Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 11 of 316
Found at i:3247904 original size:21 final size:21
Alignment explanation
Indices: 3247880--3247920 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3247870 GATCAAATAG
*
3247880 TAGTTCAATGTGATCTACTTC
1 TAGTTCAATGTGATCCACTTC
3247901 TAGTTCAATGTGATCCACTT
1 TAGTTCAATGTGATCCACTT
3247921 TTAGATTGAG
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:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (21 bp):
TAGTTCAATGTGATCCACTTC
Found at i:3248718 original size:54 final size:55
Alignment explanation
Indices: 3248632--3248745 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 55
3248622 TCAAACTTCT
* *
3248632 TCAGCCTCCTTCGAGCACTACTCGTCGGCTAACATTGCTT-ACACCTATGCTCTA
1 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAACACCTATGCTCTA
3248686 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAGACACCTATGCTCTA
1 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTA-ACACCTATGCTCTA
3248742 TCAG
1 TCAG
3248746 GAATTGGTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
54 38 0.68
56 18 0.32
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (55 bp):
TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAACACCTATGCTCTA
Found at i:3253434 original size:17 final size:17
Alignment explanation
Indices: 3253408--3253450 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3253398 TAAAAAACCA
3253408 ACTT-AATAATCAAATT
1 ACTTAAATAATCAAATT
*
3253424 ATTTAAATAATCAAATT
1 ACTTAAATAATCAAATT
3253441 ACTTAAATAA
1 ACTTAAATAA
3253451 ACACTCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
ACTTAAATAATCAAATT
Found at i:3266912 original size:36 final size:36
Alignment explanation
Indices: 3266853--3266926 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
3266843 ATTAAATTAT
*
3266853 TTATATTAAAACACTACATAATATAACAAATATTTA
1 TTATATTAAAAAACTACATAATATAACAAATATTTA
* * *
3266889 TTATATTAAAAAATTA-ATAAATATGATAAATATTTA
1 TTATATTAAAAAACTACAT-AATATAACAAATATTTA
3266925 TT
1 TT
3266927 GCATTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (36 bp):
TTATATTAAAAAACTACATAATATAACAAATATTTA
Found at i:3277069 original size:104 final size:104
Alignment explanation
Indices: 3276951--3277161 Score: 386
Period size: 104 Copynumber: 2.0 Consensus size: 104
3276941 ATTCATTAAT
3276951 TATTTTATAACTTTTTTAAAGTTGAGTAAATAAAATAGTTTTAAGTCTTAAATTTAAAATACTTT
1 TATTTTATAACTTTTTTAAAGTTGAGTAAATAAAATAGTTTTAAGTCTTAAATTTAAAATACTTT
*
3277016 ATATTTATATAAATTTTCATGTGTTAATTATTTGTATTA
66 ATATTTATATAAATTTTCATGTGTTAATAATTTGTATTA
*
3277055 TATTTTATAACTTTTTTAAAGTTGAGTAAATAATATAGTTTTAAGTCTTAAATTTAAAATACTTT
1 TATTTTATAACTTTTTTAAAGTTGAGTAAATAAAATAGTTTTAAGTCTTAAATTTAAAATACTTT
* *
3277120 ATATTTATATATATTTTCATTTGTTAATAATTTGTATTA
66 ATATTTATATAAATTTTCATGTGTTAATAATTTGTATTA
3277159 TAT
1 TAT
3277162 GAATTTTAGA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (104 bp):
TATTTTATAACTTTTTTAAAGTTGAGTAAATAAAATAGTTTTAAGTCTTAAATTTAAAATACTTT
ATATTTATATAAATTTTCATGTGTTAATAATTTGTATTA
Found at i:3277430 original size:23 final size:23
Alignment explanation
Indices: 3277401--3277466 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
3277391 GTGAATTTTG
3277401 AATTTAAATTTGATTTAAAATTT
1 AATTTAAATTTGATTTAAAATTT
* * *
3277424 AATTTAAGTTCGA-TTAAACTTT
1 AATTTAAATTTGATTTAAAATTT
*
3277446 ACTTTTAAAGTTTGAATTTAA
1 A-ATTTAAA-TTTG-ATTTAA
3277467 TTCGAGAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
22 9 0.27
23 16 0.48
24 3 0.09
25 1 0.03
26 4 0.12
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (23 bp):
AATTTAAATTTGATTTAAAATTT
Found at i:3290866 original size:17 final size:17
Alignment explanation
Indices: 3290836--3290869 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3290826 TTGGGTGAAC
*
3290836 TTATATTATAATTTTAT
1 TTATAATATAATTTTAT
*
3290853 TTATAATATTATTTTAT
1 TTATAATATAATTTTAT
3290870 ATCTTGCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATATAATTTTAT
Found at i:3291788 original size:16 final size:15
Alignment explanation
Indices: 3291767--3291815 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3291757 GAATTATTTT
3291767 ATATAAAAAATTTAAA
1 ATATAAAAAA-TTAAA
* *
3291783 ATATAATACATTAAA
1 ATATAAAAAATTAAA
3291798 ATATTAAAAAATTAAA
1 ATA-TAAAAAATTAAA
3291814 AT
1 AT
3291816 TAATATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATAAAAAATTAAA
Found at i:3297073 original size:76 final size:76
Alignment explanation
Indices: 3296991--3297137 Score: 251
Period size: 76 Copynumber: 1.9 Consensus size: 76
3296981 TAACCGAATT
* *
3296991 GAAATATTTCAATTAAATCAGTCAGTTAATTGAATTAA-CTGAAATTTAAATGTTTTTATCTTTT
1 GAAATATTTCAATTAAATCAGTCAGTTAATTGAATTAATC-AAAATTTAAATATTTTTATCTTTT
3297055 GGTTTTTGAACC
65 GGTTTTTGAACC
*
3297067 GAAATATTTCAATTAAATCAGTCAGTTAATTGAATTAATCAAAATTTATATATTTTTATCTTTTG
1 GAAATATTTCAATTAAATCAGTCAGTTAATTGAATTAATCAAAATTTAAATATTTTTATCTTTTG
3297132 GTTTTT
66 GTTTTT
3297138 AAATAAGAAC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
76 66 0.99
77 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (76 bp):
GAAATATTTCAATTAAATCAGTCAGTTAATTGAATTAATCAAAATTTAAATATTTTTATCTTTTG
GTTTTTGAACC
Found at i:3302112 original size:19 final size:21
Alignment explanation
Indices: 3302088--3302129 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3302078 TTATATGTTT
3302088 TGTATAA-ATT-TTGATAAAA
1 TGTATAATATTATTGATAAAA
*
3302107 TGTATAATATTATTGATTAAA
1 TGTATAATATTATTGATAAAA
3302128 TG
1 TG
3302130 ATACGAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (21 bp):
TGTATAATATTATTGATAAAA
Found at i:3303396 original size:14 final size:14
Alignment explanation
Indices: 3303362--3303406 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3303352 AAAAGTGATC
*
3303362 AAAAAAGTACAAAA
1 AAAAAAATACAAAA
*
3303376 AATAAAATACAAAA
1 AAAAAAATACAAAA
* *
3303390 AAAAAAAAATAAAA
1 AAAAAAATACAAAA
3303404 AAA
1 AAA
3303407 TTCTGTGGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.09
Consensus pattern (14 bp):
AAAAAAATACAAAA
Found at i:3315077 original size:29 final size:30
Alignment explanation
Indices: 3315031--3315087 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
3315021 TTTTAGAATT
3315031 AAATTTTGAAGGTCTAAT-AAAATTTTTAA
1 AAATTTTGAAGGTCTAATGAAAATTTTTAA
* *
3315060 AAATTTT-AAGAGTTTAATGATAATTTTT
1 AAATTTTGAAG-GTCTAATGAAAATTTTT
3315088 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 13 0.54
30 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (30 bp):
AAATTTTGAAGGTCTAATGAAAATTTTTAA
Found at i:3317369 original size:23 final size:24
Alignment explanation
Indices: 3317325--3317373 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
3317315 GTCCTTATAC
3317325 TTTTTGAATTTCAAAATTTTAATCT
1 TTTTTGAATTTCAAAA-TTTAATCT
3317350 TTTTTGAATTTCAAAA-TTAATCT
1 TTTTTGAATTTCAAAATTTAATCT
3317373 T
1 T
3317374 AGTTTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.33
25 16 0.67
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTTGAATTTCAAAATTTAATCT
Found at i:3319632 original size:20 final size:20
Alignment explanation
Indices: 3319579--3319632 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
3319569 AACCAAAACT
3319579 AAAATT-AAAAAAATATAAA
1 AAAATTCAAAAAAATATAAA
* *
3319598 AAGAATTCATAAAAAT-TCATA
1 AA-AATTCAAAAAAATAT-AAA
3319619 AAAATTCAAAAAAA
1 AAAATTCAAAAAAA
3319633 AAATAGCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 11 0.38
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAATTCAAAAAAATATAAA
Found at i:3320630 original size:23 final size:22
Alignment explanation
Indices: 3320583--3320630 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3320573 AATTTTTTTA
* *
3320583 AAATTTTAAAAATAAAGAGATT
1 AAATTTTAAAAATAAAGAAAAT
*
3320605 AAATTCTTAAAAATAAATAAAAT
1 AAATT-TTAAAAATAAAGAAAAT
3320628 AAA
1 AAA
