Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 10 of 132
Found at i:2654203 original size:18 final size:18
Alignment explanation
Indices: 2654172--2654206 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2654162 ATTATATTTA
**
2654172 AAAAAATTGTTTTTAAAT
1 AAAAAATTAATTTTAAAT
2654190 AAAAAATTAATTTTAAA
1 AAAAAATTAATTTTAAA
2654207 AAATTAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAAAATTAATTTTAAAT
Found at i:2661022 original size:15 final size:14
Alignment explanation
Indices: 2660995--2661024 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2660985 TTACATGCTT
2660995 TAATATTTATATTA
1 TAATATTTATATTA
2661009 TAATATTATATATTA
1 TAATATT-TATATTA
2661024 T
1 T
2661025 TATAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:2661057 original size:21 final size:21
Alignment explanation
Indices: 2661019--2661059 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2661009 TAATATTATA
*
2661019 TATTATTATAAATTCAATTTT
1 TATTATTAAAAATTCAATTTT
2661040 TATT-TTAAAAATTACAATTT
1 TATTATTAAAAATT-CAATTT
2661060 AATTTTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTAAAAATTCAATTTT
Found at i:2661064 original size:20 final size:20
Alignment explanation
Indices: 2661028--2661065 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2661018 ATATTATTAT
*
2661028 AAATTCAATTTTTATTTTAA
1 AAATTCAATTTTAATTTTAA
2661048 AAATTACAA-TTTAATTTT
1 AAATT-CAATTTTAATTTT
2661066 TACCCTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTCAATTTTAATTTTAA
Found at i:2671088 original size:20 final size:20
Alignment explanation
Indices: 2671063--2671106 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2671053 TGAAAGATGG
2671063 ATAAATTAAAAAAGAA-ATAA
1 ATAAA-TAAAAAAGAATATAA
*
2671083 ATAAATAAAATAGAATATAA
1 ATAAATAAAAAAGAATATAA
2671103 ATAA
1 ATAA
2671107 GAAAAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
ATAAATAAAAAAGAATATAA
Found at i:2671112 original size:20 final size:17
Alignment explanation
Indices: 2671070--2671114 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
2671060 TGGATAAATT
2671070 AAAAAAGAAATAAATAA
1 AAAAAAGAAATAAATAA
2671087 ATAAAATAGAATATAAATAA
1 A-AAAA-AGAA-ATAAATAA
*
2671107 GAAAAAGA
1 AAAAAAGA
2671115 TAAGGCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 8 0.33
20 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (17 bp):
AAAAAAGAAATAAATAA
Found at i:2675662 original size:186 final size:182
Alignment explanation
Indices: 2675295--2675664 Score: 491
Period size: 186 Copynumber: 2.0 Consensus size: 182
2675285 TATATATATA
2675295 GTGAGAGAGAAAATTAATTATTTATGAAAAATTATTTAAATTTTAAGGATCAAATTAAAATTTTC
1 GTGAGAGAGAAAATTAATTATTTATGAAAAATTATTTAAATTTTAAGGATCAAATTAAAA-TTTC
*
2675360 TTTTACTAAATTCAAGAATTAAATATTAGTTTACCTCGATGAAAAACCACCCTATGTTTTCGTGC
65 TTTTACTAAATTCAAGAATTAAATATTAGTTTACCTCGATG--AAA-CACCCTATATTTTCGTGC
* *
2675425 ATTGACTTGAAACTTATATAGTAGTAGTTAATACAACTAATTATATATGTATGCAT
127 AGTGACTTGAAACTTATATAGCAGTAGTTAATACAACTAATTATATATGTATGCAT
* * *
2675481 GTGAGATAGAAAATTAATTATTTATGAAAATTTATTTAAATTTTAAGGATCAAATT-GAA-TT-T
1 GTGAGAGAGAAAATTAATTATTTATGAAAAATTATTTAAATTTTAAGGATCAAATTAAAATTTCT
* * * *
2675543 TTTACTAAATTCAAGAATTAAATATTAGTTTACTTCAGGTG-GA-ACCC-ATATTTTGGTGCAGT
66 TTTACTAAATTCAAGAATTAAATATTAGTTTACCTC-GATGAAACACCCTATATTTTCGTGCAGT
* * *
2675605 GGCTTGAAACTTATATAGCAGCAGTAGTTAATACAACTATATGTATGTATGTATGTAT
130 GACTTGAAACTTATAT---AGCAGTAGTTAATACAACTA-AT-TATATATGTATGCAT
2675663 GT
1 GT
2675665 ATTGTTTATG
Statistics
Matches: 165, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
177 27 0.16
178 4 0.02
180 20 0.12
181 2 0.01
182 51 0.31
183 5 0.03
185 2 0.01
186 54 0.33
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (182 bp):
GTGAGAGAGAAAATTAATTATTTATGAAAAATTATTTAAATTTTAAGGATCAAATTAAAATTTCT
TTTACTAAATTCAAGAATTAAATATTAGTTTACCTCGATGAAACACCCTATATTTTCGTGCAGTG
ACTTGAAACTTATATAGCAGTAGTTAATACAACTAATTATATATGTATGCAT
Found at i:2675804 original size:3 final size:3
Alignment explanation
Indices: 2675796--2675826 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2675786 GCAAGATAAT
2675796 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
2675827 CCATGCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:2678304 original size:26 final size:24
Alignment explanation
Indices: 2678275--2678322 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
2678265 TTAAGATGAT
2678275 TATATAAAAAATTAATAAATATATAA
1 TATATAAAAAATT-ATAAA-ATATAA
* *
2678301 TATATATAATATTATAAAATAT
1 TATATAAAAAATTATAAAATAT
2678323 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 5 0.25
26 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TATATAAAAAATTATAAAATATAA
Found at i:2683660 original size:3 final size:3
Alignment explanation
Indices: 2683644--2683695 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
2683634 GAAACTTGGG
*
2683644 CAT CAT CAAT -AT CAT CAT C-T CCCT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT C-AT CAT CAT CAT CAT -CAT CAT CAT CAT CAT CAT CAT CAT
2683689 CAT CAT C
1 CAT CAT C
2683696 GGTATCCTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2687698 original size:99 final size:100
Alignment explanation
Indices: 2687595--2687781 Score: 220
Period size: 99 Copynumber: 1.9 Consensus size: 100
2687585 ACTATTCAAA
* * *
2687595 AAATA-ATAATATTTTAAT-AGTTTAATAAATATTAAATTAAATTAAATATTTATTTTAAT-AGT
1 AAATATATAATATTTTAATAAGATT--T-AATATTAAATTAAATTAAATATTTATTATAATAAAT
*
2687657 ATT-TAATAATTTAATGTTAAAGTGTTATATACAAGAT
63 ATTATAATAATTTAATATTAAAGTGTTATATACAAGAT
* * * * *
2687694 AAATATTTTATTATTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATTATGATAAATAT
1 AAATA-TATAATATTTTAATAAGATTTAATATTAAATTAAATTAAATATTTATTATAATAAATAT
*
2687759 TATATTAATTTAATATTAAAGTG
65 TATAATAATTTAATATTAAAGTG
2687782 ATTAAATTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
99 33 0.45
100 6 0.08
101 30 0.41
102 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (100 bp):
AAATATATAATATTTTAATAAGATTTAATATTAAATTAAATTAAATATTTATTATAATAAATATT
ATAATAATTTAATATTAAAGTGTTATATACAAGAT
Found at i:2687734 original size:12 final size:12
Alignment explanation
Indices: 2687717--2687778 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
2687707 TTTTAATAAG
2687717 ATTTAATATTAA
1 ATTTAATATTAA
2687729 ATTTAAT-TTAA
1 ATTTAATATTAA
*
2687740 TATTTATTATGATAA
1 -ATTTAATAT--TAA
2687755 ATATT-ATATT-A
1 AT-TTAATATTAA
2687766 ATTTAATATTAA
1 ATTTAATATTAA
2687778 A
1 A
2687779 GTGATTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
10 2 0.05
11 12 0.29
12 16 0.39
13 1 0.02
14 5 0.12
15 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:2687788 original size:32 final size:32
Alignment explanation
Indices: 2687712--2687795 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 32
2687702 TATTATTTTA
*
2687712 ATAA-GATTTAATATTAAATTTAATTTAATATTT
1 ATAATGATTAAATATT-AA-TTAATTTAATATTT
*
2687745 ATTATGA-TAAATATTATATTAATTTAATA-TT
1 ATAATGATTAAATATTA-ATTAATTTAATATTT
2687776 A-AAGTGATTAAAT-TTAATTA
1 ATAA-TGATTAAATATTAATTA
2687796 TAGTTGAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
30 5 0.11
31 9 0.20
32 17 0.39
33 11 0.25
34 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
ATAATGATTAAATATTAATTAATTTAATATTT
Found at i:2688738 original size:22 final size:23
Alignment explanation
Indices: 2688713--2688755 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2688703 TAATAATATC
*
2688713 TTTTATTC-CCCAAATTATAAGT
1 TTTTATTCGCCCAAACTATAAGT
*
2688735 TTTTTTTCGCCCAAACTATAA
1 TTTTATTCGCCCAAACTATAA
2688756 AAGTTACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (23 bp):
TTTTATTCGCCCAAACTATAAGT
Found at i:2701391 original size:13 final size:13
Alignment explanation
Indices: 2701373--2701397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2701363 TTTAACATTA
2701373 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
2701386 CTTTTGAAAAGT
1 CTTTTGAAAAGT
2701398 ATCGTGGAAA
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:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:2707307 original size:20 final size:20
Alignment explanation
Indices: 2707282--2707337 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2707272 TATTCTAGAA
2707282 TTATAAAAAACATAAAAAAT
1 TTATAAAAAACATAAAAAAT
* *
2707302 TTATAAAATATAT-AAAAAT
1 TTATAAAAAACATAAAAAAT
* *
2707321 TAATTAAAAACCATAAA
1 TTA-TAAAAAACATAAA
2707338 TTTTATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.29
20 18 0.64
21 2 0.07
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
TTATAAAAAACATAAAAAAT
Found at i:2707368 original size:32 final size:31
Alignment explanation
Indices: 2707310--2707369 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
2707300 ATTTATAAAA
*
2707310 TATATAAAAATTAATTAAAAACCATAAATTT
1 TATAAAAAAATTAATTAAAAACCATAAATTT
