Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 158 of 193
Found at i:48787806 original size:30 final size:31
Alignment explanation
Indices: 48787772--48787831 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
48787762 TAAAAGTACA
*
48787772 ATTTTGAA-AAAATTAAATTAAAATTTTATC
1 ATTTTGAAGAAAATTAAAATAAAATTTTATC
* * *
48787802 ATTTTTAAGAAATTTAAAATATAATTTTAT
1 ATTTTGAAGAAAATTAAAATAAAATTTTAT
48787832 TTTTACTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTTTGAAGAAAATTAAAATAAAATTTTATC
Found at i:48788249 original size:31 final size:29
Alignment explanation
Indices: 48788203--48788313 Score: 114
Period size: 31 Copynumber: 3.7 Consensus size: 29
48788193 ATATTAAAAT
* *
48788203 TATATATAAACTTTAATTTAATATGCAATTG
1 TATATATAAATTTTAATTT--GATGCAATTG
*
48788234 TATACATAAATTTTAATTTGATGCAATTG
1 TATATATAAATTTTAATTTGATGCAATTG
* *
48788263 TATATATAAAATTTTAATTGTGATTCAAATG
1 TATATAT-AAATTTTAATT-TGATGCAATTG
* *
48788294 TATATCTGAAACTTTAATTT
1 TATATAT-AAATTTTAATTT
48788314 TAATGTTAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.22
30 12 0.17
31 42 0.61
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (29 bp):
TATATATAAATTTTAATTTGATGCAATTG
Found at i:48789821 original size:24 final size:24
Alignment explanation
Indices: 48789794--48789846 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
48789784 CCTTGGGTGG
*
48789794 TGGTGCTGGACTTGGAGCTTTGTA
1 TGGTGCTGAACTTGGAGCTTTGTA
*
48789818 TGGTGCTGAATTTGGAGCTTTGTA
1 TGGTGCTGAACTTGGAGCTTTGTA
48789842 TGGTG
1 TGGTG
48789847 GTGCAGAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.13, C:0.09, G:0.38, T:0.40
Consensus pattern (24 bp):
TGGTGCTGAACTTGGAGCTTTGTA
Found at i:48789821 original size:27 final size:27
Alignment explanation
Indices: 48789791--48789850 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 27
48789781 AAGCCTTGGG
*
48789791 TGGTGGTGCTGGACTTGGAGCTTTGTA
1 TGGTGGTGCTGAACTTGGAGCTTTGTA
*
48789818 ---TGGTGCTGAATTTGGAGCTTTGTA
1 TGGTGGTGCTGAACTTGGAGCTTTGTA
48789842 TGGTGGTGC
1 TGGTGGTGC
48789851 AGAGGTGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
24 22 0.79
27 6 0.21
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (27 bp):
TGGTGGTGCTGAACTTGGAGCTTTGTA
Found at i:48789892 original size:12 final size:12
Alignment explanation
Indices: 48789874--48789903 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
48789864 CTCACTGGGA
48789874 CTGGAGTTGGAG
1 CTGGAGTTGGAG
*
48789886 TTGGAGTTGGAG
1 CTGGAGTTGGAG
48789898 CTGGAG
1 CTGGAG
48789904 CTAGTATAGG
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:0.17, C:0.07, G:0.50, T:0.27
Consensus pattern (12 bp):
CTGGAGTTGGAG
Found at i:48791939 original size:24 final size:24
Alignment explanation
Indices: 48791911--48791956 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
48791901 AACTTAAATT
48791911 TTAAA-ATCTAAAAAATAAAAAAAA
1 TTAAATATCT-AAAAATAAAAAAAA
*
48791935 TTAAATTTCTAAAAATAAAAAA
1 TTAAATATCTAAAAATAAAAAA
48791957 TTTGAACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
TTAAATATCTAAAAATAAAAAAAA
Found at i:48797546 original size:10 final size:11
Alignment explanation
Indices: 48797531--48797569 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
48797521 TAATATTTTC
48797531 ATAAA-AAATT
1 ATAAATAAATT
48797541 AT-AA-AAA-T
1 ATAAATAAATT
48797549 ATAAATAAATT
1 ATAAATAAATT
48797560 ATAAATAAAT
1 ATAAATAAAT
48797570 AAATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 3 0.12
9 7 0.27
10 5 0.19
11 11 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAATAAATT
Found at i:48797567 original size:15 final size:16
Alignment explanation
Indices: 48797549--48797649 Score: 71
Period size: 16 Copynumber: 6.1 Consensus size: 16
48797539 TTATAAAAAT
48797549 ATAAATAAAT-TATAA
1 ATAAATAAATATATAA
*
48797564 ATAAATAAATATATAT
1 ATAAATAAATATATAA
* * *
48797580 ATATATATATATATAT
1 ATAAATAAATATATAA
*
48797596 ATATATTAAAATTGATATAA
1 ATA-AAT-AAA-T-ATATAA
*
48797616 ACTAAATAAAAATATAA
1 A-TAAATAAATATATAA
*
48797633 ATATTATAAA-ATATAA
1 ATA-AATAAATATATAA
48797649 A
1 A
48797650 AATTCTAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
15 10 0.14
16 30 0.43
17 13 0.19
18 2 0.03
19 4 0.06
20 8 0.12
21 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (16 bp):
ATAAATAAATATATAA
Found at i:48797579 original size:2 final size:2
Alignment explanation
Indices: 48797572--48797601 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48797562 AAATAAATAA
48797572 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
48797602 TAAAATTGAT
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:48799593 original size:38 final size:38
Alignment explanation
Indices: 48799527--48799617 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 38
48799517 TAAATTCTAA
*
48799527 AAAAATCAA-AAAATTATAAAAAATTATTTTTTAAAAAT
1 AAAAATCAATAAAATTATTAAAAATTA-TTTTTAAAAAT
*
48799565 AAAAATCAATAAAATTATTAAAAA-TATTTTTAAAATT
1 AAAAATCAATAAAATTATTAAAAATTATTTTTAAAAAT
48799602 AAAAA--AAT-AAATTATT
1 AAAAATCAATAAAATTATT
48799618 GACATGTCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
34 8 0.16
35 3 0.06
37 15 0.30
38 11 0.22
39 13 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (38 bp):
AAAAATCAATAAAATTATTAAAAATTATTTTTAAAAAT
Found at i:48799608 original size:39 final size:40
Alignment explanation
Indices: 48799506--48799609 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 40
48799496 GTCAACATTT
*
48799506 AATTAATTTTTTAAATTCTAAAAAAATCAAAAAATTATAAAA
1 AATT-ATTTTTTAAAAT-TAAAAAAATCAAAAAATTATAAAA
* *
48799548 AATTATTTTTTAAAA--ATAAAAATCAATAAAATTATTAAA
1 AATTATTTTTTAAAATTAAAAAAATCAA-AAAATTATAAAA
48799587 AA-TA-TTTTTAAAATTAAAAAAAT
1 AATTATTTTTTAAAATTAAAAAAAT
48799610 AAATTATTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
37 9 0.16
38 12 0.22
39 20 0.36
41 10 0.18
42 4 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (40 bp):
AATTATTTTTTAAAATTAAAAAAATCAAAAAATTATAAAA
Found at i:48805337 original size:3 final size:3
Alignment explanation
Indices: 48805329--48805354 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48805319 TAGTTCTATT
48805329 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
48805355 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:48811061 original size:2 final size:2
Alignment explanation
Indices: 48811051--48811105 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
48811041 TTTTCAACAA
* *
48811051 AT AT A- AT AT AT TT AT A- AT A- AT TT A- 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
48811089 A- AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
48811106 ATGCACGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
1 6 0.14
2 37 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48811068 original size:11 final size:11
Alignment explanation
Indices: 48811051--48811105 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
48811041 TTTTCAACAA
48811051 ATATAATATAT
1 ATATAATATAT
*
48811062 TTATAATA-AT
1 ATATAATATAT
*
48811072 TTAATATATATAT
1 AT-ATA-ATATAT
48811085 ATATAATATAT
1 ATATAATATAT
48811096 ATATAATATA
1 ATATAATATA
48811106 ATGCACGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 4 0.10
11 26 0.67
12 6 0.15
13 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATAATATAT
Found at i:48811076 original size:19 final size:20
Alignment explanation
Indices: 48811054--48811105 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
48811044 TCAACAAATA
*
48811054 TAATATATTTATA-ATAATT
1 TAATATATATATATATAATT
*
48811073 TAATATATATATATATAATA
1 TAATATATATATATATAATT
48811093 T-ATATATA-ATATA
1 TAATATATATATATA
48811106 ATGCACGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 19 0.63
20 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATATATATATATAATT
Found at i:48811375 original size:22 final size:22
Alignment explanation
Indices: 48811324--48811383 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
48811314 TTTAAACTAT
*
48811324 TAAATATAATTAAAATATATTAA
1 TAAATA-AATTTAAATATATTAA
**
48811347 TTTATAAATTTAAATAT-TATAA
1 TAAATAAATTTAAATATAT-TAA
48811369 TAAAT-AATTTCAAAT
1 TAAATAAATTT-AAAT
48811384 CATTTTAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 6 0.20
22 20 0.67
23 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATAAATTTAAATATATTAA
Found at i:48814447 original size:15 final size:15
Alignment explanation
Indices: 48814427--48814456 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48814417 TAATTCAAAT
48814427 TTTATTATTTTATTA
1 TTTATTATTTTATTA
*
48814442 TTTATTTTTTTATTA
1 TTTATTATTTTATTA
48814457 AATAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTATTTTATTA
Found at i:48814462 original size:4 final size:4
Alignment explanation
Indices: 48814455--48814481 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
48814445 ATTTTTTTAT
48814455 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
48814482 TGGAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:48814762 original size:15 final size:15
Alignment explanation
Indices: 48814719--48814766 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
48814709 CTAGTTTCCA
48814719 ACCGTCGTCGCCAGCTC
1 ACCGTCGTCGCCA-C-C
** *
48814736 ACCCACGCCGCCACC
1 ACCGTCGTCGCCACC
48814751 ACCGTCGTCGCCACC
1 ACCGTCGTCGCCACC
48814766 A
1 A
48814767 ATTCCGTCGG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 14 0.56
16 1 0.04
17 10 0.40
