Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 119 of 131
Found at i:39287564 original size:200 final size:200
Alignment explanation
Indices: 39287221--39287616 Score: 729
Period size: 200 Copynumber: 2.0 Consensus size: 200
39287211 TTGATTGCAG
39287221 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
1 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
*
39287286 TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGATATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
66 TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
*
39287351 GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTATGAGATTAT
131 GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTAT
39287416 TTATA
196 TTATA
*
39287421 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAATGTATTTA
1 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
* *
39287486 TAGGAGAAGTCCTCTTGTCTGGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
66 TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
* *
39287551 GAGTAGGTGAGGACGTATAAGGTAGGGCCCATTCTATTATTCCTTTTGAGAGAGTACGAGATTAT
131 GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTAT
39287616 T
196 T
39287617 ATGTTCATTT
Statistics
Matches: 189, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 189 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (200 bp):
GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTAT
TTATA
Found at i:39293917 original size:19 final size:19
Alignment explanation
Indices: 39293895--39293955 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
39293885 TTTTTATACA
*
39293895 TTTTATATTTTTTTATAAT
1 TTTTATATTTTTTTACAAT
**
39293914 TTTTATA-AATTTTACAAT
1 TTTTATATTTTTTTACAAT
*
39293932 TTTT-TATATGTTTTACAAT
1 TTTTATAT-TTTTTTACAAT
39293951 TTTTA
1 TTTTA
39293956 CAATTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.06
18 12 0.35
19 20 0.59
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTTTTACAAT
Found at i:39293925 original size:28 final size:28
Alignment explanation
Indices: 39293885--39293971 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 28
39293875 TTAAAGGGTT
* * *
39293885 TTTTTATACATTTTATATTTTTTTATAA
1 TTTTTATAAATTTTACAATTTTTTATAA
39293913 TTTTTATAAATTTTACAATTTTTTAT-A
1 TTTTTATAAATTTTACAATTTTTTATAA
* * *
39293940 TGTTTTACAATTTTTACAA-TTTTTCTAA
1 T-TTTTATAAATTTTACAATTTTTTATAA
39293968 TTTT
1 TTTT
39293972 AACAAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 11 0.22
28 40 0.78
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTTATAAATTTTACAATTTTTTATAA
Found at i:39293954 original size:9 final size:9
Alignment explanation
Indices: 39293904--39293976 Score: 60
Period size: 9 Copynumber: 8.0 Consensus size: 9
39293894 ATTTTATATT
*
39293904 TTTTTATAA
1 TTTTTACAA
*
39293913 TTTTTATAA
1 TTTTTACAA
*
39293922 ATTTTACAA
1 TTTTTACAA
*
39293931 TTTTTTA-TA
1 -TTTTTACAA
39293940 TGTTTTACAA
1 T-TTTTACAA
39293950 TTTTTACAA
1 TTTTTACAA
39293959 TTTTT-CTAA
1 TTTTTAC-AA
*
39293968 TTTTAACAA
1 TTTTTACAA
39293977 AATTTTAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
8 2 0.04
9 43 0.81
10 8 0.15
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTTACAA
Found at i:39293982 original size:28 final size:28
Alignment explanation
Indices: 39293894--39293983 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
39293884 TTTTTTATAC
* * * *
39293894 ATTTTATATTTTTTTATAAT-TTTTATAA
1 ATTTTACAATTTTTTAT-ATGTTTAACAA
*
39293922 ATTTTACAATTTTTTATATGTTTTACAA
1 ATTTTACAATTTTTTATATGTTTAACAA
*
39293950 TTTTTACAATTTTTCTA-AT-TTTAACAAA
1 ATTTTACAATTTTT-TATATGTTTAAC-AA
39293978 ATTTTA
1 ATTTTA
39293984 ATATACTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.13
28 44 0.83
29 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (28 bp):
ATTTTACAATTTTTTATATGTTTAACAA
Found at i:39294000 original size:29 final size:28
Alignment explanation
Indices: 39293968--39294028 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
39293958 ATTTTTCTAA
*
39293968 TTTTAACAAAATTTTAATATACTTTATAT
1 TTTTAACAAAA-TTTAATAAACTTTATAT
** * *
39293997 TTTTATTAAAATTTAATAAATTTTATTT
1 TTTTAACAAAATTTAATAAACTTTATAT
39294025 TTTT
1 TTTT
39294029 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTAACAAAATTTAATAAACTTTATAT
Found at i:39294630 original size:3 final size:3
Alignment explanation
Indices: 39294622--39294675 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
39294612 NNNNNNNNNN
39294622 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39294670 TAT TAT
1 TAT TAT
39294676 CTCGCAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39297266 original size:28 final size:28
Alignment explanation
Indices: 39297226--39297279 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
39297216 AAGTTCCCAT
39297226 TTTCTTTGTCTTTATTCTCTT-TTTTTCC
1 TTTCTTTGTCTTTATTCT-TTATTTTTCC
*
39297254 TTTCTTTTTCTTTATTCTTTATTTTT
1 TTTCTTTGTCTTTATTCTTTATTTTT
39297280 ATTTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (28 bp):
TTTCTTTGTCTTTATTCTTTATTTTTCC
Found at i:39297278 original size:17 final size:17
Alignment explanation
Indices: 39297253--39297296 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
39297243 TCTTTTTTTC
*
39297253 CTTTCTTTTTCTTTATT
1 CTTTCTTTTTATTTATT
* *
39297270 CTTTATTTTTATTTTTT
1 CTTTCTTTTTATTTATT
39297287 CTTTCTTTTT
1 CTTTCTTTTT
39297297 GCTGTTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTCTTTTTATTTATT
Found at i:39297285 original size:34 final size:34
Alignment explanation
Indices: 39297225--39297296 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
39297215 CAAGTTCCCA
39297225 TTTTCTTTGTCTTTATTCTCTTTTTTTCCTTTCT
1 TTTTCTTTGTCTTTATTCTCTTTTTTTCCTTTCT
* *
39297259 TTTTCTTTATTCTTTATT-T-TTATTTTTTCTTTCT
1 TTTTCTTT-GTCTTTATTCTCTT-TTTTTCCTTTCT
39297293 TTTT
1 TTTT
39297297 GCTGTTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 2 0.06
34 24 0.71
35 8 0.24
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (34 bp):
TTTTCTTTGTCTTTATTCTCTTTTTTTCCTTTCT
Found at i:39297291 original size:28 final size:29
Alignment explanation
Indices: 39297225--39297294 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
39297215 CAAGTTCCCA
*
39297225 TTTTCTTTGTCTTTATTCTCTTTTTTTCCTT
1 TTTTC-TT-TCTTTATTCTCTTTTTTTCATT
*
39297256 TCTT-TTTCTTTATTCT-TTATTTTT-ATT
1 TTTTCTTTCTTTATTCTCTT-TTTTTCATT
39297283 TTTTCTTTCTTT
1 TTTTCTTTCTTT
39297295 TTGCTGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 7 0.21
28 22 0.65
29 2 0.06
31 3 0.09
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (29 bp):
TTTTCTTTCTTTATTCTCTTTTTTTCATT
Found at i:39297949 original size:41 final size:41
Alignment explanation
Indices: 39297859--39297936 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
39297849 TAATCTACAT
* * *
39297859 CACACGGACGTGTGGTTGGCCGTGTGTCAGGCCGTGTATGC
1 CACACGGACGTGTGGTCGACCGTGTGCCAGGCCGTGTATGC
* *
39297900 CACACGGACGTGTGGTCGACTGTGTGCCAGGTCGTGT
1 CACACGGACGTGTGGTCGACCGTGTGCCAGGCCGTGT
39297937 GGAGCACACG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.13, C:0.24, G:0.38, T:0.24
Consensus pattern (41 bp):
CACACGGACGTGTGGTCGACCGTGTGCCAGGCCGTGTATGC
Found at i:39299580 original size:53 final size:52
Alignment explanation
Indices: 39299500--39299658 Score: 203
Period size: 53 Copynumber: 3.0 Consensus size: 52
39299490 CCATGGCACT
* * *
39299500 GAAGACTATATTCTGTAAGACCGTAACTGGTTGGTTATGGAATCATATGGAAA
1 GAAGACAATA-TCTGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
*
39299553 GAAGACAATATCGTGTAAGACCATAACTGGTGGGTTATGAAATCATATGGAAA
1 GAAGACAATATC-TGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
* * * *
39299606 GAATACCATATCATGTAAGACCATAATTGATGGGTTAT-GACATCATATGGAAA
1 GAAGACAATATC-TGTAAGACCATAACTGGTGGGTTATGGA-ATCATATGGAAA
39299659 ATTTAAGAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 3 0.03
53 91 0.97
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (52 bp):
GAAGACAATATCTGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
Found at i:39299851 original size:27 final size:29
Alignment explanation
Indices: 39299808--39299874 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
39299798 AAGGATACAT
* *
39299808 CTTTGTGGCGA-ACCTCTTA-AAGG-ATGC
1 CTTTGTAGCGAGACCTC-TAGAAGGAAAGC
*
39299835 CTTTGTTGCGAGA-CTCTAGAAGGAAAGC
1 CTTTGTAGCGAGACCTCTAGAAGGAAAGC
39299863 CTTTGTAGCGAG
1 CTTTGTAGCGAG
39299875 TACTTAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 17 0.50
28 15 0.44
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (29 bp):
CTTTGTAGCGAGACCTCTAGAAGGAAAGC
Found at i:39303070 original size:15 final size:15
Alignment explanation
Indices: 39303050--39303078 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39303040 TTCAGATAAT
39303050 TTCACTTCGATTCAA
1 TTCACTTCGATTCAA
39303065 TTCACTTCGATTCA
1 TTCACTTCGATTCA
39303079 CTTTTCCAAT
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:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (15 bp):
TTCACTTCGATTCAA
Found at i:39303921 original size:16 final size:17
Alignment explanation
Indices: 39303891--39303923 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39303881 TTGTTTATTA
*
39303891 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
39303908 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
39303924 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:39311167 original size:21 final size:22
Alignment explanation
Indices: 39311129--39311171 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
39311119 AGTATGTTAT
39311129 GTCGTGACGAGAAACCCCCAAC
1 GTCGTGACGAGAAACCCCCAAC
*
39311151 GTCGTGATGAG-AACCCCCAAC
1 GTCGTGACGAGAAACCCCCAAC
