Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold451
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: 596512
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 5
Found at i:107719 original size:21 final size:20
Alignment explanation
Indices: 107683--107724 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
107673 TTTAAGTTTA
107683 ATATTATTATCTAAATCTTTT
1 ATATTATTATCTAAAT-TTTT
107704 ATATTATTATAC-AAATTTTT
1 ATATTATTAT-CTAAATTTTT
107724 A
1 A
107725 AACTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 14 0.70
22 1 0.05
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTATTATCTAAATTTTT
Found at i:108660 original size:37 final size:37
Alignment explanation
Indices: 108610--108685 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
108600 TCATGCCTCC
108610 CTAATCGTGAGAGGAACTAATCGCTCGACATATATTT
1 CTAATCGTGAGAGGAACTAATCGCTCGACATATATTT
*
108647 CTAATTGTGAGAGGAACTAATCGCTCGACATATATTT
1 CTAATCGTGAGAGGAACTAATCGCTCGACATATATTT
108684 CT
1 CT
108686 CAAGCTCTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (37 bp):
CTAATCGTGAGAGGAACTAATCGCTCGACATATATTT
Found at i:109203 original size:22 final size:23
Alignment explanation
Indices: 109177--109230 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
109167 ATACAATCAT
*
109177 ATAAACAAATATAA-ATAAATAG
1 ATAAACAAATATAATATAAAGAG
*
109199 ATAAATAAA-ATAATATAAAGAG
1 ATAAACAAATATAATATAAAGAG
*
109221 ATAAAGAAAT
1 ATAAACAAAT
109231 GTAGATCGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (23 bp):
ATAAACAAATATAATATAAAGAG
Found at i:110374 original size:20 final size:23
Alignment explanation
Indices: 110349--110395 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
110339 TAAAAAATTA
*
110349 AATATTAAGTAT-AT-AATT-TT
1 AATATTAAATATAATAAATTATT
110369 AATATTAAATATAATAAATTATT
1 AATATTAAATATAATAAATTATT
110392 AATA
1 AATA
110396 AACATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 2 0.09
22 4 0.17
23 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AATATTAAATATAATAAATTATT
Found at i:110891 original size:28 final size:29
Alignment explanation
Indices: 110849--110903 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
110839 TTACACATGA
110849 ATATAAAAAAATAAT-TAAAATATAATATG
1 ATATAAAAAAATAATAT-AAATATAATATG
*
110878 ATAT-AAAAATTAATATAAATATAATA
1 ATATAAAAAAATAATATAAATATAATA
110904 CGAATATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
ATATAAAAAAATAATATAAATATAATATG
Found at i:114212 original size:2 final size:2
Alignment explanation
Indices: 114205--114237 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
114195 CATTTAACTC
114205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
114238 ATAAGCTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:118705 original size:12 final size:13
Alignment explanation
Indices: 118688--118717 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
118678 ATGTATATTT
118688 AAATAATTT-AAA
1 AAATAATTTCAAA
118700 AAATAATTTCAAA
1 AAATAATTTCAAA
118713 AAATA
1 AAATA
118718 TACAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAATTTCAAA
Found at i:120435 original size:30 final size:31
Alignment explanation
Indices: 120374--120435 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
120364 TTTTTGTAAT
* *
120374 ATTTTTTAATTTAATCTTTAATAATTTAATA
1 ATTTTTTAATTAAATCTTTAATAATTAAATA
*
120405 ATTTTTTTATTAAAT-TTTAA-AATATAAATA
1 ATTTTTTAATTAAATCTTTAATAAT-TAAATA
120435 A
1 A
120436 CATATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.11
30 11 0.41
31 13 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTTTTTAATTAAATCTTTAATAATTAAATA
Found at i:122362 original size:27 final size:29
Alignment explanation
Indices: 122332--122387 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
122322 TAGTTAAAGA
122332 TTATTTAAT-TATTA-TATTAAAATTTTT
1 TTATTTAATATATTATTATTAAAATTTTT
* *
122359 TTATTTAATATTTTATTTTTAAAATTTTT
1 TTATTTAATATATTATTATTAAAATTTTT
122388 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
28 4 0.16
29 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTATTTAATATATTATTATTAAAATTTTT
Found at i:122363 original size:14 final size:14
Alignment explanation
Indices: 122346--122387 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
122336 TTAATTATTA
122346 TATTAAAATTTTTT
1 TATTAAAATTTTTT
*
122360 TATTTAATATTTTATT
1 TA-TTAAAATTTT-TT
122376 T-TTAAAATTTTT
1 TATTAAAATTTTT
122388 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 11 0.46
15 9 0.38
16 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTAAAATTTTTT
Found at i:122388 original size:15 final size:16
Alignment explanation
Indices: 122340--122388 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
122330 GATTATTTAA
122340 TTATTATATTAAAATTT
1 TTATTAT-TTAAAATTT
*
122357 TT-TTATTTAATA-TT
1 TTATTATTTAAAATTT
122371 TTATT-TTTAAAATTT
1 TTATTATTTAAAATTT
122386 TTA
1 TTA
122389 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.36
15 12 0.43
16 4 0.14
17 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTTAAAATTT
Found at i:122770 original size:25 final size:26
Alignment explanation
Indices: 122742--122799 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
122732 TTATTTTACC
*
122742 AAAATAAAAAATTATTTATAAT-ATA
1 AAAATAAAAAATTAATTATAATAATA
* * * *
122767 AAAATTATAATTTAATTATTATAATA
1 AAAATAAAAAATTAATTATAATAATA
122793 AAAATAA
1 AAAATAA
122800 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAAAAAATTAATTATAATAATA
Found at i:122783 original size:29 final size:29
Alignment explanation
Indices: 122751--122841 Score: 85
Period size: 30 Copynumber: 2.9 Consensus size: 29
122741 CAAAATAAAA
122751 AATTATTTATAATATAAAAATTATAATTT
1 AATTATTTATAATATAAAAATTATAATTT
* **
122780 AATTA-TTATAATAAAAATAATTTATTTTTT
1 AATTATTTATAATATAAA-AA-TTATAATTT
122810 AATTATAATTAATAAATATATAAAATTATAAT
1 AATTAT--TT-AT-AATATA-AAAATTATAAT
122842 AATAAAAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
28 11 0.23
29 7 0.15
30 12 0.25
33 2 0.04
34 7 0.15
35 7 0.15
36 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTATTTATAATATAAAAATTATAATTT
Found at i:122964 original size:21 final size:21
Alignment explanation
Indices: 122940--122985 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
122930 ATATTTTTAA
122940 AAATAAAATTATATTT-AATTT
1 AAATAAAATTAT-TTTAAATTT
**
122961 AAATCGAATTATTTTAAATTT
1 AAATAAAATTATTTTAAATTT
122982 AAAT
1 AAAT
122986 TATTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATAAAATTATTTTAAATTT
Found at i:122988 original size:16 final size:16
Alignment explanation
Indices: 122967--123014 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 16
122957 ATTTAAATCG
122967 AATTATTTTAAATTTA
1 AATTATTTTAAATTTA
122983 AATTA-TTTAAATTTA
1 AATTATTTTAAATTTA
* *
122998 AATTATATTCAATTTA
1 AATTATTTTAAATTTA
123014 A
1 A
123015 GTTAATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATTTTAAATTTA
Found at i:124003 original size:24 final size:27
Alignment explanation
Indices: 123956--124017 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
123946 CTTTTGTTCA
123956 TTATAATATTTTTTACAATAA-TTTAT
1 TTATAATATTTTTTACAATAATTTTAT
* *
123982 TT-TAATATTTTTATTC-AT-ATTTTCT
1 TTATAATATTTTT-TACAATAATTTTAT
124007 TTATAATATTT
1 TTATAATATTT
124018 ATTGTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 1 0.03
25 18 0.58
26 12 0.39
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATAATATTTTTTACAATAATTTTAT
Found at i:124108 original size:12 final size:12
Alignment explanation
Indices: 124091--124133 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
124081 ATATTTATAA
124091 ACATAATTAATT
1 ACATAATTAATT
*
124103 ACATAAAATAATTT
1 ACAT-AATTAA-TT
*
124117 ATATAATTAATT
1 ACATAATTAATT
124129 ACATA
1 ACATA
124134 TACTAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATAATTAATT
Found at i:124134 original size:14 final size:14
Alignment explanation
Indices: 124093--124135 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
124083 ATTTATAAAC
124093 ATAATTAATTACAT
1 ATAATTAATTACAT
* *
124107 A-AAATAATT-TAT
1 ATAATTAATTACAT
