Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold303
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: 874694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:10952 original size:3 final size:3
Alignment explanation
Indices: 10946--10973 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10936 ATATACTTGA
10946 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
10974 ATTAGAGTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12684 original size:18 final size:19
Alignment explanation
Indices: 12657--12706 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
12647 TTAGTTTGTA
*
12657 AATATGTTTATAATTT-AT
1 AATATTTTTATAATTTAAT
12675 AATATTTTTACT--TTTAAT
1 AATATTTTTA-TAATTTAAT
*
12693 AATAGTTTTATAAT
1 AATATTTTTATAAT
12707 CATAAAGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 4 0.15
18 20 0.77
19 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (19 bp):
AATATTTTTATAATTTAAT
Found at i:14404 original size:15 final size:15
Alignment explanation
Indices: 14384--14412 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14374 TAATCCAAAA
14384 TTTAAAACCTTAAAT
1 TTTAAAACCTTAAAT
14399 TTTAAAACCTTAAA
1 TTTAAAACCTTAAA
14413 ACTCTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAACCTTAAAT
Found at i:14428 original size:8 final size:8
Alignment explanation
Indices: 14380--14450 Score: 53
Period size: 8 Copynumber: 9.5 Consensus size: 8
14370 GGCATAATCC
14380 AAAA-TTT
1 AAAACTTT
*
14387 AAAACCTT
1 AAAACTTT
*
14395 -AAATTTT
1 AAAACTTT
*
14402 AAAACCTT
1 AAAACTTT
*
14410 AAAACTCT
1 AAAACTTT
14418 AAAA-TTT
1 AAAACTTT
*
14425 TAAACTTT
1 AAAACTTT
14433 --AACTTT
1 AAAACTTT
*
14439 TAAACTTT
1 AAAACTTT
14447 AAAA
1 AAAA
14451 TCTAAAATTC
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
6 6 0.12
7 14 0.29
8 29 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAACTTT
Found at i:14441 original size:14 final size:14
Alignment explanation
Indices: 14422--14448 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14412 AACTCTAAAA
14422 TTTTAAACTTTAAC
1 TTTTAAACTTTAAC
14436 TTTTAAACTTTAA
1 TTTTAAACTTTAA
14449 AATCTAAAAT
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:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTAAACTTTAAC
Found at i:14767 original size:33 final size:35
Alignment explanation
Indices: 14713--14779 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 35
14703 ACCCATAAAC
*
14713 CTTATATTTTAAATCCTAAATCTCAAACTTCAAAT
1 CTTAAATTTTAAATCCTAAATCTCAAACTTCAAAT
* *
14748 CTTAAATTTT-AAT-CTAAATCTTAAATTTCAAA
1 CTTAAATTTTAAATCCTAAATCTCAAACTTCAAA
14780 ACCCTAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 17 0.59
34 3 0.10
35 9 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (35 bp):
CTTAAATTTTAAATCCTAAATCTCAAACTTCAAAT
Found at i:14837 original size:20 final size:20
Alignment explanation
Indices: 14812--14849 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14802 CAAAATTTAT
14812 AACCTTAACTT-TAAACCTAA
1 AACCTTAA-TTATAAACCTAA
14832 AACCTTAATTATAAACCT
1 AACCTTAATTATAAACCT
14850 GAACTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (20 bp):
AACCTTAATTATAAACCTAA
Found at i:15210 original size:30 final size:30
Alignment explanation
Indices: 15174--15247 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
15164 TATCTAATTT
*
15174 AATTTAT-TTATATATTTAATGTTAAATTAA
1 AATTTATATT-TATATTTAATATTAAATTAA
*
15204 AATTTATATTTATGTTTAATATTAAATT--
1 AATTTATATTTATATTTAATATTAAATTAA
*
15232 TATTTATATATTATAT
1 AATTTATAT-TTATAT
15248 ATTTTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 8 0.21
29 5 0.13
30 23 0.61
31 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
AATTTATATTTATATTTAATATTAAATTAA
Found at i:16429 original size:25 final size:24
Alignment explanation
Indices: 16396--16442 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
16386 CCAATATCTA
16396 TTAAAATTCTTTTTTATAATATTG
1 TTAAAATTCTTTTTTATAATATTG
16420 TTAAATATTCTTTTTTATAATAT
1 TTAAA-ATTCTTTTTTATAATAT
16443 CTATCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
TTAAAATTCTTTTTTATAATATTG
Found at i:16452 original size:25 final size:25
Alignment explanation
Indices: 16388--16455 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 25
16378 GACTACTACC
*
16388 AATATCTATTAAAATTCTTTTTTAT
1 AATATCTATTAATATTCTTTTTTAT
*
16413 AATAT-TGTTAAATATTCTTTTTTAT
1 AATATCTATT-AATATTCTTTTTTAT
16438 AATATCTATCTATATATT
1 AATATCTAT-TA-ATATT
16456 TATCTATCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 3 0.08
25 24 0.67
26 3 0.08
27 6 0.17
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.56
Consensus pattern (25 bp):
AATATCTATTAATATTCTTTTTTAT
Found at i:17901 original size:2 final size:2
Alignment explanation
Indices: 17894--17928 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17884 ACGTAAAATC
17894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17929 AAATACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17938 original size:2 final size:2
Alignment explanation
Indices: 17933--17957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17923 TATATAAAAT
17933 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
17958 AATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23206 original size:2 final size:2
Alignment explanation
Indices: 23194--23229 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
23184 AAGAAAACTC
23194 AT AT A- 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 A
23230 CACATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27340 original size:2 final size:2
Alignment explanation
Indices: 27333--27378 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
27323 AATATGAGCA
27333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27374 AT AT A
1 AT AT A
27379 AGTAACCCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38107 original size:3 final size:3
Alignment explanation
Indices: 38101--38138 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
38091 AGAAGAAGAA
* *
38101 GAT GAT GAT GAT GAT GAC GAC GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
38139 AGAAGAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:41685 original size:4 final size:4
Alignment explanation
Indices: 41676--41706 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41666 CGAGGGGCTA
41676 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAA
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAA
41707 AGCTGCATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (4 bp):
GAAG
Found at i:45527 original size:16 final size:16
Alignment explanation
Indices: 45508--45593 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
45498 TTAAATCTAG
45508 AATGATCCGAATCCGA
1 AATGATCCGAATCCGA
* *
45524 AATGATGCAAATCTC-A
1 AATGATCCGAATC-CGA
* *
45540 AATTATCC-AAACTCGA
1 AATGATCCGAATC-CGA
* *
45556 AATGA-CTTGAATCTGA
1 AATGATC-CGAATCCGA
* *
45572 AATGATCTGAACCCGA
1 AATGATCCGAATCCGA
45588 AATGAT
1 AATGAT
