Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 6 of 13
Found at i:3117906 original size:14 final size:14
Alignment explanation
Indices: 3117887--3117913 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3117877 GATCAATTAG
3117887 TTGTGAATTGTTGT
1 TTGTGAATTGTTGT
3117901 TTGTGAATTGTTG
1 TTGTGAATTGTTG
3117914 GATCAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (14 bp):
TTGTGAATTGTTGT
Found at i:3121219 original size:23 final size:23
Alignment explanation
Indices: 3121189--3121239 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
3121179 ATTGTATTAG
* *
3121189 TATA-AAATT-ATACACTATATA
1 TATATAAATTAATACAATATACA
3121210 TAATATAAATTAATACAATATACA
1 T-ATATAAATTAATACAATATACA
3121234 TATATA
1 TATATA
3121240 GTATATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 3 0.12
23 10 0.40
24 11 0.44
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (23 bp):
TATATAAATTAATACAATATACA
Found at i:3121287 original size:22 final size:23
Alignment explanation
Indices: 3121235--3121289 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
3121225 CAATATACAT
* *
3121235 ATATAGTATATAATAATATGTTA
1 ATATAGTATACAATAATATATTA
*
3121258 AT-TA-TATACAGTAA-ATATTA
1 ATATAGTATACAATAATATATTA
3121278 ATATAGTATACA
1 ATATAGTATACA
3121290 TTATTTACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 7 0.26
21 10 0.37
22 8 0.30
23 2 0.07
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (23 bp):
ATATAGTATACAATAATATATTA
Found at i:3133775 original size:17 final size:17
Alignment explanation
Indices: 3133749--3133792 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3133739 GAGATGAAGG
* *
3133749 AAAACGAAGAAAGAAAGT
1 AAAACTAAGAAA-AAAAT
3133767 -AAACTAAGAAAAAAAT
1 AAAACTAAGAAAAAAAT
3133783 AAAACTAAGA
1 AAAACTAAGA
3133793 GTCAACCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (17 bp):
AAAACTAAGAAAAAAAT
Found at i:3141030 original size:30 final size:28
Alignment explanation
Indices: 3140964--3141066 Score: 80
Period size: 30 Copynumber: 3.5 Consensus size: 28
3140954 ATTATTAGTC
* *
3140964 ATAAAGATCTATTTGATTCAAAATACAAAT
1 ATAAAAATTTATTT-ATTCAAAATA-AAAT
*
3140994 ACAAAAATTTATTTAGTTCAAAATAAAAGT
1 ATAAAAATTTATTTA-TTCAAAATAAAA-T
* * ** *
3141024 ATAAAAACTTAATTAAACATAATAAAAAT
1 ATAAAAATTTATTTATTCAAAAT-AAAAT
*
3141053 ATAAAGATTTATTT
1 ATAAAAATTTATTT
3141067 TAATTTTTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 21 0.36
30 37 0.64
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (28 bp):
ATAAAAATTTATTTATTCAAAATAAAAT
Found at i:3142285 original size:24 final size:25
Alignment explanation
Indices: 3142258--3142305 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3142248 TTATATGGGA
*
3142258 ATTGATTTAATTTTA-TGTT-GATTT
1 ATTGATAT-ATTTTATTGTTAGATTT
3142282 ATTGATATATTTTATTGTTAGATT
1 ATTGATATATTTTATTGTTAGATT
3142306 GTAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 11 0.52
25 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.60
Consensus pattern (25 bp):
ATTGATATATTTTATTGTTAGATTT
Found at i:3143307 original size:14 final size:14
Alignment explanation
Indices: 3143290--3143319 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3143280 TGTAATCGTC
*
3143290 ATTTTTTAATTTTT
1 ATTTTTTAATTATT
3143304 ATTTTTTAATTATT
1 ATTTTTTAATTATT
3143318 AT
1 AT
3143320 AGATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTTAATTATT
Found at i:3143627 original size:2 final size:2
Alignment explanation
Indices: 3143620--3143649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3143610 TGTTAGGTAC
3143620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3143650 TAATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3154044 original size:15 final size:16
Alignment explanation
Indices: 3154021--3154066 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
3154011 GTCAAAATAT
3154021 TTATTTAATTTTTATA
1 TTATTTAATTTTTATA
3154037 TT-TTTAA-TTTTAT-
1 TTATTTAATTTTTATA
3154050 TTAATTTAATTTTTATA
1 TT-ATTTAATTTTTATA
3154067 CTCAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.08
14 6 0.23
15 10 0.38
16 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTAATTTTTATA
Found at i:3154077 original size:29 final size:29
Alignment explanation
Indices: 3154018--3154119 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 29
3154008 ATCGTCAAAA
** *
3154018 TATTT-ATTTAATTTTTATATTTTTAATTT
1 TATTTAATTTAATTTTTATA-TTAAAAATT
* *
3154047 TATTTAATTTAATTTTTATACTCAAAATT
1 TATTTAATTTAATTTTTATATTAAAAATT
** * *
3154076 TAAGTAATATAATTTTTTGATTTTAAAAATT
1 TATTTAATTTAA-TTTTT-ATATTAAAAATT
*
3154107 TATTCAATTTAAT
1 TATTTAATTTAAT
3154120 CTCCCTTAAC
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
29 19 0.34
30 20 0.36
31 17 0.30
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
TATTTAATTTAATTTTTATATTAAAAATT
Found at i:3155047 original size:15 final size:15
Alignment explanation
Indices: 3155027--3155057 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3155017 TAAATGCAGT
*
3155027 TTTTAATTTAAAAAA
1 TTTTAACTTAAAAAA
3155042 TTTTAACTTAAAAAA
1 TTTTAACTTAAAAAA
3155057 T
1 T
3155058 ATAACTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTAACTTAAAAAA
Found at i:3155111 original size:16 final size:18
Alignment explanation
Indices: 3155065--3155111 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
3155055 AATATAACTG
3155065 AAAATATTAAATAAAGTAA
1 AAAATATTAAATAAAGT-A
*
3155084 AAACATAATAAATAAA-T-
1 AAA-ATATTAAATAAAGTA
3155101 AAAATATTAAA
1 AAAATATTAAA
3155112 AAGATGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 7 0.28
17 3 0.12
19 4 0.16
20 11 0.44
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATATTAAATAAAGTA
Found at i:3157923 original size:11 final size:11
Alignment explanation
Indices: 3157903--3157939 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
3157893 CAAGTTGGAG
3157903 GAAAAA-AAAA
1 GAAAAAGAAAA
3157913 GAAAAAGAAAA
1 GAAAAAGAAAA
3157924 GAAAAAGGAAAA
1 GAAAAA-GAAAA
3157936 GAAA
1 GAAA
3157940 GGAGACATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.24
11 10 0.40
12 9 0.36
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:3157930 original size:17 final size:16
Alignment explanation
Indices: 3157903--3157939 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
3157893 CAAGTTGGAG
3157903 GAAAAAAAAAGAAAAA
1 GAAAAAAAAAGAAAAA
*
3157919 GAAAAGAAAAAGGAAAA
1 GAAAA-AAAAAGAAAAA
3157936 GAAA
1 GAAA
3157940 GGAGACATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAGAAAAA
Found at i:3166716 original size:2 final size:2
Alignment explanation
Indices: 3166709--3166734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3166699 AAGAAAGAAG
3166709 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3166735 AATGGGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3168433 original size:14 final size:16
Alignment explanation
Indices: 3168416--3168448 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3168406 TTTTTGGATA
3168416 TTTTAAAA-TA-TTAT
1 TTTTAAAATTATTTAT
3168430 TTTTAAAATTATTTAT
1 TTTTAAAATTATTTAT
3168446 TTT
1 TTT
3168449 GAGACTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTAAAATTATTTAT
Found at i:3185431 original size:2 final size:2
Alignment explanation
Indices: 3185424--3185448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3185414 TGCATTATCA
3185424 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 A
3185449 AATCTAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3189919 original size:2 final size:2
Alignment explanation
Indices: 3189912--3189944 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3189902 GAAATCCAGA
3189912 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 A
3189945 GAAACACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3190458 original size:3 final size:3
Alignment explanation
Indices: 3190450--3190484 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3190440 CCACTACCTT
3190450 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
3190485 TATAAAGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:3195659 original size:30 final size:30
Alignment explanation
Indices: 3195619--3195688 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
3195609 GTCTTCAACC
* *
3195619 AAATATTTATATTTATATTTTTAA-TTGAAT
1 AAATTTTTATATTTATA-TTTTAAGTTAAAT
*
3195649 AAATTTTTATATTTTTATTTTAAGTTAAAT
1 AAATTTTTATATTTATATTTTAAGTTAAAT
*
3195679 AAAATTTTAT
1 AAATTTTTAT
3195689 GATTAACCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 6 0.17
30 29 0.83
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
AAATTTTTATATTTATATTTTAAGTTAAAT
Found at i:3197567 original size:17 final size:18
Alignment explanation
Indices: 3197531--3197574 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
3197521 TTGTTAAATC
*
3197531 ATAAAATAATTTTTATTTT
1 ATAAAA-AATTTTTACTTT
3197550 ATAAAAAATTTTT-CTTT
1 ATAAAAAATTTTTACTTT
*
3197567 ACAAAAAA
1 ATAAAAAA
3197575 AAAAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 7 0.30
19 6 0.26
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAAAATTTTTACTTT
Found at i:3198874 original size:20 final size:21
Alignment explanation
Indices: 3198836--3198874 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3198826 ATCCGAATTT
*
3198836 CTTTTTCCTCCTTCATTTGAC
1 CTTTTTCCTCCCTCATTTGAC
*
3198857 CTTTTT-CTCCCTCTTTTG
1 CTTTTTCCTCCCTCATTTG
3198875 GAGACATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.05, C:0.33, G:0.05, T:0.56
Consensus pattern (21 bp):
CTTTTTCCTCCCTCATTTGAC
Found at i:3203186 original size:2 final size:2
Alignment explanation
Indices: 3203179--3203208 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3203169 AACCCCATCC