39311172 ATCCTGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (22 bp):
GTCGTGACGAGAAACCCCCAAC
Found at i:39319437 original size:37 final size:37
Alignment explanation
Indices: 39319387--39319462 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
39319377 TCACGAGTTC
39319387 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
1 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
*
39319424 CTTTAGCTGATTCTATGGAAGAGGTGGTGAAGCTTAA
1 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
39319461 CT
1 CT
39319463 CTTCTAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (37 bp):
CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
Found at i:39321251 original size:228 final size:228
Alignment explanation
Indices: 39320848--39321303 Score: 716
Period size: 228 Copynumber: 2.0 Consensus size: 228
39320838 TTTAGAAAGA
*
39320848 GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGTAG
1 GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGCAG
* * * * * *
39320913 TGATGACTTTTATGCCCTCTTTTTCCAGGAGCAGTGGGGTACAATAGGCCCAGCTATTTGTTATT
66 TGATAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAATAGGCCCAGCTATTTGTGATT
* *
39320978 GGGTGAAAATGGTATTTAATGGAGGCATTATTGATACTAAGCTTAATAACACATTGATTATTCTT
131 GGGTGAAAATGGTATTTAATGGAGGCATTATTAATAATAAGCTTAATAACACATTGATTATTCTT
*
39321043 ATTCCCAAGTTTTAGAGTCTTGAA-GGGTTTTCT
196 ATTCCCAAGTTTTAGAGTCCT-AAGGGGTTTTCT
* * * *
39321076 GTGGTTACTGATGAATAAATTAAAAAGGTTTTGTTTGACATGGCTCCTCTAAAAGCTCTGGGCAG
1 GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGCAG
* * *
39321141 TGGTAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAGTGGGCCCAGCTATTTGTGATT
66 TGATAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAATAGGCCCAGCTATTTGTGATT
* * *
39321206 GGGTGAAAATGGTATTTAATGGAGGCGTTATTAATAATGAGCTTAATAACACATTGATTGTTCTT
131 GGGTGAAAATGGTATTTAATGGAGGCATTATTAATAATAAGCTTAATAACACATTGATTATTCTT
39321271 ATTCCCAAGTTTTAGAGTCCTAAGGGGTTTTCT
196 ATTCCCAAGTTTTAGAGTCCTAAGGGGTTTTCT
39321304 TAGTTTTTTC
Statistics
Matches: 207, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
227 2 0.01
228 205 0.99
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (228 bp):
GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGCAG
TGATAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAATAGGCCCAGCTATTTGTGATT
GGGTGAAAATGGTATTTAATGGAGGCATTATTAATAATAAGCTTAATAACACATTGATTATTCTT
ATTCCCAAGTTTTAGAGTCCTAAGGGGTTTTCT
Found at i:39323246 original size:17 final size:17
Alignment explanation
Indices: 39323224--39323256 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39323214 ATATTTAATA
39323224 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
39323241 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
39323257 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:39324988 original size:17 final size:18
Alignment explanation
Indices: 39324968--39325009 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
39324958 CATAATTTTT
39324968 AAATATAAAATATTTA-A
1 AAATATAAAATATTTATA
*
39324985 AAAT-TGAAAATGTTTATA
1 AAATAT-AAAATATTTATA
39325003 AAATATA
1 AAATATA
39325010 TTTATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 6 0.29
19 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATATAAAATATTTATA
Found at i:39330276 original size:24 final size:24
Alignment explanation
Indices: 39330235--39330285 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
39330225 AATTCACTAA
39330235 AATAAAAAAAAAGAATATA-ATGAT
1 AATAAAAAAAAAGAATATATAT-AT
* * *
39330259 AATAAAAGAAATGCATATATATAT
1 AATAAAAAAAAAGAATATATATAT
39330283 AAT
1 AAT
39330286 TATTAGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (24 bp):
AATAAAAAAAAAGAATATATATAT
Found at i:39331639 original size:11 final size:11
Alignment explanation
Indices: 39331625--39331650 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39331615 TTTTTTAAAA
39331625 TTTTAAAATAC
1 TTTTAAAATAC
39331636 TTTTAAAATAC
1 TTTTAAAATAC
39331647 TTTT
1 TTTT
39331651 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:39331662 original size:9 final size:9
Alignment explanation
Indices: 39331648--39331708 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
39331638 TTAAAATACT
39331648 TTTTTTAAA
1 TTTTTTAAA
39331657 TTTTTTAAA
1 TTTTTTAAA
39331666 --TTTTAAA
1 TTTTTTAAA
39331673 TTTTTTTAAAAA
1 -TTTTTT--AAA
39331685 TACTTTTTAAA
1 T--TTTTTAAA
*
39331696 TTTTTTTAA
1 TTTTTTAAA
39331705 TTTT
1 TTTT
39331709 AAAATACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
7 7 0.16
9 20 0.45
10 4 0.09
11 5 0.11
12 3 0.07
13 5 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:39331667 original size:41 final size:41
Alignment explanation
Indices: 39331607--39331719 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 41
39331597 NNNNNNNNTA
*
39331607 TTTTTT-ATTTTTTTAAAATTTTAAAATACTTTT-AAAATAC
1 TTTTTTAAATTTTTT-AAATTTTAAAATACTTTTAAAAATAC
**
39331647 TTTTTTTAAATTTTTTAAATTTT-AAATTTTTTTAAAAATAC
1 -TTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAAATAC
*
39331688 -TTTTTAAATTTTTTTAATTTTAAAATACTTTT
1 TTTTTTAAATTTTTTAAATTTTAAAATACTTTT
39331720 TTTATTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
39 20 0.32
40 16 0.25
41 20 0.32
42 7 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (41 bp):
TTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAAATAC
Found at i:39337341 original size:11 final size:11
Alignment explanation
Indices: 39337327--39337352 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39337317 TTTTTTAAAA
39337327 TTTTAAAATAC
1 TTTTAAAATAC
39337338 TTTTAAAATAC
1 TTTTAAAATAC
39337349 TTTT
1 TTTT
39337353 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:39337363 original size:41 final size:41
Alignment explanation
Indices: 39337309--39337421 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 41
39337299 AATATTTTTA
*
39337309 TTTTTT-ATTTTTTTAAAATTTTAAAATACTTTT-AAAATAC
1 TTTTTTAAATTTTTT-AAATTTTAAAATACTTTTAAAAATAC
**
39337349 TTTTTTTAAATTTTTTAAATTTT-AAATTTTTTTAAAAATAC
1 -TTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAAATAC
*
39337390 -TTTTTAAATTTTTTTAATTTTAAAATACTTTT
1 TTTTTTAAATTTTTTAAATTTTAAAATACTTTT
39337422 TTTATTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
39 20 0.32
40 16 0.25
41 20 0.32
42 7 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (41 bp):
TTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAAATAC
Found at i:39337364 original size:9 final size:9
Alignment explanation
Indices: 39337350--39337410 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
39337340 TTAAAATACT
39337350 TTTTTTAAA
1 TTTTTTAAA
39337359 TTTTTTAAA
1 TTTTTTAAA
39337368 --TTTTAAA
1 TTTTTTAAA
39337375 TTTTTTTAAAAA
1 -TTTTTT--AAA
39337387 TACTTTTTAAA
1 T--TTTTTAAA
*
39337398 TTTTTTTAA
1 TTTTTTAAA
39337407 TTTT
1 TTTT
39337411 AAAATACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
7 7 0.16
9 20 0.45
10 4 0.09
11 5 0.11
12 3 0.07
13 5 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:39346050 original size:14 final size:15
Alignment explanation
Indices: 39346028--39346103 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 15
39346018 CAATCAAACA
39346028 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
39346042 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
39346057 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
39346077 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
39346091 ACGGAAAA-CATTT
1 CCAGAAAATCATTT
39346104 ACTGGCAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.43
15 14 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:39346069 original size:20 final size:20
Alignment explanation
Indices: 39346044--39346083 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39346034 AATATTTTCC
*
39346044 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
39346064 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
39346084 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:39346089 original size:34 final size:35
Alignment explanation
Indices: 39346032--39346098 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39346022 CAAACACCAG
*
39346032 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
39346067 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
39346099 CATTTACTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:39356945 original size:26 final size:26
Alignment explanation
Indices: 39356909--39356960 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
39356899 CGTTGATTTT
39356909 ATAGAATGCTTAAATAATTAGAATCA
1 ATAGAATGCTTAAATAATTAGAATCA
*
39356935 ATAGAATGCTTAAATAGTTAGAATCA
1 ATAGAATGCTTAAATAATTAGAATCA
39356961 TGTGCGTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (26 bp):
ATAGAATGCTTAAATAATTAGAATCA
Found at i:39369686 original size:41 final size:41
Alignment explanation
Indices: 39369629--39369709 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
39369619 ACCTAATTGT
*
39369629 GAAAATAATTCCCTTATTCTGATAAACTACTAAAAGATAAG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
39369670 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
39369710 AATAAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (41 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
Found at i:39372832 original size:17 final size:18
Alignment explanation
Indices: 39372799--39372832 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39372789 CAGATTGTTA
39372799 AGATAATCAAGGAAATGG
1 AGATAATCAAGGAAATGG
*
39372817 AGATAA-CAAGGGAATG
1 AGATAATCAAGGAAATG
39372833 CAGGTTACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.29, T:0.15
Consensus pattern (18 bp):
AGATAATCAAGGAAATGG
