Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 135 of 335
Found at i:39888091 original size:10 final size:11
Alignment explanation
Indices: 39888076--39888123 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
39888066 AGGCAACCCA
39888076 ATTTTTA-TTT
1 ATTTTTATTTT
39888086 ATTTTTATTTT
1 ATTTTTATTTT
39888097 ATTTTTA--TT
1 ATTTTTATTTT
39888106 ATTTATTATTTT
1 ATTT-TTATTTT
39888118 ATTTTT
1 ATTTTT
39888124 TAGATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.18
10 10 0.29
11 12 0.35
12 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:39888102 original size:21 final size:21
Alignment explanation
Indices: 39888076--39888123 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
39888066 AGGCAACCCA
39888076 ATTTTTATTTATTT-TTATTTT
1 ATTTTTA-TTATTTATTATTTT
39888097 ATTTTTATTATTTATTATTTT
1 ATTTTTATTATTTATTATTTT
39888118 ATTTTT
1 ATTTTT
39888124 TAGATATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (21 bp):
ATTTTTATTATTTATTATTTT
Found at i:39888125 original size:15 final size:15
Alignment explanation
Indices: 39888078--39888125 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
39888068 GCAACCCAAT
39888078 TTTTATTTATTT-TTA
1 TTTTATTT-TTTATTA
39888093 TTTTA-TTTTTATTA
1 TTTTATTTTTTATTA
39888107 -TTTATTATTTTATT-
1 TTTTATT-TTTTATTA
39888121 TTTTA
1 TTTTA
39888126 GATATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 7 0.24
14 6 0.21
15 16 0.55
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTTATTA
Found at i:39890119 original size:10 final size:10
Alignment explanation
Indices: 39890095--39890138 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
39890085 TAATTTTAGG
39890095 ATTTA-TTTT
1 ATTTATTTTT
39890104 ATTTATTTTT
1 ATTTATTTTT
* *
39890114 AATTATCTTT
1 ATTTATTTTT
*
39890124 ATTTATTTGT
1 ATTTATTTTT
39890134 ATTTA
1 ATTTA
39890139 CCTTTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:39890143 original size:20 final size:20
Alignment explanation
Indices: 39890101--39890143 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39890091 TAGGATTTAT
* *
39890101 TTTATTTATTTTTAATTATC
1 TTTATTTATTTGTAATTACC
*
39890121 TTTATTTATTTGTATTTACC
1 TTTATTTATTTGTAATTACC
39890141 TTT
1 TTT
39890144 TAAAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATTTATTTGTAATTACC
Found at i:39890300 original size:17 final size:17
Alignment explanation
Indices: 39890278--39890313 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39890268 CCATATTTTC
39890278 TTTAAATAAAAATTCCA
1 TTTAAATAAAAATTCCA
39890295 TTTAAATAAAAATTCCA
1 TTTAAATAAAAATTCCA
39890312 TT
1 TT
39890314 CCCATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAAATAAAAATTCCA
Found at i:39892081 original size:22 final size:20
Alignment explanation
Indices: 39892056--39892098 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
39892046 AAACACAATA
39892056 ACAAGTCAATATTCTAATATTC
1 ACAA-TCAA-ATTCTAATATTC
* *
39892078 ACAATCAAATTTTATTATTC
1 ACAATCAAATTCTAATATTC
39892098 A
1 A
39892099 TTCCTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (20 bp):
ACAATCAAATTCTAATATTC
Found at i:39893175 original size:18 final size:18
Alignment explanation
Indices: 39893149--39893186 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39893139 ATTTTTATAC
*
39893149 ATATTTTTTAATCTTATT
1 ATATATTTTAATCTTATT
*
39893167 ATATATTTTAATTTTATT
1 ATATATTTTAATCTTATT
39893185 AT
1 AT
39893187 GCACGCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATATTTTAATCTTATT
Found at i:39898570 original size:13 final size:13
Alignment explanation
Indices: 39898552--39898584 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
39898542 TTTAATATTC
39898552 AAAATT-TTTTATA
1 AAAATTATTTT-TA
39898565 AAAATTATTTTTA
1 AAAATTATTTTTA
39898578 AAAATTA
1 AAAATTA
39898585 AATATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTATTTTTA
Found at i:39899276 original size:30 final size:30
Alignment explanation
Indices: 39899240--39899300 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
39899230 CAATTTAATA
*
39899240 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
* *
39899270 AGCAAATGTCTTTAAAATAATAAAAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
39899300 A
1 A
39899301 ACAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:39901449 original size:16 final size:15
Alignment explanation
Indices: 39901423--39901465 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39901413 TATTAAGAAT
*
39901423 TGAATTGAAAAATAA
1 TGAATTAAAAAATAA
*
39901438 TAGAATT-TAAAATAA
1 T-GAATTAAAAAATAA
39901453 TGAATTAAAAAAT
1 TGAATTAAAAAAT
39901466 TGTCAACTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (15 bp):
TGAATTAAAAAATAA
Found at i:39901465 original size:15 final size:14
Alignment explanation
Indices: 39901423--39901463 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
39901413 TATTAAGAAT
39901423 TGAATTGAAAAATAA
1 TGAATT-AAAAATAA
*
39901438 TAGAATTTAAAATAA
1 T-GAATTAAAAATAA
39901453 TGAATTAAAAA
1 TGAATTAAAAA
39901464 ATTGTCAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 9 0.39
16 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (14 bp):
TGAATTAAAAATAA
Found at i:39915559 original size:15 final size:15
Alignment explanation
Indices: 39915526--39915555 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
39915516 TCCTCTCCCC
39915526 TCTCCCTCTCTCCTT
1 TCTCCCTCTCTCCTT
39915541 TCTCCC-CTCTCCTT
1 TCTCCCTCTCTCCTT
39915555 T
1 T
39915556 TCTCTCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTCCCTCTCTCCTT
Found at i:39915565 original size:22 final size:22
Alignment explanation
Indices: 39915513--39915565 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
39915503 GGCCGGAGCC
*
39915513 CTCTCCTCTCCCCTCTCCCTCT
1 CTCTCTTCTCCCCTCTCCCTCT
* *
39915535 CTC-CTTTCTCCCCTCTCCTTTT
1 CTCTC-TTCTCCCCTCTCCCTCT
39915557 CTCTCTTCT
1 CTCTCTTCT
39915566 TTTTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (22 bp):
CTCTCTTCTCCCCTCTCCCTCT
Found at i:39916140 original size:13 final size:14
Alignment explanation
Indices: 39916116--39916146 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
39916106 ATTATTATCA
39916116 ATATTGATATATGT
1 ATATTGATATATGT
39916130 ATATT-ATATATGT
1 ATATTGATATATGT
39916143 ATAT
1 ATAT
39916147 ATTCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
ATATTGATATATGT
Found at i:39922083 original size:46 final size:44
Alignment explanation
Indices: 39921979--39922086 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
39921969 TGTCTTTGAC
** * * *
39921979 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
39922023 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
39922069 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
39922087 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:39928028 original size:46 final size:44
Alignment explanation
Indices: 39927924--39928031 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
39927914 TGTCTTTGAC
** * * *
39927924 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
39927968 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
39928014 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
39928032 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:39937553 original size:74 final size:71
Alignment explanation
Indices: 39937374--39937652 Score: 387
Period size: 71 Copynumber: 3.9 Consensus size: 71
39937364 GTTTTCCAAG
* * *
39937374 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
39937439 GTTTCA
66 GTTTCA
* * * *
39937445 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
*
39937510 GATTTTTA
66 G--TTTCA
*** * *
39937518 GTTCATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTA
39937583 TGTTTCA
65 TGTTTCA
* * *
39937590 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
39937653 CTGCCTTTTA
Statistics
Matches: 179, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
71 114 0.64
72 4 0.02
73 4 0.02
74 57 0.32
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:39937645 original size:145 final size:152
Alignment explanation
Indices: 39937283--39937941 Score: 981
Period size: 160 Copynumber: 4.2 Consensus size: 152
39937273 TTGTTTTTTC
*
39937283 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
39937348 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGC-TTTT-ATTCATG-TTTCC-----AATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
39937413 GACACGTTGAGGTAATTTCAATTTATGTTT
123 GACACGTTGAGGTAATTTCAATTTATGTTT
39937443 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
* *
39937508 CTG-ATTT-TT-A-G-TT-C-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
66 CTGCTTTTATTCATGTTTCCAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
39937566 GAGGTAATTTCAATTTATGTTT
