Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 19 of 26
Found at i:3108848 original size:23 final size:24
Alignment explanation
Indices: 3108822--3108872 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
3108812 TGAGATATCA
3108822 AATTAAATTAAATTAAATTTA-TT
1 AATTAAATTAAATTAAATTTATTT
* ** *
3108845 AATTATATTATTTTAATTTTATTT
1 AATTAAATTAAATTAAATTTATTT
3108869 AATT
1 AATT
3108873 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTAAATTAAATTAAATTTATTT
Found at i:3108876 original size:23 final size:23
Alignment explanation
Indices: 3108834--3108877 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3108824 TTAAATTAAA
3108834 TTAAATTTATTAATTATATTATT
1 TTAAATTTATTAATTATATTATT
*
3108857 TTAATTTTATTTAATT-TATTA
1 TTAAATTTA-TTAATTATATTA
3108878 AAAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTAAATTTATTAATTATATTATT
Found at i:3109699 original size:39 final size:38
Alignment explanation
Indices: 3109637--3109722 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 38
3109627 TATGTTAACT
* * *
3109637 AAATAATACATATTTTTTTAATATAATAAAAATTAATTAA
1 AAATAA-AAATATTCTTTAAATATAATAAAAA-TAATTAA
3109677 AAATAAAAATATTCTTTAAATATAATAAAAATAATTAA
1 AAATAAAAATATTCTTTAAATATAATAAAAATAATTAA
3109715 AAATAAAA
1 AAATAAAA
3109723 TTAAGATACG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 15 0.35
39 22 0.51
40 6 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (38 bp):
AAATAAAAATATTCTTTAAATATAATAAAAATAATTAA
Found at i:3109714 original size:19 final size:19
Alignment explanation
Indices: 3109659--3109720 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
3109649 TTTTTTTAAT
3109659 ATAATAAAAATTAATTAAAA
1 ATAATAAAAA-TAATTAAAA
* ** *
3109679 ATAA-AAATATTCTTTAAAT
1 ATAATAAA-AATAATTAAAA
3109698 ATAATAAAAATAATTAAAA
1 ATAATAAAAATAATTAAAA
3109717 ATAA
1 ATAA
3109721 AATTAAGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAAAAATAATTAAAA
Found at i:3111711 original size:80 final size:82
Alignment explanation
Indices: 3111602--3111761 Score: 211
Period size: 80 Copynumber: 2.0 Consensus size: 82
3111592 AATCAATTAC
* *
3111602 TTTTTTTGTCTTTTCTTTTGGGATCAATTACAAATAAATTTATGTACTATACAATCTCTTTT-TA
1 TTTTTTTATCTTTTCTTTTGGGATCAATTACAAATAAATTTATATACTATACAA-CT-TTTTCTA
3111666 ATTAGGTACATGAAGAATT
64 ATTAGGTACATGAAGAATT
* * * * *
3111685 TTTTTTTATC-TTT-TTTT-GGATTAATTACAAATAAGTTTTTATACTATACTACTTTTTCTAGT
1 TTTTTTTATCTTTTCTTTTGGGATCAATTACAAATAAATTTATATACTATACAACTTTTTCTAAT
3111747 TAGGTACATGAAGAA
66 TAGGTACATGAAGAA
3111762 AATTTTTACC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 4 0.06
79 20 0.29
80 29 0.42
81 4 0.06
82 3 0.04
83 9 0.13
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (82 bp):
TTTTTTTATCTTTTCTTTTGGGATCAATTACAAATAAATTTATATACTATACAACTTTTTCTAAT
TAGGTACATGAAGAATT
Found at i:3111950 original size:7 final size:7
Alignment explanation
Indices: 3111940--3112163 Score: 81
Period size: 7 Copynumber: 30.7 Consensus size: 7
3111930 AAAATTTTAA
3111940 AAAAATT
1 AAAAATT
*
3111947 AAAAAAT
1 AAAAATT
3111954 AAAAA-T
1 AAAAATT
3111960 -AAAATT
1 AAAAATT
3111966 CAAAAAATTAT
1 --AAAAA-T-T
3111977 AAGAAATCT
1 AA-AAAT-T
3111986 ATAAAATT
1 A-AAAATT
*
3111994 AAAAAATAA
1 -AAAAAT-T
3112003 AAAGAATCT
1 AAA-AAT-T
3112012 AAAAATT
1 AAAAATT
*
3112019 AAAAAAT
1 AAAAATT
**
3112026 AATTATT
1 AAAAATT
3112033 ATAATAATTT
1 A-AA-AA-TT
*
3112043 AAAATTTT
1 AAAA-ATT
3112051 AAAAA-T
1 AAAAATT
* *
3112057 ATATA-T
1 AAAAATT
3112063 AAAAA-T
1 AAAAATT
3112069 AAAAATAT
1 AAAAAT-T
3112077 CAAAAATT
1 -AAAAATT
3112085 AAAAATT
1 AAAAATT
3112092 AAAAATT
1 AAAAATT
*
3112099 AAAATTT
1 AAAAATT
3112106 CAAAAA-T
1 -AAAAATT
*
3112113 AAAAAAT
1 AAAAATT
*
3112120 AAAAAAT
1 AAAAATT
*
3112127 ACATAATT
1 A-AAAATT
3112135 -AAAATT
1 AAAAATT
* *
3112141 TACAA--
1 AAAAATT
3112146 AAAAATT
1 AAAAATT
3112153 -AAAATT
1 AAAAATT
3112159 AAAAA
1 AAAAA
3112164 AATTGAATAA
Statistics
Matches: 167, Mismatches: 25, Indels: 50
0.69 0.10 0.21
Matches are distributed among these distances:
5 7 0.04
6 32 0.19
7 60 0.36
8 30 0.18
9 29 0.17
10 8 0.05
11 1 0.01
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:3111950 original size:8 final size:8
Alignment explanation
Indices: 3111939--3112126 Score: 73
Period size: 8 Copynumber: 23.9 Consensus size: 8
3111929 AAAAATTTTA
3111939 AAAAAATT
1 AAAAAATT
3111947 AAAAAA-T
1 AAAAAATT
3111954 -AAAAA-T
1 AAAAAATT
3111960 --AAAATT
1 AAAAAATT
3111966 CAAAAAATT
1 -AAAAAATT
3111975 ATAAGAAATCT
1 A-AA-AAAT-T
*
3111986 ATAAAATT
1 AAAAAATT
*
3111994 AAAAAATA
1 AAAAAATT
3112002 AAAAGAATCT
1 AAAA-AAT-T
3112012 -AAAAATT
1 AAAAAATT
3112019 AAAAAA-T
1 AAAAAATT
**
3112026 -AATTATT
1 AAAAAATT
*
3112033 ATAATAATTT
1 A-AA-AAATT
**
3112043 AAAATTTT
1 AAAAAATT
3112051 AAAAATATAT
1 AAAAA-AT-T
3112061 ATAAAAA-T
1 A-AAAAATT
3112069 -AAAAATAT
1 AAAAAAT-T
*
3112077 CAAAAATT
1 AAAAAATT
3112085 -AAAAATT
1 AAAAAATT
3112092 -AAAAATT
1 AAAAAATT
*
3112099 -AAAATTT
1 AAAAAATT
*
3112106 CAAAAA-T
1 AAAAAATT
3112113 AAAAAA-T
1 AAAAAATT
3112120 AAAAAAT
1 AAAAAAT
3112127 ACATAATTAA
Statistics
Matches: 143, Mismatches: 15, Indels: 44
0.71 0.07 0.22
Matches are distributed among these distances:
5 4 0.03
6 15 0.10
7 37 0.26
8 41 0.29
9 29 0.20
10 11 0.08
11 6 0.04
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.28
Consensus pattern (8 bp):
AAAAAATT
Found at i:3112002 original size:24 final size:24
Alignment explanation
Indices: 3111940--3112027 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 24
3111930 AAAATTTTAA
3111940 AAAAATTAAAAAAT-AAA-AA--T
1 AAAAATTAAAAAATAAAAGAATCT
*
3111960 -AAAATTCAAAAAATTATAAGAAATCT
1 AAAAATT-AAAAAA-TAAAAG-AATCT
3111986 ATAAAATTAAAAAATAAAAAGAATCT
1 A-AAAATTAAAAAAT-AAAAGAATCT
3112012 AAAAATTAAAAAATAA
1 AAAAATTAAAAAATAA
3112028 TTATTATAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
19 6 0.11
20 6 0.11
21 1 0.02
22 2 0.04
24 4 0.07
25 13 0.23
26 8 0.14
27 10 0.18
28 6 0.11
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAAATTAAAAAATAAAAGAATCT
Found at i:3112016 original size:25 final size:27
Alignment explanation
Indices: 3111958--3112027 Score: 99
Period size: 25 Copynumber: 2.6 Consensus size: 27
3111948 AAAAATAAAA
* *
3111958 ATAAAATTCAAAAAATTATAAGAAATCT
1 ATAAAATT-AAAAAATAAAAAGAAATCT
3111986 ATAAAATTAAAAAATAAAAAG-AATCT
1 ATAAAATTAAAAAATAAAAAGAAATCT
3112012 A-AAAATTAAAAAATAA
1 ATAAAATTAAAAAATAA
3112028 TTATTATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 15 0.38
26 6 0.15
27 11 0.28
28 8 0.20
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (27 bp):
ATAAAATTAAAAAATAAAAAGAAATCT
Found at i:3112070 original size:31 final size:31
Alignment explanation
Indices: 3111999--3112070 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
3111989 AAATTAAAAA
*
3111999 ATAAAAAGAATCTAAAAATTAAAAAATAATT
1 ATAAAAATAATCTAAAAATTAAAAAATAATT
* * * * *
3112030 ATTATAATAATTTAAAATTTTAAAAAT-ATAT
1 ATAAAAATAATCTAAAAATTAAAAAATAAT-T
3112061 ATAAAAATAA
1 ATAAAAATAA
3112071 AAATATCAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (31 bp):
ATAAAAATAATCTAAAAATTAAAAAATAATT
Found at i:3112102 original size:29 final size:29