Found at i:39373629 original size:35 final size:35
Alignment explanation
Indices: 39373580--39373651 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
39373570 GAGAAAACAG
*
39373580 AAAGAAAAATGGATCTTAGCACTTAAAAAAGCACA
1 AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
39373615 AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
1 AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
39373650 AA
1 AA
39373652 TGGCACAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.56, C:0.14, G:0.15, T:0.15
Consensus pattern (35 bp):
AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
Found at i:39375026 original size:2 final size:2
Alignment explanation
Indices: 39375019--39375061 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
39375009 CCTTTTTGCT
39375019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39375061 T
1 T
39375062 GAATATGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39379867 original size:27 final size:23
Alignment explanation
Indices: 39379837--39379889 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
39379827 TTTTTTAAGT
39379837 TAAAAAAGTAGAATTATAATATAAT-
1 TAAAAAA-TAGAATTA-AAT-TAATA
*
39379862 TATAAAATAGAATTAAATTAATA
1 TAAAAAATAGAATTAAATTAATA
39379885 TAAAA
1 TAAAA
39379890 TAGACCGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
24 8 0.32
25 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (23 bp):
TAAAAAATAGAATTAAATTAATA
Found at i:39379888 original size:21 final size:24
Alignment explanation
Indices: 39379840--39379893 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 24
39379830 TTTAAGTTAA
39379840 AAAAGTAGAATTATAATATAATTAT
1 AAAA-TAGAATTATAATATAATTAT
39379865 AAAATAGAATTA-AAT-TAA-TAT
1 AAAATAGAATTATAATATAATTAT
39379886 AAAATAGA
1 AAAATAGA
39379894 CCGATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.38
22 3 0.10
23 3 0.10
24 8 0.28
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAATAGAATTATAATATAATTAT
Found at i:39387798 original size:23 final size:23
Alignment explanation
Indices: 39387772--39387820 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
39387762 GACTTTTAGA
39387772 ACAATGGTTAGAGCTCTTCTTTG
1 ACAATGGTTAGAGCTCTTCTTTG
39387795 ACAATGGTTAGAGCTCTTCTTTG
1 ACAATGGTTAGAGCTCTTCTTTG
39387818 ACA
1 ACA
39387821 CTTAGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (23 bp):
ACAATGGTTAGAGCTCTTCTTTG
Found at i:39388647 original size:2 final size:2
Alignment explanation
Indices: 39388636--39388666 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
39388626 AAAAGGTCTG
39388636 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39388667 TTAATGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:39398306 original size:2 final size:2
Alignment explanation
Indices: 39398299--39398337 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39398289 AAGTAAAACT
39398299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39398338 TTTTTTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39412988 original size:3 final size:3
Alignment explanation
Indices: 39412956--39413005 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
39412946 TATTTTAATG
* * * *
39412956 TTA TTA TCA TTA TCA -TA TTA -TA TCA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39413002 TTA T
1 TTA T
39413006 ACGTACATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:39413653 original size:110 final size:107
Alignment explanation
Indices: 39413367--39413807 Score: 661
Period size: 108 Copynumber: 4.1 Consensus size: 107
39413357 TACGCATATT
** * *
39413367 AATATCCTTTTAAAAAAATTTAAAATAAGGCAATGTTTTGTGTTTGAAAATTCGAGGAAACGTGC
1 AATATCCTTTT--AAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGC
39413432 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
64 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
* * *
39413476 AATATCCTTTTAAAAATTCAAAATAAGGTAATGTTTTGCATTTGGAAATTCGAGAAAATGTGCCC
1 AATATCCTTTTAAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCC
39413541 TAATGTG-TCGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 TAATGTGCT-GGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCA
* *
39413584 AATATCCTTTTAAAAATTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGT
1 AATATCCTTTTAAAAATTT--AAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGC
* *
39413649 CCTAATGTGCTGGGTTTTGATTTTTCTCGTTCGACCAAATAGCCG
64 CCTAATGTGCTGGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCA
* * *
39413694 AATATCCTTTTAAAATTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGGAAACATGCCC
1 AATATCCTTTTAAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCC
* *
39413759 TAATGTGCTGGGTTTC-AATTTCTCGTTGGACCAAATAGCCA
66 TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
39413800 AATATCCT
1 AATATCCT
39413808 CTTATATCTT
Statistics
Matches: 304, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
106 30 0.10
107 64 0.21
108 99 0.33
109 11 0.04
110 99 0.33
111 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (107 bp):
AATATCCTTTTAAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCC
TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
Found at i:39413744 original size:218 final size:214
Alignment explanation
Indices: 39413367--39413807 Score: 679
Period size: 218 Copynumber: 2.0 Consensus size: 214
39413357 TACGCATATT
* *
39413367 AATATCCTTTTAAAAAAATTTAAAATAAGGCAATGTTTTGTGTTTGAAAATTCGAGGAAACGTGC
1 AATATCCTTTT-AAAAAATTTAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGC
39413432 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTCAA
65 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTCAA
* ** *
39413497 AATAAGGTAATGTTTTGCATTTGGAAATTCGAGAAAATGTGCCCTAATGTG-TCGGGTTTCGATT
130 AATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCT-GGGTTTC-A-A
39413561 TTTCTCGTTCGACCAAATAGCCA
192 TTTCTCGTTCGACCAAATAGCCA
*
39413584 AATATCCTTTT-AAAAATTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTG
1 AATATCCTTTTAAAAAATTT--AAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTG
* * * * *
39413648 TCCTAATGTGCTGGGTTTTGATTTTTCTCGTTCGACCAAATAGCCGAATATCCTTTTAAAATTTT
64 CCCTAATGTGCTGGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTC
*
39413713 AAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGGAAACATGCCCTAATGTGCTGGGTTTCAAT
128 AAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGGGTTTCAAT
*
39413778 TTCTCGTTGGACCAAATAGCCA
193 TTCTCGTTCGACCAAATAGCCA
39413800 AATATCCT
1 AATATCCT
39413808 CTTATATCTT
Statistics
Matches: 206, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
215 8 0.04
216 30 0.15
217 71 0.34
218 96 0.47
219 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (214 bp):
AATATCCTTTTAAAAAATTTAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCC
CTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTCAAA
ATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGGGTTTCAATTTC
TCGTTCGACCAAATAGCCA
Found at i:39414748 original size:16 final size:16
Alignment explanation
Indices: 39414727--39414761 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39414717 TGTTGTTTTG
*
39414727 TTTTGACTGCATGGCA
1 TTTTGACTACATGGCA
39414743 TTTTGACTACATGGCA
1 TTTTGACTACATGGCA
39414759 TTT
1 TTT
39414762 CATTAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (16 bp):
TTTTGACTACATGGCA
Found at i:39424443 original size:107 final size:108
Alignment explanation
Indices: 39424252--39424448 Score: 245
Period size: 107 Copynumber: 1.8 Consensus size: 108
39424242 TTCATCTTTG
* * * * * * *
39424252 TATCTTAGCGAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGTTTTGCTCTCAATAAATTCT
1 TATCTCAGCAAAATTTGCTATCTTGATTAATATATTCATTTAGAGATCTGCTCTCAAAAAATTCT
*
39424317 CATCTTATCCATTGCGATAA-CCTTGTATATCTTATTCATTTC
66 CATCGTATCCATTGCGATAATCCTTGTATATCTTATTCATTTC
* **
39424359 TATCTCAGCAAAATTTGCTATCTTGATTGATATATTTGTTTAGAGATCTGCTCTCAACAAAATT-
1 TATCTCAGCAAAATTTGCTATCTTGATTAATATATTCATTTAGAGATCTGCTCTCAA-AAAATTC
* **
39424423 TCATCGTGTCCATTTTGATAATCCTT
65 TCATCGTATCCATTGCGATAATCCTT
39424449 TTCAAGCATC
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
107 65 0.88
108 9 0.12
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (108 bp):
TATCTCAGCAAAATTTGCTATCTTGATTAATATATTCATTTAGAGATCTGCTCTCAAAAAATTCT
CATCGTATCCATTGCGATAATCCTTGTATATCTTATTCATTTC
Found at i:39425559 original size:44 final size:43
Alignment explanation
Indices: 39425491--39425690 Score: 104
Period size: 44 Copynumber: 4.6 Consensus size: 43
39425481 GAGCAGACTG
* *
39425491 AAATCACAA-ATTAT-TCCCCTGAAGTTACAGCGGGGCAGGTCA
1 AAATCACAATCTTATCT-CCCTGAAGTTACAGCGGAGCAGGTCA
* * * * * **
39425533 AAATCATGAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGGTTG
1 AAATCA-CAATCTTATCTCCCTGAAGTTACAGCGGAGCAGGTCA
* * ** * * * * *
39425577 AAGTTACAAGTCTTATCTCCCCAAAGTTGCGGTGGAGCA-GACTG
1 AAATCACAA-TCTTATCTCCCTGAAGTTACAGCGGAGCAGGTC-A
* * *
39425621 AAATCACAA-ATTAT-TCCCCTGAAGTTACAGCGGGGTAGGTCA
1 AAATCACAATCTTATCT-CCCTGAAGTTACAGCGGAGCAGGTCA
* *
39425663 AAATCATGAATCTTATCTCCTTGAAGTT
1 AAATCA-CAATCTTATCTCCCTGAAGTT
39425691 GCAGTGGAAC
Statistics
Matches: 114, Mismatches: 34, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.26
43 9 0.08
44 72 0.63
45 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (43 bp):
AAATCACAATCTTATCTCCCTGAAGTTACAGCGGAGCAGGTCA
Found at i:39425570 original size:130 final size:130
Alignment explanation
Indices: 39425417--39425698 Score: 528
Period size: 130 Copynumber: 2.2 Consensus size: 130
39425407 GACAAACCTG
* *
39425417 ATCTCCATGAAGTTGTAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
39425482 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
