Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 26
Found at i:5245726 original size:24 final size:24
Alignment explanation
Indices: 5245699--5245744 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5245689 TGACATGATT
5245699 TTTTCTCTACTTTTGTGGCACGCG
1 TTTTCTCTACTTTTGTGGCACGCG
**
5245723 TTTTCTCTGTTTTTGTGGCACG
1 TTTTCTCTACTTTTGTGGCACG
5245745 ATTCTCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.50
Consensus pattern (24 bp):
TTTTCTCTACTTTTGTGGCACGCG
Found at i:5253383 original size:11 final size:11
Alignment explanation
Indices: 5253367--5253392 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5253357 ACTTCTAAAA
5253367 ATTATTAAATT
1 ATTATTAAATT
5253378 ATTATTAAATT
1 ATTATTAAATT
5253389 ATTA
1 ATTA
5253393 CCATAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:5254071 original size:31 final size:31
Alignment explanation
Indices: 5254023--5254095 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
5254013 CCAAAATGAT
* *
5254023 TCTTT-GATTATAAGATGTTGTTTTGTTGAG
1 TCTTTCGACTATAAGATGTTGCTTTGTTGAG
*
5254053 TCTTTCGACTATAGGATGTTGCTTTGTTGAG
1 TCTTTCGACTATAAGATGTTGCTTTGTTGAG
*
5254084 TCTCTCGACTAT
1 TCTTTCGACTAT
5254096 TAAAAGTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.18, C:0.12, G:0.22, T:0.48
Consensus pattern (31 bp):
TCTTTCGACTATAAGATGTTGCTTTGTTGAG
Found at i:5255987 original size:18 final size:17
Alignment explanation
Indices: 5255964--5256006 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5255954 TTATTAAATT
*
5255964 ATTATAATATTACATTAA
1 ATTATAATATT-CAATAA
*
5255982 ATTATAAAATTCAATAA
1 ATTATAATATTCAATAA
5255999 ATT-TAATA
1 ATTATAATA
5256007 ATATATTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 4 0.18
17 8 0.36
18 10 0.45
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATAATATTCAATAA
Found at i:5267407 original size:25 final size:26
Alignment explanation
Indices: 5267360--5267418 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
5267350 AATAAAAGTG
5267360 AAATAT-TTTAAATTAAGTTAATAGTA
1 AAATATATTTAAATTAAGTTAATA-TA
*
5267386 AAATATATTT-AA-TAATTTAATATA
1 AAATATATTTAAATTAAGTTAATATA
5267410 AAA-ATATTT
1 AAATATATTT
5267419 TAAGTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 6 0.19
24 5 0.16
25 9 0.29
26 8 0.26
27 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (26 bp):
AAATATATTTAAATTAAGTTAATATA
Found at i:5267628 original size:55 final size:55
Alignment explanation
Indices: 5267569--5267686 Score: 227
Period size: 55 Copynumber: 2.1 Consensus size: 55
5267559 TATAATCCAC
5267569 AAACAAAGTTCAAAAATTCAAATTACATAACTAAAATAAAATTTATTAAAATTTA
1 AAACAAAGTTCAAAAATTCAAATTACATAACTAAAATAAAATTTATTAAAATTTA
5267624 AAACAAAGTTCAAAAATTCAAATTACATAACTAAAATAAAATTTATTAAAATTTA
1 AAACAAAGTTCAAAAATTCAAATTACATAACTAAAATAAAATTTATTAAAATTTA
*
5267679 AAATAAAG
1 AAACAAAG
5267687 AAATATAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (55 bp):
AAACAAAGTTCAAAAATTCAAATTACATAACTAAAATAAAATTTATTAAAATTTA
Found at i:5267785 original size:39 final size:38
Alignment explanation
Indices: 5267754--5267850 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 38
5267744 TAGAACATTA
5267754 ATGTGAAATAATTTAAGAAATTAAGAGTTTAGAATGTT
1 ATGTGAAATAATTTAAGAAATTAAGAGTTTAGAATGTT
* * *
5267792 ATGATGTCAA-AATTTAAGAAATTAGGATTTTAGAATGTT
1 ATG-TG-AAATAATTTAAGAAATTAAGAGTTTAGAATGTT
*
5267831 ATAGTGAAATAATTTGAGAA
1 AT-GTGAAATAATTTAAGAA
5267851 TTATGAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
38 5 0.10
39 42 0.84
40 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (38 bp):
ATGTGAAATAATTTAAGAAATTAAGAGTTTAGAATGTT
Found at i:5268264 original size:31 final size:31
Alignment explanation
Indices: 5268226--5268293 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
5268216 GGGTGATCAC
**
5268226 ATCTTAATTAAATAAAAACGA-AAGTGGTTAT
1 ATCTTAATTAAATAAAAAC-ATAAGTGACTAT
5268257 ATCTTAATTAAATAAAAACATAAGTGACTAT
1 ATCTTAATTAAATAAAAACATAAGTGACTAT
5268288 ATCTTA
1 ATCTTA
5268294 TGTATTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACATAAGTGACTAT
Found at i:5268607 original size:20 final size:21
Alignment explanation
Indices: 5268571--5268611 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5268561 ACAAAGAGAC
*
5268571 AACGTTAAAAGTAAAAAAAAT
1 AACGTAAAAAGTAAAAAAAAT
5268592 AACGTAAAAAGTAAAAAAAA
1 AACGTAAAAAGTAAAAAAAA
5268612 AACAACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AACGTAAAAAGTAAAAAAAAT
Found at i:5269504 original size:54 final size:56
Alignment explanation
Indices: 5269436--5269571 Score: 190
Period size: 54 Copynumber: 2.5 Consensus size: 56
5269426 CTTGGGTTTC
5269436 CCTT-TCGAACACTTGCACCAATGTCTTGGCAAGCCTGATACTCTATCTTG-A-CT
1 CCTTGTCGAACACTTGCACCAATGTCTTGGCAAGCCTGATACTCTATCTTGAACCT
* *
5269489 CCTTGTCGAACACTTGCACCAATGTCTTGGCAATCTTGATACTCTATCTTGAACCT
1 CCTTGTCGAACACTTGCACCAATGTCTTGGCAAGCCTGATACTCTATCTTGAACCT
* * *
5269545 CCCTGTC-AGACACTTGCATCGATGTCT
1 CCTTGTCGA-ACACTTGCACCAATGTCT
5269572 CAGACCCAAG
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
53 4 0.05
54 44 0.59
55 2 0.03
56 24 0.32
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.32
Consensus pattern (56 bp):
CCTTGTCGAACACTTGCACCAATGTCTTGGCAAGCCTGATACTCTATCTTGAACCT
Found at i:5269750 original size:24 final size:25
Alignment explanation
Indices: 5269723--5269771 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
5269713 TAATAAAACT
5269723 ATAAAATATA-TTTTATT-TTTAAAA
1 ATAAAATA-AGTTTTATTATTTAAAA
*
5269747 ATAATATAAGTTTTATTATTTAAAA
1 ATAAAATAAGTTTTATTATTTAAAA
5269772 TAATTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 14 0.64
25 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATAAAATAAGTTTTATTATTTAAAA
Found at i:5269772 original size:24 final size:25
Alignment explanation
Indices: 5269733--5269780 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
5269723 ATAAAATATA
5269733 TTTTATTTTTAAAAATAA-TATAAG
1 TTTTATTTTTAAAAATAATTATAAG
5269757 TTTTATTATTT-AAAATAATTATAA
1 TTTTATT-TTTAAAAATAATTATAA
5269781 TCAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTATTTTTAAAAATAATTATAAG
Found at i:5286904 original size:15 final size:15
Alignment explanation
Indices: 5286884--5286917 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5286874 TCGAAAAATA
5286884 AATTATTGGAATTTG
1 AATTATTGGAATTTG
5286899 AATTATTGGAATTTG
1 AATTATTGGAATTTG
5286914 AATT
1 AATT
5286918 CTGGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (15 bp):
AATTATTGGAATTTG
Found at i:5287187 original size:49 final size:50
Alignment explanation
Indices: 5287090--5287188 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 50
5287080 TACAAATATT
*
5287090 AAATATAATAAATAATATTATTTATCATAAAATTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAATTTAATATTATAATTTTA
* * * * *
5287140 AAATATTA-AAATAAT-TTATTTATTATTAAATATTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAAT-TTAATATTATAATTTTA
5287189 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 14 0.33
49 21 0.50
50 7 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAATTTAATATTATAATTTTA
Found at i:5287199 original size:48 final size:47
Alignment explanation
Indices: 5287088--5287203 Score: 117
Period size: 49 Copynumber: 2.4 Consensus size: 47
5287078 ATTACAAATA
*
5287088 TTAAATATAATAAATAATATTATTTATCATAAAATTTAATATTATTATT
1 TTAAA-ATAA-AAATAATATTATTTATCATAAAATTTAATATTATAATT
* * * *
5287137 TTAAAATATTAAAATAAT-TTATTTATTATTAAATATTATTTTTATAATT
1 TTAAAATA--AAAATAATATTATTTATCATAAAAT-TTAATATTATAATT
*
5287186 TTATTAATAAAAATAATA
1 TTA-AAATAAAAATAATA
5287204 ATTTTTGTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
48 25 0.45
49 26 0.46
50 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (47 bp):
TTAAAATAAAAATAATATTATTTATCATAAAATTTAATATTATAATT
Found at i:5287326 original size:23 final size:23
Alignment explanation
Indices: 5287277--5287339 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
5287267 GTGTTATATT
* **
5287277 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
5287300 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
5287323 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
5287340 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:5287363 original size:28 final size:30
Alignment explanation
Indices: 5287325--5287426 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 30
5287315 TTATTAAAAT
5287325 ATTATTTAAATATATAAATAA-TATTAT-TC
1 ATTA-TTAAATATATAAATAATTATTATATC
*
5287354 ATTATTAAATATATAAAAAAATTATTATATC
1 ATTATTAAATATAT-AAATAATTATTATATC
* *
5287385 -TTATTAAA-ATAAAAATATAATATCT-TAT-
1 ATTATTAAATATATAAATA-ATTAT-TATATC
5287413 ATTATTATAATATA
1 ATTATTA-AATATA
5287427 ATTGATTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
28 14 0.23
29 25 0.41
30 17 0.28
31 5 0.08
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTATTAAATATATAAATAATTATTATATC
Found at i:5287367 original size:19 final size:20
Alignment explanation