45594 TTGAATAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
15 6 0.11
16 43 0.80
17 5 0.09
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (16 bp):
AATGATCCGAATCCGA
Found at i:45569 original size:32 final size:32
Alignment explanation
Indices: 45475--45599 Score: 94
Period size: 32 Copynumber: 3.9 Consensus size: 32
45465 TATGAACCCG
* * * *
45475 AAATGATTCAAACCCGAAATAATTTAAATCT-
1 AAATGATCCAAACCCGAAATGACTTGAATCTC
* *
45506 AGAATGATCCGAATCCGAAATGA--TGCAAATCTC
1 A-AATGATCCAAACCCGAAATGACTTG--AATCTC
* * *
45539 AAATTATCCAAACTCGAAATGACTTGAATCTG
1 AAATGATCCAAACCCGAAATGACTTGAATCTC
** *
45571 AAATGATCTGAACCCGAAATGATTTGAAT
1 AAATGATCCAAACCCGAAATGACTTGAAT
45600 AATTAATCCG
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 68 0.93
33 1 0.01
34 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (32 bp):
AAATGATCCAAACCCGAAATGACTTGAATCTC
Found at i:45598 original size:16 final size:16
Alignment explanation
Indices: 45553--45598 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
45543 TATCCAAACT
* *
45553 CGAAATGACTTGAATC
1 CGAAATGATTTGAACC
* *
45569 TGAAATGATCTGAACC
1 CGAAATGATTTGAACC
45585 CGAAATGATTTGAA
1 CGAAATGATTTGAA
45599 TAATTAATCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (16 bp):
CGAAATGATTTGAACC
Found at i:46758 original size:15 final size:15
Alignment explanation
Indices: 46740--46776 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
46730 ATTTTATAAC
46740 TCAAAATAATTCAAA
1 TCAAAATAATTCAAA
*
46755 TCAAAATAATTCAAC
1 TCAAAATAATTCAAA
46770 TCAAAAT
1 TCAAAAT
46777 CAACTGGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (15 bp):
TCAAAATAATTCAAA
Found at i:46975 original size:15 final size:15
Alignment explanation
Indices: 46957--46993 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
46947 ATTTTATAAC
46957 TCAAAATAATTCAAA
1 TCAAAATAATTCAAA
* *
46972 TCAAAATAATTTAAC
1 TCAAAATAATTCAAA
46987 TCAAAAT
1 TCAAAAT
46994 CAGCTGACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (15 bp):
TCAAAATAATTCAAA
Found at i:48101 original size:17 final size:17
Alignment explanation
Indices: 48055--48101 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
48045 GCTTGATAAA
*
48055 TTATTTA-AATATCATT
1 TTATTTATAATATAATT
* *
48071 TTATTTGTAGTATAATT
1 TTATTTATAATATAATT
48088 TTATTTATAATATA
1 TTATTTATAATATA
48102 TTATATGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (17 bp):
TTATTTATAATATAATT
Found at i:48161 original size:18 final size:18
Alignment explanation
Indices: 48140--48190 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
48130 GTTATTGTAA
* *
48140 TATATTATTTATATTATT
1 TATATTATATATATTATG
48158 TATATT-TATATATT-TG
1 TATATTATATATATTATG
48174 TATATATATATATATTA
1 TATAT-TATATATATTA
48191 GAAAAACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 14 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATATTATATATATTATG
Found at i:48181 original size:14 final size:14
Alignment explanation
Indices: 48139--48347 Score: 57
Period size: 13 Copynumber: 14.9 Consensus size: 14
48129 TGTTATTGTA
*
48139 ATATA-TTATTTAT
1 ATATATTTATATAT
*
48152 AT-TATTTATATTT
1 ATATATTTATATAT
*
48165 ATATATTTGTATAT
1 ATATATTTATATAT
* *
48179 ATATATATAT-TAG
1 ATATATTTATATAT
* *
48192 AAAAACTATTAT-TAT
1 ATATA-T-TTATATAT
*
48207 A-AT-TTTATTTAT
1 ATATATTTATATAT
48219 AATATATTT-TATAT
1 -ATATATTTATATAT
*
48233 TTATATTTATAT-T
1 ATATATTTATATAT
* * *
48246 TTTTGTTTATATATT
1 ATATATTTATATA-T
* * *
48261 ATTTATTTTGTTTAT
1 ATATA-TTTATATAT
*
48276 AATATAATTTTATTTAT
1 -ATAT-A-TTTATATAT
48293 AATATATTT-TATAT
1 -ATATATTTATATAT
*
48307 AT-TATGTTA-AAAT
1 ATATAT-TTATATAT
48320 -TAT-TTTAATATAT
1 ATATATTT-ATATAT
48333 AATATAATTTATATA
1 -ATAT-ATTTATATA
48348 AAAAAAGAAA
Statistics
Matches: 148, Mismatches: 25, Indels: 43
0.69 0.12 0.20
Matches are distributed among these distances:
11 6 0.04
12 12 0.08
13 45 0.30
14 32 0.22
15 20 0.14
16 15 0.10
17 18 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
ATATATTTATATAT
Found at i:48255 original size:37 final size:39
Alignment explanation
Indices: 48070--48346 Score: 141
Period size: 40 Copynumber: 7.0 Consensus size: 39
48060 TAAATATCAT
* * *
48070 TTTATTTGTAGTATAATTTTATTTATAATATATTATATGAA
1 TTTATTTATAATATAATTTTATTTATAATATATTTTAT--A
* *
48111 TATTATTT-TAATAT-ATTTTGTTATTGTAATATATTATT-TA
1 T-TTATTTATAATATAATTTT-AT-TTATAATATATT-TTATA
* * * *
48151 TATTATTTATATTTATATATTTGTATATAT-ATATATATTAGA
1 T-TTATTTATA-ATATA-ATTT-TATTTATAATATATTTTATA
***
48193 AAAACTATTAT--TATAATTTTATTTATAATATATTTTATA
1 TTTA-T-TTATAATATAATTTTATTTATAATATATTTTATA
* *
48232 TTTATATT-T-ATAT-TTTTTGTTTAT-ATAT-TATTTAT-
1 TTTAT-TTATAATATAATTTTATTTATAATATAT-TTTATA
*
48267 TTTGTTTATAATATAATTTTATTTATAATATATTTTATA
1 TTTATTTATAATATAATTTTATTTATAATATATTTTATA
* * *
48306 TATTATGTTA-AA-ATTATTTTAATATATAATATAATTTATA
1 T-TTAT-TTATAATATAATTTT-ATTTATAATATATTTTATA
48346 T
1 T
48347 AAAAAAAGAA
Statistics
Matches: 184, Mismatches: 28, Indels: 49
0.70 0.11 0.19
Matches are distributed among these distances:
34 2 0.01
35 6 0.03
36 13 0.07
37 19 0.10
38 22 0.12
39 24 0.13
40 41 0.22
41 15 0.08
42 29 0.16
43 7 0.04
44 5 0.03
45 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (39 bp):
TTTATTTATAATATAATTTTATTTATAATATATTTTATA
Found at i:48285 original size:21 final size:21
Alignment explanation
Indices: 48246--48290 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
48236 TATTTATATT
*
48246 TTTTGTTTATATATTA-TTTA
1 TTTTGTTTATATATAATTTTA
48266 TTTTGTTTATAATATAATTTTA
1 TTTTGTTTAT-ATATAATTTTA
48288 TTT
1 TTT
48291 ATAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 5 0.23
22 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTGTTTATATATAATTTTA
Found at i:48291 original size:17 final size:17
Alignment explanation
Indices: 48204--48304 Score: 87
Period size: 17 Copynumber: 5.6 Consensus size: 17
48194 AAACTATTAT
48204 TATAATTTTATTTATAA
1 TATAATTTTATTTATAA
* *
48221 TATATTTTATATTTATATT
1 TATAATTT-TATTTATA-A
* *
48240 TATATTTTTTGTTTATATA
1 TATA-ATTTTATTTATA-A
* *
48259 TTATTTATTTTGTTTATAA
1 -TA-TAATTTTATTTATAA
48278 TATAATTTTATTTATAA
1 TATAATTTTATTTATAA
48295 TAT-ATTTTAT
1 TATAATTTTAT
48305 ATATTATGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.10
17 23 0.32
18 10 0.14
19 13 0.18
20 17 0.24
21 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATAATTTTATTTATAA
Found at i:48462 original size:22 final size:25
Alignment explanation
Indices: 48406--48471 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 25
48396 TCACCTGGAC
*
48406 ATTTTGTTGAATTTAAAATAATTCAA
1 ATTTTATT-AATTTAAAATAATTCAA
*
48432 AATTTATTAATTT-AAAT-ATT-AA
1 ATTTTATTAATTTAAAATAATTCAA
48454 ATTTTATTAATTTGAAAA
1 ATTTTATTAATTT-AAAA
48472 AATGGTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 14 0.40
23 3 0.09
24 7 0.20
25 5 0.14
26 6 0.17
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
ATTTTATTAATTTAAAATAATTCAA
Found at i:48891 original size:16 final size:16
Alignment explanation
