Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 6 of 29
Found at i:679842 original size:39 final size:39
Alignment explanation
Indices: 679788--679868 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
679778 TCTCACTGAG
679788 AATCAGATTCTTTCTGATATGAAAGAAGTTGATAAAACT
1 AATCAGATTCTTTCTGATATGAAAGAAGTTGATAAAACT
679827 AATCAGATTCTTTCTGATATGAAAGAAGTTGATAAAACT
1 AATCAGATTCTTTCTGATATGAAAGAAGTTGATAAAACT
679866 AAT
1 AAT
679869 GTATAAATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (39 bp):
AATCAGATTCTTTCTGATATGAAAGAAGTTGATAAAACT
Found at i:680131 original size:88 final size:90
Alignment explanation
Indices: 679968--680163 Score: 279
Period size: 88 Copynumber: 2.2 Consensus size: 90
679958 AATAAACGTG
* **
679968 ATTATATCTTAAAATTGGATTCTTTTTTATGGAAAAAAAGAAAAGTTGATTGATTATAAATGCCA
1 ATTATATCTGAAAA-TCAATTCTTTTTTAT-GAAAAAAAGAAAAGTTGATTGATTATAAATGCCA
680033 GACTGCAAGGATTAGACTAATGCATGA
64 GACTGCAAGGATTAGACTAATGCATGA
* * * *
680060 ATTATATTTGAAAATCAATTCTTTTTTAT-AGAAAAA-AAAAGTTGATTGATTGTAAATGTCAGA
1 ATTATATCTGAAAATCAATTCTTTTTTATGAAAAAAAGAAAAGTTGATTGATTATAAATGCCAGA
*
680123 CTGTAAGGATTAGACTAATGCATGA
66 CTGCAAGGATTAGACTAATGCATGA
*
680148 ATTATATCTGAGAATC
1 ATTATATCTGAAAATC
680164 GATTGTAAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 63 0.67
89 6 0.06
91 13 0.14
92 12 0.13
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (90 bp):
ATTATATCTGAAAATCAATTCTTTTTTATGAAAAAAAGAAAAGTTGATTGATTATAAATGCCAGA
CTGCAAGGATTAGACTAATGCATGA
Found at i:680195 original size:57 final size:56
Alignment explanation
Indices: 680107--680219 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 56
680097 AAAGTTGATT
*
680107 GATTGTAAATGTCAGACTGTAAGGATTAGACTAATGCATGAATTATATCTGAGAATC
1 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCT-AGAATC
680164 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTAGAATC
1 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTAGAATC
680220 AAATTCCTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
56 6 0.11
57 49 0.89
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (56 bp):
GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTAGAATC
Found at i:680201 original size:145 final size:142
Alignment explanation
Indices: 680019--680307 Score: 393
Period size: 145 Copynumber: 2.0 Consensus size: 142
680009 AAAGTTGATT
* *
680019 GATTATAAATGCCAGACTGCAAGGATTAGACTAATGCATGAATTATATTTGAAAATC-AATTCTT
1 GATTATAAATGCCAGACTGCAAGGATTAGACTAATGCATGAATTATATCT-AAAATCAAATTC-C
* * * * * *
680083 TTTTATAGAAAAAAAAAGTTGATTGATTGTAAATGTCAG-ACTGTAAGGATTAGACTAATGCATG
64 TTTTATACAAAAAAAAA-TTGACTAATTATAAATGT-AGAACTGCAAGGATAAGACTAATGCAT-
680147 AATTATATCTGAGAATC
126 AATTATATCTGAGAATC
* * *
680164 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTAGAATCAAATTCCTT
1 GATTATAAATGCCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTAAAATCAAATTCCTT
* * *
680229 TTATACAAAAAAAAATTGACTAATTATAAATGTTGAACTGCAAGGATAAGATTAATGCATTATTA
66 TTATACAAAAAAAAATTGACTAATTATAAATGTAGAACTGCAAGGATAAGACTAATGCATAATTA
680294 TATCTGAGAATC
131 TATCTGAGAATC
680306 GA
1 GA
680308 ATTCTTTTTT
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
142 19 0.15
143 36 0.28
144 21 0.16
145 52 0.41
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (142 bp):
GATTATAAATGCCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTAAAATCAAATTCCTT
TTATACAAAAAAAAATTGACTAATTATAAATGTAGAACTGCAAGGATAAGACTAATGCATAATTA
TATCTGAGAATC
Found at i:680326 original size:86 final size:87
Alignment explanation
Indices: 680169--680505 Score: 425
Period size: 86 Copynumber: 3.9 Consensus size: 87
680159 GAATCGATTG
* *
680169 TAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCT-AGAATCAAATTC-CTTTTA
1 TAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTTTTTA
*
680232 TACAAAAAAAAATTGACTAATTA
66 TA-GAAAAAAAATTGACTAATTA
* * * *
680255 TAAATGT-TGAACTGCAAGGATAAGATTAATGCAT-TATTATATCTGAGAATCGAATTCTTTTTT
1 TAAATGTCAG-ACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTTTTT
* *
680318 ATAGAAAAAAAGTTGACTGATTA
65 ATAGAAAAAAAATTGACTAATTA
*
680341 CAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATC-AGATTCTTTTTT
1 TAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGA-ATTCTTTTTT
**
680405 ATAGAAAAAAAGAAAGACTAATTGA
65 ATAGAAAAAAA-ATTGACTAATT-A
* * *
680430 TTGTAAATGTCAGACTGCAAGGATTAGACT-TTGCATGAATTATATCTGAGAATTGGATTCTTTT
1 ---TAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTTT
680494 TTATAGAAAAAA
63 TTATAGAAAAAA
680506 GAAAGACTGC
Statistics
Matches: 217, Mismatches: 22, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
85 10 0.05
86 86 0.40
87 45 0.21
88 7 0.03
89 1 0.00
91 42 0.19
92 26 0.12
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (87 bp):
TAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTTTTTA
TAGAAAAAAAATTGACTAATTA
Found at i:680551 original size:69 final size:69
Alignment explanation
Indices: 680441--680643 Score: 311
Period size: 70 Copynumber: 3.0 Consensus size: 69
680431 TGTAAATGTC
*
680441 AGACTGCAAGGATTAGACT-TTGCATGAATTATATCTGAGAATTGGATTCTTTTTTATAGAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATTGGATTCTTTTTTATAGAAAAA
680505 AGAA
66 AGAA
* *
680509 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTTTTTATAGGAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATTGGATTCTTTTTTATA-GAAAA
680574 AAGAA
65 AAGAA
* * * * *
680579 AGACTACAAGGATTACACTAATGCGTGAATTATATTTGAGAATTAGATTC-TTTTTATAGAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATTGGATTCTTTTTTATAGAAAAA
680643 A
66 A
680644 AGTTGACTAA
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
68 26 0.21
69 44 0.36
70 53 0.43
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (69 bp):
AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATTGGATTCTTTTTTATAGAAAAA
AGAA
Found at i:680686 original size:316 final size:314
Alignment explanation
Indices: 680290--680867 Score: 849
Period size: 316 Copynumber: 1.8 Consensus size: 314
680280 TTAATGCATT
* *
680290 ATTATATCTGAGAATCGAATTCTTTTTTATAGAAAAAAAGTTGACTGATTACAAATGTCAGACTG
1 ATTATATCTGAGAATAGAATTCTTTTTTATAGAAAAAAAGTTGACTAATTACAAATGTCAGACTG
* * * *
680355 CAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTAT-AGAAAAAAAGAA
66 CAAGGATTAGACTAATACATGAATTATATCTAAAAATCAGATTCTTTTTTATAAAAAAAAAAGAA
* * *
680419 AGACTAATTGATTGTAAATGTCAGACTGCAAGGATTAGACT-TTGCATGAATTATATCTGAGAAT
131 AGACCAATTGATTGTAAATGTCAAACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAAT
* * * * *
680483 TGGATTCTTTTTTATAGAAAAAAGAAAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGA
196 CGGATTATTTTTTAT--AAAAAA-AAA-ACTG-AAAGATTAAACTAATGCATAAATTATATCTGA
*
680548 GAATCGAATTCTTTTTTATAGGAAAAAAGAAAGACTACAAGGATTACACTAATGCGTGA
256 AAATCGAATTCTTTTTTATAGGAAAAAAGAAAGACTACAAGGATTACACTAATGCGTGA
* **
680607 ATTATATTTGAGAATTAG-ATTC-TTTTTATAGAAAAAAAGTTGACTAATTTTAAATGTCAGACT
1 ATTATATCTGAGAA-TAGAATTCTTTTTTATAGAAAAAAAGTTGACTAATTACAAATGTCAGACT
*
680670 GTAAGGATTAGACTAATACATGAATTATATCTAAAAATCAGATTCTTTTTTATAAAAAAAAAAAA
65 GCAAGGATTAGACTAATACATGAATTATATCTAAAAATCAGATTCTTTTTTAT--AAAAAAAAAA
* * *
680735 GAAAGACCGATTGATTGTAAATTTCAAACTGTAAGGATTAGACTAATGCATGAATTATATCTGAG
128 GAAAGACCAATTGATTGTAAATGTCAAACTGCAAGGATTAGACTAATGCATGAATTATATCTGAG
*
680800 AATCGGATTATTTTTTATAAAAAAAAAACTGAAAGATTAAACTAATGCATAAATTATATTTGAAA
193 AATCGGATTATTTTTTATAAAAAAAAAACTGAAAGATTAAACTAATGCATAAATTATATCTGAAA
680865 ATC
258 ATC
680868 AGATTCCTTT
Statistics
Matches: 233, Mismatches: 23, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
315 32 0.14
316 91 0.39
317 20 0.09
318 8 0.03
319 47 0.20
320 35 0.15
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (314 bp):
ATTATATCTGAGAATAGAATTCTTTTTTATAGAAAAAAAGTTGACTAATTACAAATGTCAGACTG
CAAGGATTAGACTAATACATGAATTATATCTAAAAATCAGATTCTTTTTTATAAAAAAAAAAGAA
AGACCAATTGATTGTAAATGTCAAACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAAT
CGGATTATTTTTTATAAAAAAAAAACTGAAAGATTAAACTAATGCATAAATTATATCTGAAAATC
GAATTCTTTTTTATAGGAAAAAAGAAAGACTACAAGGATTACACTAATGCGTGA
Found at i:680728 original size:86 final size:89
Alignment explanation
Indices: 680586--680825 Score: 254
Period size: 95 Copynumber: 2.7 Consensus size: 89
680576 GAAAGACTAC
* * * * **
680586 AAGGATTACACTAATGCGTGAATTATATTTGAGAATTAGATTC-TTTTTATAGAAAAAAAG-TTG
1 AAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATA-AAAAAAAGAAAG
* *
680649 A-C-TAATTTTAAATGTCAGACTGT
65 ACCATAATTGTAAATGTCAAACTGT
* * *
680672 AAGGATTAGACTAATACATGAATTATATCTAAAAATCAGATTCTTTTTTATAAAAAAAAAAAAGA
1 AAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTAT----AAAAAAAAGA
* *
680737 AAGACCGATTGATTGTAAATTTCAAACTGT
62 AAGACC-A-TAATTGTAAATGTCAAACTGT
* *
680767 AAGGATTAGACTAATGCATGAATTATATCTGAGAATCGGATTATTTTTTATAAAAAAAA
1 AAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAAAAAAA
680826 AACTGAAAGA
Statistics
Matches: 126, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
86 36 0.29
87 7 0.06
90 8 0.06
91 11 0.09
92 1 0.01
95 63 0.50
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (89 bp):
AAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAAAAAAAGAAAGA
CCATAATTGTAAATGTCAAACTGT
Found at i:685644 original size:127 final size:117
Alignment explanation
Indices: 685437--685792 Score: 341
Period size: 115 Copynumber: 2.9 Consensus size: 117
685427 AATAATAATA
*
685437 TATTAATTATTATTTTTAATAAAAAATAATATTTAATTAACTTTAAAGAAATTTATATTAACAAA
1 TATT-ATTATAATTTTTAAT-AAAAATAATATTTAATTAA-TTTAAA-AAA-TTATATTAACAAA
*
685502 TTAAA-AT-ATTAATTATTTTTTAATAATAAAAAATTTTAAATAAAAATAAAAAAGGTT
61 TTAAATTTAATT-ATTATTTTTTAATAATAAAAAATTTTAAATAAAAAT-AAAAAGGTT
* *
685559 TATTATTATTATTTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAAC
1 TATTATTA-TA-ATTTT--T--AA-TAAAAATAATATTTAATTAA-TTTAAAAAATTATATTAAC
* *
685624 AAATTAATATTTAATTATTATGTTTTT-ATAAAAATAAAAATTT---T-AAAATAAAAAGGTT
58 AAATTAA-ATTTAATTATTAT-TTTTTAATAATAA-AAAATTTTAAATAAAAATAAAAAGGTT
* * * *
685682 TTTTATTATAATTTTTAAT-AAAATAATATTTCATTCAATTTAAAAAGTTATATTAATAAATTAA
1 TATTATTATAATTTTTAATAAAAATAATATTTAATT-AATTTAAAAAATTATATTAACAAATT-A
* * *
685746 AATATTAATTATTATGTTTTAAAAATTAAAAATTTTAAATTAAAAAT
64 AAT-TTAATTATTATTTTTTAATAATAAAAAATTTTAAA-TAAAAAT
685793 TTTTTATTAT
Statistics
Matches: 195, Mismatches: 18, Indels: 44
0.76 0.07 0.17
Matches are distributed among these distances:
115 49 0.25
116 20 0.10
117 2 0.01
119 2 0.01
120 5 0.03
121 8 0.04
122 7 0.04
123 20 0.10
124 5 0.03
125 18 0.09
126 4 0.02
127 39 0.20
128 16 0.08
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (117 bp):
TATTATTATAATTTTTAATAAAAATAATATTTAATTAATTTAAAAAATTATATTAACAAATTAAA
TTTAATTATTATTTTTTAATAATAAAAAATTTTAAATAAAAATAAAAAGGTT
Found at i:685801 original size:14 final size:14
Alignment explanation
Indices: 685768--685795 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
685758 TATGTTTTAA
685768 AAATTAAAAATTTT
1 AAATTAAAAATTTT
685782 AAATTAAAAATTTT
1 AAATTAAAAATTTT
685796 TTATTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTAAAAATTTT
Found at i:686107 original size:23 final size:22
Alignment explanation
Indices: 686081--686154 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
686071 AATGATAAAT
*
686081 TTTTTTTAATTCCTTAAATGTTA
1 TTTTTTTAATT-ATTAAATGTTA
* * *
686104 -TTTTTTAATTTTTTAATGTAA
1 TTTTTTTAATTATTAAATGTTA
*
686125 TTTTTTTTAATTTAATTAAATATTA
1 -TTTTTTTAA-TT-ATTAAATGTTA
686150 TTTTT
1 TTTTT
686155 AATTTTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
21 8 0.20
22 10 0.25
23 8 0.20
24 7 0.17
25 7 0.17
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTTTTTAATTATTAAATGTTA
Found at i:686110 original size:22 final size:21
Alignment explanation
Indices: 686082--686130 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
686072 ATGATAAATT
*
686082 TTTTTTAATTCCTTAAATGTTA
1 TTTTTTAATT-CTTAAATGTAA
* *
686104 TTTTTTAATTTTTTAATGTAA
1 TTTTTTAATTCTTAAATGTAA
686125 TTTTTT
1 TTTTTT
686131 TTAATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTTTAATTCTTAAATGTAA
Found at i:686131 original size:22 final size:23
Alignment explanation
Indices: 686078--686137 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
686068 AATAATGATA
*
686078 AATTTTTTTTAATTCCTTAAATGT
1 AATTTTTTTTAATT-TTTAAATGT
* *
686102 --TATTTTTTAATTTTTTAATGT
1 AATTTTTTTTAATTTTTAAATGT
686123 AATTTTTTTTAATTT
1 AATTTTTTTTAATTT
686138 AATTAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 7 0.23
22 11 0.37
23 12 0.40
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (23 bp):
AATTTTTTTTAATTTTTAAATGT
Found at i:686132 original size:15 final size:15
Alignment explanation
Indices: 686112--686141 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
686102 TATTTTTTAA
686112 TTTTTTAATGTAATT
1 TTTTTTAATGTAATT
*
686127 TTTTTTAATTTAATT
1 TTTTTTAATGTAATT
686142 AAATATTATT
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:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTTTAATGTAATT
Found at i:686154 original size:45 final size:46
Alignment explanation
Indices: 686078--686165 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
686068 AATAATGATA
** *
686078 AATTTTTTTTAATTCCTTAAATGTTATTTTTTAATTTT-TTAATGT
1 AATTTTTTTTAATTAATTAAATATTATTTTTTAATTTTATTAATGT
686123 AATTTTTTTTAATTTAATTAAATATTA-TTTTTAATTTTATTAA
1 AATTTTTTTTAA-TTAATTAAATATTATTTTTTAATTTTATTAA
686166 AAATAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 23 0.61
46 15 0.39
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (46 bp):
AATTTTTTTTAATTAATTAAATATTATTTTTTAATTTTATTAATGT
Found at i:686161 original size:23 final size:22
Alignment explanation
Indices: 686094--686166 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 22
686084 TTTTAATTCC
686094 TTAAATGTTATTTTTTAATTTTTTAA
1 TTAAAT-TTA-TTTTTAA--TTTTAA
686120 TGT-AATTT-TTTTTAA-TTTAA
1 T-TAAATTTATTTTTAATTTTAA
686140 TTAAATATTATTTTTAATTTT-A
1 TTAAAT-TTATTTTTAATTTTAA
686162 TTAAA
1 TTAAA
686167 AATAATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
19 1 0.02
20 9 0.21
21 2 0.05
22 13 0.31
23 10 0.24
25 2 0.05
26 4 0.10
27 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (22 bp):
TTAAATTTATTTTTAATTTTAA
Found at i:686233 original size:36 final size:35
Alignment explanation
Indices: 686188--686258 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
686178 TAATAAACCT
*
686188 TTTTAATTTAATT-TTTAATTTTAAAAATAATTAATA
1 TTTTAATTT-ATTATGTAATTTTAAAAA-AATTAATA
*
686224 TTTTAATTTATTCATGTAATTTTTAAAAAATTAAT
1 TTTTAATTTATT-ATGTAATTTTAAAAAAATTAAT
686259 TAAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 3 0.10
36 16 0.52
37 12 0.39
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (35 bp):
TTTTAATTTATTATGTAATTTTAAAAAAATTAATA
Found at i:688719 original size:21 final size:21
Alignment explanation
Indices: 688695--688766 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 21
688685 ATTAAAATAA
688695 TATATTTTATTTAAATTTAAT
1 TATATTTTATTTAAATTTAAT
*** *
688716 TATAAAATATATAAATTTTAAT
1 TATATTTTATTTAAA-TTTAAT
*
688738 ATAAATTTT-TTTAATATTT-AT
1 -TATATTTTATTTAA-ATTTAAT
688759 TAT-TTTTA
1 TATATTTTA
688767 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 9
0.66 0.18 0.16
Matches are distributed among these distances:
19 4 0.11
20 2 0.05
21 13 0.35
22 13 0.35
23 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATTTTATTTAAATTTAAT
Found at i:688751 original size:15 final size:16
Alignment explanation
Indices: 688731--688769 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
688721 AATATATAAA
688731 TTTTAATATAAATT-T
1 TTTTAATATAAATTAT
**
688746 TTTTAATATTTATTAT
1 TTTTAATATAAATTAT
688762 TTTTAATA
1 TTTTAATA
688770 AATAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTAATATAAATTAT
Found at i:689625 original size:21 final size:21
Alignment explanation
Indices: 689578--689628 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