Alignment explanation
Indices: 3112062--3112127 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
3112052 AAAATATATA
*
3112062 TAAAAATAAAAATATCAAAAATTAAAAAT
1 TAAAAATAAAAATATCAAAAATAAAAAAT
* *
3112091 TAAAAATTAAAATTTCAAAAATAAAAAAT
1 TAAAAATAAAAATATCAAAAATAAAAAAT
*
3112120 AAAAAATA
1 TAAAAATA
3112128 CATAATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (29 bp):
TAAAAATAAAAATATCAAAAATAAAAAAT
Found at i:3112118 original size:36 final size:38
Alignment explanation
Indices: 3112069--3112164 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 38
3112059 ATATAAAAAT
*
3112069 AAAAATATCAAAAATTAAAAATTA-AAAATTAAAATTT-C
1 AAAAATA--AAAAATTAAAAAATACAAAATTAAAATTTAC
*
3112107 AAAAATAAAAAA-TAAAAAATACATAATTAAAATTTAC
1 AAAAATAAAAAATTAAAAAATACAAAATTAAAATTTAC
3112144 AAAAA-AATTAAAATTAAAAAA
1 AAAAATAA--AAAATTAAAAAA
3112165 ATTGAATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
35 8 0.16
36 19 0.37
37 6 0.12
38 11 0.22
39 7 0.14
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (38 bp):
AAAAATAAAAAATTAAAAAATACAAAATTAAAATTTAC
Found at i:3112217 original size:31 final size:31
Alignment explanation
Indices: 3112172--3112231 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3112162 AAAATTGAAT
* *
3112172 AAAAAAAACCAGAAAGAAGAGAGAGGAAAGGG
1 AAAAAAAACAAGAAAGAAGAG-GAAGAAAGGG
*
3112204 AAAAAAAA-AAGAAAGGAGAGGAAGAAAG
1 AAAAAAAACAAGAAAGAAGAGGAAGAAAG
3112232 TGTCACAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 10 0.40
32 8 0.32
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (31 bp):
AAAAAAAACAAGAAAGAAGAGGAAGAAAGGG
Found at i:3112521 original size:30 final size:30
Alignment explanation
Indices: 3112487--3112548 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3112477 CTCCTGGCTT
3112487 CAATTCTGTTACAGCTCCCAGCTCCAGCTC
1 CAATTCTGTTACAGCTCCCAGCTCCAGCTC
3112517 CAATTCTGTTACAGCTCCCAGCTCCAGCTC
1 CAATTCTGTTACAGCTCCCAGCTCCAGCTC
3112547 CA
1 CA
3112549 GCTCCAACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.21, C:0.40, G:0.13, T:0.26
Consensus pattern (30 bp):
CAATTCTGTTACAGCTCCCAGCTCCAGCTC
Found at i:3117755 original size:29 final size:30
Alignment explanation
Indices: 3117696--3117756 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
3117686 CTCCTGGCTT
3117696 CAATTCTGTTACAGCTCCCAGCTCCAGCTC
1 CAATTCTGTTACAGCTCCCAGCTCCAGCTC
3117726 CAATTCTGTTACAGCT-CCAGCTCCAGCTC
1 CAATTCTGTTACAGCTCCCAGCTCCAGCTC
3117755 CA
1 CA
3117757 GCTCTAACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.21, C:0.39, G:0.13, T:0.26
Consensus pattern (30 bp):
CAATTCTGTTACAGCTCCCAGCTCCAGCTC
Found at i:3118005 original size:13 final size:13
Alignment explanation
Indices: 3117987--3118011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3117977 ATGATTTTCT
3117987 AATCAAGAAAGAA
1 AATCAAGAAAGAA
3118000 AATCAAGAAAGA
1 AATCAAGAAAGA
3118012 GAAAGAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (13 bp):
AATCAAGAAAGAA
Found at i:3118270 original size:13 final size:13
Alignment explanation
Indices: 3118254--3118304 Score: 84
Period size: 13 Copynumber: 3.8 Consensus size: 13
3118244 CCTTTTTTCC
3118254 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
3118267 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
3118280 CTCTTTTTTTTCTT
1 CT-TTTTTTTTCTT
*
3118294 CTTTTTCTTTC
1 CTTTTTTTTTC
3118305 GTCATTTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 23 0.64
14 13 0.36
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTTTTTTTTCTT
Found at i:3118354 original size:9 final size:9
Alignment explanation
Indices: 3118325--3118354 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3118315 TTCCCTTCCC
3118325 TTCTTTTTT
1 TTCTTTTTT
3118334 TTCCTTTTTT
1 TT-CTTTTTT
3118344 TTCTTTTTT
1 TTCTTTTTT
3118353 TT
1 TT
3118355 TTAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:3118429 original size:42 final size:41
Alignment explanation
Indices: 3118342--3118507 Score: 122
Period size: 42 Copynumber: 4.0 Consensus size: 41
3118332 TTTTCCTTTT
* * * * *
3118342 TTTTCTTTTTTTTTTAATTTTTAAATTTTTATTAATTACATA
1 TTTTCTATTATTTTTAATTTTTTAATTTTTATTATTTA-AAA
* *
3118384 TTTTCTATTATTTTTCATTTTTTAATTTTTATATATTTAAGA
1 TTTTCTATTATTTTTAATTTTTTAATTTTTAT-TATTTAAAA
* * *
3118426 TTTT-AAGT-TTTTTAATATTTTT-ATTTTTATTTTTTAAAA
1 TTTTCTATTATTTTTAAT-TTTTTAATTTTTATTATTTAAAA
* ** *
3118465 TTTATATATTTATTTTTGTTTTTTTAGATTTTTACTTTTTTAA
1 TTT-TCTA-TTATTTTTAATTTTTTA-ATTTTTA-TTATTTAA
3118508 TTTAGAAATT
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
39 10 0.10
40 16 0.16
41 8 0.08
42 40 0.40
43 11 0.11
44 7 0.07
45 8 0.08
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (41 bp):
TTTTCTATTATTTTTAATTTTTTAATTTTTATTATTTAAAA
Found at i:3118453 original size:24 final size:23
Alignment explanation
Indices: 3118426--3118481 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
3118416 ATATTTAAGA
* *
3118426 TTTTAAGTTTTTTAATATTTTTAT
1 TTTTAA-TTTTTTAAAATTTATAT
3118450 TTTT-ATTTTTTAAAATTTATAT
1 TTTTAATTTTTTAAAATTTATAT
*
3118472 ATTT-ATTTTT
1 TTTTAATTTTT
3118482 GTTTTTTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.83
23 1 0.03
24 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTAATTTTTTAAAATTTATAT
Found at i:3118529 original size:50 final size:50
Alignment explanation
Indices: 3118432--3118531 Score: 114
Period size: 50 Copynumber: 2.0 Consensus size: 50
3118422 AAGATTTTAA
* ** *
3118432 GTTTTTTAATATTTTTATTTTTATTTTTTAAAATTTATATATTTATTTTT
1 GTTTTTTAAGATTTTTATTTTTATAATTTAAAATTTATATATATATTTTT
* *
3118482 GTTTTTTTAGATTTTTACTTTTT-TAATTTAGAAATTTTTA-ATATATTTTT
1 GTTTTTTAAGATTTTTA-TTTTTATAATTTA-AAATTTATATATATATTTTT
3118532 CATTTTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
50 29 0.69
51 13 0.31
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (50 bp):
GTTTTTTAAGATTTTTATTTTTATAATTTAAAATTTATATATATATTTTT
Found at i:3127831 original size:27 final size:26
Alignment explanation
Indices: 3127797--3127852 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
3127787 TACTGGGGAG
*
3127797 CAATTGGGTCGCCAAATATAGACTGC
1 CAATTGGGTCGCCAAATACAGACTGC
* * *
3127823 CAATATGGGTTGCTAAATACGGACTGC
1 CAAT-TGGGTCGCCAAATACAGACTGC
3127850 CAA
1 CAA
3127853 AGATAGACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (26 bp):
CAATTGGGTCGCCAAATACAGACTGC
Found at i:3130818 original size:2 final size:2
Alignment explanation
Indices: 3130811--3130844 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3130801 GTTTGGTTGA
*
3130811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3130845 TCACCATCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3131138 original size:9 final size:8
Alignment explanation
Indices: 3131117--3131164 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
3131107 AAAAATTTTT
*
3131117 AAATAAAA
1 AAATTAAA
3131125 AAATTAATA
1 AAATTAA-A
3131134 AAATTAAA
1 AAATTAAA
3131142 AGAATTAAA
1 A-AATTAAA
*
3131151 AATATTATA
1 AA-ATTAAA
3131160 AAATT
1 AAATT
3131165 TTCACTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 12 0.34
9 23 0.66
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (8 bp):
AAATTAAA
