Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 16 of 32
Found at i:2112300 original size:16 final size:17
Alignment explanation
Indices: 2112272--2112303 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2112262 TAAAATTTTA
2112272 AAATTATTTTTAAGTTT
1 AAATTATTTTTAAGTTT
2112289 AAATTA-TTTTAAGTT
1 AAATTATTTTTAAGTT
2112304 CGGATCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
AAATTATTTTTAAGTTT
Found at i:2113201 original size:16 final size:15
Alignment explanation
Indices: 2113170--2113218 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 15
2113160 ATTGATCAAG
2113170 TCATTTCGATTCGAA
1 TCATTTCGATTCGAA
*
2113185 TCATTTCAGATTTGAA
1 TCATTTC-GATTCGAA
2113201 TCATTTCGAGTTCGAA
1 TCATTTCGA-TTCGAA
2113217 TC
1 TC
2113219 GATCAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (15 bp):
TCATTTCGATTCGAA
Found at i:2113225 original size:31 final size:30
Alignment explanation
Indices: 2113170--2113228 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
2113160 ATTGATCAAG
2113170 TCATTTCGATTCGAATCATTTCAGATTTGAA
1 TCATTTCGATTCGAATCA-TTCAGATTTGAA
2113201 TCATTTCGAGTTCGAATCGA-TCAGATTT
1 TCATTTCGA-TTCGAATC-ATTCAGATTT
2113229 AAATTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 17 0.65
32 8 0.31
33 1 0.04
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (30 bp):
TCATTTCGATTCGAATCATTCAGATTTGAA
Found at i:2114993 original size:2 final size:2
Alignment explanation
Indices: 2114986--2115021 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2114976 AGGGTATGCC
2114986 AT AT 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 AT AT
2115022 CAGCCATGAT
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):
AT
Found at i:2116877 original size:7 final size:7
Alignment explanation
Indices: 2116842--2116891 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
2116832 TCTAAAAGAA
2116842 TTTAAAT
1 TTTAAAT
*
2116849 TAATAAAT
1 T-TTAAAT
*
2116857 TTGAAAAT
1 TT-TAAAT
*
2116865 TATAAAT
1 TTTAAAT
2116872 TTTAAAT
1 TTTAAAT
2116879 TTTAAAT
1 TTTAAAT
2116886 TTTAAA
1 TTTAAA
2116892 ATATAAATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 24 0.69
8 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
TTTAAAT
Found at i:2116884 original size:14 final size:14
Alignment explanation
Indices: 2116842--2116900 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
2116832 TCTAAAAGAA
2116842 TTTAAATTAATAAAT
1 TTTAAATT-ATAAAT
*
2116857 TTGAAAATTATAAAT
1 TT-TAAATTATAAAT
*
2116872 TTTAAATTTTAAAT
1 TTTAAATTATAAAT
*
2116886 TTTAAAATATAAAT
1 TTTAAATTATAAAT
2116900 T
1 T
2116901 CAAATATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
14 23 0.61
15 10 0.26
16 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
TTTAAATTATAAAT
Found at i:2118494 original size:28 final size:24
Alignment explanation
Indices: 2118444--2118491 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2118434 TATATTTACA
2118444 CATTTTTTATCTATTATTTGATTG
1 CATTTTTTATCTATTATTTGATTG
2118468 CATTTTTTATCTATTATTTGATTG
1 CATTTTTTATCTATTATTTGATTG
2118492 ATTAATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.62
Consensus pattern (24 bp):
CATTTTTTATCTATTATTTGATTG
Found at i:2118501 original size:20 final size:22
Alignment explanation
Indices: 2118452--2118504 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
2118442 CACATTTTTT
*
2118452 ATCTATTATTTGATTGCATTTTTT
1 ATCTATTATTTGATTGCA--TTTA
2118476 ATCTATTATTTGATTG-A-TTA
1 ATCTATTATTTGATTGCATTTA
2118496 ATCTATTAT
1 ATCTATTAT
2118505 ATTATAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 11 0.39
23 1 0.04
24 16 0.57
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (22 bp):
ATCTATTATTTGATTGCATTTA
Found at i:2120835 original size:2 final size:2
Alignment explanation
Indices: 2120822--2120862 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2120812 ACTTTTTCAC
*
2120822 AT AT AT AC 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
2120863 ACCTTCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2121886 original size:37 final size:36
Alignment explanation
Indices: 2121844--2121961 Score: 120
Period size: 35 Copynumber: 3.3 Consensus size: 36
2121834 TATTTTATAA
2121844 ATTTATTTAAATTTAATTTA-ATTTAATTATAAATAAT
1 ATTTATTTAAATTTAATTTATA-TTAATTATAAAT-AT
* * *
2121881 TTTTATTTAAATTT-ATTTATATTATTTTTAAATAT
1 ATTTATTTAAATTTAATTTATATTAATTATAAATAT
* *
2121916 ATTT-TTTAAATTTAATATATAATAATT-T-AATAT
1 ATTTATTTAAATTTAATTTATATTAATTATAAATAT
*
2121949 ATTTTTATTAAAT
1 ATTTAT-TTAAAT
2121962 ATTTTTTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
33 9 0.13
34 11 0.16
35 21 0.30
36 15 0.21
37 14 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (36 bp):
ATTTATTTAAATTTAATTTATATTAATTATAAATAT
Found at i:2121903 original size:16 final size:16
Alignment explanation
Indices: 2121841--2121903 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
2121831 TTATATTTTA
*
2121841 TAAATTTATTTAAATT
1 TAAATTTATTTATATT
2121857 T-AATTTAATTTA-ATT
1 TAAATTT-ATTTATATT
* *
2121872 ATAAA-TAATTTTTATT
1 -TAAATTTATTTATATT
2121888 TAAATTTATTTATATT
1 TAAATTTATTTATATT
2121904 ATTTTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
15 16 0.42
16 20 0.53
17 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTTATTTATATT
Found at i:2121930 original size:71 final size:72
Alignment explanation
Indices: 2121844--2121988 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 72
2121834 TATTTTATAA
*
2121844 ATTTATTTAAATTTAAT-T-TAATTTAATTATAA-ATAATTTTTATTTAA-ATTTATTT-ATATT
1 ATTTATTTAAATTTAATATATAA--TAATT-TAATAT-ATTTTTATTAAATATTTATTTAATATT
*
2121904 ATTTTTAAATAT
62 -TTTTAAAATAT
*
2121916 ATTT-TTTAAATTTAATATATAATAATTTAATATATTTTTATTAAATATTTTTTTAATATTTTTT
1 ATTTATTTAAATTTAATATATAATAATTTAATATATTTTTATTAAATATTTATTTAATATTTTTT
2121980 AAAATAT
66 AAAATAT
2121987 AT
1 AT
2121989 GATATCATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
70 14 0.22
71 38 0.58
72 10 0.15
73 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (72 bp):
ATTTATTTAAATTTAATATATAATAATTTAATATATTTTTATTAAATATTTATTTAATATTTTTT
AAAATAT
Found at i:2121973 original size:11 final size:12
Alignment explanation
Indices: 2121941--2121986 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
2121931 TATATAATAA
2121941 TTTAATATATTTT
1 TTTAA-ATATTTT
2121954 TATTAAATATTTT
1 T-TTAAATATTTT
2121967 TTT-AATATTTT
1 TTTAAATATTTT
*
2121978 TTAAAATAT
1 TTTAAATAT
2121987 ATGATATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 10 0.33
12 7 0.23
13 9 0.30
14 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAAATATTTT
Found at i:2122148 original size:19 final size:20
Alignment explanation
Indices: 2122104--2122154 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
2122094 ATTCGACTTT
2122104 AAAATTT-TTTGTTTTAAAAC
1 AAAATTTATTT-TTTTAAAAC
**
2122124 TCAATTTATTTTTTT-AAAC
1 AAAATTTATTTTTTTAAAAC
*
2122143 AAAATTAATTTT
1 AAAATTTATTTT
2122155 CTATTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 13 0.52
20 9 0.36
21 3 0.12
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (20 bp):
AAAATTTATTTTTTTAAAAC
Found at i:2122196 original size:28 final size:29
Alignment explanation
Indices: 2122131--2122207 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 29
2122121 AACTCAATTT
**
2122131 ATTTTTTTAAACAAAATTAATTTTCTATTAA
1 ATTTTTTTAAATTAAA-T-ATTTTCTATTAA
*
2122162 ATTTTTTTAAATTTAATATTTT-TATTTAA
1 ATTTTTTTAAATTAAATATTTTCTA-TTAA
*
2122191 A-TTTTTTATATTAAATA
1 ATTTTTTTAAATTAAATA
2122208 AATTTTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 16 0.40
29 10 0.25
30 1 0.03
31 13 0.32
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTTTTTAAATTAAATATTTTCTATTAA
Found at i:2122211 original size:18 final size:18
Alignment explanation
Indices: 2122188--2122227 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2122178 TATTTTTATT
