Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015163.1 Kokia drynarioides strain JFW-HI SEQ_130207, whole genome shotgun sequence
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: 290727
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 107 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2412 original size:9 final size:9
Alignment explanation
Indices: 2398--2427 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2388 TTATCTTGAA
2398 AATTAATCG
1 AATTAATCG
2407 AATTAATCG
1 AATTAATCG
2416 AATTAATC-
1 AATTAATCG
2424 AATT
1 AATT
2428 TCAAACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (9 bp):
AATTAATCG
Found at i:3813 original size:21 final size:21
Alignment explanation
Indices: 3776--3833 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
3766 ATATAAAAAT
* *
3776 TATAT-AAAAACACAAAAGTA
1 TATATAAAAAATAAAAAAGTA
* * * *
3796 TTTTTAAAAAATAAAAAATTC
1 TATATAAAAAATAAAAAAGTA
3817 TATATAAAAAATAAAAA
1 TATATAAAAAATAAAAA
3834 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (21 bp):
TATATAAAAAATAAAAAAGTA
Found at i:5041 original size:13 final size:13
Alignment explanation
Indices: 5025--5057 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5015 AAAAAATAAT
5025 TTTGGCAGGGTAG
1 TTTGGCAGGGTAG
*
5038 TTTGGCTGGGTAG
1 TTTGGCAGGGTAG
5051 TTTGGCA
1 TTTGGCA
5058 TGATTGTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.42, T:0.36
Consensus pattern (13 bp):
TTTGGCAGGGTAG
Found at i:5694 original size:88 final size:88
Alignment explanation
Indices: 5572--5762 Score: 285
Period size: 88 Copynumber: 2.2 Consensus size: 88
5562 ATTTTGACAG
* * *
5572 GGCAGTTTGGCATGATAGTCCATTTCGTCCCAATTTGAATGCTTATAGAAATGTCCTCTTAATTT
1 GGCAATTTGGCATGACAGTCCATTTCGTCCCAATTTGAATGCTTATAGAAATGTCCTCTTAATCT
*
5637 TGCATTCAATCAAAT-TTCTACCG
66 TGCATTCAATCAAATCTTCT-CCA
* * *
5660 GGTAATTTGGCATGACAGTCCATTTCGTCTCAATTTGATTGCTTATAGAAATGTCCTCTTAATCT
1 GGCAATTTGGCATGACAGTCCATTTCGTCCCAATTTGAATGCTTATAGAAATGTCCTCTTAATCT
* *
5725 TGCATTTAATCAAATCTTGTCCA
66 TGCATTCAATCAAATCTTCTCCA
5748 GGCAATTTGGCATGA
1 GGCAATTTGGCATGA
5763 GAATCTCCTA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 89 0.97
89 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (88 bp):
GGCAATTTGGCATGACAGTCCATTTCGTCCCAATTTGAATGCTTATAGAAATGTCCTCTTAATCT
TGCATTCAATCAAATCTTCTCCA
Found at i:5916 original size:13 final size:13
Alignment explanation
Indices: 5900--5950 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
5890 AAAAAGTAAT
5900 TTTGACAGGACAG
1 TTTGACAGGACAG
* * *
5913 TTTGGCTGGATAG
1 TTTGACAGGACAG
*
5926 TTTAACAGGACAG
1 TTTGACAGGACAG
*
5939 TTTGACATGACA
1 TTTGACAGGACA
5951 ATCTCCTATA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (13 bp):
TTTGACAGGACAG
Found at i:9260 original size:43 final size:44
Alignment explanation
Indices: 9200--9302 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
9190 ATATCCCATA
* * * * *
9200 ATAATATCCTATCATATCTCATTAAGAATCAAATTG-TTAATAG
1 ATAATATCTTATAATATCCCATTAAGAATCAAATTGCTAAAAAG
*
9243 ATAATATCTTATAATATCCCTTTAAGAATCAAATTGCTAAAAAG
1 ATAATATCTTATAATATCCCATTAAGAATCAAATTGCTAAAAAG
9287 ATAATAT-TTCATAATA
1 ATAATATCTT-ATAATA
9303 ATATCCTAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 34 0.65
44 18 0.35
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.37
Consensus pattern (44 bp):
ATAATATCTTATAATATCCCATTAAGAATCAAATTGCTAAAAAG
Found at i:12150 original size:29 final size:27
Alignment explanation
Indices: 12101--12199 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 27
12091 CAAATGGTTT
* * *
12101 TAAAATTTTTAATTTTTTTTTTAAATTA
1 TAAAATTATTAA-ATTTTTTTTAAAATA
* *
12129 TAACATTTTTAAAATTATTTTTTAAAATA
1 TAAAATTATT-AAATT-TTTTTTAAAATA
12158 TAAAATTATTAAATTTTTTTTAAAATAA
1 TAAAATTATTAAATTTTTTTTAAAAT-A
12186 TAAAATTATTAAAT
1 TAAAATTATTAAAT
12200 AATTTTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
27 11 0.17
28 31 0.49
29 21 0.33
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (27 bp):
TAAAATTATTAAATTTTTTTTAAAATA
Found at i:13002 original size:11 final size:11
Alignment explanation
Indices: 12986--13060 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
12976 GATGATGATT
12986 ATAATTTTAAA
1 ATAATTTTAAA
12997 ATAATTTTAAAA
1 ATAATTTT-AAA
*
13009 ATTTTATATTTAAA
1 A--TAAT-TTTAAA
*
13023 A-AA-ATTAAA
1 ATAATTTTAAA
*
13032 TTAATTTTAAA
1 ATAATTTTAAA
13043 ATAATTTT--A
1 ATAATTTTAAA
13052 ATAATTTTA
1 ATAATTTTA
13061 TATTTTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
9 14 0.27
10 2 0.04
11 21 0.41
12 4 0.08
14 7 0.14
15 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:13013 original size:20 final size:20
Alignment explanation
Indices: 12988--13097 Score: 60
Period size: 20 Copynumber: 5.8 Consensus size: 20
12978 TGATGATTAT
12988 AATTTTAAAATAATTTTAAA
1 AATTTTAAAATAATTTTAAA
13008 AATTTT---AT-A-TTTAAA
1 AATTTTAAAATAATTTTAAA
** *
13023 AAAATTAAATTAATTTTAAAA
1 AATTTTAAAATAATTTT-AAA
13044 TAATTTT--AATAATTTT--A
1 -AATTTTAAAATAATTTTAAA
*
13061 TATTTTAAAAAATAATTTT-AA
1 AATTTT--AAAATAATTTTAAA
* *
13082 TATTTTAAAATTATTT
1 AATTTTAAAATAATTT
13098 GCTGATATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 25
0.68 0.08 0.24
Matches are distributed among these distances:
15 10 0.14
16 6 0.09
17 3 0.04
18 1 0.01
19 10 0.14
20 26 0.37
21 10 0.14
22 4 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTTAAAATAATTTTAAA
Found at i:13052 original size:17 final size:16
Alignment explanation
Indices: 12998--13053 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
12988 AATTTTAAAA
12998 TAATTTT-AAAAATTT
1 TAATTTTAAAAAATTT
*
13013 TATATTTAAAAAAATTAAAT
1 TA-ATTTTAAAAAATT---T
13033 TAATTTTAAAATAATTT
1 TAATTTTAAAA-AATTT
13050 TAAT
1 TAAT
13054 AATTTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 2 0.06
16 4 0.12
17 12 0.36
19 8 0.24
20 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTTAAAAAATTT
Found at i:13057 original size:29 final size:28
Alignment explanation
Indices: 13035--13088 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
13025 AATTAAATTA
13035 ATTTT-AAAATAATTTTAATAATTTTAT
1 ATTTTAAAAATAATTTTAATAATTTTAT
13062 ATTTTAAAAAATAATTTTAAT-ATTTTA
1 ATTTT-AAAAATAATTTTAATAATTTTA
13089 AAATTATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 5 0.20
28 6 0.24
29 14 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTTTAAAAATAATTTTAATAATTTTAT
Found at i:13086 original size:21 final size:20
Alignment explanation
Indices: 13051--13091 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
13041 AAATAATTTT
13051 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
13071 AATAATTTTAATATTTTAAAA
1 AATAATTTT-ATATTTTAAAA
13092 TTATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTTTATATTTTAAAA
Found at i:17311 original size:24 final size:24
Alignment explanation
Indices: 17282--17328 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
17272 TGTACTAGTT
*
17282 ACAAGGAGATCAATTACTTAGATG
1 ACAAGGAGATCAATTACTAAGATG
*
17306 ACAAGGGGATCAATTACTAAGAT
1 ACAAGGAGATCAATTACTAAGAT
17329 TTCCAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (24 bp):
ACAAGGAGATCAATTACTAAGATG
Found at i:22785 original size:23 final size:22
Alignment explanation
Indices: 22759--22804 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
22749 ATTAAGATTC
*
22759 TAAAATTCACTATAACTGATACA
1 TAAAA-TCACTATAAATGATACA
* *
22782 TAAAATCAGTCTAAATGATACA
1 TAAAATCACTATAAATGATACA
22804 T
1 T
22805 GATTCCATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (22 bp):
TAAAATCACTATAAATGATACA
Found at i:28120 original size:16 final size:17
Alignment explanation
Indices: 28099--28137 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28089 AATAAAAGAA
*
28099 TAAAAAAT-AAATTAAT
1 TAAAAAATAAAAATAAT
28115 T-AAAAATAAAAATAAT
1 TAAAAAATAAAAATAAT
28131 TAAAAAA
1 TAAAAAA
28138 ATATCATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 9 0.45
17 5 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAATAAAAATAAT
Found at i:28135 original size:15 final size:15
Alignment explanation
Indices: 28089--28136 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
28079 AATAATCATT
* *
28089 AATAAAAGAATAAAA
1 AATAAAATAATTAAA
*
28104 AATAAATTAATTAAA
1 AATAAAATAATTAAA
28119 AATAAAAATAATTAAA
1 AAT-AAAATAATTAAA
28135 AA
1 AA
28137 AATATCATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAAAATAATTAAA
Found at i:28394 original size:146 final size:140
Alignment explanation
Indices: 28237--28583 Score: 403
Period size: 141 Copynumber: 2.4 Consensus size: 140
28227 GAACCTCAAG
* * * * ** ** *
28237 CTCAAGGATGTAATCATAATTATCTAATCATCTAATGAAAAGAGTTAATAT-TTTAAAAATATTA
1 CTCAAGAATGTAATCATAACTATCTAACCATCTAACG-AAAGAACTAATATCTAAAAAAACATTA
* * *
28301 ATTAAATTAATTTTAAAAAAAAGCTTGAAGCAGCATGAAATAAAAAATACAAATGTGAG-TAGTA
65 ATTAAA--AA-TTT---AAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAG-A
28365 GAG-AAATCAAACTCGAGA
123 GAGAAAAT-AAACTCGAGA
* *
28383 CTCAAGTATGTAATTATAACTATCTAACCATCTAACGAAAGAACTAATATGCTAAAAAAACATTA
1 CTCAAGAATGTAATCATAACTATCTAACCATCTAACGAAAGAACTAATAT-CTAAAAAAACATTA
28448 ATTAAAAATTTAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAGAGAGAAAA
65 ATTAAAAATTTAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAGAGAGAAAA
28513 TAAACTCGAGA
130 TAAACTCGAGA
*** * *
28524 CTCAAGAATGTAATTGCAACTATCTAACCATCTAACTAAAGAACTAATATGTTAAAAAAA
1 CTCAAGAATGTAATCATAACTATCTAACCATCTAACGAAAGAACTAATAT-CTAAAAAAA
28584 AAAAATTAAA
Statistics
Matches: 179, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
141 109 0.61
142 6 0.03
144 3 0.02
145 13 0.07
146 32 0.18
147 16 0.09
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.26
Consensus pattern (140 bp):
CTCAAGAATGTAATCATAACTATCTAACCATCTAACGAAAGAACTAATATCTAAAAAAACATTAA
TTAAAAATTTAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAGAGAGAAAAT
AAACTCGAGA
Found at i:28491 original size:141 final size:141
Alignment explanation
Indices: 28318--28583 Score: 428
Period size: 141 Copynumber: 1.9 Consensus size: 141
28308 TAATTTTAAA
* * *
28318 AAAAAGCTTGAAGCAGCATGAAATAAAAAATACAAATGTGAG-TAGTAGAG-AAATCAAACTCGA
1 AAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAG-AGAGAAAAT-AAACTCGA
* *
28381 GACTCAAGTATGTAATTATAACTATCTAACCATCTAACGAAAGAACTAATATGCTAAAAAAACAT
64 GACTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGCTAAAAAAACAT
28446 TAATTAAAAATTT
129 TAATTAAAAATTT
28459 AAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAGAGAGAAAATAAACTCGAGA
1 AAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAGAGAGAAAATAAACTCGAGA
* * *
28524 CTCAAGAATGTAATTGCAACTATCTAACCATCTAACTAAAGAACTAATATGTTAAAAAAA
66 CTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGCTAAAAAAA
28584 AAAAATTAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
141 109 0.95
142 6 0.05
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (141 bp):
AAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATGAGAAAGAGAGAAAATAAACTCGAGA
CTCAAGAATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGCTAAAAAAACATTA
ATTAAAAATTT
Found at i:46730 original size:27 final size:27
Alignment explanation
Indices: 46700--46753 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
46690 AACTACAAGT
46700 CCAATTGTAACAGAAACAGCAGAAGAA
1 CCAATTGTAACAGAAACAGCAGAAGAA
46727 CCAATTGTAACAGAAACAGCAGAAGAA
1 CCAATTGTAACAGAAACAGCAGAAGAA
46754 ACAACGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (27 bp):
CCAATTGTAACAGAAACAGCAGAAGAA
Found at i:57202 original size:46 final size:46
Alignment explanation
Indices: 57125--57212 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
57115 TATTGCAATT
* ** *
57125 AGAGTTTTAGATTTATTTAATTTGTTTATTATATCAGGCTTTATTA
1 AGAGTTTTAGATTTAGTTAATTTCCTCATTATATCAGGCTTTATTA
* * *
57171 AGAGTTTTAGTTTTAGTTATTTTCCTCATTATATTAGGCTTT
1 AGAGTTTTAGATTTAGTTAATTTCCTCATTATATCAGGCTTT
57213 TATTTCCCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 35 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.55
Consensus pattern (46 bp):
AGAGTTTTAGATTTAGTTAATTTCCTCATTATATCAGGCTTTATTA
Found at i:63996 original size:3 final size:3
Alignment explanation
Indices: 63988--64015 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
63978 TATAATTCAT
63988 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
64016 TTAACAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:69200 original size:30 final size:29
Alignment explanation
Indices: 69148--69205 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
69138 TAGGGATTTT
69148 CAATTTACAATTCATATCACTTTCAATTC
1 CAATTTACAATTCATATCACTTTCAATTC
*
69177 CAATTT-CACATTCACTTTCACTTTCAATT
1 CAATTTACA-ATTCA-TATCACTTTCAATT
69206 TTGATCACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 11 0.42
30 13 0.50
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (29 bp):
CAATTTACAATTCATATCACTTTCAATTC
Found at i:74618 original size:23 final size:22
Alignment explanation
Indices: 74591--74633 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
74581 ATTTTGATTT
*
74591 ACTTTCAGTTGCTTTGACAATTA
1 ACTTTCA-TTGCATTGACAATTA
*
74614 ACTTTGATTGCATTGACAAT
1 ACTTTCATTGCATTGACAAT
74634 ATTAACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (22 bp):
ACTTTCATTGCATTGACAATTA
Found at i:86642 original size:13 final size:13
Alignment explanation
Indices: 86624--86649 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86614 TCATTTCTCG
86624 TTTCTCTCTTCAC
1 TTTCTCTCTTCAC
86637 TTTCTCTCTTCAC
1 TTTCTCTCTTCAC
86650 GCATAACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTCTCTCTTCAC
Found at i:87991 original size:28 final size:27
Alignment explanation
Indices: 87959--88017 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
87949 CTGGGTGACA
* * * *
87959 CCTGTTAGGTACCCTCCATTGGATGTTG
1 CCTGTCAGGAACCCTCCACTGG-TGTCG
87987 CCTGTCAGGAACCCTCCACTGGTGTCG
1 CCTGTCAGGAACCCTCCACTGGTGTCG
88014 CCTG
1 CCTG
88018 ACAAGTACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.14, C:0.32, G:0.25, T:0.29
Consensus pattern (27 bp):
CCTGTCAGGAACCCTCCACTGGTGTCG
Found at i:97559 original size:20 final size:19
Alignment explanation
Indices: 97536--97585 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
97526 ATGCAAATAA
*
97536 ATAAATAAATATATATATAT
1 ATAAATAAATATA-ATAGAT
*
97556 ATAATATAAATTTAATAGAT
1 ATAA-ATAAATATAATAGAT
97576 ATAAAATAAA
1 AT-AAATAAA
97586 CTCAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAATAAATATAATAGAT
Found at i:97732 original size:20 final size:20
Alignment explanation
Indices: 97709--97760 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
97699 AAAATATTAG
*
97709 TTTTTTCAAAAAAGTAAGTC
1 TTTTTCCAAAAAAGTAAGTC
97729 TTTTTCCAAAAAAGTAAGTC
1 TTTTTCCAAAAAAGTAAGTC
* *
97749 ATTTTCGAAAAA
1 TTTTTCCAAAAA
97761 TCATTTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (20 bp):
TTTTTCCAAAAAAGTAAGTC
Found at i:101677 original size:39 final size:39
Alignment explanation
Indices: 101634--101713 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
101624 TAGCATTACG
101634 GTGTTTACAATGTCACAGTCAATTCAATATTGTATTGCA
1 GTGTTTACAATGTCACAGTCAATTCAATATTGTATTGCA
** * * *
101673 GTGTTTACAATGTCATTGTCAGTTTAGTATTGTATTGCA
1 GTGTTTACAATGTCACAGTCAATTCAATATTGTATTGCA
101712 GT
1 GT
101714 ATTTCCAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (39 bp):
GTGTTTACAATGTCACAGTCAATTCAATATTGTATTGCA
Found at i:101741 original size:39 final size:39
Alignment explanation
Indices: 101607--101767 Score: 101
Period size: 39 Copynumber: 4.1 Consensus size: 39
101597 TGTTTATAGT
* * * * * *
101607 TCACTACCTATTCAGTATAGCATTACGGTGTTTACAATG
1 TCACTACCAATTCAGTATTGTATTGCAGTATTTACAATG
* * *
101646 TCAC-AGTCAATTCAATATTGTATTGCAGTGTTTACAATG
1 TCACTA-CCAATTCAGTATTGTATTGCAGTATTTACAATG
* ** * * * * *
101685 TCATTGTCAGTTTAGTATTGTATTGCAGTATTTCCAGTT
1 TCACTACCAATTCAGTATTGTATTGCAGTATTTACAATG
* * * *
101724 TCACTACCAATTCAGTATCGAATT-CTAGTGTTTACAGTG
1 TCACTACCAATTCAGTATTGTATTGC-AGTATTTACAATG
101763 TCACT
1 TCACT
101768 GCCAGTTTAG
Statistics
Matches: 93, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
38 2 0.02
39 91 0.98
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (39 bp):
TCACTACCAATTCAGTATTGTATTGCAGTATTTACAATG
Found at i:105668 original size:39 final size:39
Alignment explanation
Indices: 105600--105784 Score: 194
Period size: 39 Copynumber: 4.7 Consensus size: 39
105590 TAGCATTACG
* * * *
105600 GTGTTTACAGTGTCACCGTCAATTCAGTATTGTATTGTA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTATCGTATTGTA
* ** *
105639 GTGTTTACAGTGTCACTGCCAGTTTAGTATTATATTGCA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTATCGTATTGTA
* *
105678 GTGTTT-CTAATGTCAGTGCCAGTT-AGGTATCGTATTGTA
1 GTGTTTAC-AGTGTCACTGCCAGTTCA-GTATCGTATTGTA
* * * *
105717 GTGTTTAAAGTGTCACTGCTAGTTCAGCATCGTATTATA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTATCGTATTGTA
* *
105756 GTGTTTACAGTGTCACTTCTAGTTCAGTA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTA
105785 ATTTGATAAC
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
38 2 0.02
39 119 0.98
40 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (39 bp):
GTGTTTACAGTGTCACTGCCAGTTCAGTATCGTATTGTA
Found at i:108419 original size:9 final size:9
Alignment explanation
Indices: 108407--108461 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
108397 TAATTTTTTT
108407 AAATAT-AA
1 AAATATAAA
108415 AAA-ATAAA
1 AAATATAAA
*
108423 AAATTTCAAA
1 AAATAT-AAA
108433 AAATATAAA
1 AAATATAAA
* *
108442 AATTATTAA
1 AAATATAAA
*
108451 AAATTTAAA
1 AAATATAAA
108460 AA
1 AA
108462 GTATTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 2 0.05
8 8 0.22
9 19 0.51
10 8 0.22
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATATAAA
Found at i:108452 original size:18 final size:18
Alignment explanation
Indices: 108414--108470 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
108404 TTTAAATATA
*
108414 AAAAATA-AAAAATT-TCA
1 AAAAATATAAAAATTAT-T
108431 AAAAATATAAAAATTATT
1 AAAAATATAAAAATTATT
* *
108449 AAAAATTTAAAAAGTATT
1 AAAAATATAAAAATTATT
108467 AAAA
1 AAAA
108471 TTATTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.20
18 27 0.77
19 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAATATAAAAATTATT
Found at i:108491 original size:9 final size:9
Alignment explanation