ACGTcount: A:0.17, C:0.54, G:0.19, T:0.10
Consensus pattern (15 bp):
ACCGTCGTCGCCACC
Found at i:48820686 original size:255 final size:255
Alignment explanation
Indices: 48820235--48820746 Score: 1024
Period size: 255 Copynumber: 2.0 Consensus size: 255
48820225 CGATATACAT
48820235 TTCTCCGATATATTTCTTTTGAAATTCTTTCTGAAATAGGTCCCATGTTATCTGATCCTCCGGTA
1 TTCTCCGATATATTTCTTTTGAAATTCTTTCTGAAATAGGTCCCATGTTATCTGATCCTCCGGTA
48820300 GATGTCGAACCACTGATTCTTACCATAAATAAGCTTCCCTTTGTAGCAACGATACAGCACAAATC
66 GATGTCGAACCACTGATTCTTACCATAAATAAGCTTCCCTTTGTAGCAACGATACAGCACAAATC
48820365 AAGCATTCCCGGGGGGTACATTCTAATTGCTGTAAAATTCTTTTAGTCGACTCCATCCAATTTTC
131 AAGCATTCCCGGGGGGTACATTCTAATTGCTGTAAAATTCTTTTAGTCGACTCCATCCAATTTTC
48820430 AGCTGTTGATGGATCAACTCCTTTCAGACCCATAAATTTAATGGCACCATATTTTCTCAA
196 AGCTGTTGATGGATCAACTCCTTTCAGACCCATAAATTTAATGGCACCATATTTTCTCAA
48820490 TTCTCCGATATATTTCTTTTGAAATTCTTTCTGAAATAGGTCCCATGTTATCTGATCCTCCGGTA
1 TTCTCCGATATATTTCTTTTGAAATTCTTTCTGAAATAGGTCCCATGTTATCTGATCCTCCGGTA
48820555 GATGTCGAACCACTGATTCTTACCATAAATAAGCTTCCCTTTGTAGCAACGATACAGCACAAATC
66 GATGTCGAACCACTGATTCTTACCATAAATAAGCTTCCCTTTGTAGCAACGATACAGCACAAATC
48820620 AAGCATTCCCGGGGGGTACATTCTAATTGCTGTAAAATTCTTTTAGTCGACTCCATCCAATTTTC
131 AAGCATTCCCGGGGGGTACATTCTAATTGCTGTAAAATTCTTTTAGTCGACTCCATCCAATTTTC
48820685 AGCTGTTGATGGATCAACTCCTTTCAGACCCATAAATTTAATGGCACCATATTTTCTCAA
196 AGCTGTTGATGGATCAACTCCTTTCAGACCCATAAATTTAATGGCACCATATTTTCTCAA
48820745 TT
1 TT
48820747 TTTTTATTGG
Statistics
Matches: 257, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 257 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (255 bp):
TTCTCCGATATATTTCTTTTGAAATTCTTTCTGAAATAGGTCCCATGTTATCTGATCCTCCGGTA
GATGTCGAACCACTGATTCTTACCATAAATAAGCTTCCCTTTGTAGCAACGATACAGCACAAATC
AAGCATTCCCGGGGGGTACATTCTAATTGCTGTAAAATTCTTTTAGTCGACTCCATCCAATTTTC
AGCTGTTGATGGATCAACTCCTTTCAGACCCATAAATTTAATGGCACCATATTTTCTCAA
Found at i:48822673 original size:17 final size:18
Alignment explanation
Indices: 48822639--48822674 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
48822629 TGAATTTTTA
48822639 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
48822657 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
48822674 T
1 T
48822675 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:48829122 original size:40 final size:40
Alignment explanation
Indices: 48829074--48829364 Score: 276
Period size: 40 Copynumber: 7.4 Consensus size: 40
48829064 AGTTACAACC
*
48829074 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* ** * *
48829114 TCCGATCTCTTACCCCGATCATG-GGGCAGATTGAAGACCA
1 TCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAA
* * *
48829154 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGTCAA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * *
48829194 TCCAATCTCTTACCCCAATCATG-GGGTAGATTGAA-ACAA
1 TCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAA
* *
48829233 TCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CAA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* *
48829272 T-CAATCTTTTACCCTAACCAGAAGGCAGATTGAAGATC-A
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGA-CAA
** * *
48829311 T-CAGATCTCTTACCCCGACCATG-GGGTAGATT-AAAACAA
1 TCCA-ATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAA
* *
48829350 TCAAATCTTTTACCC
1 TCCAATCTCTTACCC
48829365 CTAAAGTTAT
Statistics
Matches: 211, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
38 34 0.16
39 55 0.26
40 119 0.56
41 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (40 bp):
TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
Found at i:48829207 original size:80 final size:78
Alignment explanation
Indices: 48829074--48829285 Score: 309
Period size: 80 Copynumber: 2.7 Consensus size: 78
48829064 AGTTACAACC
* * * *
48829074 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CAATCCAATCTCTTACCCCAATCATGGG
*
48829139 GCAGATTGAAGACCA
65 GCAGATTGAA-ACAA
*
48829154 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGTCAATCCAATCTCTTACCCCAATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CAATCCAATCTCTTACCCCAATCATGGG
*
48829219 GTAGATTGAAACAA
65 GCAGATTGAAACAA
* *
48829233 TCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCAAT-CAATCTTTTACCC
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCAATCCAATCTCTTACCC
48829286 TAACCAGAAG
Statistics
Matches: 121, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
77 12 0.10
78 4 0.03
79 37 0.31
80 68 0.56
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (78 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCAATCCAATCTCTTACCCCAATCATGGGG
CAGATTGAAACAA
Found at i:48829301 original size:117 final size:119
Alignment explanation
Indices: 48829137--48829364 Score: 347
Period size: 117 Copynumber: 1.9 Consensus size: 119
48829127 CCCGATCATG
* * *
48829137 GGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG-TCAATCCA-AT
1 GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAGATC-AT-CAGAT
* * *
48829200 CTCTTACCCCAATCATGGGGTAGATTGAAACAATCTAATCTTTTACCCTAACCAGA
64 CTCTTACCCCAACCATGGGGTAGATTAAAACAATCAAATCTTTTACCCTAACCAGA
48829256 GGGCAGATTGAAG-CAAT-CAATCTTTTACCCTAACCAGAAGGCAGATTGAAGATCATCAGATCT
1 GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAGATCATCAGATCT
*
48829319 CTTACCCCGACCATGGGGTAGATTAAAACAATCAAATCTTTTACCC
66 CTTACCCCAACCATGGGGTAGATTAAAACAATCAAATCTTTTACCC
48829365 CTAAAGTTAT
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
116 2 0.02
117 80 0.80
118 5 0.05
119 13 0.13
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (119 bp):
GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAGATCATCAGATCT
CTTACCCCAACCATGGGGTAGATTAAAACAATCAAATCTTTTACCCTAACCAGA
Found at i:48832792 original size:12 final size:11
Alignment explanation
Indices: 48832765--48832809 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
48832755 TAATTAAAAG
*
48832765 TTTAAATTGAT
1 TTTAAATTTAT
48832776 TTTAAATTTATT
1 TTTAAATTTA-T
*
48832788 TTTAAATTTAAA
1 TTTAAATTT-AT
48832800 TTTAAATTTA
1 TTTAAATTTA
48832810 ATCAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.33
12 19 0.63
13 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:48832797 original size:6 final size:6
Alignment explanation
Indices: 48832776--48832839 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
48832766 TTAAATTGAT
** *
48832776 TTTAAA TTTATT TTTAAA TTTAAA TTTAAA TTT-AA -TCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
48832822 CTTAAA ATTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA
48832840 AGTCCAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
4 1 0.02
5 4 0.08
6 43 0.90
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:48832819 original size:22 final size:22
Alignment explanation
Indices: 48832791--48832832 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
48832781 ATTTATTTTT
* *
48832791 AAATTTAAATTTAAATTTAATC
1 AAATTTAAACTTAAAATTAATC
48832813 AAATTTAAACTTAAAATTAA
1 AAATTTAAACTTAAAATTAA
48832833 AATTAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTTAAACTTAAAATTAATC
Found at i:48833634 original size:15 final size:15
Alignment explanation
Indices: 48833609--48833651 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48833599 TTGATAATTT
48833609 TATTAAATATTTATAA
1 TATT-AATATTTATAA
*
48833625 TATTAATATTTTTAA
1 TATTAATATTTATAA
*
48833640 TAATAAT-TTTAT
1 TATTAATATTTAT
48833652 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAATATTTATAA
Found at i:48833643 original size:37 final size:39
Alignment explanation
Indices: 48833584--48833657 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
48833574 ACATACATTA
*
48833584 ATAATAGTAAA-TGTTT-TGATAATTTTATTAAATATTT
1 ATAATAGTAAATTGTTTATAATAATTTTATTAAATATTT
*
48833621 ATAATATTAATATT-TTTAATAATAATTTTATTAAATA
1 ATAATAGTAA-ATTGTTT-ATAATAATTTTATTAAATA
48833658 AAAAAAAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 9 0.29
38 4 0.13
39 1 0.03
40 17 0.55
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (39 bp):
ATAATAGTAAATTGTTTATAATAATTTTATTAAATATTT
Found at i:48834079 original size:30 final size:29
Alignment explanation
Indices: 48834039--48834095 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
48834029 GGCTAGAAAG
* *
48834039 TAGCGACCGGTGGATCGCGGTGGTCGGGCA
1 TAGCGACCGGTGAAGCGC-GTGGTCGGGCA
*
48834069 TAGCGGCCGGTGAAGCGCGTGGTCGGG
1 TAGCGACCGGTGAAGCGCGTGGTCGGG
48834096 GGCCTCATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.12, C:0.23, G:0.49, T:0.16
Consensus pattern (29 bp):
TAGCGACCGGTGAAGCGCGTGGTCGGGCA
Found at i:48834552 original size:29 final size:28
Alignment explanation
Indices: 48834519--48834603 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 28
48834509 TAAACTGTCC
*
48834519 AAAAATCACATTTTAACCCTAAAACTTT
1 AAAAATTACATTTTAACCCTAAAACTTT
48834547 AGAAAATTACATTTTAACCCTAAAACTTTT
1 A-AAAATTACATTTTAACCCTAAAAC-TTT
*
48834577 AAAAATTACATTTTACCCCT-AAACTTT
1 AAAAATTACATTTTAACCCTAAAACTTT
48834604 CCTAAATTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
27 3 0.06
28 5 0.09
29 41 0.77
30 4 0.08
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.35
Consensus pattern (28 bp):
AAAAATTACATTTTAACCCTAAAACTTT
Found at i:48834647 original size:58 final size:58
Alignment explanation
Indices: 48834578--48834826 Score: 228
Period size: 58 Copynumber: 4.3 Consensus size: 58
48834568 AAAACTTTTA