66 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
*
39425547 ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGTTGCGGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
*
39425612 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGTAGGTCAAAATCATGAATCTT
66 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
39425677 ATCTCCTTGAAGTTGCAGTGGA
1 ATCTCCTTGAAGTTGCAGTGGA
39425699 ACATACTAAA
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 148 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (130 bp):
ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
Found at i:39426341 original size:18 final size:20
Alignment explanation
Indices: 39426318--39426355 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
39426308 TAATGTTTAC
39426318 AGAGAA-AAAAAATA-CAAT
1 AGAGAACAAAAAATATCAAT
*
39426336 AGAGAACCAAAAATATCAAT
1 AGAGAACAAAAAATATCAAT
39426356 TAGAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.13
Consensus pattern (20 bp):
AGAGAACAAAAAATATCAAT
Found at i:39427322 original size:29 final size:31
Alignment explanation
Indices: 39427263--39427326 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
39427253 TAGATTTGAT
*
39427263 TATATATATATACATACATATCTTTGATTTA
1 TATATATATATACATACATATCTATGATTTA
*
39427294 TATATATATATGCATAC-T-TCTAT-ACTTTA
1 TATATATATATACATACATATCTATGA-TTTA
39427323 TATA
1 TATA
39427327 CTTTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 12 0.40
30 1 0.03
31 16 0.53
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (31 bp):
TATATATATATACATACATATCTATGATTTA
Found at i:39455028 original size:34 final size:34
Alignment explanation
Indices: 39454984--39455074 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
39454974 ATATTTTTTA
*
39454984 AAAATTAATTAAATTAGATTTTAAG-GGTTTTAA-
1 AAAATTAATTAAATTAGAGTTT-AGCGGTTTTAAG
* *
39455017 ATAAATTAATTAAATTAGGGTTTAGCGTTTTTAAG
1 A-AAATTAATTAAATTAGAGTTTAGCGGTTTTAAG
*
39455052 AAAATTAATTAAATTAGGGTTTA
1 AAAATTAATTAAATTAGAGTTTA
39455075 ATTTTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
33 3 0.06
34 48 0.92
35 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.42
Consensus pattern (34 bp):
AAAATTAATTAAATTAGAGTTTAGCGGTTTTAAG
Found at i:39455087 original size:34 final size:33
Alignment explanation
Indices: 39454984--39455088 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 33
39454974 ATATTTTTTA
** *
39454984 AAAATTAATTAAATTAGATTTTAAGGGTTTTAAA-
1 AAAATTAATTAAATTAGGGTTTAA--TTTTTAAAG
* *
39455018 TAAATTAATTAAATTAGGGTTTAGCGTTTTT-AAG
1 AAAATTAATTAAATTAGGGTTTA--ATTTTTAAAG
39455052 AAAATTAATTAAATTAGGGTTTAATTTTTAAAAG
1 AAAATTAATTAAATTAGGGTTTAATTTTT-AAAG
39455086 AAA
1 AAA
39455089 TAATTTTGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
32 5 0.08
33 2 0.03
34 52 0.88
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGGTTTAATTTTTAAAG
Found at i:39455348 original size:126 final size:126
Alignment explanation
Indices: 39455214--39455551 Score: 493
Period size: 126 Copynumber: 2.7 Consensus size: 126
39455204 GAAAAGATAA
* * *
39455214 TGTCAAAAACGCTTCAAGCAGAATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCTACGTGGA
1 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCTACATGGA
* * * *
39455278 CGCTAGTTTTT-TATAGTAGTT-TCTGAAAAAATAATTTTGAAAAGACGGTTCTAAATAAATAG
65 CGCT-CTTTTTCTACAATAGTTCT-TGAAAAAATAATTTTGAAAAGACGGTTCTAAACAAATAG
* *
39455340 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAGAGCTCCTACTTGGAC
1 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGAC
* *
39455405 GCTCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAG
66 GCTCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAAAAGACGGTTCTAAACAAATAG
* *
39455466 TGTCAAAAATGCTTCAAGCAGGATTCACTGTCAGCGAAATTGATGAAAAAAGCTCCTACATGGAC
1 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGAC
* *
39455531 ACTCTTTTTCTACAGTAGTTC
66 GCTCTTTTTCTACAATAGTTC
39455552 ATGTTTGGCT
Statistics
Matches: 193, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
125 5 0.03
126 186 0.96
127 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (126 bp):
TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGAC
GCTCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAAAAGACGGTTCTAAACAAATAG
Found at i:39459040 original size:18 final size:18
Alignment explanation
Indices: 39459014--39459057 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
39459004 GACTGAGAAA
* *
39459014 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
39459032 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
39459050 AGGATACA
1 AGGATACA
39459058 CACCTGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:39464358 original size:18 final size:18
Alignment explanation
Indices: 39464332--39464375 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
39464322 GACTGAGAAA
* *
39464332 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
39464350 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
39464368 AGGATACA
1 AGGATACA
39464376 CACCTGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:39465906 original size:15 final size:16
Alignment explanation
Indices: 39465878--39465910 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39465868 CAGACTGCTA
39465878 TAAAAAAATATAAAAT
1 TAAAAAAATATAAAAT
*
39465894 TAAAATAAT-TAAAAT
1 TAAAAAAATATAAAAT
39465909 TA
1 TA
39465911 CATAAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAAAATATAAAAT
Found at i:39468372 original size:264 final size:265
Alignment explanation
Indices: 39467891--39468420 Score: 1053
Period size: 264 Copynumber: 2.0 Consensus size: 265
39467881 ATTTTAAATT
39467891 GGAGGTCCTTAAATGGAAATTATACCATTGTTTATGTTATGGACAAAAATAGACATGGTTAGTAA
1 GGAGGTCCTTAAATGGAAATTATACCATTGTTTATGTTATGGACAAAAATAGACATGGTTAGTAA
39467956 GTAAATTATGTAAGGGCATTTTGGTAAAATGCCTTAATTAATGAATAAAGACAAAATAACATGAA
66 GTAAATTATGTAAGGGCATTTTGGTAAAATGCCTTAATTAATGAATAAAGACAAAATAACATGAA
39468021 ATAAGTTATCATCTTCTTCAATTCTTTTCTCCATGGCCGAATGTAGCAAGGGAACACAATGGCTA
131 ATAAGTTATCATCTTCTTCAATTCTTTTCTCCATGGCCGAATGTAGCAAGGGAACACAATGGCTA
39468086 GGGTTTTTTCATCTTCCAAGCTTCATGGTAAGTCCGTTCTAGCTCCGTTTTTCTTGTTCTTTATA
196 GGGTTTTTTCATCTTCCAAGCTTCATGGTAAGTCCGTTCTAGCTCCGTTTTTCTTGTTCTTTATA
39468151 TTTTA
261 TTTTA
39468156 GGAGGTCCTT-AATGGAAATTATACCATTGTTTATGTTATGGACAAAAATAGACATGGTTAGTAA
1 GGAGGTCCTTAAATGGAAATTATACCATTGTTTATGTTATGGACAAAAATAGACATGGTTAGTAA
39468220 GTAAATTATGTAAGGGCATTTTGGTAAAATGCCTTAATTAATGAATAAAGACAAAATAACATGAA
66 GTAAATTATGTAAGGGCATTTTGGTAAAATGCCTTAATTAATGAATAAAGACAAAATAACATGAA
39468285 ATAAGTTATCATCTTCTTCAATTCTTTTCTCCATGGCCGAATGTAGCAAGGGAACACAATGGCTA
131 ATAAGTTATCATCTTCTTCAATTCTTTTCTCCATGGCCGAATGTAGCAAGGGAACACAATGGCTA
39468350 GGGTTTTTTCATCTTCCAAGCTTCATGGTAAGTCCGTTCTAGCTCCGTTTTTCTTGTTCTTTATA
196 GGGTTTTTTCATCTTCCAAGCTTCATGGTAAGTCCGTTCTAGCTCCGTTTTTCTTGTTCTTTATA
39468415 TTTTA
261 TTTTA
39468420 G
1 G
39468421 AATCCTCATA
Statistics
Matches: 265, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
264 255 0.96
265 10 0.04
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (265 bp):
GGAGGTCCTTAAATGGAAATTATACCATTGTTTATGTTATGGACAAAAATAGACATGGTTAGTAA
GTAAATTATGTAAGGGCATTTTGGTAAAATGCCTTAATTAATGAATAAAGACAAAATAACATGAA
ATAAGTTATCATCTTCTTCAATTCTTTTCTCCATGGCCGAATGTAGCAAGGGAACACAATGGCTA
GGGTTTTTTCATCTTCCAAGCTTCATGGTAAGTCCGTTCTAGCTCCGTTTTTCTTGTTCTTTATA
TTTTA
Found at i:39469158 original size:26 final size:26
Alignment explanation
Indices: 39469124--39469174 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
39469114 GGATAAAAAA
39469124 GGGTCGCTAAGTGCAGATTCCCCGAG
1 GGGTCGCTAAGTGCAGATTCCCCGAG
* *
39469150 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTCGCTAAGTGCAGATTCCCCGA
39469175 ATTATTGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (26 bp):
GGGTCGCTAAGTGCAGATTCCCCGAG
Found at i:39469253 original size:43 final size:43
Alignment explanation
Indices: 39469148--39469385 Score: 199
Period size: 42 Copynumber: 5.6 Consensus size: 43
39469138 AGATTCCCCG
* * *
39469148 AGGGGTTGCTAAGTGCTGATTCC-CCGAAT-TATTGACTCT-AA
1 AGGGGTTGCTAAGTGCTGATTCCACCGTATCT-TTGATTGTGAA
* *
39469189 AGGTGGTTGCTAAGTGTTGATTCCACGGTATCTTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAA
** * *
39469233 AGGGGTTGC-AATGTGCTGATTCC-CCGTATCACTGAATAT-AA
1 AGGGGTTGCTAA-GTGCTGATTCCACCGTATCTTTGATTGTGAA
* * *
39469274 ATGTGGTTGCTAAGTGCTGATTTCACTGTATCTTTGATTGTGAA
1 A-GGGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAA
* * **
39469318 AGGGGTTGCTATGTGTTGATTCC-CCGTATCACTGAATT-T--A
1 AGGGGTTGCTAAGTGCTGATTCCACCGTATCTTTG-ATTGTGAA
*
39469358 AGGTGGTTGCTAAGTGCTGAATCCACCG
1 AGG-GGTTGCTAAGTGCTGATTCCACCG
39469386 AGTAACGGAT
Statistics
Matches: 157, Mismatches: 28, Indels: 23
0.75 0.13 0.11
Matches are distributed among these distances:
40 4 0.03
41 23 0.15
42 61 0.39
43 60 0.38
44 9 0.06
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (43 bp):
AGGGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAA
Found at i:39469295 original size:85 final size:84
Alignment explanation
Indices: 39469148--39469383 Score: 330
Period size: 85 Copynumber: 2.8 Consensus size: 84
39469138 AGATTCCCCG
* * * * *
39469148 AGGGGTTGCTAA-GTGCTGATTCCCCGAATTATTGACTCTAAAGGTGGTTGCTAAGTGTTGATTC
1 AGGGGTTGC-AATGTGCTGATTCCCCGTATCACTGAAT-TAAAGGTGGTTGCTAAGTGCTGATTC
39469212 CACGGTATCTTTGATTGTGAA
64 CACGGTATCTTTGATTGTGAA
* *
39469233 AGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAATATAAATGTGGTTGCTAAGTGCTGATTTC
1 AGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAAT-TAAAGGTGGTTGCTAAGTGCTGATTCC
*
39469298 ACTGTATCTTTGATTGTGAA
65 ACGGTATCTTTGATTGTGAA
* * * *
