statistics
Matches: 169, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 28 0.17
170 141 0.83
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (169 bp):
AAAGCATTGAAGGATCCACTCAACTGACAATGAAATCACGCACATCGTTCCCATTACGCAGTCTG
GGGGGCACAAATGTATGAGCACGAAAATCATCGAGACATGAGTCTACACAAGCTCCCACCGCAAC
TGGAAACAACGAACCACCTTCAGCATTCGAAACATCGGG
Found at i:2534678 original size:68 final size:68
Alignment explanation
Indices: 2534569--2534702 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 68
2534559 CCGACAATAA
* * *
2534569 ATGTGAAACTTGGATCTTTTGATTTGTTTCCTGAGTTAGGTTAAGTTAGGTGATTGAGAGATCAA
1 ATGTGAAACTTGGATCTATTGATTTGTTTCCTGAATTAGGTTAAGTTAGGTAATTGAGAGATCAA
2534634 CGC
66 CGC
2534637 ATGTGAAACTTGGATCTATTGATTTGTTTCCTGAATTAGGTTAAGTTAGGTAATTGAGAGATCAA
1 ATGTGAAACTTGGATCTATTGATTTGTTTCCTGAATTAGGTTAAGTTAGGTAATTGAGAGATCAA
2534702 C
66 C
2534703 ACTGATGAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (68 bp):
ATGTGAAACTTGGATCTATTGATTTGTTTCCTGAATTAGGTTAAGTTAGGTAATTGAGAGATCAA
CGC
Found at i:2537272 original size:64 final size:64
Alignment explanation
Indices: 2537174--2537295 Score: 208
Period size: 64 Copynumber: 1.9 Consensus size: 64
2537164 GTATATATAC
* * *
2537174 ATATATGTTTATCGTATGAATCTTTCTTATGGCTAATTCCATATTATACTATTATATAGTGTAT
1 ATATATATATATCGTATGAATATTTCTTATGGCTAATTCCATATTATACTATTATATAGTGTAT
*
2537238 ATATATATATATCGTATGAATATTTCTTATGGCTAATTTCATATTATACTATTATATA
1 ATATATATATATCGTATGAATATTTCTTATGGCTAATTCCATATTATACTATTATATA
2537296 TAATTTAACG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (64 bp):
ATATATATATATCGTATGAATATTTCTTATGGCTAATTCCATATTATACTATTATATAGTGTAT
Found at i:2541997 original size:22 final size:22
Alignment explanation
Indices: 2541972--2542018 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2541962 GCTCCTTGAT
2541972 AGCTCCTTACTTTCCATTATTG
1 AGCTCCTTACTTTCCATTATTG
2541994 AGCTCCTTACTTTCCATTATTG
1 AGCTCCTTACTTTCCATTATTG
2542016 AGC
1 AGC
2542019 AGGTTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.43
Consensus pattern (22 bp):
AGCTCCTTACTTTCCATTATTG
Found at i:2545786 original size:16 final size:16
Alignment explanation
Indices: 2545762--2545796 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2545752 GAGGATTAAA
* *
2545762 TTTATTTTAATTTATT
1 TTTAATTTAATATATT
2545778 TTTAATTTAATATATT
1 TTTAATTTAATATATT
2545794 TTT
1 TTT
2545797 CTCACCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTTAATATATT
Found at i:2546134 original size:12 final size:13
Alignment explanation
Indices: 2546107--2546135 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2546097 TCAATTAGGA
2546107 TTTAGAATATTAT
1 TTTAGAATATTAT
2546120 TTTA-AATATTAT
1 TTTAGAATATTAT
2546132 TTTA
1 TTTA
2546136 TCTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTAGAATATTAT
Found at i:2546736 original size:18 final size:18
Alignment explanation
Indices: 2546713--2546755 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2546703 CTTTAGATTA
*
2546713 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
2546731 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
2546749 TTTATTT
1 TTTATTT
2546756 TAATAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2546909 original size:30 final size:31
Alignment explanation
Indices: 2546874--2546932 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
2546864 CAAATTTAAC
2546874 ACTTCTTTTTTT-TATTT-TTTTTATTTTCCT
1 ACTTCTTTTTTTAT-TTTATTTTTATTTTCCT
2546904 ACTTCTTTTTTTATTTTATTTTTATTTTC
1 ACTTCTTTTTTTATTTTATTTTTATTTTC
2546933 TCTTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (31 bp):
ACTTCTTTTTTTATTTTATTTTTATTTTCCT
Found at i:2546926 original size:31 final size:30
Alignment explanation
Indices: 2546874--2546932 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 30
2546864 CAAATTTAAC
2546874 ACTTCTTTTTTTTATTTTTTTTATTTTCCT
1 ACTTCTTTTTTTTATTTTTTTTATTTTCCT
2546904 ACTTC-TTTTTTTATTTTATTTTTATTTTC
1 ACTTCTTTTTTTTA-TTT-TTTTTATTTTC
2546933 TCTTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.30
30 8 0.30
31 11 0.41
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (30 bp):
ACTTCTTTTTTTTATTTTTTTTATTTTCCT
Found at i:2546931 original size:18 final size:17
Alignment explanation
Indices: 2546883--2546959 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 17
2546873 CACTTCTTTT
2546883 TTTTA-TTTTTTTTAT-
1 TTTTATTTTTTTTTATA
*
2546898 TTTCCTACTTCTTTTTT-TA
1 TTT--TA-TTTTTTTTTATA
* *
2546917 TTTTATTTTTATTTTCTC
1 TTTTATTTTT-TTTTATA
*
2546935 TTTTAATATTTTTTTATA
1 TTTT-ATTTTTTTTTATA
2546953 TTTTATT
1 TTTTATT