3320631 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATTTTAAAAATAAAGAAAAT
Found at i:3320987 original size:109 final size:109
Alignment explanation
Indices: 3320848--3321059 Score: 329
Period size: 109 Copynumber: 1.9 Consensus size: 109
3320838 TGCACAAAAA
* * *
3320848 TCCACCCAACATGTTTCCCACATCTTTTTTTCATTAATTTATTTTGTTTTTATTTTATTAATTAA
1 TCCACCCAACATGTCTACCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
* *
3320913 T-AATGTTAAATTTTA-TAAAAATAATTCATTTACCACTAGATGTG
66 TAAAAGTTAAATTTTATTAAAAA-AAATCATTTA-CACTAGATGTG
* *
3320957 TCCACCCAACATGTCTATCACATCTTTTTTTCATTCATTTATTTTGTTTTTATCTTATTAATTAA
1 TCCACCCAACATGTCTACCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
3321022 TAAAAGTTAAATTTTATTAAAAAAAATCATTTACACTA
66 TAAAAGTTAAATTTTATTAAAAAAAATCATTTACACTA
3321060 AAGGTGTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
109 66 0.70
110 22 0.23
111 6 0.06
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (109 bp):
TCCACCCAACATGTCTACCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
TAAAAGTTAAATTTTATTAAAAAAAATCATTTACACTAGATGTG
Found at i:3322989 original size:20 final size:20
Alignment explanation
Indices: 3322964--3323004 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3322954 TACAAACAAG
*
3322964 TTAGTTTTTAGCTTTATTAT
1 TTAGTTTTTAGCTTCATTAT
3322984 TTAGTTTTTAGCTTCATTAT
1 TTAGTTTTTAGCTTCATTAT
3323004 T
1 T
3323005 CAATTAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (20 bp):
TTAGTTTTTAGCTTCATTAT
Found at i:3326592 original size:3 final size:3
Alignment explanation
Indices: 3326584--3326642 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
3326574 TACGTTTTCA
3326584 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3326632 TTC TTC TTC TT
1 TTC TTC TTC TT
3326643 TTTATAAAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3343066 original size:3 final size:3
Alignment explanation
Indices: 3343058--3343085 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3343048 GTTCACTCTC
3343058 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3343086 TTTTTCGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3344203 original size:31 final size:31
Alignment explanation
Indices: 3344168--3344242 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
3344158 TTAATATAAT
*
3344168 ATTTGGTATTTAAACTTAACACTTTTTCCTA
1 ATTTGGTACTTAAACTTAACACTTTTTCCTA
* * *
3344199 ATTTGGTACCTAAACTTGACACTTTTTCTTA
1 ATTTGGTACTTAAACTTAACACTTTTTCCTA
*
3344230 AGTTGGTACTTAA
1 ATTTGGTACTTAA
3344243 TCTTTTTTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTAACACTTTTTCCTA
Found at i:3344452 original size:23 final size:20
Alignment explanation
Indices: 3344426--3344482 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
3344416 ATATAATTTT
3344426 TTTTATTTTATATATTCAATTA
1 TTTTATTTTATA-ATT-AATTA
*
3344448 CTTTTAGTTT-TAATTAATTA
1 -TTTTATTTTATAATTAATTA
3344468 -TTTATTTTATTAATT
1 TTTTATTTTA-TAATT
3344483 GAAAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 7 0.23
20 10 0.33
21 3 0.10
22 2 0.07
23 8 0.27
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATTTTATAATTAATTA
Found at i:3344479 original size:16 final size:18
Alignment explanation
Indices: 3344450--3344482 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3344440 TTCAATTACT
3344450 TTTAGTTTTAATTAATTA
1 TTTAGTTTTAATTAATTA
3344468 TTTA-TTTT-ATTAATT
1 TTTAGTTTTAATTAATT
3344483 GAAAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTAGTTTTAATTAATTA
Found at i:3352317 original size:21 final size:21
Alignment explanation
Indices: 3352291--3352331 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3352281 AGACGAGCAA
* *
3352291 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3352312 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3352332 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3358491 original size:17 final size:17
Alignment explanation
Indices: 3358466--3358498 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3358456 CTGAATATTG
3358466 TTTTAAAATTATAAGTT
1 TTTTAAAATTATAAGTT
*
3358483 TTTTTAAATTATAAGT
1 TTTTAAAATTATAAGT
3358499 AATATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTTAAAATTATAAGTT
Found at i:3359743 original size:15 final size:15
Alignment explanation
Indices: 3359702--3359746 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3359692 TTAATTGTTT
* *
3359702 ATTTTTATATATAAA
1 ATTTTTATAAATTAA
*
3359717 ATTTTTATTAAATTTA
1 ATTTTTA-TAAATTAA
3359733 ATTTTTATAAATTA
1 ATTTTTATAAATTA
3359747 TTAATATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTATAAATTAA
Found at i:3366355 original size:30 final size:29
Alignment explanation
Indices: 3366316--3366404 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 29
3366306 TTTACGTATT
3366316 TTATTAATTTAATTTTAAATATTAAAAAAG
1 TTATTAATTTAA-TTTAAATATTAAAAAAG
* * *
3366346 TTATAAATTTAATTTATAATATTTAGAAAAT
1 TTATTAATTTAATTTA-AATA-TTAAAAAAG
*
3366377 TTATTTATTTAATTTAAAT-TCTAAAAAA
1 TTATTAATTTAATTTAAATAT-TAAAAAA
3366405 TTTAAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 1 0.02
29 10 0.20
30 18 0.36
31 21 0.42
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (29 bp):
TTATTAATTTAATTTAAATATTAAAAAAG
Found at i:3366429 original size:14 final size:15
Alignment explanation
Indices: 3366410--3366439 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3366400 AAAAATTTAA
3366410 AAAAAT-ATTTTTTT
1 AAAAATAATTTTTTT
3366424 AAAAATAATTTTTTT
1 AAAAATAATTTTTTT
3366439 A
1 A
3366440 CTTTAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAAATAATTTTTTT
Found at i:3369789 original size:21 final size:20
Alignment explanation
Indices: 3369765--3369821 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
3369755 AATGTTTTTA
*
3369765 CCAAACAAAATAAATTTAATC
1 CCAAA-AAAATAAATATAATC
*
3369786 CCAAAAAAGAAGAAAATATAATC
1 CC-AAAAA-AA-TAAATATAATC
*
3369809 CCAAAAATATAAA
1 CCAAAAAAATAAA
3369822 CTACTGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.10
21 5 0.17
22 10 0.34
23 11 0.38
ACGTcount: A:0.63, C:0.16, G:0.04, T:0.18
Consensus pattern (20 bp):
CCAAAAAAATAAATATAATC
Found at i:3370822 original size:29 final size:29
Alignment explanation
Indices: 3370783--3370850 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
3370773 GGAGCTGAAG
3370783 AAGAAATGAAAGTAAAAATTTTCTATGGA
1 AAGAAATGAAAGTAAAAATTTTCTATGGA
3370812 AAGAAATGAAAGTAAAAATTTTCTATGGA
1 AAGAAATGAAAGTAAAAATTTTCTATGGA
3370841 AAGAAATGAA
1 AAGAAATGAA
3370851 GGAAAGAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.25
Consensus pattern (29 bp):
AAGAAATGAAAGTAAAAATTTTCTATGGA
Found at i:3371379 original size:14 final size:14
Alignment explanation
Indices: 3371360--3371392 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3371350 GTTCAAAAGT
3371360 GAAAGGATTTTGAC
1 GAAAGGATTTTGAC
3371374 GAAAGGATTTTGAC
1 GAAAGGATTTTGAC
*
3371388 AAAAG
1 GAAAG
3371393 TATAAGCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (14 bp):
GAAAGGATTTTGAC
Found at i:3376307 original size:46 final size:44
Alignment explanation
Indices: 3376248--3376362 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
3376238 ACAGGACAGA
* *
3376248 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
3376294 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
3376338 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
3376363 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:3376343 original size:44 final size:45
Alignment explanation
Indices: 3376248--3376381 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
3376238 ACAGGACAGA
* *
3376248 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
3376294 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
3376338 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3376382 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:3382325 original size:17 final size:18