Indices: 5287315--5287367 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
5287305 TTAAATATCT
5287315 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
5287334 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
5287355 TTATTAAATATAT
1 TTATTAAATATAT
5287368 AAAAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:5287368 original size:30 final size:30
Alignment explanation
Indices: 5287325--5287399 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
5287315 TTATTAAAAT
* *
5287325 ATTATTTAAATATATAAATAA-TATTAT-TC
1 ATTATTAAAATATA-AAAAAATTATTATATC
5287354 ATTATTAAATATATAAAAAAATTATTATATC
1 ATTATTAAA-ATATAAAAAAATTATTATATC
5287385 -TTATTAAAATA-AAAA
1 ATTATTAAAATATAAAA
5287400 TATAATATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 4 0.10
29 16 0.39
30 19 0.46
31 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
ATTATTAAAATATAAAAAAATTATTATATC
Found at i:5289849 original size:31 final size:31
Alignment explanation
Indices: 5289811--5289874 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
5289801 GAGTCGAGGG
*
5289811 TTTACCTATGTTCTAAGGAACATATGGACAA
1 TTTACCTAGGTTCTAAGGAACATATGGACAA
** * *
5289842 TTTACCTAGGTTCTTCGGGACCTATGGACAA
1 TTTACCTAGGTTCTAAGGAACATATGGACAA
5289873 TT
1 TT
5289875 ACCGAGGATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
TTTACCTAGGTTCTAAGGAACATATGGACAA
Found at i:5289909 original size:30 final size:30
Alignment explanation
Indices: 5289873--5289932 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5289863 CTATGGACAA
5289873 TTACCGAGGATCTTTATGACATCTGGATAG
1 TTACCGAGGATCTTTATGACATCTGGATAG
*
5289903 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACATCTGGATAG
5289933 GTCCTTCGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACATCTGGATAG
Found at i:5295977 original size:21 final size:21
Alignment explanation
Indices: 5295953--5295992 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5295943 ACAATATTGC
5295953 ATATTGTGATAAGAGAATGCA
1 ATATTGTGATAAGAGAATGCA
5295974 ATATTGTGATAAGAGAATG
1 ATATTGTGATAAGAGAATG
5295993 GACGTATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (21 bp):
ATATTGTGATAAGAGAATGCA
Found at i:5296621 original size:60 final size:60
Alignment explanation
Indices: 5296548--5296680 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
5296538 TTTAAAGGAC
* *
5296548 AAAG-TACATAAATTATC-CTTCAACTATAAAATATT-ATCTTGTTAAGTCTTCTAACTATTA
1 AAAGTTACA-AAATTATCTCTT-AACTATAAAACATTGCT-TTGTTAAGTCTTCTAACTATTA
* * * * *
5296608 AAAGTTACAAAATTATCTCTTGATTATAGAACGTTGCTTTGTTAAGTCTTTTAACTATTA
1 AAAGTTACAAAATTATCTCTTAACTATAAAACATTGCTTTGTTAAGTCTTCTAACTATTA
5296668 AAAGTTACAAAAT
1 AAAGTTACAAAAT
5296681 ACACTATTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
60 55 0.87
61 8 0.13
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (60 bp):
AAAGTTACAAAATTATCTCTTAACTATAAAACATTGCTTTGTTAAGTCTTCTAACTATTA
Found at i:5299384 original size:28 final size:28
Alignment explanation
Indices: 5299340--5299404 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
5299330 TAATGACTTG
* * *
5299340 AGTGATCATTTTTTGATAAATCGATATT
1 AGTGACCATTTTGTGATAAATCAATATT
5299368 AGTGACCATTTTGTGATAAATCAATATT
1 AGTGACCATTTTGTGATAAATCAATATT
5299396 AGTGACCAT
1 AGTGACCAT
5299405 AGTATAACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (28 bp):
AGTGACCATTTTGTGATAAATCAATATT
Found at i:5299544 original size:36 final size:37
Alignment explanation
Indices: 5299504--5299580 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 37
5299494 GTTATATAGT
5299504 TAATGTTAT-AGAGAGAATTACCATAGTTTGCATCTC
1 TAATGTTATAAGAGAGAATTACCATAGTTTGCATCTC
5299540 TAATGTTATAGGAAGAGAGAATTACCATAGTTTGCATCTC
1 TAATGTTAT---AAGAGAGAATTACCATAGTTTGCATCTC
5299580 T
1 T
5299581 TCTAAACTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 9 0.24
40 28 0.76
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (37 bp):
TAATGTTATAAGAGAGAATTACCATAGTTTGCATCTC
Found at i:5307952 original size:9 final size:9
Alignment explanation
Indices: 5307938--5307968 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5307928 ATTACAAACT
5307938 AAATAATAA
1 AAATAATAA
5307947 AAATAATAA
1 AAATAATAA
5307956 AAATAATTAA
1 AAATAA-TAA
5307966 AAA
1 AAA
5307969 GAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAATAA
Found at i:5309323 original size:20 final size:20
Alignment explanation
Indices: 5309298--5309335 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5309288 CAATGTAATA
5309298 AAAAAATTCA-TTATATACTC
1 AAAAAATT-ATTTATATACTC
5309318 AAAAAATTATTTATATAC
1 AAAAAATTATTTATATAC
5309336 AAATTCAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATTATTTATATACTC
Found at i:5311087 original size:15 final size:15
Alignment explanation
Indices: 5311061--5311108 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
5311051 TTTAAACATC
*
5311061 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
5311077 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
5311094 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
5311109 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:5316602 original size:22 final size:21
Alignment explanation
Indices: 5316560--5316599 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5316550 GAGTTTATTT
* *
5316560 TCATTTTTTTATTTTGAAACA
1 TCATTTTTATATTTTAAAACA
5316581 TCATTTTTATATTTTAAAA
1 TCATTTTTATATTTTAAAA
5316600 ACAATTTCTC
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:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAACA
Found at i:5330858 original size:73 final size:73
Alignment explanation
Indices: 5330739--5330886 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
5330729 CCGAGAACGA
5330739 ACAAGATTCACACGACCTCGATCCGGATACGTACAAAATCCCTGTATTCGACGAAAAGGACGTAG
1 ACAAGATTCACACGACCTCGATCCGGATACGTACAAAATCCCTGTATTCGACGAAAAGGACGTAG
5330804 TCGTTTTG
66 TCGTTTTG
*
5330812 ACAAGATTCGCACGACCTCGATCCGGATACGTACAAAATCCCTGTATTCGACGAAAAGGACGTAG
1 ACAAGATTCACACGACCTCGATCCGGATACGTACAAAATCCCTGTATTCGACGAAAAGGACGTAG
5330877 TCGTTTTG
66 TCGTTTTG
5330885 AC
1 AC
5330887 GGAAGGAAAC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (73 bp):
ACAAGATTCACACGACCTCGATCCGGATACGTACAAAATCCCTGTATTCGACGAAAAGGACGTAG
TCGTTTTG
Found at i:5333451 original size:88 final size:88
Alignment explanation
Indices: 5333302--5333473 Score: 326
Period size: 88 Copynumber: 2.0 Consensus size: 88
5333292 TGAATCAGTC
* *
5333302 TGAACGATTAAAGCAATAACCTGTTTAATGAAAAGGGATAAGACGCAAATGCTAAGCCTGGAATG
1 TGAACGATTAAAGCAATAACCTGTTTAACGAAAAGGGATAAGACGCAAATGCTAACCCTGGAATG
5333367 AGACATCATAGTAAGAAGTGGTG
66 AGACATCATAGTAAGAAGTGGTG
5333390 TGAACGATTAAAGCAATAACCTGTTTAACGAAAAGGGATAAGACGCAAATGCTAACCCTGGAATG
1 TGAACGATTAAAGCAATAACCTGTTTAACGAAAAGGGATAAGACGCAAATGCTAACCCTGGAATG
5333455 AGACATCATAGTAAGAAGT
66 AGACATCATAGTAAGAAGT
5333474 TGTTTATTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (88 bp):
TGAACGATTAAAGCAATAACCTGTTTAACGAAAAGGGATAAGACGCAAATGCTAACCCTGGAATG
AGACATCATAGTAAGAAGTGGTG
Found at i:5334426 original size:20 final size:20
Alignment explanation
Indices: 5334401--5334535 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
5334391 AATTGGGAAA
*
5334401 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATAATGACT
* *
5334421 ATCGCAATGCGATATTTACT
1 ATCGCAATGCGATAATGACT
* *
5334441 ATCGCAATCCGATAAT-ACAAA
1 ATCGCAATGCGATAATGAC--T
* * *
5334462 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATAATGACT
* * **
5334482 TTCGCAACGCGATTTTGACT
1 ATCGCAATGCGATAATGACT
* *
5334502 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATAATGAC-T
5334522 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
5334536 TTTCAAAGCG
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.04
20 63 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATAATGACT
Found at i:5334463 original size:61 final size:61
Alignment explanation
Indices: 5334398--5334535 Score: 190
Period size: 61 Copynumber: 2.3 Consensus size: 61
5334388 GTGAATTGGG
*
5334398 AAAATCGCAATGCGATACTGACTATCGCAATGCGATATTT-ACTATCGCAATC-CGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGAT-TTTGACTATCGCAA-CGCGATAATAC
* * * *
5334459 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTTTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATTTTGACTATCGCAACGCGATAATAC
*
5334520 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
5334536 TTTCAAAGCG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 4 0.06
61 63 0.94
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATTTTGACTATCGCAACGCGATAATAC
Found at i:5334732 original size:22 final size:22
Alignment explanation
Indices: 5334704--5334747 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5334694 ACTCTCTCAC
5334704 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
5334726 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
5334748 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:5335049 original size:20 final size:20
Alignment explanation