*
3203179 TA TA TA TA TA CA 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
3203209 AATTTGCAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3222170 original size:23 final size:25
Alignment explanation
Indices: 3222126--3222172 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
3222116 AGAAAAGTGG
*
3222126 AAATAGAACACGAAAACCAAGAGAA
1 AAATAGAACACGAAAACAAAGAGAA
*
3222151 AAATAGAA-A-GAAAAGAAAGAGA
1 AAATAGAACACGAAAACAAAGAGA
3222173 GAGAGGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 1 0.05
25 8 0.40
ACGTcount: A:0.68, C:0.09, G:0.19, T:0.04
Consensus pattern (25 bp):
AAATAGAACACGAAAACAAAGAGAA
Found at i:3225190 original size:18 final size:16
Alignment explanation
Indices: 3225167--3225204 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
3225157 GATGTTCTCC
3225167 TTTCTTTTTCCTTTTTCT
1 TTTCTTTTT-CTTTTT-T
3225185 TTTCTTTTTCTTTTTT
1 TTTCTTTTTCTTTTTT
3225201 TTTC
1 TTTC
3225205 CTCCAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTT
Found at i:3225199 original size:6 final size:6
Alignment explanation
Indices: 3225167--3225203 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
3225157 GATGTTCTCC
3225167 TTTCTT TTTCCTT TTTC-T TTTCTT TTTCTT TTT-TT TT
1 TTTCTT TTT-CTT TTTCTT TTTCTT TTTCTT TTTCTT TT
3225204 CCTCCAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 9 0.31
6 14 0.48
7 6 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:3237635 original size:10 final size:10
Alignment explanation
Indices: 3237610--3237638 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
3237600 ATAAAAATAA
3237610 AAAATTATTT
1 AAAATTATTT
3237620 -AAATTATTT
1 AAAATTATTT
3237629 AAAATTATTT
1 AAAATTATTT
3237639 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAAATTATTT
Found at i:3240273 original size:133 final size:133
Alignment explanation
Indices: 3240035--3240283 Score: 462
Period size: 133 Copynumber: 1.9 Consensus size: 133
3240025 TTTTTTTTTA
*
3240035 AAAAAAAAACGATTGCTTTGTTGTTAAGAATATGATTGTGGAGAGATATGGGAGGTCCGAGCCTT
1 AAAAAAAAACGATTGCTTTGTTGTTAAGAATATGATTGTGGAGAGATATGGGAGGTCCGAGCCTG
3240100 CTTTACTTCACATTGCGACGAATTTTCTGTCTTGGCCAACTAATCTTGATTATTTGTAATATGAT
66 CTTTACTTCACATTGCGACGAATTTTCTGTCTTGGCCAACTAATCTTGATTATTTGTAATATGAT
3240165 TAT
131 TAT
* *
3240168 AAAAAAAAACGATTGCTTTGTTGTTAAGAATATGATTGTGGGGAGATATGGGAGGTCTGAGCCTG
1 AAAAAAAAACGATTGCTTTGTTGTTAAGAATATGATTGTGGAGAGATATGGGAGGTCCGAGCCTG
*
3240233 CTTTGCTTCACATTGCGACGAATTTTCTGTCTTGGCCAACTAATCTTGATT
66 CTTTACTTCACATTGCGACGAATTTTCTGTCTTGGCCAACTAATCTTGATT
3240284 CTATATTCCC
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 112 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (133 bp):
AAAAAAAAACGATTGCTTTGTTGTTAAGAATATGATTGTGGAGAGATATGGGAGGTCCGAGCCTG
CTTTACTTCACATTGCGACGAATTTTCTGTCTTGGCCAACTAATCTTGATTATTTGTAATATGAT
TAT
Found at i:3244725 original size:2 final size:2
Alignment explanation
Indices: 3244718--3244763 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
3244708 TGAAATTAAG
* * *
3244718 AT AT AT AT AT AT AT AT AC AC AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3244760 AT AT
1 AT AT
3244764 TTCACCCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3247350 original size:21 final size:23
Alignment explanation
Indices: 3247294--3247350 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
3247284 CTATCGATAT
*
3247294 ATTTTAAATTAGTTTTAGTTTCTA
1 ATTTT-AATTAGTTTTAATTTCTA
3247318 A-TTT-ATTAGTTTTAATTT-TA
1 ATTTTAATTAGTTTTAATTTCTA
3247338 ATTTTAATT-GTTT
1 ATTTTAATTAGTTT
3247351 AGATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 20 0.67
22 3 0.10
23 3 0.10
24 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (23 bp):
ATTTTAATTAGTTTTAATTTCTA
Found at i:3253307 original size:2 final size:2
Alignment explanation
Indices: 3253300--3253331 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3253290 ATTAAAAATG
3253300 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
3253332 AAGATATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3256806 original size:18 final size:18
Alignment explanation
Indices: 3256773--3256807 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3256763 CAAAAGCTAT
*
3256773 GTTTGTTCAACCAATTAA
1 GTTTGTTCAAACAATTAA
*
3256791 GTTTGTTCAAATAATTA
1 GTTTGTTCAAACAATTA
3256808 TGTTGGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
GTTTGTTCAAACAATTAA
Found at i:3256850 original size:24 final size:23
Alignment explanation
Indices: 3256813--3256870 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
3256803 AATTATGTTG
* *
3256813 GAAAATAAAAAATTATGT-TTGTC
1 GAAAATAGACAATTAT-TATTGTC
*
3256836 AGAAAATAGACAATTCTTATTGTC
1 -GAAAATAGACAATTATTATTGTC
3256860 GAAAATAGACA
1 GAAAATAGACA
3256871 TGCGTTGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (23 bp):
GAAAATAGACAATTATTATTGTC
Found at i:3262063 original size:22 final size:22
Alignment explanation
Indices: 3262015--3262086 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
3262005 AGTTTTGATG
*
3262015 ATTTTTGGACATTGCATAATTA
1 ATTTTTGGACATTGCGTAATTA
* * *
3262037 GTTTTTGGACATTACGTAACTA
1 ATTTTTGGACATTGCGTAATTA
*
3262059 ATTTTTAGG-CATTGCGTTATTA
1 ATTTTT-GGACATTGCGTAATTA
3262081 ATTTTT
1 ATTTTT
3262087 AGATAGTGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 39 0.95
23 2 0.05
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (22 bp):
ATTTTTGGACATTGCGTAATTA
Found at i:3262217 original size:23 final size:23
Alignment explanation
Indices: 3262154--3262242 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
3262144 ACTGATTGAT
** *
3262154 AGGCATTGCGTGATTAGTTAGAA
1 AGGCATTATGTGATTAGTTAGTA
* *
3262177 AGGTATTACT-TGACTAGTTAGTA
1 AGGCATTA-TGTGATTAGTTAGTA
* * *
3262200 AGACATTATGTGATTAGTT-TTT
1 AGGCATTATGTGATTAGTTAGTA
3262222 AGGCATTATGTGACTTAGTTA
1 AGGCATTATGTGA-TTAGTTA
3262243 TTGTTTAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
22 14 0.27
23 37 0.73
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (23 bp):
AGGCATTATGTGATTAGTTAGTA
Found at i:3262302 original size:21 final size:21
Alignment explanation
Indices: 3262250--3262317 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
3262240 TTATTGTTTA
*
3262250 AAAATCAGTCACGTAATGCCT
1 AAAATCAGTTACGTAATGCCT
* *
3262271 AAAAACTAGTTACATAATGTCC-
1 AAAATC-AGTTACGTAATG-CCT
*
3262293 AAAATCAGTTACGTAATGCTT
1 AAAATCAGTTACGTAATGCCT
3262314 AAAA
1 AAAA
3262318 ACTAGAGATG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.53
22 15 0.39
23 2 0.05
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (21 bp):
AAAATCAGTTACGTAATGCCT
Found at i:3262412 original size:22 final size:22
Alignment explanation
Indices: 3262372--3262413 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3262362 CTCACATTAT
*
3262372 CTAAAAACCAGTGACACAATGC
1 CTAAAAACCAGTAACACAATGC
* *
3262394 CTAAAAACTAGTAATACAAT
1 CTAAAAACCAGTAACACAAT
3262414 ATTTAATAAC
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:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (22 bp):
CTAAAAACCAGTAACACAATGC
Found at i:3264729 original size:20 final size:20
Alignment explanation
Indices: 3264690--3264729 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3264680 TAATACTTGA
*
3264690 AAAAAATTTTAAATTATTTT
1 AAAAAATTTTAAATAATTTT
3264710 AAAAAA-TTTAAATAAGTTTT
1 AAAAAATTTTAAATAA-TTTT
3264730 TTATTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAAAATTTTAAATAATTTT
Found at i:3278547 original size:13 final size:12
Alignment explanation
Indices: 3278528--3278557 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3278518 AAATTTATTT
3278528 AAATTTTTTAAA
1 AAATTTTTTAAA
*
3278540 ATATTTTTTAAA
1 AAATTTTTTAAA
3278552 AAATTT
1 AAATTT
3278558 AAACATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AAATTTTTTAAA
Found at i:3321268 original size:37 final size:37
Alignment explanation
Indices: 3321200--3321274 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
3321190 ATCTTAAAGC
*
3321200 TAATATATAATTGAATTAAAGATAAGTTTAATAAATT
1 TAATATATAATTGAATTAAAGATAAGATTAATAAATT
* * * *
3321237 TAATATGTCATTGAATTAGAATATAA-ATTAATTAATT
1 TAATATATAATTGAATTA-AAGATAAGATTAATAAATT
3321274 T
1 T
3321275 TTATTTACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 26 0.81
38 6 0.19
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (37 bp):
TAATATATAATTGAATTAAAGATAAGATTAATAAATT
Found at i:3342120 original size:20 final size:20
Alignment explanation
Indices: 3342077--3342120 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3342067 CAAGGGGAGG
**
3342077 AAATATAACAATAAAATGTG
1 AAATATAACAATAAAATGAA
* *
3342097 AAATATAATAATAAAGTGAA
1 AAATATAACAATAAAATGAA
3342117 AAAT
1 AAAT
3342121 GATGAGTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (20 bp):
AAATATAACAATAAAATGAA
Found at i:3343825 original size:2 final size:2
Alignment explanation
Indices: 3343818--3343851 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3343808 TATTACAGTT
3343818 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3343852 ATGTTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3347575 original size:35 final size:35
Alignment explanation
Indices: 3347534--3347605 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
3347524 TCTGTAAGTT
*
3347534 AGTCTTCCCTATGTATCGCATAAAAACAATTGTAA
1 AGTCTTCCCTACGTATCGCATAAAAACAATTGTAA
* *
3347569 AGTCTTCCCTACGTATCGCATCAAAACCATTGTAA
1 AGTCTTCCCTACGTATCGCATAAAAACAATTGTAA
3347604 AG
1 AG
3347606 GCTTTGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (35 bp):
AGTCTTCCCTACGTATCGCATAAAAACAATTGTAA
Found at i:3364488 original size:80 final size:79
Alignment explanation
Indices: 3364357--3364509 Score: 238