689568 TTTAAATTAT
* *
689578 TAATTTTAATTAAATTTTATA
1 TAATTTTAAATAAATTTTAGA
*
689599 TCATTTTAAAT-AATTTTAGA
1 TAATTTTAAATAAATTTTAGA
*
689619 TAAATTTAAA
1 TAATTTTAAA
689629 AGTTTAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATTTTAAATAAATTTTAGA
Found at i:690911 original size:23 final size:23
Alignment explanation
Indices: 690885--690957 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
690875 TTTTTCAATC
690885 ATATTTAATAATTTATTATATTT
1 ATATTTAATAATTTATTATATTT
*
690908 ATATTTAA-AA-TT-TTA-A--A
1 ATATTTAATAATTTATTATATTT
690925 ATATTTAATAATTTATATTATATTT
1 ATATTTAATAA-TT-TATTATATTT
690950 ATAATTTA
1 AT-ATTTA
690958 TATTATGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 1 0.03
20 4 0.10
21 3 0.08
22 5 0.13
23 9 0.23
25 2 0.05
26 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTTAATAATTTATTATATTT
Found at i:690953 original size:18 final size:18
Alignment explanation
Indices: 690900--690963 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
690890 TAATAATTTA
*
690900 TTATATTTATATTTAAAAT
1 TTATA-TTATATTTATAAT
**
690919 TT-TAAAATATTTAATAAT
1 TTATATTATATTT-ATAAT
690937 TTATATTATATTTATAAT
1 TTATATTATATTTATAAT
690955 TTATATTAT
1 TTATATTAT
690964 GCTTATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.16
18 22 0.58
19 10 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTATATTTATAAT
Found at i:690969 original size:18 final size:18
Alignment explanation
Indices: 690932--690974 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
690922 AAAATATTTA
*
690932 ATAATTTATATTATATTT
1 ATAATTTATATTATACTT
*
690950 ATAATTTATATTATGCTT
1 ATAATTTATATTATACTT
690968 AT-ATTTA
1 ATAATTTA
690975 CATAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATAATTTATATTATACTT
Found at i:696114 original size:2 final size:2
Alignment explanation
Indices: 696101--696144 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
696091 TACCCTTTTT
* *
696101 AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
696143 AG
1 AG
696145 GGAAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (2 bp):
AG
Found at i:696239 original size:2 final size:2
Alignment explanation
Indices: 696232--696257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
696222 ATACTTTTAA
696232 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
696258 ATGGCTGTGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:697044 original size:20 final size:19
Alignment explanation
Indices: 697019--697059 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
697009 TAAGAAAATT
*
697019 AAAAATTATCCTATTTATAA
1 AAAAATAATCC-ATTTATAA
*
697039 AAAAATAATTCATTTATAA
1 AAAAATAATCCATTTATAA
697058 AA
1 AA
697060 TTATTTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATAATCCATTTATAA
Found at i:697096 original size:19 final size:18
Alignment explanation
Indices: 697072--697107 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
697062 ATTTATGTTT
697072 TAAATATAAATATATTTAA
1 TAAATAT-AATATATTTAA
*
697091 TAAATATATTATATTTA
1 TAAATATAATATATTTA
697108 TATTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATATAATATATTTAA
Found at i:697811 original size:32 final size:34
Alignment explanation
Indices: 697775--697838 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 34
697765 CGAATAGATA
*
697775 AATATA-TAATAATTTATATAAA-ATA-AATTATT
1 AATATATTAA-AATTAATATAAATATATAATTATT
697807 AATATATTAAAATTAATATAAATATATAATTA
1 AATATATTAAAATTAATATAAATATATAATTA
697839 ATTGAACACG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 17 0.61
33 6 0.21
34 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AATATATTAAAATTAATATAAATATATAATTATT
Found at i:697812 original size:20 final size:19
Alignment explanation
Indices: 697789--697835 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
697779 TATAATAATT
*
697789 TATATAAAATAAATTATTAA
1 TATATAAAATAAA-TATAAA
*
697809 TATATTAAAATTAATATAAA
1 TATA-TAAAATAAATATAAA
697829 TATATAA
1 TATATAA
697836 TTAATTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 13 0.54
21 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATAAAATAAATATAAA
Found at i:697837 original size:17 final size:17
Alignment explanation
Indices: 697778--697840 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
697768 ATAGATAAAT
*
697778 ATATAATAATTTATATAA
1 ATAT-ATAATTAATATAA
697796 A-ATA-AATT-AT-TAA
1 ATATATAATTAATATAA
*
697809 TATATTAAAATTAATATAA
1 -ATA-TATAATTAATATAA
697828 ATATATAATTAAT
1 ATATATAATTAAT
697841 TGAACACGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 3 0.08
14 3 0.08
15 5 0.13
16 3 0.08
17 15 0.39
18 6 0.16
19 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATTAATATAA
Found at i:698089 original size:18 final size:18
Alignment explanation
Indices: 698046--698095 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
698036 ATGTAAAAAT
698046 CTAAAT-TAAATAAATTA
1 CTAAATATAAATAAATTA
698063 CTAATATATAAA-AAATTA
1 CTAA-ATATAAATAAATTA
*
698081 TTTAAATATATAATA
1 -CTAAATATA-AATA
698096 CCTTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 4 0.15
18 13 0.48
19 9 0.33
20 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAAATATAAATAAATTA
Found at i:703985 original size:3 final size:3
Alignment explanation
Indices: 703977--704010 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
703967 AACCTTTATT
*
703977 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
704011 TATTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:704015 original size:3 final size:3
Alignment explanation
Indices: 704009--704035 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
703999 AATAATAATA
704009 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
704036 GCCAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:704869 original size:19 final size:19
Alignment explanation
Indices: 704837--704874 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
704827 ATTATTTATT
704837 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
704856 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
704875 AATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:704913 original size:20 final size:19
Alignment explanation
Indices: 704855--704914 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
704845 ATTATAAAAT
*
704855 ATAAATATT-AAT-ATAAA
1 ATAAATTTTAAATAATAAA
* * **
704872 ATAAATTTTTAATATTTTA
1 ATAAATTTTAAATAATAAA
704891 ATAACATTTTAAATAATAAA
1 ATAA-ATTTTAAATAATAAA
704911 ATAA
1 ATAA
704915 GTTACCAAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 8 0.25
18 3 0.09
19 6 0.19
20 15 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATTTTAAATAATAAA
Found at i:705042 original size:2 final size:2
Alignment explanation
Indices: 705035--705061 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
705025 ATTTCCCGAT
705035 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
705062 TCTTTTCATC
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:707084 original size:19 final size:20
Alignment explanation
Indices: 707054--707091 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
707044 CATCTTTATT
*
707054 TATAATTTATAATCTATATC
1 TATAATTTATAATATATATC
707074 TATAA-TTATAATATATAT
1 TATAATTTATAATATATAT
707092 AAGTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATTTATAATATATATC
Found at i:707171 original size:14 final size:15
Alignment explanation
Indices: 707148--707185 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
707138 TTGTTTATTA
*
707148 TATTACTAATTTTAT
1 TATTATTAATTTTAT
*
707163 TATT-TTAATTTTTT
1 TATTATTAATTTTAT
707177 TATTATTAA
1 TATTATTAA
707186 AACTTATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTATTAATTTTAT
Found at i:707274 original size:23 final size:24
Alignment explanation
Indices: 707243--707298 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
707233 TGATTCAATA
707243 AATT-TATTTGAT-AATAAAAATTT
1 AATTATATTT-ATAAATAAAAATTT
*