* * *
48834578 AAAATTA-CATTTTACCCCTAAACT-TTCCTAAATT-CTA-TTTTAACCCTGATTTTACCC
1 AAAATTACCATTTTACCCCTAAA-TATTCCAAAATTACCATTTTTAA-CCTGATTTCA-CC
* *
48834635 AAAATTACCATTTTACCCCTGAATATTCCAAAATTACCATTTTTGACCTGATTTCACC
1 AAAATTACCATTTTACCCCTAAATATTCCAAAATTACCATTTTTAACCTGATTTCACC
** * *
48834693 AAAATTACCATTTTACCCCCGAATCTTCCAACAA-T-CCATTTTT-ACCTCAATTTCACC
1 AAAATTACCATTTTACCCCTAAATATTCCAA-AATTACCATTTTTAACCT-GATTTCACC
* * * ** *
48834750 AAAATTACCGTTTTACCCTCGAACT-TTCCAAAA-CCCCATTTTTAACCTCGATTTCACTA
1 AAAATTACCATTTTACCC-CTAAATATTCCAAAATTACCATTTTTAACCT-GATTTCAC-C
48834809 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
48834827 TCGAACCTTC
Statistics
Matches: 166, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
56 6 0.04
57 55 0.33
58 70 0.42
59 30 0.18
60 5 0.03
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAATATTCCAAAATTACCATTTTTAACCTGATTTCACC
Found at i:48834665 original size:29 final size:28
Alignment explanation
Indices: 48834578--48834782 Score: 138
Period size: 29 Copynumber: 7.1 Consensus size: 28
48834568 AAAACTTTTA
*
48834578 AAAATTA-CATTTTACCCCTAAACTTTCC
1 AAAATTACCATTTTACCCCTGAA-TTTCC
* * * *
48834606 TAAATT-CTATTTTAACCCTGATTTTACCC
1 AAAATTACCATTTTACCCCTGAATTT--CC
48834635 AAAATTACCATTTTACCCCTGAATATTCC
1 AAAATTACCATTTTACCCCTGAAT-TTCC
***
48834664 AAAATTACCATTTTTGACCTG-ATTTCACC
1 AAAATTACCATTTTACCCCTGAATTT--CC
*
48834693 AAAATTACCATTTTACCCCCGAATCTTCC
1 AAAATTACCATTTTACCCCTGAAT-TTCC
*
48834722 AACAA-T-CCATTTTTA--CCTCAATTTCACC
1 AA-AATTACCA-TTTTACCCCTGAATTT--CC
*
48834750 AAAATTACCGTTTTA-CCCTCGAACTTTCC
1 AAAATTACCATTTTACCCCT-GAA-TTTCC
48834779 AAAA
1 AAAA
48834783 CCCCATTTTT
Statistics
Matches: 139, Mismatches: 20, Indels: 35
0.72 0.10 0.18
Matches are distributed among these distances:
26 2 0.01
27 12 0.09
28 31 0.22
29 67 0.48
30 20 0.14
31 7 0.05
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCTGAATTTCC
Found at i:48834824 original size:59 final size:57
Alignment explanation
Indices: 48834578--48834886 Score: 269
Period size: 59 Copynumber: 5.3 Consensus size: 57
48834568 AAAACTTTTA
* * * * *
48834578 AAAATTA-CATTTTACCCCTAAACTTTCCTAAATTCTA-TTTTAACC-CTGATTTTACCC
1 AAAATTACCATTTTACCCC-GAACTTTCCAAAATCCCATTTTTAACCTC-GATTTCA-CC
* *
48834635 AAAATTACCATTTTACCCCTGAA-TATTCCAAAATTACCATTTTTGACCT-GATTTCACC
1 AAAATTACCATTTTACCCC-GAACT-TTCCAAAA-TCCCATTTTTAACCTCGATTTCACC
*
48834693 AAAATTACCATTTTACCCCCGAA-TCTTCCAACAAT-CCATTTTT-ACCTCAATTTCACC
1 AAAATTACCATTTTA-CCCCGAACT-TTCCAA-AATCCCATTTTTAACCTCGATTTCACC
* * *
48834750 AAAATTACCGTTTTACCCTCGAACTTTCCAAAACCCCATTTTTAACCTCGATTTCACTA
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC-C
* * * *
48834809 AAAATTACCATTTTACCCTCGAACCTTCTAAAATCCTATTTTTAACCCCGAATTTTC-CC
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATCCCATTTTTAACCTCG-A-TTTCACC
*
48834868 AAAGTTA-CATTTTTACCCC
1 AAAATTACCA-TTTTACCCC
48834887 CGAGAGTCAA
Statistics
Matches: 216, Mismatches: 20, Indels: 31
0.81 0.07 0.12
Matches are distributed among these distances:
56 9 0.04
57 56 0.26
58 65 0.30
59 73 0.34
60 9 0.04
61 4 0.02
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
Found at i:48841824 original size:23 final size:23
Alignment explanation
Indices: 48841798--48841911 Score: 126
Period size: 23 Copynumber: 5.0 Consensus size: 23
48841788 TTACCATTCA
*
48841798 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
*
48841821 GCACTTTGTGTGCCTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
48841844 GCACT-TCGTGTGCCTACTGATTT-
1 GCACTGT-GTGTGCCTACTG-TTTC
* * * *
48841867 GCGCTATGTGCGCCTACTGATT-
1 GCACTGTGTGTGCCTACTGTTTC
*
48841889 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
48841912 TCCAACACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
22 20 0.26
23 53 0.69
24 4 0.05
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (23 bp):
GCACTGTGTGTGCCTACTGTTTC
Found at i:48841882 original size:46 final size:45
Alignment explanation
Indices: 48841798--48841911 Score: 142
Period size: 46 Copynumber: 2.5 Consensus size: 45
48841788 TTACCATTCA
* * *
48841798 GCACTGTGTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGTTT
1 GCACTGTGTGTGCTTACTGTTTCGCACTATGTGCGCCTACTGATT
* *
48841843 CGCACT-TCGTGTGCCTACTGATTT-GCGCTATGTGCGCCTACTGATT
1 -GCACTGT-GTGTGCTTACTG-TTTCGCACTATGTGCGCCTACTGATT
48841889 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCTTACTGTTTC
48841912 TCCAACACTT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
44 3 0.05
45 17 0.29
46 35 0.60
47 3 0.05
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (45 bp):
GCACTGTGTGTGCTTACTGTTTCGCACTATGTGCGCCTACTGATT
Found at i:48849822 original size:48 final size:48
Alignment explanation
Indices: 48849751--48849917 Score: 253
Period size: 48 Copynumber: 3.5 Consensus size: 48
48849741 CTTCGAACCC
* *
48849751 AGCTTCCTGATAAGACACTGAGAGGCAGGTTGAAGCAATAAAAAGGTT
1 AGCTTCCAGATGAGACACTGAGAGGCAGGTTGAAGCAATAAAAAGGTT
48849799 AGCTTCCAGATGAGACACTGAGAGGCAGGTTGAAGCAATAAAAAGGTT
1 AGCTTCCAGATGAGACACTGAGAGGCAGGTTGAAGCAATAAAAAGGTT
* * * **
48849847 AGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAATAATAAAAAGGTT
1 AGCTTCCAGATGAGACACTGAGAGGCAGGTTGAAGCAATAAAAAGGTT
* *
48849895 AGCTTCCTGATGAGACACAGAGA
1 AGCTTCCAGATGAGACACTGAGA
48849918 AGTGGACCAA
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 110 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (48 bp):
AGCTTCCAGATGAGACACTGAGAGGCAGGTTGAAGCAATAAAAAGGTT
Found at i:48850178 original size:195 final size:196
Alignment explanation
Indices: 48849846--48850361 Score: 752
Period size: 195 Copynumber: 2.6 Consensus size: 196
48849836 ATAAAAAGGT
* * *
48849846 TAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAATAATAAAAAGGTTAGCTTCCTGATGAGAC
1 TAGCTTCCATATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGAC
*
48849911 ACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAATGAGCGAGG
66 ACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACGAGCGAGG
*
48849976 CGGTCATCTTCTTGATGAGATACAAAG-AAGA-ATGCCAACTCAA-AACACGAGCAAATCTTCGA
131 CGGTCATCTTCCTGATGAGATACAAAGAAAGACA--CCAACTCAACAACACGAGCAAATCTTCGA
48850038 ACC
194 ACC
* * *
48850041 TAGCTTCCATATGAGATACTGAGAAGCAAGTTGAAGCAATAAAATGGTTAGCTTCCTGATGAGAC
1 TAGCTTCCATATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGAC
* *
48850106 ACAGAGAAATGGACCAAATTCGTCTTCCTAAGGAGATCCAGAGAAGCGAATTAAAACGAGCGAGG
66 ACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACGAGCGAGG
* ** *
48850171 CGGTCATCTTCCTGATGAGATACAGAGAAAGACACCAACTCAACGCTCAATGCGAGCAAATCTTT
131 CGGTCATCTTCCTGATGAGATACAAAGAAAGACACCAACTCAA----CAACACGAGCAAATCTTC
48850236 GAACC
192 GAACC
* * * *
48850241 CAACTTCC-TGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCGTCCTGATGAGA
1 TAGCTTCCAT-ATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGA
* * *
48850305 TACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCTAGAGAAGCGAATTAAAA
65 CACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
48850362 TAGATAATTG
Statistics
Matches: 287, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
195 155 0.54
196 4 0.01
197 1 0.00
199 1 0.00
200 126 0.44
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.20
Consensus pattern (196 bp):
TAGCTTCCATATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGAC
ACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACGAGCGAGG
CGGTCATCTTCCTGATGAGATACAAAGAAAGACACCAACTCAACAACACGAGCAAATCTTCGAAC
C
Found at i:48850796 original size:16 final size:17
Alignment explanation
Indices: 48850770--48850804 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
48850760 ATTGATTTTA
*
48850770 AATCTAAATTTAAATTT
1 AATCTAAATTTAAACTT
48850787 AATC-AAATTTAAACTT
1 AATCTAAATTTAAACTT
48850803 AA
1 AA
48850805 AATTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
AATCTAAATTTAAACTT
Found at i:48850799 original size:22 final size:22
Alignment explanation
Indices: 48850769--48850810 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
48850759 AATTGATTTT
* *
48850769 AAATCTAAATTTAAATTTAATC
1 AAATCTAAACTTAAAATTAATC
*
48850791 AAATTTAAACTTAAAATTAA
1 AAATCTAAACTTAAAATTAA
48850811 AATTAAAAGT
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:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATCTAAACTTAAAATTAATC
Found at i:48851606 original size:15 final size:15
Alignment explanation
Indices: 48851581--48851623 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48851571 TTGATAATTT
48851581 TATTAAATATTTATAA
1 TATT-AATATTTATAA
*
48851597 TATTAATATTTTTAA
1 TATTAATATTTATAA
*
48851612 TAATAAT-TTTAT
1 TATTAATATTTAT
48851624 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAATATTTATAA
Found at i:48851615 original size:37 final size:39
Alignment explanation
Indices: 48851556--48851629 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
48851546 ACATACATTA
*
48851556 ATAATAGTAAA-TGTTT-TGATAATTTTATTAAATATTT
1 ATAATAGTAAATTGTTTATAATAATTTTATTAAATATTT
*
48851593 ATAATATTAATATT-TTTAATAATAATTTTATTAAATA
1 ATAATAGTAA-ATTGTTT-ATAATAATTTTATTAAATA
48851630 AAAAAAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 9 0.29
38 4 0.13
39 1 0.03
40 17 0.55
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (39 bp):
ATAATAGTAAATTGTTTATAATAATTTTATTAAATATTT
Found at i:48852534 original size:29 final size:29
Alignment explanation