Found at i:3131575 original size:19 final size:20
Alignment explanation
Indices: 3131551--3131597 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3131541 CATTAATAAT
3131551 TTATATTAT-ATCAA-TTTTA
1 TTATATTATAAT-AATTTTTA
*
3131570 TTATATTTTAATAATTTTTA
1 TTATATTATAATAATTTTTA
3131590 TTATATTA
1 TTATATTA
3131598 ACTTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTATAATAATTTTTA
Found at i:3133601 original size:25 final size:26
Alignment explanation
Indices: 3133553--3133601 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3133543 TGTTTTTGAT
* *
3133553 ATATTTAAAAATCGTATTTTATATTC
1 ATATTTAAAAATCATATTTAATATTC
*
3133579 ATATTTTAAAAT-ATATTTAATAT
1 ATATTTAAAAATCATATTTAATAT
3133602 GTATTAAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATTTAAAAATCATATTTAATATTC
Found at i:3134394 original size:17 final size:17
Alignment explanation
Indices: 3134372--3134407 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3134362 GTTTGAAATT
3134372 CAAAGGTCGTTAAGAAA
1 CAAAGGTCGTTAAGAAA
*
3134389 CAAAGGTTGTTAAGAAA
1 CAAAGGTCGTTAAGAAA
3134406 CA
1 CA
3134408 TGGTAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.19
Consensus pattern (17 bp):
CAAAGGTCGTTAAGAAA
Found at i:3135420 original size:22 final size:22
Alignment explanation
Indices: 3135356--3135427 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
3135346 GTATTTAGAA
* * *
3135356 TATATTAAATGTTAAAAATATT
1 TATATTAAATCTTAAATATTTT
*
3135378 TATATTAATATCTAAATATATTTT
1 TATATTAA-ATCTTAA-ATATTTT
3135402 TATAATTAAAT-TTAAATATTTCT
1 TAT-ATTAAATCTTAAATATTT-T
3135425 TAT
1 TAT
3135428 TATGAAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
22 14 0.34
23 12 0.29
24 10 0.24
25 5 0.12
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (22 bp):
TATATTAAATCTTAAATATTTT
Found at i:3136000 original size:11 final size:10
Alignment explanation
Indices: 3135970--3136058 Score: 58
Period size: 11 Copynumber: 8.4 Consensus size: 10
3135960 AACGTAAGCA
3135970 AAAATATAAT
1 AAAATATAAT
*
3135980 ACAAAAATAATT
1 A-AAATATAA-T
3135992 AAAATATAAATAT
1 AAAATAT--A-AT
3136005 AAAATATAATT
1 AAAATATAA-T
*
3136016 TAAA-ATAAT
1 AAAATATAAT
3136025 AAATATATAAT
1 AAA-ATATAAT
3136036 AAGAATAT-AT
1 AA-AATATAAT
*
3136046 -AAATTTAAT
1 AAAATATAAT
3136055 AAAA
1 AAAA
3136059 AATTTTATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
8 4 0.06
9 6 0.10
10 12 0.19
11 28 0.44
12 3 0.05
13 9 0.14
14 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAATATAAT
Found at i:3136021 original size:12 final size:12
Alignment explanation
Indices: 3135970--3136110 Score: 89
Period size: 12 Copynumber: 11.8 Consensus size: 12
3135960 AACGTAAGCA
*
3135970 AAAATATAATAC
1 AAAATATAATAT
3135982 AAAA-ATAAT-T
1 AAAATATAATAT
3135992 AAAATATAAATAT
1 AAAATAT-AATAT
*
3136005 AAAATATAATTT
1 AAAATATAATAT
3136017 AAAATAATAAATAT
1 AAAAT-AT-AATAT
* *
3136031 ATAATAAGAATAT
1 AAAAT-ATAATAT
* *
3136044 ATAAATTTAATAA
1 A-AAATATAATAT
* *
3136057 AAAATTTTATAT
1 AAAATATAATAT
3136069 AAAATA-AAT-T
1 AAAATATAATAT
*
3136079 ATTAATAT-AT-T
1 A-AAATATAATAT
3136090 AAAAT-TAATAT
1 AAAATATAATAT
3136101 AAATATATAA
1 AAA-ATATAA
3136111 AATTTTAATT
Statistics
Matches: 102, Mismatches: 15, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
9 1 0.01
10 11 0.11
11 21 0.21
12 32 0.31
13 24 0.24
14 13 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:3136036 original size:26 final size:24
Alignment explanation
Indices: 3135970--3136036 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 24
3135960 AACGTAAGCA
*
3135970 AAAATAT-AATACAAAA-ATAATT
1 AAAATATAAATATAAAATATAATT
3135992 AAAATATAAATATAAAATATAATTT
1 AAAATATAAATATAAAATATAA-TT
*
3136017 AAAATAATAAATATATAATA
1 AAAAT-ATAAATATAAAATA
3136037 AGAATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.18
23 8 0.21
24 4 0.10
25 7 0.18
26 13 0.33
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATATAAATATAAAATATAATT
Found at i:3136046 original size:34 final size:35
Alignment explanation
Indices: 3135983--3136053 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
3135973 ATATAATACA
3135983 AAAATAATTAAAATATAAATATAAAATAT-AATTT
1 AAAATAATTAAAATATAAATATAAAATATAAATTT
3136017 AAAATAA-T-AAATATATAATA-AGAATATATAAATTT
1 AAAATAATTAAAATATA-AATATA-AA-ATATAAATTT
3136052 AA
1 AA
3136054 TAAAAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
32 8 0.24
33 7 0.21
34 11 0.33
35 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (35 bp):
AAAATAATTAAAATATAAATATAAAATATAAATTT
Found at i:3136105 original size:20 final size:20
Alignment explanation
Indices: 3136064--3136129 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
3136054 TAAAAAATTT
* *
3136064 TATATAAAATAAATTATTAA
1 TATATAAAATTAATTATAAA
3136084 TATATTAAAATTAA-TATAAA
1 TATA-TAAAATTAATTATAAA
*
3136104 TATATAAAATTTTAATTATAAT
1 TATATAAAA--TTAATTATAAA
3136126 TATA
1 TATA
3136130 CTATATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.13
20 13 0.33
21 12 0.31
22 9 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAAAATTAATTATAAA
Found at i:3136113 original size:19 final size:19
Alignment explanation
Indices: 3135988--3136114 Score: 71
Period size: 20 Copynumber: 6.2 Consensus size: 19
3135978 ATACAAAAAT
*
3135988 AATTAAAATATAA-ATATAA
1 AATTAATATA-AATATATAA
*
3136007 AATATAATTTAAA-ATAATAA
1 AAT-TAATATAAATAT-ATAA
3136027 ATATATAATA-AGAATATATAA
1 A-AT-TAATATA-AATATATAA
* *
3136048 ATTTAATAAAAAATTTTATATAA
1 AATTAAT-ATAAA---TATATAA
* *
3136071 AATAAATTATTAATATATTAA
1 AATTAA-TATAAATATA-TAA
3136092 AATTAATATAAATATATAA
1 AATTAATATAAATATATAA
3136111 AATT
1 AATT
3136115 TTAATTATAA
Statistics
Matches: 86, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
19 18 0.21
20 28 0.33
21 23 0.27
22 2 0.02
23 14 0.16
24 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
AATTAATATAAATATATAA
Found at i:3136488 original size:26 final size:27
Alignment explanation
Indices: 3136442--3136542 Score: 76
Period size: 24 Copynumber: 4.0 Consensus size: 27
3136432 AATATTTTAT
3136442 ATATTTTATAATTAAATATAAATAAAA
1 ATATTTTATAATTAAATATAAATAAAA
3136469 ATATTTT-TAA-T--ATAT-AATAAATA
1 ATATTTTATAATTAAATATAAATAAA-A
** *
3136492 A-ATTAAATTAATTAAAAATAAA-AAAA
1 ATATTTTA-TAATTAAATATAAATAAAA
*
3136518 TTA-TTTA-AATTAAATATAACATAAA
1 ATATTTTATAATTAAATATAA-ATAAA
3136543 TGGAATGAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 21
0.67 0.08 0.25
Matches are distributed among these distances:
22 9 0.16
23 6 0.11
24 14 0.25
25 3 0.05
26 9 0.16
27 14 0.25
28 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATTTTATAATTAAATATAAATAAAA
Found at i:3136494 original size:36 final size:35
Alignment explanation
Indices: 3136432--3136499 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
3136422 ATAATAAACT
* * *
3136432 AATATTTTATATATTTTATAATTAAATATAAATAAA
1 AATATTTTATATATATAATAAATAAAT-TAAATAAA
3136468 AATATTTT-TAATATATAATAAATAAATTAAAT
1 AATATTTTAT-ATATATAATAAATAAATTAAAT
3136500 TAATTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
AATATTTTATATATATAATAAATAAATTAAATAAA
Found at i:3137490 original size:18 final size:19
Alignment explanation