* *
2707341 TATAAAAATAATTTATTAAAAATCATAAA
1 TATAAAAA-AATTAATTAAAAACCATAAA
2707370 AATTAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (31 bp):
TATAAAAAAATTAATTAAAAACCATAAATTT
Found at i:2707380 original size:32 final size:33
Alignment explanation
Indices: 2707318--2707386 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
2707308 AATATATAAA
** *
2707318 AATTAATTAAAAACCATAAATTTTA-TAAAAAT
1 AATTAATTAAAAACCATAAAAATTAGAAAAAAT
* *
2707350 AATTTATTAAAAATCATAAAAATTAGAAAAAAT
1 AATTAATTAAAAACCATAAAAATTAGAAAAAAT
2707383 AATT
1 AATT
2707387 CATAAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (33 bp):
AATTAATTAAAAACCATAAAAATTAGAAAAAAT
Found at i:2707611 original size:9 final size:9
Alignment explanation
Indices: 2707599--2707658 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 9
2707589 TTTCATAAAA
2707599 TTTTATTATT
1 TTTTATTA-T
2707609 TTTTAATTAAT
1 TTTT-ATT-AT
*
2707620 TTCTATTATT
1 TTTTATTA-T
*
2707630 TTTTATAAT
1 TTTTATTAT
2707639 TTTTA-TAT
1 TTTTATTAT
2707647 TTTTA-TAT
1 TTTTATTAT
2707655 TTTT
1 TTTT
2707659 GTATAACTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 14 0.33
9 7 0.16
10 14 0.33
11 7 0.16
12 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATTAT
Found at i:2707612 original size:10 final size:9
Alignment explanation
Indices: 2707599--2707663 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 9
2707589 TTTCATAAAA
2707599 TTTTATTATT
1 TTTTA-TATT
2707609 TTTTA-ATT
1 TTTTATATT
2707617 AATTTCTATTATT
1 --TTT-TA-TATT
*
2707630 TTTTATAAT
1 TTTTATATT
2707639 TTTTATA-T
1 TTTTATATT
2707647 TTTTATATT
1 TTTTATATT
2707656 TTTGTATA
1 TTT-TATA
2707664 ACTCCATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
8 11 0.23
9 14 0.30
10 14 0.30
11 5 0.11
13 3 0.06
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTATATT
Found at i:2707628 original size:21 final size:18
Alignment explanation
Indices: 2707597--2707650 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 18
2707587 AATTTCATAA
2707597 AATTTTATTATTTTTTAATT
1 AATTTTATTATTTTTT-A-T
2707617 AATTTCTATTATTTTTTAT
1 AATTT-TATTATTTTTTAT
2707636 AATTTT-TATATTTTT
1 AATTTTAT-TATTTTT
2707651 ATATTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.03
18 8 0.25
19 6 0.19
20 6 0.19
21 11 0.34
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
AATTTTATTATTTTTTAT
Found at i:2715734 original size:23 final size:22
Alignment explanation
Indices: 2715708--2715777 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
2715698 TTCATTTAAC
2715708 TTAATCGAACATGTTCACGAACA
1 TTAAT-GAACATGTTCACGAACA
*
2715731 TTAAATGAACATGTTCATGAACA
1 TT-AATGAACATGTTCACGAACA
* *
2715754 TATAATTGAAAACGTTCACGAACA
1 T-TAA-TGAACATGTTCACGAACA
2715778 ATGTTAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (22 bp):
TTAATGAACATGTTCACGAACA
Found at i:2715770 original size:24 final size:23
Alignment explanation
Indices: 2715720--2715777 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
2715710 AATCGAACAT
* *
2715720 GTTCACGAACATTAAATGAACAT
1 GTTCACGAACATTAAATGAAAAC
* *
2715743 GTTCATGAACATATAATTGAAAAC
1 GTTCACGAACAT-TAAATGAAAAC
2715767 GTTCACGAACA
1 GTTCACGAACA
2715778 ATGTTAATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (23 bp):
GTTCACGAACATTAAATGAAAAC
Found at i:2719400 original size:36 final size:36
Alignment explanation
Indices: 2719354--2719423 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
2719344 TTGAAGAGAA
*
2719354 AAAAAAGAAGGAGAAGGA-TTAAGAAGAAGAAAAAGG
1 AAAAAAGAAGGAGAAGGAGTGAA-AAGAAGAAAAAGG
* **
2719390 AAAAGAGAAGGTTAAGGAGTGAAAAGAAGAAAAA
1 AAAAAAGAAGGAGAAGGAGTGAAAAGAAGAAAAA
2719424 TTACCATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 26 0.90
37 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.30, T:0.07
Consensus pattern (36 bp):
AAAAAAGAAGGAGAAGGAGTGAAAAGAAGAAAAAGG
Found at i:2722301 original size:18 final size:18
Alignment explanation
Indices: 2722278--2722326 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 18
2722268 TATGATGATA
2722278 TATATGTGATGAACAATG
1 TATATGTGATGAACAATG
2722296 TATATGTGAAATATGAACAATG
1 TATATGTG----ATGAACAATG
2722318 TATATGTGA
1 TATATGTGA
2722327 AATATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 9 0.33
22 18 0.67
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (18 bp):
TATATGTGATGAACAATG
Found at i:2722311 original size:22 final size:22
Alignment explanation
Indices: 2722286--2722331 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2722276 TATATATGTG
2722286 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
2722308 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
2722330 AT
1 AT
2722332 TATATGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (22 bp):
ATGAACAATGTATATGTGAAAT
Found at i:2722493 original size:6 final size:6
Alignment explanation
Indices: 2722482--2722520 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
2722472 TGATCAAAAT
*
2722482 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
2722521 TATGAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:2732646 original size:21 final size:20
Alignment explanation
Indices: 2732631--2732682 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
2732621 AACATTTTTA
2732631 TAAAATTTTAATACATATTT
1 TAAAATTTTAATACATATTT
*
2732651 TAAATTTTTATATGACA-ATTT
1 TAAAATTTTA-AT-ACATATTT
2732672 TGCAAAATTTT
1 T--AAAATTTT
2732683 GAATCGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.35
21 7 0.27
22 3 0.12
23 7 0.27
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (20 bp):
TAAAATTTTAATACATATTT
Found at i:2739362 original size:6 final size:6
Alignment explanation
Indices: 2739348--2739400 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
2739338 TTCCTAGTGT
* * *
2739348 ACAACA ACAAGA AC-ATA ACAATGGA ACAAGA TCAAGA ACAAGA ACAAGA
1 ACAAGA ACAAGA ACAAGA ACAA--GA ACAAGA ACAAGA ACAAGA ACAAGA
2739397 ACAA
1 ACAA
2739401 AGCCGGCCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 4 0.10
6 30 0.77
8 5 0.13
ACGTcount: A:0.62, C:0.19, G:0.13, T:0.06
Consensus pattern (6 bp):
ACAAGA
Found at i:2740305 original size:2 final size:2
Alignment explanation
Indices: 2740298--2740323 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2740288 GTTCTTAAGC
2740298 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
2740324 CTTGAGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2742906 original size:26 final size:26
Alignment explanation
Indices: 2742864--2742915 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2742854 TTTTTGAATT
* *
2742864 AATTCAATTTGATTCGAAT-CTAAAA
1 AATTCAAATTGAGTCGAATGCTAAAA
*
2742889 AATTCCAAATTGAGTCGATTGCTAAAA
1 AATT-CAAATTGAGTCGAATGCTAAAA
2742916 TAGGATTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (26 bp):
AATTCAAATTGAGTCGAATGCTAAAA
Found at i:2746556 original size:28 final size:28
Alignment explanation
Indices: 2746516--2746572 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2746506 TTCTAGCTTC
*
2746516 ACCCTTGATTTTACCATATGCTATTTGT
1 ACCCTTGAATTTACCATATGCTATTTGT
2746544 ACCCTTGAATTTACCATATGCTATTTGT
1 ACCCTTGAATTTACCATATGCTATTTGT
2746572 A
1 A
2746573 AAATTAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.44
Consensus pattern (28 bp):
ACCCTTGAATTTACCATATGCTATTTGT
Found at i:2765284 original size:51 final size:51
Alignment explanation
Indices: 2765229--2765351 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
2765219 TCCTCTTCTG
* *
2765229 GGTTCTGCTTTAAACCATTGGCACTTC-CCTTAGGTGTATGCTGCTCTCCTC
1 GGTTCTGCTTTAAACCATTGGCACTTCTCC-TAGGTGCACGCTGCTCTCCTC
* * *
2765280 GGTTCTGCTTTAAACCATTGGCGCTTCTCCTAGGTGCACGCTTCTCTCCTG
1 GGTTCTGCTTTAAACCATTGGCACTTCTCCTAGGTGCACGCTGCTCTCCTC
*
2765331 GGTTCTTCTTTAAACCATTGG
1 GGTTCTGCTTTAAACCATTGG
2765352 AAACCGAGAC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 63 0.97
52 2 0.03
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.37
Consensus pattern (51 bp):
GGTTCTGCTTTAAACCATTGGCACTTCTCCTAGGTGCACGCTGCTCTCCTC
Found at i:2767322 original size:6 final size:6
Alignment explanation
Indices: 2767311--2767337 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2767301 TTTTTTTTCT
2767311 TCCTTC TCCTTC TCCTTC TCCTTC TCC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCC
2767338 CTCTTCCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTTC
Found at i:2767480 original size:81 final size:81
Alignment explanation
Indices: 2767392--2767581 Score: 308
Period size: 81 Copynumber: 2.3 Consensus size: 81
2767382 GGTCAAATTA
*
2767392 TTGCTCGACTCAGTAGCTTTAGATTTCTTCTTCAACTCAGTAGCTGTAGATTTCTTGCTCGACTC
1 TTGCTCGACTCAGTAGCTTTAGATTTCTTCTTCAACTCAGTAGCAGTAGATTTCTTGCTCGACTC
2767457 AGTAGCAGTAGATTTC
66 AGTAGCAGTAGATTTC
** * ** * *
2767473 TTGCTCGACTCAGTAGCAGTAGATTTCTTGTTTGACTCAGTAGCAGTAGATTTCTTGTTTGACTC