Indices: 48852493--48852570 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
48852483 TAAACTGTCC
* *
48852493 AAAAATCACATTTTGACCCCAAAA-TTTT
1 AAAAATTACATTTTAACCCCAAAACTTTT
*
48852521 AAAAAATTACATTTTAACCCTAAAACTTTT
1 -AAAAATTACATTTTAACCCCAAAACTTTT
*
48852551 AAAAATTACATTTTTACCCC
1 AAAAATTACATTTTAACCCC
48852571 CGAACTTTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 39 0.91
30 4 0.09
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCCAAAACTTTT
Found at i:48852688 original size:29 final size:28
Alignment explanation
Indices: 48852609--48852710 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
48852599 CCGATTTTGC
*
48852609 CCAAAATTACCATTTTACCCTCAAATCTT
1 CCAAAATTACCATTTTACCC-CTAATCTT
* *
48852638 CTAAAATT-CCATTTTTGA-CCCTAATTTT
1 CCAAAATTACCA-TTTT-ACCCCTAATCTT
48852666 ACCAAAATTACCATTTTACCCCTGAATCTT
1 -CCAAAATTACCATTTTACCCCT-AATCTT
*
48852696 CCAACATT-CCATTTT
1 CCAAAATTACCATTTT
48852711 TGACCTCGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
28 17 0.28
29 35 0.57
30 9 0.15
ACGTcount: A:0.31, C:0.28, G:0.02, T:0.38
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCTAATCTT
Found at i:48852705 original size:117 final size:117
Alignment explanation
Indices: 48852550--48852827 Score: 277
Period size: 117 Copynumber: 2.4 Consensus size: 117
48852540 CTAAAACTTT
48852550 TAAAAATTA-CATTTTTACCCCCGAACTTTCCTAAATTCCATTTTAAACCCCGATTTTGC-CCAA
1 TAAAAATTACCA-TTTTACCCCCGAACTTTCCTAAATTCCATTTTAAACCCCGA-TTT-CACCAA
* * *
48852613 AATTACCATTTTACCCTCAAA-TCTTCTAAAA-TTCCATTTTTGACC-CTAATTTTAC
63 AATTACCATTTTACCCTCAAACT-TTCCAAAACCT-CATTTTTAACCTCT-ATTTTAC
* * ** *
48852668 -CAAAATTACCATTTTACCCCTGAA-TCTTCC-AACATTCCATTTTTGACCTCGATTTCACCAAA
1 TAAAAATTACCATTTTACCCCCGAACT-TTCCTAA-ATTCCATTTTAAACCCCGATTTCACCAAA
* * *
48852730 ATTACCGTTTTACTCTCGAACTTTCCAAAACCTCATTTTTAACCTCTATTTTAC
64 ATTACCATTTTACCCTCAAACTTTCCAAAACCTCATTTTTAACCTCTATTTTAC
* * * *
48852784 TAAAAATTACCATTTTATCCCCAAACCTT-CTAAAATCCCATTTT
1 TAAAAATTACCATTTTACCCCCGAACTTTCCT-AAATTCCATTTT
48852828 TAACGTTAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
115 1 0.01
116 53 0.40
117 74 0.56
118 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (117 bp):
TAAAAATTACCATTTTACCCCCGAACTTTCCTAAATTCCATTTTAAACCCCGATTTCACCAAAAT
TACCATTTTACCCTCAAACTTTCCAAAACCTCATTTTTAACCTCTATTTTAC
Found at i:48852828 original size:59 final size:57
Alignment explanation
Indices: 48852552--48852831 Score: 235
Period size: 58 Copynumber: 4.8 Consensus size: 57
48852542 AAAACTTTTA
* * * *
48852552 AAAATTA-CATTTTTACCCCCGAACTTTCCT-AAATTCCATTTTAAACCCCGATTTTGCCC
1 AAAATTACCA-TTTTA-CCCCGAACCTT-CTAAAATTCCATTTTTAACCTCGATTTT-ACC
* * * *
48852611 AAAATTACCATTTTACCCTCAAATCTTCTAAAATTCCATTTTTGACC-CTAATTTTACC
1 AAAATTACCATTTTACCC-CGAACCTTCTAAAATTCCATTTTTAACCTC-GATTTTACC
* * * * *
48852669 AAAATTACCATTTTACCCCTGAATCTTCCAACATTCCATTTTTGACCTCGATTTCACC
1 AAAATTACCATTTTACCCC-GAACCTTCTAAAATTCCATTTTTAACCTCGATTTTACC
* * * * * * *
48852727 AAAATTACCGTTTTACTCTCGAACTTTCCAAAA-CCTCATTTTTAACCTCTATTTTACTA
1 AAAATTACCATTTTAC-CCCGAACCTTCTAAAATTC-CATTTTTAACCTCGATTTTAC-C
* *
48852786 AAAATTACCATTTTATCCCCAAACCTTCTAAAATCCCATTTTTAAC
1 AAAATTACCATTTTA-CCCCGAACCTTCTAAAATTCCATTTTTAAC
48852832 GTTAAATTTT
Statistics
Matches: 183, Mismatches: 27, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
57 2 0.01
58 100 0.55
59 76 0.42
60 5 0.03
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCGAACCTTCTAAAATTCCATTTTTAACCTCGATTTTACC
Found at i:48862759 original size:20 final size:19
Alignment explanation
Indices: 48862734--48862772 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
48862724 AAAAATTCCT
48862734 TTTATTATTAAATAGATTAA
1 TTTATTATTAAATA-ATTAA
* *
48862754 TTTATTTTTGAATAATTAA
1 TTTATTATTAAATAATTAA
48862773 AAAAATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTATTATTAAATAATTAA
Found at i:48864947 original size:17 final size:18
Alignment explanation
Indices: 48864915--48864948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48864905 TTCCAATAAT
48864915 TTAAAAATGAATTACTGC
1 TTAAAAATGAATTACTGC
*
48864933 TTAAACATG-ATTACTG
1 TTAAAAATGAATTACTG
48864949 TCAAAACGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TTAAAAATGAATTACTGC
Found at i:48869969 original size:28 final size:29
Alignment explanation
Indices: 48869938--48869998 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
48869928 AAAATGCAAT
* * *
48869938 TTTTGGATAC-TCGAGGGCAAAACGGTAA
1 TTTTAGATACTTCGAGGGAAAAACAGTAA
*
48869966 TTTTAGATACTTCGAGGGAAAAATAGTAA
1 TTTTAGATACTTCGAGGGAAAAACAGTAA
48869995 TTTT
1 TTTT
48869999 TGGAGGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (29 bp):
TTTTAGATACTTCGAGGGAAAAACAGTAA
Found at i:48870011 original size:29 final size:28
Alignment explanation
Indices: 48869979--48870060 Score: 65
Period size: 29 Copynumber: 2.8 Consensus size: 28
48869969 TAGATACTTC
*
48869979 GAGGGAAAAATAGTAATTTTTGGAGGTTT
1 GAGGGAAAAAT-GTAATTTTTGGAGATTT
* * * *
48870008 GAGGTTAAAAATGGAAATTTTGGATATTT
1 GAGG-GAAAAATGTAATTTTTGGAGATTT
* * *
48870037 GGGGGTAAAATGGTATTTTTTGGA
1 GAGGGAAAAAT-GTAATTTTTGGA
48870061 AAGTTCGGGA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
28 5 0.12
29 29 0.73
30 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (28 bp):
GAGGGAAAAATGTAATTTTTGGAGATTT
Found at i:48870117 original size:60 final size:59
Alignment explanation
Indices: 48869966--48870175 Score: 185
Period size: 59 Copynumber: 3.5 Consensus size: 59
48869956 AAAACGGTAA
* * * * * *
48869966 TTTTAGATACTTCGAGGGAAAAATAGTAATTTTTGG-AGGTTTGAGG-TTAAAAATGGAAA-
1 TTTTAGACA-TTCG-GGGTAAAATAGTAATTTTTGGAAAGTTCG-GGATCAAAAATAGAAAT
* * * * * *
48870025 TTTTGGATATTTGGGGGTAAAATGGTATTTTTTGGAAAGTTCGGGATCAAAAAAAGAAAT
1 TTTTAGACA-TTCGGGGTAAAATAGTAATTTTTGGAAAGTTCGGGATCAAAAATAGAAAT
**
48870085 TTTTAGACATTCGGGAGTAAAATAGTAATTTTTGGAAAGTTCAAGATCAAAAATA-AAAT
1 TTTTAGACATTCGGG-GTAAAATAGTAATTTTTGGAAAGTTCGGGATCAAAAATAGAAAT
* * *
48870144 TCTTAGACATCCGAGGGTAAAATGGTAATTTT
1 TTTTAGACATTCG-GGGTAAAATAGTAATTTT
48870176 AAAAATTTCG
Statistics
Matches: 124, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
58 20 0.16
59 61 0.49
60 43 0.35
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (59 bp):
TTTTAGACATTCGGGGTAAAATAGTAATTTTTGGAAAGTTCGGGATCAAAAATAGAAAT
Found at i:48870166 original size:59 final size:59
Alignment explanation
Indices: 48870038--48870175 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 59
48870028 TGGATATTTG
* ** * *
48870038 GGGGTAAAATGGTATTTTTTGGAAAGTTCGGGATCAAAAAAAGAAATTTTTAGACATTC
1 GGGGTAAAATGGTAATTTTTGGAAAGTTCAAGATCAAAAAAAGAAATTCTTAGACATCC
* *
48870097 GGGAGTAAAATAGTAATTTTTGGAAAGTTCAAGATCAAAAATA-AAATTCTTAGACATCC
1 GGG-GTAAAATGGTAATTTTTGGAAAGTTCAAGATCAAAAAAAGAAATTCTTAGACATCC
48870156 GAGGGTAAAATGGTAATTTT
1 G-GGGTAAAATGGTAATTTT
48870176 AAAAATTTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 33 0.48
60 36 0.52
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGAAAGTTCAAGATCAAAAAAAGAAATTCTTAGACATCC
Found at i:48870255 original size:30 final size:29
Alignment explanation
Indices: 48870191--48870381 Score: 176
Period size: 29 Copynumber: 6.6 Consensus size: 29
48870181 TTTCGGAGGT
* *
48870191 TAAAAATGGAA-TTTTGGAAGTTGAGGGGG
1 TAAAAATGTAATTTTTGGAAGTTTA-GGGG
*
48870220 T-AAAATGTAATTTTTGGAAAGTTTAGGGT
1 TAAAAATGTAATTTTTGG-AAGTTTAGGGG
* *
48870249 TAAAAATGTAATATTT-AAATGTTTAGGGG
1 TAAAAATGTAATTTTTGGAA-GTTTAGGGG
* * **
48870278 TAAAAATGTGATTTTTGTGAAGTTCAAAGG
1 TAAAAATGTAATTTTTG-GAAGTTTAGGGG
* *
48870308 AAAAAATGTAATTTTTAGG-AGTTCAGGGG
1 TAAAAATGTAATTTTT-GGAAGTTTAGGGG
* *
48870337 AAAAAATGTAAATTTTGTGAAGTTTAGGGG
1 TAAAAATGTAATTTTTG-GAAGTTTAGGGG
48870367 T-AAAATGTAATTTTT
1 TAAAAATGTAATTTTT
48870382 AGAAAGATCG
Statistics
Matches: 133, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
28 11 0.08
29 70 0.53
30 49 0.37
31 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (29 bp):
TAAAAATGTAATTTTTGGAAGTTTAGGGG
Found at i:48870284 original size:59 final size:58
Alignment explanation
Indices: 48870191--48870385 Score: 193
Period size: 59 Copynumber: 3.3 Consensus size: 58
48870181 TTTCGGAGGT
* * *
48870191 TAAAAATGGAA-TTTTGGAAGTTGAGGGGGT-AAAATGTAATTTTTG-GAAAGTTTAGGG
1 TAAAAATGTAATTTTTAGAAGTTCA-GGGGTAAAAATGTAATTTTTGTG-AAGTTTAGGG
* * * * *
48870248 TTAAAAATGTAATATTTA-AATGTTTAGGGGTAAAAATGTGATTTTTGTGAAGTTCAAAGG
1 -TAAAAATGTAATTTTTAGAA-GTTCAGGGGTAAAAATGTAATTTTTGTGAAGTT-TAGGG
* * * *
48870308 AAAAAATGTAATTTTTAGGAGTTCAGGGGAAAAAATGTAAATTTTGTGAAGTTTAGGGG
1 TAAAAATGTAATTTTTAGAAGTTCAGGGGTAAAAATGTAATTTTTGTGAAGTTTA-GGG
48870367 T-AAAATGTAATTTTTAGAA
1 TAAAAATGTAATTTTTAGAA
48870386 AGATCGAGGT
Statistics
Matches: 112, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
58 35 0.31
59 72 0.64
60 5 0.04
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.35
Consensus pattern (58 bp):
TAAAAATGTAATTTTTAGAAGTTCAGGGGTAAAAATGTAATTTTTGTGAAGTTTAGGG
Found at i:48871460 original size:3 final size:3
Alignment explanation
Indices: 48871454--48871501 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
48871444 TTATTTAATA
*
48871454 ATT ATT AAT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
48871501 A
1 A
48871502 ATGTTATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:48872186 original size:18 final size:17
Alignment explanation
Indices: 48872147--48872239 Score: 105