Indices: 5334990--5335053 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
5334980 GCGATTTTAG
*
5334990 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
5335010 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
5335030 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
5335050 TTTC
1 TTTC
5335054 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:5335244 original size:25 final size:24
Alignment explanation
Indices: 5335190--5335244 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
5335180 TGTTTATTAT
* *
5335190 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
5335214 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
5335240 TGTTT
1 TGTTT
5335245 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:5336394 original size:18 final size:18
Alignment explanation
Indices: 5336373--5336417 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5336363 TCCATTTCAG
*
5336373 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
5336391 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
5336409 GAGCCATCA
1 GAGCCATCA
5336418 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:5336918 original size:20 final size:20
Alignment explanation
Indices: 5336893--5336938 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5336883 TAGTTTACTT
5336893 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
5336913 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
*
5336933 TTGCAA
1 TCGCAA
5336939 TGGAAATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:5336966 original size:14 final size:14
Alignment explanation
Indices: 5336947--5336986 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
5336937 AATGGAAATG
5336947 AAAATCGCAACGAC
1 AAAATCGCAACGAC
5336961 AAAATCGCAACGAC
1 AAAATCGCAACGAC
5336975 AAAATCGCAACG
1 AAAATCGCAACG
5336987 CGAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5337039 original size:14 final size:14
Alignment explanation
Indices: 5337020--5337110 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
5337010 TTGTGTTTCG
5337020 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5337034 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
5337050 CGCATTGCGATTTTGC
1 CG--TTGCGATTTTGT
*
5337066 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
5337083 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
5337099 CGTTGCGATTTT
1 CGTTGCGATTTT
5337111 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 27 0.44
15 3 0.05
16 11 0.18
17 3 0.05
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5337084 original size:33 final size:33
Alignment explanation
Indices: 5337015--5337126 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
5337005 GCGATTTGTG
*
5337015 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
5337047 TTTCGCATTGCGATTTTGCCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
5337080 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
5337113 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
5337127 AGCCATTTCC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 25 0.33
33 51 0.67
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:5337145 original size:20 final size:19
Alignment explanation
Indices: 5337111--5337166 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
5337101 TTGCGATTTT
*
5337111 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5337130 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
5337150 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
5337167 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5339258 original size:20 final size:20
Alignment explanation
Indices: 5339205--5339288 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
5339195 ACTATCGCAA
*
5339205 CGATAGTCAGTTTCGCATTG
1 CGATAGCCAGTTTCGCATTG
*** *
5339225 CGATTTTTCA-TTTCGAATTG
1 CGA-TAGCCAGTTTCGCATTG
*
5339245 CGATAGCCAGTTTCGCGTTG
1 CGATAGCCAGTTTCGCATTG
*
5339265 CGATAGCCATTTTCGCATTG
1 CGATAGCCAGTTTCGCATTG
5339285 CGAT
1 CGAT
5339289 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.06
20 45 0.87
21 4 0.08
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
CGATAGCCAGTTTCGCATTG
Found at i:5339527 original size:20 final size:20
Alignment explanation
Indices: 5339511--5339568 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
5339501 ATTGCGATTT
*
5339511 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCTCGTTGCGATAG
5339531 TCAGAATCTCGTTGCGATAG
1 TCAGAATCTCGTTGCGATAG
* * *
5339551 TCAGTATCGCATTGCGAT
1 TCAGAATCTCGTTGCGAT
5339569 TTTCCAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
TCAGAATCTCGTTGCGATAG
Found at i:5340416 original size:24 final size:24
Alignment explanation
Indices: 5340359--5340418 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
5340349 TAGTCAGTAT
*
5340359 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
* * *
5340383 CCGGACTTTGATATTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
*
5340407 TCGAATTTTGAT
1 TCGAAATTTGAT
5340419 GATGTTTCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGGTCAATAC
Found at i:5340610 original size:12 final size:12
Alignment explanation
Indices: 5340593--5340617 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5340583 ATATAATCCT
5340593 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5340605 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5340617 G
1 G
5340618 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5341872 original size:19 final size:19
Alignment explanation
Indices: 5341850--5341908 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
5341840 GGAAATTACT
5341850 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5341869 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5341883 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5341902 ATCGCAA
1 ATCGCAA
5341909 CGCTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5341892 original size:33 final size:33
Alignment explanation
Indices: 5341850--5341976 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
5341840 GGAAATTACT
5341850 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
5341883 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
5341915 TTTTGTAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5341949 ATCGCAATGCGAAATTAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5341977 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5341961 original size:66 final size:66
Alignment explanation
Indices: 5341855--5341983 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
5341845 TTACTATCGC
*
5341855 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTTG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTTG
5341920 T
66 T
* *
5341921 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATTAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
5341984 AATTTCGCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.19
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTTG
T
Found at i:5341991 original size:19 final size:19
Alignment explanation
Indices: 5341948--5341985 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5341938 GCAACGAGGG
*
5341948 AATCGCAATGCGAAATTAA
1 AATCGCAACGCGAAATTAA
*
5341967 AATCGCAACGCGAATTTAA
1 AATCGCAACGCGAAATTAA
5341986 TTTCGCGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (19 bp):
AATCGCAACGCGAAATTAA
Found at i:5341998 original size:19 final size:18
Alignment explanation
Indices: 5341976--5342083 Score: 52
Period size: 19 Copynumber: 6.2 Consensus size: 18
5341966 AAATCGCAAC
5341976 GCGAATTTAATTTCGCGTT
1 GCGAATTT-ATTTCGCGTT
* *
5341995 GCG-A--T-TCTCTCGTT
1 GCGAATTTATTTCGCGTT
*
5342009 GCGATTTTTATTTCGCGTT
1 GCGA-ATTTATTTCGCGTT
* *
5342028 GCG-A--T-TCTCTCGTT
1 GCGAATTTATTTCGCGTT
*
5342042 GCGATTTTCATTTCGCGTT
1 GCGAATTT-ATTTCGCGTT
* *
5342061 GCGATTTTCATTTCGCATT
1 GCGAATTT-ATTTCGCGTT
5342080 GCGA
1 GCGA
5342084 TAGTACTTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
14 20 0.30
15 1 0.01
16 1 0.01
17 1 0.01
18 2 0.03
19 42 0.63
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (18 bp):
GCGAATTTATTTCGCGTT
Found at i:5342008 original size:14 final size:14
Alignment explanation
Indices: 5341991--5342047 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
5341981 TTTAATTTCG
5341991 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
5342005 CGTTGCGATTTTTATTTCG
1 CGTTGCGA----T-TCTCT
5342024 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5342038 CGTTGCGATT
1 CGTTGCGATT
5342048 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
15 1 0.03
18 1 0.03
19 11 0.32
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5342027 original size:33 final size:33
Alignment explanation
Indices: 5341976--5342066 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
5341966 AAATCGCAAC
*
5341976 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
*
5342009 GCGATTTTTATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