*
2122188 TAAATTTTTTATATTAAA
1 TAAATTTTTAATATTAAA
*
2122206 TAAA-TTTTAATTTTAAA
1 TAAATTTTTAATATTAAA
2122223 TAAAT
1 TAAAT
2122228 AATTTAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTTTTAATATTAAA
Found at i:2122242 original size:20 final size:17
Alignment explanation
Indices: 2122202--2122244 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
2122192 TTTTTTATAT
*
2122202 TAAATAAATTTTAATTT
1 TAAATAAATTTTAATTA
2122219 TAAATAAATAATTTAACTTA
1 TAAATAAAT--TTTAA-TTA
2122239 TAAATA
1 TAAATA
2122245 GTATTACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
19 5 0.23
20 8 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATAAATTTTAATTA
Found at i:2122389 original size:2 final size:2
Alignment explanation
Indices: 2122382--2122411 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2122372 GTACACCAAA
2122382 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
2122412 GGTCAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2122538 original size:33 final size:31
Alignment explanation
Indices: 2122501--2122593 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 31
2122491 ATATTTTTAT
2122501 ATTTTATAATATATCATAATTTTATTTAAATAA
1 ATTTTA-AATAT-TCATAATTTTATTTAAATAA
* *
2122534 ATTTTAATATATTTAATAA-TTTATATTATATAA
1 ATTTTAA-ATA-TTCATAATTTTAT-TTAAATAA
2122567 ATTTTAAAATATTCATACATTTATATT
1 ATTTT-AAATATTCATA-ATTT-TATT
2122594 GTATTTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
32 11 0.22
33 30 0.60
34 6 0.12
35 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTTAAATATTCATAATTTTATTTAAATAA
Found at i:2128689 original size:14 final size:14
Alignment explanation
Indices: 2128670--2128699 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2128660 GAGGAGAAAA
*
2128670 AGGGGGGGGGGGGG
1 AGGGGGCGGGGGGG
2128684 AGGGGGCGGGGGGG
1 AGGGGGCGGGGGGG
2128698 AG
1 AG
2128700 AGTCGACGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.03, G:0.87, T:0.00
Consensus pattern (14 bp):
AGGGGGCGGGGGGG
Found at i:2129564 original size:19 final size:18
Alignment explanation
Indices: 2129507--2129574 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
2129497 ATTATATTAT
* *
2129507 TTTTATGTTTATAAAAAA
1 TTTTATATTTATATAAAA
*
2129525 TATTATATTTATATAATAA
1 TTTTATATTTATATAA-AA
*
2129544 TTTTATATTATATTTAAAA
1 TTTTATATT-TATATAAAA
*
2129563 TTATCATATTTA
1 TT-TTATATTTA
2129575 AATTATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
18 13 0.32
19 16 0.39
20 12 0.29
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TTTTATATTTATATAAAA
Found at i:2129573 original size:15 final size:14
Alignment explanation
Indices: 2129552--2129587 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2129542 AATTTTATAT
2129552 TATATTTAAAATTA
1 TATATTTAAAATTA
2129566 TCATATTT-AAATTA
1 T-ATATTTAAAATTA
2129580 TATATTTA
1 TATATTTA
2129588 CTTTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.30
14 8 0.40
15 6 0.30
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATTTAAAATTA
Found at i:2129586 original size:13 final size:13
Alignment explanation
Indices: 2129552--2129597 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2129542 AATTTTATAT
2129552 TATATTTAAAATTA
1 TATATTT-AAATTA
2129566 TCATATTTAAATTA
1 T-ATATTTAAATTA
**
2129580 TATATTTACTTTA
1 TATATTTAAATTA
2129593 TATAT
1 TATAT
2129598 ATATACATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 15 0.52
14 8 0.28
15 6 0.21
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTTAAATTA
Found at i:2130090 original size:8 final size:8
Alignment explanation
Indices: 2130077--2130192 Score: 63
Period size: 8 Copynumber: 13.1 Consensus size: 8
2130067 CTTTAAATAT
2130077 TATATAAA
1 TATATAAA
2130085 TATATAAA
1 TATATAAA
2130093 TATATTAAA
1 TATA-TAAA
* **
2130102 TTTATATTT
1 TATATA-AA
*
2130111 TATATTAA
1 TATATAAA
2130119 TATATTAAAA
1 TATA-T-AAA
2130129 TTTATATAAA
1 --TATATAAA
2130139 TATATATTAA
1 TATATA--AA
* *
2130149 TTTAAAAA
1 TATATAAA
2130157 TA-ATTATAA
1 TATA-TA-AA
2130166 TATATTAAAA
1 TATA-T-AAA
2130176 TATATAAA
1 TATATAAA
2130184 TATATAAA
1 TATATAAA
2130192 T
1 T
2130193 TATCAAATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
7 1 0.01
8 40 0.48
9 17 0.20
10 20 0.24
11 2 0.02
12 4 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
TATATAAA
Found at i:2130097 original size:10 final size:10
Alignment explanation
Indices: 2130040--2130189 Score: 73
Period size: 10 Copynumber: 16.3 Consensus size: 10
2130030 AATAAGTATA
2130040 ATATAAAT-T
1 ATATAAATAT
2130049 A-ATAAATA-
1 ATATAAATAT
*
2130057 A-ATAAAAAT
1 ATATAAATAT
*
2130066 ACTTTAAATAT
1 A-TATAAATAT
2130077 -TATATAA-AT
1 ATATA-AATAT
2130086 ATATAAATAT
1 ATATAAATAT
2130096 AT-TAAAT-T
1 ATATAAATAT
* *
2130104 -TAT-ATTTT
1 ATATAAATAT
*
2130112 ATATTAATAT
1 ATATAAATAT
*
2130122 AT-TAAAATTT
1 ATAT-AAATAT
2130132 ATATAAATAT
1 ATATAAATAT
*
2130142 ATATTAAT-T
1 ATATAAATAT
*
2130151 -TAAAAATA-
1 ATATAAATAT
2130159 AT-TATAATAT
1 ATATA-AATAT
2130169 AT-TAAA-AT
1 ATATAAATAT
2130177 ATATAAATAT
1 ATATAAATAT
2130187 ATA
1 ATA
2130190 AATTATCAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 37
0.68 0.09 0.23
Matches are distributed among these distances:
7 3 0.03
8 26 0.24
9 30 0.28
10 42 0.39
11 7 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATAAATAT
Found at i:2130121 original size:26 final size:27
Alignment explanation
Indices: 2130085--2130135 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
2130075 ATTATATAAA
2130085 TATATAAATATATT-AAATTTATATTT
1 TATATAAATATATTAAAATTTATATTT
*
2130111 TATATTAATATATTAAAATTTATAT
1 TATATAAATATATTAAAATTTATAT
2130136 AAATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TATATAAATATATTAAAATTTATATTT
Found at i:2130124 original size:47 final size:45
Alignment explanation
Indices: 2130059--2130193 Score: 127
Period size: 47 Copynumber: 3.0 Consensus size: 45
2130049 AATAAATAAA
*
2130059 TAAAAATACTTTAA-ATATTATATAAATATATAAATATATTAAATT
1 TAAAAATAATTTAATATATTATA-AAATATATAAATATATTAAATT
* ** * * *
2130104 TATATTTTATATTAATATATTA-AAATTTATATAAATATATATTAATT
1 TAAAAATAAT-TTAATATATTATAAA-ATATATAAATATAT-TAAATT
2130151 TAAAAATAATTATAATATA-T-TAAAATATATAAATATA-TAAATT
1 TAAAAATAATT-TAATATATTATAAAATATATAAATATATTAAATT
2130194 ATCAAATTTA
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
43 5 0.07
45 19 0.27
46 23 0.32
47 24 0.34
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (45 bp):
TAAAAATAATTTAATATATTATAAAATATATAAATATATTAAATT
Found at i:2130141 original size:26 final size:27
Alignment explanation
Indices: 2130043--2130144 Score: 102
Period size: 27 Copynumber: 3.7 Consensus size: 27
2130033 AAGTATAATA
* *
2130043 TAAA-TTA-ATAAATAAATAAAAATACTT
1 TAAATTTATATAAATATATAAATATA--T
2130070 TAAATATTATATAAATATATAAATATAT
1 TAAAT-TTATATAAATATATAAATATAT
** *
2130098 TAAATTTATAT-TTTATATTAATATAT
1 TAAATTTATATAAATATATAAATATAT
2130124 TAAAATTTATATAAATATATA
1 T-AAATTTATATAAATATATA
2130145 TTAATTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
26 13 0.21
27 20 0.32
28 11 0.18
29 3 0.05
30 15 0.24
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTTATATAAATATATAAATATAT
Found at i:2130184 original size:27 final size:24
Alignment explanation
Indices: 2130029--2130190 Score: 69
Period size: 26 Copynumber: 6.2 Consensus size: 24
2130019 AAATTTTTTA
*
2130029 AAATAAGTATAATATAAATTAATAAAT
1 AAATAA-TATATTA-AAATT-ATAAAT
*
2130056 AAATAAAAATACTTTAAATATTATATAAAT
1 AAAT-AATATA--TTAAA-A-T-TATAAAT
* * **
2130086 ATATAAATATATTAAATTTATATTTT
1 AAAT-AATATATTAAAATTATA-AAT
* *
2130112 ATATTAATATATTAAAATT-TATAT
1 A-AATAATATATTAAAATTATAAAT
* *
2130136 AAAT-ATATATT-AATTTAAAAAT
1 AAATAATATATTAAAATTATAAAT
2130158 AATTATAATATATTAAAATATATAAAT
1 AA--ATAATATATTAAAAT-TATAAAT
*
2130185 ATATAA
1 AAATAA
2130191 ATTATCAAAT