Indices: 108407--108491 Score: 50
Period size: 10 Copynumber: 9.3 Consensus size: 9
108397 TAATTTTTTT
*
108407 AAATATAAA
1 AAATTTAAA
108416 AAA--TAAA
1 AAATTTAAA
108423 AAATTTCAAA
1 AAATTT-AAA
*
108433 AAATAT-AA
1 AAATTTAAA
*
108441 AAATTATTAA
1 AAATT-TAAA
108451 AAATTTAAA
1 AAATTTAAA
*
108460 AAGTATTAAA
1 AAAT-TTAAA
* **
108470 ATTATTTTTA
1 A-AATTTAAA
108480 AAATTTAAA
1 AAATTTAAA
108489 AAA
1 AAA
108492 ATAATAATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
7 7 0.12
8 6 0.10
9 19 0.33
10 25 0.43
11 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (9 bp):
AAATTTAAA
Found at i:108501 original size:28 final size:25
Alignment explanation
Indices: 108421--108501 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 25
108411 ATAAAAAATA
108421 AAAAATTTCAAAAAATATAAAAATTATT
1 AAAAATTT-AAAAAA-AT-AAAATTATT
*
108449 AAAAATTTAAAAAGTATTAAAATTATTTT
1 AAAAATTTAAAAA--AATAAAATTA--TT
*
108478 TAAAATTTAAAAAAATAATAATTA
1 AAAAATTTAAAAAAATAA-AATTA
108502 ATACGTGGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 16 0.36
28 14 0.31
29 15 0.33
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (25 bp):
AAAAATTTAAAAAAATAAAATTATT
Found at i:109273 original size:26 final size:26
Alignment explanation
Indices: 109235--109285 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
109225 AAATTAATTT
*
109235 AATTCATTAAAAATTAAAAATATATA
1 AATTCATTAAAAAATAAAAATATATA
*
109261 AATT-ATTAAAAAAATAAAATTATAT
1 AATTCATT-AAAAAATAAAAATATAT
109286 TTTTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
AATTCATTAAAAAATAAAAATATATA
Found at i:109280 original size:17 final size:18
Alignment explanation
Indices: 109247--109283 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
109237 TTCATTAAAA
*
109247 ATTAAAAATATATAAATT
1 ATTAAAAAAATATAAATT
109265 ATTAAAAAAATA-AAATT
1 ATTAAAAAAATATAAATT
109282 AT
1 AT
109284 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTAAAAAAATATAAATT
Found at i:110554 original size:3 final size:3
Alignment explanation
Indices: 110546--110571 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
110536 CACCGACAAT
110546 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
110572 ATCTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:115181 original size:22 final size:22
Alignment explanation
Indices: 115150--115194 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
115140 TCTCTTTTTC
115150 TTTATAACTTATATAAACATAG
1 TTTATAACTTATATAAACATAG
*
115172 TTTATCACTTATATAAACATAG
1 TTTATAACTTATATAAACATAG
115194 T
1 T
115195 GTTAATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (22 bp):
TTTATAACTTATATAAACATAG
Found at i:115540 original size:14 final size:14
Alignment explanation
Indices: 115514--115552 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
115504 TTAAAAAGTG
115514 TAATTATTATTTTAA
1 TAATTA-TATTTTAA
*
115529 TAATTGTATTTTAA
1 TAATTATATTTTAA
115543 TAATTATATT
1 TAATTATATT
115553 GTGGTGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TAATTATATTTTAA
Found at i:116567 original size:28 final size:28
Alignment explanation
Indices: 116514--116567 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
116504 TTTAATATAA
**
116514 TTTTTAAGAAAATTATATAATTTTTTAG
1 TTTTTAAGAAAATTATATAAAATTTTAG
*
116542 TTTTTAA-AATAATTTTATAAAATTTT
1 TTTTTAAGAA-AATTATATAAAATTTT
116568 GTAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TTTTTAAGAAAATTATATAAAATTTTAG
Found at i:116586 original size:11 final size:11
Alignment explanation
Indices: 116543--116588 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
116533 ATTTTTTAGT
116543 TTTTA-AAATAA
1 TTTTATAAAT-A
116554 TTTTATAAA-A
1 TTTTATAAATA
*
116564 TTTTGT-AATA
1 TTTTATAAATA
116574 TTTTATAAATA
1 TTTTATAAATA
116585 TTTT
1 TTTT
116589 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 2 0.07
10 12 0.40
11 13 0.43
12 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:116597 original size:20 final size:20
Alignment explanation
Indices: 116554--116619 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
116544 TTTAAAATAA
* *
116554 TTTTATAAA-ATTTTGTAATA
1 TTTTATAAATATTTTG-ATTT
116574 TTTTATAAATATTTTGATTT
1 TTTTATAAATATTTTGATTT
*
116594 TTTT-TGAAACTATTTTCAATTT
1 TTTTAT-AAA-TATTTT-GATTT
116616 TTTT
1 TTTT
116620 TGTATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.03
20 18 0.46
21 12 0.31
22 8 0.21
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATAAATATTTTGATTT
Found at i:116598 original size:21 final size:22
Alignment explanation
Indices: 116580--116621 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
116570 AATATTTTAT
*
116580 AAATATTTT-GATTTTTTTTGA
1 AAATATTTTCAATTTTTTTTGA
*
116601 AACTATTTTCAATTTTTTTTG
1 AAATATTTTCAATTTTTTTTG
116622 TATATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (22 bp):
AAATATTTTCAATTTTTTTTGA
Found at i:120733 original size:9 final size:9
Alignment explanation
Indices: 120719--120749 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
120709 CACTTTTGGA
120719 GAAGATGGT
1 GAAGATGGT
120728 GAAGATGGT
1 GAAGATGGT
*
120737 GAAGATGAT
1 GAAGATGGT
120746 GAAG
1 GAAG
120750 TGTTTAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (9 bp):
GAAGATGGT
Found at i:125491 original size:26 final size:26
Alignment explanation
Indices: 125422--125493 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
125412 CATCATCCCA
* * *
125422 ATTTTAC-CCTGGTAAAATTTTGATG
1 ATTTTACTCTTGGTAAAATTTTAACG
** *
125447 ATTTTACTCTCAGTCAAATTTTAACG
1 ATTTTACTCTTGGTAAAATTTTAACG
125473 ATTTTACTCTTGGTAAAATTT
1 ATTTTACTCTTGGTAAAATTT
125494 CGAGAGAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (26 bp):
ATTTTACTCTTGGTAAAATTTTAACG
Found at i:126371 original size:6 final size:6
Alignment explanation
Indices: 126351--126427 Score: 77
Period size: 6 Copynumber: 13.0 Consensus size: 6
126341 CTAAACACAT
* ***
126351 TTTAAA TTT-AT TTTAAA TTTAAA TTTGTT TTTAAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* *
126398 TTTAAG TTTAAA TTTATA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
126428 ATTATTCTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
5 9 0.16
6 44 0.79
7 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:126389 original size:19 final size:17
Alignment explanation
Indices: 126351--126445 Score: 109
Period size: 17 Copynumber: 5.4 Consensus size: 17
126341 CTAAACACAT
126351 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
126368 TTTAAATTTGTTTTTAAAA
1 TTTAAATTT-ATTTT-AAA
* *
126387 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
126404 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
126422 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
*
126439 CTTAAAT
1 TTTAAAT
126446 AAATAAAAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
17 31 0.48
18 22 0.34
19 12 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:126391 original size:36 final size:35
Alignment explanation
Indices: 126351--126445 Score: 118
Period size: 36 Copynumber: 2.7 Consensus size: 35
126341 CTAAACACAT
* *
126351 TTTAAATTTATTTTAAATTTAAATTTGTTTTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATATTT-AAA
* *
126387 TTTAAATTTAATTTAAGTTTAAATTTATATTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTATATTTAAA
* * *
126422 TTTAAAATTATTCTAAACTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
126446 AAATAAAAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 22 0.44
36 28 0.56
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATATTTAAA
Found at i:127176 original size:24 final size:24
Alignment explanation
Indices: 127128--127176 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
127118 AATAGTTTTG
* *
127128 ACAATATTAATAATGATAACCATA
1 ACAATATTAATAATAATAACAATA
*
127152 ACAATATTAATAATAATAATAATA
1 ACAATATTAATAATAATAACAATA
127176 A
1 A
127177 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (24 bp):
ACAATATTAATAATAATAACAATA
Found at i:128354 original size:29 final size:28
Alignment explanation
Indices: 128325--128479 Score: 84
Period size: 29 Copynumber: 5.4 Consensus size: 28
128315 CCCCTTAACT
128325 TTCCAAAAATTACATTTTCACCCCAAAC
1 TTCCAAAAATTACATTTTCACCCCAAAC
** * ** *
128353 TTCCAAGTATT-CAATTTTAGATTCCAAATT
1 TTCCAAAAATTAC-ATTTT-CACCCCAAA-C
128383 TTCC-AAAATTACCA-TTT-ACCCCTAAAC
1 TTCCAAAAATTA-CATTTTCACCCC-AAAC
* * * **
128410 TTCCAAATATTCCATTTTTTACCCCGAATT
1 TTCCAAAAATTACA-TTTTCACCCC-AAAC
* *
128440 TTCTAAAAATTACATTTTCACCTCAAAAC
1 TTCCAAAAATTACATTTTCACC-CCAAAC
*
128469 ATCCAAAAATT
1 TTCCAAAAATT
128480 CTATTTTTAA
Statistics
Matches: 91, Mismatches: 25, Indels: 21
0.66 0.18 0.15
Matches are distributed among these distances:
27 10 0.11
28 22 0.24
29 34 0.37
30 24 0.26
31 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (28 bp):
TTCCAAAAATTACATTTTCACCCCAAAC
Found at i:128440 original size:57 final size:58
Alignment explanation
Indices: 128324--128564 Score: 211
Period size: 58 Copynumber: 4.2 Consensus size: 58
128314 GCCCCTTAAC
** * * **
128324 TTTCCAAAAATTACATTTTCACCCC-AAACTTCCAAGTATTCAATTTTAGATTCCAAAT
1 TTTCC-AAAATTACATTTTCACCCCAAAACTTCCAAAAATTCCATTTTTGACCCCAAAT
* * * *