Alignment explanation
Indices: 3382293--3382326 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3382283 TTTCACTTAT
3382293 ATTATTAAATAAATACAA
1 ATTATTAAATAAATACAA
3382311 ATTATTAAA-AAATACA
1 ATTATTAAATAAATACA
3382327 TGGAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTATTAAATAAATACAA
Found at i:3390939 original size:27 final size:26
Alignment explanation
Indices: 3390891--3390960 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 26
3390881 AAAGTAAACA
*
3390891 ATAAAACAATTTAAAATGAATAATAC
1 ATAAAACAATTTAAAATAAATAATAC
**
3390917 ATAAAACAAGTTTAAAATAAATAATGT
1 ATAAAACAA-TTTAAAATAAATAATAC
* *
3390944 ATAAAGCATTTTAAAAT
1 ATAAAACAATTTAAAAT
3390961 CTATAATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 17 0.45
27 21 0.55
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (26 bp):
ATAAAACAATTTAAAATAAATAATAC
Found at i:3392945 original size:21 final size:21
Alignment explanation
Indices: 3392889--3392946 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
3392879 TGCGATGAAA
3392889 ATTTTGTTTTGTA-TTTTTAAGCC
1 ATTTT-TTTT-TATTTTTTAA-CC
*
3392912 ATTTATTTTTATTTTTTAA-C
1 ATTTTTTTTTATTTTTTAACC
3392932 ATTTTTTTTCTATTT
1 ATTTTTTTT-TATTT
3392947 ATAATGGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 9 0.29
21 7 0.23
22 11 0.35
23 4 0.13
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (21 bp):
ATTTTTTTTTATTTTTTAACC
Found at i:3399933 original size:24 final size:21
Alignment explanation
Indices: 3399895--3399946 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
3399885 TGATTTAATT
*
3399895 TTTTAAAAATTATAAAGATATAAA
1 TTTT-AAAATAATAAA-AT-TAAA
3399919 TTATTAAAATAATAAAATTAAA
1 TT-TTAAAATAATAAAATTAAA
3399941 TTTTAA
1 TTTTAA
3399947 CTATGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 2 0.08
24 12 0.46
25 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTTAAAATAATAAAATTAAA
Found at i:3412005 original size:7 final size:7
Alignment explanation
Indices: 3411993--3412020 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3411983 TTTTGACAAC
3411993 CCGAAAT
1 CCGAAAT
3412000 CCGAAAT
1 CCGAAAT
3412007 CCGAAAT
1 CCGAAAT
3412014 CCGAAAT
1 CCGAAAT
3412021 TCTAAACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (7 bp):
CCGAAAT
Found at i:3413297 original size:29 final size:31
Alignment explanation
Indices: 3413240--3413297 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
3413230 TATGAGGACC
* *
3413240 TAATTAATATACACTCAATAGTTTTGGGATG
1 TAATTAAAATACACTCAATAGTTTAGGGATG
*
3413271 TAATTAAAATA-ACTTAA-AGTTTAGGGA
1 TAATTAAAATACACTCAATAGTTTAGGGA
3413298 CTAATTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (31 bp):
TAATTAAAATACACTCAATAGTTTAGGGATG
Found at i:3418331 original size:15 final size:15
Alignment explanation
Indices: 3418304--3418351 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3418294 TGTTTATAAA
3418304 TATTT-AATCATTATT
1 TATTTAAAT-ATTATT
*
3418319 TATTTAAATATTATG
1 TATTTAAATATTATT
* *
3418334 AATTTAAATAATATT
1 TATTTAAATATTATT
3418349 TAT
1 TAT
3418352 ATCAGCATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 24 0.89
16 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAAATATTATT
Found at i:3419039 original size:83 final size:83
Alignment explanation
Indices: 3418890--3419052 Score: 204
Period size: 83 Copynumber: 2.0 Consensus size: 83
3418880 GCTTCTCGCC
* * * *
3418890 ACCTCGCGATGTGGAGCACAAAGGAGATGTGTGAGCCGCAAGATGGATCGCCCCATCGTGTGTCA
1 ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAAGATGGATCACCCCATCGTGTCTCA
3418955 CA-TCTCATCAACATGATG
66 CACTC-CATCAACATGATG
* ** * * *
3418973 ACCTCGCTAGGTGGAGCAC-AAGAGAGATATGTGAGTTGCGAGATGGATCACCTCATTGTGTCTC
1 ACCTCGCGAGGTGGAGCACAAAG-GAGATATGTGAGCCGCAAGATGGATCACCCCATCGTGTCTC
3419037 ACACTCCATCAACATG
65 ACACTCCATCAACATG
3419053 GCAACCTCGT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
82 3 0.04
83 63 0.93
84 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (83 bp):
ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAAGATGGATCACCCCATCGTGTCTCA
CACTCCATCAACATGATG
Found at i:3419060 original size:83 final size:83
Alignment explanation
Indices: 3418890--3419071 Score: 197
Period size: 83 Copynumber: 2.2 Consensus size: 83
3418880 GCTTCTCGCC
* * * *
3418890 ACCTCGCGATGTGGAGCACAAAGGAGATGTGTGAGCCGCAAGATGGATCGCCCCATCGTGTGTCA
1 ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAAGATGGATCACCCCATCGTGTCTCA
**
3418955 CATCTCATCAACATGATG
66 CATCTCATCAACATGACA
* ** * * *
3418973 ACCTCGCTAGGTGGAGCAC-AAGAGAGATATGTGAGTTGCGAGATGGATCACCTCATTGTGTCTC
1 ACCTCGCGAGGTGGAGCACAAAG-GAGATATGTGAGCCGCAAGATGGATCACCCCATCGTGTCTC
*
3419037 ACA-CTCCATCAACATGGCA
65 ACATCT-CATCAACATGACA
* *
3419056 ACCTCGTGAAGTGGAG
1 ACCTCGCGAGGTGGAG
3419072 AGTAAAGAAC
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
82 5 0.06
83 76 0.94
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (83 bp):
ACCTCGCGAGGTGGAGCACAAAGGAGATATGTGAGCCGCAAGATGGATCACCCCATCGTGTCTCA
CATCTCATCAACATGACA
Found at i:3419620 original size:31 final size:31
Alignment explanation
Indices: 3419580--3419675 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 31
3419570 ATATGTTTCA
3419580 AATT-TATATATGAATTTTGATTTAATGTGT
1 AATTATATATATGAATTTTGATTTAATGTGT
* * *
3419610 AA-TATAATATATTAATTTTAATTTGA--TGT
1 AATTAT-ATATATGAATTTTGATTTAATGTGT
* *
3419639 AATTATATATACGAAATTTAGATTTAA--TGT
1 AATTATATATATG-AATTTTGATTTAATGTGT
3419669 AATTATA
1 AATTATA
3419676 CATAAAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 11 0.20
30 26 0.48
31 17 0.31
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (31 bp):
AATTATATATATGAATTTTGATTTAATGTGT
Found at i:3419695 original size:30 final size:29
Alignment explanation
Indices: 3419627--3419702 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
3419617 TATATTAATT
* * ** *
3419627 TTAATTTGATGTAATTATATATACGAAAT
1 TTAATTTAATGTAATTATACATAAAAAAA
3419656 TTAGATTTAATGTAATTATACATAAAAAAA
1 TTA-ATTTAATGTAATTATACATAAAAAAA
*
3419686 TTAATTTTAATTTAATT
1 TTAA-TTTAATGTAATT
3419703 GTATAATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (29 bp):
TTAATTTAATGTAATTATACATAAAAAAA
Found at i:3424939 original size:31 final size:31
Alignment explanation
Indices: 3424904--3424970 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3424894 TTAATATACT
* *
3424904 ATTTGATATTTGAGTTT-GACTTTAATGTTCA
1 ATTTGATACTCGAGTTTAGA-TTTAATGTTCA
* *
3424935 ATTTGGTACTCGAGTTTAGATTTATTGTTCA
1 ATTTGATACTCGAGTTTAGATTTAATGTTCA
3424966 ATTTG
1 ATTTG
3424971 GTACCAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.18, T:0.51
Consensus pattern (31 bp):
ATTTGATACTCGAGTTTAGATTTAATGTTCA
Found at i:3424971 original size:31 final size:31
Alignment explanation
Indices: 3424915--3424974 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
3424905 TTTGATATTT
3424915 GAGTTTGACTTTAATGTTCAATTTGGTACTC
1 GAGTTTGACTTTAATGTTCAATTTGGTACTC
*
3424946 GAGTTTAGA-TTTATTGTTCAATTTGGTAC
1 GAGTTT-GACTTTAATGTTCAATTTGGTAC
3424975 CAAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (31 bp):
GAGTTTGACTTTAATGTTCAATTTGGTACTC
Found at i:3426667 original size:21 final size:22
Alignment explanation
Indices: 3426643--3426693 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
3426633 AAAAAATCCA
*
3426643 AAAATTAAATCATA-A-AAAAAT
1 AAAATTAAAT-ATATAGAAAAAG
**
3426664 AAAACAAAATATATAGAAAAAG
1 AAAATTAAATATATAGAAAAAG
3426686 AAAATTAA
1 AAAATTAA
3426694 TGTTGTTCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.13
21 9 0.39
22 11 0.48
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAATTAAATATATAGAAAAAG
Found at i:3433953 original size:20 final size:20
Alignment explanation
Indices: 3433928--3433969 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3433918 AATAACGTCG
3433928 TGTTCGAACTTGCATCTCCT
1 TGTTCGAACTTGCATCTCCT
3433948 TGTTCGAACTTGCATCTCCT
