Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 8 of 135
Found at i:3607875 original size:67 final size:67
Alignment explanation
Indices: 3607767--3608031 Score: 503
Period size: 67 Copynumber: 4.0 Consensus size: 67
3607757 TTTATATTAC
3607767 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
3607832 GT
66 GT
3607834 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
3607899 GT
66 GT
3607901 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
3607966 GT
66 GT
* * *
3607968 AGGGGATTTAGCCTGGACTGGTAATCCCGCTATAAGAAATAAGGTTCGTGGGAGTGTGCTCTCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
3608032 GAATTGGAAA
Statistics
Matches: 195, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 195 1.00
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
GT
Found at i:3614093 original size:131 final size:132
Alignment explanation
Indices: 3613859--3614121 Score: 519
Period size: 131 Copynumber: 2.0 Consensus size: 132
3613849 TTATGATTAT
3613859 TTTCAGAATATGAATAATAAATTATTCAGAATTATTGAAAATATTCAGTAAACTCCAGTAGGAGG
1 TTTCAGAATATGAATAATAAATTATTCAGAATTATTGAAAATATTCAGTAAACTCCAGTAGGAGG
3613924 ATCTTGTCCTTTCCCACCATCTCCATTATTACCATCTTTCCCTTTTCCCTTCTT-TTTGTCCTCA
66 ATCTTGTCCTTTCCCACCATCTCCATTATTACCATCTTTCCCTTTTCCCTTCTTCTTTGTCCTCA
3613988 AG
131 AG
3613990 TTTCAGAATATGAATAATAAATTATTCAGAATTATTGAAAATATTCAGTAAACTCCAGTAGGAGG
1 TTTCAGAATATGAATAATAAATTATTCAGAATTATTGAAAATATTCAGTAAACTCCAGTAGGAGG
3614055 ATCTTGTCCTTTCCCACCATCTCCATTATTACCATCTTTCCCTTTTCCCTTCTTCTTTGTCCTCA
66 ATCTTGTCCTTTCCCACCATCTCCATTATTACCATCTTTCCCTTTTCCCTTCTTCTTTGTCCTCA
3614120 AG
131 AG
3614122 AACCTCTTCC
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 119 0.91
132 12 0.09
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (132 bp):
TTTCAGAATATGAATAATAAATTATTCAGAATTATTGAAAATATTCAGTAAACTCCAGTAGGAGG
ATCTTGTCCTTTCCCACCATCTCCATTATTACCATCTTTCCCTTTTCCCTTCTTCTTTGTCCTCA
AG
Found at i:3617958 original size:17 final size:17
Alignment explanation
Indices: 3617936--3617983 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
3617926 ATAATGTTTT
3617936 AGTTCTTTTTAAAAATA
1 AGTTCTTTTTAAAAATA
**
3617953 AGTTC--TTTAATTATA
1 AGTTCTTTTTAAAAATA
*
3617968 AGTACTTTTTAAAAAT
1 AGTTCTTTTTAAAAAT
3617984 GATATTAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 12 0.50
17 12 0.50
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
AGTTCTTTTTAAAAATA
Found at i:3633278 original size:33 final size:34
Alignment explanation
Indices: 3633241--3633309 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
3633231 CTCTAGGTTG
3633241 ATAGCAGATTACTTTTAGAATGGATCAAA-CTTT
1 ATAGCAGATTACTTTTAGAATGGATCAAACCTTT
3633274 ATAGCAGATTACTTTTAGAATGGATCAAACCTTT
1 ATAGCAGATTACTTTTAGAATGGATCAAACCTTT
3633308 AT
1 AT
3633310 TTTTCTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (34 bp):
ATAGCAGATTACTTTTAGAATGGATCAAACCTTT
Found at i:3661833 original size:293 final size:294
Alignment explanation
Indices: 3661306--3661892 Score: 1167
Period size: 293 Copynumber: 2.0 Consensus size: 294
3661296 CAGAGGTGGC
3661306 AAAGCATTGGTGGAGGTAGAAATTGGTTTGGATTTAGTATTTGACTTTTTTGGAAGGCCGCCTAT
1 AAAGCATTGGTGGAGGTAGAAATTGGTTTGGATTTAGTATTTGACTTTTTTGGAAGGCCGCCTAT
3661371 AAATTTATCCGGAAATAATGTAGAAACAAAATGTTTTCATAGTAATTCAGCTTTTTTTTTATGGA
66 AAATTTATCCGGAAATAATGTAGAAACAAAATGTTTTCATAGTAATTCAGCTTTTTTTTTATGGA
3661436 TTTTTTTTTAAATAAGCTCAATTTTTTTTCTTAATTTGATTGTTATTGCTATTTAGTTAATTTGA
131 TTTTTTTTTAAATAAGCTCAATTTTTTTTCTTAATTTGATTGTTATTGCTATTTAGTTAATTTGA
3661501 TCAATAATTTTCTAAAAATAGATAATTTATTTTTAATGTAAATGATAACTATAATATTAACTTTT
196 TCAATAATTTTCTAAAAATAGATAATTTATTTTTAATGTAAATGATAACTATAATATTAACTTTT
3661566 TAATAATATTTATCTTATATGTC-TATCAATAAA
261 TAATAATATTTATCTTATATGTCATATCAATAAA
3661599 AAAGCATTGGTGGAGGTAGAAATTGGTTTGGATTTAGTATTTGACTTTTTTGGAAGGCCGCCTAT
1 AAAGCATTGGTGGAGGTAGAAATTGGTTTGGATTTAGTATTTGACTTTTTTGGAAGGCCGCCTAT
3661664 AAATTTATCCGGAAATAATGTAGAAACAAAATGTTTTCATAGTAATTCAGCTTTTTTTTTATGGA
66 AAATTTATCCGGAAATAATGTAGAAACAAAATGTTTTCATAGTAATTCAGCTTTTTTTTTATGGA
3661729 TTTTTTTTTAAATAAGCTCAATTTTTTTTCTTAATTTGATTGTTATTGCTATTTAGTTAATTTGA
131 TTTTTTTTTAAATAAGCTCAATTTTTTTTCTTAATTTGATTGTTATTGCTATTTAGTTAATTTGA
3661794 TCAATAATTTTCTAAAAATAGATAATTTATTTTTAATGTAAATGATAACTATAATATTAACTTTT
196 TCAATAATTTTCTAAAAATAGATAATTTATTTTTAATGTAAATGATAACTATAATATTAACTTTT
3661859 TAATAATATTTATCTTATATGTCATATCAATAAA
261 TAATAATATTTATCTTATATGTCATATCAATAAA
3661893 CAATTAAAAA
Statistics
Matches: 293, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
293 283 0.97
294 10 0.03
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.46
Consensus pattern (294 bp):
AAAGCATTGGTGGAGGTAGAAATTGGTTTGGATTTAGTATTTGACTTTTTTGGAAGGCCGCCTAT
AAATTTATCCGGAAATAATGTAGAAACAAAATGTTTTCATAGTAATTCAGCTTTTTTTTTATGGA
TTTTTTTTTAAATAAGCTCAATTTTTTTTCTTAATTTGATTGTTATTGCTATTTAGTTAATTTGA
TCAATAATTTTCTAAAAATAGATAATTTATTTTTAATGTAAATGATAACTATAATATTAACTTTT
TAATAATATTTATCTTATATGTCATATCAATAAA
Found at i:3662077 original size:30 final size:31
Alignment explanation
Indices: 3662010--3662080 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
3662000 TAAAAATAAC
*
3662010 AATTTGACTATTTTTAAAAAATTAATAATTA
1 AATTTAACTATTTTTAAAAAATTAATAATTA
* * *
3662041 AGTTTAACTCTTTTTAAAATATTAA-AATTA
1 AATTTAACTATTTTTAAAAAATTAATAATTA
3662071 AATTTAACTA
1 AATTTAACTA
3662081 AGAATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (31 bp):
AATTTAACTATTTTTAAAAAATTAATAATTA
Found at i:3662402 original size:40 final size:40
Alignment explanation
Indices: 3662286--3662403 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 40
3662276 AATTTATTTA
3662286 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGAT
1 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGAT
* * * * *
3662326 GAAATAATATTAAACAAATCTAT-A---GA-A-T-T-AATAT
1 G-AA-AATCTAAAACAAATATATAATTTTATATTATAAAGAT
3662360 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGAT
1 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGAT
3662400 GAAA
1 GAAA
3662404 TAATATTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 20
0.66 0.11 0.23
Matches are distributed among these distances:
32 15 0.26
33 3 0.05
34 5 0.09
35 1 0.02
36 2 0.03
37 2 0.03
38 2 0.03
39 1 0.02
40 9 0.16
41 3 0.05
42 15 0.26
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (40 bp):
GAAAATCTAAAACAAATATATAATTTTATATTATAAAGAT
Found at i:3662407 original size:74 final size:75
Alignment explanation
Indices: 3662286--3662434 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
3662276 AATTTATTTA
3662286 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGATGAAATAATATTAAACAAATCTAT-A
1 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGATGAAATAATATTAAACAAATCTATAA
3662350 GAATTAATAT
66 GAATTAATAT
3662360 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGATGAAATAATATTAAACAAATCTATAA
1 GAAAATCTAAAACAAATATATAATTTTATATTATAAAGATGAAATAATATTAAACAAATCTATAA
3662425 GAATTAATAT
66 GAATTAATAT
3662435 TATAATTAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 63 0.85
75 11 0.15
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (75 bp):
GAAAATCTAAAACAAATATATAATTTTATATTATAAAGATGAAATAATATTAAACAAATCTATAA
GAATTAATAT
Found at i:3663482 original size:22 final size:22
Alignment explanation
Indices: 3663456--3663502 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3663446 TATTTTAAGT
3663456 AATTTATA-AGAAATTTAATCTA
1 AATTT-TACAGAAATTTAATCTA
**
3663478 AATTTTACATCAATTTAATCTA
1 AATTTTACAGAAATTTAATCTA
3663500 AAT
1 AAT
3663503 CTTAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTTACAGAAATTTAATCTA
Found at i:3663853 original size:19 final size:19
Alignment explanation
Indices: 3663829--3663868 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3663819 CAAATTAAAG
3663829 ATATAATTAGTGGTCAATA
1 ATATAATTAGTGGTCAATA
*
3663848 ATATAATTAGTGGTTAATA
1 ATATAATTAGTGGTCAATA
3663867 AT
1 AT
3663869 TACTTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (19 bp):
ATATAATTAGTGGTCAATA
Found at i:3663902 original size:15 final size:15
Alignment explanation
Indices: 3663879--3663915 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3663869 TACTTCTGTT