128382 TTTCCAAAATTACCA-TTT-ACCCCTAAACTTCCAAATATTCCATTTTTTACCCCGAAT
1 TTTCCAAAATTA-CATTTTCACCCCAAAACTTCCAAAAATTCCATTTTTGACCCCAAAT
* * * * * **
128439 TTTCTAAAAATTACATTTTCACCTCAAAACATCCAAAAATTCTATTTTTAACCTTAAAT
1 TTTC-CAAAATTACATTTTCACCCCAAAACTTCCAAAAATTCCATTTTTGACCCCAAAT
* * * * * *
128498 TTTTCAAAATTATCATTTT-ACACCAAAACTTCAAAAAAATCCATTTTTGACCTCGAAT
1 TTTCCAAAATTA-CATTTTCACCCCAAAACTTCCAAAAATTCCATTTTTGACCCCAAAT
128556 TTTCCAAAA
1 TTTCCAAAA
128565 ATCCCATTTT
Statistics
Matches: 148, Mismatches: 29, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
56 5 0.03
57 42 0.28
58 62 0.42
59 39 0.26
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (58 bp):
TTTCCAAAATTACATTTTCACCCCAAAACTTCCAAAAATTCCATTTTTGACCCCAAAT
Found at i:128456 original size:30 final size:30
Alignment explanation
Indices: 128422--128658 Score: 96
Period size: 30 Copynumber: 8.0 Consensus size: 30
128412 CCAAATATTC
128422 CATTTTTTACCCCGAATTTTCTAAAAATTA
1 CATTTTTTACCCCGAATTTTCTAAAAATTA
* * * *** *
128452 CA-TTTTCACCTCAAAACATCCAAAAATT-
1 CATTTTTTACCCCGAATTTTCTAAAAATTA
* *** *
128480 CTATTTTTAACCTTAAATTTT-TCAAAATTA
1 C-ATTTTTTACCCCGAATTTTCTAAAAATTA
* * ** * * *
128510 TCA--TTTTACACCAAAACTTCAAAAAAATC
1 -CATTTTTTACCCCGAATTTTCTAAAAATTA
* * * **
128539 CATTTTTGACCTCGAATTTTCCAAAAATCC
1 CATTTTTTACCCCGAATTTTCTAAAAATTA
* *
128569 CATTTTTTACCTCGAATTCTCTAAAAATTA
1 CATTTTTTACCCCGAATTTTCTAAAAATTA
*
128599 CCA--TTTTACCCCCGAA-CTTCTAAAAAATT-
1 -CATTTTTTA-CCCCGAATTTTCT-AAAAATTA
* * *
128628 CATTTTTGACCCCTAATTTTCCAAAAATTA
1 CATTTTTTACCCCGAATTTTCTAAAAATTA
128658 C
1 C
128659 CATCTTACCC
Statistics
Matches: 148, Mismatches: 45, Indels: 28
0.67 0.20 0.13
Matches are distributed among these distances:
28 15 0.10
29 52 0.35
30 78 0.53
31 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (30 bp):
CATTTTTTACCCCGAATTTTCTAAAAATTA
Found at i:128565 original size:29 final size:30
Alignment explanation
Indices: 128532--128661 Score: 99
Period size: 30 Copynumber: 4.4 Consensus size: 30
128522 AAAACTTCAA
*
128532 AAAAAT-CCATTTTTGACCTCGAATTTTCC
1 AAAAATACCATTTTTGACCCCGAATTTTCC
* * * * *
128561 AAAAATCCCATTTTTTACCTCGAATTCTCT
1 AAAAATACCATTTTTGACCCCGAATTTTCC
* *
128591 AAAAATTACCA-TTTT-ACCCCCGAA-CTTCT
1 AAAAA-TACCATTTTTGA-CCCCGAATTTTCC
* *
128620 AAAAA-ATTCATTTTTGACCCCTAATTTTCC
1 AAAAATA-CCATTTTTGACCCCGAATTTTCC
128650 AAAAATTACCAT
1 AAAAA-TACCAT
128662 CTTACCCTCG
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 2 0.03
29 25 0.31
30 44 0.55
31 7 0.09
32 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAAATACCATTTTTGACCCCGAATTTTCC
Found at i:128624 original size:59 final size:61
Alignment explanation
Indices: 128561--128701 Score: 160
Period size: 59 Copynumber: 2.3 Consensus size: 61
128551 CGAATTTTCC
* * * *
128561 AAAAATCCCATTTTTTACCTCGAATTCTCTAAAAATTACCATTTTACCCCCGAACTT-C-TA
1 AAAAAT-CCATTTTTAACCTCGAATTCTCCAAAAATTACCATCTTACCCCCGAACTTCCAAA
* * * * * *
128621 AAAAATTCATTTTTGACCCCTAATTTTCCAAAAATTACCATCTTACCCTCGAACTTCCAAA
1 AAAAATCCATTTTTAACCTCGAATTCTCCAAAAATTACCATCTTACCCCCGAACTTCCAAA
*
128682 AAAATTCCATTTTTAACCTC
1 AAAAATCCATTTTTAACCTC
128702 AAACATTACC
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
59 42 0.64
60 7 0.11
61 17 0.26
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.35
Consensus pattern (61 bp):
AAAAATCCATTTTTAACCTCGAATTCTCCAAAAATTACCATCTTACCCCCGAACTTCCAAA
Found at i:128671 original size:89 final size:89
Alignment explanation
Indices: 128503--128694 Score: 221
Period size: 89 Copynumber: 2.2 Consensus size: 89
128493 TAAATTTTTC
* * *
128503 AAAATTATCATTTTACACCAAAACTTCAAAAAAATCCATTTTTGACCTCGAATTTTCCAAAAATC
1 AAAATTACCATTTTACACCAAAACTTCAAAAAAATCCATTTTTGACCCCGAATTTTCCAAAAATA
* *
128568 CCATTTTTTACCTCGAA-TTCTC-TA
66 CCA-TTCTTACCTCGAACTTC-CAAA
* ** * * *
128592 AAAATTACCATTTTACCCCCGAACTTCTAAAAAATTCATTTTTGACCCCTAATTTTCCAAAAATT
1 AAAATTACCATTTTACACCAAAACTTCAAAAAAATCCATTTTTGACCCCGAATTTTCCAAAAA-T
128657 ACCA-TCTTACCCTCGAACTTCCAAA
65 ACCATTCTTA-CCTCGAACTTCCAAA
128682 AAAATT-CCATTTT
1 AAAATTACCATTTT
128695 TAACCTCAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
88 4 0.05
89 70 0.80
90 14 0.16
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (89 bp):
AAAATTACCATTTTACACCAAAACTTCAAAAAAATCCATTTTTGACCCCGAATTTTCCAAAAATA
CCATTCTTACCTCGAACTTCCAAA
Found at i:128678 original size:29 final size:30
Alignment explanation
Indices: 128573--128812 Score: 117
Period size: 29 Copynumber: 8.4 Consensus size: 30
128563 AAATCCCATT
128573 TTTTA-CCTCGAA-TTCTCTAAAAATTACCA
1 TTTTACCCTCGAACTTCTC-AAAAATTACCA
* *
128602 TTTTACCCCCGAACTTCTAAAAAATT--CA
1 TTTTACCCTCGAACTTCTCAAAAATTACCA
* *
128630 TTTTTGACCC-CTAA-TTTTCCAAAAATTACCA
1 -TTTT-ACCCTCGAACTTCT-CAAAAATTACCA
*
128661 TCTTACCCTCGAACTTC-CAAAAAAATT-CCA
1 TTTTACCCTCGAACTTCTC--AAAAATTACCA
*
128691 TTTT----T--AAC--CTCAAACATTACCA
1 TTTTACCCTCGAACTTCTCAAAAATTACCA
** *
128713 TTTTACCCTTAAACTT-TCAAAAATT-CTA
1 TTTTACCCTCGAACTTCTCAAAAATTACCA
* * * **
128741 TTTTTCGCCCCGAACTTC-CAAAAAATATTA
1 TTTTAC-CCTCGAACTTCTCAAAAATTACCA
*
128771 TTTTACCCCCGAACATTC-C-AAAATTACCA
1 TTTTACCCTCGAAC-TTCTCAAAAATTACCA
128800 TTTTCACCCTCGA
1 TTTT-ACCCTCGA
128813 GAGTCCATAA
Statistics
Matches: 162, Mismatches: 23, Indels: 51
0.69 0.10 0.22
Matches are distributed among these distances:
21 6 0.04
22 8 0.05
23 1 0.01
24 3 0.02
26 2 0.01
28 15 0.09
29 65 0.40
30 47 0.29
31 15 0.09
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
TTTTACCCTCGAACTTCTCAAAAATTACCA
Found at i:128773 original size:30 final size:30
Alignment explanation
Indices: 128731--128793 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
128721 TTAAACTTTC
*
128731 AAAAATTCTATTTTTCGCCCCGAAC-TTCCA
1 AAAAATTCTATTTTAC-CCCCGAACATTCCA
128761 AAAAATAT-TATTTTACCCCCGAACATTCCA
1 AAAAAT-TCTATTTTACCCCCGAACATTCCA
128791 AAA
1 AAA
128794 TTACCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 8 0.27
30 21 0.70
31 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (30 bp):
AAAAATTCTATTTTACCCCCGAACATTCCA
Found at i:130053 original size:18 final size:17
Alignment explanation
Indices: 130012--130074 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
130002 CTAAACCCAT
130012 TTTAAATTTA-TTTTAA
1 TTTAAATTTATTTTTAA
*
130028 GATTAAATTTATTTTCTAA
1 -TTTAAATTTATTTT-TAA
* *
130047 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-TAA
130065 TTTAAATTTA
1 TTTAAATTTA
130075 AAATTTTTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 9 0.24
18 26 0.68
19 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTTAA
Found at i:130092 original size:23 final size:24
Alignment explanation
Indices: 130045--130094 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
130035 TTTATTTTCT
*
130045 AATTTAAATTTGTTTTAAAATTTA
1 AATTTAAATTTGTTCTAAAATTTA
130069 AATTTAAAATTT-TTCT-AAATTTA
1 AATTT-AAATTTGTTCTAAAATTTA
130092 AAT
1 AAT
130095 AAATAAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 8 0.33
25 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AATTTAAATTTGTTCTAAAATTTA
Found at i:130799 original size:3 final size:3
Alignment explanation
Indices: 130786--130838 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
130776 TAGTTTTGAC
* * * * *
130786 AAT ATT AAT AAT AAT AAC CAT AAC AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
130834 AAT AA
1 AAT AA
130839 ATATAAAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:130832 original size:24 final size:24
Alignment explanation
Indices: 130784--130837 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
130774 AATAGTTTTG
*
130784 ACAATATTAATAATAATAACCATA
1 ACAATATTAATAATAATAACAATA
*
130808 ACAATATTAATAATAATAATAATA
1 ACAATATTAATAATAATAACAATA
*
130832 ATAATA
1 ACAATA
130838 AATATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (24 bp):
ACAATATTAATAATAATAACAATA
Found at i:131189 original size:2 final size:2
Alignment explanation
Indices: 131182--131207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
131172 TGAACACAGG
131182 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
131208 AGAGGGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:132059 original size:58 final size:57
Alignment explanation
Indices: 131979--132280 Score: 261
Period size: 58 Copynumber: 5.1 Consensus size: 57
131969 GAAAATTATA
*
131979 TTTTAGCCCTAAATTTTCAAAAATTA-CATTTTCACCCTTGAATTTCCTAAAATTCCAT
1 TTTTA-CCCTAAATTTTCAAAAATTACCATTTT-ACCCTTGAATTTCCAAAAATTCCAT
** * *
132037 TTTTACCCTAAATTTTCTAAAAATTACCATTTTACCCACGAACTTCCAAAAATTTCAT
1 TTTTACCCTAAATTTTC-AAAAATTACCATTTTACCCTTGAATTTCCAAAAATTCCAT
* * * *** *
132095 TTTTCACCCTTAATTTTCCAAAAATTACTATTTTACCC--CAAGTTTTTGAAAATCCCAT
1 TTTT-ACCCTAAATTTT-CAAAAATTACCATTTTACCCTTGAA-TTTCCAAAAATTCCAT
* * *
132153 TTTTGCCCATGAATCTTCCAAAAATTACCATTTTACCCTTGAATTTCCAAAAAATTCCAT
1 TTTTACCC-TAAAT-TTTCAAAAATTACCATTTTACCCTTGAATTTCC-AAAAATTCCAT
* * * * ** *
132213 TTTTGACCCCGAACTTTTCAGAAATTATCATTTTACCCTCAAACTTT-CAAAAATTCAAT
1 TTTT-A-CCCTAAATTTTCAAAAATTACCATTTTACCCTTGAA-TTTCCAAAAATTCCAT
132272 TCTTTACCC
1 T-TTTACCC
132281 CGAACTTCCA
Statistics
Matches: 197, Mismatches: 33, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