1 TGTTCGAACTTGCATCTCCT
3433968 TG
1 TG
3433970 AGAGTGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTTCGAACTTGCATCTCCT
Found at i:3434938 original size:18 final size:19
Alignment explanation
Indices: 3434915--3434953 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3434905 ATTTAACCGA
*
3434915 ATTTAATATATAT-TATTT
1 ATTTAATATAAATATATTT
*
3434933 ATTTAATTTAAATATATTT
1 ATTTAATATAAATATATTT
3434952 AT
1 AT
3434954 AATATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAATATAAATATATTT
Found at i:3434950 original size:22 final size:22
Alignment explanation
Indices: 3434914--3434967 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
3434904 AATTTAACCG
* *
3434914 AATTT-AATATATATTATTTATTT
1 AATTTAAATATAT-TTA-TAATAT
3434937 AATTTAAATATATTTATAATAT
1 AATTTAAATATATTTATAATAT
3434959 AATTTAAAT
1 AATTTAAAT
3434968 TAATCTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.46
23 8 0.29
24 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTAAATATATTTATAATAT
Found at i:3435029 original size:22 final size:22
Alignment explanation
Indices: 3434986--3435049 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
3434976 TCTAAATCGA
*
3434986 TTATAATATATATTT-TATATATT
1 TTATAATATA-ATTTAAATATA-T
* *
3435009 TTATATTTTTAATTTAAATATAT
1 TTATA-ATATAATTTAAATATAT
3435032 TTATAATATAATTTAAAT
1 TTATAATATAATTTAAAT
3435050 GAATATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 11 0.32
23 15 0.44
24 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATAATATAATTTAAATATAT
Found at i:3439772 original size:28 final size:30
Alignment explanation
Indices: 3439699--3439773 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 30
3439689 TTTCGCTTTA
* **
3439699 AAAATAATAAAATT-TATATTTATATTTTT
1 AAAATAATAAAATTATATAATTATATAATT
*
3439728 AAAATTATTAAAA-TATA-AATTAT-TAATT
1 AAAA-TAATAAAATTATATAATTATATAATT
3439756 AAAATAATAAAATTATAT
1 AAAATAATAAAATTATAT
3439774 TTTTACTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
27 7 0.19
28 11 0.30
29 10 0.27
30 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATAATAAAATTATATAATTATATAATT
Found at i:3439784 original size:28 final size:28
Alignment explanation
Indices: 3439678--3439784 Score: 78
Period size: 30 Copynumber: 3.8 Consensus size: 28
3439668 ATTAATAAGG
**
3439678 ATAAAATTATA-TTTCGCT-TTAAAAATA
1 ATAAAATTATATTTTTACTATT-AAAATA
* * *
3439705 ATAAAATTTATATTTATATTTTTAAAATTA
1 ATAAAA-TTATATTTTTACTATTAAAA-TA
* * *
3439735 TTAAAATATAAATTATTA--ATTAAAATA
1 ATAAAAT-TATATTTTTACTATTAAAATA
3439762 ATAAAATTATATTTTTACTATTA
1 ATAAAATTATATTTTTACTATTA
3439785 TATAAATTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
26 8 0.13
27 14 0.23
28 15 0.25
29 8 0.13
30 16 0.26
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (28 bp):
ATAAAATTATATTTTTACTATTAAAATA
Found at i:3443521 original size:149 final size:144
Alignment explanation
Indices: 3443328--3443614 Score: 441
Period size: 149 Copynumber: 2.0 Consensus size: 144
3443318 AAAACACCCA
* * *
3443328 TAGGGATTTTTTAAGGGGATTTTACAGGATCTTATAATCGTTGAAATTTTGAAATAAATTGATGG
1 TAGGGATTTTTTAAGGGGATTTTACAGGATCTCATAACCCTTGAAATTTTGAAATAAATTGATGG
* * *
3443393 GTTATATTCCCTAAAACTATACTTAAAGCTTAACTTCACAGAACAA-ACTAATAATTCTGCAATT
66 GTTAAATTCCCTAAAACTATAATTAAAGCTTAACTTCACAGAACAAGA-TAATAATGCTGCAA--
3443457 TTCTCTTCCTTAAAAAT
128 TTCTCTTCCTTAAAAAT
3443474 TAGGGATTTTTTAAGAATGGGATTTTACAGGATCTCATAACCCTTGAAATTTTGAAATAAATTGA
1 TAGGGATTTTTTAAG---GGGATTTTACAGGATCTCATAACCCTTGAAATTTTGAAATAAATTGA
* *
3443539 TGGGTTAAATTCCCTAAAACTATAATTAGAGCTTAACTTCACAGAACAAGATACTAATGCTGCAA
63 TGGGTTAAATTCCCTAAAACTATAATTAAAGCTTAACTTCACAGAACAAGATAATAATGCTGCAA
3443604 TTCTCTTCCTT
128 TTCTCTTCCTT
3443615 GAACTGGCAA
Statistics
Matches: 129, Mismatches: 8, Indels: 7
0.90 0.06 0.05
Matches are distributed among these distances:
146 15 0.12
147 11 0.09
149 102 0.79
150 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (144 bp):
TAGGGATTTTTTAAGGGGATTTTACAGGATCTCATAACCCTTGAAATTTTGAAATAAATTGATGG
GTTAAATTCCCTAAAACTATAATTAAAGCTTAACTTCACAGAACAAGATAATAATGCTGCAATTC
TCTTCCTTAAAAAT
Found at i:3444276 original size:12 final size:14
Alignment explanation
Indices: 3444245--3444273 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3444235 CAATTTCTAC
3444245 AGAAAATTTCGAAG
1 AGAAAATTTCGAAG
3444259 AGAAAATTTCGAAG
1 AGAAAATTTCGAAG
3444273 A
1 A
3444274 AAAGAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AGAAAATTTCGAAG
Found at i:3445373 original size:14 final size:14
Alignment explanation
Indices: 3445338--3445374 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3445328 TTTGACAATA
3445338 CTTTTG-AAAAGTG
1 CTTTTGAAAAAGTG
*
3445351 -TTGTGAAAAAGTG
1 CTTTTGAAAAAGTG
3445364 CTTTTGAAAAA
1 CTTTTGAAAAA
3445375 TTTGGTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 4 0.20
13 7 0.35
14 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (14 bp):
CTTTTGAAAAAGTG
Found at i:3448052 original size:12 final size:12
Alignment explanation
Indices: 3448035--3448063 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3448025 ATAATCTAAT
3448035 CTCACGATCTCA
1 CTCACGATCTCA
3448047 CTCACGATCTCA
1 CTCACGATCTCA
3448059 CTCAC
1 CTCAC
3448064 TGACCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.45, G:0.07, T:0.24
Consensus pattern (12 bp):
CTCACGATCTCA
Found at i:3452946 original size:15 final size:15
Alignment explanation
Indices: 3452926--3452980 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
3452916 TAATCTCTGT
3452926 ATTTTAATTTAATTA
1 ATTTTAATTTAATTA
*
3452941 ATTTTAATTT-TTTA
1 ATTTTAATTTAATTA
*
3452955 ATTTTTTATTTAATTA
1 A-TTTTAATTTAATTA
*
3452971 ATATTAATTT
1 ATTTTAATTT
3452981 TTATATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 4 0.12
15 25 0.76
16 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTAATTTAATTA
Found at i:3452968 original size:30 final size:30
Alignment explanation
Indices: 3452927--3452992 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
3452917 AATCTCTGTA
*
3452927 TTTTAATTTAATTAATTTTAATTTTT-TAAT
1 TTTTAATTTAATTAATATTAATTTTTAT-AT
*
3452957 TTTTTATTTAATTAATATTAATTTTTATAT
1 TTTTAATTTAATTAATATTAATTTTTATAT
3452987 TTTTAA
1 TTTTAA
3452993 AATTTGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTAATTTAATTAATATTAATTTTTATAT
Found at i:3455105 original size:3 final size:3
Alignment explanation
Indices: 3455097--3455141 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3455087 GTATATACAT
* *
3455097 ATA ATA ATA ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3455142 TGAAAATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3457426 original size:91 final size:91
Alignment explanation
Indices: 3457278--3457445 Score: 255
Period size: 91 Copynumber: 1.8 Consensus size: 91
3457268 CGAGATTCTT
* *** *
3457278 TTTTTGTTGCGTGGTTAAGAAAATGTTTGGCTTGAAATCGCACTAGAATTTTCTGTTTGTTTGCT
1 TTTTCGTTGCGTGGTTAAGAAAATGTTTAAATTGAAATCGCACTAGAATTTTCTGTTTGCTTGCT
3457343 GAGAAACACTGTTTGAATTCTTTTTA
66 GAGAAACACTGTTTGAATTCTTTTTA
* * * *
3457369 TTTTCGTTGCGTGGTTCAGAAACTGTTTAAATTGAATTCGCACTAGAATTTTTTGTTTGCTTGCT
1 TTTTCGTTGCGTGGTTAAGAAAATGTTTAAATTGAAATCGCACTAGAATTTTCTGTTTGCTTGCT
3457434 GAGAAACACTGT
66 GAGAAACACTGT
3457446 GAGAAAAACT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 68 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.43
Consensus pattern (91 bp):
TTTTCGTTGCGTGGTTAAGAAAATGTTTAAATTGAAATCGCACTAGAATTTTCTGTTTGCTTGCT
GAGAAACACTGTTTGAATTCTTTTTA
Found at i:3457533 original size:100 final size:101
Alignment explanation
Indices: 3457342--3457724 Score: 468
Period size: 100 Copynumber: 3.8 Consensus size: 101
3457332 GTTTGTTTGC
* * * * *
3457342 TGAGAAACACTGTTTGAATTCTTTTTATTTTCGTTGCGTGGTTCAGAAACTGTTTAAATTGAATT
1 TGAGAAAAACTGTTTGAATTC-TTTT-TTTTCGTTGCATGGTTAAGAAAATGTTTAATTTGAATT
* *
