Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 117 of 129
Found at i:19637000 original size:39 final size:39
Alignment explanation
Indices: 19636895--19637148 Score: 107
Period size: 45 Copynumber: 6.0 Consensus size: 39
19636885 TTTTACTTAT
* * *
19636895 AAATAATATTATATAAATAAATAATATACTATTAATATA
1 AAATAATATTATATTAATAAATATTATAATATTAATATA
* * *
19636934 ATATACTAATAAATAATATTAAAAAATATTATAATA-TATTCATA
1 A-A-A-TAAT--ATTATATTAATAAATATTATAATATTAAT-ATA
* *
19636978 AAATAATATTATATTAATAAATATTATTACAAATAAATATTA
1 AAATAATATTATATTAATAAATATTA-TA-ATATTAATA-TA
* * * * * *
19637020 TACTAATGTATTAATTTTAATAAATAATATTATATTAATACATC
1 AAATAA--TATT-ATATTAATAAATATTATAATATTAAT--ATA
* * * *
19637064 ATATTATAATATATTAATAAATTTTATTAAT-TTAATTAATA
1 AAATAATATTATATTAATAAATATTA-TAATATTAA-T-ATA
* * * *
19637105 AATTTTATAACAATATATTAATAAATAATATACTATTAATATA
1 AA----ATAATATTATATTAATAAATATTATAATATTAATATA
19637148 A
1 A
19637149 TATATTAATA
Statistics
Matches: 157, Mismatches: 36, Indels: 40
0.67 0.15 0.17
Matches are distributed among these distances:
39 18 0.11
40 3 0.02
41 28 0.18
42 20 0.13
43 14 0.09
44 35 0.22
45 39 0.25
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (39 bp):
AAATAATATTATATTAATAAATATTATAATATTAATATA
Found at i:19637136 original size:23 final size:23
Alignment explanation
Indices: 19636931--19637204 Score: 124
Period size: 23 Copynumber: 12.0 Consensus size: 23
19636921 TACTATTAAT
*
19636931 ATAATATACTAATAAATAATATTA
1 ATAATATATTAATAAATAATA-TA
* *
19636955 A-AAAATATT-ATAATATATTCATA
1 ATAATATATTAATAA-ATAAT-ATA
*
19636978 A-AATAATATT-AT-ATTAATA-A
1 ATAAT-ATATTAATAAATAATATA
* ** *
19636998 ATATTATTACAAATAAATATTATA
1 ATAATA-TATTAATAAATAATATA
* * *
19637022 CTAATGTATTAATTTTAATAA-ATA
1 ATAATATATTAA--TAAATAATATA
* * * *
19637046 ATATTATATTAATACATCATATT
1 ATAATATATTAATAAATAATATA
*
19637069 ATAATATATTAATAAAT--TTTA
1 ATAATATATTAATAAATAATATA
* * **
19637090 TTAATTTAATTAATAAATTTTATA
1 ATAATAT-ATTAATAAATAATATA
*
19637114 ACAATATATTAATAAATAATATA
1 ATAATATATTAATAAATAATATA
* * *
19637137 CTATTA-ATATAATATATTAATA-A
1 ATAATATAT-TAATA-AATAATATA
* *
19637160 AT-AT-TTTTAATAAATAATATT
1 ATAATATATTAATAAATAATATA
*
19637181 ATAATATATTAATAAATAAAATA
1 ATAATATATTAATAAATAATATA
19637204 A
1 A
19637205 AGAATAATAA
Statistics
Matches: 181, Mismatches: 49, Indels: 41
0.67 0.18 0.15
Matches are distributed among these distances:
20 9 0.05
21 19 0.10
22 29 0.16
23 81 0.45
24 38 0.21
25 5 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATATATTAATAAATAATATA
Found at i:19637175 original size:13 final size:12
Alignment explanation
Indices: 19636893--19637198 Score: 93
Period size: 13 Copynumber: 25.6 Consensus size: 12
19636883 AATTTTACTT
19636893 ATAAATAATATTA
1 ATAAAT-ATATTA
*
19636906 TATAAATA-AATA
1 -ATAAATATATTA
19636918 AT--ATACTATTA
1 ATAAATA-TATTA
*
19636929 ATATAATATACTA
1 ATA-AATATATTA
19636942 ATAAATAATATTA
1 ATAAAT-ATATTA
19636955 A-AAA-ATATT-
1 ATAAATATATTA
*
19636964 AT-AATATATTC
1 ATAAATATATTA
19636975 AT-AA-A-A-TA
1 ATAAATATATTA
*
19636983 AT-ATTATATTA
1 ATAAATATATTA
19636994 ATAAATATTATTA
1 ATAAATA-TATTA
*
19637007 CA-AATAAATATT-
1 -ATAA-ATATATTA
*
19637019 ATACTAATGTATTA
1 ATA--AATATATTA
* *
19637033 ATTTTAATA-AATA
1 A--TAAATATATTA
*
19637046 AT-ATTATATTA
1 ATAAATATATTA
*
19637057 ATACATCATATT-
1 ATAAAT-ATATTA
19637069 AT-AATATATTA
1 ATAAATATATTA
19637080 ATAAAT-T-TT-
1 ATAAATATATTA
* *
19637089 ATTAATTTAATTA
1 ATAAATAT-ATTA
*
19637102 ATAAAT-TTTATA
1 ATAAATATAT-TA
* *
19637114 ACAATATATTAATAA
1 ATAA-ATA-T-ATTA
19637129 ATAATATACTATTA
1 ATAA-ATA-TATTA
19637143 ATATAATATATTA
1 ATA-AATATATTA
*
19637156 ATAAATATTTTTA
1 ATAAATA-TATTA
19637169 ATAAATAATATT-
1 ATAAAT-ATATTA
19637181 AT-AATATATTA
1 ATAAATATATTA
19637192 ATAAATA
1 ATAAATA
19637199 AAATAAAGAA
Statistics
Matches: 222, Mismatches: 29, Indels: 84
0.66 0.09 0.25
Matches are distributed among these distances:
8 4 0.02
9 13 0.06
10 28 0.13
11 33 0.15
12 37 0.17
13 67 0.30
14 27 0.12
15 11 0.05
16 2 0.01
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAAATATATTA
Found at i:19637309 original size:15 final size:15
Alignment explanation
Indices: 19637289--19637329 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
19637279 TATAATTATT
*
19637289 TTTTAATATTAATAA
1 TTTTAATATAAATAA
19637304 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
19637320 TTTAAATATA
1 TTTTAATATA
19637330 GTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:19637983 original size:16 final size:16
Alignment explanation
Indices: 19637947--19637985 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
19637937 CATGAATATC
*
19637947 ATAAATTTATGAATGG
1 ATAAATTTATGAATGA
19637963 ATAAATTTATGAAT-A
1 ATAAATTTATGAATGA
19637978 ATTAAATT
1 A-TAAATT
19637986 AATGCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (16 bp):
ATAAATTTATGAATGA
Found at i:19638024 original size:20 final size:20
Alignment explanation
Indices: 19638001--19638043 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
19637991 AATTTAAGTT
*
19638001 TGATTAATGATTGTTTATTA
1 TGATTAATGATTATTTATTA
19638021 TGATTAATGATTATTTATTA
1 TGATTAATGATTATTTATTA
19638041 TGA
1 TGA
19638044 ATTTAGACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (20 bp):
TGATTAATGATTATTTATTA
Found at i:19638775 original size:19 final size:19
Alignment explanation
Indices: 19638751--19638787 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19638741 ATTAAGATTT
19638751 ATAAATAAATTTTAAATTA
1 ATAAATAAATTTTAAATTA
* *
19638770 ATAAATATATTTTGAATT
1 ATAAATAAATTTTAAATT
19638788 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATAAATAAATTTTAAATTA
Found at i:19641041 original size:2 final size:2
Alignment explanation
Indices: 19641036--19641068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19641026 GGGTTAACTT
19641036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19641069 TTTGGTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19649676 original size:21 final size:21
Alignment explanation
Indices: 19649652--19649692 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19649642 GAGGTTGCAG
*
19649652 AAGCTGATGCAGAGGCAGCAC
1 AAGCTGATGCAGAAGCAGCAC
**
19649673 AAGCTTTTGCAGAAGCAGCA
1 AAGCTGATGCAGAAGCAGCA
19649693 ATGAAGACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (21 bp):
AAGCTGATGCAGAAGCAGCAC
Found at i:19659393 original size:18 final size:18
Alignment explanation
Indices: 19659370--19659405 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19659360 CTGGCCCAAA
19659370 GTCATCTTTGAAAGTATT
1 GTCATCTTTGAAAGTATT
19659388 GTCATCTTTGAAAGTATT
1 GTCATCTTTGAAAGTATT
19659406 AATTGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (18 bp):
GTCATCTTTGAAAGTATT
Found at i:19659536 original size:23 final size:23
Alignment explanation
Indices: 19659510--19659563 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
19659500 GGCAAGCAAT
*
19659510 TCTTCATACTTGTGATCTCAAAG
1 TCTTCAGACTTGTGATCTCAAAG
19659533 TCTTCAGACTTGTGATCTCAAAG
1 TCTTCAGACTTGTGATCTCAAAG
19659556 TCTTCAGA
1 TCTTCAGA
19659564 TAAAACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (23 bp):
TCTTCAGACTTGTGATCTCAAAG
Found at i:19662852 original size:2 final size:2
Alignment explanation
Indices: 19662847--19662872 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19662837 TAAAAAATTA
19662847 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
19662873 TGGTTACATC
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:19666514 original size:2 final size:2
Alignment explanation
Indices: 19666507--19666533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19666497 AACTGGCAAT
19666507 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19666534 GCATGTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19668354 original size:12 final size:12
Alignment explanation
Indices: 19668337--19668389 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
19668327 TTTTTTAAAA
19668337 TTTATATTTAAT
1 TTTATATTTAAT
*
19668349 TTTATATATT-TT
1 TTTATAT-TTAAT
19668361 TATATATATTTAAT
1 T-T-TATATTTAAT
19668375 TTTATATTTATAT
1 TTTATATTTA-AT
19668388 TT
1 TT
19668390 AAAATAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 17 0.50
13 10 0.29
14 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATTTAAT
Found at i:19677423 original size:29 final size:29
Alignment explanation
Indices: 19677358--19677425 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
19677348 ATTGAATTTA