707266 -ATTATATTTATAAATAAAATTTT
1 AATTATATTTATAAATAAAAATTT
*
707289 AATTCTATTT
1 AATTATATTT
707299 TTTTGGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 5 0.18
23 15 0.54
24 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AATTATATTTATAAATAAAAATTT
Found at i:707523 original size:24 final size:23
Alignment explanation
Indices: 707459--707523 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
707449 ATTTTAAATG
*
707459 TTAATA-AAAATTT-TAGTTATT
1 TTAATATAAAATTTATATTTATT
* *
707480 TT-ATATAATATGTA-ACTTTATAT
1 TTAATATAAAATTTATA-TTTAT-T
707503 TTAATATAAAATTTATATTTA
1 TTAATATAAAATTTATATTTA
707524 AATAATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
20 3 0.09
21 8 0.24
22 4 0.12
23 3 0.09
24 14 0.42
25 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (23 bp):
TTAATATAAAATTTATATTTATT
Found at i:707535 original size:18 final size:18
Alignment explanation
Indices: 707496--707562 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
707486 AATATGTAAC
**
707496 TTTATATTTAATATAA-AA
1 TTTATATTTAA-ATAATTT
707514 TTTATATTTAAATAATTT
1 TTTATATTTAAATAATTT
* *
707532 TTTATAATATAAATATTTT
1 TTTAT-ATTTAAATAATTT
707551 ATATTATATTTA
1 -T-TTATATTTA
707563 TAAACATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 4 0.10
18 16 0.40
19 11 0.28
20 5 0.12
21 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATATTTAAATAATTT
Found at i:710730 original size:2 final size:2
Alignment explanation
Indices: 710725--710749 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
710715 TCAGTTAGAT
710725 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
710750 TTATTAAAAA
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:711355 original size:19 final size:19
Alignment explanation
Indices: 711310--711356 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
711300 AAATTAGTTT
*
711310 AAATAACTATTTAATTATA
1 AAATAATTATTTAATTATA
*
711329 AAAT-ATTATTTTATT-TA
1 AAATAATTATTTAATTATA
711346 AATATAATTAT
1 AA-ATAATTAT
711357 AAAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 11 0.46
19 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATAATTATTTAATTATA
Found at i:711366 original size:16 final size:16
Alignment explanation
Indices: 711347--711390 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
711337 TTTTATTTAA
*
711347 ATATAATTATAAAAAT
1 ATATAAATATAAAAAT
* *
711363 ATATAAATATTAATAT
1 ATATAAATATAAAAAT
711379 ATATAAA-ATAAA
1 ATATAAATATAAA
711391 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAAATATAAAAAT
Found at i:711975 original size:21 final size:21
Alignment explanation
Indices: 711924--711977 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
711914 AATATTATTT
*
711924 TATTTAAATTTAATTATAAAA
1 TATTTAATTTTAATTATAAAA
* *
711945 TAAATAAATTTTAA-TATAAAAA
1 T-ATTTAATTTTAATTAT-AAAA
711967 TATTTAATTTT
1 TATTTAATTTT
711978 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTAATTTTAATTATAAAA
Found at i:714488 original size:13 final size:14
Alignment explanation
Indices: 714471--714503 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
714461 TATCAATTTT
714471 TTAAAATAATTATA
1 TTAAAATAATTATA
*
714485 -TAAATTAATTATA
1 TTAAAATAATTATA
714498 TTAAAA
1 TTAAAA
714504 ATTTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 2
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATAATTATA
Found at i:719661 original size:30 final size:30
Alignment explanation
Indices: 719601--719662 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
719591 TATTAACAGT
* * *
719601 ATATAAATTTATAAATTATTATTATATTAA
1 ATATAAATTAATAAATAAATATTATATTAA
*
719631 ATATAAATTAATAAA-AAATATTAATTTTAA
1 ATATAAATTAATAAATAAATATT-ATATTAA
719661 AT
1 AT
719663 TTTAAATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATAAATTAATAAATAAATATTATATTAA
Found at i:719680 original size:15 final size:15
Alignment explanation
Indices: 719660--719693 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
719650 ATTAATTTTA
719660 AATTTT-AAATCATAT
1 AATTTTAAAAT-ATAT
719675 AATTTTAAAATATAT
1 AATTTTAAAATATAT
719690 AATT
1 AATT
719694 ATATTGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTTAAAATATAT
Found at i:721317 original size:7 final size:7
Alignment explanation
Indices: 721296--721334 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
721286 GATTTGGAGC
*
721296 TTTTCTC
1 TTTTCTT
721303 TTTT-TT
1 TTTTCTT
721309 TTTTCTT
1 TTTTCTT
721316 TTTTCTT
1 TTTTCTT
*
721323 TGTTCTT
1 TTTTCTT
721330 TTTTC
1 TTTTC
721335 ATTCACATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:722430 original size:15 final size:16
Alignment explanation
Indices: 722412--722441 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
722402 AACAATCAAT
722412 TTAT-TAAAAAATTAA
1 TTATATAAAAAATTAA
722427 TTATATAAAAAATTA
1 TTATATAAAAAATTA
722442 TAACAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTATATAAAAAATTAA
Found at i:726745 original size:15 final size:15
Alignment explanation
Indices: 726725--726780 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
726715 GTTTCAGTTT
*
726725 ATTTATATTTTT-TTA
1 ATTTA-ATTTTTAATA
* *
726740 ATTTATTTTTTAAAA
1 ATTTAATTTTTAATA
*
726755 ATTTAATTTTTGATA
1 ATTTAATTTTTAATA
726770 ATTTAATTTTT
1 ATTTAATTTTT
726781 TATGATGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 5 0.15
15 29 0.85
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
ATTTAATTTTTAATA
Found at i:726772 original size:30 final size:31
Alignment explanation
Indices: 726725--726782 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
726715 GTTTCAGTTT
*
726725 ATTTATATTTTTTTAATTT-ATTTTTTAAAA
1 ATTTATATTTTTATAATTTAATTTTTTAAAA
726755 ATTTA-ATTTTTGATAATTTAATTTTTTA
1 ATTTATATTTTT-ATAATTTAATTTTTTA
726783 TGATGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 11 0.44
31 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (31 bp):
ATTTATATTTTTATAATTTAATTTTTTAAAA
Found at i:727919 original size:37 final size:35
Alignment explanation
Indices: 727877--727977 Score: 96
Period size: 37 Copynumber: 2.7 Consensus size: 35
727867 TTAATTTAAT
*
727877 TTAATTTACATTAATTTAAATATTAAAATCAATCAAA
1 TTAATTTATATTAATTTAAA-ATTAAAAT-AATCAAA
* * *
727914 TTAATTAATAATAATTTTAAAATTAAAATAATTAAA
1 TTAATTTATATTAA-TTTAAAATTAAAATAATCAAA
727950 -TAATATTAATATTAATTTATACAATTAA
1 TTAAT-TT-ATATTAATTTA-A-AATTAA
727978 TTTTTTTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
35 4 0.08
36 11 0.21
37 26 0.49
38 12 0.23
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (35 bp):
TTAATTTATATTAATTTAAAATTAAAATAATCAAA
Found at i:728018 original size:12 final size:13
Alignment explanation
Indices: 727987--728022 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
727977 ATTTTTTTAA
727987 TTTTAAATATATT
1 TTTTAAATATATT
728000 TTATTAAATATA-T
1 TT-TTAAATATATT
728013 TTTTAAATAT
1 TTTTAAATAT
728023 TTTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 5 0.23
14 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTAAATATATT
Found at i:728029 original size:21 final size:21
Alignment explanation
Indices: 728003--728055 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
727993 ATATATTTTA
728003 TTAAATATATTTTTAAATATT
1 TTAAATATATTTTTAAATATT
* *
728024 TTAAATAT-TAATTTAATTATT
1 TTAAATATAT-TTTTAAATATT
728045 TT-AATATATTT
1 TTAAATATATTT
728056 AATTTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATATATTTTTAAATATT
Found at i:728066 original size:22 final size:21
Alignment explanation
Indices: 728006--728072 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
727996 TATTTTATTA
728006 AATATATT--TTTAAATATTTT
1 AATATATTAATTT-AATATTTT
728026 AA-ATATTAATTTAATTATTTT
1 AATATATTAATTTAA-TATTTT
*
728047 AATATATTTAATTTTATATTTT
1 AATATA-TTAATTTAATATTTT
728069 AATA
1 AATA
728073 ATAAAAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 5 0.12
20 4 0.10
21 11 0.27
22 13 0.32
23 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATATATTAATTTAATATTTT
Found at i:728102 original size:9 final size:9
Alignment explanation
Indices: 728077--728168 Score: 78
Period size: 9 Copynumber: 10.0 Consensus size: 9
728067 TTAATAATAA
*
728077 AAATTAATCG
1 AAATTAAT-T
728087 AAA-TAATT
1 AAATTAATT
728095 AAATTAATT
1 AAATTAATT
*
728104 AATTTAAATT
1 AAATT-AATT
728114 AAATTAATT
1 AAATTAATT
*
728123 GAATTAATT
1 AAATTAATT
*
728132 AAATCAAATT
1 AAAT-TAATT
*
728142 TAATTAATT
1 AAATTAATT
***
728151 TTTTTAATT
1 AAATTAATT
728160 AAATTAATT
1 AAATTAATT
728169 TTAATCCATT
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
8 3 0.05
9 45 0.68
10 18 0.27
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (9 bp):
AAATTAATT
Found at i:728115 original size:19 final size:19
Alignment explanation
Indices: 728091--728151 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 19
728081 TAATCGAAAT
728091 AATTAAATTAATTAATTTA
1 AATTAAATTAATTAATTTA
728110 AATTAAATTAATTGAATTAATTA
1 AATTAAATTAATT-AA-T--TTA
*
728133 AATCAAATTTAATTAATTT
1 AATTAAA-TTAATTAATTT
728152 TTTTAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 13 0.36
20 4 0.11
21 1 0.03
22 1 0.03
23 11 0.31
24 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
AATTAAATTAATTAATTTA
Found at i:728157 original size:28 final size:28
Alignment explanation
Indices: 728090--728173 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
728080 TTAATCGAAA
* * *
728090 TAATTAAATTAATTAATTTAAATTAAAT
1 TAATTGAATTAATTAAATTAAATTTAAT
*
728118 TAATTGAATTAATTAAATCAAATTTAAT
1 TAATTGAATTAATTAAATTAAATTTAAT
*** *
728146 TAATTTTTTTAATTAAATTAATTTTAAT
1 TAATTGAATTAATTAAATTAAATTTAAT
728174 CCATTTTTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
TAATTGAATTAATTAAATTAAATTTAAT
Found at i:728166 original size:5 final size:5
Alignment explanation
Indices: 728091--728148 Score: 59
Period size: 5 Copynumber: 12.2 Consensus size: 5
728081 TAATCGAAAT
* * *
728091 AATTA AATT- AATTA ATTTA AATTA AATT- AATTG AATT- AATTA AATCA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA
*
728138 AATTT AATTA A
1 AATTA AATTA A
728149 TTTTTTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 12 0.27
5 32 0.73
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:728826 original size:27 final size:28
Alignment explanation
Indices: 728793--728863 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
728783 GCTACCCATT
728793 TGTTTGTCAAAAATGGTGGTTAT-TTTA
1 TGTTTGTCAAAAATGGTGGTTATCTTTA
* *
728820 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTA
* *
728848 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
728864 AAGCTTGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTATCTTTA
Found at i:733596 original size:3 final size:3
Alignment explanation
Indices: 733568--733606 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
733558 CATGGTTTTT
733568 TTA TT- TTA TT- TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
733607 GACCATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.25
3 24 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:733606 original size:6 final size:5
Alignment explanation
Indices: 733566--733604 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
733556 CTCATGGTTT
733566 TTTTA TTTTA TTTTA TTTTA TTTTA TTATTA TTATTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA TT
733605 ATGACCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 22 0.67
6 11 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:736041 original size:22 final size:22
Alignment explanation
Indices: 736016--736059 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
736006 CATTTCAAAG
736016 TATTTAATTTTACCTTGTAATA
1 TATTTAATTTTACCTTGTAATA
736038 TATTTAATTTTACCTTGTAATA
1 TATTTAATTTTACCTTGTAATA
736060 CATAAGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTAATTTTACCTTGTAATA
Found at i:741492 original size:22 final size:21
Alignment explanation
Indices: 741444--741496 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
741434 TTTCATCCAC
* *
741444 CGCTATTGCGACAATAGTAGA
1 CGCTATTGTGACAATAGCAGA
*
741465 CTGCTATTGTGACAATAGCGGA
1 C-GCTATTGTGACAATAGCAGA
741487 TCGCTATTGT
1 -CGCTATTGT
741497 CGCTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (21 bp):
CGCTATTGTGACAATAGCAGA
Found at i:743874 original size:24 final size:24
Alignment explanation
Indices: 743846--743891 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
743836 AATAAAAATT
743846 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* * *
743870 AGCCACCATTTTTTACATACAA
1 AGCCACCAATTTTGACAAACAA
743892 AAATAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:743917 original size:28 final size:28
Alignment explanation
Indices: 743886--743949 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
743876 CATTTTTTAC
743886 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
*
743914 ATACAAAGGAAACCACCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
743942 ATACAAAG
1 ATACAAAG
743950 GGTGGCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:743950 original size:28 final size:28
Alignment explanation
Indices: 743896--743950 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
743886 ATACAAAAAT
743896 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
743924 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
743951 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:745405 original size:13 final size:13
Alignment explanation
Indices: 745387--745443 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
745377 TTCAATGGTT
745387 TGTATCGATACAA
1 TGTATCGATACAA
745400 TGTATCGATACATAA
1 TGTATCGATAC--AA
745415 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
745432 TGTATCGATACA
1 TGTATCGATACA
745444 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:745424 original size:19 final size:18
Alignment explanation
Indices: 745400--745462 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
745390 ATCGATACAA
745400 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
745419 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
745432 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
745451 TGTATCGATACA
1 TGTATCGATACA
745463 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:745427 original size:32 final size:32
Alignment explanation
Indices: 745386--745470 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
745376 TTTCAATGGT
745386 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
745418 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
745450 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
745471 CTACGAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:745591 original size:52 final size:52
Alignment explanation
Indices: 745548--745676 Score: 195
Period size: 52 Copynumber: 2.5 Consensus size: 52
745538 CACTGATCTT
* * *
745548 TGTATCAATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCAATACATACAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
745600 TGTATCGATACATACAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCAATACATACAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * *
745652 TTTATCGATACATACAGGCAAATTT
1 TGTATCAATACATACAAGCAAATTT
745677 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCAATACATACAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:755865 original size:18 final size:19
Alignment explanation
Indices: 755831--755866 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
755821 TTTTAACACA
755831 TTTATTTATTAATATTATG
1 TTTATTTATTAATATTATG
*
755850 TTTATTT-TTTATATTAT
1 TTTATTTATTAATATTAT
755867 ATCGTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTATTTATTAATATTATG
Found at i:756343 original size:19 final size:19
Alignment explanation
Indices: 756297--756344 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
756287 TATTTTTTAA
756297 TTTGTATACATTTATTTATT
1 TTTGT-TACATTTATTTATT
* *
756317 CTTATTACA-TTATTATATT