131 GAGGTAATTTCAATTTATGTTT
39937588 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
39937653 CTGCCTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTG-CTTTT-ATTCATG-TTTCC-----AATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
39937718 GACACGTTGAGGTAATTTCAATTTATGTTT
123 GACACGTTGAGGTAATTTCAATTTATGTTT
39937748 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
39937813 TTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGC-TTTT-ATTCATG-TTTCC-----AATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
39937878 GACACGTTGAGGTAATTTCAATTTATGTTT
123 GACACGTTGAGGTAATTTCAATTTATGTTT
* * *
39937908 CAAAAATCAACTCATATTACGAGAGGTGGGTTGA
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
39937942 ACCTTTTAAT
Statistics
Matches: 473, Mismatches: 10, Indels: 32
0.92 0.02 0.06
Matches are distributed among these distances:
145 133 0.28
147 3 0.01
149 2 0.00
150 1 0.00
151 2 0.00
152 2 0.00
153 2 0.00
154 2 0.00
155 1 0.00
156 2 0.00
158 3 0.01
159 1 0.00
160 319 0.67
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (152 bp):
CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTGCTTTTATTCATGTTTCCAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
GAGGTAATTTCAATTTATGTTT
Found at i:39937800 original size:71 final size:71
Alignment explanation
Indices: 39937679--39937812 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
39937669 GTTTTCCAAG
* * *
39937679 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
39937744 GTTTCA
66 GTTTCA
* * *
39937750 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
39937813 TTGCTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:39937989 original size:125 final size:130
Alignment explanation
Indices: 39937839--39938139 Score: 405
Period size: 140 Copynumber: 2.3 Consensus size: 130
39937829 GTTTTCCAAG
*
39937839 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-T-AA-TTTCAATT
1 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTTCAATTTTCAATT
*
39937901 TATG-T-TTCAAAAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTC
66 TACGTTGTTCAAAAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTC
* * *
39937964 AAAATCAGCTCATATTGCGAAAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT
1 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG----TTCAA-----
*
39938029 GTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTT
57 -TTTTCAATTTACGTTGTTCAAAAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTT
39938094 CTACTTTTTC
121 CTACTTTTTC
* *
39938104 AAAATCAACTCATATTGCGAGATGTGAGTTGAGCCT
1 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCT
39938140 TGGATTCACA
Statistics
Matches: 152, Mismatches: 9, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
125 47 0.31
130 1 0.01
131 2 0.01
138 11 0.07
139 1 0.01
140 90 0.59
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (130 bp):
AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTTCAATTTTCAATT
TACGTTGTTCAAAAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTC
Found at i:39939479 original size:22 final size:24
Alignment explanation
Indices: 39939427--39939479 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
39939417 GGCCGGAGCC
*
39939427 CTCTCCTCTCCCCTCTCCCTCTTT
1 CTCTCTTCTCCCCTCTCCCTCTTT
39939451 C-CT-TTCTCCCCTCT-CCT-TTT
1 CTCTCTTCTCCCCTCTCCCTCTTT
39939471 CTCTCTTCT
1 CTCTCTTCT
39939480 TTTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 14 0.54
23 2 0.08
24 1 0.04
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (24 bp):
CTCTCTTCTCCCCTCTCCCTCTTT
Found at i:39940055 original size:13 final size:14
Alignment explanation
Indices: 39940031--39940061 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
39940021 ATTATTATCA
39940031 ATATTGATATATGT
1 ATATTGATATATGT
39940045 ATATT-ATATATGT
1 ATATTGATATATGT
39940058 ATAT
1 ATAT
39940062 ATTCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
ATATTGATATATGT
Found at i:39947107 original size:15 final size:16
Alignment explanation
Indices: 39947089--39947135 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
39947079 TGATAATGTA
39947089 AATAAC-AATAATACT
1 AATAACGAATAATACT
* *
39947104 AAT-ACTAATAATAAT
1 AATAACGAATAATACT
39947119 AATAACGAATAAT-CT
1 AATAACGAATAATACT
39947134 AA
1 AA
39947136 ATTTTTGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 17 0.63
16 8 0.30
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (16 bp):
AATAACGAATAATACT
Found at i:39947341 original size:3 final size:3
Alignment explanation
Indices: 39947333--39947357 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39947323 TAAAATGGTT
39947333 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
39947358 TGTACAAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:39948831 original size:28 final size:29
Alignment explanation
Indices: 39948785--39948840 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
39948775 TATATATATA
* *
39948785 TTTTATATTATGTCTATATTTTATGTATTT
1 TTTTACATTATG-CTATATATTATGTATTT
39948815 TTTTACATTATG-TATATATTATGTAT
1 TTTTACATTATGCTATATATTATGTAT
39948841 ATACTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
30 11 0.46
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (29 bp):
TTTTACATTATGCTATATATTATGTATTT
Found at i:39948849 original size:30 final size:30
Alignment explanation
Indices: 39948773--39948849 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
39948763 CTTTTTAAAC
* *
39948773 ATTATATATATATTTTATATTATGTCTATAT
1 ATTATGTATATATTTTACATTATG-CTATAT
* *
39948804 TTTATGTAT-TTTTTTACATTATG-TATAT
1 ATTATGTATATATTTTACATTATGCTATAT
39948832 ATTATGTATATACTTTTA
1 ATTATGTATATA-TTTTA
39948850 ATATCATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 13 0.34
29 1 0.03
30 17 0.45
31 7 0.18
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (30 bp):
ATTATGTATATATTTTACATTATGCTATAT
Found at i:39948858 original size:23 final size:22
Alignment explanation
Indices: 39948828--39948888 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
39948818 TACATTATGT
*
39948828 ATATATTATGTATATACTTTTA
1 ATATATTATATATATACTTTTA
* *
39948850 ATATCATTATATATTTATTTTTA
1 ATAT-ATTATATATATACTTTTA
*
39948873 ATATATACATATATAT
1 ATATAT-TATATATAT
39948889 TTATCTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 6 0.19
23 26 0.81
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (22 bp):
ATATATTATATATATACTTTTA
Found at i:39948889 original size:21 final size:23
Alignment explanation
Indices: 39948838--39948899 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
39948828 ATATATTATG
* *
39948838 TATATACTTTTAATATCATTATA
1 TATATATTTTTAATATCATTACA
*
39948861 TATTTATTTTTAATAT-A-TACA
1 TATATATTTTTAATATCATTACA
39948882 TATATATTTATCTAATAT
1 TATATATTT-T-TAATAT
39948900 TATTGATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.33
22 2 0.06
23 20 0.61
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATATTTTTAATATCATTACA
Found at i:39949294 original size:13 final size:13
Alignment explanation
Indices: 39949276--39949300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39949266 TATTATTATA
39949276 TATATATTTCTTT
1 TATATATTTCTTT
39949289 TATATATTTCTT
1 TATATATTTCTT
39949301 ATTACTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTCTTT
Found at i:39953188 original size:9 final size:9
Alignment explanation
Indices: 39953174--39953232 Score: 93
Period size: 9 Copynumber: 6.7 Consensus size: 9
39953164 ATCAACGCTT
39953174 TTGCATTCA
1 TTGCATTCA
39953183 TTGCATTCA
1 TTGCATTCA
*
39953192 TCGCATTCA
1 TTGCATTCA
39953201 TTGCATTCA
1 TTGCATTCA
*
39953210 TCGCATTCA
1 TTGCATTCA
39953219 TTGCATTCA
1 TTGCATTCA
39953228 -TGCAT
1 TTGCAT
39953233 CAGCATTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
8 5 0.11
9 41 0.89
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (9 bp):
TTGCATTCA
Found at i:39953199 original size:18 final size:18
Alignment explanation
Indices: 39953176--39953232 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
39953166 CAACGCTTTT
39953176 GCATTCATTGCATTCATC
1 GCATTCATTGCATTCATC
39953194 GCATTCATTGCATTCATC
1 GCATTCATTGCATTCATC
39953212 GCATTCATTGCATTCAT-
1 GCATTCATTGCATTCATC
39953229 GCAT
1 GCAT
39953233 CAGCATTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
17 4 0.10
18 35 0.90
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (18 bp):
GCATTCATTGCATTCATC
Found at i:39961327 original size:43 final size:43
Alignment explanation
Indices: 39961263--39961644 Score: 217
Period size: 43 Copynumber: 8.8 Consensus size: 43
39961253 AGAATCAGTG
* * *
39961263 AATTCACCAGACCTTAACCCCCTAAGCAGTAGGGTAACATGTTA
1 AATTCA-CAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* *
39961307 AATTCACAGATCTCAACCCCCTAAGCAGTAGTGTAACAGGTTG