39469318 AGGGGTTGCTATGTGTTGATTCCCCGTATCACTGAATTTAAGGTGGTTGCTAAGTGCTGAATCCA
1 AGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGCTGATTCCA
39469383 C
66 C
39469384 CGAGTAACGG
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 27 0.20
85 108 0.80
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (84 bp):
AGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGCTGATTCCA
CGGTATCTTTGATTGTGAA
Found at i:39475716 original size:397 final size:396
Alignment explanation
Indices: 39474975--39475740 Score: 920
Period size: 397 Copynumber: 1.9 Consensus size: 396
39474965 TCTAGTGTCT
* * *
39474975 TAAGTGTAGTATTTTCGTCTATATACAATTGTATTTTTTCAAACATATTAGCTAATAAAATTATT
1 TAAGTGTAGTATTTTCGTCAATATACAATTGTATTTTTTCAAACAGATTAGATAATAAAATTATT
* **
39475040 CATGAATTACATTAATATCCTTTGTATATTATCCTCAATGGTTTTTGTATGCAAAGCAAAATGAA
66 CATGAATTACATTAATA-CCTTTGTATAATATCCTCAATGGTTTTTGTACACAAAGCAAAATGAA
* * **
39475105 AGCAAATATTAGCTCATTGGTTGTCTAATGTTTAACTAATACTAAACAGTATTATGTGATTAGAT
130 AGCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACAGTATTATATGACCAGAT
* * * * *
39475170 CGTAATACAGAAAGATAGTTTATATTAGTAGATGAACCTAAAGATATCCTTAATCTGATATAAAA
195 CGTAATACAGAAAGATAATTTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAATAGAAAA
** * *
39475235 TGAGCAAACTGATTAAAAGAGTAATATGTCATCTATCAAGTTCAATTGGAGAGATGCTTTGTCTT
260 TGAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATTGGAGAGATGCTTTGTCTT
* * * * *
39475300 GGCCATCGGAGCAGATGACTCCTAGAATATAGAGACATAGATGTCATTGACCGGCTATTGGATTA
325 AGACATCGAAGCAGATGACTCCTAAAAGATAGAGACATAGATGTCATTGACCGGCTATTGGATTA
39475365 GGTGCCC
390 GGTGCCC
* * ** *
39475372 TAAGTGTAGTATTTTCGTCAATGTACACTTGTAATTTTTTTGAACAGGTT-GATAAATAAAATTA
1 TAAGTGTAGTATTTTCGTCAATATACAATTGT-ATTTTTTCAAACAGATTAGAT-AATAAAATTA
* *
39475436 TTCATGAATTACATTAATA-CTTTGTATAATGTCCTCATGTGGTTTTTGTACACAAAGCAAAAT-
64 TTCATGAATTACATTAATACCTTTGTATAATATCCTCA-ATGGTTTTTGTACACAAAGCAAAATG
* * * ** *
39475499 AGGAGCAAATGTT-GCTCACTGGTTGTTTAATGTTTAAACTAATACT-AAGTGATATTATATGGC
128 A-AAGCAAATATTAGCTCACTGGTTGTCTAATGTTT-AACTAATACTAAACAG-TATTATATGAC
* * * * *
39475562 CGGATTGTAATAC-GAAA-ATACATCTTATATTAGTAGACGAACCTAAATATGTCCCTAGTCTAA
190 CAGATCGTAATACAGAAAGATA-AT-TTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAA
* * * **
39475625 TCGAAAATGAGTAAACCAATTGAAAGACTAATATGTTGTCTATCAAGTCCAATTAGG-GAGATG-
253 TAGAAAATGAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATT-GGAGAGATGC
** *
39475688 TTTCGTCTTAGACATCGAAGTGGATGACTCCTAAAAGATAGAGACATGGATGT
317 TTT-GTCTTAGACATCGAAGCAGATGACTCCTAAAAGATAGAGACATAGATGT
39475741 GACTGACTAG
Statistics
Matches: 309, Mismatches: 50, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
395 3 0.01
396 48 0.16
397 214 0.69
398 44 0.14
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (396 bp):
TAAGTGTAGTATTTTCGTCAATATACAATTGTATTTTTTCAAACAGATTAGATAATAAAATTATT
CATGAATTACATTAATACCTTTGTATAATATCCTCAATGGTTTTTGTACACAAAGCAAAATGAAA
GCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACAGTATTATATGACCAGATC
GTAATACAGAAAGATAATTTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAATAGAAAAT
GAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATTGGAGAGATGCTTTGTCTTA
GACATCGAAGCAGATGACTCCTAAAAGATAGAGACATAGATGTCATTGACCGGCTATTGGATTAG
GTGCCC
Found at i:39476580 original size:63 final size:66
Alignment explanation
Indices: 39476479--39476612 Score: 213
Period size: 63 Copynumber: 2.1 Consensus size: 66
39476469 ATAGAAATTG
*
39476479 TGAAAATGGAGAAATTGAAATCATTTGGAAATTATTATGGTTTTCTCCAAAATGAAAAT-GA-AA
1 TGAAAATGGAGAAATGGAAATCATTTGGAAATTATTATGGTTTTCTCCAAAATGAAAATGGAGAA
39476542 A
66 A
*
39476543 TGAAAATGGAGAAATGGAAA-CATTTGG-AATTGATTATGGTTTTTTCCAAAATGAAAATGGAGA
1 TGAAAATGGAGAAATGGAAATCATTTGGAAATT-ATTATGGTTTTCTCCAAAATGAAAATGGAGA
39476606 AA
65 AA
39476608 TGAAA
1 TGAAA
39476613 TCATTTGGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
62 4 0.06
63 32 0.49
64 21 0.32
65 8 0.12
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (66 bp):
TGAAAATGGAGAAATGGAAATCATTTGGAAATTATTATGGTTTTCTCCAAAATGAAAATGGAGAA
A
Found at i:39476595 original size:51 final size:51
Alignment explanation
Indices: 39476539--39476652 Score: 176
Period size: 51 Copynumber: 2.2 Consensus size: 51
39476529 AATGAAAATG
* * *
39476539 AAAATGAAAATGGAGAAATGGAAA-CATTTGGAATTGATTATGGTTTTTTCC
1 AAAATGAAAATGGAGAAAT-GAAATCATTTGGAAATGAATATGGTTTTCTCC
*
39476590 AAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCC
1 AAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATATGGTTTTCTCC
39476641 AAAATGAAAATG
1 AAAATGAAAATG
39476653 ACCTGAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 4 0.07
51 54 0.93
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (51 bp):
AAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATATGGTTTTCTCC
Found at i:39479055 original size:19 final size:20
Alignment explanation
Indices: 39479014--39479056 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39479004 ATGTTTCCTT
39479014 CTTTCTCTATTTTTTTTCTA
1 CTTTCTCTATTTTTTTTCTA
39479034 CTTTCTCT-TTTCTTTTTC-A
1 CTTTCTCTATTT-TTTTTCTA
39479053 CTTT
1 CTTT
39479057 TGATACTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (20 bp):
CTTTCTCTATTTTTTTTCTA
Found at i:39484898 original size:2 final size:2
Alignment explanation
Indices: 39484891--39484915 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39484881 CGGTTGCCAT
39484891 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
39484916 TTCTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39497999 original size:150 final size:148
Alignment explanation
Indices: 39497643--39498228 Score: 840
Period size: 150 Copynumber: 4.0 Consensus size: 148
39497633 TAGGCGATCT
* * *
39497643 GGAGGCACATTCCACTGAGGATCTACTACTAGCCATCACATTGGATGGAGAAGAGTGCGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
** * * *
39497708 CACTGTATGTCTCACTTCTAGTAGTCC-T--TCCACTCTTCTTATTAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTT-TTATCAGTTTTCCTTCCAAGATTT
39497770 TCTTCACTGTGCAATTT--
130 TCTTCACTGTGCAATTTGG
* * *
39497787 GGAGGCACCTTCCACTGAGGATCTACTACTGCCCATCACGTTGGATGGAGAAGAGTGGGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
*
39497852 CACCGTGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCATTTTATCAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATTT
39497917 TCTTCACTGTGCAATTTGGG
130 TCTTCACTGTGCAATTT-GG
* * * *
39497937 GGAGGCACCTTTCACTGAGGATCTACTACTACCGATCACATTGGACGGAGAAGGGTGAGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
* ** * * * *
39498002 CACTATGCATCTCACTCCTAGGAATCCTTCCTCCACCCTTTATATCAGTTTTCCTTACAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTT-TATCAGTTTTCCTTCCAAGATTT
39498067 TCTTCACTGTGCAATTTGG
130 TCTTCACTGTGCAATTTGG
39498086 AGGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATT
1 -GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATT
* * **
39498151 CCATCATGTGTCTCACTTCTAGGAGTCCGTCCTCCACTCTTTTTATCAGTTTTCCTTCCATTATT
65 CCACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATT
39498216 TTCTTCACTGTGC
129 TTCTTCACTGTGC
39498229 TTTCTCTTCT
Statistics
Matches: 393, Mismatches: 39, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
144 84 0.21
145 1 0.00
147 47 0.12
148 2 0.01
149 5 0.01
150 251 0.64
151 3 0.01
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (148 bp):
GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTTTATCAGTTTTCCTTCCAAGATTTT
CTTCACTGTGCAATTTGG
Found at i:39499938 original size:30 final size:29
Alignment explanation
Indices: 39499897--39499953 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 29
39499887 ATATAAAAGC
39499897 AAAAGAAGAAAACATAAGAGGG-GAGAGAGGT
1 AAAAGAAG-AAA-A-AAGAGGGAGAGAGAGGT
39499928 AAAA-AAGAAAAAAGAGGGAGAGAGAG
1 AAAAGAAGAAAAAAGAGGGAGAGAGAG
39499954 AGAAGAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 7 0.28
28 8 0.32
29 3 0.12
30 3 0.12
31 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.35, T:0.04
Consensus pattern (29 bp):
AAAAGAAGAAAAAAGAGGGAGAGAGAGGT
Found at i:39517345 original size:27 final size:27
Alignment explanation
Indices: 39517315--39517371 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
39517305 TAAATATTCA
*
39517315 TGGGACATTTCGCAATATAGGTGTCCG
1 TGGGACATTCCGCAATATAGGTGTCCG
* * *
39517342 TGGGACATTCCGTAATATATGTGTTCG
1 TGGGACATTCCGCAATATAGGTGTCCG
39517369 TGG
1 TGG
39517372 AAAAGTCCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (27 bp):
TGGGACATTCCGCAATATAGGTGTCCG
Found at i:39526455 original size:76 final size:76
Alignment explanation
Indices: 39526329--39526480 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
39526319 TATATATTTT
39526329 TAATAACACGTTATTACATTTTACCTTTTTAATAGTTTATATATACAAGGATAAAATGGTAAGTG
1 TAATAACACGTTATTACATTTTACCTTTTTAATAGTTTATATATACAAGGATAAAATGGTAAGTG
39526394 TACATTGTGGA
66 TACATTGTGGA
*
39526405 TAATATCACGTTATTACATTTTACCTTTTTAATAGTTTATATATACAAGGATAAAATGGTAAGTG
1 TAATAACACGTTATTACATTTTACCTTTTTAATAGTTTATATATACAAGGATAAAATGGTAAGTG
39526470 TACATTGTGGA
66 TACATTGTGGA
39526481 GCGAGTTGGA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40
Consensus pattern (76 bp):
TAATAACACGTTATTACATTTTACCTTTTTAATAGTTTATATATACAAGGATAAAATGGTAAGTG
TACATTGTGGA
Found at i:39526779 original size:9 final size:9
Alignment explanation
Indices: 39526765--39526816 Score: 50
Period size: 9 Copynumber: 5.2 Consensus size: 9
39526755 CCAATTTAAT
39526765 TTTTTAAAA
1 TTTTTAAAA
39526774 TTTTTAAAA
1 TTTTTAAAA
39526783 TTTTTTAATTATTA
1 -TTTTTAA--A--A
39526797 TTTTTAAAA
1 TTTTTAAAA
*
39526806 TTTTTATAA
1 TTTTTAAAA
39526815 TT
1 TT
39526817 AGGATTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
9 20 0.54
10 7 0.19
11 1 0.03
