Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008273.1 Hibiscus syriacus cultivar Beakdansim tig00110930_pilon, 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: 1042195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:576607 original size:28 final size:29
Alignment explanation
Indices: 576568--576634 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
576558 AATAGTGAAA
* *
576568 TTTTAATAATTTGATCTTTGAACTTTAT-
1 TTTTAATTATTTGATCTTCGAACTTTATG
*
576596 TTTTAATTATTTGATCTTCGAACTTTGTG
1 TTTTAATTATTTGATCTTCGAACTTTATG
576625 TTTTAATTAT
1 TTTTAATTAT
576635 ACAAACCGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 25 0.71
29 10 0.29
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.58
Consensus pattern (29 bp):
TTTTAATTATTTGATCTTCGAACTTTATG
Found at i:586016 original size:14 final size:15
Alignment explanation
Indices: 585997--586032 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
585987 TATAATTTTC
585997 TTTT-AAATTTTTAT
1 TTTTAAAATTTTTAT
586011 TTTTAAAATTTTTA-
1 TTTTAAAATTTTTAT
586025 TTTTAAAA
1 TTTTAAAA
586033 AATTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAAAATTTTTAT
Found at i:586021 original size:15 final size:14
Alignment explanation
Indices: 585992--586032 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
585982 AATTGTATAA
*
585992 TTTTCTTTT-AAAT
1 TTTTATTTTAAAAT
586005 TTTTATTTTTAAAAT
1 TTTTA-TTTTAAAAT
586020 TTTTATTTTAAAA
1 TTTTATTTTAAAA
586033 AATTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 12 0.48
15 9 0.36
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTATTTTAAAAT
Found at i:586033 original size:15 final size:15
Alignment explanation
Indices: 586001--586033 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
585991 ATTTTCTTTT
*
586001 AAATTTTTATTTTTA
1 AAATTTTTATTTTAA
586016 AAATTTTTATTTTAA
1 AAATTTTTATTTTAA
586031 AAA
1 AAA
586034 ATTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AAATTTTTATTTTAA
Found at i:589147 original size:171 final size:170
Alignment explanation
Indices: 588775--589265 Score: 556
Period size: 171 Copynumber: 2.8 Consensus size: 170
588765 ACACAAGATG
* * * * *
588775 AGACTTAA-CCAACCACATTGTAAAACTAAACATCTAATTTCATAGATTTTGCATGCAAAAACCA
1 AGACTCAACCCAA-CACATTATAAAACTAAACATCT-ATTTCAAAGTTTTTGCATGCAAAAACTA
* * *
588839 AACCTTATTCATAAGTAATTTTAACACGAAA-ATCGCACTTACAAGCATATGATGTCTTGCATAG
64 AACCTTATTCATAAGTAATTTTAACAC-AAAGACCGCACTTTCAAGCATATGATG-C---C-T-T
* * * * *
588903 CCATAGTTGTAACTTGCAATAATATATGTACGTTATACAGCTCAAGACT
122 CCTTAGTTGTAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
* *
588952 AGACTCAACCCACCACATTATAAAACTAAACATCGTATTTCAAAGTTTTTGCATGCAAAAACTAC
1 AGACTCAACCCAACACATTATAAAACTAAACATC-TATTTCAAAGTTTTTGCATGCAAAAACTAA
* * * * *
589017 ACTTTATTCCTATGAAATTTCAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTT
65 ACCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTT
* *
589082 GTAACTTGCCACAATATATGTACATTACGCAGCCCAAGACT
130 GTAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
* * * * *
589123 AGACTCAACCCAACTCATTATAAAACTAGACATCTTATCTCAAA-TATTTTGCAAGCAAAATCTA
1 AGACTCAACCCAACACATTATAAAACTAAACATC-TATTTCAAAGT-TTTTGCATGCAAAAACTA
** * * * *
589187 AACCTTATTCATAAGTAATTTTAATGCAAAGACCACACTTTCAAGCATGTGATGCATTGCTTAGT
64 AACCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGT
589252 TGTAACTTGCAACA
129 TGTAACTTGCAACA
589266 GTGACACAGC
Statistics
Matches: 268, Mismatches: 42, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
170 1 0.00
171 163 0.61
172 1 0.00
173 1 0.00
176 4 0.01
177 94 0.35
178 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (170 bp):
AGACTCAACCCAACACATTATAAAACTAAACATCTATTTCAAAGTTTTTGCATGCAAAAACTAAA
CCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTTG
TAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
Found at i:596095 original size:2 final size:2
Alignment explanation
Indices: 596090--596116 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
596080 ATATTTTTTT
596090 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
596117 TAGTGGTTGG
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:596435 original size:34 final size:34
Alignment explanation
Indices: 596372--596483 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
596362 AAAACAATCC
* *
596372 TCAATTTCATTATAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
596407 TCAATTTCATTCTAAACCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
* * *
596441 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
596476 TCAATTTC
1 TCAATTTC
596484 TGTCTTTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 26 0.38
35 42 0.62
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:597577 original size:35 final size:34
Alignment explanation
Indices: 597529--597640 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
597519 ATTCCTCCTT
* *
597529 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
597564 CAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
597599 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
597634 AAATTGA
1 AAATTGA
597641 GGAATGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:613066 original size:60 final size:60
Alignment explanation
Indices: 612973--613130 Score: 171
Period size: 60 Copynumber: 2.6 Consensus size: 60
612963 TTTGGTTCTT
* * * *
612973 AAAC-TTTTAAATATTACAATTCCATCCCTAAACTAT-TACTATCATTCTAAATTTA-TCCTC
1 AAACTTTTTCAATATTTCAATTTCATCCC-AAACTATATACT-TCATTCTAAA-TTAGTCCCC
* * *
613033 AAACTTTTT-AATATTTTATTTTCATTCCCAAACTATATCCTTCATTCTAAATTAGTCCCC
1 AAACTTTTTCAATATTTCAATTTCA-TCCCAAACTATATACTTCATTCTAAATTAGTCCCC
* *
613093 AAACTTTTTCAGTATTTCAATTTCATCCCAAATTATAT
1 AAACTTTTTCAATATTTCAATTTCATCCCAAACTATAT
613131 GTATATACTA
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
59 3 0.04
60 57 0.69
61 23 0.28
ACGTcount: A:0.34, C:0.22, G:0.01, T:0.43
Consensus pattern (60 bp):