1 TTTGTTACATTTATT-TATT
756336 TTTGTTACA
1 TTTGTTACA
756345 AGATATTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 15 0.65
20 3 0.13
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTGTTACATTTATTTATT
Found at i:756425 original size:10 final size:10
Alignment explanation
Indices: 756410--756444 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
756400 TCTTATGATA
*
756410 ATAAAAAATT
1 ATAAAATATT
756420 ATAAAATATT
1 ATAAAATATT
756430 ATAAAATATT
1 ATAAAATATT
756440 ATAAA
1 ATAAA
756445 CTAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
ATAAAATATT
Found at i:757118 original size:34 final size:34
Alignment explanation
Indices: 757075--757175 Score: 121
Period size: 37 Copynumber: 2.9 Consensus size: 34
757065 TAGGTTTACT
*
757075 TAACACACTTAATATGTTTACTTAACACATCACC
1 TAACACACTTAATATGTTTACTTAACACACCACC
* * *
757109 TAACACACTTAATATATTGTTCACTTAACATACCACT
1 TAACACACTT-A-ATA-TGTTTACTTAACACACCACC
* *
757146 TAACATACTTAATATGTTTACCTAACACAC
1 TAACACACTTAATATGTTTACTTAACACAC
757176 TTAATAAAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
34 23 0.41
35 4 0.07
36 4 0.07
37 25 0.45
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.34
Consensus pattern (34 bp):
TAACACACTTAATATGTTTACTTAACACACCACC
Found at i:760944 original size:3 final size:3
Alignment explanation
Indices: 760936--760965 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
760926 AATGTCATCG
760936 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
760966 CAAAATAATG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:761611 original size:18 final size:21
Alignment explanation
Indices: 761584--761635 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 21
761574 TATAATTATA
*
761584 AATAAAATAAATATT-AT-TT
1 AATAATATAAATATTAATATT
*
761603 AA-AATATAAATGTTAATATT
1 AATAATATAAATATTAATATT
761623 AATAATA-AAATAT
1 AATAATATAAATAT
761636 ATCAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 10 0.37
19 4 0.15
20 9 0.33
21 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAATATAAATATTAATATT
Found at i:762257 original size:16 final size:16
Alignment explanation
Indices: 762211--762300 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
762201 TTTAAAATTT
*
762211 AATTTAAATTATTTTA
1 AATTTAATTTATTTTA
* * *
762227 ATTTTGA-TCATTTTTA
1 AATTTAATTTA-TTTTA
*
762243 TATTTAATTTATTTTA
1 AATTTAATTTATTTTA
*
762259 AATTTCAA-TAATTTTA
1 AATTT-AATTTATTTTA
* *
762275 ACTTTAAATTATTTTA
1 AATTTAATTTATTTTA
762291 AATTTAATTT
1 AATTTAATTT
762301 TATATAATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
15 4 0.07
16 49 0.86
17 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (16 bp):
AATTTAATTTATTTTA
Found at i:762274 original size:32 final size:32
Alignment explanation
Indices: 762208--762295 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
762198 TTTTTTAAAA
** *
762208 TTTAATTTAAATTATTTT-AATTTTGATCATT
1 TTTAATTTAAATTATTTTAAATTTCAATCAAT
*
762239 TTTATATTTAATTTATTTTAAATTTCAAT-AAT
1 TTTA-ATTTAAATTATTTTAAATTTCAATCAAT
762271 TTTAACTTTAAATTATTTTAAATTT
1 TTTAA-TTTAAATTATTTTAAATTT
762296 AATTTTATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
31 5 0.10
32 37 0.76
33 7 0.14
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (32 bp):
TTTAATTTAAATTATTTTAAATTTCAATCAAT
Found at i:764224 original size:13 final size:13
Alignment explanation
Indices: 764208--764232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
764198 ATAAAAATTT
764208 AATTATATAAAAA
1 AATTATATAAAAA
764221 AATTATATAAAA
1 AATTATATAAAA
764233 TATAAGATAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTATATAAAAA
Found at i:765298 original size:34 final size:34
Alignment explanation
Indices: 765232--765298 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
765222 ACAAATTAGT
* * * *
765232 CATATATAAAAAATATATAAAATATATTATTTTA
1 CATATATAAAAAATAAATAAAACACATAATTTTA
765266 CATATA-AAAAAATAAATACAAACACATAATTTT
1 CATATATAAAAAATAAATA-AAACACATAATTTT
765299 TTTCTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.34
Consensus pattern (34 bp):
CATATATAAAAAATAAATAAAACACATAATTTTA
Found at i:765348 original size:8 final size:9
Alignment explanation
Indices: 765322--765359 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
765312 TTTTTTTATC
765322 CTTTCTCTTT
1 CTTTCT-TTT
*
765332 CGTTCTTTT
1 CTTTCTTTT
765341 CTTT-TTTT
1 CTTTCTTTT
765349 CTTTCTTTT
1 CTTTCTTTT
765358 CT
1 CT
765360 GCCTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.32
9 12 0.48
10 5 0.20
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:766008 original size:10 final size:10
Alignment explanation
Indices: 765993--766018 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
765983 ATAAATTATT
765993 AATATATAAA
1 AATATATAAA
766003 AATATATAAA
1 AATATATAAA
766013 AATATA
1 AATATA
766019 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATATATAAA
Found at i:766242 original size:11 final size:10
Alignment explanation
Indices: 766217--766252 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
766207 TGAACATAAC
766217 AATAATAAAA
1 AATAATAAAA
766227 AATAATTAAAA
1 AATAA-TAAAA
*
766238 CATAATAAAA
1 AATAATAAAA
766248 AATAA
1 AATAA
766253 CATGAACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (10 bp):
AATAATAAAA
Found at i:766260 original size:21 final size:20
Alignment explanation
Indices: 766209--766261 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
766199 ACACGATATG
766209 AACATAACAATAATAAAAAAT
1 AACATAAC-ATAATAAAAAAT
* *
766230 AATTAAAACATAATAAAAAAT
1 AA-CATAACATAATAAAAAAT
766251 AACATGAACAT
1 AACAT-AACAT
766262 GATACGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (20 bp):
AACATAACATAATAAAAAAT
Found at i:766452 original size:38 final size:40
Alignment explanation
Indices: 766401--766475 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 40
766391 AATACAAAAA
766401 ATAAATATGACATAAATATATAA-A-TATAAAAAATATTT
1 ATAAATATGACATAAATATATAATATTATAAAAAATATTT
* * * *
766439 ATAACTATTACATAAATTTATAATATTATAAATAATA
1 ATAAATATGACATAAATATATAATATTATAAAAAATA
766476 AAAACTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 20 0.65
39 1 0.03
40 10 0.32
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (40 bp):
ATAAATATGACATAAATATATAATATTATAAAAAATATTT
Found at i:766535 original size:10 final size:10
Alignment explanation
Indices: 766515--766584 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
766505 CATATATAAA
766515 ATAATAAATAT
1 ATAA-AAATAT
766526 ATAAAAATAT
1 ATAAAAATAT
*
766536 ACATAAAATA-
1 ATA-AAAATAT
766546 A-AATAAAT-T
1 ATAA-AAATAT
* *
766555 ATTAATATAT
1 ATAAAAATAT
766565 -TAAAAATAT
1 ATAAAAATAT
766574 ATAAAAATAT
1 ATAAAAATAT
766584 A
1 A
766585 ATATTTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
8 1 0.02
9 16 0.33
10 21 0.44
11 10 0.21
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:766545 original size:21 final size:20
Alignment explanation
Indices: 766506--766585 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 20
766496 TTTTTCTCTC
*
766506 ATATATAAA-ATAAT-AAAT
1 ATATAAAAATATAATAAAAT
766524 ATATAAAAATATACATAAAAT
1 ATATAAAAATATA-ATAAAAT
* *
766545 A-A-AATAAAT-TATTAATAT
1 ATATAA-AAATATAATAAAAT
766563 AT-TAAAAATAT-ATAAAA-
1 ATATAAAAATATAATAAAAT
766580 ATATAA
1 ATATAA
766586 TATTTTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
17 2 0.04
18 25 0.51
19 10 0.20
20 7 0.14
21 5 0.10
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAAAATATAATAAAAT
Found at i:766601 original size:32 final size:35
Alignment explanation
Indices: 766508--766615 Score: 102
Period size: 37 Copynumber: 3.2 Consensus size: 35
766498 TTTCTCTCAT
* * *
766508 ATATAA-AATAATAAATATATAAAAATATACATAAA
1 ATATAATAATTATTAATATATAAAAATATATA-AAA
*
766543 ATAAAATAAATTATTAATATATTAAAAATATATAAAA
1 ATATAAT-AATTATTAATATA-TAAAAATATATAAAA
*
766580 ATATAAT-ATT-TTAA-ATATAAAAA-AT-TATAA
1 ATATAATAATTATTAATATATAAAAATATATAAAA
766610 ATATAA