3663879 ATATATTATAAAAAA
1 ATATATTATAAAAAA
* *
3663894 ATATTTTATAAAAAT
1 ATATATTATAAAAAA
3663909 ATATATT
1 ATATATT
3663916 GTTATTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATTATAAAAAA
Found at i:3665249 original size:28 final size:27
Alignment explanation
Indices: 3665196--3665260 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
3665186 TGTGACAAAA
3665196 AATATAAAAAATAAAAATTATTAAATTTT
1 AATA-AAAAAATAAAAATTA-TAAATTTT
3665225 AATAAAAAACATAAAAATTGA-AAATTTT
1 AATAAAAAA-ATAAAAATT-ATAAATTTT
*
3665253 TATAAAAA
1 AATAAAAA
3665261 TTACAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 19 0.58
29 13 0.39
30 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AATAAAAAAATAAAAATTATAAATTTT
Found at i:3665535 original size:30 final size:30
Alignment explanation
Indices: 3665470--3665537 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
3665460 TTCTTTACAT
* *
3665470 TTTTTTTATAATTTTCTATATATTTTATAA
1 TTTTTTTATAATTTTCTATAAATTTCATAA
*
3665500 TTTTTTTCTAATTTT-TAATAAATTTCA-AA
1 TTTTTTTATAATTTTCT-ATAAATTTCATAA
*
3665529 TATTTTTAT
1 TTTTTTTAT
3665538 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTTTTATAATTTTCTATAAATTTCATAA
Found at i:3665553 original size:20 final size:21
Alignment explanation
Indices: 3665508--3665558 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3665498 AATTTTTTTC
*
3665508 TAATTTTTA-ATAAATTTCAA
1 TAATTTTTATTTAAATTTCAA
3665528 -ATATTTTTATTTAAATTT-AA
1 TA-ATTTTTATTTAAATTTCAA
3665548 TAA-TTTTATTT
1 TAATTTTTATTT
3665559 TTATACCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.33
20 10 0.37
21 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTTATTTAAATTTCAA
Found at i:3675918 original size:2 final size:2
Alignment explanation
Indices: 3675911--3675936 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3675901 TCAACTTTGG
3675911 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
3675937 TTTTTTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3677144 original size:19 final size:19
Alignment explanation
Indices: 3677110--3677162 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3677100 TTTTATATTA
* *
3677110 TTAAATTATGTAATT-ATC
1 TTAAATTATATTATTAATC
*
3677128 TTTAATATATATTATTAATC
1 TTAAAT-TATATTATTAATC
*
3677148 TTAAATTTTATTATT
1 TTAAATTATATTATT
3677163 TAACAGAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 5 0.18
19 15 0.54
20 8 0.29
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAAATTATATTATTAATC
Found at i:3693088 original size:2 final size:2
Alignment explanation
Indices: 3693081--3693111 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3693071 TTAAAATCCT
*
3693081 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3693112 TCACACGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:3694325 original size:25 final size:25
Alignment explanation
Indices: 3694290--3694365 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 25
3694280 CGGCCCGGCC
* *
3694290 CATTTTTAAAATAAACATTAAAAAT
1 CATTTTAAAAATAAAAATTAAAAAT
* *
3694315 TATTTTAAAAATAAAAACTAAAAAAT
1 CATTTTAAAAATAAAAA-TTAAAAAT
* *
3694341 CATTTTAAAATTAAAAAATAAAAAT
1 CATTTTAAAAATAAAAATTAAAAAT
3694366 AAAAATATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 20 0.48
26 22 0.52
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (25 bp):
CATTTTAAAAATAAAAATTAAAAAT
Found at i:3701030 original size:2 final size:2
Alignment explanation
Indices: 3701023--3701054 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3701013 ACAGAGACAC
3701023 AG AG 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 AG AG
3701055 GTGTGTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3704864 original size:224 final size:224
Alignment explanation
Indices: 3704474--3704914 Score: 855
Period size: 224 Copynumber: 2.0 Consensus size: 224
3704464 ATAGATTGAT
*
3704474 TGCTCTCTTTTTTCCTCTTTTCTTTTTAAGTTTGTCCCGCTATAAATATTGTAGAATACAAGAAG
1 TGCTCTCTTTTTTCCTCTTTTCCTTTTAAGTTTGTCCCGCTATAAATATTGTAGAATACAAGAAG
*
3704539 AATAGAACATCTTCAAGTGCTATGGAAAAAGTTATATACCAAAGGAAAACATAACTAGAACTAGA
66 AATAGAACATCTTCAAGTGCTATGGAAAAAGCTATATACCAAAGGAAAACATAACTAGAACTAGA
3704604 AGCCCTCAAAAGAACTATGAGATTTAGAATTCAACCAAATCCTAACAATTACCTAGAATCTAATA
131 AGCCCTCAAAAGAACTATGAGATTTAGAATTCAACCAAATCCTAACAATTACCTAGAATCTAATA
3704669 TCTAAAGCTTGCTGTACCTCTATTGATTG
196 TCTAAAGCTTGCTGTACCTCTATTGATTG
3704698 TGCTCTCTTTTTTCCTCTTTTCCTTTTAAGTTTGTCCCGCTATAAATATTGTAGAATACAAGAAG
1 TGCTCTCTTTTTTCCTCTTTTCCTTTTAAGTTTGTCCCGCTATAAATATTGTAGAATACAAGAAG
*
3704763 AATAGAACATCTTCAAGTGCTATGGAAAAAGCTATATACCAAGGGAAAACATAACTAGAACTAGA
66 AATAGAACATCTTCAAGTGCTATGGAAAAAGCTATATACCAAAGGAAAACATAACTAGAACTAGA
3704828 AGCCCTCAAAAGAACTATGAGATTTAGAATTCAACCAAATCCTAACAATTACCTAGAATCTAATA
131 AGCCCTCAAAAGAACTATGAGATTTAGAATTCAACCAAATCCTAACAATTACCTAGAATCTAATA
3704893 TCTAAAGCTTGCTGTACCTCTA
196 TCTAAAGCTTGCTGTACCTCTA
3704915 CCCATTCCTT
Statistics
Matches: 214, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
224 214 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (224 bp):
TGCTCTCTTTTTTCCTCTTTTCCTTTTAAGTTTGTCCCGCTATAAATATTGTAGAATACAAGAAG
AATAGAACATCTTCAAGTGCTATGGAAAAAGCTATATACCAAAGGAAAACATAACTAGAACTAGA
AGCCCTCAAAAGAACTATGAGATTTAGAATTCAACCAAATCCTAACAATTACCTAGAATCTAATA
TCTAAAGCTTGCTGTACCTCTATTGATTG
Found at i:3723338 original size:34 final size:34
Alignment explanation
Indices: 3723295--3723360 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
3723285 CAAACACTAG
*
3723295 AAAATATTTT-CTGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAG-AAATCATTTTACAGAAAAGT
3723329 AAAATATTTTCCAGAAATCATTTTACAGAAAA
1 AAAATATTTTCCAGAAATCATTTTACAGAAAA
3723361 TATTTTACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (34 bp):
AAAATATTTTCCAGAAATCATTTTACAGAAAAGT
Found at i:3723357 original size:14 final size:14
Alignment explanation
Indices: 3723329--3723368 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3723319 ACAGAAAAGT
*
3723329 AAAATATTTTCCAG
1 AAAATATTTTACAG
3723343 -AAATCATTTTACAG
1 AAAAT-ATTTTACAG
3723357 AAAATATTTTAC
1 AAAATATTTTAC
3723369 TGGCAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 15 0.65
15 4 0.17
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAATATTTTACAG
Found at i:3723555 original size:13 final size:13
Alignment explanation
Indices: 3723538--3723607 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
3723528 CGAGTATTAA
3723538 ATTAAATATTAAAT
1 ATTAAAT-TTAAAT
3723552 -TTAAATTTAAAT
1 ATTAAATTTAAAT
*
3723564 ACTAAA-TTAAGAT
1 ATTAAATTTAA-AT
** *
3723577 AAAAAATTTAAGT
1 ATTAAATTTAAAT
3723590 ATTAAATTT-AAT
1 ATTAAATTTAAAT
3723602 ATTAAA
1 ATTAAA
3723608 ACTGTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
12 18 0.39
13 24 0.52
14 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:3723563 original size:19 final size:18
Alignment explanation
Indices: 3723534--3723571 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3723524 AATTCGAGTA
*
3723534 TTAAATTAAATATTAAAT
1 TTAAATTAAATACTAAAT
3723552 TTAAATTTAAATACTAAAT
1 TTAAA-TTAAATACTAAAT
3723571 T
1 T
3723572 AAGATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAATTAAATACTAAAT
Found at i:3733112 original size:55 final size:55
Alignment explanation
Indices: 3733028--3733195 Score: 336
Period size: 55 Copynumber: 3.1 Consensus size: 55
3733018 ATAAAGCGTG
3733028 GTAAGTCTCCTCTTTCTTCTTCCTTACATGTATGTATATATTTCTCTATTTGTGT
1 GTAAGTCTCCTCTTTCTTCTTCCTTACATGTATGTATATATTTCTCTATTTGTGT
3733083 GTAAGTCTCCTCTTTCTTCTTCCTTACATGTATGTATATATTTCTCTATTTGTGT
1 GTAAGTCTCCTCTTTCTTCTTCCTTACATGTATGTATATATTTCTCTATTTGTGT
3733138 GTAAGTCTCCTCTTTCTTCTTCCTTACATGTATGTATATATTTCTCTATTTGTGT
1 GTAAGTCTCCTCTTTCTTCTTCCTTACATGTATGTATATATTTCTCTATTTGTGT
3733193 GTA
1 GTA
3733196 TACATTCGCA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 113 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.52
Consensus pattern (55 bp):
GTAAGTCTCCTCTTTCTTCTTCCTTACATGTATGTATATATTTCTCTATTTGTGT
Found at i:3741614 original size:36 final size:36
Alignment explanation
Indices: 3741542--3741614 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