AAACTTTTTCAATATTTCAATTTCATCCCAAACTATATACTTCATTCTAAATTAGTCCCC
Found at i:613331 original size:60 final size:59
Alignment explanation
Indices: 613258--613434 Score: 189
Period size: 60 Copynumber: 3.0 Consensus size: 59
613248 TGAATTTGGG
* * *
613258 GATGAAATTGGAATATTTAAATGTTT-GGGTACCAATTTAGACTGAGGGTCATAGTTTGAA
1 GATGAAATTGGAATATTTAAATGTTTAGGG-ACCAATTTAAAATGAGGATCATAGTTTG-A
* * * * * *
613318 GATGAAATTGGAATGA-TCAAAAGTTTAAGGACTAACTTAAAATGAGTATCATAGTTTGA
1 GATGAAATTGGAAT-ATTTAAATGTTTAGGGACCAATTTAAAATGAGGATCATAGTTTGA
* *
613377 GTATGAAATTGGAATATTTAAAAT-TTTAGGGACCAATTTAAAATGAGAATAATAGTTT
1 G-ATGAAATTGGAATATTT-AAATGTTTAGGGACCAATTTAAAATGAGGATCATAGTTT
613435 AGGGACATAT
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
59 3 0.03
60 87 0.91
61 6 0.06
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.34
Consensus pattern (59 bp):
GATGAAATTGGAATATTTAAATGTTTAGGGACCAATTTAAAATGAGGATCATAGTTTGA
Found at i:617588 original size:31 final size:31
Alignment explanation
Indices: 617553--617641 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
617543 GTACATGTGG
617553 TATGTGTCACATCATCACTTTGAACACGTGA
1 TATGTGTCACATCATCACTTTGAACACGTGA
*
617584 TATGTGTCACATCATCACTTTGAACACGTGG
1 TATGTGTCACATCATCACTTTGAACACGTGA
* *
617615 TATGTGTCACGTCGGT-ACTTTGAACAC
1 TATGTGTCACATC-ATCACTTTGAACAC
617642 ATATAACTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 53 0.98
32 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (31 bp):
TATGTGTCACATCATCACTTTGAACACGTGA
Found at i:619513 original size:15 final size:15
Alignment explanation
Indices: 619495--619525 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
619485 GCCCCTTAAA
619495 CATTGATGCCCTGTG
1 CATTGATGCCCTGTG
619510 CATTGATGCCCTGTG
1 CATTGATGCCCTGTG
619525 C
1 C
619526 GATCGCCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.26, T:0.32
Consensus pattern (15 bp):
CATTGATGCCCTGTG
Found at i:626850 original size:21 final size:21
Alignment explanation
Indices: 626811--626873 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
626801 CTTAGTAAAA
*
626811 TTTCCGATTATTGTCTTTTTT
1 TTTCCGATTTTTGTCTTTTTT
626832 TTT-CGATTTTTGTCTTTTTT
1 TTTCCGATTTTTGTCTTTTTT
626852 TTTCCGATTTTTGTCTTTTTT
1 TTTCCGATTTTTGTCTTTTTT
626873 T
1 T
626874 CCGTCGTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 19 0.47
21 21 0.52
ACGTcount: A:0.06, C:0.13, G:0.10, T:0.71
Consensus pattern (21 bp):
TTTCCGATTTTTGTCTTTTTT
Found at i:630827 original size:51 final size:51
Alignment explanation
Indices: 630707--630813 Score: 187
Period size: 51 Copynumber: 2.1 Consensus size: 51
630697 CATTTTAATT
* * *
630707 TGCAATAACATATCATTTTTGGATTTTGATAGGCAATTTTTCTACAAAGGG
1 TGCAATAACATACCATTTTTGGATTTTGATAAGCAATTTTTCCACAAAGGG
630758 TGCAATAACATACCATTTTTGGATTTTGATAAGCAATTTTTCCACAAAGGG
1 TGCAATAACATACCATTTTTGGATTTTGATAAGCAATTTTTCCACAAAGGG
630809 TGCAA
1 TGCAA
630814 ATAGCTCTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (51 bp):
TGCAATAACATACCATTTTTGGATTTTGATAAGCAATTTTTCCACAAAGGG
Found at i:632489 original size:11 final size:11
Alignment explanation
Indices: 632473--632504 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
632463 AATAAAGATC
632473 GGAGGAAGGAA
1 GGAGGAAGGAA
632484 GGAGGAAGGAA
1 GGAGGAAGGAA
632495 GGAGGAAGGA
1 GGAGGAAGGA
632505 GGAATTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (11 bp):
GGAGGAAGGAA
Found at i:633118 original size:2 final size:2
Alignment explanation
Indices: 633111--633140 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
633101 TGCATGCGCG
633111 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
633141 ATTAACCTTG
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
Found at i:640763 original size:18 final size:17
Alignment explanation
Indices: 640734--640769 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
640724 ATAATATAAG
640734 TTTATATATAAACTATA
1 TTTATATATAAACTATA
*
640751 TTTATATTATAAATTATA
1 TTTATA-TATAAACTATA
640769 T
1 T
640770 AATTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATATATAAACTATA
Found at i:640792 original size:2 final size:2
Alignment explanation
Indices: 640785--641015 Score: 72
Period size: 2 Copynumber: 116.5 Consensus size: 2
640775 TTATAAGTTT
* *
640785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG TT TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * * * * *
640827 -A T- TA TA TA TA GA AA CTA TA TA TG TA TA AA TA T- TA AA AA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
640867 TA TA -A TT TA TA AA CTA TA -A TT TA TA T- TA -A TA TA GTG TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
640907 TA TA TA TG TA TA AA CTA TA -A CTA TA TA AA CTA TA TA TT TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA
* * * * * * * *
640949 AA CTA TA -A AA AA TT TA -A GTA TA AA TT TA -A AA TA AA TGA TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA
640989 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
641016 TCACATGAGT
Statistics
Matches: 167, Mismatches: 40, Indels: 44
0.67 0.16 0.18
Matches are distributed among these distances:
1 12 0.07
2 144 0.86
3 11 0.07
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:640893 original size:34 final size:33
Alignment explanation
Indices: 640855--640956 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 33
640845 ATATGTATAA
*
640855 ATATTAAAAATATATAATTTATAAACTATAATTT
1 ATATTAAAAATATATAATTTATAAACTATAA-CT
*
640889 ATATTAATATAGTGTATATATATATGTATAAACTATAACT
1 ATATTAA-A-A----ATATATA-ATTTATAAACTATAACT
*
640929 ATA-T-AAACTATAT-ATTTATAAACTATAA
1 ATATTAAAAATATATAATTTATAAACTATAA
640957 AAAATTTAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
30 14 0.25
32 5 0.09
34 7 0.12
35 1 0.02
36 2 0.04
37 1 0.02
38 1 0.02
39 1 0.02
40 11 0.19
41 14 0.25
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (33 bp):
ATATTAAAAATATATAATTTATAAACTATAACT
