Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 122 of 128
Found at i:40389056 original size:9 final size:9
Alignment explanation
Indices: 40389038--40389095 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
40389028 TTTGGTTAAA
40389038 AATTAACCG
1 AATTAACCG
*
40389047 AATTACCCG
1 AATTAACCG
40389056 AATTAACCG
1 AATTAACCG
* *
40389065 GATTACCCG
1 AATTAACCG
*
40389074 AATTATCCG
1 AATTAACCG
40389083 AATTAACCG
1 AATTAACCG
40389092 AATT
1 AATT
40389096 GAATCACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:40389061 original size:18 final size:18
Alignment explanation
Indices: 40389038--40389095 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
40389028 TTTGGTTAAA
40389038 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
40389056 AATTAACCGGATTACCCG
1 AATTAACCGAATTACCCG
* *
40389074 AATTATCCGAATTAACCG
1 AATTAACCGAATTACCCG
40389092 AATT
1 AATT
40389096 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:40389220 original size:18 final size:18
Alignment explanation
Indices: 40389197--40389240 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40389187 TAATTTTATG
*
40389197 ATTGGGTTGAGTTGGGTA
1 ATTGGGTTGAGTTGAGTA
*
40389215 ATTGGGTTGGGTTGAGTA
1 ATTGGGTTGAGTTGAGTA
*
40389233 CTTGGGTT
1 ATTGGGTT
40389241 TGGATTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGAGTTGAGTA
Found at i:40389579 original size:118 final size:118
Alignment explanation
Indices: 40389433--40389662 Score: 415
Period size: 118 Copynumber: 1.9 Consensus size: 118
40389423 CCGAATTCAG
* * *
40389433 TCGGTTAACCGAATTTTTTCGGTTTTACCCGAATTTTGCACACCCCTACTTATGGCTGTAGATAT
1 TCGGTTAACCAAATTTTTTCGGTTTTACCCGAATTTTACACACCCCTACTTATGGCCGTAGATAT
*
40389498 TGAAGAATCATTTTATACATTTATGTTTTAATAAATAATATATTATTAATCGT
66 TGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATTAATCGT
*
40389551 TCGGTTAATCAAATTTTTTCGGTTTTACCCGAATTTTACACACCCCTACTTATGGCCGTAGATAT
1 TCGGTTAACCAAATTTTTTCGGTTTTACCCGAATTTTACACACCCCTACTTATGGCCGTAGATAT
40389616 TGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATT
66 TGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATT
40389663 GGTTAAAAAG
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 107 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (118 bp):
TCGGTTAACCAAATTTTTTCGGTTTTACCCGAATTTTACACACCCCTACTTATGGCCGTAGATAT
TGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATTAATCGT
Found at i:40390395 original size:28 final size:31
Alignment explanation
Indices: 40390364--40390429 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
40390354 AAAGCATATA
40390364 TAATAAATTAT-T-ATAATTA-AA-ATTATTT
1 TAATAAATTATCTAAT-ATTACAATATTATTT
*
40390392 TAATAAAATTATCTAATATTACAATTTTATTT
1 TAAT-AAATTATCTAATATTACAATATTATTT
40390424 TAATAA
1 TAATAA
40390430 TAAATTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 4 0.12
29 7 0.22
30 5 0.16
31 6 0.19
32 10 0.31
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
TAATAAATTATCTAATATTACAATATTATTT
Found at i:40390398 original size:14 final size:14
Alignment explanation
Indices: 40390362--40390403 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
40390352 AGAAAGCATA
40390362 TATAAT-AAATTAT
1 TATAATAAAATTAT
40390375 TATAATTAAAATTAT
1 TATAA-TAAAATTAT
*
40390390 TTTAATAAAATTAT
1 TATAATAAAATTAT
40390404 CTAATATTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 10 0.38
15 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATAAAATTAT
Found at i:40390575 original size:25 final size:24
Alignment explanation
Indices: 40390546--40390605 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
40390536 AATATTTTAA
* *
40390546 ATTTTTTATAGTATAAAATATGAAT
1 ATTTTTTATAATAT-AAATATCAAT
* *
40390571 ATTTTTTAGAATATAAATATCATT
1 ATTTTTTATAATATAAATATCAAT
40390595 ATTTATTTATA
1 ATTT-TTTATA
40390606 TCCTACTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (24 bp):
ATTTTTTATAATATAAATATCAAT
Found at i:40399371 original size:29 final size:28
Alignment explanation
Indices: 40399330--40399387 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
40399320 CTTTTATAAA
40399330 AGATTAAGAGCTAAACTT-AGCTAAAAAAT
1 AGATTAAGAGCTAAA-TTGA-CTAAAAAAT
40399359 AGATTAA-AGGCTAAATTGACTAAAAAAT
1 AGATTAAGA-GCTAAATTGACTAAAAAAT
40399387 A
1 A
40399388 TGTAAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (28 bp):
AGATTAAGAGCTAAATTGACTAAAAAAT
Found at i:40402394 original size:24 final size:23
Alignment explanation
Indices: 40402367--40402432 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 23
40402357 AGTTTAAAGG
40402367 ATGTATAATGCTTTCCTTTAAATA
1 ATGTATAATGC-TTCCTTTAAATA
* *
40402391 ATGTA-ACA-GC-TCCTTTGAATG
1 ATGTATA-ATGCTTCCTTTAAATA
*
40402412 ATGCATAATGCTCTCCTTTAA
1 ATGTATAATGCT-TCCTTTAA
40402433 TTGATGTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
21 14 0.42
22 3 0.09
23 3 0.09
24 13 0.39
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (23 bp):
ATGTATAATGCTTCCTTTAAATA
Found at i:40402559 original size:11 final size:11
Alignment explanation
Indices: 40402543--40402575 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40402533 ACCTACAATC
40402543 AAAACACATTA
1 AAAACACATTA
40402554 AAAACACATT-
1 AAAACACATTA
40402564 -AAACACATTA
1 AAAACACATTA
40402574 AA
1 AA
40402576 CCACATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAACACATTA
Found at i:40405205 original size:33 final size:33
Alignment explanation
Indices: 40405167--40405229 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
40405157 ATATATTTTG
* *
40405167 TTTAACTTGACTTGCAAGCAATCTTTTAGATTT
1 TTTAACTTGACATGCAAGCAATCTCTTAGATTT
40405200 TTTAACTTGACATGCAAGCAATCTCTTAGA
1 TTTAACTTGACATGCAAGCAATCTCTTAGA
40405230 ATTCGGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (33 bp):
TTTAACTTGACATGCAAGCAATCTCTTAGATTT
Found at i:40410250 original size:211 final size:211
Alignment explanation
Indices: 40409883--40410305 Score: 774
Period size: 211 Copynumber: 2.0 Consensus size: 211
40409873 GAAACCCTAG
*
40409883 TAGTGTTGCCCCCTTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
1 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
*
40409948 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCTGTTTCCCTCAATTTTCTC
66 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCTGATTCCCTCAATTTTCTC
* *
40410013 TATTTTCTTCCCCTCTATACCGCCCATAATACCCCAAAACTCTACTATTGTGCCGCCTCATTGAT
131 TATTTTCTTCCCCTCTATACCGCCCATAATACCCCAAAACTCTACTATTATGCCACCTCATTGAT
*
40410078 CATCAACTCCTATTGT
196 CATCAACTCATATTGT
40410094 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
1 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
* *
40410159 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCCTTCTTCCTCTCTGATTCTCTCAATTTTCTC
66 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCTGATTCCCTCAATTTTCTC
*
40410224 TATTTTCTTCCCCTCTATAGCGCCCATAATACCCCAAAACTCTACTATTATGCCACCTCATTGAT
131 TATTTTCTTCCCCTCTATACCGCCCATAATACCCCAAAACTCTACTATTATGCCACCTCATTGAT
40410289 CATCAACTCATATTGT
196 CATCAACTCATATTGT
40410305 T
1 T
40410306 TCCTATTTTA
Statistics
Matches: 204, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
211 204 1.00
ACGTcount: A:0.20, C:0.30, G:0.08, T:0.42
Consensus pattern (211 bp):
TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCTGATTCCCTCAATTTTCTC
TATTTTCTTCCCCTCTATACCGCCCATAATACCCCAAAACTCTACTATTATGCCACCTCATTGAT
CATCAACTCATATTGT
Found at i:40412951 original size:21 final size:21
Alignment explanation
Indices: 40412927--40413080 Score: 146
Period size: 21 Copynumber: 7.3 Consensus size: 21
40412917 GTACATCGTT
*
40412927 AACAGAAGCTTGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
* *
40412948 AACAAAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTA
* ** * *
40412969 AACAGAAACTCACAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTA
* *
40412990 AATAGAAGCTCGTAAGAGCTT
1 AACAGAAGCTCGTAAGAGCTA
* * * * *
40413011 AACGGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTA
40413032 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
**
40413053 AACAGAAGCTCACAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
*
40413074 AAGAGAA
1 AACAGAA
40413081 AGTAAAACAC
Statistics
Matches: 105, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 105 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTA
Found at i:40412986 original size:42 final size:42
Alignment explanation
Indices: 40412940--40413080 Score: 174
Period size: 42 Copynumber: 3.4 Consensus size: 42
40412930 AGAAGCTTGT
* *
40412940 AAGAGCTAAACAAAAGCTCGTAAGAGCTGAACAGAAACTCAC
1 AAGAGCTAAACAGAAGCTCGTAAGAGCTAAACAGAAACTCAC
* * * * * *
40412982 AAGAGTTGAATAGAAGCTCGTAAGAGCTTAACGGAAACTCAT
1 AAGAGCTAAACAGAAGCTCGTAAGAGCTAAACAGAAACTCAC
* * *
40413024 AAGAGTTGAACAGAAGCTCGTAAGAGCTAAACAGAAGCTCAC
1 AAGAGCTAAACAGAAGCTCGTAAGAGCTAAACAGAAACTCAC