* *
19677358 AAATAT-TAATTTTTTAAATTAAAATATC
1 AAATATATAATTTTTTAAAATAAAACATC
*
19677386 AAATA-ATAATTTTATTAAAATAATACAT-
1 AAATATATAATTTT-TTAAAATAAAACATC
19677414 AAATATATAATT
1 AAATATATAATT
19677426 AAATTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATATATAATTTTTTAAAATAAAACATC
Found at i:19677431 original size:29 final size:24
Alignment explanation
Indices: 19677371--19677432 Score: 61
Period size: 29 Copynumber: 2.4 Consensus size: 24
19677361 TATTAATTTT
19677371 TTAAATTAAAATATCAAATAATAA
1 TTAAATTAAAATATCAAATAATAA
**
19677395 TTTTATTAAAATAATACATAAATATATAA
1 TTAAATTAAAAT-AT-C--AAATA-ATAA
19677424 TTAAATTAA
1 TTAAATTAA
19677433 TAAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 10 0.34
25 2 0.07
26 1 0.03
28 5 0.17
29 11 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAAATTAAAATATCAAATAATAA
Found at i:19678286 original size:363 final size:367
Alignment explanation
Indices: 19677861--19678616 Score: 1033
Period size: 363 Copynumber: 2.1 Consensus size: 367
19677851 ATAATTTTAT
19677861 TAATTAAAAAATAAAAAATAAAGAAAAAAAAGGAAGATAATTGAGATACCATGTTAACATTTAAA
1 TAATT-AAAAATAAAAAATAAAGAAAAAAAA-GAAGATAATTGAGATACCATGTTAACATTTAAA
* * *
19677926 TTGAGTTTAAAATATTAATATCTTAACTTAAAGTATAAAATCATACTTTTTTAATATAATATATG
64 TTGAATTTAAAATATTAATATCTTAAATTAAAGTATAAAATCATACTTTTTTAATATAATATATA
* *
19677991 CATATAAATATAAAATTAAATAGATAA-ATATATATATATATATATATATATCATGGAATGACTT
129 CATATAAATATAAAATTAAATAGATAATA-AAATATATATATATATATATATCATGGAATGACCT
* * *
19678055 GGGTAGAGCACCCTAAATTTATTTTGGTCTATCGTTACCTTTAAT-AAA-AAAA-AATCCAACAA
193 -GATAGAGCACCCTAAATCTATTTTGGTCTATCCTTACCTTTAATAAAATAAAATAATCCAACAA
* * * * * *
19678117 ACTTTATATTGATTTTTTAAAAAAA-ATCAAATCGAGATAAATGGATACCTATAAGATACTAATT
257 ACTTAATATTAAATTTTTAAAAAAATATCAAATCGAGACAAATGAATACCTATAAAATACTAATT
* ** * * **
19678181 ATTTTGTTGTTGTTATTGATTGATTCATCTTATTGTAAAATTGATA
322 ATTTTGTTATTGTTAGAGATCGACTCATCTTATTGTAAAACAGATA
* *
19678227 TAATTAAAAATAAGTAAAA-AAA-AAAAAAAA-AAGATAATTGAGATAGCATGTTGACATTTAAA
1 TAATTAAAAATAA--AAAATAAAGAAAAAAAAGAAGATAATTGAGATACCATGTTAACATTTAAA
* *
19678289 TTGAATTTAAAATGTTAATATCTTAAATTAAAGTATAAAGTCATACTTTTTTAATATAATATATA
64 TTGAATTTAAAATATTAATATCTTAAATTAAAGTATAAAATCATACTTTTTTAATATAATATATA
*
19678354 CATATAAATATAAAATTAAATAGATAATAAAATATATATATATATATATATCATTGAATGACCTG
129 CATATAAATATAAAATTAAATAGATAATAAAATATATATATATATATATATCATGGAATGACCTG
* * * **
19678419 ATAGAGCACCCTAAATCTGTTTTGGTTTATCCTTACCTTTTATAAAATAAAATAATCCAACTGAC
194 ATAGAGCACCCTAAATCTATTTTGGTCTATCCTTACCTTTAATAAAATAAAATAATCCAACAAAC
* ** *
19678484 TTAATATTAAATTTTTAAAAAAATATTAAATCGAGACGGATGAATACCTATAAAATACTAATTGT
259 TTAATATTAAATTTTTAAAAAAATATCAAATCGAGACAAATGAATACCTATAAAATACTAATTAT
* * *
19678549 TTTGTTATTGTTAGAGATCGACTCATTTTGTTGTAAAACAGATC
324 TTTGTTATTGTTAGAGATCGACTCATCTTATTGTAAAACAGATA
19678593 TAATTAAAAAATATGAAAAATAAA
1 TAATT-AAAAATA--AAAAATAAA
19678617 TAAATAAAGA
Statistics
Matches: 341, Mismatches: 38, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
362 38 0.11
363 152 0.45
364 5 0.01
365 46 0.13
366 81 0.24
367 15 0.04
368 3 0.01
369 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (367 bp):
TAATTAAAAATAAAAAATAAAGAAAAAAAAGAAGATAATTGAGATACCATGTTAACATTTAAATT
GAATTTAAAATATTAATATCTTAAATTAAAGTATAAAATCATACTTTTTTAATATAATATATACA
TATAAATATAAAATTAAATAGATAATAAAATATATATATATATATATATCATGGAATGACCTGAT
AGAGCACCCTAAATCTATTTTGGTCTATCCTTACCTTTAATAAAATAAAATAATCCAACAAACTT
AATATTAAATTTTTAAAAAAATATCAAATCGAGACAAATGAATACCTATAAAATACTAATTATTT
TGTTATTGTTAGAGATCGACTCATCTTATTGTAAAACAGATA
Found at i:19679028 original size:20 final size:20
Alignment explanation
Indices: 19678990--19679029 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19678980 GAAATTTTAT
*
19678990 TAAATTTATATATTAAATAA
1 TAAATTTATATAATAAATAA
19679010 TAAATTTAT-TAATATAATAA
1 TAAATTTATATAATA-AATAA
19679030 AATATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTTATATAATAAATAA
Found at i:19680175 original size:13 final size:13
Alignment explanation
Indices: 19680157--19680181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19680147 ATTAATTTTA
19680157 AATATAATATAAT
1 AATATAATATAAT
19680170 AATATAATATAA
1 AATATAATATAA
19680182 AAACAATATA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:19680525 original size:6 final size:6
Alignment explanation
Indices: 19680502--19680535 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
19680492 AATTATTTTT
19680502 ATATTA ATAATATA ATATTA ATATTA ATATTA AT
1 ATATTA AT-AT-TA ATATTA ATATTA ATATTA AT
19680536 CTTATACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:19680886 original size:19 final size:19
Alignment explanation
Indices: 19680838--19680886 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
19680828 AATAAATATA
19680838 TTATATT-TATATTTAAAAT
1 TTATATTATAT-TTTAAAAT
* *
19680857 TTA-AATATATTTTATAAT
1 TTATATTATATTTTAAAAT
19680875 TTATATTATATT
1 TTATATTATATT
19680887 ATTTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATTATATTTTAAAAT
Found at i:19680899 original size:23 final size:23
Alignment explanation
Indices: 19680834--19680903 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
19680824 GTATAATAAA
19680834 TATATTATATTTATATTTAA-AATT
1 TATATTATA-TTAT-TTTAATAATT
19680858 TA-A--ATA-TATTTT-ATAATT
1 TATATTATATTATTTTAATAATT
19680876 TATATTATATTATTTTAATAATT
1 TATATTATATTATTTTAATAATT
19680899 TATAT
1 TATAT
19680904 CATCGAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 4 0.10
21 6 0.15
22 6 0.15
23 12 0.30
24 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTATATTATTTTAATAATT
Found at i:19686584 original size:79 final size:79
Alignment explanation
Indices: 19686453--19686610 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
19686443 GATCGGCTTG
*
19686453 GCAATGGCTGGTGGTGGGGCTTATCTTGTTTACAGATATAGATTAAGGGTAAGTTCGTGCATTAC
1 GCAATGGCTGGTGGTGGGGCTTATCTTGTTTACAGATATAGATTAAGGGTAAGCTCGTGCATTAC
19686518 ATTATAAAATAAGC
66 ATTATAAAATAAGC
19686532 GCAATGGCTGGTGGTGGGGCTTATCTTGTTTACAGATATAGATTAAGGGTAAGCTCGTGCATTAC
1 GCAATGGCTGGTGGTGGGGCTTATCTTGTTTACAGATATAGATTAAGGGTAAGCTCGTGCATTAC
19686597 ATTATAAAATAAGC
66 ATTATAAAATAAGC
19686611 CTACAGTATG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (79 bp):
GCAATGGCTGGTGGTGGGGCTTATCTTGTTTACAGATATAGATTAAGGGTAAGCTCGTGCATTAC
ATTATAAAATAAGC
Found at i:19697307 original size:23 final size:23
Alignment explanation
Indices: 19697281--19697343 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
19697271 AAATTTGATA
19697281 TAAATAAATTTAAAAATATATAT
1 TAAATAAATTTAAAAATATATAT
19697304 TAAATAAATTTAAAAATATATAT
1 TAAATAAATTTAAAAATATATAT
*
19697327 GAAATAAAATTTAAAAA
1 TAAAT-AAATTTAAAAA
19697344 CTCTTTAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 27 0.71
24 11 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAATAAATTTAAAAATATATAT
Found at i:19698692 original size:2 final size:2
Alignment explanation
Indices: 19698681--19698730 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
19698671 ATTACCAACT
* * *
19698681 TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TT TA TT TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19698721 TA TA TT TA TA
1 TA TA TA TA TA
19698731 GTATTAATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:19698745 original size:25 final size:25
Alignment explanation
Indices: 19698694--19698745 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
19698684 AATATATATA
* *
19698694 TATATATATATATTATTTATTTATT
1 TATATATATATAGTATTTAATTATT
*
19698719 TATATATTTATAGTA-TTAATTAGTT
1 TATATATATATAGTATTTAATTA-TT
19698744 TA
1 TA
19698746 GTGGAATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TATATATATATAGTATTTAATTATT
Found at i:19706949 original size:20 final size:21
Alignment explanation
Indices: 19706911--19706950 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
19706901 GATGATTTTA
*
19706911 TAGTATTTTGATAAAATTATG
1 TAGTATTTTAATAAAATTATG
*
19706932 TAGTA-TTTAATAATATTAT
1 TAGTATTTTAATAAAATTAT
19706951 TTATACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (21 bp):
TAGTATTTTAATAAAATTATG
Found at i:19713929 original size:27 final size:29
Alignment explanation
Indices: 19713894--19713958 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
19713884 AATTAATATA
* * *
19713894 TTTATAATTTATATATTA-ATTATAATTT
1 TTTATAATTTAAATATAATATTAAAATTT
19713922 TTTA-AATTTAAATATAATATTAAAATTTT
1 TTTATAATTTAAATATAATATTAAAA-TTT
19713951 TTTATAAT
1 TTTATAAT