124119 ATAATTAATTACAT
1 ATAATTAATTACAT
124133 ATA
1 ATA
124136 CTAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.13
13 14 0.61
14 6 0.26
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATTAATTACAT
Found at i:124477 original size:3 final size:3
Alignment explanation
Indices: 124469--124501 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
124459 ATATGAAAGT
124469 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
124502 AACATTTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:128085 original size:20 final size:21
Alignment explanation
Indices: 128047--128085 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
128037 TAATATAATT
*
128047 TAATATAAATTATTATTTATG
1 TAATAAAAATTATTATTTATG
128068 TAATAAAAATTA-TATTTA
1 TAATAAAAATTATTATTTA
128086 AATTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TAATAAAAATTATTATTTATG
Found at i:128603 original size:2 final size:2
Alignment explanation
Indices: 128596--128636 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
128586 TCTTTTCAAG
128596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
128637 CTCTTCACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:128812 original size:16 final size:14
Alignment explanation
Indices: 128784--128817 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
128774 ATAAAATATT
128784 TTAAAATATTTATA
1 TTAAAATATTTATA
128798 TTAAATATATATTATA
1 TTAAA-ATAT-TTATA
128814 TTAA
1 TTAA
128818 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAAATATTTATA
Found at i:129513 original size:2 final size:2
Alignment explanation
Indices: 129506--129550 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
129496 AATTATAGTG
*
129506 TA TA TA TA TA TA TA TA TA TA TA GA 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
129548 TA T
1 TA T
129551 CAAGCAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:132948 original size:14 final size:14
Alignment explanation
Indices: 132929--132990 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 14
132919 TATTTTATAT
132929 ATATATAAATTTTA
1 ATATATAAATTTTA
132943 ATATATTAATAATTTATA
1 ATATA-T-A-AATTT-TA
*
132961 ATATAAAAATTTTA
1 ATATATAAATTTTA
* *
132975 AAATATATATTTTA
1 ATATATAAATTTTA
132989 AT
1 AT
132991 TATTTTATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.49
15 6 0.15
16 2 0.05
17 5 0.13
18 7 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATAAATTTTA
Found at i:132948 original size:16 final size:16
Alignment explanation
Indices: 132920--132983 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
132910 TCTTTAAAGT
132920 ATTTTATATATATATAA
1 ATTTTA-ATATATATAA
132937 ATTTTAATATAT-TAATA
1 ATTTTAATATATAT-A-A
132954 ATTTATAATATA-A-AA
1 ATTT-TAATATATATAA
*
132969 ATTTTAAAATATATA
1 ATTTTAATATATATA
132984 TTTTAATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
14 6 0.15
15 7 0.17
16 9 0.22
17 11 0.28
18 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTAATATATATAA
Found at i:132948 original size:18 final size:17
Alignment explanation
Indices: 132920--132983 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
132910 TCTTTAAAGT
132920 ATTTTATATATATATAA
1 ATTTTATATATATATAA
132937 ATTTTA-ATATAT-TAA
1 ATTTTATATATATATAA
* *
132952 TAATTTATA-ATATAAAA
1 -ATTTTATATATATATAA
*
132969 ATTTTA-AAATATATA
1 ATTTTATATATATATA
132984 TTTTAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.10
16 26 0.67
17 9 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTATATATATATAA
Found at i:134286 original size:27 final size:27
Alignment explanation
Indices: 134227--134286 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
134217 TAAATTACTA
134227 TTTATTTTTTATTAAAATATTTAAAAAT
1 TTTATTTTTTATT-AAATATTTAAAAAT
* * *
134255 ATTATTTTTATATT-AATATTTATATAT
1 TTTATTTTT-TATTAAATATTTAAAAAT
134282 TTTAT
1 TTTAT
134287 AATTAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 15 0.56
28 8 0.30
29 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTATTTTTTATTAAATATTTAAAAAT
Found at i:134580 original size:23 final size:25
Alignment explanation
Indices: 134542--134587 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
134532 AGATGTATTA
134542 AAAATATATAATAAATATAAATACT
1 AAAATATATAATAAATATAAATACT
*
134567 AAAATATA-AA-AAATCTAAATA
1 AAAATATATAATAAATATAAATA
134588 ACTATGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATATATAATAAATATAAATACT
Found at i:135316 original size:24 final size:26
Alignment explanation
Indices: 135282--135329 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
135272 TATCTTCATG
*
135282 TCATATCATATCATATTT-TATAACT
1 TCATATCATATCAGATTTATATAACT
135307 TCATA-CATATCAGATTTATATAA
1 TCATATCATATCAGATTTATATAA
135330 TCATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.44
Consensus pattern (26 bp):
TCATATCATATCAGATTTATATAACT
Found at i:135333 original size:23 final size:24
Alignment explanation
Indices: 135282--135335 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
135272 TATCTTCATG
*
135282 TCATATCATATCATATTTTATAAC
1 TCATATCATATCAGATTTTATAAC
135306 TTCATA-CATATCAGATTTATATAA-
1 -TCATATCATATCAGATTT-TATAAC
135330 TCATAT
1 TCATAT
135336 TAAATATTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 5 0.19
24 11 0.42
25 10 0.38
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.44
Consensus pattern (24 bp):
TCATATCATATCAGATTTTATAAC
Found at i:135925 original size:2 final size:2
Alignment explanation
Indices: 135918--135956 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
135908 GAGATCCTTT
135918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
135957 CAAACTTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:143357 original size:24 final size:23
Alignment explanation
Indices: 143330--143374 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
143320 AGGTTAACCC
143330 AAAGAAGTGATTGATCTTTATTTA
1 AAAGAAGTGATT-ATCTTTATTTA
* *
143354 AAAGAATTGATTATTTTTATT
1 AAAGAAGTGATTATCTTTATT
143375 CAACTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (23 bp):
AAAGAAGTGATTATCTTTATTTA
Found at i:143828 original size:19 final size:20
Alignment explanation
Indices: 143798--143854 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
143788 TTTAATAAAA
143798 ATTAATTTAAAAT-ATTATTT
1 ATTAATTTAAAATAATT-TTT
143818 ATTAA-TTAAAATAATTTTT
1 ATTAATTTAAAATAATTTTT
143837 ATTTAAATTTAATAATAA
1 A-TT-AATTTAA-AATAA
143855 AATATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 11 0.34
20 10 0.31
21 2 0.06
22 4 0.12
23 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAATTTAAAATAATTTTT
Found at i:144145 original size:14 final size:14
Alignment explanation
Indices: 144126--144159 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
144116 CGGATAGAGT
144126 AATAAAAAATTGAA
1 AATAAAAAATTGAA
*
144140 AATAAAAAATTTAA
1 AATAAAAAATTGAA
144154 AA-AAAA
1 AATAAAA
144160 TATAATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAAAAATTGAA
Found at i:144591 original size:17 final size:19
Alignment explanation
Indices: 144566--144605 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
144556 TTTAATTTTA
144566 AAATATT-AAAAATTAAAT
1 AAATATTAAAAAATTAAAT
*
144584 AAAT-TTAAAAAATTAATT
1 AAATATTAAAAAATTAAAT
144602 AAAT
1 AAAT
144606 CGATCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATTAAAAAATTAAAT
Found at i:145459 original size:30 final size:29
Alignment explanation
Indices: 145421--145485 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
145411 CAAGATGAAA
* *
145421 ATAAATT-AAAATATGATTGTAAATATGAT
1 ATAAATTAAAAATAT-AGTATAAATATGAT
*
145450 ATAATATTAAAAATATAGTATAAATATTAT
1 ATAA-ATTAAAAATATAGTATAAATATGAT
145480 ATAAAT
1 ATAAAT
145486 GTATGTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 6 0.19
30 18 0.58
31 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (29 bp):
ATAAATTAAAAATATAGTATAAATATGAT
Found at i:145465 original size:19 final size:20
Alignment explanation
Indices: 145452--145502 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
145442 AATATGATAT
145452 AATATTAAAAATATAGTATA
1 AATATTAAAAATATAGTATA