Indices: 48840--49002 Score: 60
Period size: 16 Copynumber: 9.6 Consensus size: 16
48830 TATTCTTGTC
*
48840 ATTTAAATTTTAAATT
1 ATTTTAATTTTAAATT
* * * *
48856 ATTTTGAGTTCAGATT
1 ATTTTAATTTTAAATT
*
48872 ATTTTAATTTTAAATA
1 ATTTTAATTTTAAATT
*
48888 ATTTTAAATTCATATAATT
1 ATTTT-AATT-TTA-AATT
* * *
48907 AAGTTTAACATTAAAATT
1 -ATTTTAA-TTTTAAATT
* * *
48925 A-ATCAATTTTGAATT
1 ATTTTAATTTTAAATT
48940 ATTTTAAATTTTAATTAATT
1 ATTTT-AATTTT-A--AATT
* *
48960 AAATTTAATATTTAATTT
1 -ATTTTAAT-TTTAAATT
*
48978 A-ATTAATTTTAAATT
1 ATTTTAATTTTAAATT
*
48993 ATTTAAATTT
1 ATTTTAATTT
49003 ATCAAATATA
Statistics
Matches: 104, Mismatches: 30, Indels: 26
0.65 0.19 0.16
Matches are distributed among these distances:
15 15 0.14
16 42 0.40
17 12 0.12
18 9 0.09
19 6 0.06
20 13 0.12
21 7 0.07
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTTAATTTTAAATT
Found at i:48967 original size:21 final size:22
Alignment explanation
Indices: 48942--48992 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
48932 TTTGAATTAT
48942 TTTAAATTTTAA-TTAATTAAA
1 TTTAAATTTTAATTTAATTAAA
*
48963 TTT-AATATTTAATTTAATTAAT
1 TTTAAAT-TTTAATTTAATTAAA
48985 TTTAAATT
1 TTTAAATT
48993 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 8 0.31
22 12 0.46
23 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAAATTTTAATTTAATTAAA
Found at i:48980 original size:53 final size:54
Alignment explanation
Indices: 48877--49016 Score: 153
Period size: 53 Copynumber: 2.6 Consensus size: 54
48867 AGATTATTTT
* * *
48877 AATTTTAAATAATTTTAAA--TTCATATAATTAAGTTTAACATTAAAATTAATC
1 AATTTTAAATTATTTTAAATTTTAATATAATTAAATTTAACATTAAAATTAATC
* * * * *
48929 AATTTTGAATTATTTTAAATTTTAAT-TAATTAAATTTAATATTTAATTTAATT
1 AATTTTAAATTATTTTAAATTTTAATATAATTAAATTTAACATTAAAATTAATC
48982 AATTTTAAATTA-TTTAAATTTATCAAATATAATTA
1 AATTTTAAATTATTTTAAATTT-T--AATATAATTA
49017 TTTTAAATTG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
52 26 0.36
53 34 0.47
54 4 0.05
55 3 0.04
56 6 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (54 bp):
AATTTTAAATTATTTTAAATTTTAATATAATTAAATTTAACATTAAAATTAATC
Found at i:48998 original size:15 final size:15
Alignment explanation
Indices: 48964--49025 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
48954 TTAATTAAAT
*
48964 TTAATATTTAATTTAA
1 TTAAT-TTTAAATTAA
*
48980 TTAATTTTAAATTAT
1 TTAATTTTAAATTAA
48995 TTAAATTTATCAAATATAA
1 TT-AATTT-T-AAAT-TAA
49014 TT-ATTTTAAATT
1 TTAATTTTAAATT
49026 GAGACCATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 1 0.03
15 14 0.36
16 11 0.28
17 5 0.13
18 4 0.10
19 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTTAAATTAA
Found at i:50597 original size:2 final size:2
Alignment explanation
Indices: 50590--50620 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50580 TATCTATCAT
50590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50621 GCATGCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50839 original size:1 final size:1
Alignment explanation
Indices: 50833--50858 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
50823 ATTCTATTTG
50833 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
50859 CTCCGATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:57304 original size:3 final size:3
Alignment explanation
Indices: 57296--57321 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57286 CAAAAAATAG
57296 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
57322 ATCCTATCAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:60397 original size:21 final size:21
Alignment explanation
Indices: 60371--60414 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
60361 ACGTTCTAAG
60371 AAGAACCAGATATCATGGCAA
1 AAGAACCAGATATCATGGCAA
60392 AAGAACCAGATATCATGGCAA
1 AAGAACCAGATATCATGGCAA
60413 AA
1 AA
60415 CCTAGATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (21 bp):
AAGAACCAGATATCATGGCAA
Found at i:65566 original size:3 final size:3
Alignment explanation
Indices: 65558--65656 Score: 123
Period size: 3 Copynumber: 32.7 Consensus size: 3
65548 TATTAGTCTT
*
65558 TTA TTA TTA TTG TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA
*
65604 TT- TATC TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65649 TTA TTA TT
1 TTA TTA TT
65657 TATCATGTTA
Statistics
Matches: 86, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
2 5 0.06
3 72 0.84
4 9 0.10
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:66262 original size:24 final size:24
Alignment explanation
Indices: 66235--66323 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 24
66225 AAATTGTTAT
66235 TAAATTTATAATATTTTTAGTGAA
1 TAAATTTATAATATTTTTAGTGAA
*
66259 TAAATTTATAATCAATTTTAATA-TAAAA
1 TAAATTTATAAT--ATTTT--TAGT-GAA
*
66287 TAATATGT-TAATATTTTTAGTGAA
1 TAA-ATTTATAATATTTTTAGTGAA
66311 TAAAATATTATAA
1 T-AAAT-TTATAA
66324 AAATAATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
24 19 0.37
25 4 0.08
26 13 0.25
27 1 0.02
28 11 0.22
29 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (24 bp):
TAAATTTATAATATTTTTAGTGAA
Found at i:67156 original size:2 final size:2
Alignment explanation
Indices: 67149--67173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67139 CATATGTAAA
67149 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 A
67174 CACTTTAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83619 original size:12 final size:12
Alignment explanation
Indices: 83599--83632 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
83589 ATACATTAAT
83599 TATATATATAGA
1 TATATATATAGA
*
83611 TATAGATATAGA
1 TATATATATAGA
83623 TATATATATA
1 TATATATATA
83633 TAAATCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (12 bp):
TATATATATAGA
Found at i:83634 original size:6 final size:6
Alignment explanation
Indices: 83599--83632 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
83589 ATACATTAAT
* *
83599 TATATA TATAGA TATAGA TATAGA TATATA TATA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATA
83633 TAAATCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (6 bp):
TATAGA
Found at i:84920 original size:2 final size:2
Alignment explanation
Indices: 84915--84942 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84905 ATATATATAC
84915 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
84943 ACAAAATAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:85394 original size:5 final size:5
Alignment explanation
Indices: 85384--85408 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
85374 TGCCGGAGTG
85384 TGCAT TGCAT TGCAT TGCAT TGCAT
1 TGCAT TGCAT TGCAT TGCAT TGCAT
85409 CCTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TGCAT
Found at i:85849 original size:20 final size:22
Alignment explanation
Indices: 85821--85861 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
85811 ATGAGTTATA
*
85821 GTAATATAAT-TA-TTTGATTC
1 GTAAAATAATATATTTTGATTC
85841 GTAAAATAATATATTTTGATT
1 GTAAAATAATATATTTTGATT
85862 TTATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (22 bp):