Period size: 80 Copynumber: 1.9 Consensus size: 79
3364347 ATCCAGACAA
**
3364357 AGATAATAAATTTTTTTTCATATATATATATATATATGATTGCTGATTATAACAT-AAAGGGTAT
1 AGATAATAAAAATTTTTTCATATATATATATATATATGATTGCTGATTATAACATAAAAGGGTAT
3364421 GCTTAGTTCAGGAC
66 GCTTAGTTCAGGAC
3364435 AGATAATAAAAATTTTTTCATATATATATATATATATATGATTGC-GAATTATAACATAAAAGGG
1 AGATAATAAAAATTTTTTC--ATATATATATATATATATGATTGCTG-ATTATAACATAAAAGGG
*
3364499 TATGTTTAGTT
63 TATGCTTAGTT
3364510 GGGGAGAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
78 17 0.25
79 1 0.01
80 34 0.50
81 16 0.24
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (79 bp):
AGATAATAAAAATTTTTTCATATATATATATATATATGATTGCTGATTATAACATAAAAGGGTAT
GCTTAGTTCAGGAC
Found at i:3365389 original size:2 final size:2
Alignment explanation
Indices: 3365382--3365408 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3365372 TTTTTCTCGC
3365382 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
3365409 CTTCGCAGTC
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:3385211 original size:21 final size:21
Alignment explanation
Indices: 3385158--3385222 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
3385148 AAATTACTTC
*
3385158 AATGATCTTTGAACTTCTTTG
1 AATGATCTTTGAACTTGTTTG
* * *
3385179 AGTAATCCTTGAACTTGTTTG
1 AATGATCTTTGAACTTGTTTG
* *
3385200 AATGATTTTTGAAATTGTTTG
1 AATGATCTTTGAACTTGTTTG
3385221 AA
1 AA
3385223 AATGTTTTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (21 bp):
AATGATCTTTGAACTTGTTTG
Found at i:3385230 original size:21 final size:21
Alignment explanation
Indices: 3385187--3385230 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3385177 TGAGTAATCC
* *
3385187 TTGAACTTGTTTGAATGATTT
1 TTGAAATTGTTTGAATAATTT
3385208 TTGAAATTGTTTGAA-AATGTT
1 TTGAAATTGTTTGAATAAT-TT
3385229 TT
1 TT
3385231 TGAACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.27, C:0.02, G:0.18, T:0.52
Consensus pattern (21 bp):
TTGAAATTGTTTGAATAATTT
Found at i:3385361 original size:21 final size:21
Alignment explanation
Indices: 3385335--3385420 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
3385325 ATCTTTGAAT
3385335 TTATTTGAATAATTTTTAAAG
1 TTATTTGAATAATTTTTAAAG
* * *
3385356 TTATTTGAATGAGTTTTTGAAT
1 TTATTTGAAT-AATTTTTAAAG
* *
3385378 TTGTTTGAATAATTTTTAAAT
1 TTATTTGAATAATTTTTAAAG
* * * *
3385399 TTTTTTAAATAAGTTTTGAAG
1 TTATTTGAATAATTTTTAAAG
3385420 T
1 T
3385421 GTCTAAGTGT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 36 0.68
22 17 0.32
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.55
Consensus pattern (21 bp):
TTATTTGAATAATTTTTAAAG
Found at i:3385376 original size:43 final size:43
Alignment explanation
Indices: 3385328--3385415 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
3385318 TTAAATGATC
* *
3385328 TTTGAATTTATTTGAATAATTTTTAAAGTTATTTGAATGAGTT
1 TTTGAATTTATTTGAATAATTTTTAAAGTTATTTAAATAAGTT
* * *
3385371 TTTGAATTTGTTTGAATAATTTTTAAATTTTTTTAAATAAGTT
1 TTTGAATTTATTTGAATAATTTTTAAAGTTATTTAAATAAGTT
3385414 TT
1 TT
3385416 GAAGTGTCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (43 bp):
TTTGAATTTATTTGAATAATTTTTAAAGTTATTTAAATAAGTT
Found at i:3385474 original size:22 final size:22
Alignment explanation
Indices: 3385449--3385494 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3385439 GAAAGGTTTC
3385449 AAAATTACTTAAATAAGTTTTG
1 AAAATTACTTAAATAAGTTTTG
* * * *
3385471 AAAATTGCTTTAATGATTTTTG
1 AAAATTACTTAAATAAGTTTTG
3385493 AA
1 AA
3385495 CTTCTTTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (22 bp):
AAAATTACTTAAATAAGTTTTG
Found at i:3385705 original size:20 final size:20
Alignment explanation
Indices: 3385680--3385747 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
3385670 GTTTTGCCCA
*
3385680 AAATGTACGAATACATTTCT
1 AAATGTATGAATACATTTCT
*
3385700 AAATGTATGAATATATTTCT
1 AAATGTATGAATACATTTCT
*
3385720 AAATGTATGGATACATTT-T
1 AAATGTATGAATACATTTCT
3385739 AAAATGTAT
1 -AAATGTAT
3385748 CGATATATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (20 bp):
AAATGTATGAATACATTTCT
Found at i:3385724 original size:40 final size:40
Alignment explanation
Indices: 3385680--3385755 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
3385670 GTTTTGCCCA
3385680 AAATGTACGAATACATTTCT-AAATGTAT-GAATATATTTCT
1 AAATGTACGAATACATTT-TAAAATGTATCG-ATATATTTCT
* *
3385720 AAATGTATGGATACATTTTAAAATGTATCGATATAT
1 AAATGTACGAATACATTTTAAAATGTATCGATATAT
3385756 GTGGTTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 1 0.03
40 30 0.94
41 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (40 bp):
AAATGTACGAATACATTTTAAAATGTATCGATATATTTCT
Found at i:3391260 original size:14 final size:14
Alignment explanation
Indices: 3391241--3391267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3391231 GGAATGTTTT
3391241 TTTTTTTTTTTTGC
1 TTTTTTTTTTTTGC
3391255 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
3391268 TTTATAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTTTTGC
Found at i:3407447 original size:32 final size:32
Alignment explanation
Indices: 3407397--3407457 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3407387 CTCTTGCAAC
* *
3407397 CTCAATCTCCTACAGCAAAAATCATGAAAGCT
1 CTCAACCTCCCACAGCAAAAATCATGAAAGCT
*
3407429 CTCAACCTCCCACGGCAAAAATCATGAAA
1 CTCAACCTCCCACAGCAAAAATCATGAAA
3407458 AATCAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.31, G:0.10, T:0.18
Consensus pattern (32 bp):
CTCAACCTCCCACAGCAAAAATCATGAAAGCT
Found at i:3424710 original size:57 final size:58
Alignment explanation
Indices: 3424642--3424757 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
3424632 CATTCTTTCC
* * *
3424642 TTAAGGTGGAGAA-AATATGTTTCCTAAAGCCATAAGCTTGAAGAAGATACTAACTTA
1 TTAAGGTGGAGAAGAATATGCTTCCTAAAGCCAAAAGCATGAAGAAGATACTAACTTA
* * *
3424699 TTAAGGTGGAGAAGAATATGCTTGCTAAAGCTAAAAGCATGAAGAAGATGCTAACTTA
1 TTAAGGTGGAGAAGAATATGCTTCCTAAAGCCAAAAGCATGAAGAAGATACTAACTTA
3424757 T
1 T
3424758 GAATGACAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 13 0.25
58 39 0.75
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (58 bp):
TTAAGGTGGAGAAGAATATGCTTCCTAAAGCCAAAAGCATGAAGAAGATACTAACTTA
Found at i:3430211 original size:2 final size:2
Alignment explanation
Indices: 3430204--3430228 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3430194 ATAAAGTTGG
3430204 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 A
3430229 GTACTAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3434067 original size:18 final size:18
Alignment explanation
Indices: 3434044--3434099 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
3434034 TCTGACAAGT
3434044 ATAAAACTTGTATAAACA
1 ATAAAACTTGTATAAACA
3434062 ATAAAACTTGTATAAACA
1 ATAAAACTTGTATAAACA
3434080 ATAAAACTTGTATAAACA
1 ATAAAACTTGTATAAACA
3434098 AT
1 AT
3434100 CTTTAGCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (18 bp):
ATAAAACTTGTATAAACA
Found at i:3436237 original size:58 final size:58
Alignment explanation
Indices: 3436123--3436239 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 58
3436113 GATTCTTTCC
* * * *
3436123 TTAAGATGGAGAAGAATATGTTTCCTAAACCCAAAAGCATGAAGAAGATGCTAACTTA
1 TTAAGATGGAGAAGAATATGATTCCTAAACCCAAAAGCATAAAGAAGATACAAACTTA
* * * * *
3436181 TTAAGGTGGAGAAGAATATGATTCCTAAAGCTAAAAGCTTAAAGAAGTTACAAACTTA
1 TTAAGATGGAGAAGAATATGATTCCTAAACCCAAAAGCATAAAGAAGATACAAACTTA
3436239 T
1 T
3436240 GAATGACAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.26
Consensus pattern (58 bp):
TTAAGATGGAGAAGAATATGATTCCTAAACCCAAAAGCATAAAGAAGATACAAACTTA
Found at i:3436628 original size:20 final size:20
Alignment explanation
Indices: 3436603--3436663 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
3436593 AATATTTTAT
3436603 AATATTATAATTAAAATAAA
1 AATATTATAATTAAAATAAA
* *
3436623 AATATTAT-AGTAAAATATAT
1 AATATTATAATTAAAATA-AA
* * *
3436643 AATATAAAAATAAAAATAAA
1 AATATTATAATTAAAATAAA
3436663 A
1 A
3436664 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AATATTATAATTAAAATAAA
Found at i:3436667 original size:19 final size:20
Alignment explanation
Indices: 3436614--3437234 Score: 116
Period size: 20 Copynumber: 30.1 Consensus size: 20
3436604 ATATTATAAT
* * *
3436614 TAAAATA-AAAATATTATAG
1 TAAAATATAAAATATAAAAA
*
3436633 TAAAATATATAATATAAAAA
1 TAAAATATAAAATATAAAAA
3436653 TAAAA-ATAAAATATAAAAAA
1 TAAAATATAAAATAT-AAAAA
* *
3436673 TTAACATTTATATAATATAGGTAAAA
1 -TAA-A-ATATAAAATATA---AAAA
*
3436699 -AAAAT-TAAAATTTAAAAGTA
1 TAAAATATAAAATATAAAA--A
*
3436719 TATAATATAAAAATATATTAAAGAAA
1 TA-AA-ATATAAA-ATA-T-AA-AAA
* *
3436745 TGAAATAAAAAATATAAAAA
1 TAAAATATAAAATATAAAAA
* *
3436765 TTAAATA-ATAA-ATAAAAA
1 TAAAATATAAAATATAAAAA
*
3436783 TAAAAATATATGACAT-TAAAAA
1 T-AAAATATA--AAATATAAAAA
* * * *
3436805 T-ATATTTAAAA-AT-GATA
1 TAAAATATAAAATATAAAAA
* * *
3436822 TTATATA-AAAAT-TAATAA
1 TAAAATATAAAATATAAAAA
3436840 TATAAATATAAATATATTAAAAA
1 TA-AAATATAAA-ATA-TAAAAA
* *
3436863 TAAAATATAAAATATTATAA
1 TAAAATATAAAATATAAAAA
3436883 TAATAA-ATAAAATA-AAATATA
1 TAA-AATATAAAATATAAA-A-A
* * **
3436904 TGACAT-TAAAAATATATTTAA
1 TAAAATAT-AAAATATA-AAAA
* **
3436925 -GAAATGATATTATATAAAAA
1 TAAAAT-ATAAAATATAAAAA
3436945 TTAATAATA-AAAATATAAATATA
1 -TAA-AATATAAAATATAAA-A-A
*
3436968 TTAAAATA-AAATATATAAAAT
1 -TAAAATATAAA-ATATAAAAA
* *
3436989 TATAATA-ATAA-ATAAAAA
1 TAAAATATAAAATATAAAAA
** *
3437007 TAAAATATATGATATTAAAA
1 TAAAATATAAAATATAAAAA
* * *
3437027 T-ATAT-TAAAATAT-GATA
1 TAAAATATAAAATATAAAAA
* * *
3437044 TTATATA-AAAAT-TAATAA
1 TAAAATATAAAATATAAAAA
*
3437062 TATAATATAAATATATTAAAAA
1 TAAAATATAAA-ATA-TAAAAA
* *
3437084 T-AAATATAAAATATTATAA
1 TAAAATATAAAATATAAAAA
3437103 TAATAA-ATAAAATA-AAAATA
1 TAA-AATATAAAATATAAAA-A
* *
3437123 TATGACATTAAAAATATATTTAAGAAA