Statistics
Matches: 103, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
21 4 0.04
22 12 0.12
23 2 0.02
24 5 0.05
25 17 0.17
26 19 0.18
27 15 0.15
28 9 0.09
29 3 0.03
30 16 0.16
31 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (24 bp):
AAATAATATATTAAAATTATAAAT
Found at i:2130206 original size:45 final size:43
Alignment explanation
Indices: 2130082--2130209 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 43
2130072 AATATTATAT
* *
2130082 AAATATATAAATATATTAAATTTATATTTTA-TATTAATATATTA
1 AAATATATAAATATA-TAAATTTAAATTTAATTA-TAATATATTA
**
2130126 AAATTTATATAAATATATATTAATTTAAAAATAATTATAATATATTA
1 AAA--TATATAAATATATA--AATTTAAATTTAATTATAATATATTA
2130173 AAATATATAAATATATAAATTATCAAATTTAATTATA
1 AAATATATAAATATATAAATT-T-AAATTTAATTATA
2130210 CTTTATTCAC
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
43 4 0.06
44 4 0.06
45 27 0.38
46 12 0.17
47 22 0.31
48 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (43 bp):
AAATATATAAATATATAAATTTAAATTTAATTATAATATATTA
Found at i:2130485 original size:14 final size:14
Alignment explanation
Indices: 2130462--2130498 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2130452 TAAATATAAT
2130462 ATAT-ATATTAAAC
1 ATATCATATTAAAC
*
2130475 ATATCATATTAATC
1 ATATCATATTAAAC
2130489 ATATCATATT
1 ATATCATATT
2130499 TATTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATCATATTAAAC
Found at i:2130683 original size:13 final size:14
Alignment explanation
Indices: 2130665--2130693 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2130655 AAATATATAG
2130665 TAATAT-TTAAAAT
1 TAATATATTAAAAT
2130678 TAATATATTAAAAT
1 TAATATATTAAAAT
2130692 TA
1 TA
2130694 TGAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATATATTAAAAT
Found at i:2131351 original size:15 final size:15
Alignment explanation
Indices: 2131331--2131360 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2131321 TCAGTATCTA
*
2131331 TAAATAAATATTAAT
1 TAAATAAAAATTAAT
2131346 TAAATAAAAATTAAT
1 TAAATAAAAATTAAT
2131361 ATATTCTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATAAAAATTAAT
Found at i:2131598 original size:3 final size:3
Alignment explanation
Indices: 2131590--2131628 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2131580 TTTTTATTTA
2131590 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2131629 TATTTTCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2134746 original size:19 final size:20
Alignment explanation
Indices: 2134724--2134767 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
2134714 AATTTTAAGT
*
2134724 AAATTTATAAAT-TTATT-TA
1 AAATTTA-AAATATGATTATA
2134743 AAATTTAAAATATGATTATA
1 AAATTTAAAATATGATTATA
2134763 AAATT
1 AAATT
2134768 ACTCTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 11 0.50
20 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATTTAAAATATGATTATA
Found at i:2135603 original size:12 final size:12
Alignment explanation
Indices: 2135588--2135624 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2135578 AATTCATATA
2135588 ATTATTTAAAAT
1 ATTATTTAAAAT
2135600 ATTATTTAAAAT
1 ATTATTTAAAAT
*
2135612 -TT-TTAAAAAT
1 ATTATTTAAAAT
2135622 ATT
1 ATT
2135625 TTATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 7 0.30
11 4 0.17
12 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTATTTAAAAT
Found at i:2135655 original size:20 final size:19
Alignment explanation
Indices: 2135632--2135679 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2135622 ATTTTATATT
2135632 AATATAATTAAATTTAAATA
1 AATATAATT-AATTTAAATA
* *
2135652 AATATAATTATTTTACATA
1 AATATAATTAATTTAAATA
2135671 AATAATAAT
1 AAT-ATAAT
2135680 ATGAGTTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATAATTAATTTAAATA
Found at i:2136459 original size:11 final size:11
Alignment explanation
Indices: 2136434--2136470 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
2136424 TATAATCATT
2136434 ATAATTTTTTAA
1 ATAATTTTTT-A
2136446 ATAATTTTTTA
1 ATAATTTTTTA
2136457 ATAATTTTTGTA
1 ATAATTTTT-TA
2136469 AT
1 AT
2136471 TGAATTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
ATAATTTTTTA
Found at i:2136534 original size:17 final size:18
Alignment explanation
Indices: 2136497--2136535 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2136487 ACTCAATTAA
*
2136497 AAATTTTATTAATAATAT
1 AAATTTAATTAATAATAT
*
2136515 AAATTTAATTATTAAT-T
1 AAATTTAATTAATAATAT
2136532 AAAT
1 AAAT
2136536 AATTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTTAATTAATAATAT
Found at i:2136977 original size:19 final size:19
Alignment explanation
Indices: 2136931--2136978 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2136921 ACTCAAAATT
*
2136931 TAATTTAAT-TAATTTATA
1 TAATTTAATAAAATTTATA
2136949 TAATTATAATAAAATTTA-A
1 TAATT-TAATAAAATTTATA
2136968 TAAATTTAATA
1 T-AATTTAATA
2136979 TTTAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTTAATAAAATTTATA
Found at i:2136978 original size:9 final size:9
Alignment explanation
Indices: 2136932--2136978 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
2136922 CTCAAAATTT
*
2136932 AATTTAATT
1 AATTTAATA
2136941 AATTT-ATA
1 AATTTAATA
2136949 TAATTATAATAA
1 -AATT-TAAT-A
2136961 AATTTAATA
1 AATTTAATA
2136970 AATTTAATA
1 AATTTAATA
2136979 TTTAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 2 0.06
9 19 0.58
10 5 0.15
11 6 0.18
12 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTTAATA
Found at i:2136992 original size:33 final size:34
Alignment explanation
Indices: 2136925--2136992 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
2136915 ATATAAACTC
*
2136925 AAAATTTAATTTAATTAATTTATATAATTATAAT
1 AAAATTTAATTAAATTAATTTATATAATTATAAT
2136959 AAAATTTAA-TAAATTTAATATT-TA-AATTATAAT
1 AAAATTTAATTAAA-TTAAT-TTATATAATTATAAT
2136992 A
1 A
2136993 TTTTTTATCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 13 0.42
34 16 0.52
35 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (34 bp):
AAAATTTAATTAAATTAATTTATATAATTATAAT
Found at i:2137402 original size:32 final size:32
Alignment explanation
Indices: 2137325--2137402 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 32
2137315 ATATTTAAAT
* *
2137325 TATTTTATATTTATATAAAATTTAATATATTAA
1 TATTTT-TAATTATATAAAATTTAAAATATTAA
* * * *
2137358 TA-ATATATATTATATAAATTTTAAAATATTTA
1 TATTTTTA-ATTATATAAAATTTAAAATATTAA
2137390 TATTTTTAATTAT
1 TATTTTTAATTAT
2137403 TTTTATATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
31 2 0.06
32 28 0.80
33 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATTTTTAATTATATAAAATTTAAAATATTAA
Found at i:2139360 original size:2 final size:2
Alignment explanation
Indices: 2139353--2139389 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2139343 AATGTGATAC
2139353 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 T
2139390 GCAGTCAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2139544 original size:2 final size:2
Alignment explanation
Indices: 2139537--2139561 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2139527 TCTTCGCAAT
2139537 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 T
2139562 CCTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2139782 original size:3 final size:3
Alignment explanation
Indices: 2139774--2139807 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2139764 AAATGTTTCA
2139774 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2139808 TTGGTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2140884 original size:27 final size:27
Alignment explanation
Indices: 2140848--2140915 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
2140838 AACAACATTA
*
2140848 TAATTTTATTAAATATTT-ATTA-TATT
1 TAATATTATTAAATATTTCATTACT-TT
*
2140874 TAATACTTATTTAATATTTCATTACTTT
1 TAATA-TTATTAAATATTTCATTACTTT
*
2140902 TAATATAATTAAAT
1 TAATATTATTAAAT