*
40413066 AAGAGCTAAAGAGAA
1 AAGAGCTAAACAGAA
40413081 AGTAAAACAC
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (42 bp):
AAGAGCTAAACAGAAGCTCGTAAGAGCTAAACAGAAACTCAC
Found at i:40413009 original size:63 final size:63
Alignment explanation
Indices: 40412927--40413075 Score: 165
Period size: 63 Copynumber: 2.4 Consensus size: 63
40412917 GTACATCGTT
* * * *
40412927 AACAGAAGCTTGTAAGAGCTAAAC-AAAAGCTCGTAAGAGCTGAACAGAAACTCACAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTAAACGAAAA-CTCATAAGAGCTGAACAGAAACTCACAAGAGCTA
* * * * * **
40412990 AATAGAAGCTCGTAAGAGCTTAACGGAAACTCATAAGAGTTGAACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAGAGCTGAACAGAAACTCACAAGAGCTA
**
40413053 AACAGAAGCTCACAAGAGCTAAA
1 AACAGAAGCTCGTAAGAGCTAAA
40413076 GAGAAAGTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
63 67 0.96
64 3 0.04
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (63 bp):
AACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAGAGCTGAACAGAAACTCACAAGAGCTA
Found at i:40418142 original size:25 final size:26
Alignment explanation
Indices: 40418113--40418164 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40418103 TATATGTACC
40418113 TAGATTTTTTTT-CATAAAAAATGTT
1 TAGATTTTTTTTCCATAAAAAATGTT
40418138 TAGATTTTTTTTCCATAAAAAATGTT
1 TAGATTTTTTTTCCATAAAAAATGTT
40418164 T
1 T
40418165 TTCTTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (26 bp):
TAGATTTTTTTTCCATAAAAAATGTT
Found at i:40421366 original size:14 final size:14
Alignment explanation
Indices: 40421347--40421373 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40421337 CATTATGGCT
40421347 TTTCAGCAATTTTC
1 TTTCAGCAATTTTC
40421361 TTTCAGCAATTTT
1 TTTCAGCAATTTT
40421374 GGCATATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTCAGCAATTTTC
Found at i:40426158 original size:18 final size:18
Alignment explanation
Indices: 40426135--40426170 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40426125 TAAAGAACCC
*
40426135 GAAGTTTCTTTAATTTAA
1 GAAGTTTCTCTAATTTAA
40426153 GAAGTTTCTCTAATTTAA
1 GAAGTTTCTCTAATTTAA
40426171 AGAATTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.47
Consensus pattern (18 bp):
GAAGTTTCTCTAATTTAA
Found at i:40428852 original size:33 final size:33
Alignment explanation
Indices: 40428815--40428882 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
40428805 AAAGACAAGT
40428815 ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
1 ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
40428848 ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
1 ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
40428881 AT
1 AT
40428883 GTGATATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (33 bp):
ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
Found at i:40429413 original size:16 final size:17
Alignment explanation
Indices: 40429392--40429437 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
40429382 AATAGAAATA
40429392 TTTATTATTAATTA-CT
1 TTTATTATTAATTAGCT
* *
40429408 TTTATTGTTAATAAGCT
1 TTTATTATTAATTAGCT
*
40429425 TTTAATA-TAATTA
1 TTTATTATTAATTA
40429438 TATAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTATTATTAATTAGCT
Found at i:40430338 original size:18 final size:19
Alignment explanation
Indices: 40430315--40430350 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
40430305 TGACAATTTC
40430315 TTTTTTATATT-TGTAATG
1 TTTTTTATATTATGTAATG
40430333 TTTTTTATATTATGTAAT
1 TTTTTTATATTATGTAAT
40430351 TTATAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTTTTATATTATGTAATG
Found at i:40430481 original size:18 final size:19
Alignment explanation
Indices: 40430458--40430493 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
40430448 TGACAATTTC
40430458 TTTTTTATATT-TGTAATG
1 TTTTTTATATTATGTAATG
40430476 TTTTTTATATTATGTAAT
1 TTTTTTATATTATGTAAT
40430494 TTATAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTTTTATATTATGTAATG
Found at i:40430509 original size:143 final size:143
Alignment explanation
Indices: 40430251--40430526 Score: 543
Period size: 143 Copynumber: 1.9 Consensus size: 143
40430241 TTTGAGGAGA
40430251 TTTAAACAAAAACATTAGGCATGAAAAATGGGTTGGTTAAAAAAAATTATGGCTTGACAATTTCT
1 TTTAAACAAAAACATTAGGCATGAAAAATGGGTTGGTTAAAAAAAATTATGGCTTGACAATTTCT
40430316 TTTTTATATTTGTAATGTTTTTTATATTATGTAATTTATAACACATAAAAATTAAATCTATAAAA
66 TTTTTATATTTGTAATGTTTTTTATATTATGTAATTTATAACACATAAAAATTAAATCTATAAAA
40430381 ATAGTTCCTCAAG
131 ATAGTTCCTCAAG
40430394 TTTAAACAAAAACATTAGGCATGAAAAATGGGTTGGTTAAAAAAAATTATGGCTTGACAATTTCT
1 TTTAAACAAAAACATTAGGCATGAAAAATGGGTTGGTTAAAAAAAATTATGGCTTGACAATTTCT
*
40430459 TTTTTATATTTGTAATGTTTTTTATATTATGTAATTTATAACACATAAAAATTAAATCTATAATA
66 TTTTTATATTTGTAATGTTTTTTATATTATGTAATTTATAACACATAAAAATTAAATCTATAAAA
40430524 ATA
131 ATA
40430527 TATATAATAC
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 132 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (143 bp):
TTTAAACAAAAACATTAGGCATGAAAAATGGGTTGGTTAAAAAAAATTATGGCTTGACAATTTCT
TTTTTATATTTGTAATGTTTTTTATATTATGTAATTTATAACACATAAAAATTAAATCTATAAAA
ATAGTTCCTCAAG
Found at i:40440433 original size:159 final size:159
Alignment explanation
Indices: 40440221--40440537 Score: 501
Period size: 159 Copynumber: 2.0 Consensus size: 159
40440211 CTTTACTCAT
* * *
40440221 TTTTTGCTCTTCTTTGCCCTATTGGCTTCGACTTTTCCCTTGCTCGAACCAAACTTCTTAGGCTC
1 TTTTTGCTCCTCTTTGCCCTATTGGCTTCGACTTTTCCCTTACTCAAACCAAACTTCTTAGGCTC
* *
40440286 CTTGTCTGCTCTATCGTTTCCTTCGATGATAGACTTCCTTGAACACTTCCGCAACTTATGC-AGA
66 CTTGTCTGCTCTAACGTTTCCTTCGATGAAAGACTTCCTTGAACACTTCCGCAACTTATGCGA-A
*
40440350 CCATGACACAAGAAGCACTCCACTTGCTTA
130 CCATGACACAAGAAGCACTCCACTGGCTTA
* * *
40440380 TTTTTGCTCCTCTTTGCCCTCTTGGCTTTGACTTTTCCCTTACTCAAATCAAACTTCTTAGGCTC
1 TTTTTGCTCCTCTTTGCCCTATTGGCTTCGACTTTTCCCTTACTCAAACCAAACTTCTTAGGCTC
* * * *
40440445 CTTGTCTGCTCTAACGTTTTCTTTGATGAAAGACTTCCTTGGACACTTTCGCAACTTATGCGAAC
66 CTTGTCTGCTCTAACGTTTCCTTCGATGAAAGACTTCCTTGAACACTTCCGCAACTTATGCGAAC
40440510 CATGACACAAGAAGCACTCCACTGGCTT
131 CATGACACAAGAAGCACTCCACTGGCTT
40440538 CTTCTCACTT
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
159 143 0.99
160 1 0.01
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (159 bp):
TTTTTGCTCCTCTTTGCCCTATTGGCTTCGACTTTTCCCTTACTCAAACCAAACTTCTTAGGCTC
CTTGTCTGCTCTAACGTTTCCTTCGATGAAAGACTTCCTTGAACACTTCCGCAACTTATGCGAAC
CATGACACAAGAAGCACTCCACTGGCTTA
Found at i:40443180 original size:7 final size:8
Alignment explanation
Indices: 40443153--40443189 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
40443143 CGAGCAAAAG
40443153 AAAAATAA
1 AAAAATAA
40443161 AAAAATCAGA
1 AAAAAT-A-A
40443171 AAAAATAA
1 AAAAATAA
40443179 AAAAATAA
1 AAAAATAA
40443187 AAA
1 AAA
40443190 GTGCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.67
9 2 0.07
10 7 0.26
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:40443199 original size:26 final size:27
Alignment explanation
Indices: 40443153--40443207 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
40443143 CGAGCAAAAG
*
40443153 AAAAATAAAAAAATCAGAAAA-AATAA
1 AAAAATAAAAAAATCAAAAAAGAATAA
*
40443179 AAAAAT-AAAAAGTGCAAAAAAGAATAA
1 AAAAATAAAAAAAT-CAAAAAAGAATAA
40443206 AA
1 AA
40443208 TAATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 12 0.48
27 7 0.28
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (27 bp):
AAAAATAAAAAAATCAAAAAAGAATAA
Found at i:40450548 original size:21 final size:20
Alignment explanation
Indices: 40450506--40450576 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
40450496 TTCAAGGATG
40450506 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGTATA
*
40450525 TGCAATGTTAGATATGATATA
1 TGCAATCTTAGATATG-TATA
*
40450546 TGCAATGTTAGATATGT-TA
1 TGCAATCTTAGATATGTATA
40450565 TGCAATCTTAGA
1 TGCAATCTTAGA
40450577 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 28 0.58
20 1 0.02
21 19 0.40
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (20 bp):
TGCAATCTTAGATATGTATA
Found at i:40450583 original size:22 final size:23
Alignment explanation
Indices: 40450515--40450599 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 23
40450505 GTGCAATCTT
*
40450515 AGATATGA-TATGCAATGTT---
1 AGATATGATTATGCAATCTTAGA
*
40450534 AGATATGATATATGCAATGTT---
1 AGATATGAT-TATGCAATCTTAGA
40450555 AGATATG-TTATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
40450577 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
40450600 GATTTAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
19 18 0.32
20 1 0.02
21 18 0.32
22 7 0.12
23 13 0.23
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:40450602 original size:22 final size:22
Alignment explanation
Indices: 40450555--40450599 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
40450545 ATGCAATGTT