2546960 ATGTTTCCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
15 3 0.06
16 4 0.09
17 10 0.21
18 15 0.32
19 15 0.32
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTTTTTATA
Found at i:2549378 original size:20 final size:20
Alignment explanation
Indices: 2549353--2549396 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2549343 GATCCATCAA
2549353 GCTGGAGCAGTACAGTCTAC
1 GCTGGAGCAGTACAGTCTAC
*
2549373 GCTGGAGCAGTACCGTCTAC
1 GCTGGAGCAGTACAGTCTAC
2549393 GCTG
1 GCTG
2549397 CACCAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.20
Consensus pattern (20 bp):
GCTGGAGCAGTACAGTCTAC
Found at i:2553525 original size:42 final size:41
Alignment explanation
Indices: 2553478--2553698 Score: 105
Period size: 42 Copynumber: 5.2 Consensus size: 41
2553468 CAGACCCGCA
2553478 AAGGGGAACCACCTGAAGAATATACTACATGACTTTCCCGTG
1 AAGGGGAACCACCTGAAGAATATACTACATG-CTTTCCCGTG
** * * *
2553520 AAGGGGATTCATCC-AAAG-ATCAT-CTCACATG-GTTCAGACCCTCG
1 AAGGGGAACCA-CCTGAAGAAT-ATACT-ACATGCTTTC---CCGT-G
* *
2553564 AAGGGGAACCACCTGAAGAATATACAACATGACTTTCCTGTG
1 AAGGGGAACCACCTGAAGAATATACTACATG-CTTTCCCGTG
** * * * *
2553606 AAGGGGAGTCATCC-AAAG-ATCAT-CTCACCTGGTTTAGACCCGCG
1 AAGGGGAACCA-CCTGAAGAAT-ATACT-ACATGCTTT---CCCGTG
* * *
2553650 AAGGGGAACCACCTGAAGAATATACCACTTGGCTTTCCCGTA
1 AAGGGGAACCACCTGAAGAATATACTACAT-GCTTTCCCGTG
2553692 AAGGGGA
1 AAGGGGA
2553699 GTCATTTAAA
Statistics
Matches: 129, Mismatches: 28, Indels: 44
0.64 0.14 0.22
Matches are distributed among these distances:
40 3 0.02
41 10 0.08
42 49 0.38
43 13 0.10
44 41 0.32
45 10 0.08
46 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (41 bp):
AAGGGGAACCACCTGAAGAATATACTACATGCTTTCCCGTG
Found at i:2553710 original size:86 final size:86
Alignment explanation
Indices: 2553418--2553703 Score: 428
Period size: 86 Copynumber: 3.3 Consensus size: 86
2553408 AGAACATCTC
* * * * * *
2553418 ACATGACTTTCCCGTGAAAGGAAGTTATCCGAAGATAATCTCACCTGGTTCAGACCCGCAAAGGG
1 ACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGGG
*
2553483 GAACCACCTGAAGAATATACT
66 GAACCACCTGAAGAATATACA
* * *
2553504 ACATGACTTTCCCGTGAAGGGGATTCATCCAAAGATCATCTCACATGGTTCAGACCCTCGAAGGG
1 ACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGGG
2553569 GAACCACCTGAAGAATATACA
66 GAACCACCTGAAGAATATACA
* *
2553590 ACATGACTTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTTAGACCCGCGAAGGG
1 ACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGGG
*
2553655 GAACCACCTGAAGAATATACC
66 GAACCACCTGAAGAATATACA
* * *
2553676 ACTTGGCTTTCCCGTAAAGGGGAGTCAT
1 ACATGACTTTCCCGTGAAGGGGAGTCAT
2553704 TTAAAGAATT
Statistics
Matches: 180, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 180 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (86 bp):
ACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGGG
GAACCACCTGAAGAATATACA
Found at i:2554634 original size:12 final size:12
Alignment explanation
Indices: 2554601--2554634 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2554591 GGGAATAAAA
2554601 TCTC-ATTTTTC
1 TCTCTATTTTTC
*
2554612 TCTCTAGTTTTC
1 TCTCTATTTTTC
2554624 TCTCTATTTTT
1 TCTCTATTTTT
2554635 TGCACACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.09, C:0.24, G:0.03, T:0.65
Consensus pattern (12 bp):
TCTCTATTTTTC
Found at i:2555043 original size:18 final size:18
Alignment explanation
Indices: 2555020--2555058 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2555010 TTTTAGATTA
*
2555020 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
2555038 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
2555056 TTT
1 TTT
2555059 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2555401 original size:16 final size:16
Alignment explanation
Indices: 2555371--2555416 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
2555361 TCCTTCTTTG
*
2555371 ATTTT-TTTTTTTTTA
1 ATTTTATTTTTATTTA
2555386 ATTTTATTTTTATTTA
1 ATTTTATTTTTATTTA
2555402 ATATTTA-TTTTATTT
1 AT-TTTATTTTTATTT
2555417 TATAATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.18
16 19 0.68
17 4 0.14
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTATTTTTATTTA
Found at i:2555826 original size:30 final size:30
Alignment explanation
Indices: 2555792--2556051 Score: 200
Period size: 30 Copynumber: 8.9 Consensus size: 30
2555782 TTAAAATAAA
* *
2555792 AAATATATTTTATTTTTATATTAACTTATT
1 AAATATATTTTATTCTTATCTTAACTTATT
* * * *
2555822 AAATATATTTTATTATTGTCTTAACCTA-A
1 AAATATATTTTATTCTTATCTTAACTTATT
*
2555851 AAATATATTTTATTCTTATTTTAACTTA--
1 AAATATATTTTATTCTTATCTTAACTTATT
* **
2555879 AAATATATTTTAGTCTTTATCTTAACTTAAA