Found at i:640925 original size:15 final size:15
Alignment explanation
Indices: 640907--640955 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
640897 ATAGTGTATA
*
640907 TATATATGTATAAAC
1 TATATATATATAAAC
640922 TATA-ACTATATAAAC
1 TATATA-TATATAAAC
*
640937 TATATATTTATAAAC
1 TATATATATATAAAC
640952 TATA
1 TATA
640956 AAAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:641477 original size:14 final size:14
Alignment explanation
Indices: 641460--641498 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
641450 TTATGTTTAA
641460 TTATATATATAAAT
1 TTATATATATAAAT
* **
641474 TTATGTATATACTT
1 TTATATATATAAAT
641488 TTATATATATA
1 TTATATATATA
641499 TATTATTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (14 bp):
TTATATATATAAAT
Found at i:641838 original size:17 final size:15
Alignment explanation
Indices: 641811--641849 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
641801 ATATATATAT
*
641811 ATATGTATGTATATAA
1 ATATATATGTATA-AA
641827 ACTATATATGTATAAA
1 A-TATATATGTATAAA
641843 ATATATA
1 ATATATA
641850 GCTTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 4 0.19
17 11 0.52
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (15 bp):
ATATATATGTATAAA
Found at i:642154 original size:2 final size:2
Alignment explanation
Indices: 642077--642145 Score: 68
Period size: 2 Copynumber: 34.0 Consensus size: 2
642067 ATAAACAATG
642077 TA TA GTA TA TA TA -A CTA 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 TA TA
* * * **
642120 CA CA CA CC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
642146 AACTATATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
1 1 0.02
2 56 0.93
3 3 0.05
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:642252 original size:7 final size:7
Alignment explanation
Indices: 642242--642296 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
642232 TCCTAAATCA
642242 TAAACCC
1 TAAACCC
642249 TAAACCC
1 TAAACCC
**
642256 TAAACTT
1 TAAACCC
*
642263 TAAACCA
1 TAAACCC
**
642270 TAAATAC
1 TAAACCC
642277 TAAACCC
1 TAAACCC
642284 TAAACCC
1 TAAACCC
642291 TAAACC
1 TAAACC
642297 TTAATATAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:642252 original size:14 final size:14
Alignment explanation
Indices: 642233--642296 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
642223 TTATAGAAAT
*
642233 CCTAAATCATAAAC
1 CCTAAACCATAAAC
*
642247 CCTAAACCCTAAAC
1 CCTAAACCATAAAC
** *
642261 TTTAAACCATAAAT
1 CCTAAACCATAAAC
* *
642275 ACTAAACCCTAAAC
1 CCTAAACCATAAAC
642289 CCTAAACC
1 CCTAAACC
642297 TTAATATAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:642259 original size:21 final size:20
Alignment explanation
Indices: 642233--642296 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
642223 TTATAGAAAT
642233 CCTAAATCATAAACCCTAAAC
1 CCTAAA-CATAAACCCTAAAC
* * *
642254 CCTAAACTTTAAACCATAAAT
1 CCTAAAC-ATAAACCCTAAAC
* *
642275 ACTAAACCCTAAACCCTAAAC
1 CCTAAA-CATAAACCCTAAAC
642296 C
1 C
642297 TTAATATAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (20 bp):
CCTAAACATAAACCCTAAAC
Found at i:642676 original size:4 final size:4
Alignment explanation
Indices: 642667--642739 Score: 132
Period size: 4 Copynumber: 18.8 Consensus size: 4
642657 GCTATATGTA
642667 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
642715 TATG TATG --TG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
642740 ATATACTTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
4 65 0.97
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:643602 original size:14 final size:14
Alignment explanation
Indices: 643583--643675 Score: 80
Period size: 14 Copynumber: 6.6 Consensus size: 14
643573 TAAAATATAA
* *
643583 AAACCCTAAGTCTT
1 AAACCCTAAATCAT
643597 AAACCCTAAATCAT
1 AAACCCTAAATCAT
*
643611 AAACCCTAAATCCT
1 AAACCCTAAATCAT
** *
643625 AAACTTTAAACCAT
1 AAACCCTAAATCAT
* *
643639 AATCCATAAA-CACT
1 AAACCCTAAATCA-T
* *
643653 AAACCATAAACCAT
1 AAACCCTAAATCAT
643667 AAACCCTAA
1 AAACCCTAA
643676 TATAAATGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
13 2 0.03
14 61 0.94
15 2 0.03
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:643662 original size:7 final size:7
Alignment explanation
Indices: 643596--643671 Score: 66
Period size: 7 Copynumber: 10.9 Consensus size: 7
643586 CCCTAAGTCT
*
643596 TAAACCC
1 TAAACCA
*
643603 TAAATCA
1 TAAACCA
*
643610 TAAACCC
1 TAAACCA
643617 TAAATCC-
1 TAAA-CCA
**
643624 TAAACTT
1 TAAACCA
643631 TAAACCA
1 TAAACCA
*
643638 TAATCCA
1 TAAACCA
643645 TAAA-CA
1 TAAACCA
643651 CTAAACCA
1 -TAAACCA
643659 TAAACCA
1 TAAACCA
643666 TAAACC
1 TAAACC
643672 CTAATATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
6 3 0.05
7 49 0.88
8 4 0.07
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:643675 original size:21 final size:21
Alignment explanation
Indices: 643596--643675 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
643586 CCCTAAGTCT
* *
643596 TAAACCCTAAATCA-TAAACCC
1 TAAACCATAAA-CACTAAACCA
**
643617 TAAATCC-TAAACTTTAAACCA
1 TAAA-CCATAAACACTAAACCA
*
643638 TAATCCATAAACACTAAACCA
1 TAAACCATAAACACTAAACCA
*
643659 TAAACCATAAACCCTAA
1 TAAACCATAAACACTAA
643676 TATAAATGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 3 0.06
21 44 0.90
22 2 0.04
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCATAAACACTAAACCA
Found at i:644130 original size:16 final size:16
Alignment explanation
Indices: 644111--644148 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
644101 CAGATCATTT
644111 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
644127 ACAGGTCATGTTGAAA
1 ACAGGTCAGGTTAAAA
644143 A-AGGTC
1 ACAGGTC
644149 GGATAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:655097 original size:60 final size:59
Alignment explanation
Indices: 654944--655098 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
654934 GTATTCAAGG
* * * * *