Indices: 3137464--3137506 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3137454 TATTTAATAA
3137464 AAATATTTTAATC-AAATT
1 AAATATTTTAATCAAAATT
* *
3137482 AAATTTTTTATTCATAAATT
1 AAATATTTTAATCA-AAATT
3137502 AAATA
1 AAATA
3137507 AATATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATATTTTAATCAAAATT
Found at i:3137517 original size:25 final size:23
Alignment explanation
Indices: 3137481--3137529 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
3137471 TTAATCAAAT
* *
3137481 TAAATTTTTTATTCATAAATTAAA
1 TAAATTTATTATTAATAAA-TAAA
3137505 TAAATATTATTATTAATAAATAAA
1 TAAAT-TTATTATTAATAAATAAA
3137529 T
1 T
3137530 TTTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTATTATTAATAAATAAA
Found at i:3137524 original size:20 final size:19
Alignment explanation
Indices: 3137501--3137542 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3137491 ATTCATAAAT
*
3137501 TAAATAAATATTATTATTAA
1 TAAATAAAT-TTATTAATAA
*
3137521 TAAATAAATTTTTTAATAA
1 TAAATAAATTTATTAATAA
3137540 TAA
1 TAA
3137543 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATAAATTTATTAATAA
Found at i:3137548 original size:44 final size:44
Alignment explanation
Indices: 3137455--3137548 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
3137445 AGTTATTATT
* *
3137455 ATTT-AATAAAAATATTTTAATCAAATTAAATTTTTTATTCATA
1 ATTTAAATAAAAATATTTTAATCAAATTAAATTTTTTAATAATA
* *
3137498 AATTAAATAAATATTATTATTAAT-AAA-TAAATTTTTTAATAATA
1 ATTTAAATAAA-AATATT-TTAATCAAATTAAATTTTTTAATAATA
3137542 ATTTAAA
1 ATTTAAA
3137549 AATTAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
43 3 0.07
44 27 0.63
45 8 0.19
46 5 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (44 bp):
ATTTAAATAAAAATATTTTAATCAAATTAAATTTTTTAATAATA
Found at i:3138084 original size:16 final size:15
Alignment explanation
Indices: 3138053--3138085 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3138043 ATATTAATAA
3138053 TTAAAATTTTTTATT
1 TTAAAATTTTTTATT
*
3138068 TTAAAATTTTTTAAT
1 TTAAAATTTTTTATT
3138083 TTA
1 TTA
3138086 CTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAAAATTTTTTATT
Found at i:3138116 original size:25 final size:24
Alignment explanation
Indices: 3138077--3138125 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3138067 TTTAAAATTT
3138077 TTTAATTTACTTAAAAAATAATATA
1 TTTAATTTACTTAAAAAA-AATATA
*
3138102 TTTAATTTA-TATAAATAAAATATA
1 TTTAATTTACT-TAAAAAAAATATA
3138126 AAATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAATTTACTTAAAAAAAATATA
Found at i:3138173 original size:29 final size:31
Alignment explanation
Indices: 3138110--3138173 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
3138100 TATTTAATTT
*
3138110 ATAT-AAATAAAATATAAAATATAATAATCA
1 ATATCAAATAAAATATAAAAAATAATAATCA
*
3138140 A-ATCAAAT-AAATATAAAAAATTATAAT-A
1 ATATCAAATAAAATATAAAAAATAATAATCA
3138168 ATATCA
1 ATATCA
3138174 CTAATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.07
29 23 0.77
30 5 0.17
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (31 bp):
ATATCAAATAAAATATAAAAAATAATAATCA
Found at i:3139703 original size:17 final size:16
Alignment explanation
Indices: 3139683--3139721 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3139673 ATTTATTTAT
*
3139683 TTTATTATATTATAATA
1 TTTATAATATTAT-ATA
*
3139700 TTTAAAATATTATATA
1 TTTATAATATTATATA
3139716 TTTATA
1 TTTATA
3139722 TAAATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATAATATTATATA
Found at i:3139864 original size:34 final size:35
Alignment explanation
Indices: 3139817--3139888 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
3139807 TCCAATACTC
* *
3139817 AAATATTTGATTTAGATTATTATT-TAAATTA-ATA
1 AAATATTTGATTTAAATTA-AATTATAAATTATATA
3139851 AAATAATTT-ATTTAAATTAAATTATAAATTATATA
1 AAAT-ATTTGATTTAAATTAAATTATAAATTATATA
3139886 AAA
1 AAA
3139889 ATTAATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 3 0.09
34 20 0.61
35 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (35 bp):
AAATATTTGATTTAAATTAAATTATAAATTATATA
Found at i:3139882 original size:21 final size:22
Alignment explanation
Indices: 3139835--3139887 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
3139825 GATTTAGATT
3139835 ATTATTTAAATTAATAAAATAA
1 ATTATTTAAATTAATAAAATAA
* **
3139857 TTTATTTAAATTAA-ATTATAA
1 ATTATTTAAATTAATAAAATAA
*
3139878 ATTATATAAA
1 ATTATTTAAA
3139888 AATTAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATTTAAATTAATAAAATAA
Found at i:3139902 original size:23 final size:22
Alignment explanation
Indices: 3139842--3139902 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
3139832 ATTATTATTT
**
3139842 AAATTAATA-AAATAATTTATTT
1 AAATTAATATAAA-AATTTATAA
*
3139864 AAATTAA-ATTATAAATTATATAA
1 AAATTAATA-TAAAAATT-TATAA
3139887 AAATTAATATAAAAAT
1 AAATTAATATAAAAAT
3139903 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 1 0.03
22 11 0.35
23 18 0.58
24 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTAATATAAAAATTTATAA
Found at i:3141356 original size:32 final size:30
Alignment explanation
Indices: 3141283--3141358 Score: 75
Period size: 32 Copynumber: 2.4 Consensus size: 30
3141273 AAAATTATGA
*
3141283 CTATTTAAAT-AAATATTTATTTAAATAAT
1 CTATTTAAATAAAATATCTATTTAAATAAT
*
3141312 -TATATCTAAAATAAAATATCTATTTGAGATATAT
1 CTAT-T-T-AAATAAAATATCTATTT-AAATA-AT
3141346 CTATTTAAATAAA
1 CTATTTAAATAAA
3141359 TTATACCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
28 3 0.08
29 1 0.03
30 1 0.03
31 4 0.11
32 18 0.47
33 5 0.13
34 3 0.08
35 3 0.08
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (30 bp):
CTATTTAAATAAAATATCTATTTAAATAAT
Found at i:3141907 original size:2 final size:2
Alignment explanation
Indices: 3141853--3141887 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3141843 ATAAGGTTGA
3141853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3141888 ATGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3143176 original size:33 final size:33
Alignment explanation
Indices: 3143113--3143176 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
3143103 GTAAATTTAC
** *
3143113 ATATTCAAATTTTTTAATGTTTATAATTCATAA
1 ATATTCAAATTTAATAATGATTATAATTCATAA
* *
3143146 ATATTCAAATTTAATAATGATTGTAGTTCAT
1 ATATTCAAATTTAATAATGATTATAATTCAT
3143177 GAACGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (33 bp):
ATATTCAAATTTAATAATGATTATAATTCATAA
Found at i:3145927 original size:21 final size:21
Alignment explanation
Indices: 3145889--3145936 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3145879 TTTTATTTTA
***
3145889 TTTTATTAATTTTTTTAATAT
1 TTTTATTAATTAAATTAATAT
3145910 TTTTATTAATTAAATTAATAT
1 TTTTATTAATTAAATTAATAT
3145931 TATTTA
1 T-TTTA
3145937 ACTTATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTAATTAAATTAATAT
Found at i:3146343 original size:22 final size:22
Alignment explanation
Indices: 3146317--3146362 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3146307 AATATAATAT
* *
3146317 AAAACATTAAGTAAAGTTTTAA
1 AAAACATCAAGTAAAGTTTCAA
3146339 AAAACATCAAGTAAAGTTTCAA
1 AAAACATCAAGTAAAGTTTCAA
3146361 AA
1 AA
3146363 CAGGACGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (22 bp):