GTAAAATAATATATTTTGATTC
Found at i:86498 original size:3 final size:3
Alignment explanation
Indices: 86490--86527 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
86480 ATTTAAGAGA
86490 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 AA
86528 AAGAAGAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:87526 original size:24 final size:22
Alignment explanation
Indices: 87475--87536 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
87465 ATTTTAACAT
*
87475 TTTAATATATATTATAAAAATA
1 TTTAATATATATTATAAAAAAA
**
87497 CATAATATAATATTTATAAAAAAA
1 TTTAATAT-ATA-TTATAAAAAAA
87521 TTTAATTGATATATTA
1 TTTAA-T-ATATATTA
87537 CATTTTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 6 0.19
23 3 0.10
24 16 0.52
25 4 0.13
26 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTAATATATATTATAAAAAAA
Found at i:93290 original size:14 final size:14
Alignment explanation
Indices: 93271--93302 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
93261 TAATATGCAG
*
93271 ATAAATTATTTTAA
1 ATAAATTATTTAAA
93285 ATAAATTATTTAAA
1 ATAAATTATTTAAA
93299 ATAA
1 ATAA
93303 GTTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAATTATTTAAA
Found at i:94310 original size:21 final size:22
Alignment explanation
Indices: 94266--94311 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
94256 GATATAATCT
*
94266 AATTTAATATAATATATTTATA
1 AATTTAATATAATATATGTATA
94288 AATTTAATATTAAT-T-TGTATA
1 AATTTAATA-TAATATATGTATA
94309 AAT
1 AAT
94312 CATTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AATTTAATATAATATATGTATA
Found at i:99713 original size:3 final size:3
Alignment explanation
Indices: 99705--99736 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
99695 ACTGATTATT
99705 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
99737 AGTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:101743 original size:2 final size:2
Alignment explanation
Indices: 101733--101770 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
101723 TATATCCAAC
*
101733 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
101771 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:102579 original size:6 final size:6
Alignment explanation
Indices: 102568--102601 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
102558 ATTTGTACAC
102568 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGG
1 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGG
102602 TAATGGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:103425 original size:5 final size:5
Alignment explanation
Indices: 103415--103471 Score: 91
Period size: 5 Copynumber: 11.6 Consensus size: 5
103405 CACGTCCTAT
103415 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- ATAGTA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA-TA
103465 AT-TA ATA
1 ATATA ATA
103472 CCAATTAGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
4 7 0.14
5 40 0.82
6 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:104034 original size:2 final size:2
Alignment explanation
Indices: 104029--104053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104019 ATATACAAAT
104029 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
104054 TAGCACGTTA
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:104956 original size:2 final size:2
Alignment explanation
Indices: 104949--104980 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
104939 TGAAACTCAC
104949 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
104981 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:104985 original size:2 final size:2
Alignment explanation
Indices: 104980--105056 Score: 84
Period size: 2 Copynumber: 37.0 Consensus size: 2
104970 TCTCTCTCTC
*
104980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A CTCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A
* *
105023 CTT TCA TA TA TT TA TA TA TA TA TA TA TA TA TA TA
1 -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
105057 GTAGTCGTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
1 1 0.02
2 60 0.92
3 1 0.02
4 3 0.05
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:105895 original size:2 final size:2
Alignment explanation
Indices: 105888--105915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
105878 ATAATGTCTG
105888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
105916 GCATTATGAA
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):
TA
Found at i:109121 original size:15 final size:17
Alignment explanation
Indices: 109092--109123 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
109082 AACACGTGAA
109092 ATTTATATTTATGTTAT
1 ATTTATATTTATGTTAT
109109 ATTTAT-TTT-TGTTAT
1 ATTTATATTTATGTTAT
109124 TTGACCTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
ATTTATATTTATGTTAT
Found at i:109780 original size:2 final size:2
Alignment explanation
Indices: 109773--109801 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
109763 AGAAACCATT
109773 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
109802 TTCCTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:115353 original size:10 final size:10
Alignment explanation
Indices: 115295--115369 Score: 51
Period size: 10 Copynumber: 7.5 Consensus size: 10
115285 GTAGGCTTGC
*
115295 CTTTCCTTGG
1 CTTTCCTTTG
*
115305 CTTTCCTGTG
1 CTTTCCTTTG
* *
115315 CTTTGCTTTC
1 CTTTCCTTTG
* **
115325 CTTCCCTTCC
1 CTTTCCTTTG
*
115335 CTTCCCTTTG
1 CTTTCCTTTG
*
115345 CTTTGCTTTG
1 CTTTCCTTTG
* *
115355 TTTTCCTTTC
1 CTTTCCTTTG
115365 CTTTC
1 CTTTC
115370 ATTTCCTAAT
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
10 49 1.00
ACGTcount: A:0.00, C:0.35, G:0.11, T:0.55
Consensus pattern (10 bp):
CTTTCCTTTG
Found at i:117160 original size:23 final size:24
Alignment explanation
Indices: 117134--117186 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
117124 TATTTTTAAA
117134 ATATTAAAAAT-TATATTATTTAT
1 ATATTAAAAATATATATTATTTAT
* * *
117157 ATA-TATATATATATGTTATTTAT
1 ATATTAAAAATATATATTATTTAT
*
117180 AAATTAA
1 ATATTAA
117187 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
22 5 0.22
23 16 0.70
24 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTAAAAATATATATTATTTAT
Found at i:123309 original size:2 final size:2
Alignment explanation
Indices: 123302--123332 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
123292 AAACAACTTG
123302 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123333 GTAATAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:123462 original size:2 final size:2
Alignment explanation
Indices: 123455--123480 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
123445 CCAACTGCAG
123455 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
123481 GAGAAAATGA
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):
AT
Found at i:123567 original size:5 final size:5
Alignment explanation
Indices: 123557--123584 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