12 1 0.03
13 7 0.19
14 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:39526800 original size:23 final size:24
Alignment explanation
Indices: 39526773--39526817 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
39526763 ATTTTTTAAA
39526773 ATTTTTAAAATTTTT-TAATTATT
1 ATTTTTAAAATTTTTATAATTATT
39526796 ATTTTTAAAATTTTTATAATTA
1 ATTTTTAAAATTTTTATAATTA
39526818 GGATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTTAAAATTTTTATAATTATT
Found at i:39528438 original size:19 final size:19
Alignment explanation
Indices: 39528392--39528439 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
39528382 GTATACATTT
39528392 TAAA-TTTATTTAAGTAGA
1 TAAATTTTATTTAAGTAGA
* *
39528410 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAAGTAGA
39528429 TAAATTTTATT
1 TAAATTTTATT
39528440 CATATTCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAAGTAGA
Found at i:39535716 original size:41 final size:41
Alignment explanation
Indices: 39535663--39535745 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
39535653 TATCTAAAAT
*
39535663 AATATAAAATATTATATTAATAAGATTCAAATTAGAAATAA
1 AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAA
* *
39535704 AATATAAAATATTATATTATTAAGATCCTAATTAGAAATAA
1 AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAA
39535745 A
1 A
39535746 TAATCTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (41 bp):
AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAA
Found at i:39537703 original size:174 final size:175
Alignment explanation
Indices: 39537416--39537765 Score: 693
Period size: 174 Copynumber: 2.0 Consensus size: 175
39537406 TTAAATCAAA
39537416 TTTTTATCATTTTAGGGAATTAAAGTATAATTTTACCATTATTAATTTAAAATTTTTTAAATTAT
1 TTTTTATCATTTTAGGGAATTAAAGTATAATTTTACCATTATTAATTTAAAATTTTTTAAATTAT
39537481 AAAAAAAAGTTAAAATAAAAATTTATTAGGAGAATCCATGGGCCTACTGGCTCTCCACTACGGTA
66 AAAAAAAAGTTAAAATAAAAATTTATTAGGAGAATCCATGGGCCTACTGGCTCTCCACTACGGTA
39537546 CTCCGCTGGTTGTCACGATTTGGCTTAATTCGATATTACAGAAAT
131 CTCCGCTGGTTGTCACGATTTGGCTTAATTCGATATTACAGAAAT
39537591 TTTTTATCA-TTTAGGGAATTAAAGTATAATTTTACCATTATTAATTTAAAATTTTTTAAATTAT
1 TTTTTATCATTTTAGGGAATTAAAGTATAATTTTACCATTATTAATTTAAAATTTTTTAAATTAT
39537655 AAAAAAAAGTTAAAATAAAAATTTATTAGGAGAATCCATGGGCCTACTGGCTCTCCACTACGGTA
66 AAAAAAAAGTTAAAATAAAAATTTATTAGGAGAATCCATGGGCCTACTGGCTCTCCACTACGGTA
39537720 CTCCGCTGGTTGTCACGATTTGGCTTAATTCGATATTACAGAAAT
131 CTCCGCTGGTTGTCACGATTTGGCTTAATTCGATATTACAGAAAT
39537765 T
1 T
39537766 ATTTCGAATT
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
174 166 0.95
175 9 0.05
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (175 bp):
TTTTTATCATTTTAGGGAATTAAAGTATAATTTTACCATTATTAATTTAAAATTTTTTAAATTAT
AAAAAAAAGTTAAAATAAAAATTTATTAGGAGAATCCATGGGCCTACTGGCTCTCCACTACGGTA
CTCCGCTGGTTGTCACGATTTGGCTTAATTCGATATTACAGAAAT
Found at i:39547921 original size:2 final size:2
Alignment explanation
Indices: 39547914--39547938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39547904 TATTTATGGA
39547914 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
39547939 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39551380 original size:3 final size:3
Alignment explanation
Indices: 39551358--39551410 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
39551348 ATAATGACAG
* *
39551358 TAA TAA AAA T-A TAA TAAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39551403 TAAA TAA T
1 T-AA TAA T
39551411 GGTAATTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:39552180 original size:3 final size:3
Alignment explanation
Indices: 39552172--39552215 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
39552162 ATATCCCCAA
39552172 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
39552216 TAAAAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:39553049 original size:50 final size:50
Alignment explanation
Indices: 39552995--39553222 Score: 233
Period size: 50 Copynumber: 4.6 Consensus size: 50
39552985 CACCAGGGAG
* * **
39552995 ATAAGATCCACCGTCGTGGCTTCAATCTGCTCCGCTGCGACGCCAGGAAA
1 ATAAGATCCGCCGTTGTGGCTTCAATCTGCTCAACTGCGACGCCAGGAAA
** * * * *** *
39553045 ATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATTTCAGGGAA
1 ATAAGATCCGCCGTTGTGGCTTCAATCTGCTCAACTGCGACGCCAGGAAA
** * * * * *
39553095 ACCAGATCCGCCGTCGTAGCTTCAATCTGTTCAACTAC-ACCGCCAGGGAA
1 ATAAGATCCGCCGTTGTGGCTTCAATCTGCTCAACTGCGA-CGCCAGGAAA
* **
39553145 GTAAGATCCGCCGTTGTGGCTTCAATCTGCTCTGCTGCGACGCCAGGAAA
1 ATAAGATCCGCCGTTGTGGCTTCAATCTGCTCAACTGCGACGCCAGGAAA
39553195 ATAAGATCCGCCGTTGTGGCTTCAATCT
1 ATAAGATCCGCCGTTGTGGCTTCAATCT
39553223 TTTTAACTGC
Statistics
Matches: 141, Mismatches: 35, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
49 1 0.01
50 139 0.99
51 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
ATAAGATCCGCCGTTGTGGCTTCAATCTGCTCAACTGCGACGCCAGGAAA
Found at i:39553391 original size:70 final size:70
Alignment explanation
Indices: 39553278--39553408 Score: 208
Period size: 70 Copynumber: 1.9 Consensus size: 70
39553268 TTTCACTGCC
**
39553278 AGTACAGGAAGGCAAGATCTATTATTTTCAACCTACTCCACTACTGCCCAGGGAGATAAGGTTCG
1 AGTACAGGAAGGCAAGATCTACCATTTTCAACCTACTCCACTACTGCCCAGGGAGATAAGGTTCG
39553343 CTGTA
66 CTGTA
* * * *
39553348 AGTACAGGAAGGCCATATCTGCCATTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGG
1 AGTACAGGAAGGCAAGATCTACCATTTTCAACCTACTCCACTACTGCCCAGGGAGATAAGG
39553409 CTGGTATCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 55 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (70 bp):
AGTACAGGAAGGCAAGATCTACCATTTTCAACCTACTCCACTACTGCCCAGGGAGATAAGGTTCG
CTGTA
Found at i:39556993 original size:3 final size:3
Alignment explanation
Indices: 39556971--39557023 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
39556961 ATAATGACAG
* *
39556971 TAA TAA AAA T-A TAA TAAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39557016 TAAA TAA T
1 T-AA TAA T
39557024 GGTAATTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:39563822 original size:18 final size:19
Alignment explanation
Indices: 39563793--39563830 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39563783 TAAATGAATA
*
39563793 ATTATATATTTTTAAAGAC
1 ATTATATATTTTGAAAGAC
39563812 ATTAT-TATTTTGAAAGAC
1 ATTATATATTTTGAAAGAC
39563830 A
1 A
39563831 CCTATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTATATATTTTGAAAGAC
Found at i:39564425 original size:30 final size:30
Alignment explanation
Indices: 39564384--39564539 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 30
39564374 GTGTTTTAAA
* *
39564384 AAAATTGTATTTTCACCCCTAAACTTTTTT
1 AAAATTATATTTTCACCCCTAAACTTTCTT
* * *
39564414 AAAATCATATTTTGACCCTTAAACTTTCTT
1 AAAATTATATTTTCACCCCTAAACTTTCTT
*
39564444 AAAATTACA-TTTCAACCCCTAAAC-TT-TT
1 AAAATTATATTTTC-ACCCCTAAACTTTCTT
* *
39564472 ATAAATTACT-TTTTAACCCCTAAACTTTCTC
1 A-AAATTA-TATTTTCACCCCTAAACTTTCTT
* * *
39564503 AAAATTATATTTTGACCCCTAAAATTTATT
1 AAAATTATATTTTCACCCCTAAACTTTCTT
*
39564533 GAAATTA
1 AAAATTA
39564540 CGTTTTAGTC
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
28 3 0.03
29 22 0.22
30 75 0.74
31 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.42
Consensus pattern (30 bp):
AAAATTATATTTTCACCCCTAAACTTTCTT
Found at i:39564507 original size:59 final size:59
Alignment explanation
Indices: 39564394--39564525 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 59
39564384 AAAATTGTAT
* * * *
39564394 TTTCACCCCTAAACTTTTTTAAAATCATATTTTGACCCTTAAACTTTCTTAAAATTACA
1 TTTCACCCCTAAACTTTTATAAAATCATATTTTAACCCCTAAACTTTCTCAAAATTACA
* *
39564453 TTTCAACCCCTAAACTTTTAT-AAATTACT-TTTTAACCCCTAAACTTTCTCAAAATTATA
1 TTTC-ACCCCTAAACTTTTATAAAATCA-TATTTTAACCCCTAAACTTTCTCAAAATTACA
*
39564512 TTTTGACCCCTAAA
1 -TTTCACCCCTAAA
39564526 ATTTATTGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 44 0.70
60 19 0.30
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (59 bp):
TTTCACCCCTAAACTTTTATAAAATCATATTTTAACCCCTAAACTTTCTCAAAATTACA
Found at i:39564557 original size:89 final size:89
Alignment explanation
Indices: 39564393--39564561 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 89
39564383 AAAAATTGTA
* * * * * *
39564393 TTTTCACCCCTAAACTTTTTTAAAATCATATTTTGACCCTTAAACTTTCTTAAAATTACATTTCA
1 TTTTAACCCCTAAACTTTCTCAAAATCATATTTTGACCCCTAAAATTTATTAAAATTACATTTCA
*
39564458 ACCCCTAAACTTTTATAAATTACT
66 ACCCCAAAACTTTTATAAATTACT
* * * *
39564482 TTTTAACCCCTAAACTTTCTCAAAATTATATTTTGACCCCTAAAATTTATTGAAATTACGTTTTA
1 TTTTAACCCCTAAACTTTCTCAAAATCATATTTTGACCCCTAAAATTTATTAAAATTACATTTCA
**
39564547 GTCCCAAAACTTTTA
66 ACCCCAAAACTTTTA
39564562 CTGAGTTCAC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
89 67 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (89 bp):
TTTTAACCCCTAAACTTTCTCAAAATCATATTTTGACCCCTAAAATTTATTAAAATTACATTTCA
ACCCCAAAACTTTTATAAATTACT
Found at i:39564912 original size:14 final size:14
Alignment explanation
Indices: 39564895--39564925 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39564885 AAAAATAAAA
39564895 AAAAAACAGCAAAG
1 AAAAAACAGCAAAG
*
39564909 AAAAAAGAGCAAAG
1 AAAAAACAGCAAAG
39564923 AAA
1 AAA
39564926 GAAAAGAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.10, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAACAGCAAAG
Found at i:39565043 original size:24 final size:24
Alignment explanation
Indices: 39565015--39565087 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
39565005 GGGAAAGAAG
39565015 GAAAGGAAGAAA-AAAGAAGAAAAA
1 GAAA-GAAGAAAGAAAGAAGAAAAA
*
39565039 GAAAGAAGAAAGAAAGAAGAAAAGG
1 GAAAGAAGAAAGAAAGAAGAAAA-A
* * *
39565064 GGAAGAAGAAAGAAGGAAAAAAAA
1 GAAAGAAGAAAGAAAGAAGAAAAA
39565088 AGAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 7 0.17