1 TA--A-AATATAAA-ATA--TAA-AAA
* *
3437150 TGATATTATATAAAAT-TAATAA
1 T-A-A-AATATAAAATATAAAAA
*
3437172 TATAAATATAAATATATTAAAA
1 TA-AAATATAAA-ATATAAAAA
* *
3437194 TAAAATATAAAATATTATAA
1 TAAAATATAAAATATAAAAA
3437214 TAATAA-ATAAAA-ATAAAAA
1 TAA-AATATAAAATATAAAAA
3437233 TA
1 TA
3437235 TATGATATTA
Statistics
Matches: 445, Mismatches: 85, Indels: 144
0.66 0.13 0.21
Matches are distributed among these distances:
17 12 0.03
18 52 0.12
19 52 0.12
20 117 0.26
21 70 0.16
22 53 0.12
23 36 0.08
24 23 0.05
25 4 0.01
26 9 0.02
27 12 0.03
28 5 0.01
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAATATAAAATATAAAAA
Found at i:3436849 original size:6 final size:6
Alignment explanation
Indices: 3436838--3436903 Score: 50
Period size: 5 Copynumber: 11.0 Consensus size: 6
3436828 AAAAATTAAT
* *
3436838 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
3436888 AATA-A AATA-A AATATA
1 AATATA AATATA AATATA
3436904 TGACATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
5 18 0.36
6 16 0.32
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:3436849 original size:23 final size:23
Alignment explanation
Indices: 3436823--3436891 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
3436813 AAAATGATAT
3436823 TATATAAAAATTAATAATATAAA
1 TATATAAAAATTAATAATATAAA
*
3436846 TATA-AATATATTAA-AA-ATAAA
1 TATATAA-AAATTAATAATATAAA
3436867 -ATATAAAATATT-ATAATAATAAA
1 TATATAAAA-ATTAATAAT-ATAAA
3436890 TA
1 TA
3436892 AAATAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
20 5 0.14
21 12 0.32
22 4 0.11
23 15 0.41
24 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TATATAAAAATTAATAATATAAA
Found at i:3436855 original size:12 final size:12
Alignment explanation
Indices: 3436838--3436903 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 12
3436828 AAAAATTAAT
3436838 AATATAAATATA
1 AATATAAATATA
* *
3436850 AATAT-ATTAAA
1 AATATAAATATA
3436861 AATA-AAATATAA
1 AATATAAATAT-A
3436873 AATATTATAATAATA
1 AATA-TA-AAT-ATA
3436888 AATA-AAATA-A
1 AATATAAATATA
3436898 AATATA
1 AATATA
3436904 TGACATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
10 5 0.12
11 13 0.30
12 13 0.30
13 1 0.02
14 1 0.02
15 8 0.19
16 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAAATATA
Found at i:3436868 original size:63 final size:62
Alignment explanation
Indices: 3436756--3437105 Score: 197
Period size: 63 Copynumber: 5.7 Consensus size: 62
3436746 GAAATAAAAA
* * * *
3436756 ATATAAAAATTAAATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAAAATGAT
1 ATATAAAAATT-AATAAT--AT--AAATATAAATATATTAAAAT-AAAATATATTTAAAAATGAT
3436821 ATT
60 ATT
*
3436824 ATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATA---AAATAT--TA-T
1 ATATAAAAATTAATAATATAAATATAAATATATT-AAAATAAAATATATTTAAAAATGATATT
*
3436881 A-ATAATAAA-TAA-AATA-AAATAT--ATGACATT-AAA-A--ATATATTTAAGAAATGATATT
1 ATATAA-AAATTAATAATATAAATATAAAT-ATATTAAAATAAAATATATTTAA-AAATGATATT
* * *
3436936 ATATAAAAATTAATAATAAAAATATAAATATATTAAAATAAAATATA--TAAAATTATAATAAT
1 ATATAAAAATTAATAATATAAATATAAATATATTAAAATAAAATATATTTAAAA--ATGATATT
* * ** * *
3436998 AAATAAAAA-TAA-AATATATGATATTAAAATATATTAAAATATGATATTATATAAAAATTAATA
1 ATATAAAAATTAATAATATA-AATA-T-AAATATATTAAAATAAAATA-TATTTAAAAA-TGAT-
3437061 ATAT
60 AT-T
*
3437065 AATATAAATATATTAA-AA-ATAAATATAAA-ATATTATAATAA
1 -ATATAAA-A-ATTAATAATATAAATATAAATATATTAAAATAA
3437106 TAAATAAAAT
Statistics
Matches: 227, Mismatches: 20, Indels: 72
0.71 0.06 0.23
Matches are distributed among these distances:
48 5 0.02
50 1 0.00
51 5 0.02
52 5 0.02
53 4 0.02
54 8 0.04
55 9 0.04
56 14 0.06
57 9 0.04
58 8 0.04
59 4 0.02
60 17 0.07
61 10 0.04
62 15 0.07
63 44 0.19
64 6 0.03
65 6 0.03
66 16 0.07
67 10 0.04
68 18 0.08
69 4 0.02
70 4 0.02
71 5 0.02
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (62 bp):
ATATAAAAATTAATAATATAAATATAAATATATTAAAATAAAATATATTTAAAAATGATATT
Found at i:3436911 original size:111 final size:114
Alignment explanation
Indices: 3436753--3437304 Score: 931
Period size: 112 Copynumber: 5.0 Consensus size: 114
3436743 AATGAAATAA
3436753 AAAATATAAAA-ATTA-AATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAA-A
1 AAAATATAAAATATTATAATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAGA
3436815 AATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
66 AATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
3436864 AAAATATAAAATATTATAATAATAAAT-AAAAT-AAAATATATGACATTAAAAATATATTTAAGA
1 AAAATATAAAATATTATAATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAGA
*
3436927 AATGATATTATATAAAAATTAATAATAAAAATATAAATATATT-AAAAT
66 AATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
*
3436975 AAAATATATAAA-ATTATAATAATAAATAAAAAT-AAAATATATGATATT-AAAATATA-TTAA-
1 AAAATATA-AAATATTATAATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAG
3437035 AATATGATATTATATAAAAATTAATAATAT-AATATAAATATATTAAAAAT
65 AA-ATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
3437085 -AAATATAAAATATTATAATAATAAAT-AAAATAAAAATATATGACATTAAAAATATATTTAAGA
1 AAAATATAAAATATTATAATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAGA
3437148 AATGATATTATAT-AAAATTAATAATATAAATATAAATATATT-AAAAT
66 AATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
*
3437195 AAAATATAAAATATTATAATAATAAATAAAAATAAAAATATATGATATTAAAAATATATTTAAGA
1 AAAATATAAAATATTATAATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAGA
*
3437260 AATGATATTATATAAAAATTAATAATA-AAAAATAAATATATTAAA
66 AATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAA
3437305 CTTATATTTT
Statistics
Matches: 418, Mismatches: 6, Indels: 32
0.92 0.01 0.07
Matches are distributed among these distances:
108 8 0.02
109 52 0.12
110 62 0.15
111 132 0.32
112 139 0.33
113 25 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (114 bp):
AAAATATAAAATATTATAATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAGA
AATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
Found at i:3437181 original size:6 final size:6
Alignment explanation
Indices: 3437170--3437236 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
3437160 TAAAATTAAT
*
3437170 AATATA AATATA AATAT- ATTA-A AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
* *
3437219 AATAAA AATAAA AATATA
1 AATATA AATATA AATATA
3437237 TGATATTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
5 11 0.22
6 24 0.47
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:3437213 original size:220 final size:222
Alignment explanation
Indices: 3436753--3437304 Score: 972
Period size: 220 Copynumber: 2.5 Consensus size: 222
3436743 AATGAAATAA
*
3436753 AAAATATAAAAATTA-AATAATAAATAAAAATAAAAATATATGACATTAAAAATATATTTAAAAA
1 AAAATATAAAAATTATAATAATAAATAAAAATAAAAATATATGATATTAAAAATATATTTAAAAA
3436817 TGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATATTATA
66 TGATATTATATAAAAATTAATAATAT-AATATAAATATATTAAAAATAAAATATAAAATATTATA
3436882 ATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAATT
130 ATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAATT
3436947 AATAATAAAAATATAAATATATTAAAAT
195 AATAATAAAAATATAAATATATTAAAAT
3436975 AAAATATATAAAATTATAATAATAAATAAAAAT-AAAATATATGATATT-AAAATATA-TTAAAA
1 AAAATATA-AAAATTATAATAATAAATAAAAATAAAAATATATGATATTAAAAATATATTTAAAA
3437037 TATGATATTATATAAAAATTAATAATATAATATAAATATATTAAAAAT-AAATATAAAATATTAT
65 -ATGATATTATATAAAAATTAATAATATAATATAAATATATTAAAAATAAAATATAAAATATTAT
3437101 AATAATAAATAAAATAAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATAT-AAAA
129 AATAATAAATAAAAT-AAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAA
*
3437165 TTAATAATATAAATATAAATATATTAAAAT
193 TTAATAATAAAAATATAAATATATTAAAAT
3437195 AAAATATAAAATATTATAATAATAAATAAAAATAAAAATATATGATATTAAAAATATATTTAAGA
1 AAAATATAAAA-ATTATAATAATAAATAAAAATAAAAATATATGATATTAAAAATATATTTAA-A
* *
3437260 AATGATATTATATAAAAATTAATAATAAAAAATAAATATATTAAA
64 AATGATATTATATAAAAATTAATAATATAATATAAATATATTAAA
3437305 CTTATATTTT
Statistics
Matches: 317, Mismatches: 4, Indels: 17
0.94 0.01 0.05
Matches are distributed among these distances:
219 3 0.01
220 93 0.29
221 85 0.27
222 51 0.16
223 67 0.21
224 18 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (222 bp):
AAAATATAAAAATTATAATAATAAATAAAAATAAAAATATATGATATTAAAAATATATTTAAAAA
TGATATTATATAAAAATTAATAATATAATATAAATATATTAAAAATAAAATATAAAATATTATAA
TAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAATTA
ATAATAAAAATATAAATATATTAAAAT
Found at i:3437276 original size:28 final size:26
Alignment explanation
Indices: 3436783--3437097 Score: 63
Period size: 23 Copynumber: 12.9 Consensus size: 26
3436773 TAAATAAAAA
* *
3436783 TAAAAATATATGACATTAAAAATATATT
1 TAAAAATATATTATA-T-AAAATATATT
3436811 TAAAAATGATATTATAT-AAA-A-A-T
1 TAAAAAT-ATATTATATAAAATATATT
* *
3436834 TAATAATATA-AATAT-AAATATAT-
1 TAAAAATATATTATATAAAATATATT
* *
3436857 TAAAAATA-A-AATATAAAATAT-TA
1 TAAAAATATATTATATAAAATATATT
* * * *
3436880 TAATAATAAATAAAATAAAATATATGACAT
1 TAAAAATATATTATATAAAATATAT----T
3436910 TAAAAATATATT-TA-AGAAATGATATT
1 TAAAAATATATTATATA-AAAT-ATATT
*
3436936 ATATAAAA-AT-TAATAATAAAA-ATA--
1 -TA-AAAATATATTAT-ATAAAATATATT
*
3436960 T--AAATATATTAAAATAAAATATA--
1 TAAAAATATATT-ATATAAAATATATT
* * * **
3436983 TAAAATTATAATA-AT-AAATAAAAA
1 TAAAAATATATTATATAAAATATATT
*
3437007 T-AAAATATATGATATTAAAATATA-T
1 TAAAAATATATTATA-TAAAATATATT
3437032 TAAAATATGATATTATAT-AAA-A-A-T
1 TAAAA-AT-ATATTATATAAAATATATT
*
3437056 TAATAATATA--ATAT-AAATATA-T
1 TAAAAATATATTATATAAAATATATT
3437078 TAAAAATA-A--ATATAAAATAT
1 TAAAAATATATTATATAAAATAT
3437098 TATAATAATA
Statistics
Matches: 224, Mismatches: 26, Indels: 80
0.68 0.08 0.24
Matches are distributed among these distances:
20 10 0.04
21 15 0.07
22 42 0.19
23 46 0.21
24 11 0.05