3741532 AATCAACATA
* *
3741542 AAAATCCCTAAGGTTATGTTAGAATATTTATGTAAT
1 AAAATCCCTAAGGTTATGCTAGAATATTTATATAAT
* *
3741578 AAAATTCCTGAGGTTATGCTAGAATATTT-TCATAAT
1 AAAATCCCTAAGGTTATGCTAGAATATTTAT-ATAAT
3741614 A
1 A
3741615 TTATCTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (36 bp):
AAAATCCCTAAGGTTATGCTAGAATATTTATATAAT
Found at i:3757294 original size:20 final size:21
Alignment explanation
Indices: 3757242--3757294 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3757232 ATAAGGAAAT
3757242 AAAA-AAATTATAAAAATTATA
1 AAAATAAATT-TAAAAATTATA
**
3757263 AAAATATTTTTAAAAA-TATA
1 AAAATAAATTTAAAAATTATA
*
3757283 ACAATAAATTTA
1 AAAATAAATTTA
3757295 TATTTATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 10 0.38
22 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATAAATTTAAAAATTATA
Found at i:3757441 original size:26 final size:26
Alignment explanation
Indices: 3757405--3757454 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3757395 GTGGGAGAGT
*
3757405 ATTTTATATTTAATATCAATATAATG
1 ATTTTATATTTAATATAAATATAATG
*
3757431 ATTTTTTATTTAATATAAATATAA
1 ATTTTATATTTAATATAAATATAA
3757455 ATATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTTATATTTAATATAAATATAATG
Found at i:3757900 original size:20 final size:20
Alignment explanation
Indices: 3757834--3757903 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
3757824 TCAATAGAAA
3757834 TTTAAAAATT-ATAAAAA-T
1 TTTAAAAATTCATAAAAATT
* * *
3757852 ATTAAAAACTCAAAAAAAATAT
1 TTTAAAAATTC-ATAAAAAT-T
**
3757874 TAAAAAAATTCATAAAAATT
1 TTTAAAAATTCATAAAAATT
3757894 TTTAAAAATT
1 TTTAAAAATT
3757904 AACATGAAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
18 8 0.21
20 15 0.39
21 7 0.18
22 8 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTAAAAATTCATAAAAATT
Found at i:3762443 original size:21 final size:21
Alignment explanation
Indices: 3762418--3762458 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3762408 CCCTCCTCCG
*
3762418 TCAACTCCTTCAACCCCACCC
1 TCAACTCCGTCAACCCCACCC
*
3762439 TCAACTCCGTCGACCCCACC
1 TCAACTCCGTCAACCCCACC
3762459 GTCTCCACCA
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:0.22, C:0.56, G:0.05, T:0.17
Consensus pattern (21 bp):
TCAACTCCGTCAACCCCACCC
Found at i:3762501 original size:15 final size:15
Alignment explanation
Indices: 3762481--3762519 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3762471 ACCATCATCT
*
3762481 CCACCATCTCCAAAA
1 CCACCAGCTCCAAAA
3762496 CCACCAGCTCCAAAA
1 CCACCAGCTCCAAAA
*
3762511 CCACTAGCT
1 CCACCAGCT
3762520 GCAGCGGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.46, G:0.05, T:0.13
Consensus pattern (15 bp):
CCACCAGCTCCAAAA
Found at i:3764852 original size:14 final size:14
Alignment explanation
Indices: 3764833--3764869 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3764823 CAGCAAAAAG
3764833 AAACAGAAGTTGCA
1 AAACAGAAGTTGCA
*
3764847 AAACAGAATTTGCA
1 AAACAGAAGTTGCA
*
3764861 AAACTGAAG
1 AAACAGAAG
3764870 CACGAAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (14 bp):
AAACAGAAGTTGCA
Found at i:3766458 original size:230 final size:231
Alignment explanation
Indices: 3766033--3766526 Score: 920
Period size: 230 Copynumber: 2.1 Consensus size: 231
3766023 GAGCTCTTAA
* *
3766033 ATTATTT-TTGTAGTTAAATAAGTCCTTAAATCATGATTTTTATTCATAAAAGTCTTTGATTTTA
1 ATTATTTATT-TAG-TAAATTATTCCTTAAATCATGATTTTTATTCATAAAAGTCTTTGATTTTA
3766097 ATATTAAAGCAGGTATTATCTAATTTTTTTATTAATGCAGTGGAAATTATATATACTTTAACATA
64 ATATTAAAGCAGGTATTATCTAATTTTTTTATTAATGCAGTGGAAATTATATATACTTTAACATA
3766162 GTAATCAAAATTTTGAAAAGAGTAATTGTGTTATGGATATAAACACTTTAAATAAATTTTAAAAT
129 GTAATCAAAATTTTGAAAAGAGTAATTGTGTTATGGATATAAACACTTTAAATAAATTTTAAAAT
3766227 ATTATTTTATTTTAGTACTTTTTAAAAAAATATATTTT
194 ATTATTTTATTTTAGTACTTTTTAAAAAAATATATTTT
3766265 ATTATTTA-TTAGTAAATTATTCCTTAAATCATGATTTTTATTCATAAAAGTCTTTGATTTTAAT
1 ATTATTTATTTAGTAAATTATTCCTTAAATCATGATTTTTATTCATAAAAGTCTTTGATTTTAAT
3766329 ATTAAAGCAGGTATTATCTAATTTTTTTATTAATGCAGTGGAAATTATATATACTTTAACATAGT
66 ATTAAAGCAGGTATTATCTAATTTTTTTATTAATGCAGTGGAAATTATATATACTTTAACATAGT
3766394 AATCAAAATTTTGAAAAGAGTAATTGTGTTATGGATATAAACACTTTAAATAAATTTTAAAATAT
131 AATCAAAATTTTGAAAAGAGTAATTGTGTTATGGATATAAACACTTTAAATAAATTTTAAAATAT
3766459 TATTTTATTTTAGTACTTTTTAAAAAAATATATTTT
196 TATTTTATTTTAGTACTTTTTAAAAAAATATATTTT
3766495 ATTATTTATTTAGTAAATTATTCTCATTAAAT
1 ATTATTTATTTAGTAAATTATTC-C-TTAAAT
3766527 TAGTTTAAAA
Statistics
Matches: 256, Mismatches: 2, Indels: 7
0.97 0.01 0.03
Matches are distributed among these distances:
230 224 0.88
231 17 0.07
232 9 0.04
233 6 0.02
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (231 bp):
ATTATTTATTTAGTAAATTATTCCTTAAATCATGATTTTTATTCATAAAAGTCTTTGATTTTAAT
ATTAAAGCAGGTATTATCTAATTTTTTTATTAATGCAGTGGAAATTATATATACTTTAACATAGT
AATCAAAATTTTGAAAAGAGTAATTGTGTTATGGATATAAACACTTTAAATAAATTTTAAAATAT
TATTTTATTTTAGTACTTTTTAAAAAAATATATTTT
Found at i:3769014 original size:31 final size:32
Alignment explanation
Indices: 3768964--3769025 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
3768954 ACTAGGTCCT
3768964 AAACATTGACAATTATTCCCACATTGAGACTA
1 AAACATTGACAATTATTCCCACATTGAGACTA
* * *
3768996 AAAC-TTGATAATTTTTCCCGCATTGAGACT
1 AAACATTGACAATTATTCCCACATTGAGACT
3769026 TGAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (32 bp):
AAACATTGACAATTATTCCCACATTGAGACTA
Found at i:3785803 original size:3 final size:3
Alignment explanation
Indices: 3785795--3785819 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3785785 TTCAACTCAA
3785795 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3785820 TGAGTGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3787746 original size:14 final size:15
Alignment explanation
Indices: 3787727--3787758 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3787717 CGAAAACCCG
3787727 AAAAATGGAAAAA-A
1 AAAAATGGAAAAAGA
3787741 AAAAATGGAAAAAGA
1 AAAAATGGAAAAAGA
3787756 AAA
1 AAA
3787759 CCAATCCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAAATGGAAAAAGA
Found at i:3799114 original size:29 final size:29
Alignment explanation
Indices: 3799056--3799114 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3799046 ATTTATTAAA
* * **
3799056 AATTAGGTGACTATTTTATAGCTTTTCAT
1 AATTAAGTGACTATTTTATAACTTACCAT
3799085 AATTAAGTGACTATTTTATAACTTACCAT
1 AATTAAGTGACTATTTTATAACTTACCAT
3799114 A
1 A
3799115 TTATTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (29 bp):
AATTAAGTGACTATTTTATAACTTACCAT
Found at i:3801587 original size:4 final size:4
Alignment explanation
Indices: 3801578--3801602 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3801568 ATCTAAGAGG
3801578 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
3801603 AGTATTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:3804766 original size:16 final size:18
Alignment explanation
Indices: 3804729--3804776 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
3804719 GGATTACTTT
*
3804729 TTTTAAATTAATTTTGAG
1 TTTTAGATTAATTTTGAG
3804747 -TTTAGATT-ATTTT-AG
1 TTTTAGATTAATTTTGAG
*
3804762 TTTTAGATTGATTTT
1 TTTTAGATTAATTTT
3804777 TACTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 2 0.07
16 13 0.48
17 12 0.44
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.60
Consensus pattern (18 bp):
TTTTAGATTAATTTTGAG
Found at i:3804927 original size:43 final size:43
Alignment explanation
Indices: 3804879--3804965 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
3804869 GAATCATCTC
3804879 GATTCTAAATTATTTCAAGTTTAATTTGTATGAGATTAATTAT
1 GATTCTAAATTATTTCAAGTTTAATTTGTATGAGATTAATTAT
3804922 GATTCTAAATTATTTCAAGTTTAATTTGTATGAGATTAATTAT
1 GATTCTAAATTATTTCAAGTTTAATTTGTATGAGATTAATTAT
3804965 G
1 G
3804966 CTTTGATTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (43 bp):
GATTCTAAATTATTTCAAGTTTAATTTGTATGAGATTAATTAT
Found at i:3813050 original size:13 final size:13
Alignment explanation
Indices: 3813016--3813065 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
3813006 TCTTCATTGT
3813016 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
* *
3813029 -TATGTAAAAGTAC
1 TTTTG-AAAAGTGC