3457407 CGCACTAGAATTTTTTGTTTGCTTGCTGAGAAACACTG
64 CGCACTAGAATTTTCTGATTGCTTGCTGAGAAACACTG
* * * * * * *
3457445 TGAGAAAAACTGGTTGAATTCTTTTTTTTGGTCGCGT-GATAAGAAAATGTTTGATTCGAATTCG
1 TGAGAAAAACTGTTTGAATTCTTTTTTTTCGTTGCATGGTTAAGAAAATGTTTAATTTGAATTCG
* * *
3457509 CATTAGAGTTTTCTGATTGTTTGCTGAGAAACACTG
66 CACTAGAATTTTCTGATTGCTTGCTGAGAAACACTG
3457545 TGAGAAAAACTGTTTGAATTCTTTTTTTTCGTTGCATGGTTAAGAAAATG-TTAATTTGAATTCG
1 TGAGAAAAACTGTTTGAATTCTTTTTTTTCGTTGCATGGTTAAGAAAATGTTTAATTTGAATTCG
* * * *
3457609 CACTAGAATTCTCTGACTGGTAGCTGAGAAACAC--
66 CACTAGAATTTTCTGATTGCTTGCTGAGAAACACTG
* * * * *
3457643 TGAGAAAAAATCGTTTGAATTTTTTTTATTTTGTTGCATGGTTAAGAAATTGTTTAATTTGAACT
1 TGAGAAAAACT-GTTTGAATTCTTTTT-TTTCGTTGCATGGTTAAGAAAATGTTTAATTTGAATT
3457708 CGCACTAGAATTTTCTG
64 CGCACTAGAATTTTCTG
3457725 TTTTTGGTTG
Statistics
Matches: 242, Mismatches: 34, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
98 10 0.04
99 14 0.06
100 147 0.61
101 48 0.20
102 4 0.02
103 19 0.08
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (101 bp):
TGAGAAAAACTGTTTGAATTCTTTTTTTTCGTTGCATGGTTAAGAAAATGTTTAATTTGAATTCG
CACTAGAATTTTCTGATTGCTTGCTGAGAAACACTG
Found at i:3457735 original size:56 final size:55
Alignment explanation
Indices: 3457671--3457779 Score: 155
Period size: 56 Copynumber: 2.0 Consensus size: 55
3457661 ATTTTTTTTA
*
3457671 TTTTGTTGCATGGTTAAGAAATTGTTTAATTTGAACTCGCACTAGAATTTTCTGT
1 TTTTGTTGCATGGTTAAGAAAATGTTTAATTTGAACTCGCACTAGAATTTTCTGT
* * * * *
3457726 TTTTGGTTGCGTGGTTAATAAAATGTTTAATTTGAATTCGCATTAGAGTTTTCT
1 TTTT-GTTGCATGGTTAAGAAAATGTTTAATTTGAACTCGCACTAGAATTTTCT
3457780 CATTGTTTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
55 4 0.09
56 43 0.91
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (55 bp):
TTTTGTTGCATGGTTAAGAAAATGTTTAATTTGAACTCGCACTAGAATTTTCTGT
Found at i:3457878 original size:157 final size:156
Alignment explanation
Indices: 3457569--3457862 Score: 385
Period size: 157 Copynumber: 1.9 Consensus size: 156
3457559 TGAATTCTTT
* *
3457569 TTTTTCGTTGCATGGTTAAGAAAATGTTAATTTGAATTCGCACTAGAATTCTCTGACTGGTAGCT
1 TTTTTCGTTGCATGGTTAAGAAAATGTTAATTTGAATTCGCACTAGAATTCTCTCACTGGTACCT
* * *
3457634 GAGAAACACTGAGAAAAAATCGTTTGAATTTTTTTTATTTTGTTGCATGGTTAAGAAATTGTTTA
66 GAGAAACACTGAGAAAAAATCGTTTGAATTTTTTTTATTTCGTTGCATGGTTAAGAAAATATTTA
**
3457699 ATTTGAACTCGCACTAGAATTTTCTG
131 ATTCAAACTCGCACTAGAATTTTCTG
* * * * * * * * *
3457725 TTTTTGGTTGCGTGGTTAATAAAATGTTTAATTTGAATTCGCATTAGAGTTTTCTCATTGTTTCC
1 TTTTTCGTTGCATGGTTAAGAAAATG-TTAATTTGAATTCGCACTAGAATTCTCTCACTGGTACC
*
3457790 TGAGAAACACTGAG-AAAAATTGTTTGAATTCCTTTTTT-TTTCGTTGCATGGTTAAGAAAATAT
65 TGAGAAACACTGAGAAAAAATCGTTTGAATT--TTTTTTATTTCGTTGCATGGTTAAGAAAATAT
*
3457853 TTTATTCAAA
128 TTAATTCAAA
3457863 TTCGGATCAG
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
156 38 0.32
157 73 0.62
158 6 0.05
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (156 bp):
TTTTTCGTTGCATGGTTAAGAAAATGTTAATTTGAATTCGCACTAGAATTCTCTCACTGGTACCT
GAGAAACACTGAGAAAAAATCGTTTGAATTTTTTTTATTTCGTTGCATGGTTAAGAAAATATTTA
ATTCAAACTCGCACTAGAATTTTCTG
Found at i:3460313 original size:15 final size:15
Alignment explanation
Indices: 3460293--3460321 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3460283 AAATCGCCTC
3460293 TTTAATTCTTGTTTT
1 TTTAATTCTTGTTTT
3460308 TTTAATTCTTGTTT
1 TTTAATTCTTGTTT
3460322 CCATTTATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTAATTCTTGTTTT
Found at i:3466837 original size:23 final size:24
Alignment explanation
Indices: 3466811--3466855 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3466801 TGATGAATAT
3466811 TGGGTTT-TGATTGCTA-TATTTTC
1 TGGGTTTGTG-TTGCTATTATTTTC
3466834 TGGGTTTGTGTTGCTATTATTT
1 TGGGTTTGTGTTGCTATTATTT
3466856 GTAACAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.11, C:0.07, G:0.24, T:0.58
Consensus pattern (24 bp):
TGGGTTTGTGTTGCTATTATTTTC
Found at i:3478789 original size:14 final size:14
Alignment explanation
Indices: 3478770--3478796 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3478760 TATTATAAGG
3478770 TCAAACTACAAAAT
1 TCAAACTACAAAAT
3478784 TCAAACTACAAAA
1 TCAAACTACAAAA
3478797 ATAGTCACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (14 bp):
TCAAACTACAAAAT
Found at i:3481376 original size:47 final size:46
Alignment explanation
Indices: 3481231--3481381 Score: 164
Period size: 47 Copynumber: 3.3 Consensus size: 46
3481221 CACAACTGGT
* * * **
3481231 CATTCGGCCTTATCACATAT-TCACTTACACATAT-ATCACATTAAC
1 CATTCGACCTTATCACATATAACACTTTCACAT-TCATCACATTGGC
* * *
3481276 CATTC-AGCCTTATCTCATGTATGCACTTTCACATTCATCACATTGGC
1 CATTCGA-CCTTATCACATATA-ACACTTTCACATTCATCACATTGGC
3481323 CATTCGACCTTATCACATATACACACTTTCACATTCATCACATTGGC
1 CATTCGACCTTATCACATATA-ACACTTTCACATTCATCACATTGGC
*
3481370 CATTCGATCTTA
1 CATTCGACCTTA
3481382 AGCTAGATAT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
45 16 0.18
46 1 0.01
47 71 0.80
48 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.34
Consensus pattern (46 bp):
CATTCGACCTTATCACATATAACACTTTCACATTCATCACATTGGC
Found at i:3486013 original size:9 final size:9
Alignment explanation
Indices: 3485995--3486077 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 9
3485985 GGATGTTAAA
*
3485995 GACGATGAT
1 GACGACGAT
3486004 GACGACGAT
1 GACGACGAT
* * *
3486013 GAAGGCGAA
1 GACGACGAT
* **
3486022 GGCGACGGC
1 GACGACGAT
*
3486031 GACGGCGAT
1 GACGACGAT
*
3486040 GACGACGAC
1 GACGACGAT
3486049 GACGACGAT
1 GACGACGAT
*
3486058 GATGAC-AGT
1 GACGACGA-T
*
3486067 GATGACGAT
1 GACGACGAT
3486076 GA
1 GA
3486078 AGAAGGTGAA
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
8 1 0.02
9 53 0.96
10 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.39, T:0.11
Consensus pattern (9 bp):
GACGACGAT
Found at i:3486819 original size:24 final size:24
Alignment explanation
Indices: 3486792--3486844 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3486782 ATTTTGAACC
* *
3486792 AGAAGAAAATGGTGAAGAGGAAGA
1 AGAAGAAAATGATGAAGACGAAGA
* *
3486816 AGAAGAAGATGATGAAGACGATGA
1 AGAAGAAAATGATGAAGACGAAGA
3486840 AGAAG
1 AGAAG
3486845 GTAGTGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.36, T:0.09
Consensus pattern (24 bp):
AGAAGAAAATGATGAAGACGAAGA
Found at i:3492366 original size:13 final size:13
Alignment explanation
Indices: 3492348--3492373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3492338 ATAAAGCTTT
3492348 GGTTGAGTGATAA
1 GGTTGAGTGATAA
3492361 GGTTGAGTGATAA
1 GGTTGAGTGATAA
3492374 ATTTAATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
GGTTGAGTGATAA
Found at i:3493546 original size:31 final size:32
Alignment explanation
Indices: 3493511--3493579 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
3493501 TTTAATACTC
*
3493511 AAACTTGACAATTTTTT-C-TAATTTGGTACCT
1 AAACTTGAC-ATTTTTTCCTTAAGTTGGTACCT
* *
3493542 AAACTTGACCTTTTTTCCTTAAGTTGGTACTT
1 AAACTTGACATTTTTTCCTTAAGTTGGTACCT
3493574 AAACTT
1 AAACTT
3493580 TTTGGGGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 6 0.18
31 10 0.30
32 17 0.52
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (32 bp):
AAACTTGACATTTTTTCCTTAAGTTGGTACCT
Found at i:3499921 original size:14 final size:14
Alignment explanation
Indices: 3499902--3499929 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3499892 GGCCTGTGAT
3499902 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
3499916 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
3499930 AACAACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TCAAGATTTTAAAC
Found at i:3508759 original size:14 final size:14
Alignment explanation
Indices: 3508739--3508783 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3508729 CTCAAGTTCG
3508739 AGGATTTAAGATTT
1 AGGATTTAAGATTT
* *
3508753 GGGATTTAAAATTT
1 AGGATTTAAGATTT
**
3508767 AAAATTTAAGATTT
1 AGGATTTAAGATTT
3508781 AGG
1 AGG