19713959 ACAGATATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 11 0.35
28 10 0.32
29 7 0.23
30 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTATAATTTAAATATAATATTAAAATTT
Found at i:19714437 original size:21 final size:21
Alignment explanation
Indices: 19714413--19714479 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
19714403 AAAAATGAAA
19714413 TAAAAATTTTTATTATTTATT
1 TAAAAATTTTTATTATTTATT
***
19714434 TAAAAATAAATATT-TTTATT
1 TAAAAATTTTTATTATTTATT
*
19714454 TAAATTATTTTTA-TATTTAATT
1 TAAA-AATTTTTATTATTT-ATT
19714476 TAAA
1 TAAA
19714480 TAATAAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 11 0.31
21 18 0.50
22 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAAAATTTTTATTATTTATT
Found at i:19714677 original size:22 final size:23
Alignment explanation
Indices: 19714634--19714689 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
19714624 AATTTAATAT
19714634 TTTAAATTAAATATAAAAAT-AA
1 TTTAAATTAAATATAAAAATAAA
* * **
19714656 TTTAAATTAATTTTAATCATAAA
1 TTTAAATTAAATATAAAAATAAA
19714679 TTT-AATTAAAT
1 TTTAAATTAAAT
19714690 GCATCTAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAATTAAATATAAAAATAAA
Found at i:19733189 original size:15 final size:15
Alignment explanation
Indices: 19733169--19733199 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19733159 TGTTGCTGCT
19733169 GAAGAAGAAGAGGAA
1 GAAGAAGAAGAGGAA
*
19733184 GAAGAAGAAGTGGAA
1 GAAGAAGAAGAGGAA
19733199 G
1 G
19733200 GAGAGGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (15 bp):
GAAGAAGAAGAGGAA
Found at i:19733925 original size:21 final size:22
Alignment explanation
Indices: 19733899--19733946 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
19733889 GCAAAATTAA
19733899 TAAAATAATATATTTTATTTT-
1 TAAAATAATATATTTTATTTTC
* * *
19733920 TAAAATTATTTTTTTTATTTTC
1 TAAAATAATATATTTTATTTTC
19733942 TAAAA
1 TAAAA
19733947 ATTATACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TAAAATAATATATTTTATTTTC
Found at i:19734721 original size:111 final size:113
Alignment explanation
Indices: 19734514--19734743 Score: 335
Period size: 111 Copynumber: 2.1 Consensus size: 113
19734504 CTTTGAAAAT
* * *
19734514 TAAATTATATTTAGTATGGTAGATCTAGCTCAGTACATAAGAAGCAATATCATTTTTTTTTAAGT
1 TAAATTATATTTAGTATGGTAGATCTAGCGCAGTACATAAGAAGCAATATCATTTTTTTTAAAAT
19734579 TATATTTATAATTAAGTATTACATTCATATAATAATATAATCAATTAA
66 TATATTTATAATTAAGTATTACATTCATATAATAATATAATCAATTAA
* * *
19734627 TAAATTGTATTTGGTATGGTAGATCTAGCGCA-TGACACT-GGAAG-AA-AT-ATTATTTTTTAA
1 TAAATTATATTTAGTATGGTAGATCTAGCGCAGT-ACA-TAAGAAGCAATATCATT-TTTTTTAA
*
19734687 AATTATATTTATAATTAAGTATTACATTCATATAATGATATAATCAATTAA
63 AATTATATTTATAATTAAGTATTACATTCATATAATAATATAATCAATTAA
19734738 TAAATT
1 TAAATT
19734744 TTAATTTAAT
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
110 3 0.03
111 64 0.60
112 3 0.03
113 36 0.34
114 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (113 bp):
TAAATTATATTTAGTATGGTAGATCTAGCGCAGTACATAAGAAGCAATATCATTTTTTTTAAAAT
TATATTTATAATTAAGTATTACATTCATATAATAATATAATCAATTAA
Found at i:19735281 original size:27 final size:27
Alignment explanation
Indices: 19735229--19735282 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
19735219 TTATTTAATT
*
19735229 TTTTAAATTAAAATAAAATGTGTTATA
1 TTTTAAATTAAAATAAAATGTATTATA
19735256 TTTTAAATTTTAAAAT-AAATG-ATTATA
1 TTTTAAA--TTAAAATAAAATGTATTATA
19735283 AATTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 12 0.50
28 5 0.21
29 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (27 bp):
TTTTAAATTAAAATAAAATGTATTATA
Found at i:19741549 original size:62 final size:63
Alignment explanation
Indices: 19741450--19741577 Score: 222
Period size: 62 Copynumber: 2.0 Consensus size: 63
19741440 AATATATCAA
19741450 AAATTAAAATTTTTAATTAAAAGATTAAAAATTCAAAAAATATAATAATATTTGAAGAAAAAT
1 AAATTAAAATTTTTAATTAAAAGATTAAAAATTCAAAAAATATAATAATATTTGAAGAAAAAT
* * *
19741513 AAATTAAAATTTTTAATTAAAA-ATTAAAATTTCAAAACATATAATAATATTTGAAGAAAACT
1 AAATTAAAATTTTTAATTAAAAGATTAAAAATTCAAAAAATATAATAATATTTGAAGAAAAAT
19741575 AAA
1 AAA
19741578 ATATCTTAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 40 0.65
63 22 0.35
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (63 bp):
AAATTAAAATTTTTAATTAAAAGATTAAAAATTCAAAAAATATAATAATATTTGAAGAAAAAT
Found at i:19741747 original size:22 final size:20
Alignment explanation
Indices: 19741718--19741757 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19741708 TATACATCTG
19741718 TAAATTTATATAATTTTAAGA
1 TAAATTTAT-TAATTTTAAGA
*
19741739 TAAATTTTATTTATTTTAA
1 TAAA-TTTATTAATTTTAA
19741758 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TAAATTTATTAATTTTAAGA
Found at i:19743228 original size:25 final size:25
Alignment explanation
Indices: 19743190--19743241 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
19743180 TATAAAAAAA
19743190 AATTTTAAAGATTTTCTTACATATC
1 AATTTTAAAGATTTTCTTACATATC
*
19743215 AATTTT-AAGAATTTTTTTACATATC
1 AATTTTAAAG-ATTTTCTTACATATC
19743240 AA
1 AA
19743242 AAAGAGAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (25 bp):
AATTTTAAAGATTTTCTTACATATC
Found at i:19746877 original size:29 final size:29
Alignment explanation
Indices: 19746845--19746901 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
19746835 ATTATATATT
*
19746845 TTTTATATTCAAATAAAATTTTACTTTTA
1 TTTTATATTCAAATAAAATTTTAATTTTA
* *
19746874 TTTTATATTTAAATAAATTTTTAATTTT
1 TTTTATATTCAAATAAAATTTTAATTTT
19746902 TAATTTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTATATTCAAATAAAATTTTAATTTTA
Found at i:19753820 original size:4 final size:4
Alignment explanation
Indices: 19753813--19753839 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19753803 ACACACACAC
19753813 ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATA
19753840 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:19754101 original size:21 final size:22
Alignment explanation
Indices: 19754077--19754120 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19754067 TAAATTAAAA
*
19754077 AATAAAGTT-AATTTATAATTT
1 AATAAAGTTAAATTTAAAATTT
*
19754098 AATAAATTTAAATTTAAAATTT
1 AATAAAGTTAAATTTAAAATTT
19754120 A
1 A
19754121 TGTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATAAAGTTAAATTTAAAATTT
Found at i:19754238 original size:2 final size:2
Alignment explanation
Indices: 19754231--19754268 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19754221 CCAATTTAAC
19754231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19754269 CACACACACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19754503 original size:14 final size:14
Alignment explanation
Indices: 19754483--19754513 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
19754473 TTGAAATCTA
19754483 AAAAAAAATAAAAAC
1 AAAAAAAA-AAAAAC
19754498 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
19754512 AA
1 AA
19754514 TTTAACAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:19754563 original size:8 final size:8
Alignment explanation
Indices: 19754546--19754592 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
19754536 TTTTAAAACT
19754546 AAAAAA-A
1 AAAAAATA
*
19754553 AAATAATA
1 AAAAAATA
*
19754561 AAAGAATA
1 AAAAAATA
19754569 AAAAAATA
1 AAAAAATA
**
19754577 AAAGCATA
1 AAAAAATA
19754585 AAAAAATA
1 AAAAAATA
19754593 TATGTATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
7 5 0.16
8 27 0.84
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:19754576 original size:16 final size:16
Alignment explanation
Indices: 19754551--19754592 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
19754541 AAACTAAAAA
19754551 AAAAATAATAAAAGAAT
1 AAAAA-AATAAAAGAAT
*
19754568 AAAAAAATAAAAGCAT
1 AAAAAAATAAAAGAAT
19754584 AAAAAAATA
1 AAAAAAATA
19754593 TATGTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (16 bp):
AAAAAAATAAAAGAAT
Found at i:19761283 original size:19 final size:19
Alignment explanation
Indices: 19761261--19761321 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
19761251 AAGTCAGACA
*
19761261 TAAATTAAAAAATAAATAT
1 TAAATTAAATAATAAATAT
* *
19761280 TAAATTTACATAATAAA-CT
1 TAAA-TTAAATAATAAATAT
* *
19761299 TAATTTATATAATAAATAT
1 TAAATTAAATAATAAATAT
19761318 TAAA
1 TAAA
19761322 ATTTTTTGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 11 0.33
19 12 0.36
20 10 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTAAATAATAAATAT
Found at i:19761399 original size:13 final size:13
Alignment explanation
Indices: 19761364--19761403 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