40450555 AGATATGTTATGCAATCTTAGA
1 AGATATGTTATGCAATCTTAGA
* *
40450577 AGATATGATTTTGTAATCTTAGA
1 AGATATG-TTATGCAATCTTAGA
40450600 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (22 bp):
AGATATGTTATGCAATCTTAGA
Found at i:40450916 original size:3 final size:3
Alignment explanation
Indices: 40450908--40450937 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40450898 TGTTATTAAG
*
40450908 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40450938 CTATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40464435 original size:12 final size:12
Alignment explanation
Indices: 40464418--40464443 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40464408 TCTTTCAGCT
40464418 CATTAGTATCAA
1 CATTAGTATCAA
40464430 CATTAGTATCAA
1 CATTAGTATCAA
40464442 CA
1 CA
40464444 AGCAATGGTA
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:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (12 bp):
CATTAGTATCAA
Found at i:40465199 original size:22 final size:22
Alignment explanation
Indices: 40465174--40465222 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
40465164 AAAAATCACA
*
40465174 AAAAATAATTTTA-AAAATTCTT
1 AAAAATAATTTTACAAAAAT-TT
*
40465196 AAAAATATTTTTACAAAAATTT
1 AAAAATAATTTTACAAAAATTT
40465218 AAAAA
1 AAAAA
40465223 AAATGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATAATTTTACAAAAATTT
Found at i:40467424 original size:45 final size:44
Alignment explanation
Indices: 40467360--40467447 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
40467350 ATTAGAGGTG
*
40467360 TAATGAAATAGAGGTGTAATAGCAAATC-AACTGTTTGGTTGAATA
1 TAATGAAATAGAGGCGTAATAG-AAATCTAA-TGTTTGGTTGAATA
* * *
40467405 TAATGGAATAGAGGCGTAATAGTAATCTTATGTTTGGTTGAAT
1 TAATGAAATAGAGGCGTAATAGAAATCTAATGTTTGGTTGAAT
40467448 GGAATAGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 17 0.45
45 21 0.55
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (44 bp):
TAATGAAATAGAGGCGTAATAGAAATCTAATGTTTGGTTGAATA
Found at i:40467634 original size:18 final size:17
Alignment explanation
Indices: 40467613--40467647 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40467603 TTATTATTAA
*
40467613 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40467631 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40467648 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40470999 original size:31 final size:30
Alignment explanation
Indices: 40470964--40471067 Score: 77
Period size: 31 Copynumber: 3.4 Consensus size: 30
40470954 TAAAATTGGG
*
40470964 AAATTTTTATTTCTCCATTGAAATTTTTAGA
1 AAATTTTAATTTCTCC-TTGAAATTTTTAGA
** ** *
40470995 AAATTTTAATTAAGTCCGTCAAAATTTTT-GG
1 AAATTTTAATT-TCTCC-TTGAAATTTTTAGA
* *
40471026 AAATTTTCATTTCTCTCTTGAAGTTTTTAG-
1 AAATTTTAATTTCTC-CTTGAAATTTTTAGA
40471056 AAATATTTAATT
1 AAAT-TTTAATT
40471068 AGGCCCCTTC
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
30 14 0.25
31 29 0.53
32 12 0.22
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.49
Consensus pattern (30 bp):
AAATTTTAATTTCTCCTTGAAATTTTTAGA
Found at i:40471086 original size:62 final size:62
Alignment explanation
Indices: 40470962--40471094 Score: 155
Period size: 62 Copynumber: 2.1 Consensus size: 62
40470952 AATAAAATTG
* * *
40470962 GGAAATTTTTATTTCTCCATTGAAATTTTTAGAAAATTTTAATTAAGTCCGTCAAAATTTTT
1 GGAAATTTTCATTTCTCCATTGAAATTTTTAGAAAATTTTAATTAAGCCCGTCAAAACTTTT
* * *
40471024 GGAAATTTTCATTTCTCTC-TTGAAGTTTTTAG-AAATATTTAATTAGGCCCCTTC-AAACTTTT
1 GGAAATTTTCATTTCTC-CATTGAAATTTTTAGAAAAT-TTTAATTAAG-CCCGTCAAAACTTTT
*
40471086 GAAAATTTT
1 GGAAATTTT
40471095 AATCAAGCTC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
61 4 0.07
62 52 0.85
63 5 0.08
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (62 bp):
GGAAATTTTCATTTCTCCATTGAAATTTTTAGAAAATTTTAATTAAGCCCGTCAAAACTTTT
Found at i:40488215 original size:19 final size:18
Alignment explanation
Indices: 40488191--40488235 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
40488181 TAAATACCAA
40488191 GTTTTTTAGTTAAAAAAAT
1 GTTTTTTAG-TAAAAAAAT
*
40488210 GTTTTTGAGTAAAAAAAT
1 GTTTTTTAGTAAAAAAAT
40488228 -TTTTTTAG
1 GTTTTTTAG
40488236 GAGGGCCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
GTTTTTTAGTAAAAAAAT
Found at i:40488540 original size:52 final size:52
Alignment explanation
Indices: 40488457--40488646 Score: 362
Period size: 52 Copynumber: 3.7 Consensus size: 52
40488447 ATTATCATTA
*
40488457 TACACTTATATTAATCATATTTATTGGATAAAAAAAGACTTGATCTTGACTG
1 TACATTTATATTAATCATATTTATTGGATAAAAAAAGACTTGATCTTGACTG
40488509 TACATTTATATTAATCATATTTATTGGATAAAAAAAGACTTGATCTTGACTG
1 TACATTTATATTAATCATATTTATTGGATAAAAAAAGACTTGATCTTGACTG
40488561 TACATTTATATTAATCATATTTATTGGATAAAAAAAGACTTGATCTTGACTG
1 TACATTTATATTAATCATATTTATTGGATAAAAAAAGACTTGATCTTGACTG
*
40488613 TACATTTATATTAATCATATTTATTGGATCAAAA
1 TACATTTATATTAATCATATTTATTGGATAAAAA
40488647 GCGTCTGTTC
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 136 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.41
Consensus pattern (52 bp):
TACATTTATATTAATCATATTTATTGGATAAAAAAAGACTTGATCTTGACTG
Found at i:40498258 original size:12 final size:12
Alignment explanation
Indices: 40498241--40498270 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
40498231 CACAGGTTTG
40498241 AAAATAATTACC
1 AAAATAATTACC
40498253 AAAATAATTACC
1 AAAATAATTACC
40498265 AAAATA
1 AAAATA
40498271 GGGTTGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAATTACC
Found at i:40499025 original size:113 final size:107
Alignment explanation
Indices: 40498831--40499230 Score: 324
Period size: 94 Copynumber: 3.8 Consensus size: 107
40498821 CGCCTCTAGT
* *
40498831 CGGCACCACCTTTTTTGGGGAAATTTTTTTTCACTTTTTTTCGTGTCAATAGCAGGTATTAGTAT
1 CGGCACCACCTTTTTTGGGGAAATTTTTTTTCACTTTTTTTCGTGTCAATAGCAGGTATCAATAT
* *
40498896 ATAAAAAAAGTAAAAAAAAAATTTGGTGGTGGCTTGCCAATGGC
66 ACAAAAAAAGT-AAAAAAAAA-TTGGTGGTGGCCTGCCAATGGC
* * *
40498940 CGGCACCATCTTTTTTGGGGGGAGAATTTTTTTTTTTAC-TTTTTTCGTGTCAATAGCTGGTATC
1 CGGCACCACCTTTTTT--GGGGA-AA--TTTTTTTTCACTTTTTTTCGTGTCAATAGCAGGTATC
*
40499004 AATATACGAAAAAAGTAAAAAAAAATTGGTGGTGGCCTGCCACCTTTTATGG-
61 AATATACAAAAAAAGTAAAAAAAAATTGGTGGTGGCCTGCCA------ATGGC
* *
40499056 -GG-A--A--TTTTTT-------T----TTTCAC-TTTTTTCGTGTCAATAGCAGGTATTAGTAT
1 CGGCACCACCTTTTTTGGGGAAATTTTTTTTCACTTTTTTTCGTGTCAATAGCAGGTATCAATAT
* * *
40499103 ACGAAAAAAGTAAAAAAAAAATT-GTGGTGGCCTGCCAACGGT
66 ACAAAAAAAGT-AAAAAAAAATTGGTGGTGGCCTGCCAATGGC
* * * * *
40499145 TGGCACCACCTTTTTT-GTGAGAATTTTTTTTTAC-TTTTTTCGTGTCAATAACAGGTATCAGTA
1 CGGCACCACCTTTTTTGGGGA-AATTTTTTTTCACTTTTTTTCGTGTCAATAGCAGGTATCAATA
* *
40499208 TACGAGAAAAGTAAAAAAAAATT
65 TACAAAAAAAGTAAAAAAAAATT
40499231 CCCCCAAAAA
Statistics
Matches: 244, Mismatches: 17, Indels: 64
0.75 0.05 0.20
Matches are distributed among these distances:
88 3 0.01
90 2 0.01
91 1 0.00
93 1 0.00
94 57 0.23
95 17 0.07
98 1 0.00
102 1 0.00
105 11 0.05
106 43 0.18
109 15 0.06
110 6 0.02
111 21 0.09
112 12 0.05
113 36 0.15
114 11 0.05
115 2 0.01
117 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (107 bp):
CGGCACCACCTTTTTTGGGGAAATTTTTTTTCACTTTTTTTCGTGTCAATAGCAGGTATCAATAT
ACAAAAAAAGTAAAAAAAAATTGGTGGTGGCCTGCCAATGGC
Found at i:40499408 original size:41 final size:41
Alignment explanation
Indices: 40499363--40499558 Score: 144
Period size: 41 Copynumber: 4.9 Consensus size: 41
40499353 AAATATATTT
* * *
40499363 ATTTTTTAAAATTTTAAAATATTTTTTACATACTTTTTTAA
1 ATTTTTTAAAATTTTAAAATATTTTTAAAATACTTTTTAAA
**
40499404 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAA
1 ATTTTTTAAAATTTTAAAATATTTTTAAAATACTTTTTAAA
* * **
40499445 A-TTTTAAAATATTTTTACAAT-TTTTT--AAT--TTTAAAATA
1 ATTTTTTAAA-A-TTTTAAAATATTTTTAAAATACTTTTTAA-A
** **
40499483 ATTTTAAAATACATTTTTTAA-A-TTTTAAAATA-TTTTTAAA
1 ATTTTTTAA-A-ATTTTAAAATATTTTTAAAATACTTTTTAAA
*
40499523 ATTTTTT--AATTATAAAATATTTTTAAAATACTTTTT
1 ATTTTTTAAAATTTTAAAATATTTTTAAAATACTTTTT
40499559 TTTATTTTTA
Statistics
Matches: 121, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
36 6 0.05
37 7 0.06
38 16 0.13
39 20 0.17
40 16 0.13
41 48 0.40
42 8 0.07
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (41 bp):
ATTTTTTAAAATTTTAAAATATTTTTAAAATACTTTTTAAA
Found at i:40499420 original size:17 final size:17
Alignment explanation
Indices: 40499398--40499431 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40499388 TTACATACTT
* *
40499398 TTTTAAATTTTTTTTAA
1 TTTTAAAATATTTTTAA
40499415 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
40499432 AATACTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:40499442 original size:12 final size:11
Alignment explanation
Indices: 40499362--40499579 Score: 92
Period size: 11 Copynumber: 21.6 Consensus size: 11
40499352 TAAATATATT
*
40499362 TATTTTTTAAA
1 TATTTTTAAAA
40499373 -A-TTTTAAAA