1 TTGCTCGACTCAGTAGCTTTAGATTTCTTCTTCAACTCAGTAGCAGTAGATTTCTTGCTCGACTC
2767538 AGTAGCAGTAGATTTC
66 AGTAGCAGTAGATTTC
2767554 TTGCTCGACTCAGTAGCTTTAGATTTCT
1 TTGCTCGACTCAGTAGCTTTAGATTTCT
2767582 CTTGTGATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 99 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (81 bp):
TTGCTCGACTCAGTAGCTTTAGATTTCTTCTTCAACTCAGTAGCAGTAGATTTCTTGCTCGACTC
AGTAGCAGTAGATTTC
Found at i:2767493 original size:33 final size:27
Alignment explanation
Indices: 2767392--2767581 Score: 274
Period size: 27 Copynumber: 7.0 Consensus size: 27
2767382 GGTCAAATTA
**
2767392 TTGCTCGACTCAGTAGCTTTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
* *
2767419 TT-CTTCAACTCAGTAGCTGTAGATTTC
1 TTGC-TCGACTCAGTAGCAGTAGATTTC
2767446 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2767473 TTGCTCGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
* *
2767500 TTGTTTGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
* *
2767527 TTGTTTGACTCAGTAGCAGTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
**
2767554 TTGCTCGACTCAGTAGCTTTAGATTTC
1 TTGCTCGACTCAGTAGCAGTAGATTTC
2767581 T
1 T
2767582 CTTGTGATTT
Statistics
Matches: 151, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
26 1 0.01
27 149 0.99
28 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (27 bp):
TTGCTCGACTCAGTAGCAGTAGATTTC
Found at i:2768979 original size:38 final size:38
Alignment explanation
Indices: 2768937--2769033 Score: 149
Period size: 38 Copynumber: 2.6 Consensus size: 38
2768927 TGATTAAAGA
* * *
2768937 TTAGCTGAGTTAAGCTTACAATCTCTAGATTATTTGGG
1 TTAGCTGAGTTAAGCTCACAATCTCTAGATCATTTGAG
*
2768975 TTAGCTGAGTTAAGCTCGCAATCTCTAGATCATTTGAG
1 TTAGCTGAGTTAAGCTCACAATCTCTAGATCATTTGAG
*
2769013 TTAGTTGAGTTAAGCTCACAA
1 TTAGCTGAGTTAAGCTCACAA
2769034 CTTCAAAACA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (38 bp):
TTAGCTGAGTTAAGCTCACAATCTCTAGATCATTTGAG
Found at i:2769094 original size:105 final size:105
Alignment explanation
Indices: 2768973--2769247 Score: 370
Period size: 105 Copynumber: 2.6 Consensus size: 105
2768963 AGATTATTTG
* * * * * *
2768973 GGTTAGCTGAGTTAAGCTCGCAATCTCTAGATCATTTGAGTTAGTTGAGTTAAGCTCACAACTTC
1 GGTTAGCTGAGTTAAGCTCGCAACCTCCAGATTATTTGAGTTAGCTGAGTTAAACTCGCAACTTC
* * *
2769038 AAAACAACTCACAGACCTACGATCTCAGCTGATTATTAAA
66 AAAACAACTCACAGACCTACGATCCCAACTGATGATTAAA
* *
2769078 GGTTAGTTGAGTTAAGCTCGCAACCTCCAGATTATTTAAGTTAGCTGAGTTAAACTCGCAACTTC
1 GGTTAGCTGAGTTAAGCTCGCAACCTCCAGATTATTTGAGTTAGCTGAGTTAAACTCGCAACTTC
* ** * *
2769143 GAAACAGTTCACAGACTTACGTTCCCAACTGATGATTAAA
66 AAAACAACTCACAGACCTACGATCCCAACTGATGATTAAA
* * * *
2769183 GGTTAGCTAAGTTAAGCTCGCAACCTCCAAATTATTTGAGTCAGCTAAGTTAAACTCGCAACTTC
1 GGTTAGCTGAGTTAAGCTCGCAACCTCCAGATTATTTGAGTTAGCTGAGTTAAACTCGCAACTTC
2769248 CAAATTATTT
Statistics
Matches: 148, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 148 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (105 bp):
GGTTAGCTGAGTTAAGCTCGCAACCTCCAGATTATTTGAGTTAGCTGAGTTAAACTCGCAACTTC
AAAACAACTCACAGACCTACGATCCCAACTGATGATTAAA
Found at i:2769127 original size:38 final size:37
Alignment explanation
Indices: 2769068--2769286 Score: 134
Period size: 38 Copynumber: 6.0 Consensus size: 37
2769058 GATCTCAGCT
* *
2769068 GATTATTAAAGGTTAGTTGAGTTAAGCTCGCAACCTCCA
1 GATTATTTAA-GTTAGCTGAGTTAAGCTCGCAA-CTCCA
* *
2769107 GATTATTTAAGTTAGCTGAGTTAAACTCGCAACTTC-
1 GATTATTTAAGTTAGCTGAGTTAAGCTCGCAACTCCA
* * * * *
2769143 GA--A---ACAGTTCA-CAGACTTACGTTCCCAACT---
1 GATTATTTA-AGTT-AGCTGAGTTAAGCTCGCAACTCCA
* * *
2769173 GATGATTAAAGGTTAGCTAAGTTAAGCTCGCAACCTCCA
1 GATTATTTAA-GTTAGCTGAGTTAAGCTCGCAA-CTCCA
* * * * *
2769212 AATTATTTGAGTCAGCTAAGTTAAACTCGCAACTTCCA
1 GATTATTTAAGTTAGCTGAGTTAAGCTCGCAAC-TCCA
* *
2769250 AATTATTTGAGTTAGCTGAGTTAAGCTCGCAACTCCA
1 GATTATTTAAGTTAGCTGAGTTAAGCTCGCAACTCCA
2769287 AAACATCTCG
Statistics
Matches: 141, Mismatches: 25, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
30 2 0.01
31 1 0.01
32 18 0.13
33 1 0.01
34 3 0.02
35 15 0.11
36 4 0.03
37 8 0.06
38 74 0.52
39 15 0.11
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (37 bp):
GATTATTTAAGTTAGCTGAGTTAAGCTCGCAACTCCA
Found at i:2769136 original size:143 final size:143
Alignment explanation
Indices: 2768875--2769138 Score: 386
Period size: 143 Copynumber: 1.8 Consensus size: 143
2768865 TAAGGTTAAC
* *
2768875 TGAGTTAAGCTCACAACTTCAAAACAACTCGCGGACCTACATTCCCAACTGATGATTAAAGATTA
1 TGAGTTAAGCTCACAACTTCAAAACAACTCACAGACCTACATTCCCAACTGATGATTAAAGATTA
* * * ** *
2768940 GCTGAGTTAAGCTTACAATCTCTAGATTATTTGGGTTAGCTGAGTTAAGCTCGCAATCTCTAGAT
66 GCTGAGTTAAGCTCACAACCTCCAGATTATTTAAGTTAGCTGAGTTAAACTCGCAATCTCTAGAT
2769005 CATTTGAGTTAGT
131 CATTTGAGTTAGT
* * * *
2769018 TGAGTTAAGCTCACAACTTCAAAACAACTCACAGACCTACGA-TCTCAGCTGATTATTAAAGGTT
1 TGAGTTAAGCTCACAACTTCAAAACAACTCACAGACCTAC-ATTCCCAACTGATGATTAAAGATT
* *
2769082 AGTTGAGTTAAGCTCGCAACCTCCAGATTATTTAAGTTAGCTGAGTTAAACTCGCAA
65 AGCTGAGTTAAGCTCACAACCTCCAGATTATTTAAGTTAGCTGAGTTAAACTCGCAA
2769139 CTTCGAAACA
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
143 105 0.99
144 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (143 bp):
TGAGTTAAGCTCACAACTTCAAAACAACTCACAGACCTACATTCCCAACTGATGATTAAAGATTA
GCTGAGTTAAGCTCACAACCTCCAGATTATTTAAGTTAGCTGAGTTAAACTCGCAATCTCTAGAT
CATTTGAGTTAGT
Found at i:2769366 original size:248 final size:248
Alignment explanation
Indices: 2768864--2769388 Score: 558
Period size: 248 Copynumber: 2.1 Consensus size: 248
2768854 CATCAGATGA
* * *
2768864 TTAAGGTTAACTGAGTTAAGCTCACAACTTCAAAACAACTCGCGGACCTACATTCCCAACTGATG
1 TTAA-GTTAACTGAGTTAAACTCACAACTTCAAAACAACTCACAGACCTACATTCCCAACTGATG
* * * * * * * * *
2768929 ATTAAAGATTAGCTGAGTTAAGCTTACAATCTCTAGATTATTTGGGTTAGCTGAGTTAAGCTCGC
65 ATTAAAGATTAGCTAAGTTAAGCTCACAACCTCCAAATTATTTGAGTCAGCTAAGTTAAACTCGC
* * * *
2768994 AATCTCTAGATCATTTGAGTTAGTTGAGTTAAGCTCACAACTTCAAAACAACTCACAGACCTACG
130 AATCTCCAAATCATTTGAGTTAGCTGAGTTAAGCTCACAACTCCAAAACAACTCACAGACCTACG
* * * * * *
2769059 ATCTCAGCTGATTATTAAAGGTTAGTTGAGTTAAGCTCGCAACCTCCAGATTAT
195 ATCCCAACTAATTATTAAAGGTCAGCTGAGTTAAGATCGCAACCTCCAGATTAT
* * * ** * *
2769113 TTAAGTTAGCTGAGTTAAACTCGCAACTTCGAAACAGTTCACAGACTTACGTTCCCAACTGATGA
1 TTAAGTTAACTGAGTTAAACTCACAACTTCAAAACAACTCACAGACCTACATTCCCAACTGATGA
* *
2769178 TTAAAGGTTAGCTAAGTTAAGCTCGCAACCTCCAAATTATTTGAGTCAGCTAAGTTAAACTCGCA
66 TTAAAGATTAGCTAAGTTAAGCTCACAACCTCCAAATTATTTGAGTCAGCTAAGTTAAACTCGCA
* * * ** *
2769243 A-CTTCCAAATTATTTGAGTTAGCTGAGTTAAGCTCGCAACTCCAAAACATCTC-GTGCACTTAC
131 ATC-TCCAAATCATTTGAGTTAGCTGAGTTAAGCTCACAACTCCAAAACAACTCACAG-ACCTAC
* * * * *
2769306 GTTCCCAACTAATT-TTACTAAGGCTCA-CTGATTTAGGATCGTAACCTCCA-ATTGT
194 GATCCCAACTAATTATTA--AAGG-TCAGCTGAGTTAAGATCGCAACCTCCAGATTAT
*
2769361 TTAAGTTAACTGATTTAATA-TCACAACT
1 TTAAGTTAACTGAGTTAA-ACTCACAACT
2769389 CTTAACAGCA
Statistics
Matches: 225, Mismatches: 45, Indels: 13
0.80 0.16 0.05
Matches are distributed among these distances:
247 5 0.02
248 191 0.85
249 27 0.12
250 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (248 bp):
TTAAGTTAACTGAGTTAAACTCACAACTTCAAAACAACTCACAGACCTACATTCCCAACTGATGA
TTAAAGATTAGCTAAGTTAAGCTCACAACCTCCAAATTATTTGAGTCAGCTAAGTTAAACTCGCA
ATCTCCAAATCATTTGAGTTAGCTGAGTTAAGCTCACAACTCCAAAACAACTCACAGACCTACGA
TCCCAACTAATTATTAAAGGTCAGCTGAGTTAAGATCGCAACCTCCAGATTAT
Found at i:2770617 original size:33 final size:33
Alignment explanation
Indices: 2770579--2770651 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
2770569 TCAGAATATG
2770579 CATTGTCAAACGTACATCTCCTTAATTCACAAC
1 CATTGTCAAACGTACATCTCCTTAATTCACAAC
2770612 CATTGTCAAACGTACATCTCCTTAATTCACAAC
1 CATTGTCAAACGTACATCTCCTTAATTCACAAC
2770645 CATTGTC
1 CATTGTC
2770652 CTGCACTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (33 bp):
CATTGTCAAACGTACATCTCCTTAATTCACAAC
Found at i:2777881 original size:2 final size:2
Alignment explanation
Indices: 2777874--2777914 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2777864 GCAAAAGTTG
2777874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2777915 GTTATCTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2778526 original size:78 final size:80
Alignment explanation
Indices: 2778436--2778588 Score: 206
Period size: 80 Copynumber: 1.9 Consensus size: 80
2778426 TTTTTAAAAT
* * *
2778436 AATTTGACAAAAAAAGTTA-AAAATTGAAGTGAT-AAAAATATTAGTATC-AAGTTATAAAATAT
1 AATTTGACAAAAAAA-TTATAAAATTGAAGTGATAAAAAAGATTAGTA-CAAAATAATAAAATAT
2778498 ATAAAT-ATTAGAGAAA
64 ATAAATCATTAGAGAAA
* *
2778514 AATTTGGCAAAAAAATTATAAGATTGAAGTGATAAAAAAAGATTAGTACAAAATAATAAAATATA
1 AATTTGACAAAAAAATTATAAAATTGAAGTGAT-AAAAAAGATTAGTACAAAATAATAAAATATA
2778579 TAAATCATTA
65 TAAATCATTA
2778589 ATGACAAGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
77 3 0.05
78 27 0.42
79 1 0.02
