Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 114 of 131
Found at i:20418125 original size:7 final size:7
Alignment explanation
Indices: 20418113--20418150 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
20418103 TTAAGGTTCG
20418113 GGATTTT
1 GGATTTT
20418120 GGATTTT
1 GGATTTT
20418127 AGGA-TTT
1 -GGATTTT
20418134 GAGATTTT
1 G-GATTTT
20418142 GGATTTT
1 GGATTTT
20418149 GG
1 GG
20418151 GGTTTCGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 1 0.04
7 20 0.71
8 7 0.25
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (7 bp):
GGATTTT
Found at i:20418139 original size:22 final size:21
Alignment explanation
Indices: 20418095--20418148 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
20418085 AATTTTAAGG
* *
20418095 TTTTGGATTTAAGGTTCGGGA
1 TTTTGGATTTTAGGTTCGAGA
*
20418116 TTTTGGATTTTAGGATTTGAGA
1 TTTTGGATTTTAGG-TTCGAGA
20418138 TTTTGGATTTT
1 TTTTGGATTTT
20418149 GGGGTTTCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.19, C:0.02, G:0.28, T:0.52
Consensus pattern (21 bp):
TTTTGGATTTTAGGTTCGAGA
Found at i:20418149 original size:15 final size:15
Alignment explanation
Indices: 20418113--20418150 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
20418103 TTAAGGTTCG
20418113 GGATTTTGGATTTTA
1 GGATTTTGGATTTTA
20418128 GGA-TTTGAGATTTT-
1 GGATTTTG-GATTTTA
20418142 GGATTTTGG
1 GGATTTTGG
20418151 GGTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (15 bp):
GGATTTTGGATTTTA
Found at i:20424149 original size:13 final size:13
Alignment explanation
Indices: 20424111--20424487 Score: 137
Period size: 13 Copynumber: 29.7 Consensus size: 13
20424101 TTTTATTTAC
20424111 AAATAATATTATATT
1 AAATAATATTA-A-T
20424126 ATAAT-ATATTAAT
1 A-AATAATATTAAT
*
20424139 AAATAACATTATAT
1 AAATAATATTA-AT
*
20424153 GAATAA-A-TAAT
1 AAATAATATTAAT
*
20424164 --ATATTATTAAT
1 AAATAATATTAAT
*
20424175 ATAAT-ATCTTAAT
1 A-AATAATATTAAT
*
20424188 AAAAAATATTAAT
1 AAATAATATTAAT
*
20424201 AAAAAATATT-AT
1 AAATAATATTAAT
* *
20424213 AATATATTAATAAAT
1 AA-ATAAT-ATTAAT
*
20424228 AATATAATATTCAT
1 AA-ATAATATTAAT
20424242 AAATAATATATTAAT
1 AAAT-A-ATATTAAT
*
20424257 AAATAA-A-TCAT
1 AAATAATATTAAT
*
20424268 --ATTATATTAAT
1 AAATAATATTAAT
*
20424279 AAATCATA-T-AT
1 AAATAATATTAAT
20424290 AAATAATATACTAAT
1 AAATAATAT--TAAT
* *
20424305 AAATAGTATTAAG
1 AAATAATATTAAT
20424318 AAATAATATT-AT
1 AAATAATATTAAT
20424330 -AAT-ATATTAAT
1 AAATAATATTAAT
*
20424341 AAAT-AT-TAAAT
1 AAATAATATTAAT
*
20424352 ATTATTAAT-TTAATT
1 A--AATAATATTAA-T
*
20424367 AATAAAATATT-AT
1 AA-ATAATATTAAT
20424380 -AATAATATATGAAT
1 AAATAATAT-T-AAT
20424394 AAATAATA-T-AT
1 AAATAATATTAAT
***
20424405 TGTTAATA--AAT
1 AAATAATATTAAT
* *
20424416 AATATACTATTATT
1 AA-ATAATATTAAT
20424430 ATAAT-ATATTAAT
1 A-AATAATATTAAT
*
20424443 AAATATTATTAAT
1 AAATAATATTAAT
* *
20424456 ATATAACA-T-AT
1 AAATAATATTAAT
*
20424467 TAAT-ATATTAAT
1 AAATAATATTAAT
20424479 AAATAATAT
1 AAATAATAT
20424488 AAAGAATAAG
Statistics
Matches: 272, Mismatches: 47, Indels: 88
0.67 0.12 0.22
Matches are distributed among these distances:
9 6 0.02
10 9 0.03
11 51 0.19
12 34 0.12
13 83 0.31
14 37 0.14
15 49 0.18
16 3 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (13 bp):
AAATAATATTAAT
Found at i:20424164 original size:33 final size:31
Alignment explanation
Indices: 20424126--20424471 Score: 170
Period size: 33 Copynumber: 11.5 Consensus size: 31
20424116 ATATTATATT
*
20424126 ATAATATATTAATAAATAACATTATATGAATAA
1 ATAATATATTAATAAATAA-A-TATATTAATAA
* *
20424159 ATAATATATT-ATTAATATAATATCTTAATAA
1 ATAATATATTAATAAATA-AATATATTAATAA
20424190 A-AA-ATATTAAT-AA-AAA-ATA-T--T--
1 ATAATATATTAATAAATAAATATATTAATAA
*
20424211 ATAATATATTAATAAATAATATAATATTCATAA
1 ATAATATATTAATAAATAA-AT-ATATTAATAA
*
20424244 ATAATATATTAATAAATAAATCATATTATATTA
1 ATAATATATTAATAAATAAAT-ATATTA-ATAA
*
20424277 ATAA-ATCA-TATATAAAT-AATATACTAATAA
1 ATAATAT-ATTA-ATAAATAAATATATTAATAA
* * * *
20424307 AT-A-GTATTAAGAAATAATATTATAATATATTA
1 ATAATATATTAATAAATAA-A-TATATTA-ATAA
* * * *
20424339 ATAA-ATATTAA-ATATTATTA-ATTTAATTA
1 ATAATATATTAATAAATAAATATA-TTAATAA
* *
20424368 ATAAAATATT-AT-AAT-AATATATGAATAA
1 ATAATATATTAATAAATAAATATATTAATAA
*
20424396 ATAATATATTGTTAATAAATAATATACTATT-AT-T
1 ATAATATA---TTAATAAATAA-ATA-TATTAATAA
*
20424430 ATAATATATTAATAAAT--AT-TATTAATAT
1 ATAATATATTAATAAATAAATATATTAATAA
*
20424458 ATAACATATTAATA
1 ATAATATATTAATA
20424472 TATTAATAAA
Statistics
Matches: 250, Mismatches: 26, Indels: 79
0.70 0.07 0.22
Matches are distributed among these distances:
21 1 0.00
22 2 0.01
23 9 0.04
24 2 0.01
25 3 0.01
26 7 0.03
27 4 0.02
28 41 0.16
29 26 0.10
30 19 0.08
31 33 0.13
32 32 0.13
33 54 0.22
34 9 0.04
35 5 0.02
36 3 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (31 bp):
ATAATATATTAATAAATAAATATATTAATAA
Found at i:20424275 original size:37 final size:33
Alignment explanation
Indices: 20424131--20424488 Score: 172
Period size: 36 Copynumber: 10.5 Consensus size: 33
20424121 ATATTATAAT
*
20424131 ATATTAATAAATAACATTATATGAATAAATAATATA
1 ATATTAATAAAT-A-A-TATATTAATAAATAATATA
* * *
20424167 TTATTAAT--ATAATATCTTAATAAAAAATATTA
1 ATATTAATAAATAATATATTAATAAATAATA-TA
** *
20424199 ATAAAAAATATTATAATATATTAATAAATAATATA
1 AT-ATTAATA-AATAATATATTAATAAATAATATA
*
20424234 ATATTCATAAATAATATATTAATAAATAAATCATA
1 ATATTAATAAATAATATATTAATAAAT-AAT-ATA
* *
20424269 TTATATTAATAAATCATATATAAATAATATACTAATAAATA
1 --ATATTAATAAAT-A-ATAT-ATTAATA-AATAAT--ATA
* * *
20424310 GTATTAAGAAATAATAT-TATAATATATTAATA-A
1 ATATTAATAAATAATATAT-TAATA-AATAATATA
* *
20424343 ATA-T--TAAAT-AT-TATTAATTTAATTAATAAA
1 ATATTAATAAATAATATATTAA--TAAATAATATA
*
20424373 ATATT-AT-AATAATATATGAATAAATAATATA
1 ATATTAATAAATAATATATTAATAAATAATATA
* * * * *
20424404 TTGTTAATAAATAATATACT-AT-TATTATA-A
1 ATATTAATAAATAATATATTAATAAATAATATA
*
20424434 TATATTAATAAAT-AT-TATTAATATATAACATATTAA
1 -ATATTAATAAATAATATATTAATAAAT-A-ATA-T-A
20424470 TATATTAATAAATAATATA
1 -ATATTAATAAATAATATA
20424489 AAGAATAAGA
Statistics
Matches: 251, Mismatches: 36, Indels: 68
0.71 0.10 0.19
Matches are distributed among these distances:
28 4 0.02
29 13 0.05
30 15 0.06
31 48 0.19
32 12 0.05
33 42 0.17
34 10 0.04
35 7 0.03
36 51 0.20
37 17 0.07
38 4 0.02
39 14 0.06
40 9 0.04
41 5 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (33 bp):
ATATTAATAAATAATATATTAATAAATAATATA
Found at i:20424341 original size:36 final size:36
Alignment explanation
Indices: 20424174--20424487 Score: 181
Period size: 36 Copynumber: 8.6 Consensus size: 36
20424164 ATATTATTAA
* * *
20424174 TATAATATCTTAATAAAAAATATTAATAAAAAATAT
1 TATAATATATTAATAAATAATATTAATAAATAATAT
20424210 TATAATATATTAATAAATAATATAATATTCATAAATAATA-
1 TATAATATATTAATAAATAATAT--TA---ATAAATAATAT
* * * *
20424250 TATTAATAAATAAATCATATTATATTAATAAATCATATAT
1 TA-TAATATATTAAT-AAATAATATTAATAAAT-A-ATAT
* * * *
20424290 AAATAATATACTAATAAATAGTATTAAGAAATAATAT
1 -TATAATATATTAATAAATAATATTAATAAATAATAT
* *
20424327 TATAATATATTAATAAATATTAAATATTATTAATTTAAT-T
1 TATAATATATTAAT-AA-A-T-AATATTAATAA-ATAATAT
* *
20424367 AATAAAATATT-AT-AATAATATATGAATAAAT-A-A-
1 TATAATATATTAATAAATAATAT-T-AATAAATAATAT
* *
20424400 TAT-AT-TGTTAATAAATAATA-TACT--AT--TAT
1 TATAATATATTAATAAATAATATTAATAAATAATAT
* * *
20424429 TATAATATATTAATAAATATTATTAATATATAACA-
1 TATAATATATTAATAAATAATATTAATAAATAATAT
20424464 TATTAATATATTAATAAATAATAT
1 TA-TAATATATTAATAAATAATAT
20424488 AAAGAATAAG
Statistics
Matches: 213, Mismatches: 34, Indels: 62
0.69 0.11 0.20
Matches are distributed among these distances:
28 3 0.01
29 3 0.01
30 4 0.02
31 17 0.08
32 6 0.03
33 9 0.04
34 8 0.04
35 5 0.02
36 59 0.28
37 13 0.06
38 5 0.02
39 19 0.09
40 31 0.15
41 24 0.11
42 7 0.03
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (36 bp):
TATAATATATTAATAAATAATATTAATAAATAATAT
Found at i:20424344 original size:23 final size:23
Alignment explanation
Indices: 20424193--20424487 Score: 112
Period size: 23 Copynumber: 12.7 Consensus size: 23
20424183 TTAATAAAAA
*
20424193 ATATTAATAAAAAATATTATAAT
1 ATATTAATAAATAATATTATAAT
20424216 ATATTAATAAAT-A-A-TAT-A-
1 ATATTAATAAATAATATTATAAT
*
20424234 ATATTCATAAATAATA-TATTAAT
1 ATATTAATAAATAATATTA-TAAT
* * * *
20424257 AAATAAATCATATTATATTAATAA-
1 ATATTAAT-AAATAATATT-ATAAT
20424281 ATCA-TATATAAATAATATACTAATAAAT
1 AT-ATTA-ATAAATAATAT--T-AT-AAT
*
20424309 AGTATTAAGAAATAATATTATAAT
1 A-TATTAATAAATAATATTATAAT
*
20424333 ATATTAATAAATATTAAATATTATTA-
1 ATATTAAT-AA-A-T-AATATTATAAT
*
20424359 AT-TTAATTAATAAAATATTATAAT