24 15 0.36
25 20 0.48
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (24 bp):
GAAAGAAGAAAGAAAGAAGAAAAA
Found at i:39565045 original size:4 final size:4
Alignment explanation
Indices: 39565007--39565060 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
39564997 GGCTGATCGG
* * *
39565007 GAAA GAAG GAAA GGAA GAAA -AAA GAAGA AAAA GAAA G-AA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
39565054 G-AA GAAA
1 GAAA GAAA
39565061 AGGGGAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
3 9 0.22
4 28 0.70
5 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:39565045 original size:32 final size:33
Alignment explanation
Indices: 39565007--39565091 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 33
39564997 GGCTGATCGG
*
39565007 GAAAGAAGGAAAGGAAGAA-AAAAGAAGAAAAA
1 GAAAGAAGGAAAGAAAGAAGAAAAGAAGAAAAA
** *
39565039 GAAAGAA-GAAAGAAAGAAGAAAAGGGGAAGAA
1 GAAAGAAGGAAAGAAAGAAGAAAAGAAGAAAAA
*
39565071 GAAAGAAGGAAA-AAAAAAGAA
1 GAAAGAAGGAAAGAAAGAAGAA
39565092 TAATTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 10 0.22
32 32 0.70
33 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (33 bp):
GAAAGAAGGAAAGAAAGAAGAAAAGAAGAAAAA
Found at i:39565563 original size:12 final size:13
Alignment explanation
Indices: 39565546--39565574 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39565536 TTTATACATT
39565546 TTTATATTTTT-A
1 TTTATATTTTTAA
39565558 TTTATATTTTTAA
1 TTTATATTTTTAA
39565571 TTTA
1 TTTA
39565575 ATCCAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATATTTTTAA
Found at i:39565788 original size:38 final size:39
Alignment explanation
Indices: 39565724--39565826 Score: 93
Period size: 38 Copynumber: 2.7 Consensus size: 39
39565714 ATCGAAAATA
* * * *
39565724 TTCAAAAAAATTTGTGTTTTC-GAAAAAAATTCCCGTGT
1 TTCAAAAATATTCGTGTCTTCAAAAAAAAATTCCCGTGT
* * ** *
39565762 TTC-GAAATTTTCGTGTCTTCAAAAAAATTTTCTCGTGT
1 TTCAAAAATATTCGTGTCTTCAAAAAAAAATTCCCGTGT
*
39565800 TTCAAAAAATATTCGTGTTTTCAAAAA
1 TTC-AAAAATATTCGTGTCTTCAAAAA
39565827 TAAGGCAACG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 12 0.24
38 19 0.38
40 19 0.38
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (39 bp):
TTCAAAAATATTCGTGTCTTCAAAAAAAAATTCCCGTGT
Found at i:39565791 original size:20 final size:19
Alignment explanation
Indices: 39565724--39565826 Score: 74
Period size: 20 Copynumber: 5.4 Consensus size: 19
39565714 ATCGAAAATA
39565724 TTCAAAAAAA-TTT-GTGTT
1 TTCAAAAAAATTTTCGTG-T
**
39565742 TTCGAAAAAAATTCCCGTGT
1 TTC-AAAAAAATTTTCGTGT
*
39565762 TTC---GAAATTTTCGTGT
1 TTCAAAAAAATTTTCGTGT
39565778 CTTCAAAAAAATTTTCTCGTGT
1 -TTCAAAAAAA-TTT-TCGTGT
*
39565800 TTC-AAAAAATATTCGTGTT
1 TTCAAAAAAATTTTCGTG-T
39565819 TTCAAAAA
1 TTCAAAAA
39565827 TAAGGCAACG
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
16 10 0.15
17 3 0.04
18 8 0.12
19 13 0.19
20 18 0.27
21 9 0.13
22 6 0.09
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (19 bp):
TTCAAAAAAATTTTCGTGT
Found at i:39565815 original size:18 final size:18
Alignment explanation
Indices: 39565724--39565826 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 18
39565714 ATCGAAAATA
*
39565724 TTCAAAAAA-ATTTGTGTT
1 TTCAAAAAATATTCGTG-T
39565742 TTCGAAAAAA-ATTCCCGTGT
1 TTC-AAAAAATATT--CGTGT
* *
39565762 TTC--GAAATTTTCGTGT
1 TTCAAAAAATATTCGTGT
*
39565778 CTTCAAAAAAATTTTCTCGTGT
1 -TTC-AAAAAA-TAT-TCGTGT
39565800 TTCAAAAAATATTCGTGTT
1 TTCAAAAAATATTCGTG-T
39565819 TTCAAAAA
1 TTCAAAAA
39565827 TAAGGCAACG
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
16 5 0.07
17 6 0.09
18 10 0.14
19 20 0.29
20 13 0.19
21 9 0.13
22 6 0.09
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (18 bp):
TTCAAAAAATATTCGTGT
Found at i:39565984 original size:18 final size:18
Alignment explanation
Indices: 39565943--39565984 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39565933 AATTTGTGTA
*
39565943 AAAAAATCTTCGTGGTTT
1 AAAAAATATTCGTGGTTT
* *
39565961 CAAAAATATTCGTGTTTT
1 AAAAAATATTCGTGGTTT
39565979 AAAAAA
1 AAAAAA
39565985 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (18 bp):
AAAAAATATTCGTGGTTT
Found at i:39566039 original size:18 final size:17
Alignment explanation
Indices: 39566018--39566338 Score: 138
Period size: 18 Copynumber: 18.0 Consensus size: 17
39566008 TTTTTAAATT
*
39566018 TTTCATGTTTTCAAAAAA
1 TTTCGTGTTTTC-AAAAA
*
39566036 TTTCCGTGTTTTAAAAAAAA
1 TTT-CGTGTTTT--CAAAAA
* * *
39566056 TTCCAT-TTTTCAAAAT
1 TTTCGTGTTTTCAAAAA
39566072 TATTCGTGTTTTCAAAAA
1 T-TTCGTGTTTTCAAAAA
* * *
39566090 ATTCCTATGTTTCAAAAA
1 TTTCGTGT-TTTCAAAAA
* *
39566108 TCTTTGTGTTTTCAAAAG
1 T-TTCGTGTTTTCAAAAA
*
39566126 TTCCG-GTGTTTCAAAAA
1 TTTCGTGT-TTTCAAAAA
*
39566143 TTTTCATGTTTTCAAAAA
1 -TTTCGTGTTTTCAAAAA
*
39566161 TTCCCGTGTTTT-AAAAA
1 TT-TCGTGTTTTCAAAAA
39566178 TTTCCGTGTTTTCAAAAA
1 TTT-CGTGTTTTCAAAAA
*
39566196 TTT-GTGTTTT-AAAATT
1 TTTCGTGTTTTCAAAA-A
*
39566212 TTTCGTG-CTTCAAAAAGAAA
1 TTTCGTGTTTTC---AA-AAA
* *
39566232 ATTAGTGTTTTCAAAAAAAAAA
1 TTTCGTGTTTTC-----AAAAA
*
39566254 TTCTCGTG-TTTCAAAAT
1 TT-TCGTGTTTTCAAAAA
**
39566271 TTTCGTGTTTAAAAAAA
1 TTTCGTGTTTTCAAAAA
** * *
39566288 AATCATG-TTTCTAAAA
1 TTTCGTGTTTTCAAAAA
*
39566304 -TTCTGTTGTTTTAAAAAA
1 TTTC-G-TGTTTTCAAAAA
39566322 TTTCGTGTTTTCAAAAA
1 TTTCGTGTTTTCAAAAA
39566339 AAAAAGGTTG
Statistics
Matches: 226, Mismatches: 48, Indels: 59
0.68 0.14 0.18
Matches are distributed among these distances:
15 6 0.03
16 30 0.13
17 67 0.30
18 69 0.31
19 18 0.08
20 14 0.06
21 5 0.02
22 8 0.04
23 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (17 bp):
TTTCGTGTTTTCAAAAA
Found at i:39566143 original size:35 final size:34
Alignment explanation
Indices: 39566026--39566197 Score: 157
Period size: 35 Copynumber: 4.8 Consensus size: 34
39566016 TTTTTCATGT
* * *
39566026 TTTCAAAAAATTTCCGTGTTTTAAAAAAAATT-CCATT
1 TTTC-AAAAATTT-CGTGTTTT--CAAAAATTCCCGTG
* **
39566063 TTTCAAAATTATTCGTGTTTTCAAAAAATTCCTATG
1 TTTCAAAAAT-TTCGTGTTTTC-AAAAATTCCCGTG
* * *
39566099 TTTCAAAAATCTTTGTGTTTTCAAAAGTTCCGGTG
1 TTTCAAAAAT-TTCGTGTTTTCAAAAATTCCCGTG
*
39566134 TTTCAAAAATTTTCATGTTTTCAAAAATTCCCGTG
1 TTTCAAAAA-TTTCGTGTTTTCAAAAATTCCCGTG
*
39566169 TTTTAAAAATTTCCGTGTTTTCAAAAATT
1 TTTCAAAAATTT-CGTGTTTTCAAAAATT
39566198 TGTGTTTTAA
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
34 3 0.03
35 69 0.61
36 36 0.32
37 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (34 bp):
TTTCAAAAATTTCGTGTTTTCAAAAATTCCCGTG
Found at i:39566269 original size:21 final size:20
Alignment explanation
Indices: 39566213--39566269 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
39566203 TTTAAAATTT
*
39566213 TTCGTGCTTCAAAAAGAAAA
1 TTCGTGTTTCAAAAAGAAAA
* *
39566233 TTAGTGTTTTCAAAAAAAAAA
1 TTCGTG-TTTCAAAAAGAAAA
39566254 TTCTCGTGTTTCAAAA
1 -T-TCGTGTTTCAAAA
39566270 TTTTCGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.17
21 12 0.40
22 9 0.30
23 4 0.13
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
TTCGTGTTTCAAAAAGAAAA
Found at i:39566285 original size:16 final size:16
Alignment explanation
Indices: 39566249--39566285 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
39566239 TTTTCAAAAA
39566249 AAAAATTCTCGTGTTT
1 AAAAATTCTCGTGTTT
* *
39566265 CAAAATTTTCGTGTTT
1 AAAAATTCTCGTGTTT
39566281 AAAAA
1 AAAAA
39566286 AAAATCATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (16 bp):
AAAAATTCTCGTGTTT
Found at i:39566339 original size:18 final size:18
Alignment explanation
Indices: 39566018--39566339 Score: 126
Period size: 17 Copynumber: 18.0 Consensus size: 18
39566008 TTTTTAAATT
*
39566018 TTTCATGTTTTCAAAAAA
1 TTTCGTGTTTTCAAAAAA
*
39566036 TTTCCGTGTTTTAAAAAAAA
1 TTT-CGTGTTTT-CAAAAAA
* * *
39566056 TTCCAT-TTTTC-AAAAT
1 TTTCGTGTTTTCAAAAAA
39566072 TATTCGTGTTTTCAAAAAA
1 T-TTCGTGTTTTCAAAAAA
* *
39566091 -TTCCTATGTTTC-AAAAA
1 TTTCGTGT-TTTCAAAAAA
* *
39566108 TCTTTGTGTTTTC-AAAAG
1 T-TTCGTGTTTTCAAAAAA
* *
39566126 TTCCG-GTGTTTCAAAAAT
1 TTTCGTGT-TTTCAAAAAA
*
39566144 TTTCATGTTTTC-AAAAA
1 TTTCGTGTTTTCAAAAAA
*
39566161 TTCCCGTGTTTT--AAAAA
1 TT-TCGTGTTTTCAAAAAA
39566178 TTTCCGTGTTTTC-AAAAA
1 TTT-CGTGTTTTCAAAAAA
**
39566196 TTT-GTGTTTT-AAAATT
1 TTTCGTGTTTTCAAAAAA
*
39566212 TTTCGTG-CTTCAAAAAGAAA
1 TTTCGTGTTTTC--AAA-AAA
* *
39566232 ATTAGTGTTTTCAAAAAAAAAA
1 TTTCGTGTTTTC----AAAAAA
*
39566254 TTCTCGTG-TTTC-AAAAT
1 TT-TCGTGTTTTCAAAAAA
*
39566271 TTTCGTG-TTTAAAAAAA
1 TTTCGTGTTTTCAAAAAA
** * *
39566288 AATCATG-TTTC-TAAAA
1 TTTCGTGTTTTCAAAAAA
39566304 -TTCTGTTGTTTT-AAAAAA
1 TTTC-G-TGTTTTCAAAAAA
39566322 TTTCGTGTTTTCAAAAAA
1 TTTCGTGTTTTCAAAAAA
39566340 AAAAGGTTGC
Statistics
Matches: 228, Mismatches: 45, Indels: 62
0.68 0.13 0.19
Matches are distributed among these distances:
15 2 0.01
16 34 0.15
17 68 0.30
18 65 0.29
19 25 0.11
20 14 0.06
21 3 0.01
22 8 0.04
23 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
TTTCGTGTTTTCAAAAAA
Found at i:39568421 original size:33 final size:31
Alignment explanation
Indices: 39568379--39568445 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 31
39568369 ATTTAATTAA
39568379 TTTTTAAATTTTTAAA-AAATTCTAAAAATATT
1 TTTTTAAATTTTTAAATAAATT-TAAAAAT-TT
*
39568411 TTTTATAAATTTTTAAATAAATTTAATAATTT
1 TTTT-TAAATTTTTAAATAAATTTAAAAATTT
39568443 TTT
1 TTT
39568446 AAAAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 9 0.28
33 18 0.56
34 5 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTTTAAATTTTTAAATAAATTTAAAAATTT
Found at i:39568428 original size:21 final size:21
Alignment explanation
Indices: 39568415--39568458 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
39568405 AATATTTTTT
39568415 ATAAATTTTTAAATAAATTTA
1 ATAAATTTTTAAATAAATTTA