*
3813042 TTTTGAAAAGTGT
1 TTTTGAAAAGTGC
3813055 TTTTGAAAAGT
1 TTTTGAAAAGT
3813066 TTGGTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 3 0.10
13 24 0.80
14 3 0.10
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:3816696 original size:25 final size:25
Alignment explanation
Indices: 3816668--3816732 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
3816658 AATTTGATCC
*
3816668 TTCAAAAATGATAAAAAATTAATCA
1 TTCAAAAATGATAAAAAATAAATCA
* *
3816693 TTCAAAAATTATAAAGATATAAATCA
1 TTCAAAAATGATAAA-AAATAAATCA
3816719 TT--AAAATGATAAAA
1 TTCAAAAATGATAAAA
3816733 TTATATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 10 0.29
25 14 0.40
26 10 0.29
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (25 bp):
TTCAAAAATGATAAAAAATAAATCA
Found at i:3820443 original size:31 final size:31
Alignment explanation
Indices: 3820373--3820431 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
3820363 AAATAGTAAT
* * *
3820373 TGAATTATTTTAAAATTTTCATTTAAGTCAC
1 TGAACTATTCTAAAATTTTCATTTAAATCAC
*
3820404 TGAACTATTCTAAAATTTTTATTTAAAT
1 TGAACTATTCTAAAATTTTCATTTAAAT
3820432 GACTAGACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (31 bp):
TGAACTATTCTAAAATTTTCATTTAAATCAC
Found at i:3823388 original size:19 final size:17
Alignment explanation
Indices: 3823353--3823397 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
3823343 TTTAAAAATA
3823353 AAAAATATTAAAAGGTT
1 AAAAATATTAAAAGGTT
*
3823370 AAAAATCATTAGAATGGTT
1 AAAAAT-ATTA-AAAGGTT
3823389 AAAATATAT
1 AAAA-ATAT
3823398 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 12 0.50
20 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.31
Consensus pattern (17 bp):
AAAAATATTAAAAGGTT
Found at i:3823586 original size:19 final size:17
Alignment explanation
Indices: 3823551--3823595 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
3823541 TTTAAAAATA
3823551 AAAAATATTAAAAGGTT
1 AAAAATATTAAAAGGTT
*
3823568 AAAAATCATTAGAATGGTT
1 AAAAAT-ATTA-AAAGGTT
3823587 AAAATATAT
1 AAAA-ATAT
3823596 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 12 0.50
20 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.31
Consensus pattern (17 bp):
AAAAATATTAAAAGGTT
Found at i:3823670 original size:198 final size:199
Alignment explanation
Indices: 3823332--3823732 Score: 788
Period size: 198 Copynumber: 2.0 Consensus size: 199
3823322 CGTGAGTATT
3823332 TAATTAAATTTTTTAAAAATAAAAAATATTAAAAGGTTAAAAATCATTAGAATGGTTAAAATATA
1 TAATTAAATTTTTTAAAAATAAAAAATATTAAAAGGTTAAAAATCATTAGAATGGTTAAAATATA
3823397 TATATTTAAAATTTAATTCACGCTATATCAACAAAGCTCATCAACGCTAATTTTTCCATTTCTTT
66 TATATTTAAAATTTAATTCACGCTATATCAACAAAGCTCATCAACGCTAATTTTTCCATTTCTTT
3823462 ATAAAATTTAAGAGTTAAAAGAGATAAAAAAAATTAAAAAAATTATTTTTTTTAT-AAATTAAAG
131 ATAAAATTTAAGAGTTAAAAGAGATAAAAAAAATTAAAAAAATTATTTTTTTTATAAAATTAAAG
3823526 TACC
196 TACC
3823530 TAATTAAATTTTTTAAAAATAAAAAATATTAAAAGGTTAAAAATCATTAGAATGGTTAAAATATA
1 TAATTAAATTTTTTAAAAATAAAAAATATTAAAAGGTTAAAAATCATTAGAATGGTTAAAATATA
3823595 TATATTTAAAATTTAATTCACGCTATATCAACAAAGCTCATCAACGCTAATTTTTCCATTTCTTT
66 TATATTTAAAATTTAATTCACGCTATATCAACAAAGCTCATCAACGCTAATTTTTCCATTTCTTT
3823660 ATAAAATTTAAGAGTTAAAAGAGATAAAAAAAATTAAAAAAATTATTTTTTTTATAAAATTAAAG
131 ATAAAATTTAAGAGTTAAAAGAGATAAAAAAAATTAAAAAAATTATTTTTTTTATAAAATTAAAG
3823725 TACC
196 TACC
3823729 -AATT
1 TAATT
3823733 GTAGAAGGGG
Statistics
Matches: 202, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
198 189 0.94
199 13 0.06
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (199 bp):
TAATTAAATTTTTTAAAAATAAAAAATATTAAAAGGTTAAAAATCATTAGAATGGTTAAAATATA
TATATTTAAAATTTAATTCACGCTATATCAACAAAGCTCATCAACGCTAATTTTTCCATTTCTTT
ATAAAATTTAAGAGTTAAAAGAGATAAAAAAAATTAAAAAAATTATTTTTTTTATAAAATTAAAG
TACC
Found at i:3829810 original size:97 final size:95
Alignment explanation
Indices: 3829639--3829825 Score: 302
Period size: 97 Copynumber: 1.9 Consensus size: 95
3829629 GATAGTAAAA
* *
3829639 TAGTTGTAAATTCTCAAAACCACAAAACCAACTAACAATTTTGTTGTCGAGAATAGAGATTAGGA
1 TAGTTGTAAATTCTCAAAACCACAAAACCAACCAACAATTTTGTTGTCGAGAATAGAAATTAGGA
*
3829704 GAGACGACTCTCTCTGTAATCAGATTTTTTAC
66 GAGACGA--CTCTATGTAATCAGATTTTTTAC
* *
3829736 TAGTTGTAAATTCTCGAAACCACAAAACCAACCAACAGTTTTGTTGTCGAGAATAGAAATTAGGA
1 TAGTTGTAAATTCTCAAAACCACAAAACCAACCAACAATTTTGTTGTCGAGAATAGAAATTAGGA
*
3829801 GAGATGACTCTATGTAATCAGATTT
66 GAGACGACTCTATGTAATCAGATTT
3829826 GATATGTAAC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 17 0.20
97 67 0.80
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (95 bp):
TAGTTGTAAATTCTCAAAACCACAAAACCAACCAACAATTTTGTTGTCGAGAATAGAAATTAGGA
GAGACGACTCTATGTAATCAGATTTTTTAC
Found at i:3856165 original size:13 final size:13
Alignment explanation
Indices: 3856132--3856174 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
3856122 TGAGATTTTG
3856132 TTATTAATTTATTA
1 TTATTAA-TTATTA
*
3856146 TTA-TAATTATAA
1 TTATTAATTATTA
3856158 TTATTAATTATTA
1 TTATTAATTATTA
3856171 TTAT
1 TTAT
3856175 GGTTTTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 8 0.31
13 15 0.58
14 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTAATTATTA
Found at i:3856932 original size:15 final size:16
Alignment explanation
Indices: 3856902--3856934 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3856892 TAAGGTAGGT
3856902 ATGAATATTGAAATGA
1 ATGAATATTGAAATGA
*
3856918 ATGAA-ATTGAGATGA
1 ATGAATATTGAAATGA
3856933 AT
1 AT
3856935 TATGATTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (16 bp):
ATGAATATTGAAATGA
Found at i:3858629 original size:13 final size:15
Alignment explanation
Indices: 3858613--3858645 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3858603 TGTTAACCAA
3858613 ATAAACA-TAT-AGC
1 ATAAACATTATAAGC
3858626 ATAAACATTATAAGC
1 ATAAACATTATAAGC
3858641 ATAAA
1 ATAAA
3858646 TGAGCACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 3 0.17
15 8 0.44
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (15 bp):
ATAAACATTATAAGC
Found at i:3860191 original size:11 final size:12
Alignment explanation
Indices: 3860172--3860196 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3860162 TGGACAAAAA
3860172 TTGGTTTTTAAT
1 TTGGTTTTTAAT
3860184 TTGGTTTTTAAT
1 TTGGTTTTTAAT
3860196 T
1 T
3860197 CATTTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TTGGTTTTTAAT
Found at i:3863285 original size:16 final size:16
Alignment explanation
Indices: 3863256--3863303 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
3863246 CACTTAATTT
3863256 GATTTAAACATGAAAA
1 GATTTAAACATGAAAA
* *
3863272 GATTTGAACCTGAAAA
1 GATTTAAACATGAAAA
* *
3863288 GGTTTAAACTTGAAAA
1 GATTTAAACATGAAAA
3863304 AAAAAATCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (16 bp):
GATTTAAACATGAAAA
Found at i:3863337 original size:15 final size:17
Alignment explanation
Indices: 3863313--3863355 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
3863303 AAAAAAATCT
*
3863313 AATCTTAAAAAA-TTTG
1 AATCTAAAAAAATTTTG
3863329 AA-CTAAAAAAATTTTG
1 AATCTAAAAAAATTTTG
3863345 AATCTAAAAAA
1 AATCTAAAAAA
3863356 TCTTAGCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (17 bp):
AATCTAAAAAAATTTTG
Found at i:3863338 original size:16 final size:17
Alignment explanation
Indices: 3863302--3863355 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
3863292 TAAACTTGAA
*
3863302 AAAAAAAATCT-AATCT
1 AAAAAAAATTTGAATCT
*
3863318 -TAAAAAATTTGAA-CT
1 AAAAAAAATTTGAATCT
*
3863333 AAAAAAATTTTGAATCT
1 AAAAAAAATTTGAATCT
3863350 AAAAAA
1 AAAAAA
3863356 TCTTAGCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 10 0.32
16 13 0.42
17 8 0.26
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAAAAAATTTGAATCT
Found at i:3864345 original size:16 final size:16
Alignment explanation
Indices: 3864324--3864354 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3864314 GTTCCAACAT
*
3864324 GATATTTTCATATTCG
1 GATATTTTCAAATTCG
3864340 GATATTTTCAAATTC
1 GATATTTTCAAATTC
3864355 AACTCGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (16 bp):
GATATTTTCAAATTCG
Found at i:3865135 original size:73 final size:73
Alignment explanation
Indices: 3864996--3865141 Score: 186