1 ATATTAA-TAA-ATAATATTATAAT
20424383 AATATATGAATAAAT-A-A-TAT-AT
1 -ATAT-T-AATAAATAATATTATAAT
*
20424405 -TGTTAATAAATAATA-TACT-AT
1 ATATTAATAAATAATATTA-TAAT
20424426 -TATT-AT-AAT-ATATTAATAAAT
1 ATATTAATAAATAATATT-AT-AAT
* *
20424447 ATTATTAATATATAACA-TATTAAT
1 A-TATTAATAAATAATATTA-TAAT
20424471 ATATTAATAAATAATAT
1 ATATTAATAAATAATAT
20424488 AAAGAATAAG
Statistics
Matches: 209, Mismatches: 23, Indels: 79
0.67 0.07 0.25
Matches are distributed among these distances:
18 21 0.10
19 9 0.04
20 14 0.07
21 10 0.05
22 4 0.02
23 51 0.24
24 29 0.14
25 25 0.12
26 14 0.07
27 15 0.07
28 14 0.07
29 3 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (23 bp):
ATATTAATAAATAATATTATAAT
Found at i:20424427 original size:49 final size:51
Alignment explanation
Indices: 20424318--20424448 Score: 149
Period size: 49 Copynumber: 2.6 Consensus size: 51
20424308 TAGTATTAAG
* * *
20424318 AAATAATATTATAATATATTAATAAATATTAAATATTATTAATTTAATTAATA
1 AAATATTATAATAATATATTAATAAATA-TAAATATTATTAA-TTAAATAATA
* * *
20424371 AAATATTATAATAATATATGAATAAATA-ATATATTGTTAA-TAAATAATA
1 AAATATTATAATAATATATTAATAAATATAAATATTATTAATTAAATAATA
* * *
20424420 TACTATTATTATAATATATTAATAAATAT
1 AAATATTATAATAATATATTAATAAATAT
20424449 TATTAATATA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 32 0.48
51 10 0.15
53 25 0.37
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (51 bp):
AAATATTATAATAATATATTAATAAATATAAATATTATTAATTAAATAATA
Found at i:20424620 original size:26 final size:27
Alignment explanation
Indices: 20424585--20424641 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
20424575 TTTTAATATT
20424585 AATA-ATTTTAACAATAAA-AATTTTC
1 AATATATTTTAACAATAAATAATTTTC
* *
20424610 AATATATTTTAATAATAAATAATTTTT
1 AATATATTTTAACAATAAATAATTTTC
20424637 AATAT
1 AATAT
20424642 TTTAATAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 13 0.46
27 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATATTTTAACAATAAATAATTTTC
Found at i:20424641 original size:27 final size:26
Alignment explanation
Indices: 20424583--20424648 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
20424573 TCTTTTAATA
*
20424583 TTAATA-ATTTTAACAATAAAAATTT
1 TTAATATATTTTAATAATAAAAATTT
*
20424608 TCAATATATTTTAATAATAAATAATTT
1 TTAATATATTTTAATAATAAA-AATTT
20424635 TT-A-ATATTTTAATA
1 TTAATATATTTTAATA
20424649 GTTATATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 16 0.44
26 14 0.39
27 6 0.17
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATATATTTTAATAATAAAAATTT
Found at i:20424647 original size:25 final size:24
Alignment explanation
Indices: 20424583--20424648 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 24
20424573 TCTTTTAATA
*
20424583 TTAATAATTTTAACAATAAAAATTT
1 TTAAT-ATTTTAATAATAAAAATTT
*
20424608 TCAATATATTTTAATAATAAATAATTT
1 T-TA-ATATTTTAATAATAAA-AATTT
20424635 TTAATATTTTAATA
1 TTAATATTTTAATA
20424649 GTTATATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 12 0.34
26 15 0.43
27 8 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAATATTTTAATAATAAAAATTT
Found at i:20425017 original size:24 final size:23
Alignment explanation
Indices: 20424954--20425021 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
20424944 TGTTTAATGT
*
20424954 TTGTATAATATATTTATTTAATA
1 TTGTATAATATATTTATTTAAAA
*
20424977 -TATA-AATACCTAGTTTATTTAACAA
1 TTGTATAATA--TA-TTTATTTAA-AA
20425002 TTGTATAATATATTTATTTA
1 TTGTATAATATATTTATTTA
20425022 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.11
22 3 0.08
23 2 0.06
24 17 0.47
25 3 0.08
26 3 0.08
27 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
TTGTATAATATATTTATTTAAAA
Found at i:20425639 original size:17 final size:17
Alignment explanation
Indices: 20425617--20425649 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20425607 TGATAGGATA
20425617 AAATAAGATAATATTAT
1 AAATAAGATAATATTAT
*
20425634 AAATAAGATTATATTA
1 AAATAAGATAATATTA
20425650 AATAATGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATAAGATAATATTAT
Found at i:20427988 original size:17 final size:17
Alignment explanation
Indices: 20427966--20428005 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20427956 ATTACATTAT
*
20427966 TATAATGATATTGCAAA
1 TATAATGATACTGCAAA
*
20427983 TATAATGATGCTGCAAA
1 TATAATGATACTGCAAA
20428000 TGATAA
1 T-ATAA
20428006 CAACCGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
TATAATGATACTGCAAA
Found at i:20428866 original size:12 final size:11
Alignment explanation
Indices: 20428840--20428867 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20428830 TTACTCGTAT
20428840 AAAAATCAAAC
1 AAAAATCAAAC
20428851 AAAAATCAAAC
1 AAAAATCAAAC
20428862 AAAAAT
1 AAAAAT
20428868 ATAGAGCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAATCAAAC
Found at i:20431695 original size:17 final size:17
Alignment explanation
Indices: 20431673--20431724 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
20431663 AGATTAGGAT
* *
20431673 AAGTTTCAGACAAAACA
1 AAGTTTAAGACAAGACA
*
20431690 AAGTTTGAGACAAGACA
1 AAGTTTAAGACAAGACA
20431707 AAGTTTAAGACAAGACA
1 AAGTTTAAGACAAGACA
20431724 A
1 A
20431725 CCATTTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (17 bp):
AAGTTTAAGACAAGACA
Found at i:20435797 original size:12 final size:12
Alignment explanation
Indices: 20435782--20435808 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20435772 CTGTTGAAAT
20435782 AATTAAATATTA
1 AATTAAATATTA
20435794 AATTAAATATTA
1 AATTAAATATTA
20435806 AAT
1 AAT
20435809 AAAAGGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATTAAATATTA
Found at i:20435821 original size:16 final size:16
Alignment explanation
Indices: 20435802--20435834 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20435792 TAAATTAAAT
*
20435802 ATTAAATAAAAGGATA
1 ATTAAATAAAACGATA
20435818 ATTAAATAAAACGATA
1 ATTAAATAAAACGATA
20435834 A
1 A
20435835 ATAATAAAGA
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:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (16 bp):
ATTAAATAAAACGATA
Found at i:20436310 original size:131 final size:124
Alignment explanation
Indices: 20436069--20436324 Score: 316
Period size: 131 Copynumber: 2.0 Consensus size: 124
20436059 TCCGAGTAGC
20436069 GGCATAGTATCTTCTAAAAGAGATAGATATTGATATATATATATTTAAAAAAATTTAAAAGTAGA
1 GGCATAGTATCTTCTAAAAGAGATAGATATTGATATATATATATTTAAAAAAATTTAAAAGTAGA
** * * * *
20436134 TAGATTGTTCAGTCTCTCAGATTAGGGCAAAATGTGGCATACTTGACATTTTAAAAGAA
66 TAGACCGCTCAATCTCTCAGATTAGGGCAAAATGTGGCATACTTGACACTCTAAAAGAA
*
20436193 GGCATAGTATCTTCTAAAAGAGATAGATATCAATATATATATATATATATTTAAAAAAAATTCT-
1 GGCATAGTATCTTCTAAAAGAGATAG--AT--AT-T-GATATATATATATTT-AAAAAAATT-TA
* * * * * *
20436257 GAAGTAGATAGACCGCTCAATCTCTTAGGTTATGGTAAAATGTGTCATACTTGACACTCTAAAAG
58 AAAGTAGATAGACCGCTCAATCTCTCAGATTAGGGCAAAATGTGGCATACTTGACACTCTAAAAG
20436322 AA
123 AA
20436324 G
1 G
20436325 TGGTAGCAGG
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
124 26 0.23
126 2 0.02
128 2 0.02
129 1 0.01
130 14 0.13
131 65 0.59
132 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (124 bp):
GGCATAGTATCTTCTAAAAGAGATAGATATTGATATATATATATTTAAAAAAATTTAAAAGTAGA
TAGACCGCTCAATCTCTCAGATTAGGGCAAAATGTGGCATACTTGACACTCTAAAAGAA
Found at i:20438347 original size:17 final size:17
Alignment explanation
Indices: 20438325--20438365 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20438315 TTAATTATTA
* *
20438325 TCGAGTCGAATTCGAAC
1 TCGAGTAGAACTCGAAC
*
20438342 TCGAGTAGAACTCGAGC
1 TCGAGTAGAACTCGAAC
20438359 TCGAGTA
1 TCGAGTA
20438366 ATTCGACTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (17 bp):
TCGAGTAGAACTCGAAC
Found at i:20438740 original size:16 final size:16
Alignment explanation
Indices: 20438716--20438750 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20438706 ATTACACCTC
20438716 TAACATTTATTCAGCT
1 TAACATTTATTCAGCT
*
20438732 TAACCTTTATTCAGCT
1 TAACATTTATTCAGCT
20438748 TAA
1 TAA
20438751 AGTTAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (16 bp):
TAACATTTATTCAGCT
Found at i:20438996 original size:22 final size:22
Alignment explanation
Indices: 20438954--20438997 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
20438944 CTTTTGTTCA
*
20438954 TTTTCTTTAAAAACCTTTAATTT
1 TTTTCTTTAAAAA-CTATAATTT
20438977 TTTTCTCTTAAAAA-TATAATT
1 TTTTCT-TTAAAAACTATAATT
20438998 CAAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTCTTTAAAAACTATAATTT
Found at i:20442869 original size:18 final size:18
Alignment explanation
Indices: 20442846--20442885 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20442836 CAATCCCCTG