Period size: 18 Copynumber: 5.3 Consensus size: 17
48872137 ACTTTTATTC
*
48872147 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
* *
48872164 TTTTACATTTAAATATAA
1 ATTTAAATTTAAA-ATAA
* *
48872182 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
48872199 ATTTAAATTCTAAAACAA
1 ATTTAAATT-TAAAATAA
48872217 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
48872235 ATTTA
1 ATTTA
48872240 GTTTGAGTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
17 22 0.35
18 40 0.65
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:48872224 original size:6 final size:6
Alignment explanation
Indices: 48872147--48872239 Score: 68
Period size: 6 Copynumber: 15.8 Consensus size: 6
48872137 ACTTTTATTC
* * * *
48872147 ATTTAA ATTTAGA A--TAA TTTTAC ATTTAA ATATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** **
48872194 A-TTAA ATTTAA ATTCTAA A-ACAA ATTTAA ATTTAA AAATAA ATTTA
1 ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA
48872240 GTTTGAGTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
4 1 0.02
5 10 0.15
6 49 0.74
7 6 0.09
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:48883964 original size:42 final size:43
Alignment explanation
Indices: 48883918--48884019 Score: 106
Period size: 42 Copynumber: 2.4 Consensus size: 43
48883908 ATATAATTTT
48883918 AAAAAATATATTTTT-ATTTAATTTAGGA-TTTTTTT-TAAGA
1 AAAAAATATATTTTTGATTTAATTTAGGAGTTTTTTTGTAAGA
* * *
48883958 AGAAAAAT-TGATTTTTGGTTTAGTTTATGAGTTTTTTTGTAAGA
1 A-AAAAATAT-ATTTTTGATTTAATTTAGGAGTTTTTTTGTAAGA
* *
48884002 ACAAAAT-TATATTTGATT
1 AAAAAATATATTTTTGATT
48884020 AAGATAAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
40 2 0.04
41 12 0.24
42 18 0.35
43 13 0.25
44 6 0.12
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (43 bp):
AAAAAATATATTTTTGATTTAATTTAGGAGTTTTTTTGTAAGA
Found at i:48883972 original size:41 final size:44
Alignment explanation
Indices: 48883919--48884015 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
48883909 TATAATTTTA
*
48883919 AAAAATATATTTTT-ATTTAATTTAGGA-TTTTTTT-TAAGAAG
1 AAAAATATATTTTTGATTTAATTTAGGAGTTTTTTTGTAAGAAC
* * *
48883960 AAAAAT-TGATTTTTGGTTTAGTTTATGAGTTTTTTTGTAAGAAC
1 AAAAATAT-ATTTTTGATTTAATTTAGGAGTTTTTTTGTAAGAAC
*
48884004 AAAATTATATTT
1 AAAAATATATTT
48884016 GATTAAGATA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.02
41 12 0.26
42 10 0.22
43 7 0.15
44 15 0.33
45 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (44 bp):
AAAAATATATTTTTGATTTAATTTAGGAGTTTTTTTGTAAGAAC
Found at i:48884209 original size:18 final size:18
Alignment explanation
Indices: 48884186--48884223 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
48884176 TAATATAGTT
*
48884186 TTATTCG-GTTTATTTGAA
1 TTATTCGAG-TTATTCGAA
48884204 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
48884222 TT
1 TT
48884224 CGAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:48884302 original size:14 final size:14
Alignment explanation
Indices: 48884285--48884334 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
48884275 TTCGTTTAAC
*
48884285 TCGAATAACTCGAT
1 TCGAATAATTCGAT
48884299 TCGAATAATTCGAAAT
1 TCGAATAATTCG--AT
**
48884315 TCGAATTTTTCGAT
1 TCGAATAATTCGAT
48884329 TCGAAT
1 TCGAAT
48884335 CGAATTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 19 0.61
16 12 0.39
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (14 bp):
TCGAATAATTCGAT
Found at i:48887221 original size:6 final size:6
Alignment explanation
Indices: 48887210--48887234 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48887200 AGAATAAAAG
48887210 CAATTT CAATTT CAATTT CAATTT C
1 CAATTT CAATTT CAATTT CAATTT C
48887235 CATATTCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (6 bp):
CAATTT
Found at i:48892957 original size:23 final size:23
Alignment explanation
Indices: 48892902--48893039 Score: 111
Period size: 23 Copynumber: 6.0 Consensus size: 23
48892892 AGCGCGTCTC
48892902 GTGCTCTCTGATTAGCA-TTGTGT
1 GTGCTCTCTGATTAGCACTT-TGT
* *
48892925 GTGGTATCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
48892948 ATGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
** * * *
48892971 GTATTCTATGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
48892994 GTGCTCTCTGTTGCCTAGCAC-TTAT
1 GTGCTCTCTGAT---TAGCACTTTGT
*
48893019 GTGCTCTCTG-TTAGTACTTTG
1 GTGCTCTCTGATTAGCACTTTG
48893040 GCACTCTCTG
Statistics
Matches: 90, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
21 5 0.06
22 2 0.02
23 62 0.69
24 3 0.03
25 12 0.13
26 6 0.07
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:48915564 original size:59 final size:57
Alignment explanation
Indices: 48915433--48915566 Score: 180
Period size: 59 Copynumber: 2.3 Consensus size: 57
48915423 TAACAATAAC
* *
48915433 AATAATTATATTAAAAATATATTTAAATTATATATTATTTTATTAAATTATATTTAAT
1 AATAATTATATT-AAAATACAATTAAATTATATATTATTTTATTAAATTATATTTAAT
* * *
48915491 AATAATTATGTTAAAATACAATTAAATTATTTATTATTTATTATTAATTTATATTTAAT
1 AATAATTATATTAAAATACAATTAAATTATATATTA-TT-TTATTAAATTATATTTAAT
48915550 AATAATCT-TATTAAAAT
1 AATAAT-TATATTAAAAT
48915567 TTAATAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 21 0.31
58 13 0.19
59 32 0.48
60 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (57 bp):
AATAATTATATTAAAATACAATTAAATTATATATTATTTTATTAAATTATATTTAAT
Found at i:48915744 original size:16 final size:16
Alignment explanation
Indices: 48915723--48915792 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
48915713 TAAATTACTG
*
48915723 ATTACAACCCTATTCC
1 ATTACAACTCTATTCC
** *
48915739 ATTACAGTTCTATTTC
1 ATTACAACTCTATTCC
* *
48915755 ATTACAACTTTATTCT
1 ATTACAACTCTATTCC
48915771 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
48915787 ATTACA
1 ATTACA
48915793 GTGAACCAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.31, C:0.26, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:48917396 original size:5 final size:5
Alignment explanation
Indices: 48917386--48917413 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
48917376 CCACCCACTT
48917386 GCCAA GCCAA GCCAA GCCAA GCCAA GCC
1 GCCAA GCCAA GCCAA GCCAA GCCAA GCC
48917414 TGTGGTCCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.43, G:0.21, T:0.00
Consensus pattern (5 bp):
GCCAA
Found at i:48920394 original size:40 final size:40
Alignment explanation
Indices: 48920350--48920467 Score: 184
Period size: 40 Copynumber: 3.0 Consensus size: 40
48920340 TGTGATAAAG
*
48920350 ACTTATAACTCGGTAGAGCATAAGATTGTTAAAAAGGAAA
1 ACTTATGACTCGGTAGAGCATAAGATTGTTAAAAAGGAAA
**
48920390 ACTTATGACTCGGTAGAGCATAAGATTGTT-AAAAGGAGT
1 ACTTATGACTCGGTAGAGCATAAGATTGTTAAAAAGGAAA
* *
48920429 ACTTATGACTCGGTAAAGCATAATATTGTTAAAAAGGAA
1 ACTTATGACTCGGTAGAGCATAAGATTGTTAAAAAGGAA
48920468 GACACATAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
39 35 0.49
40 36 0.51
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (40 bp):
ACTTATGACTCGGTAGAGCATAAGATTGTTAAAAAGGAAA
Found at i:48921177 original size:21 final size:21
Alignment explanation
Indices: 48921153--48921209 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
48921143 TAGAAGTAAG
* *
48921153 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
48921174 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
48921195 ACTTGTATCGGTAGA
1 ACTTGTATCGGTAGA
48921210 GGTCTGCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:48931949 original size:15 final size:16
Alignment explanation
Indices: 48931924--48931954 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
48931914 TCATCCTTTA
48931924 AAAAATATTAAAAAAT
1 AAAAATATTAAAAAAT
48931940 AAAAAT-TTAAAAAAT
1 AAAAATATTAAAAAAT
48931955 GTGTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATATTAAAAAAT
Found at i:48934793 original size:57 final size:57
Alignment explanation
Indices: 48934680--48934793 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 57
48934670 CTCCACTCCA
* * ** **
48934680 ACATTTACAGTTTCACCTCCATTTATTTGAACGGAAGTGGAGCTTTTATTGTGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTTTTATTCAGCTGC
*
48934737 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTTTTATTCAGCTGC
48934794 TCTTCAACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
57 48 0.98
58 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (57 bp):
ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTTTTATTCAGCTGC
Found at i:48935873 original size:2 final size:2
Alignment explanation
Indices: 48935826--48935853 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48935816 ATATATATAT
48935826 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
48935854 TACCAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48942544 original size:2 final size:2
Alignment explanation
Indices: 48942537--48942589 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
48942527 CATGGGTAGC
48942537 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
48942579 GA GA GA GA GA G
1 GA GA GA GA GA G
48942590 GAGTTTCATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:48943673 original size:56 final size:56
Alignment explanation
Indices: 48943587--48943697 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 56
48943577 ATTTCTTGAA
* * *
48943587 CCATAATAATATTCTATAATATCCCATTAGGAATCAAATTGCTAAGAGATAATATT
1 CCATAATAATATCCTATAATATCCCATTAGGAATCAAATTGCTAAAAAATAATATT
*
48943643 CCATAATAATATCCTATAATATCCCATTAGGAATTAAATTGCTAAAAAATAATAT