1 TATTTTTAAAA
* *
40499382 TATTTTTTACA
1 TATTTTTAAAA
*
40499393 TACTTTTTTAAA
1 TA-TTTTTAAAA
*
40499405 T-TTTTT---T
1 TATTTTTAAAA
*
40499412 TAATTTTAAAA
1 TATTTTTAAAA
40499423 TATTTTTAAAA
1 TATTTTTAAAA
40499434 TACTTTTT-AAA
1 TA-TTTTTAAAA
40499445 -A-TTTTAAAA
1 TATTTTTAAAA
*
40499454 TATTTTTACAA
1 TATTTTTAAAA
40499465 T-TTTTT---A
1 TATTTTTAAAA
40499472 -A-TTTTAAAA
1 TATTTTTAAAA
*
40499481 TAATTTTAAAA
1 TATTTTTAAAA
*
40499492 TACATTTTT-TAA
1 T--ATTTTTAAAA
40499504 -A-TTTTAAAA
1 TATTTTTAAAA
40499513 TATTTTTAAAA
1 TATTTTTAAAA
40499524 T-TTTTT---A
1 TATTTTTAAAA
*
40499531 -A-TTATAAAA
1 TATTTTTAAAA
40499540 TATTTTTAAAA
1 TATTTTTAAAA
**
40499551 TACTTTTT--TT
1 TA-TTTTTAAAA
40499561 TATTTTTAAAA
1 TATTTTTAAAA
40499572 TATATTTT
1 TAT-TTTT
40499580 TGGTATTTTA
Statistics
Matches: 157, Mismatches: 18, Indels: 63
0.66 0.08 0.26
Matches are distributed among these distances:
6 7 0.04
7 3 0.02
8 12 0.08
9 20 0.13
10 24 0.15
11 61 0.39
12 25 0.16
13 5 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:40499566 original size:58 final size:58
Alignment explanation
Indices: 40499397--40499579 Score: 267
Period size: 59 Copynumber: 3.1 Consensus size: 58
40499387 TTTACATACT
* *
40499397 TTTTTAAATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAATTTTAAAATA
1 TTTTTAAA-ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTAAAATA
* *
40499456 TTTTTACAATTTTTTAATTTTAAAATAATTTTAAAATACATTTTTTAAATTTTAAAATA
1 TTTTTAAAATTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAAATTTTAAAATA
* * *
40499515 TTTTTAAAATTTTTTAATTATAAAATATTTTTAAAATACTTTTTTTTATTTTTAAAATA
1 TTTTTAAAATTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAAATTTTAAAATA
40499574 TATTTT
1 T-TTTT
40499580 TGGTATTTTA
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
58 29 0.26
59 79 0.71
60 4 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (58 bp):
TTTTTAAAATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTAAAATA
Found at i:40499589 original size:21 final size:21
Alignment explanation
Indices: 40499540--40499588 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
40499530 AATTATAAAA
*
40499540 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATACTTTTTTG
40499561 TATTTTTAAAATA-TATTTTTGG
1 TATTTTTAAAATACT-TTTTT-G
40499583 TATTTT
1 TATTTT
40499589 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.72
22 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
TATTTTTAAAATACTTTTTTG
Found at i:40502789 original size:23 final size:23
Alignment explanation
Indices: 40502748--40502791 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40502738 GTTTTAAGTC
* * *
40502748 ATGATAATTAAATTTTAATTTTT
1 ATGATAATAAAAATGTAATTTTT
40502771 ATGATAATAAAAATGTAATTT
1 ATGATAATAAAAATGTAATTT
40502792 CATCATTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
ATGATAATAAAAATGTAATTTTT
Found at i:40502938 original size:23 final size:23
Alignment explanation
Indices: 40502899--40502952 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
40502889 TTAAATTTTA
*
40502899 AAAACTTTAAAAAACTTAAAT-G
1 AAAATTTTAAAAAACTTAAATAG
*
40502921 AAAATTTTAAATAGACTTAAATAG
1 AAAATTTTAAA-AAACTTAAATAG
40502945 AAAATTTT
1 AAAATTTT
40502953 CCATTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.36
23 9 0.32
24 9 0.32
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (23 bp):
AAAATTTTAAAAAACTTAAATAG
Found at i:40509826 original size:42 final size:42
Alignment explanation
Indices: 40509779--40509864 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
40509769 GGCAGCAATG
* *
40509779 TCAATTTCAAGCGGCGGGCAAGGACCCACAGAAAGTTCTCTT
1 TCAATTTCAACCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
40509821 TCAATTTCAACCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
1 TCAATTTCAACCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
40509863 TC
1 TC
40509865 GTTCATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (42 bp):
TCAATTTCAACCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
Found at i:40512052 original size:85 final size:85
Alignment explanation
Indices: 40511957--40512125 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 85
40511947 TTTTTTTGAC
40511957 TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAGGAGGAATCTCC-TTTACATAACAAACA
1 TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAGGAGGAATCTCCGTTT-CATAACAAACA
40512021 AACAACCTTTTTGACTCATAT
65 AACAACCTTTTTGACTCATAT
** *
40512042 TTATCCCTAAGACTATTTTTACAGGCGAATATGATAAGGAGGAATCTCCGTTTCATAACAAACAA
1 TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAGGAGGAATCTCCGTTTCATAACAAACAA
40512107 ACAACCTTTTTGACTCATA
66 ACAACCTTTTTGACTCATA
40512126 CTTTTATGAC
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 77 0.96
86 3 0.04
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (85 bp):
TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAGGAGGAATCTCCGTTTCATAACAAACAA
ACAACCTTTTTGACTCATAT
Found at i:40513351 original size:14 final size:15
Alignment explanation
Indices: 40513327--40513357 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
40513317 TAAATGATTT
40513327 TTTTTATAATTTTTA
1 TTTTTATAATTTTTA
40513342 TTTTTA-AATTTTTA
1 TTTTTATAATTTTTA
40513356 TT
1 TT
40513358 ATTTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATAATTTTTA
Found at i:40513383 original size:21 final size:21
Alignment explanation
Indices: 40513329--40513383 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
40513319 AATGATTTTT
*
40513329 TTTATAATTTTTATTTTTAAA
1 TTTATAATTTTTATTTATAAA
* *
40513350 TTTTTATTATTTTA-TTATAAA
1 TTTATAAT-TTTTATTTATAAA
40513371 TTTATAACTTTTT
1 TTTATAA-TTTTT
40513384 TAAAATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATAATTTTTATTTATAAA
Found at i:40514300 original size:27 final size:27
Alignment explanation
Indices: 40514228--40514300 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
40514218 GTCGGGTGGC
* *
40514228 GCCTCATAGGGAGGCACCATCAAAAGT
1 GCCTCATAGGGAGGCGCCATCAAAAAT
* * *
40514255 GCCTCATAAGGAGGTGCCATTAAAAAT
1 GCCTCATAGGGAGGCGCCATCAAAAAT
40514282 GCCTCATAGGGAGGCGCCA
1 GCCTCATAGGGAGGCGCCA
40514301 ATGGGTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.16
Consensus pattern (27 bp):
GCCTCATAGGGAGGCGCCATCAAAAAT
Found at i:40514354 original size:19 final size:19
Alignment explanation
Indices: 40514305--40514369 Score: 94
Period size: 19 Copynumber: 3.3 Consensus size: 19
40514295 GCGCCAATGG
*
40514305 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
40514324 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
40514345 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
40514364 GTAATT
1 GTAATT
40514370 ATTTTATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 24 0.59
21 17 0.41
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:40514650 original size:14 final size:14
Alignment explanation
Indices: 40514631--40514666 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40514621 TTTGATTTTG
40514631 TATTTATTTAACAA
1 TATTTATTTAACAA
*
40514645 TATTTATTTAACAG
1 TATTTATTTAACAA
40514659 TATTTATT
1 TATTTATT
40514667 AATTTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTTATTTAACAA
Found at i:40514773 original size:27 final size:27
Alignment explanation
Indices: 40514700--40514777 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
40514690 ATAAAATAAT
*
40514700 ACCATTGGCGCCTATCAGATAGGCACC
1 ACCATTGGCGCCTCTCAGATAGGCACC
40514727 ACCATTGGCGCCTCTCAGATAGGCACC
1 ACCATTGGCGCCTCTCAGATAGGCACC
* *
40514754 ACCATTGGCGCATCTGAGATAGGC
1 ACCATTGGCGCCTCTCAGATAGGC
40514778 TCCAATATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (27 bp):
ACCATTGGCGCCTCTCAGATAGGCACC
Found at i:40515755 original size:29 final size:29
Alignment explanation
Indices: 40515723--40515779 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
40515713 AACTCACTAC
*
40515723 TTTGTGTTTAAACAAGCACTCAACCTATT
1 TTTGTGGTTAAACAAGCACTCAACCTATT
* * *
40515752 TTTGTGGTTAAATAAGCTCTTAACCTAT
1 TTTGTGGTTAAACAAGCACTCAACCTAT
40515780 GATTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTGTGGTTAAACAAGCACTCAACCTATT
Found at i:40516616 original size:29 final size:29
Alignment explanation
Indices: 40516584--40516704 Score: 104
Period size: 29 Copynumber: 4.1 Consensus size: 29
40516574 GTCAAAATTT
*
40516584 TTTTCAAAATTATATTTTTAACCCCTAAAT
1 TTTTCAAAATTATA-TTTTAACCCCTAAAG
* *
40516614 TTTTCCAAAATTATATTTTAA-CCCTTAAC
1 TTTT-CAAAATTATATTTTAACCCCTAAAG
* * * *
40516643 TTTTTAAAATTACATTTTGA-CCTTAAA-
1 TTTTCAAAATTATATTTTAACCCCTAAAG
* *
40516670 TATTCTCAAAATTATACTTTAACCCCAAAAG
1 T-TT-TCAAAATTATATTTTAACCCCTAAAG
40516701 TTTT
1 TTTT
40516705 GCTGTGTTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 20 0.27
29 24 0.33
30 17 0.23
31 11 0.15