* *
20442846 ACTTTTGACTTCGGTATC
1 ACTTTTGACTCCGATATC
20442864 ACTTTTGACTCCGATATC
1 ACTTTTGACTCCGATATC
20442882 ACTT
1 ACTT
20442886 GTTGGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (18 bp):
ACTTTTGACTCCGATATC
Found at i:20456181 original size:16 final size:16
Alignment explanation
Indices: 20456155--20456199 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
20456145 AATAATATTG
20456155 AATTCATAAAAAATTAA
1 AATT-ATAAAAAATTAA
*
20456172 AATTAT-AAAAATGAA
1 AATTATAAAAAATTAA
20456187 AA-TATAAAAAATT
1 AATTATAAAAAATT
20456200 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 3 0.12
15 16 0.64
16 2 0.08
17 4 0.16
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
AATTATAAAAAATTAA
Found at i:20457222 original size:23 final size:24
Alignment explanation
Indices: 20457178--20457235 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
20457168 ATATATTTAA
20457178 TAAAATATATTAATTTTAATTAATC
1 TAAAATATATTAATTTTAATT-ATC
*
20457203 TAAAATA-A-TAA-TTTATATTATT
1 TAAAATATATTAATTTTA-ATTATC
*
20457225 TAAAATCTATT
1 TAAAATATATT
20457236 TATTAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 12 0.43
23 7 0.25
24 2 0.07
25 7 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATATATTAATTTTAATTATC
Found at i:20463351 original size:22 final size:22
Alignment explanation
Indices: 20463309--20463352 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20463299 ATAATATTCT
*
20463309 TATTAAATTATATATATATATA
1 TATTAAATTATACATATATATA
*
20463331 TATTAAATTTTAACATA-ATATA
1 TATTAAATTAT-ACATATATATA
20463353 AAATTAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAAATTATACATATATATA
Found at i:20463371 original size:17 final size:18
Alignment explanation
Indices: 20463327--20463378 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
20463317 TATATATATA
*
20463327 TATATATTAAATTTTAAC
1 TATATATTAAATATTAAC
20463345 -ATA-ATATAAA-ATTAAC
1 TATATAT-TAAATATTAAC
20463361 TATATATTAAATTATTAA
1 TATATATTAAA-TATTAA
20463379 TTTCACTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
16 7 0.25
17 14 0.50
18 2 0.07
19 5 0.18
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATATTAAATATTAAC
Found at i:20465542 original size:13 final size:11
Alignment explanation
Indices: 20465532--20465569 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20465522 GATGATATGA
20465532 TATAAAAATAT
1 TATAAAAATAT
20465543 TATAAAAATA-
1 TATAAAAATAT
* *
20465553 TATAAAGATAA
1 TATAAAAATAT
20465564 TATAAA
1 TATAAA
20465570 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:20466616 original size:19 final size:17
Alignment explanation
Indices: 20466592--20466627 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
20466582 ATATATTATC
20466592 TTGACTTAGAACTGTGAAA
1 TTGACTT-GAACT-TGAAA
20466611 TTGACTTGAACTTGAAA
1 TTGACTTGAACTTGAAA
20466628 AATTAATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (17 bp):
TTGACTTGAACTTGAAA
Found at i:20467272 original size:28 final size:26
Alignment explanation
Indices: 20467217--20467273 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
20467207 AAATATTTTT
**
20467217 ATAATTTTTTATTTAAATAATTTTAA
1 ATAATTTTTTATTTAAATAATTAAAA
20467243 ATAATTTTTTAAATTTAATATAA-TAAAA
1 ATAATTTTTT--ATTTAA-ATAATTAAAA
20467271 ATA
1 ATA
20467274 TTATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
28 12 0.46
29 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATAATTTTTTATTTAAATAATTAAAA
Found at i:20468045 original size:23 final size:23
Alignment explanation
Indices: 20468010--20468062 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
20468000 TATGAAGATC
*
20468010 ATAAAGATAAAATAAAATTTATT
1 ATAAATATAAAATAAAATTTATT
* ** *
20468033 ATAAATATTAAATATTATTTTTT
1 ATAAATATAAAATAAAATTTATT
20468056 ATAAATA
1 ATAAATA
20468063 ATTATATGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAAATATAAAATAAAATTTATT
Found at i:20470169 original size:3 final size:3
Alignment explanation
Indices: 20470155--20470191 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
20470145 GCCACTACTT
* *
20470155 CCA CCA CTA CCA CCA CCA CCA CCA CCA CCA CCC CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
20470192 TAGTTACACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.68, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:20471057 original size:14 final size:14
Alignment explanation
Indices: 20471038--20471070 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20471028 GAAGAGGCTG
20471038 GGAGGGGAAGGAA-A
1 GGAGGGG-AGGAAGA
20471052 GGAGGGGAGGAAGA
1 GGAGGGGAGGAAGA
20471066 GGAGG
1 GGAGG
20471071 AACAAAGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
GGAGGGGAGGAAGA
Found at i:20473070 original size:19 final size:19
Alignment explanation
Indices: 20473009--20473135 Score: 70
Period size: 17 Copynumber: 7.0 Consensus size: 19
20472999 AATTAAATTT
* * *
20473009 TTTTAAAAATTTAAAATAT
1 TTTTAAAAATATAAAAAAA
*
20473028 TTTTAAAAATATATAAAAA
1 TTTTAAAAATATAAAAAAA
* *
20473047 --GTAAAAAAATAAAAAAA
1 TTTTAAAAATATAAAAAAA
***
20473064 TTTTAAAAAT-TATGTAAA
1 TTTTAAAAATATAAAAAAA
*
20473082 -TTTAAAAAT-TCAAAAAA
1 TTTTAAAAATATAAAAAAA
* * * *
20473099 -TTTCAAAATTTTAATAAA
1 TTTTAAAAATATAAAAAAA
20473117 TTTCTAAAAAT-TAAAAAAA
1 TTT-TAAAAATATAAAAAAA
20473136 GAAAAATTTT
Statistics
Matches: 81, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
17 35 0.43
18 11 0.14
19 29 0.36
20 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TTTTAAAAATATAAAAAAA
Found at i:20473081 original size:11 final size:9
Alignment explanation
Indices: 20473009--20473128 Score: 59
Period size: 9 Copynumber: 13.2 Consensus size: 9
20472999 AATTAAATTT
20473009 TTTTAAAAA
1 TTTTAAAAA
20473018 -TTTAAAATA
1 TTTTAAAA-A
20473027 TTTTTAAAAA
1 -TTTTAAAAA
*
20473037 TATATAAAAA
1 T-TTTAAAAA
* *
20473047 -GTAAAAAA
1 TTTTAAAAA
* **
20473055 ATAAAAAAA
1 TTTTAAAAA
20473064 TTTTAAAAA
1 TTTTAAAAA
* **
20473073 TTATGTAAA
1 TTTTAAAAA
20473082 -TTTAAAAA
1 TTTTAAAAA
*
20473090 -TTCAAAAA
1 TTTTAAAAA
* *
20473098 ATTTCAAAA
1 TTTTAAAAA
20473107 TTTTAATAAA
1 TTTTAA-AAA
20473117 TTTCTAAAAA
1 TTT-TAAAAA
20473127 TT
1 TT
20473129 AAAAAAAGAA
Statistics
Matches: 83, Mismatches: 20, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
8 24 0.29
9 30 0.36
10 19 0.23
11 10 0.12
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:20473263 original size:26 final size:25
Alignment explanation
Indices: 20473233--20473298 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
20473223 TTAAAGATTA
* **
20473233 TAAAAAAT-TAAAATATTGAATTTTT
1 TAAAAAATAAAAAATA-TGAAAATTT
20473258 TAAAAAATAAAAAATATGAAAATTT
1 TAAAAAATAAAAAATATGAAAATTT
20473283 TAAAAAATAAAAAATA
1 TAAAAAATAAAAAATA
20473299 AAAAATTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 31 0.84
26 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
TAAAAAATAAAAAATATGAAAATTT
Found at i:20473311 original size:25 final size:25
Alignment explanation
Indices: 20473258--20473313 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
20473248 TTGAATTTTT
* *
20473258 TAAAAAATAAAAAATATGAAAATTT
1 TAAAAAATAAAAAATATAAAAATTA
20473283 TAAAAAATAAAAAATA-AAAAATTGA
1 TAAAAAATAAAAAATATAAAAATT-A
20473308 TAAAAA
1 TAAAAA
20473314 TCTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
TAAAAAATAAAAAATATAAAAATTA
Found at i:20473369 original size:30 final size:31
Alignment explanation
Indices: 20473307--20473368 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
20473297 TAAAAAATTG
*
20473307 ATAAAAATCTAAAATTTTTTTGAAAAATAAAA
1 ATAAAAA-CTAAAATTTATTTGAAAAATAAAA
*
20473339 ATAAAAA-TAAAATTTATTT-AAAATTAAAA
1 ATAAAAACTAAAATTTATTTGAAAAATAAAA
20473368 A
1 A
20473369 AAAGGTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
32 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (31 bp):
ATAAAAACTAAAATTTATTTGAAAAATAAAA
Found at i:20473507 original size:19 final size:20
Alignment explanation
Indices: 20473470--20473509 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20473460 AATTTACATC
*
20473470 TTAATATTTTTTTGAATTTT
1 TTAATATTTTCTTGAATTTT
*
20473490 TTAA-ATTTTCTTGGATTTT
1 TTAATATTTTCTTGAATTTT
20473509 T
1 T
20473510 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (20 bp):
TTAATATTTTCTTGAATTTT
Found at i:20473704 original size:25 final size:26
Alignment explanation
Indices: 20473676--20473729 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
20473666 TTTAAGAAAA
20473676 TTTTATTTTATT-AAAATTTTTTATT