25 22 0.10
26 21 0.09
27 8 0.04
28 24 0.11
29 12 0.05
30 13 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (26 bp):
TAAAAATATATTATATAAAATATATT
Found at i:3437299 original size:28 final size:27
Alignment explanation
Indices: 3436823--3437300 Score: 170
Period size: 27 Copynumber: 17.2 Consensus size: 27
3436813 AAAATGATAT
*
3436823 TATATAAAAATTAATAATATAAATATAAA
1 TATATAAAAA-TAATAATA-AAAAATAAA
* *
3436852 TATATTAAAAATAA-AATATAAAAT-AT
1 TATA-TAAAAATAATAATAAAAAATAAA
* *
3436878 TATAATAATAAATAA-AATAAAATATATGA
1 TAT-ATAA-AAATAATAATAAAAAATA-AA
* * * *
3436907 CAT-TAAAAAT-ATATTTAAGAAATGATAT
1 TATATAAAAATAATA-ATAAAAAAT-A-AA
3436935 TATATAAAAATTAATAATAAAAATATAAA
1 TATATAAAAA-TAATAATAAAAA-ATAAA
* *
3436964 TATATTAAAATAA-AATATATAAAAT-TA
1 TATATAAAAATAATAATA-A-AAAATAAA
* *
3436991 TA-ATAATAAATAA-AA-ATAAAATATA
1 TATATAA-AAATAATAATAAAAAATAAA
* * * *
3437016 TGATATTAAAAT-ATATTAAAATATGATAT
1 T-ATATAAAAATAATAATAAAAAAT-A-AA
* *
3437045 TATATAAAAATTAATAATATAATATAAA
1 TATATAAAAA-TAATAATAAAAAATAAA
* *
3437073 TATATTAAAAAT-A-AATATAAAAT-AT
1 TATA-TAAAAATAATAATAAAAAATAAA
*
3437098 TATAATAATAAATAA-AAT-AAAAATATA
1 TAT-ATAA-AAATAATAATAAAAAATAAA
* * * *
3437125 TGACATTAAAAAT-ATATTTAAGAAATGATAT
1 T-ATA-TAAAAATAATA-ATAAAAAAT-A-AA
* *
3437156 TATATAAAATTAATAATATAAATATAAA
1 TATATAAAAATAATAATA-AAAAATAAA
* * *
3437184 TATATTAAAATAA-AATATAAAAT-AT
1 TATATAAAAATAATAATAAAAAATAAA
* *
3437209 TATAATAATAAATAAAAAT-AAAAATATA
1 TAT-ATAA-AAATAATAATAAAAAATAAA
* * *
3437237 TGATATTAAAAAT-ATATTTAAGAAATGATAT
1 T-ATA-TAAAAATAATA-ATAAAAAAT-A-AA
3437268 TATATAAAAATTAATAATAAAAAATAAA
1 TATATAAAAA-TAATAATAAAAAATAAA
3437296 TATAT
1 TATAT
3437301 TAAACTTATA
Statistics
Matches: 335, Mismatches: 64, Indels: 101
0.67 0.13 0.20
Matches are distributed among these distances:
24 5 0.01
25 16 0.05
26 49 0.15
27 80 0.24
28 62 0.19
29 68 0.20
30 45 0.13
31 10 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
TATATAAAAATAATAATAAAAAATAAA
Found at i:3441001 original size:3 final size:3
Alignment explanation
Indices: 3440993--3441024 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3440983 TGATACCAAA
3440993 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3441025 AGTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3444377 original size:1 final size:1
Alignment explanation
Indices: 3444357--3444410 Score: 81
Period size: 1 Copynumber: 54.0 Consensus size: 1
3444347 GTTTCTCTCC
* * *
3444357 TTTTTCTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3444411 GAGATGCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:3444866 original size:2 final size:2
Alignment explanation
Indices: 3444859--3444888 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3444849 CATACAAACG
3444859 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
3444889 AAGTAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3454600 original size:2 final size:2
Alignment explanation
Indices: 3454593--3454629 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3454583 CAGCTTACTA
*
3454593 AT AT AT AT AT GT 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 AT A
3454630 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3454634 original size:2 final size:2
Alignment explanation
Indices: 3454629--3454659 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3454619 ATATATATAT
3454629 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3454660 AAGTCTTTGT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3457798 original size:3 final size:3
Alignment explanation
Indices: 3457790--3457825 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3457780 TGGAAGATGG
*
3457790 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3457826 TTGGTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:3458415 original size:21 final size:22
Alignment explanation
Indices: 3458373--3458417 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3458363 ATCATATCTA
*
3458373 CATCATTCATGAAATATTACAT
1 CATCATTCATCAAATATTACAT
3458395 CATCATT-ATCAAAT-TTAACAT
1 CATCATTCATCAAATATT-ACAT
3458416 CA
1 CA
3458418 AATCAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 12 0.57
22 7 0.33
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (22 bp):
CATCATTCATCAAATATTACAT
Found at i:3458435 original size:19 final size:21
Alignment explanation
Indices: 3458411--3458461 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
3458401 TATCAAATTT
3458411 AACATCAAATCAACA-AA-AA
1 AACATCAAATCAACATAATAA
** *
3458430 AACATCACGTCAACATAATTA
1 AACATCAAATCAACATAATAA
3458451 AACATCAAATC
1 AACATCAAATC
3458462 TATATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 13 0.52
20 2 0.08
21 10 0.40
ACGTcount: A:0.57, C:0.24, G:0.02, T:0.18
Consensus pattern (21 bp):
AACATCAAATCAACATAATAA
Found at i:3467232 original size:21 final size:21
Alignment explanation
Indices: 3467203--3467242 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3467193 TAATAACTAT
*
3467203 TATATATATATATACTTTTAA
1 TATAAATATATATACTTTTAA
*
3467224 TATAAATATATTTACTTTT
1 TATAAATATATATACTTTT
3467243 TATTTTATGT
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:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATAAATATATATACTTTTAA
Found at i:3467917 original size:23 final size:23
Alignment explanation
Indices: 3467876--3467942 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 23
3467866 TAATTACTGT
*
3467876 TATATATACACTAAAATACTTTTAA
1 TATATATACA-T-ATATACTTTTAA
3467901 TATATATACATATATAC-TTTAA
1 TATATATACATATATACTTTTAA
* *
3467923 -ATATAAACATATTTACTTTT
1 TATATATACATATATACTTTT
3467943 TATTTTGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 14 0.37
22 8 0.21
23 5 0.13
24 1 0.03
25 10 0.26
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (23 bp):
TATATATACATATATACTTTTAA
Found at i:3467981 original size:15 final size:15
Alignment explanation
Indices: 3467963--3468009 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
3467953 TAACATTACA
3467963 AAAATTATAATTTAT
1 AAAATTATAATTTAT
3467978 AAAATTACTAA-TTAT
1 AAAATTA-TAATTTAT
*
3467993 AACAAATATACATTTAT
1 AA-AATTATA-ATTTAT
3468010 TTATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 15 0.56
16 8 0.30
17 4 0.15
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTATAATTTAT
Found at i:3468139 original size:348 final size:341
Alignment explanation
Indices: 3467203--3468334 Score: 1370
Period size: 348 Copynumber: 3.3 Consensus size: 341
3467193 TAATAACTAT
* * *
3467203 TATATATATATATACTTTTAATATAAATATATTTACTTTTTATTTTATGTTAACATTACAAAAAT
1 TATATACATATATACTTTAAATATAAACATATTTACTTTTTATTTTATGTTAACATTACAAAAAT
* *
3467268 TATAATTTATAAAATTATTAATTATCATATATATATATATATATATACCATTGTTTATATAAACT
66 TATAACTTATAAAATTATTAATTAT-A-ATA-A-ATATACAT-T-T---A---TTTATATAAACT
* * * * * * *
3467333 TATAATATAGATACTAAAATAAAGTCTTTGAAATTAGAATATTTTTGGAACCTAACTATTTCTTT
119 TATAATATAGAAACTAAAA-AAAGT-TATGAGATTAGAATAGTTTT-GAAACTTAGT-TTT-TTT
* * *
3467398 TTAATTTCATGCAATTAAACACAAACCTATATAGTTAAGTAAATTAATTTATGAAACTATGATTA
179 TTAATTTCATGTAATTAAAGACAAACC-ATATAGTTAATTAAATTAATTTATGAAACTATGATTA
* * * * * *
3467463 TTTATTAACTTGTAATGTCTTTTAATATATATAGTTTATATATTGTGCTAATTTATAAGAAATAT
243 TTAATTAACTTGTAATGTCTTTTAATATATATACTTTATATATTGGGTTCATTTATAAGGAATAT
* * *
3467528 AGTTACTATTATATATATACTTAAATACTTTTAG
308 AATTACTATTATATATATACTAAAATACTTTTAA
* * * * *
3467562 TATAT--ATAT-T-CTTTACATAAAAACATATTTACTTTCTATTTTATGTTAATATTATAAAAAT
1 TATATACATATATACTTTAAATATAAACATATTTACTTTTTATTTTATGTTAACATTACAAAAAT
* *
3467623 TATAACTTATAAAATTATT-ATTATAATATATAT-C-TTTATTTATATAAACTTATAATATATAA
66 TATAACTTATAAAATTATTAATTATAATAAATATACATTTATTTATATAAACTTATAATATAGAA
* * * * * *
3467685 ACCTAAAGAAAAGTTATGAGATCATAATAGCTTT-ATTACCTAGTTATTTTTTAATTTCATGTAA
131 A-CTAAA-AAAAGTTATGAGATTAGAATAGTTTTGA-AACTTAGTTTTTTTTTAATTTCATGTAA
*
3467749 TTAAAGACAAACTCTTATAGTTAATTAAATTAATTTATGAAACTATGATTATTAATTAACTTGTA
193 TTAAAGACAAAC-CATATAGTTAATTAAATTAATTTATGAAACTATGATTATTAATTAACTTGTA
* * *
3467814 ATGCCTTTTAATGTATATACTTTATATATATTGGGTTCATTTATAAGGAATATAATTACTGTTAT
257 ATGTCTTTTAATATATATAC-TT-TATATATTGGGTTCATTTATAAGGAATATAATTACTATTAT
*
3467879 ATATACACTAAAATACTTTTAATA
320 ATATATACTAAAATACTTTT-A-A
* *
3467903 TATATACATATATACTTTAAATATAAACATATTTACTTTTTATTTTGTATTAACATTACAAAAAT
1 TATATACATATATACTTTAAATATAAACATATTTACTTTTTATTTTATGTTAACATTACAAAAAT
* * * *
3467968 TATAATTTATAAAATTACTAATTATAACAAATATACATTTATTTATATAAATTTATAATATAGAA
66 TATAACTTATAAAATTATTAATTATAATAAATATACATTTATTTATATAAACTTATAATATAGAA
* * *
3468033 ATCTAAAAAGAAGTTGTGAGATTAGAATAGTTTTGAAACTTAGTTTTTTTTTAATTTTATGTAAG
131 A-CTAAAAA-AAGTTATGAGATTAGAATAGTTTTGAAACTTAGTTTTTTTTTAATTTCATGTAAT
* **
3468098 TAAGGACAAACACATATAGTTAATTAAATTAATAAATGAAACTATGATTATTAATTAACTTGTAA
194 TAAAGACAAAC-CATATAGTTAATTAAATTAATTTATGAAACTATGATTATTAATTAACTTGTAA
* *
3468163 TATCTTTTAATATATATACTTTATATATTGGGTTCATTTATATGGAATATAATTACTATTATATA
258 TGTCTTTTAATATATATACTTTATATATTGGGTTCATTTATAAGGAATATAATTACTATTATATA
3468228 TATACTAAAATAC-TTTAGA
323 TATACTAAAATACTTTTA-A
* * *
3468247 TATATAC--ATATAGTTTAAATATAAACATATTTA-TTTTCTATTTTGTGTTAACAATACAAAAA
1 TATATACATATATACTTTAAATATAAACATATTTACTTTT-TATTTTATGTTAACATTACAAAAA
3468309 TTATAACTTATAAAATTATTAATTAT
65 TTATAACTTATAAAATTATTAATTAT
3468335 GTTTGAATTT
Statistics
Matches: 674, Mismatches: 81, Indels: 53
0.83 0.10 0.07
Matches are distributed among these distances:
337 92 0.14
338 6 0.01
339 56 0.08
340 38 0.06
341 19 0.03
342 72 0.11
343 5 0.01
344 10 0.01
345 64 0.09
346 67 0.10
347 6 0.01
348 153 0.23
349 1 0.00
350 4 0.01
352 3 0.00
353 1 0.00
354 5 0.01
355 62 0.09
356 1 0.00
357 4 0.01
359 5 0.01