Period size: 73 Copynumber: 2.0 Consensus size: 73
3864986 AATATTTATA
* * * ***
3864996 TGTAACACCACTAACCCGTATTCGTAGCCGGAACATGGTTACCGAGTATTACAAGATAAGGGAAT
1 TGTAACACCACTAACCCGTATCCGTAGCCGGAACAGGGTTACCGAGTATTACAAGACAACAAAAT
3865061 AGTAAATC
66 AGTAAATC
* * * *
3865069 TGTAACACTC-CTGACCCGTATCCGTCGCCGGAACAGGGTTACGGAGTATTACAGGACAACAAAA
1 TGTAACAC-CACTAACCCGTATCCGTAGCCGGAACAGGGTTACCGAGTATTACAAGACAACAAAA
3865133 TAGTAAATC
65 TAGTAAATC
3865142 ATTCAAATCA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
73 61 0.98
74 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (73 bp):
TGTAACACCACTAACCCGTATCCGTAGCCGGAACAGGGTTACCGAGTATTACAAGACAACAAAAT
AGTAAATC
Found at i:3866023 original size:21 final size:21
Alignment explanation
Indices: 3865999--3866041 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3865989 CGAAAATACC
3865999 AACAGAAGCTCGTAAAAGCTG
1 AACAGAAGCTCGTAAAAGCTG
*
3866020 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAAAGCTG
3866041 A
1 A
3866042 TCCACCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCGTAAAAGCTG
Found at i:3868959 original size:30 final size:29
Alignment explanation
Indices: 3868920--3868986 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
3868910 ACCAATAAAA
* *
3868920 GCCGTTTTTTTTCAAAATTTACCTAAATGG
1 GCCGATTTTTTT-AAAATTTACCGAAATGG
** *
3868950 GCCGATTTTTTTATTATTTACCGGAATGG
1 GCCGATTTTTTTAAAATTTACCGAAATGG
3868979 GCC-ATTTT
1 GCCGATTTT
3868987 CCGCGAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 5 0.16
29 16 0.50
30 11 0.34
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (29 bp):
GCCGATTTTTTTAAAATTTACCGAAATGG
Found at i:3883159 original size:2 final size:2
Alignment explanation
Indices: 3883115--3883151 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3883105 GCAATTAGGA
3883115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3883152 AAATATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3886488 original size:1 final size:1
Alignment explanation
Indices: 3886484--3886518 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
3886474 GGGGGGGGGG
* *
3886484 AAAAAAAAAAAAAAAAAAAAAAAGAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3886519 GGGGGGGGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:3887325 original size:6 final size:7
Alignment explanation
Indices: 3887296--3887323 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3887286 GACTATGGAG
3887296 TAATTTT
1 TAATTTT
3887303 TAATTTT
1 TAATTTT
3887310 TAATTTT
1 TAATTTT
3887317 TAATTTT
1 TAATTTT
3887324 AAGAAAATGT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TAATTTT
Found at i:3887611 original size:15 final size:16
Alignment explanation
Indices: 3887591--3887624 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3887581 AATCTTTTAA
3887591 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
3887606 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
3887622 AAA
1 AAA
3887625 ATAATAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:3902059 original size:4 final size:4
Alignment explanation
Indices: 3902050--3902075 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3902040 GTTACCATAC
3902050 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
3902076 ACGAAACTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:3904433 original size:17 final size:16
Alignment explanation
Indices: 3904408--3904441 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
3904398 ATGGGAATTT
3904408 TTTAAAAAAGAAAAAAA
1 TTTAAAAAA-AAAAAAA
3904425 TTTACAAAAAAAAAAAA
1 TTTA-AAAAAAAAAAAA
3904442 AAAGGGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
TTTAAAAAAAAAAAAA
Found at i:3907644 original size:19 final size:18
Alignment explanation
Indices: 3907605--3907638 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3907595 TCTAACCCTT
*
3907605 TATTTTTAAAGATTTAAA
1 TATTTTTAAAGAATTAAA
3907623 TATTTTTAAA-AATTAA
1 TATTTTTAAAGAATTAA
3907639 TGATATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTTTTAAAGAATTAAA
Found at i:3911128 original size:31 final size:31
Alignment explanation
Indices: 3911090--3911152 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3911080 AAAAAGCGTA
3911090 AGTTATTTTCTGGAAAAGAGCTCCTCAATAG
1 AGTTATTTTCTGGAAAAGAGCTCCTCAATAG
3911121 AGTTATTTTCTGGAAAAGAGCTCCTCAATAG
1 AGTTATTTTCTGGAAAAGAGCTCCTCAATAG
3911152 A
1 A
3911153 TGATTTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (31 bp):
AGTTATTTTCTGGAAAAGAGCTCCTCAATAG
Found at i:3911247 original size:9 final size:9
Alignment explanation
Indices: 3911233--3911280 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
3911223 TTTATTTTTA
3911233 AAAATATTT
1 AAAATATTT
3911242 AAAATATTT
1 AAAATATTT
3911251 AAAATA-TT
1 AAAATATTT
*
3911259 AATATATTAT
1 AAAATATT-T
**
3911269 TTAATATTT
1 AAAATATTT
3911278 AAA
1 AAA
3911281 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
8 7 0.23
9 18 0.58
10 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAAATATTT
Found at i:3911286 original size:18 final size:18
Alignment explanation
Indices: 3911246--3911303 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
3911236 ATATTTAAAA
* *
3911246 TATTTAAAATATTAATATAT
1 TATTTAATAT-TTAA-ATTT
3911266 TATTTAATATTTAAATTT
1 TATTTAATATTTAAATTT
*
3911284 TATTTTAATA-GTAAATTT
1 TA-TTTAATATTTAAATTT
3911302 TA
1 TA
3911304 AAAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.41
19 11 0.32
20 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATTTAATATTTAAATTT
Found at i:3911840 original size:33 final size:33
Alignment explanation
Indices: 3911788--3911870 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
3911778 GACTTTTATA
* * * **
3911788 AAACAAAAGCAAATGTTTTACACAGATTCATTT
1 AAACACAAGAAAATATTTTACACAGATTCATCC
* *
3911821 AAACACCAGAAAATATTTTATACAGATTCATCC
1 AAACACAAGAAAATATTTTACACAGATTCATCC
3911854 AAACACAAGAAAATATT
1 AAACACAAGAAAATATT
3911871 AGCTTTTCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (33 bp):
AAACACAAGAAAATATTTTACACAGATTCATCC
Found at i:3933211 original size:24 final size:24
Alignment explanation
Indices: 3933184--3933235 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3933174 TTAGTAAGTC
*
3933184 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3933208 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3933232 AAAT
1 AAAT
3933236 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3934025 original size:5 final size:5
Alignment explanation
Indices: 3934015--3934060 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
3934005 GATTATGTTT
3934015 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TATATA T
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA T-TATA T
3934061 ATAACAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 23 0.62
6 10 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:3934040 original size:19 final size:17
Alignment explanation
Indices: 3934016--3934062 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 17
3934006 ATTATGTTTT
3934016 TATATTATATTATTATTAA
1 TATATTATATTA-TATT-A
3934035 TATATTATATTATATTA
1 TATATTATATTATATTA
3934052 TATATATATAT
1 TATAT-TATAT
3934063 AACAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTATATTATATTA
Found at i:3935494 original size:37 final size:36
Alignment explanation
Indices: 3935393--3935527 Score: 92
Period size: 39 Copynumber: 3.5 Consensus size: 36
3935383 CGACCTTGAG
3935393 TCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCA-AC--TTACTTCGGAT--AT
** ** *
3935434 TCGATGAGGTACTGGGTACCAACTTACTTCGGCT-T
1 TCGATGAGACACTGGGTGTCAACTTACTTCGGATAT
* *
3935469 TGCCGATGAGACACTGGGTGTCAACTATTGCTTCGAACTAT
1 T--CGATGAGACACTGGGTGTCAAC--TTACTTCGGA-TAT
* *
3935510 CCGATGAGGCACTGGGTG
1 TCGATGAGACACTGGGTG
3935528 CCGTACTGGT
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
35 2 0.03
37 18 0.24
38 10 0.14
39 23 0.31
40 3 0.04
41 18 0.24
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (36 bp):
TCGATGAGACACTGGGTGTCAACTTACTTCGGATAT
Found at i:3935986 original size:17 final size:18
Alignment explanation