2140916 GATTAAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.11
27 19 0.54
28 11 0.31
29 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TAATATTATTAAATATTTCATTACTTT
Found at i:2141115 original size:16 final size:16
Alignment explanation
Indices: 2141090--2141129 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2141080 TAATAATAAT
2141090 ATAA-TAAATAAACAA
1 ATAATTAAATAAACAA
* *
2141105 TTAATTAAATAAATAA
1 ATAATTAAATAAACAA
2141121 ATAATTAAA
1 ATAATTAAA
2141130 AGAGGCCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATTAAATAAACAA
Found at i:2141754 original size:18 final size:18
Alignment explanation
Indices: 2141728--2141762 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2141718 TTTTATACTA
*
2141728 TAATAAAAAATTAAAAAT
1 TAATAAAAAAATAAAAAT
*
2141746 TAATTAAAAAATAAAAA
1 TAATAAAAAAATAAAAA
2141763 ACATATGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAAAAAAATAAAAAT
Found at i:2148238 original size:3 final size:3
Alignment explanation
Indices: 2148230--2148270 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2148220 GTCATACTGA
2148230 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2148271 AAGATACTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2148971 original size:14 final size:14
Alignment explanation
Indices: 2148952--2148978 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2148942 TATCACGATT
2148952 AATTTTATAAATAA
1 AATTTTATAAATAA
2148966 AATTTTATAAATA
1 AATTTTATAAATA
2148979 TATTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTTTATAAATAA
Found at i:2149820 original size:49 final size:49
Alignment explanation
Indices: 2149767--2149866 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
2149757 ACATGATAAA
*
2149767 AAATATACAAACATGACATAAATAACAAATATTACCATCAACCTGCATT
1 AAATACACAAACATGACATAAATAACAAATATTACCATCAACCTGCATT
* * * *
2149816 AAATACACAAATATGATATGAATAACAAATATTATCATCAACCTGCATT
1 AAATACACAAACATGACATAAATAACAAATATTACCATCAACCTGCATT
2149865 AA
1 AA
2149867 TCATACGAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (49 bp):
AAATACACAAACATGACATAAATAACAAATATTACCATCAACCTGCATT
Found at i:2150097 original size:22 final size:22
Alignment explanation
Indices: 2150072--2150218 Score: 107
Period size: 22 Copynumber: 6.5 Consensus size: 22
2150062 GGACATAACT
*
2150072 ATATGTATATATGATAATAAAA
1 ATATGTATATATGATAATAATA
* *
2150094 ATATGAATATATGATTATAA-A
1 ATATGTATATATGATAATAATA
* * * * *
2150115 ACTATATACATATCACAATAATT
1 A-TATGTATATATGATAATAATA
* * * *
2150138 GTAAGTATATATAAAAATAATA
1 ATATGTATATATGATAATAATA
* *
2150160 ATATGTACATATGATTATAATA
1 ATATGTATATATGATAATAATA
*
2150182 ATATGCATATAATATTATAATAATA
1 ATATG--TAT-ATATGATAATAATA
*
2150207 ATATATATATAT
1 ATATGTATATAT
2150219 ATGTAAATTC
Statistics
Matches: 94, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
21 2 0.02
22 71 0.76
23 3 0.03
24 2 0.02
25 16 0.17
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (22 bp):
ATATGTATATATGATAATAATA
Found at i:2150163 original size:66 final size:65
Alignment explanation
Indices: 2150045--2150179 Score: 162
Period size: 66 Copynumber: 2.1 Consensus size: 65
2150035 GCAAATCAAA
* * * * * *
2150045 ATAAAAGTATATACATAGGACATAACTATATGTATATATGATAATAAAAATATGAATATATGATT
1 ATAAAACTATATACATAGCACATAACTATAAGTATATATAAAAATAAAAATATGAACATATGATT
* * * * *
2150110 ATAAAACTATATACATATCACAATAATTGTAAGTATATATAAAAATAATAATATGTACATATGAT
1 ATAAAACTATATACATAGCAC-ATAACTATAAGTATATATAAAAATAAAAATATGAACATATGAT
2150175 T
65 T
2150176 ATAA
1 ATAA
2150180 TAATATGCAT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
65 18 0.31
66 40 0.69
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (65 bp):
ATAAAACTATATACATAGCACATAACTATAAGTATATATAAAAATAAAAATATGAACATATGATT
Found at i:2150216 original size:25 final size:26
Alignment explanation
Indices: 2150147--2150217 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
2150137 TGTAAGTATA
* *
2150147 TATAAAAATAATA-ATATGTACATAT
1 TATAATAATAATATATATATACATAT
* * **
2150172 GATTATAATAATATGCATATA-ATAT
1 TATAATAATAATATATATATACATAT
2150197 TATAATAATAATATATATATA
1 TATAATAATAATATATATATA
2150218 TATGTAAATT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
25 31 0.89
26 4 0.11
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (26 bp):
TATAATAATAATATATATATACATAT
Found at i:2150904 original size:22 final size:22
Alignment explanation
Indices: 2150879--2150921 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2150869 ATATATACAC
*
2150879 ATTTTACTGCAAACATATGTAT
1 ATTTTACTACAAACATATGTAT
* *
2150901 ATTTTATTATAAACATATGTA
1 ATTTTACTACAAACATATGTA
2150922 CATATTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTTACTACAAACATATGTAT
Found at i:2152048 original size:34 final size:34
Alignment explanation
Indices: 2151986--2152170 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
2151976 GTAAAAACCA
* *
2151986 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * * * *
2152020 CCATTTAGTCAATAATGATAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
*
2152054 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
2152088 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
2152122 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
2152155 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2152171 TCTCCCACTT
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 15 0.11
34 117 0.89
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:2152128 original size:102 final size:101
Alignment explanation
Indices: 2151986--2152170 Score: 307
Period size: 102 Copynumber: 1.8 Consensus size: 101
2151976 GTAAAAACCA
*
2151986 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAATAATGATAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGATAAACCACCAAAT
2152051 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * * *
2152088 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGATAAACCACCAAAT
2152153 CACCATTTAATCAACAAT
66 CACCATTTAATCAACAAT
2152171 TCTCCCACTT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 16 0.21
102 61 0.79
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGATAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:2156263 original size:19 final size:19
Alignment explanation
Indices: 2156236--2156298 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2156226 TCACGTGTAC
* *
2156236 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2156255 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2156274 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2156293 AGTACC
1 AGTACC
2156299 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2156647 original size:34 final size:34
Alignment explanation
Indices: 2156601--2156783 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
2156591 GTAAAAACCA
*
2156601 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2156635 TCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
2156669 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2156703 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
2156737 TCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2156770 CCATTTAATCAACA
1 CCATTTAATCAACA
2156784 CAAATAAAAT
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.11
34 112 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2156743 original size:102 final size:101
Alignment explanation
Indices: 2156601--2156783 Score: 321
Period size: 102 Copynumber: 1.8 Consensus size: 101
2156591 GTAAAAACCA
2156601 CCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAACCACCAAAT
2156666 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
2156703 CCATTTAATCAACAATGGTAAGCTACCAAATTTCTCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAACCACCAAAT
2156768 CACCATTTAATCAACA
66 CACCATTTAATCAACA