123547 CCAAGTTCCA
123557 ACCTC ACCTC ACCTC ACCTC ACCTC ACC
1 ACCTC ACCTC ACCTC ACCTC ACCTC ACC
123585 ATGGCATGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.61, G:0.00, T:0.18
Consensus pattern (5 bp):
ACCTC
Found at i:123784 original size:2 final size:2
Alignment explanation
Indices: 123777--123805 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
123767 CTGCCACGCA
123777 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
123806 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:124459 original size:5 final size:5
Alignment explanation
Indices: 124445--124480 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
124435 TGTAGGTAGG
* *
124445 ATAGG ATAGA ATAGA ATTGA ATAGA ATAGA ATAGA A
1 ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA A
124481 AAACTAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (5 bp):
ATAGA
Found at i:129623 original size:19 final size:19
Alignment explanation
Indices: 129601--129650 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 19
129591 AATGGATATT
129601 TTAAATTAATAAAAATTTA-
1 TTAAATTAATAAAAA-TTAG
129620 TT-AA-TAA-AAAAATTAG
1 TTAAATTAATAAAAATTAG
129636 TTAAGATTAATAAAA
1 TTAA-ATTAATAAAA
129651 GATATATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 3 0.12
16 7 0.27
17 4 0.15
18 3 0.12
19 5 0.19
20 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
TTAAATTAATAAAAATTAG
Found at i:131801 original size:3 final size:3
Alignment explanation
Indices: 131795--131824 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
131785 TTGATGTTTT
131795 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
131825 GTAGTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:133120 original size:2 final size:2
Alignment explanation
Indices: 133115--133139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
133105 TTTAAAAAAA
133115 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 A
133140 ATGAAACTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137169 original size:32 final size:33
Alignment explanation
Indices: 137128--137192 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
137118 TTTATAATTA
137128 AAATAAATAA-AAAATTTATGATAAAAT-TTATTT
1 AAATAAATAATAAAATTT-T-ATAAAATATTATTT
*
137161 AAAT-AATAATATAATTTTATAAAATATTATTT
1 AAATAAATAATAAAATTTTATAAAATATTATTT
137193 TTATTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 7 0.24
32 12 0.41
33 10 0.34
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (33 bp):
AAATAAATAATAAAATTTTATAAAATATTATTT
Found at i:138017 original size:23 final size:24
Alignment explanation
Indices: 137976--138031 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
137966 ATATTGTTAT
* *
137976 TTATATTAAACATATTCAACTT-A
1 TTATATTATACATACTCAACTTAA
* *
137999 TTATATTATATATACTCAATTTAA
1 TTATATTATACATACTCAACTTAA
*
138023 TTATCTTAT
1 TTATATTAT
138032 TCAATTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATATTATACATACTCAACTTAA
Found at i:138713 original size:50 final size:50
Alignment explanation
Indices: 138624--138864 Score: 405
Period size: 50 Copynumber: 4.9 Consensus size: 50
138614 TTGATTATCA
* * *
138624 TTCATCAACTTTTGACAATAG-A-GAGGTGGCCATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTC
138672 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTC
1 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTC
* **
138722 TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGATGATTC
1 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTC
138772 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTC
1 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTC
*
138822 TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTG
1 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTG
138865 GCTCTAAGTA
Statistics
Matches: 181, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
48 19 0.10
49 1 0.01
50 161 0.89
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (50 bp):
TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTGTTGACAATTC
Found at i:143328 original size:50 final size:50
Alignment explanation
Indices: 143259--143515 Score: 376
Period size: 50 Copynumber: 5.1 Consensus size: 50
143249 AGTTGTTGTC
* *
143259 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
143309 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
143359 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
143409 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGACCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* * * *
143459 ATTATTGACAATTCTTCATCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
143509 ATTGTTG
1 ATTGTTG
143516 GTTCTAAGTA
Statistics
Matches: 190, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
49 1 0.01
50 187 0.98
51 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:143432 original size:100 final size:100
Alignment explanation
Indices: 143259--143515 Score: 435
Period size: 100 Copynumber: 2.6 Consensus size: 100
143249 AGTTGTTGTC
* * *
143259 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTC
*
143323 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTGACCATA
143359 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
143424 TCACCAACCTTTGACAATAGAAGGAGGTGACCATA
66 TCACCAACCTTTGACAATAGAAGGAGGTGACCATA
* * *
143459 ATTATTGACAATTCTTCATCAACCTTTGACAATAGAGGGAGGTGACCATAATTGTTG
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTG
143516 GTTCTAAGTA
Statistics
Matches: 149, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
100 147 0.99
101 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
TCACCAACCTTTGACAATAGAAGGAGGTGACCATA
Found at i:145945 original size:23 final size:24
Alignment explanation
Indices: 145919--145968 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
145909 CTCTTCAATT
145919 TTCAAACTATTTTTTTT-AAACGA
1 TTCAAACTATTTTTTTTGAAACGA
145942 TTCAAACTATTTTTTTTGAAACGA
1 TTCAAACTATTTTTTTTGAAACGA
145966 TTC
1 TTC
145969 TTTTAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (24 bp):
TTCAAACTATTTTTTTTGAAACGA
Found at i:146923 original size:13 final size:13
Alignment explanation
Indices: 146905--146933 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
146895 CTAATGAAGA
146905 TTATCATGGTAAT
1 TTATCATGGTAAT
146918 TTATCATGGTAAT
1 TTATCATGGTAAT
146931 TTA
1 TTA
146934 GGTTATCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (13 bp):
TTATCATGGTAAT
Found at i:147142 original size:2 final size:2
Alignment explanation
Indices: 147137--147170 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
147127 TATATATATA
147137 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
147171 CCCTTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:151901 original size:16 final size:15
Alignment explanation
Indices: 151880--151910 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
151870 GAGGGTGCTT
151880 TTATTTATTTATTTAA
1 TTATTTATTT-TTTAA
151896 TTATTTATTTTTTAA
1 TTATTTATTTTTTAA