19761354 AATTTGCATA
19761364 TATATACTTTATAAT
1 TATATA-TTT-TAAT
19761379 TATAATATTTTAAT
1 TAT-ATATTTTAAT
19761393 TATATATTTTA
1 TATATATTTTA
19761404 TTTAGGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.33
14 7 0.29
15 6 0.25
16 3 0.12
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TATATATTTTAAT
Found at i:19762056 original size:21 final size:17
Alignment explanation
Indices: 19762007--19762058 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
19761997 TGATATTATT
*
19762007 TAATTTAATTTTATTTA
1 TAATATAATTTTATTTA
*
19762024 TAATATCATTTTATTTGA
1 TAATATAATTTTATTT-A
19762042 TACTATTATAATTTTAT
1 TA--A-TATAATTTTAT
19762059 ATACCAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 14 0.50
18 3 0.11
20 1 0.04
21 10 0.36
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATATAATTTTATTTA
Found at i:19763161 original size:12 final size:12
Alignment explanation
Indices: 19763138--19763207 Score: 63
Period size: 12 Copynumber: 5.7 Consensus size: 12
19763128 TTATATAAAA
*
19763138 TTTATTTTTAAT
1 TTTATATTTAAT
19763150 TATT-TATTTAAT
1 T-TTATATTTAAT
19763162 TTTATATTTATAT
1 TTTATATTTA-AT
* *
19763175 TTAAAATATT-AT
1 TTTATAT-TTAAT
19763187 TTTATATTTATAT
1 TTTATATTTA-AT
19763200 TTTATATT
1 TTTATATT
19763208 AAAAAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 4 0.09
12 22 0.47
13 19 0.40
14 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATATTTAAT
Found at i:19763164 original size:18 final size:18
Alignment explanation
Indices: 19763154--19763207 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
19763144 TTTAATTATT
19763154 TATTTAATTTTATATTTA
1 TATTTAATTTTATATTTA
*
19763172 TATTTAAAATATTAT-TTTA
1 TATTT--AATTTTATATTTA
19763191 TATTTATATTTTATATT
1 TATTTA-ATTTTATATT
19763208 AAAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 1 0.03
18 11 0.37
19 11 0.37
20 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTAATTTTATATTTA
Found at i:19763171 original size:6 final size:6
Alignment explanation
Indices: 19763150--19763207 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
19763140 TATTTTTAAT
* *
19763150 TATTTA T-TTAA T-TTTA TATTTA TATTTAA AATATTA T-TTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTT-A TAT-TTA TATTTA TATTTA
19763197 TATTTTA TATT
1 TA-TTTA TATT
19763208 AAAAAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 12 0.28
6 19 0.44
7 10 0.23
8 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:19763200 original size:13 final size:13
Alignment explanation
Indices: 19763154--19763207 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
19763144 TTTAATTATT
19763154 TATTTA-ATTTTA
1 TATTTATATTTTA
*
19763166 TATTTATATTTAA
1 TATTTATATTTTA
* *
19763179 AATAT-TATTTTA
1 TATTTATATTTTA
19763191 TATTTATATTTTA
1 TATTTATATTTTA
19763204 TATT
1 TATT
19763208 AAAAAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
12 15 0.44
13 19 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTTATATTTTA
Found at i:19763200 original size:31 final size:32
Alignment explanation
Indices: 19763153--19763217 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
19763143 TTTTAATTAT
*
19763153 TTATTTAATTTTATA-TTTATATT-TAAAATA
1 TTATTTAATTTTATATTTTATATTAAAAAATA
*
19763183 TTATTTTATATTTATATTTTATATTAAAAAATA
1 TTATTTAAT-TTTATATTTTATATTAAAAAATA
19763216 TT
1 TT
19763218 TCATTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 8 0.27
31 6 0.20
32 8 0.27
33 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TTATTTAATTTTATATTTTATATTAAAAAATA
Found at i:19768685 original size:20 final size:22
Alignment explanation
Indices: 19768660--19768702 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19768650 TACATAAAAA
19768660 AATTTA-C-GAGAAGACAAATC
1 AATTTACCTGAGAAGACAAATC
19768680 AATTTACCTGAGAAGACAAATC
1 AATTTACCTGAGAAGACAAATC
19768702 A
1 A
19768703 GCAGCTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (22 bp):
AATTTACCTGAGAAGACAAATC
Found at i:19775420 original size:10 final size:10
Alignment explanation
Indices: 19775405--19775435 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
19775395 GACACGACAG
19775405 ACAATGAAGT
1 ACAATGAAGT
19775415 ACAATGAAGT
1 ACAATGAAGT
19775425 ACAATGAAGT
1 ACAATGAAGT
19775435 A
1 A
19775436 GTTGCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (10 bp):
ACAATGAAGT
Found at i:19779719 original size:22 final size:23
Alignment explanation
Indices: 19779682--19779726 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
19779672 ACGAATTATA
* *
19779682 AAATATATTTAAATTTTAAATAT
1 AAATATATATAAATTTAAAATAT
19779705 AAATATA-ATAAATTTAAAATAT
1 AAATATATATAAATTTAAAATAT
19779727 GATATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATATATAAATTTAAAATAT
Found at i:19779811 original size:24 final size:24
Alignment explanation
Indices: 19779781--19779846 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
19779771 CATAACATAA
19779781 ATAAATAAA-ATAATATAAATATAC
1 ATAAATAAATATAAT-TAAATATAC
* *
19779805 ATGAATAAATATCATTAAATATAC
1 ATAAATAAATATAATTAAATATAC
* * *
19779829 GTAAATAAACATGATTAA
1 ATAAATAAATATAATTAA
19779847 TAAGAATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (24 bp):
ATAAATAAATATAATTAAATATAC
Found at i:19779825 original size:14 final size:14
Alignment explanation
Indices: 19779775--19779837 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
19779765 TTTAAACATA
19779775 ACATAAATAAATA-
1 ACATAAATAAATAT
*
19779788 AAATAATATAAATAT
1 ACATAA-ATAAATAT
*
19779803 ACATGAATAAATAT
1 ACATAAATAAATAT
19779817 -CAT---TAAATAT
1 ACATAAATAAATAT
*
19779827 ACGTAAATAAA
1 ACATAAATAAA
19779838 CATGATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
10 7 0.17
11 2 0.05
13 8 0.20
14 19 0.47
15 4 0.10
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (14 bp):
ACATAAATAAATAT
Found at i:19785616 original size:21 final size:20
Alignment explanation
Indices: 19785591--19785634 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 20
19785581 CGAAGATGGG
19785591 TTTTTCTTCTTTTCTTTTTAT
1 TTTTTC-TCTTTTCTTTTTAT
19785612 TTTTTCTCTTTT-TTTTT-T
1 TTTTTCTCTTTTCTTTTTAT
19785630 TTTTT
1 TTTTT
19785635 TTGGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 5 0.22
20 6 0.26
21 6 0.26
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTCTCTTTTCTTTTTAT
Found at i:19785635 original size:21 final size:21
Alignment explanation
Indices: 19785591--19785636 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
19785581 CGAAGATGGG
19785591 TTTTTCTTCTTTTCTTTTTAT
1 TTTTTCTTCTTTTCTTTTTAT
* *
19785612 TTTTTC-TCTTTTTTTTTTTT
1 TTTTTCTTCTTTTCTTTTTAT
19785632 TTTTT
1 TTTTT
19785637 GGTTTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (21 bp):
TTTTTCTTCTTTTCTTTTTAT
Found at i:19785925 original size:19 final size:18
Alignment explanation
Indices: 19785901--19785942 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
19785891 TAATTTTATC
19785901 TATAATTTTTATTATAATT
1 TATAA-TTTTATTATAATT
19785920 TATAA--TTATTATAATT
1 TATAATTTTATTATAATT
19785936 TATAATT
1 TATAATT
19785943 GTTCAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 16 0.76
19 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATAATTTTATTATAATT
Found at i:19785928 original size:16 final size:16
Alignment explanation
Indices: 19785909--19785942 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19785899 TCTATAATTT
19785909 TTATTATAATTTATAA
1 TTATTATAATTTATAA
19785925 TTATTATAATTTATAA
1 TTATTATAATTTATAA
19785941 TT
1 TT
19785943 GTTCAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATAATTTATAA
Found at i:19786543 original size:14 final size:14
Alignment explanation
Indices: 19786524--19786551 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19786514 TTTTTTGTCA
19786524 CCAAAAAATTAAAT
1 CCAAAAAATTAAAT
19786538 CCAAAAAATTAAAT
1 CCAAAAAATTAAAT
19786552 TTGGTTGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (14 bp):
CCAAAAAATTAAAT
Found at i:19794793 original size:48 final size:48
Alignment explanation
Indices: 19794735--19794829 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
19794725 ACTAATGTTG
*
19794735 TGGTACTCGACTACAACTGATTTTCACCAACTTTTATCTTTTTCACAA
1 TGGTAATCGACTACAACTGATTTTCACCAACTTTTATCTTTTTCACAA
19794783 TGGTAATCGACTACAACTGATTTTCACCAACTTTTATCTTTTTCACA
1 TGGTAATCGACTACAACTGATTTTCACCAACTTTTATCTTTTTCACA
19794830 GTGCCATAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.40
Consensus pattern (48 bp):
TGGTAATCGACTACAACTGATTTTCACCAACTTTTATCTTTTTCACAA