1 TTTTATTTTATTGAAAATTTTTTATT
*
20473701 TTTTATTTTTTTGAAAATTTTTTATT
1 TTTTATTTTATTGAAAATTTTTTATT
20473727 TTT
1 TTT
20473730 ATTAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTATTTTATTGAAAATTTTTTATT
Found at i:20473736 original size:18 final size:17
Alignment explanation
Indices: 20473698--20473759 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 17
20473688 AAAATTTTTT
20473698 ATTTTTTATTTTTTTGAAA
1 ATTTTTTATTTTTTT--AA
20473717 ATTTTTTATTTTTATTAA
1 ATTTTTTATTTTT-TTAA
* * *
20473735 ATTATTGATTTTTTTTCA
1 ATTTTTTA-TTTTTTTAA
20473753 ATTTTTT
1 ATTTTTT
20473760 TTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 16 0.44
19 18 0.50
20 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTTTTATTTTTTTAA
Found at i:20473797 original size:19 final size:19
Alignment explanation
Indices: 20473762--20473809 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
20473752 AATTTTTTTT
*
20473762 AAAATTTCATATATTTTAA
1 AAAATTTTATATATTTTAA
*
20473781 AAAATTTTATA-ACTTTTTA
1 AAAATTTTATATA-TTTTAA
20473800 AAAATGTTTA
1 AAAAT-TTTA
20473810 AGATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 20 0.80
20 4 0.16
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAATTTTATATATTTTAA
Found at i:20473841 original size:28 final size:28
Alignment explanation
Indices: 20473785--20473856 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
20473775 TTTTAAAAAA
* *
20473785 TTTTATAACTTTTTAAAAATGTTTAAGAT
1 TTTTTTAA-TTTTTAAAAATATTTAAGAT
20473814 TTTTTTAATTTTTAAAAATA-TTATAGAT
1 TTTTTTAATTTTTAAAAATATTTA-AGAT
20473842 TTTTTTGAAATTTTT
1 TTTTTT--AATTTTT
20473857 TTGAAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 3 0.08
28 21 0.55
29 7 0.18
30 7 0.18
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (28 bp):
TTTTTTAATTTTTAAAAATATTTAAGAT
Found at i:20473858 original size:12 final size:11
Alignment explanation
Indices: 20473840--20473866 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20473830 AATATTATAG
20473840 ATTTTTTTGAA
1 ATTTTTTTGAA
20473851 ATTTTTTTGAA
1 ATTTTTTTGAA
20473862 ATTTT
1 ATTTT
20473867 CTTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
ATTTTTTTGAA
Found at i:20476834 original size:2 final size:2
Alignment explanation
Indices: 20476827--20476855 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20476817 TTTTCAAATT
20476827 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20476856 AGTGGACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20477798 original size:8 final size:8
Alignment explanation
Indices: 20477770--20477808 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
20477760 CATAGTAATT
20477770 CATATATA
1 CATATATA
*
20477778 CATACATA
1 CATATATA
20477786 CATATATA
1 CATATATA
*
20477794 TATATATA
1 CATATATA
*
20477802 TATATAT
1 CATATAT
20477809 GAATTACCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (8 bp):
CATATATA
Found at i:20478234 original size:31 final size:29
Alignment explanation
Indices: 20478165--20478240 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
20478155 TAATAGATTC
*
20478165 ATAATTTAAATAATATATTAAAAATTTTT
1 ATAATTTAAATATTATATTAAAAATTTTT
* *
20478194 AAAATTTAAATATTATATTAAATATTTTATT
1 ATAATTTAAATATTATATTAAA-AATTT-TT
*
20478225 ATAATTTAAAAATTAT
1 ATAATTTAAATATTAT
20478241 TCATAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 20 0.50
30 4 0.10
31 16 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAATTTAAATATTATATTAAAAATTTTT
Found at i:20478241 original size:29 final size:30
Alignment explanation
Indices: 20478165--20478259 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 30
20478155 TAATAGATTC
*
20478165 ATAATTTAAATAATATATTAAA-AATTTTT
1 ATAATTTAAATAATATATTAAATATTTTTT
* *
20478194 AAAATTTAAATATTATATTAAATATTTTATT
1 ATAATTTAAATAATATATTAAATATTTT-TT
20478225 ATAATTTAAA-AAT-TATTCATAATATTAATTTT
1 ATAATTTAAATAATATATT-A-AATATT--TTTT
20478257 ATA
1 ATA
20478260 TTAATATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
29 24 0.44
30 7 0.13
31 17 0.31
32 5 0.09
33 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATAATTTAAATAATATATTAAATATTTTTT
Found at i:20480701 original size:12 final size:12
Alignment explanation
Indices: 20480684--20480709 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20480674 TCTTGTGAAT
20480684 TTTAAGTATGGC
1 TTTAAGTATGGC
20480696 TTTAAGTATGGC
1 TTTAAGTATGGC
20480708 TT
1 TT
20480710 ATGATACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (12 bp):
TTTAAGTATGGC
Found at i:20482998 original size:3 final size:3
Alignment explanation
Indices: 20482990--20483043 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
20482980 GTGATTTTAG
* * * * *
20482990 TCA TCA TCA CCA CCA TCA TCA TCA TCC TCA TCA TCA TCT TGA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
20483038 TCA TCA
1 TCA TCA
20483044 GAGTCATCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:20483389 original size:30 final size:30
Alignment explanation
Indices: 20483324--20483413 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
20483314 TTTATTGCAG
* **
20483324 TTCAAA-AAGCCCTTAACCTTTAATTTAAA
1 TTCAAATAAGCCCTTAAACTTTAATTTGTA
**
20483353 CCCAAATAAGCCCTTAAACTTTAATTTGTA
1 TTCAAATAAGCCCTTAAACTTTAATTTGTA
* *
20483383 TTCAAATAAACTCTT-AACTTTTAATTTGTA
1 TTCAAATAAGCCCTTAAAC-TTTAATTTGTA
20483413 T
1 T
20483414 CTAAGTAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
29 7 0.14
30 43 0.86
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (30 bp):
TTCAAATAAGCCCTTAAACTTTAATTTGTA
Found at i:20483423 original size:30 final size:30
Alignment explanation
Indices: 20483355--20483430 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
20483345 AATTTAAACC
* *
20483355 CAAATAAGCCCTTAAAC-TTTAATTTGTATT
1 CAAATAAACTCTT-AACTTTTAATTTGTATT
20483385 CAAATAAACTCTTAACTTTTAATTTGTA-T
1 CAAATAAACTCTTAACTTTTAATTTGTATT
*
20483414 CTAAGTAAACTCTTAAC
1 C-AAATAAACTCTTAAC
20483431 ATAAATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 5 0.12
30 36 0.88
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.39
Consensus pattern (30 bp):
CAAATAAACTCTTAACTTTTAATTTGTATT
Found at i:20483586 original size:14 final size:15
Alignment explanation
Indices: 20483559--20483596 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
20483549 CTTTTTTAAT
*
20483559 ATTTTATCCAAAAAA
1 ATTTAATCCAAAAAA
20483574 ATTTAATCCAAAAAA
1 ATTTAATCCAAAAAA
*
20483589 ATTCAATC
1 ATTTAATC
20483597 TGACTTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTTAATCCAAAAAA
Found at i:20483917 original size:126 final size:126
Alignment explanation
Indices: 20483749--20484000 Score: 441
Period size: 126 Copynumber: 2.0 Consensus size: 126
20483739 AAAAGCAGTA
* * * *
20483749 ACAAATTCCAATAGGGTTATACCTAAACAGTGACCTAGATGCAAGTATTCCCTAGAATAAAGAGA
1 ACAAATTCCAATAGAGTTATAACTAAACAGTGACCTACATGCAAGCATTCCCTAGAATAAAGAGA
*
20483814 TAATGTATCTAACGTTTTCTCAAATCACCACAATTTTCATTATTGCTATTTCAACCTCATT
66 TAATGTATCCAACGTTTTCTCAAATCACCACAATTTTCATTATTGCTATTTCAACCTCATT
*
20483875 ACAAATTCCAATAGAGTTATAACTAAACAGTGACCTACATGCAAGCATTCCTTAGAATAAAGAGA
1 ACAAATTCCAATAGAGTTATAACTAAACAGTGACCTACATGCAAGCATTCCCTAGAATAAAGAGA
*
20483940 TAATGTATCCAATGTTTTCTCAAATCACCACAATTTTCATTATTGCTATTTCAACCTCATT
66 TAATGTATCCAACGTTTTCTCAAATCACCACAATTTTCATTATTGCTATTTCAACCTCATT
20484001 CTCCCACTTT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (126 bp):
ACAAATTCCAATAGAGTTATAACTAAACAGTGACCTACATGCAAGCATTCCCTAGAATAAAGAGA
TAATGTATCCAACGTTTTCTCAAATCACCACAATTTTCATTATTGCTATTTCAACCTCATT
Found at i:20492473 original size:2 final size:2
Alignment explanation
Indices: 20492466--20492496 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20492456 TTTTCAAGCC
*
20492466 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20492497 GTATGTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20494274 original size:12 final size:12
Alignment explanation
Indices: 20494257--20494281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20494247 GCTCTGTTTT
20494257 TTTTCTTTTTAA
1 TTTTCTTTTTAA
20494269 TTTTCTTTTTAA
1 TTTTCTTTTTAA
20494281 T
1 T
20494282 GGTTCAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTAA
Found at i:20495369 original size:2 final size:2
Alignment explanation
Indices: 20495362--20495391 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20495352 ACTTGCTGCA
*
20495362 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20495392 GACTGACTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:20500572 original size:80 final size:80