151911 ATCTGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTATTTTTTAA
Found at i:162955 original size:3 final size:3
Alignment explanation
Indices: 162949--162983 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
162939 AATAATAATA
162949 ATT ATT ATT ATT A-T ATTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT
162984 AGTTGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 26 0.87
4 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:163967 original size:16 final size:16
Alignment explanation
Indices: 163942--163999 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
163932 TTTTGAGTTG
*
163942 ATTTTGAGTTTAAATC
1 ATTTTGAGTTTAAATA
*
163958 ATTTTAAGTTTAAATA
1 ATTTTGAGTTTAAATA
* *
163974 ATTTTGAGTTTGAATT
1 ATTTTGAGTTTAAATA
*
163990 ATTTCGAGTT
1 ATTTTGAGTT
164000 GTGTCATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (16 bp):
ATTTTGAGTTTAAATA
Found at i:164451 original size:26 final size:28
Alignment explanation
Indices: 164391--164453 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
164381 TGATAATAAT
* * *
164391 AATTATAAATGTAATTTTTTATTATACCA
1 AATTA-AAAAGTAATTTTCTATTATACAA
164420 AA-TAAAAAGTAATTTTCTATTA-A-AA
1 AATTAAAAAGTAATTTTCTATTATACAA
164445 AATTAAAAA
1 AATTAAAAA
164454 TAAAATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 3 0.10
26 7 0.23
27 16 0.53
28 2 0.07
29 2 0.07
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (28 bp):
AATTAAAAAGTAATTTTCTATTATACAA
Found at i:167609 original size:18 final size:18
Alignment explanation
Indices: 167582--167617 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
167572 AATTAACCCC
167582 CTTTGACTCATATAAGTT
1 CTTTGACTCATATAAGTT
* *
167600 CTTTGCCTCATCTAAGTT
1 CTTTGACTCATATAAGTT
167618 TAATAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (18 bp):
CTTTGACTCATATAAGTT
Found at i:173499 original size:1 final size:1
Alignment explanation
Indices: 173495--173522 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
173485 ACCCCCCCTG
173495 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
173523 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:175753 original size:2 final size:2
Alignment explanation
Indices: 175746--175770 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
175736 TTGGATGGTT
175746 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
175771 TTCTTTTTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:175950 original size:2 final size:2
Alignment explanation
Indices: 175943--175980 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
175933 AGTGTGCGTG
175943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
175981 AATGTTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:180393 original size:15 final size:15
Alignment explanation
Indices: 180373--180403 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
180363 ATGCGTAGAT
*
180373 ATATATATATAATAA
1 ATATATAAATAATAA
180388 ATATATAAATAATAA
1 ATATATAAATAATAA
180403 A
1 A
180404 AATTTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATATAAATAATAA
Found at i:180437 original size:16 final size:17
Alignment explanation
Indices: 180411--180448 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
180401 AAAAATTTCA
*
180411 AATACTAATATTATTAT
1 AATACTAATATAATTAT
180428 AATA-TAATATAATTAT
1 AATACTAATATAATTAT
*
180444 TATAC
1 AATAC
180449 AGAATAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AATACTAATATAATTAT
Found at i:181393 original size:2 final size:2
Alignment explanation
Indices: 181386--181423 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
181376 CCTCTTTCTT
181386 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
181424 TTTGAATTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:182611 original size:17 final size:18
Alignment explanation
Indices: 182575--182612 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
182565 TTTCAACAAC
*
182575 ATAAAAATAAAACATTTA
1 ATAAAAATAAAACATATA
*
182593 ATAAAATTAAAA-ATATA
1 ATAAAAATAAAACATATA
182610 ATA
1 ATA
182613 TTTATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAATAAAACATATA
Found at i:188020 original size:2 final size:2
Alignment explanation
Indices: 188013--188046 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
188003 CCTTTCACAC
188013 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
188047 ATAGACTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:189244 original size:12 final size:12
Alignment explanation
Indices: 189211--189237 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
189201 GTATCAATGC
189211 AAAAGAAAAAGG
1 AAAAGAAAAAGG
189223 AAAAGAAAAAGG
1 AAAAGAAAAAGG
189235 AAA
1 AAA
189238 TAAAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGG
Found at i:193902 original size:33 final size:33
Alignment explanation
Indices: 193860--193959 Score: 116
Period size: 33 Copynumber: 3.0 Consensus size: 33
193850 AAGGAGAAAA
*
193860 AAAAAATTATATATTTGTAT-TATTTTTTTATAT
1 AAAATATTATATATTT-TATATATTTTTTTATAT
193893 AAAATATTATAT-TTTTATATATTTTTTTTATATT
1 AAAATATTATATATTTTATATA-TTTTTTTATA-T
* *
193927 AATAAT-TTATTTATTTTATATATATTTTTATAT
1 AA-AATATTATATATTTTATATATTTTTTTATAT
193960 GTACATATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
31 3 0.05
32 5 0.08
33 22 0.37
34 17 0.29
35 12 0.20
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
AAAATATTATATATTTTATATATTTTTTTATAT
Found at i:193925 original size:26 final size:26
Alignment explanation
Indices: 193896--193959 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 26
193886 TTTATATAAA
*
193896 ATATTATATTTTTATATATTTTTTTT
1 ATATTATATTTTTATATATTTATTTT
* *
193922 ATATTA-A---TAATTTATTTATTTT
1 ATATTATATTTTTATATATTTATTTT
193944 ATA-TATATTTTTATAT
1 ATATTATATTTTTATAT
193960 GTACATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 9
0.67 0.12 0.21
Matches are distributed among these distances:
21 2 0.07
22 16 0.55
25 5 0.17
26 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
ATATTATATTTTTATATATTTATTTT
Found at i:193944 original size:35 final size:34
Alignment explanation
Indices: 193866--193975 Score: 120
Period size: 34 Copynumber: 3.2 Consensus size: 34
193856 AAAAAAAAAA
193866 TTATATATTTGTAT-TATTTTTTTATA-TAA-AAT
1 TTATATATTT-TATATATTTTTTTATATTAATAAT
193898 ATTATAT-TTTTATATATTTTTTTTATATTAATAAT
1 -TTATATATTTTATATA-TTTTTTTATATTAATAAT
* *
193933 TTATTTATTTTATATATATTTTTATATGTACATATAT
1 TTATATATTTTATATATTTTTTTATAT-TA-ATA-AT
193970 TTATAT
1 TTATAT
193976 TATGTGTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
31 3 0.05
32 5 0.08
33 16 0.24
34 18 0.27
35 14 0.21
36 3 0.05
37 7 0.11
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.64
Consensus pattern (34 bp):
TTATATATTTTATATATTTTTTTATATTAATAAT
Found at i:193972 original size:37 final size:35
Alignment explanation
Indices: 193866--193992 Score: 108
Period size: 34 Copynumber: 3.7 Consensus size: 35
193856 AAAAAAAAAA
*
193866 TTATA-TATTTGTAT-TATTTTTTTATA-TAA-AAT