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * *
39961350 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGAAATAGATCGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGT-TA
* * * * * *
39961394 AGATGAT-A-AG-CCTTAACCCCTTATGCAGTAAGGTAACAGGCTAAA
1 A-AT--TCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGG-T-TA
* * * * * *
39961439 AATT-ACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGT-TA
* * * * * *
39961482 AGA-TGA-AGAACCTTAAACCCCTAAGTAGTAGGGTAACAGGTTG
1 A-ATTCACAG-ATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * * *
39961525 AATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAGATCGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGT-TA
* * *
39961569 AGATGAT-A-AG-CCTTAA-CCCCTAAGCAGTAGGGTAACAGGTTG
1 A-AT--TCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * *
39961611 AATTTATAGATCTTAACCCCCCTAAGCAGTAGGG
1 AATTCACAGATCTCAA-CCCCCTAAGCAGTAGGG
39961645 AAATAGATCA
Statistics
Matches: 259, Mismatches: 58, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 4 0.02
42 9 0.03
43 127 0.49
44 102 0.39
45 11 0.04
46 2 0.01
47 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (43 bp):
AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
Found at i:39961469 original size:88 final size:87
Alignment explanation
Indices: 39961324--39961713 Score: 475
Period size: 87 Copynumber: 4.5 Consensus size: 87
39961314 AGATCTCAAC
* * *
39961324 CCCCTAAGCAGTAGTGTAACAGGTTG-AATTCACAGATCTCAACCCCCTAAGCAGTAGGGAAATA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAAATT-ACAGATCTCACCCCCCTAAGCAGTAGGGAAACA
39961388 GATCGAAGATGATAAGCCTT-AA
65 GATCGAAGATGATAAGCCTTAAA
* * ** * * *
39961410 CCCCTTATGCAGTAAGGTAACAGGCTAAAAATTACAGATCTTATCACCCTAAGCAGTAGGGAAAC
1 CCCC-TAAGCAGTAGGGTAACAGG-TTGAAATTACAGATCTCACCCCCCTAAGCAGTAGGGAAAC
*
39961475 AGATCGAAGATGA-AGAACCTTAAA
64 AGATCGAAGATGATA-AGCCTTAAA
* *
39961499 CCCCTAAGTAGTAGGGTAACAGGTTGAATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAG
1 CCCCTAAGCAGTAGGGTAACAGGTTGAAATTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAG
39961564 ATCGAAGATGATAAGCCTT-AA
66 ATCGAAGATGATAAGCCTTAAA
* * * *
39961585 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTATAGATCTTAACCCCCCTAAGCAGTAGGGAAATA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAAATTACAGATC-TCACCCCCCTAAGCAGTAGGGAAACA
* *
39961650 GATC-AGGAGTGATGAGCCTTAAA
65 GATCGAAGA-TGATAAGCCTTAAA
* * * *
39961673 CCCCTAAGCAATAGGGTCACAGGCTGGAAATTACAAATCTC
1 CCCCTAAGCAGTAGGGTAACAGG-TTGAAATTACAGATCTC
39961714 TTCTCCCTGA
Statistics
Matches: 261, Mismatches: 33, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
86 45 0.17
87 107 0.41
88 88 0.34
89 21 0.08
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (87 bp):
CCCCTAAGCAGTAGGGTAACAGGTTGAAATTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAG
ATCGAAGATGATAAGCCTTAAA
Found at i:39961504 original size:44 final size:45
Alignment explanation
Indices: 39961367--39961688 Score: 186
Period size: 44 Copynumber: 7.4 Consensus size: 45
39961357 AGATCTCAAC
* *
39961367 CCCCTAAGCAGTAGGGAAATAGATCGAAGATGATA-AGCCTT-AA
1 CCCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGAACCTTAAA
* * * * * * * * * *
39961410 CCCCTTATGCAGTAAGGTAACAG-GCTAAAAATTACAG-ATCTT-AT
1 CCCC-TAAGCAGTAGGGAAACAGATC-GAAGATGATAGAACCTTAAA
39961454 CACCCTAAGCAGTAGGGAAACAGATCGAAGATGA-AGAACCTTAAA
1 C-CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGAACCTTAAA
* * * * * * * * * **
39961499 CCCCTAAGTAGTAGGGTAACAGGTTGAA-TTTACAG-ATCTCACC
1 CCCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGAACCTTAAA
*
39961542 CCCCTAAGCAGTAGGGAAACAGATCGAAGATGATA-AGCCTT-AA
1 CCCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGAACCTTAAA
* * * * * * *
39961585 CCCCTAAGCAGTAGGGTAACAGGTTGAA-TTTATAG-ATCTTAACC
1 CCCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGAACCTTAA-A
* * *
39961629 CCCCTAAGCAGTAGGGAAATAGATC-AGGAGTGAT-GAGCCTTAAA
1 CCCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATAGAACCTTAAA
*
39961673 CCCCTAAGCAATAGGG
1 CCCCTAAGCAGTAGGG
39961689 TCACAGGCTG
Statistics
Matches: 201, Mismatches: 62, Indels: 31
0.68 0.21 0.11
Matches are distributed among these distances:
42 7 0.03
43 64 0.32
44 116 0.58
45 14 0.07
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (45 bp):
CCCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGAACCTTAAA
Found at i:39963444 original size:11 final size:11
Alignment explanation
Indices: 39963412--39963482 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
39963402 CTTTTTAAAC
*
39963412 ATTATATATAT
1 ATTATGTATAT
39963423 ATT-T-T-TAT
1 ATTATGTATAT
*
39963431 ATTATGTCTAT
1 ATTATGTATAT
*
39963442 ATT-T-TATGT
1 ATTATGTATAT
*
39963451 ATT-T-TTTAT
1 ATTATGTATAT
39963460 ATTATGTATAT
1 ATTATGTATAT
39963471 ATTATGTATAT
1 ATTATGTATAT
39963482 A
1 A
39963483 CTTTTAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
8 6 0.12
9 15 0.30
10 4 0.08
11 25 0.50
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (11 bp):
ATTATGTATAT
Found at i:39963469 original size:27 final size:28
Alignment explanation
Indices: 39963424--39963479 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
39963414 TATATATATA
*
39963424 TTTTTATATTATGTCTATATTTTATGTAT
1 TTTTTATATTATG-CTATATATTATGTAT
39963453 TTTTTATATTATG-TATATATTATGTAT
1 TTTTTATATTATGCTATATATTATGTAT
39963480 ATACTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.50
29 13 0.50
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTTATATTATGCTATATATTATGTAT
Found at i:39963475 original size:16 final size:16
Alignment explanation
Indices: 39963427--39963475 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
39963417 ATATATATTT
*
39963427 TTATATTATGTCTATA
1 TTATATTATGTATATA
* *
39963443 -T-T-TTATGTATTTT
1 TTATATTATGTATATA
39963456 TTATATTATGTATATA
1 TTATATTATGTATATA
39963472 TTAT
1 TTAT
39963476 GTATATACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
13 8 0.32
14 2 0.08
15 2 0.08
16 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (16 bp):
TTATATTATGTATATA
Found at i:39963510 original size:23 final size:22
Alignment explanation
Indices: 39963467--39963517 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
39963457 TATATTATGT
*
39963467 ATATATTATGTATATACTTTTA
1 ATATATTATATATATACTTTTA
* *
39963489 ATATCATTATATATTTATTTTTA
1 ATAT-ATTATATATATACTTTTA
39963512 ATATAT
1 ATATAT
39963518 ACGTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATATTATATATATACTTTTA
Found at i:39963829 original size:2 final size:2
Alignment explanation
Indices: 39963822--39963859 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
39963812 TATTGCTAAC
39963822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
39963860 ATTCCATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39963957 original size:13 final size:13
Alignment explanation
Indices: 39963939--39963963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39963929 ATTATATATA
39963939 TATATATTTCTTT
1 TATATATTTCTTT
39963952 TATATATTTCTT
1 TATATATTTCTT
39963964 ATTACTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTCTTT
Found at i:39965041 original size:3 final size:3
Alignment explanation
Indices: 39965035--39965085 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
39965025 TGGTTACGAC
39965035 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39965083 AAT
1 AAT
39965086 TGAAGTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39970823 original size:25 final size:25
Alignment explanation
Indices: 39970767--39970832 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 25
39970757 AAATTATATA
*
39970767 ATTTTTT-AAAAAATTATAAAAACT
1 ATTTTTTAAAAAAATTCTAAAAACT
***
39970791 AAAATTTAAAAAAATTCTAAAAACT
1 ATTTTTTAAAAAAATTCTAAAAACT
* * *
39970816 TTTTTTTATAACAATTC
1 ATTTTTTAAAAAAATTC
39970833 AAATATTCAA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTTTTTAAAAAAATTCTAAAAACT
Found at i:39971922 original size:22 final size:23
Alignment explanation
Indices: 39971865--39971923 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
39971855 AGTGTTTGGG
39971865 AAATATTAAA-AT-AAATATATA
1 AAATATTAAATATAAAATATATA
* *
39971886 AAAAAGT-AATAATAAAATAT-TA
1 AAATATTAAAT-ATAAAATATATA
39971908 AAATATTAAATATAAA
1 AAATATTAAATATAAA
39971924 TTACACTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.07
21 5 0.17
22 14 0.47
23 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATATTAAATATAAAATATATA
Found at i:39977874 original size:20 final size:22
Alignment explanation
Indices: 39977851--39977891 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
39977841 TAAATTTAAC
39977851 TAAAAAAATA-AAA-ATTAAAT
1 TAAAAAAATATAAATATTAAAT
39977871 TAAAAAAATATAAATATTAAA
1 TAAAAAAATATAAATATTAAA