Alignment explanation
Indices: 20500439--20500595 Score: 269
Period size: 80 Copynumber: 2.0 Consensus size: 80
20500429 GTATTTCGGA
* * *
20500439 GGAAACTGACTTCGACCTTGTTCTGTTCTATGTCCCGTCAAAAGAAAAATTTCTATGTCCGAAAT
1 GGAAACTGACTTCGAACTGGTTCTGTTCTATGTCCCGTCAAAAGAAAAATTTCTATATCCGAAAT
20500504 AAAAAGCTTAAATTT
66 AAAAAGCTTAAATTT
* *
20500519 GGAAACTGACTTCGAACTGGTTCTGTTCTATGTCTCGTCAAAAGAAAATTTTCTATATCCGAAAT
1 GGAAACTGACTTCGAACTGGTTCTGTTCTATGTCCCGTCAAAAGAAAAATTTCTATATCCGAAAT
20500584 AAAAAGCTTAAA
66 AAAAAGCTTAAA
20500596 ATTAAATGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (80 bp):
GGAAACTGACTTCGAACTGGTTCTGTTCTATGTCCCGTCAAAAGAAAAATTTCTATATCCGAAAT
AAAAAGCTTAAATTT
Found at i:20506813 original size:17 final size:18
Alignment explanation
Indices: 20506775--20506827 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
20506765 ATTATTTTTT
*
20506775 AAAATATAAATATAATAT
1 AAAATATAAATATAATAC
20506793 AAAAT-TAAATA-AATAAC
1 AAAATATAAATATAAT-AC
20506810 AAAA-AT-AATATATATAC
1 AAAATATAAATATA-ATAC
20506827 A
1 A
20506828 GAATCGGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
16 7 0.23
17 16 0.53
18 7 0.23
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATAAATATAATAC
Found at i:20510497 original size:32 final size:32
Alignment explanation
Indices: 20510461--20510537 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
20510451 GTTTAGATTA
* *
20510461 TTTGGATTT-ATATTTTTTTGGATTTGGATACT
1 TTTGGATTTGA-ATTTTTTTGGATTTGAATAAT
*
20510493 TTTGGATTTGAGTTTTTTTGGATTTGAATAAT
1 TTTGGATTTGAATTTTTTTGGATTTGAATAAT
* *
20510525 TTTAGATTCGAAT
1 TTTGGATTTGAAT
20510538 AAATTTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 37 0.97
33 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (32 bp):
TTTGGATTTGAATTTTTTTGGATTTGAATAAT
Found at i:20510518 original size:16 final size:17
Alignment explanation
Indices: 20510461--20510519 Score: 70
Period size: 16 Copynumber: 3.6 Consensus size: 17
20510451 GTTTAGATTA
*
20510461 TTTGGATTT-ATATTTT
1 TTTGGATTTGAGATTTT
**
20510477 TTTGGATTTG-GATACT
1 TTTGGATTTGAGATTTT
20510493 TTTGGATTTGAG-TTTT
1 TTTGGATTTGAGATTTT
20510509 TTTGGATTTGA
1 TTTGGATTTGA
20510520 ATAATTTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (17 bp):
TTTGGATTTGAGATTTT
Found at i:20510527 original size:16 final size:16
Alignment explanation
Indices: 20510476--20510544 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
20510466 ATTTATATTT
* *
20510476 TTTTGGATTTGGATAC
1 TTTTGGATTTGAATAA
* **
20510492 TTTTGGATTTGAGTTT
1 TTTTGGATTTGAATAA
20510508 TTTTGGATTTGAATAA
1 TTTTGGATTTGAATAA
* *
20510524 TTTTAGATTCGAATAAA
1 TTTTGGATTTGAAT-AA
20510541 TTTT
1 TTTT
20510545 AAATTCAAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 37 0.86
17 6 0.14
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.54
Consensus pattern (16 bp):
TTTTGGATTTGAATAA
Found at i:20510542 original size:17 final size:16
Alignment explanation
Indices: 20510508--20510550 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
20510498 ATTTGAGTTT
* *
20510508 TTTTGGATTTGAATAA
1 TTTTAGATTCGAATAA
20510524 TTTTAGATTCGAATAAA
1 TTTTAGATTCGAAT-AA
*
20510541 TTTTAAATTC
1 TTTTAGATTC
20510551 AAACCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (16 bp):
TTTTAGATTCGAATAA
Found at i:20510777 original size:17 final size:17
Alignment explanation
Indices: 20510744--20510776 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
20510734 TAAATTTTAA
20510744 AAATAATATATTTATAT
1 AAATAATATATTTATAT
20510761 AAAT-ATATA-TTATAT
1 AAATAATATATTTATAT
20510776 A
1 A
20510777 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATAATATATTTATAT
Found at i:20511895 original size:14 final size:16
Alignment explanation
Indices: 20511870--20511906 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
20511860 CGATCTTGAA
20511870 ATTTTTTGGGTT-TAG
1 ATTTTTTGGGTTATAG
20511885 ATTTTTT-GGTTATAG
1 ATTTTTTGGGTTATAG
20511900 ATTTTTT
1 ATTTTTT
20511907 TTGGATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (16 bp):
ATTTTTTGGGTTATAG
Found at i:20513502 original size:15 final size:15
Alignment explanation
Indices: 20513463--20513502 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
20513453 AAATATATTA
20513463 ATTTTTAAAATAAAT
1 ATTTTTAAAATAAAT
* **
20513478 ATATAAAAAATAAAT
1 ATTTTTAAAATAAAT
20513493 ATTTTTAAAA
1 ATTTTTAAAA
20513503 AATTTATTTA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTTTAAAATAAAT
Found at i:20514305 original size:2 final size:2
Alignment explanation
Indices: 20514298--20514328 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20514288 GAACCTGGGC
20514298 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20514329 GTGGAAGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20515522 original size:21 final size:22
Alignment explanation
Indices: 20515478--20515524 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
20515468 ACCAAAATAA
20515478 AAAATTTATTAACTTAATAGTT
1 AAAATTTATTAACTTAATAGTT
*
20515500 AAAATTTA-TAATTTAACTA-TT
1 AAAATTTATTAACTTAA-TAGTT
20515521 AAAA
1 AAAA
20515525 ATTAACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATTTATTAACTTAATAGTT
Found at i:20515525 original size:22 final size:23
Alignment explanation
Indices: 20515477--20515527 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
20515467 GACCAAAATA
20515477 AAAAATTTATTAACTTAATAGTT
1 AAAAATTTATTAACTTAATAGTT
*
20515500 -AAAATTTA-TAATTTAACTA-TT
1 AAAAATTTATTAACTTAA-TAGTT
20515521 AAAAATT
1 AAAAATT
20515528 AACAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
AAAAATTTATTAACTTAATAGTT
Found at i:20516135 original size:13 final size:13
Alignment explanation
Indices: 20516117--20516142 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20516107 CAAGAAATAT
20516117 GATATTTGACAAC
1 GATATTTGACAAC
20516130 GATATTTGACAAC
1 GATATTTGACAAC
20516143 AAAAATTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
GATATTTGACAAC
Found at i:20518369 original size:2 final size:2
Alignment explanation
Indices: 20518364--20518391 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20518354 AATTATATTC
20518364 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
20518392 TGCAACAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20522225 original size:15 final size:15
Alignment explanation
Indices: 20522190--20522219 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20522180 TACCAAGTCT
*
20522190 GATAAAACAAATATC
1 GATAAAACAAACATC
20522205 GATAAAACAAACATC
1 GATAAAACAAACATC
20522220 ATTAAATGTC
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:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (15 bp):
GATAAAACAAACATC
Found at i:20523601 original size:2 final size:2
Alignment explanation
Indices: 20523594--20523621 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20523584 CCATAAATAA
20523594 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
20523622 GCATTAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20527349 original size:1 final size:1
Alignment explanation
Indices: 20527343--20527367 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20527333 TTGTGGCCTT
20527343 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
20527368 ATTCCTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:20528402 original size:23 final size:22
Alignment explanation
Indices: 20528362--20528404 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
20528352 ATTAATTAGT
* *
20528362 TTTATTTATTTATTTAATATTA
1 TTTATTTATATATGTAATATTA
20528384 TTTATTTTATATATGTAATAT
1 TTTA-TTTATATATGTAATAT
20528405 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATTTATATATGTAATATTA
Found at i:20530252 original size:19 final size:20
Alignment explanation
Indices: 20530223--20530260 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20530213 GTTTACATTA
*
20530223 TTTTTGCTTTGTTTTTGTTG
1 TTTTTGCTTTGGTTTTGTTG
20530243 TTTTTG-TTTGGTTTTGTT
1 TTTTTGCTTTGGTTTTGTT
20530261 TCTGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.00, C:0.03, G:0.21, T:0.76
Consensus pattern (20 bp):
TTTTTGCTTTGGTTTTGTTG
Found at i:20530257 original size:10 final size:10
Alignment explanation
Indices: 20530223--20530261 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
20530213 GTTTACATTA
20530223 TTTTTGCTTTG
1 TTTTTG-TTTG
20530234 TTTTTG-TTG
1 TTTTTGTTTG
20530243 TTTTTGTTTG
1 TTTTTGTTTG
*
20530253 GTTTTGTTT
1 TTTTTGTTT
20530262 CTGTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.35