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (29 bp):
TTTTCAAAATTATATTTTAACCCCTAAAG
Found at i:40516623 original size:31 final size:30
Alignment explanation
Indices: 40516583--40516704 Score: 110
Period size: 30 Copynumber: 4.2 Consensus size: 30
40516573 GGTCAAAATT
40516583 TTTTTCAAAATTATATTTTTAACCCCTAAA
1 TTTTTCAAAATTATATTTTTAACCCCTAAA
* *
40516613 TTTTTCCAAAATTATA-TTTTAACCCTTAAC
1 TTTTT-CAAAATTATATTTTTAACCCCTAAA
* * *
40516643 TTTTT-AAAATTACA-TTTTGA-CCTTAAA
1 TTTTTCAAAATTATATTTTTAACCCCTAAA
* * *
40516670 TATTCTCAAAATTATA-CTTTAACCCCAAAA
1 T-TTTTCAAAATTATATTTTTAACCCCTAAA
*
40516700 GTTTT
1 TTTTT
40516705 GCTGTGTTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
27 7 0.09
28 16 0.21
29 15 0.20
30 27 0.36
31 10 0.13
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTTTCAAAATTATATTTTTAACCCCTAAA
Found at i:40517085 original size:25 final size:25
Alignment explanation
Indices: 40517057--40517104 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
40517047 CAAGCAAGCA
*
40517057 AAAGAGGAAAAAA-AAGAGAAAGAGT
1 AAAGAAGAAAAAAGAAGA-AAAGAGT
40517082 AAAGAAGAAAAAAGAAGAAAAGA
1 AAAGAAGAAAAAAGAAGAAAAGA
40517105 AGGAGAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (25 bp):
AAAGAAGAAAAAAGAAGAAAAGAGT
Found at i:40517113 original size:18 final size:18
Alignment explanation
Indices: 40517057--40517113 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
40517047 CAAGCAAGCA
* * *
40517057 AAAGAGGAAAAAAAAGAG
1 AAAGAAGAAAAGAAGGAG
* * *
40517075 AAAG-AGTAAAGAAGAAA
1 AAAGAAGAAAAGAAGGAG
40517092 AAAGAAGAAAAGAAGGAG
1 AAAGAAGAAAAGAAGGAG
40517110 AAAG
1 AAAG
40517114 GAGAGCTCCA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (18 bp):
AAAGAAGAAAAGAAGGAG
Found at i:40517233 original size:13 final size:13
Alignment explanation
Indices: 40517197--40517244 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
40517187 CTGCCGAAGG
40517197 AGAAGAA-AAA-A
1 AGAAGAAGAAAGA
*
40517208 AGAAGAAAAAAGA
1 AGAAGAAGAAAGA
*
40517221 AGAAGAAGGAAGA
1 AGAAGAAGAAAGA
*
40517234 GGAAGAAGAAA
1 AGAAGAAGAAA
40517245 TAAAAAAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 21 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAAGA
Found at i:40517284 original size:11 final size:11
Alignment explanation
Indices: 40517203--40517293 Score: 53
Period size: 11 Copynumber: 8.3 Consensus size: 11
40517193 AAGGAGAAGA
40517203 AAAAAAG-AAG
1 AAAAAAGAAAG
40517213 AAAAAAG-AAG
1 AAAAAAGAAAG
* *
40517223 AAGAAGGAAGAG
1 AAAAAAGAA-AG
* * *
40517235 GAAGAAGAAAT
1 AAAAAAGAAAG
**
40517246 AAAAAA-AGGGG
1 AAAAAAGA-AAG
*
40517257 AAAGAAAAAAAG
1 AAA-AAAGAAAG
40517269 AAAAAAGAAAG
1 AAAAAAGAAAG
*
40517280 CAAAAAGAAAG
1 AAAAAAGAAAG
40517291 AAA
1 AAA
40517294 TTTTTTTAAC
Statistics
Matches: 59, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
10 16 0.27
11 28 0.47
12 14 0.24
13 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.01
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:40517577 original size:14 final size:13
Alignment explanation
Indices: 40517553--40517627 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 13
40517543 GGCGGCCCAG
40517553 AAGAGAGGAAAAAA
1 AAGA-AGGAAAAAA
40517567 ATAGAAGGAAAAAA
1 A-AGAAGGAAAAAA
*
40517581 AAGAAAAAAGAAAAAGA
1 AAG---AAGGAAAAA-A
* *
40517598 AAAAAGAAAAAAA
1 AAGAAGGAAAAAA
40517611 AAGAA-GAAAAAA
1 AAGAAGGAAAAAA
*
40517623 GAGAA
1 AAGAA
40517628 AAAAAGGGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
12 10 0.20
13 7 0.14
14 18 0.37
15 3 0.06
16 8 0.16
17 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (13 bp):
AAGAAGGAAAAAA
Found at i:40517589 original size:7 final size:7
Alignment explanation
Indices: 40517577--40517630 Score: 76
Period size: 7 Copynumber: 7.9 Consensus size: 7
40517567 ATAGAAGGAA
40517577 AAAAAAG
1 AAAAAAG
40517584 AAAAAAG
1 AAAAAAG
40517591 -AAAAAG
1 AAAAAAG
40517597 AAAAAAG
1 AAAAAAG
40517604 AAAAAA-
1 AAAAAAG
*
40517610 AAAGAAG
1 AAAAAAG
40517617 AAAAAAG
1 AAAAAAG
40517624 AGAAAAA
1 A-AAAAA
40517631 AAGGGTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 11 0.26
7 26 0.62
8 5 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:40517594 original size:13 final size:13
Alignment explanation
Indices: 40517578--40517621 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
40517568 TAGAAGGAAA
40517578 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
40517591 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
40517604 AAAAA-AAAAGAAG
1 AAAAAGAAAA-AAG
40517617 AAAAA
1 AAAAA
40517622 AGAGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.13
13 26 0.87
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:40517612 original size:10 final size:10
Alignment explanation
Indices: 40517575--40517633 Score: 75
Period size: 10 Copynumber: 5.9 Consensus size: 10
40517565 AAATAGAAGG
40517575 AAAAAAAAGA
1 AAAAAAAAGA
40517585 AAAAAGAAA-A
1 AAAAA-AAAGA
*
40517595 AGAAAAAAGA
1 AAAAAAAAGA
40517605 AAAAAAAAGA
1 AAAAAAAAGA
*
40517615 AGAAAAAAGA
1 AAAAAAAAGA
*
40517625 GAAAAAAAG
1 AAAAAAAAG
40517634 GGTTCAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 3 0.07
10 36 0.86
11 3 0.07
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:40517622 original size:13 final size:13
Alignment explanation
Indices: 40517564--40517632 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 13
40517554 AGAGAGGAAA
* *
40517564 AAAATAGAAGGAA
1 AAAAAAGAAGAAA
40517577 AAAAAAGAA-AAA
1 AAAAAAGAAGAAA
*
40517589 AGAAAAAGAAAAAA
1 A-AAAAAGAAGAAA
* *
40517603 GAAAAAAAAAGAAG
1 -AAAAAAGAAGAAA
40517617 AAAAAAG-AGAAA
1 AAAAAAGAAGAAA
40517629 AAAA
1 AAAA
40517633 GGGTTCAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
12 11 0.24
13 22 0.48
14 12 0.26
15 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:40517808 original size:17 final size:17
Alignment explanation
Indices: 40517780--40517820 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40517770 ATATTTTTGT
40517780 ATTTATATTTTTAATTTA
1 ATTTA-ATTTTTAATTTA
*
40517798 ATTTAATTTTTATTTTA
1 ATTTAATTTTTAATTTA
*
40517815 TTTTAA
1 ATTTAA
40517821 GTAATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTAATTTTTAATTTA
Found at i:40518162 original size:17 final size:17
Alignment explanation
Indices: 40518118--40518217 Score: 64
Period size: 17 Copynumber: 5.7 Consensus size: 17
40518108 AAAATTCATT
*
40518118 TTTTCAAAATATTCCCCTG
1 TTTTCAAAAT-TT-CCATG
40518137 -TTTCAAAAATTTCCATG
1 TTTTC-AAAATTTCCATG
*
40518154 TTTTCAAAATTTTCATG
1 TTTTCAAAATTTCCATG
* * *
40518171 TTTTTAAAAATT-CGTG
1 TTTTCAAAATTTCCATG
40518187 -TTT-AAAATTTTTTCCATG
1 TTTTCAAAA---TTTCCATG
40518205 TTTTCACAAATTT
1 TTTTCA-AAATTT
40518218 TCGTGTTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
14 4 0.06
15 3 0.05
16 3 0.05
17 27 0.42
18 16 0.25
19 8 0.12
20 1 0.02
21 3 0.05
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (17 bp):
TTTTCAAAATTTCCATG
Found at i:40518259 original size:30 final size:30
Alignment explanation
Indices: 40518194--40518258 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
40518184 GTGTTTAAAA
40518194 TTTTTTCCATGTTTTCACAAATTTTCGTGT
1 TTTTTTCCATGTTTTCACAAATTTTCGTGT
*
40518224 TTTTTTCCATGTTTTCACAAATTTT-TTGT
1 TTTTTTCCATGTTTTCACAAATTTTCGTGT
40518253 TTTTTT
1 TTTTTT
40518259 TTTAAATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.15, C:0.14, G:0.08, T:0.63
Consensus pattern (30 bp):
TTTTTTCCATGTTTTCACAAATTTTCGTGT
Found at i:40518330 original size:17 final size:17
Alignment explanation
Indices: 40518310--40518548 Score: 54
Period size: 18 Copynumber: 13.2 Consensus size: 17
40518300 CCGGTGCATC
40518310 AAAAATTTGTGTTTTTAA
1 AAAAATTTGTGTTTTT-A
* *
40518328 AAAAATTCT-TCGTGTTTC
1 AAAAATT-TGT-GTTTTTA
*
40518346 AAAAATTTCCGTGTTTTCA
1 AAAAATTT--GTGTTTTTA
*
40518365 AAAAATTTTCGTGTTTTCA
1 AAAAA-TTT-GTGTTTTTA
* * * *
40518384 AAAAAATTCTCGTGTTTC
1 AAAAATTTGT-GTTTTTA
* *
40518402 ACAAATTTCCGTG-TTTTC
1 AAAAATTT--GTGTTTTTA
* *
40518420 AAAAATTTTTGTGTTTCA
1 AAAAATTTGTGT-TTTTA
** **
40518438 AACATTTTTGTGTTTCAAAA
1 AA-AAATTTGTGTTT--TTA
* *
40518458 AAAAAATTGTGTTTTCA
1 AAAAATTTGTGTTTTTA
* *
40518475 AAAAATTTCTCGTGTTT-
1 AAAAATTTGT-GTTTTTA
* *
40518492 CAAAATTATCGTGTTTTCA
1 AAAAATT-T-GTGTTTTTA
40518511 AAAAATTTCGTG-TTTTA
1 AAAAATTT-GTGTTTTTA
* * *
40518528 AGAATTTTCGTGTTTCTA
1 AAAAATTT-GTGTTTTTA
40518546 AAA
1 AAA
40518549 TTCTCGTGTT
Statistics
Matches: 160, Mismatches: 42, Indels: 38
0.67 0.17 0.16
Matches are distributed among these distances:
16 2 0.01
17 31 0.19
18 65 0.41
19 54 0.34
20 8 0.05
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (17 bp):
AAAAATTTGTGTTTTTA
Found at i:40518348 original size:36 final size:34
Alignment explanation
Indices: 40518308--40518568 Score: 161
Period size: 36 Copynumber: 7.3 Consensus size: 34