Indices: 3935955--3935988 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3935945 ATAAATAGAA
3935955 ATGATAATGAATGAGTTG
1 ATGATAATGAATGAGTTG
*
3935973 ATGA-AATGATTGAGTT
1 ATGATAATGAATGAGTT
3935989 TGTATGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (18 bp):
ATGATAATGAATGAGTTG
Found at i:3938271 original size:24 final size:24
Alignment explanation
Indices: 3938244--3938295 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3938234 TTAGTAAGTC
3938244 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
* *
3938268 AAATATATTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
3938292 AAAT
1 AAAT
3938296 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATGCT
Found at i:3942398 original size:17 final size:18
Alignment explanation
Indices: 3942365--3942398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3942355 AAAAAATTGT
3942365 AATAACTATACATTTAAA
1 AATAACTATACATTTAAA
*
3942383 AATAATTATA-ATTTAA
1 AATAACTATACATTTAA
3942399 TTCACAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAACTATACATTTAAA
Found at i:3944714 original size:21 final size:21
Alignment explanation
Indices: 3944672--3944715 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3944662 TTTTCCTAGG
* *
3944672 ATGTGAATTGGATGGAATTGA
1 ATGTGAATTGGATGAAAATGA
* *
3944693 ATGTGAATTGTATTAAAATGA
1 ATGTGAATTGGATGAAAATGA
3944714 AT
1 AT
3944716 TAAATTTACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (21 bp):
ATGTGAATTGGATGAAAATGA
Found at i:3946491 original size:25 final size:25
Alignment explanation
Indices: 3946463--3946553 Score: 139
Period size: 25 Copynumber: 3.6 Consensus size: 25
3946453 ACCTTAGCGC
*
3946463 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
*
3946488 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTCAGT
*
3946513 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
3946538 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
3946554 TGCATGATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 2 0.03
25 58 0.97
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:3948702 original size:19 final size:19
Alignment explanation
Indices: 3948640--3948702 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
3948630 TTTTGTTTTT
*
3948640 ATTATAATTTATATATTAATA
1 ATTAT-ATTTATAAATT-ATA
*
3948661 A--ATATATATAACATTA-A
1 ATTATATTTATAA-ATTATA
*
3948678 AATATATTTATAAATTATA
1 ATTATATTTATAAATTATA
3948697 ATTATA
1 ATTATA
3948703 AAAAATCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 2 0.06
18 11 0.32
19 20 0.59
21 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTATATTTATAAATTATA
Found at i:3952872 original size:3 final size:3
Alignment explanation
Indices: 3952864--3952890 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3952854 AGTAAAATTG
3952864 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3952891 TACTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3956863 original size:22 final size:21
Alignment explanation
Indices: 3956828--3956888 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
3956818 ATTAACAATT
3956828 AATAATTTTATAATTTTACTAACA
1 AATAA-TTT-TAATTTTACTAA-A
* * *
3956852 ATTAGTTTTAATTTTATTAAA
1 AATAATTTTAATTTTACTAAA
3956873 AATAATTTTAATTTTA
1 AATAATTTTAATTTTA
3956889 ATTAAAAACG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 15 0.47
22 11 0.34
23 3 0.09
24 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (21 bp):
AATAATTTTAATTTTACTAAA
Found at i:3956883 original size:21 final size:21
Alignment explanation
Indices: 3956828--3956896 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
3956818 ATTAACAATT
*
3956828 AATAATTTTATAATTTTACTAACA
1 AATAA-TTT-TAATTTTATTAA-A
* *
3956852 ATTAGTTTTAATTTTATTAAA
1 AATAATTTTAATTTTATTAAA
3956873 AATAATTTTAATTTTAATTAAA
1 AATAATTTTAATTTT-ATTAAA
3956895 AA
1 AA
3956897 CGGGCCGGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 14 0.36
22 19 0.49
23 3 0.08
24 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
AATAATTTTAATTTTATTAAA
Found at i:3978966 original size:2 final size:2
Alignment explanation
Indices: 3978959--3978987 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3978949 TAAGCAAGGA
3978959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3978988 NNNNNNNTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3979903 original size:42 final size:42
Alignment explanation
Indices: 3979844--3979929 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
3979834 TCTCTGGTTT
3979844 ATTTGGCCATTTTGGGAGCTGCTAAG-TTTCCACCCACCCTTC
1 ATTTGGCCATTTTGGGAGCTGCTAAGCTTT-CACCCACCCTTC
* * *
3979886 ATTTGGCCATTTTGGGAGCTTCTTAGCTTTTACCCACCCTTC
1 ATTTGGCCATTTTGGGAGCTGCTAAGCTTTCACCCACCCTTC
3979928 AT
1 AT
3979930 GGTTCAGGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.37
Consensus pattern (42 bp):
ATTTGGCCATTTTGGGAGCTGCTAAGCTTTCACCCACCCTTC
Found at i:4000322 original size:2 final size:2
Alignment explanation
Indices: 4000315--4000341 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4000305 ACAGAACATG
4000315 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4000342 GCATTGAGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4002701 original size:15 final size:15
Alignment explanation
Indices: 4002681--4002720 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
4002671 CTCCTTTGGC
4002681 TTTTTGTTTTATTGT
1 TTTTTGTTTTATTGT
4002696 TTTTTGTTTTATTGT
1 TTTTTGTTTTATTGT
4002711 TTTTTGTTTT
1 TTTTTGTTTT
4002721 CTGTTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.05, C:0.00, G:0.12, T:0.82
Consensus pattern (15 bp):
TTTTTGTTTTATTGT
Found at i:4002704 original size:7 final size:7
Alignment explanation
Indices: 4002681--4002725 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
4002671 CTCCTTTGGC
4002681 TTTTTGT
1 TTTTTGT
4002688 TTTATTGT
1 TTT-TTGT
4002696 TTTTTGT
1 TTTTTGT
4002703 TTTATTGT
1 TTT-TTGT
4002711 TTTTTGT
1 TTTTTGT
*
4002718 TTTCTGT
1 TTTTTGT
4002725 T
1 T
4002726 CTCTTTTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
7 21 0.60
8 14 0.40
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.80
Consensus pattern (7 bp):
TTTTTGT
Found at i:4012981 original size:21 final size:21
Alignment explanation
Indices: 4012957--4013005 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4012947 TGGAATTATT
*
4012957 ATTTTTACAATTATACCAAAC
1 ATTTTTAAAATTATACCAAAC
* **
4012978 ATTTTTAAAATTTTAGGAAAC
1 ATTTTTAAAATTATACCAAAC
4012999 ATTTTTA
1 ATTTTTA
4013006 TTCTTACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTTTTAAAATTATACCAAAC
Found at i:4015520 original size:30 final size:30
Alignment explanation
Indices: 4015486--4015697 Score: 424
Period size: 30 Copynumber: 7.1 Consensus size: 30
4015476 AATTAAGGTT
4015486 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
4015516 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
4015546 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
4015576 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
4015606 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
4015636 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
4015666 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
4015696 TG
1 TG
4015698 TAGTAGTCTA
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 182 1.00
ACGTcount: A:0.20, C:0.07, G:0.37, T:0.37
Consensus pattern (30 bp):
TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
Found at i:4019453 original size:11 final size:11
Alignment explanation
Indices: 4019424--4019461 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4019414 TTCTACAAGT
4019424 TTTTAATAA-A
1 TTTTAATAATA
*
4019434 TTTAAAATAATA
1 TTT-TAATAATA
4019446 TTTTAATAATA
1 TTTTAATAATA
4019457 TTTTA
1 TTTTA
4019462 TATTTTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 3 0.12
11 17 0.71
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAATAATA
Found at i:4019812 original size:15 final size:16
Alignment explanation
Indices: 4019792--4019824 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4019782 AGCTCTCATG
4019792 TATTTTAAAT-TAATT
1 TATTTTAAATATAATT
4019807 TATTTTAAATATAATT
1 TATTTTAAATATAATT
4019823 TA