80 30 0.46
81 4 0.06
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.29
Consensus pattern (80 bp):
AATTTGACAAAAAAATTATAAAATTGAAGTGATAAAAAAGATTAGTACAAAATAATAAAATATAT
AAATCATTAGAGAAA
Found at i:2781897 original size:21 final size:21
Alignment explanation
Indices: 2781873--2781913 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2781863 AAACATTGAC
* *
2781873 CTTGAACCTCAAACATCAAAT
1 CTTGAACCACAAACACCAAAT
2781894 CTTGAACCACAAACACCAAA
1 CTTGAACCACAAACACCAAA
2781914 CCATAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.32, G:0.05, T:0.17
Consensus pattern (21 bp):
CTTGAACCACAAACACCAAAT
Found at i:2785404 original size:29 final size:28
Alignment explanation
Indices: 2785354--2785416 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
2785344 TTGACCTGTA
2785354 TATATTATGTTATAAAAAAATTATATTAGT
1 TATA-TATGTTATAAAAAAATTATA-TAGT
* *
2785384 TATATATGTTA-AATAATAATTATATATT
1 TATATATGTTATAA-AAAAATTATATAGT
2785412 TATAT
1 TATAT
2785417 TTATATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
29 16 0.53
30 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (28 bp):
TATATATGTTATAAAAAAATTATATAGT
Found at i:2785417 original size:6 final size:6
Alignment explanation
Indices: 2785406--2785441 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2785396 ATAATAATTA
2785406 TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT
2785442 AAATCACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:2789083 original size:29 final size:28
Alignment explanation
Indices: 2789051--2789278 Score: 137
Period size: 29 Copynumber: 7.8 Consensus size: 28
2789041 CTTTGGATGC
*
2789051 TCGGGGGTGAAATGGTAATTTTGATGAAA
1 TCGGGGGTAAAATGGTAATTTTG-TGAAA
**
2789080 TCGGGATTAAAATTGG-AATTTTG-GAAA
1 TCGGGGGTAAAA-TGGTAATTTTGTGAAA
* * *
2789107 GTTCGAGGGTCAAAAT-ATACTTTTTGGTGAAA
1 --TCGGGGGT-AAAATGGTA-ATTTT-GTGAAA
*
2789139 TCGGGGTTAAAAATGG-AATTTTG-GAAA
1 TCGGGGGT-AAAATGGTAATTTTGTGAAA
2789166 GTTCGGGGGTAAAATGGTAATTTTTGGTGAAA
1 --TCGGGGGTAAAATGGTAA-TTTT-GTGAAA
* * * *
2789198 TCGAGGTTAAAAATGG-AATTTTGGGAAGT
1 TCGGGGGT-AAAATGGTAATTTTGTGAA-A
*
2789227 TCGAGGGTAAAATGGTAATTTTTGGTGAAA
1 TCGGGGGTAAAATGGTAA-TTTT-GTGAAA
*
2789257 TCGGGGTTAAAAATGG-AATTTT
1 TCGGGGGT-AAAATGGTAATTTT
2789279 AGAAAGTTTG
Statistics
Matches: 155, Mismatches: 23, Indels: 42
0.70 0.10 0.19
Matches are distributed among these distances:
27 8 0.05
28 19 0.12
29 53 0.34
30 47 0.30
31 20 0.13
32 8 0.05
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (28 bp):
TCGGGGGTAAAATGGTAATTTTGTGAAA
Found at i:2789138 original size:59 final size:59
Alignment explanation
Indices: 2789055--2789303 Score: 333
Period size: 59 Copynumber: 4.2 Consensus size: 59
2789045 GGATGCTCGG
* * * * *
2789055 GGGTGAAATGGTAA-TTTTGATGAAATCGGGATTAAAATTGGAATTTTGGAAAGTTCGA
1 GGGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* *
2789113 GGGTCAAAAT-ATACTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGG
1 GGGT-AAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * *
2789172 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTCGA
1 GGGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * * *
2789231 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTGG
1 GGGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
2789290 GGGTCAAAAT-ATAA
1 GGGT-AAAATGATAA
2789304 CTTCTGAACA
Statistics
Matches: 169, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
58 11 0.07
59 153 0.91
60 5 0.03
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
Found at i:2789152 original size:30 final size:29
Alignment explanation
Indices: 2789118--2789271 Score: 113
Period size: 30 Copynumber: 5.2 Consensus size: 29
2789108 TTCGAGGGTC
*
2789118 AAAATATACTTTTTGGTGAAATCGGGGTTA
1 AAAATGTA-TTTTTGGTGAAATCGGGGTTA
* * *
2789148 AAAATGGAATTTT-G-GAAAGTTCGGGGGT-
1 AAAATGTATTTTTGGTGAAA--TCGGGGTTA
*
2789176 AAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAAT-GT-ATTTTTGGTGAAATCGGGGTTA
* * *
2789207 AAAATGGAATTTTGG-GAAGTTCGAGGG-T-
1 AAAATGTATTTTTGGTGAA-ATCG-GGGTTA
2789235 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAAT-GT-ATTTTTGGTGAAATCGGGGTTA
2789266 AAAATG
1 AAAATG
2789272 GAATTTTAGA
Statistics
Matches: 95, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
27 4 0.04
28 14 0.15
29 27 0.28
30 32 0.34
31 14 0.15
32 4 0.04
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (29 bp):
AAAATGTATTTTTGGTGAAATCGGGGTTA
Found at i:2789228 original size:118 final size:117
Alignment explanation
Indices: 2789051--2789299 Score: 376
Period size: 118 Copynumber: 2.1 Consensus size: 117
2789041 CTTTGGATGC
* *
2789051 TCGGGGGTGAAATGGTAATTTTGATGAAATCGGGATTAAAATTGGAATTTTGGAAAGTTCGAGGG
1 TCGGGGGTAAAATGGTAATTTTGATGAAATCGGGATTAAAAATGGAATTTTGGAAAGTTCGAGGG
* *
2789116 TCAAAAT-ATACTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGT
66 T-AAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGT
* *
2789168 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TTAAAAATGGAATTTTGGGAAGTTCGAG
1 TCGGGGGTAAAATGGTAA-TTTTGATGAAATCG-GGATTAAAAATGGAATTTTGGAAAGTTCGAG
*
2789232 GGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGT
64 GGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGT
*
2789286 TTGGGGGTCAAAAT
1 TCGGGGGT-AAAAT
2789300 ATAACTTCTG
Statistics
Matches: 120, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
117 22 0.18
118 91 0.76
119 7 0.06
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.32
Consensus pattern (117 bp):
TCGGGGGTAAAATGGTAATTTTGATGAAATCGGGATTAAAAATGGAATTTTGGAAAGTTCGAGGG
TAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGT
Found at i:2789291 original size:29 final size:29
Alignment explanation
Indices: 2789080--2789291 Score: 140
Period size: 29 Copynumber: 7.2 Consensus size: 29
2789070 TTTGATGAAA
* *
2789080 TCGGGATTAAAATTGGAATTTTGGAAAGT
1 TCGGGGTTAAAAATGGAATTTTGGAAAGT
* *
2789109 TCGAGGGTCAAAATAT--ACTTTTTGGTGAAA--
1 TCG-GGGTTAAAA-ATGGA-ATTTT-G-GAAAGT
2789139 TCGGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGGTTAAAAATGGAATTTTGGAAAGT
*
2789168 TCGGGGGT-AAAATGGTAATTTTTGGTGAAA--
1 TCGGGGTTAAAAATGG-AA-TTTT-G-GAAAGT
* *
2789198 TCGAGGTTAAAAATGGAATTTTGGGAAGT
1 TCGGGGTTAAAAATGGAATTTTGGAAAGT
2789227 TCGAGGG-T-AAAATGGTAATTTTTGGTGAAA--
1 TCG-GGGTTAAAAATGG-AA-TTTT-G-GAAAGT
*
2789257 TCGGGGTTAAAAATGGAATTTTAGAAAGT
1 TCGGGGTTAAAAATGGAATTTTGGAAAGT
*
2789286 TTGGGG
1 TCGGGG
2789292 GTCAAAATAT
Statistics
Matches: 144, Mismatches: 14, Indels: 50
0.69 0.07 0.24
Matches are distributed among these distances:
27 11 0.08
28 18 0.12
29 47 0.33
30 39 0.27
31 18 0.12
32 11 0.08
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (29 bp):
TCGGGGTTAAAAATGGAATTTTGGAAAGT
Found at i:2789647 original size:32 final size:32
Alignment explanation
Indices: 2789583--2789653 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
2789573 AATTATTGGG
2789583 CTAAATTAAAAATAATTAAAAATATGAAAAGGA
1 CTAAATTAAAAATAATTAAAAATATG-AAAGGA
2789616 CTAAATT-AAAATAATTAAAAAATACTG-AAGGA
1 CTAAATTAAAAATAATT-AAAAATA-TGAAAGGA
*
2789648 CCAAAT
1 CTAAAT
2789654 GCGTAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 19 0.54
33 14 0.40
34 2 0.06
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.24
Consensus pattern (32 bp):
CTAAATTAAAAATAATTAAAAATATGAAAGGA
Found at i:2790013 original size:14 final size:13
Alignment explanation
Indices: 2789960--2790003 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
2789950 AAGTCCCCCC
2789960 TTTTCTTTCCCTT
1 TTTTCTTTCCCTT
*
2789973 TTTTC-TT--ATT
1 TTTTCTTTCCCTT
2789983 TTTTCTTTCCCTT
1 TTTTCTTTCCCTT
2789996 TTTTCTTT
1 TTTTCTTT
2790004 TTCGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 2 0.08
13 15 0.58
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTCTTTCCCTT
Found at i:2790342 original size:16 final size:16
Alignment explanation
Indices: 2790321--2790353 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2790311 ATTATTTAAA
*
2790321 ATTATTAATTATTATT
1 ATTATTAATTACTATT
2790337 ATTATTAATTACTATT
1 ATTATTAATTACTATT
2790353 A
1 A
2790354 ATGCCAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATTAATTACTATT
Found at i:2791087 original size:17 final size:18
Alignment explanation
Indices: 2791065--2791110 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
2791055 TTATTTGGAT
*
2791065 ATTT-AATTTTATTTTAA
1 ATTTAAATTTTATATTAA
2791082 ATTTAAATTTT-TATTAA
1 ATTTAAATTTTATATTAA
*
2791099 GTTTAAATTTTA
1 ATTTAAATTTTA
2791111 GAAAAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTAAATTTTATATTAA
Found at i:2795156 original size:16 final size:17
Alignment explanation
Indices: 2795125--2795158 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2795115 TAATTTAATG
2795125 TTTAATTATTATAATTT
1 TTTAATTATTATAATTT
*