AAAACATCAAGTAAAGTTTCAA
Found at i:3146693 original size:18 final size:17
Alignment explanation
Indices: 3146672--3146738 Score: 59
Period size: 18 Copynumber: 4.0 Consensus size: 17
3146662 TATTAGTGTC
*
3146672 ATTTTTAATATATAAATA
1 ATTTTAAATATA-AAATA
3146690 ATTTTAAATATAAAATA
1 ATTTTAAATATAAAATA
*
3146707 A-ATT-AA-ATAAAATAA
1 ATTTTAAATATAAAAT-A
* *
3146722 ATTTTATATATCAAATA
1 ATTTTAAATATAAAATA
3146739 CCCATTATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
14 7 0.17
15 4 0.10
16 4 0.10
17 8 0.20
18 17 0.43
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTTAAATATAAAATA
Found at i:3146726 original size:32 final size:33
Alignment explanation
Indices: 3146676--3146738 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
3146666 AGTGTCATTT
3146676 TTAATATATAAATAATTTTAAATATAAAATAAA
1 TTAATATATAAATAATTTTAAATATAAAATAAA
* *
3146709 TTAA-ATA-AAATAAATTTTATATATCAAATA
1 TTAATATATAAAT-AATTTTAAATATAAAATA
3146739 CCCATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 19 0.70
33 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (33 bp):
TTAATATATAAATAATTTTAAATATAAAATAAA
Found at i:3147416 original size:27 final size:27
Alignment explanation
Indices: 3147378--3147430 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3147368 TGCAACCTTC
* *
3147378 ACTATTTCAAATTGAATTTCATAATTT
1 ACTATTTCAAATTGAATGTCAAAATTT
3147405 ACTATTTCAAATTGAATGTCAAAATT
1 ACTATTTCAAATTGAATGTCAAAATT
3147431 GGCGGCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (27 bp):
ACTATTTCAAATTGAATGTCAAAATTT
Found at i:3147444 original size:12 final size:12
Alignment explanation
Indices: 3147436--3147460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3147426 AAATTGGCGG
3147436 CACAGTTGGCAA
1 CACAGTTGGCAA
3147448 CACAGTTGGCAA
1 CACAGTTGGCAA
3147460 C
1 C
3147461 CTTTGTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (12 bp):
CACAGTTGGCAA
Found at i:3151004 original size:2 final size:2
Alignment explanation
Indices: 3150997--3151034 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3150987 TACAACATAA
*
3150997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3151035 TTAGAGATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3151413 original size:3 final size:3
Alignment explanation
Indices: 3151405--3151442 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3151395 ATTCAAAAAG
3151405 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3151443 GTTCATTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3152230 original size:6 final size:6
Alignment explanation
Indices: 3152182--3152227 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
3152172 AAAAAATTGG
* *
3152182 ATATCT ATATCT ATATCT ATATCT ATATCT ATATAT ATATAT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
3152228 ATAACATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATCT
Found at i:3152435 original size:11 final size:12
Alignment explanation
Indices: 3152420--3152448 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3152410 ATTTATTTAC
3152420 ATATTTAATTTT
1 ATATTTAATTTT
3152432 -TATTTAATTTT
1 ATATTTAATTTT
3152443 ATATTT
1 ATATTT
3152449 TTATCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:3152450 original size:19 final size:19
Alignment explanation
Indices: 3152411--3152452 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3152401 AAATTTAAAA
3152411 TTTATTTACATATTTAATT
1 TTTATTTACATATTTAATT
3152430 TTTATTTA-AT-TTTATATT
1 TTTATTTACATATTTA-ATT
3152448 TTTAT
1 TTTAT
3152453 CTCTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 8 0.36
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTTACATATTTAATT
Found at i:3153343 original size:23 final size:24
Alignment explanation
Indices: 3153300--3153344 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3153290 GTTGAATTGA
*
3153300 CTTAATTTTAATATTCTTTTCCCT
1 CTTAATTTTAATATTCATTTCCCT
*
3153324 CTTAATTTTTA-ATTCATTTCC
1 CTTAATTTTAATATTCATTTCC
3153345 ATAAATATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.58
Consensus pattern (24 bp):
CTTAATTTTAATATTCATTTCCCT
Found at i:3154682 original size:19 final size:19
Alignment explanation
Indices: 3154641--3154682 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3154631 AGATTTGATC
** *
3154641 CTTTTTTAGATAGGTATTA
1 CTTTTTTAGATAAATATGA
3154660 -TTTTTTAGATAAATATGA
1 CTTTTTTAGATAAATATGA
3154678 CTTTT
1 CTTTT
3154683 GAAATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (19 bp):
CTTTTTTAGATAAATATGA
Found at i:3155544 original size:3 final size:3
Alignment explanation
Indices: 3155536--3155568 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3155526 AGTCATTGTC
3155536 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3155569 CTGCTAGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3157107 original size:22 final size:21
Alignment explanation
Indices: 3157082--3157124 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3157072 ACATTTCATT
*
3157082 TAATCGATTTATTTTTAAATAA
1 TAATCAATTTA-TTTTAAATAA
*
3157104 TAATTAATTTATTTTAAATAA
1 TAATCAATTTATTTTAAATAA
3157125 AAATAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATCAATTTATTTTAAATAA
Found at i:3157151 original size:29 final size:27
Alignment explanation
Indices: 3157098--3157151 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
3157088 ATTTATTTTT
* * *
3157098 AAATAATAATTAATTTATTTTAAATAA
1 AAATAATAAATAATTTATCTCAAATAA
3157125 AAATAATATAATATATTTATCTCAAAT
1 AAATAATA-AATA-ATTTATCTCAAAT
3157152 TTAATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 3 0.14
29 11 0.50
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATAATAAATAATTTATCTCAAATAA
Found at i:3157928 original size:4 final size:4
Alignment explanation
Indices: 3157921--3157946 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3157911 TTAGCATTCA
3157921 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3157947 TGGCCAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:3160178 original size:6 final size:7
Alignment explanation
Indices: 3160161--3160188 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3160151 ATCAAACTAG
3160161 TTTTTTA
1 TTTTTTA
3160168 TTTTTTA
1 TTTTTTA
3160175 TTTTTTA
1 TTTTTTA
3160182 TTTTTTA
1 TTTTTTA
3160189 GTTACGCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:3161564 original size:18 final size:17
Alignment explanation
Indices: 3161532--3161565 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3161522 AATTTATGTG
3161532 AATGAAAAATAAAATAC
1 AATGAAAAATAAAATAC
*
3161549 AATGATAAAATTAAATA
1 AATGA-AAAATAAAATA
3161566 TATATTAATC
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:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (17 bp):
AATGAAAAATAAAATAC
Found at i:3162427 original size:18 final size:18
Alignment explanation
Indices: 3162400--3162440 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3162390 TATAATCGAA
3162400 TAAA-AAATATAAAAATT
1 TAAATAAATATAAAAATT
*
3162417 TAAATAAATATTAAAATT
1 TAAATAAATATAAAAATT
3162435 TAAATA
1 TAAATA
3162441 TTAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAATAAATATAAAAATT
Found at i:3163406 original size:29 final size:30
Alignment explanation
Indices: 3163365--3163436 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
3163355 TTAACTTTTA
3163365 AAAT-AATTTTTATACTTTT-ATTT-TATCC
1 AAATAAATTTTTATA-TTTTGATTTGTATCC
* *
3163393 AAATAAATTATTATATTTTGATTTGTATCT
1 AAATAAATTTTTATATTTTGATTTGTATCC
3163423 AAATAAATTTTTAT
1 AAATAAATTTTTAT
3163437 TTCAAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.21
29 13 0.34
30 17 0.45
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTGATTTGTATCC
Found at i:3164255 original size:11 final size:10
Alignment explanation
Indices: 3164234--3164263 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3164224 ATATTTTTTG
3164234 TTTTTTAAAT
1 TTTTTTAAAT
3164244 TTTTTTATAAT
1 TTTTTTA-AAT
3164255 TTTTTTAAA
1 TTTTTTAAA
3164264 AAATTAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:3164647 original size:20 final size:21
Alignment explanation
Indices: 3164612--3164653 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3164602 TTTGGGCCAC
* *
3164612 TTTGACCTTTTTTTTTTTAAT
1 TTTGACCTTTTATTTTGTAAT
3164633 TTTGA-CTTTTATTTTGTAAT
1 TTTGACCTTTTATTTTGTAAT
3164653 T
1 T
3164654 CACAGCATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (21 bp):
TTTGACCTTTTATTTTGTAAT
Found at i:3166209 original size:2 final size:2
Alignment explanation
Indices: 3166202--3166237 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3166192 ATCCTTTTAT
3166202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3166238 AATACTAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3167098 original size:42 final size:43
Alignment explanation
Indices: 3167047--3167130 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 43
3167037 ATTTCATTTT
*
3167047 TTTATTAATTATA-TT-ATAAAAATATTATTTT-TATATTAATA
1 TTTATTAATTAAATTTAATAAAAATATTATTTTAT-TATTAATA
3167088 TTTATATAATTAAATTTAAATAAAAATATTATTTTATTATTAA
1 TTTAT-TAATTAAATTT-AATAAAAATATTATTTTATTATTAA
3167131 ATAGAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 5 0.14
42 7 0.19
43 2 0.05
45 22 0.59
46 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (43 bp):
TTTATTAATTAAATTTAATAAAAATATTATTTTATTATTAATA
Found at i:3171062 original size:21 final size:21
Alignment explanation
Indices: 3171037--3171086 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3171027 ATCATCTTTT
*
3171037 ATGAAA-AGATGCACTAGTTGG
1 ATGAAATA-ATGCACTAATTGG
*
3171058 ATGAAATAATGTACTAATTGG
1 ATGAAATAATGCACTAATTGG
*
3171079 ATGGAATA
1 ATGAAATA
3171087 TGTAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.28
Consensus pattern (21 bp):
ATGAAATAATGCACTAATTGG
Found at i:3177824 original size:2 final size:2
Alignment explanation
Indices: 3177812--3177840 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3177802 TCCATTTTGG
3177812 AT AT A- 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
3177841 TAATCCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3184007 original size:50 final size:49
Alignment explanation
Indices: 3183943--3184102 Score: 214
Period size: 50 Copynumber: 3.2 Consensus size: 49
3183933 AGGTGTTACC
* *
3183943 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGATGTGGCTATA
1 ATTGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGA-GTGGCTATA
* * * *
3183993 ATTGTTGACGATTCTTCACCAATCTTTGATAATTGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGA-GTGGCTATA
*
3184043 ATTGTTGACTATTCTTCACCAACCTTTAATAATAGAGAGAGATGG-TCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAG-TGGCT-ATA
3184093 ATTGTTGACT
1 ATTGTTGACT
3184103 CTAAGCAACT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
49 1 0.01
50 96 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (49 bp):
ATTGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGTGGCTATA
Found at i:3184434 original size:2 final size:2
Alignment explanation
Indices: 3184421--3184452 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3184411 AGCTTAAGTT
*
3184421 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3184453 CATAAGATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3185713 original size:21 final size:21
Alignment explanation
Indices: 3185664--3185715 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3185654 AAATTGTTGC
3185664 TGAAAA-TATTTTTAATAGCA
1 TGAAAATTATTTTTAATAGCA
* *
3185684 T-AAATTTATTTTTATATA-TA
1 TGAAAATTATTTTTA-ATAGCA
3185704 TGAAAATTATTT
1 TGAAAATTATTT
3185716 ATTAGTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.12
20 11 0.42
21 12 0.46
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (21 bp):
TGAAAATTATTTTTAATAGCA
Found at i:3187855 original size:19 final size:21
Alignment explanation
Indices: 3187833--3187874 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3187823 AAAATATGCT
*
3187833 AAAATAT-TTAAAAATA-ATA
1 AAAATATAATAAAAATATATA
3187852 AAAATATAATAAAAATATATA
1 AAAATATAATAAAAATATATA
3187873 AA
1 AA
3187875 TTTGTAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 8 0.40
21 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATATAATAAAAATATATA
Found at i:3187864 original size:29 final size:29
Alignment explanation
Indices: 3187795--3187874 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
3187785 TTATAAGGTC
* *
3187795 AAATATAATAAAATACAAAAAAAAAAGTA
1 AAATATAATAAAATATATAAAAAAAAGTA
** * *
3187824 AAATATGCTAAAATATTTAAAAATAA-TAA
1 AAATATAATAAAATATATAAAAAAAAGT-A
3187853 AAATATAATAAAAATATATAAA
1 AAATATAAT-AAAATATATAAA
3187875 TTTGTAAAAC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.70
30 11 0.28
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (29 bp):
AAATATAATAAAATATATAAAAAAAAGTA
Found at i:3187873 original size:13 final size:11
Alignment explanation
Indices: 3187842--3187874 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3187832 TAAAATATTT
3187842 AAAA-ATAATA
1 AAAATATAATA
3187852 AAAATATAATA
1 AAAATATAATA
3187863 AAAATAT-ATA
1 AAAATATAATA
3187873 AA
1 AA
3187875 TTTGTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATATAATA
Found at i:3187916 original size:17 final size:18
Alignment explanation
Indices: 3187887--3187920 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3187877 TGTAAAACTC
3187887 TTATATATAAATTATTAA
1 TTATATATAAATTATTAA
3187905 TTATAT-TAAATTATTA
1 TTATATATAAATTATTA
3187921 TAAATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATATAAATTATTAA
Found at i:3188162 original size:2 final size:2
Alignment explanation
Indices: 3188155--3188199 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3188145 CCCTGCTCAC
3188155 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3188197 CT C
1 CT C
3188200 AAACACACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3188373 original size:2 final size:2
Alignment explanation
Indices: 3188366--3188392 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3188356 ACTTTTCTTA
3188366 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
3188393 AATCATTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3189245 original size:2 final size:2
Alignment explanation
Indices: 3189238--3189281 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3189228 CTTTTTCTTT