1 AAATATATTTTATTC-TTATCTTAACTTATT
* *
2555910 AAATATATTGTATTCTTATCTTAATTTATT
1 AAATATATTTTATTCTTATCTTAACTTATT
* * ** *
2555940 ACATA-A----ATT-ATAAATTAAATTATT
1 AAATATATTTTATTCTTATCTTAACTTATT
* *
2555964 AAATATATTATATTCTTA-CTTTAAATTATT
1 AAATATATTTTATTCTTATC-TTAACTTATT
* * * *
2555994 AAATATATTTAATTATTATTTTAACTTA-A
1 AAATATATTTTATTCTTATCTTAACTTATT
*
2556023 AACATATTTTTTATTCTTATCTTAACTTA
1 AA-ATATATTTTATTCTTATCTTAACTTA
2556052 AAAGTATATT
Statistics
Matches: 184, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
24 15 0.08
25 4 0.02
28 14 0.08
29 42 0.23
30 96 0.52
31 13 0.07
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (30 bp):
AAATATATTTTATTCTTATCTTAACTTATT
Found at i:2555855 original size:59 final size:59
Alignment explanation
Indices: 2555790--2556051 Score: 254
Period size: 59 Copynumber: 4.5 Consensus size: 59
2555780 TCTTAAAATA
* * * *
2555790 AAAAATATATTTTATTTTTATATTAACTTATTAAATATATTTTATTATTGTCTTAACCT
1 AAAAATATATTTTATTCTTATCTTAACTTATTAAATATATTTTATTATTATCTTAACTT
*
2555849 AAAAATATATTTTATTCTTATTTTAACTTA--AAATATATTTTAGTCT-TTATCTTAACTT
1 AAAAATATATTTTATTCTTATCTTAACTTATTAAATATATTTTA-T-TATTATCTTAACTT
* * * * * * **
2555907 AAAAAATATATTGTATTCTTATCTTAATTTATTACATAAATTATA-AATTAAATT-A-TT
1 -AAAAATATATTTTATTCTTATCTTAACTTATTAAATATATTTTATTATTATCTTAACTT
* * * *
2555964 --AAATATATTATATTCTTA-CTTTAAATTATTAAATATATTTAATTATTATTTTAACTT
1 AAAAATATATTTTATTCTTATC-TTAACTTATTAAATATATTTTATTATTATCTTAACTT
*
2556021 AAAACATATTTTTTATTCTTATCTTAACTTA
1 AAAA-ATATATTTTATTCTTATCTTAACTTA
2556052 AAAGTATATT
Statistics
Matches: 164, Mismatches: 25, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
53 1 0.01
54 34 0.21
55 6 0.04
56 1 0.01
57 16 0.10
58 12 0.07
59 63 0.38
60 21 0.13
61 10 0.06
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (59 bp):
AAAAATATATTTTATTCTTATCTTAACTTATTAAATATATTTTATTATTATCTTAACTT
Found at i:2555962 original size:24 final size:24
Alignment explanation
Indices: 2555930--2555975 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2555920 TATTCTTATC
* *
2555930 TTAATTTATTACATAAATTATAAA
1 TTAAATTATTAAATAAATTATAAA
*
2555954 TTAAATTATTAAATATATTATA
1 TTAAATTATTAAATAAATTATA
2555976 TTCTTACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAATTATTAAATAAATTATAAA
Found at i:2556109 original size:30 final size:31
Alignment explanation
Indices: 2556068--2556134 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
2556058 TATTGCCCTT
* * * *
2556068 TTAACTACAAAAATATGTGTTAT-TTTTATC
1 TTAAATACAAAAAAATATATTATATTTTATC
2556098 TTAAATACAAAAAAATATATTATATTTTATC
1 TTAAATACAAAAAAATATATTATATTTTATC
2556129 TTAAAT
1 TTAAAT
2556135 TTAAAATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (31 bp):
TTAAATACAAAAAAATATATTATATTTTATC
Found at i:2556220 original size:30 final size:29
Alignment explanation
Indices: 2556181--2556255 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
2556171 CATATAAGAA
*
2556181 TAAATTATATTTTTAAATTTAAGATAAGATT
1 TAAA-TATATTTTTAAA-TTAAAATAAGATT
*
2556212 TAAATATATGTTTTAAATTAAAATAAGCTT
1 TAAATATAT-TTTTAAATTAAAATAAGATT
*
2556242 AAAATATATTTTTA
1 TAAATATATTTTTA
2556256 GGTTACGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.12
30 24 0.60
31 11 0.28
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (29 bp):
TAAATATATTTTTAAATTAAAATAAGATT
Found at i:2556779 original size:17 final size:18
Alignment explanation
Indices: 2556757--2556791 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2556747 TAATTATACG
2556757 TTAAATCTTT-TAAAATT
1 TTAAATCTTTATAAAATT
*
2556774 TTAAATTTTTATAAAATT
1 TTAAATCTTTATAAAATT
2556792 AAATTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAATCTTTATAAAATT
Found at i:2557634 original size:17 final size:18
Alignment explanation
Indices: 2557596--2557643 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
2557586 GTTTATGATA
2557596 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGTGAAG
*
2557614 GAATTGGAATCTGT-CAG
1 GAATTGGAATCTGTGAAG
2557631 GAATTGGAATCTG
1 GAATTGGAATCTG
2557644 AATCTGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (18 bp):
GAATTGGAATCTGTGAAG
Found at i:2558232 original size:16 final size:17
Alignment explanation
Indices: 2558196--2558233 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2558186 TTAAAATAAA
*
2558196 TAATTATAAAAATATAG
1 TAATTATAAAAATATAC
*
2558213 TAATTA-AAAAATTTAC
1 TAATTATAAAAATATAC
2558229 TAATT
1 TAATT
2558234 TTTTTCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
TAATTATAAAAATATAC
Found at i:2560605 original size:20 final size:20