1 CCATAATAATATCCTATAATATCCCATTAGGAATCAAATTGCTAAAAAATAATAT
48943698 CTAACAACCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (56 bp):
CCATAATAATATCCTATAATATCCCATTAGGAATCAAATTGCTAAAAAATAATATT
Found at i:48953495 original size:85 final size:85
Alignment explanation
Indices: 48953352--48953522 Score: 218
Period size: 85 Copynumber: 2.0 Consensus size: 85
48953342 GAATGGCTCT
* * * *
48953352 AGTGGTAAAAAAGATGTTATACATTTTAGAAAATTCGGATTCGAGCACCTGTGTGTACAAGGTGT
1 AGTGGTAAAAAAGATGTTATACATCTTAAAAAATTCAGATTCGAGCACCTGTGTGTACAAAGTGT
*
48953417 ATGTACGTTGTTTTCTATTA
66 ATGTACGTTATTTTCTATTA
* * * *
48953437 AGTGGTAAAAATGATGTTATTCATCTTAAAAAATTCA-AGTTCGAGTATCTGTGTGTACAAAGTG
1 AGTGGTAAAAAAGATGTTATACATCTTAAAAAATTCAGA-TTCGAGCACCTGTGTGTACAAAGTG
* * *
48953501 TGTGTGCGTTATTTTTTATTA
65 TATGTACGTTATTTTCTATTA
48953522 A
1 A
48953523 AAAAATATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 1 0.01
85 72 0.99
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (85 bp):
AGTGGTAAAAAAGATGTTATACATCTTAAAAAATTCAGATTCGAGCACCTGTGTGTACAAAGTGT
ATGTACGTTATTTTCTATTA
Found at i:48968996 original size:18 final size:18
Alignment explanation
Indices: 48968956--48968998 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
48968946 TATTTACACT
* **
48968956 AATTTGATTCGAATTATCC
1 AATTT-ATTCAAATTATAA
48968975 AATTTATTCAAATTATAA
1 AATTTATTCAAATTATAA
48968993 AATTTA
1 AATTTA
48968999 ACTCGACTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (18 bp):
AATTTATTCAAATTATAA
Found at i:48994093 original size:28 final size:28
Alignment explanation
Indices: 48994040--48994120 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
48994030 CTTTCAAGTG
*
48994040 TTGGGTTTTAGATTTTTGAATTTTGAATT
1 TTGGATTTTAGA-TTTTGAATTTTGAATT
*
48994069 TTGGATTTTAGATTTTGGATTTTGAATT
1 TTGGATTTTAGATTTTGAATTTTGAATT
* * *
48994097 TTGAATTTTAAATTTT-AACTTTGA
1 TTGGATTTTAGATTTTGAATTTTGA
48994121 GATATAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.13
28 29 0.63
29 11 0.24
ACGTcount: A:0.25, C:0.01, G:0.17, T:0.57
Consensus pattern (28 bp):
TTGGATTTTAGATTTTGAATTTTGAATT
Found at i:48994114 original size:7 final size:7
Alignment explanation
Indices: 48994053--48994112 Score: 77
Period size: 7 Copynumber: 8.6 Consensus size: 7
48994043 GGTTTTAGAT
48994053 TTTTGAA
1 TTTTGAA
48994060 TTTTGAA
1 TTTTGAA
*
48994067 TTTTGGA
1 TTTTGAA
48994074 TTTT-AGA
1 TTTTGA-A
*
48994081 TTTTGGA
1 TTTTGAA
48994088 TTTTGAA
1 TTTTGAA
48994095 TTTTGAA
1 TTTTGAA
*
48994102 TTTTAAA
1 TTTTGAA
48994109 TTTT
1 TTTT
48994113 AACTTTGAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (7 bp):
TTTTGAA
Found at i:49004069 original size:17 final size:19
Alignment explanation
Indices: 49004041--49004080 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
49004031 ACGTAAATAA
*
49004041 AAAATAATAAAAATTA-TT
1 AAAATAATAAAAAATATTT
49004059 AAAAT-ATAAAAAATATTT
1 AAAATAATAAAAAATATTT
49004077 AAAA
1 AAAA
49004081 ATTATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAATAAAAAATATTT
Found at i:49004150 original size:17 final size:16
Alignment explanation
Indices: 49004122--49004160 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
49004112 AAGACACATG
49004122 ATAAAAAT-AAAAATT
1 ATAAAAATAAAAAATT
49004137 ATTAAAAATAAAAAAATT
1 A-TAAAAAT-AAAAAATT
49004155 ATAAAA
1 ATAAAA
49004161 TTTAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 7 0.33
17 5 0.24
18 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATAAAAAATT
Found at i:49004160 original size:16 final size:16
Alignment explanation
Indices: 49004123--49004161 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
49004113 AGACACATGA
*
49004123 TAAAAATAAAAATTAT
1 TAAAAATAAAAATAAT
49004139 TAAAAATAAAAA-AAT
1 TAAAAATAAAAATAAT
49004154 TATAAAAT
1 TA-AAAAT
49004162 TTAAATATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAATAAAAATAAT
Found at i:49007563 original size:25 final size:26
Alignment explanation
Indices: 49007535--49007587 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
49007525 ATCATATAAA
49007535 AAATTTCAATAAATA-AAAAAT-ATAT
1 AAATTT-AATAAATATAAAAATAATAT
* *
49007560 AAATTTATTAAATATTAAAATAATAT
1 AAATTTAATAAATATAAAAATAATAT
49007586 AA
1 AA
49007588 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 11 0.46
26 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATTTAATAAATATAAAAATAATAT
Found at i:49007996 original size:28 final size:28
Alignment explanation
Indices: 49007963--49008023 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
49007953 AATAATTAAT
*
49007963 AAAATTATATAT-TATATATTAAA-ATATA
1 AAAATTAAATATCTA-AT-TTAAACATATA
*
49007991 AAAATTAAATCTCTAATTTAAACATATA
1 AAAATTAAATATCTAATTTAAACATATA
49008019 AAAAT
1 AAAAT
49008024 ATCAAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 22 0.76
29 2 0.07
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAATTAAATATCTAATTTAAACATATA
Found at i:49016215 original size:42 final size:43
Alignment explanation
Indices: 49016147--49016230 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 43
49016137 AATACGCTTT
49016147 CAAAATTATAAAAAAAAACACATAAAAGGAATTAAATAAGTTC
1 CAAAATTATAAAAAAAAACACATAAAAGGAATTAAATAAGTTC
49016190 CAAAATTAT-AAAAAAAACACATAAAAGGAATTAAATAAGTT
1 CAAAATTATAAAAAAAAACACATAAAAGGAATTAAATAAGTT
49016231 TAAGTTTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 32 0.78
43 9 0.22
ACGTcount: A:0.63, C:0.08, G:0.07, T:0.21
Consensus pattern (43 bp):
CAAAATTATAAAAAAAAACACATAAAAGGAATTAAATAAGTTC
Found at i:49019742 original size:62 final size:59
Alignment explanation
Indices: 49019587--49019759 Score: 154
Period size: 58 Copynumber: 2.9 Consensus size: 59
49019577 TTAATATAAT
* * * * ** * *
49019587 ATTTGGTACCTGAACTTGATATTTTTTATTAATTTGATATTTAA-ATTTTTTTGACTCA
1 ATTTAGTACCTAAACTTGACACTTTTTCCTAATTTGATACTTAATATTTTTTTGACCCA
*
49019645 ATTTAGTATCTAAACTTGACACTTTTTCCTAATTTGATACTTAAATATTTTTTTAGACCCA
1 ATTTAGTACCTAAACTTGACACTTTTTCCTAATTTGATACTT-AATATTTTTTT-GACCCA
* * * * *
49019706 ATTT-GATACCTGAACTT-AGCATTTATTTCCTAATTTGGTACCTAATCTTTTTTT
1 ATTTAG-TACCTAAACTTGA-CACTT-TTTCCTAATTTGATACTTAATATTTTTTT
49019760 TAGATTTAAT
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
58 34 0.36
59 2 0.02
60 10 0.11
61 32 0.34
62 16 0.17
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.50
Consensus pattern (59 bp):
ATTTAGTACCTAAACTTGACACTTTTTCCTAATTTGATACTTAATATTTTTTTGACCCA
Found at i:49022283 original size:9 final size:9
Alignment explanation
Indices: 49022258--49022502 Score: 56
Period size: 9 Copynumber: 26.0 Consensus size: 9
49022248 GTTCAGTTCA
49022258 AATTTTTAT
1 AATTTTTAT
49022267 AACTTTTTTAT
1 AA--TTTTTAT
49022278 AA-TTTTAT
1 AATTTTTAT
*
49022286 AAGTTTATAT
1 AA-TTTTTAT
*
49022296 CAA--TTTAA
1 -AATTTTTAT
*
49022304 AATTTTTTT
1 AATTTTTAT
*
49022313 AATATTTTTT
1 AAT-TTTTAT
49022323 ACATTTTTAT
1 A-ATTTTTAT
*
49022333 TATTTTTA-
1 AATTTTTAT
* *
49022341 AGAATTCTATT
1 A-ATTTTTA-T
* *
49022352 ACTTTTTAAAA
1 AATTTTT--AT
* *
49022363 AAATTTAAAT
1 AATTTTTA-T
49022373 AAGTTTTTATT
1 AA-TTTTTA-T
49022384 AA-TTTTAT
1 AATTTTTAT
*
49022392 AGTTTTTTTAT
1 A-ATT-TTTAT
*
49022403 AATTTATTAG
1 AATTT-TTAT
*
49022413 AAATTTTAT
1 AATTTTTAT
*
49022422 AATATTTAT
1 AATTTTTAT
*
49022431 AAGTTTTAAT
1 AA-TTTTTAT
*
49022441 ATTTTTTAT
1 AATTTTTAT
*
49022450 AATTTTAATT
1 AATTTTTA-T
* *
49022460 AGTTTATAT
1 AATTTTTAT
*
49022469 CAATTTTAAT
1 -AATTTTTAT
49022479 -A-TTTT-T
1 AATTTTTAT
*
49022485 AATATTTAT
1 AATTTTTAT
*
49022494 AAATTTTAT
1 AATTTTTAT
49022503 GAGAAAATAT
Statistics
Matches: 166, Mismatches: 44, Indels: 52
0.63 0.17 0.20
Matches are distributed among these distances:
6 1 0.01
7 6 0.04
8 17 0.10
9 60 0.36
10 50 0.30
11 31 0.19
12 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (9 bp):
AATTTTTAT
Found at i:49022450 original size:19 final size:18
Alignment explanation
Indices: 49022426--49022484 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
49022416 TTTTATAATA
49022426 TTTATAAGTTTTAATATTT
1 TTTATAA-TTTTAATATTT
*
49022445 TTTATAATTTTAATTAGTT
1 TTTATAATTTTAA-TATTT
*
49022464 TATATCAATTTTAATATTT
1 TTTAT-AATTTTAATATTT
49022483 TT
1 TT
49022485 AATATTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.18
19 20 0.59
20 8 0.24
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTATAATTTTAATATTT
Found at i:49022485 original size:29 final size:25
Alignment explanation
Indices: 49022443--49022501 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
49022433 GTTTTAATAT
*
49022443 TTTTTATAATTTTAATTAGTTTATATCAA
1 TTTTAATAATTTTAA-TA-TTTATA--AA
*
49022472 TTTTAATATTTTTAATATTTATAAA
1 TTTTAATAATTTTAATATTTATAAA
49022497 TTTTA
1 TTTTA
49022502 TGAGAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.25
27 6 0.21
28 2 0.07
29 13 0.46
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTAATAATTTTAATATTTATAAA
Found at i:49025545 original size:21 final size:21
Alignment explanation
Indices: 49025521--49025579 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
49025511 GCAAAAGCAG
*
49025521 CACCAAAATAGTAAAAAACAA
1 CACCAAAATAATAAAAAACAA
49025542 CACCAAAATAATAAAAAACAA
1 CACCAAAATAATAAAAAACAA
* * *
49025563 AACCAAAACAACAAAAA
1 CACCAAAATAATAAAAA
49025580 TAGCACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.07
Consensus pattern (21 bp):
CACCAAAATAATAAAAAACAA
Found at i:49025599 original size:21 final size:21