3189238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3189280 TA
1 TA
3189282 AAGTTAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3191625 original size:3 final size:3
Alignment explanation
Indices: 3191617--3191642 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3191607 TTTTAATTGG
3191617 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3191643 ATGAAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3192147 original size:18 final size:18
Alignment explanation
Indices: 3192126--3192168 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3192116 ATCAGATATT
*
3192126 TAAATTTTTTATTTA-AAA
1 TAAATTTATT-TTTATAAA
3192144 TAAATTTATTTTTATAAA
1 TAAATTTATTTTTATAAA
3192162 T-AATTTA
1 TAAATTTA
3192169 AATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTTATTTTTATAAA
Found at i:3192250 original size:17 final size:18
Alignment explanation
Indices: 3192221--3192258 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
3192211 TATTTTTAAA
3192221 AAATAATTTAATAAATTT
1 AAATAATTTAATAAATTT
3192239 AAATAA-TTAATAAATTT
1 AAATAATTTAATAAATTT
3192256 AAA
1 AAA
3192259 ATTTTAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAATTTAATAAATTT
Found at i:3193875 original size:2 final size:2
Alignment explanation
Indices: 3193868--3193900 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3193858 TTAAACTTCA
3193868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3193901 TTACATGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3197366 original size:13 final size:13
Alignment explanation
Indices: 3197348--3197372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3197338 AGTATTGGTT
3197348 TTATTTTTTTATC
1 TTATTTTTTTATC
3197361 TTATTTTTTTAT
1 TTATTTTTTTAT
3197373 TAAAAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTATC
Found at i:3197507 original size:11 final size:11
Alignment explanation
Indices: 3197487--3197526 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
3197477 AAATTTTAAA
3197487 ATATTTATATT
1 ATATTTATATT
*
3197498 ATATTCATATT
1 ATATTTATATT
3197509 ATATTTTATATT
1 ATA-TTTATATT
3197521 ATATTT
1 ATATTT
3197527 TAATTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATTTATATT
Found at i:3197760 original size:28 final size:29
Alignment explanation
Indices: 3197729--3197795 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
3197719 AATAATTTGA
*
3197729 TATATTTTTAATATTTAAATTATA-ATAT
1 TATATTTTTAATATTTAAATAATATATAT
* *
3197757 TATATATTTATTATTTAAATAATATATAT
1 TATATTTTTAATATTTAAATAATATATAT
3197786 TATATTTTTA
1 TATATTTTTA
3197796 TATAATTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATATTTTTAATATTTAAATAATATATAT
Found at i:3197782 original size:22 final size:22
Alignment explanation
Indices: 3197752--3197801 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3197742 TTTAAATTAT
*
3197752 AATATTATATATT-TATTATTTA
1 AATAATATATATTATATT-TTTA
3197774 AATAATATATATTATATTTTTA
1 AATAATATATATTATATTTTTA
*
3197796 TATAAT
1 AATAAT
3197802 TCAAAAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATAATATATATTATATTTTTA
Found at i:3197791 original size:27 final size:27
Alignment explanation
Indices: 3197718--3197796 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
3197708 TTAAAATAAA
* * *
3197718 AAATAATTTGATA-TATTTTTAATATTT
1 AAATAATAT-ATATTATATTTATTATTT
*
3197745 AAATTATA-ATATTATATATTTATTATTT
1 AAATAATATATA-T-TATATTTATTATTT
3197773 AAATAATATATATTATATTT-TTAT
1 AAATAATATATATTATATTTATTAT
3197797 ATAATTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 3 0.07
26 4 0.09
27 13 0.30
28 20 0.47
29 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
AAATAATATATATTATATTTATTATTT
Found at i:3198742 original size:29 final size:27
Alignment explanation
Indices: 3198710--3198776 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
3198700 AAATATGATA
3198710 AAATTTTAAATATAAATATAATATATATT
1 AAATTTTAAATAT-AATAT-ATATATATT
* *
3198739 AAATTTATTAAATATATTATATTTATATT
1 AAA-TT-TTAAATATAATATATATATATT
*
3198768 ATATTTTAA
1 AAATTTTAA
3198777 TTTTGTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 13 0.39
30 6 0.18
31 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATTTTAAATATAATATATATATATT
Found at i:3198771 original size:18 final size:18
Alignment explanation
Indices: 3198726--3198776 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3198716 TAAATATAAA
*
3198726 TATAATATATATTAAATT
1 TATATTATATATTAAATT
* *
3198744 TAT-TAAATATATTATATT
1 TATAT-TATATATTAAATT
*
3198762 TATATTATATTTTAA
1 TATATTATATATTAA
3198777 TTTTGTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTATATATTAAATT
Found at i:3199574 original size:8 final size:8
Alignment explanation
Indices: 3199547--3199577 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
3199537 ATAATTTTAA
3199547 ATTATTTTT
1 ATTA-TTTT
3199556 ATTATTTT
1 ATTATTTT
3199564 ATTATTTT
1 ATTATTTT
3199572 ATTATT
1 ATTATT
3199578 AAATTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTATTTT
Found at i:3199578 original size:19 final size:19
Alignment explanation
Indices: 3199523--3199578 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
3199513 CTTATTAATA
*
3199523 TATTATCTTTATTTATAATTT
1 TATTAT-TTTA-TTATTATTT
3199544 TAAATTA-TTT-TTATTATTT
1 T--ATTATTTTATTATTATTT
3199563 TATTATTTTATTATTA
1 TATTATTTTATTATTA
3199579 AATTAATATC
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
19 15 0.50
21 4 0.13
23 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTATTTTATTATTATTT
Found at i:3199608 original size:11 final size:11
Alignment explanation
Indices: 3199592--3199639 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
3199582 TAATATCACT
3199592 TAATTTAATAA
1 TAATTTAATAA
3199603 TAATTTAATAA
1 TAATTTAATAA
* * *
3199614 AAATTTTATTA
1 TAATTTAATAA
*
3199625 TAATATATATAA
1 TAATTTA-ATAA
3199637 TAA
1 TAA
3199640 ATATAAAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 23 0.79
12 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATTTAATAA
Found at i:3199724 original size:18 final size:17
Alignment explanation
Indices: 3199695--3199748 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
3199685 ATATTAATTA
*
3199695 TATTAAATTTTTTTATT
1 TATTAAATTTTTATATT
*
3199712 TTTTAATATTTTTATATT
1 TATTAA-ATTTTTATATT
*
3199730 TATTAAATATATTATATT
1 TATTAAAT-TTTTATATT
3199748 T
1 T
3199749 TTATATTCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTAAATTTTTATATT
Found at i:3199728 original size:8 final size:8
Alignment explanation
Indices: 3199704--3199755 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
3199694 ATATTAAATT
3199704 TTTTTAT-
1 TTTTTATA
3199711 TTTTTAATA
1 TTTTT-ATA
3199720 TTTTTATA
1 TTTTTATA
*
3199728 TTTATTAAA
1 TTT-TTATA
*
3199737 TATATTATA
1 T-TTTTATA
3199746 TTTTTATA
1 TTTTTATA
3199754 TT
1 TT
3199756 CTGTATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.14
8 16 0.43
9 15 0.41
10 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTTATA
Found at i:3200293 original size:15 final size:15
Alignment explanation
Indices: 3200273--3200302 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3200263 TTTAATTTAA