654944 TATGACCTTAATTTTAAAATGGTCTCTAAACTTTTAAATATTACAATTTTATCCTTAAAC
1 TATGACCTTCA-TTTAAATTGGTCCCCAAACTTTTAAATATTACAATTTTATCCCTAAAC
* * * * *
655004 TATGA-TTATCAATTTAAATTAGTTCTCAGACTTTTAAATATTACAATTTTATTCCCT-AAC
1 TATGACCT-TC-ATTTAAATTGGTCCCCAAACTTTTAAATATTACAATTTTA-TCCCTAAAC
655064 TATGACCTTCATTCTAAATTGGTCCCCAAACTTTT
1 TATGACCTTCATT-TAAATTGGTCCCCAAACTTTT
655099 TGAACATTCT
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
59 4 0.05
60 65 0.87
61 6 0.08
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (59 bp):
TATGACCTTCATTTAAATTGGTCCCCAAACTTTTAAATATTACAATTTTATCCCTAAAC
Found at i:655350 original size:28 final size:27
Alignment explanation
Indices: 655259--655350 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 27
655249 TTGGGTATGG
**
655259 AATTTGAATATTCGAAAGACTGGGGACT
1 AATTTGAATATTC-AAAGTTTGGGGACT
* *
655287 AATTTAAAAATAAATTCATAGTTTGGGGA-T
1 AATTT--GAAT--ATTCAAAGTTTGGGGACT
655317 GCAATTTGAATATTCAAAAGTTTGGGGACT
1 --AATTTGAATATTC-AAAGTTTGGGGACT
655347 AATT
1 AATT
655351 AAAAACAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
28 13 0.26
29 11 0.22
30 8 0.16
31 9 0.18
32 9 0.18
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (27 bp):
AATTTGAATATTCAAAGTTTGGGGACT
Found at i:655404 original size:29 final size:28
Alignment explanation
Indices: 655367--655458 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
655357 AATACCATAG
*
655367 TTTATGGATGAAATTAGAATGTTAAAAAA
1 TTTAAGGATGAAATTAGAATGTT-AAAAA
* * * * * *
655396 TTTAAGGATTAATTTAGAATGAGTCATAT
1 TTTAAGGATGAAATTAGAATG-TTAAAAA
* *
655425 TTTAAGGATGAAATTAGAATATTCAAAAG
1 TTTAAGGATGAAATTAGAATGTT-AAAAA
655454 TTTAA
1 TTTAA
655459 TGACCAATTT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
28 1 0.02
29 45 0.96
30 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (28 bp):
TTTAAGGATGAAATTAGAATGTTAAAAA
Found at i:655437 original size:58 final size:58
Alignment explanation
Indices: 655362--655476 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 58
655352 AAAACAATAC
* * ** *
655362 CATAGTTTATGGATGAAATTAGAATGTTAAAAAATTTAAGGATTAATTTAGAATGAGT
1 CATAGTTTAAGGATGAAATTAGAATATTAAAAAATTTAAGGACCAATTTAAAATGAGT
* * * *
655420 CATATTTTAAGGATGAAATTAGAATATTCAAAAGTTTAATGACCAATTTAAAATGAG
1 CATAGTTTAAGGATGAAATTAGAATATTAAAAAATTTAAGGACCAATTTAAAATGAG
655477 GGTTATAGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (58 bp):
CATAGTTTAAGGATGAAATTAGAATATTAAAAAATTTAAGGACCAATTTAAAATGAGT
Found at i:658128 original size:32 final size:32
Alignment explanation
Indices: 658092--658157 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
658082 TACCTTATAG
*
658092 AGTGCAGCTTAGGTTAAATTTGAAACATTGAA
1 AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
658124 AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
1 AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
658156 AG
1 AG
658158 GTTAGAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (32 bp):
AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
Found at i:660404 original size:14 final size:14
Alignment explanation
Indices: 660387--660415 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
660377 ATAACTATTC
660387 AAATTCAGAAAATG
1 AAATTCAGAAAATG
660401 AAATTCAGAAAATG
1 AAATTCAGAAAATG
660415 A
1 A
660416 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAATTCAGAAAATG
Found at i:660497 original size:70 final size:67
Alignment explanation
Indices: 660411--660538 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 67
660401 AAATTCAGAA
* * * * *
660411 AATGAGTTTTAGTTAGATAAATTTTTTATTTTTGTATTAATAACATATAAAAAGAATTTGTATAA
1 AATGAGTTTTACTTAGAT--A-TTTTTATGTTTGTACTAATAAAATAGAAAAAGAATTTGTATAA
660476 TACTT
63 TACTT
*
660481 AATGAGTTTTACTTAGATATTTTTATGTTTGTACTAATAAAATAGAAAAATAATTTGT
1 AATGAGTTTTACTTAGATATTTTTATGTTTGTACTAATAAAATAGAAAAAGAATTTGT
660539 CATTATACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
67 34 0.65
68 1 0.02
70 17 0.33
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (67 bp):
AATGAGTTTTACTTAGATATTTTTATGTTTGTACTAATAAAATAGAAAAAGAATTTGTATAATAC
TT
Found at i:660666 original size:19 final size:19
Alignment explanation
Indices: 660642--660680 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
660632 AACTTTATTT
* *
660642 AAAAAATATTTATATTTTA
1 AAAAAATAATTAGATTTTA
660661 AAAAAATAATTAGATTTTA
1 AAAAAATAATTAGATTTTA
660680 A
1 A
660681 TTTTAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAAATAATTAGATTTTA
Found at i:661832 original size:19 final size:19
Alignment explanation
Indices: 661781--661832 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
661771 AAATATCCTA
*
661781 ATTACATTTTTAA-TTTAT
1 ATTATATTTTTAATTTTAT
* * *
661799 ATTTATAATTATAATTTTTT
1 A-TTATATTTTTAATTTTAT
661819 ATTATATTTTTAAT
1 ATTATATTTTTAAT
661833 ATTTCGTCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 1 0.04
19 20 0.77
20 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTATATTTTTAATTTTAT
Found at i:664584 original size:78 final size:78
Alignment explanation
Indices: 664455--664615 Score: 277
Period size: 78 Copynumber: 2.1 Consensus size: 78
664445 TTTATCGAGG
664455 AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
1 AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
664520 ATATATTACTATT
66 ATATATTACTATT
* * * *
664533 AAAAAATGAAATTAGAAGAAGAAAAAATCACCCTGTGAACAACTGTAGGATAGCAGACTTGTCAA
1 AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
*
664598 GTATATTACTATT
66 ATATATTACTATT
664611 AAAAA
1 AAAAA
664616 GCTTAGACTT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.24
Consensus pattern (78 bp):
AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
ATATATTACTATT
Found at i:667627 original size:60 final size:60
Alignment explanation
Indices: 667475--667647 Score: 195
Period size: 60 Copynumber: 2.9 Consensus size: 60
667465 GTTTATACGT
* * ** *
667475 ATAGTTT-GGGATGAAACTATAATATTCAAAAAGTTTGGGGAATAATTTAGAATGAAAGTC