1 ATATAA
766616 ACATATAGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
30 10 0.16
31 2 0.03
32 6 0.09
33 3 0.05
34 4 0.06
35 8 0.12
37 20 0.31
38 11 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (35 bp):
ATATAATAATTATTAATATATAAAAATATATAAAA
Found at i:766615 original size:16 final size:16
Alignment explanation
Indices: 766506--766616 Score: 71
Period size: 16 Copynumber: 6.4 Consensus size: 16
766496 TTTTTCTCTC
* *
766506 ATATATAAAATAATAA
1 ATATAAAAAATTATAA
766522 ATATATAAAAATATACATAA
1 ATATA-AAAAAT-T--ATAA
766542 A-ATAAAATAAATTATTAA
1 ATAT-AAA-AAATTA-TAA
*
766560 TATATTAAAAATATATAA
1 -ATATAAAAAAT-TATAA
* * * *
766578 AAATATAATATTTTAA
1 ATATAAAAAATTATAA
766594 ATATAAAAAATTATAA
1 ATATAAAAAATTATAA
766610 ATATAAA
1 ATATAAA
766617 CATATAGATT
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
16 28 0.38
17 13 0.18
18 10 0.14
19 10 0.14
20 12 0.16
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAAAAATTATAA
Found at i:766622 original size:48 final size:45
Alignment explanation
Indices: 766509--766622 Score: 117
Period size: 48 Copynumber: 2.4 Consensus size: 45
766499 TTCTCTCATA
766509 TATAAA-ATAATAAATATATAAAAATATACATAAAATAAAATAAAT
1 TATAAATATAA-AAATATATAAAAATATACATAAAATAAAATAAAT
766554 TATTAATATATTAAAAATATATAAAAATATA-ATATTTTAAATATAAA-AAAT
1 TA-TAA-ATA-TAAAAATATATAAAAATATACATA----AAATA-AAATAAAT
*
766605 TATAAATATAAACATATA
1 TATAAATATAAAAATATA
766623 GATTTTTTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
45 2 0.03
46 3 0.05
47 4 0.07
48 27 0.46
49 6 0.10
50 3 0.05
51 11 0.19
52 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (45 bp):
TATAAATATAAAAATATATAAAAATATACATAAAATAAAATAAAT
Found at i:767196 original size:20 final size:20
Alignment explanation
Indices: 767165--767215 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
767155 TAAATTTAAT
* * *
767165 TTTATATATTTTCATATCAA
1 TTTATATTTTTTAATATAAA
*
767185 TTTATATTTTTTAATCTAAA
1 TTTATATTTTTTAATATAAA
767205 TATTATATTTT
1 T-TTATATTTT
767216 ATATTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATATTTTTTAATATAAA
Found at i:770982 original size:32 final size:31
Alignment explanation
Indices: 770946--771107 Score: 89
Period size: 33 Copynumber: 5.4 Consensus size: 31
770936 TTATATGATT
770946 ATATAAATATGATATATAATATTAAAAATATA
1 ATATAAATAT-ATATATAATATTAAAAATATA
* * * *
770978 ATATAAAAAAATAAATATATTTTTAAAATTTATATA
1 ATAT--AAATATATATATAATATTAAAA---ATATA
*
771014 ATATAAAT-TATAAAT-ATATT-AAAAT-TA
1 ATATAAATATATATATAATATTAAAAATATA
771041 ATATAAATATA-A-A-AAT-TT--AAATATA
1 ATATAAATATATATATAATATTAAAAATATA
* * *
771066 AT-TATAATATAT-TAAAATA-TATAAATATT
1 ATATA-AATATATATATAATATTAAAAATATA
*
771095 ATTTAAATATATA
1 ATATAAATATATA
771108 AATCATCAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
24 6 0.06
25 12 0.12
26 4 0.04
27 15 0.15
28 4 0.04
29 15 0.15
30 2 0.02
31 3 0.03
32 7 0.07
33 18 0.17
34 8 0.08
36 9 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
ATATAAATATATATATAATATTAAAAATATA
Found at i:771021 original size:15 final size:13
Alignment explanation
Indices: 771007--771105 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 13
770997 TTTTTAAAAT
771007 TTATATAATATAAA
1 TTATA-AATATAAA
771021 TTATAAATAT--A
1 TTATAAATATAAA
771032 TTA-AAAT-T-AA
1 TTATAAATATAAA
771042 -TATAAATATAAAAA
1 TTATAAATAT--AAA
771056 TT-TAAATAT-AA
1 TTATAAATATAAA
771067 TTATAATATATTAAAA
1 TTATAA-ATA-T-AAA
*
771083 TATATAAATAT-TA
1 T-TATAAATATAAA
771096 TT-TAAATATA
1 TTATAAATATA
771106 TAAATCATCA
Statistics
Matches: 70, Mismatches: 1, Indels: 30
0.69 0.01 0.30
Matches are distributed among these distances:
9 3 0.04
10 9 0.13
11 16 0.23
12 4 0.06
13 10 0.14
14 15 0.21
15 2 0.03
16 6 0.09
17 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTATAAATATAAA
Found at i:771044 original size:27 final size:25
Alignment explanation
Indices: 771012--771110 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 25
771002 AAAATTTATA
*
771012 TAATATAAATTATAAATATATTAAAAT
1 TAATATAAA-TATAAAAAT-TTAAAAT
771039 TAATATAAATATAAAAATTT-AAAT
1 TAATATAAATATAAAAATTTAAAAT
*
771063 ATAATTATAATATATTAAAATATATAAATAT
1 -TAA-TATAA-ATA-TAAAA-ATTTAAA-AT
* *
771094 T-ATTTAAATATATAAAT
1 TAATATAAATATAAAAAT
771111 CATCAAATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
24 4 0.07
25 7 0.11
26 17 0.28
27 15 0.25
28 9 0.15
29 4 0.07
30 3 0.05
31 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATATAAATATAAAAATTTAAAAT
Found at i:771050 original size:18 final size:17
Alignment explanation
Indices: 771000--771095 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 17
770990 AAATATATTT
771000 TTAAAATT-TATATAATA
1 TTAAAATTATATA-AATA
771017 -T-AAATTATA-AATATA
1 TTAAAATTATATAA-ATA
771032 TTAAAATTAATATAAATA
1 TTAAAATT-ATATAAATA
*
771050 -TAAAA--ATTTAAATA
1 TTAAAATTATATAAATA
*
771064 -T--AATTATA-ATATA
1 TTAAAATTATATAAATA
771077 TTAAAA-TATATAAATA
1 TTAAAATTATATAAATA
771093 TTA
1 TTA
771096 TTTAAATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 25
0.68 0.04 0.27
Matches are distributed among these distances:
12 2 0.03
13 4 0.06
14 13 0.21
15 13 0.21
16 13 0.21
17 10 0.16
18 6 0.10
19 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAATTATATAAATA
Found at i:771106 original size:21 final size:22
Alignment explanation
Indices: 771013--771107 Score: 67
Period size: 20 Copynumber: 4.4 Consensus size: 22
771003 AAATTTATAT
* *
771013 AATATAAATTATAAATATATTAA
1 AATATATATTAT-AATATATTTA
* *
771036 AATTAATATAAATATAA-AAATTTA
1 AA-T-ATAT-ATTATAATATATTTA
771060 AATATA-ATTATAATATA-TTA
1 AATATATATTATAATATATTTA
771080 AA-ATATA-TA-AATATTATTTA
1 AATATATATTATAATA-TATTTA
771100 AATATATA
1 AATATATA
771108 AATCATCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
18 4 0.07
19 7 0.12
20 17 0.29
21 7 0.12
22 3 0.05
23 3 0.05
24 8 0.14
25 5 0.09
26 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATATTATAATATATTTA
Found at i:772744 original size:17 final size:16
Alignment explanation
Indices: 772724--772757 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
772714 TGTATTTGAA
772724 TCAAAATATTACTAAAT
1 TCAAAA-ATTACTAAAT
*
772741 TCAATAATTACTAAAT
1 TCAAAAATTACTAAAT
772757 T
1 T
772758 TTATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
TCAAAAATTACTAAAT
Found at i:773078 original size:24 final size:25
Alignment explanation
Indices: 773032--773079 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
773022 ACATAATGAA
*
773032 AAGCATTAAACATAGTTACAAACAT
1 AAGCATTAAACATAATTACAAACAT
* *
773057 AAGCA-TAAGCATAATTATAAACA
1 AAGCATTAAACATAATTACAAACA
773080 CAACGGTGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (25 bp):
AAGCATTAAACATAATTACAAACAT
Found at i:775897 original size:25 final size:25
Alignment explanation
Indices: 775852--775900 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
775842 TTTTAATTTA
* *
775852 TATAAAATGTAATACGTAAATTAAT
1 TATAAAATATAATACATAAATTAAT
775877 TATAAAATATAATA-ATCAAATTAA
1 TATAAAATATAATACAT-AAATTAA
775901 AATAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
TATAAAATATAATACATAAATTAAT
Found at i:776493 original size:57 final size:57
Alignment explanation
Indices: 776422--776532 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 57
776412 GTCGATCTAC
* *
776422 TTCTAATTGTTGTTGCCAATTATTACAGTTGCTGTTAAGTTTAGTAGTTTAGTTACT
1 TTCTAATTGCTGTTGCCAATTATTACAGTTGCTGTTAAGTTTAGTACTTTAGTTACT
* *
776479 TTCTAATTGCTGTTGTCGATTATTACAGTTGCTGTTAAGTTTAGTACTTTAGTT
1 TTCTAATTGCTGTTGCCAATTATTACAGTTGCTGTTAAGTTTAGTACTTTAGTT
776533 GCTGGTAGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.50
Consensus pattern (57 bp):
TTCTAATTGCTGTTGCCAATTATTACAGTTGCTGTTAAGTTTAGTACTTTAGTTACT
Found at i:776585 original size:17 final size:18
Alignment explanation
Indices: 776565--776598 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
776555 TTTAATTTTA
776565 TTTTGTT-TTTTATTAAG
1 TTTTGTTATTTTATTAAG