39977892 AGTTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAAAAATATAAATATTAAAT
Found at i:39979506 original size:117 final size:116
Alignment explanation
Indices: 39979281--39979513 Score: 430
Period size: 116 Copynumber: 2.0 Consensus size: 116
39979271 CCAACATGGC
*
39979281 CTGATTTTGCAAAAACAACAAAAAAGTCGATTGTTTTCTCACTATATTATTGTTGTTTTTTTTGC
1 CTGAATTTGCAAAAACAACAAAAAAGTCGATTGTTTTCTCACTATATTATTGTTGTTTTTTTTGC
39979346 TATTTTTTTCACTGTTTAGTTGTCATTTCACTAATATTTTGTTACATTTTT
66 TATTTTTTTCACTGTTTAGTTGTCATTTCACTAATATTTTGTTACATTTTT
39979397 CTGAATTTGCAAAAACAACAAAAAAGTCGATTGTTTTCTCACTATATTATTGTTGTTTTTTTTGC
1 CTGAATTTGCAAAAACAACAAAAAAGTCGATTGTTTTCTCACTATATTATTGTTGTTTTTTTTGC
* *
39979462 TATTTTTTTTCACTGTTTTGTTGTCATTTCACTAGTATTTTGTTACATTTTT
66 TA-TTTTTTTCACTGTTTAGTTGTCATTTCACTAATATTTTGTTACATTTTT
39979514 TTTTGTTATT
Statistics
Matches: 113, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
116 66 0.58
117 47 0.42
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (116 bp):
CTGAATTTGCAAAAACAACAAAAAAGTCGATTGTTTTCTCACTATATTATTGTTGTTTTTTTTGC
TATTTTTTTCACTGTTTAGTTGTCATTTCACTAATATTTTGTTACATTTTT
Found at i:39979971 original size:43 final size:42
Alignment explanation
Indices: 39979923--39980055 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 42
39979913 TTATGTGGAA
* * *
39979923 AAACGCCGCTATAGAACATTACATTTAGCGGCGCTTTCTCCAC
1 AAACGCCGCTAAAGAACGTGACATTTAGCGGCGCTTTC-CCAC
* * *
39979966 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTTCCCCAT
1 AAACGCCGCTAAAGAACGTGACATTTAGCGGCGCTTT-CCCAC
* * *
39980009 AAACGCCACTAAAGAACGTGACTTTTAGCTGCGCTTTCCCAC
1 AAACGCCGCTAAAGAACGTGACATTTAGCGGCGCTTTCCCAC
39980051 AAACG
1 AAACG
39980056 TTTCTAAGAG
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 9 0.12
43 68 0.87
44 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACGTGACATTTAGCGGCGCTTTCCCAC
Found at i:39980084 original size:41 final size:40
Alignment explanation
Indices: 39979923--39980104 Score: 150
Period size: 43 Copynumber: 4.3 Consensus size: 40
39979913 TTATGTGGAA
* * * *
39979923 AAACGCCGCTATAGAACATTACATTTAGCGGCGCTTTCTCCAC
1 AAACGCCACTAAAGAAC-TGACCTTTAGC-GCGCTTTC-CCAC
* *
39979966 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTTCCCCAT
1 AAACGCCACTAAAGAAC-TGACCTTTAGCG-CGCTTT-CCCAC
*
39980009 AAACGCCACTAAAGAACGTGACTTTTAGCTGCGCTTTCCCAC
1 AAACGCCACTAAAGAAC-TGACCTTTAGC-GCGCTTTCCCAC
*** * *
39980051 AAACGTTTCTAAGAGAA-TGACCTTTAGCAGCGCTTTTCTCAA
1 AAACGCCACTAA-AGAACTGACCTTTAGC-GCGC-TTTCCCAC
39980093 AAACGCCACTAA
1 AAACGCCACTAA
39980105 GGTCATGTTC
Statistics
Matches: 116, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
41 14 0.12
42 29 0.25
43 71 0.61
44 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (40 bp):
AAACGCCACTAAAGAACTGACCTTTAGCGCGCTTTCCCAC
Found at i:39980101 original size:84 final size:85
Alignment explanation
Indices: 39979921--39980104 Score: 212
Period size: 86 Copynumber: 2.2 Consensus size: 85
39979911 GTTTATGTGG
* * *
39979921 AAAAACGCCGCTATAGAACATTACATTTAGCGGCGCTTTCTCCACAAACGCCGCTAAAGAACGTG
1 AAAAACGCCACTAAAGAACATGACATTTAGCGGCGCTTTCTCCACAAACGCCGCTAAAGAAC-TG
39979986 ACCTTTAGCGACGCTTTCCCC
65 ACCTTTAGCGACGCTTTCCCC
* * * * ***
39980007 ATAAACGCCACTAAAGAACGTGACTTTTAGCTGCGCTTTC-CCACAAACGTTTCTAAGAGAA-TG
1 AAAAACGCCACTAAAGAACATGACATTTAGCGGCGCTTTCTCCACAAACGCCGCTAA-AGAACTG
* *
39980070 ACCTTTAGC-AGCGCTTTTCTC
65 ACCTTTAGCGA-CGCTTTCCCC
39980091 AAAAACGCCACTAA
1 AAAAACGCCACTAA
39980105 GGTCATGTTC
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
83 1 0.01
84 32 0.39
85 13 0.16
86 37 0.45
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (85 bp):
AAAAACGCCACTAAAGAACATGACATTTAGCGGCGCTTTCTCCACAAACGCCGCTAAAGAACTGA
CCTTTAGCGACGCTTTCCCC
Found at i:39980153 original size:42 final size:42
Alignment explanation
Indices: 39980106--39980187 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
39980096 CGCCACTAAG
* *
39980106 GTCATGTTCTTTAACGGCGTTT-TAGTAAAAGCGTTGTTAAAA
1 GTCATGTTCTTTAACGGCGTTTGTAG-AAAAACGCTGTTAAAA
**
39980148 GTCATGTTCTTTGGCGGCGTTTGTAGAAAAACGCTGTTAA
1 GTCATGTTCTTTAACGGCGTTTGTAGAAAAACGCTGTTAA
39980188 CTTTAGTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.91
43 3 0.09
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (42 bp):
GTCATGTTCTTTAACGGCGTTTGTAGAAAAACGCTGTTAAAA
Found at i:39980589 original size:66 final size:65
Alignment explanation
Indices: 39980461--39980594 Score: 164
Period size: 66 Copynumber: 2.0 Consensus size: 65
39980451 ATTCTGAAGC
* * * *
39980461 TGTAGCTGGAGTTTGTCATATTTTCTGCTTGCCTCTGCTTCCCTCGCTGCTACCTTTGCTTTAAG
1 TGTAGCTGGAGTTTGTCATATTTTCT-CTTGCCTCTACTTCCCTCGATGCTACCTCTACTTTAAG
39980526 T
65 T
* *
39980527 TGTAGCTGGAGTTCT-TCATATTTTCT-TTGAGCCTCTACTTCTCTCGATGCTGCCTCTACTTTA
1 TGTAGCTGGAGTT-TGTCATATTTTCTCTT--GCCTCTACTTCCCTCGATGCTACCTCTACTTTA
39980590 AGT
63 AGT
39980593 TG
1 TG
39980595 AGCAATTTGC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
64 2 0.03
66 56 0.95
67 1 0.02
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (65 bp):
TGTAGCTGGAGTTTGTCATATTTTCTCTTGCCTCTACTTCCCTCGATGCTACCTCTACTTTAAGT
Found at i:39982659 original size:28 final size:27
Alignment explanation
Indices: 39982607--39982659 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
39982597 CTATTCAGAA
* *
39982607 ATCAGTGTTAACTAGGCCTTAGCCCAT
1 ATCAGTATTAACTAGGCCATAGCCCAT
*
39982634 ATCAGTATTAATCTGGGCCATAGCCC
1 ATCAGTATTAA-CTAGGCCATAGCCC
39982660 CTTACAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (27 bp):
ATCAGTATTAACTAGGCCATAGCCCAT
Found at i:39982744 original size:60 final size:59
Alignment explanation
Indices: 39982621--39982755 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 59
39982611 GTGTTAACTA
* *
39982621 GGCCTTAGCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTATACTG
1 GGCC-TAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGT-ACAGAGTATACTG
* * *
39982682 GGCCTAGCCCATATCAGTATCAATCTGGGTCGTAGCCCTATTACAAGT-C-GAGATATATTG
1 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCC-ATTAC-AGTACAGAG-TATACTG
*
39982742 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
39982756 TAACACAGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 3 0.05
60 51 0.78
61 8 0.12
62 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (59 bp):
GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTACAGAGTATACTG
Found at i:39982791 original size:19 final size:20
Alignment explanation
Indices: 39982748--39982803 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
39982738 ATTGGGCCTT
39982748 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
39982768 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
* *
39982787 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
39982804 CTCATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:39986043 original size:5 final size:5
Alignment explanation
Indices: 39986033--39986156 Score: 180
Period size: 5 Copynumber: 24.0 Consensus size: 5
39986023 AATAATTAAG
39986033 TATAT TATA- T-TAT TATAT TATATT TATATT TATATT TATATT TATATT
1 TATAT TATAT TATAT TATAT TATA-T TATA-T TATA-T TATA-T TATA-T
39986081 TATATT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
39986132 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
39986157 ATAAAAGAAA
Statistics
Matches: 116, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.02
4 2 0.02
5 77 0.66
6 35 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:39986830 original size:45 final size:45
Alignment explanation
Indices: 39986765--39986869 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 45
39986755 ATGTGCCGAC
* *
39986765 TACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGT
1 TACCGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGT
* * *
39986810 TACCGTTATTGTTACAGATTCAACATTTTGTGTGTTGAATACTGT
1 TACCGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGT
*
39986855 TACTGTTACTGTTAC
1 TACCGTTACTGTTAC
39986870 TGCTACCGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (45 bp):
TACCGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGT
Found at i:39986860 original size:6 final size:6
Alignment explanation
Indices: 39986849--39986890 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
39986839 GTGTGTTGAA
* *
39986849 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
39986891 ATTAGGTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:39990103 original size:46 final size:46
Alignment explanation
Indices: 39990043--39990270 Score: 323
Period size: 46 Copynumber: 5.0 Consensus size: 46
39990033 TTTGACATGA
* * * * * * *
39990043 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
** * *
39990089 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