1 ATAGTTTAGGGATGAAATTAAAATATTC-AAAAGTTTAAGGAATAATTTAAAATGAAAGTC
* * * * **
667535 ATAGTTTAGGGATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAAAATGATGGTC
1 ATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGGAATAATTTAAAATGAAAGTC
* * * *
667595 ATAGTTTAGGGATAAAATTAAAACATTCAAAAGTTTAATGATTAATTTAAAAT
1 ATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGGAATAATTTAAAAT
667648 TAAGATCATA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 79 0.84
61 15 0.16
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.34
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGGAATAATTTAAAATGAAAGTC
Found at i:668616 original size:2 final size:2
Alignment explanation
Indices: 668609--668640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
668599 TTGGTTACTT
668609 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
668641 CATCAGCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:671530 original size:27 final size:28
Alignment explanation
Indices: 671487--671541 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
671477 GCTCTTTTCG
* *
671487 AAAATATATTTTTATAATTTTATTAAAAT
1 AAAATATA-TTTTATAATTATAATAAAAT
671516 AAAATATA-TTTATAATTATAATAAAA
1 AAAATATATTTTATAATTATAATAAAA
671542 ATTTATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
29 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAATATATTTTATAATTATAATAAAAT
Found at i:671573 original size:25 final size:23
Alignment explanation
Indices: 671499--671573 Score: 57
Period size: 25 Copynumber: 3.2 Consensus size: 23
671489 AATATATTTT
* *
671499 TATAATT-TTATTAAAAT-AAAA
1 TATAATTATAATTATAATAAAAA
*
671520 TATATTTATAATTATAATAAAAA
1 TATAATTATAATTATAATAAAAA
671543 TTTATAATTATAATCT-TAAATTAAAAA
1 --TATAATTATAAT-TAT-AA-TAAAAA
671570 TATA
1 TATA
671574 TTTCATACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 6 0.14
22 8 0.19
23 4 0.09
25 16 0.37
26 3 0.07
27 6 0.14
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATTATAATTATAATAAAAA
Found at i:672109 original size:18 final size:18
Alignment explanation
Indices: 672086--672127 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
672076 ATAAAAAATC
*
672086 TTTATTATAGGAAGATGT
1 TTTATTATAGGAAAATGT
672104 TTTATTATAGGAAAATGT
1 TTTATTATAGGAAAATGT
672122 TTTATT
1 TTTATT
672128 GAGTTTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTATTATAGGAAAATGT
Found at i:672493 original size:20 final size:22
Alignment explanation
Indices: 672452--672494 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
672442 TATATTTTTT
*
672452 TAAAAATTTATTTTATAAAAAA
1 TAAAAATATATTTTATAAAAAA
672474 TAAAAATAT-TTTTA-AAAAAA
1 TAAAAATATATTTTATAAAAAA
672494 T
1 T
672495 GTTTTTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATATATTTTATAAAAAA
Found at i:677854 original size:2 final size:2
Alignment explanation
Indices: 677847--677882 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
677837 GTCAAAGATC
*
677847 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
677883 CCTAAAGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:679691 original size:30 final size:31
Alignment explanation
Indices: 679655--679712 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
679645 ACTAGTTTGA
*
679655 CCTTAAA-TTCATATAAAATATCAATTTAAC
1 CCTTAAATTTCAGATAAAATATCAATTTAAC
* *
679685 CCTTAAATTTTAGATAAAATCTCAATTT
1 CCTTAAATTTCAGATAAAATATCAATTT
679713 GACCGCTCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.40
Consensus pattern (31 bp):
CCTTAAATTTCAGATAAAATATCAATTTAAC
Found at i:680327 original size:20 final size:19
Alignment explanation
Indices: 680262--680328 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
680252 TATTTTAATT
*
680262 TTAAAATATAAAAATATATA
1 TTAAAA-ATTAAAATATATA
*
680282 -TAAAAATTAAAATAAAATA
1 TTAAAAATTAAAAT-ATATA
*
680301 CTAAAAATGTAAAATATATA
1 TTAAAAAT-TAAAATATATA
*
680321 TTTAAAAT
1 TTAAAAAT
680329 ACCAAAAGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.18
19 9 0.23
20 17 0.44
21 6 0.15
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
TTAAAAATTAAAATATATA
Found at i:680702 original size:16 final size:17
Alignment explanation
Indices: 680637--680703 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 17
680627 ACATATAATA
680637 TATGTTTTTTAATATTT
1 TATGTTTTTTAATATTT
** *
680654 T-TAATTTTTAATAATT
1 TATGTTTTTTAATATTT
** *
680670 TATG-ACTTTATAGATTT
1 TATGTTTTTTA-ATATTT
680687 TATGTTTTTTAA-ATTT
1 TATGTTTTTTAATATTT
680703 T
1 T
680704 TAATATATAT
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
16 22 0.59
17 11 0.30
18 4 0.11
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.64
Consensus pattern (17 bp):
TATGTTTTTTAATATTT
Found at i:680749 original size:6 final size:7
Alignment explanation
Indices: 680727--680756 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
680717 TAAACAGAAA
680727 TTTAATT
1 TTTAATT
680734 TTTAATT
1 TTTAATT
680741 TTTAATT
1 TTTAATT
680748 TTTATATT
1 TTTA-ATT
680756 T
1 T
680757 AAAATTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTAATT
Found at i:680757 original size:13 final size:14
Alignment explanation
Indices: 680726--680772 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
680716 ATAAACAGAA
680726 ATTTAATTTTTAAT
1 ATTTAATTTTTAAT
*
680740 TTTTAATTTTT-AT
1 ATTTAATTTTTAAT
*
680753 ATTTAAAATTTTGAAT
1 ATTT--AATTTTTAAT
680769 ATTT
1 ATTT
680773 CTATATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.19
14 10 0.37
15 6 0.22
16 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
ATTTAATTTTTAAT
Found at i:680777 original size:24 final size:23
Alignment explanation
Indices: 680737--680802 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
680727 TTTAATTTTT
*
680737 AATTTTTAAT-TTTTATATTTAA
1 AATTTTAAATATTTTATATTTAA
* *
680759 AATTTTGAATATTTCTATATTTTA
1 AATTTTAAATATTT-TATATTTAA
*
680783 AATTTAAAATATTTT-TATTT
1 AATTTTAAATATTTTATATTT