*
5342042 GCGATTTTCATTTCGCGTTGCGATT
1 GCGATTTTAATTTCGCGTTGCGATT
5342067 TTCATTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (33 bp):
GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
Found at i:5342084 original size:19 final size:19
Alignment explanation
Indices: 5342005--5342084 Score: 98
Period size: 19 Copynumber: 4.5 Consensus size: 19
5341995 GCGATTCTCT
*
5342005 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
*
5342024 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
5342038 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
5342057 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
5342076 CATTGCGAT
1 CGTTGCGAT
5342085 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 10 0.19
16 3 0.06
17 2 0.04
19 37 0.71
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:5342210 original size:14 final size:14
Alignment explanation
Indices: 5342191--5342227 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5342181 CATCAATTAA
5342191 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5342205 ACAAATCACCTTTT
1 ACAAATCAACTTTT
5342219 ACAAATCAA
1 ACAAATCAA
5342228 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5343670 original size:42 final size:42
Alignment explanation
Indices: 5343624--5343703 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
5343614 CGATGACAGT
* *
5343624 GGCCTCTTGAACGGTAGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
5343666 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
5343704 CAGGCGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:5344100 original size:91 final size:90
Alignment explanation
Indices: 5343924--5344108 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
5343914 ATTTCAAACT
*
5343924 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
5343989 AAAATTGGCAGCAACCGAATAAATTTAC
63 AAAATTGGCAGCAACCGAATAAATTTAC
5344017 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
**
5344081 GTATTGGCAGCAACCGAATAAATTTAC
64 AAATTGGCAGCAACCGAATAAATTTAC
5344108 T
1 T
5344109 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAAA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:5345878 original size:33 final size:33
Alignment explanation
Indices: 5345820--5345954 Score: 153
Period size: 33 Copynumber: 3.9 Consensus size: 33
5345810 ACGAGATAAT
* *
5345820 GAGAATCGCAACGCGGAAATAACTATCGTAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
5345854 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
5345887 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA--CG--A
* **
5345924 TGAAAATCGCAACGCGAAATGAAAATCGCAA
1 -GAGAATCGCAACGCGAAATGACTATCGCAA
5345955 TGCGATTTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
33 45 0.49
34 14 0.15
35 2 0.02
37 1 0.01
38 29 0.32
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:5345882 original size:19 final size:19
Alignment explanation
Indices: 5345857--5345959 Score: 135
Period size: 19 Copynumber: 5.7 Consensus size: 19
5345847 GTAACGAGAG
*
5345857 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
* *
5345876 TATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
5345890 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
5345909 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
5345928 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
5345947 AATCGCAATGCGA
1 AATCGCAACGCGA
5345960 TTTTGGTTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 59 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:5345941 original size:38 final size:35
Alignment explanation
Indices: 5345795--5345959 Score: 151
Period size: 33 Copynumber: 4.6 Consensus size: 35
5345785 TCTTTTGGTT
*
5345795 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GCG--AA-GAGAATCGCAACGC
* *
5345834 GGAAAT-AACTATCGTAA-CG-AGAGAATCGCAACGC
1 -GAAATGAA-AATCGCAAGCGAAGAGAATCGCAACGC
**
5345868 GAAATGACTATCGCAA-CG-AGAGAATCGCAACGC
1 GAAATGAAAATCGCAAGCGAAGAGAATCGCAACGC
*
5345901 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAA-GCG-AA-GAGAATCGCAACGC
5345939 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAA-GCGA
5345960 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
33 43 0.39
34 15 0.14
35 3 0.03
37 2 0.02
38 33 0.30
39 2 0.02
40 11 0.10
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (35 bp):
GAAATGAAAATCGCAAGCGAAGAGAATCGCAACGC
Found at i:5346559 original size:20 final size:20
Alignment explanation
Indices: 5346534--5346586 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
5346524 GTGCTATGTA
*
5346534 AATCGCGTTGCGAAATTCAG
1 AATCGCGTTGCGAAAGTCAG
5346554 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
5346574 TATCTCGTTGCGA
1 AATCGCGTTGCGA
5346587 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:5346620 original size:20 final size:20
Alignment explanation
Indices: 5346595--5346645 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5346585 GATTTTGTAT
5346595 TATCGCATTGCGATAGTAAA
1 TATCGCATTGCGATAGTAAA
* *
5346615 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAA
5346635 TATCGCATTGC
1 TATCGCATTGC
5346646 AATTTTCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAA
Found at i:5347434 original size:17 final size:18
Alignment explanation
Indices: 5347405--5347450 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5347395 TTTAAAGAAT
*
5347405 ATATATAAATATTTTAC-A
1 ATATAT-AATATTATACAA
*
5347423 ATTTATAATATTATACAA
1 ATATATAATATTATACAA
5347441 ATATATAATA
1 ATATATAATA
5347451 AGTACAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATAATATTATACAA
Found at i:5348274 original size:17 final size:16
Alignment explanation
Indices: 5348254--5348291 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
5348244 AATCTAATTC
5348254 AAAATTTCGAATATCT
1 AAAATTTCGAATATCT
5348270 GAAAATTTCGAATATCT
1 -AAAATTTCGAATATCT
5348287 AAAAT
1 AAAAT
5348292 AGTGATCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (16 bp):
AAAATTTCGAATATCT
Found at i:5356562 original size:23 final size:23
Alignment explanation
Indices: 5356542--5356586 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5356532 AATATACTTC
*
5356542 TGTGCTGAATCATTCAGTACTGT
1 TGTGCTGAATCAGTCAGTACTGT
* *
5356565 TTTGCTGAATCAGTCAGCACTG
1 TGTGCTGAATCAGTCAGTACTG
5356587 AATCATTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (23 bp):
TGTGCTGAATCAGTCAGTACTGT
Found at i:5358379 original size:26 final size:28
Alignment explanation
Indices: 5358343--5358412 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
5358333 GCTAATGGCA
*
5358343 TGCATGGCGACCTGT-CA-CGGTGGGAG
1 TGCATGGCGACCTATACAGCGGTGGGAG
*
5358369 TGCATGGCGACCTATACAGGTCGTTGGGAG
1 TGCATGGCGACCTATACA-G-CGGTGGGAG
5358399 TGCATGGCGACCTA
1 TGCATGGCGACCTA
5358413 CGTGGGGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 14 0.37
27 2 0.05
30 22 0.58
ACGTcount: A:0.19, C:0.23, G:0.37, T:0.21
Consensus pattern (28 bp):
TGCATGGCGACCTATACAGCGGTGGGAG
Found at i:5358923 original size:2 final size:2
Alignment explanation
Indices: 5358916--5358965 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5358906 CTTATAAGAA
5358916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5358958 AT AT AT AT
1 AT AT AT AT
5358966 TGGTACAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5360569 original size:3 final size:3
Alignment explanation
Indices: 5360561--5360602 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5360551 TCAACCAATC
5360561 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5360603 CAACAACATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5360693 original size:12 final size:12
Alignment explanation
Indices: 5360666--5360717 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
5360656 AGAACTCCAG
* *
5360666 GAAGTTGAGGAG
1 GAAGTTGAAGAA
5360678 GAAGTTGAAGAA
1 GAAGTTGAAGAA
** *
5360690 GAAGCAGAAGAG
1 GAAGTTGAAGAA
*
5360702 GAGGTTGAAGAA
1 GAAGTTGAAGAA
5360714 GAAG
1 GAAG
5360718 AGGAAGTGGA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.44, C:0.02, G:0.42, T:0.12
Consensus pattern (12 bp):
GAAGTTGAAGAA
Found at i:5373822 original size:28 final size:28
Alignment explanation
Indices: 5373762--5373823 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
5373752 TTGTTCTGCG
*
5373762 ATAA-TTTAATTTAAGATTAATTTAATAC
1 ATAACTTTAATTTAAAATTAATTT-ATAC
*
5373790 A-AACTTTAATTTAAAATGTTATTT-TAC
1 ATAACTTTAATTTAAAAT-TAATTTATAC
5373817 ATAACTT
1 ATAACTT
5373824 AAAAAGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 6 0.21
28 18 0.62
29 5 0.17
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (28 bp):
ATAACTTTAATTTAAAATTAATTTATAC
Found at i:5376912 original size:7 final size:7
Alignment explanation
Indices: 5376900--5376929 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5376890 ACATAGCTAC
5376900 AGGAGTT
1 AGGAGTT
5376907 AGGAGTT
1 AGGAGTT
5376914 AGGAGTT
1 AGGAGTT
*
5376921 AGAAGTT
1 AGGAGTT
5376928 AG
1 AG