3508784 GTTAGTTTAA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (14 bp):
AGGATTTAAGATTT
Found at i:3509747 original size:7 final size:7
Alignment explanation
Indices: 3509735--3509773 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
3509725 TCGTTTTTTA
3509735 TTTAGGG
1 TTTAGGG
3509742 TTTAGGG
1 TTTAGGG
*
3509749 TTTAAGG
1 TTTAGGG
3509756 TTTAGGG
1 TTTAGGG
3509763 TTTAGGG
1 TTTAGGG
3509770 TTTA
1 TTTA
3509774 TATCAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:3520461 original size:22 final size:20
Alignment explanation
Indices: 3520430--3520471 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3520420 ATTTTTTATA
3520430 AAAATGAAAATAAAAATACTTG
1 AAAATGAAAA-AAAAA-ACTTG
*
3520452 AAAATTAAAAAAAAAACTTG
1 AAAATGAAAAAAAAAACTTG
3520472 TTTTCATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (20 bp):
AAAATGAAAAAAAAAACTTG
Found at i:3523194 original size:33 final size:30
Alignment explanation
Indices: 3523123--3523197 Score: 80
Period size: 33 Copynumber: 2.4 Consensus size: 30
3523113 ATTTTAAAAT
* *
3523123 TATATATG-AACTTTGATTTGGTCCAATTA
1 TATATATGAAACTCTGATTTGGTCAAATTA
* *
3523152 TACACATGAAACTCTGATTGTGGTTCAAATATA
1 TATATATGAAACTCTGATT-TGG-TCAAAT-TA
3523185 TATATATGAAACT
1 TATATATGAAACT
3523198 TCAATTTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 6 0.17
30 9 0.25
31 3 0.08
32 5 0.14
33 13 0.36
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (30 bp):
TATATATGAAACTCTGATTTGGTCAAATTA
Found at i:3526467 original size:17 final size:17
Alignment explanation
Indices: 3526445--3526498 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
3526435 TTTTAGTATT
3526445 AAATAAACTCAGTATAA
1 AAATAAACTCAGTATAA
* * *
3526462 AAATAAATTTTAGTAT-T
1 AAATAAA-CTCAGTATAA
3526479 AAATAAACTCAGTATAA
1 AAATAAACTCAGTATAA
3526496 AAA
1 AAA
3526499 AAGCTAGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30
Consensus pattern (17 bp):
AAATAAACTCAGTATAA
Found at i:3526475 original size:34 final size:34
Alignment explanation
Indices: 3526432--3526498 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
3526422 TACAATGTGC
3526432 AAATTTTAGTATTAAATAAACTCAGTATAAAAAT
1 AAATTTTAGTATTAAATAAACTCAGTATAAAAAT
3526466 AAATTTTAGTATTAAATAAACTCAGTATAAAAA
1 AAATTTTAGTATTAAATAAACTCAGTATAAAAA
3526499 AAGCTAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (34 bp):
AAATTTTAGTATTAAATAAACTCAGTATAAAAAT
Found at i:3526519 original size:34 final size:34
Alignment explanation
Indices: 3526438--3526509 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
3526428 GTGCAAATTT
**
3526438 TAGTATTAAATAAACTCAGTATAAAAATAAATTT
1 TAGTATTAAATAAACTCAGTATAAAAATAAATGC
3526472 TAGTATTAAATAAACTCAGTAT-AAAA-AAA-GC
1 TAGTATTAAATAAACTCAGTATAAAAATAAATGC
3526503 TAGTATT
1 TAGTATT
3526510 GGTAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 7 0.19
32 3 0.08
33 4 0.11
34 22 0.61
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.33
Consensus pattern (34 bp):
TAGTATTAAATAAACTCAGTATAAAAATAAATGC
Found at i:3529285 original size:16 final size:15
Alignment explanation
Indices: 3529259--3529292 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3529249 CGGTTTTTGC
3529259 TATATATTATAAAAA
1 TATATATTATAAAAA
*
3529274 TATATGATTATAAAGA
1 TATAT-ATTATAAAAA
3529290 TAT
1 TAT
3529293 TTTTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
TATATATTATAAAAA
Found at i:3536299 original size:53 final size:52
Alignment explanation
Indices: 3536236--3536339 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 52
3536226 AATACTAGGC
3536236 ATACCTCCACACAAACATTGTATTTGATGCTCTCGTGTACTATCATCCTCGCA
1 ATACCTCCACACAAACATTGTATTTGATGCTCTCGTGTAC-ATCATCCTCGCA
3536289 ATACCTCCACACAAACATTGTATTTGATGCTCTCGTGTACATCATCCTCGC
1 ATACCTCCACACAAACATTGTATTTGATGCTCTCGTGTACATCATCCTCGC
3536340 TATATGATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 11 0.22
53 40 0.78
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.32
Consensus pattern (52 bp):
ATACCTCCACACAAACATTGTATTTGATGCTCTCGTGTACATCATCCTCGCA
Found at i:3537010 original size:5 final size:5
Alignment explanation
Indices: 3536997--3537031 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
3536987 AAGACTACTT
3536997 TTTTAG TTTTG TTTTG TTTTG TTTT- TTTTG TTTTG
1 TTTT-G TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
3537032 AGAGGGGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 20 0.71
6 4 0.14
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:3537411 original size:10 final size:10
Alignment explanation
Indices: 3537392--3537421 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3537382 ATTTTACTAA
3537392 TATATATATG
1 TATATATATG
*
3537402 TATATGTATG
1 TATATATATG
3537412 TATATATATG
1 TATATATATG
3537422 CTTCAGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:3544688 original size:88 final size:87
Alignment explanation
Indices: 3544521--3544695 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
3544511 AATTTGGATT
*
3544521 AGTACGAATTTAAATTAAAGGTTTATATGTTAAAAAGTCCTTAAGAAATTGCAAAAAATCAATTA
1 AGTACGAATTTAAATTAAAGGTTTATATGTTAAAAAATCCTTAAGAAATTGCAAAAAATCAATTA
3544586 AGCCCTTATATTAAATTCTCAC
66 AGCCCTTATATTAAATTCTCAC
*
3544608 AGTACGAATTTAAATTAAAGGTTTATATGTTAAAAAATCCTTAAGAAATTGTAAAAAGATCAATT
1 AGTACGAATTTAAATTAAAGGTTTATATGTTAAAAAATCCTTAAGAAATTGCAAAAA-ATCAATT
3544673 AAGCCCTTATATTAAATTCTCAC
65 AAGCCCTTATATTAAATTCTCAC
3544696 CTAATTAAGC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
87 55 0.65
88 30 0.35
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (87 bp):
AGTACGAATTTAAATTAAAGGTTTATATGTTAAAAAATCCTTAAGAAATTGCAAAAAATCAATTA
AGCCCTTATATTAAATTCTCAC
Found at i:3544752 original size:13 final size:13
Alignment explanation
Indices: 3544730--3544760 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3544720 AAAAAATCAA
*
3544730 TTAACTCCCTTCG
1 TTAACACCCTTCG
3544743 TTAACACCCTTCG
1 TTAACACCCTTCG
3544756 TTAAC
1 TTAAC
3544761 GGTTTTCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.35
Consensus pattern (13 bp):
TTAACACCCTTCG
Found at i:3544874 original size:9 final size:9
Alignment explanation
Indices: 3544838--3544935 Score: 67
Period size: 9 Copynumber: 10.8 Consensus size: 9
3544828 AATATTTTTC
3544838 TATAAAAAT
1 TATAAAAAT
3544847 TATTAAAAAT
1 TA-TAAAAAT
* *
3544857 CATACAAAT
1 TATAAAAAT
3544866 TATAAAAATAT
1 TAT-AAAA-AT
*
3544877 TATTAAAATT
1 TA-TAAAAAT
* *
3544887 TATATAACT
1 TATAAAAAT
*
3544896 TATAATAA-
1 TATAAAAAT
*
3544904 T-TAATAAT
1 TATAAAAAT
3544912 TATAAAAA-
1 TATAAAAAT
3544920 TATAAAAAT
1 TATAAAAAT
*
3544929 AATAAAA
1 TATAAAA
3544936 CATATTTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
7 6 0.09
8 10 0.14
9 31 0.44
10 14 0.20
11 8 0.11
12 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
TATAAAAAT
Found at i:3545563 original size:27 final size:28
Alignment explanation
Indices: 3545532--3545592 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
3545522 TTTTTTTATA
3545532 ATTTTTATAAGTTTAT-ATAATTTTAATG
1 ATTTTTATAAGTTTATAATAA-TTTAATG
* * *
3545560 -TTTTTATTATTTTTTAATAATTTAATG
1 ATTTTTATAAGTTTATAATAATTTAATG
3545587 ATTTTT
1 ATTTTT
3545593 TATTAATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
ATTTTTATAAGTTTATAATAATTTAATG
Found at i:3545590 original size:19 final size:19
Alignment explanation
Indices: 3545568--3545637 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
3545558 TGTTTTTATT
3545568 ATTTTTTAATAATTTAATG
1 ATTTTTTAATAATTTAATG
* *
3545587 ATTTTTTATTAATTCT-ATA
1 ATTTTTTAATAATT-TAATG
*
3545606 ATTTGTTT-ATAATTTATTAG
1 ATTT-TTTAATAATTTAAT-G
3545626 A-TTTTTAATAAT
1 ATTTTTTAATAAT
3545638 ATTTATAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 4 0.10
19 32 0.78
20 5 0.12
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTTTTTAATAATTTAATG
Found at i:3553337 original size:24 final size:24