680803 TCTGAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.37
23 4 0.11
24 20 0.53
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
AATTTTAAATATTTTATATTTAA
Found at i:680805 original size:31 final size:31
Alignment explanation
Indices: 680731--680805 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
680721 CAGAAATTTA
*
680731 ATTTTTAATTTT-TAATTTTTATATTTAAAAT
1 ATTTTT-ATTTTCTAATTTTTAAATTTAAAAT
**
680762 -TTTGAATATTTCT-ATATTTTAAATTTAAAAT
1 ATTTTTAT-TTTCTAAT-TTTTAAATTTAAAAT
680793 ATTTTTATTTTCT
1 ATTTTTATTTTCT
680806 GAAAAAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
29 2 0.06
30 8 0.23
31 20 0.57
32 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (31 bp):
ATTTTTATTTTCTAATTTTTAAATTTAAAAT
Found at i:684521 original size:19 final size:19
Alignment explanation
Indices: 684476--684512 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
684466 AGCCATCGAC
*
684476 TGCTTTGAATAAATGGGGA
1 TGCTTTGAATAAATGAGGA
684495 TGCTTTGAATAAATGAGG
1 TGCTTTGAATAAATGAGG
684513 CTGTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (19 bp):
TGCTTTGAATAAATGAGGA
Found at i:690870 original size:77 final size:75
Alignment explanation
Indices: 690659--690883 Score: 325
Period size: 71 Copynumber: 3.0 Consensus size: 75
690649 TGTTGCTGTA
*
690659 TTGCTCTTTATTATCCCCATCTTCTGTAATAGGTGTCAGAGCTTCCACGATTTCGGACAT-C-T-
1 TTGCTCTTTATCATCCCCATCTTCTGTAATAGGTGTCAGAGCTTCCACGATTTCGGACATGCGTG
* * *
690721 GT-TG-CTGTA
66 GTCCGAAT-TC
* *
690730 TTGCTCTTTGTCATCCCCATCTTCTGTAATAGGTGTCAGAGCTTCCACGATTTCGAACATGCGTG
1 TTGCTCTTTATCATCCCCATCTTCTGTAATAGGTGTCAGAGCTTCCACGATTTCGGACATGCGTG
*
690795 GTCGGAATTC
66 GTCCGAATTC
690805 TTGCTCTTTATCATCCCCATCTTCTGTAATAGAAGTGTCAGAGCTTCCACGATTTCGGACATGCG
1 TTGCTCTTTATCATCCCCATCTTCTGTAATAG--GTGTCAGAGCTTCCACGATTTCGGACATGCG
690870 TGGTCCGAATTC
64 TGGTCCGAATTC
690882 TT
1 TT
690884 TCTCGGGCTG
Statistics
Matches: 138, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
71 57 0.41
72 1 0.01
73 1 0.01
74 2 0.01
75 33 0.24
76 1 0.01
77 43 0.31
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (75 bp):
TTGCTCTTTATCATCCCCATCTTCTGTAATAGGTGTCAGAGCTTCCACGATTTCGGACATGCGTG
GTCCGAATTC
Found at i:696177 original size:211 final size:214
Alignment explanation
Indices: 695778--696207 Score: 814
Period size: 211 Copynumber: 2.0 Consensus size: 214
695768 AAAAAAGCAA
695778 TGGCAAAACAGAGAAAGAAGAAGAAGACGACGATTATATGGGAGATTTGTCTCATTTTCTTCCCC
1 TGGCAAAACAGAGAAAGAAGAAGAAGACGACGATTATATGGGAGATTTG-CTCATTTTCTTCCCC
695843 CTGAACCCTCTAACTCTGCGAAATTATCTCTCAAAAAGGTTTGTTTTTTTTTCTTTTTTAATACC
65 CTGAACCCTCTAACTCTGCGAAATTATCTCTCAAAAAGGTTTGTTTTTTTTTCTTTTTTAATACC
695908 AATTTGTTCTATTTTAGATTTTGCAAATAAGCCTCTGAATTAAGTTCCTCTGTTAATTCTTTCTT
130 AATTTGTTCTATTTTAGATTTTGCAAATAAGCCTCTGAATTAAGTTCCTCTGTTAATTCTTTCTT
695973 CTCAAGCAATGATGTAATTG
195 CTCAAGCAATGATGTAATTG
695993 TGGCAAAACAGAGAAAGAAGAAGAAGACGACGATTATATGGGAGATTTG-TCATTTTCTTCCCCC
1 TGGCAAAACAGAGAAAGAAGAAGAAGACGACGATTATATGGGAGATTTGCTCATTTTCTTCCCCC
696057 TGAACCCTCTAACTCTGCGAAATTATCTCTC-AAAAGGTTTGTTTTTTTTTCTTTTTTAATACCA
66 TGAACCCTCTAACTCTGCGAAATTATCTCTCAAAAAGGTTTGTTTTTTTTTCTTTTTTAATACCA
696121 A-TTGTTCTATTTTAGA-TTTGCAAATTAAGCCTCTGAATTAAGTTCCTCTGTTAATTCTTTCTT
131 ATTTGTTCTATTTTAGATTTTGCAAA-TAAGCCTCTGAATTAAGTTCCTCTGTTAATTCTTTCTT
696184 CTCAAGCAATGATGTAATTG
195 CTCAAGCAATGATGTAATTG
696204 TGGC
1 TGGC
696208 TTTCTTTTCC
Statistics
Matches: 214, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
210 8 0.04
211 77 0.36
212 34 0.16
213 46 0.21
215 49 0.23
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (214 bp):
TGGCAAAACAGAGAAAGAAGAAGAAGACGACGATTATATGGGAGATTTGCTCATTTTCTTCCCCC
TGAACCCTCTAACTCTGCGAAATTATCTCTCAAAAAGGTTTGTTTTTTTTTCTTTTTTAATACCA
ATTTGTTCTATTTTAGATTTTGCAAATAAGCCTCTGAATTAAGTTCCTCTGTTAATTCTTTCTTC
TCAAGCAATGATGTAATTG
Found at i:696268 original size:26 final size:26
Alignment explanation
Indices: 696239--696296 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
696229 AGTAAAAAAT
*
696239 GGTTTTTATCGTAGCTTAGGGTTTTG
1 GGTTTTTATCGTAGCTTAGGGTTATG
696265 GGTTTTTATCGTAGCTTAGGGTTATG
1 GGTTTTTATCGTAGCTTAGGGTTATG
696291 GGTTTT
1 GGTTTT
696297 AGCTGTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.12, C:0.07, G:0.31, T:0.50
Consensus pattern (26 bp):
GGTTTTTATCGTAGCTTAGGGTTATG
Found at i:698023 original size:40 final size:40
Alignment explanation
Indices: 697897--698023 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 40
697887 GATCATTTAT
*
697897 TCTGTATCCGTAAATTCTGTCGCATGTCATTCTGTTATTA
1 TCTGCATCCGTAAATTCTGTCGCATGTCATTCTGTTATTA
** * * * * *
697937 TCTAAATCCGTGAATTTTGTCGCATGCCATTATGTTACTA
1 TCTGCATCCGTAAATTCTGTCGCATGTCATTCTGTTATTA
* * * *
697977 TATGCATCCATAAATTCTGACGCATATCATTCTGTTATTA
1 TCTGCATCCGTAAATTCTGTCGCATGTCATTCTGTTATTA
698017 TCTGCAT
1 TCTGCAT
698024 TGAATCTGGA
Statistics
Matches: 68, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.42
Consensus pattern (40 bp):
TCTGCATCCGTAAATTCTGTCGCATGTCATTCTGTTATTA
Found at i:699747 original size:29 final size:29
Alignment explanation
Indices: 699713--699771 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
699703 CCTAAATTAA
699713 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
699742 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
699771 T
1 T
699772 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:699983 original size:16 final size:16
Alignment explanation
Indices: 699962--699993 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
699952 CCCTTTTGCA
699962 ATTTTGTGAGATTATT
1 ATTTTGTGAGATTATT
699978 ATTTTGTGAGATTATT
1 ATTTTGTGAGATTATT
699994 CTAAAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (16 bp):
ATTTTGTGAGATTATT
Found at i:702896 original size:29 final size:29
Alignment explanation
Indices: 702862--702920 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
702852 CCTAAATTAA