2156784 CAAATAAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 63 0.82
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:2157794 original size:34 final size:34
Alignment explanation
Indices: 2157754--2157830 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 34
2157744 TTAAAAAATT
* *
2157754 TTAAAAACAACATTCAT-TCTAATATTGCT-AAA
1 TTAAAAAAAACATTCATCTCTAATATAGCTAAAA
*
2157786 TTAAAAAAAATATTCATCTCTAATATAGCTAAAA
1 TTAAAAAAAACATTCATCTCTAATATAGCTAAAA
2157820 TTAAAATAAAA
1 TTAAAA-AAAA
2157831 AGAACATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 15 0.38
33 11 0.28
34 9 0.23
35 4 0.10
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (34 bp):
TTAAAAAAAACATTCATCTCTAATATAGCTAAAA
Found at i:2158215 original size:21 final size:21
Alignment explanation
Indices: 2158191--2158230 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2158181 TATTTTTATT
*
2158191 TAAATATAATTATAAAATATA
1 TAAATATAAGTATAAAATATA
*
2158212 TAAATATTAGTATAAAATA
1 TAAATATAAGTATAAAATA
2158231 AATTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAATATAAGTATAAAATATA
Found at i:2158268 original size:19 final size:19
Alignment explanation
Indices: 2158223--2158279 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2158213 AAATATTAGT
*
2158223 ATAAAATAAATTTTTAATA
1 ATAAAATAAATTTTAAATA
* ** *
2158242 TTTTAATATATTTTAAATA
1 ATAAAATAAATTTTAAATA
2158261 ATAAAATAAAATTTTAAAT
1 ATAAAAT-AAATTTTAAAT
2158280 TAAATCAAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAAATAAATTTTAAATA
Found at i:2159831 original size:21 final size:21
Alignment explanation
Indices: 2159807--2159855 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2159797 AATTAATCAT
2159807 CATATAAGTAAATAAATCTAA
1 CATATAAGTAAATAAATCTAA
* * * * *
2159828 CATAAAATTGAATTAATCTTA
1 CATATAAGTAAATAAATCTAA
2159849 CATATAA
1 CATATAA
2159856 TAAGACTTGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (21 bp):
CATATAAGTAAATAAATCTAA
Found at i:2160042 original size:13 final size:13
Alignment explanation
Indices: 2160024--2160050 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2160014 CAACTTATGA
2160024 TTAAGTTGTCGAG
1 TTAAGTTGTCGAG
2160037 TTAAGTTGTCGAG
1 TTAAGTTGTCGAG
2160050 T
1 T
2160051 GTGGTACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (13 bp):
TTAAGTTGTCGAG
Found at i:2161662 original size:223 final size:223
Alignment explanation
Indices: 2161273--2161697 Score: 566
Period size: 223 Copynumber: 1.9 Consensus size: 223
2161263 GTTTATTGAA
* * * * * * * *
2161273 TGTTCATTTTGTAGAATAACTTATCATAGTTTTATTTCACAAAGTCTCGAAATAATCATTTAGTG
1 TGTTCATTTCGCAGAATAACCTATCATAGTTTTACTTCACAAAATCTCAAAATAACCATTTAATG
* * *
2161338 ACTCCTCTACTGAATGACTATTTCGGTTTTGAGCATGATATAAAATTATTCAAGTGAATTAGTCA
66 ACTCCTCTACTGAATGACTATTTCGGTTTTAAGCACGATACAAAATTATTCAAGTGAATTAGTCA
* ** * *
2161403 TCTCTATGAAAGCTAATTTATATTTTATTCTTGTTCCACCAAATCGAACATGGTCATATGAGTTG
131 TCTCTATGAAAGCTAATTTATATTTTATTCTTGTTCCACCAAATCAAACATGACCATATGAATCG
2161468 ATATCATTACTATGTGTAGAAAGAATTG
196 ATATCATTACTATGTGTAGAAAGAATTG
* **
2161496 TGTTCATTTCGCAGAATAACCTATTATA-TTCTTACTTCGTAAAATCTCAAAATAACCATTTAAT
1 TGTTCATTTCGCAGAATAACCTATCATAGTT-TTACTTCACAAAATCTCAAAATAACCATTTAAT
* * * * *
2161560 GTCTTCTCTATTGAATGACTATTTCTGTTTTAAGCACGATACAAAATTATTCAAGTGGATTAGTC
65 GACTCCTCTACTGAATGACTATTTCGGTTTTAAGCACGATACAAAATTATTCAAGTGAATTAGTC
* * * *
2161625 ATCTCT-TCGAAAGTTAATTTCTATTTTATTTTTGTTCCTCCAAATCAAACATGACCATATGAAT
130 ATCTCTAT-GAAAGCTAATTTATATTTTATTCTTGTTCCACCAAATCAAACATGACCATATGAAT
2161689 CGATATCAT
194 CGATATCAT
2161698 CATTATATAT
Statistics
Matches: 172, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
222 3 0.02
223 169 0.98
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (223 bp):
TGTTCATTTCGCAGAATAACCTATCATAGTTTTACTTCACAAAATCTCAAAATAACCATTTAATG
ACTCCTCTACTGAATGACTATTTCGGTTTTAAGCACGATACAAAATTATTCAAGTGAATTAGTCA
TCTCTATGAAAGCTAATTTATATTTTATTCTTGTTCCACCAAATCAAACATGACCATATGAATCG
ATATCATTACTATGTGTAGAAAGAATTG
Found at i:2162100 original size:16 final size:16
Alignment explanation
Indices: 2162057--2162102 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2162047 TTGAATCAAA
*
2162057 TTATTATTATTATTATT
1 TTATT-TTATTTTTATT
*
2162074 TTAATTTATTTTTATT
1 TTATTTTATTTTTATT
2162090 TTATTTTATTTTT
1 TTATTTTATTTTT
2162103 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTATTTTTATT
Found at i:2162102 original size:6 final size:5
Alignment explanation
Indices: 2162057--2162101 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
2162047 TTGAATCAAA
*
2162057 TTATT ATTATT ATTATT TTAAT TTATTT TTATT TTATT TTATT TT
1 TTATT -TTATT -TTATT TTATT TTA-TT TTATT TTATT TTATT TT
2162102 TTAAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 21 0.58
6 15 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:2163173 original size:20 final size:19
Alignment explanation
Indices: 2163150--2163196 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2163140 ATGGTATGAA
2163150 TTATATTTAAAAATATTATT
1 TTATATTT-AAAATATTATT
**
2163170 TTATATTTATTATATTATT
1 TTATATTTAAAATATTATT
*
2163189 TTTTATTT
1 TTATATTT
2163197 TTAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATATTTAAAATATTATT
Found at i:2164293 original size:2 final size:2
Alignment explanation
Indices: 2164286--2164331 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2164276 ATTCGGGTGT
2164286 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2164328 TC TC
1 TC TC
2164332 CCCCCCCCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2169445 original size:51 final size:50
Alignment explanation
Indices: 2169385--2169566 Score: 176
Period size: 51 Copynumber: 3.6 Consensus size: 50
2169375 CCAGTCGTTT
* *
2169385 GAAATGAAATCTCCTCTCAATGTCAAATCCTCACAGGAAATGCAGCAGTCC
1 GAAACGAAATCTCC-CGCAATGTCAAATCCTCACAGGAAATGCAGCAGTCC
* * *
2169436 GAAACGAAATCCCCTCGCAATG-CGAAGTCCTCAGAGGAAATGCAGCAGTCC
1 GAAACGAAATCTCC-CGCAATGTC-AAATCCTCACAGGAAATGCAGCAGTCC
* * *
2169487 GAAACGAAA--TCCCGCAATGTCAAGTCCTC-CAAGCAAATGCAGCAATCC
1 GAAACGAAATCTCCCGCAATGTCAAATCCTCAC-AGGAAATGCAGCAGTCC
* * *
2169535 CAAATGACATCTCCC-CGACATGTCAAATCCTC
1 GAAACGAAATCTCCCGC-A-ATGTCAAATCCTC
2169567 TAAAGAACAC
Statistics
Matches: 111, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
48 36 0.32
49 4 0.04
50 6 0.05
51 65 0.59
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.18
Consensus pattern (50 bp):
GAAACGAAATCTCCCGCAATGTCAAATCCTCACAGGAAATGCAGCAGTCC
Found at i:2169525 original size:48 final size:50
Alignment explanation
Indices: 2169385--2169530 Score: 183
Period size: 51 Copynumber: 2.9 Consensus size: 50
2169375 CCAGTCGTTT
* * *
2169385 GAAATGAAATCTCCTCTCAATGTCAAATCCTCACAGGAAATGCAGCAGTCC
1 GAAACGAAATC-CCTCGCAATGTCAAGTCCTCACAGGAAATGCAGCAGTCC
*
2169436 GAAACGAAATCCCCTCGCAATG-CGAAGTCCTCAGAGGAAATGCAGCAGTCC
1 GAAACGAAAT-CCCTCGCAATGTC-AAGTCCTCACAGGAAATGCAGCAGTCC
*
2169487 GAAACGAAAT-CC-CGCAATGTCAAGTCCTC-CAAGCAAATGCAGCA
1 GAAACGAAATCCCTCGCAATGTCAAGTCCTCAC-AGGAAATGCAGCA
2169531 ATCCCAAATG
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
48 27 0.32
49 3 0.04
50 1 0.01
51 53 0.62
52 1 0.01
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.16
Consensus pattern (50 bp):
GAAACGAAATCCCTCGCAATGTCAAGTCCTCACAGGAAATGCAGCAGTCC
Found at i:2170279 original size:13 final size:13
Alignment explanation
Indices: 2170261--2170286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2170251 GATTTAATCC
2170261 GATTTAATATAAT
1 GATTTAATATAAT
2170274 GATTTAATATAAT
1 GATTTAATATAAT
2170287 AATTCAAATC
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
GATTTAATATAAT
Found at i:2173154 original size:2 final size:2
Alignment explanation
Indices: 2173147--2173174 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2173137 ATCATTTTTA
2173147 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