39990135 TGCCATGGTATCATTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
39990181 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
39990227 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
39990271 AGAGAACACT
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 164 0.98
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:39994743 original size:46 final size:46
Alignment explanation
Indices: 39994693--39994868 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
39994683 TGGTTGAGCA
39994693 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
39994739 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
39994784 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39994832 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39994869 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 63 0.58
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39994849 original size:93 final size:93
Alignment explanation
Indices: 39994690--39994860 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
39994680 GGATGGTTGA
* * *
39994690 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
39994755 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
39994783 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
39994848 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39994861 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:39999447 original size:5 final size:5
Alignment explanation
Indices: 39999437--39999484 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
39999427 AATAATTAAG
39999437 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
39999485 ATAAAAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:40000122 original size:6 final size:6
Alignment explanation
Indices: 40000111--40000137 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40000101 ATGTGCCGAC
40000111 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
40000138 CGATTCGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:40000167 original size:45 final size:45
Alignment explanation
Indices: 40000117--40000223 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
40000107 CGACTACTGT
*
40000117 TACTGTTACTGTTACTGTTACCGATTC-GACACTTTGTGTGTCAAA
1 TACTGTTACTGTTACTGTTACAGATTCAG-CACTTTGTGTGTCAAA
* * **
40000162 TACTGTTACCGTTACTGTTACAGATTCAGCATTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAA
40000207 TACTGTTACTGTTACTG
1 TACTGTTACTGTTACTG
40000224 CTATTGTTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 54 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAA
Found at i:40000217 original size:51 final size:50
Alignment explanation
Indices: 40000111--40000235 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 50
40000101 ATGTGCCGAC
*
40000111 TACTGTTACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCAA
1 TACTGTTACTGTTACTGTTACTGTTACAGATTCGACACTTTGTGTGTCAA
* * *
40000161 -A----TACTGTTACCGTTACTGTTACAGATTC-AGCATTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACTGTTACAGATTCGA-CACTTTGTGTG-TCAA
* *
40000207 TACTGTTACTGTTACTGCTATTGTTACAG
1 TACTGTTACTGTTACTGTTACTGTTACAG
40000236 TTACTGATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
44 1 0.02
45 35 0.57
46 3 0.05
47 1 0.02
49 1 0.02
51 20 0.33
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (50 bp):
TACTGTTACTGTTACTGTTACTGTTACAGATTCGACACTTTGTGTGTCAA
Found at i:40010570 original size:49 final size:49
Alignment explanation
Indices: 40010498--40010593 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
40010488 TGGTTTAAGA
40010498 AAAACTCAATTACAAAAATGTTGTTTATGTATAGAGAATTAATTACATC
1 AAAACTCAATTACAAAAATGTTGTTTATGTATAGAGAATTAATTACATC
40010547 AAAACTCAATTACAAAAATGTTGTTTATGTATAGAGAATTAATTACA
1 AAAACTCAATTACAAAAATGTTGTTTATGTATAGAGAATTAATTACA
40010594 CCAAGTATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.34
Consensus pattern (49 bp):
AAAACTCAATTACAAAAATGTTGTTTATGTATAGAGAATTAATTACATC
Found at i:40013443 original size:10 final size:11
Alignment explanation
Indices: 40013427--40013456 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
40013417 GAAGTTAATT
40013427 TTTTATTTTAA
1 TTTTATTTTAA
40013438 -TTTATTTTAA
1 TTTTATTTTAA
40013448 TTTTATTTT
1 TTTTATTTT
40013457 TATATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:40013451 original size:23 final size:22
Alignment explanation
Indices: 40013421--40013467 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
40013411 GAATTAGAAG
*
40013421 TTAATTTTTTATTTTA-ATTTATT
1 TTAATTTTAT-TTTTATATTT-TT
40013444 TTAATTTTATTTTTATATTTTT
1 TTAATTTTATTTTTATATTTTT
40013466 TT
1 TT
40013468 CGAATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (22 bp):
TTAATTTTATTTTTATATTTTT
Found at i:40014748 original size:22 final size:22
Alignment explanation
Indices: 40014720--40014769 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
40014710 AACTATTGTA
40014720 CATATTAGATGAATTCAATAAT
1 CATATTAGATGAATTCAATAAT
*
40014742 CATATTAGATGAATTCAATAGT
1 CATATTAGATGAATTCAATAAT
40014764 CATATT
1 CATATT
40014770 TGATTCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (22 bp):
CATATTAGATGAATTCAATAAT
Found at i:40017430 original size:15 final size:15
Alignment explanation
Indices: 40017410--40017439 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40017400 TTCACTCTTT
40017410 TATGTTTTCTTTGTA
1 TATGTTTTCTTTGTA
40017425 TATGTTTTCTTTGTA
1 TATGTTTTCTTTGTA
40017440 GTAAGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TATGTTTTCTTTGTA
Found at i:40017448 original size:15 final size:15
Alignment explanation
Indices: 40017413--40017447 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40017403 ACTCTTTTAT
*
40017413 GTTTTCTTTGTATAT
1 GTTTTCTTTGTATAA
40017428 GTTTTCTTTGTAGTAA
1 GTTTTCTTTGTA-TAA
40017444 GTTT
1 GTTT
40017448 CATTGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (15 bp):
GTTTTCTTTGTATAA
Found at i:40017680 original size:51 final size:50
Alignment explanation
Indices: 40017613--40017790 Score: 175
Period size: 52 Copynumber: 3.5 Consensus size: 50
40017603 CGGATACTCG
*
40017613 GTGG-CTTGCACATAGTACCAC-CATTGTAGTTAAAGCTACATTCTTCACAAA
1 GTGGCCTT-CACATAGTACCACAC-TTGT-GATAAAGCTACATTCTTCACAAA
* * * *
40017664 ATGGCCTTCACATAGTACTACACTTGTGACTAAAACTATCTTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-TAAAGCTA-CATTCTTCACAAA
* * ** *
40017716 GTGGCCTTCATATAGTACCATACTTGTGACCAAGCT--ATCTCTTCTCAAA
1 GTGGCCTTCACATAGTACCACACTTGTGATAAAGCTACAT-TCTTCACAAA
*
40017765 GTGGCCTTCACATAGTACCACGCTTG
1 GTGGCCTTCACATAGTACCACACTTG
40017791 AGTCACTAGT
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
48 1 0.01
49 32 0.30
50 1 0.01
51 30 0.29
52 41 0.39
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (50 bp):
GTGGCCTTCACATAGTACCACACTTGTGATAAAGCTACATTCTTCACAAA
Found at i:40017780 original size:49 final size:51
Alignment explanation
Indices: 40017653--40017790 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 51
40017643 TAAAGCTACA
* *
40017653 TTCTTCACAAAATGGCCTTCACATAGTACTACACTTGTGACTAAAACTATC
1 TTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGACTAAAACTATC
* * * *
40017704 TTTCTTCACAAAGTGGCCTTCATATAGTACCATACTTGTGAC-CAAGCTATC
1 -TTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGACTAAAACTATC
* *
40017755 -TCTTCTCAAAGTGGCCTTCACATAGTACCACGCTTG
1 TTCTTCACAAAGTGGCCTTCACATAGTACCACACTTG
40017791 AGTCACTAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
49 32 0.42
51 7 0.09
52 37 0.49
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
TTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGACTAAAACTATC
Found at i:40023682 original size:49 final size:51
Alignment explanation
Indices: 40023570--40023695 Score: 159
Period size: 49 Copynumber: 2.5 Consensus size: 51
40023560 GATATACCTG
* * *
40023570 ATGGCCTGCACATAATACCACCCTTGTAAGCAAAGCTACCTTCTTCATAAA
1 ATGGCCTTCACATAGTACCACACTTGTAAGCAAAGCTACCTTCTTCATAAA
* * *
40023621 ATGGCCTTCACATAGTACCACACTTGTGA-CCAAGCTATC-TCTTC-TCAAA
1 ATGGCCTTCACATAGTACCACACTTGTAAGCAAAGCTACCTTCTTCAT-AAA
*
40023670 GTGGCCTTCACATAGTACCACACTTG
1 ATGGCCTTCACATAGTACCACACTTG
40023696 AGTCACTAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.01
49 33 0.49
50 8 0.12
51 25 0.37
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.27
Consensus pattern (51 bp):
ATGGCCTTCACATAGTACCACACTTGTAAGCAAAGCTACCTTCTTCATAAA
Found at i:40028254 original size:23 final size:23
Alignment explanation
Indices: 40028200--40028301 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
40028190 GAGTCATGGT
*
40028200 CGGTAAGCTCT-TTCGAGCTGAATA
1 CGGTAAGCTCTAAT-GAGCTGAA-A
*
40028224 --GTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
* *
40028245 CGGTAAGCTCCAATAAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