40518298 TTCCGGTGCA
40518308 TCAAAAATTTGTGTTTTTAAAAAAATTCTTCGTGTT
1 TCAAAAATTTGTGTTTTT-AAAAAATT-TTCGTGTT
*
40518344 TCAAAAATTTCCGTGTTTTCAAAAAATTTTCGTGTTT
1 TCAAAAATTT--GTGTTTTTAAAAAATTTTCGTG-TT
* * * * * *
40518381 TCAAAAAAATTCTCGTGTTTCACAAATTTCCGTGTTT
1 TC-AAAAATTTGT-GTTTTTAAAAAATTTTCGTG-TT
* * * * *
40518418 TCAAAAATTTTTGTGTTTCAAACATTTTTGTGTT
1 TCAAAAATTTGTGTTTTTAAAAAATTTTCGTGTT
* *
40518452 TCAAAAAAAAAATTGTGTTTTCAAAAAATTTCTCGTGTT
1 TC----AAAAATTTGTGTTTTTAAAAAATTT-TCGTGTT
*
40518491 TC-AAAATTATCGTGTTTTCAAAAAA-TTTCGTGTT
1 TCAAAAATT-T-GTGTTTTTAAAAAATTTTCGTGTT
* * * *
40518525 TTAAGAATTTTCGTGTTTCT--AAAATTCTCGTGTT
1 TCAA-AAATTT-GTGTTTTTAAAAAATTTTCGTGTT
*
40518559 TTAAAAATTT
1 TCAAAAATTT
40518569 TCCATGTTTT
Statistics
Matches: 182, Mismatches: 28, Indels: 33
0.75 0.12 0.14
Matches are distributed among these distances:
33 9 0.05
34 29 0.16
35 28 0.15
36 43 0.24
37 32 0.18
38 33 0.18
39 8 0.04
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (34 bp):
TCAAAAATTTGTGTTTTTAAAAAATTTTCGTGTT
Found at i:40518451 original size:91 final size:88
Alignment explanation
Indices: 40518328--40518565 Score: 277
Period size: 90 Copynumber: 2.6 Consensus size: 88
40518318 GTGTTTTTAA
*
40518328 AAAAATTCTTCGTGTTTCAAAAATTTCCGTGTTTTCAAAAAATTTTCGTGTTTTCAAAAAAATTC
1 AAAAATT-TTCGTGTTTC-AAAATTTTCGTG-TTTCAAAAAATTTTCGTGTTTTCAAAAAAATTC
40518393 TCGTGTTTCACAAATT-TCCGTGTTTTC
63 TCGTGTTTCA-AAATTAT-CGTGTTTTC
* * ** *
40518420 AAAAATTTTTGTGTTTCAAACATTTTTGTGTTTCAAAAAAAAAATT-GTGTTTTCAAAAAATTTC
1 AAAAATTTTCGTGTTTCAAA-ATTTTCGTGTTTC--AAAAAATTTTCGTGTTTTCAAAAAAATTC
40518484 TCGTGTTTCAAAATTATCGTGTTTTC
63 TCGTGTTTCAAAATTATCGTGTTTTC
* * * *
40518510 AAAAAATTTCGTGTTTTAAGAATTTTCGTGTTTC-TAAAATTCTCGTGTTTT-AAAAA
1 AAAAATTTTCGTGTTTCAA-AATTTTCGTGTTTCAAAAAATTTTCGTGTTTTCAAAAA
40518566 TTTTCCATGT
Statistics
Matches: 126, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
87 10 0.08
88 7 0.06
90 49 0.39
91 45 0.36
92 15 0.12
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (88 bp):
AAAAATTTTCGTGTTTCAAAATTTTCGTGTTTCAAAAAATTTTCGTGTTTTCAAAAAAATTCTCG
TGTTTCAAAATTATCGTGTTTTC
Found at i:40518550 original size:17 final size:17
Alignment explanation
Indices: 40518328--40518584 Score: 203
Period size: 17 Copynumber: 14.3 Consensus size: 17
40518318 GTGTTTTTAA
40518328 AAAAATTCTTCGTGTTTC
1 AAAAATT-TTCGTGTTTC
*
40518346 AAAAATTTCCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
40518364 AAAAAATTTTCGTGTTTTC
1 -AAAAATTTTCGTG-TTTC
*
40518383 AAAAAAATTCTCGTGTTTC
1 --AAAAATTTTCGTGTTTC
* *
40518402 ACAAATTTCCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
40518420 AAAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
40518437 AAACATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
**
40518454 AAAAAAAAAATT-GTGTTTTC
1 ---AAAAATTTTCGTG-TTTC
40518474 AAAAAATTTCTCGTGTTTC
1 -AAAAATTT-TCGTGTTTC
*
40518493 -AAAATTATCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
40518510 AAAAAATTTCGTGTTTT
1 AAAAATTTTCGTGTTTC
*
40518527 AAGAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * *
40518544 TAAAATTCTCGTGTTTT
1 AAAAATTTTCGTGTTTC
*
40518561 AAAAATTTTCCATGTTTTC
1 AAAAATTTT-CGTG-TTTC
40518580 AAAAA
1 AAAAA
40518585 AAATTGTTTT
Statistics
Matches: 195, Mismatches: 30, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
16 5 0.03
17 82 0.42
18 45 0.23
19 37 0.19
20 26 0.13
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:40519705 original size:9 final size:9
Alignment explanation
Indices: 40519687--40519735 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
40519677 TTTGGTTAAA
40519687 AATTAACCG
1 AATTAACCG
*
40519696 AATTATCCG
1 AATTAACCG
*
40519705 AATTAACTG
1 AATTAACCG
40519714 AATT-ACTCG
1 AATTAAC-CG
40519723 AATTAACCG
1 AATTAACCG
40519732 AATT
1 AATT
40519736 GAATCACTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 2 0.06
9 30 0.88
10 2 0.06
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
AATTAACCG
Found at i:40519710 original size:18 final size:18
Alignment explanation
Indices: 40519687--40519735 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
40519677 TTTGGTTAAA
40519687 AATTAACCGAATTA-TCCG
1 AATTAACCGAATTACT-CG
*
40519705 AATTAACTGAATTACTCG
1 AATTAACCGAATTACTCG
40519723 AATTAACCGAATT
1 AATTAACCGAATT
40519736 GAATCACTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (18 bp):
AATTAACCGAATTACTCG
Found at i:40522980 original size:14 final size:15
Alignment explanation
Indices: 40522956--40522984 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40522946 TATAAATTTT
40522956 AATATTCTTTTTAAA
1 AATATTCTTTTTAAA
40522971 AATA-TCTTTTTAAA
1 AATATTCTTTTTAAA
40522985 TTTTTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTCTTTTTAAA
Found at i:40527236 original size:25 final size:27
Alignment explanation
Indices: 40527208--40527259 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
40527198 ATTACAACAA
* *
40527208 GGAAAACATGTACA-TATT-ATAAATT
1 GGAAAACATATAAATTATTAATAAATT
40527233 GGAAAACATATAAATTATTAATAAATT
1 GGAAAACATATAAATTATTAATAAATT
40527260 AAACTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 4 0.17
27 7 0.30
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.33
Consensus pattern (27 bp):
GGAAAACATATAAATTATTAATAAATT
Found at i:40532220 original size:2 final size:2
Alignment explanation
Indices: 40532213--40532244 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
40532203 ATTTGTGGTT
40532213 TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40532245 GCATCAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40536143 original size:23 final size:24
Alignment explanation
Indices: 40536113--40536159 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
40536103 AAATTAAATC
40536113 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
40536136 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
40536160 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:40536159 original size:24 final size:23
Alignment explanation
Indices: 40536113--40536178 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 23
40536103 AAATTAAATC
* *
40536113 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGCAATATCATATCT
40536136 TCTAAGATTGCATATATCATA---
1 TCTAAGATTGCA-ATATCATATCT
40536157 TCTAAGATTGC-ATATCATATCT
1 TCTAAGATTGCAATATCATATCT
40536179 AAAACTGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 8 0.22
21 11 0.30
23 11 0.30
24 7 0.19
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
TCTAAGATTGCAATATCATATCT
Found at i:40536162 original size:21 final size:21
Alignment explanation
Indices: 40536136--40536190 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
40536126 AATCATATCT
40536136 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
40536157 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
* *
40536176 TCTAAAACTGCATAT
1 TCTAAGATTGCATAT
40536191 CCTCAACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:40540747 original size:28 final size:30
Alignment explanation
Indices: 40540697--40540763 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 30
40540687 AATGTGTTTA
*
40540697 AATAAAATAATGTTAAGTTTTTTTATATTT
1 AATAAAATAATGTTAAGCTTTTTTATATTT
40540727 AA-AAAATAATGTTAA-CTTTTTTATATTT
1 AATAAAATAATGTTAAGCTTTTTTATATTT
40540755 AATAAAATA
1 AATAAAATA
40540764 TATATAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 14 0.40
29 19 0.54
30 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (30 bp):
AATAAAATAATGTTAAGCTTTTTTATATTT
Found at i:40543991 original size:14 final size:16
Alignment explanation
Indices: 40543972--40544004 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40543962 ACCCCTTTTA
40543972 TTTTT-ATTT-TTATT
1 TTTTTAATTTCTTATT
40543986 TTTTTAATTTCTTATT
1 TTTTTAATTTCTTATT
40544002 TTT
1 TTT
40544005 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 4 0.24
16 8 0.47
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTAATTTCTTATT
Found at i:40545538 original size:7 final size:7
Alignment explanation
Indices: 40545513--40545570 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
40545503 ACATTGAACA
40545513 TTAAACC
1 TTAAACC
*
40545520 TCAAACC
1 TTAAACC
* *
40545527 CTAAATC
1 TTAAACC
*
40545534 TTAAATC
1 TTAAACC
40545541 TTAAACC
1 TTAAACC
40545548 TTAAACC
1 TTAAACC
*
40545555 CTAAA-C
1 TTAAACC
40545561 TTAAAACC
1 TT-AAACC
40545569 TT
1 TT
40545571 GCATCTTGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
6 2 0.05
7 36 0.88
8 3 0.07
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAACC
Found at i:40545544 original size:28 final size:27
Alignment explanation
Indices: 40545513--40545565 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
40545503 ACATTGAACA
40545513 TTAAACCTCAAACCCTAAATCTTAAATC
1 TTAAACCTCAAACCCTAAA-CTTAAATC