2795142 TTTATTTATTA-AATTT
1 TTTAATTATTATAATTT
2795158 T
1 T
2795159 ATATATAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTATTATAATTT
Found at i:2795820 original size:29 final size:29
Alignment explanation
Indices: 2795788--2795844 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2795778 ATACTTTTTA
* *
2795788 AATAATTTTAATGATTTTTAATTTTTAAG
1 AATAATTGTAATGATTTTTAAATTTTAAG
**
2795817 AATAATTGTAATTTTTTTTAAATTTTAA
1 AATAATTGTAATGATTTTTAAATTTTAA
2795845 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (29 bp):
AATAATTGTAATGATTTTTAAATTTTAAG
Found at i:2797475 original size:19 final size:19
Alignment explanation
Indices: 2797449--2797492 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
2797439 TATGTTCTTT
*
2797449 ATTTTTTTTTAAAAGTATTA
1 ATTTTTTTTTAAAA-TATAA
2797469 ATTTTTTTTTAAAATATAA
1 ATTTTTTTTTAAAATATAA
2797488 ATTTT
1 ATTTT
2797493 GAAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTTTTTTAAAATATAA
Found at i:2800145 original size:23 final size:22
Alignment explanation
Indices: 2800119--2800287 Score: 114
Period size: 23 Copynumber: 7.3 Consensus size: 22
2800109 TTTCGCACCT
* *
2800119 TGTGTGCCTACTGATTTGCGCTA
1 TGTGTGCCTACTGA-TTGCACTG
* * *
2800142 TGTGCGCTTACTGATTACACTG
1 TGTGTGCCTACTGATTGCACTG
2800164 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACT-GATTGCACTG
*
2800187 TGTGTGCTCT-CTGTTTAGCAC-G
1 TGTGTGC-CTACTGATT-GCACTG
*
2800209 TATCGTGCTCT-CTGTTATTAGCACTG
1 TGT-GTGC-CTACTG--ATT-GCACTG
*
2800235 TGTGTGCTCT-CTGATTAGCACTT
1 TGTGTGC-CTACTGATT-GCACTG
2800258 TGTGTGCTCT-CTGATTAGCACTG
1 TGTGTGC-CTACTGATT-GCACTG
2800281 TGTGTGC
1 TGTGTGC
2800288 TCTCTGTTGC
Statistics
Matches: 125, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
22 21 0.17
23 82 0.66
24 2 0.02
25 17 0.14
26 3 0.02
ACGTcount: A:0.13, C:0.22, G:0.25, T:0.40
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTG
Found at i:2800237 original size:48 final size:46
Alignment explanation
Indices: 2800177--2800295 Score: 170
Period size: 48 Copynumber: 2.6 Consensus size: 46
2800167 GTGCCTACTG
2800177 GATT-GCACTGTGTGTGCTCTCTGTTTAGCACGTAT-CGTGCTCTCT
1 GATTAGCACTGTGTGTGCTCTCTGTTTAGCAC-TATGCGTGCTCTCT
* * *
2800222 GTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCT
1 G--ATTAGCACTGTGTGTGCTCTCTGTTTAGCACTATGCGTGCTCTCT
2800270 GATTAGCACTGTGTGTGCTCTCTGTT
1 GATTAGCACTGTGTGTGCTCTCTGTT
2800296 GCCCAGCACT
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
45 1 0.02
46 24 0.36
47 5 0.08
48 36 0.55
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (46 bp):
GATTAGCACTGTGTGTGCTCTCTGTTTAGCACTATGCGTGCTCTCT
Found at i:2800237 original size:71 final size:70
Alignment explanation
Indices: 2800155--2800295 Score: 198
Period size: 71 Copynumber: 2.0 Consensus size: 70
2800145 GCGCTTACTG
*
2800155 ATTACACTGTGTGTGC-CTACTGGATT-GCACTGTGTGTGCTCTCTGTTTAGCAC-GTATCGTGC
1 ATTACACTGTGTGTGCTCT-CT-GATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTAT-GTGC
2800217 TCTCTGTT
63 TCTCTGTT
* *
2800225 ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTGTGTGTGCTC
1 ATTA-CACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTATGTGCTC
2800290 TCTGTT
65 TCTGTT
2800296 GCCCAGCACT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
70 8 0.12
71 51 0.80
72 5 0.08
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (70 bp):
ATTACACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTATGTGCTCT
CTGTT
Found at i:2800288 original size:23 final size:23
Alignment explanation
Indices: 2800152--2800293 Score: 184
Period size: 23 Copynumber: 6.1 Consensus size: 23
2800142 TGTGCGCTTA
2800152 CTGATTA-CACTGTGTGTGC-CT
1 CTGATTAGCACTGTGTGTGCTCT
2800173 ACTGGATT-GCACTGTGTGTGCTCT
1 -CT-GATTAGCACTGTGTGTGCTCT
* *
2800197 CTGTTTAGCAC-GTATCGTGCTCT
1 CTGATTAGCACTGTGT-GTGCTCT
2800220 CTGTTATTAGCACTGTGTGTGCTCT
1 CTG--ATTAGCACTGTGTGTGCTCT
*
2800245 CTGATTAGCACTTTGTGTGCTCT
1 CTGATTAGCACTGTGTGTGCTCT
2800268 CTGATTAGCACTGTGTGTGCTCT
1 CTGATTAGCACTGTGTGTGCTCT
2800291 CTG
1 CTG
2800294 TTGCCCAGCA
Statistics
Matches: 106, Mismatches: 6, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
22 8 0.08
23 76 0.72
24 2 0.02
25 17 0.16
26 3 0.03
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.40
Consensus pattern (23 bp):
CTGATTAGCACTGTGTGTGCTCT
Found at i:2800312 original size:48 final size:44
Alignment explanation
Indices: 2800177--2800318 Score: 169
Period size: 48 Copynumber: 3.0 Consensus size: 44
2800167 GTGCCTACTG
*
2800177 GATT-GCACTGTGTGTGCTCTCTGTTTAGCACGTATCGTGCTCTCT
1 GATTAGCACTGTGTGTGCTCTCTG-TTAGCACTTAT-GTGCTCTCT
*
2800222 GTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCT
1 G--ATTAGCACTGTGTGTGCTCTCTG-TTAGCAC-TTATGTGCTCTCT
2800270 GATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCT
1 GATTAGCACTGTGTGTGCTCTCTGTT----AGCACTTATGTGCTCTCT
2800318 G
1 G
2800319 TTCAGTACTT
Statistics
Matches: 85, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
45 3 0.04
46 23 0.27
47 3 0.04
48 49 0.58
49 7 0.08
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (44 bp):
GATTAGCACTGTGTGTGCTCTCTGTTAGCACTTATGTGCTCTCT
Found at i:2800330 original size:71 final size:71
Alignment explanation
Indices: 2800159--2800318 Score: 184
Period size: 71 Copynumber: 2.3 Consensus size: 71
2800149 TTACTGATTA
* * *
2800159 CACTGTGTGTGC-CTACTGGATT-GCACTGTGTGTGCTCTCTGTTTAGCACGTATCGTGCTCTCT
1 CACTGTATGTGCTCT-CT-GATTAGCACTTTGTGTGCTCTCTGATTAGCACGTATCGTGCTCTCT
**
2800222 GTTATTAG
64 GTTACCAG
* *
2800230 CACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTGTGT-GTGCTCTCTG
1 CACTGTATGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCAC-GTATCGTGCTCTCTG
*
2800294 TTGCCCAG
65 TT-ACCAG
2800302 CACT-TATGTGCTCTCTG
1 CACTGTATGTGCTCTCTG
2800319 TTCAGTACTT
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
70 4 0.05
71 63 0.81
72 11 0.14
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (71 bp):
CACTGTATGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACGTATCGTGCTCTCTGT
TACCAG
Found at i:2816004 original size:14 final size:14
Alignment explanation
Indices: 2815985--2816014 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2815975 GAATAAATAT
2815985 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
2815999 TTAATTAATTAAAA
1 TTAATTAAATAAAA
2816013 TT
1 TT
2816015 TTTAAACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:2816132 original size:22 final size:22
Alignment explanation
Indices: 2816104--2816146 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2816094 TTTGATTCCA
2816104 ATATCTTTAGTTACAAATCTGT
1 ATATCTTTAGTTACAAATCTGT
2816126 ATATCTTTAGTTACAAATCTG
1 ATATCTTTAGTTACAAATCTG
2816147 ACTCAAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
ATATCTTTAGTTACAAATCTGT
Found at i:2816268 original size:113 final size:113
Alignment explanation
Indices: 2816126--2816343 Score: 348
Period size: 113 Copynumber: 1.9 Consensus size: 113
2816116 ACAAATCTGT
* **
2816126 ATATCTTTAGTTACAAATCTGACTCAAAGCTTGAATATTTAAAACCCATTAACCAAAAGATTTGA
1 ATATATTTAGTTACAAATCTGACTCAAAGCTTGAATATTTAAAACCCATTAACCAAAAGATTCAA
*
2816191 TATCTTTGGTT-TCAATATCTTCTTCCCGTTAAATTTCTTTTGATTCCA
66 TATCATTGGTTCT-AATATCTTCTTCCCGTTAAATTTCTTTTGATTCCA
* * *
2816239 ATATATTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCGTTAACCAAAAGATTCAA
1 ATATATTTAGTTACAAATCTGACTCAAAGCTTGAATATTTAAAACCCATTAACCAAAAGATTCAA
*
2816304 TATCATTGGTTCTAATATCTTCTTCCCGTTAAGTTTCTTT
66 TATCATTGGTTCTAATATCTTCTTCCCGTTAAATTTCTTT
2816344 GGGTTAATGG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
113 95 0.99
114 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (113 bp):
ATATATTTAGTTACAAATCTGACTCAAAGCTTGAATATTTAAAACCCATTAACCAAAAGATTCAA
TATCATTGGTTCTAATATCTTCTTCCCGTTAAATTTCTTTTGATTCCA
Found at i:2816699 original size:31 final size:29
Alignment explanation
Indices: 2816635--2816703 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2816625 ATAATAATAT
* *
2816635 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
2816664 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
2816695 AAGTGACTA
1 AAGTGACTA
2816704 TTTTTGTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:2826625 original size:20 final size:21
Alignment explanation
Indices: 2826587--2826625 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2826577 TTATATGCTT
* *
2826587 ATTTTTAATTATTATACTTGA
1 ATTTTTAATTAATACACTTGA
2826608 ATTTTTAA-TAATACACTT
1 ATTTTTAATTAATACACTT
2826626 AACCCTCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTTAATTAATACACTTGA
Found at i:2828803 original size:11 final size:11
Alignment explanation
Indices: 2828787--2828823 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
2828777 TAGTGTAATA
2828787 CATCCCAAAGT
1 CATCCCAAAGT
2828798 CATCCCAAAGT
1 CATCCCAAAGT
2828809 CATCCCAAAGT