5376930 AAGTACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (7 bp):
AGGAGTT
Found at i:5382636 original size:23 final size:23
Alignment explanation
Indices: 5382600--5382644 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5382590 CAGACATTAG
* *
5382600 TCAATTGAAGCTCAAACACGAAC
1 TCAATTCAAACTCAAACACGAAC
*
5382623 TCAATTCAAACTCAAACTCGAA
1 TCAATTCAAACTCAAACACGAA
5382645 TTTGAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.27, G:0.09, T:0.20
Consensus pattern (23 bp):
TCAATTCAAACTCAAACACGAAC
Found at i:5386729 original size:32 final size:32
Alignment explanation
Indices: 5386684--5386756 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
5386674 TACATTTGTT
* *
5386684 TGAATGTAGGATTAAC-TCTGGTATGCATTATA
1 TGAATGCAAGATTAACTTC-GGTATGCATTATA
*
5386716 TGAATGCAAGATTAACTTCGGTATGCATTATC
1 TGAATGCAAGATTAACTTCGGTATGCATTATA
*
5386748 TAAATGCAA
1 TGAATGCAA
5386757 TACTGGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (32 bp):
TGAATGCAAGATTAACTTCGGTATGCATTATA
Found at i:5387793 original size:19 final size:19
Alignment explanation
Indices: 5387766--5387823 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 19
5387756 TTTTGTTGCA
5387766 TAAAGTATCGATACTCTTG
1 TAAAGTATCGATACTCTTG
* *
5387785 TAAAATATCGATACTCTGAGG
1 TAAAGTATCGATACTCT--TG
5387806 TAAAGTATCGATACTCTT
1 TAAAGTATCGATACTCTT
5387824 AGCCTGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (19 bp):
TAAAGTATCGATACTCTTG
Found at i:5391984 original size:182 final size:182
Alignment explanation
Indices: 5391677--5392098 Score: 754
Period size: 182 Copynumber: 2.3 Consensus size: 182
5391667 ATTTAAGGTA
* * * * * *
5391677 TAAATTATAAGTTGATCAAAATTTTAGTTTAATAAAAAATGTTATTGAAAAAATAAATAAAGTTA
1 TAAATTATACGTTAATCGAGATTTCATTTTAATAAAAAATGTTATTGAAAAAATAAATAAAGTTA
5391742 AACTTATTAAAATTCAAATTCAAATAATTTTAATTTTAGAATTATATATGTTATTATTAGATTAA
66 AACTTATTAAAATTCAAATTCAAATAATTTTAATTTTAGAATTATATATGTTATTATTAGATTAA
5391807 AATTTTTAAATAAATACTATCTTAAGAAAGAGAAATAAGATTATTTAAAGAG
131 AATTTTTAAATAAATACTATCTTAAGAAAGAGAAATAAGATTATTTAAAGAG
5391859 TAAATTATACGTTAATCGAGATTTCATTTTAATAAAAAATGTTATTGAAAAAATAAATAAAGTTA
1 TAAATTATACGTTAATCGAGATTTCATTTTAATAAAAAATGTTATTGAAAAAATAAATAAAGTTA
*
5391924 AACTTATTAAAATTCCAATTCAAATAATTTTAATTTTAGAATTATATATGTTATTATTAGATTAA
66 AACTTATTAAAATTCAAATTCAAATAATTTTAATTTTAGAATTATATATGTTATTATTAGATTAA
5391989 AATTTTTAAATAAATACTATCTTAAGAAAGAGAAATAAGATTATTTAAAGAG
131 AATTTTTAAATAAATACTATCTTAAGAAAGAGAAATAAGATTATTTAAAGAG
* *
5392041 TAAATTATACGTTAATCGAGATTTCATTTTAATAAAAAATATTATTTAAAAACATAAA
1 TAAATTATACGTTAATCGAGATTTCATTTTAATAAAAAATGTTATTGAAAAA-ATAAA
5392099 AGAATTAATT
Statistics
Matches: 230, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
182 225 0.98
183 5 0.02
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.39
Consensus pattern (182 bp):
TAAATTATACGTTAATCGAGATTTCATTTTAATAAAAAATGTTATTGAAAAAATAAATAAAGTTA
AACTTATTAAAATTCAAATTCAAATAATTTTAATTTTAGAATTATATATGTTATTATTAGATTAA
AATTTTTAAATAAATACTATCTTAAGAAAGAGAAATAAGATTATTTAAAGAG
Found at i:5392957 original size:20 final size:21
Alignment explanation
Indices: 5392923--5392962 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5392913 AAAAACAATG
5392923 ATAAATTATACG-TTTAGTAC
1 ATAAATTATACGTTTTAGTAC
5392943 ATAAATTATTA-GTTTTAGTA
1 ATAAATTA-TACGTTTTAGTA
5392963 TGTTTTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (21 bp):
ATAAATTATACGTTTTAGTAC
Found at i:5399526 original size:87 final size:87
Alignment explanation
Indices: 5399423--5399594 Score: 290
Period size: 87 Copynumber: 2.0 Consensus size: 87
5399413 TCATTTAACC
* * *
5399423 AGAAATATTATCAAGCACAATAACATATTATATATCGCTTATATAATGTAATAGGTAGCGCTTAT
1 AGAAACATTATCAAGCACAATAACATATTAGATAGCGCTTATATAATGTAATAGGTAGCGCTTAT
5399488 ATAATAAAATATCTTAATTACT
66 ATAATAAAATATCTTAATTACT
* *
5399510 AGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTGT
1 AGAAACATTATCAAGCACAATAACATATTAGATAGCGCTTATATAATGTAATAGGTAGCGCTTAT
*
5399575 ATAATAAAATATGTTAATTA
66 ATAATAAAATATCTTAATTA
5399595 TTTAATTTGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (87 bp):
AGAAACATTATCAAGCACAATAACATATTAGATAGCGCTTATATAATGTAATAGGTAGCGCTTAT
ATAATAAAATATCTTAATTACT
Found at i:5399555 original size:23 final size:23
Alignment explanation
Indices: 5399529--5399578 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
5399519 ATCAAGCACA
*
5399529 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
5399552 ATAATGTAATAGGTAGCGCTTGT
1 ATAACATAATAGGTAGCGCTTAT
5399575 ATAA
1 ATAA
5399579 TAAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:5399585 original size:23 final size:23
Alignment explanation
Indices: 5399538--5399585 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5399528 AATAACATAT
**
5399538 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
5399561 TAGGTAGCGCTTGTATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
5399584 TA
1 TA
5399586 TGTTAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:5400081 original size:183 final size:180
Alignment explanation
Indices: 5399852--5400180 Score: 525
Period size: 183 Copynumber: 1.8 Consensus size: 180
5399842 AAATGTATTA
* * *
5399852 ATACTTTACAATATAACAGGTAAATATGACAAAACCATTTTCATTATGACAAAATCGGTAAAATT
1 ATACTTTACAATATAACAGGTAAATATGACAAAACCAGTTTCATTATGACAAAACCAGTAAAATT
* *
5399917 TACCGGATATGTTGAAAGTATCGAT-ACTTTTTATAAAAATGTATTAATACTTTACAATATAACA
66 TACCCGATATGTTGAAAGTATCGATCA-TTTTTATAAAAATG-ATCAATACTTTACAATATAACA
*
5399981 GGTAAAAATATGACAAAACCGGTAAAATTTACCCGATATGTTGAAAGGATCG
129 GATAAAAATATGACAAAACCGGTAAAATTTACCCGATATGTTGAAAGGATCG
* *
5400033 ATACTTTACAATTTAACAGGTAAAAATATGACAAAACCAGTTTCATTATGATAAAACCAGTAAAA
1 ATACTTTACAATATAACAGGT--AAATATGACAAAACCAGTTTCATTATGACAAAACCAGTAAAA
*
5400098 TTTACCCGATATGTTGAAAGTATCGATCATTTTTATAAAAATGATCGATACTTTACAATATAACA
64 TTTACCCGATATGTTGAAAGTATCGATCATTTTTATAAAAATGATCAATACTTTACAATATAACA
*
5400163 TATAAAAATATGACAAAA
129 GATAAAAATATGACAAAA
5400181 TCAATTTCAT
Statistics
Matches: 135, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
181 20 0.15
182 36 0.27
183 78 0.58
184 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.31
Consensus pattern (180 bp):
ATACTTTACAATATAACAGGTAAATATGACAAAACCAGTTTCATTATGACAAAACCAGTAAAATT
TACCCGATATGTTGAAAGTATCGATCATTTTTATAAAAATGATCAATACTTTACAATATAACAGA
TAAAAATATGACAAAACCGGTAAAATTTACCCGATATGTTGAAAGGATCG
Found at i:5400106 original size:90 final size:89
Alignment explanation
Indices: 5399852--5400124 Score: 291
Period size: 93 Copynumber: 3.0 Consensus size: 89
5399842 AAATGTATTA
* * *
5399852 ATACTTTACAATATAACAGGT-AAATATGACAAAACCATTTTCATTATGACAAAATCGGTAAAAT
1 ATACTTTACAATTTAACAGGTAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAAT
*
5399916 TTACCGGATATGTTGAAAGTATCG
66 TTACCCGATATGTTGAAAGTATCG
** * * * * * * *** *
5399940 ATACTTT-TTA-TAAAAATGTATTAATACTTTACAATATAACAGGTAAAAATATGACAAAACCGG
1 ATACTTTACAATTTAACAGGTA-AAATA--TGACAA-A-ACCA-GTTTCATTATGACAAAACCGG
*
5400003 TAAAATTTACCCGATATGTTGAAAGGATCG
60 TAAAATTTACCCGATATGTTGAAAGTATCG
* *
5400033 ATACTTTACAATTTAACAGGTAAAAATATGACAAAACCAGTTTCATTATGATAAAACCAGTAAAA
1 ATACTTTACAATTTAACAGGT-AAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAA
5400098 TTTACCCGATATGTTGAAAGTATCG
65 TTTACCCGATATGTTGAAAGTATCG
5400123 AT
1 AT
5400125 CATTTTTATA
Statistics
Matches: 143, Mismatches: 32, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
86 5 0.03
87 1 0.01
88 11 0.08
90 51 0.36
91 4 0.03
92 4 0.03
93 55 0.38
94 1 0.01
95 10 0.07
96 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (89 bp):
ATACTTTACAATTTAACAGGTAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAAT
TTACCCGATATGTTGAAAGTATCG
Found at i:5400225 original size:112 final size:112
Alignment explanation
Indices: 5400028--5400373 Score: 498
Period size: 112 Copynumber: 3.1 Consensus size: 112
5400018 ATGTTGAAAG
*
5400028 GATCGATACTTTACAATTTAACAGGTAAAAATATGACAAAACCAGTTTCATTATGATAAAACCAG
1 GATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGATAAAACCAG
*
5400093 TAAAATTTACCCGATATGTTGAAAGTATCGATCATTTTTATAAAAAT
66 TAAAATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAT
** * * *
5400140 GATCGATACTTTACAATATAACATATAAAAATATGACAAAATCAATTTCATTATGACAAAACCAG
1 GATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGATAAAACCAG
* * * *
5400205 TAAAATTTACCTGATATGTTGAAATTATCGATCCTTCTTATAAAAAG
66 TAAAATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAT
* *
5400252 GATCGATATTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTATCATTATGATAAAATC-
1 GATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTT-TCATTATGATAAAACCA
* **
5400316 GATAAAATTTACCTAATATGTTGAAAGTATAAAT-ACTTTTTATAAAAAT
65 G-TAAAATTTACCTGATATGTTGAAAGTATCGATCA-TTTTTATAAAAAT
5400365 GTATCGATA
1 G-ATCGATA
5400374 TTTTGTTGAA
Statistics
Matches: 205, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
112 144 0.70
113 54 0.26
114 7 0.03
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (112 bp):
GATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGATAAAACCAG
TAAAATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAT
Found at i:5400839 original size:87 final size:87
Alignment explanation
Indices: 5400694--5400899 Score: 333
Period size: 87 Copynumber: 2.4 Consensus size: 87
5400684 TTTTCTACAG
* * *
5400694 AGGTAGCACTTATATAATAAAATAGGTT-ATTACTATAAACATTATCAAACACAATAACATATTA
1 AGGTAGCGCTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAACACAATAACATATTA
* *
5400758 TGTACCGCTTATATAATGTAAT
66 GGTACCGCTTATATAACGTAAT
*
5400780 AGGTAGCGCTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAGCACAATAACATATTA
1 AGGTAGCGCTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAACACAATAACATATTA
*
5400845 GGTAGCGCTTATATAACGTAAT
66 GGTACCGCTTATATAACGTAAT
*
5400867 AGATAGCGCTTATATAATAAAATAGATTAATTA
1 AGGTAGCGCTTATATAATAAAATAGATTAATTA
5400900 TTTAATTTGT
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
86 26 0.23
87 85 0.77
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (87 bp):
AGGTAGCGCTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAACACAATAACATATTA
GGTACCGCTTATATAACGTAAT
Found at i:5400860 original size:23 final size:23
Alignment explanation
Indices: 5400834--5400893 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
5400824 ATCAAGCACA
* *
5400834 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
*
5400857 ATAACGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
* *
5400880 ATAATAAAATAGAT
1 ATAACATAATAGAT
5400894 TAATTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:5401415 original size:114 final size:114
Alignment explanation
Indices: 5401142--5401614 Score: 679
Period size: 112 Copynumber: 4.2 Consensus size: 114
5401132 ATCGATACTT
* *
5401142 TATAAATATGTATCGATACTTTACAATATAACA-ATAAAAATATGACAAAACCAGTTTCATTATG
1 TATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATG
* * * *
5401206 ACAAAACCGGTAAAATTTACCGGATATATTTAAAGTATCGAT-CTTTT-
66 ACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATATTTTTA
* * *
5401253 TATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAGTATGACAAAATCAATTTCATTATG
1 TATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATG
* *
5401318 ACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTATCGGTCATTTTTA
66 ACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGAT-ATTTTTA
* *
5401368 TAAAAAAATG-ATCGATACTTTACAATTTAACAGGTAAAAATATGACAAAACCAGTTTCATTATG
1 TATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATG
* *
5401432 AAAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATTGATATTTTT-
66 ACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATATTTTTA
* * * *
5401480 TATAAAAA-GGATCGATACTTTACAATATAACATGTAAAAATATGACAAAAACAGTTTTATTATG
1 TATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATG
** ** *
5401544 ACAAAACCAATAAAATTTACCTGATATGTTGAAAGTATAAATATTTTTT
66 ACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATATTTTTA
5401593 TATAAAAATGTATCGATACTTT
1 TATAAAAATGTATCGATACTTT
5401615 GTTGAAAGTT
Statistics
Matches: 324, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
111 33 0.10
112 164 0.51
113 14 0.04
114 104 0.32
115 9 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (114 bp):
TATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATG
ACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATATTTTTA
Found at i:5401573 original size:226 final size:225
Alignment explanation
Indices: 5401149--5401614 Score: 693
Period size: 226 Copynumber: 2.1 Consensus size: 225
5401139 CTTTATAAAT
*
5401149 ATGTATCGATACTTTACAATATAACAATAAAAATATGACAAAACCAGTTTCATTATGACAAAACC
1 ATGTATCGATACTTTACAATATAACAATAAAAATATGACAAAACCAGTTTCATTATGAAAAAACC
* *
5401214 GGTAAAATTTACCGGATATATTTAAAGTATCGATCTTTTTATAAAAATGTATCGATACTTTACAA
66 GGTAAAATTTACCGGATATATTGAAAGTATCGATCTTTTTATAAAAATGGATCGATACTTTACAA
* * **
5401279 TATAACAGGTAAAAGTATGACAAAATCAATTTCATTATGACAAAACCGGTAAAATTTACCTAATA
131 TATAACAGGTAAAAATATGACAAAAACAATTTCATTATGACAAAACCAATAAAATTTACCTAATA
***
5401344 TGTTGAAAGTATCGGTCATTTTTATAAAAAA
196 TGTTGAAAGTATAAAT-ATTTTTATAAAAAA
* *
5401375 ATG-ATCGATACTTTACAATTTAACAGGTAAAAATATGACAAAACCAGTTTCATTATGAAAAAAC
1 ATGTATCGATACTTTACAATATAACA-ATAAAAATATGACAAAACCAGTTTCATTATGAAAAAAC
* * * *
5401439 CGGTAAAATTTACCTGATATGTTGAAAGTATTGATATTTTTTATAAAAA-GGATCGATACTTTAC
65 CGGTAAAATTTACCGGATATATTGAAAGTATCGAT-CTTTTTATAAAAATGGATCGATACTTTAC
* * * *
5401503 AATATAACATGTAAAAATATGACAAAAACAGTTTTATTATGACAAAACCAATAAAATTTACCTGA
129 AATATAACAGGTAAAAATATGACAAAAACAATTTCATTATGACAAAACCAATAAAATTTACCTAA
* *
5401568 TATGTTGAAAGTATAAATATTTTTTTATAAAA
194 TATGTTGAAAGTATAAATATTTTTATAAAAAA
5401600 ATGTATCGATACTTT
1 ATGTATCGATACTTT
5401615 GTTGAAAGTT
Statistics
Matches: 215, Mismatches: 22, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
225 36 0.17
226 167 0.78
227 12 0.06
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (225 bp):
ATGTATCGATACTTTACAATATAACAATAAAAATATGACAAAACCAGTTTCATTATGAAAAAACC
GGTAAAATTTACCGGATATATTGAAAGTATCGATCTTTTTATAAAAATGGATCGATACTTTACAA
TATAACAGGTAAAAATATGACAAAAACAATTTCATTATGACAAAACCAATAAAATTTACCTAATA
TGTTGAAAGTATAAATATTTTTATAAAAAA
Found at i:5407043 original size:69 final size:69
Alignment explanation
Indices: 5406935--5407122 Score: 277
Period size: 69 Copynumber: 2.7 Consensus size: 69
5406925 AAACAAATTA
* * * * * *
5406935 TTTTTTGTTTTACCGTTAATCGAATCAAAGTTTATTTGAAAATTATTAACCGAACCAAATTAACC
1 TTTTTTCTTTAACCATTAATCGAACCAAAATTTAGTTGAAAATTATTAACCGAACCAAATTAACC
*
5407000 TAAT
66 GAAT
*
5407004 TTTTTTCTTTAACCATTAATCGAACCAAAATTTAGTTGAAAATTATTAACCGAACCGAATTAACC
1 TTTTTTCTTTAACCATTAATCGAACCAAAATTTAGTTGAAAATTATTAACCGAACCAAATTAACC
5407069 GAAT
66 GAAT
* * *
5407073 TTTTTTCTTTAAACATTAATCAAACCGAAATTTAGTTGAAAATTATTAAC
1 TTTTTTCTTTAACCATTAATCGAACCAAAATTTAGTTGAAAATTATTAAC
5407123 TTAACCGAAC
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 108 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (69 bp):
TTTTTTCTTTAACCATTAATCGAACCAAAATTTAGTTGAAAATTATTAACCGAACCAAATTAACC
GAAT
Found at i:5407362 original size:179 final size:179
Alignment explanation
Indices: 5407042--5407375 Score: 508
Period size: 179 Copynumber: 1.9 Consensus size: 179
5407032 AATTTAGTTG
5407042 AAAATTATTAACCGAACCGAATTAACCGAATTTTTTTCTTTAAACATTAATCAAACCGAAATTTA
1 AAAATTATTAACCGAACCGAATTAACCGAATTTTTTTCTTTAAACATTAATCAAACCGAAATTTA
* ** * *
5407107 GTTGAAAATTATTAACTTAACCGAACAAATTTTGGTTAATTCGGTCAATTTTTGAATTAACCAAC
66 GTTGAAAATTATAAACCAAACCGAACAAATTTTGATTAATTCGGTCAATTTTTGAATTAACCAAA
*****
5407172 TTTTTTTAAAATTTTCTAATTTATATAACAATTCAATATTTTTAATTCA
131 AAAAATTAAAATTTTCTAATTTATATAACAATTCAATATTTTTAATTCA
* *
5407221 AAAATTATTAACCGAACCGAATTAACTGAATTTTTTTCTTTAACCATTAATCAAACTC-AAATTT
1 AAAATTATTAACCGAACCGAATTAACCGAATTTTTTTCTTTAAACATTAATCAAAC-CGAAATTT
* * * *
5407285 ATTTGAAAATTATAAACCAAATCGAACAAATTTTGATTAATTTGGTCAATTTTTTAATTAACCAA
65 AGTTGAAAATTATAAACCAAACCGAACAAATTTTGATTAATTCGGTCAATTTTTGAATTAACCAA
5407350 AAAAAATTAAAATTTTCTAATTTATA
130 AAAAAATTAAAATTTTCTAATTTATA
5407376 CCATTTTTTC
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
179 137 0.99
180 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (179 bp):
AAAATTATTAACCGAACCGAATTAACCGAATTTTTTTCTTTAAACATTAATCAAACCGAAATTTA
GTTGAAAATTATAAACCAAACCGAACAAATTTTGATTAATTCGGTCAATTTTTGAATTAACCAAA
AAAAATTAAAATTTTCTAATTTATATAACAATTCAATATTTTTAATTCA
Found at i:5407609 original size:8 final size:8
Alignment explanation
Indices: 5407590--5407623 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
5407580 TATTCAATTG
5407590 TTATATAAA
1 TTATA-AAA
5407599 TTATAAAA
1 TTATAAAA
5407607 TTATAAAA
1 TTATAAAA
5407615 TTATAAAA
1 TTATAAAA
5407623 T
1 T
5407624 ATTTTGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 20 0.80
9 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:5410621 original size:36 final size:36
Alignment explanation
Indices: 5410562--5410635 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
5410552 GTTAGAAAAT
* *
5410562 ATTTATATATATTTTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATATTTTTTAAAAAATTGAAAAT-ATAAA
*
5410599 ATTTATATA-ATTTTTTAGAAAATTGAAAATATAAA
1 ATTTATATATATTTTTTAAAAAATTGAAAATATAAA
5410634 AT
1 AT
5410636 AGTTTAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
36 18 0.53
37 9 0.26
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (36 bp):
ATTTATATATATTTTTTAAAAAATTGAAAATATAAA
Found at i:5422206 original size:20 final size:20
Alignment explanation
Indices: 5421959--5422206 Score: 116
Period size: 20 Copynumber: 12.2 Consensus size: 20
5421949 AACCGACGAA
* **
5421959 TTCGCAACACGAACTCCAAT
1 TTCGCAACACGAATTTTAAT
* * *
5421979 TTCGCAACAC-AGTTTCCAAA
1 TTCGCAACACGAATTT-TAAT
* *
5421999 TTCGCAACACAAAATTTTAAA
1 TTCGCAACAC-GAATTTTAAT
*
5422020 TTCGCAACACAGAATTTAACAAT
1 TTCGCAACAC-GAATTT--TAAT
*
5422043 TTCGCAACACGAATTTCT-TT
1 TTCGCAACACGAATTT-TAAT
* * *
5422063 TTCGCAAAACGATTTTTAAA
1 TTCGCAACACGAATTTTAAT