2173175 GATCAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2173556 original size:2 final size:2
Alignment explanation
Indices: 2173549--2173578 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2173539 GCATCAGTTT
2173549 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2173579 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2174549 original size:45 final size:45
Alignment explanation
Indices: 2174508--2174823 Score: 146
Period size: 45 Copynumber: 7.3 Consensus size: 45
2174498 TGTTTCTTTG
* *
2174508 TCTTCTCAGCTGAGCCATTCACTGTCGCAG-CCATCTCTTTCTTCA
1 TCTTCTCAGCTGAGCCATTTACTGT-GAAGCCCATCTCTTTCTTCA
* * * * *
2174553 TCCTCTCGGATAAGCCATTTACTGTTAAGCCCATCTCTTTCTTCA
1 TCTTCTCAGCTGAGCCATTTACTGTGAAGCCCATCTCTTTCTTCA
* * * *** *
2174598 TCTTTTCAGCTGAGCTATTTAC--TGCAG-TTGTCTCTGGTC-TCA
1 TCTTCTCAGCTGAGCCATTTACTGTGAAGCCCATCTCT-TTCTTCA
* **
2174640 TCTTCTCAGCTGATCCATTTACTGT--AGCTACC-TCT-TTTC-GAA
1 TCTTCTCAGCTGAGCCATTTACTGTGAAGC--CCATCTCTTTCTTCA
* * * * * *
2174682 TCTTCTCAGCTGAGCTATTTCCTGCCG-TGGCCATCTCTTTCTTCC
1 TCTTCTCAGCTGAGCCATTTACTG-TGAAGCCCATCTCTTTCTTCA
* * * **
2174727 TCTTCTCAGATGAGCTATTCAC---G--G-CTGTCTCTTTCTGT-A
1 TCTTCTCAGCTGAGCCATTTACTGTGAAGCCCATCTCTTTCT-TCA
* * * * *
2174766 TCTTCTCAGCTGAGCTATTTACTGTCATGACCGTCTCTTTCTTCA
1 TCTTCTCAGCTGAGCCATTTACTGTGAAGCCCATCTCTTTCTTCA
*
2174811 TTTTCTCAGCTGA
1 TCTTCTCAGCTGA
2174824 ATTATTTACA
Statistics
Matches: 204, Mismatches: 47, Indels: 40
0.70 0.16 0.14
Matches are distributed among these distances:
39 30 0.15
40 2 0.01
41 1 0.00
42 55 0.27
43 9 0.04
44 13 0.06
45 94 0.46
ACGTcount: A:0.16, C:0.30, G:0.15, T:0.40
Consensus pattern (45 bp):
TCTTCTCAGCTGAGCCATTTACTGTGAAGCCCATCTCTTTCTTCA
Found at i:2174649 original size:42 final size:41
Alignment explanation
Indices: 2174586--2174865 Score: 174
Period size: 45 Copynumber: 6.5 Consensus size: 41
2174576 GTTAAGCCCA
* *
2174586 TCTCTTTCTTCATCTTTTCAGCTGAGCTATTTACTGCAGTTG
1 TCTCTTTC-TCATCTTCTCAGCTGAGCTATTTACTGCAGCTG
* * * * *
2174628 TCTCTGGTCTCATCTTCTCAGCTGATCCATTTACTGTAGCTA
1 TCTCT-TTCTCATCTTCTCAGCTGAGCTATTTACTGCAGCTG
* * *
2174670 CCTCTTT-TCGAATCTTCTCAGCTGAGCTATTTCCTGCCG-TGG
1 TCTCTTTCTC--ATCTTCTCAGCTGAGCTATTTACTGCAGCT-G
* * *
2174712 CCATCTCTTTCTTCCTCTTCTCAGATGAGCTATTCAC-G--GCTG
1 ---TCTCTTTC-TCATCTTCTCAGCTGAGCTATTTACTGCAGCTG
* *
2174754 TCTCTTTCTGTATCTTCTCAGCTGAGCTATTTACTGTCATGACCG
1 TCTCTTTCT-CATCTTCTCAGCTGAGCTATTTACTG-CA-G-CTG
* ** *
2174799 TCTCTTTCTTCATTTTCTCAGCTGAATTATTTACAGTCACGGCTG
1 TCTCTTTC-TCATCTTCTCAGCTGAGCTATTTACTG-CA--GCTG
**
2174844 TCTCTTTGCTTGTCTTCTCAGC
1 TCTCTTT-CTCATCTTCTCAGC
2174866 CGAATTATTC
Statistics
Matches: 183, Mismatches: 35, Indels: 37
0.72 0.14 0.15
Matches are distributed among these distances:
38 1 0.01
39 28 0.15
40 3 0.02
41 2 0.01
42 61 0.33
43 3 0.02
44 2 0.01
45 78 0.43
46 3 0.02
47 2 0.01
ACGTcount: A:0.14, C:0.28, G:0.15, T:0.42
Consensus pattern (41 bp):
TCTCTTTCTCATCTTCTCAGCTGAGCTATTTACTGCAGCTG
Found at i:2180862 original size:20 final size:18
Alignment explanation
Indices: 2180837--2181001 Score: 91
Period size: 17 Copynumber: 9.3 Consensus size: 18
2180827 TGTATGCATG
*
2180837 TATTTATAATATGTTTTATA
1 TATTTATAATA--TATTATA
2180857 TATTTATAATATATTATA
1 TATTTATAATATATTATA
*
2180875 TATTT-TAATA-ATTTAAA
1 TATTTATAATATA-TTATA
*
2180892 TATTTATATATTATATAATTA
1 TATTTATA-A-TATATTA-TA
*
2180913 TATTTTTAATATATTA-A
1 TATTTATAATATATTATA
* * *
2180930 TAATTTATATTA-AATAAA
1 T-ATTTATAATATATTATA
* *
2180948 TTTTTATAA-AT-TTTTA
1 TATTTATAATATATTATA
2180964 TATTTAT-ATAT-TT-T-
1 TATTTATAATATATTATA
2180978 TA-TTATTAATTATATTATA
1 TATTTA-TAA-TATATTATA
2180997 TATTT
1 TATTT
2181002 TTTATATTAA
Statistics
Matches: 113, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
13 3 0.03
14 3 0.03
15 3 0.03
16 17 0.15
17 27 0.24
18 24 0.21
19 9 0.08
20 18 0.16
21 9 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
TATTTATAATATATTATA
Found at i:2180864 original size:8 final size:8
Alignment explanation
Indices: 2180851--2181001 Score: 94
Period size: 8 Copynumber: 18.4 Consensus size: 8
2180841 TATAATATGT
2180851 TTTATATA
1 TTTATATA
2180859 TTTATAATA
1 TTTAT-ATA
2180868 TATTATATA
1 T-TTATATA
2180877 TTT-TAATAA
1 TTTAT-AT-A
*
2180886 TTTAAATA
1 TTTATATA
2180894 TTTATATA
1 TTTATATA
2180902 -TTATATA
1 TTTATATA
* *
2180909 ATTATATT
1 TTTATATA
2180917 TTTAATATA
1 TTT-ATATA
*
2180926 TTAATA-A
1 TTTATATA
2180933 TTTATATTA
1 TTTATA-TA
** * *
2180942 AATAAATT
1 TTTATATA
*
2180950 TTTATAAA
1 TTTATATA
*
2180958 TTTTTATA
1 TTTATATA
2180966 TTTATATA
1 TTTATATA
*
2180974 TTTTTATTA
1 TTTATA-TA
*
2180983 TTAAT-TA
1 TTTATATA
2180990 TATTATATA
1 T-TTATATA
2180999 TTT
1 TTT
2181002 TTTATATTAA
Statistics
Matches: 108, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
7 17 0.16
8 55 0.51
9 32 0.30
10 4 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:2180868 original size:9 final size:9
Alignment explanation
Indices: 2180837--2180910 Score: 66
Period size: 9 Copynumber: 8.1 Consensus size: 9
2180827 TGTATGCATG
2180837 TATTTATAA
1 TATTTATAA
*
2180846 TATGTTTTATA
1 TAT-TTATA-A
2180857 TATTTATAA
1 TATTTATAA
2180866 TATATTAT-A
1 TAT-TTATAA
2180875 TATTT-TAA
1 TATTTATAA
2180883 TAATTTA-AA
1 T-ATTTATAA
2180892 TATTTAT-A
1 TATTTATAA
2180900 TATTATATAA
1 TATT-TATAA
2180910 T
1 T
2180911 TATATTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
7 1 0.02
8 14 0.26
9 21 0.39
10 14 0.26
11 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (9 bp):
TATTTATAA
Found at i:2180920 original size:39 final size:43
Alignment explanation
Indices: 2180852--2181012 Score: 116
Period size: 39 Copynumber: 3.9 Consensus size: 43
2180842 ATAATATGTT
2180852 TTATATATTTATAATATATTATATATTTTAATA-ATTTAA-ATAT
1 TTATATATTTATAATATATTATATATTTTAATATA-TTAATA-AT
2180895 TTATATA-TTAT-ATA-ATTATAT-TTTTAATATATTAATAAT
1 TTATATATTTATAATATATTATATATTTTAATATATTAATAAT
** * * *
2180934 TTATAT-TAAATAA-ATTTTTATAAATTTT--TATATTTATATAT
1 TTATATATTTATAATA-TATTATATATTTTAATATATTAATA-AT
*
2180975 TT-T-TA-TTATTAATTATATTATATATTTT-TTATATTAAT
1 TTATATATTTA-TAA-TATATTATATATTTTAATATATTAAT
2181013 TGTGACAGGC
Statistics
Matches: 95, Mismatches: 10, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
39 25 0.26
40 23 0.24
41 23 0.24
42 17 0.18
43 7 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (43 bp):
TTATATATTTATAATATATTATATATTTTAATATATTAATAAT
Found at i:2180937 original size:24 final size:23
Alignment explanation
Indices: 2180873--2180940 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
2180863 TAATATATTA
* * *
2180873 TATATTTTAATAATTTAAATATT
1 TATATATTAATAATTTATATTTT
2180896 TATATATTATATAA-TTATATTTT
1 TATATATTA-ATAATTTATATTTT
2180919 TAATATATTAATAATTTATATT
1 T-ATATATTAATAATTTATATT
2180941 AAATAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATATATTAATAATTTATATTTT
Found at i:2180948 original size:56 final size:58
Alignment explanation
Indices: 2180855--2180997 Score: 143
Period size: 56 Copynumber: 2.5 Consensus size: 58
2180845 ATATGTTTTA
* * * *
2180855 TATATTTATAATATATT-ATATATTT-TAATAATTTAAATATTTATATA-TTATATAAT
1 TATATTTTTAATATATTAATA-ATTTATATTAATATAAATATTTATAAATTTATATAAT
* * *
2180911 TATATTTTTAATATATTAATAATTTATATTAA-ATAAATTTTTATAAATTTTTATATT
1 TATATTTTTAATATATTAATAATTTATATTAATATAAATATTTATAAATTTATATAAT
* *
2180968 TATATATTTTTAT-TATTAATTATATTATAT
1 TATAT-TTTTAATATATTAATAAT-TTATAT
2180998 ATTTTTTATA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
56 32 0.44
57 29 0.40
58 12 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (58 bp):
TATATTTTTAATATATTAATAATTTATATTAATATAAATATTTATAAATTTATATAAT
Found at i:2180949 original size:15 final size:13
Alignment explanation
Indices: 2180922--2180994 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 13
2180912 ATATTTTTAA