* * *
39568436 ATAATTTTTTAAAAAAAATTA
1 ATAAATTTTTAAATAAATTTA
39568457 AT
1 AT
39568459 GTTTGTACGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAATTTTTAAATAAATTTA
Found at i:39569697 original size:18 final size:17
Alignment explanation
Indices: 39569670--39569714 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
39569660 AAAATATTTT
**
39569670 AAAAAATATTTTCAATA
1 AAAAAATATTTAAAATA
39569687 AAAAAACTATTTAAAATA
1 AAAAAA-TATTTAAAATA
39569705 AAAATAATAT
1 AAAA-AATAT
39569715 GAAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 16 0.67
19 2 0.08
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATATTTAAAATA
Found at i:39571014 original size:16 final size:15
Alignment explanation
Indices: 39570994--39571034 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
39570984 AAATTAAGAG
39570994 TTATTTTTTAATTTA
1 TTATTTTTTAATTTA
* *
39571009 TGTATTATTTATTTTA
1 T-TATTTTTTAATTTA
39571025 TTATTTTTTA
1 TTATTTTTTA
39571035 CATATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TTATTTTTTAATTTA
Found at i:39580368 original size:10 final size:10
Alignment explanation
Indices: 39580335--39580380 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
39580325 TAAAAACCAT
39580335 AAAAATTATA
1 AAAAATTATA
39580345 AACAAGATTTATA
1 AA-AA-A-TTATA
39580358 AAAAATTAT-
1 AAAAATTATA
39580367 -AAAATTATA
1 AAAAATTATA
39580376 AAAAA
1 AAAAA
39580381 ACTTTATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 8 0.26
10 10 0.32
11 3 0.10
12 3 0.10
13 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:39580371 original size:31 final size:31
Alignment explanation
Indices: 39580336--39580394 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39580326 AAAAACCATA
*
39580336 AAAATTATAAACAAGA-TTTATAAAAAATTAT
1 AAAATTATAAA-AAAACTTTATAAAAAATTAT
*
39580367 AAAATTATAAAAAAACTTTATTAAAAAT
1 AAAATTATAAAAAAACTTTATAAAAAAT
39580395 AACAATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (31 bp):
AAAATTATAAAAAAACTTTATAAAAAATTAT
Found at i:39587332 original size:11 final size:11
Alignment explanation
Indices: 39587315--39587344 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39587305 ACCCATATTA
39587315 AATTTTTATAT
1 AATTTTTATAT
*
39587326 TATTTTTATAT
1 AATTTTTATAT
39587337 AATTTTTA
1 AATTTTTA
39587345 AATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTTATAT
Found at i:39587514 original size:30 final size:30
Alignment explanation
Indices: 39587469--39587530 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
39587459 CTTAACAAGT
*
39587469 AAATTCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
*
39587499 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
39587529 AA
1 AA
39587531 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:39587585 original size:22 final size:22
Alignment explanation
Indices: 39587560--39587602 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39587550 TATCTAAATA
39587560 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
39587582 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
39587603 AATAGAGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:39592201 original size:2 final size:2
Alignment explanation
Indices: 39592194--39592229 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
39592184 TTGCTTGTTT
*
39592194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39592230 GTAACTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39604679 original size:12 final size:12
Alignment explanation
Indices: 39604662--39604687 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39604652 GTTTGGCATG
39604662 TACCTATCTAGT
1 TACCTATCTAGT
39604674 TACCTATCTAGT
1 TACCTATCTAGT
39604686 TA
1 TA
39604688 AGTCACTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (12 bp):
TACCTATCTAGT
Found at i:39607339 original size:25 final size:25
Alignment explanation
Indices: 39607311--39607373 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
39607301 ACAAGCACAT
*
39607311 TAACGGGAAGCTCTTCCGAGCCATA
1 TAACGGGAAGCTCATCCGAGCCATA
** *
39607336 TAACGGGAAGCTCATGTGAGCCATG
1 TAACGGGAAGCTCATCCGAGCCATA
39607361 TAACGGGAAGCTC
1 TAACGGGAAGCTC
39607374 GCAAGAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.19
Consensus pattern (25 bp):
TAACGGGAAGCTCATCCGAGCCATA
Found at i:39607617 original size:21 final size:20
Alignment explanation
Indices: 39607567--39607617 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
39607557 TATGACAATT
*
39607567 TATACAATTCACACATATAA
1 TATACAAATCACACATATAA
*
39607587 TATTCAAAATCA-ATCATATAAA
1 TATAC-AAATCACA-CATAT-AA
39607609 TATACAAAT
1 TATACAAAT
39607618 TAGTTACACG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.20
21 14 0.56
22 6 0.24
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (20 bp):
TATACAAATCACACATATAA
Found at i:39611269 original size:23 final size:23
Alignment explanation
Indices: 39611239--39611285 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
39611229 ATTACAACTT
*
39611239 ATCTATACTTATATAGTAAAGTA
1 ATCTATACCTATATAGTAAAGTA
*
39611262 ATCTATACCTATATATTAAAGTA
1 ATCTATACCTATATAGTAAAGTA
39611285 A
1 A
39611286 GGTCCAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (23 bp):
ATCTATACCTATATAGTAAAGTA
Found at i:39612735 original size:29 final size:30
Alignment explanation
Indices: 39612700--39612758 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
39612690 TCTTGGTTGA
*
39612700 TGTGTAATTTTATATA-AAAACTTTGATTT
1 TGTGTAATTTTATACATAAAACTTTGATTT
*
39612729 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGTAATTTTATACATAAAACTTTGATTT
39612759 GATTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (30 bp):
TGTGTAATTTTATACATAAAACTTTGATTT
Found at i:39615188 original size:17 final size:17
Alignment explanation
Indices: 39615166--39615199 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39615156 AGATAATTGT
39615166 CATTTGGAAGCTTTAGA
1 CATTTGGAAGCTTTAGA
39615183 CATTTGGAAGCTTTAGA
1 CATTTGGAAGCTTTAGA
39615200 ACCTCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
CATTTGGAAGCTTTAGA
Found at i:39620915 original size:15 final size:16
Alignment explanation
Indices: 39620895--39620925 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39620885 AATAAAAAAG
39620895 AGAAAC-AAAAAGAGA
1 AGAAACAAAAAAGAGA
39620910 AGAAACAAAAAAGAGA
1 AGAAACAAAAAAGAGA
39620926 GAGAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAACAAAAAAGAGA
Found at i:39625950 original size:26 final size:25
Alignment explanation
Indices: 39625914--39625965 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
39625904 TTCTAAAAAC
* *
39625914 GGGATGCTAGAAAATTTATGTTATTT
1 GGGATACTAGAAAAATTA-GTTATTT
39625940 GGGATACTAGAAAAATTAGTTATTT
1 GGGATACTAGAAAAATTAGTTATTT
39625965 G
1 G
39625966 AGTATTTACG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (25 bp):
GGGATACTAGAAAAATTAGTTATTT
Found at i:39635836 original size:19 final size:20
Alignment explanation
Indices: 39635800--39635837 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39635790 ATCAAAATCA
*
39635800 TTTTTTCTTGATTCAAAAGT
1 TTTTTTCTTGAATCAAAAGT
*
39635820 TTTTTTTTTGAAT-AAAAG
1 TTTTTTCTTGAATCAAAAG
39635838 CAATATTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTTTCTTGAATCAAAAGT
Found at i:39636521 original size:30 final size:29
Alignment explanation
Indices: 39636484--39636579 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
39636474 TATTCATAAC
*
39636484 AATAAAAA-CATATTAAAATTCTTAAAAACT
1 AATAAAAATCATA-TAAAATTATTAAAAA-T
*
39636514 TATAAAAATCATATAAAATTATTAAAAAT
1 AATAAAAATCATATAAAATTATTAAAAAT
* * *
39636543 AATAAAATTGATATAAACTTA-TAAAAATT
1 AATAAAAATCATATAAAATTATTAAAAA-T
*
39636572 ATTAAAAA
1 AATAAAAA
39636580 AACATAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.11
29 25 0.45
30 21 0.38
31 4 0.07
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (29 bp):
AATAAAAATCATATAAAATTATTAAAAAT
Found at i:39636531 original size:20 final size:20
Alignment explanation
Indices: 39636494--39636579 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
39636484 AATAAAAACA
* *
39636494 TATTAAAATTCTTA-AAAACT
1 TATTAAAAATCATATAAAA-T
39636514 TA-TAAAAATCATATAAAAT
1 TATTAAAAATCATATAAAAT
39636533 TATTAAAAAT-A-ATAAAAT
1 TATTAAAAATCATATAAAAT
* *
39636551 TGA-TATAAA-CTTATAAAAAT
1 T-ATTAAAAATCATAT-AAAAT
39636571 TATTAAAAA
1 TATTAAAAA
39636580 AACATAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
18 13 0.24
19 17 0.31
20 24 0.44
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (20 bp):
TATTAAAAATCATATAAAAT
Found at i:39637018 original size:9 final size:9
Alignment explanation
Indices: 39637006--39637188 Score: 67
Period size: 9 Copynumber: 19.9 Consensus size: 9
39636996 TTTTATGATT
39637006 TTTTTATAA
1 TTTTTATAA
39637015 TTTTTATAA
1 TTTTTATAA
*
39637024 GTTTATATCAA
1 -TTTTTAT-AA
* *
39637035 -TTTAAGTAT
1 TTTTTA-TAA
* *
39637044 TTTTTTTAT
1 TTTTTATAA
39637053 TTTTTA-AGA
1 TTTTTATA-A
* *
39637062 CTTCTAATACA
1 -TTTTTATA-A
39637073 TTTTT-TAA
1 TTTTTATAA
*
39637081 GTTTTACTAA
1 TTTTTA-TAA
**
39637091 -TTTTATTT
1 TTTTTATAA
39637099 TTTTTATAA
1 TTTTTATAA
39637108 TTTATTAT-A
1 TTT-TTATAA
39637117 TTTTTATAA
1 TTTTTATAA
* *
39637126 TATTTACAA
1 TTTTTATAA
39637135 GTTTTTTTATAA
1 ---TTTTTATAA
* *
39637147 CTTTAAT-A
1 TTTTTATAA
*
39637155 TTCTTT-TTA
1 TT-TTTATAA
39637164 TTTTT-TAA
1 TTTTTATAA
39637172 TTTTTATAA
1 TTTTTATAA
39637181 TTTTTATA
1 TTTTTATA
39637189 CACAATGCGT
Statistics
Matches: 129, Mismatches: 27, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
8 24 0.19
9 70 0.54
10 24 0.19
11 4 0.03
12 7 0.05
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Done.