***
5422083 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTTAAT
* *
5422103 TTCGCAACAAGATTTTCTAA-
1 TTCGCAACACGAATTT-TAAT
** *
5422123 TTCGCAA-AGCGCGTTTCAAT
1 TTCGCAACA-CGAATTTTAAT
*
5422143 TTCGCAACGCGAATTTT-AT
1 TTCGCAACACGAATTTTAAT
*
5422162 TGTCGCAACTCG-ATTTTCGAA-
1 T-TCGCAACACGAATTTT--AAT
*
5422183 TTCGCATCACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
5422203 TTCG
1 TTCG
5422207 GAAAATAACT
Statistics
Matches: 172, Mismatches: 38, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
19 17 0.10
20 106 0.62
21 26 0.15
22 11 0.06
23 12 0.07
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:5423044 original size:20 final size:20
Alignment explanation
Indices: 5422984--5423045 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
5422974 CCATATTCGC
*
5422984 AACTCAAATTTGCAACTCAA
1 AACTCAAATTTGCAACTCGA
* * *
5423004 AAATCAAA-TTCCTAATTCGA
1 AACTCAAATTTGC-AACTCGA
*
5423024 AACTCAAATTTGCAACACGA
1 AACTCAAATTTGCAACTCGA
5423044 AA
1 AA
5423046 ATCGCAACTC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.24
Consensus pattern (20 bp):
AACTCAAATTTGCAACTCGA
Found at i:5423072 original size:20 final size:20
Alignment explanation
Indices: 5423043--5423119 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
5423033 TTGCAACACG
* *
5423043 AAAA-TCGCAACTCGATATT
1 AAAATTCGCAACTCGAAAAT
5423062 AAAATTCGCAACTCGAAAAT
1 AAAATTCGCAACTCGAAAAT
* *
5423082 ATAATTGGCAACTCGAAAAT
1 AAAATTCGCAACTCGAAAAT
*
5423102 GAAATTCGCAACTCGAAA
1 AAAATTCGCAACTCGAAA
5423120 TCGATTTCGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 4 0.08
20 46 0.92
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (20 bp):
AAAATTCGCAACTCGAAAAT
Found at i:5423166 original size:20 final size:20
Alignment explanation
Indices: 5423135--5423260 Score: 137
Period size: 20 Copynumber: 6.3 Consensus size: 20
5423125 TTCGATTTTC
*
5423135 ATTTTCGCA-TTGCGAATTTG
1 ATTTTCG-AGTTGCGAATTCG
* * *
5423155 ATTTTTGAATTGCGAAATCG
1 ATTTTCGAGTTGCGAATTCG
*
5423175 ATTTTCGTGTTGCGAATTCG
1 ATTTTCGAGTTGCGAATTCG
* *
5423195 ATTTTTGAGTTGTGAATTCG
1 ATTTTCGAGTTGCGAATTCG
*
5423215 ATTTTCGAGTTGCGAATTGG
1 ATTTTCGAGTTGCGAATTCG
* * *
5423235 AATATCGAGTTGCGAATTTG
1 ATTTTCGAGTTGCGAATTCG
5423255 ATTTTC
1 ATTTTC
5423261 TTAAAGGTAG
Statistics
Matches: 87, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
19 1 0.01
20 86 0.99
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.44
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTCG
Found at i:5425126 original size:21 final size:21
Alignment explanation
Indices: 5425102--5425152 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5425092 ATGTGAATCC
*
5425102 TGAACGATGGGAGGGGCCTCT
1 TGAACGATGGGAGGGGCCTAT
5425123 TGAACGATGGGAGGGGCCTAT
1 TGAACGATGGGAGGGGCCTAT
5425144 TGAACGATG
1 TGAACGATG
5425153 AGAGATGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.20
Consensus pattern (21 bp):
TGAACGATGGGAGGGGCCTAT
Found at i:5425527 original size:21 final size:20
Alignment explanation
Indices: 5425503--5425678 Score: 122
Period size: 21 Copynumber: 8.4 Consensus size: 20
5425493 TAGAACACCC
5425503 ACCTCATCACGTAAAGCAGCT
1 ACCTCATCACGTAAAGCA-CT
*
5425524 ACCTCA-CTACGTAAAGCACC
1 ACCTCATC-ACGTAAAGCACT
** * *
5425544 ATTGTCATCACGTAAAACAGTT
1 A-CCTCATCACGTAAAGCA-CT
*
5425566 ACCTCA-CTACGTAAAGACCCT
1 ACCTCATC-ACGTAAAG-CACT
* * *
5425587 ACCTCATCACGTCATGCACC
1 ACCTCATCACGTAAAGCACT
** * *
5425607 ATTTTTATCACGTAAAGCACCG
1 A-CCTCATCACGTAAAGCA-CT
5425629 ACCTCATCACGTAAAGCACT
1 ACCTCATCACGTAAAGCACT
5425649 GACCTCATCACGTAAAGCACCT
1 -ACCTCATCACGTAAAGCA-CT
*
5425671 AACTCATC
1 ACCTCATC
5425679 CCGTGGAGGT
Statistics
Matches: 118, Mismatches: 26, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
20 8 0.07
21 102 0.86
22 8 0.07
ACGTcount: A:0.33, C:0.34, G:0.11, T:0.22
Consensus pattern (20 bp):
ACCTCATCACGTAAAGCACT
Found at i:5425578 original size:63 final size:62
Alignment explanation
Indices: 5425488--5425669 Score: 206
Period size: 63 Copynumber: 2.9 Consensus size: 62
5425478 TGAAACAATC
* *
5425488 TCACGTAGAACACCCACCTCATCACGTAAAGCAGCTACCTCA-CTACGTAAAGCACCATTGTCA
1 TCACGTAAAACACCGACCTCATCACGTAAAGCA-CTACCTCATC-ACGTAAAGCACCATTGTCA
*** * * * * *
5425551 TCACGTAAAACAGTTACCTCA-CTACGTAAAGACCCTACCTCATCACGTCATGCACCATTTTTA
1 TCACGTAAAACACCGACCTCATC-ACGTAAAG-CACTACCTCATCACGTAAAGCACCATTGTCA
*
5425614 TCACGTAAAGCACCGACCTCATCACGTAAAGCACTGACCTCATCACGTAAAGCACC
1 TCACGTAAAACACCGACCTCATCACGTAAAGCACT-ACCTCATCACGTAAAGCACC
5425670 TAACTCATCC
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
62 4 0.04
63 91 0.93
64 3 0.03
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.21
Consensus pattern (62 bp):
TCACGTAAAACACCGACCTCATCACGTAAAGCACTACCTCATCACGTAAAGCACCATTGTCA
Found at i:5425659 original size:42 final size:41
Alignment explanation
Indices: 5425488--5425678 Score: 149
Period size: 42 Copynumber: 4.6 Consensus size: 41
5425478 TGAAACAATC
*
5425488 TCACGTAGAA-CACCCACCTCATCACGTAAAGCAGCTACCTCA
1 TCACGTA-AAGCACCTACCTCATCACGTAAAGCA-CTACCTCA
** * *
5425530 -CTACGTAAAGCACC-ATTGTCATCACGTAAAACAGTTACCTCA
1 TC-ACGTAAAGCACCTA-CCTCATCACGTAAAGCA-CTACCTCA
* * * ** *
5425572 -CTACGTAAAG-ACCCTACCTCATCACGTCATGCACCATTTTTA
1 TC-ACGTAAAGCA-CCTACCTCATCACGTAAAGCACTA-CCTCA
*
5425614 TCACGTAAAGCACCGACCTCATCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACT-ACCTCA
*
5425656 TCACGTAAAGCACCTAACTCATC
1 TCACGTAAAGCACCTACCTCATC
5425679 CCGTGGAGGT
Statistics
Matches: 117, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
41 6 0.05
42 107 0.91
43 4 0.03
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.21
Consensus pattern (41 bp):
TCACGTAAAGCACCTACCTCATCACGTAAAGCACTACCTCA
Found at i:5425932 original size:42 final size:42
Alignment explanation
Indices: 5425780--5425943 Score: 199
Period size: 42 Copynumber: 4.0 Consensus size: 42
5425770 GATGGAATAT
* * *
5425780 GTGATGGATCTCGGTGTCGATGTGTAGAGTCGGCT--A-GAG
1 GTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAG
* * * * *
5425819 GTGATGGCTCTCGGTGTCGAGGTGTGGAATCGGCTCGATCAG
1 GTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAG
*
5425861 GTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATGAG
1 GTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAG
* * *
5425903 GTGATGGATCTCGGTGTTGAAGTGAAGAATCAACTCGATGA
1 GTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGA
5425944 AAAAGTGGGG
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
39 31 0.29
41 1 0.01
42 76 0.70
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (42 bp):
GTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAG
Found at i:5432809 original size:2 final size:2
Alignment explanation
Indices: 5432802--5432852 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5432792 CACCCGAGTC
5432802 GA GA GA GA GA GA GA GA 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 GA GA GA GA GA GA GA GA
5432844 GA GA GA GA G
1 GA GA GA GA G
5432853 GACCTGCAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5440548 original size:138 final size:138
Alignment explanation
Indices: 5440311--5440587 Score: 554
Period size: 138 Copynumber: 2.0 Consensus size: 138
5440301 TATGTTAAAT
5440311 ATTAAAATATTAATTTTAAATATAAATGTATAATATATTTAAATCACGTTGATTAAATTATAAAT
1 ATTAAAATATTAATTTTAAATATAAATGTATAATATATTTAAATCACGTTGATTAAATTATAAAT
5440376 GATTATACTATAAGCGTGTCCTATGTTAGACTCAAATTAATGTTTAACGTTTAAATTAATGACTA
66 GATTATACTATAAGCGTGTCCTATGTTAGACTCAAATTAATGTTTAACGTTTAAATTAATGACTA
5440441 TGCCGACA
131 TGCCGACA
5440449 ATTAAAATATTAATTTTAAATATAAATGTATAATATATTTAAATCACGTTGATTAAATTATAAAT
1 ATTAAAATATTAATTTTAAATATAAATGTATAATATATTTAAATCACGTTGATTAAATTATAAAT
5440514 GATTATACTATAAGCGTGTCCTATGTTAGACTCAAATTAATGTTTAACGTTTAAATTAATGACTA
66 GATTATACTATAAGCGTGTCCTATGTTAGACTCAAATTAATGTTTAACGTTTAAATTAATGACTA
5440579 TGCCGACA
131 TGCCGACA
5440587 A
1 A
5440588 AAAAACTGGA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (138 bp):
ATTAAAATATTAATTTTAAATATAAATGTATAATATATTTAAATCACGTTGATTAAATTATAAAT
GATTATACTATAAGCGTGTCCTATGTTAGACTCAAATTAATGTTTAACGTTTAAATTAATGACTA
TGCCGACA
Found at i:5440919 original size:4 final size:4
Alignment explanation
Indices: 5440905--5440940 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
5440895 GAGTACCCAA
5440905 TTCT CTTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
5440941 ATTTTCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:5442098 original size:60 final size:61
Alignment explanation
Indices: 5441997--5442112 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 61
5441987 TTATATTCAA
*
5441997 CTCATACAATTAATAATTAATGTGTGCATATCAACTCT-AAAAAATATTTATAAACCATCG
1 CTCATACAATTAATAATTAATGTGTGAATATCAACTCTAAAAAAATATTTATAAACCATCG
* *
5442057 CTCATACAATTAATAATTAATGTGTGAATA-CACATTTTAAAAAAAATATTTATAAA
1 CTCATACAATTAATAATTAATGTGTGAATATCA-ACTCT-AAAAAAATATTTATAAA
5442113 TCTCCAGCTG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 2 0.04
60 32 0.64
62 16 0.32