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (341 bp):
TATATACATATATACTTTAAATATAAACATATTTACTTTTTATTTTATGTTAACATTACAAAAAT
TATAACTTATAAAATTATTAATTATAATAAATATACATTTATTTATATAAACTTATAATATAGAA
ACTAAAAAAAGTTATGAGATTAGAATAGTTTTGAAACTTAGTTTTTTTTTAATTTCATGTAATTA
AAGACAAACCATATAGTTAATTAAATTAATTTATGAAACTATGATTATTAATTAACTTGTAATGT
CTTTTAATATATATACTTTATATATTGGGTTCATTTATAAGGAATATAATTACTATTATATATAT
ACTAAAATACTTTTAA
Found at i:3469500 original size:17 final size:17
Alignment explanation
Indices: 3469452--3469503 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
3469442 CAGATGATGT
3469452 GTAAGCTGACCAAATAG
1 GTAAGCTGACCAAATAG
*
3469469 GTTAGCTG-----A-AG
1 GTAAGCTGACCAAATAG
3469480 GTAAGCTGACCAAATAG
1 GTAAGCTGACCAAATAG
3469497 GTAAGCT
1 GTAAGCT
3469504 ACTACTTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
11 9 0.33
12 1 0.04
16 1 0.04
17 16 0.59
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (17 bp):
GTAAGCTGACCAAATAG
Found at i:3474891 original size:14 final size:14
Alignment explanation
Indices: 3474845--3474893 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
3474835 ATTGTGTAAA
**
3474845 ATTTTATATATCGT
1 ATTTTATATATTAT
*
3474859 ATTTAACTAT-TTAT
1 ATTTTA-TATATTAT
3474873 ATTTTATATATTAT
1 ATTTTATATATTAT
3474887 ATTTTAT
1 ATTTTAT
3474894 GAAAAGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 3 0.10
14 23 0.79
15 3 0.10
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (14 bp):
ATTTTATATATTAT
Found at i:3476511 original size:17 final size:17
Alignment explanation
Indices: 3476489--3476521 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3476479 ACTATTTTAC
*
3476489 TGAAAATATAATAAAAA
1 TGAAAATAAAATAAAAA
3476506 TGAAAATAAAATAAAA
1 TGAAAATAAAATAAAA
3476522 CGAAAACCAC
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:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
TGAAAATAAAATAAAAA
Found at i:3478841 original size:22 final size:20
Alignment explanation
Indices: 3478816--3478862 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
3478806 CATATTATAT
3478816 TTTAATA-GTTTAACTTAATAA
1 TTTAATATG-TTAA-TTAATAA
3478837 CTTTAATATGTTAATTAATAA
1 -TTTAATATGTTAATTAATAA
3478858 TTTAA
1 TTTAA
3478863 AAGATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.21
21 7 0.29
22 11 0.46
23 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTAATATGTTAATTAATAA
Found at i:3496515 original size:20 final size:20
Alignment explanation
Indices: 3496492--3496529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3496482 TTTTTTATTT
* *
3496492 AAAAAGTTGATTTTTTTAAA
1 AAAAAATTGATTATTTTAAA
3496512 AAAAAATTGATTATTTTA
1 AAAAAATTGATTATTTTA
3496530 TATAATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
AAAAAATTGATTATTTTAAA
Found at i:3503316 original size:22 final size:22
Alignment explanation
Indices: 3503274--3503316 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3503264 CCGTTCATTA
* *
3503274 TTTAATTACTTTTTGATATATT
1 TTTAATTACTTTTTAAAATATT
3503296 TTTAATTA-TTATTTAAAATAT
1 TTTAATTACTT-TTTAAAATAT
3503317 AATAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTAATTACTTTTTAAAATATT
Found at i:3503710 original size:15 final size:15
Alignment explanation
Indices: 3503675--3503711 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
3503665 TATCATGTGA
3503675 ATATA-ATATCATTT
1 ATATATATATCATTT
3503689 ATATATATAT-ATTT
1 ATATATATATCATTT
3503703 ATAT-TATAT
1 ATATATATAT
3503712 GTCTTAGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATATATATCATTT
Found at i:3506832 original size:32 final size:31
Alignment explanation
Indices: 3506775--3506834 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
3506765 GAAATGAATA
* * *
3506775 TTAATAATAAAAATATATATTTTATATAAAT
1 TTAAAAATAAAAATATAAATATTATATAAAT
3506806 TTAAAAATAATAAATATAAATATTATATA
1 TTAAAAATAA-AAATATAAATATTATATA
3506835 TTATATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAAAAATAAAAATATAAATATTATATAAAT
Found at i:3516072 original size:17 final size:17
Alignment explanation
Indices: 3516050--3516082 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3516040 CTGAGAGAGC
3516050 TTTGGT-TTTGTCTTGTG
1 TTTGGTGTTTGT-TTGTG
3516067 TTTGGTGTTTGTTTGT
1 TTTGGTGTTTGTTTGT
3516083 TTGTTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.00, C:0.03, G:0.30, T:0.67
Consensus pattern (17 bp):
TTTGGTGTTTGTTTGTG
Found at i:3519982 original size:15 final size:15
Alignment explanation
Indices: 3519954--3520007 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 15
3519944 ATCCAAAACT
3519954 TATATTTA-TAAATA
1 TATATTTATTAAATA
3519968 TATATTTATTAAATA
1 TATATTTATTAAATA
*
3519983 -ATAATTATTGAAATA
1 TATATTTATT-AAATA
*
3519998 T-TTTTTATTA
1 TATATTTATTA
3520008 TAATTATTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 17 0.50
15 17 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATATTTATTAAATA
Found at i:3522415 original size:27 final size:27
Alignment explanation
Indices: 3522377--3522443 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
3522367 TGCAAGTACA
3522377 GAAAAGCAATTATACCTGTTATTTGAT
1 GAAAAGCAATTATACCTGTTATTTGAT
*
3522404 GAAATGCAATTATACCTGTTATTTGAT
1 GAAAAGCAATTATACCTGTTATTTGAT
3522431 GAAAAGCAATTAT
1 GAAAAGCAATTAT
3522444 CCTAGCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (27 bp):
GAAAAGCAATTATACCTGTTATTTGAT
Found at i:3524257 original size:24 final size:24
Alignment explanation
Indices: 3524229--3524312 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
3524219 ATCAGACGAC
3524229 GAAGAAACCAAGAATTGGGAGTCG
1 GAAGAAACCAAGAATTGGGAGTCG
* * * * *
3524253 GAAGAAAACAACAA-CGGATCAGACG
1 GAAGAAACCAAGAATTGG--GAGTCG
*
3524278 AAGAAGAAGCCAAGAATTGGGAGTCG
1 --GAAGAAACCAAGAATTGGGAGTCG
3524304 GAAGGAAAC
1 GAA-GAAAC
3524313 AATGACGGAT
Statistics
Matches: 42, Mismatches: 12, Indels: 11
0.65 0.18 0.17
Matches are distributed among these distances:
23 2 0.05
24 15 0.36
25 8 0.19
26 4 0.10
27 11 0.26
28 2 0.05
ACGTcount: A:0.46, C:0.14, G:0.31, T:0.08
Consensus pattern (24 bp):
GAAGAAACCAAGAATTGGGAGTCG
Found at i:3524262 original size:51 final size:51
Alignment explanation
Indices: 3524201--3524401 Score: 260
Period size: 51 Copynumber: 3.9 Consensus size: 51
3524191 AAATATGTGA
* *
3524201 GGAAGGAAACAACAACGGATCAGACGACGAAGAAACCAAGAATTGGGAGTC
1 GGAAGAAAACAACAACGGATCAGACGAAGAAGAAACCAAGAATTGGGAGTC
*
3524252 GGAAGAAAACAACAACGGATCAGACGAAGAAGAAGCCAAGAATTGGGAGTC
1 GGAAGAAAACAACAACGGATCAGACGAAGAAGAAACCAAGAATTGGGAGTC
* ** * * ** * *
3524303 GGAAGGAAACAATGACGGATCAAACAAAGAAGAAGTCGAGAATTGGGAGTG
1 GGAAGAAAACAACAACGGATCAGACGAAGAAGAAACCAAGAATTGGGAGTC
* *
3524354 GGAAGAAAACAACGACGGATCAGACGAAGAAG-AACTCGAGAATTGGGA
1 GGAAGAAAACAACAACGGATCAGACGAAGAAGAAAC-CAAGAATTGGGA
3524402 ATCGAAATTT
Statistics
Matches: 132, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
50 1 0.01
51 131 0.99
ACGTcount: A:0.46, C:0.14, G:0.31, T:0.09
Consensus pattern (51 bp):
GGAAGAAAACAACAACGGATCAGACGAAGAAGAAACCAAGAATTGGGAGTC
Found at i:3524285 original size:27 final size:26
Alignment explanation
Indices: 3524202--3524285 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
3524192 AATATGTGAG
*
3524202 GAAGGAAACAACAACGGATCAGACGA
1 GAAGAAAACAACAACGGATCAGACGA
* * * * *
3524228 CGAAGAAACCAAGAATTGG--GAGTCG-
1 -GAAGAAAACAACAA-CGGATCAGACGA
3524253 GAAGAAAACAACAACGGATCAGACGAA
1 GAAGAAAACAACAACGGATCAGACG-A
3524280 GAAGAA
1 GAAGAA
3524286 GCCAAGAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
23 2 0.05
24 12 0.29
25 4 0.10
26 4 0.10
27 17 0.41
28 2 0.05
ACGTcount: A:0.50, C:0.17, G:0.27, T:0.06
Consensus pattern (26 bp):
GAAGAAAACAACAACGGATCAGACGA
Found at i:3524307 original size:27 final size:26
Alignment explanation
Indices: 3524229--3524307 Score: 60
Period size: 27 Copynumber: 3.0 Consensus size: 26
3524219 ATCAGACGAC
3524229 GAAGAAACCAAGAATTGGGAGTCGGAA
1 GAAG-AACCAAGAATTGGGAGTCGGAA
* *
3524256 GAA-AA-CAACAA--CGGA-TCAGACGAA
1 GAAGAACCAAGAATTGGGAGTC-G--GAA
3524280 GAAGAAGCCAAGAATTGGGAGTCGGAA
1 GAAGAA-CCAAGAATTGGGAGTCGGAA
3524307 G
1 G
3524308 GAAACAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 18
0.64 0.07 0.30
Matches are distributed among these distances:
21 2 0.05
22 4 0.10
24 11 0.28
25 4 0.10
27 12 0.31
29 4 0.10
30 2 0.05
ACGTcount: A:0.46, C:0.14, G:0.32, T:0.09
Consensus pattern (26 bp):
GAAGAACCAAGAATTGGGAGTCGGAA
Found at i:3524377 original size:102 final size:102
Alignment explanation
Indices: 3524201--3524401 Score: 287
Period size: 102 Copynumber: 2.0 Consensus size: 102
3524191 AAATATGTGA
* * *
3524201 GGAAGGAAACAACAACGGATCAGACGACGAAGAAACCAAGAATTGGGAGTCGGAAGAAAACAACA
1 GGAAGGAAACAACAACGGATCAAACAAAGAAGAAACCAAGAATTGGGAGTCGGAAGAAAACAACA
3524266 ACGGATCAGACGAAGAAGAAGC-CAAGAATTGGGAGTC
66 ACGGATCAGACGAAGAAGAA-CTCAAGAATTGGGAGTC
** ** * * *
3524303 GGAAGGAAACAATGACGGATCAAACAAAGAAGAAGTCGAGAATTGGGAGTGGGAAGAAAACAACG
1 GGAAGGAAACAACAACGGATCAAACAAAGAAGAAACCAAGAATTGGGAGTCGGAAGAAAACAACA
*
3524368 ACGGATCAGACGAAGAAGAACTCGAGAATTGGGA
66 ACGGATCAGACGAAGAAGAACTCAAGAATTGGGA
3524402 ATCGAAATTT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 1 0.01
102 86 0.99
ACGTcount: A:0.46, C:0.14, G:0.31, T:0.09
Consensus pattern (102 bp):
GGAAGGAAACAACAACGGATCAAACAAAGAAGAAACCAAGAATTGGGAGTCGGAAGAAAACAACA
ACGGATCAGACGAAGAAGAACTCAAGAATTGGGAGTC
Found at i:3532490 original size:18 final size:19
Alignment explanation
Indices: 3532467--3532515 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
3532457 TCAATTGTGT
3532467 AAATA-TTATT-TTTTATAA
1 AAATATTTATTATTTTA-AA
3532485 AAATATTTATTATTTTAAA
1 AAATATTTATTATTTTAAA
*
3532504 AAGAGATTTATT
1 AA-ATATTTATT
3532516 TTAATTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 5 0.19