57 17 0.09
58 77 0.39
59 52 0.26
60 43 0.22
61 5 0.03
62 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (57 bp):
TTTTACCCTAAATTTTCAAAAATTACCATTTTACCCTTGAATTTCCAAAAATTCCAT
Found at i:132069 original size:30 final size:29
Alignment explanation
Indices: 131979--132280 Score: 167
Period size: 29 Copynumber: 10.3 Consensus size: 29
131969 GAAAATTATA
131979 TTTTAGCCCTAAATTTTCAAAAATTA-CAT
1 TTTTA-CCCTAAATTTTCAAAAATTACCAT
* * * *
132008 TTTCACCCTTGAATTTCCTAAAATT-CCAT
1 TTTTACCC-TAAATTTTCAAAAATTACCAT
132037 TTTTACCCTAAATTTTCTAAAAATTACCA-
1 TTTTACCCTAAATTTTC-AAAAATTACCAT
* * *
132066 TTTTACCC-ACGAACTTCCAAAAATT-TCAT
1 TTTTACCCTA--AATTTTCAAAAATTACCAT
* *
132095 TTTTCACCCTTAATTTTCCAAAAATTACTA-
1 TTTT-ACCCTAAATTTT-CAAAAATTACCAT
* * ** *
132125 TTTTACCCCAAGTTTTTGAAAA-TCCCAT
1 TTTTACCCTAAATTTTCAAAAATTACCAT
* * *
132153 TTTTGCCCATGAATCTTCCAAAAATTACCA-
1 TTTTACCC-TAAAT-TTTCAAAAATTACCAT
* *
132183 TTTTACCCTTGAATTTCCAAAAAATT-CCAT
1 TTTTACCC-TAAATTTTC-AAAAATTACCAT
* * * *
132213 TTTTGACCCCGAACTTTTCAGAAATTATCA-
1 TTTT-A-CCCTAAATTTTCAAAAATTACCAT
* *
132243 TTTTACCCTCAAACTTTCAAAAATT-CAAT
1 TTTTACCCT-AAATTTTCAAAAATTACCAT
132272 TCTTTACCC
1 T-TTTACCC
132281 CGAACTTCCA
Statistics
Matches: 205, Mismatches: 45, Indels: 45
0.69 0.15 0.15
Matches are distributed among these distances:
27 3 0.01
28 28 0.14
29 88 0.43
30 70 0.34
31 13 0.06
32 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTTACCCTAAATTTTCAAAAATTACCAT
Found at i:132286 original size:29 final size:28
Alignment explanation
Indices: 132202--132293 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 28
132192 TGAATTTCCA
132202 AAAAATTCCATT-TTTGACCCCGAACTTTTC
1 AAAAATT-CATTCTTT-ACCCCGAAC-TTTC
* *
132232 AGAAATT-A-TCATTTTACCCTCAAACTTTC
1 AAAAATTCATTC--TTTACCC-CGAACTTTC
*
132261 AAAAATTCAATTCTTTACCCCGAACTTCC
1 AAAAATTC-ATTCTTTACCCCGAACTTTC
132290 AAAA
1 AAAA
132294 TTTTCCAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 25 0.50
30 20 0.40
31 1 0.02
32 2 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAAATTCATTCTTTACCCCGAACTTTC
Found at i:132305 original size:59 final size:59
Alignment explanation
Indices: 132063--132319 Score: 154
Period size: 58 Copynumber: 4.4 Consensus size: 59
132053 CTAAAAATTA
* * * * ** * * *
132063 CCATTTTACCCACGAACTTCCAAAAATTTC-ATTTTTCACCCTTAATTTTCCAAAAATTA
1 CCATTTTACCCTCGAACTTTCAAAAAATTCAATTTTTGACCCCGAA-CTTCCAAAATTTT
* * *** * * * * *
132122 CTATTTTACCC-C-AAGTTTTTGAAAATCCCATTTTTG-CCCATGAATCTTCCAAAAATTA
1 CCATTTTACCCTCGAACTTTCAAAAAATTCAATTTTTGACCC-CGAA-CTTCCAAAATTTT
* * * *
132180 CCATTTTACCCTTGAA-TTTCCAAAAAATTCCATTTTTGACCCCGAACTTTTCAGAAATTAT
1 CCATTTTACCCTCGAACTTT-CAAAAAATTCAATTTTTGACCCCGAAC-TTCCA-AAATTTT
*
132241 -CATTTTACCCTCAAACTTTC-AAAAATTCAATTCTTT-ACCCCGAACTTCCAAAATTTT
1 CCATTTTACCCTCGAACTTTCAAAAAATTCAATT-TTTGACCCCGAACTTCCAAAATTTT
132298 CCAATTTT-CCCTCGAACATTTC
1 CC-ATTTTACCCTCGAAC-TTTC
132320 GAAATTACCA
Statistics
Matches: 157, Mismatches: 28, Indels: 26
0.74 0.13 0.12
Matches are distributed among these distances:
57 18 0.11
58 46 0.29
59 43 0.27
60 40 0.25
61 10 0.06
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (59 bp):
CCATTTTACCCTCGAACTTTCAAAAAATTCAATTTTTGACCCCGAACTTCCAAAATTTT
Found at i:136331 original size:23 final size:24
Alignment explanation
Indices: 136301--136345 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
136291 TTAAAAATCA
*
136301 ATGCATTTTCTT-GCATTACATAC
1 ATGCATTTTATTCGCATTACATAC
136324 ATGCATTTTATTCGCATTACAT
1 ATGCATTTTATTCGCATTACAT
136346 CTTTGCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (24 bp):
ATGCATTTTATTCGCATTACATAC
Found at i:136352 original size:24 final size:23
Alignment explanation
Indices: 136301--136363 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
136291 TTAAAAATCA
136301 ATGCATTTTCTT-GCATTACATAC
1 ATGCATTTT-TTCGCATTACATAC
136324 ATGCATTTTATTCGCATTACAT-C
1 ATGCATTTT-TTCGCATTACATAC
* *
136347 TTTGCATATTTTCGCAT
1 -ATGCATTTTTTCGCAT
136364 AATTAATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.46
Consensus pattern (23 bp):
ATGCATTTTTTCGCATTACATAC
Found at i:137468 original size:173 final size:173
Alignment explanation
Indices: 137179--137524 Score: 692
Period size: 173 Copynumber: 2.0 Consensus size: 173
137169 AGATCTAATG
137179 CAGGCCTTCTTAAAACAATACGGCCACGTAACAGAAATAACTCCTGATCGACTCATACTACAAAA
1 CAGGCCTTCTTAAAACAATACGGCCACGTAACAGAAATAACTCCTGATCGACTCATACTACAAAA
137244 CATGGAAAAAAGGTCAAATGAGAGTTTTAGGCAGTATGCACAAAGGTGGCGAGATATGGCAACTC
66 CATGGAAAAAAGGTCAAATGAGAGTTTTAGGCAGTATGCACAAAGGTGGCGAGATATGGCAACTC
137309 AGGTGCAACCACCGCTAATAGAAAAAGAAATAACGATGTTGTT
131 AGGTGCAACCACCGCTAATAGAAAAAGAAATAACGATGTTGTT
137352 CAGGCCTTCTTAAAACAATACGGCCACGTAACAGAAATAACTCCTGATCGACTCATACTACAAAA
1 CAGGCCTTCTTAAAACAATACGGCCACGTAACAGAAATAACTCCTGATCGACTCATACTACAAAA
137417 CATGGAAAAAAGGTCAAATGAGAGTTTTAGGCAGTATGCACAAAGGTGGCGAGATATGGCAACTC
66 CATGGAAAAAAGGTCAAATGAGAGTTTTAGGCAGTATGCACAAAGGTGGCGAGATATGGCAACTC
137482 AGGTGCAACCACCGCTAATAGAAAAAGAAATAACGATGTTGTT
131 AGGTGCAACCACCGCTAATAGAAAAAGAAATAACGATGTTGTT
137525 TGTTAGCACC
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 173 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (173 bp):
CAGGCCTTCTTAAAACAATACGGCCACGTAACAGAAATAACTCCTGATCGACTCATACTACAAAA
CATGGAAAAAAGGTCAAATGAGAGTTTTAGGCAGTATGCACAAAGGTGGCGAGATATGGCAACTC
AGGTGCAACCACCGCTAATAGAAAAAGAAATAACGATGTTGTT
Found at i:138614 original size:14 final size:14
Alignment explanation
Indices: 138595--138628 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
138585 AGAAAGAGAT
138595 CAATAAAGGGAAGG
1 CAATAAAGGGAAGG
* *
138609 CAATAATGTGAAGG
1 CAATAAAGGGAAGG
138623 CAATAA
1 CAATAA
138629 TGTGTGAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.26, T:0.15
Consensus pattern (14 bp):
CAATAAAGGGAAGG
Found at i:138629 original size:14 final size:14
Alignment explanation
Indices: 138604--138632 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
138594 TCAATAAAGG
138604 GAAGGCAATAATGT
1 GAAGGCAATAATGT
138618 GAAGGCAATAATGT
1 GAAGGCAATAATGT
138632 G
1 G
138633 TGAGCCAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (14 bp):
GAAGGCAATAATGT
Found at i:140523 original size:21 final size:21
Alignment explanation
Indices: 140477--140537 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
140467 CGATTTGAGG
*
140477 AAAAATAGAAGAAACA-AAATT
1 AAAAATAAAAGAAA-ATAAATT
140498 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATA-AATT
140520 -AAAATAAATAGAAAATAA
1 AAAAATAAA-AGAAAATAA
140538 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 1 0.03
21 23 0.64
22 12 0.33
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAAATAAAAGAAAATAAATT
Found at i:142961 original size:6 final size:6
Alignment explanation
Indices: 142947--142986 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
142937 AATAAGATAG
*
142947 AAAAAT AATAAT AATAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT -A-AAAAT AAAAAT AAAAAT AAAAAT AA
142987 TTGGGTTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 24 0.80
7 2 0.07
8 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:142984 original size:32 final size:33
Alignment explanation
Indices: 142913--142987 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 33
142903 TTTCCTAGAC
*
142913 AAAAATAAATAAATAAATAAATAAAATAAGATAG
1 AAAAAT-AATAAATAAATAAATAAAATAAGAAAG
*
142947 AAAAATAAT-AAT-AATAAAATAAAAATAA-AAAT
1 AAAAATAATAAATAAAT-AAAT-AAAATAAGAAAG
142979 AAAAATAAT
1 AAAAATAAT
142988 TGGGTTGCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
31 3 0.08
32 18 0.49
33 10 0.27
34 6 0.16
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (33 bp):
AAAAATAATAAATAAATAAATAAAATAAGAAAG
Found at i:148616 original size:22 final size:22
Alignment explanation
Indices: 148574--148633 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
148564 CAATATGAGG
* *
148574 AAAAATAGAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
148595 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATAGAATT
*
148617 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
148634 AAGAAGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 22 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:148635 original size:16 final size:16
Alignment explanation
Indices: 148594--148635 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
148584 GAAACAGAAT
148594 TAAAAATAAAAGAAAA
1 TAAAAATAAAAGAAAA
* *
148610 TATAATTAAAAG-AAA
1 TAAAAATAAAAGAAAA
148625 TAGAAAATAAA
1 TA-AAAATAAA
148636 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAAGAAAA
Found at i:151955 original size:3 final size:3
Alignment explanation
Indices: 151947--151973 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
151937 CGATTCCTAA
151947 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
151974 CGAGATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:153506 original size:6 final size:6
Alignment explanation
Indices: 153495--153535 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
153485 CTAAACCCAT
153495 TTTAAA TTTAAA TTTAAA TTTAAA TTT--A TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