1 CATCCCAAAGT
2828820 CATC
1 CATC
2828824 AATCTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.38, G:0.08, T:0.19
Consensus pattern (11 bp):
CATCCCAAAGT
Found at i:2831893 original size:19 final size:19
Alignment explanation
Indices: 2831855--2831894 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2831845 AAAACATCAT
*
2831855 ATTAATTTTAATTAATTTG
1 ATTAATTTTAATTAACTTG
2831874 ATTAA-TTTAATTATACTTG
1 ATTAATTTTAATTA-ACTTG
2831893 AT
1 AT
2831895 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATTTTAATTAACTTG
Found at i:2835073 original size:26 final size:28
Alignment explanation
Indices: 2835037--2835096 Score: 88
Period size: 26 Copynumber: 2.2 Consensus size: 28
2835027 AATATATTTT
*
2835037 AAAATAATTAAAAAT-ATATTA-TTTAA
1 AAAATAATTAAAAATCATATGACTTTAA
*
2835063 AAAATAATTAAAAATCATATGACTTTAG
1 AAAATAATTAAAAATCATATGACTTTAA
2835091 AAAATA
1 AAAATA
2835097 GTATAAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 15 0.50
27 5 0.17
28 10 0.33
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATAATTAAAAATCATATGACTTTAA
Found at i:2847567 original size:32 final size:32
Alignment explanation
Indices: 2847506--2847578 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
2847496 ATATTTTTAA
*
2847506 ATTTAAATTTAAATAAAAATATTTAAAAAATT
1 ATTTAAATTTAAATAAAAATAATTAAAAAATT
* *
2847538 ATTT-AATTTAAATTAAAATTAAATTAAAAAAAT
1 ATTTAAATTTAAA-TAAAAAT-AATTAAAAAATT
*
2847571 ATCTAAAT
1 ATTTAAAT
2847579 CCAACCTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 8 0.24
32 10 0.29
33 13 0.38
34 3 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
ATTTAAATTTAAATAAAAATAATTAAAAAATT
Found at i:2853036 original size:27 final size:27
Alignment explanation
Indices: 2852982--2853036 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 27
2852972 AATCCCTTTT
2852982 AATAATTATATATTTTTTTGTTCAAAAAAG
1 AATAATTATATATTTTTTTG-T--AAAAAG
2853012 AATAATTATATATTTTGTTTG-AAAA
1 AATAATTATATATTTT-TTTGTAAAA
2853037 TTGAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 4 0.17
30 16 0.67
31 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (27 bp):
AATAATTATATATTTTTTTGTAAAAAG
Found at i:2862465 original size:3 final size:3
Alignment explanation
Indices: 2862457--2862493 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2862447 GGGATTTCAC
2862457 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2862494 TACTAGTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2864491 original size:6 final size:6
Alignment explanation
Indices: 2864480--2864508 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2864470 CAAAAGGGAA
2864480 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
2864509 AGAGAGGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:2865396 original size:30 final size:29
Alignment explanation
Indices: 2865362--2865418 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
2865352 TATTTTTTGG
*
2865362 AAATTGAATAAAATCAAAATTTCATATAAA
1 AAATTGAATAAAATC-AAAGTTCATATAAA
*
2865392 AAATTGCATAAAATCAAAGTTCATATA
1 AAATTGAATAAAATCAAAGTTCATATA
2865419 TAATATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (29 bp):
AAATTGAATAAAATCAAAGTTCATATAAA
Found at i:2867375 original size:2 final size:2
Alignment explanation
Indices: 2867368--2867401 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2867358 AACAATCTGC
2867368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2867402 TTCTTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2883261 original size:20 final size:20
Alignment explanation
Indices: 2883224--2883261 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2883214 TATATTTTCG
*
2883224 AAATATTATAATAAGTTTAA
1 AAATATTATAAAAAGTTTAA
2883244 AAATA-TATAAAAATGTTT
1 AAATATTATAAAAA-GTTT
2883262 TTAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
AAATATTATAAAAAGTTTAA
Found at i:2885224 original size:15 final size:15
Alignment explanation
Indices: 2885183--2885233 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
2885173 GGAGCATAGG
2885183 GAGGAGGGTATCCCT
1 GAGGAGGGTATCCCT
* *
2885198 GAGCAGGATATCCCT
1 GAGGAGGGTATCCCT
* *
2885213 GCGGAGGGTATCCTT
1 GAGGAGGGTATCCCT
2885228 GAGGAG
1 GAGGAG
2885234 AATAACCTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.39, T:0.20
Consensus pattern (15 bp):
GAGGAGGGTATCCCT
Found at i:2885249 original size:30 final size:30
Alignment explanation
Indices: 2885183--2885249 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2885173 GGAGCATAGG
* *
2885183 GAGGAGGGTATCCCTGAGCAGGATATCCCT
1 GAGGAGGGTATCCCTGAGCAGAATAACCCT
* * * *
2885213 GCGGAGGGTATCCTTGAGGAGAATAACCTT
1 GAGGAGGGTATCCCTGAGCAGAATAACCCT
2885243 GAGGAGG
1 GAGGAGG
2885250 ATGTCCTGGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.19
Consensus pattern (30 bp):
GAGGAGGGTATCCCTGAGCAGAATAACCCT
Found at i:2891389 original size:21 final size:22
Alignment explanation
Indices: 2891365--2891428 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 22
2891355 AAATGAAAAT
2891365 AAATATATAAAAAATTC-AGAA
1 AAATATATAAAAAATTCTAGAA
2891386 AAATATAT--AAAA-TCTAGAA
1 AAATATATAAAAAATTCTAGAA
* *
2891405 AAATAAATAAACAAATTATAGAA
1 AAATATATAAA-AAATTCTAGAA
2891428 A
1 A
2891429 GGTTATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 2 0.06
19 15 0.42
21 9 0.25
22 3 0.08
23 7 0.19
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (22 bp):
AAATATATAAAAAATTCTAGAA
Found at i:2891677 original size:20 final size:19
Alignment explanation
Indices: 2891636--2891692 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
2891626 TTTAAATACT
2891636 TTTTCAATTTTTATAACA-A
1 TTTTCAATTTTTATAA-ATA
2891655 TTTTCAATTTTTATAAATTA
1 TTTTCAATTTTTATAAA-TA
* *
2891675 TTTTGACTTTTTA-AAATA
1 TTTTCAATTTTTATAAATA
2891693 AATAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
19 19 0.56
20 12 0.35
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTCAATTTTTATAAATA
Found at i:2891970 original size:20 final size:20
Alignment explanation
Indices: 2891928--2891988 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
2891918 ATTTTTTAAT
*
2891928 ATTTAA-ATATTTAATATTATA
1 ATTTAATATTTTTAAT-TT-TA
**
2891949 ATTTTCTATTTTTAATTTTA
1 ATTTAATATTTTTAATTTTA
2891969 ATTTAATATTTTT-ATTTTA
1 ATTTAATATTTTTAATTTTA
2891988 A
1 A
2891989 ATAAATCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.21
20 13 0.38
21 6 0.18
22 8 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAATATTTTTAATTTTA
Found at i:2903380 original size:19 final size:19
Alignment explanation
Indices: 2903341--2903396 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2903331 TGAAAGTACA
2903341 ATATTATTACT-TTTAATAT
1 ATATTATTA-TATTTAATAT
2903360 ATATTATTATATATTAA-AT
1 ATATTATTATAT-TTAATAT
*
2903379 ATTTTATTATATTTAATA
1 ATATTATTATATTTAATA
2903397 AAATATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.15
19 24 0.73
20 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTATTATATTTAATAT
Found at i:2910537 original size:249 final size:249
Alignment explanation
Indices: 2910099--2910599 Score: 1002
Period size: 249 Copynumber: 2.0 Consensus size: 249
2910089 TCAATGCAAG
2910099 TTATGTCAGTGATACCATCCTTGTAGAGCTCTTCACACAACTGTGAGTTCCCACAACCCAGTTCC
1 TTATGTCAGTGATACCATCCTTGTAGAGCTCTTCACACAACTGTGAGTTCCCACAACCCAGTTCC
2910164 AGCACCTTCATCATGCAAAATTTTTCATCATTATCATGTTAAAGTAAACCGAATCCCATTCTAAC
66 AGCACCTTCATCATGCAAAATTTTTCATCATTATCATGTTAAAGTAAACCGAATCCCATTCTAAC
2910229 CAGAACTGAGCAAAACAGTGATGAAAATCCAACTAGCAATCCATAATTATGAATTAAGCATATAA
131 CAGAACTGAGCAAAACAGTGATGAAAATCCAACTAGCAATCCATAATTATGAATTAAGCATATAA
2910294 CTTATAACCCCAACTCAAAAACCGACAAATTTAACTGCCATTTTGCTACAATAT
196 CTTATAACCCCAACTCAAAAACCGACAAATTTAACTGCCATTTTGCTACAATAT
2910348 TTATGTCAGTGATACCATCCTTGTAGAGCTCTTCACACAACTGTGAGTTCCCACAACCCAGTTCC
1 TTATGTCAGTGATACCATCCTTGTAGAGCTCTTCACACAACTGTGAGTTCCCACAACCCAGTTCC
2910413 AGCACCTTCATCATGCAAAATTTTTCATCATTATCATGTTAAAGTAAACCGAATCCCATTCTAAC
66 AGCACCTTCATCATGCAAAATTTTTCATCATTATCATGTTAAAGTAAACCGAATCCCATTCTAAC
2910478 CAGAACTGAGCAAAACAGTGATGAAAATCCAACTAGCAATCCATAATTATGAATTAAGCATATAA
131 CAGAACTGAGCAAAACAGTGATGAAAATCCAACTAGCAATCCATAATTATGAATTAAGCATATAA
2910543 CTTATAACCCCAACTCAAAAACCGACAAATTTAACTGCCATTTTGCTACAATAT
196 CTTATAACCCCAACTCAAAAACCGACAAATTTAACTGCCATTTTGCTACAATAT
2910597 TTA
1 TTA
2910600 ACTAAAATAT
Statistics
Matches: 252, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 252 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (249 bp):
TTATGTCAGTGATACCATCCTTGTAGAGCTCTTCACACAACTGTGAGTTCCCACAACCCAGTTCC
AGCACCTTCATCATGCAAAATTTTTCATCATTATCATGTTAAAGTAAACCGAATCCCATTCTAAC
CAGAACTGAGCAAAACAGTGATGAAAATCCAACTAGCAATCCATAATTATGAATTAAGCATATAA
CTTATAACCCCAACTCAAAAACCGACAAATTTAACTGCCATTTTGCTACAATAT
Found at i:2928395 original size:22 final size:20
Alignment explanation