2180922 TATATTAATAATT
1 TATATTAATAATT
2180935 TATATTAAATAAATT
1 TATATT-AAT-AATT
* * *
2180950 TTTATAAAT-TTT
1 TATATTAATAATT
*
2180962 TATATTTATATATT
1 TATATTAATA-ATT
* *
2180976 TTTATTATTAA-T
1 TATATTAATAATT
2180988 TATATTA
1 TATATTA
2180995 TATATTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
12 15 0.33
13 7 0.16
14 15 0.33
15 8 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATATTAATAATT
Found at i:2181003 original size:25 final size:26
Alignment explanation
Indices: 2180961--2181013 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
2180951 TTATAAATTT
2180961 TTATATTTATATA-TTTTTATTATTAA
1 TTATATTTATATATTTTTTA-TATTAA
2180987 TTATA-TTATATATTTTTTATATTAA
1 TTATATTTATATATTTTTTATATTAA
2181012 TT
1 TT
2181014 GTGACAGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATATTTATATATTTTTTATATTAA
Found at i:2181320 original size:25 final size:25
Alignment explanation
Indices: 2181249--2181320 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 25
2181239 ATTAAAAAGA
*
2181249 AAAAAGTAATGAATTATTTTATTTTTT
1 AAAAATTAAT-AATT-TTTTATTTTTT
2181276 --AAATTAAGT--TTTTATATATTTTTT
1 AAAAATTAA-TAATTTT-T-TATTTTTT
2181300 AAAAATTAATAATTTTTTATT
1 AAAAATTAATAATTTTTTATT
2181321 ATTTGTATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 16
0.69 0.02 0.30
Matches are distributed among these distances:
22 2 0.05
23 3 0.08
24 8 0.22
25 11 0.30
26 9 0.24
27 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
AAAAATTAATAATTTTTTATTTTTT
Found at i:2181427 original size:28 final size:26
Alignment explanation
Indices: 2181372--2181464 Score: 73
Period size: 30 Copynumber: 3.4 Consensus size: 26
2181362 GACTAAATTG
2181372 TTAAA-AAATAATTAT-TTTATATTTT
1 TTAAATAAATAATTATATTT-TATTTT
* *
2181397 TTACATGAATAATTATATTTTATTATAT
1 TTAAATAAATAATTATATTTTATT-T-T
**
2181425 TTAAATAAATTTTTATATTTTTATTTATCT
1 TTAAATAAATAATTATA-TTTTA-TT-T-T
2181455 TTAAATAAAT
1 TTAAATAAAT
2181465 TTTTATTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
25 4 0.07
26 13 0.24
27 4 0.07
28 14 0.25
29 5 0.09
30 15 0.27
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (26 bp):
TTAAATAAATAATTATATTTTATTTT
Found at i:2181460 original size:30 final size:28
Alignment explanation
Indices: 2181409--2181470 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 28
2181399 ACATGAATAA
2181409 TTATATTTTATTATATTTAAATAAATTT
1 TTATATTTTATTATATTTAAATAAATTT
*
2181437 TTATATTTTTATTTATCTTTAAATAAATTT
1 TTATA-TTTTA-TTATATTTAAATAAATTT
2181467 TTAT
1 TTAT
2181471 TTCAGATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 5 0.16
29 5 0.16
30 21 0.68
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTATATTTTATTATATTTAAATAAATTT
Found at i:2181617 original size:16 final size:15
Alignment explanation
Indices: 2181592--2181626 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2181582 TTTTTATTGT
*
2181592 TTTAGTTAAGATTAA
1 TTTAGTTAAGACTAA
2181607 TTTATGTTAAGACTAA
1 TTTA-GTTAAGACTAA
2181623 TTTA
1 TTTA
2181627 AGTACAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (15 bp):
TTTAGTTAAGACTAA
Found at i:2181995 original size:14 final size:13
Alignment explanation
Indices: 2181953--2182000 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
2181943 TATTTAAAAA
*
2181953 TTTATAATTTTTT
1 TTTAAAATTTTTT
*
2181966 TTAAACAATTTTTT
1 TTTAA-AATTTTTT
2181980 TTT-AAATTTTTAT
1 TTTAAAATTTTT-T
2181993 TTTAAAAT
1 TTTAAAAT
2182001 ACGAACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.24
13 8 0.28
14 14 0.48
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTAAAATTTTTT
Found at i:2182955 original size:29 final size:30
Alignment explanation
Indices: 2182907--2182967 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2182897 TAATTTAAAT
*
2182907 TTTAAATTTAAATTCTTTAATTAAATT-AA
1 TTTAAATTTAAATTCATTAATTAAATTCAA
*
2182936 TTTAAATTTAATATT-ATTAATTTAATTCAA
1 TTTAAATTTAA-ATTCATTAATTAAATTCAA
2182966 TT
1 TT
2182968 CGATTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTAAATTTAAATTCATTAATTAAATTCAA
Found at i:2183608 original size:17 final size:17
Alignment explanation
Indices: 2183586--2183619 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2183576 ATTAATAGCG
*
2183586 AAAATAATTATTATTAT
1 AAAATAATAATTATTAT
2183603 AAAATAATAATTATTAT
1 AAAATAATAATTATTAT
2183620 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATAATAATTATTAT
Found at i:2183613 original size:20 final size:19
Alignment explanation
Indices: 2183588--2183626 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
2183578 TAATAGCGAA
2183588 AATAATTATTATTATAAAAT
1 AATAATTATTATT-TAAAAT
2183608 AATAATTATTATTTAAAAT
1 AATAATTATTATTTAAAAT
2183627 TTTGATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTATTATTTAAAAT
Found at i:2187573 original size:20 final size:19
Alignment explanation
Indices: 2187548--2187618 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
2187538 ATAATTTATG
2187548 TATTTATTATATTATAATCA
1 TATTTATTATATTATAAT-A
** *
2187568 TATTTAAAATA-TATTATA
1 TATTTATTATATTATAATA
* *
2187586 TTTTTA-TAAATTATAATAA
1 TATTTATTATATTATAAT-A
*
2187605 TTTTTATTATATTA
1 TATTTATTATATTA
2187619 ATTTTAAAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 2 0.05
18 11 0.28
19 12 0.30
20 15 0.38
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTATTATATTATAATA
Found at i:2187607 original size:19 final size:19
Alignment explanation
Indices: 2187558--2187611 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2187548 TATTTATTAT
* *
2187558 ATTATAATCATATTTA-AA
1 ATTATAATAATTTTTATAA
*
2187576 A-TATATTATATTTTTATAA
1 ATTATAATA-ATTTTTATAA
2187595 ATTATAATAATTTTTAT
1 ATTATAATAATTTTTAT
2187612 TATATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 11 0.38
20 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTATAATAATTTTTATAA
Found at i:2192407 original size:14 final size:14
Alignment explanation
Indices: 2192388--2192414 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2192378 AAAAAAATAA
2192388 TATATTATTTTAAT
1 TATATTATTTTAAT
2192402 TATATTATTTTAA
1 TATATTATTTTAA
2192415 ATTAAATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTATTTTAAT
Found at i:2195885 original size:35 final size:35
Alignment explanation
Indices: 2195812--2195886 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 35
2195802 GTTAAGTATC
2195812 TAATTTAAAATCAAATATTAAAAAGATAAAAATAT
1 TAATTTAAAATCAAATATTAAAAAGATAAAAATAT
*
2195847 TAATTTAAATAT-AAA-ATTATAAACGATATAAAAT-T
1 TAATTTAAA-ATCAAATATTA-AAAAGATA-AAAATAT
2195882 TAATT
1 TAATT
2195887 GATATGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
34 4 0.11
35 25 0.69
36 7 0.19
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (35 bp):
TAATTTAAAATCAAATATTAAAAAGATAAAAATAT
Found at i:2197936 original size:21 final size:21
Alignment explanation
Indices: 2197897--2197936 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2197887 ATTGAAGATT
* **
2197897 ATAAATAATTATTTTTAAAAG
1 ATAAAAAATTATTCATAAAAG
2197918 ATAAAAAATTATTCATAAA
1 ATAAAAAATTATTCATAAA
2197937 GTTTTAAAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATAAAAAATTATTCATAAAAG
Found at i:2198169 original size:13 final size:13
Alignment explanation
Indices: 2198153--2198177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2198143 TAACATATTA
2198153 AATAAAAATATAT
1 AATAAAAATATAT
2198166 AATAAAAATATA
1 AATAAAAATATA
2198178 ATACAAGCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAAATATAT
Found at i:2199150 original size:12 final size:12
Alignment explanation
Indices: 2199133--2199157 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2199123 AAGAAACAAC
2199133 AAATATATATAT
1 AAATATATATAT
2199145 AAATATATATAT
1 AAATATATATAT
2199157 A
1 A
2199158 TACACAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATATAT
Found at i:2199235 original size:50 final size:50