10 11 0.42
11 6 0.23
ACGTcount: A:0.00, C:0.03, G:0.21, T:0.77
Consensus pattern (10 bp):
TTTTTGTTTG
Found at i:20541057 original size:2 final size:2
Alignment explanation
Indices: 20541050--20541075 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20541040 TCCAATTTTA
20541050 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
20541076 GTTTCACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20543576 original size:18 final size:18
Alignment explanation
Indices: 20543531--20543569 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20543521 CAAAATCTAA
*
20543531 CAAATCAGTATTTATAAT
1 CAAATCAATATTTATAAT
20543549 CAAATCAATATTTATAAT
1 CAAATCAATATTTATAAT
20543567 CAA
1 CAA
20543570 CTGAATACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.36
Consensus pattern (18 bp):
CAAATCAATATTTATAAT
Found at i:20556772 original size:25 final size:27
Alignment explanation
Indices: 20556742--20556802 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
20556732 ATACGGATAT
*
20556742 AAATAAAAAATA-AAAAA-TTATTTAG
1 AAATAAAAAATATAAAAATTTATTTAA
*
20556767 AGATAATAAAATATAAAAATTTATTTAA
1 AAATAA-AAAATATAAAAATTTATTTAA
20556795 AAATAAAA
1 AAATAAAA
20556803 CAATTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 6 0.20
27 7 0.23
28 12 0.40
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
AAATAAAAAATATAAAAATTTATTTAA
Found at i:20557379 original size:21 final size:22
Alignment explanation
Indices: 20557349--20557397 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
20557339 CCTAAAATTA
*
20557349 ATAAAATATTATTT-TTAAAAT
1 ATAAATTATTATTTTTTAAAAT
20557370 ATAAATTATTATTTTTTAAAAT
1 ATAAATTATTATTTTTTAAAAT
20557392 ATAAAT
1 ATAAAT
20557398 ATAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAATTATTATTTTTTAAAAT
Found at i:20557388 original size:22 final size:21
Alignment explanation
Indices: 20557349--20557397 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
20557339 CCTAAAATTA
*
20557349 ATAAAATATTATTTTTAAAAT
1 ATAAATTATTATTTTTAAAAT
20557370 ATAAATTATTATTTTTTAAAAT
1 ATAAATTATTA-TTTTTAAAAT
20557392 ATAAAT
1 ATAAAT
20557398 ATAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATTATTATTTTTAAAAT
Found at i:20558935 original size:144 final size:144
Alignment explanation
Indices: 20558787--20559053 Score: 322
Period size: 144 Copynumber: 1.9 Consensus size: 144
20558777 CAGATCTTCA
* *
20558787 CGAAAAACTCCAAATCATG-ATTAATTATTATTTTATAATTTTTAATGCATTAAAAACCTTAATT
1 CGAAAAACTCCAAATCATGTATTAA-TATTATTTCATAATTTTTAATGCATTAAAAACATTAATT
* * *
20558851 AAACATTGAAAGGTGA-GAAATTATCAAAATACCATTTAAGGGTATTTTTGTAATTTGACGTTCA
65 AAACATTAAAAGGT-ATGAAATTACCAAAATACCATTTAAGAGTATTTTTGTAATTTGACGTTCA
20558915 CGAGGTCCCTTATTTG
129 CGAGGTCCCTTATTTG
** * * * * * * * * *
20558931 CGAAAAGTTTCAGATCATGTTTTGATATTATTTCATGATTTTTGATGGATTAAAAACATTGATTG
1 CGAAAAACTCCAAATCATGTATTAATATTATTTCATAATTTTTAATGCATTAAAAACATTAATTA
* * * *
20558996 TACTTTAAAAGGTATGAAATTACCAAAATACCTTTTATGAGTATTTTTGTAATTTGAC
66 AACATTAAAAGGTATGAAATTACCAAAATACCATTTAAGAGTATTTTTGTAATTTGAC
20559054 CTTTCTGAAG
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
143 1 0.01
144 97 0.96
145 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (144 bp):
CGAAAAACTCCAAATCATGTATTAATATTATTTCATAATTTTTAATGCATTAAAAACATTAATTA
AACATTAAAAGGTATGAAATTACCAAAATACCATTTAAGAGTATTTTTGTAATTTGACGTTCACG
AGGTCCCTTATTTG
Found at i:20559079 original size:144 final size:143
Alignment explanation
Indices: 20558812--20559088 Score: 308
Period size: 144 Copynumber: 1.9 Consensus size: 143
20558802 CATGATTAAT
* * * *
20558812 TATTATTTTATAATTTTTAATGCATTAAAAACCTTAATTAAACATTGAAAGGTGAGAAATTATCA
1 TATTATTTCATAATTTTTAATGCATTAAAAACATTAATTAAACATTAAAAGGTGAGAAATTACCA
* * * *
20558877 AAATACCATTTAAGGGTATTTTTGTAATTTGACGTTCACGAGGTCCCTTATTTGCGAAAAGTTTC
66 AAATACCATTTAAGAGTATTTTTGTAATTTGACGTTCACGAAGTCCATTATTTACGAAAAG-TTC
20558942 AGATCATGTTTTGA
130 AGATCATGTTTTGA
* * * * ** *
20558956 TATTATTTCATGATTTTTGATGGATTAAAAACATTGATTGTACTTTAAAAGGT-ATGAAATTACC
1 TATTATTTCATAATTTTTAATGCATTAAAAACATTAATTAAACATTAAAAGGTGA-GAAATTACC
* * * * **
20559020 AAAATACCTTTTATGAGTATTTTTGTAATTTGACCTTTC-TGAAGTTGATT-TTTCACGAAAAGT
65 AAAATACCATTTAAGAGTATTTTTGTAATTTGA-CGTTCACGAAGTCCATTATTT-ACGAAAAGT
20559083 TCAGAT
128 TCAGAT
20559089 TATAGTATTA
Statistics
Matches: 109, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
143 11 0.10
144 94 0.86
145 4 0.04
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (143 bp):
TATTATTTCATAATTTTTAATGCATTAAAAACATTAATTAAACATTAAAAGGTGAGAAATTACCA
AAATACCATTTAAGAGTATTTTTGTAATTTGACGTTCACGAAGTCCATTATTTACGAAAAGTTCA
GATCATGTTTTGA
Found at i:20560118 original size:20 final size:20
Alignment explanation
Indices: 20560088--20560145 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
20560078 AAAACCAAAT
*
20560088 CTTAAATCCCAAAGTCAA-C
1 CTTAAACCCCAAAGTCAACC
20560107 CTCTAAACCCCAAAGTCAACC
1 CT-TAAACCCCAAAGTCAACC
**
20560128 CTTAAACCTTAAAGTCAA
1 CTTAAACCCCAAAGTCAA
20560146 AATTTAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.85
21 3 0.09
ACGTcount: A:0.41, C:0.33, G:0.05, T:0.21
Consensus pattern (20 bp):
CTTAAACCCCAAAGTCAACC
Found at i:20560342 original size:12 final size:13
Alignment explanation
Indices: 20560311--20560347 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
20560301 TATCCCAACC
20560311 TTAAACCCTAAAA
1 TTAAACCCTAAAA
20560324 TTAAACCCTAAAA
1 TTAAACCCTAAAA
20560337 -TAAACCCTAAA
1 TTAAACCCTAAA
20560348 CCCTTTACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (13 bp):
TTAAACCCTAAAA
Found at i:20562437 original size:19 final size:21
Alignment explanation
Indices: 20562399--20562437 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20562389 ATTATTGTAT
20562399 AAATATAAATATAGATTTTTA
1 AAATATAAATATAGATTTTTA
*
20562420 AAATATCAAT-TA-ATTTTT
1 AAATATAAATATAGATTTTT
20562438 TTATATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
AAATATAAATATAGATTTTTA
Found at i:20562648 original size:20 final size:22
Alignment explanation
Indices: 20562620--20562660 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
20562610 AAAAATTTAT
*
20562620 AATTTAAAA-TATA-TTTTAAA
1 AATTAAAAATTATACTTTTAAA
20562640 AATTAAAAATTATACTTTTAA
1 AATTAAAAATTATACTTTTAA
20562661 TCACATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTAAAAATTATACTTTTAAA
Found at i:20563537 original size:21 final size:20
Alignment explanation
Indices: 20563494--20563537 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
20563484 TATTTTATTT
*
20563494 TATAAAAATTTAAAAAAAGA
1 TATAAAAATTTAAAAAAAAA
20563514 TATATAAAA-TTAATAAAAAAA
1 TATA-AAAATTTAA-AAAAAAA
20563535 TAT
1 TAT
20563538 TTTAATTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
TATAAAAATTTAAAAAAAAA
Found at i:20564942 original size:3 final size:3
Alignment explanation
Indices: 20564927--20565010 Score: 52
Period size: 3 Copynumber: 29.0 Consensus size: 3
20564917 TATTTTTGTG
* * * * *
20564927 TTA TTA GTA TTA TTA TTTG TTA TTA TTA TTA CTA -TA GTA -TA GTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
20564971 -TA TTG TTA TTA -TA TTA TTA TCA TTA TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
20565011 GTATAGTATG
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
2 10 0.15
3 51 0.78
4 4 0.06
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:20564985 original size:11 final size:11
Alignment explanation
Indices: 20564934--20565015 Score: 50
Period size: 11 Copynumber: 7.9 Consensus size: 11
20564924 GTGTTATTAG
20564934 TATTATTAT-T
1 TATTATTATAT
*
20564944 TGTTA-T-TAT
1 TATTATTATAT
* *
20564953 TATTACTATAG
1 TATTATTATAT
*
20564964 TA-TAGTATAT
1 TATTATTATAT
*
20564974 TGTTATTATAT
1 TATTATTATAT
*
20564985 TATTATCATTAT
1 TATTATTA-TAT
20564997 TA-TATT-TAT
1 TATTATTATAT
*
20565006 TATTAGTATA
1 TATTATTATA
20565016 GTATGTTATT
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
8 1 0.02
9 11 0.20
10 15 0.28
11 22 0.41
12 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (11 bp):
TATTATTATAT
Found at i:20565932 original size:22 final size:22
Alignment explanation
Indices: 20565902--20566007 Score: 56
Period size: 23 Copynumber: 4.4 Consensus size: 22
20565892 AAATTTTATT
20565902 TTTACTTTTTGATTTTATTTTTA
1 TTTA-TTTTTGATTTTATTTTTA
20565925 TTTATTTTAT-ATTTTGAATTTTTTGAA
1 TTTATTTT-TGATTTT--A-TTTTT--A
* * *
20565952 TTT-TATTTTCAGTTT-TGTTTA
1 TTTAT-TTTTGATTTTATTTTTA
20565973 TTTATTTTATTGACTTTTATTATTTA
1 TTTA-TTT-TTGA-TTTTATT-TTTA
20565999 TTTATTTTT
1 TTTATTTTT