Alignment explanation
Indices: 3553307--3553353 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3553297 TTTGGTGTTA
3553307 TTTTCTTGTGGAACACTTCCTTTG
1 TTTTCTTGTGGAACACTTCCTTTG
3553331 TTTTCTTGTGGAACACTTCCTTT
1 TTTTCTTGTGGAACACTTCCTTT
3553354 TGATTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (24 bp):
TTTTCTTGTGGAACACTTCCTTTG
Found at i:3553789 original size:29 final size:30
Alignment explanation
Indices: 3553707--3553790 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
3553697 TTTATATAAC
* * *
3553707 TTTTAAAGGG-TTAAATTATGAAATTTTTAT
1 TTTTAAAGGGATCAAA-TATGAAATTTTAAA
3553737 TTTTAAAGGGATCAAATATG-AATTTTAAA
1 TTTTAAAGGGATCAAATATGAAATTTTAAA
3553766 TTTT-AAGAGGATCAAA-ATGAAATTT
1 TTTTAAAG-GGATCAAATATGAAATTT
3553791 CACCCTTAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.12
29 24 0.50
30 14 0.29
31 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (30 bp):
TTTTAAAGGGATCAAATATGAAATTTTAAA
Found at i:3554885 original size:23 final size:25
Alignment explanation
Indices: 3554850--3554907 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
3554840 AGGAGTGGTA
*
3554850 AATAAACTATTAAT-TTT-ATTTTT
1 AATAAAATATTAATATTTAATTTTT
*
3554873 AATAAAATTTTAATACTTTAATTTTT
1 AATAAAATATTAATA-TTTAATTTTT
*
3554899 AATGAAATA
1 AATAAAATA
3554908 AAGAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 12 0.43
25 3 0.11
26 13 0.46
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (25 bp):
AATAAAATATTAATATTTAATTTTT
Found at i:3557747 original size:12 final size:14
Alignment explanation
Indices: 3557730--3557785 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 14
3557720 GATTAAATAA
3557730 TAATTATTATAAA-
1 TAATTATTATAAAT
*
3557743 T-ATTATTTTAAAT
1 TAATTATTATAAAT
3557756 TAATTATTATATAAT
1 TAATTATTATA-AAT
3557771 TAA-TATTA-AAAT
1 TAATTATTATAAAT
3557783 TAA
1 TAA
3557786 AATTTATCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 16 0.42
13 3 0.08
14 13 0.34
15 6 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATTATAAAT
Found at i:3557779 original size:26 final size:26
Alignment explanation
Indices: 3557721--3557785 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
3557711 GACTTAACCG
*
3557721 ATTAAATAATAATTATTATAAATATTAT
1 ATTAAAT--TAATTATTATAAATATAAT
*
3557749 TTTAAATTAATTATTATATAAT-TAAT
1 ATTAAATTAATTATTATA-AATATAAT
3557775 ATTAAAATTAA
1 ATT-AAATTAA
3557786 AATTTATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 16 0.50
27 10 0.31
28 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTAAATTAATTATTATAAATATAAT
Found at i:3570199 original size:21 final size:21
Alignment explanation
Indices: 3570168--3570217 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
3570158 TCTAATAAAG
* *
3570168 AATATAA-ATATACATTTAATC
1 AATATAATATA-AAATTAAATC
3570189 AACTATAATATAAAATTAAATC
1 AA-TATAATATAAAATTAAATC
3570211 AATATAA
1 AATATAA
3570218 AATATAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 15 0.60
23 3 0.12
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (21 bp):
AATATAATATAAAATTAAATC
Found at i:3571176 original size:21 final size:21
Alignment explanation
Indices: 3571129--3571179 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3571119 TTGTTTTAAA
3571129 TTTAATTATAAAATATAATAAT
1 TTTAA-TATAAAATATAATAAT
* *
3571151 ATTAATATAAAATA-ATATATT
1 TTTAATATAAAATATA-ATAAT
3571172 TTTAATAT
1 TTTAATAT
3571180 TTTATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAATATAAAATATAATAAT
Found at i:3571840 original size:24 final size:22
Alignment explanation
Indices: 3571779--3571840 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
3571769 TGGCGACATG
*
3571779 TTTCCCACTTAACTAGGTTTTT
1 TTTCCCAATTAACTAGGTTTTT
* *
3571801 TTTCCCTAGTTAAACTATGTTATTT
1 TTTCCC-AATT-AACTAGGTT-TTT
3571826 TTTCCCAATCTAACT
1 TTTCCCAAT-TAACT
3571841 TTGATTGTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.18
23 3 0.09
24 14 0.42
25 10 0.30
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (22 bp):
TTTCCCAATTAACTAGGTTTTT
Found at i:3574109 original size:24 final size:24
Alignment explanation
Indices: 3574081--3574126 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3574071 TGGTAGGGGC
3574081 AGAGACGAGAGTGGGAGAGGCAGT
1 AGAGACGAGAGTGGGAGAGGCAGT
3574105 AGAGACGAGAGTGGGAGAGGCA
1 AGAGACGAGAGTGGGAGAGGCA
3574127 AAGGCTCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.50, T:0.07
Consensus pattern (24 bp):
AGAGACGAGAGTGGGAGAGGCAGT
Found at i:3576785 original size:25 final size:23
Alignment explanation
Indices: 3576740--3576787 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
3576730 AGCAAAGCAA
*
3576740 AGCAAAACCCATCATTAATCTAC
1 AGCAAAACCCATCAGTAATCTAC
*
3576763 AGCAAAACCACCATCAGTCATCTAC
1 AGCAAAA-C-CCATCAGTAATCTAC
3576788 TACAGTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 13 0.62
ACGTcount: A:0.42, C:0.33, G:0.06, T:0.19
Consensus pattern (23 bp):
AGCAAAACCCATCAGTAATCTAC
Found at i:3577456 original size:37 final size:37
Alignment explanation
Indices: 3577415--3577491 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
3577405 AAATAAAGTA
3577415 AATTCAATATCAACAATCAATCGTAAAAATTCGATCC
1 AATTCAATATCAACAATCAATCGTAAAAATTCGATCC
3577452 AATTCAATATCAACAATCAATCGTAAAAATTCGATCC
1 AATTCAATATCAACAATCAATCGTAAAAATTCGATCC
3577489 AAT
1 AAT
3577492 CGAGAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.27
Consensus pattern (37 bp):
AATTCAATATCAACAATCAATCGTAAAAATTCGATCC
Found at i:3578194 original size:30 final size:29
Alignment explanation
Indices: 3578128--3578195 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
3578118 AATTTATGCG
* * *
3578128 TGTAATGTTATATATAAAATTTGATTTTA
1 TGTAATTTTATACATAAAATTTGATTTGA
*
3578157 TGAAATTTTATACATAAAATTTTGATTTGA
1 TGTAATTTTATACATAAAA-TTTGATTTGA
*
3578187 TTTAATTTT
1 TGTAATTTT
3578196 CACAAATCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (29 bp):
TGTAATTTTATACATAAAATTTGATTTGA
Found at i:3582856 original size:28 final size:28
Alignment explanation
Indices: 3582816--3582878 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
3582806 GCCATTATTA
3582816 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * *
3582844 ACCCCATAAGTTATGAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
3582872 ACCCCAT
1 ACCCCAT
3582879 TAATATGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:3583038 original size:14 final size:14
Alignment explanation
Indices: 3582998--3583038 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3582988 AAAAAGAAGA
3582998 TACACTCTCTCTTC
1 TACACTCTCTCTTC
3583012 TACA-T-TCTC-TC
1 TACACTCTCTCTTC
*
3583023 TACACTCTTTCTTC
1 TACACTCTCTCTTC
3583037 TA
1 TA
3583039 TCACATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 6 0.26
12 5 0.22
13 4 0.17
14 8 0.35
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (14 bp):
TACACTCTCTCTTC
Found at i:3588293 original size:28 final size:28
Alignment explanation
Indices: 3588241--3588299 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3588231 TTATCAACCC
*
3588241 CATAAGTTATAAAACTCTTCTTATACCT
1 CATAAGTTATAAAACTCTTCCTATACCT
* * *
3588269 CATAAGTTATGAGACTTTTCCTATACCT
1 CATAAGTTATAAAACTCTTCCTATACCT
3588297 CAT
1 CAT
3588300 TAATATGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (28 bp):
CATAAGTTATAAAACTCTTCCTATACCT
Found at i:3588459 original size:14 final size:14
Alignment explanation
Indices: 3588419--3588459 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3588409 AAAAAGAAGA
3588419 TACACTCTCTCTTC
1 TACACTCTCTCTTC
3588433 TACA-T-TCTC-TC
1 TACACTCTCTCTTC
*
3588444 TACACTCTTTCTTC
1 TACACTCTCTCTTC
3588458 TA
1 TA
3588460 TCACATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 6 0.26
12 5 0.22
13 4 0.17
14 8 0.35
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (14 bp):
TACACTCTCTCTTC
Found at i:3594048 original size:49 final size:49