153536 AAATAAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
6 29 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:155518 original size:41 final size:40
Alignment explanation
Indices: 155455--155535 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
155445 ACTTTCTAAA
*
155455 AATTACATTTTCACCCCTAACTTCTAAAAATTCCATTTTT
1 AATTACATTTTCACCCCTAACTTCCAAAAATTCCATTTTT
* *
155495 AATTATCATTTT-ACCCTTAAACTTCCAAAAATTCTATTTTT
1 AATTA-CATTTTCACCCCT-AACTTCCAAAAATTCCATTTTT
155536 GACCTCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 10 0.28
41 26 0.72
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (40 bp):
AATTACATTTTCACCCCTAACTTCCAAAAATTCCATTTTT
Found at i:155535 original size:29 final size:29
Alignment explanation
Indices: 155503--155850 Score: 192
Period size: 29 Copynumber: 11.8 Consensus size: 29
155493 TTAATTATCA
*
155503 TTTTACCCTTAAACTTCCAAAAATTCTAT
1 TTTTACCCTTAAACTTCCAAAAATTCCAT
* * * * *
155532 TTTTGA-CCTCAAATTTTTCAAATATTACAT
1 TTTT-ACCCTTAAA-CTTCCAAAAATTCCAT
* *
155562 TTTCACCCCTAAACTTCCAAAAATTCCAT
1 TTTTACCCTTAAACTTCCAAAAATTCCAT
* *
155591 TTTTAACCC-TAAATTTTTCAAAAATTACCA-
1 TTTT-ACCCTTAAA-CTTCCAAAAATT-CCAT
* * *
155621 TTTTACCCCTAAATTTCCAAAAATCCCAT
1 TTTTACCCTTAAACTTCCAAAAATTCCAT
** * * *
155650 TTTTAATCTCAAAATTCCAAAAAATACCA-
1 TTTTACCCTTAAACTTCC-AAAAATTCCAT
* *
155679 TTTTACCCTTAAACTTCTAAAAATTCCTT
1 TTTTACCCTTAAACTTCCAAAAATTCCAT
* ** *
155708 TTTTGACCCCTAATTTTCTAAAAATTACCA-
1 TTTT-ACCCTTAAACTTCCAAAAATT-CCAT
** *
155738 TTTTACCCCCAAGCTTCCAAAAA-TCTCATT
1 TTTTACCCTTAAACTTCCAAAAATTC-CA-T
* * *
155768 TTTTATCAC-TAATCTTCTAAAAATTACCA-
1 TTTTA-CCCTTAAACTTCCAAAAATT-CCAT
* *
155797 TTTTACCCTCAAACTTTCAAAAAAATTCCAT
1 TTTTACCCTTAAAC-TTC-CAAAAATTCCAT
* *
155828 TTTTGA-CCTCAAACTTCAAAAAA
1 TTTT-ACCCTTAAACTTCCAAAAA
155851 AAATTTCATT
Statistics
Matches: 249, Mismatches: 47, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.00
28 16 0.06
29 103 0.41
30 98 0.39
31 29 0.12
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (29 bp):
TTTTACCCTTAAACTTCCAAAAATTCCAT
Found at i:155576 original size:59 final size:58
Alignment explanation
Indices: 155495--155849 Score: 351
Period size: 59 Copynumber: 6.0 Consensus size: 58
155485 TTCCATTTTT
* * *
155495 AATTATCATTTTACCCTTAAACTTCCAAAAATTCTATTTTTGACCTCAAATTTTTCAAA
1 AATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCAAA-TTTTCAAA
* *
155554 TATTA-CATTTTCACCCCTAAACTTCCAAAAATTCCATTTTTAACC-CTAAATTTTTCAAA
1 AATTACCATTTT-ACCCCTAAACTTCCAAAAATTCCATTTTTGACCTC-AAA-TTTTCAAA
* * * * * *
155613 AATTACCATTTTACCCCTAAATTTCCAAAAATCCCATTTTTAATCTCAAAATTCCAAA
1 AATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCAAATTTTCAAA
* * * * * *
155671 AAATACCATTTTACCCTTAAACTTCTAAAAATTCCTTTTTTGACCCCTAATTTTCTAAA
1 AATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCAAATTTTC-AAA
* * * * * * *
155730 AATTACCATTTTACCCCCAAGCTTCCAAAAA-TCTCATTTTTTATCACTAATCTTCTAAA
1 AATTACCATTTTACCCCTAAACTTCCAAAAATTC-CATTTTTGACCTCAAATTTTC-AAA
* *
155789 AATTACCATTTTA-CCCTCAAACTTTCAAAAAAATTCCATTTTTGACCTCAAA-CTTCAAA
1 AATTACCATTTTACCCCT-AAAC-TTC-CAAAAATTCCATTTTTGACCTCAAATTTTCAAA
155848 AA
1 AA
155850 AAAATTTCAT
Statistics
Matches: 247, Mismatches: 39, Indels: 20
0.81 0.13 0.07
Matches are distributed among these distances:
58 61 0.25
59 153 0.62
60 14 0.06
61 17 0.07
62 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.38
Consensus pattern (58 bp):
AATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCAAATTTTCAAA
Found at i:155820 original size:30 final size:29
Alignment explanation
Indices: 155495--155891 Score: 180
Period size: 29 Copynumber: 13.4 Consensus size: 29
155485 TTCCATTTTT
* *
155495 AATTATCATTTTACCCTTAAACTTCCAAA
1 AATTACCATTTTACCCTCAAACTTCCAAA
* * *
155524 AATT-CTATTTTTGA-CCTCAAATTTTTCAAA
1 AATTACCA-TTTT-ACCCTCAAA-CTTCCAAA
*
155554 TATTA-CATTTTCACCC-CTAAACTTCCAAA
1 AATTACCATTTT-ACCCTC-AAACTTCCAAA
* *
155583 AATT-CCATTTTTAACCCT-AAATTTTTCAAA
1 AATTACCA-TTTT-ACCCTCAAA-CTTCCAAA
*
155613 AATTACCATTTTACCC-CTAAATTTCCAAA
1 AATTACCATTTTACCCTC-AAACTTCCAAA
* ** *
155642 AA-TCCCATTTTTAATCTCAAAATTCCAAA
1 AATTACCA-TTTTACCCTCAAACTTCCAAA
* * *
155671 AAATACCATTTTACCCTTAAACTTCTAAA
1 AATTACCATTTTACCCTCAAACTTCCAAA
* ** *
155700 AATT-CCTTTTTTGACCC-CTAATTTTCTAAA
1 AATTACC-ATTTT-ACCCTC-AAACTTCCAAA
* *
155730 AATTACCATTTTACCCCCAAGCTTCCAAA
1 AATTACCATTTTACCCTCAAACTTCCAAA
* * *
155759 AA-T-CTCATTTTTTATCACT-AATCTTCTAAA
1 AATTAC-CA--TTTTA-CCCTCAAACTTCCAAA
*
155789 AATTACCATTTTACCCTCAAACTTTCAAAAA
1 AATTACCATTTTACCCTCAAAC-TTC-CAAA
*
155820 AATT-CCATTTTTGA-CCTCAAACTTCAAAAAAA
1 AATTACCA-TTTT-ACCCTCAAACTTC---CAAA
* *
155852 AATT-TCATTTTACCCTCGAACATTCC-AA
1 AATTACCATTTTACCCTCAAAC-TTCCAAA
*
155880 AATTAGCATTTT
1 AATTACCATTTT
155892 CGTCCCCGAG
Statistics
Matches: 286, Mismatches: 45, Indels: 74
0.71 0.11 0.18
Matches are distributed among these distances:
27 1 0.00
28 19 0.07
29 116 0.41
30 94 0.33
31 40 0.14
32 16 0.06
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AATTACCATTTTACCCTCAAACTTCCAAA
Found at i:155821 original size:31 final size:30
Alignment explanation
Indices: 155786--155868 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 30
155776 CTAATCTTCT
155786 AAAAATTACCATTTTACCCTCAAACTTTC-AA
1 AAAAATT-CCATTTTACCCTCAAAC-TTCAAA
155817 AAAAATTCCATTTTTGA-CCTCAAACTTCAAAA
1 AAAAATTCCA-TTTT-ACCCTCAAACTTC-AAA
*
155849 AAAAATTTCATTTTACCCTC
1 AAAAATTCCATTTTACCCTC
155869 GAACATTCCA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
30 7 0.15
31 27 0.59
32 12 0.26
ACGTcount: A:0.41, C:0.24, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAAATTCCATTTTACCCTCAAACTTCAAA
Found at i:157491 original size:32 final size:32
Alignment explanation
Indices: 157450--157515 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
157440 TGAGATTAAT
*
157450 TATGTGTGTCGTACATCTCATATGTATATATC
1 TATGTGTGTCGCACATCTCATATGTATATATC
*
157482 TATGTGTGTCGCACATCTCATATGTATATTTC
1 TATGTGTGTCGCACATCTCATATGTATATATC
157514 TA
1 TA
157516 CCATTCGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (32 bp):
TATGTGTGTCGCACATCTCATATGTATATATC
Found at i:159857 original size:113 final size:113
Alignment explanation
Indices: 159654--159909 Score: 381
Period size: 113 Copynumber: 2.3 Consensus size: 113
159644 GAATAAAAAG
* *
159654 AAACAGAGACACTCGAACCACATCCATGGATGCAATAAAAATAACAAGTCGATCACCCGAATCAC
1 AAACAGAGACACCCGAATCACATCCATGGATGCAATAAAAATAACAAGTCGATCACCCGAATCAC
** * *
159719 ATCCATGGAGACAGTGATGATTGATAGTTTAAAATAATTGTCACACCC
66 ATCCACAGAGACAATGATGATTGATAGTTTAAAATAATTATCACACCC
* * *
159767 GAACAGGGACATCCGAATCACATCCATGGATGCAATAAAAATAACAAGTCGATC-CCTCGAATCA
1 AAACAGAGACACCCGAATCACATCCATGGATGCAATAAAAATAACAAGTCGATCACC-CGAATCA
* *
159831 TATCCACAGAGACAATGAT-ATATGATAGTTTAAAATAATTATCACACTC
65 CATCCACAGAGACAATGATGAT-TGATAGTTTAAAATAATTATCACACCC
159880 AAACAGAGACACCCGAATCACATCCATGGA
1 AAACAGAGACACCCGAATCACATCCATGGA
159910 GACAATGATG
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
112 4 0.03
113 123 0.97
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (113 bp):
AAACAGAGACACCCGAATCACATCCATGGATGCAATAAAAATAACAAGTCGATCACCCGAATCAC
ATCCACAGAGACAATGATGATTGATAGTTTAAAATAATTATCACACCC
Found at i:163586 original size:17 final size:17
Alignment explanation
Indices: 163564--163597 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
163554 ATGTTATTTA
*
163564 GATATTGATAGATGTTT
1 GATATTGATACATGTTT
*
163581 GATATTTATACATGTTT
1 GATATTGATACATGTTT
163598 TATAGCGACG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (17 bp):
GATATTGATACATGTTT
Found at i:163924 original size:21 final size:22
Alignment explanation
Indices: 163900--163946 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
163890 TTCGATTTAT
*
163900 TTGAGAATAGAT-ATAAACCGA
1 TTGAGAATAGATAAAAAACCGA
* *
163921 TTGA-ACTAGATAAAAAATCGA
1 TTGAGAATAGATAAAAAACCGA
163942 TTGAG
1 TTGAG
163947 TTGGGCAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (22 bp):
TTGAGAATAGATAAAAAACCGA
Found at i:167087 original size:21 final size:20
Alignment explanation
Indices: 167063--167110 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
167053 CCTTTAAGCT
167063 CAAACCAAAGTGAACCAAGTC
1 CAAACCAAA-TGAACCAAGTC
*
167084 CAAATCCAAATGAATCAAGTC
1 CAAA-CCAAATGAACCAAGTC
167105 CAAACC
1 CAAACC
167111 TAACCTAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 18 0.72
22 5 0.20
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.12
Consensus pattern (20 bp):
CAAACCAAATGAACCAAGTC
Found at i:167164 original size:11 final size:11
Alignment explanation
Indices: 167123--167165 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
167113 ACCTAAGTCA
*
167123 GACCGTTGATC
1 GACCGTTGACC
*
167134 GGCCGTTGACC
1 GACCGTTGACC
*
167145 GACCTTTGACC
1 GACCGTTGACC
*
167156 GATCGTTGAC
1 GACCGTTGAC
167166 TGTTGACAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (11 bp):
GACCGTTGACC
Found at i:167170 original size:7 final size:7
Alignment explanation
Indices: 167160--167227 Score: 79
Period size: 7 Copynumber: 10.0 Consensus size: 7
167150 TTGACCGATC
167160 GTTGACT