702862 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
702891 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
702920 T
1 T
702921 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:706041 original size:20 final size:20
Alignment explanation
Indices: 706018--706057 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
706008 TTGGTAAAAG
*
706018 TTATTGAAAATATTATTATT
1 TTATCGAAAATATTATTATT
* *
706038 TTATCGGAAATGTTATTATT
1 TTATCGAAAATATTATTATT
706058 AGGTGTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (20 bp):
TTATCGAAAATATTATTATT
Found at i:709807 original size:6 final size:6
Alignment explanation
Indices: 709796--709822 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
709786 CATTTTCTTC
709796 TATTGT TATTGT TATTGT TATTGT TAT
1 TATTGT TATTGT TATTGT TATTGT TAT
709823 CACATCTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
TATTGT
Found at i:722126 original size:111 final size:111
Alignment explanation
Indices: 721928--722141 Score: 383
Period size: 111 Copynumber: 1.9 Consensus size: 111
721918 ATATATCTCT
* *
721928 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
721993 TGATTTATTTAATGCATAATTATTAGATTAAGAATTAAATATATCG
66 TGATTTATTTAATGCATAATTATTAGATTAAGAATTAAATATATCG
* *
722039 ACACTTTGCTGATACAGTAACGTTTTAATGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
722104 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
722142 TTTTTGTAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 98 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (111 bp):
ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATAATTATTAGATTAAGAATTAAATATATCG
Found at i:723993 original size:3 final size:3
Alignment explanation
Indices: 723985--724043 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
723975 ACCTGCTCAG
* * ** *
723985 GAC GAC GAC GAC GAC GAT GAC GAT GGT GAC GAT GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
724033 GAC GAC GAC GA
1 GAC GAC GAC GA
724044 TGATGACAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.25, G:0.36, T:0.07
Consensus pattern (3 bp):
GAC
Found at i:726365 original size:40 final size:39
Alignment explanation
Indices: 726310--726386 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 39
726300 CAATAAGTAT
726310 AATTAAAAAATTATAACAAAATTATCTTATAACGAAAAAA
1 AATTAAAAAATTATAACAAAATTATCTTATAAC-AAAAAA
726350 AATTAAAAAATTATAACAAAATTATCTTATAACAAAA
1 AATTAAAAAATTATAACAAAATTATCTTATAACAAAA
726387 CTTCTAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 4 0.11
40 33 0.89
ACGTcount: A:0.62, C:0.08, G:0.01, T:0.29
Consensus pattern (39 bp):
AATTAAAAAATTATAACAAAATTATCTTATAACAAAAAA
Found at i:730417 original size:43 final size:43
Alignment explanation
Indices: 730356--730454 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
730346 GGATTTGAAT
730356 ATACTCATGGCTTTTCAAAGCAATAATCAATGAGGGCCTTTTC
1 ATACTCATGGCTTTTCAAAGCAATAATCAATGAGGGCCTTTTC
730399 ATACTCATGGCTTTTCAAAGCAATAATCAATGAGGGCCTTTTC
1 ATACTCATGGCTTTTCAAAGCAATAATCAATGAGGGCCTTTTC
730442 ATACTCATGGCTT
1 ATACTCATGGCTT
730455 GTTTTCTTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (43 bp):
ATACTCATGGCTTTTCAAAGCAATAATCAATGAGGGCCTTTTC
Found at i:732782 original size:84 final size:84
Alignment explanation
Indices: 732650--732818 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
732640 TCCAAACTCG
*
732650 TCCTTATCTATTAAAAATTGATGATCCCTTGAACTAGACGTTAACATGTTGATTTGGATATAATA
1 TCCTTATCCATTAAAAATTGATGATCCCTTGAACTAGACGTTAACATGTTGATTTGGATATAATA
*
732715 AAATATGATCCCAAAACCA
66 AAATATAATCCCAAAACCA
*
732734 TCCTTATCCATTAAAAATTGATGGTCCCTTGAACTAGACGTTAACATGTTGATTTGGATATAATA
1 TCCTTATCCATTAAAAATTGATGATCCCTTGAACTAGACGTTAACATGTTGATTTGGATATAATA
732799 AAATATAATCCCAAAACCA
66 AAATATAATCCCAAAACCA
732818 T
1 T
732819 TTGAATTGTA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (84 bp):
TCCTTATCCATTAAAAATTGATGATCCCTTGAACTAGACGTTAACATGTTGATTTGGATATAATA
AAATATAATCCCAAAACCA
Found at i:738951 original size:23 final size:23
Alignment explanation
Indices: 738921--738980 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
738911 TTCGCACCTC
*
738921 TGAATGATTCAGCAAAATAGTGT
1 TGAATGATTCAGCAAAACAGTGT
738944 TGAATGATTCAGCAAAACAGTGT
1 TGAATGATTCAGCAAAACAGTGT
738967 TGAATGATTCAGCA
1 TGAATGATTCAGCA
738981 CAGAAGTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (23 bp):
TGAATGATTCAGCAAAACAGTGT
Found at i:739691 original size:21 final size:21
Alignment explanation
Indices: 739642--739691 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
739632 GTTAATATGG
*
739642 TAATTTATGATCTTAACGTGA
1 TAATTTATGATATTAACGTGA
* ** *
739663 CAGCTTATGGTATTAACGTGA
1 TAATTTATGATATTAACGTGA
739684 TAATTTAT
1 TAATTTAT
739692 AATGTTTAAA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (21 bp):
TAATTTATGATATTAACGTGA
Found at i:742311 original size:173 final size:165
Alignment explanation
Indices: 742022--742360 Score: 597
Period size: 173 Copynumber: 2.0 Consensus size: 165
742012 ATCATTCAAG
742022 AGAAACATAACTCTTGAAGAGCTGATAACGAAGATTTCGAGGAAGAATCATGTTGGAAGTAGTAG
1 AGAAACATAACTCTTGAAGAGCTGATAACGAAGATTTCGAGGAAGAATCATGTTGGAAGTAGTAG
742087 AAGAATGTCATCGTTGCAGTACAGATTTCCAACATCATTGTTGTCATTAACTTATATAGCGTTCG
66 AAGAATGTCATCGTTGCAGTACAGATTTCCAACATCATTGTTGTCATTAACTTATATAGCGTTCG
742152 AACTTTCGAACAATGATGATGTTCAAATGATGGTTGAAGCTCA
131 AAC-TT-------TGATGATGTTCAAATGATGGTTGAAGCTCA
*
742195 AGAAACATAACTCTTGAAGAGCTGATAACGAAGATTTCGAGGAAGATTCATGTTGGAAGTAGTAG
1 AGAAACATAACTCTTGAAGAGCTGATAACGAAGATTTCGAGGAAGAATCATGTTGGAAGTAGTAG
742260 AAGAATGTCATCGTTGCAGTACAGATTTCCAACATCATTGTTGTCATTAACTTATATAGCGTTCG
66 AAGAATGTCATCGTTGCAGTACAGATTTCCAACATCATTGTTGTCATTAACTTATATAGCGTTCG
742325 AACTTTGATGATGTTCAAATGATGGTTGAAGCTCA
131 AACTTTGATGATGTTCAAATGATGGTTGAAGCTCA
742360 A
1 A
742361 AGTAATTATT
Statistics
Matches: 165, Mismatches: 1, Indels: 8
0.95 0.01 0.05