20566008 ACTGAGTAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 27
0.67 0.05 0.28
Matches are distributed among these distances:
21 4 0.06
22 11 0.17
23 13 0.20
24 6 0.09
25 9 0.14
26 10 0.16
27 11 0.17
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.72
Consensus pattern (22 bp):
TTTATTTTTGATTTTATTTTTA
Found at i:20570835 original size:22 final size:24
Alignment explanation
Indices: 20570792--20570835 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
20570782 TTATTTTTTT
*
20570792 ATTTTTATATATTATTTTAATAAG
1 ATTTTTATATATTATTTAAATAAG
20570816 ATTTTTA-ATA-TATTTAAATA
1 ATTTTTATATATTATTTAAATA
20570836 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
24 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTTTATATATTATTTAAATAAG
Found at i:20572222 original size:2 final size:2
Alignment explanation
Indices: 20572217--20572243 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20572207 TCATTGTGTG
20572217 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 A
20572244 ATAATATCCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20573727 original size:31 final size:31
Alignment explanation
Indices: 20573689--20573751 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
20573679 AAAAAATTTA
20573689 TTCATTAATAAGATAACATCAT-CTGATTCAC
1 TTCATTAATAAGATAACATCATCCT-ATTCAC
* *
20573720 TTCATTAATGAGATGACATCATCCTATTCAC
1 TTCATTAATAAGATAACATCATCCTATTCAC
20573751 T
1 T
20573752 AATAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (31 bp):
TTCATTAATAAGATAACATCATCCTATTCAC
Found at i:20577289 original size:20 final size:21
Alignment explanation
Indices: 20577264--20577311 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
20577254 GTGAGAAAAA
20577264 TAGAGAAAAAAACTTTTAG-G
1 TAGAGAAAAAAACTTTTAGAG
20577284 TAGAGAAAAAAACTTTTAGAG
1 TAGAGAAAAAAACTTTTAGAG
20577305 -AGAGAAA
1 TAGAGAAA
20577312 CAGATTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (21 bp):
TAGAGAAAAAAACTTTTAGAG
Found at i:20581856 original size:15 final size:16
Alignment explanation
Indices: 20581836--20581871 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20581826 CATGAGTTAC
20581836 AAAAAA-AAAAAAGGA
1 AAAAAATAAAAAAGGA
*
20581851 AAAAAATAGAAAAGGA
1 AAAAAATAAAAAAGGA
20581867 AAAAA
1 AAAAA
20581872 TAGAGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAAATAAAAAAGGA
Found at i:20581872 original size:15 final size:16
Alignment explanation
Indices: 20581836--20581875 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
20581826 CATGAGTTAC
20581836 AAAAAAA-A-AAAAGG
1 AAAAAAATAGAAAAGG
20581850 AAAAAAATAGAAAAGG
1 AAAAAAATAGAAAAGG
20581866 -AAAAAATAGA
1 AAAAAAATAGA
20581876 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.29
15 11 0.46
16 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAAAATAGAAAAGG
Found at i:20582002 original size:22 final size:22
Alignment explanation
Indices: 20581974--20582016 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20581964 CTTTTTAATA
* * *
20581974 AAAAGTATCTATATTTGAAATG
1 AAAAGTAGCCATATTTCAAATG
20581996 AAAAGTAGCCATATTTCAAAT
1 AAAAGTAGCCATATTTCAAAT
20582017 TCCTCTCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAAGTAGCCATATTTCAAATG
Found at i:20583338 original size:9 final size:9
Alignment explanation
Indices: 20583313--20583364 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
20583303 GGACATATGG
*
20583313 TATGGATTT
1 TATGCATTT
*
20583322 CATGCATTT
1 TATGCATTT
*
20583331 TATTCATTGT
1 TATGCATT-T
20583341 T-TGCATTT
1 TATGCATTT
*
20583349 TATGCATTA
1 TATGCATTT
20583358 TATGCAT
1 TATGCAT
20583365 CACATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 2 0.06
9 31 0.89
10 2 0.06
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.52
Consensus pattern (9 bp):
TATGCATTT
Found at i:20583819 original size:147 final size:145
Alignment explanation
Indices: 20583638--20584041 Score: 391
Period size: 146 Copynumber: 2.8 Consensus size: 145
20583628 AAGCCCTTTG
* * * * *
20583638 GGCATGATCTTTTTATAACTTTCGAGTATCTTTCTAAATGTTAAAGTTATGGAGCCTTCATATGA
1 GGCATGATC-TTTTAAAAATTTCTAGTATCTTTCTAAATTTTAAAGTTATGGAGTCTTCATATGA
** * *
20583703 AATGAACTTTTTCAAAATTTGATTTGTAAGATCTTTGAGGCATAATCACCAAGTCCTT-TGAGCA
65 AA-GAACTTTTTCAAAATTCAATTTGTAAGACCTTTGAGGCATAATCACCAAGTCCTTCAG-GCA
*
20583767 TGATCTATAAGTCATCCA
128 TGATCTATAAGACATCCA
* * ** *
20583785 GGCATGATCTTTTAAAAATTTGCTAGTATCTTTCTAAATTTTAAAGTTATAGAGTTTTTGTATAA
1 GGCATGATCTTTTAAAAATTT-CTAGTATCTTTCTAAATTTTAAAGTTATGGAGTCTTCATAT-G
** * ** *
20583850 AAAGAGTTTTTTCTAAATTCAATTTGTAAGACCTCCG-GGTATAATCACCAAGTCCTTCAGGCAT
64 AAAGAACTTTTTCAAAATTCAATTTGTAAGACCTTTGAGGCATAATCACCAAGTCCTTCAGGCAT
* * ***
20583914 GATCTTTAAGACCTTTG
129 GATCTATAAGACATCCA
* * ** * * * * *
20583931 GGTATGATCTTTTTAAAACCTCTAGATATCTTTCTAAGTTTTAAATTTATGAAGTCTTCATGTGG
1 GGCATGATCTTTTAAAAATTTCTAG-TATCTTTCTAAATTTTAAAGTTATGGAGTCTTCATATGA
* *
20583996 AAGAAGCTTTTTCAAAATTCAATTTATAAGACCTTT-AGGCTTAATC
65 AAGAA-CTTTTTCAAAATTCAATTTGTAAGACCTTTGAGGCATAATC
20584042 TTTAAGTCAT
Statistics
Matches: 203, Mismatches: 48, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
145 8 0.04
146 122 0.60
147 70 0.34
148 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (145 bp):
GGCATGATCTTTTAAAAATTTCTAGTATCTTTCTAAATTTTAAAGTTATGGAGTCTTCATATGAA
AGAACTTTTTCAAAATTCAATTTGTAAGACCTTTGAGGCATAATCACCAAGTCCTTCAGGCATGA
TCTATAAGACATCCA
Found at i:20584291 original size:8 final size:8
Alignment explanation
Indices: 20584278--20584324 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
20584268 AGCTTGTCAC
20584278 AAAAAAT-
1 AAAAAATA
20584285 AAAAAA-A
1 AAAAAATA
20584292 AAAAAATA
1 AAAAAATA
20584300 AAAAAATAA
1 AAAAAAT-A
*
20584309 TAAAAAAGA
1 -AAAAAATA
20584318 AAAAAAT
1 AAAAAAT
20584325 TGAATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 12 0.35
8 14 0.41
9 2 0.06
10 6 0.18
ACGTcount: A:0.87, C:0.00, G:0.02, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:20587415 original size:60 final size:60
Alignment explanation
Indices: 20587337--20587488 Score: 139
Period size: 59 Copynumber: 2.5 Consensus size: 60
20587327 ACGATGAACT
* * * **
20587337 ATTACTACATTTATTTAAAGAAACACAGTAAT-AGTGTTTTTAAAAAAATTACTTGTCTTA
1 ATTACTGCGTTTAATTAAAGAAACACAGTAATGAGTGTTTTT-AAAAAATTACTTCACTTA
* * * * * *
20587397 GTTATTGTGTTTAATTAAA-AAA-ATAATAATTGATTGTTTTTAAAAAATTACTTCACTTA
1 ATTACTGCGTTTAATTAAAGAAACACAGTAA-TGAGTGTTTTTAAAAAATTACTTCACTTA
* *
20587456 ATTACTGCGTTTACTTAAAAGAAACGCAGTAAT
1 ATTACTGCGTTTAATT-AAAGAAACACAGTAAT
20587489 TGATATATTT
Statistics
Matches: 69, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
58 5 0.07
59 32 0.46
60 24 0.35
61 4 0.06
62 4 0.06
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (60 bp):
ATTACTGCGTTTAATTAAAGAAACACAGTAATGAGTGTTTTTAAAAAATTACTTCACTTA
Found at i:20588688 original size:166 final size:166
Alignment explanation
Indices: 20588408--20588706 Score: 472
Period size: 166 Copynumber: 1.8 Consensus size: 166
20588398 ACATAGAATG
* * * * * *
20588408 AATATACAAAACAAATTGTTTATTGTGTTTGCTATGTGTTATGCCTAAAGATCACAATGCAAAAG
1 AATATACAAAACAAACTGTTTATTATGTTTGCTATATGTTATGCCAAAAGATCAAAATGCAAAAC
* * * * *
20588473 CATCGTTCATATTGTCATGTATTAATATGCAAAACAAACTATTTGCTACTAATTCAACATAGAAT
66 CATCCTTCATATTATCATGCATCAATATGCAAAACAAACTATTTGCTACTAATTCAACATAAAAT
20588538 GAAAATGCAAAAGCATCATTCATATTGTCATGTATC
131 GAAAATGCAAAAGCATCATTCATATTGTCATGTATC
* *
20588574 AATATGCAAAACAAACTGTTTGTTATGTTTGCTATATGTTATGCCAAAAGATCAAAATGCAAAAC
1 AATATACAAAACAAACTGTTTATTATGTTTGCTATATGTTATGCCAAAAGATCAAAATGCAAAAC
*
20588639 CATCCTTCATATTATCATGCATCAATATGCAAAATAAACTATTTGCTACTAATTCAACATAAAAT
66 CATCCTTCATATTATCATGCATCAATATGCAAAACAAACTATTTGCTACTAATTCAACATAAAAT
20588704 GAA
131 GAA
20588707 TACTCCTAAG
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
166 119 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (166 bp):
AATATACAAAACAAACTGTTTATTATGTTTGCTATATGTTATGCCAAAAGATCAAAATGCAAAAC
CATCCTTCATATTATCATGCATCAATATGCAAAACAAACTATTTGCTACTAATTCAACATAAAAT
GAAAATGCAAAAGCATCATTCATATTGTCATGTATC
Found at i:20600196 original size:17 final size:16
Alignment explanation
Indices: 20600166--20600205 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
20600156 AGTTTTTTGT
20600166 TTATTAA-TATTAAAA
1 TTATTAATTATTAAAA
20600181 TTATTAATTAATTAAAA
1 TTATTAATT-ATTAAAA
20600198 TTATTAAT
1 TTATTAAT
20600206 AAGTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTAATTATTAAAA
Found at i:20600217 original size:3 final size:3
Alignment explanation