1 GTTGACT
*
167167 GTTGACA
1 GTTGACT
167174 GTTGACT
1 GTTGACT
167181 GTTGACT
1 GTTGACT
*
167188 -TTGACC
1 GTTGACT
167194 GTTGACT
1 GTTGACT
167201 GTTGACT
1 GTTGACT
167208 -TTGA-T
1 GTTGACT
*
167213 CGTTGACC
1 -GTTGACT
167221 GTTGACT
1 GTTGACT
167228 TTTTCGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 1 0.02
6 9 0.18
7 41 0.80
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (7 bp):
GTTGACT
Found at i:167197 original size:20 final size:20
Alignment explanation
Indices: 167160--167229 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
167150 TTGACCGATC
*
167160 GTTGACTGTTGACAGTTGACT
1 GTTGACT-TTGACCGTTGACT
167181 GTTGACTTTGACCGTTGACT
1 GTTGACTTTGACCGTTGACT
* *
167201 GTTGACTTTGATCGTTGACC
1 GTTGACTTTGACCGTTGACT
167221 GTTGACTTT
1 GTTGACTTT
167230 TTCGAAAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 39 0.85
21 7 0.15
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (20 bp):
GTTGACTTTGACCGTTGACT
Found at i:167227 original size:27 final size:28
Alignment explanation
Indices: 167156--167227 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 28
167146 ACCTTTGACC
* *
167156 GATCGTTGACTGTTGACAGTTGACTGTT
1 GATCGTTGACCGTTGACTGTTGACTGTT
*
167184 GA-CTTTGACCGTTGACTGTTGACT-TT
1 GATCGTTGACCGTTGACTGTTGACTGTT
167210 GATCGTTGACCGTTGACT
1 GATCGTTGACCGTTGACT
167228 TTTTCGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 4 0.10
27 33 0.85
28 2 0.05
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (28 bp):
GATCGTTGACCGTTGACTGTTGACTGTT
Found at i:168320 original size:22 final size:22
Alignment explanation
Indices: 168278--168328 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
168268 TACAAATTTA
* *
168278 TATTATTTTATTTTATTATTAT
1 TATTATTTGATTTTATGATTAT
168300 TATTACTTTGATTTTA-GATTAT
1 TATTA-TTTGATTTTATGATTAT
168322 TATTATT
1 TATTATT
168329 ATACTCTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 9 0.35
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TATTATTTGATTTTATGATTAT
Found at i:173582 original size:15 final size:15
Alignment explanation
Indices: 173562--173595 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
173552 ACCTTTAAGC
173562 CCAAACCAAAGTGAA
1 CCAAACCAAAGTGAA
* *
173577 CCAAACCCATGTGAA
1 CCAAACCAAAGTGAA
173592 CCAA
1 CCAA
173596 GTCCAAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.32, G:0.12, T:0.09
Consensus pattern (15 bp):
CCAAACCAAAGTGAA
Found at i:173601 original size:21 final size:21
Alignment explanation
Indices: 173577--173624 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
173567 CCAAAGTGAA
173577 CCAAACCC-ATGTGAACCAAGT
1 CCAAACCCAAT-TGAACCAAGT
173598 CCAAACCCAATTGAACCAAGT
1 CCAAACCCAATTGAACCAAGT
173619 CCAAAC
1 CCAAAC
173625 ACAACTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.42, C:0.35, G:0.10, T:0.12
Consensus pattern (21 bp):
CCAAACCCAATTGAACCAAGT
Found at i:173657 original size:11 final size:11
Alignment explanation
Indices: 173638--173690 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
173628 ACTTATGTTA
173638 GACCGTTGACC
1 GACCGTTGACC
* *
173649 GACCATTGATC
1 GACCGTTGACC
173660 GACCGTTGACC
1 GACCGTTGACC
** *
173671 GGTCGTTGATC
1 GACCGTTGACC
*
173682 GAACGTTGA
1 GACCGTTGA
173691 TTGTTGACCG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (11 bp):
GACCGTTGACC
Found at i:173666 original size:22 final size:22
Alignment explanation
Indices: 173638--173690 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
173628 ACTTATGTTA
173638 GACCGTTGACCGACCATTGATC
1 GACCGTTGACCGACCATTGATC
** *
173660 GACCGTTGACCGGTCGTTGATC
1 GACCGTTGACCGACCATTGATC
*
173682 GAACGTTGA
1 GACCGTTGA
173691 TTGTTGACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (22 bp):
GACCGTTGACCGACCATTGATC
Found at i:174728 original size:2 final size:2
Alignment explanation
Indices: 174723--174755 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
174713 AAAAGCAAAC
174723 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
174756 GAATAGCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:186653 original size:21 final size:21
Alignment explanation
Indices: 186602--186641 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
186592 TATTACATGT
*
186602 ATGAGCATGAACGAGCAAGCC
1 ATGAGCTTGAACGAGCAAGCC
186623 ATGAGCTTGAACGAGCAAG
1 ATGAGCTTGAACGAGCAAG
186642 GCATAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (21 bp):
ATGAGCTTGAACGAGCAAGCC
Found at i:186762 original size:72 final size:72
Alignment explanation
Indices: 186644--186782 Score: 224
Period size: 72 Copynumber: 1.9 Consensus size: 72
186634 CGAGCAAGGC
* * * **
186644 ATAGTCTTGACAGACAAAAGGTAGAGGTGCCAAGAACCTTACATGGTAACTTGTATTACATGCAT
1 ATAGTCTTGACAGACAAAAGCTAGAGATGCCAAGAACCTTAAATGGTAACTCATATTACATGCAT
186709 GATGAAA
66 GATGAAA
*
186716 ATAGTCTTGACAGACAAATGCTAGAGATGCCAAGAACCTTAAATGGTAACTCATATTACATGCAT
1 ATAGTCTTGACAGACAAAAGCTAGAGATGCCAAGAACCTTAAATGGTAACTCATATTACATGCAT
186781 GA
66 GA
186783 GCAGAAGAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (72 bp):
ATAGTCTTGACAGACAAAAGCTAGAGATGCCAAGAACCTTAAATGGTAACTCATATTACATGCAT
GATGAAA
Found at i:187288 original size:78 final size:78
Alignment explanation
Indices: 187159--187319 Score: 268
Period size: 78 Copynumber: 2.1 Consensus size: 78
187149 TATCGGTGGT
* * *
187159 TGCTTTGCTTCACTTGATGTATAGTGCCCAACTAATTCTAAATTCTTATGATTATTGGCTACATC
1 TGCTTTGCTTCACTTGATGTATAGTGCCCAACTAATACTAAATTCATATGATTATTGACTACATC
187224 TAAACAAGTTGCA
66 TAAACAAGTTGCA
* * *
187237 TGCTTTGCTTTACTTGATGTTTAGTGCCCAACTAATACTAAATTCATATGATTATTGATTACATC
1 TGCTTTGCTTCACTTGATGTATAGTGCCCAACTAATACTAAATTCATATGATTATTGACTACATC
187302 TAAACAAGTTGCA
66 TAAACAAGTTGCA
187315 TGCTT
1 TGCTT
187320 ACATGGATAC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (78 bp):
TGCTTTGCTTCACTTGATGTATAGTGCCCAACTAATACTAAATTCATATGATTATTGACTACATC
TAAACAAGTTGCA
Found at i:188159 original size:29 final size:29
Alignment explanation
Indices: 188117--188175 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
188107 TCAACACTAT
188117 ACCCACGCTGGCTTCAGCTCATGCATGTA
1 ACCCACGCTGGCTTCAGCTCATGCATGTA
188146 ACCCACGCTGGCTTCAGCTCATGCATGTA
1 ACCCACGCTGGCTTCAGCTCATGCATGTA
188175 A
1 A
188176 TACGAGTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (29 bp):
ACCCACGCTGGCTTCAGCTCATGCATGTA
Found at i:188292 original size:75 final size:76
Alignment explanation
Indices: 188157--188389 Score: 247
Period size: 84 Copynumber: 3.0 Consensus size: 76
188147 CCCACGCTGG
* * * *
188157 CTTCA-GCTCATGCATGTAATACGAGTTACCATTTAAAGTTCTTGGCATCTCTATCATTTGTCTG
1 CTTCATGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTA-CTTTTGTCTG
188221 TCAAGACTAT-T
65 TCAAGACTATCT
*
188232 -TTCATGCTCATGCATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCTTTTGTCTG
1 CTTCATGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTA-CTTTTGTCTG
*
188296 TCAAGATTATGCCTTGCT
65 TCAAGACTA-----T-CT
* * * * *
188314 CGTTCATGCTCATACATGTATTACAAGTTATCATTTATGGTTCTTGGCACCTCTACTACTTGTCT
1 C-TTCATGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACT-TTTGTCT
*
188379 GTGAAGACTAT
64 GTCAAGACTAT
188390 GCCTTACTCG
Statistics
Matches: 132, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
74 4 0.03
75 61 0.46
79 1 0.01
80 1 0.01
82 1 0.01
83 2 0.02
84 62 0.47
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (76 bp):
CTTCATGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACTTTTGTCTGT
CAAGACTATCT
Found at i:188377 original size:84 final size:84
Alignment explanation
Indices: 188232--188407 Score: 246
Period size: 84 Copynumber: 2.1 Consensus size: 84
188222 CAAGACTATT
* *
188232 TTCATGCTCATGCATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCTTTTGTCTGT
1 TTCATGCTCATACATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCTCTTGTCTGT
* *
188297 CAAGATTATGCCTTGCTCG
66 CAAGACTATGCCTTACTCG
* * * *
188316 TTCATGCTCATACATGTATTACAAGTTATCATTTATGGTTCTTGGCACCTCTA-CTACTTGTCTG
1 TTCATGCTCATACATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCT-CTTGTCTG
*
188380 TGAAGACTATGCCTTACTCG
65 TCAAGACTATGCCTTACTCG
*
188400 TTTATGCT
1 TTCATGCT
188408 TATGCTCGTG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
83 2 0.02
84 79 0.98
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (84 bp):
TTCATGCTCATACATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCTCTTGTCTGT
CAAGACTATGCCTTACTCG
Found at i:190833 original size:18 final size:18
Alignment explanation
Indices: 190796--190846 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
190786 GTAATATATA
* *
190796 TTTATAAAAATTTTATAAT
1 TTTAT-AAATTTTTACAAT
*
190815 TCTT-TAATTTTTTACAAT
1 T-TTATAAATTTTTACAAT
190833 TTTATAAATTTTTA
1 TTTATAAATTTTTA
190847 TTTTTGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 2 0.08
18 20 0.77
19 2 0.08
20 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATAAATTTTTACAAT
Found at i:193763 original size:3 final size:3
Alignment explanation
Indices: 193751--193793 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
193741 TTTTTTTTTT
193751 TAA TACA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