*
40545541 TTAAACCTTAAACCCTAAACTTAAA
1 TTAAACCTCAAACCCTAAACTTAAA
40545566 ACCTTGCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (27 bp):
TTAAACCTCAAACCCTAAACTTAAATC
Found at i:40545568 original size:14 final size:14
Alignment explanation
Indices: 40545514--40545565 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
40545504 CATTGAACAT
*
40545514 TAAACCTCAAACCC
1 TAAACCTTAAACCC
* * *
40545528 TAAATCTTAAATCT
1 TAAACCTTAAACCC
40545542 TAAACCTTAAACCC
1 TAAACCTTAAACCC
40545556 TAAA-CTTAAA
1 TAAACCTTAAA
40545566 ACCTTGCATC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 6 0.19
14 25 0.81
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:40547071 original size:16 final size:17
Alignment explanation
Indices: 40547030--40547071 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
40547020 AAATTTCCAT
40547030 TTAATTAAATGCTAAAA
1 TTAATTAAATGCTAAAA
40547047 -TAACTTAAA-GCTAAAA
1 TTAA-TTAAATGCTAAAA
*
40547063 TTAAATAAA
1 TTAATTAAA
40547072 ATTTCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (17 bp):
TTAATTAAATGCTAAAA
Found at i:40550988 original size:14 final size:13
Alignment explanation
Indices: 40550936--40550990 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
40550926 TTTGCCCTCC
40550936 TTTCTTTATTTA-
1 TTTCTTTATTTAT
*
40550948 TTTCTCTATTTAT
1 TTTCTTTATTTAT
*
40550961 TTAT-TATTAGTTAT
1 TT-TCT-TTATTTAT
40550975 TTTCTTTTATTTAT
1 TTTC-TTTATTTAT
40550989 TT
1 TT
40550991 CTTGTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 11 0.32
13 4 0.12
14 18 0.53
15 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTCTTTATTTAT
Found at i:40553483 original size:14 final size:14
Alignment explanation
Indices: 40553460--40553490 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40553450 TGTCGCGTTC
*
40553460 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
40553474 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
40553488 TTA
1 TTA
40553491 AAACAATTCC
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:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:40555614 original size:27 final size:28
Alignment explanation
Indices: 40555577--40555635 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
40555567 CTAAGATGAC
* *
40555577 TATATAAAAATTTTCAATAATAAAA-AA
1 TATATAAAAATATTAAATAATAAAATAA
*
40555604 TATATAAAAATATTAAATATTAAAATAA
1 TATATAAAAATATTAAATAATAAAATAA
40555632 TATA
1 TATA
40555636 ATATAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
TATATAAAAATATTAAATAATAAAATAA
Found at i:40557025 original size:3 final size:3
Alignment explanation
Indices: 40557010--40557052 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
40557000 TGAGCAACTC
* *
40557010 TTG TTG TTA TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
40557053 CATCATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.05, C:0.00, G:0.28, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:40558499 original size:31 final size:31
Alignment explanation
Indices: 40558464--40558529 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
40558454 ACAAAATGGT
*
40558464 CACTGAACTATTCAAAAGTTTTCATTTAAGC
1 CACTGAACAATTCAAAAGTTTTCATTTAAGC
* * *
40558495 CACTGAACAATTCAGAAGTTTTTATTTAAGT
1 CACTGAACAATTCAAAAGTTTTCATTTAAGC
40558526 CACT
1 CACT
40558530 AGGCTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (31 bp):
CACTGAACAATTCAAAAGTTTTCATTTAAGC
Found at i:40567637 original size:59 final size:59
Alignment explanation
Indices: 40567566--40567698 Score: 162
Period size: 62 Copynumber: 2.2 Consensus size: 59
40567556 ATCACTTTAA
* * * * *
40567566 TATTAAATTAATATAATATTTA-T-CAAGATAAATAATAGATTAAATTTAATTTTAAATC
1 TATTAAAATAATATAATATTTACTGCAAGATAAACAATAAATTAAATTAAATATTAAA-C
* *
40567624 TTATTAAAATAATATAATGTTTATCTGCAAGATAAACATTAAATTAAATTAAATATTAAAC
1 -TATTAAAATAATATAATATTTA-CTGCAAGATAAACAATAAATTAAATTAAATATTAAAC
40567685 TATTAAAATAATAT
1 TATTAAAATAATAT
40567699 TATTTTTGGA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 20 0.31
60 14 0.22
61 2 0.03
62 28 0.44
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (59 bp):
TATTAAAATAATATAATATTTACTGCAAGATAAACAATAAATTAAATTAAATATTAAAC
Found at i:40572642 original size:19 final size:21
Alignment explanation
Indices: 40572611--40572654 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
40572601 AAAAATACTC
40572611 AAAA-AAATAATTTTTAAT-A
1 AAAATAAATAATTTTTAATGA
*
40572630 AAAATAAAT-ATTTTTTATGA
1 AAAATAAATAATTTTTAATGA
40572650 AAAAT
1 AAAAT
40572655 TATAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATAAATAATTTTTAATGA
Found at i:40575111 original size:16 final size:16
Alignment explanation
Indices: 40575090--40575121 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40575080 GTACCACCCA
40575090 TGTGACCATTGTCATC
1 TGTGACCATTGTCATC
40575106 TGTGACCATTGTCATC
1 TGTGACCATTGTCATC
40575122 CGATACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (16 bp):
TGTGACCATTGTCATC
Found at i:40575244 original size:51 final size:52
Alignment explanation
Indices: 40575131--40575312 Score: 230
Period size: 51 Copynumber: 3.6 Consensus size: 52
40575121 CCGATACATG
* * * * *
40575131 TAGTAGCCTACACATAGTACTACACACGTGATC-AAG-CTTTCCAGTTCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAAGTCTATCCAGTACACA
*
40575181 TAGTAGCCTGCACATAGTACTACACACGTAACCAAAGTC-ATCCAGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAAGTCTATCCAGTACACA
* * *
40575232 TAGTAGCCTGCACATAGTACTACACATGTGACCATCA-TCTATCGA-TACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-AAGTCTATCCAGTACACA
*
40575283 TAGTAGCCTGCACTTAGTACTACACACGTG
1 TAGTAGCCTGCACATAGTACTACACACGTG
40575313 TTCATAAGTA
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
50 30 0.26
51 80 0.69
52 6 0.05
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCAAAGTCTATCCAGTACACA
Found at i:40575257 original size:26 final size:26
Alignment explanation
Indices: 40575226--40575308 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
40575216 AGTCATCCAG
40575226 TACACATAGTAGCCTGCACATAGTAC
1 TACACATAGTAGCCTGCACATAGTAC
*
40575252 TACACAT-GT-GACCAT-CATCTATCG-A-
1 TACACATAGTAG-CC-TGCA-C-ATAGTAC
*
40575277 TACACATAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACATAGTAC
40575303 TACACA
1 TACACA
40575309 CGTGTTCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 18
0.68 0.05 0.27
Matches are distributed among these distances:
24 3 0.07
25 16 0.36
26 22 0.49
27 4 0.09
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (26 bp):
TACACATAGTAGCCTGCACATAGTAC
Found at i:40579117 original size:19 final size:18
Alignment explanation
Indices: 40579075--40579118 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
40579065 TTAATATTAC
*
40579075 ACATTTTAATTTCACATT
1 ACATTTTAATTTCACACT
40579093 ACATTTTAATTTTCACACT
1 ACATTTTAA-TTTCACACT
*
40579112 ATATTTT
1 ACATTTT
40579119 GCTTATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (18 bp):
ACATTTTAATTTCACACT
Found at i:40579889 original size:45 final size:46
Alignment explanation
Indices: 40579811--40579936 Score: 186
Period size: 46 Copynumber: 2.8 Consensus size: 46
40579801 TACATATGAT
* * *
40579811 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGACTAA
*
40579854 CACTTATCACTTTGTCACTTGATTAGATAAGTGTAGCTAAGACTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGACTAA
*
40579900 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
40579937 ACTTATCNNN
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 10 0.14
44 5 0.07
45 19 0.26
46 40 0.54
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGACTAA
Found at i:40582400 original size:14 final size:13
Alignment explanation
Indices: 40582383--40582419 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
40582373 GTTTCTCTCA
40582383 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
40582396 TTTTTCTTTCTTTC
1 TTTTTC-TTCTTTC
40582410 TTTTTTCTTC
1 -TTTTTCTTC
40582420 AATTTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:40582404 original size:10 final size:11
Alignment explanation
Indices: 40582385--40582418 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40582375 TTCTCTCATT
40582385 TTTCTTCTTTC
1 TTTCTTCTTTC
40582396 TTT-TTCTTTC
1 TTTCTTCTTTC
*
40582406 TTTCTTTTTTC
1 TTTCTTCTTTC
40582417 TT
1 TT
40582419 CAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:40584185 original size:20 final size:19
Alignment explanation
Indices: 40584129--40584183 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
40584119 ACAAAAAATT
*
40584129 AAATTCAAAATAATTT-TTA
1 AAATTCAAAAT-ATTTATAA
40584148 AAATTCAAAATATTTATAA
1 AAATTCAAAATATTTATAA
*
40584167 AAATTCCAAA-ATTTATA
1 AAATTCAAAATATTTATA
40584184 TATTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTCAAAATATTTATAA
Found at i:40584213 original size:18 final size:18
Alignment explanation
Indices: 40584147--40584214 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 18
40584137 AATAATTTTT
40584147 AAAA-TTCAAAATATTTATA
1 AAAATTTCAAAA-A-TTATA
* *
40584166 AAAATTCCAAAATTTAT-
1 AAAATTTCAAAAATTATA
* * *
40584183 ATATTTTAAAAAAATTATA
1 AAAATTT-CAAAAATTATA
40584202 AAAATTTCAAAAA
1 AAAATTTCAAAAA
40584215 AAATCTATAA
Statistics
Matches: 36, Mismatches: 10, Indels: 7
0.68 0.19 0.13
Matches are distributed among these distances:
17 4 0.11
18 17 0.47
19 9 0.25
20 6 0.17
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTTCAAAAATTATA
Found at i:40584213 original size:19 final size:18
Alignment explanation
Indices: 40584129--40584215 Score: 66
Period size: 19 Copynumber: 4.7 Consensus size: 18
40584119 ACAAAAAATT
* *
40584129 AAATTCAAAATAATTTTTA
1 AAATTCAAAA-AATTATAA
*
40584148 AAATTCAAAATATTTATAA
1 AAATTCAAAA-AATTATAA
* * *
40584167 AAATTCCAAAATTTATAT
1 AAATTCAAAAAATTATAA
** *
40584185 ATTTTAAAAAAATTATAA
1 AAATTCAAAAAATTATAA
40584203 AAATTTCAAAAAA
1 AAA-TTCAAAAAA
40584216 AATCTATAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
18 20 0.38
19 33 0.62
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTCAAAAAATTATAA
Found at i:40584234 original size:21 final size:21
Alignment explanation
Indices: 40584190--40584234 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40584180 TATATATTTT
* *
40584190 AAAAAAATTATAAAAATTTCA
1 AAAAAAATTATAAAAATATAA
40584211 AAAAAAATCTAT-AAAATATAA
1 AAAAAAAT-TATAAAAATATAA
40584232 AAA
1 AAA
40584235 GAAAGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAAATTATAAAAATATAA
Found at i:40592418 original size:23 final size:24
Alignment explanation
Indices: 40592378--40592425 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
40592368 CAGTACAAAT
*
40592378 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
40592402 AACAAAAACAGCA-CAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
40592425 A
1 A
40592426 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.71, C:0.19, G:0.04, T:0.06
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:40592588 original size:18 final size:20
Alignment explanation
Indices: 40592565--40592601 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
40592555 AAACACATTT
40592565 TTCAAATT-T-TTATTTTTA
1 TTCAAATTCTATTATTTTTA
40592583 TTCAAATTCTATTATTTTT
1 TTCAAATTCTATTATTTTT
40592602 TGGGCGGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (20 bp):
TTCAAATTCTATTATTTTTA
Found at i:40597027 original size:22 final size:24
Alignment explanation
Indices: 40596991--40597037 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
40596981 GTCCTCAAGA
40596991 TCGAAGATCTTTATTTAA-TTTCTT
1 TCGAAGATCTTTA-TTAAGTTTCTT
40597015 TCGAAG-T-TTTATTAAGTTTCTT
1 TCGAAGATCTTTATTAAGTTTCTT
40597037 T
1 T
40597038 ATATCTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 11 0.50
23 1 0.05
24 6 0.27
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (24 bp):
TCGAAGATCTTTATTAAGTTTCTT
Found at i:40599489 original size:17 final size:18
Alignment explanation
Indices: 40599452--40599494 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
40599442 TTTATATTTT
* *
40599452 TAAAAATATTAATTATTA
1 TAAAAATATTAAGTATGA
40599470 TAAAAATATT-AGTATGA
1 TAAAAATATTAAGTATGA
40599487 TAAAAATA
1 TAAAAATA
40599495 ATTTCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
TAAAAATATTAAGTATGA
Found at i:40600461 original size:18 final size:18
Alignment explanation
Indices: 40600410--40600464 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
40600400 TTTTTTTTGC
* *
40600410 TATAATTTTATAAAATACA
1 TATAATTTTTTAATATA-A
40600429 TA-AATTATTTT--TATAA
1 TATAATT-TTTTAATATAA
40600445 TATAATTTTTTAATATAA
1 TATAATTTTTTAATATAA
40600463 TA
1 TA
40600465 ATCTCAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 11 0.37
19 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAATTTTTTAATATAA
Found at i:40602394 original size:12 final size:12
Alignment explanation
Indices: 40602374--40602420 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
40602364 TTCCTAAATC
40602374 AGAGACCAAACA
1 AGAGACCAAACA
*
40602386 AGAGGCCAAACA
1 AGAGACCAAACA
* *
40602398 GGAGACCAAACC
1 AGAGACCAAACA
40602410 AGAGACCAAAC
1 AGAGACCAAAC
40602421 CGGAAACTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.51, C:0.28, G:0.21, T:0.00
Consensus pattern (12 bp):
AGAGACCAAACA
Found at i:40602402 original size:24 final size:24
Alignment explanation
Indices: 40602375--40602420 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
40602365 TCCTAAATCA
*
40602375 GAGACCAAACAAGAGGCCAAACAG
1 GAGACCAAACAAGAGACCAAACAG
*
40602399 GAGACCAAACCAGAGACCAAAC
1 GAGACCAAACAAGAGACCAAAC
40602421 CGGAAACTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.28, G:0.22, T:0.00
Consensus pattern (24 bp):
GAGACCAAACAAGAGACCAAACAG
Found at i:40604882 original size:18 final size:19
Alignment explanation
Indices: 40604851--40604887 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40604841 TCAAACTATG
40604851 AAAACCTATTTTTACATTT
1 AAAACCTATTTTTACATTT
*
40604870 AAAACCT-TTTTTAGATTT
1 AAAACCTATTTTTACATTT
40604888 TCCAGTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.49
Consensus pattern (19 bp):
AAAACCTATTTTTACATTT
Found at i:40622295 original size:19 final size:19
Alignment explanation
Indices: 40622271--40622314 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
40622261 TCATTAAATC
40622271 AACTCTTAAACCCAGATTA
1 AACTCTTAAACCCAGATTA
*
40622290 AACTCTTAAACCCGGATTA
1 AACTCTTAAACCCAGATTA
*
40622309 AGCTCT
1 AACTCT
40622315 AAAAAGCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (19 bp):
AACTCTTAAACCCAGATTA
Found at i:40629773 original size:44 final size:43
Alignment explanation
Indices: 40629716--40629844 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 43
40629706 ATAGGATTTT
*
40629716 GATTTGAGATTTCGTGTAAGACCACGTCTGGGACATTGGTATC
1 GATTTGAGATTTCGTGTAAGACCACGTCTGGGACATTGGCATC
* * *
40629759 GATTTGAGACTTTCGTGTAAAACC-CTGTCTAGGACAGTGGCATC
1 GATTTGAGA-TTTCGTGTAAGACCAC-GTCTGGGACATTGGCATC
* * *
40629803 GATATTTA-ATTACATGTAAGACCACGTCTGGGACATTGGCAT
1 GAT-TTGAGATTTCGTGTAAGACCACGTCTGGGACATTGGCAT
40629845 TGTACGAGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 36 0.50
44 33 0.46
45 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
GATTTGAGATTTCGTGTAAGACCACGTCTGGGACATTGGCATC
Found at i:40633868 original size:10 final size:10
Alignment explanation
Indices: 40633853--40633912 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
40633843 TATTCTTTAG
40633853 AATTTTTATA
1 AATTTTTATA
40633863 AATTTTT-TA
1 AATTTTTATA
*
40633872 AA---ATATA
1 AATTTTTATA
*
40633879 AATTTTTA-G
1 AATTTTTATA
40633888 AATTTTTATA
1 AATTTTTATA
40633898 AATATTTTA-A
1 AAT-TTTTATA
40633908 AATTT
1 AATTT
40633913 AAAAATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
6 1 0.03
7 4 0.10
9 14 0.35
10 16 0.40
11 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
AATTTTTATA
Found at i:40633890 original size:35 final size:36
Alignment explanation
Indices: 40633839--40633949 Score: 127
Period size: 35 Copynumber: 3.0 Consensus size: 36
40633829 TTACTTTCTC
* *
40633839 TATATATTCTTTAGAATTTTTATAAATTTTTTAAAA
1 TATAAATTCTTTAGAATTTTTATAAATATTTTAAAA
40633875 TATAAATT-TTTAGAATTTTTATAAATATTTTAAAA
1 TATAAATTCTTTAGAATTTTTATAAATATTTTAAAA
* * *
40633910 TTTAAAAATTATTTTGAATTTTTGA-AAATCATTTTAAAA
1 --TATAAATTCTTTAGAATTTTT-ATAAAT-ATTTTAAAA
40633949 T
1 T
40633950 TTTTATTGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
35 26 0.39
36 7 0.11
37 8 0.12
38 15 0.23
39 10 0.15
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (36 bp):
TATAAATTCTTTAGAATTTTTATAAATATTTTAAAA
Found at i:40636473 original size:15 final size:16
Alignment explanation
Indices: 40636453--40636482 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40636443 TTTAGAATTT
40636453 TAAATTAAAA-ATAAC
1 TAAATTAAAATATAAC
40636468 TAAATTAAAATATAA
1 TAAATTAAAATATAA
40636483 AAACTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATTAAAATATAAC
Found at i:40636859 original size:52 final size:51
Alignment explanation
Indices: 40636762--40636859 Score: 117
Period size: 52 Copynumber: 1.9 Consensus size: 51
40636752 CCCCTCAAAC
* * * * * *
40636762 TTTTTTTCTTTTATTTTCTTCTAAATTTTTTACTTTCCTCTAAACCTCATT
1 TTTTTTTCTTTTACTTTCTCCCAAAATTTTTACTTTCATCCAAACCTCATT
40636813 TTTTTTTCCTTTTACTTTCTCCCCAAAATTTTTAC-TTCATCCAAACC
1 TTTTTTT-CTTTTACTTTCT-CCCAAAATTTTTACTTTCATCCAAACC
40636860 CCCCAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
51 7 0.18
52 21 0.54
53 11 0.28
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.56
Consensus pattern (51 bp):
TTTTTTTCTTTTACTTTCTCCCAAAATTTTTACTTTCATCCAAACCTCATT
Done.