Indices: 20600211--20600304 Score: 116
Period size: 3 Copynumber: 31.3 Consensus size: 3
20600201 TTAATAAGTA
* * * * * *
20600211 AAT AAT AAT AAT AAT AAT GAT GAT GAT AAT GAG AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
20600259 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT GAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20600305 TTAGTTTAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20601427 original size:3 final size:3
Alignment explanation
Indices: 20601419--20601479 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
20601409 TTATTGTTTT
20601419 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
20601467 ATA ATG ATA ATA A
1 ATA ATA ATA ATA A
20601480 CAACTTTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20601864 original size:14 final size:14
Alignment explanation
Indices: 20601817--20601920 Score: 91
Period size: 14 Copynumber: 7.2 Consensus size: 14
20601807 TGTGTTTTTA
20601817 AAAATCAAAACCCT
1 AAAATCAAAACCCT
* * *
20601831 AAATCCTCCAAATCCT
1 AAA--ATCAAAACCCT
*
20601847 AAAATCAAAACTCT
1 AAAATCAAAACCCT
* *
20601861 AAAACCTTAAACCCT
1 AAAATC-AAAACCCT
*
20601876 AAAATCAAAACACT
1 AAAATCAAAACCCT
* *
20601890 AAAACCTAAACCCT
1 AAAATCAAAACCCT
*
20601904 ACAATCAAAACCCT
1 AAAATCAAAACCCT
20601918 AAA
1 AAA
20601921 CCCTTTAAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
14 45 0.67
15 11 0.16
16 11 0.16
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATCAAAACCCT
Found at i:20601878 original size:7 final size:7
Alignment explanation
Indices: 20601862--20602001 Score: 50
Period size: 7 Copynumber: 19.0 Consensus size: 7
20601852 CAAAACTCTA
*
20601862 AAACCTT
1 AAACCCT
20601869 AAACCCT
1 AAACCCT
** *
20601876 AAAATCA
1 AAACCCT
*
20601883 AAACACT
1 AAACCCT
*
20601890 AAAACCT
1 AAACCCT
20601897 AAACCCT
1 AAACCCT
* *
20601904 ACAA-TCA
1 A-AACCCT
20601911 AAACCCT
1 AAACCCT
20601918 AAACCCTTT
1 AAACCC--T
20601927 AAAACCC-
1 -AAACCCT
*
20601934 AAACACT
1 AAACCCT
20601941 AAAACCCT
1 -AAACCCT
*
20601949 AAATCCTTT
1 AAA-CC-CT
*
20601958 AAACCCC
1 AAACCCT
*
20601965 AAACACT
1 AAACCCT
*
20601972 AAAACTCT
1 -AAACCCT
*
20601980 AAACCTT
1 AAACCCT
*
20601987 AGAAACCT
1 A-AACCCT
20601995 AAACCCT
1 AAACCCT
20602002 TCAAAACCTA
Statistics
Matches: 95, Mismatches: 27, Indels: 22
0.66 0.19 0.15
Matches are distributed among these distances:
6 7 0.07
7 54 0.57
8 23 0.24
9 5 0.05
10 6 0.06
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:20601909 original size:28 final size:28
Alignment explanation
Indices: 20601817--20601920 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 28
20601807 TGTGTTTTTA
* *
20601817 AAAATCAAAACCCTAAATCCTCCAAATCCT
1 AAAATCAAAACCCTAAAACCT--AAACCCT
*
20601847 AAAATCAAAACTCTAAAACCTTAAACCCT
1 AAAATCAAAACCCTAAAACC-TAAACCCT
*
20601876 AAAATCAAAACACTAAAACCTAAACCCT
1 AAAATCAAAACCCTAAAACCTAAACCCT
*
20601904 ACAATCAAAACCCTAAA
1 AAAATCAAAACCCTAAA
20601921 CCCTTTAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 23 0.34
29 25 0.37
30 18 0.27
31 1 0.01
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (28 bp):
AAAATCAAAACCCTAAAACCTAAACCCT
Found at i:20601945 original size:31 final size:31
Alignment explanation
Indices: 20601910--20601984 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
20601900 CCCTACAATC
20601910 AAAACCCTAAACCCTTTAAAACCCAAACACT
1 AAAACCCTAAACCCTTTAAAACCCAAACACT
* *
20601941 AAAACCCTAAATCCTTTAAACCCCAAACACT
1 AAAACCCTAAACCCTTTAAAACCCAAACACT
*
20601972 AAAACTCTAAACC
1 AAAACCCTAAACC
20601985 TTAGAAACCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (31 bp):
AAAACCCTAAACCCTTTAAAACCCAAACACT
Found at i:20601950 original size:8 final size:8
Alignment explanation
Indices: 20601853--20602028 Score: 53
Period size: 8 Copynumber: 23.5 Consensus size: 8
20601843 TCCTAAAATC
*
20601853 AAAACTCT
1 AAAACCCT
20601861 AAAA-CCT
1 AAAACCCT
*
20601868 TAAACCCT
1 AAAACCCT
*
20601876 AAAA-TC-
1 AAAACCCT
*
20601882 AAAACACT
1 AAAACCCT
20601890 AAAA-CCT
1 AAAACCCT
20601897 -AAACCCT
1 AAAACCCT
* *
20601904 ACAA-TC-
1 AAAACCCT
20601910 AAAACCCT
1 AAAACCCT
20601918 -AAACCCTTT
1 AAAACCC--T
20601927 AAAACCC-
1 AAAACCCT
*
20601934 -AAACACT
1 AAAACCCT
20601941 AAAACCCT
1 AAAACCCT
* *
20601949 AAATCCTT
1 AAAACCCT
*
20601957 TAAACCC-
1 AAAACCCT
* *
20601964 CAAACACT
1 AAAACCCT
*
20601972 AAAACTCT
1 AAAACCCT
*
20601980 -AAACCTT
1 AAAACCCT
20601987 AGAAA-CCT
1 A-AAACCCT
20601995 -AAACCCTT
1 AAAACCC-T
20602003 CAAAA-CCT
1 -AAAACCCT
*
20602011 AAAA-TC-
1 AAAACCCT
20602017 AAAACCCT
1 AAAACCCT
20602025 AAAA
1 AAAA
20602029 ATAAAAAACC
Statistics
Matches: 121, Mismatches: 26, Indels: 42
0.64 0.14 0.22
Matches are distributed among these distances:
6 22 0.18
7 38 0.31
8 46 0.38
9 6 0.05
10 9 0.07
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.18
Consensus pattern (8 bp):
AAAACCCT
Found at i:20601993 original size:31 final size:31
Alignment explanation
Indices: 20601910--20601993 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
20601900 CCCTACAATC
20601910 AAAACCCTAAACCCTTTAAAA-CCCAAACACT
1 AAAACCCTAAACCC-TTAAAACCCCAAACACT
* *
20601941 AAAACCCTAAATCCTTTAAACCCCAAACACT
1 AAAACCCTAAACCCTTAAAACCCCAAACACT
*
20601972 AAAACTCTAAA-CCTTAGAAACC
1 AAAACCCTAAACCCTTA-AAACC
20601994 TAAACCCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
30 9 0.19
31 38 0.81
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.18
Consensus pattern (31 bp):
AAAACCCTAAACCCTTAAAACCCCAAACACT
Found at i:20602059 original size:21 final size:21
Alignment explanation
Indices: 20602033--20602072 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20602023 CTAAAAATAA
* *
20602033 AAAACCTTAAAACCTCAAATC
1 AAAACCCTAAAACCCCAAATC
20602054 AAAACCCTAAAACCCCAAA
1 AAAACCCTAAAACCCCAAA
20602073 CCTAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.33, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAACCCTAAAACCCCAAATC
Found at i:20604532 original size:43 final size:42
Alignment explanation
Indices: 20604444--20604558 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 42
20604434 GAATACTTTG
*
20604444 ATTTTTCAAAGTTGTTAAGCCTCTACTTAGAGGAGATTTTCAA
1 ATTTTT-AAAGTTGTTAAGCCTCTACTTAGAGAAGATTTTCAA
* * *
20604487 ATTTTTAAAGTTATTGAGCCTCTACTTAGAGAAGTTTTTCAAA
1 ATTTTTAAAGTTGTTAAGCCTCTACTTAGAGAAGATTTTC-AA
* *
20604530 ATTTTTAAAATTGTTAAGCCTTTACTTAG
1 ATTTTTAAAGTTGTTAAGCCTCTACTTAG
20604559 GTGAGCCTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 30 0.48
43 33 0.52
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (42 bp):
ATTTTTAAAGTTGTTAAGCCTCTACTTAGAGAAGATTTTCAA
Found at i:20606254 original size:34 final size:32
Alignment explanation
Indices: 20606216--20606279 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
20606206 AAAAACAAAA
*
20606216 ATAAAACAAATAATAAAAATTAAATAAAAATAGG
1 ATAAAACAAACAAT-AAAATTAAA-AAAAATAGG
*
20606250 ATAAAACTAACAATAAAATTAAAAAAAATA
1 ATAAAACAAACAATAAAATTAAAAAAAATA
20606280 CAAATGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.25
33 9 0.32
34 12 0.43
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (32 bp):
ATAAAACAAACAATAAAATTAAAAAAAATAGG
Found at i:20606394 original size:16 final size:17
Alignment explanation
Indices: 20606363--20606399 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20606353 AAAATAAAAT
20606363 AAAACAATAAAGACAAA
1 AAAACAATAAAGACAAA
*
20606380 AAAATAATAAA-ACAAA
1 AAAACAATAAAGACAAA
20606396 AAAA
1 AAAA
20606400 AATTAAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.81, C:0.08, G:0.03, T:0.08
Consensus pattern (17 bp):
AAAACAATAAAGACAAA
Found at i:20606400 original size:17 final size:17
Alignment explanation
Indices: 20606342--20606400 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
20606332 AAAATTTCAT
* * *
20606342 AAAAACACAAGAAAATA
1 AAAAAAACAATAAAACA
20606359 AAATAAAACAATAAAGAC-
1 AAA-AAAACAATAAA-ACA
*
20606377 AAAAAAATAATAAAACA
1 AAAAAAACAATAAAACA
20606394 AAAAAAA
1 AAAAAAA
20606401 ATTAAGCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.06
17 20 0.57
18 12 0.34
19 1 0.03
ACGTcount: A:0.80, C:0.08, G:0.03, T:0.08
Consensus pattern (17 bp):
AAAAAAACAATAAAACA
Found at i:20606569 original size:3 final size:3
Alignment explanation
Indices: 20606561--20606613 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
20606551 TTCCTAAGTA
20606561 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20606609 AAT AA
1 AAT AA
20606614 ATGTTATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.