1 TA
4019825 AAAATACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTAAATATAATT
Found at i:4026558 original size:22 final size:22
Alignment explanation
Indices: 4026532--4026573 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4026522 TTCTTAAACT
4026532 TTAAAATATTTGA-ATTATATTC
1 TTAAAATA-TTGATATTATATTC
*
4026554 TTAAATTATTGATATTATAT
1 TTAAAATATTGATATTATAT
4026574 CCATCAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TTAAAATATTGATATTATATTC
Found at i:4027017 original size:86 final size:87
Alignment explanation
Indices: 4026872--4027055 Score: 343
Period size: 86 Copynumber: 2.1 Consensus size: 87
4026862 ATAACACTAA
4026872 TAATTGAATATGTAATTAGAATATCTTGAAGTTTGATATGTAAGATGAACGTAACTCTAAATTTA
1 TAATTGAATATGTAATTAGAATATCTTGAAGTTTGATATGTAAGATGAACGTAACTCTAAATTTA
4026937 TGTATAATAAA-AAAATATTTT
66 TGTATAATAAATAAAATATTTT
4026958 TAATTGAATATGTAATTAGAATATCTTGAAGTTTGATATGTAAGATGAACGTAACTCTAAATTTA
1 TAATTGAATATGTAATTAGAATATCTTGAAGTTTGATATGTAAGATGAACGTAACTCTAAATTTA
4027023 TGTATAATAAATAAAATATTTT
66 TGTATAATAAATAAAATATTTT
*
4027045 TATATTAAATA
1 TA-ATTGAATA
4027056 AATGATTACA
Statistics
Matches: 95, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
86 76 0.80
87 12 0.13
88 7 0.07
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.40
Consensus pattern (87 bp):
TAATTGAATATGTAATTAGAATATCTTGAAGTTTGATATGTAAGATGAACGTAACTCTAAATTTA
TGTATAATAAATAAAATATTTT
Found at i:4028074 original size:20 final size:21
Alignment explanation
Indices: 4028050--4028091 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
4028040 TGTTTATACC
*
4028050 TTTTTTTAATTTTAAAAAATA
1 TTTTTTAAATTTTAAAAAATA
4028071 TTTTTTAAAATTTTAAAAAAT
1 TTTTTT-AAATTTTAAAAAAT
4028092 TCATTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTTAAATTTTAAAAAATA
Found at i:4034247 original size:5 final size:5
Alignment explanation
Indices: 4034237--4034261 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4034227 TATCAGTAAT
4034237 TCATA TCATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA
4034262 GTTGTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TCATA
Found at i:4050324 original size:15 final size:15
Alignment explanation
Indices: 4050305--4050370 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
4050295 TATTTGATAA
4050305 ACTGAAAAATTAAGT
1 ACTGAAAAATTAAGT
* *
4050320 GCTGAAAAAATAAGT
1 ACTGAAAAATTAAGT
** *
4050335 GTTGAAAAATTAAAT
1 ACTGAAAAATTAAGT
* *
4050350 ATTGAAAATTTAAGT
1 ACTGAAAAATTAAGT
4050365 ACTGAA
1 ACTGAA
4050371 TTTAAGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.29
Consensus pattern (15 bp):
ACTGAAAAATTAAGT
Found at i:4057444 original size:1 final size:1
Alignment explanation
Indices: 4057438--4057522 Score: 98
Period size: 1 Copynumber: 85.0 Consensus size: 1
4057428 TTAGCCACAC
** * * *
4057438 AAAAAAAAAAAAAAAAAAAAAATTAAAACACAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
4057503 CAAAAAACAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAA
4057523 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:4057472 original size:31 final size:29
Alignment explanation
Indices: 4057434--4057522 Score: 112
Period size: 29 Copynumber: 3.0 Consensus size: 29
4057424 AGTATTAGCC
4057434 ACACAAAAAAAAAAAAAAAAAAAAAATTAAA
1 ACACAAAAAAAAAAAAAAAAAAAAAA--AAA
4057465 ACAC--AAAAAAAAAAAAAAAAAAAAAAA
1 ACACAAAAAAAAAAAAAAAAAAAAAAAAA
*
4057492 ACA-AAAAAAAACAAAAAACAAAAAAACAAA
1 ACACAAAAAAAA-AAAAAA-AAAAAAAAAAA
4057522 A
1 A
4057523 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
27 6 0.11
28 6 0.11
29 26 0.49
30 11 0.21
31 4 0.08
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.02
Consensus pattern (29 bp):
ACACAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:4057480 original size:27 final size:25
Alignment explanation
Indices: 4057441--4057522 Score: 119
Period size: 25 Copynumber: 3.2 Consensus size: 25
4057431 GCCACACAAA
4057441 AAAAAAAAAAAAAAAAAAATTAAAACAC
1 AAAAAAAAAAAAAAAAAAA--AAAA-AC
4057469 AAAAAAAAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAC
* *
4057494 AAAAAAAAACAAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAC
4057519 AAAA
1 AAAA
4057523 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
25 29 0.56
26 4 0.08
28 19 0.37
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAAAAAAAAAAC
Found at i:4057480 original size:33 final size:32
Alignment explanation
Indices: 4057433--4057522 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
4057423 AAGTATTAGC
**
4057433 CACACAAAAAAAAAAAAAAAAAAAAAATTAAAA
1 CACA-AAAAAAAAAAAAAAAAAAAAAAACAAAA
4057466 CACAAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 CACAAAAAAAAAAAAAAAAAAAAAAAACAAAA
* * *
4057498 -A-AAAACAAAAAACAAAAAAACAAAA
1 CACAAAAAAAAAAAAAAAAAAAAAAAA
4057523 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 21 0.40
31 1 0.02
32 26 0.50
33 4 0.08
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (32 bp):
CACAAAAAAAAAAAAAAAAAAAAAAAACAAAA
Found at i:4061076 original size:26 final size:26
Alignment explanation
Indices: 4061023--4061074 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4061013 AATAACATGA
**
4061023 ATTTAATATTTTTTACTACTTATTTT
1 ATTTAATATTTTTTACTAAATATTTT
*
4061049 ATTTAATATTTTTTATTGAAATATTT
1 ATTTAATATTTTTTACT-AAATATTT
4061075 ATCAAGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTAATATTTTTTACTAAATATTTT
Found at i:4063127 original size:18 final size:18
Alignment explanation
Indices: 4063106--4063163 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
4063096 ATGTAAAATT
4063106 GTAATATTTTATAAAGTC
1 GTAATATTTTATAAAGTC
* ** *
4063124 GTAAGAGAATTATAAA-TT
1 GTAATA-TTTTATAAAGTC
4063142 GTAATATTTTATAAAGTC
1 GTAATATTTTATAAAGTC
4063160 GTAA
1 GTAA
4063164 GAGAATTATA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 7 0.23
18 16 0.53
19 7 0.23
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (18 bp):
GTAATATTTTATAAAGTC
Found at i:4063138 original size:19 final size:19
Alignment explanation
Indices: 4063114--4063174 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
4063104 TTGTAATATT
4063114 TTATAAAGTCGTAAGAGAA
1 TTATAAAGTCGTAAGAGAA
* * **
4063133 TTATAAA-TTGTAATA-TT
1 TTATAAAGTCGTAAGAGAA
4063150 TTATAAAGTCGTAAGAGAA
1 TTATAAAGTCGTAAGAGAA
4063169 TTATAA
1 TTATAA
4063175 TAATGTAAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 7 0.22
18 12 0.38
19 13 0.41
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (19 bp):
TTATAAAGTCGTAAGAGAA
Found at i:4063141 original size:36 final size:36
Alignment explanation
Indices: 4063101--4063174 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
4063091 GTAAAATGTA
4063101 AAATTGTAATATTTTATAAAGTCGTAAGAGAATTAT
1 AAATTGTAATATTTTATAAAGTCGTAAGAGAATTAT
4063137 AAATTGTAATATTTTATAAAGTCGTAAGAGAATTAT
1 AAATTGTAATATTTTATAAAGTCGTAAGAGAATTAT
4063173 AA
1 AA
4063175 TAATGTAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.38
Consensus pattern (36 bp):
AAATTGTAATATTTTATAAAGTCGTAAGAGAATTAT
Found at i:4063470 original size:10 final size:10
Alignment explanation
Indices: 4063390--4063506 Score: 60
Period size: 10 Copynumber: 11.6 Consensus size: 10
4063380 TTTTGATGCA
4063390 TTTTTATATAT
1 TTTTTATA-AT
*
4063401 TTTTTATGA-
1 TTTTTATAAT
*
4063410 TTTTTATAAA
1 TTTTTATAAT
* * *
4063420 ATTTCACTATT
1 TTTTTA-TAAT
*
4063431 TTTTTATATT
1 TTTTTATAAT
**
4063441 TCTTTTACGA-
1 T-TTTTATAAT
4063451 TTTTTATAAT
1 TTTTTATAAT
*
4063461 TTTTTCTAAT
1 TTTTTATAAT
*
4063471 TTTTAATAA-
1 TTTTTATAAT
** *
4063480 AATTTAAATAT
1 TTTTTATA-AT
4063491 TTTTTATAAT
1 TTTTTATAAT
4063501 TTTTTA
1 TTTTTA
4063507 CCACATGTCA
Statistics
Matches: 77, Mismatches: 23, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
9 18 0.23
10 36 0.47
11 23 0.30
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:4063480 original size:61 final size:59
Alignment explanation
Indices: 4063389--4063507 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 59
4063379 TTTTTGATGC
* * * *
4063389 ATTTTTATATATTTTTTATGATTTTTATAAAATTTCACTATTTTTTTATATTTCTTTTACG
1 ATTTTTATATATTTTTTATAATTTTTATAAAATTTAAATA-TTTTTTATAATT-TTTTACG
*