Alignment explanation
Indices: 49025513--49025624 Score: 70
Period size: 21 Copynumber: 5.5 Consensus size: 21
49025503 AAATAACAGC
* *
49025513 AAAAGCAGCACCAAAATAGTA
1 AAAAACAGCACCAAAATAGCA
* **
49025534 AAAAACAACACCAAAATAATA
1 AAAAACAGCACCAAAATAGCA
** * *
49025555 AAAAACAAAACCAAAACAAC-
1 AAAAACAGCACCAAAATAGCA
* *
49025575 AAAAATAGCACCAAAACAGCA
1 AAAAACAGCACCAAAATAGCA
*
49025596 AAAAA-A--ACCAGAAATAGAA
1 AAAAACAGCACCA-AAATAGCA
*
49025615 AAAAATAGCA
1 AAAAACAGCA
49025625 ATATTATTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
18 4 0.05
19 11 0.15
20 18 0.24
21 40 0.54
22 1 0.01
ACGTcount: A:0.68, C:0.19, G:0.07, T:0.06
Consensus pattern (21 bp):
AAAAACAGCACCAAAATAGCA
Found at i:49031932 original size:68 final size:68
Alignment explanation
Indices: 49031849--49031984 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
49031839 TAGTAAAACA
49031849 TTGCTTCTTTCATTCATGTATTGGATTTTCCCAAATGAAAATGAAAAATTATTGTTTTCACCAAT
1 TTGCTTCTTTCATTCATGTATTGGATTTTCCCAAATGAAAATGAAAAATTATTGTTTTCACCAAT
49031914 AAT
66 AAT
49031917 TTGCTTCTTTCATTCATGTATTGGATTTTCCCAAATGAAAATGAAAAATTATTGTTTTCACCAAT
1 TTGCTTCTTTCATTCATGTATTGGATTTTCCCAAATGAAAATGAAAAATTATTGTTTTCACCAAT
49031982 AAT
66 AAT
49031985 CTTTATAGCC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (68 bp):
TTGCTTCTTTCATTCATGTATTGGATTTTCCCAAATGAAAATGAAAAATTATTGTTTTCACCAAT
AAT
Found at i:49037480 original size:13 final size:13
Alignment explanation
Indices: 49037459--49037516 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
49037449 TTATTAGAAT
* *
49037459 AATAATAAAATTG
1 AATATTAAAATTA
49037472 AATATTAAAATTAA
1 AATATTAAAATT-A
* * *
49037486 AATATTTAATTTT
1 AATATTAAAATTA
49037499 AATATT-AAATTA
1 AATATTAAAATTA
49037511 AATATT
1 AATATT
49037517 TTATCCGACC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
12 10 0.27
13 17 0.46
14 10 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AATATTAAAATTA
Found at i:49038416 original size:19 final size:19
Alignment explanation
Indices: 49038383--49038422 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
49038373 ATATTTTTTT
*
49038383 ATTAGAATGAAAAAGTTTA
1 ATTAGAATGAAAAAGTATA
49038402 ATTAGAAT-AGAAAAGTATA
1 ATTAGAATGA-AAAAGTATA
49038421 AT
1 AT
49038423 AAAAGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (19 bp):
ATTAGAATGAAAAAGTATA
Found at i:49038562 original size:17 final size:17
Alignment explanation
Indices: 49038540--49038573 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49038530 CCTTGCAACT
49038540 TCAAATAACCCGATAGA
1 TCAAATAACCCGATAGA
*
49038557 TCAAATAACTCGATAGA
1 TCAAATAACCCGATAGA
49038574 ATAGATCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (17 bp):
TCAAATAACCCGATAGA
Found at i:49052850 original size:17 final size:17
Alignment explanation
Indices: 49052814--49052857 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
49052804 TTTTTTTTTA
*
49052814 AAATTTAAACTTAATAT
1 AAATTTAAATTTAATAT
49052831 AAATTTAAATTTAA-ATT
1 AAATTTAAATTTAATA-T
*
49052848 AAAATTAAAT
1 AAATTTAAAT
49052858 GCCCAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTAAATTTAATAT
Found at i:49054144 original size:59 final size:59
Alignment explanation
Indices: 49054065--49054382 Score: 419
Period size: 59 Copynumber: 5.4 Consensus size: 59
49054055 CTTGAACTGT
49054065 CCAAAAATTA-CATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
** *
49054123 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * *
49054182 CCAAAAATTACCATTTT-CCCCTGAACTTTCCAAAATTCCA-TTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * * * * * *
49054239 CCAAAAATTGCAATTTTACCCCCTAACTTTCCAAAACCCCATTTTTAGCCTCGATTTTA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * * * **
49054298 CCAAAAATTATCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
*
49054357 CAAAAAATTA-CATTTTTACCCCCGAA
1 CCAAAAATTACCA-TTTTACCCCCGAA
49054383 AGTCAAAAAT
Statistics
Matches: 224, Mismatches: 32, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
57 30 0.13
58 52 0.23
59 142 0.63
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
Found at i:49054270 original size:116 final size:117
Alignment explanation
Indices: 49054065--49054379 Score: 456
Period size: 116 Copynumber: 2.7 Consensus size: 117
49054055 CTTGAACTGT
* * *
49054065 CCAAAAATTACATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAA
1 CCAAAAATTACATTTT-CCCCTGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAA
* *
49054130 TTACCATTTTA-CCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
65 TTACAATTTTACCCCCTAAACTTTCCAAAACCCCATTTTTAACCTCGATTTCA
49054182 CCAAAAATTACCATTTTCCCCTGAACTTTCCAAAATTCCA-TTTTAACCCCAATTTCACCAAAAA
1 CCAAAAATTA-CATTTTCCCCTGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAA
* * *
49054246 TTGCAATTTTACCCCCT-AACTTTCCAAAACCCCATTTTTAGCCTCGATTTTA
65 TTACAATTTTACCCCCTAAACTTTCCAAAACCCCATTTTTAACCTCGATTTCA
* * * *
49054298 CCAAAAATTATCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACAAAAA
1 CCAAAAATTA-CATTTTCCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAA
*
49054363 ATTACATTTTTACCCCC
64 ATTACAATTTTACCCCC
49054380 GAAAGTCAAA
Statistics
Matches: 179, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
116 84 0.47
117 53 0.30
118 42 0.23
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (117 bp):
CCAAAAATTACATTTTCCCCTGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAAT
TACAATTTTACCCCCTAAACTTTCCAAAACCCCATTTTTAACCTCGATTTCA
Found at i:49058305 original size:13 final size:15
Alignment explanation
Indices: 49058287--49058318 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
49058277 ATAGTCTATC
49058287 AACACA-AAATA-AA
1 AACACATAAATATAA
49058300 AACACATAAATATAA
1 AACACATAAATATAA
49058315 AACA
1 AACA
49058319 TACGACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.72, C:0.16, G:0.00, T:0.12
Consensus pattern (15 bp):
AACACATAAATATAA
Found at i:49059417 original size:25 final size:25
Alignment explanation
Indices: 49059380--49059434 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
49059370 AGAATAATAC
49059380 TAAAATAAATAAATTGAAAATAAAA
1 TAAAATAAATAAATTGAAAATAAAA
* *
49059405 TAAAATGATTAAATTGAAAATAAAA
1 TAAAATAAATAAATTGAAAATAAAA
49059430 TAAAA
1 TAAAA
49059435 ACAATGATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (25 bp):
TAAAATAAATAAATTGAAAATAAAA
Found at i:49059430 original size:30 final size:28
Alignment explanation
Indices: 49059396--49059463 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
49059386 AAATAAATTG
*
49059396 AAAATAAAATAAAATGATTAAATTGAAAA
1 AAAATAAAA-AAAATGATCAAATTGAAAA
* *
49059425 TAAAATAAAAACAATGATCAAATTTAAAA
1 -AAAATAAAAAAAATGATCAAATTGAAAA
*
49059454 AAAATTAAAA
1 AAAATAAAAA
49059464 GATTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 9 0.26
29 16 0.47
30 9 0.26
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (28 bp):
AAAATAAAAAAAATGATCAAATTGAAAA
Found at i:49059440 original size:29 final size:27
Alignment explanation
Indices: 49059389--49059463 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 27
49059379 CTAAAATAAA
49059389 TAAATTGAAAATAAAAT--AAAATGAT
1 TAAATTGAAAATAAAATAAAAAATGAT
49059414 TAAATTGAAAATAAAATAAAAACAATGAT
1 TAAATTGAAAATAAAAT-AAAA-AATGAT
* * *
49059443 CAAATTTAAAA-AAAATTAAAA
1 TAAATTGAAAATAAAATAAAAA
49059464 GATTTAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 17 0.40
26 1 0.02
27 3 0.07
28 7 0.16
29 15 0.35
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (27 bp):
TAAATTGAAAATAAAATAAAAAATGAT
Found at i:49059482 original size:19 final size:19
Alignment explanation
Indices: 49059446--49059481 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
49059436 CAATGATCAA
49059446 ATTTAAAAAAAATTAAAAG
1 ATTTAAAAAAAATTAAAAG
49059465 ATTT-AAAAAAATTAAAA
1 ATTTAAAAAAAATTAAAA
49059482 AACATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
ATTTAAAAAAAATTAAAAG
Found at i:49065979 original size:22 final size:22
Alignment explanation
Indices: 49065954--49065996 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
49065944 CTGGGTTTGG
*
49065954 ATTC-ATCCATCTTTGTTTCTTC
1 ATTCTATCCAACTTT-TTTCTTC
*
49065976 ATTCTTTCCAACTTTTTTCTT
1 ATTCTATCCAACTTTTTTCTT
49065997 ATGGGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.14, C:0.26, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTCTATCCAACTTTTTTCTTC
Found at i:49068862 original size:16 final size:16
Alignment explanation
Indices: 49068841--49068910 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
49068831 TTTGGTTCGT
*
49068841 TGTAATGGAATAGAAA
1 TGTAATGGAATAGAGA
** *
49068857 TGTAATATAATAGAGT
1 TGTAATGGAATAGAGA
*
49068873 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGA
*
49068889 TGTAATGAAATAG-GA
1 TGTAATGGAATAGAGA
49068904 CTGTAAT
1 -TGTAAT
49068911 CAGTAATTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 1 0.02
16 43 0.98
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:49069190 original size:58 final size:58
Alignment explanation
Indices: 49069079--49069187 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 58
49069069 AATTTTAATG
* * *
49069079 ATTATTATTAAATATAATTTAATAAAAATATTAATTAATTTAATTATATTTTAACATA
1 ATTATTATTAAATACAATTTAATAAAAATAATAATTAATTTAATAATATTTTAACATA
49069137 ATTATTATTAAATACAATTTAAT-AAAATAAT-ATATAATTTAATAATATTTT
1 ATTATTATTAAATACAATTTAATAAAAATAATAAT-TAATTTAATAATATTTT
49069188 TAATATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