19 9 0.33
20 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
AAATATTTATTATTTTAAA
Found at i:3532512 original size:20 final size:19
Alignment explanation
Indices: 3532472--3532517 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3532462 TGTGTAAATA
*
3532472 TTATTTTTTATAAAAATAT
1 TTATTTTTTATAAAAAGAT
3532491 TTATTATTTTA-AAAAGAGAT
1 TTATT-TTTTATAAAA-AGAT
3532511 TTATTTT
1 TTATTTT
3532518 AATTTAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TTATTTTTTATAAAAAGAT
Found at i:3534175 original size:20 final size:21
Alignment explanation
Indices: 3534147--3534185 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3534137 AAACTTTAGC
3534147 TTCAATTTT-GGATTTTTTTT
1 TTCAATTTTAGGATTTTTTTT
* *
3534167 TTCATTTTTAGTATTTTTT
1 TTCAATTTTAGGATTTTTT
3534186 AATGATCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (21 bp):
TTCAATTTTAGGATTTTTTTT
Found at i:3543672 original size:46 final size:47
Alignment explanation
Indices: 3543604--3543707 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 47
3543594 CAGAGAAACC
* * *
3543604 AAGAGATTTATTATATGGAATACACCATGGTGGTGTATGTGCAAAAA
1 AAGAGATATATTATATGGAATACACCATGATCGTGTATGTGCAAAAA
* *
3543651 AAGAGATAT-TTATGTGGAATACACCATGATCTTGTATGTGCAAAAA
1 AAGAGATATATTATATGGAATACACCATGATCGTGTATGTGCAAAAA
* *
3543697 TAGGGATATAT
1 AAGAGATATAT
3543708 AAGCAGATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
46 40 0.82
47 9 0.18
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (47 bp):
AAGAGATATATTATATGGAATACACCATGATCGTGTATGTGCAAAAA
Found at i:3544408 original size:125 final size:124
Alignment explanation
Indices: 3544169--3544417 Score: 372
Period size: 125 Copynumber: 2.0 Consensus size: 124
3544159 TAACACTGAA
* *
3544169 ATAAAAAGATATCAAACATTGTAGACAGTTCAAGAAATAGAAAAGATTGCATCACTGAGAAGAAA
1 ATAAAAAGATAACAAACATTATAGACAGTTCAAGAAATAGAAAAGATTGCATCACTGAGAAGAAA
* *
3544234 AATACTTTGCTGTGTCAGTATCCTCAACTACAAGTTACAACGCATGTTTGACCGTCAGC
66 AATACTTTGCTGTGTCAGTATCCTCAACTACAAGTTACAAAGCACGTTTGACCGTCAGC
* * * * * *
3544293 ATAAAAATATAACAAAGATTATAGACAGTTCAAGTACTAGAAAAGATTGTATCAGTGAGAAGATA
1 ATAAAAAGATAACAAACATTATAGACAGTTCAAGAAATAGAAAAGATTGCATCACTGAGAAGA-A
* * *
3544358 ACATACTTTGCTGTGTCAGTATCCTCAACTACAAGTTGCAAAGCACGTTTGACTGTCAGC
65 AAATACTTTGCTGTGTCAGTATCCTCAACTACAAGTTACAAAGCACGTTTGACCGTCAGC
3544418 CAATTGCTTT
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
124 55 0.50
125 56 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (124 bp):
ATAAAAAGATAACAAACATTATAGACAGTTCAAGAAATAGAAAAGATTGCATCACTGAGAAGAAA
AATACTTTGCTGTGTCAGTATCCTCAACTACAAGTTACAAAGCACGTTTGACCGTCAGC
Found at i:3550324 original size:13 final size:13
Alignment explanation
Indices: 3550306--3550330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3550296 AATTATTAAT
3550306 TATAAAAATAAAA
1 TATAAAAATAAAA
3550319 TATAAAAATAAA
1 TATAAAAATAAA
3550331 TAAAAATAAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TATAAAAATAAAA
Found at i:3570636 original size:74 final size:75
Alignment explanation
Indices: 3570509--3570652 Score: 227
Period size: 74 Copynumber: 1.9 Consensus size: 75
3570499 CTGTTGATGG
*** * *
3570509 TGTTGTTCTTCTTATGAAATCCATGGGCATTGATAAGGTGAGCTTTGCATGTATTTTGTT-TTTG
1 TGTTGTTCTTCTTATGAAATCCACAAGCATTGATAAGGTGAGCATTGCATGTATTTCGTTGTTTG
3570573 TCTTTAATGT
66 TCTTTAATGT
*
3570583 TGTTGTTCTTCTTATGAAATCCACAAGCATTGATAAGGTGAGCATTGCGTGTATTTCGTTGTTTG
1 TGTTGTTCTTCTTATGAAATCCACAAGCATTGATAAGGTGAGCATTGCATGTATTTCGTTGTTTG
3570648 TCTTT
66 TCTTT
3570653 TTCTCTTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 54 0.86
75 9 0.14
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.47
Consensus pattern (75 bp):
TGTTGTTCTTCTTATGAAATCCACAAGCATTGATAAGGTGAGCATTGCATGTATTTCGTTGTTTG
TCTTTAATGT
Found at i:3573250 original size:2 final size:2
Alignment explanation
Indices: 3573243--3573288 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
3573233 ATATTCTACG
* * * *
3573243 CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA AA CA CA TA CG CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3573285 CA CA
1 CA CA
3573289 TATATGTTCT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.43, G:0.02, T:0.02
Consensus pattern (2 bp):
CA
Found at i:3575387 original size:24 final size:24
Alignment explanation
Indices: 3575370--3575415 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3575360 GATACATATG
*
3575370 TTATCTTTACACGTGATAAGTCTA
1 TTATCTTTACACGTGATAAGTATA
*
3575394 TTATCTTTACATGTGA-AAGTAT
1 TTATCTTTACACGTGATAAGTAT
3575416 CAAAGTATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (24 bp):
TTATCTTTACACGTGATAAGTATA
Found at i:3576878 original size:2 final size:2
Alignment explanation
Indices: 3576867--3576900 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3576857 ACACACATAC
*
3576867 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3576901 TTGTGGACAA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3576880 original size:10 final size:10
Alignment explanation
Indices: 3576861--3576900 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3576851 AACATGACAC
*
3576861 ACATACATAT
1 ACATATATAT
3576871 ACATATATAT
1 ACATATATAT
*
3576881 ATATATATAT
1 ACATATATAT
*
3576891 ATATATATAT
1 ACATATATAT
3576901 TTGTGGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (10 bp):
ACATATATAT
Found at i:3577714 original size:12 final size:12
Alignment explanation
Indices: 3577694--3577735 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3577684 AAGGGTCAAT
*
3577694 TATACATACATA
1 TATATATACATA
3577706 TATATATACATA
1 TATATATACATA
* *
3577718 CATATATATATA
1 TATATATACATA
3577730 TATATA
1 TATATA
3577736 AAATATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATATACATA
Found at i:3577715 original size:16 final size:16
Alignment explanation
Indices: 3577694--3577729 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3577684 AAGGGTCAAT
3577694 TATACATACATATATA
1 TATACATACATATATA
3577710 TATACATACATATATA
1 TATACATACATATATA
3577726 TATA
1 TATA
3577730 TATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (16 bp):
TATACATACATATATA
Found at i:3577720 original size:20 final size:20
Alignment explanation
Indices: 3577695--3577733 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3577685 AGGGTCAATT
3577695 ATACATACATATATATATAC
1 ATACATACATATATATATAC
*
3577715 ATACATATATATATATATA
1 ATACATACATATATATATA
3577734 TAAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
ATACATACATATATATATAC
Found at i:3579982 original size:17 final size:17
Alignment explanation
Indices: 3579960--3579992 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3579950 CCCATTTCCC
3579960 TTTCTTTTCTTT-TCTTT
1 TTTC-TTTCTTTCTCTTT
3579977 TTTCTTTCTTTCTCTT
1 TTTCTTTCTTTCTCTT
3579993 CTATCGTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTCTTTCTCTTT
Found at i:3594162 original size:45 final size:45
Alignment explanation
Indices: 3594094--3594198 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
3594084 CACGCTATGA
* * * *
3594094 TGTTACATGCCATGTACAGAAACATGTTACACG-CTATAGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTTACACGTC-ATAGTCAGGT
* *
3594139 TGTTACACGTCATGTGCAAAAACATGTTACACGTCATGGTCAGGT
1 TGTTACACGTCATGTACAAAAACATGTTACACGTCATAGTCAGGT
*
3594184 TATTACACGTCATGT
1 TGTTACACGTCATGT
3594199 TAAAAAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (45 bp):
TGTTACACGTCATGTACAAAAACATGTTACACGTCATAGTCAGGT
Found at i:3594332 original size:29 final size:29
Alignment explanation
Indices: 3594264--3594352 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 29
3594254 TTAATAAAAG
*
3594264 TTGTTACACGTCATATTGAAAAAAAATATA
1 TTGTTACACGTCATATTGAAAAAATAT-TA
3594294 TTGTTATTACACGTCATATTGAAAAAATATTA
1 TTG---TTACACGTCATATTGAAAAAATATTA
*
3594326 TTGTTACACGTCATATT-TAAAAATATT
1 TTGTTACACGTCATATTGAAAAAATATT
3594353 TTAGTACACT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
28 9 0.17
29 14 0.26
30 3 0.06
32 5 0.09
33 23 0.43
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (29 bp):
TTGTTACACGTCATATTGAAAAAATATTA
Found at i:3594360 original size:27 final size:29
Alignment explanation
Indices: 3594268--3594361 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
3594258 TAAAAGTTGT
* *
3594268 TACACGTCATATTGAAAAAAAATATATTGTTAT
1 TACACGTCATATTG---AAAAA-ATATTATTAG
3594301 TACACGTCATATTGAAAAAATATTATT-G
1 TACACGTCATATTGAAAAAATATTATTAG
*
3594329 TTACACGTCATATT-TAAAAATATT-TTAG
1 -TACACGTCATATTGAAAAAATATTATTAG
3594357 TACAC
1 TACAC
3594362 TTTAATGCCT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
27 7 0.12
28 10 0.18
29 20 0.36
30 5 0.09
33 14 0.25
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (29 bp):
TACACGTCATATTGAAAAAATATTATTAG
Found at i:3595150 original size:28 final size:28
Alignment explanation
Indices: 3595118--3595178 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
3595108 AAGCCACCAC
*
3595118 AAAAAGAATGAAAAAGAGAAAGAAAGGA-
1 AAAAAGAAT-AAAAAGAGAAAAAAAGGAG
*
3595146 AAAAAGAATAAAGAGAGAAAAAAAGGAG
1 AAAAAGAATAAAAAGAGAAAAAAAGGAG
3595174 AAAAA
1 AAAAA
3595179 CAAAATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (28 bp):
AAAAAGAATAAAAAGAGAAAAAAAGGAG
Found at i:3595670 original size:29 final size:29
Alignment explanation
Indices: 3595586--3595674 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
3595576 TCTCTCTTTT
* * *
3595586 GTTTTGTTCTATTGTACTTGTTCATGCATA
1 GTTTT-TTCTCTTGTACTTATTCATGTATA
** * *
3595616 ACTTTTTCTCTTATACCTATTCATGTATA
1 GTTTTTTCTCTTGTACTTATTCATGTATA
3595645 GTTTTTTCTCTTGTACTTATTCATGTATA
1 GTTTTTTCTCTTGTACTTATTCATGTATA
3595674 G
1 G