4063450 ATTTTTATA-ATTTTTTCTAATTTTTAATAAAATTTAAATATTTTTTATAATTTTTTAC
1 ATTTTTATATATTTTTTATAATTTTT-ATAAAATTTAAATATTTTTTATAATTTTTTAC
4063508 CACATGTCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 6 0.12
60 25 0.48
61 21 0.40
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (59 bp):
ATTTTTATATATTTTTTATAATTTTTATAAAATTTAAATATTTTTTATAATTTTTTACG
Found at i:4063701 original size:79 final size:81
Alignment explanation
Indices: 4063587--4063739 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 81
4063577 AGTCAAATGA
* * *
4063587 TCTTTTTGATGTATTTTAATGGTTTAAGGTACAATT-TAGTAAAAAA-AAGGACTTAATT-ATTA
1 TCTTTTTGATGTATTTTAATAGTTCAAGATACAATTATAG-AAAAAATAAGGACTTAATTAATTA
4063649 TTTTTTAAAATTAAGGG
65 TTTTTTAAAATTAAGGG
*
4063666 TCTTTTT-ATGTATTTTAATAGTTCAA-ATATCCAATTGAATAGAAAAAATAATGACTTAATTAA
1 TCTTTTTGATGTATTTTAATAGTTCAAGATA--CAATT--ATAGAAAAAATAAGGACTTAATTAA
*
4063729 TTTTTTTTTAA
62 TTATTTTTTAA
4063740 GCTTGAAAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
77 2 0.03
78 17 0.27
79 12 0.19
81 6 0.10
82 14 0.23
83 11 0.18
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (81 bp):
TCTTTTTGATGTATTTTAATAGTTCAAGATACAATTATAGAAAAAATAAGGACTTAATTAATTAT
TTTTTAAAATTAAGGG
Found at i:4064295 original size:6 final size:6
Alignment explanation
Indices: 4064286--4064316 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
4064276 TTTAAAATTT
*
4064286 ATATTA ATATTA CTATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA ATATTA A
4064317 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:4067385 original size:9 final size:9
Alignment explanation
Indices: 4067371--4067395 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4067361 TTAAAACAAG
4067371 TATAAAACA
1 TATAAAACA
4067380 TATAAAACA
1 TATAAAACA
4067389 TATAAAA
1 TATAAAA
4067396 AATAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
TATAAAACA
Found at i:4072979 original size:27 final size:27
Alignment explanation
Indices: 4072949--4073015 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
4072939 CCTATCAGGT
4072949 AGGCGCCAATGAAGATGCCTCACAGAG
1 AGGCGCCAATGAAGATGCCTCACAGAG
* *
4072976 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGATGCCTCACAGAG
4073003 AGGCGCCAATGAA
1 AGGCGCCAATGAA
4073016 TATTCATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.31, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGATGCCTCACAGAG
Found at i:4073051 original size:21 final size:21
Alignment explanation
Indices: 4073014--4073068 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
4073004 GGCGCCAATG
4073014 AATATTCATAC--AAAATTAC
1 AATATTCATACAAAAAATTAC
*
4073033 AATATTCATATAAAAAATTAC
1 AATATTCATACAAAAAATTAC
4073054 AATATTCATACAAAA
1 AATATTCATACAAAA
4073069 TACTAATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.31
21 22 0.69
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATTCATACAAAAAATTAC
Found at i:4073240 original size:17 final size:17
Alignment explanation
Indices: 4073218--4073250 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4073208 TTAAAAATAT
4073218 AAAAAAATATT-TTATTC
1 AAAAAAA-ATTATTATTC
4073235 AAAAAAAATTATTATT
1 AAAAAAAATTATTATT
4073251 ATTTTATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAAAAATTATTATTC
Found at i:4083939 original size:19 final size:20
Alignment explanation
Indices: 4083917--4083960 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
4083907 ATTTGTTTAA
*
4083917 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
4083936 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
4083955 -ATTTTT
1 AATTTTT
4083961 TTTTTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:4083947 original size:18 final size:18
Alignment explanation
Indices: 4083920--4083959 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4083910 TGTTTAAAAT
*
4083920 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTG-A
4083938 TTTTAAAAATTATTTTGA
1 TTTTAAAAATTATTTTGA
4083956 TTTT
1 TTTT
4083960 TTTTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATTATTTTGA
Found at i:4086672 original size:2 final size:2
Alignment explanation
Indices: 4086665--4086744 Score: 74
Period size: 2 Copynumber: 40.0 Consensus size: 2
4086655 CAATAACTTA
* * * *
4086665 AT AT AT AT AT AT AT AT AT AT AT AT AA ACT CAT -T TT TT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT
* *
4086708 A- AA AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4086745 TTTTATGTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.03
2 64 0.94
3 1 0.01
4 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4117760 original size:211 final size:212
Alignment explanation
Indices: 4117396--4117819 Score: 841
Period size: 211 Copynumber: 2.0 Consensus size: 212
4117386 AATTAGCCAA
4117396 AACTAATTTTAATCGAGTTTCTACATTGTTATTATTTGCATCATCAATTTTTTCTAATCTATATT
1 AACTAATTTTAATCGAGTTTCTACATTGTTATTATTTGCATCATCAATTTTTTCTAATCTATATT
4117461 AATGTGTGAGTATTTCTTTCTAAAGCTTTTCTATGAATTAATTTGAATTGTGACCAAAACCATGG
66 AATGTGTGAGTATTTCTTTCTAAAGCTTTTCTATGAATTAATTTGAATTGTGACCAAAACCATGG
4117526 CATTTCTACTCATTGTCAATGA-TTTTTTTTTTTTGGATGAGTAGTCATTATTAATTAGTTATGT
131 CATTTCTACTCATTGTCAATGATTTTTTTTTTTTTGGATGAGTAGTCATTATTAATTAGTTATGT
4117590 TTTATTATCATACTAAT
196 TTTATTATCATACTAAT
4117607 AACTAATTTTAATCGAGTTTCTACATTGTTATTATTTGCATCATCAATTTTTTCTAATCTATATT
1 AACTAATTTTAATCGAGTTTCTACATTGTTATTATTTGCATCATCAATTTTTTCTAATCTATATT
4117672 AATGTGTGAGTATTTCTTTCTAAAGCTTTTCTATGAATTAATTTGAATTGTGACCAAAACCATGG
66 AATGTGTGAGTATTTCTTTCTAAAGCTTTTCTATGAATTAATTTGAATTGTGACCAAAACCATGG
4117737 CATTTCTACTCATTGTCAATGATTTTTTTTTTTTTGGATGAGTAGTCATTATTAATTAGTTATGT
131 CATTTCTACTCATTGTCAATGATTTTTTTTTTTTTGGATGAGTAGTCATTATTAATTAGTTATGT
4117802 TTTATTATCATACTAAT
196 TTTATTATCATACTAAT
4117819 A
1 A
4117820 TTGGTCGTAT
Statistics
Matches: 212, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
211 152 0.72
212 60 0.28
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (212 bp):
AACTAATTTTAATCGAGTTTCTACATTGTTATTATTTGCATCATCAATTTTTTCTAATCTATATT
AATGTGTGAGTATTTCTTTCTAAAGCTTTTCTATGAATTAATTTGAATTGTGACCAAAACCATGG
CATTTCTACTCATTGTCAATGATTTTTTTTTTTTTGGATGAGTAGTCATTATTAATTAGTTATGT
TTTATTATCATACTAAT
Found at i:4121529 original size:23 final size:23
Alignment explanation
Indices: 4121485--4121534 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4121475 GCCAAGGTTC
* * **
4121485 CCACTGATATGTAGTCGTAGCTA
1 CCACTGAAATGTAGCCAAAGCTA
4121508 CCACTGAAATGTAGCCAAAGCTA
1 CCACTGAAATGTAGCCAAAGCTA
4121531 CCAC
1 CCAC
4121535 AGATCAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (23 bp):
CCACTGAAATGTAGCCAAAGCTA
Found at i:4123585 original size:36 final size:36
Alignment explanation
Indices: 4123533--4123625 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
4123523 TATCACTTCT
* * *
4123533 CATAAGCCTTCCCCCATGTGTAGGAGTACGACCTCC
1 CATAAGCCTTCTCCCATGTGTAGGAGCACGACCTCA
* *
4123569 CATAAGCCTTCTCCCATGTATAGGAGCAGGACCTCA
1 CATAAGCCTTCTCCCATGTGTAGGAGCACGACCTCA
*
4123605 CGTAAGCCTT-TCCCCATGTGT
1 CATAAGCCTTCT-CCCATGTGT
4123626 GGGACCAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
35 1 0.02
36 48 0.98
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (36 bp):
CATAAGCCTTCTCCCATGTGTAGGAGCACGACCTCA
Found at i:4130667 original size:2 final size:2
Alignment explanation
Indices: 4130660--4130694 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4130650 ATATAACACA
4130660 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4130695 TTTTCCAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4146469 original size:21 final size:21
Alignment explanation
Indices: 4146427--4146514 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
4146417 GATCAATATA
* *
4146427 GACACAT-AAGTACCTGAAAC
1 GACACATAAAGTGCCTGATAC
** *
4146447 GACACACGAGGTGCCTGATAC
1 GACACATAAAGTGCCTGATAC
4146468 GACACATAAAGTGCCTGAGATAC
1 GACACATAAAGTGCCT--GATAC
4146491 GACACATAAAGTGCCTGAT-C
1 GACACATAAAGTGCCTGATAC
4146511 GACA
1 GACA
4146515 AAGTCGATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.19
21 26 0.45
23 21 0.36
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (21 bp):
GACACATAAAGTGCCTGATAC
Done.