Alignment explanation
Indices: 2560580--2560633 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2560570 ATCCAAAGTG
2560580 GGTAGTATCGATACTCTACT
1 GGTAGTATCGATACTCTACT
2560600 GGTAGTATCGATACTCTACT
1 GGTAGTATCGATACTCTACT
* *
2560620 TGTAGTATTGATAC
1 GGTAGTATCGATAC
2560634 CCTAAGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (20 bp):
GGTAGTATCGATACTCTACT
Found at i:2564863 original size:17 final size:18
Alignment explanation
Indices: 2564843--2564876 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2564833 TGGACTTTTT
2564843 AATTT-AGACAAAGATAG
1 AATTTCAGACAAAGATAG
*
2564860 AATTTCAGATAAAGATA
1 AATTTCAGACAAAGATA
2564877 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (18 bp):
AATTTCAGACAAAGATAG
Found at i:2565971 original size:17 final size:17
Alignment explanation
Indices: 2565912--2565977 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
2565902 TAAATCCTAA
*
2565912 TTAAAATAATTAAAACTAT
1 TTAAAATAA-TATAA-TAT
* *
2565931 TTAAATTAAAATACATAT
1 TTAAAATAATATA-ATAT
**
2565949 AAAAAATAATATAATAT
1 TTAAAATAATATAATAT
2565966 TTAAAATAATAT
1 TTAAAATAATAT
2565978 CCTAAAACTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
17 14 0.38
18 14 0.38
19 9 0.24
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAATAATATAATAT
Found at i:2567636 original size:23 final size:23
Alignment explanation
Indices: 2567583--2567636 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2567573 TAAGTATTTT
* **
2567583 AAATTTTTAAAGAAATCAAATTG
1 AAATTTTTAAAAAAATCAAATAC
*
2567606 AAAATTTTAAAAAAATCAAATAC
1 AAATTTTTAAAAAAATCAAATAC
*
2567629 TAATTTTT
1 AAATTTTT
2567637 TAAGGGTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (23 bp):
AAATTTTTAAAAAAATCAAATAC
Found at i:2569187 original size:27 final size:27
Alignment explanation
Indices: 2569147--2569207 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
2569137 CATGGCACAC
*
2569147 TGTT-ATGCAGCACCCCATCCTCTACA
1 TGTTGATGCAACACCCCATCCTCTACA
* *
2569173 TGTTGATGCAACACCTCATCCTCTACT
1 TGTTGATGCAACACCCCATCCTCTACA
2569200 TGTTGATG
1 TGTTGATG
2569208 AGCTGGTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (27 bp):
TGTTGATGCAACACCCCATCCTCTACA
Found at i:2579828 original size:2 final size:2
Alignment explanation
Indices: 2579821--2579861 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2579811 TTTGTAGAAC
2579821 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
2579862 TTAAAGTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2584266 original size:35 final size:35
Alignment explanation
Indices: 2584221--2584341 Score: 170
Period size: 36 Copynumber: 3.4 Consensus size: 35
2584211 AGATGAACAA
* *
2584221 TTGAACCGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
* *
2584256 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC-AC
* *
2584292 TTGAGTCGAAAGTGTCGATGCTTCTTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
2584327 TTTGAATCGAAAGTG
1 -TTGAATCGAAAGTG
2584342 CTAATACTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
35 31 0.41
36 44 0.59
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
Found at i:2584302 original size:36 final size:35
Alignment explanation
Indices: 2584221--2584360 Score: 167
Period size: 36 Copynumber: 3.9 Consensus size: 35
2584211 AGATGAACAA
* * *
2584221 TTGAACCGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCAC
*
2584256 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC-AC
*
2584292 TTGAGTCGAAAGTGTCGATGCTT-CTTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTT-CGTTCAC
* *
2584327 TTTGAATCGAAAGTG-CTAATACTTCCTTTCGTTC
1 -TTGAATCGAAAGTGTC-GATGCTTCCTTTCGTTC
2584361 TTCTTATTCA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
35 36 0.40
36 51 0.56
37 4 0.04
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCAC
Found at i:2584362 original size:72 final size:71
Alignment explanation
Indices: 2584227--2584365 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 71
2584217 ACAATTGAAC
* * *
2584227 CGAAAGTGTTGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 CGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCAATACTTCCTTTCGTTCTTC
2584292 TTGAGT
66 TTGAGT
*
2584298 CGAAAGTGTCGATGCTTCTTTCCGTTCACTTTGAATCGAAAGTG-CTAATACTTCCTTTCGTTCT
1 CGAAAGTGTCGATGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGTC-AATACTTCCTTTCGTTCT
2584362 TCTT
64 TCTT
2584366 ATTCACCTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
71 28 0.45
72 34 0.55
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (71 bp):
CGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCAATACTTCCTTTCGTTCTTC
TTGAGT
Found at i:2587074 original size:15 final size:16
Alignment explanation
Indices: 2587041--2587074 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2587031 TCTTATGAAC
2587041 ACATGGTGACTACTCTT
1 ACATGGTGACTA-TCTT
2587058 ACATGGTGACT-TCTT
1 ACATGGTGACTATCTT
2587073 AC
1 AC
2587075 CAGCGGAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (16 bp):
ACATGGTGACTATCTT
Found at i:2591320 original size:3 final size:3
Alignment explanation
Indices: 2591312--2591363 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2591302 AATTGAGTAA
*
2591312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AGT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2591358 ATAT AA
1 A-AT AA
2591364 AAAAACAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2592202 original size:9 final size:9
Alignment explanation
Indices: 2592164--2592264 Score: 66
Period size: 9 Copynumber: 10.8 Consensus size: 9
2592154 GCATGCAAAA
2592164 AATAA-AAT
1 AATAATAAT
*
2592172 AAAAATAAAT
1 AATAAT-AAT
* *
2592182 AAAAATATT
1 AATAATAAT
*
2592191 AATATTAAT
1 AATAATAAT
2592200 AATAATAAT
1 AATAATAAT
2592209 AATAATAAAT
1 AATAAT-AAT
2592219 AAATAAATATAT
1 -AAT-AATA-AT
2592231 AAT-ATAAT
1 AATAATAAT
2592239 AAATAAATATAT
1 -AAT-AATA-AT
2592251 AAT-ATAAT
1 AATAATAAT
2592259 AA-AATA
1 AATAATA
2592265 TTTTTGTAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
8 13 0.17
9 31 0.41
10 12 0.16
11 13 0.17
12 7 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATAAT
Found at i:2592206 original size:28 final size:28
Alignment explanation
Indices: 2592169--2592264 Score: 83
Period size: 33 Copynumber: 3.4 Consensus size: 28
2592159 CAAAAAATAA
*
2592169 AATAAAAATAAATAAAAATATTAATATT
1 AATAATAATAAATAAAAATATTAATATT
*
2592197 AATAATAATAATAATAATAAATAAATAAATATAT
1 AATAATAAT-A-AATAA-AAAT--ATTAATAT-T
*
2592231 AAT-ATAATAAATAAATATA-TAATA-T
1 AATAATAATAAATAAAAATATTAATATT
2592256 AATAA-AATA
1 AATAATAATA
2592265 TTTTTGTAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
25 8 0.14
26 1 0.02
27 4 0.07
28 9 0.16
29 1 0.02
30 8 0.14
31 9 0.16
32 1 0.02
33 12 0.21
34 4 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
AATAATAATAAATAAAAATATTAATATT
Found at i:2592213 original size:12 final size:12
Alignment explanation
Indices: 2592164--2592264 Score: 66
Period size: 12 Copynumber: 8.1 Consensus size: 12
2592154 GCATGCAAAA
*
2592164 AATAA-AATAAA
1 AATAATAATAAT
*
2592175 AATAAATAAAAAT
1 AAT-AATAATAAT
* *
2592188 ATTAATATTAAT
1 AATAATAATAAT
2592200 AATAATAATAAT
1 AATAATAATAAT
2592212 AATAAATAAATAAAT
1 AAT-AAT-AAT-AAT
2592227 ATATAAT-ATAAT
1 A-ATAATAATAAT
2592239 AAATAAATATATAAT
1 -AAT-AATA-ATAAT
2592254 -ATAATAA-AAT
1 AATAATAATAAT
2592264 A
1 A
2592265 TTTTTGTAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
10 3 0.04
11 4 0.06
12 31 0.43
13 17 0.24
14 3 0.04
15 12 0.17
16 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:2592225 original size:8 final size:8
Alignment explanation
Indices: 2592212--2592261 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
2592202 TAATAATAAT
2592212 AATAAATA
1 AATAAATA
2592220 AATAAATA
1 AATAAATA
*
2592228 TAT-AATA
1 AATAAATA
2592235 TAATAAATA
1 -AATAAATA
*
2592244 AATATAT-
1 AATAAATA
2592251 AATATAATA
1 AATA-AATA
2592260 AA
1 AA
2592262 ATATTTTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
7 8 0.24
8 20 0.59
9 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AATAAATA
Found at i:2592239 original size:20 final size:20
Alignment explanation
Indices: 2592175--2592261 Score: 108
Period size: 20 Copynumber: 4.3 Consensus size: 20
2592165 ATAAAATAAA
*
2592175 AATAAATAAAAATATTAATATT
1 AATAAATAAATATA-TAATA-T
2592197 AAT-AAT-AATA-ATAATAAT
1 AATAAATAAATATATAAT-AT
2592215 AAATAAATAAATATATAATAT
1 -AATAAATAAATATATAATAT
2592236 AATAAATAAATATATAATAT
1 AATAAATAAATATATAATAT
2592256 AATAAA
1 AATAAA
2592262 ATATTTTTGT
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
18 5 0.08
19 5 0.08
20 32 0.54
21 9 0.15
22 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAATAAATATATAATAT
Found at i:2593598 original size:6 final size:6
Alignment explanation
Indices: 2593569--2593648 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
2593559 GCCTGCAAAA
* * *
2593569 AATAA- AATAA- AAAAAT AA-AA- AATATT AATATT AATAAT AATAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
2593613 AATAAT AAATATAT ATATATAT ATATAAT -ATAAT AA
1 AATAAT -AATA-AT A-ATA-AT A-ATAAT AATAAT AA
2593649 AATGTTTTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