Found at i:19797779 original size:19 final size:20
Alignment explanation
Indices: 19797755--19797794 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19797745 TTTGATTATG
19797755 GAAAA-CAAGGGGCGGGAAT
1 GAAAACCAAGGGGCGGGAAT
* *
19797774 GAAAACCGAGGGGTGGGAAT
1 GAAAACCAAGGGGCGGGAAT
19797794 G
1 G
19797795 GGATAGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.10, G:0.45, T:0.07
Consensus pattern (20 bp):
GAAAACCAAGGGGCGGGAAT
Found at i:19798052 original size:2 final size:2
Alignment explanation
Indices: 19798039--19798071 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19798029 ATTCCTTTAG
*
19798039 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19798072 TTTATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19799881 original size:2 final size:2
Alignment explanation
Indices: 19799874--19799901 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19799864 AAATAAATAA
19799874 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
19799902 TAAAGTAGAT
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:19809235 original size:22 final size:22
Alignment explanation
Indices: 19809210--19809254 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
19809200 ATTAAATTAC
19809210 TCTTTATTTTCATTGGACTTCA
1 TCTTTATTTTCATTGGACTTCA
19809232 TCTTTATTTTCATTGGACTTCA
1 TCTTTATTTTCATTGGACTTCA
19809254 T
1 T
19809255 GGATTTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.56
Consensus pattern (22 bp):
TCTTTATTTTCATTGGACTTCA
Found at i:19810445 original size:36 final size:35
Alignment explanation
Indices: 19810395--19810464 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
19810385 TAGACGTCAC
*
19810395 TATTTTTATATATTTTATAAGTGTTAAAATTTATA
1 TATTTATATATATTTTATAAGTGTTAAAATTTATA
* *
19810430 TATTTATATTATATTTTTTAAGTGTTATAATTTAT
1 TATTTATA-TATATTTTATAAGTGTTAAAATTTAT
19810465 GTTAACACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (35 bp):
TATTTATATATATTTTATAAGTGTTAAAATTTATA
Found at i:19811001 original size:33 final size:34
Alignment explanation
Indices: 19810937--19811006 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 34
19810927 ATAAAAAAAT
*
19810937 TATTTTTTAATTATTTATATATATTATATAATGA
1 TATTTTTTAATTATTTATATATATTAAATAATGA
*
19810971 TATTTTTTAA-TATTTATAT-T-TTAAA-AATAA
1 TATTTTTTAATTATTTATATATATTAAATAATGA
19811001 TATTTT
1 TATTTT
19811007 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 10 0.29
31 4 0.12
32 1 0.03
33 9 0.26
34 10 0.29
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (34 bp):
TATTTTTTAATTATTTATATATATTAAATAATGA
Found at i:19811003 original size:20 final size:21
Alignment explanation
Indices: 19810978--19811031 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
19810968 TGATATTTTT
19810978 TAATATTTATATTTT-AAAAA
1 TAATATTTATATTTTAAAAAA
19810998 TAATATTTTATATTTTAAAAAA
1 TAATA-TTTATATTTTAAAAAA
19811020 TAATATTT-TATT
1 TAATATTTATATT
19811032 AAATTTCTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.28
21 13 0.41
22 10 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATATTTATATTTTAAAAAA
Found at i:19811009 original size:21 final size:22
Alignment explanation
Indices: 19810978--19811030 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
19810968 TGATATTTTT
19810978 TAATA-TTTATATTTT-AAAAA
1 TAATATTTTATATTTTAAAAAA
19810998 TAATATTTTATATTTTAAAAAA
1 TAATATTTTATATTTTAAAAAA
19811020 TAATATTTTAT
1 TAATATTTTAT
19811031 TAAATTTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 5 0.16
21 10 0.32
22 16 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATATTTTATATTTTAAAAAA
Found at i:19823146 original size:17 final size:16
Alignment explanation
Indices: 19823124--19823155 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
19823114 AATTCCTTTC
19823124 AAAATTATACAAAATTA
1 AAAATTATA-AAAATTA
19823141 AAAATTATAAAAATT
1 AAAATTATAAAAATT
19823156 TATATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTATAAAAATTA
Found at i:19823241 original size:20 final size:20
Alignment explanation
Indices: 19823223--19823266 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 20
19823213 AATAAATATC
19823223 ATTTTATTAATAAAAATATTAA
1 ATTTTA-TAATAAAAATA-TAA
19823245 ATTTTATAATAAAATATATAA
1 ATTTTATAATAAAA-ATATAA
19823266 A
1 A
19823267 AATTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTTATAATAAAAATATAA
Found at i:19824055 original size:30 final size:31
Alignment explanation
Indices: 19824001--19824186 Score: 114
Period size: 30 Copynumber: 6.0 Consensus size: 31
19823991 CTCCAGTGAC
19824001 AGCTTCTCCTCCTCCAGTTTCAACTCCTCCACCT
1 AGCTTCTCCTCCTCCAG---CAACTCCTCCACCT
*
19824035 AGC-TCTCCTCCTCCAGCAACTCCCCCACCCGTT
1 AGCTTCTCCTCCTCCAGCAACTCCTCCA-CC--T
* * * *
19824068 AGC-CCTCCTCC-ACAGGCTACGCCTCCACC-
1 AGCTTCTCCTCCTCCA-GCAACTCCTCCACCT
* * * *
19824097 AGCTTCTCCACCTCCTGCCACTCCGCCACCT
1 AGCTTCTCCTCCTCCAGCAACTCCTCCACCT
* * *
19824128 -GCTTCTCCCCCTCCTGCTACTCCTCCACCT
1 AGCTTCTCCTCCTCCAGCAACTCCTCCACCT
* * * * *
19824158 -GCATCACCCCCTCCAGCAACCCCACCACC
1 AGCTTCTCCTCCTCCAGCAACTCCTCCACC
19824187 AGCACCCTTG
Statistics
Matches: 123, Mismatches: 22, Indels: 18
0.75 0.13 0.11
Matches are distributed among these distances:
29 3 0.02
30 77 0.63
31 3 0.02
32 4 0.03
33 33 0.27
34 3 0.02
ACGTcount: A:0.15, C:0.55, G:0.09, T:0.22
Consensus pattern (31 bp):
AGCTTCTCCTCCTCCAGCAACTCCTCCACCT
Found at i:19824128 original size:15 final size:15
Alignment explanation
Indices: 19824110--19824159 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
19824100 TTCTCCACCT
* *
19824110 CCTGCCACTCCGCCA
1 CCTGCTACTCCCCCA
* *
19824125 CCTGCTTCTCCCCCT
1 CCTGCTACTCCCCCA
*
19824140 CCTGCTACTCCTCCA
1 CCTGCTACTCCCCCA
19824155 CCTGC
1 CCTGC
19824160 ATCACCCCCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.08, C:0.58, G:0.10, T:0.24
Consensus pattern (15 bp):
CCTGCTACTCCCCCA
Found at i:19826890 original size:25 final size:26
Alignment explanation
Indices: 19826832--19826892 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
19826822 AAAATTTTAA
* *
19826832 ATCATA-TTAATTTTATATTTTTTAT
1 ATCATATTTTATTTTATATTTATTAT
*
19826857 ATCAT-TTTTATTTTATA-TTATTGT
1 ATCATATTTTATTTTATATTTATTAT
19826881 ATCATATTTTAT
1 ATCATATTTTAT
19826893 ATTAAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (26 bp):
ATCATATTTTATTTTATATTTATTAT
Found at i:19830174 original size:12 final size:12
Alignment explanation
Indices: 19830157--19830183 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19830147 CTAAATATAT
19830157 AAAATTAAATTA
1 AAAATTAAATTA
19830169 AAAATTAAATTA
1 AAAATTAAATTA
19830181 AAA
1 AAA
19830184 TTTTTTATAT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATTAAATTA
Found at i:19837171 original size:11 final size:10
Alignment explanation
Indices: 19837154--19837193 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
19837144 TATTTATTTA
19837154 TTCTTTTTTT
1 TTCTTTTTTT
19837164 TCTCTTTTCTTT
1 T-TCTTTT-TTT
*
19837176 TTCTTTTTCT
1 TTCTTTTTTT
19837186 TTCTTTTT
1 TTCTTTTT
19837194 CTGGCAACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 11 0.41
11 12 0.44
12 4 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:19837175 original size:16 final size:16
Alignment explanation
Indices: 19837154--19837195 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
19837144 TATTTATTTA
19837154 TTCTTTTT-TTTCTCTT
1 TTCTTTTTCTTTCTC-T
*
19837170 TTCTTTTTCTTTTTCT
1 TTCTTTTTCTTTCTCT
19837186 TTCTTTTTCT
1 TTCTTTTTCT
19837196 GGCAACGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTTTCTTTCTCT
Found at i:19837179 original size:22 final size:22
Alignment explanation
Indices: 19837154--19837195 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19837144 TATTTATTTA
19837154 TTCTTTTT-TTTCTCTTTTCTTT
1 TTCTTTTTCTTTCT-TTTTCTTT
19837176 TTCTTTTTCTTTCTTTTTCT
1 TTCTTTTTCTTTCTTTTTCT
19837196 GGCAACGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTCTTTTTCTTTCTTTTTCTTT
Found at i:19838951 original size:17 final size:17
Alignment explanation
Indices: 19838908--19838951 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
19838898 ACTAAATAAG
19838908 AAAAAATCAAATAACAA
1 AAAAAATCAAATAACAA
**
19838925 AAAATTTCAACA-AACAA
1 AAAAAATCAA-ATAACAA
19838942 AAAAAATCAA
1 AAAAAATCAA
19838952 GAAAATTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAAATCAAATAACAA
Found at i:19839904 original size:17 final size:17
Alignment explanation
Indices: 19839884--19839936 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