Indices: 2928364--2928409 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2928354 TGATGAATCA
2928364 AAATTGAATATGTTTTTAATTT
1 AAATTGAATA--TTTTTAATTT
* *
2928386 AAATTTAATATTTTTATTTT
1 AAATTGAATATTTTTAATTT
2928406 AAAT
1 AAAT
2928410 AAACTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
22 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
AAATTGAATATTTTTAATTT
Found at i:2937493 original size:15 final size:15
Alignment explanation
Indices: 2937473--2937502 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2937463 CAAGTTTAAA
*
2937473 TTAAACAACACTATT
1 TTAAACAACAATATT
2937488 TTAAACAACAATATT
1 TTAAACAACAATATT
2937503 ACAATTAAGG
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:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAACAACAATATT
Found at i:2964283 original size:9 final size:9
Alignment explanation
Indices: 2964271--2964296 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2964261 AGTTATGTAC
2964271 TTGTCGCCG
1 TTGTCGCCG
2964280 TTGTCGCCG
1 TTGTCGCCG
2964289 TTGTCGCC
1 TTGTCGCC
2964297 TCTTTCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (9 bp):
TTGTCGCCG
Found at i:2966447 original size:30 final size:30
Alignment explanation
Indices: 2966413--2966486 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
2966403 ATATCGTATT
2966413 AATAATTAATTGCTTTTTAAATTTTTTAAA
1 AATAATTAATTGCTTTTTAAATTTTTTAAA
** *
2966443 AATAA-TAATTAATTTTTAATTTTTTTAAA
1 AATAATTAATTGCTTTTTAAATTTTTTAAA
2966472 AATAATTAATTGCTT
1 AATAATTAATTGCTT
2966487 ACGTGAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 26 0.68
30 12 0.32
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (30 bp):
AATAATTAATTGCTTTTTAAATTTTTTAAA
Found at i:2966448 original size:26 final size:28
Alignment explanation
Indices: 2966426--2966482 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
2966416 AATTAATTGC
2966426 TTTTTAAATTTTTTAAAAATAATAATTAA
1 TTTTTAAATTTTTT-AAAATAATAATTAA
*
2966455 TTTTT-AATTTTTTTAAA-AATAATTAA
1 TTTTTAAATTTTTTAAAATAATAATTAA
2966481 TT
1 TT
2966483 GCTTACGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.41
27 3 0.11
28 8 0.30
29 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTTAAATTTTTTAAAATAATAATTAA
Found at i:2968743 original size:2 final size:2
Alignment explanation
Indices: 2968736--2968760 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2968726 CATCCTTTAA
2968736 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
2968761 AACATAGAAT
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:2969580 original size:176 final size:175
Alignment explanation
Indices: 2969287--2969638 Score: 659
Period size: 176 Copynumber: 2.0 Consensus size: 175
2969277 AACCAAACTG
2969287 ATATACACCCTCTCCAATATACATACGATATTCAACATTCTCTTAAATCCAAATAACATAGATAA
1 ATATACACCCTCTCCAATATACATACGATATTCAACATTCTCTTAAATCCAAATAACATAGATAA
* *
2969352 TAGAAGTACTACATTATTAAAGTTTCATCATTTCATGCATGCAAATACGAAGATAAATGGGGCAA
66 TAGAAGTACCACATTATTAAAGTTTCATCATTTCATGCATGCAAATACGAAGACAAATGGGGCAA
2969417 GTAGTGGAATCCGAATAACATAGATAATAGCACTAAAACATCATT
131 GTAGTGGAATCCGAATAACATAGATAATAGCACTAAAACATCATT
* *
2969462 ATATACACCCTCTCCAATATACATGCGATATTCAACATTCTCTTCAAATTCAAATAACATAGATA
1 ATATACACCCTCTCCAATATACATACGATATTCAACATTCTCTT-AAATCCAAATAACATAGATA
2969527 ATAGAAGTACCACATTATTAAAGTTTCATCATTTCATGCATGCAAATACGAAGACAAATGGGGCA
65 ATAGAAGTACCACATTATTAAAGTTTCATCATTTCATGCATGCAAATACGAAGACAAATGGGGCA
2969592 AGTAGTGGAATCCGAATAACATAGATAATAGCACTAAAACATCATT
130 AGTAGTGGAATCCGAATAACATAGATAATAGCACTAAAACATCATT
2969638 A
1 A
2969639 AAGTTTCATC
Statistics
Matches: 172, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
175 43 0.25
176 129 0.75
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (175 bp):
ATATACACCCTCTCCAATATACATACGATATTCAACATTCTCTTAAATCCAAATAACATAGATAA
TAGAAGTACCACATTATTAAAGTTTCATCATTTCATGCATGCAAATACGAAGACAAATGGGGCAA
GTAGTGGAATCCGAATAACATAGATAATAGCACTAAAACATCATT
Found at i:2969671 original size:92 final size:92
Alignment explanation
Indices: 2969514--2969700 Score: 284
Period size: 92 Copynumber: 2.0 Consensus size: 92
2969504 TTCAAATTCA
* ** * *
2969514 AATAACATAGATAATAGAAGTACCACATTATTAAAGTTTCATCATTTCATGCATGCAAATACGAA
1 AATAACATAGATAATAGAACTAAAACATCATTAAAGTTTCATCATTTCATGCAGGCAAATACGAA
*
2969579 GACAAATGGGGCAAGTAGTGGAATCCG
66 GACAAAGGGGGCAAGTAGTGGAATCCG
* *
2969606 AATAACATAGATAATAGCACTAAAACATCATTAAAGTTTCATCATTTCATGCAGGCAAGTACGAA
1 AATAACATAGATAATAGAACTAAAACATCATTAAAGTTTCATCATTTCATGCAGGCAAATACGAA
* *
2969671 GATAAAGGGGGTAAGTAGTGGAATCCG
66 GACAAAGGGGGCAAGTAGTGGAATCCG
2969698 AAT
1 AAT
2969701 TTATCAGTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (92 bp):
AATAACATAGATAATAGAACTAAAACATCATTAAAGTTTCATCATTTCATGCAGGCAAATACGAA
GACAAAGGGGGCAAGTAGTGGAATCCG
Found at i:2973728 original size:8 final size:8
Alignment explanation
Indices: 2973715--2973748 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2973705 AAATAATTTT
2973715 TAAAAAAA
1 TAAAAAAA
2973723 TAAAAAAA
1 TAAAAAAA
*
2973731 TTTAAAAAA
1 -TAAAAAAA
2973740 TAAAAAAA
1 TAAAAAAA
2973748 T
1 T
2973749 TTAAAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
TAAAAAAA
Found at i:2973736 original size:18 final size:18
Alignment explanation
Indices: 2973713--2973756 Score: 81
Period size: 17 Copynumber: 2.5 Consensus size: 18
2973703 ACAAATAATT
2973713 TTTAAAAAAATAAAAAAA
1 TTTAAAAAAATAAAAAAA
2973731 TTT-AAAAAATAAAAAAA
1 TTTAAAAAAATAAAAAAA
2973748 TTTAAAAAA
1 TTTAAAAAA
2973757 GTTCATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
TTTAAAAAAATAAAAAAA
Found at i:2982331 original size:7 final size:7
Alignment explanation
Indices: 2982319--2982344 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2982309 TTTTTTTACT
2982319 AAAAATA
1 AAAAATA
2982326 AAAAATA
1 AAAAATA
2982333 AAAAATA
1 AAAAATA
2982340 AAAAA
1 AAAAA
2982345 AACCTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2995375 original size:42 final size:42
Alignment explanation
Indices: 2995311--2995392 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
2995301 CAAAGGCAGA
* *
2995311 TACATGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACATC
1 TACAAGAATTACAGAGGCTTCAAATTCGGGATCAAGAACATC
2995353 TACAAGAATTACAGAGGCTTCAAATTCGGGATCAAGAACA
1 TACAAGAATTACAGAGGCTTCAAATTCGGGATCAAGAACA
2995393 GCTCGCTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (42 bp):
TACAAGAATTACAGAGGCTTCAAATTCGGGATCAAGAACATC
Found at i:2998138 original size:23 final size:23
Alignment explanation
Indices: 2998090--2998138 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
2998080 TTGAAGGTCG
* * *
2998090 AAAACTAAAATGATAAAAAATTT
1 AAAACCAAAATGACAAAAAATAT
2998113 AAAACCAAAATGACAAAATAA-AT
1 AAAACCAAAATGACAAAA-AATAT
2998136 AAA
1 AAA
2998139 CATTTCAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAACCAAAATGACAAAAAATAT
Found at i:3006491 original size:51 final size:55
Alignment explanation
Indices: 3006407--3006534 Score: 165
Period size: 57 Copynumber: 2.4 Consensus size: 55
3006397 GTCAGTCCTA
*
3006407 ATGACCCAAATACGGTCGTTACTCATG--CTCCTCCT-C-CTCCTGTCGGTGCTG
1 ATGACCCAAATACGGTCGTTACTCACGCCCTCCTCCTCCTCTCCTGTCGGTGCTG
* ** *
3006458 ATGGCCCAAATACGGTCGTTTTTCGCGCCCCTCCTCCTCCTTCTCCTGTCGGTGCTG
1 ATGACCCAAATACGGTCGTTACTCACG-CCCTCCTCCTCC-TCTCCTGTCGGTGCTG
3006515 ATGACCCAAATACGGTCGTT
1 ATGACCCAAATACGGTCGTT
3006535 GATCCTGCCC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
51 22 0.34
54 8 0.12
55 1 0.02
57 34 0.52
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.30
Consensus pattern (55 bp):
ATGACCCAAATACGGTCGTTACTCACGCCCTCCTCCTCCTCTCCTGTCGGTGCTG
Found at i:3006545 original size:57 final size:57
Alignment explanation
Indices: 3006434--3006548 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 57
3006424 GTTACTCATG
* **
3006434 CTCCTCCTCCTCCTGTCGGTGCTGATGGCCCAAATACGGTCGTTTTTCGCGCCCCTC
1 CTCCTCCTCCTCCTGTCGGTGCTGATGACCCAAATACGGTCGTTGATCGCGCCCCTC
*
3006491 CTCCTCCTTCTCCTGTCGGTGCTGATGACCCAAATACGGTCGTTGATC-CTGCCCCTC
1 CTCCTCCTCCTCCTGTCGGTGCTGATGACCCAAATACGGTCGTTGATCGC-GCCCCTC
3006548 C
1 C
3006549 AACGGATCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 1 0.02
57 52 0.98
ACGTcount: A:0.10, C:0.40, G:0.20, T:0.30
Consensus pattern (57 bp):
CTCCTCCTCCTCCTGTCGGTGCTGATGACCCAAATACGGTCGTTGATCGCGCCCCTC
Found at i:3009531 original size:29 final size:30
Alignment explanation
Indices: 3009488--3009547 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
3009478 TTTTGGTTTA
3009488 TTGTGTAAATGTATAAAT-AAACTTTGATT
1 TTGTGTAAATGTATAAATGAAACTTTGATT
* * * *
3009517 TTGTGTAATTTTATACATGAAATTTTGATT
1 TTGTGTAAATGTATAAATGAAACTTTGATT
3009547 T
1 T
3009548 GATCTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (30 bp):
TTGTGTAAATGTATAAATGAAACTTTGATT
Found at i:3010542 original size:30 final size:30