4 2 0.03
5 17 0.26
6 26 0.40
7 7 0.11
8 13 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATAAT
Found at i:2593606 original size:9 final size:9
Alignment explanation
Indices: 2593569--2593648 Score: 53
Period size: 9 Copynumber: 8.9 Consensus size: 9
2593559 GCCTGCAAAA
2593569 AATAA-AAT
1 AATAATAAT
*
2593577 AA-AAAAAT
1 AATAATAAT
2593585 AA-AA-AAT
1 AATAATAAT
* *
2593592 ATTAATATT
1 AATAATAAT
2593601 AATAATAAT
1 AATAATAAT
2593610 AATAATAAT
1 AATAATAAT
2593619 AAATATATATAT
1 -AATA-ATA-AT
2593631 ATATATATAAT
1 A-ATA-ATAAT
2593642 -ATAATAA
1 AATAATAA
2593649 AATGTTTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.10
8 15 0.25
9 21 0.34
10 4 0.07
11 6 0.10
12 9 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AATAATAAT
Found at i:2594288 original size:32 final size:32
Alignment explanation
Indices: 2594252--2594338 Score: 156
Period size: 32 Copynumber: 2.7 Consensus size: 32
2594242 GGTGTTACAG
2594252 ATGACCCCTTCGTCGTGAAGTTGTATATGTAT
1 ATGACCCCTTCGTCGTGAAGTTGTATATGTAT
*
2594284 ATGACCCATTCGTCGTGAAGTTGTATATGTAT
1 ATGACCCCTTCGTCGTGAAGTTGTATATGTAT
*
2594316 ATGGCCCCTTCGTCGTGAAGTTG
1 ATGACCCCTTCGTCGTGAAGTTG
2594339 AGCCTGAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (32 bp):
ATGACCCCTTCGTCGTGAAGTTGTATATGTAT
Found at i:2594583 original size:106 final size:106
Alignment explanation
Indices: 2594398--2594609 Score: 284
Period size: 106 Copynumber: 2.0 Consensus size: 106
2594388 TGTATTGCTC
* * *
2594398 CGAGTCCAATATCCTCCGTCGTGAAGTTTGAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTTGAATTGACTCCGAAACTGGGAAATTGTTTGTTGACA
**
2594463 GTCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
2594504 CGAGTCTAATATCCTTCG-CTGTGAAG-TTGAAATTGACTCCGAAATTGGGAAGTTGTTTGTTGA
1 CGAGTCCAATATCCTCCGTC-GTGAAGTTTG-AATTGACTCCGAAACTGGGAAATTGTTTGTTGA
* * *
2594567 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
2594610 TAAGTGTTGA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
105 4 0.04
106 88 0.96
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCGTCGTGAAGTTTGAATTGACTCCGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:2594808 original size:106 final size:106
Alignment explanation
Indices: 2594682--2594995 Score: 501
Period size: 106 Copynumber: 3.0 Consensus size: 106
2594672 TTGCTCCGAG
* *
2594682 TCCAATATCCTTC-TTCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAACC
1 TCCAATATCCTTCGCT-GTGAAGTTGAAATTGGTTCTGGAATTGGGAAATTGTTTGTTGACAACC
*
2594746 AGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT-CTCGAC
65 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCT-GAC
* * *
2594788 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTTACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGGAATTGGGAAATTGTTTGTTGACAACCA
*
2594853 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCTGAG
66 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCTGAC
2594894 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTT-T-GAAGTTGGGAAATTGTTTGTTGACAAC
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGG-TTCTGGAA-TTGGGAAATTGTTTGTTGACAAC
2594957 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
64 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
2594996 CGAGTGGCAC
Statistics
Matches: 194, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
105 2 0.01
106 188 0.97
107 4 0.02
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (106 bp):
TCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGGAATTGGGAAATTGTTTGTTGACAACCA
GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCTGAC
Found at i:2594842 original size:280 final size:280
Alignment explanation
Indices: 2594335--2594888 Score: 932
Period size: 280 Copynumber: 2.0 Consensus size: 280
2594325 TCGTCGTGAA
2594335 GTTGAGCCTGAGAATTGGATATCCTTCGTCGAGAAGTTGAAATCCAAGTAAGTTGTATTGCTCCG
1 GTTGAGCCTGAGAATTGGATATCCTTCGTCGAGAAGTTGAAATCCAAGTAAGTTGTATTGCTCCG
**
2594400 AGTCCAATATCCTCCGTCGTGAAGTTTGAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAGT
66 AGTCCAATATCCTCCGTCGTGAAGTTTGAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
* *
2594465 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAG
131 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGACTCCAATATCCTTCGCTGTGAAG
*
2594530 TTGAAATTGACTCCGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
196 TTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
2594595 GAACTTGTGTTGTCTTAAGT
261 GAACTTGTGTTGTCTTAAGT
*
2594615 GTTGAGCCTG-GTAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGCTCC
1 GTTGAGCCTGAG-AATTGGATATCCTTCGTCGAGAAGTTGAAATCCAAGTAAGTTGTATTGCTCC
* * *
2594679 GAGTCCAATATCCTTCTTCGTGAAG-TTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
65 GAGTCCAATATCCTCCGTCGTGAAGTTTG-AATTGGCTCTGGAACTGGGAAATTGTTTGTTGACA
* * * *
2594743 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGACTCCAATATCCTTCGCTGTGA
129 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGACTCCAATATCCTTCGCTGTGA
* * *
2594808 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTTACAACCAGCCGTCCCTTCGTTGTGAAG
194 AGTTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAG
2594873 TTGAACTTGTGTTGTC
259 TTGAACTTGTGTTGTC
2594889 CTGAGTCCAA
Statistics
Matches: 256, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
279 4 0.02
280 252 0.98
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (280 bp):
GTTGAGCCTGAGAATTGGATATCCTTCGTCGAGAAGTTGAAATCCAAGTAAGTTGTATTGCTCCG
AGTCCAATATCCTCCGTCGTGAAGTTTGAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGACTCCAATATCCTTCGCTGTGAAG
TTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
GAACTTGTGTTGTCTTAAGT
Found at i:2595776 original size:36 final size:36
Alignment explanation
Indices: 2595725--2595837 Score: 145
Period size: 36 Copynumber: 3.1 Consensus size: 36
2595715 AAGATTTTAG
* *
2595725 GTTTCAAAAGTAATTGTCTCAAGGGAGACAAAATTT
1 GTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTT
** *
2595761 GTTTCAAGGGAAATTGTCTCAAGAGAGACAAAACTTA
1 GTTTCAAAAGAAATTGTCTCAAGAGAGACAAAA-TTT
* * *
2595798 GTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTT
1 GTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTT
2595834 GTTT
1 GTTT
2595838 TAAGAAAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 34 0.53
37 30 0.47
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
GTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTT
Found at i:2595820 original size:37 final size:36
Alignment explanation
Indices: 2595729--2595832 Score: 127
Period size: 37 Copynumber: 2.9 Consensus size: 36
2595719 TTTTAGGTTT
* * * *
2595729 CAAAAGTAATTGTCTCAAGGGAGACAAAATTTGTTT
1 CAAAAGAAATTGTCTCAAGAGAGACAAAATTAGTTC
**
2595765 CAAGGGAAATTGTCTCAAGAGAGACAAAACTTAGTTC
1 CAAAAGAAATTGTCTCAAGAGAGACAAAA-TTAGTTC
* *
2595802 CAAAAGAAACTGTCTCAAGAGAGACGAAATT
1 CAAAAGAAATTGTCTCAAGAGAGACAAAATT
2595833 TGTTTTAAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 27 0.47
37 30 0.53
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (36 bp):
CAAAAGAAATTGTCTCAAGAGAGACAAAATTAGTTC
Found at i:2597419 original size:36 final size:36
Alignment explanation
Indices: 2597379--2597455 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
2597369 TGATTTTTGT
* * *
2597379 TCTTTCCTTTTTCCTTTTGTTCTTGTTTTTCTTTTC
1 TCTTTCCTTTTTCCTTTTGTTATTGATTATCTTTTC
** * *
2597415 TCTTTGTTTTTTCTTTTTGTTATTGATTATCTTTTT
1 TCTTTCCTTTTTCCTTTTGTTATTGATTATCTTTTC
2597451 TCTTT
1 TCTTT
2597456 TTGTTATGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.74
Consensus pattern (36 bp):
TCTTTCCTTTTTCCTTTTGTTATTGATTATCTTTTC
Found at i:2600500 original size:3 final size:3
Alignment explanation
Indices: 2600492--2600530 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
2600482 AATTGAGTAA
*
2600492 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2600531 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2601346 original size:3 final size:3
Alignment explanation
Indices: 2601323--2601384 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
2601313 GTATGCAAAA
* *
2601323 AAT AA- AAT AA- AAA AAT AAAT AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
2601367 AAAT ATAT AAT -AT AAT AA
1 -AAT A-AT AAT AAT AAT AA
2601385 AATGTTTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
2 6 0.12
3 35 0.70
4 9 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2605173 original size:15 final size:15
Alignment explanation
Indices: 2605153--2605246 Score: 66
Period size: 15 Copynumber: 7.0 Consensus size: 15
2605143 TATAATTGAT
*
2605153 TTAATTTTTTTAATA
1 TTAATTTTTTAAATA
2605168 TTAATTTTTTAAATA
1 TTAATTTTTTAAATA
2605183 --AA----TTAAATA
1 TTAATTTTTTAAATA
2605192 TTAATTTTTT-AATA
1 TTAATTTTTTAAATA
* * *
2605206 TT-ATATTATAGATA
1 TTAATTTTTTAAATA
2605220 TTAA--TTTT-AATA
1 TTAATTTTTTAAATA
*
2605232 TTAACTTTTTAAATA
1 TTAATTTTTTAAATA
2605247 AATTATATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
9 7 0.11
11 2 0.03
12 7 0.11
13 10 0.16
14 15 0.24
15 21 0.34
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (15 bp):
TTAATTTTTTAAATA
Found at i:2605213 original size:26 final size:27