*
776582 TTTTGTTATTTTTTTAA
1 TTTTGTTATTTTATTAA
776599 ATAGGTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTTGTTATTTTATTAAG
Found at i:776641 original size:45 final size:46
Alignment explanation
Indices: 776592--776687 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 46
776582 TTTTGTTATT
*
776592 TTTTTAAATAG-GTTTTAATT-GAGTATGGGTTTAAATTTATAT-AGA
1 TTTTTAAATAGAGTTTTAATTAG-GTATGAGTTTAAATTTATATGA-A
* *
776637 TTTTT-AATTGAGTTTTAATTAGGTTTGAGTTTAAATTTATATGAA
1 TTTTTAAATAGAGTTTTAATTAGGTATGAGTTTAAATTTATATGAA
776682 TTTTTA
1 TTTTTA
776688 GTTTATTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
44 4 0.09
45 38 0.86
46 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (46 bp):
TTTTTAAATAGAGTTTTAATTAGGTATGAGTTTAAATTTATATGAA
Found at i:776838 original size:22 final size:21
Alignment explanation
Indices: 776803--776901 Score: 60
Period size: 22 Copynumber: 4.6 Consensus size: 21
776793 CATATTTCAA
776803 TAATTAA--AAATCGATCTAAT
1 TAATTAATTAAATCGAT-TAAT
*
776823 TAATTAATTAAATCGATTATT
1 TAATTAATTAAATCGATTAAT
* ** *
776844 TAAATTGATTAAA-AAATAAAT
1 T-AATTAATTAAATCGATTAAT
**
776865 TAAATTAATTAAATTAATTAAATT
1 T-AATTAATTAAATCGATT-AA-T
776889 TAATTTAATTAAA
1 TAA-TTAATTAAA
776902 ATTTTCAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
20 7 0.11
21 20 0.32
22 21 0.33
23 4 0.06
24 11 0.17
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
TAATTAATTAAATCGATTAAT
Found at i:776869 original size:9 final size:9
Alignment explanation
Indices: 776857--776900 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
776847 ATTGATTAAA
*
776857 AAATAAATT
1 AAATTAATT
776866 AAATTAATT
1 AAATTAATT
776875 AAATTAATT
1 AAATTAATT
776884 AAATTTAATT
1 AAA-TTAATT
*
776894 TAATTAA
1 AAATTAA
776901 AATTTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATTAATT
Found at i:776870 original size:5 final size:5
Alignment explanation
Indices: 776860--776901 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
776850 GATTAAAAAA
* *
776860 TAAAT TAAAT T-AAT TAAAT T-AAT TAAAT TTAAT TTAAT TAAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAA
776902 ATTTTCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 8 0.24
5 25 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TAAAT
Found at i:776896 original size:15 final size:15
Alignment explanation
Indices: 776841--776901 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
776831 TAAATCGATT
*
776841 ATTTAAATTGATTAAA
1 ATTTAAATTAATT-AA
**
776857 AAATAAATTAAATT-A
1 ATTTAAATT-AATTAA
776872 A-TTAAATTAATTAA
1 ATTTAAATTAATTAA
*
776886 ATTTAATTTAATTAA
1 ATTTAAATTAATTAA
776901 A
1 A
776902 ATTTTCAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 4 0.11
14 8 0.22
15 15 0.41
16 7 0.19
17 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTTAAATTAATTAA
Found at i:780681 original size:34 final size:34
Alignment explanation
Indices: 780642--780710 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
780632 ATATGGGGTA
*
780642 GGATTAAGTCATATACTAAAGTTAAATAGAAGGG
1 GGATTAAGTCATATACTAAAATTAAATAGAAGGG
780676 GGATTAAGTCATATACTAAAATTAAATAGAAGGG
1 GGATTAAGTCATATACTAAAATTAAATAGAAGGG
780710 G
1 G
780711 CAATCCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (34 bp):
GGATTAAGTCATATACTAAAATTAAATAGAAGGG
Found at i:781683 original size:17 final size:17
Alignment explanation
Indices: 781661--781694 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
781651 ATCAAAATGA
781661 TTATTATTCTATTATGC
1 TTATTATTCTATTATGC
781678 TTATTATTCTATTATGC
1 TTATTATTCTATTATGC
781695 ATCAAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (17 bp):
TTATTATTCTATTATGC
Found at i:784058 original size:39 final size:39
Alignment explanation
Indices: 784007--784084 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
783997 TGTTACATGA
* *
784007 TTATATAAATTTA-ATTAATGTATCAAATAAAATATAAAT
1 TTATATAAATTTATATTAATGTA-AAAATAAAATAAAAAT
* *
784046 TTATATATATTTATATTAATTTAAAAATAAAATAAAAAT
1 TTATATAAATTTATATTAATGTAAAAATAAAATAAAAAT
784085 CATGAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 26 0.76
40 8 0.24
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
TTATATAAATTTATATTAATGTAAAAATAAAATAAAAAT
Found at i:784288 original size:3 final size:3
Alignment explanation
Indices: 784280--784305 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
784270 CTTTTGAATA
784280 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
784306 GTTTTTACAC
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:784793 original size:22 final size:21
Alignment explanation
Indices: 784745--784793 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
784735 TGAACACAAA
784745 AATATTATTTTATATATTATT
1 AATATTATTTTATATATTATT
* *
784766 ATTATTACTTTTAT-TAATTTTT
1 AATATTA-TTTTATAT-ATTATT
784788 AATATT
1 AATATT
784794 TACTAAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTATTTTATATATTATT
Found at i:784930 original size:24 final size:23
Alignment explanation
Indices: 784905--784965 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
784895 TCCATTATTA
784905 ATTATTAATTTTATTATTATAAT
1 ATTATTAATTTTATTATTATAAT
* * *
784928 A--ATTAATTTCATTTTTATCATT
1 ATTATTAATTTTATTATTAT-AAT
*
784950 ATTTTTAATTTTATTA
1 ATTATTAATTTTATTA
784966 GAATTAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 15 0.52
22 3 0.10
23 1 0.03
24 10 0.34
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTATTAATTTTATTATTATAAT
Found at i:784932 original size:21 final size:21
Alignment explanation
Indices: 784898--784945 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
784888 TATATACTCC
* *
784898 ATTATTAATTATTAATTTTATT
1 ATTA-TAATAATTAATTTCATT
784920 ATTATAATAATTAATTTCATT
1 ATTATAATAATTAATTTCATT
*
784941 TTTAT
1 ATTAT
784946 CATTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTATAATAATTAATTTCATT
Found at i:785035 original size:2 final size:2
Alignment explanation
Indices: 785028--785063 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
785018 AACTAAGAAA
785028 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
785064 TAAAATGCAA
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:792291 original size:15 final size:15
Alignment explanation
Indices: 792267--792298 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
792257 ATACCAAATA
*
792267 TAAAATTTTAATTTT
1 TAAAAATTTAATTTT
792282 TAAAAATTTAATTTT
1 TAAAAATTTAATTTT
792297 TA
1 TA
792299 CGAAACTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAAAATTTAATTTT
Found at i:795211 original size:33 final size:33
Alignment explanation
Indices: 795172--795253 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
795162 AAAAATATAA
* * *
795172 ATATAATATAAATATATAAACATTTTAAATTTT
1 ATATAATATAAATATATAAACATGTCAAAATTT
* * *
795205 ATATAATATGAAT-TATTAATATGTCAAAATTT
1 ATATAATATAAATATATAAACATGTCAAAATTT
795237 ATATAAATATAAA-ATAT
1 ATAT-AATATAAATATAT
795254 TTTATATATG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 18 0.45
33 22 0.55
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (33 bp):
ATATAATATAAATATATAAACATGTCAAAATTT
Found at i:801576 original size:14 final size:15
Alignment explanation
Indices: 801547--801576 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
801537 TGTATGGTTA
801547 TTTTCCTTTATTTGC
1 TTTTCCTTTATTTGC
801562 TTTTCCTTT-TTTGC
1 TTTTCCTTTATTTGC
801576 T
1 T
801577 GAAAGAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.03, C:0.20, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTTCCTTTATTTGC
Found at i:805007 original size:21 final size:20
Alignment explanation
Indices: 804983--805035 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
804973 TTAAAATTTA
** *
804983 TTTTCTTTCATTTTTTCACT
1 TTTTCTTTCAACTTTTAACT
* *
805003 CTTTTTTTTTAACTTTTAACT
1 -TTTTCTTTCAACTTTTAACT
805024 TTTTCTTTCAAC
1 TTTTCTTTCAAC
805036 CAAACATACT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCTTTCAACTTTTAACT
Done.