* *
145472 AATATTATATAAATGTA-TGTA
1 AATATTA-A-AAATATAGTATA
145493 AATATTAAAA
1 AATATTAAAA
145503 TTTATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 8 0.30
21 11 0.41
22 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (20 bp):
AATATTAAAAATATAGTATA
Found at i:145569 original size:22 final size:22
Alignment explanation
Indices: 145539--145596 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
145529 TGTATCAAAA
*
145539 TAAATATAAATATATAATATTT
1 TAAAAATAAATATATAATATTT
145561 TAAAAAT-AAT-TATAATATTT
1 TAAAAATAAATATATAATATTT
*
145581 AAAATATATAAATATA
1 TAAA-A-ATAAATATA
145597 GTAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 13 0.43
21 4 0.13
22 8 0.27
23 3 0.10
24 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAAATAAATATATAATATTT
Found at i:149905 original size:33 final size:33
Alignment explanation
Indices: 149863--149934 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
149853 TGAGTTGAAC
149863 ATTATTCTTAGTT-ACTAAGAAAATTAT-TAGATA
1 ATTATTCTTAGTTAACTAA-AAAATTATAT-GATA
* *
149896 ATTATTCTTAGTTAATTAAATAATTATATGATA
1 ATTATTCTTAGTTAACTAAAAAATTATATGATA
149929 ATTATT
1 ATTATT
149935 TAATTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 30 0.86
34 5 0.14
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (33 bp):
ATTATTCTTAGTTAACTAAAAAATTATATGATA
Found at i:151100 original size:16 final size:16
Alignment explanation
Indices: 151079--151109 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
151069 TTATAAATAA
151079 TTATTTTATTATAATT
1 TTATTTTATTATAATT
*
151095 TTATTTTATTTTAAT
1 TTATTTTATTATAAT
151110 GAACTAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTATTATAATT
Found at i:154375 original size:18 final size:18
Alignment explanation
Indices: 154341--154385 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
154331 TTTATAGTAG
154341 TTAAATAAATCATTTATAT
1 TTAAATAAATCATTTAT-T
*
154360 TTAAATATAT-ATTTATT
1 TTAAATAAATCATTTATT
154377 TTAAATAAA
1 TTAAATAAA
154386 ATATTAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAATAAATCATTTATT
Found at i:154389 original size:18 final size:18
Alignment explanation
Indices: 154341--154390 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
154331 TTTATAGTAG
154341 TTAAATAAATCATTTATAT
1 TTAAATAAAT-ATTTATAT
*
154360 TTAAATATATATTTAT-T
1 TTAAATAAATATTTATAT
154377 TTAAATAAAATATT
1 TTAAAT-AAATATT
154391 AGCATATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.25
18 12 0.43
19 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAATAAATATTTATAT
Found at i:155071 original size:2 final size:2
Alignment explanation
Indices: 155064--155095 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
155054 GCAACAATTA
155064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155096 GGCCATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:155779 original size:21 final size:20
Alignment explanation
Indices: 155738--155780 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
155728 ATTAAATATA
*
155738 ATATAAAATATGACATAAAT
1 ATATAAAATATGAAATAAAT
* *
155758 ATATAAATATATTAAATTAAT
1 ATATAAA-ATATGAAATAAAT
155779 AT
1 AT
155781 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
ATATAAAATATGAAATAAAT
Found at i:156098 original size:28 final size:26
Alignment explanation
Indices: 156061--156115 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
156051 ATGTTATTTT
* *
156061 TTATATTATAATTATATTTAATATATTA
1 TTATATTATAA--AAATTTAACATATTA
*
156089 TTATTTTATAAAAATTTAACATATTA
1 TTATATTATAAAAATTTAACATATTA
156115 T
1 T
156116 CAATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.58
28 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTATATTATAAAAATTTAACATATTA
Found at i:163465 original size:26 final size:23
Alignment explanation
Indices: 163436--163487 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 23
163426 TATTTATGAT
163436 TATATTTTATAATATATATAATATAA
1 TATATTTTA-AA-ATAT-TAATATAA
*
163462 TATATTTTAAAGTATTAATATAA
1 TATATTTTAAAATATTAATATAA
163485 TAT
1 TAT
163488 TAGAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 11 0.44
24 3 0.12
25 2 0.08
26 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAATATTAATATAA
Found at i:163530 original size:23 final size:24
Alignment explanation
Indices: 163447--163531 Score: 59
Period size: 23 Copynumber: 3.6 Consensus size: 24
163437 ATATTTTATA
***
163447 ATATATATAATATAATA-TATTTT
1 ATATATATAATATAATATTAGAAT
*
163470 AAAGTAT-TAATATAATATTAGAAT
1 ATA-TATATAATATAATATTAGAAT
* * *
163494 ATATATATATATATGATTTTAGTAT
1 ATATATATA-ATATAATATTAGAAT
*
163519 ATAT-TCTAATATA
1 ATATATATAATATA
163532 TATACTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
23 19 0.40
24 13 0.27
25 16 0.33
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (24 bp):
ATATATATAATATAATATTAGAAT
Found at i:165104 original size:7 final size:7
Alignment explanation
Indices: 165094--165147 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
165084 AATAATTAAT
165094 AAATTTA
1 AAATTTA
165101 AAATTTAA
1 AAATTT-A
165109 AATATTTA
1 AA-ATTTA
*
165117 ATATTTTA
1 A-AATTTA
165125 AAATTTA
1 AAATTTA
*
165132 AATTTTA
1 AAATTTA
*
165139 ATATTTA
1 AAATTTA
165146 AA
1 AA
165148 TTTTTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 23 0.61
8 10 0.26
9 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
AAATTTA
Found at i:165108 original size:16 final size:15
Alignment explanation
Indices: 165089--165139 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
165079 AAAATAATAA
165089 TTAATAAATTTAAAAT
1 TTAA-AAATTTAAAAT
*
165105 TTAAAATATTTAATAT
1 TTAAAA-ATTTAAAAT
* *
165121 TTTAAAATTTAAATT
1 TTAAAAATTTAAAAT
165136 TTAA
1 TTAA
165140 TATTTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAAAATTTAAAAT
Found at i:165111 original size:14 final size:14
Alignment explanation
Indices: 165094--165151 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
165084 AATAATTAAT
*
165094 AAATTTAAAATTTAA
1 AAATTT-AAATTTTA
165109 AATATTTAATATTTTA
1 AA-ATTTAA-ATTTTA
165125 AAATTTAAATTTTA
1 AAATTTAAATTTTA
*
165139 ATATTTAAATTTT
1 AAATTTAAATTTT
165152 TTTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 18 0.46
15 10 0.26
16 11 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:165129 original size:24 final size:22
Alignment explanation
Indices: 165097--165144 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
165087 AATTAATAAA
165097 TTTAAAATTTAAAATATTTAATAT
1 TTTAAAATTT-AAAT-TTTAATAT
165121 TTTAAAATTTAAATTTTAATAT
1 TTTAAAATTTAAATTTTAATAT
165143 TT
1 TT
165145 AAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 10 0.42
23 4 0.17
24 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAAAATTTAAATTTTAATAT
Found at i:166606 original size:19 final size:19
Alignment explanation
Indices: 166582--166618 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
166572 CATCTGGGTC
166582 TGAGTAACATAGGTATACA
1 TGAGTAACATAGGTATACA
166601 TGAGTAACATAGGTATAC
1 TGAGTAACATAGGTATAC
166619 TCAAGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (19 bp):
TGAGTAACATAGGTATACA
Found at i:172229 original size:16 final size:16
Alignment explanation
Indices: 172208--172240 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
172198 AAAGCAATCT
172208 ATAAA-TTATAAACAAA
1 ATAAATTTATAAA-AAA
172224 ATAAATTTATAAAAAA
1 ATAAATTTATAAAAAA
172240 A
1 A
172241 AAAAAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAATTTATAAAAAA
Found at i:172241 original size:17 final size:16
Alignment explanation
Indices: 172208--172241 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
172198 AAAGCAATCT
*
172208 ATAAATTATAAACAAA
1 ATAAATTATAAAAAAA
172224 ATAAATTTATAAAAAAA
1 ATAAA-TTATAAAAAAA
172241 A
1 A
172242 AAAAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAATTATAAAAAAA
Found at i:172787 original size:15 final size:13
Alignment explanation
Indices: 172749--172790 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
172739 GCAGGCTGAG
172749 AAAGAAGAAAATAA
1 AAAGAAGAAAA-AA
172763 AAAGAA-AAAAAA
1 AAAGAAGAAAAAA