56 2 0.04
57 23 0.49
58 22 0.47
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAAATAATAATTAATTTAATAATATTTTAACATA
Found at i:49072809 original size:2 final size:2
Alignment explanation
Indices: 49072802--49072828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49072792 GCTCCAAATT
49072802 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
49072829 ATATATATAT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:49072940 original size:59 final size:59
Alignment explanation
Indices: 49072848--49072968 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
49072838 TATATATATA
*
49072848 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
49072907 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
49072966 TAT
1 TAT
49072969 GGATACTATG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (59 bp):
TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
Found at i:49074257 original size:2 final size:2
Alignment explanation
Indices: 49074250--49074278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49074240 GCTCCAAATT
49074250 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
49074279 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:49074386 original size:59 final size:59
Alignment explanation
Indices: 49074294--49074414 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
49074284 TATATATATA
* *
49074294 TATAGGTACTGTGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
49074353 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
49074412 TAT
1 TAT
49074415 GGATACTATG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.36
Consensus pattern (59 bp):
TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
Found at i:49075699 original size:2 final size:2
Alignment explanation
Indices: 49075692--49075722 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49075682 GCTCCAAATT
49075692 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
49075723 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:49075826 original size:59 final size:59
Alignment explanation
Indices: 49075734--49075854 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
49075724 TATATATATA
* *
49075734 TATAGGTACTGTGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
49075793 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
49075852 TAT
1 TAT
49075855 GGATACTATG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.36
Consensus pattern (59 bp):
TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAAAAAGC
Found at i:49078779 original size:29 final size:29
Alignment explanation
Indices: 49078707--49078784 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
49078697 GGACCTGGAA
*
49078707 TTTAAAATTTGAAAATAAATAAACTAAAT
1 TTTAAAATTTAAAAATAAATAAACTAAAT
* *
49078736 TCCTAAAA-ATAAAAATACAAT-AACTAAAT
1 T-TTAAAATTTAAAAATA-AATAAACTAAAT
*
49078765 TTTAAAATTTTAAAA-AAATA
1 TTTAAAATTTAAAAATAAATA
49078785 TAAAGATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
27 3 0.08
28 6 0.15
29 22 0.56
30 8 0.21
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.32
Consensus pattern (29 bp):
TTTAAAATTTAAAAATAAATAAACTAAAT
Found at i:49086318 original size:28 final size:28
Alignment explanation
Indices: 49086275--49086337 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
49086265 TGCTAACTTA
* *
49086275 TTTAAA-TTTATATAAATTTTTTTAT-AT
1 TTTAAATTTTATATAAA-TATTGTATCAT
*
49086302 TTTAAATTTTATTTAAATATTGTATCAT
1 TTTAAATTTTATATAAATATTGTATCAT
49086330 TTTAAATT
1 TTTAAATT
49086338 ATTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTAAATTTTATATAAATATTGTATCAT
Found at i:49087315 original size:30 final size:31
Alignment explanation
Indices: 49087246--49087315 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
49087236 GCCTTTTATC
* *
49087246 TTTAAATTTGATAACTAGATTCATTTTGGTA
1 TTTAAATTTGACAACTAGATTCATTTTCGTA
* *
49087277 TTTAAATTTGACAATTAGATTTA-TTTCG-A
1 TTTAAATTTGACAACTAGATTCATTTTCGTA
49087306 TTCTAAATTT
1 TT-TAAATTT
49087316 AAATTCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 20 0.59
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (31 bp):
TTTAAATTTGACAACTAGATTCATTTTCGTA
Found at i:49089465 original size:19 final size:20
Alignment explanation
Indices: 49089428--49089471 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
49089418 GACTCTACTC
* *
49089428 AAATTAAAAAAAATTAAATT
1 AAATTAAAAAAAATAAAATA
*
49089448 AAATT-AAAATAATAAAATA
1 AAATTAAAAAAAATAAAATA
49089467 AAATT
1 AAATT
49089472 TATTAACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATTAAAAAAAATAAAATA
Found at i:49090446 original size:59 final size:59
Alignment explanation
Indices: 49090376--49090491 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 59
49090366 TATTGGATTA
* * **
49090376 CATCCCTAACAAAGTAACAATCCGCTTCAATTGTAATATGCAACGCAGATTAACTATTG
1 CATCCCGAACAAAGTAACAATCCACTTCAATTACAATATGCAACGCAGATTAACTATTG
* * * *
49090435 CATCCCGAACAAAGTGACAATCCACTTCAATTACAATATGCAATGTAGATTGACTAT
1 CATCCCGAACAAAGTAACAATCCACTTCAATTACAATATGCAACGCAGATTAACTAT
49090492 GGCCTCGAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (59 bp):
CATCCCGAACAAAGTAACAATCCACTTCAATTACAATATGCAACGCAGATTAACTATTG
Found at i:49092250 original size:17 final size:17
Alignment explanation
Indices: 49092203--49092250 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
49092193 ATTAAACCCA
* *
49092203 ATTTTTAATTTTAATTT
1 ATTTTAAATTTAAATTT
* *
49092220 TTTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
49092237 ATTTTAAATTTAAA
1 ATTTTAAATTTAAA
49092251 ATTTGAAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:49092957 original size:11 final size:11
Alignment explanation
Indices: 49092941--49093002 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
49092931 TTTCAGTATT
49092941 TAATAAATA-A
1 TAATAAATATA
49092951 GTAATAAATATA
1 -TAATAAATATA
*
49092963 TAATAAACATAA
1 TAATAAATAT-A
49092975 TAAGTATAATAT-
1 TAA-TA-AATATA
49092987 TAAT-AATA-A
1 TAATAAATATA
49092996 TAATAAA
1 TAATAAA
49093003 AAAAAAGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
9 8 0.19
10 2 0.05
11 19 0.44
12 8 0.19
13 2 0.05
14 4 0.09
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (11 bp):
TAATAAATATA
Found at i:49094031 original size:29 final size:29
Alignment explanation
Indices: 49093985--49094327 Score: 177
Period size: 29 Copynumber: 11.7 Consensus size: 29
49093975 GGCCCCTAAG
*
49093985 CTTTCCAAAAATCACATTTTGACCCCCAAA
1 CTTTCCAAAAATTACATTTT-ACCCCCAAA
* * * *
49094015 CTTTCC-AAAATAACATTTTTGCCCTCGAA
1 CTTTCCAAAAATTACA-TTTTACCCCCAAA
* * *
49094044 CTTTTCTAAAATTGCATTTTA-CCCCAGAA
1 CTTTCCAAAAATTACATTTTACCCCCA-AA
* * *
49094073 C-ATCCTAAAATTACTATTTTACCCCCGAA
1 CTTTCCAAAAATTAC-ATTTTACCCCCAAA
* *
49094102 C-ATCCAAAAATTACCATTTTCCCCCCAAA
1 CTTTCCAAAAATTA-CATTTTACCCCCAAA
* * * **
49094131 -TTTCCAAAAATCACATTTCCAACTTCAAA
1 CTTTCCAAAAATTACATTT-TACCCCCAAA
* * **
49094160 TTTTTCCAAAAGTT-CAATTTTAATCCCAAA
1 -CTTTCCAAAAATTAC-ATTTTACCCCCAAA
** * *
49094190 -TTTCTCCCAAATTTCAATTTTGATCCCCAAA
1 CTTTC-CAAAAATTAC-ATTTT-ACCCCCAAA
* *
49094221 -TTCCTCGAAAATTACATTTTTACCCCCAAA
1 CTTTC-CAAAAATTACA-TTTTACCCCCAAA
*
49094251 CTTTTCC-AAAATTACATTTTTACCCCCGAA
1 C-TTTCCAAAAATTACA-TTTTACCCCCAAA
* *
49094281 C-ATCCAAAAATTACCATTTTGCCCCCAAA
1 CTTTCCAAAAATTA-CATTTTACCCCCAAA
*
49094310 -TTTCCAAAAATCACATTT
1 CTTTCCAAAAATTACATTT
49094328 CCAACTTCAA
Statistics
Matches: 246, Mismatches: 47, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
28 30 0.12
29 106 0.43
30 70 0.28
31 37 0.15
32 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
CTTTCCAAAAATTACATTTTACCCCCAAA
Found at i:49094200 original size:31 final size:30
Alignment explanation
Indices: 49094156--49094222 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
49094146 TTTCCAACTT
*
49094156 CAAATTTTTCCAAAAGTTCAATTTTAAT-CC
1 CAAA-TTTTCCCAAAGTTCAATTTTAATCCC
* *
49094186 CAAATTTCTCCCAAATTTCAATTTTGATCCC
1 CAAATTT-TCCCAAAGTTCAATTTTAATCCC
49094217 CAAATT
1 CAAATT
49094223 CCTCGAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 21 0.66
31 8 0.25
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CAAATTTTCCCAAAGTTCAATTTTAATCCC
Found at i:49094233 original size:31 final size:31
Alignment explanation
Indices: 49094164--49094411 Score: 92
Period size: 30 Copynumber: 8.3 Consensus size: 31
49094154 TTCAAATTTT
* *
49094164 TCCAAAAGTTCAATTTTAAT-CCCAAATTTC
1 TCCAAAATTTCAATTTTAATCCCCAAATTCC
* *
49094194 TCCCAAATTTCAATTTTGATCCCCAAATTCC
1 TCCAAAATTTCAATTTTAATCCCCAAATTCC
* * * * *
49094225 TCGAAAATTAC-ATTTTTACCCCCAAACTT-T
1 TCCAAAATTTCAATTTTAATCCCCAAA-TTCC
* * * * *
49094255 TCCAAAATTAC-ATTTTTACCCCCGAA--CA
1 TCCAAAATTTCAATTTTAATCCCCAAATTCC
* * **
49094283 TCCAAAAATTACCATTTT-GCCCCCAAATT--
1 TCC-AAAATTTCAATTTTAATCCCCAAATTCC
* * ** *
49094312 TCCAAAA-ATCACATTTCCAA-CTTCAAATT-T
1 TCCAAAATTTCA-ATTT-TAATCCCCAAATTCC
* *
49094342 TCCAAAAGTTCGATTTTAAT-CCCAAATTTCC
1 TCCAAAATTTCAATTTTAATCCCCAAA-TTCC
* * *
49094373 -CCTAAATTTTAATTTTGATCCCCAAATTCC
1 TCCAAAATTTCAATTTTAATCCCCAAATTCC
*
49094403 TCGAAAATT
1 TCCAAAATT
49094412 ATATTTTCAT
Statistics
Matches: 166, Mismatches: 35, Indels: 33
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.01
28 11 0.07
29 31 0.19
30 90 0.54
31 33 0.20
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (31 bp):
TCCAAAATTTCAATTTTAATCCCCAAATTCC
Done.