19839874 AGTTATGTGT
*
19839884 AAAAAAAAAACACAAAC
1 AAAAAAAAAACAAAAAC
*
19839901 AAAAAAAAAATAAAAAC
1 AAAAAAAAAACAAAAAC
*
19839918 -AAAACAAAACAAAAA-
1 AAAAAAAAAACAAAAAC
19839933 AAAA
1 AAAA
19839937 TCTTAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAC
Found at i:19839915 original size:27 final size:27
Alignment explanation
Indices: 19839883--19839936 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
19839873 AAGTTATGTG
*
19839883 TAAAAAAAAAACACAAACAAAAAAAAAA
1 TAAAAACAAAACA-AAACAAAAAAAAAA
19839911 TAAAAACAAAACAAAACAAAAAAAAA
1 TAAAAACAAAACAAAACAAAAAAAAA
19839937 TCTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.85, C:0.11, G:0.00, T:0.04
Consensus pattern (27 bp):
TAAAAACAAAACAAAACAAAAAAAAAA
Found at i:19841257 original size:34 final size:34
Alignment explanation
Indices: 19841214--19841285 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
19841204 AGCTTCAAAG
19841214 AGTATGCACATAGATAGAAAGATATGGCTATACA
1 AGTATGCACATAGATAGAAAGATATGGCTATACA
19841248 AGTATGCACATAGATAGAAAGATATGGCTATACA
1 AGTATGCACATAGATAGAAAGATATGGCTATACA
19841282 AGTA
1 AGTA
19841286 CAACATTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (34 bp):
AGTATGCACATAGATAGAAAGATATGGCTATACA
Found at i:19843190 original size:21 final size:21
Alignment explanation
Indices: 19843165--19843204 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19843155 CAGAAAAATC
19843165 AAAAGTAAA-AAAAAAAGAAGA
1 AAAAG-AAAGAAAAAAAGAAGA
19843186 AAAAGAAAGAAAAAAAGAA
1 AAAAGAAAGAAAAAAAGAA
19843205 ATGATTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (21 bp):
AAAAGAAAGAAAAAAAGAAGA
Found at i:19843202 original size:12 final size:12
Alignment explanation
Indices: 19843166--19843205 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
19843156 AGAAAAATCA
19843166 AAAGTAAAAAAA-
1 AAAG-AAAAAAAG
19843178 AAAGAAGAAAAAG
1 AAAGAA-AAAAAG
19843191 AAAGAAAAAAAG
1 AAAGAAAAAAAG
19843203 AAA
1 AAA
19843206 TGATTGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.08
12 18 0.69
13 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:19844963 original size:42 final size:42
Alignment explanation
Indices: 19844858--19844968 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
19844848 CATTAAAAAA
* *
19844858 ATCATTTACATTTTTTCTCGATGGTGATATCTGAGTGTCAAGAT
1 ATCATTTACA-TATTT-TCGGTGGTGATATCTGAGTGTCAAGAT
* * * * * *
19844902 TTGAATCACATCTTCTCGGTGGTGATATCTGAGTGTCAA-AGT
1 ATCATTTACATATTTTCGGTGGTGATATCTGAGTGTCAAGA-T
19844944 ATCATTTACATATTTTCGGTGGTGA
1 ATCATTTACATATTTTCGGTGGTGA
19844969 CATTCGAATG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
41 1 0.02
42 43 0.81
43 3 0.06
44 6 0.11
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (42 bp):
ATCATTTACATATTTTCGGTGGTGATATCTGAGTGTCAAGAT
Found at i:19844981 original size:42 final size:42
Alignment explanation
Indices: 19844917--19845006 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
19844907 TCACATCTTC
* * *
19844917 TCGGTGGTGATATCTGAGTGTCAAAGTATCATTTACATATTT
1 TCGGTGGTGACATCTGAATGTCAAAGTATCAATTACATATTT
* * * *
19844959 TCGGTGGTGACAT-TCGAATGTCAAGGTTTGAATTACATTTTT
1 TCGGTGGTGACATCT-GAATGTCAAAGTATCAATTACATATTT
19845001 TCGGTG
1 TCGGTG
19845007 ACGATATCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.40
Consensus pattern (42 bp):
TCGGTGGTGACATCTGAATGTCAAAGTATCAATTACATATTT
Found at i:19844989 original size:84 final size:86
Alignment explanation
Indices: 19844858--19845015 Score: 196
Period size: 84 Copynumber: 1.9 Consensus size: 86
19844848 CATTAAAAAA
* * *
19844858 ATCATTTACATTTTTTCTCGATGGTGATATCTGAGTGTCAAGATTTGAATCACATCTTCTCGGTG
1 ATCATTTACATTATTTCTCGATGGTGACATCTGAATGTCAAGATTTGAATCACATCTTCTCGGTG
**
19844923 GTGATATCTGAGTGTCAAAGT
66 ACGATATCTGAGTGTCAAAGT
* * * * *
19844944 ATCATTTACA-TATTT-TCGGTGGTGACAT-TCGAATGTCAAGGTTTGAATTACATTTTTTCGGT
1 ATCATTTACATTATTTCTCGATGGTGACATCT-GAATGTCAAGATTTGAATCACATCTTCTCGGT
19845006 GACGATATCT
65 GACGATATCT
19845016 AAAGTCATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
83 1 0.02
84 46 0.75
85 4 0.07
86 10 0.16
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (86 bp):
ATCATTTACATTATTTCTCGATGGTGACATCTGAATGTCAAGATTTGAATCACATCTTCTCGGTG
ACGATATCTGAGTGTCAAAGT
Found at i:19845074 original size:14 final size:14
Alignment explanation
Indices: 19845055--19845084 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19845045 ATCCGAGTGC
19845055 CAAGGTTTGAATTG
1 CAAGGTTTGAATTG
19845069 CAAGGTTTGAATTG
1 CAAGGTTTGAATTG
19845083 CA
1 CA
19845085 TTTTCTCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (14 bp):
CAAGGTTTGAATTG
Found at i:19845131 original size:89 final size:89
Alignment explanation
Indices: 19844980--19845157 Score: 259
Period size: 89 Copynumber: 2.0 Consensus size: 89
19844970 ATTCGAATGT
* *
19844980 CAAGGTTTGAATTACATTTTTTCGGTGACGATATCTAAAGTCATTTACCTTTTCTCGATGGTGAT
1 CAAGGTTTGAATTACATTTTCTCGGTGACAATATCTAAAGTCATTTACCTTTTCTCGATGGTGAT
19845045 ATCCGAGTGCCAAGGTTTGAATTG
66 ATCCGAGTGCCAAGGTTTGAATTG
* * * * *
19845069 CAAGGTTTGAATTGCATTTTCTCGGTGGCAATATCTGAAA-TCATTTGCCTTTTTTCGGTGGTGA
1 CAAGGTTTGAATTACATTTTCTCGGTGACAATATCT-AAAGTCATTTACCTTTTCTCGATGGTGA
* *
19845133 TATTCGAGTGTCAAGGTTTGAATTG
65 TATCCGAGTGCCAAGGTTTGAATTG
19845158 TATTTTCTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 76 0.96
90 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (89 bp):
CAAGGTTTGAATTACATTTTCTCGGTGACAATATCTAAAGTCATTTACCTTTTCTCGATGGTGAT
ATCCGAGTGCCAAGGTTTGAATTG
Found at i:19845196 original size:75 final size:76
Alignment explanation
Indices: 19845069--19845241 Score: 253
Period size: 75 Copynumber: 2.3 Consensus size: 76
19845059 GTTTGAATTG
* * *
19845069 CAAGGTTTGAATTGCATTTTCTCGGTGGCAATATCTGAAATCATTTGCCTTTTTTCGGTGGTGAT
1 CAAGGTTTGAATTGCATTTTCTCGATGGCAATATCTCAAATCATTTGCCTTTTCTCGGTGGTGAT
*
19845134 ATTCGAGTGT-
66 ATCCGAGTGTC
* *
19845144 CAAGGTTTGAATTGTATTTTCTCGATGGCAATAT-TCAAAGTCATTTGTCTTTTCTCGGTGGTGA
1 CAAGGTTTGAATTGCATTTTCTCGATGGCAATATCTCAAA-TCATTTGCCTTTTCTCGGTGGTGA
19845208 TATCCGAGTGTC
65 TATCCGAGTGTC
*
19845220 CAA-GTTTGAATTGCATATTCTC
1 CAAGGTTTGAATTGCATTTTCTC
19845242 ATTGGTGATA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
74 4 0.05
75 81 0.92
76 3 0.03
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (76 bp):
CAAGGTTTGAATTGCATTTTCTCGATGGCAATATCTCAAATCATTTGCCTTTTCTCGGTGGTGAT
ATCCGAGTGTC
Found at i:19845258 original size:42 final size:42
Alignment explanation
Indices: 19845202--19845359 Score: 133
Period size: 42 Copynumber: 4.0 Consensus size: 42
19845192 CTTTTCTCGG
* *
19845202 TGGTGATATCCGAGTGTCCAAGTTTGAATTGCATATTCTCAT
1 TGGTGATATCCGAGTGTCAAAGTTTGAATTACATATTCTCAT
* * *
19845244 TGGTGATATTCGAGTGTCAAAGTTTGAATTACATTTTCT-AGG
1 TGGTGATATCCGAGTGTCAAAGTTTGAATTACATATTCTCA-T
*
19845286 TGGTGATATCCGA-AGTC--A-TTTG-----CATATTC-C-T
1 TGGTGATATCCGAGTGTCAAAGTTTGAATTACATATTCTCAT
* *
19845317 GGTGGTGATATCCGAGTGTCAAAGTTTGAATTGCATTTTCTCA
1 --TGGTGATATCCGAGTGTCAAAGTTTGAATTACATATTCTCA
19845360 GTGACAATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
33 19 0.21
34 3 0.03
36 1 0.01
37 4 0.04
38 4 0.04
39 1 0.01
41 4 0.04
42 53 0.59
43 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (42 bp):
TGGTGATATCCGAGTGTCAAAGTTTGAATTACATATTCTCAT
Found at i:19845323 original size:75 final size:75
Alignment explanation
Indices: 19845230--19845507 Score: 382
Period size: 75 Copynumber: 3.7 Consensus size: 75
19845220 CAAGTTTGAA
* **
19845230 TTGCATATTCTC-ATTGGTGATATTCGAGTGTCAAAGTTTGAATTACATTTTCTAGGTGGTGATA
1 TTGCATATTCTCGA-TGGTGATATCCGAGTGTCAAAGTTTGAATTACATTTTCTAGGTGACGATA
19845294 TCCGAAGTCAT
65 TCCGAAGTCAT
* * *
19845305 TTGCATATTC-CTGGTGGTGATATCCGAGTGTCAAAGTTTGAATTGCATTTTCTCA-GTGACAAT
1 TTGCATATTCTC-GATGGTGATATCCGAGTGTCAAAGTTTGAATTACATTTTCT-AGGTGACGAT
19845368 ATCCGAAGTCAT
64 ATCCGAAGTCAT
* * *
19845380 TTGCATATTCTCGATAGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTTGGTGACGATAT
1 TTGCATATTCTCGATGGTGATATCCGAGTGTCAAAGTTTGAATTACATTTTCTAGGTGACGATAT
**
19845445 TAGAAGTCAT
66 CCGAAGTCAT
* * *
19845455 TTGCATATTCTCGATGGTGATATTCGAGTGTTAAAGGTTGAATTACATTTTCT
1 TTGCATATTCTCGATGGTGATATCCGAGTGTCAAAGTTTGAATTACATTTTCT
19845508 TAATGATGAT
Statistics
Matches: 179, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
74 1 0.01
75 176 0.98
76 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (75 bp):
TTGCATATTCTCGATGGTGATATCCGAGTGTCAAAGTTTGAATTACATTTTCTAGGTGACGATAT
CCGAAGTCAT
Found at i:19845333 original size:117 final size:117