172775 AGAAGAGAGAAAAAA
1 A-AAGA-AGAAAAAA
172790 A
1 A
172791 TGATGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 8 0.32
14 7 0.28
15 7 0.28
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAGAAGAAAAAA
Found at i:172851 original size:11 final size:12
Alignment explanation
Indices: 172827--172855 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
172817 TTTAAAATAT
172827 TATATTTTTATA
1 TATATTTTTATA
172839 TATATTTTT-TA
1 TATATTTTTATA
172850 TATATT
1 TATATT
172856 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATATTTTTATA
Found at i:172869 original size:33 final size:32
Alignment explanation
Indices: 172796--172870 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 32
172786 AAAAATGATG
* *
172796 TATTTGTATTTATATTTTTTATTTAAAATATTA
1 TATTT-TATATATATTTTTTATATAAAATATTA
*
172829 TATTTTTATATATATTTTTTATATATTAATAATT-
1 TA-TTTTATATATATTTTTTATATA-AAAT-ATTA
172863 TATTTTAT
1 TATTTTAT
172871 TTTATAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 25 0.69
34 8 0.22
35 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (32 bp):
TATTTTATATATATTTTTTATATAAAATATTA
Found at i:174040 original size:17 final size:17
Alignment explanation
Indices: 174018--174075 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
174008 GAAATTTTTT
*
174018 GATATAATAGATTATAC
1 GATATAATAAATTATAC
*
174035 GATATAAAAAATTATA-
1 GATATAATAAATTATAC
*
174051 -ATATAATATAA-AATAC
1 GATATAATA-AATTATAC
174067 GATATAATA
1 GATATAATA
174076 TGAAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 10 0.29
16 2 0.06
17 22 0.65
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (17 bp):
GATATAATAAATTATAC
Found at i:174140 original size:20 final size:20
Alignment explanation
Indices: 174099--174140 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
174089 TAAAAATAAA
*
174099 TATATAAATATATTAAATTT
1 TATATAAATATATTAAACTT
174119 TATATAAATATA-TAATACTT
1 TATATAAATATATTAA-ACTT
174139 TA
1 TA
174141 AATATGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATAAATATATTAAACTT
Found at i:174468 original size:20 final size:21
Alignment explanation
Indices: 174426--174469 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
174416 ATTATGATAA
**
174426 ATAAATTAATAAATTAATTTT
1 ATAAATTAATAAATTAAAATT
*
174447 ATAAA-TAATAATTTAAAATT
1 ATAAATTAATAAATTAAAATT
174467 ATA
1 ATA
174470 CAAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATTAATAAATTAAAATT
Found at i:174772 original size:22 final size:22
Alignment explanation
Indices: 174722--174776 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
174712 TAATATTATT
*
174722 TATAAAAATTTTATTAAAATTA
1 TATAAAAATATTATTAAAATTA
*
174744 TAT--AAATCATTATT-TAATTA
1 TATAAAAAT-ATTATTAAAATTA
174764 TATAAAAATATTA
1 TATAAAAATATTA
174777 CCTAACTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 12 0.43
21 9 0.32
22 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATAAAAATATTATTAAAATTA
Found at i:174862 original size:19 final size:19
Alignment explanation
Indices: 174815--174894 Score: 99
Period size: 20 Copynumber: 4.2 Consensus size: 19
174805 ATAATTTTTG
*
174815 TTAC-AATTAGATAAAACA
1 TTACTAATTATATAAAACA
*
174833 TTACTTAATTATATAAAACT
1 TTAC-TAATTATATAAAACA
*
174853 TTACTAATTATATAAAGCA
1 TTACTAATTATATAAAACA
*
174872 TTATCTAATTATATAAAATA
1 TTA-CTAATTATATAAAACA
174892 TTA
1 TTA
174895 TTTAAGAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
18 4 0.08
19 16 0.30
20 33 0.62
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (19 bp):
TTACTAATTATATAAAACA
Found at i:174862 original size:39 final size:38
Alignment explanation
Indices: 174815--174889 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
174805 ATAATTTTTG
174815 TTACAATTAGATAAAACATTA-CTTAATTATATAAAACT
1 TTACAATTAGATAAAACATTATC-TAATTATATAAAACT
* *
174853 TTACTAATTATATAAAGCATTATCTAATTATATAAAA
1 TTAC-AATTAGATAAAACATTATCTAATTATATAAAA
174890 TATTATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 4 0.12
39 28 0.85
40 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (38 bp):
TTACAATTAGATAAAACATTATCTAATTATATAAAACT
Found at i:175199 original size:21 final size:21
Alignment explanation
Indices: 175145--175206 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
175135 TTTTCATTAG
175145 AATTACAT-AAAACATTATAT
1 AATTACATAAAAACATTATAT
* *
175165 AATTTAAATAAAAACATTATCT
1 AA-TTACATAAAAACATTATAT
175187 AATTACATAAAAAACATTAT
1 AATTACAT-AAAAACATTAT
175207 TAGTTATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.06
21 10 0.28
22 24 0.67
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTACATAAAAACATTATAT
Found at i:175421 original size:19 final size:19
Alignment explanation
Indices: 175375--175424 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
175365 ATAAAATTAC
*
175375 ATAAAATATATCTAATTATT
1 ATAAAATAT-TATAATTATT
*
175395 AAAAAATATTATAAGTTA-T
1 ATAAAATATTATAA-TTATT
175414 ATAAAATATTA
1 ATAAAATATTA
175425 CTTAAGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAAAATATTATAATTATT
Found at i:175470 original size:19 final size:20
Alignment explanation
Indices: 175441--175495 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
175431 AATAATTTTT
*
175441 ATTATCTAATTACATAAAAA
1 ATTACCTAATTACATAAAAA
* **
175461 ATTA-CTAATTATATAAAGC
1 ATTACCTAATTACATAAAAA
175480 ATTACCTAATTACATA
1 ATTACCTAATTACATA
175496 GAAATATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTACCTAATTACATAAAAA
Found at i:175586 original size:12 final size:13
Alignment explanation
Indices: 175569--175613 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
175559 TTACTAGCTT
175569 CATAAAATA-TTA
1 CATAAAATATTTA
*
175581 CATAAAAATATTTT
1 CAT-AAAATATTTA
175595 CAT-AAATATTTA
1 CATAAAATATTTA
175607 CATAAAA
1 CATAAAA
175614 AATACCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 14 0.50
13 9 0.32
14 5 0.18
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAAAATATTTA
Found at i:175590 original size:13 final size:13
Alignment explanation
Indices: 175572--175614 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
175562 CTAGCTTCAT
175572 AAAATATTACATA
1 AAAATATTACATA
*
175585 AAAATATTTTCATA
1 AAAATA-TTACATA
*
175599 AATAT-TTACATA
1 AAAATATTACATA
175611 AAAA
1 AAAA
175615 ATACCATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 9 0.36
13 6 0.24
14 10 0.40
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATATTACATA
Found at i:176172 original size:27 final size:29
Alignment explanation
Indices: 176137--176210 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 29
176127 TTATGGACAC
* *
176137 ATTAATAAATTTAATTTGTATGAA-TTAA
1 ATTATTAAATTTAATTTGTATAAATTTAA
** *
176165 ATT-TTAAATAAAATTTTTATAAATTTAA
1 ATTATTAAATTTAATTTGTATAAATTTAA
* *
176193 ATTATTTAGTTTAATTTG
1 ATTATTAAATTTAATTTG
176211 AAATATTATT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
27 15 0.44
28 10 0.29
29 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTATTAAATTTAATTTGTATAAATTTAA
Found at i:177146 original size:2 final size:2
Alignment explanation
Indices: 177141--177176 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
177131 TCTAATTTTT
177141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
177177 AACTTAGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:180287 original size:6 final size:6
Alignment explanation
Indices: 180276--180315 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
180266 TAATTTTTAT
*
180276 AATTAA AATTAA AATTAA AATTTAA TAATTTA AATTAA AA
1 AATTAA AATTAA AATTAA AA-TTAA -AATTAA AATTAA AA
180316 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 21 0.70
7 7 0.23
8 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
AATTAA
Found at i:180291 original size:26 final size:26
Alignment explanation
Indices: 180259--180315 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
180249 ATCAAATATG
* * *
180259 TAAAATTTAATTTTTATAATTAAAAT
1 TAAAATTAAAATTTAATAATTAAAAT
*
180285 TAAAATTAAAATTTAATAATTTAAAT
1 TAAAATTAAAATTTAATAATTAAAAT
180311 TAAAA
1 TAAAA
180316 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAATTAAAATTTAATAATTAAAAT
Found at i:180310 original size:20 final size:19
Alignment explanation
Indices: 180278--180315 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
180268 ATTTTTATAA
180278 TTAAAATTAAAATTAAAAT
1 TTAAAATTAAAATTAAAAT
*
180297 TTAATAATTTAAATTAAAA
1 TTAA-AATTAAAATTAAAA
180316 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAATTAAAATTAAAAT
Found at i:180400 original size:19 final size:17
Alignment explanation
Indices: 180368--180421 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 17
180358 TTTTAAATAA
180368 AATAATTTTATTATATT
1 AATAATTTTATTATATT
*
180385 AATATATTTATATTATTTT
1 AATA-ATTT-TATTATATT
*
180404 AAATAATTTTTTTATATT
1 -AATAATTTTATTATATT
180422 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.13
18 11 0.35
19 12 0.39
20 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATAATTTTATTATATT
Found at i:180927 original size:20 final size:19
Alignment explanation
Indices: 180900--180940 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
180890 TATATATTAT
180900 TTAAAATAAATTTAATTTA
1 TTAAAATAAATTTAATTTA
* *
180919 TTAATAATATATTTTATTTA
1 TTAA-AATAAATTTAATTTA
180939 TT
1 TT
180941 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAAATAAATTTAATTTA
Found at i:181973 original size:7 final size:7
Alignment explanation
Indices: 181963--182020 Score: 50
Period size: 8 Copynumber: 8.0 Consensus size: 7
181953 TTAAAAATTA
181963 AAATTTT
1 AAATTTT
181970 AAATTTTTT
1 AAA--TTTT
181979 AATATTTT
1 AA-ATTTT
181987 AAA-TTT
1 AAATTTT
181993 AAA-TTT
1 AAATTTT
181999 -AATTTT
1 AAATTTT
182005 ATAATTTAT
1 A-AATTT-T
182014 AAATTTT
1 AAATTTT
182021 GTTTTGATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
5 2 0.05
6 12 0.27
7 5 0.11
8 16 0.36
9 8 0.18
10 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AAATTTT
Found at i:181980 original size:17 final size:17
Alignment explanation
Indices: 181960--181992 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
181950 TTTTTAAAAA
181960 TTAAAATTTTAAATTTT
1 TTAAAATTTTAAATTTT
*
181977 TTAATATTTTAAATTT
1 TTAAAATTTTAAATTT
181993 AAATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAAAATTTTAAATTTT
Found at i:181990 original size:24 final size:23
Alignment explanation
Indices: 181949--181998 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
181939 ACATAAAATT
181949 TTTTTTAAAAATTAAAATTTTAAA
1 TTTTTTAAAAATTAAAA-TTTAAA
* * *
181973 TTTTTTAATATTTTAAATTTAAA
1 TTTTTTAAAAATTAAAATTTAAA
181996 TTT
1 TTT
181999 AATTTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTTAAAAATTAAAATTTAAA
Found at i:184437 original size:21 final size:20
Alignment explanation
Indices: 184391--184438 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
184381 CTAGTGTCTA
*
184391 TTAAATTATAATAATATAAT
1 TTAAATTATAATAATAAAAT
** *
184411 AAAAATTATAAATATTAAAAT
1 TTAAATTAT-AATAATAAAAT
184432 TTAAATT
1 TTAAATT
184439 GTGAATCTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAATTATAATAATAAAAT
Found at i:185703 original size:2 final size:2
Alignment explanation
Indices: 185696--185726 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
185686 CACATCTATT
185696 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
185727 TTGAAGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:185956 original size:22 final size:22
Alignment explanation
Indices: 185929--185970 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
185919 GATAAAAAAT
185929 AAAAA-TTATATTTTAATTCTTA
1 AAAAATTTATA-TTTAATTCTTA
185951 AAAAATTTATATTTAATTCT
1 AAAAATTTATATTTAATTCT
185971 GACTTTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAAATTTATATTTAATTCTTA
Found at i:187507 original size:18 final size:19
Alignment explanation
Indices: 187471--187507 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
187461 CATCTAATAC
187471 AATTAAGAACTTTATATAT
1 AATTAAGAACTTTATATAT
187490 AATT-AGAA-TTTATCATAT
1 AATTAAGAACTTTAT-ATAT
187508 CTACTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
AATTAAGAACTTTATATAT
Found at i:187556 original size:18 final size:17
Alignment explanation
Indices: 187521--187563 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
187511 CTTTATACAT
187521 AAAAATATATATTCTTA
1 AAAAATATATATTCTTA
187538 AAAAATTATCATATT-TT-
1 AAAAA-TAT-ATATTCTTA
187555 AAAAATATA
1 AAAAATATA
187564 AGTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 10 0.42
18 5 0.21
19 5 0.21
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAAATATATATTCTTA
Found at i:187683 original size:19 final size:20
Alignment explanation
Indices: 187659--187704 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
187649 TAAATGTCAC
187659 TAATTTT-ATTT-TCTTATTA
1 TAATTTTGATTTAT-TTATTA
*
187678 TAATTTTGATTTATTTTTTA
1 TAATTTTGATTTATTTATTA
187698 TAATTTT
1 TAATTTT
187705 TTTGATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 16 0.67
21 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TAATTTTGATTTATTTATTA
Found at i:187707 original size:23 final size:24
Alignment explanation
Indices: 187663--187711 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
187653 TGTCACTAAT
*
187663 TTTATTTTCTTATTATAATTTTGA
1 TTTATTTTCTTATAATAATTTTGA
**
187687 TTTATTTT-TTATAATTTTTTTGA
1 TTTATTTTCTTATAATAATTTTGA
187710 TT
1 TT
187712 AAATTAGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTATTTTCTTATAATAATTTTGA
Found at i:188118 original size:2 final size:2
Alignment explanation
Indices: 188111--188156 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
188101 CAAACTCTTA
** * *
188111 AT AT AT AT CG AT AT AT AT AT CT AT AT AT AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
188153 AT AT
1 AT AT
188157 TTGTATGAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:188340 original size:11 final size:11
Alignment explanation
Indices: 188326--188460 Score: 50
Period size: 11 Copynumber: 12.2 Consensus size: 11
188316 TAAAATAAGA
188326 TATAAATATAT
1 TATAAATATAT
*
188337 TATAAAACGATAT
1 TAT-AAA-TATAT
* *
188350 AAAAAATATAT
1 TATAAATATAT
*
188361 ATATAACA-ATGT
1 -TATAA-ATATAT
*
188373 ATATTAATATAT
1 -TATAAATATAT
* *
188385 CA-AAATTTAT
1 TATAAATATAT
*
188395 ATATATATAATAT
1 -TATAAAT-ATAT
*
188408 TTTAAATATAT
1 TATAAATATAT
*
188419 T-TACGATATA-
1 TATA-AATATAT
188429 TA-AAA-AT-T
1 TATAAATATAT
*
188437 TATAAATATAA
1 TATAAATATAT
188448 TATAAATATAT
1 TATAAATATAT
188459 TA
1 TA
188461 ATTATCAAAA
Statistics
Matches: 89, Mismatches: 21, Indels: 28
0.64 0.15 0.20
Matches are distributed among these distances:
8 4 0.04
9 4 0.04
10 12 0.13
11 32 0.36
12 28 0.31
13 9 0.10
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (11 bp):
TATAAATATAT
Found at i:188400 original size:18 final size:18
Alignment explanation
Indices: 188355--188404 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
188345 GATATAAAAA
188355 ATATATATATAACAATGT
1 ATATATATATAACAATGT
*
188373 ATATTAATATATCAA-AATTT
1 ATA-T-ATATAT-AACAATGT
188393 ATATATATATAA
1 ATATATATATAA
188405 TATTTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 9 0.32
19 2 0.07
20 13 0.46
21 2 0.07
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
ATATATATATAACAATGT
Found at i:188416 original size:16 final size:18
Alignment explanation
Indices: 188378--188418 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
188368 AATGTATATT
188378 AATATATCAAAATTTATA
1 AATATATCAAAATTTATA
* *
188396 TATATAT-AATATTT-TA
1 AATATATCAAAATTTATA
188412 AATATAT
1 AATATAT
188419 TTACGATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 8 0.40
17 6 0.30
18 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATCAAAATTTATA
Found at i:189663 original size:15 final size:15
Alignment explanation
Indices: 189643--189675 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
189633 GTTATATTCA
*
189643 TTTTTTTATATTGTG
1 TTTTTTTATATCGTG
189658 TTTTTTTATATCGTG
1 TTTTTTTATATCGTG
189673 TTT
1 TTT
189676 ATATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.12, T:0.73
Consensus pattern (15 bp):
TTTTTTTATATCGTG
Found at i:192582 original size:32 final size:32
Alignment explanation