1 TTATATTATTT-TATATATATTTTTATATTAATAAT
*
193898 ATTATA-T-TTTTATATATTTTTTTTATATTAATAAT
1 -TTATATTATTTTATATA-TATTTTTATATTAATAAT
193933 TTAT-TTATTTTATATATATTTTTATATGTACATATAT
1 TTATATTATTTTATATATATTTTTATAT-TA-ATA-AT
*
193970 TTATATTATGTGTATAT-TATTTT
1 TTATATTAT-TTTATATATATTTT
193993 CAAGTAATGT
Statistics
Matches: 81, Mismatches: 2, Indels: 17
0.81 0.02 0.17
Matches are distributed among these distances:
31 3 0.04
32 5 0.06
33 16 0.20
34 18 0.22
35 14 0.17
36 3 0.04
37 6 0.07
38 10 0.12
39 6 0.07
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (35 bp):
TTATATTATTTTATATATATTTTTATATTAATAAT
Found at i:194127 original size:24 final size:23
Alignment explanation
Indices: 194083--194128 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
194073 TTTTTACACG
* *
194083 TTAATTATTTATTTATCTATATT
1 TTAATTATTCATGTATCTATATT
*
194106 TTAATATATTCATGTATTTATAT
1 TTAAT-TATTCATGTATCTATAT
194129 CGTATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTAATTATTCATGTATCTATATT
Found at i:194618 original size:12 final size:13
Alignment explanation
Indices: 194597--194662 Score: 61
Period size: 12 Copynumber: 5.3 Consensus size: 13
194587 TGTATTTAAA
194597 ATATTATTTTTAT
1 ATATTATTTTTAT
194610 ATATT-TTTTTAT
1 ATATTATTTTTAT
*
194622 ATATTAATAATTTAT
1 ATATT-AT-TTTTAT
194637 -T-TTA-TTTTAT
1 ATATTATTTTTAT
*
194647 GTA-TATTTTTAT
1 ATATTATTTTTAT
194659 ATAT
1 ATAT
194663 ATGTGTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 5 0.12
11 3 0.07
12 21 0.49
13 7 0.16
14 2 0.05
15 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
ATATTATTTTTAT
Found at i:194663 original size:12 final size:12
Alignment explanation
Indices: 194597--194728 Score: 55
Period size: 12 Copynumber: 11.0 Consensus size: 12
194587 TGTATTTAAA
194597 ATAT-TATTTTT
1 ATATATATTTTT
*
194608 ATATATTTTTTT
1 ATATATATTTTT
*
194620 ATATATTAATAATTT
1 ATATA-T-AT-TTTT
*
194635 AT-TTTA-TTTT
1 ATATATATTTTT
*
194645 ATGTATATTTTT
1 ATATATATTTTT
194657 ATATATATGTGTATT
1 ATATATAT-T-T-TT
* *
194672 A-ATATAATGTGT
1 ATATAT-ATTTTT
194684 ATAT-TATTTTT
1 ATATATATTTTT
*
194695 ATGT-TATATTTT
1 ATATATAT-TTTT
*
194707 AAATAT-TTTTT
1 ATATATATTTTT
*
194718 ATGT-TATTTTT
1 ATATATATTTTT
194729 TTATGTTTAA
Statistics
Matches: 91, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
10 6 0.07
11 28 0.31
12 33 0.36
13 7 0.08
14 7 0.08
15 10 0.11
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (12 bp):
ATATATATTTTT
Found at i:195048 original size:13 final size:13
Alignment explanation
Indices: 195030--195099 Score: 52
Period size: 13 Copynumber: 5.2 Consensus size: 13
195020 TTATTTTATA
195030 TTTTATATAAATT
1 TTTTATATAAATT
*
195043 TTTTATATATTAAAT
1 TTTTATATA--AATT
* * *
195058 TTTAATTTTAAATA
1 TTTTA-TATAAATT
195072 TTTTAT-TAAATAT
1 TTTTATATAAAT-T
*
195085 TTTTAAATAAATT
1 TTTTATATAAATT
195098 TT
1 TT
195100 ATTAACTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
12 5 0.11
13 18 0.41
14 11 0.25
15 7 0.16
16 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTATATAAATT
Found at i:196527 original size:6 final size:6
Alignment explanation
Indices: 196518--196547 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
196508 AATTCCAATT
196518 CCAACC CCAACC CCAACC CCAACC CCAACC
1 CCAACC CCAACC CCAACC CCAACC CCAACC
196548 AACAACAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAACC
Found at i:199222 original size:2 final size:2
Alignment explanation
Indices: 199215--199250 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
199205 CCATTTGGCG
*
199215 CT CT CT CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
199251 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:199255 original size:2 final size:2
Alignment explanation
Indices: 199250--199274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
199240 TCTCTCTCTC
199250 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
199275 GTGTGTGTGT
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:199279 original size:2 final size:2
Alignment explanation
Indices: 199274--199304 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
199264 TATATATATA
199274 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
199305 ATGTATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:199321 original size:12 final size:12
Alignment explanation
Indices: 199306--199330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
199296 TGTGTGTGTA
199306 TGTATTTAGATT
1 TGTATTTAGATT
199318 TGTATTTAGATT
1 TGTATTTAGATT
199330 T
1 T
199331 AAACATGGCA
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TGTATTTAGATT
Found at i:203907 original size:77 final size:77
Alignment explanation
Indices: 203779--203928 Score: 255
Period size: 77 Copynumber: 1.9 Consensus size: 77
203769 CGAAGCCATG
* * *
203779 ATGGAGGCCATGCAGAAAGAGATGGGGGAGCTCAAAGGTGAGCTCTCGTCATATAAAGCAGCTAT
1 ATGGAAGCCATGCAGAAAGAGATGGAGGAGCTCAAAGGCGAGCTCTCGTCATATAAAGCAGCTAT
203844 TGGTGGTAGCGT
66 TGGTGGTAGCGT
* *
203856 ATGGAAGCCATGCAGAAAGAGATGGAGGAGCTCAAAGGCGAGCTCTTGTCATGTAAAGCAGCTAT
1 ATGGAAGCCATGCAGAAAGAGATGGAGGAGCTCAAAGGCGAGCTCTCGTCATATAAAGCAGCTAT
203921 TGGTGGTA
66 TGGTGGTA
203929 ACGTGCTAGC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (77 bp):
ATGGAAGCCATGCAGAAAGAGATGGAGGAGCTCAAAGGCGAGCTCTCGTCATATAAAGCAGCTAT
TGGTGGTAGCGT
Found at i:210339 original size:3 final size:3
Alignment explanation
Indices: 210333--210388 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
210323 CCACAACAAA
* * *
210333 AAT AAT AAT AA- AAT AAC AAC AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
210380 AAT AAT AAT
1 AAT AAT AAT
210389 GATGATAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:210344 original size:23 final size:23
Alignment explanation
Indices: 210317--210366 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
210307 TAATTATGGT
*
210317 ATAAAACCACAACAAAAATAATA
1 ATAAAACAACAACAAAAATAATA
* *
210340 ATAAAATAACAACAACAATAATA
1 ATAAAACAACAACAAAAATAATA
210363 ATAA
1 ATAA
210367 TAATAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (23 bp):
ATAAAACAACAACAAAAATAATA
Found at i:210953 original size:2 final size:2
Alignment explanation
Indices: 210948--210981 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
210938 ATATATTGCC
*
210948 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
210982 GCTGTAGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:212808 original size:2 final size:2
Alignment explanation
Indices: 212801--212838 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
212791 TTTACAGAAA
212801 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
212839 TAAGAAATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:219368 original size:28 final size:26
Alignment explanation
Indices: 219326--219389 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 26
219316 GGATCTTTCG
219326 ATAAAATTAATTAATTTTAATAAAAA
1 ATAAAATTAATTAATTTTAATAAAAA
*
219352 ATAAAATATAAATTAATTTTATTAAAAA
1 ATAAAAT-T-AATTAATTTTAATAAAAA