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (61 bp):
CTCATACAATTAATAATTAATGTGTGAATATCAACTCTAAAAAAATATTTATAAACCATCG
Found at i:5447232 original size:14 final size:14
Alignment explanation
Indices: 5447207--5447241 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5447197 ACACGTGACA
5447207 TTTTATAATTTTT-T
1 TTTTA-AATTTTTAT
5447221 TTTTAAATTTTTAT
1 TTTTAAATTTTTAT
5447235 TTTTAAA
1 TTTTAAA
5447242 AACAAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTAAATTTTTAT
Found at i:5447817 original size:21 final size:21
Alignment explanation
Indices: 5447791--5447844 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5447781 ATTTACCGTG
*
5447791 ATTGCGACCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
* *
5447812 ATTGCGGTCGTCGTGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
5447833 ATTGCGGCCGTC
1 ATTGCGGCCGTC
5447845 ACGAACCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:5450979 original size:16 final size:16
Alignment explanation
Indices: 5450933--5450979 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
5450923 ACAACAAAAA
* *
5450933 AGAGAGGGAGAGGGAG
1 AGAGAGGGAGAAGGCG
*
5450949 AGGGAGGGAG-A-GCG
1 AGAGAGGGAGAAGGCG
5450963 AGAGAGGGAGAAGGCG
1 AGAGAGGGAGAAGGCG
5450979 A
1 A
5450980 TGGAACGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 13 0.52
ACGTcount: A:0.36, C:0.04, G:0.60, T:0.00
Consensus pattern (16 bp):
AGAGAGGGAGAAGGCG
Found at i:5451230 original size:16 final size:14
Alignment explanation
Indices: 5451207--5451245 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
5451197 ATTTAAATAA
*
5451207 TATTAAATTATTTAC
1 TATTAAATTAATT-C
5451222 TACTTAAATTAATTC
1 TA-TTAAATTAATTC
5451237 TATTAAATT
1 TATTAAATT
5451246 GTGCGTGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTAAATTAATTC
Found at i:5452882 original size:20 final size:20
Alignment explanation
Indices: 5452857--5452895 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5452847 TTGGTTCACG
5452857 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGTGA
5452877 GAATGTAAGATTACCAGTG
1 GAATGTAAGATTACCAGTG
5452896 GGAGTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (20 bp):
GAATGTAAGATTACCAGTGA
Found at i:5452906 original size:20 final size:20
Alignment explanation
Indices: 5452863--5452913 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5452853 CACGGAATGT
**
5452863 AAGATTACCAGTGAGAATGT
1 AAGATTACCAGTGAGAATAA
* *
5452883 AAGATTACCAGTGGGAGTAA
1 AAGATTACCAGTGAGAATAA
5452903 AAGATTACCAG
1 AAGATTACCAG
5452914 GGAATAGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:5453581 original size:18 final size:19
Alignment explanation
Indices: 5453546--5453582 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5453536 CACGGAATGT
5453546 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
5453566 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
5453583 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:5458774 original size:183 final size:183
Alignment explanation
Indices: 5458421--5458804 Score: 716
Period size: 183 Copynumber: 2.1 Consensus size: 183
5458411 ATATGTTTTT
5458421 TATATTTAAAAAATTAAATTTAAATGTTAACATCCTTAAAACTCTTCTGATAAATTTAGACTTAA
1 TATATTT--AAAATTAAATTTAAATGTTAACATCCTTAAAACTCTTCTGATAAATTTAGACTTAA
5458486 GGACACATGAAGTATCAAACTTTTGAGAAAAAATTAAACCTGTCAAAATTTAAAATCATTTCAAC
64 GGACACATGAAGTATCAAACTTTTGAGAAAAAATTAAACCTGTCAAAATTTAAAATCATTTCAAC
5458551 TTTTTGTTTTGTATAAGTCATGATTTTTTTATAAAAAAATTCATATATATGTATA
129 TTTTTGTTTTGTATAAGTCATGATTTTTTTATAAAAAAATTCATATATATGTATA
5458606 TATATTTAAAATTAAATTTAAATGTTAACATCCTTAAAACTCTTCTGATAAATTTAGACTTAAGG
1 TATATTTAAAATTAAATTTAAATGTTAACATCCTTAAAACTCTTCTGATAAATTTAGACTTAAGG
5458671 ACACATGAAGTATCAAACTTTTGAGGAAAAAATTAAACCTGTCAAAATTTAAAATCATTTCAACT
66 ACACATGAAGTATCAAACTTTTGA-GAAAAAATTAAACCTGTCAAAATTTAAAATCATTTCAACT
**
5458736 TTTTGTTTTGTATAAGTCATGATTTTTTT-TTTAAAAATTCATATATATGTATA
130 TTTTGTTTTGTATAAGTCATGATTTTTTTATAAAAAAATTCATATATATGTATA
5458789 TATATTTAAAATTAAA
1 TATATTTAAAATTAAA
5458805 AATATAAGTG
Statistics
Matches: 196, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
183 120 0.61
184 69 0.35
185 7 0.04
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (183 bp):
TATATTTAAAATTAAATTTAAATGTTAACATCCTTAAAACTCTTCTGATAAATTTAGACTTAAGG
ACACATGAAGTATCAAACTTTTGAGAAAAAATTAAACCTGTCAAAATTTAAAATCATTTCAACTT
TTTGTTTTGTATAAGTCATGATTTTTTTATAAAAAAATTCATATATATGTATA
Found at i:5467070 original size:93 final size:93
Alignment explanation
Indices: 5466928--5467112 Score: 246
Period size: 93 Copynumber: 2.0 Consensus size: 93
5466918 GTCTAATCAA
* ** * *
5466928 CACTTCCGTTAACTGTTAACGGCTAGTGGCCTAATTGAATACATTTAAATAATTGGGT-GATTTG
1 CACTTCCGTTAACTGTTAACGGCTAGTGGCCTAATTGAATACATGTAAATAATCAGATAG-TCTG
5466992 ATTGACAAGAATTCAAAAATAATGGTCAG
65 ATTGACAAGAATTCAAAAATAATGGTCAG
* * ** *
5467021 CACTTCCGTTAACTGTTAACGGCTAGTGGTCTGATTGAATGTATGTAAATAGTCAGATAGTCTGA
1 CACTTCCGTTAACTGTTAACGGCTAGTGGCCTAATTGAATACATGTAAATAATCAGATAGTCTGA
* *
5467086 TTTACAAGAATTCAAAAATAGTGGTCA
66 TTGACAAGAATTCAAAAATAATGGTCA
5467113 AAATAAAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
93 78 0.99
94 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (93 bp):
CACTTCCGTTAACTGTTAACGGCTAGTGGCCTAATTGAATACATGTAAATAATCAGATAGTCTGA
TTGACAAGAATTCAAAAATAATGGTCAG
Found at i:5470314 original size:19 final size:21
Alignment explanation
Indices: 5470290--5470328 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5470280 CTGAGATGTT
5470290 TTCAAGAG-AA-GACATATTA
1 TTCAAGAGCAATGACATATTA
*
5470309 TTCAAGGGCAATGACATATT
1 TTCAAGAGCAATGACATATT
5470329 CTCCTGGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 2 0.12
21 8 0.47
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (21 bp):
TTCAAGAGCAATGACATATTA
Found at i:5474165 original size:40 final size:40
Alignment explanation
Indices: 5474117--5474193 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
5474107 CGACTGATTT
*
5474117 GGATAGAAAGTCATTCGAACCTAAGTTGAAAATATTTGAA
1 GGATAGAAAGTCATTCGAACCTAAATTGAAAATATTTGAA
*
5474157 GGATAGAAAGTCGTTCGAACCTAAATTGAAAATATTT
1 GGATAGAAAGTCATTCGAACCTAAATTGAAAATATTT
5474194 AAAAATTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (40 bp):
GGATAGAAAGTCATTCGAACCTAAATTGAAAATATTTGAA
Found at i:5494565 original size:35 final size:35
Alignment explanation
Indices: 5494492--5494566 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
5494482 CGTCACTAAC
**
5494492 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
5494527 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
5494562 AGTAA
1 AGTAA
5494567 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:5494671 original size:24 final size:24
Alignment explanation
Indices: 5494644--5494718 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
5494634 CATAATTCAA
*
5494644 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
5494668 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
5494692 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
5494715 GTCA
1 GTCA
5494719 GGATCATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:5494724 original size:23 final size:23
Alignment explanation
Indices: 5494648--5494724 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
5494638 ATTCAAGTCA
*
5494648 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
5494671 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
5494695 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
5494718 AGGATCA
1 AGTATCA
5494725 TAATAGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:5494751 original size:47 final size:47
Alignment explanation
Indices: 5494627--5494740 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
5494617 TATATCAAAA
* * * * *
5494627 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
5494675 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
*
5494721 ATCATAAT-AGAATTCAAGTC
1 ATCA-AATCAGAATCCAAGTC
5494741 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 15 0.27
47 23 0.42
48 17 0.31
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:5495893 original size:18 final size:18
Alignment explanation
Indices: 5495872--5495907 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5495862 CTTCCATCCG
*
5495872 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5495890 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5495908 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:5497202 original size:7 final size:7
Alignment explanation
Indices: 5497182--5497227 Score: 74
Period size: 7 Copynumber: 6.3 Consensus size: 7
5497172 GTCAAAGTTT
5497182 GGTCAAC
1 GGTCAAC
5497189 GGGTCAAC
1 -GGTCAAC
5497197 GGTCAAC
1 GGTCAAC
5497204 GGTCAAC
1 GGTCAAC
5497211 GGGTCAAC
1 -GGTCAAC
5497219 GGTCAAC
1 GGTCAAC
5497226 GG
1 GG
5497228 GTCGGGTCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
7 23 0.62
8 14 0.38
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Done.