Alignment explanation
Indices: 3593995--3594092 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
3593985 ACACAAAAAG
3593995 TTAAATTTAATCCAATGCTTACTTTGCTATTTGAACTGTTCAAATTGAT
1 TTAAATTTAATCCAATGCTTACTTTGCTATTTGAACTGTTCAAATTGAT
3594044 TTAAATTTAATCCAATGCTTACTTTGCTATTTGAACTGTTCAAATTGAT
1 TTAAATTTAATCCAATGCTTACTTTGCTATTTGAACTGTTCAAATTGAT
3594093 GATAACCAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (49 bp):
TTAAATTTAATCCAATGCTTACTTTGCTATTTGAACTGTTCAAATTGAT
Found at i:3598390 original size:8 final size:8
Alignment explanation
Indices: 3598377--3598410 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
3598367 TACAATTTAA
3598377 TATTTTTT
1 TATTTTTT
3598385 TATTTTTT
1 TATTTTTT
3598393 TATTTTTT
1 TATTTTTT
3598401 TATTTTTT
1 TATTTTTT
3598409 TA
1 TA
3598411 AAATTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:3599518 original size:16 final size:16
Alignment explanation
Indices: 3599461--3599520 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
3599451 GTTAACTGAG
3599461 AATGA-CTAAAATAGA
1 AATGATCTAAAATAGA
* *
3599476 AATGATCT-AAATCGTG
1 AATGATCTAAAATAG-A
* *
3599492 AGTGAT-AAAAATAGA
1 AATGATCTAAAATAGA
3599507 AATGATCTAAAATA
1 AATGATCTAAAATA
3599521 TTAGTGACTA
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
15 15 0.45
16 18 0.55
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (16 bp):
AATGATCTAAAATAGA
Found at i:3599527 original size:31 final size:32
Alignment explanation
Indices: 3599463--3599532 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
3599453 TAACTGAGAA
*
3599463 TGACT-AAAATAGAAATGATCTAAATCGTGAG
1 TGACTAAAAATAGAAATGATCTAAATCATGAG
*
3599494 TGA-TAAAAATAGAAATGATCTAAAAT-ATTAG
1 TGACTAAAAATAGAAATGATCT-AAATCATGAG
3599525 TGACTAAA
1 TGACTAAA
3599533 TTAAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 25 0.74
32 8 0.24
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (32 bp):
TGACTAAAAATAGAAATGATCTAAATCATGAG
Found at i:3602263 original size:14 final size:14
Alignment explanation
Indices: 3602244--3602273 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3602234 TAAAAATTTA
3602244 AGCAATTAGTGATT
1 AGCAATTAGTGATT
3602258 AGCAATTAGTGATT
1 AGCAATTAGTGATT
3602272 AG
1 AG
3602274 TTGATAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (14 bp):
AGCAATTAGTGATT
Found at i:3602482 original size:12 final size:12
Alignment explanation
Indices: 3602465--3602492 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3602455 TAAATACCAC
3602465 TAAATTTTCTTT
1 TAAATTTTCTTT
3602477 TAAATTTTCTTT
1 TAAATTTTCTTT
3602489 TAAA
1 TAAA
3602493 AAATTGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
TAAATTTTCTTT
Found at i:3610352 original size:32 final size:32
Alignment explanation
Indices: 3610307--3610370 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3610297 TAGTTAAGAA
3610307 AAAAAAACAAAAATTAGATATAAAAATAAATG
1 AAAAAAACAAAAATTAGATATAAAAATAAATG
*
3610339 AAAAAAACGAAAATTAGATATAAAAATAAATG
1 AAAAAAACAAAAATTAGATATAAAAATAAATG
3610371 GAACATTGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.19
Consensus pattern (32 bp):
AAAAAAACAAAAATTAGATATAAAAATAAATG
Found at i:3610363 original size:19 final size:18
Alignment explanation
Indices: 3610309--3610364 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 18
3610299 GTTAAGAAAA
3610309 AAAAACAAAAATTAGATAT
1 AAAAAC-AAAATTAGATAT
*
3610328 AAAAA-TAAA-T-GA-A-
1 AAAAACAAAATTAGATAT
3610341 AAAAACGAAAATTAGATAT
1 AAAAAC-AAAATTAGATAT
3610360 AAAAA
1 AAAAA
3610365 TAAATGGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
13 5 0.17
14 1 0.03
15 5 0.17
16 2 0.07
17 5 0.17
18 1 0.03
19 10 0.34
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (18 bp):
AAAAACAAAATTAGATAT
Found at i:3610960 original size:17 final size:17
Alignment explanation
Indices: 3610938--3610995 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
3610928 TTTAATTTTT
3610938 ATATAAAAATTAAAAAA
1 ATATAAAAATTAAAAAA
* *
3610955 ATATAATACATCAAAAACA
1 ATATAA-AAATTAAAAA-A
3610974 ATA-AAAATATTAAAATAA
1 ATATAAAA-ATTAAAA-AA
3610992 ATAT
1 ATAT
3610996 TTCTCAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 7 0.22
18 20 0.62
19 5 0.16
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATAAAAATTAAAAAA
Found at i:3612395 original size:45 final size:46
Alignment explanation
Indices: 3612328--3612451 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
3612318 CATATGACCT
*
3612328 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3612371 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3612417 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3612452 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:3612434 original size:46 final size:45
Alignment explanation
Indices: 3612328--3612525 Score: 207
Period size: 37 Copynumber: 4.8 Consensus size: 45
3612318 CATATGACCT
*
3612328 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3612371 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
3612417 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3612454 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
3612491 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3612526 CACTTATCAC
Statistics
Matches: 140, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
37 64 0.46
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.06
44 6 0.04
45 21 0.15
46 34 0.24
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:3612455 original size:37 final size:37
Alignment explanation
Indices: 3612414--3612551 Score: 233
Period size: 37 Copynumber: 3.8 Consensus size: 37
3612404 GCTGAAGCTA
* *
3612414 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3612451 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3612488 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
3612525 CCACTTATCACTTTGT-TCTTGATCAGA
1 CCACTTATCACTTTGTCTCTTGATCAGA
3612552 AGTACTCAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 11 0.11
37 85 0.89
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:3614072 original size:45 final size:45
Alignment explanation
Indices: 3614008--3614101 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
3613998 AAACAGTGAG
3614008 AAAATAATAATTTCCTTTTACAAATTCGAGCCAAGCCCAGGCCAA
1 AAAATAATAATTTCCTTTTACAAATTCGAGCCAAGCCCAGGCCAA
* *
3614053 AAAATAATAATTTCTTTTTACAAATTCGAGCGAAGCCCAGGCCAA
1 AAAATAATAATTTCCTTTTACAAATTCGAGCCAAGCCCAGGCCAA
3614098 AAAA
1 AAAA
3614102 ACTTACCTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (45 bp):
AAAATAATAATTTCCTTTTACAAATTCGAGCCAAGCCCAGGCCAA
Found at i:3615777 original size:27 final size:28
Alignment explanation
Indices: 3615747--3615799 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
3615737 TATATAATAC
3615747 TAATAAAACTAAAATTAAATC-ATATTT
1 TAATAAAACTAAAATTAAATCTATATTT
* * *
3615774 TAATAAAATTAATATTCAATCTATAT
1 TAATAAAACTAAAATTAAATCTATAT
3615800 AAATTAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATAAAACTAAAATTAAATCTATATTT
Found at i:3630183 original size:26 final size:26
Alignment explanation
Indices: 3630154--3630205 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3630144 ACATGATTGT
3630154 TTAAATTAAATCAGAACGATCAGTTC
1 TTAAATTAAATCAGAACGATCAGTTC
3630180 TTAAATTAAATCAGAACGATCAGTTC
1 TTAAATTAAATCAGAACGATCAGTTC
3630206 AAGAATCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
TTAAATTAAATCAGAACGATCAGTTC
Found at i:3634776 original size:17 final size:18
Alignment explanation
Indices: 3634754--3634792 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3634744 GGAAAGCTTC
*
3634754 AAAAAAGAAAAAAGAA-A
1 AAAAAACAAAAAAGAATA
*
3634771 AAAAAACAAAATAGAATA
1 AAAAAACAAAAAAGAATA
3634789 AAAA
1 AAAA
3634793 TGAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.85, C:0.03, G:0.08, T:0.05
Consensus pattern (18 bp):
AAAAAACAAAAAAGAATA
Done.