Indices: 192537--192607 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
192527 GTTGGAGGGA
192537 GCTGCTGCTGGAGTTGCTCATG-GCTGCTGGA-G
1 GCTGCTGCTGGAGTTGCT--TGAGCTGCTGGATG
192569 GCTGCTG-TGGGAGTTGCTTGAGCTGCTGGATG
1 GCTGCTGCT-GGAGTTGCTTGAGCTGCTGGATG
*
192601 GTTGCTG
1 GCTGCTG
192608 AGCTGCTGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 2 0.06
31 10 0.29
32 23 0.66
ACGTcount: A:0.08, C:0.18, G:0.42, T:0.31
Consensus pattern (32 bp):
GCTGCTGCTGGAGTTGCTTGAGCTGCTGGATG
Found at i:192611 original size:19 final size:19
Alignment explanation
Indices: 192581--192633 Score: 97
Period size: 19 Copynumber: 2.7 Consensus size: 19
192571 TGCTGTGGGA
192581 GTTGCTTGAGCTGCTGGATG
1 GTTGC-TGAGCTGCTGGATG
192601 GTTGCTGAGCTGCTGGATG
1 GTTGCTGAGCTGCTGGATG
192620 GTTGCTGAGCTGCT
1 GTTGCTGAGCTGCT
192634 AGCCTGCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 28 0.85
20 5 0.15
ACGTcount: A:0.09, C:0.17, G:0.40, T:0.34
Consensus pattern (19 bp):
GTTGCTGAGCTGCTGGATG
Found at i:193341 original size:19 final size:19
Alignment explanation
Indices: 193293--193330 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
193283 TTTTTTTGGA
*
193293 TATTTGATATTTTTATTTT
1 TATTTGATTTTTTTATTTT
193312 TATTTGATTTTTTTATTTT
1 TATTTGATTTTTTTATTTT
193331 ATTATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (19 bp):
TATTTGATTTTTTTATTTT
Found at i:194255 original size:31 final size:31
Alignment explanation
Indices: 194220--194306 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
194210 AACTTGTGTG
194220 GGCTTTGACTGAGGTGCCGCCAACTCATGCA
1 GGCTTTGACTGAGGTGCCGCCAACTCATGCA
* *
194251 GGCTTTGACT-AGGGTACCGCTAACTCATGCA
1 GGCTTTGACTGA-GGTGCCGCCAACTCATGCA
194282 GGCTTTGACTGAGGTGCCGCCAACT
1 GGCTTTGACTGAGGTGCCGCCAACT
194307 TGTGGGCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 48 0.96
32 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.29, T:0.24
Consensus pattern (31 bp):
GGCTTTGACTGAGGTGCCGCCAACTCATGCA
Found at i:194365 original size:28 final size:28
Alignment explanation
Indices: 194304--194572 Score: 339
Period size: 28 Copynumber: 9.6 Consensus size: 28
194294 GGTGCCGCCA
* * *
194304 ACTTGTGGGCTTTAAAAGGGGATGCCACTA
1 ACTTGTGGGCTTTGAAA-TGG-TGCCACTG
** *
194334 ACTTGTGGATTTTGAAATGGTACCACTG
1 ACTTGTGGGCTTTGAAATGGTGCCACTG
* *
194362 ACTTGT-GGCTTTTGAAATGATGCCATTG
1 ACTTGTGGGC-TTTGAAATGGTGCCACTG
* *
194390 ACTTGTGGGCTTTGAAATGTTGCCACTA
1 ACTTGTGGGCTTTGAAATGGTGCCACTG
* *
194418 ATTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAATGGTGCCACTG
*
194446 ACTTGTGGGCTTTGAAA-GGATGCCACTA
1 ACTTGTGGGCTTTGAAATGG-TGCCACTG
194474 ACTTGTGGGCTTTGAAATGGTGCCACTG
1 ACTTGTGGGCTTTGAAATGGTGCCACTG
194502 ACTT-TGGGCTTTGAAA-GGATGCCACTG
1 ACTTGTGGGCTTTGAAATGG-TGCCACTG
*
194529 ACTTGTGGGCTTTGAAATGTTGCCACTG
1 ACTTGTGGGCTTTGAAATGGTGCCACTG
194557 ACTTGTGGGCTTTGAA
1 ACTTGTGGGCTTTGAA
194573 GGAAATGGAT
Statistics
Matches: 210, Mismatches: 22, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.01
27 27 0.13
28 159 0.76
29 8 0.04
30 14 0.07
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAATGGTGCCACTG
Found at i:194728 original size:34 final size:32
Alignment explanation
Indices: 194589--194773 Score: 97
Period size: 33 Copynumber: 5.4 Consensus size: 32
194579 GGATGCTAAT
* * *
194589 GAGTTGTGGGCTTTGAAGAGAAAAATGTGCCATG
1 GAGTTGTGGACTTT-AAAAGAAAAA-GTGCCACG
*
194623 GGGTTGTGGAC-TTAAAAGGAACAAAGTGCCACG
1 GAGTTGTGGACTTTAAAA-GAA-AAAGTGCCACG
* * * * * *
194656 AAGTTATGGACCTTAAAGGAAAATA-TGCTATG
1 GAGTTGTGGACTTTAAAAGAAAA-AGTGCCACG
*
194688 GAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGGG
1 GAGTTGTGGACTTT-AAAAGAAAAA-GTGCCAC---G
* *
194725 TTGTGTTGTGGAC-TTAAAAGGAACAAGGTGCCACG
1 --GAGTTGTGGACTTTAAAA-GAA-AAAGTGCCACG
*
194760 AAGTTGTGGACTTT
1 GAGTTGTGGACTTT
194774 GAAGGAAATG
Statistics
Matches: 114, Mismatches: 22, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
32 21 0.18
33 41 0.36
34 23 0.20
35 1 0.01
37 5 0.04
38 12 0.11
39 11 0.10
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.25
Consensus pattern (32 bp):
GAGTTGTGGACTTTAAAAGAAAAAGTGCCACG
Found at i:194767 original size:33 final size:32
Alignment explanation
Indices: 194625--194804 Score: 110
Period size: 33 Copynumber: 5.3 Consensus size: 32
194615 GTGCCATGGG
*
194625 GTTGTGGACTTAAAAGGAACAAAGTGCCACGAA
1 GTTGTGGACTTAAAAGGAA-AAGGTGCCACGAA
* ** * * *
194658 GTTATGGACCTT-AAAGGAAAATATGCTATGGA
1 GTTGTGGA-CTTAAAAGGAAAAGGTGCCACGAA
* * **
194690 GTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGGGTTGT
1 GTTGTGGAC-TT-AAAAGGAAAAGGTGCCAC---G--AA
194729 GTTGTGGACTTAAAAGGAACAAGGTGCCACGAA
1 GTTGTGGACTTAAAAGGAA-AAGGTGCCACGAA
** * *
194762 GTTGTGGACTTTGAAGGAAATGGATGCCACTAA
1 GTTGTGGACTTAAAAGGAAAAGG-TGCCACGAA
*
194795 GTCGTGGACT
1 GTTGTGGACT
194805 CAGAAAAAGG
Statistics
Matches: 113, Mismatches: 23, Indels: 22
0.72 0.15 0.14
Matches are distributed among these distances:
31 1 0.01
32 19 0.17
33 48 0.42
34 15 0.13
35 1 0.01
37 8 0.07
38 12 0.11
39 9 0.08
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (32 bp):
GTTGTGGACTTAAAAGGAAAAGGTGCCACGAA
Found at i:194779 original size:104 final size:100
Alignment explanation
Indices: 194559--194781 Score: 290
Period size: 104 Copynumber: 2.2 Consensus size: 100
194549 TGCCACTGAC
* * * *
194559 TTGTGGGCTTTGAAGG-AAATGGATGCTAATGAGTTGTGGGCTTTGAAGAGAAAAATGTGCCATG
1 TTGTGGACTTTGAAGGAAAAT-GATGCTAATGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCAGG
194623 GGGTTGTGGACTTAAAAGGAACAAAGTGCCACGAAG
65 GGGTTGTGGACTTAAAAGGAACAAAGTGCCACGAAG
* * *
194659 TTATGGACCTTAAAGGAAAAT-ATGCT-ATGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACG
1 TTGTGGACTTTGAAGGAAAATGATGCTAAT-GAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCA--
*
194722 GGGTTGTGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAG
63 GGG--G-GTTGTGGACTTAAAAGGAACAAAGTGCCACGAAG
194763 TTGTGGACTTTGAAGGAAA
1 TTGTGGACTTTGAAGGAAA
194782 TGGATGCCAC
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
98 2 0.02
99 35 0.33
100 12 0.11
101 6 0.06
103 1 0.01
104 49 0.47
ACGTcount: A:0.32, C:0.10, G:0.33, T:0.25
Consensus pattern (100 bp):
TTGTGGACTTTGAAGGAAAATGATGCTAATGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCAGGG
GGTTGTGGACTTAAAAGGAACAAAGTGCCACGAAG
Found at i:194819 original size:30 final size:30
Alignment explanation
Indices: 194749--194960 Score: 178
Period size: 30 Copynumber: 6.8 Consensus size: 30
194739 TAAAAGGAAC
* *
194749 AAGG-TGCCAC-GAAGTTGTGGACTTTGAAGGA
1 AAGGATGCCACTG-AGTCGTGGACTTAGAA--A
* *
194780 AATGGATGCCACTAAGTCGTGGACTCAGAAA
1 AA-GGATGCCACTGAGTCGTGGACTTAGAAA
*
194811 AAGGATGCCACTGAGTAGTGGACTTTTAAGAAA
1 AAGGATGCCACTGAGTCGTGGAC--TT-AGAAA
* *
194844 AAGGACGCCACTGAGTCGTGGAATTAGAAA
1 AAGGATGCCACTGAGTCGTGGACTTAGAAA
* *
194874 AAGGATGCCACTAAGTCATGGACTTTAGAGAAA
1 AAGGATGCCACTGAGTCGTGGAC-TT--AGAAA
* * *
194907 AAAGATG-CATTGAGTCATGGACTTAGAAA
1 AAGGATGCCACTGAGTCGTGGACTTAGAAA
* * *
194936 AATGATGCCATTGAGTAGTGGACTT
1 AAGGATGCCACTGAGTCGTGGACTT
194961 TTAGGAAATG
Statistics
Matches: 151, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
29 11 0.07
30 58 0.38
31 11 0.07
32 16 0.11
33 55 0.36
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (30 bp):
AAGGATGCCACTGAGTCGTGGACTTAGAAA
Found at i:194835 original size:63 final size:62
Alignment explanation
Indices: 194749--194961 Score: 236
Period size: 63 Copynumber: 3.4 Consensus size: 62
194739 TAAAAGGAAC
* * * * *
194749 AAGG-TGCCAC-GAAGTTGTGGACTTTGAAGGAAATGGATGCCACTAAGTCGTGGACTCAGAAA
1 AAGGATGCCACTG-AGTAGTGGACTTT-AAGAAAAAGGATGCCACTGAGTCGTGGACTTAGAAA
* *
194811 AAGGATGCCACTGAGTAGTGGACTTTTAAGAAAAAGGACGCCACTGAGTCGTGGAATTAGAAA
1 AAGGATGCCACTGAGTAGTGGAC-TTTAAGAAAAAGGATGCCACTGAGTCGTGGACTTAGAAA
* * * *
194874 AAGGATGCCACTAAGTCA-TGGACTTTAGAGAAAAAAGATG-CATTGAGTCATGGACTTAGAAA
1 AAGGATGCCACTGAGT-AGTGGACTTTA-AGAAAAAGGATGCCACTGAGTCGTGGACTTAGAAA
* *
194936 AATGATGCCATTGAGTAGTGGACTTT
1 AAGGATGCCACTGAGTAGTGGACTTT
194962 TAGGAAATGT
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.01