3200273 TAAATATTATAAAAT
1 TAAATATTATAAAAT
*
3200288 TAAATATTATTAAAT
1 TAAATATTATAAAAT
3200303 CATATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATATTATAAAAT
Found at i:3200569 original size:17 final size:18
Alignment explanation
Indices: 3200527--3200569 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3200517 ATATTATTTT
3200527 AAATATAAATAAAAAATTA
1 AAATATAAAT-AAAAATTA
**
3200546 ATTTATAAAT-AAAATTA
1 AAATATAAATAAAAATTA
3200563 AAATATA
1 AAATATA
3200570 TATTATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAAATAAAAATTA
Found at i:3200625 original size:30 final size:29
Alignment explanation
Indices: 3200561--3200625 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3200551 TAAATAAAAT
*
3200561 TAAAATATATATTATTTTTAAAATATATA
1 TAAAATATATATAATTTTTAAAATATATA
* ** *
3200590 AAAAATATATGATAATTTTTAATTTATTTA
1 TAAAATATAT-ATAATTTTTAAAATATATA
3200620 TAAAAT
1 TAAAAT
3200626 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TAAAATATATATAATTTTTAAAATATATA
Found at i:3206243 original size:2 final size:2
Alignment explanation
Indices: 3206236--3206276 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3206226 TTTGCCACAT
3206236 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
3206277 TCATACAACA
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:3210920 original size:2 final size:2
Alignment explanation
Indices: 3210913--3210953 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3210903 AAATGATGAA
*
3210913 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3210954 ATAAATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3211581 original size:17 final size:18
Alignment explanation
Indices: 3211530--3211577 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
3211520 ATGGAAAGCT
*
3211530 GTTATTTTTTTGCTTTTTCA
1 GTTATTTTTTT--ATTTTCA
3211550 GTTATTTTTTTATTTT-A
1 GTTATTTTTTTATTTTCA
3211567 GTT-TTTTTTTA
1 GTTATTTTTTTA
3211578 ATTTGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 4 0.15
18 4 0.15
20 11 0.41
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.75
Consensus pattern (18 bp):
GTTATTTTTTTATTTTCA
Found at i:3212114 original size:16 final size:16
Alignment explanation
Indices: 3212080--3212125 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3212070 TTAAAATTAA
* *
3212080 TTAAATTTTAATTTTTT
1 TTAAA-TTTAAATTATT
3212097 TTAAATTTAAATTATT
1 TTAAATTTAAATTATT
*
3212113 TTAAATCTAAATT
1 TTAAATTTAAATT
3212126 TATTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATTTAAATTATT
Found at i:3212128 original size:17 final size:17
Alignment explanation
Indices: 3212089--3212129 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3212079 ATTAAATTTT
* *
3212089 AATTTTTTTTAAATTTA
1 AATTTATTTTAAATCTA
3212106 AA-TTATTTTAAATCTA
1 AATTTATTTTAAATCTA
3212122 AATTTATT
1 AATTTATT
3212130 AATTTAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTATTTTAAATCTA
Found at i:3212235 original size:25 final size:25
Alignment explanation
Indices: 3212185--3212238 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3212175 TTCGAATTAA
*
3212185 TTAAATTTAATTTTTTTTAAATATT
1 TTAAATTTAATTTTTATTAAATATT
3212210 TTAAATTT-ATTATTTAATTAAA-ATT
1 TTAAATTTAATT-TTT-ATTAAATATT
3212235 TTAA
1 TTAA
3212239 TCAATTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 3 0.12
25 18 0.69
26 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAAATTTAATTTTTATTAAATATT
Found at i:3212441 original size:23 final size:23
Alignment explanation
Indices: 3212410--3212484 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
3212400 GACCATACTT
*
3212410 AAATCTTAATTCATTTATTATTA
1 AAATATTAATTCATTTATTATTA
**
3212433 AAATATTAATT-ATATTAAGATTCA
1 AAATATTAATTCAT-TTATTATT-A
*
3212457 AAATCTT-A-TCA-TTATTATTA
1 AAATATTAATTCATTTATTATTA
*
3212477 AAACATTA
1 AAATATTA
3212485 TTTTATATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
20 6 0.15
21 6 0.15
22 3 0.08
23 18 0.45
24 7 0.17
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (23 bp):
AAATATTAATTCATTTATTATTA
Found at i:3212547 original size:22 final size:22
Alignment explanation
Indices: 3212516--3212557 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3212506 ATATTTACAT
*
3212516 AAATAATAAATATTAATTATTA
1 AAATAATAAAAATTAATTATTA
* *
3212538 AAATATTAAAAATTATTTAT
1 AAATAATAAAAATTAATTAT
3212558 CATTAAACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATAATAAAAATTAATTATTA
Found at i:3212661 original size:25 final size:25
Alignment explanation
Indices: 3212611--3212663 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3212601 ATTTTAATGA
* *
3212611 TAATATTTAATGCTAAAATATTATAT
1 TAATATTAAATACTAAAATA-TATAT
3212637 TAATATTAAATACTTAAAATA-ATAT
1 TAATATTAAATAC-TAAAATATATAT
3212662 TA
1 TA
3212664 TTTGTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 11 0.46
27 7 0.29
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATATTAAATACTAAAATATATAT
Found at i:3212874 original size:30 final size:31
Alignment explanation
Indices: 3212815--3212906 Score: 77
Period size: 30 Copynumber: 3.1 Consensus size: 31
3212805 TAAATTTTAT
* * *
3212815 TAATATTTTATTA-ATTATTATTAAA-ATAAA
1 TAATATTATATTATAGTATTA-AAAATATAAA
3212845 TAATATTATATTATA-TATTAAAAATATAAA
1 TAATATTATATTATAGTATTAAAAATATAAA
* * *
3212875 T-ATGTAAT-TTAATAGTATTCAAAATATAAA
1 TAATATTATATT-ATAGTATTAAAAATATAAA
3212905 TA
1 TA
3212907 TTAACAATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
28 2 0.04
29 11 0.21
30 38 0.73
31 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (31 bp):
TAATATTATATTATAGTATTAAAAATATAAA
Found at i:3214198 original size:2 final size:2
Alignment explanation
Indices: 3214191--3214221 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3214181 TATCTTTGTG
3214191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3214222 AGCCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3215481 original size:19 final size:19
Alignment explanation
Indices: 3215457--3215506 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3215447 TCTTTTAAAT
3215457 AAAAAACTATTCACT-TATA
1 AAAAAACTATTCA-TATATA
*
3215476 AAAAAACTAGTCATATATA
1 AAAAAACTATTCATATATA
*
3215495 ATAAAAATTATT
1 A-AAAAACTATT
3215507 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 17 0.65
20 8 0.31
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAACTATTCATATATA
Found at i:3216485 original size:13 final size:13
Alignment explanation
Indices: 3216469--3216502 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3216459 AATTTTATTT
*
3216469 TTTATCATCGATA
1 TTTATCATCAATA
*
3216482 TTTATAATCAATA
1 TTTATCATCAATA
3216495 TTTATCAT
1 TTTATCAT
3216503 AATTAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (13 bp):
TTTATCATCAATA
Found at i:3223367 original size:16 final size:16
Alignment explanation
Indices: 3223342--3223372 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3223332 ACTATATTTT
3223342 TATTTATATTTTTCTA
1 TATTTATATTTTTCTA
*
3223358 TATTTGTATTTTTCT
1 TATTTATATTTTTCT
3223373 TTTTGAGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.71
Consensus pattern (16 bp):
TATTTATATTTTTCTA
Done.