Alignment explanation
Indices: 2199173--2199270 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
2199163 AAAGTTTTAT
** *
2199173 AGTAATTATTTTATTTTGTTTCTTCAATTTGTGTCAAACAAAACATAATA
1 AGTAATTATTTTATTTAATTTCTTCAATTTGTATCAAACAAAACATAATA
*
2199223 AGTAATTATTTTATTTAATTTCTTCCATTTGTATCAAACAAAACATAA
1 AGTAATTATTTTATTTAATTTCTTCAATTTGTATCAAACAAAACATAA
2199271 AAATATACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (50 bp):
AGTAATTATTTTATTTAATTTCTTCAATTTGTATCAAACAAAACATAATA
Found at i:2199797 original size:16 final size:16
Alignment explanation
Indices: 2199768--2199807 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
2199758 CAATGCTACC
*
2199768 TCTCATTCTTTTTTTT
1 TCTCTTTCTTTTTTTT
2199784 T-TCTTTCTTTTTTTT
1 TCTCTTTCTTTTTTTT
2199799 TCTCTTTCT
1 TCTCTTTCT
2199808 AATTTGGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
TCTCTTTCTTTTTTTT
Found at i:2201451 original size:23 final size:23
Alignment explanation
Indices: 2201401--2201449 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
2201391 AAAATCTTAA
* *
2201401 TTTTAATTTTTATATTTATAATT
1 TTTTAATTTTTATAATTACAATT
2201424 TTTTAATTTTTA-AATTACAATT
1 TTTTAATTTTTATAATTACAATT
2201446 TTTT
1 TTTT
2201450 TATAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTAATTTTTATAATTACAATT
Found at i:2201971 original size:2 final size:2
Alignment explanation
Indices: 2201966--2201990 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2201956 TCTCTCTATC
2201966 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 T
2201991 TGATCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2202451 original size:2 final size:2
Alignment explanation
Indices: 2202444--2202492 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2202434 ATAACTCTTC
2202444 AT AT AT AT AT 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 AT AT AT AT AT
2202486 AT AT AT A
1 AT AT AT A
2202493 AGCCATTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2204075 original size:19 final size:17
Alignment explanation
Indices: 2204034--2204076 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2204024 TTATTTATTT
2204034 TTATTTTTTACTCAAAA
1 TTATTTTTTACTCAAAA
*
2204051 -TATTTTTTAACTATAAAA
1 TTATTTTTT-ACT-CAAAA
2204069 TTATTTTT
1 TTATTTTT
2204077 AATTACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 4 0.18
19 7 0.32
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATTTTTTACTCAAAA
Found at i:2204553 original size:25 final size:24
Alignment explanation
Indices: 2204497--2204559 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
2204487 TATTTTAAAT
*
2204497 TTATTTTTAATTTAATTGTGTATA
1 TTATTTTTAATTTAATTATGTATA
* *
2204521 TTAATTTTAATTTTAATATAT-TATG
1 TTATTTTTAA-TTTAAT-TATGTATA
2204546 TTATTTTT-ATTTAA
1 TTATTTTTAATTTAA
2204560 AAATAAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 5 0.15
24 10 0.30
25 16 0.48
26 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (24 bp):
TTATTTTTAATTTAATTATGTATA
Found at i:2206196 original size:10 final size:10
Alignment explanation
Indices: 2206181--2206215 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2206171 TGATATATAC
2206181 GCATAGATAT
1 GCATAGATAT
2206191 GCATAGATAT
1 GCATAGATAT
* *
2206201 ACATACATAT
1 GCATAGATAT
2206211 GCATA
1 GCATA
2206216 TGTTATGTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (10 bp):
GCATAGATAT
Found at i:2206948 original size:2 final size:2
Alignment explanation
Indices: 2206941--2206972 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2206931 AACAATGCAA
2206941 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
2206973 GTATGCATAA
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:2208597 original size:29 final size:30
Alignment explanation
Indices: 2208537--2208598 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
2208527 TTTGATTTGA
* **
2208537 ATTTATATTTAATAAATAAAAAATATTTTT
1 ATTTAAATTTAATAAATAAAAAATATAATT
* *
2208567 ATTTAAATTTAAT-TATAAAATATATAATT
1 ATTTAAATTTAATAAATAAAAAATATAATT
2208596 ATT
1 ATT
2208599 AATATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAAATTTAATAAATAAAAAATATAATT
Found at i:2208600 original size:22 final size:19
Alignment explanation
Indices: 2208570--2208620 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
2208560 TATTTTTATT
2208570 TAAA-TTTAATTATAAAATA
1 TAAATTTTAATTATAAAA-A
2208589 TATAATTATTAA-TATAAAAA
1 TA-AATT-TTAATTATAAAAA
2208609 TAAATTTTAATT
1 TAAATTTTAATT
2208621 TATTAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 4 0.14
19 7 0.25
20 5 0.18
21 8 0.29
22 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTTTAATTATAAAAA
Found at i:2210417 original size:6 final size:6
Alignment explanation
Indices: 2210383--2210408 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2210373 AAAACAGTTT
2210383 TAATTA TAATTA TAATTA TAATTA TA
1 TAATTA TAATTA TAATTA TAATTA TA
2210409 TTTTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:2217078 original size:14 final size:14
Alignment explanation
Indices: 2217059--2217090 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2217049 TGAGACATTT
2217059 ATATATTAATATTA
1 ATATATTAATATTA
2217073 ATATATTAATATTA
1 ATATATTAATATTA
2217087 ATAT
1 ATAT
2217091 CATTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATTAATATTA
Found at i:2219088 original size:13 final size:13
Alignment explanation
Indices: 2219070--2219099 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2219060 ACTAAGAAAT
*
2219070 TATATGTGTTTAA
1 TATATGTATTTAA
2219083 TATATGTATTTAA
1 TATATGTATTTAA
2219096 TATA
1 TATA
2219100 CATTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATATGTATTTAA
Found at i:2223604 original size:26 final size:24
Alignment explanation
Indices: 2223572--2223622 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
2223562 CATTTTACAA
2223572 TTATATAATATATATTAATTTTATATTT
1 TTATAT-AT-TATA-TAATTTT-TATTT
2223600 TTATATATTATATAATTTTTATT
1 TTATATATTATATAATTTTTATT
2223623 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 7 0.30
26 4 0.17
27 2 0.09
28 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATATATTATATAATTTTTATTT
Found at i:2224426 original size:17 final size:17
Alignment explanation
Indices: 2224404--2224441 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2224394 CATAATAAAT
*
2224404 AAAACTATAAAA-ATTTA
1 AAAACT-TAAAACATCTA
2224421 AAAACTTAAAACATCTA
1 AAAACTTAAAACATCTA
2224438 AAAA
1 AAAA
2224442 GAACTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAACTTAAAACATCTA
Found at i:2225057 original size:15 final size:14
Alignment explanation
Indices: 2225033--2225080 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
2225023 AAAGTACTTT
2225033 AATTTTATATTATTA
1 AATTTTATATT-TTA
*
2225048 AATTTAATATTTT-
1 AATTTTATATTTTA
2225061 AATTTCTATATTTTTA
1 AATTT-TATA-TTTTA
2225077 AATT
1 AATT
2225081 GTAGTGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 5 0.18
14 5 0.18
15 14 0.50
16 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTTATATTTTA
Found at i:2227223 original size:16 final size:15
Alignment explanation
Indices: 2227204--2227243 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2227194 AAAATTTTTA
*
2227204 AATTTAAATTTAATT
1 AATTTAAATTGAATT
2227219 CAATTTAAATTGAATT
1 -AATTTAAATTGAATT
*
2227235 AACTTAAAT
1 AATTTAAAT
2227244 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (15 bp):
AATTTAAATTGAATT
Found at i:2227584 original size:19 final size:19
Alignment explanation
Indices: 2227545--2227586 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2227535 TATATAAATA
*
2227545 TTAATATAAAATTAATATT
1 TTAATATAAAATAAATATT
2227564 TTAATGATAAAATAAAT-TT
1 TTAAT-ATAAAATAAATATT
2227583 TTAA
1 TTAA
2227587 ATTAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TTAATATAAAATAAATATT
Done.