Alignment explanation
Indices: 3010508--3010591 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
3010498 TAAATTGGAG
* *
3010508 TTTTGAATTCCTTAAAAG-TTGATAAAAAAA
1 TTTTGAATCCCTTAAAAGCTAGA-AAAAAAA
*
3010538 TTTTGAACCCCTTAAAAGCTAGAAAAAAAA
1 TTTTGAATCCCTTAAAAGCTAGAAAAAAAA
* *
3010568 -ATTGAATCCCTTAAAAACT-GAAAA
1 TTTTGAATCCCTTAAAAGCTAGAAAA
3010592 TATTTTTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.11
29 16 0.34
30 23 0.49
31 3 0.06
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (30 bp):
TTTTGAATCCCTTAAAAGCTAGAAAAAAAA
Found at i:3021519 original size:28 final size:28
Alignment explanation
Indices: 3021466--3021522 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
3021456 TATAATTTTT
* * *
3021466 AATAATTTATATTTTTAATTTTTTTAAA
1 AATAAATTAAATTTTTAATTTATTTAAA
3021494 AATAAATTAAATTTTT-ATTATATTTAAA
1 AATAAATTAAATTTTTAATT-TATTTAAA
3021522 A
1 A
3021523 GAATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATAAATTAAATTTTTAATTTATTTAAA
Found at i:3021568 original size:36 final size:37
Alignment explanation
Indices: 3021487--3021568 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 37
3021477 TTTTTAATTT
3021487 TTTTAAAAATAAATTAAATTTTTATTATATTTAAAAG
1 TTTTAAAAATAAATTAAATTTTTATTATATTTAAAAG
** **
3021524 AATT-AAAATATAATTTTATTTTTATTA-ATTTAAAA-
1 TTTTAAAAATA-AATTAAATTTTTATTATATTTAAAAG
3021559 TTTTAAAAAT
1 TTTTAAAAAT
3021569 TTTAAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
35 2 0.05
36 19 0.51
37 16 0.43
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (37 bp):
TTTTAAAAATAAATTAAATTTTTATTATATTTAAAAG
Found at i:3022117 original size:26 final size:27
Alignment explanation
Indices: 3022063--3022117 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
3022053 CTTATAAAAA
*
3022063 TATTATATTAATTATATGTTAAATAAT
1 TATTATATTAATTATATATTAAATAAT
*
3022090 TATTATA-TATATT-TATATTAAATCAT
1 TATTATATTA-ATTATATATTAAATAAT
3022116 TA
1 TA
3022118 ACCCAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTATATTAATTATATATTAAATAAT
Found at i:3022822 original size:30 final size:31
Alignment explanation
Indices: 3022769--3022827 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
3022759 TTTTAATTCG
3022769 ATTAATTTTAGTCTTCATACTTTTCGAATGA
1 ATTAATTTTAGTCTTCATACTTTTCGAATGA
*
3022800 ATTAA-TTTAGT-TTCTATGCTTTTCGAAT
1 ATTAATTTTAGTCTTC-ATACTTTTCGAAT
3022828 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTAATTTTAGTCTTCATACTTTTCGAATGA
Found at i:3026095 original size:15 final size:16
Alignment explanation
Indices: 3026075--3026106 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3026065 TCAAAGTTTA
3026075 AATTTTTT-TAAATTT
1 AATTTTTTATAAATTT
3026090 AATTTTTTATAAATTT
1 AATTTTTTATAAATTT
3026106 A
1 A
3026107 TTCTATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTTTATAAATTT
Found at i:3026096 original size:16 final size:16
Alignment explanation
Indices: 3026071--3026106 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3026061 GTCCTCAAAG
*
3026071 TTTAAATTTTTTTAAA
1 TTTAAATTTTTATAAA
*
3026087 TTTAATTTTTTATAAA
1 TTTAAATTTTTATAAA
3026103 TTTA
1 TTTA
3026107 TTCTATGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTAAATTTTTATAAA
Found at i:3029432 original size:89 final size:90
Alignment explanation
Indices: 3029323--3029495 Score: 222
Period size: 89 Copynumber: 1.9 Consensus size: 90
3029313 AACTTTAAAG
* * *
3029323 TTTAGGCCCTAATCTAGGAACAATTGTCAAGTTCAGGGATTAATTTGAACAAAAA-AAGTTCAAG
1 TTTAGGCCCTAATCTAGGAACAATTGTCAAGTTCAGGGACTAACTTGAACAAAAATAAATTCAAG
3029387 CCCTAATGTGAAAATAATTACCTAA
66 CCCTAATGTGAAAATAATTACCTAA
* * * * * * *
3029412 TTTAGGTCCTAATGTGGGAACAATTGTCAAGTTTAGGGCCTAACTTGGACAAAAATAAATTTAAG
1 TTTAGGCCCTAATCTAGGAACAATTGTCAAGTTCAGGGACTAACTTGAACAAAAATAAATTCAAG
* * *
3029477 TCTTAATGTGAGAATAATT
66 CCCTAATGTGAAAATAATT
3029496 GACAAGTTCA
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
89 47 0.67
90 23 0.33
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (90 bp):
TTTAGGCCCTAATCTAGGAACAATTGTCAAGTTCAGGGACTAACTTGAACAAAAATAAATTCAAG
CCCTAATGTGAAAATAATTACCTAA
Found at i:3037592 original size:23 final size:23
Alignment explanation
Indices: 3037541--3037682 Score: 110
Period size: 23 Copynumber: 6.1 Consensus size: 23
3037531 AAATCAGTAG
*
3037541 GCACACGAAGTGCGAAACAGTAG-
1 GCACACAAAGTGCGAAACAG-AGA
3037564 GCACACAAAGTGCGAAACAGAGA
1 GCACACAAAGTGCGAAACAGAGA
* * *
3037587 GTACACAAAGTACTG-ATCAGAGA
1 GCACACAAAGTGC-GAAACAGAGA
* *
3037610 GCACACACAGTGCTAATAACAGAGA
1 GCACACAAAGTGC-GA-AACAGAGA
* * *
3037635 GCACGA-GACGTGCTAAACAGAGA
1 GCAC-ACAAAGTGCGAAACAGAGA
* * *
3037658 GCACACACAGTGCTAATCAGAGA
1 GCACACAAAGTGCGAAACAGAGA
3037681 GC
1 GC
3037683 GCGCTAGTGT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
22 3 0.03
23 75 0.78
24 2 0.02
25 15 0.16
26 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
GCACACAAAGTGCGAAACAGAGA
Found at i:3037593 original size:25 final size:23
Alignment explanation
Indices: 3037486--3037597 Score: 113
Period size: 23 Copynumber: 4.9 Consensus size: 23
3037476 AAGTGTTGGG
* *
3037486 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* * * *
3037509 -AATCAGTAGGCGCACATAGCGC
1 GAAACAGTAGGCACACAAAGTGC
*
3037531 -AAATCAGTAGGCACACGAAGTGC
1 GAAA-CAGTAGGCACACAAAGTGC
3037554 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACAAAGTGC
*
3037577 GAAACAG-AGAGTACACAAAGT
1 GAAACAGTAG-GCACACAAAGT
3037598 ACTGATCAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
22 21 0.28
23 50 0.68
24 3 0.04
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (23 bp):
GAAACAGTAGGCACACAAAGTGC
Found at i:3048792 original size:28 final size:28
Alignment explanation
Indices: 3048760--3048825 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 28
3048750 AAATTAAATA
3048760 AAAAATTAAAATAATATTATTATA-TAATT
1 AAAAATT-AAATAA-ATTATTATACTAATT
3048789 AAAAAATTAAATAAATTATTATACTAATT
1 -AAAAATTAAATAAATTATTATACTAATT
3048818 AAAAATTA
1 AAAAATTA
3048826 TAATCATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 17 0.49
29 11 0.31
30 7 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAAATTAAATAAATTATTATACTAATT
Found at i:3048802 original size:29 final size:30
Alignment explanation
Indices: 3048758--3048822 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
3048748 AAAAATTAAA
3048758 TAAAAAATTAAAATAATATTATTATA-TAAT
1 TAAAAAATTAAAATAA-ATTATTATACTAAT
3048788 TAAAAAATT-AAATAAATTATTATACTAAT
1 TAAAAAATTAAAATAAATTATTATACTAAT
3048817 TAAAAA
1 TAAAAA
3048823 TTATAATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 9 0.26
29 16 0.47
30 9 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAAAAATTAAAATAAATTATTATACTAAT
Found at i:3051208 original size:12 final size:13
Alignment explanation
Indices: 3051183--3051207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3051173 GAAATATAAA
3051183 AAAATAATTTTTT
1 AAAATAATTTTTT
3051196 AAAATAATTTTT
1 AAAATAATTTTT
3051208 ATGTACTACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATAATTTTTT
Found at i:3058536 original size:18 final size:18
Alignment explanation
Indices: 3058513--3058548 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3058503 TGAATTTTTC
3058513 GTTTGATCAATTCAATTA
1 GTTTGATCAATTCAATTA
* *
3058531 GTTTGATTAATTTAATTA
1 GTTTGATCAATTCAATTA
3058549 AATAAATTAT
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:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
GTTTGATCAATTCAATTA
Found at i:3062027 original size:15 final size:15
Alignment explanation
Indices: 3062009--3062052 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3061999 CCATCATCTG
*
3062009 CATCATCATCTTTAT
1 CATCATCATCTTCAT
*
3062024 CATCATCTTCTTCAT
1 CATCATCATCTTCAT
* *
3062039 CAACACCATCTTCA
1 CATCATCATCTTCA
3062053 GTGCCGAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.27, C:0.34, G:0.00, T:0.39
Consensus pattern (15 bp):
CATCATCATCTTCAT
Found at i:3062032 original size:12 final size:12
Alignment explanation
Indices: 3062000--3062040 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3061990 TCATCAGATC
*
3062000 CATCATCTGCAT
1 CATCATCTTCAT
*
3062012 CATCATCTTTAT
1 CATCATCTTCAT
*
3062024 CATCATCTTCTT
1 CATCATCTTCAT
3062036 CATCA
1 CATCA
3062041 ACACCATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.41
Consensus pattern (12 bp):
CATCATCTTCAT
Found at i:3064058 original size:13 final size:12
Alignment explanation
Indices: 3064040--3064073 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3064030 TAATTTGATA
3064040 TAATTTAATAGGT
1 TAATTTAATA-GT
3064053 TAATTTAATAGT
1 TAATTTAATAGT
3064065 TAA-TTAATA
1 TAATTTAATA
3064074 ATATTAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.29
12 5 0.24
13 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (12 bp):
TAATTTAATAGT
Done.