193794 AAAGTCGCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:200179 original size:27 final size:27
Alignment explanation
Indices: 200141--200196 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
200131 ATCACTAACT
200141 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
200168 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
200195 AA
1 AA
200197 AAAATAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:200181 original size:5 final size:6
Alignment explanation
Indices: 200138--200188 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
200128 GGGATCACTA
* *
200138 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
200182 ACTAAT A
1 ACTAAT A
200189 GAATAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (6 bp):
ACTAAT
Found at i:200204 original size:14 final size:14
Alignment explanation
Indices: 200185--200212 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
200175 ATCTAATACT
200185 AATAGAATAGAAAA
1 AATAGAATAGAAAA
200199 AATAGAATAGAAAA
1 AATAGAATAGAAAA
200213 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:208872 original size:17 final size:18
Alignment explanation
Indices: 208844--208877 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
208834 CAATTAAACC
*
208844 GTTTTTGAAAAGTTGATT
1 GTTTTTGAAAAGGTGATT
208862 GTTTTTG-AAAGGTGAT
1 GTTTTTGAAAAGGTGAT
208878 GATGAAGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (18 bp):
GTTTTTGAAAAGGTGATT
Found at i:209554 original size:2 final size:2
Alignment explanation
Indices: 209541--209570 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
209531 ATTTATTATT
*
209541 TA TA TT 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
209571 GTTATGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:210396 original size:20 final size:20
Alignment explanation
Indices: 210357--210396 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
210347 ATAATTAATC
* *
210357 TTTTTAAGAAAATTATATTT
1 TTTTTAAGAAAATGAAATTT
*
210377 TTTTTAAGATAATGAAATTT
1 TTTTTAAGAAAATGAAATTT
210397 CTTAGAAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTTTAAGAAAATGAAATTT
Found at i:231903 original size:20 final size:20
Alignment explanation
Indices: 231854--231906 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
231844 CAAAATTCAA
* *
231854 AAAT-GATTTAAACTTTTTT
1 AAATCGATTGAAACATTTTT
*
231873 AAACTCAATTGAAACATTTTT
1 AAA-TCGATTGAAACATTTTT
231894 AAATCGATTGAAA
1 AAATCGATTGAAA
231907 AATTGTTCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 10 0.36
21 15 0.54
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (20 bp):
AAATCGATTGAAACATTTTT
Found at i:256190 original size:137 final size:137
Alignment explanation
Indices: 255944--256218 Score: 550
Period size: 137 Copynumber: 2.0 Consensus size: 137
255934 TACATAACAA
255944 GTGGTAGAAGTACGACCATCAGGCACAATTAAAATCAGAATAGACAAGCAAGCTATTACTAAGGT
1 GTGGTAGAAGTACGACCATCAGGCACAATTAAAATCAGAATAGACAAGCAAGCTATTACTAAGGT
256009 CTTAGGAAATGTTAAGACCATAATTAGAAGTACCACTAAGATACCAAAGAACTCTCGTTACAGCT
66 CTTAGGAAATGTTAAGACCATAATTAGAAGTACCACTAAGATACCAAAGAACTCTCGTTACAGCT
256074 TTCCAAT
131 TTCCAAT
256081 GTGGTAGAAGTACGACCATCAGGCACAATTAAAATCAGAATAGACAAGCAAGCTATTACTAAGGT
1 GTGGTAGAAGTACGACCATCAGGCACAATTAAAATCAGAATAGACAAGCAAGCTATTACTAAGGT
256146 CTTAGGAAATGTTAAGACCATAATTAGAAGTACCACTAAGATACCAAAGAACTCTCGTTACAGCT
66 CTTAGGAAATGTTAAGACCATAATTAGAAGTACCACTAAGATACCAAAGAACTCTCGTTACAGCT
256211 TTCCAAT
131 TTCCAAT
256218 G
1 G
256219 ACACTCTTTA
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 138 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (137 bp):
GTGGTAGAAGTACGACCATCAGGCACAATTAAAATCAGAATAGACAAGCAAGCTATTACTAAGGT
CTTAGGAAATGTTAAGACCATAATTAGAAGTACCACTAAGATACCAAAGAACTCTCGTTACAGCT
TTCCAAT
Found at i:260994 original size:185 final size:185
Alignment explanation
Indices: 260682--261243 Score: 1007
Period size: 185 Copynumber: 3.0 Consensus size: 185
260672 TACTTTCTTC
260682 AGATAAAGGTAAGTAAAGAGTGCAATGACTACAAGCTAAATTGATATAAGATCCATAGTTCCCTG
1 AGATAAAGGTAAGTAAAGAGTGCAATGACTACAAGCTAAATTGATATAAGATCCATAGTTCCCTG
* *
260747 GTCAAAAGAAACAGGAGTTTTGTTTCTTTTCTATGGCTTTGAAACAGTTAAATGTTTTCTAACTA
66 GTCAAAAGAAACAGGAATTTTGTTTCTTTTCTATGGTTTTGAAACAGTTAAATGTTTTCTAACTA
* *
260812 GTGAACCAGATTCAATATAGTAGCACAATGAAAATTCTAGTGAAACACAAAGTGT
131 GTGAACCAGATTCAATATAGTAGCACAACGAAAAATCTAGTGAAACACAAAGTGT
*
260867 AGATAAAGGTAAGTAAAGAGTGCAATGACTACAAGCTAAATTGATATAAGATCCATAATTCCCTG
1 AGATAAAGGTAAGTAAAGAGTGCAATGACTACAAGCTAAATTGATATAAGATCCATAGTTCCCTG
*
260932 GTCAAAAGAAACAGGAATTCTGTTTCTTTTCTATGGTTTTGAAACAGTTAAATGTTTTCTAACTA
66 GTCAAAAGAAACAGGAATTTTGTTTCTTTTCTATGGTTTTGAAACAGTTAAATGTTTTCTAACTA
* * *
260997 GTGAACCAGATTCAATATAGTAGCACAACAAAAAATCTGGTGAAACACAAAGTAT
131 GTGAACCAGATTCAATATAGTAGCACAACGAAAAATCTAGTGAAACACAAAGTGT
*
261052 CGATAAAGGTAAGTAAAGAGTGCAATGACTACAAGCTAAATTGATATAAGATCCATAGTTCCCTG
1 AGATAAAGGTAAGTAAAGAGTGCAATGACTACAAGCTAAATTGATATAAGATCCATAGTTCCCTG
*
261117 GTCAAAAGCAACAGGAATTTTGTTTCTTTTCTATGGTTTTGAAACAGTTAAATGTTTTCTAACTA
66 GTCAAAAGAAACAGGAATTTTGTTTCTTTTCTATGGTTTTGAAACAGTTAAATGTTTTCTAACTA
*
261182 CTGAACCAGATTCAATATAGTAGCACAACGAAAAATCTAGTGAAACACAAAGTGT
131 GTGAACCAGATTCAATATAGTAGCACAACGAAAAATCTAGTGAAACACAAAGTGT
261237 AGTATAA
1 AG-ATAA
261244 GAACGTCTTC
Statistics
Matches: 358, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
185 354 0.99
186 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (185 bp):
AGATAAAGGTAAGTAAAGAGTGCAATGACTACAAGCTAAATTGATATAAGATCCATAGTTCCCTG
GTCAAAAGAAACAGGAATTTTGTTTCTTTTCTATGGTTTTGAAACAGTTAAATGTTTTCTAACTA
GTGAACCAGATTCAATATAGTAGCACAACGAAAAATCTAGTGAAACACAAAGTGT
Found at i:262209 original size:124 final size:124
Alignment explanation
Indices: 262067--262388 Score: 581
Period size: 124 Copynumber: 2.6 Consensus size: 124
262057 AATTTTGTTG
262067 TTGCTACCTCACACACCAACAACCCAAGCTCCCACATCAGAATTTATATTATTCGAAGACATCAC
1 TTGCTACCTCACACACCAACAACCCAAGCTCCCACATCAGAATTTATATTATTCGAAGACATCAC
262132 ATCTGTCTTTGAAATATTTGCCTTCCACAATTATCAACATGTTTTCTCATCTAATTTGT
66 ATCTGTCTTTGAAATATTTGCCTTCCACAATTATCAACATGTTTTCTCATCTAATTTGT
262191 TTGCTACCTCACACACCAACAACCCAAGCTCCCACATCAGAATTTATATTATTCGAAGACATCAC
1 TTGCTACCTCACACACCAACAACCCAAGCTCCCACATCAGAATTTATATTATTCGAAGACATCAC
262256 ATCTGTCTTTGAAATATTTGCCTTCCACAATTATCAACATGTTTTCTCATCTAATTTGT
66 ATCTGTCTTTGAAATATTTGCCTTCCACAATTATCAACATGTTTTCTCATCTAATTTGT
* * * * * * *
262315 TCGCTACGTCACACACCAACAGCCCAAGCTCCCATATCAGAATTTATAGTATCCCAAGACATCAC
1 TTGCTACCTCACACACCAACAACCCAAGCTCCCACATCAGAATTTATATTATTCGAAGACATCAC
262380 ATCTGTCTT
66 ATCTGTCTT
262389 GGATGTTCAT
Statistics
Matches: 191, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 191 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.32
Consensus pattern (124 bp):
TTGCTACCTCACACACCAACAACCCAAGCTCCCACATCAGAATTTATATTATTCGAAGACATCAC
ATCTGTCTTTGAAATATTTGCCTTCCACAATTATCAACATGTTTTCTCATCTAATTTGT
Found at i:264389 original size:125 final size:125
Alignment explanation
Indices: 264167--264417 Score: 457
Period size: 125 Copynumber: 2.0 Consensus size: 125
264157 AGTTGTTGCC
264167 AGTAACAACACAGATACAATTGTAATAGGCAATAATAAGAAAAAGGATACTTATCCATGTGTTTT
1 AGTAACAACACAGATACAATTGTAATAGGCAATAATAAGAAAAAGGATACTTATCCATGTGTTTT
*
264232 TCAATTGTATAAGAAAAAATTGCTTTCTTTAGATGGAAAATTGGCACTCACTTGTGAACG
66 TCAATTGTATAAGAAAAAATTGCTTTCTTTAGATGGAAAATTGACACTCACTTGTGAACG
* *
264292 AGTAACAATACATATACAATTGTAATAGGCAATAATAAGAAAAAGGATACTTATCCATGTGTTTT
1 AGTAACAACACAGATACAATTGTAATAGGCAATAATAAGAAAAAGGATACTTATCCATGTGTTTT
* *
264357 TCAATTGTATAAGAAAAGATTGCTTTCTTTAGATGGCAAATTGACACTCACTTGTGAACG
66 TCAATTGTATAAGAAAAAATTGCTTTCTTTAGATGGAAAATTGACACTCACTTGTGAACG
264417 A
1 A
264418 AGCAATTCCT
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (125 bp):
AGTAACAACACAGATACAATTGTAATAGGCAATAATAAGAAAAAGGATACTTATCCATGTGTTTT
TCAATTGTATAAGAAAAAATTGCTTTCTTTAGATGGAAAATTGACACTCACTTGTGAACG
Found at i:265703 original size:3 final size:3
Alignment explanation
Indices: 265695--265723 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
265685 GGTGTCCATG
265695 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
265724 AAAAAAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:276215 original size:22 final size:21
Alignment explanation
Indices: 276166--276212 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
276156 CGATTTAAGG
*
276166 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAAAAACAGAATT
*
276187 AAAAATAAAAAAAATAGAATT
1 AAAAATAAAAAAAACAGAATT
276208 AAAAA
1 AAAAA
276213 ATAGAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAAAAACAGAATT
Found at i:276957 original size:30 final size:29
Alignment explanation
Indices: 276919--276995 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
276909 AGATAAACAT
276919 AAATTAAATACAAATAAATAATATA-TTTA
1 AAATTAAATACAAATAAA-AATATATTTTA
* **
276948 AATATTAAATCCTTATAAAAATATATTTTA
1 AA-ATTAAATACAAATAAAAATATATTTTA
*
276978 AAATAAAATA-AAATAAAA
1 AAATTAAATACAAATAAAA
276996 CCAAGTCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 6 0.15
29 14 0.36
30 19 0.49
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (29 bp):
AAATTAAATACAAATAAAAATATATTTTA
Done.