Alignment explanation
Indices: 19845127--19845359 Score: 326
Period size: 117 Copynumber: 2.0 Consensus size: 117
19845117 CTTTTTTCGG
* ** * *
19845127 TGGTGATATTCGAGTGTCAAGGTTTGAATTGTATTTTCTCGATGGCAATATTCAAAGTCATTTGT
1 TGGTGATATTCGAGTGTCAAAGTTTGAATTACATTTTCTAGATGGCAATATCCAAAGTCATTTGT
* *
19845192 CTTTTCTCGGTGGTGATATCCGAGTGTCCAAGTTTGAATTGCATATTCTCAT
66 CTTTCCTCGGTGGTGATATCCGAGTGTCAAAGTTTGAATTGCATATTCTCAT
* ** *
19845244 TGGTGATATTCGAGTGTCAAAGTTTGAATTACATTTTCTAGGTGGTGATATCCGAAGTCATTTG-
1 TGGTGATATTCGAGTGTCAAAGTTTGAATTACATTTTCTAGATGGCAATATCCAAAGTCATTTGT
*
19845308 CATATTCCT-GGTGGTGATATCCGAGTGTCAAAGTTTGAATTGCATTTTCTCA
66 C-T-TTCCTCGGTGGTGATATCCGAGTGTCAAAGTTTGAATTGCATATTCTCA
19845360 GTGACAATAT
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
116 1 0.01
117 97 0.95
118 4 0.04
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (117 bp):
TGGTGATATTCGAGTGTCAAAGTTTGAATTACATTTTCTAGATGGCAATATCCAAAGTCATTTGT
CTTTCCTCGGTGGTGATATCCGAGTGTCAAAGTTTGAATTGCATATTCTCAT
Found at i:19845402 original size:192 final size:189
Alignment explanation
Indices: 19845073--19845438 Score: 470
Period size: 192 Copynumber: 1.9 Consensus size: 189
19845063 GAATTGCAAG
* * * * ** *
19845073 GTTTGAATTGCATTTTCTCGGTGGCAATATCTGAAATCATTTGCCTTTTTTCGGTGGTGATATTC
1 GTTTGAATTACATTTTCTAGGTGGCAATATCCGAAATCATTTGCATTTCCTCGGTGGTGATATCC
* * * * * *
19845138 GAGTGTCAAGGTTTGAATTGTATTTTCTCGATGGCAATATTCAAAGTCATTTGTCTTTTCTCGGT
66 GAGTGTCAAAGTTTGAATTGCATTTTCTCGATGACAATATCCAAAGTCATTTGTCTATTCTCGAT
* *
19845203 GGTGATATCCGAGTGTCCAA-GTTTGAATTGCATATTCTCATTGGTGATATTCGAGTGTCAAA
131 AGTGATATCCGAGTGT-CAAGGTTTGAATTACAT-TT-TC-TTGGTGATATTCGAGTGTCAAA
** *
19845265 GTTTGAATTACATTTTCTAGGTGGTGATATCCGAAGTCATTTGCATATTCCT-GGTGGTGATATC
1 GTTTGAATTACATTTTCTAGGTGGCAATATCCGAAATCATTTGCAT-TTCCTCGGTGGTGATATC
*
19845329 CGAGTGTCAAAGTTTGAATTGCATTTTCTC-AGTGACAATATCCGAAGTCATTTG-CATATTCTC
65 CGAGTGTCAAAGTTTGAATTGCATTTTCTCGA-TGACAATATCCAAAGTCATTTGTC-TATTCTC
19845392 GATAGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTTGGTGA
128 GATAGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTTGGTGA
19845439 CGATATTAGA
Statistics
Matches: 151, Mismatches: 19, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
189 7 0.05
190 2 0.01
191 7 0.05
192 132 0.87
193 3 0.02
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (189 bp):
GTTTGAATTACATTTTCTAGGTGGCAATATCCGAAATCATTTGCATTTCCTCGGTGGTGATATCC
GAGTGTCAAAGTTTGAATTGCATTTTCTCGATGACAATATCCAAAGTCATTTGTCTATTCTCGAT
AGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTTGGTGATATTCGAGTGTCAAA
Found at i:19845775 original size:49 final size:50
Alignment explanation
Indices: 19845722--19845835 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 50
19845712 AAATTTTTTG
** * *
19845722 AGCCTCTGCTTTTATAAGCTTTTTCAAGATGA-GAATTGTAAAGTTATTA
1 AGCCTCTGCTTAGAGAAACTTTTTCAAGATGATGAATTGTAAAGTTATTA
* * *
19845771 AGCCTCTGCTTAGAGAAACTTTTTCAAGATGATGAATTTTAAAGTTGTTG
1 AGCCTCTGCTTAGAGAAACTTTTTCAAGATGATGAATTGTAAAGTTATTA
*
19845821 AGCCTCTGTTTAGAG
1 AGCCTCTGCTTAGAG
19845836 GGGTTTTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 28 0.50
50 28 0.50
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (50 bp):
AGCCTCTGCTTAGAGAAACTTTTTCAAGATGATGAATTGTAAAGTTATTA
Found at i:19845834 original size:50 final size:50
Alignment explanation
Indices: 19845706--19845867 Score: 175
Period size: 50 Copynumber: 3.3 Consensus size: 50
19845696 TTAATAGTTT
* * * *
19845706 AATTTTAAATTTTTTGAGCCTCTGCTTT-TATAAGCTTTTTCAAGATGA-G
1 AATTTTAAAGTTGTTGAGCCTCTG-TTTAGAGAAGCTTTTTCAAGATGATG
* * * * *
19845755 AATTGTAAAGTTATTAAGCCTCTGCTTAGAGAAACTTTTTCAAGATGATG
1 AATTTTAAAGTTGTTGAGCCTCTGTTTAGAGAAGCTTTTTCAAGATGATG
** * * *
19845805 AATTTTAAAGTTGTTGAGCCTCTGTTTAGAGGGGTTTTTTTAAGATGATA
1 AATTTTAAAGTTGTTGAGCCTCTGTTTAGAGAAGCTTTTTCAAGATGATG
19845855 AATTTTAAAGTTG
1 AATTTTAAAGTTG
19845868 AATTTTAAAG
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
48 2 0.02
49 37 0.40
50 54 0.58
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (50 bp):
AATTTTAAAGTTGTTGAGCCTCTGTTTAGAGAAGCTTTTTCAAGATGATG
Found at i:19845873 original size:13 final size:13
Alignment explanation
Indices: 19845855--19845880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19845845 TAAGATGATA
19845855 AATTTTAAAGTTG
1 AATTTTAAAGTTG
19845868 AATTTTAAAGTTG
1 AATTTTAAAGTTG
19845881 TTGAGACCCT
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:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
AATTTTAAAGTTG
Found at i:19845913 original size:63 final size:63
Alignment explanation
Indices: 19845803--19845930 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 63
19845793 TTCAAGATGA
** * * **
19845803 TGAATTTTAAAGTTGTTGAGCCTCTGTTTAGAGGGGTTTTTTTAAGATGATAAATTTTAAAGT
1 TGAATTTTAAAGTTGTTGAGCCTCTGCCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGT
19845866 TGAATTTTAAAGTTGTTGAGACC-CTGCCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGT
1 TGAATTTTAAAGTTGTTGAG-CCTCTGCCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGT
19845929 TG
1 TG
19845931 TTGAGCCCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 56 0.97
64 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (63 bp):
TGAATTTTAAAGTTGTTGAGCCTCTGCCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGT
Found at i:19845946 original size:50 final size:50
Alignment explanation
Indices: 19845868--19846130 Score: 295
Period size: 50 Copynumber: 5.3 Consensus size: 50
19845858 TTTAAAGTTG
*
19845868 AATTTTAAAGTTGTTGAGACC-CTGCCTAGAGGAGCTTTTCCAAGATGATA
1 AATTTTAAAGTTGTTGAG-CCTCTGCTTAGAGGAGCTTTTCCAAGATGATA
* * *
19845918 AATTTTAAAGTTGTTGAGCC-CTTACCTAGAGGAGCTTTTCCAAGATGATG
1 AATTTTAAAGTTGTTGAGCCTC-TGCTTAGAGGAGCTTTTCCAAGATGATA
* * * *
19845968 AATTTTAAAATTATTGAGCCTCTACTTAGAGGAGCTTTTTCAAGATG--A
1 AATTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTCCAAGATGATA
* * **
19846016 AATTTTAAAGTTATTGAGCCTCTGCTTAGAAGAGCTTTTTTAAGATG--A
1 AATTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTCCAAGATGATA
* * * * * * *
19846064 ATTTTTAAAGTTGTTAAGCATATGCTTATATGAGCTTTTCCAAGATGATG
1 AATTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTCCAAGATGATA
19846114 AATTTTAAAGTTGTTGA
1 AATTTTAAAGTTGTTGA
19846131 ACTTTTGATT
Statistics
Matches: 186, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
48 82 0.44
49 3 0.02
50 100 0.54
51 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (50 bp):
AATTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTCCAAGATGATA
Found at i:19845963 original size:113 final size:113
Alignment explanation
Indices: 19845754--19845976 Score: 272
Period size: 113 Copynumber: 2.0 Consensus size: 113
19845744 TTCAAGATGA
* * *
19845754 GAATTGTAAAGTTATTAAGCCTCTGCTTAGAGAAACTTTTTCAAGATGATGAATTTTAAAGTTGT
1 GAATTGTAAAGTTATTAAGCCTCTGCCTAGAGAAACTTTTCCAAGATGATAAATTTTAAAGTTGT
* * * **
19845819 TGAGCCTCTGTTTAGAGGGGTTTTTTTAAGATGATAAATTTTAAAGTT
66 TGAGCCTCTGTCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGTT
* * * * *
19845867 GAATTTTAAAGTTGTTGAGACC-CTGCCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGTTG
1 GAATTGTAAAGTTATTAAG-CCTCTGCCTAGAGAAACTTTTCCAAGATGATAAATTTTAAAGTTG
*
19845931 TTGAGCC-CT-TACCTAGAGGAGCTTTTCCAAGATGATGAATTTTAAA
65 TTGAGCCTCTGT--CTAGAGGAGCTTTTCCAAGATGATAAATTTTAAA
19845977 ATTATTGAGC
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
111 1 0.01
112 2 0.02
113 88 0.95
114 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (113 bp):
GAATTGTAAAGTTATTAAGCCTCTGCCTAGAGAAACTTTTCCAAGATGATAAATTTTAAAGTTGT
TGAGCCTCTGTCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGTT
Found at i:19846153 original size:146 final size:147
Alignment explanation
Indices: 19845868--19846132 Score: 338
Period size: 146 Copynumber: 1.8 Consensus size: 147
19845858 TTTAAAGTTG
* *
19845868 AATTTTAAAGTTGTTGAGACCCTGCCTAGAGGAGCTTTTCCAAGATGATAAATTTTAAAGTTGTT
1 AATTTTAAAGTTATTGAGACCCTGCCTAGAAGAGCTTTTCCAAGATGA-AAATTTTAAAGTTGTT
* * *
19845933 GAGCCCTTACCTAGAGGAGCTTTTCCAAGATGATGAATTTTAAAATTATTGAGCCTCTACTTAGA
65 AAGCCATTACCTAGAGGAGCTTTTCCAAGATGATGAATTTTAAAATTATTGAACCTCTACTTAGA
*
19845998 GGAGCTTTTTCAAGATGA
130 GAAGCTTTTTCAAGATGA
* ** *
19846016 AATTTTAAAGTTATTGAG-CCTCTGCTTAGAAGAGCTTTTTTAAGATG-AATTTTTAAAGTTGTT
1 AATTTTAAAGTTATTGAGACC-CTGCCTAGAAGAGCTTTTCCAAGATGAAAATTTTAAAGTTGTT
* * * * * *
19846079 AAG-CATATGCTTATATGAGCTTTTCCAAGATGATGAATTTTAAAGTTGTTGAAC
65 AAGCCAT-TACCTAGAGGAGCTTTTCCAAGATGATGAATTTTAAAATTATTGAAC