Alignment explanation
Indices: 2605163--2605235 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 27
2605153 TTAATTTTTT
2605163 TAATATTAATTTTTTAA-A-TAAATTA
1 TAATATTAATTTTTTAATATTAAATTA
*
2605188 -AATATTAATTTTTTAATATTATATTA
1 TAATATTAATTTTTTAATATTAAATTA
2605214 TAGATATTAA--TTTTAATATTAA
1 TA-ATATTAATTTTTTAATATTAA
2605236 CTTTTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 16 0.38
25 1 0.02
26 17 0.40
27 1 0.02
28 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
TAATATTAATTTTTTAATATTAAATTA
Found at i:2605232 original size:40 final size:37
Alignment explanation
Indices: 2605188--2605271 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 37
2605178 AAATAAATTA
* *
2605188 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAACTTTTTAA-A-TAAATTAT--ATATTAATTTTT
2605228 AATATTAACTTTTTAAATAAATTATATATTAATTTTT
1 AATATTAACTTTTTAAATAAATTATATATTAATTTTT
2605265 AATATTA
1 AATATTA
2605272 TATTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
36 7 0.17
37 11 0.27
38 7 0.17
39 1 0.02
40 15 0.37
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAACTTTTTAAATAAATTATATATTAATTTTT
Found at i:2605243 original size:64 final size:64
Alignment explanation
Indices: 2605160--2605292 Score: 223
Period size: 64 Copynumber: 2.1 Consensus size: 64
2605150 GATTTAATTT
*
2605160 TTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA-TTAA
1 TTTTAATATTAACTTTTTAAATAAATTAAATATTAA-TTTTTAATATTATATTATAGATATTTAA
* *
2605224 TTTTAATATTAACTTTTTAAATAAATTATATATTAATTTTTAATATTATATTATATATATTTAA
1 TTTTAATATTAACTTTTTAAATAAATTAAATATTAATTTTTAATATTATATTATAGATATTTAA
2605288 TTTTA
1 TTTTA
2605293 TATCATATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 22 0.34
64 43 0.66
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (64 bp):
TTTTAATATTAACTTTTTAAATAAATTAAATATTAATTTTTAATATTATATTATAGATATTTAA
Found at i:2605288 original size:21 final size:21
Alignment explanation
Indices: 2605199--2605301 Score: 65
Period size: 21 Copynumber: 4.9 Consensus size: 21
2605189 ATATTAATTT
*
2605199 TTTAATATTATATTATAGATA
1 TTTAATATTATATTATATATA
*
2605220 -TTAATTTTAATATTA-ACT-T-
1 TTTAATATT-ATATTATA-TATA
*
2605239 TTTAAATAAATTATA-TAT-TAATT
1 TTT-AAT--ATTATATTATAT-ATA
2605262 TTTAATATTATATTATATATA
1 TTTAATATTATATTATATATA
* *
2605283 TTTAATTTTATATCATATA
1 TTTAATATTATATTATATA
2605302 AATTATTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
20 18 0.28
21 33 0.52
22 8 0.12
23 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTAATATTATATTATATATA
Found at i:2606028 original size:31 final size:31
Alignment explanation
Indices: 2605971--2606029 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2605961 AGTTGTATGG
*
2605971 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
2606002 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
2606030 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:2606678 original size:34 final size:32
Alignment explanation
Indices: 2606611--2606686 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
2606601 ACAAATAAAT
* ** *
2606611 ATATAATAATAATTAATAATATTAATTATTAA
1 ATATAATAATAATTAAAAATATTAAAAAATAA
2606643 ATATAATAAATAATTAAAATATATTAAAAAATAA
1 ATATAAT-AATAATTAAAA-ATATTAAAAAATAA
*
2606677 ATATAGTAAT
1 ATATAATAAT
2606687 TAAAATAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 7 0.19
33 13 0.35
34 17 0.46
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
ATATAATAATAATTAAAAATATTAAAAAATAA
Found at i:2606680 original size:16 final size:16
Alignment explanation
Indices: 2606603--2606681 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 16
2606593 AATTAACAAC
2606603 AAATAAATATA-TAATA
1 AAATAAATATATTAA-A
* *
2606619 ATAATTAATAATATTAAT
1 A-AATAAAT-ATATTAAA
* * *
2606637 TATTAAATATAATAAA
1 AAATAAATATATTAAA
*
2606653 TAATTAAAATATATTAAA
1 -AAAT-AAATATATTAAA
2606671 AAATAAATATA
1 AAATAAATATA
2606682 GTAATTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
16 14 0.29
17 17 0.35
18 14 0.29
19 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAAATATATTAAA
Found at i:2606777 original size:14 final size:14
Alignment explanation
Indices: 2606758--2606810 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
2606748 AAATTATATG
*
2606758 TATAATATATTAAA
1 TATAATATATTAAT
*
2606772 TATAATA-AATAAT
1 TATAATATATTAAT
2606785 TACTAATAT-TATAAT
1 TA-TAATATAT-TAAT
2606800 TATAATATATT
1 TATAATATATT
2606811 TTGAAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 6 0.19
14 19 0.59
15 7 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAATATATTAAT
Done.