3595675 CTATTCTTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 45 0.94
30 3 0.06
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.54
Consensus pattern (29 bp):
GTTTTTTCTCTTGTACTTATTCATGTATA
Found at i:3596526 original size:249 final size:247
Alignment explanation
Indices: 3596212--3597642 Score: 1452
Period size: 249 Copynumber: 5.9 Consensus size: 247
3596202 GAGGGGGGGA
* * * * * *
3596212 TTTGGAAATGTTGAGGAGAGTTTTGAGTTTGCAATCGATATTAGCGCCC-GAAATGATTGAAAAT
1 TTTGGAAATGTCGAGGAGAGCTTTGAGTTTGCTATCG-TTTTGGTGCCCAG-AATGATTGAAAAT
* *
3596276 CTCATCCACCTAACCATCCAGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAAT
64 CTCATCCACCCAACCATCTAGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAAT
* **
3596341 GAAAAATCGAAAATACCCTTTTAAATTGATAAAATACCATGAACAAATGTTAGATGTAGAGAAGG
129 GAAAAATCAAAAATACCCTTTTAAATTGATAAAATACCATGAACAGGTGTTAGATGTAGAGAAGG
* * *
3596406 TATATAAGTAGAAATCAATATAAGTTTTTTGGTTTCGAACAGTTGGGAAGGGAAC
194 TATGTAGGTAGAAATCAATATAAGTTTTTTGGTTTCGAACAGTTGGG-AGGGAGC
* * *
3596461 TTTGGAAATGTCGAGGAGAGCTTTGAGTTTGTTATCAGTTTTGGTGCCTAAAATGATTGAAAATC
1 TTTGGAAATGTCGAGGAGAGCTTTGAGTTTGCTATC-GTTTTGGTGCCCAGAATGATTGAAAATC
* *
3596526 TCATCCACCCACCCATCTAGAAAATCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAATG
65 TCATCCACCCAACCATCTAGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAATG
* * * *
3596591 AAAAATAAAAAATACCCTTTTAAATTGATAATATAACATGAACAGGTGTGAGATGTAGAGAAGGT
130 AAAAATCAAAAATACCCTTTTAAATTGATAAAATACCATGAACAGGTGTTAGATGTAGAGAAGGT
* * * * *
3596656 ATGTAGGTAAAAAGCAATATAGGTTTTTTGGTTTTGAAC----GGGAGGGCA-A
195 ATGTAGGTAGAAATCAATATAAGTTTTTTGGTTTCGAACAGTTGGGAGGG-AGC
* * ** *
3596705 TTATAGAAATGTCGAGGAGAGCTTTGAGTTTGCTGTCGATTTTGGCACTCAGAATGATTGAAAAT
1 TT-TGGAAATGTCGAGGAGAGCTTTGAGTTTGCTATCG-TTTTGGTGCCCAGAATGATTGAAAAT
* * * * *
3596770 TTCATCCACCCAACCATTTAGAAAACCCAATAATGTCACTCAAGAACTTAAATGAGAAAAGAAAT
64 CTCATCCACCCAACCATCTAGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAAT
** * * *
3596835 GAAAAATTGAAAATACCTTTTTAAATTGATAAAATAACATGAATAGGTGTTAGATGTAGAGAAGG
129 GAAAAATCAAAAATACCCTTTTAAATTGATAAAATACCATGAACAGGTGTTAGATGTAGAGAAGG
* * * *
3596900 TATGTAGGT--AAA--AAT-CAA-TTTTTT-GTTTCGAACAGTTACGAAAGGAGC
194 TATGTAGGTAGAAATCAATATAAGTTTTTTGGTTTCGAACAGTT-GGGAGGGAGC
* * * ** ***
3596948 TTTGGAAATGTCGATGAGAGCTTTGAGTTTGTTGTCGGTTTTGGCACTTGGAATGATTGAAAATC
1 TTTGGAAATGTCGAGGAGAGCTTTGAGTTTGCTATC-GTTTTGGTGCCCAGAATGATTGAAAATC
* * * * *
3597013 TCATCCATCCAGCCAT-TCAGAAAACCTAATAATGT-CC--AGGAACTTAAAAGAGAAAAAAAAT
65 TCATCCACCCAACCATCT-AGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAAT
* * ** * * *
3597074 GAAAAACCAAAAATGCTTTTTTAAATTGATAAAATACCATGAATAGGTGTTAGATGTAAAAAAGG
129 GAAAAATCAAAAATACCCTTTTAAATTGATAAAATACCATGAACAGGTGTTAGATGTAGAGAAGG
* * *
3597139 TATGTAGGGAGAAATC-----AA--TTTTTGGTTTTGAACAGCTGAGTG-GGGAGC
194 TATGTAGGTAGAAATCAATATAAGTTTTTTGGTTTCGAACAGTTG-G-GAGGGAGC
* * * *
3597187 TTTGGAAATGTCGAAGAGAGATTTGAGTTTGTTATCGGTTTTGGTGCCCAGAATGACTG---AT-
1 TTTGGAAATGTCGAGGAGAGCTTTGAGTTTGCTATC-GTTTTGGTGCCCAGAATGATTGAAAATC
* * *
3597248 T-AGCCATCC-A--A---A-AAAA-CCAATAATGTCCCTCAAGAACTTAAAAGAGAAAAGAAATG
65 TCATCCACCCAACCATCTAGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAATG
** * * * *
3597304 AAAAGCCAAAAATA-CCTTTTCAAATTGATAAAATACCATGAACATGTATTAAATGTAAAGAAGG
130 AAAAATCAAAAATACCCTTTT-AAATTGATAAAATACCATGAACAGGTGTTAGATGTAGAGAAGG
* * * * **
3597368 TATGTAGGGAGAAATCAATAGAGGTTTTTTGGTTTCAAACAGTAAGGAGGGTAGC
194 TATGTAGGTAGAAATCAATATAAGTTTTTTGGTTTCGAACAGTTGGGAGGG-AGC
* * * * *
3597423 -TTGGAAATGTCGAGGACAGATTTGAGTTTGCTATCAGTTTTGGTGCCCGGAATGACTGAAAGTC
1 TTTGGAAATGTCGAGGAGAGCTTTGAGTTTGCTATC-GTTTTGGTGCCCAGAATGATTGAAAATC
* * * *
3597487 TTATCCACCCAGCCATCTAGAAAACCCAATAACGTCCCTTAAAAACTTAAAAGAGAAAAGAAAT-
65 TCATCCACCCAACCATCTAGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAATG
* * * * * *
3597551 AAAAAACTAAAAATATCCTTTTTAAATTGACAAAATACCATGAACAAGTGTTAGATATAGATAAG
130 AAAAATC-AAAAATA-CCCTTTTAAATTGATAAAATACCATGAACAGGTGTTAGATGTAGAGAAG
*
3597616 GTATG-CGAGTAGAAATCAATATAAGTT
193 GTATGTAG-GTAGAAATCAATATAAGTT
3597643 AGATTATACT
Statistics
Matches: 995, Mismatches: 137, Indels: 100
0.81 0.11 0.08
Matches are distributed among these distances:
226 9 0.01
227 6 0.01
228 5 0.01
229 89 0.09
231 1 0.00
234 9 0.01
235 58 0.06
236 20 0.02
238 14 0.01
239 162 0.16
240 7 0.01
241 8 0.01
242 86 0.09
243 11 0.01
244 7 0.01
245 182 0.18
246 1 0.00
247 9 0.01
248 44 0.04
249 261 0.26
250 6 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (247 bp):
TTTGGAAATGTCGAGGAGAGCTTTGAGTTTGCTATCGTTTTGGTGCCCAGAATGATTGAAAATCT
CATCCACCCAACCATCTAGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAATGA
AAAATCAAAAATACCCTTTTAAATTGATAAAATACCATGAACAGGTGTTAGATGTAGAGAAGGTA
TGTAGGTAGAAATCAATATAAGTTTTTTGGTTTCGAACAGTTGGGAGGGAGC
Found at i:3597370 original size:229 final size:237
Alignment explanation
Indices: 3596295--3597596 Score: 870
Period size: 245 Copynumber: 5.4 Consensus size: 237
3596285 CTAACCATCC
* * * * *
3596295 AGAAAACCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAATGAAAAATCGAAAATACCCT
1 AGAAAACCCAATAACGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAACCAAAAATACCTT
** * * * * * * *
3596360 TTTAAATTGATAAAATACCATGAACAAATGTTAGATGTAGAGAAGGTATATAAGTAGAAATCAAT
66 TTTAAATTGATAAAATACCATGAACAGGTATTAAATGTAAAAAAGGTATGTAGGGAGAAATC-A-
* * ** * * * *
3596425 ATAAGTTTTTTGGTTTCGAACAGTTGGGAAGGG-AACTTTGGAAATGTCGAGGAGAGCTTTGAGT
129 A-GAG-TTTTTGGTTTCAAACAGTAAGG-AGGGTAGC-TTGGAAATGTCGAAGACAGATTTGAGT
* * * * * *
3596489 TTGTTATCAGTTTTGGTGCCTAAAATGATTGAAAATCTCATCCACCCACCCATCT
190 TTGCTATCAGTTTTGGTGCCCAGAATGACTG--AA-CTTAGCCACCCA--CA--T
* * * ** *
3596544 AGAAAATCCAATAATGTCCCTTAAGAACTTAAAAGAGAAAAGAAATGAAAAATAAAAAATACCCT
1 AGAAAACCCAATAACGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAACCAAAAATACCTT
* * * * * * * * * *
3596609 TTTAAATTGATAATATAACATGAACAGGTGTGAGATGTAGAGAAGGTATGTAGGTAAAAAGCAAT
66 TTTAAATTGATAAAATACCATGAACAGGTATTAAATGTAAAAAAGGTATGTAGGGAGAAATC-A-
* ** * ** * * * *
3596674 ATAGGTTTTTTGGTTTTGAAC-G---GGAGGGCAATTATAGAAATGTCGAGGAGAGCTTTGAGTT
129 AGA-G-TTTTTGGTTTCAAACAGTAAGGAGGGTAGCT-TGGAAATGTCGAAGACAGATTTGAGTT
* ** * * * *
3596735 TGCTGTC-GATTTTGGCACTCAGAATGATTGAAAATTTCATCCACCCAACCATTT
191 TGCTATCAG-TTTTGGTGCCCAGAATGACTG--AACTT-AGCCACCC-A-CA--T
* * * ***
3596789 AGAAAACCCAATAATGTCACTCAAGAACTTAAATGAGAAAAGAAATGAAAAATTGAAAATACCTT
1 AGAAAACCCAATAACGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAACCAAAAATACCTT
* * * * * * * *
3596854 TTTAAATTGATAAAATAACATGAATAGGTGTTAGATGTAGAGAAGGTATGTAGGTAAAAATC-A-
66 TTTAAATTGATAAAATACCATGAACAGGTATTAAATGTAAAAAAGGTATGTAGGGAGAAATCAAG
* * * * * * * * *
3596917 A-TTTTTTGTTTCGAACAGTTACGAAAGG-AGCTTTGGAAATGTCGATGAGAGCTTTGAGTTTGT
131 AGTTTTTGGTTTCAAACAG-TAAGGAGGGTAGC-TTGGAAATGTCGAAGACAGATTTGAGTTTGC
* * ** *** * * * *
3596980 TGTCGGTTTTGGCACTTGGAATGATTGAAAATCTCATCCATCCAGCCATT
194 TATCAGTTTTGGTGCCCAGAATGACTG--AA-CTTAGCCACCCA--CA-T
* * * * * *
3597030 CAGAAAACCTAATAATGT--C-CAGGAACTTAAAAGAGAAAAAAAATGAAAAACCAAAAATGCTT
1 -AGAAAACCCAATAACGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAACCAAAAATACCT
* * *
3597092 TTTTAAATTGATAAAATACCATGAATAGGTGTTAGATGTAAAAAAGGTATGTAGGGAGAAATC-A
65 TTTTAAATTGATAAAATACCATGAACAGGTATTAAATGTAAAAAAGGTATGTAGGGAGAAATCAA
** * *
3597156 -A-TTTTTGGTTTTGAACAGCTGAGTG-GGG-AGCTTTGGAAATGTCGAAGAGAGATTTGAGTTT
130 GAGTTTTTGGTTTCAAACAG-TAAG-GAGGGTAGC-TTGGAAATGTCGAAGACAGATTTGAGTTT
* * *
3597217 GTTATCGGTTTTGGTGCCCAGAATGACTG-A-TTAGCCATCCA-A-
192 GCTATCAGTTTTGGTGCCCAGAATGACTGAACTTAGCCACCCACAT
* *
3597259 A-AAAA-CCAATAATGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAGCCAAAAATACCTT
1 AGAAAACCCAATAACGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAACCAAAAATACCTT
* * *
3597322 TTCAAATTGATAAAATACCATGAACATGTATTAAATGTAAAGAAGGTATGTAGGGAGAAATCAAT
66 TTTAAATTGATAAAATACCATGAACAGGTATTAAATGTAAAAAAGGTATGTAGGGAGAAATC-A-
*
3597387 AGAGGTTTTTTGGTTTCAAACAGTAAGGAGGGTAGCTTGGAAATGTCGAGGACAGATTTGAGTTT
129 AGA-G-TTTTTGGTTTCAAACAGTAAGGAGGGTAGCTTGGAAATGTCGAAGACAGATTTGAGTTT
* *
3597452 GCTATCAGTTTTGGTGCCCGGAATGACTGAAAGTCTTATCCACCCAGCCATCT
192 GCTATCAGTTTTGGTGCCCAGAATGACTG-AA--CTTAGCCACCCA--CA--T
* * * *
3597505 AGAAAACCCAATAACGTCCCTTAAAAACTTAAAAGAGAAAAGAAATAAAAAACTAAAAATATCCT
1 AGAAAACCCAATAACGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAACCAAAAATA-CCT
*
3597570 TTTTAAATTGACAAAATACCATGAACA
65 TTTTAAATTGATAAAATACCATGAACA
3597597 AGTGTTAGAT
Statistics
Matches: 897, Mismatches: 113, Indels: 86
0.82 0.10 0.08
Matches are distributed among these distances:
226 9 0.01
227 4 0.00
228 2 0.00
229 95 0.11
231 1 0.00
232 1 0.00
233 1 0.00
234 10 0.01
235 59 0.07
236 19 0.02
237 1 0.00
238 13 0.01
239 168 0.19
240 10 0.01
241 4 0.00
242 82 0.09
243 8 0.01
244 7 0.01
245 184 0.21
246 2 0.00
247 4 0.00
248 50 0.06
249 163 0.18
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (237 bp):
AGAAAACCCAATAACGTCCCTCAAGAACTTAAAAGAGAAAAGAAATGAAAAACCAAAAATACCTT
TTTAAATTGATAAAATACCATGAACAGGTATTAAATGTAAAAAAGGTATGTAGGGAGAAATCAAG
AGTTTTTGGTTTCAAACAGTAAGGAGGGTAGCTTGGAAATGTCGAAGACAGATTTGAGTTTGCTA
TCAGTTTTGGTGCCCAGAATGACTGAACTTAGCCACCCACAT
Found at i:3599094 original size:17 final size:17
Alignment explanation
Indices: 3599074--3599126 Score: 63
Period size: 16 Copynumber: 3.0 Consensus size: 17
3599064 TTTATAATGT
3599074 TATAATTAAAATAAAAA
1 TATAATTAAAATAAAAA
*
3599091 TAT-ATTAAAACAAAATA
1 TATAATTAAAATAAAA-A
3599108 TATAATATAAGAATAAAAA
1 TATAAT-TAA-AATAAAAA
3599127 ATTAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 11 0.37
17 7 0.23
18 2 0.07
19 4 0.13
20 6 0.20
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
TATAATTAAAATAAAAA
Done.