19846133 TTTTGATTAG
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
145 2 0.02
146 57 0.57
147 2 0.02
148 39 0.39
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (147 bp):
AATTTTAAAGTTATTGAGACCCTGCCTAGAAGAGCTTTTCCAAGATGAAAATTTTAAAGTTGTTA
AGCCATTACCTAGAGGAGCTTTTCCAAGATGATGAATTTTAAAATTATTGAACCTCTACTTAGAG
AAGCTTTTTCAAGATGA
Found at i:19847181 original size:24 final size:24
Alignment explanation
Indices: 19847145--19847193 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
19847135 CGATTCAGGT
19847145 AAAAAGTTTTTTTTATT-TTTTAA
1 AAAAAGTTTTTTTTATTATTTTAA
* *
19847168 AAAAATTTTATTTTTGTTATTTTAA
1 AAAAAGTTT-TTTTTATTATTTTAA
19847193 A
1 A
19847194 TTTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 7 0.32
25 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AAAAAGTTTTTTTTATTATTTTAA
Found at i:19847209 original size:21 final size:21
Alignment explanation
Indices: 19847170--19847210 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19847160 TTTTTTAAAA
* **
19847170 AAATTTTATTTTTGTTATTTT
1 AAATTTTATTATTAATATTTT
19847191 AAATTTTATTATTAATATTT
1 AAATTTTATTATTAATATTT
19847211 AAGCATGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
AAATTTTATTATTAATATTTT
Found at i:19848875 original size:25 final size:26
Alignment explanation
Indices: 19848840--19848891 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
19848830 TGGTTCATTT
19848840 ACATTCAACCCAAAAAGAACTATACC
1 ACATTCAACCCAAAAAGAACTATACC
19848866 ACATTC-ACCCAAAAAGAACTATACC
1 ACATTCAACCCAAAAAGAACTATACC
19848891 A
1 A
19848892 ATAATAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.50, C:0.31, G:0.04, T:0.15
Consensus pattern (26 bp):
ACATTCAACCCAAAAAGAACTATACC
Found at i:19849590 original size:12 final size:12
Alignment explanation
Indices: 19849573--19849613 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
19849563 TAATTGATTC
19849573 TCTGATAAACAA
1 TCTGATAAACAA
19849585 TCTGATAAACAA
1 TCTGATAAACAA
*
19849597 ---AATAAACAA
1 TCTGATAAACAA
19849606 TCTGATAA
1 TCTGATAA
19849614 CTACATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.33
12 16 0.67
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (12 bp):
TCTGATAAACAA
Found at i:19849775 original size:18 final size:17
Alignment explanation
Indices: 19849731--19849774 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
19849721 CTCATGAAAC
19849731 AACATGAAAACAAAAAT
1 AACATGAAAACAAAAAT
*
19849748 AGCATGAAAACAAAAAT
1 AACATGAAAACAAAAAT
*
19849765 AATATGAAAA
1 AACATGAAAA
19849775 ATAAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (17 bp):
AACATGAAAACAAAAAT
Found at i:19861761 original size:34 final size:33
Alignment explanation
Indices: 19861658--19861760 Score: 111
Period size: 34 Copynumber: 3.1 Consensus size: 33
19861648 AAAATTTTTC
**
19861658 AAAATTT-TGATTTTTTTCAAATTTATTCTCGAA
1 AAAATTTATGATTTTTTAAAAATTTATTCTC-AA
** * * *
19861691 AAGGTTTATAATTTTTTGAAATTTTATTCTCAA
1 AAAATTTATGATTTTTTAAAAATTTATTCTCAA
19861724 AAAATTATATGATTTTTTAAAAATTTATT-TCAA
1 AAAATT-TATGATTTTTTAAAAATTTATTCTCAA
19861757 AAAA
1 AAAA
19861761 AATAACTTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
33 19 0.33
34 38 0.67
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (33 bp):
AAAATTTATGATTTTTTAAAAATTTATTCTCAA
Found at i:19866285 original size:20 final size:21
Alignment explanation
Indices: 19866254--19866308 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
19866244 ATTTGAGTTG
19866254 TAAATCAAATTTAAATA-TAAA
1 TAAAT-AAATTTAAATATTAAA
19866275 TAAATAAATTTAAA-ATTAAA
1 TAAATAAATTTAAATATTAAA
19866295 TATAA-AAA-TTAAAT
1 TA-AATAAATTTAAAT
19866309 TCATTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.19
20 18 0.58
21 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATAAATTTAAATATTAAA
Found at i:19866385 original size:21 final size:21
Alignment explanation
Indices: 19866345--19866385 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19866335 ATTGAACAAA
*
19866345 TTCAAATAATTTAATTTTTAT
1 TTCAAATAATTTAATATTTAT
19866366 TTCAAATTAATTTAA-ATTTA
1 TTCAAA-TAATTTAATATTTA
19866386 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTCAAATAATTTAATATTTAT
Found at i:19867019 original size:24 final size:25
Alignment explanation
Indices: 19866990--19867037 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
19866980 AATAAAAATT
*
19866990 TTAATTTTATGATA-ATTTGATATC
1 TTAATTATATGATATATTTGATATC
* *
19867014 TTAATTATATTATATATTTTATAT
1 TTAATTATATGATATATTTGATAT
19867038 ATGTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (25 bp):
TTAATTATATGATATATTTGATATC
Found at i:19868211 original size:22 final size:22
Alignment explanation
Indices: 19868155--19868244 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 22
19868145 ATTCGATCAA
**
19868155 TAAATTAAA-TTATTTAA-ATT
1 TAAATTAAATTTAAATAATATT
* *
19868175 TAATTTTAA-TTAAATAATATT
1 TAAATTAAATTTAAATAATATT
**
19868196 TAAATT-AATTTCAAATTTTATT
1 TAAATTAAATTT-AAATAATATT
*
19868218 CAAATTAAATTTAAATAAT-TT
1 TAAATTAAATTTAAATAATATT
19868239 ATAAAT
1 -TAAAT
19868245 ATTAATATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
20 15 0.28
21 12 0.22
22 22 0.41
23 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAATTAAATTTAAATAATATT
Found at i:19868230 original size:33 final size:32
Alignment explanation
Indices: 19868176--19868238 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
19868166 ATTTAAATTT
19868176 AATTTTAATTAAATAATATTTAAATTAATTTCA
1 AATTTTAATTAAATAATATTTAAA-TAATTTCA
19868209 AATTTT-ATTCAAATTAA-ATTTAAATAATTT
1 AATTTTAATT-AAA-TAATATTTAAATAATTT
19868239 ATAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 9 0.32
33 16 0.57
34 3 0.11
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
AATTTTAATTAAATAATATTTAAATAATTTCA
Found at i:19869037 original size:16 final size:16
Alignment explanation
Indices: 19868999--19869038 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
19868989 TTAATTAATT
19868999 TATATAATTTTAAAAAA
1 TATAT-ATTTTAAAAAA
19869016 TA-ATATTTTAAAAAA
1 TATATATTTTAAAAAA
19869031 TATATATT
1 TATATATT
19869039 AAAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.59
16 7 0.32
17 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATATTTTAAAAAA
Found at i:19869215 original size:37 final size:37
Alignment explanation
Indices: 19869183--19869257 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
19869173 TTGTACTAAT
19869183 GCAACACACAACCAAAGTGATGATAGCGTGTACCAAAG
1 GCAACAC-CAACCAAAGTGATGATAGCGTGTACCAAAG
** * *
19869221 GTGACGCCAACCAAAGTGATGATAGCGTGCACCAAAG
1 GCAACACCAACCAAAGTGATGATAGCGTGTACCAAAG
19869258 TTGACGCCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (37 bp):
GCAACACCAACCAAAGTGATGATAGCGTGTACCAAAG
Found at i:19869219 original size:21 final size:21
Alignment explanation
Indices: 19869192--19869258 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
19869182 TGCAACACAC
19869192 AACCAAAGTGATGATAGCGTG
1 AACCAAAGTGATGATAGCGTG
* **
19869213 TACCAAAG-G-TG--A-CGCC
1 AACCAAAGTGATGATAGCGTG
19869229 AACCAAAGTGATGATAGCGTG
1 AACCAAAGTGATGATAGCGTG
*
19869250 CACCAAAGT
1 AACCAAAGT
19869259 TGACGCCACG
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
16 9 0.26
17 2 0.06
18 2 0.06
19 2 0.06
20 2 0.06
21 17 0.50
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.16
Consensus pattern (21 bp):
AACCAAAGTGATGATAGCGTG
Found at i:19869263 original size:37 final size:37
Alignment explanation
Indices: 19869191--19869266 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
19869181 ATGCAACACA
*
19869191 CAACCAAAGTGATGATAGCGTGTACCAAAGGTGACGC
1 CAACCAAAGTGATGATAGCGTGCACCAAAGGTGACGC
*
19869228 CAACCAAAGTGATGATAGCGTGCACCAAAGTTGACGC
1 CAACCAAAGTGATGATAGCGTGCACCAAAGGTGACGC
19869265 CA
1 CA
19869267 CGATTTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.16
Consensus pattern (37 bp):
CAACCAAAGTGATGATAGCGTGCACCAAAGGTGACGC
Found at i:19871944 original size:2 final size:2
Alignment explanation
Indices: 19871937--19871969 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19871927 TTCCATACTC
19871937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19871970 TCTAAAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19872567 original size:2 final size:2
Alignment explanation
Indices: 19872560--19872589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19872550 AACTTTTTAT
19872560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19872590 AAACTTGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.