*
219380 AT-TAATTAAT
1 ATAAAATTAAT
219390 GAAAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 4 0.12
28 19 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAAAATTAATTAATTTTAATAAAAA
Found at i:219422 original size:18 final size:17
Alignment explanation
Indices: 219375--219422 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
219365 TAATTTTATT
219375 AAAA-AATTAATTAATG
1 AAAATAATTAATTAATG
219391 AAAATAATTAAATTAACT-
1 AAAATAATT-AATTAA-TG
219409 AAAATTAATTAATT
1 AAAA-TAATTAATT
219423 TGATTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 14 0.50
19 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATAATTAATTAATG
Found at i:220631 original size:2 final size:2
Alignment explanation
Indices: 220624--220656 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
220614 CAATTCCAAT
*
220624 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
220657 GCAGTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:222677 original size:28 final size:28
Alignment explanation
Indices: 222612--222684 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
222602 CTTCTTATAA
222612 TAATAAATTTATAAAATATAAAATGTTAT
1 TAAT-AATTTATAAAATATAAAATGTTAT
* * *
222641 TAATTATTTATGAAATATAAAATTTTA-
1 TAATAATTTATAAAATATAAAATGTTAT
222668 TATATAATTTATAAAAT
1 TA-ATAATTTATAAAAT
222685 GTTATAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 2 0.05
28 32 0.84
29 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
TAATAATTTATAAAATATAAAATGTTAT
Found at i:222692 original size:17 final size:17
Alignment explanation
Indices: 222670--222715 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
222660 AAATTTTATA
222670 TATAATTTATAAAATGT
1 TATAATTTATAAAATGT
*
222687 TATAA-TTATAAAATTT
1 TATAATTTATAAAATGT
222703 TAT-ATTT-TAAAAT
1 TATAATTTATAAAAT
222716 TATATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 7 0.26
16 15 0.56
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TATAATTTATAAAATGT
Found at i:222715 original size:15 final size:15
Alignment explanation
Indices: 222674--222729 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
222664 TTTATATATA
*
222674 ATTTATAAAATGTTAT
1 ATTT-TAAAATTTTAT
*
222690 AATTATAAAATTTTAT
1 -ATTTTAAAATTTTAT
*
222706 ATTTTAAAATTATAT
1 ATTTTAAAATTTTAT
222721 -TTTTAAAAT
1 ATTTTAAAAT
222730 AATTTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 9 0.26
15 13 0.37
16 10 0.29
17 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTTAAAATTTTAT
Found at i:222726 original size:14 final size:14
Alignment explanation
Indices: 222695--222737 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
222685 GTTATAATTA
*
222695 TAAAATTTTATATTT
1 TAAAATTATAT-TTT
222710 TAAAATTATATTTT
1 TAAAATTATATTTT
222724 TAAAA-TA-ATTTT
1 TAAAATTATATTTT
222736 TA
1 TA
222738 TTAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 8 0.30
15 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAAATTATATTTT
Found at i:225377 original size:2 final size:2
Alignment explanation
Indices: 225370--225405 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
225360 CAAGAACAGG
*
225370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225406 CTTGAATCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228129 original size:158 final size:155
Alignment explanation
Indices: 227427--228129 Score: 712
Period size: 154 Copynumber: 4.5 Consensus size: 155
227417 AACACCAAAA
* * *
227427 AAACCATAAAAACTGGAATGGCTATGGGCTTTAAAATGTTGCCAGGTTCATTGATTTGACTTCGG
1 AAACCATAAAAACTGGAATGGCTATGGGCTGTAAAATGTTGCCAGGTCCATTGATTTGACTTAGG
* * *
227492 CTCTACAAAAAGTG-ACCCATGGGCCACAAGT-AGAAGTGCTGATTGATCTTTGGTTCTCTACAA
66 CTCCAC-AAAAG-GCACCCATGGGCCACAAGTCA-AAGTGCTGATTGATCTTGGGTTCTTTACAA
* *** * *
227555 TTGGATTTTTCCAATCCTC-TGCCTGATA
128 TTGGACTAGGCCAAGCCTCAT-CCTGATG
* * *
227583 AAACCATAAAAACTAGAATGGTTATGGGCTGTAGAAA-GTTGCCAGCTCCATTGATTTGACTTAG
1 AAACCATAAAAACTGGAATGGCTATGGGCTGTA-AAATGTTGCCAGGTCCATTGATTTGACTTAG
* *
227647 GCTCCACAAAAGGGCACCCATCGGCCACAAG--AAAGTGCTG-TCGATCTTGGGTTCTTTACAAT
65 GCTCCACAAAA-GGCACCCATGGGCCACAAGTCAAAGTGCTGATTGATCTTGGGTTCTTTACAAT
* * *
227709 TGGGACTTGTCCAAGCCTCAGCCTGATG
129 T-GGACTAGGCCAAGCCTCATCCTGATG
* * * * * * **
227737 AAACCATAAAAACTGGAATGGTTATGCGCTGTAGAATGTTACCAGGTCAATTGATATGACTTAAA
1 AAACCATAAAAACTGGAATGGCTATGGGCTGTAAAATGTTGCCAGGTCCATTGATTTGACTTAGG
* * * *
227802 TTCGACACAAAGGCAGCCATGGGCCACAAGTCAAAGTGCTGATTGGTCTTGGGTTCTTTACAATT
66 CTCCACA-AAAGGCACCCATGGGCCACAAGTCAAAGTGCTGATTGATCTTGGGTTCTTTACAATT
*
227867 GTACTAGGCCAAGCCTCA---TG--G
130 GGACTAGGCCAAGCCTCATCCTGATG
* * *
227888 -AACCATAAAAACTGGAATGGCTTTGGGCTGTAGAAAGCTGCCAGATGCCCAGGTCAATTGATTT
1 AAACCATAAAAACTGGAATGGCTATGGGCTGTA-AAA--T----GTTG-CCAGGTCCATTGATTT
* * *
227952 GACTTAGGCTCCACAAAAAGGCACCCAAGGGCCACAGGTCGAAGTGCTGATTGATCTTGGGTTCT
58 GACTTAGGCTCCAC-AAAAGGCACCCATGGGCCACAAGTCAAAGTGCTGATTGATCTTGGGTTCT
*
228017 TTACAATTGGACTAGGCCAATCCTCATCCTGATG
122 TTACAATTGGACTAGGCCAAGCCTCATCCTGATG
* ** * * * *
228051 TAACCCGAAGAAATGCTGGGATGGCTATGGGCTATAAAATGTTGGCAGGTCCATTGATTTGACGT
1 AAACCATAA-AAA--CTGGAATGGCTATGGGCTGTAAAATGTTGCCAGGTCCATTGATTTGACTT
228116 AGGCTCCACAAAAG
63 AGGCTCCACAAAAG
228130 TGCTGATTGG
Statistics
Matches: 458, Mismatches: 61, Indels: 54
0.80 0.11 0.09
Matches are distributed among these distances:
150 29 0.06
151 3 0.01
153 25 0.05
154 103 0.22
155 9 0.02
156 100 0.22
157 26 0.06
158 98 0.21
159 28 0.06
160 3 0.01
161 2 0.00
163 1 0.00
164 7 0.02
165 3 0.01
166 3 0.01
167 18 0.04
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (155 bp):
AAACCATAAAAACTGGAATGGCTATGGGCTGTAAAATGTTGCCAGGTCCATTGATTTGACTTAGG
CTCCACAAAAGGCACCCATGGGCCACAAGTCAAAGTGCTGATTGATCTTGGGTTCTTTACAATTG
GACTAGGCCAAGCCTCATCCTGATG
Found at i:239812 original size:2 final size:2
Alignment explanation
Indices: 239807--239833 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
239797 AACTTTTATT
239807 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 T
239834 GTGAACTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:243114 original size:6 final size:6
Alignment explanation
Indices: 243103--243128 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
243093 GGAGCGGATA
243103 TTTGTT TTTGTT TTTGTT TTTGTT TT
1 TTTGTT TTTGTT TTTGTT TTTGTT TT
243129 GCCTTTTGGA
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:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:249869 original size:27 final size:28
Alignment explanation
Indices: 249832--249912 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
249822 TTATAATTAA
* *
249832 ATTTAAAATATTATATATTTATATAA-T
1 ATTTAATATATTATATTTTTATATAAGT
* *
249859 ATTTAATATATTAATAATTTTTGTGTAAGT
1 ATTTAATATATT-AT-ATTTTTATATAAGT
249889 -TTTAATATATTTATATTTTTATAT
1 ATTTAATATA-TTATATTTTTATAT
249913 CTTATTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 11 0.25
28 10 0.23
29 20 0.45
30 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
ATTTAATATATTATATTTTTATATAAGT
Done.