* *
40028268 CAGTAAGCTCCAATGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
*
40028291 CGGCAAGCTCT
1 CGGTAAGCTCT
40028302 TACGAGCTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
21 1 0.01
22 17 0.25
23 49 0.73
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (23 bp):
CGGTAAGCTCTAATGAGCTGAAA
Found at i:40028309 original size:23 final size:23
Alignment explanation
Indices: 40028224--40028300 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
40028214 GAGCTGAATA
* *
40028224 GTAAGCTCTATTGAGCTGAAACG
1 GTAAGCTCCAATGAGCTGAAACG
* *
40028247 GTAAGCTCCAATAAGCTGAAACA
1 GTAAGCTCCAATGAGCTGAAACG
40028270 GTAAGCTCCAATGAGCTGAAACG
1 GTAAGCTCCAATGAGCTGAAACG
*
40028293 GCAAGCTC
1 GTAAGCTC
40028301 TTACGAGCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.19
Consensus pattern (23 bp):
GTAAGCTCCAATGAGCTGAAACG
Found at i:40031372 original size:26 final size:25
Alignment explanation
Indices: 40031330--40031382 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
40031320 AACATTTGAC
*
40031330 AAGTTTAGGTACAAAATTAGATAAAA
1 AAGTTCAGGTACAAAATTAGA-AAAA
*
40031356 AAGTTCAGGTATC-AAATTGGAAAAA
1 AAGTTCAGGTA-CAAAATTAGAAAAA
40031381 AA
1 AA
40031383 TGTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 17 0.71
27 1 0.04
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (25 bp):
AAGTTCAGGTACAAAATTAGAAAAA
Found at i:40031441 original size:29 final size:30
Alignment explanation
Indices: 40031365--40031462 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 30
40031355 AAAGTTCAGG
*
40031365 TATCAAATTGGAAAAAAATGTTAAATTTAGA
1 TATCAAATT-GAAAAAAAAGTTAAATTTAGA
* ** *
40031396 TACCAAATTGTGTAAAAAAG-T-AGTTTAGA
1 TATCAAATTG-AAAAAAAAGTTAAATTTAGA
* *
40031425 TATCAAATTAGAAAAAAAA-TCAAATTTAAA
1 TATCAAATT-GAAAAAAAAGTTAAATTTAGA
*
40031455 TACCAAAT
1 TATCAAAT
40031463 GTTATATTAA
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
29 21 0.41
30 16 0.31
31 14 0.27
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (30 bp):
TATCAAATTGAAAAAAAAGTTAAATTTAGA
Found at i:40031938 original size:10 final size:10
Alignment explanation
Indices: 40031925--40031995 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 10
40031915 TCCTAATTCT
40031925 TAAAAAAATA
1 TAAAAAAATA
40031935 TAAAAAAATA
1 TAAAAAAATA
40031945 T--AAAAATA
1 TAAAAAAATA
* * * *
40031953 CATAAATATT
1 TAAAAAAATA
*
40031963 TAAAAAAAGA
1 TAAAAAAATA
40031973 TAAAAAAAT-
1 TAAAAAAATA
* *
40031982 TAAATATATA
1 TAAAAAAATA
40031992 TAAA
1 TAAA
40031996 TTACATTGTA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
8 7 0.15
9 7 0.15
10 33 0.70
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:40034706 original size:15 final size:15
Alignment explanation
Indices: 40034686--40034717 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40034676 AACAAACAAC
40034686 AACAACAATAATAAT
1 AACAACAATAATAAT
40034701 AACAACAATAATAAT
1 AACAACAATAATAAT
40034716 AA
1 AA
40034718 TAATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (15 bp):
AACAACAATAATAAT
Found at i:40034706 original size:18 final size:18
Alignment explanation
Indices: 40034683--40034720 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
40034673 ATCAACAAAC
40034683 AACAACAACAATAATAAT
1 AACAACAACAATAATAAT
*
40034701 AACAACAATAATAATAAT
1 AACAACAACAATAATAAT
40034719 AA
1 AA
40034721 TAATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (18 bp):
AACAACAACAATAATAAT
Found at i:40034710 original size:12 final size:12
Alignment explanation
Indices: 40034689--40034725 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40034679 AAACAACAAC
40034689 AACAATAATAAT
1 AACAATAATAAT
*
40034701 AACAACAATAAT
1 AACAATAATAAT
*
40034713 AATAATAATAAT
1 AACAATAATAAT
40034725 A
1 A
40034726 TAAAAATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AACAATAATAAT
Found at i:40034713 original size:3 final size:3
Alignment explanation
Indices: 40034692--40034725 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
40034682 CAACAACAAC
* *
40034692 AAT AAT AAT AAC AAC AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40034726 TAAAAATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:40034869 original size:10 final size:10
Alignment explanation
Indices: 40034854--40034886 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
40034844 AAAAGAATAG
40034854 ATAAATAAAT
1 ATAAATAAAT
40034864 ATAAATAAAT
1 ATAAATAAAT
40034874 ATAAA-AAAT
1 ATAAATAAAT
40034883 ATAA
1 ATAA
40034887 TAGTAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:40037179 original size:40 final size:40
Alignment explanation
Indices: 40037120--40037261 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
40037110 AAATTGAATG
* * *
40037120 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
40037160 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
40037200 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
40037240 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
40037262 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:40037262 original size:40 final size:39
Alignment explanation
Indices: 40037159--40037287 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
40037149 TGCTGGAAAT
* * *
40037159 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
40037199 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
40037239 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
40037279 TATATCCGG
1 TATATCCGG
40037288 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:40042917 original size:14 final size:15
Alignment explanation
Indices: 40042884--40042919 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
40042874 ATTTTTTTAA
40042884 AAAAAGTCGATTTCC
1 AAAAAGTCGATTTCC
40042899 AAAAAGTCGATTTCC
1 AAAAAGTCGATTTCC
40042914 AAAAAG
1 AAAAAG
40042920 GTTTTGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (15 bp):
AAAAAGTCGATTTCC
Found at i:40047429 original size:26 final size:26
Alignment explanation
Indices: 40047391--40047474 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
40047381 CATGAAATTC
* *
40047391 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
40047417 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
*
40047443 TTATCATGGAACATTTATCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
40047469 TTATCA
1 TTATCA
40047475 ATTTGTACCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:40048571 original size:35 final size:36
Alignment explanation
Indices: 40048524--40048595 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
40048514 AACTTTTGTC
*
40048524 TAAATTCTAATTTAG-CCCTAAATCGAGACTAACTT
1 TAAATTCTAATTTAGCCCCTAAACCGAGACTAACTT
40048559 TAAATT-TCAATTTAGCCCCTAAACCGAGACTAACTT
1 TAAATTCT-AATTTAGCCCCTAAACCGAGACTAACTT
40048595 T
1 T
40048596 TATTCTTCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 1 0.03
35 13 0.38
36 20 0.59
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.33
Consensus pattern (36 bp):
TAAATTCTAATTTAGCCCCTAAACCGAGACTAACTT
Found at i:40049058 original size:20 final size:22
Alignment explanation
Indices: 40049020--40049059 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40049010 TTTCGTTTGC
40049020 TTTGTTTCTCTTATTCATTTCT
1 TTTGTTTCTCTTATTCATTTCT
40049042 TTTGTTTC-CTT-TTCATTT
1 TTTGTTTCTCTTATTCATTT
40049060 ATTATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTGTTTCTCTTATTCATTTCT
Found at i:40049236 original size:14 final size:15
Alignment explanation
Indices: 40049212--40049257 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
40049202 ATAAATATCT
40049212 TATAATATAATTATAA
1 TATAAT-TAATTATAA
40049228 TA-AATTAATT-TAA
1 TATAATTAATTATAA
*
40049241 TATAATTTATTACTAA
1 TATAATTAATTA-TAA
40049257 T
1 T
40049258 TCGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 3 0.12
16 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTAATTATAA
Found at i:40054927 original size:71 final size:71
Alignment explanation
Indices: 40054843--40055006 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
40054833 CGATTTGTCT
40054843 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
40054908 CTTTCA
66 CTTTCA
40054914 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
40054979 CTTTCA
66 CTTTCA
40054985 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
40055007 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:40055044 original size:71 final size:70
Alignment explanation
Indices: 40054843--40055040 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
40054833 CGATTTGTCT
* * * *
40054843 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
40054908 CTTTCA
65 CTTTCA
* * * *
40054914 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
40054979 CTTTCA
65 CTTTCA
* *