62 48 0.37
63 75 0.58
64 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (62 bp):
AAGGATGCCACTGAGTAGTGGACTTTAAGAAAAAGGATGCCACTGAGTCGTGGACTTAGAAA
Found at i:196272 original size:8 final size:8
Alignment explanation
Indices: 196261--196286 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
196251 TTTTTTTTCA
196261 TTTTGTTT
1 TTTTGTTT
196269 TTTTGTTT
1 TTTTGTTT
196277 TTTTGTTT
1 TTTTGTTT
196285 TT
1 TT
196287 ACTTCTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTGTTT
Found at i:202195 original size:19 final size:19
Alignment explanation
Indices: 202150--202197 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
202140 GGAGGGAGCT
*
202150 GCTGCTGGAGTTGCTCCTG
1 GCTGTTGGAGTTGCTCCTG
* * *
202169 GTTATTGGAGTTGCTCGTG
1 GCTGTTGGAGTTGCTCCTG
202188 GCTGTTGGAG
1 GCTGTTGGAG
202198 GCTGTTATGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.08, C:0.17, G:0.40, T:0.35
Consensus pattern (19 bp):
GCTGTTGGAGTTGCTCCTG
Found at i:202869 original size:8 final size:8
Alignment explanation
Indices: 202856--202913 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 8
202846 ATGATATTTA
202856 ATTTTTTT
1 ATTTTTTT
202864 ATTTTTTT
1 ATTTTTTT
*
202872 A---TTTG
1 ATTTTTTT
202877 ATTTTTTT
1 ATTTTTTT
*
202885 CTTTTTTT
1 ATTTTTTT
* *
202893 CTTTTATT
1 ATTTTTTT
*
202901 ATTTTTTA
1 ATTTTTTT
202909 ATTTT
1 ATTTT
202914 ATAAAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
5 4 0.10
8 36 0.90
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (8 bp):
ATTTTTTT
Found at i:202874 original size:21 final size:21
Alignment explanation
Indices: 202850--202906 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
202840 TTTCTTATGA
202850 TATTTAATTTTTTTATTTTTT
1 TATTTAATTTTTTTATTTTTT
* *
202871 TATTTGATTTTTTTCTTTTTT
1 TATTTAATTTTTTTATTTTTT
* *
202892 TCTTTTATTATTTTT
1 TATTTAATT-TTTTT
202907 TAATTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.81
Consensus pattern (21 bp):
TATTTAATTTTTTTATTTTTT
Found at i:208877 original size:21 final size:21
Alignment explanation
Indices: 208844--208916 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
208834 TAGCCCATTA
* * *
208844 TATCAATATATGTTAGGATTG
1 TATCGATACATGTTAAGATTG
*
208865 TATCGATACATGTCAAGATTG
1 TATCGATACATGTTAAGATTG
* *
208886 TATCGATATATGATAAGATTG
1 TATCGATACATGTTAAGATTG
208907 TATCGATACA
1 TATCGATACA
208917 AATAAAGGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
TATCGATACATGTTAAGATTG
Found at i:210741 original size:19 final size:19
Alignment explanation
Indices: 210717--210842 Score: 117
Period size: 19 Copynumber: 7.6 Consensus size: 19
210707 AACTGTAACG
210717 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
210736 GTATCGATAC--AA----T
1 GTATCGATACATAAGTGTT
210749 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
*
210768 TTATCGATAC--AA----T
1 GTATCGATACATAAGTGTT
210781 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
210800 GTATCGATAC--AA----T
1 GTATCGATACATAAGTGTT
210813 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
210832 GTATCGATACA
1 GTATCGATACA
210843 ATGTATCGCT
Statistics
Matches: 87, Mismatches: 2, Indels: 36
0.70 0.02 0.29
Matches are distributed among these distances:
13 32 0.37
15 6 0.07
17 6 0.07
19 43 0.49
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (19 bp):
GTATCGATACATAAGTGTT
Found at i:210753 original size:13 final size:13
Alignment explanation
Indices: 210735--210823 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
210725 ACATAAGTGT
210735 TGTATCGATACAA
1 TGTATCGATACAA
210748 TGTATCGATACATAA
1 TGTATCGATAC--AA
210763 GTGTTTTATCGATACAA
1 -TG---TATCGATACAA
210780 TGTATCGATACATAA
1 TGTATCGATAC--AA
210795 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
210812 TGTATCGATACA
1 TGTATCGATACA
210824 TAAGTGTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 32 0.50
15 4 0.06
16 4 0.06
17 4 0.06
19 20 0.31
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:210758 original size:32 final size:32
Alignment explanation
Indices: 210717--210850 Score: 259
Period size: 32 Copynumber: 4.2 Consensus size: 32
210707 AACTGTAACG
210717 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
*
210749 GTATCGATACATAAGTGTTTTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
210781 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
210813 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
210845 GTATCG
1 GTATCG
210851 CTACGAAGCT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 100 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
GTATCGATACATAAGTGTTGTATCGATACAAT
Found at i:216717 original size:12 final size:11
Alignment explanation
Indices: 216681--216745 Score: 58
Period size: 12 Copynumber: 5.6 Consensus size: 11
216671 GTAAACACAC
216681 AAAAAAAAACA
1 AAAAAAAAACA
* ** *
216692 ACAGCAACACA
1 AAAAAAAAACA
216703 AAAAACAAAACA
1 AAAAA-AAAACA
216715 AAAATAAAAACA
1 AAAA-AAAAACA
*
216727 AAAAAATACACA
1 AAAAAA-AAACA
216739 AAAAAAA
1 AAAAAAA
216746 GGAAAAGAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
11 12 0.29
12 29 0.69
13 1 0.02
ACGTcount: A:0.80, C:0.15, G:0.02, T:0.03
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:218089 original size:35 final size:34
Alignment explanation
Indices: 217952--218331 Score: 273
Period size: 34 Copynumber: 11.6 Consensus size: 34
217942 CTCTCCTTCA
* * *
217952 AAGTCCACAACTCAGTGGCATCCCTTTTTCC-TAT
1 AAGTCCACAACTCCGTGGCA-CTCTTTTTCCTTTT
* *
217986 AAGTCCACAACTCAGTGGTA-TCTCTTTT-C---T
1 AAGTCCACAACTCCGTGGCACTCT-TTTTCCTTTT
* *
218016 AAGTCCACGACTCCGTGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
218049 AAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACTC-TTTTTCCTTTT
* *
218085 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * **
218119 AAAGTCTACGACTCCGTGGCA-TCTCTTTCCTTCA
1 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
218153 AAGTCCA-AACTCAGTGGCATCCCTTTTTCC-TGT
1 AAGTCCACAACTCCGTGGCA-CTCTTTTTCCTTTT
* *
218186 AAGTCCACAACTCAGTGGCA-TC-TCTT--TTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * *
218216 AAGTCCACGACTCAGTGGCAC-ATTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* **
218249 AAAGCCCACAACTCCGTGATACTCTTTTTCCCTTTT
1 -AAGTCCACAACTCCGTGGCACTCTTTTT-CCTTTT
* *
218285 AAGTCCATAACTCCATGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
218312 AAGTCCACAACTCCGTGGCA
1 AAGTCCACAACTCCGTGGCA
218332 TCAAGTCAGT
Statistics
Matches: 281, Mismatches: 44, Indels: 49
0.75 0.12 0.13
Matches are distributed among these distances:
27 24 0.09
29 4 0.01
30 41 0.15
31 6 0.02
32 14 0.05
33 24 0.09
34 92 0.33
35 61 0.22
36 15 0.05
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:218308 original size:27 final size:27
Alignment explanation
Indices: 218278--218331 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
218268 TACTCTTTTT
*
218278 CCCTTTTAAGTCCATAACTCCATGGCA
1 CCCTTTTAAGTCCACAACTCCATGGCA
*
218305 CCCTTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCATGGCA
218332 TCAAGTCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCATGGCA
Found at i:218354 original size:200 final size:197
Alignment explanation
Indices: 217946--218333 Score: 570
Period size: 200 Copynumber: 2.0 Consensus size: 197
217936 AAATCTCTCT
*
217946 CCTTCAAAGTCCACAACTCAGTGGCATCCCTTTTTCCTATAAGTCCACAACTCAGTGGTATCTCT
1 CCTTCAAAGTCCACAACTCAGTGGCATCCCTTTTTCCTATAAGTCCACAACTCAGTGGCATCTCT
* * *
218011 TTTCTAAGTCCACGACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTT
66 TTTCTAAGTCCACGACTCAGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGACACTCTTT
* * * *
218076 TTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTTAAAGTCTACGACTCCGTGGCAT
131 TTCCCTTTTAAGCCCACAACTCCATGGCACTC----TCTTTTTAAAGTCCACAACTCCGTGGCAT
**
218141 CTCTTT
192 CTCTGG
*
218147 CCTTCAAAGTCCA-AACTCAGTGGCATCCCTTTTTCCTGTAAGTCCACAACTCAGTGGCATCTCT
1 CCTTCAAAGTCCACAACTCAGTGGCATCCCTTTTTCCTATAAGTCCACAACTCAGTGGCATCTCT
* *
218211 TTTTTAAGTCCACGACTCAGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGATACTCTTT
66 TTTCTAAGTCCACGACTCAGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGACACTCTTT
* *
218276 TTCCCTTTTAAGTCCATAACTCCATGGCAC-C-C-TTTT-AAGTCCACAACTCCGTGGCATC
131 TTCCCTTTTAAGCCCACAACTCCATGGCACTCTCTTTTTAAAGTCCACAACTCCGTGGCATC
218334 AAGTCAGTGG
Statistics
Matches: 174, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
192 20 0.11
193 4 0.02
194 1 0.01
199 1 0.01
200 135 0.78
201 13 0.07
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (197 bp):
CCTTCAAAGTCCACAACTCAGTGGCATCCCTTTTTCCTATAAGTCCACAACTCAGTGGCATCTCT
TTTCTAAGTCCACGACTCAGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGACACTCTTT
TTCCCTTTTAAGCCCACAACTCCATGGCACTCTCTTTTTAAAGTCCACAACTCCGTGGCATCTCT
GG
Found at i:218575 original size:21 final size:21
Alignment explanation
Indices: 218551--218619 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
218541 ATGTCGCTGG
218551 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
218572 CCTTTAAGTCCAATATCGTTGG--
1 CCTTGAA-T-CAGCA-CATTGGCA
*
218594 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
218615 CCTTG
1 CCTTG
218620 TTTTTAAGGC
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 12 0.35
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:218595 original size:43 final size:43
Alignment explanation
Indices: 218538--218992 Score: 451
Period size: 43 Copynumber: 9.9 Consensus size: 43
218528 GTCTTTAACA
218538 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* * * *
218581 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAGG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-----TTTAAGT
218629 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* * * *
218672 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C----CTTTAAGT
218720 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* * *
218763 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C----CTTTAAGT
*
218811 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* * * *
218854 CCAATGTCGCTGGCCTTGAATCAGTATATTAGCACCTTCATCTTTAACT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
* * * * *
218903 CCAATATTGCTGGCCTTAAATCAGCATATTGGCGCCTTTGTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATT---G-----G-CACCTTTAAGT
218955 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
218993 CATCTTTAAG
Statistics
Matches: 342, Mismatches: 40, Indels: 60
0.77 0.09 0.14
Matches are distributed among these distances:
43 152 0.44
44 3 0.01
47 1 0.00
48 116 0.34
49 34 0.10
52 33 0.10
57 1 0.00
58 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
Found at i:218668 original size:91 final size:91
Alignment explanation
Indices: 218478--219041 Score: 777
Period size: 91 Copynumber: 6.0 Consensus size: 91
218468 GCACCTTCAT
*
218478 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTTGTCTTTAACACCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TTGTCTTTAAGACCAAT
218543 GTCGCTGGCCTTGAATCAGCACATTGGCAC
62 GTCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
218573 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAGGCCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
218638 CTGGCCTTGAATCAGCACATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
*
218664 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
218729 CTGGCCTTGAATCAGCACATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
218755 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
*
218820 CTGGCCTTGAATCAGCACATTGGCAT
66 CTGGCCTTGAATCAGCACATTGGCAC
* * * * ** * *
218846 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTATATTAGCACCTTCATCTTTAACTCCAATATT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTC
* * *
218911 GCTGGCCTTAAATCAGCATATTGGCGCCTTTGTCAT
65 GCTGGCCTTGAATCAGCACATT---G-----G-CAC
* * * * *
218947 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAGTATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTC
* *
219012 GCTGGCCTTGAATCAGCATATTGGCGC
65 GCTGGCCTTGAATCAGCACATTGGCAC
219039 CTT
1 CTT
219042 CGTCATCTTT
Statistics
Matches: 429, Mismatches: 30, Indels: 23
0.89 0.06 0.05
Matches are distributed among these distances:
91 263 0.61
92 37 0.09
93 1 0.00
95 44 0.10
98 1 0.00
100 1 0.00
101 82 0.19
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (91 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCAC
Found at i:218789 original size:182 final size:182
Alignment explanation
Indices: 218382--219041 Score: 888
Period size: 182 Copynumber: 3.5 Consensus size: 182
218372 GGCATCTTCT
* * *
218382 TTTAAGCCCAATATCGCTGGCCTTGAATAAGCATATTGGCACCTCATCTTTAAGACCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
218447 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
66 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
218512 TATTGGCACCTTTGTTGTCTTTAACACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
125 TATTGGCACC----TTGTCTTTAACACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
* * * *
218574 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAGGCCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
*
218639 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGG
66 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
*
218704 CACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
131 CACCTTGTCTTTAACACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
*
218756 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
* * * *
218821 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTATATTAG
66 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
* * * * * * *
218886 CACCTTCATCTTTAACTCCAATATTGCTGGCCTTAAATCAGCATATTGGCGCCTTTGTCATC
131 CACCTT-GTCTTTAACACCAATGTCGCTGGCCTTGAATCAGCACATT---G-----G-CACC
* * * *
218948 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAGTATCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTCG
* *
219013 CTGGCCTTGAATCAGCATATTGGCGCCTT
65 CTGGCCTTGAATCAGCACATTGGCACCTT
219042 CGTCATCTTT
Statistics
Matches: 424, Mismatches: 33, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
182 175 0.41
183 33 0.08
186 44 0.10
188 1 0.00
191 1 0.00
192 128 0.30
193 42 0.10
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (182 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
CACCTTGTCTTTAACACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
Found at i:219843 original size:19 final size:19
Alignment explanation
Indices: 219819--219877 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
219809 ACAGTAACTA
219819 TATCGATATATAAGTGTTG
1 TATCGATATATAAGTGTTG
*
219838 TATCG--ATACAA----TG
1 TATCGATATATAAGTGTTG
219851 TATCGATATATAAGTGTTG
1 TATCGATATATAAGTGTTG
219870 TATCGATA
1 TATCGATA
219878 CAATGTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 7 0.22
15 5 0.16
17 5 0.16
19 15 0.47
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (19 bp):
TATCGATATATAAGTGTTG
Found at i:219860 original size:32 final size:32
Alignment explanation
Indices: 219819--219886 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
219809 ACAGTAACTA
219819 TATCGATATATAAGTGTTGTATCGATACAATG
1 TATCGATATATAAGTGTTGTATCGATACAATG
219851 TATCGATATATAAGTGTTGTATCGATACAATG
1 TATCGATATATAAGTGTTGTATCGATACAATG
219883 TATC
1 TATC
219887 TCTACAAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (32 bp):
TATCGATATATAAGTGTTGTATCGATACAATG
Found at i:227394 original size:20 final size:20
Alignment explanation
Indices: 227369--227422 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
227359 TACCTAGATG
227369 TGTATCGATACATGTA-TGAA
1 TGTATCGATACAT-TATTGAA
*
227389 TGTATCGATACATTATTTAA
1 TGTATCGATACATTATTGAA
227409 TGTATCGATACATT
1 TGTATCGATACATT
227423 CTGTCTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTATTGAA
Found at i:230862 original size:22 final size:22
Alignment explanation
Indices: 230830--230872 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
230820 TCCAACATAT
230830 GTAACAAATCACATACAATTAC
1 GTAACAAATCACATACAATTAC
*
230852 GTAACACATCACATACAATTA
1 GTAACAAATCACATACAATTA
230873 AGGTATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (22 bp):
GTAACAAATCACATACAATTAC
Done.