40054985 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
40055041 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:40062029 original size:71 final size:71
Alignment explanation
Indices: 40061945--40062108 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
40061935 CGATTTGTCT
40061945 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
40062010 CTTTCA
66 CTTTCA
40062016 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
40062081 CTTTCA
66 CTTTCA
40062087 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
40062109 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:40062146 original size:71 final size:70
Alignment explanation
Indices: 40061945--40062142 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
40061935 CGATTTGTCT
* * * *
40061945 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
40062010 CTTTCA
65 CTTTCA
* * * *
40062016 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
40062081 CTTTCA
65 CTTTCA
* *
40062087 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
40062143 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:40065229 original size:27 final size:27
Alignment explanation
Indices: 40064701--40065228 Score: 722
Period size: 27 Copynumber: 19.6 Consensus size: 27
40064691 AAAGTACTCC
40064701 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
40064728 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
40064755 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
40064782 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
40064809 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
40064836 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
40064863 CGATTTATAGAATTACCGTTTTACCTT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
40064890 TGATTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
40064917 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
40064944 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
40064971 CAATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
40064998 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
40065025 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
40065051 CTAATTTACATAATTACCATTTTACCC-
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
40065078 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
40065105 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
40065132 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
40065159 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
40065186 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
40065213 CGGTTTACAAAATTAC
1 CGATTTACAGAATTAC
40065229 TAAAATACCC
Statistics
Matches: 445, Mismatches: 50, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
26 25 0.06
27 418 0.94
28 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:40066564 original size:9 final size:9
Alignment explanation
Indices: 40066552--40066608 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40066542 TTTGATAAAC
40066552 ATGATATGT
1 ATGATATGT
*
40066561 ATGATATGCAC
1 ATGATATG--T
*
40066572 ATGACATGT
1 ATGATATGT
*
40066581 ATGATATGCAC
1 ATGATATG--T
40066592 ATGATATGT
1 ATGATATGT
40066601 ATGATATG
1 ATGATATG
40066609 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:40066575 original size:20 final size:20
Alignment explanation
Indices: 40066550--40066620 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40066540 ATTTTGATAA
40066550 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40066570 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
40066590 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40066610 ACATGAGATGT
1 ACATGATATGT
40066621 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40066597 original size:11 final size:11
Alignment explanation
Indices: 40066561--40066615 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40066551 CATGATATGT
40066561 ATGATATGCAC
1 ATGATATGCAC
* *
40066572 ATGACATG--T
1 ATGATATGCAC
40066581 ATGATATGCAC
1 ATGATATGCAC
*
40066592 ATGATATG--T
1 ATGATATGCAC
40066601 ATGATATGCAC
1 ATGATATGCAC
40066612 ATGA
1 ATGA
40066616 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40066722 original size:24 final size:24
Alignment explanation
Indices: 40066665--40066831 Score: 241
Period size: 24 Copynumber: 7.0 Consensus size: 24
40066655 GGAGGAAGTG
40066665 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
40066689 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
40066712 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
40066736 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
40066760 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
40066783 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
40066807 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
40066832 ATGATAAAGC
Statistics
Matches: 132, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
23 44 0.33
24 77 0.58
25 11 0.08
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:40066734 original size:47 final size:47
Alignment explanation
Indices: 40066665--40066831 Score: 239
Period size: 47 Copynumber: 3.5 Consensus size: 47
40066655 GGAGGAAGTG
40066665 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
*
40066712 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
* *
40066760 -TAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTAT
* *
40066807 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
40066832 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 6, Indels: 8
0.89 0.05 0.07
Matches are distributed among these distances:
47 67 0.61
48 31 0.28
49 11 0.10
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (47 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:40066781 original size:71 final size:71
Alignment explanation
Indices: 40066665--40066831 Score: 273
Period size: 71 Copynumber: 2.3 Consensus size: 71
40066655 GGAGGAAGTG
40066665 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
40066730 AGTTAT
66 AGTTAT
* *
40066736 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
40066801 AGTTAT
66 AGTTAT
* *
40066807 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
40066832 ATGATAAAGC
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
71 79 0.88
72 11 0.12
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (71 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
AGTTAT
Found at i:40068487 original size:22 final size:22
Alignment explanation
Indices: 40068460--40068517 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
40068450 CTCCCTTGTT
*
40068460 TTTCTCTGTTTCGTTTGC-TTTG
1 TTTCTCTGTTTCATTT-CTTTTG
*
40068482 TTTCTCTTTTTCATTTCTTTTG
1 TTTCTCTGTTTCATTTCTTTTG
40068504 TTTCT-T-TTTCATTT
1 TTTCTCTGTTTCATTT
40068518 ATTATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.24
21 2 0.06
22 23 0.70
ACGTcount: A:0.03, C:0.17, G:0.09, T:0.71
Consensus pattern (22 bp):
TTTCTCTGTTTCATTTCTTTTG
Found at i:40069321 original size:2 final size:2
Alignment explanation
Indices: 40069314--40069364 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
40069304 TGTAACAATT
* * *
40069314 TA TA TA TA TG TA TG CA 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
40069356 TA TA TA TA T
1 TA TA TA TA T
40069365 CGAATTCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40070482 original size:179 final size:179
Alignment explanation
Indices: 40070179--40070524 Score: 570
Period size: 179 Copynumber: 1.9 Consensus size: 179
40070169 TAATAACCAT
* *
40070179 TTAGGTCATCAAATATTTTTTTAATATAAAACTCAATAGCGATTGGATTTTTACAATTTAATCTC
1 TTAGGTCATCAAATATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAATCTC
* *
40070244 TGAACTTTAATTAATAAATTTTTCGATTAAATTTTTGCACCAATCTTTAATATATTTTCATACTA
66 TGAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTA
40070309 ACTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAA
131 ACTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAA
* * * *
40070358 TTAGGTCATCAAGTA-TTTTCTAATATGAAACTCAATAGCAATTGGATTTTTATAATTTAGTCTC
1 TTAGGTCATCAAATATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAATCTC
* *
40070422 TGAACTTTAATTAACT-ATTTTTCTCGGTTAAATTTCTGAACCAATCTTTAATATATTTTCATAC
66 TGAACTTTAATTAA-TAAATTTT-TCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATAC
40070486 TAACTCCATAAAACCTCTTATTATAATCTCACGGACTTG
129 TAACTCCATAAAACCTCTTATTATAATCTCACGGACTTG
40070525 GTTTATAGAA
Statistics
Matches: 155, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
178 63 0.41
179 92 0.59
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (179 bp):
TTAGGTCATCAAATATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAATCTC
TGAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTA
ACTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAA
Found at i:40072129 original size:16 final size:16
Alignment explanation
Indices: 40072105--40072135 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40072095 ATGATAACCC
*
40072105 AATGGTTTTTTTTTTA
1 AATGATTTTTTTTTTA
40072121 AATGATTTTTTTTTT
1 AATGATTTTTTTTTT
40072136 GTGTTCTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (16 bp):
AATGATTTTTTTTTTA
Found at i:40077609 original size:21 final size:23
Alignment explanation
Indices: 40077584--40077625 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40077574 TGATTTTTTA
*
40077584 TTTAA-AAAAA-TGAGAATTACG
1 TTTAAGAAAAAGTGAAAATTACG
40077605 TTTAAGAAAAAGTGAAAATTA
1 TTTAAGAAAAAGTGAAAATTA
40077626 AATCAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (23 bp):
TTTAAGAAAAAGTGAAAATTACG
Found at i:40080325 original size:21 final size:21
Alignment explanation
Indices: 40080296--40080335 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40080286 TTTCAACAAA
* *
40080296 CAGCTAAAATAACCCAATATT
1 CAGCAAAAAGAACCCAATATT
40080317 CAGCAAAAAGAACCCAATA
1 CAGCAAAAAGAACCCAATA
40080336 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.25, G:0.07, T:0.15
Consensus pattern (21 bp):
CAGCAAAAAGAACCCAATATT
Found at i:40080995 original size:2 final size:2
Alignment explanation
Indices: 40080988--40081020 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40080978 TGTTTTAGCA
*
40080988 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40081021 AATTTCGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:40085155 original size:23 final size:23
Alignment explanation
Indices: 40085131--40085223 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 23
40085121 AATTGTGATG
* * *
40085131 TTAAAGTGCTGCAAATTGAAGTGT
1 TTAAAGTGTTGTAAATTGAAGT-A
*
40085155 TTAAA-TGTTGTGAATTGAAGTA
1 TTAAAGTGTTGTAAATTGAAGTA
40085177 TTAAAGTGTTGTAAATTGAAGTA
1 TTAAAGTGTTGTAAATTGAAGTA
*
40085200 TTTAAA-TTTTGTAAATTGAAGTA
1 -TTAAAGTGTTGTAAATTGAAGTA
40085223 T
1 T
40085224 CTAAGTACTG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.10
23 45 0.74
24 10 0.16
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (23 bp):
TTAAAGTGTTGTAAATTGAAGTA
Found at i:40085160 original size:46 final size:46
Alignment explanation
Indices: 40085131--40085241 Score: 152
Period size: 46 Copynumber: 2.4 Consensus size: 46
40085121 AATTGTGATG
* *
40085131 TTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTGAATTGAAGTA
1 TTAAAGTGCTGCAAATTGAAGTATTTAAATGTTGTAAATTGAAGTA
* * *
40085177 TTAAAGTGTTGTAAATTGAAGTATTTAAATTTTGTAAATTGAAGTA
1 TTAAAGTGCTGCAAATTGAAGTATTTAAATGTTGTAAATTGAAGTA
*
40085223 TCT-AAGTACTGCAAATTGA
1 T-TAAAGTGCTGCAAATTGA
40085242 GATGTTTTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 55 0.98
47 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (46 bp):
TTAAAGTGCTGCAAATTGAAGTATTTAAATGTTGTAAATTGAAGTA
Found at i:40085238 original size:23 final size:22
Alignment explanation
Indices: 40085143--40085241 Score: 81
Period size: 23 Copynumber: 4.3 Consensus size: 22
40085133 AAAGTGCTGC
* * *
40085143 AAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGT-ATTAAGTATTGT
* *
40085166 GAATTGAAGTATTAAAGTGTTGT
1 AAATTGAAGTATT-AAGTATTGT
* *
40085189 AAATTGAAGTATTTAAATTTTGT
1 AAATTGAAGTA-TTAAGTATTGT
* *
40085212 AAATTGAAGTATCTAAGTACTGC
1 AAATTGAAGTAT-TAAGTATTGT
40085235 AAATTGA
1 AAATTGA
40085242 GATGTTTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
22 3 0.05
23 58 0.92
24 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.39
Consensus pattern (22 bp):
AAATTGAAGTATTAAGTATTGT
Found at i:40090639 original size:25 final size:25
Alignment explanation
Indices: 40090618--40090670 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
40090608 AAGAAAAGTG
40090618 AAATAAGAA-AGAAAGAACAAAAGAA
1 AAATAAGAACA-AAAGAACAAAAGAA
*
40090643 AAATAAGAACAAAAGAAGAAAA-AA
1 AAATAAGAACAAAAGAACAAAAGAA
40090667 AAAT
1 AAAT
40090671 TAAAGAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.23
25 19 0.73
26 1 0.04
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (25 bp):
AAATAAGAACAAAAGAACAAAAGAA
Found at i:40091086 original size:27 final size:28
Alignment explanation
Indices: 40091031--40091089 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
40091021 ATAACATTTG
*
40091031 AAAAGTTTAGGTACCAAATTAGATAAAA
1 AAAAGTTTAGGTACCAAATTAGAGAAAA
* * *
40091059 AAAAGTTTATGTATCAAATTAGGGAAAA
1 AAAAGTTTAGGTACCAAATTAGAGAAAA
40091087 AAA
1 AAA
40091090 TGTCAAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.25
Consensus pattern (28 bp):
AAAAGTTTAGGTACCAAATTAGAGAAAA
Found at i:40091180 original size:29 final size:27
Alignment explanation
Indices: 40091138--40091194 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
40091128 AAAAAGTATC
*
40091138 AAGTTCAGGTACCAAATTAGGTAAAAAAA
1 AAGTTCAGATACCAAATTA-G-AAAAAAA
*
40091167 AAGTTTAGATACCAAATTAGAAAAAAA
1 AAGTTCAGATACCAAATTAGAAAAAAA
40091194 A
1 A
40091195 TGTCAAGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 8 0.31
28 1 0.04
29 17 0.65
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (27 bp):
AAGTTCAGATACCAAATTAGAAAAAAA
Found at i:40093563 original size:31 final size:28
Alignment explanation
Indices: 40093487--40093565 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
40093477 AACATCTGAT
* *
40093487 AAGTTCAGGTACCAAATTAGATAAAAAA
1 AAGTTCAGGTATCAAATTAGAAAAAAAA
* *
40093515 AAGTTTAGGTATTAAATTAGAAAAAAATA
1 AAGTTCAGGTATCAAATTAGAAAAAAA-A
*
40093544 TCAAGTTCATGTATCAAATTAG
1 --AAGTTCAGGTATCAAATTAG
40093566 GTATTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 23 0.56
29 1 0.02
31 17 0.41
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (28 bp):
AAGTTCAGGTATCAAATTAGAAAAAAAA
Found at i:40093603 original size:44 final size:43
Alignment explanation
Indices: 40093519--40093610 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 43
40093509 AAAAAAAAGT
* **
40093519 TTAGGTATTAAATTAGAAAAAAATATCAAGTTCATGTATCAAA
1 TTAGGTATTAAATTAGAAAAAAATATAAAGTTCAAATATCAAA
* *
40093562 TTAGGTATTAAATTAAGAAAAAAATGTAAAGTTTAAATATCAAA
1 TTAGGTATTAAATT-AGAAAAAAATATAAAGTTCAAATATCAAA
40093606 TTAGG
1 TTAGG
40093611 GGAAAAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 14 0.33
44 29 0.67
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (43 bp):
TTAGGTATTAAATTAGAAAAAAATATAAAGTTCAAATATCAAA
Found at i:40093644 original size:28 final size:28
Alignment explanation
Indices: 40093568--40093645 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 28
40093558 CAAATTAGGT
* *
40093568 ATTAAATTAAGAAAAAAATGTAAAGTTTAAAT
1 ATTAAATT-AGAAAAAAA---AAAGCTTAAAA
* ***
40093600 ATCAAATTAGGGGAAAAAAAGCTTAAAA
1 ATTAAATTAGAAAAAAAAAAGCTTAAAA
40093628 ATTAAATTAGAAAAAAAA
1 ATTAAATTAGAAAAAAAA
40093646 TGTCATATTC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
28 23 0.64
31 6 0.17
32 7 0.19
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.24
Consensus pattern (28 bp):
ATTAAATTAGAAAAAAAAAAGCTTAAAA
Found at i:40094096 original size:98 final size:98
Alignment explanation
Indices: 40093927--40094124 Score: 317
Period size: 98 Copynumber: 2.0 Consensus size: 98
40093917 TTTTTACAAC
* *
40093927 ATTTAAATTGGTTATTCAATTAATTAAGTTTATTCTTTTTATCCATTTCTGTTAAGTGCCATTAA
1 ATTTAAATTGGTTATTCAATTAATCAAGTTTATTCTTTTTATCCATTTATGTTAAGTGCCATTAA
*
40093992 ATATTTGATGGGAGAATAAGGAGACAGTCCAAA
66 ATATTTGATGGGAGAATAAGCAGACAGTCCAAA
*
40094025 ATTTAAATTGGTTATTCAGTTAATCAAGTTTATTCTTTTTGATCCATTTATGTTAAGTG-CATTA
1 ATTTAAATTGGTTATTCAATTAATCAAGTTTATTCTTTTT-ATCCATTTATGTTAAGTGCCATTA
* * *
40094089 AATATTTGATGGGAGGATAAGCTGAGAGTCCAAA
65 AATATTTGATGGGAGAATAAGCAGACAGTCCAAA
40094123 AT
1 AT
40094125 CTAGTTTAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
98 75 0.82
99 17 0.18
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.41
Consensus pattern (98 bp):
ATTTAAATTGGTTATTCAATTAATCAAGTTTATTCTTTTTATCCATTTATGTTAAGTGCCATTAA
ATATTTGATGGGAGAATAAGCAGACAGTCCAAA
Found at i:40094297 original size:20 final size:19
Alignment explanation
Indices: 40094272--40094313 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
40094262 ATACACAAAT
40094272 ATTTTAAA-ATATTATAATAA
1 ATTTTAAATATA-TAT-ATAA
40094292 ATTTTAAATATATATATAA
1 ATTTTAAATATATATATAA
40094311 ATT
1 ATT
40094314 ACATTGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTAAATATATATATAA
Found at i:40094302 original size:19 final size:20
Alignment explanation
Indices: 40094272--40094313 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
40094262 ATACACAAAT
40094272 ATTTTAAAATAT-TATAATAA
1 ATTTTAAAATATATAT-ATAA
40094292 ATTTT-AAATATATATATAA
1 ATTTTAAAATATATATATAA
40094311 ATT
1 ATT
40094314 ACATTGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTTAAAATATATATATAA
Done.