Matches are distributed among these distances:
165 31 0.19
172 2 0.01
173 132 0.80
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (165 bp):
AGAAACATAACTCTTGAAGAGCTGATAACGAAGATTTCGAGGAAGAATCATGTTGGAAGTAGTAG
AAGAATGTCATCGTTGCAGTACAGATTTCCAACATCATTGTTGTCATTAACTTATATAGCGTTCG
AACTTTGATGATGTTCAAATGATGGTTGAAGCTCA
Found at i:745166 original size:35 final size:36
Alignment explanation
Indices: 745081--745183 Score: 101
Period size: 35 Copynumber: 2.9 Consensus size: 36
745071 ATTTGGTATT
*
745081 TAAATACAACAAACTTACAATAA-GA-ATTAAATGG
1 TAAATACAACAAAATTACAATAATGATATTAAATGG
* *
745115 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA-TGATATTAAATGG
745153 T-AATA-AACAAAATTA-AATGAAAT-ATATTAAA
1 TAAATACAACAAAATTACAAT--AATGATATTAAA
745184 AAAAGTCCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
34 16 0.27
35 25 0.42
36 3 0.05
37 5 0.08
38 10 0.17
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.27
Consensus pattern (36 bp):
TAAATACAACAAAATTACAATAATGATATTAAATGG
Found at i:747431 original size:17 final size:18
Alignment explanation
Indices: 747411--747449 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
747401 ATTATATTAA
747411 TAAAATA-TTAAATAAAG
1 TAAAATAGTTAAATAAAG
*
747428 TAAAATAGTTAAATAAAT
1 TAAAATAGTTAAATAAAG
747446 TAAA
1 TAAA
747450 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
TAAAATAGTTAAATAAAG
Found at i:747944 original size:2 final size:2
Alignment explanation
Indices: 747939--747963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
747929 GAATATATTC
747939 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
747964 TAACACCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:748098 original size:14 final size:15
Alignment explanation
Indices: 748071--748099 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
748061 TATGTTTAAT
748071 TATTTAATAAATATA
1 TATTTAATAAATATA
748086 TATTTAA-AAATATA
1 TATTTAATAAATATA
748100 AAAACACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAATAAATATA
Found at i:752374 original size:20 final size:20
Alignment explanation
Indices: 752340--752379 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
752330 GCTCAATTAT
*
752340 AGAAGGAAAAAAGGA-AGAA
1 AGAAAGAAAAAAGGATAGAA
752359 AGAAAGAAAAAGAGGATAGAA
1 AGAAAGAAAAA-AGGATAGAA
752380 GAGATGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 4 0.22
21 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (20 bp):
AGAAAGAAAAAAGGATAGAA
Found at i:768431 original size:229 final size:227
Alignment explanation
Indices: 768021--768469 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
768011 GTAAATTATC
* * *
768021 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
768086 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
768151 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
768216 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
768249 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
768314 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
768379 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
768444 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
768470 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 40 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:768558 original size:20 final size:19
Alignment explanation
Indices: 768535--768581 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
768525 CGATATACCA
768535 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
768555 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
768575 GGTAAAA
1 GGTAAAA
768582 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:768725 original size:20 final size:19
Alignment explanation
Indices: 768702--768748 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
768692 CGATATAACA
*
768702 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
768722 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
768742 GGTAAAA
1 GGTAAAA
768749 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:770728 original size:18 final size:18
Alignment explanation
Indices: 770705--770766 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
770695 ATCGGTCGCA
* * *
770705 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
770723 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
770741 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
770759 GAAGATGA
1 GAAGATGA
770767 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:770729 original size:6 final size:6
Alignment explanation
Indices: 770705--770766 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
770695 ATCGGTCGCA
* * * * * *
770705 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
770753 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
770767 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:770740 original size:3 final size:3
Alignment explanation
Indices: 770720--770770 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
770710 TGAAGCTGAC
* * * *
770720 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
770768 GAT
1 GAT
770771 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:770767 original size:12 final size:12
Alignment explanation
Indices: 770708--770770 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
770698 GGTCGCAGAA
* *
770708 GATGAAGCTGAC
1 GATGAAGATGAT
*
770720 GATGAAGATGAC
1 GATGAAGATGAT
*
770732 GATGATGATGAT
1 GATGAAGATGAT
*
770744 GATGACGATGAT
1 GATGAAGATGAT
770756 GATGAAGATGAT
1 GATGAAGATGAT
770768 GAT
1 GAT
770771 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:772456 original size:184 final size:184
Alignment explanation
Indices: 772138--772806 Score: 1254
Period size: 184 Copynumber: 3.7 Consensus size: 184
772128 CTTTCAACAT
* *
772138 ATTATAAT-AAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
772202 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
772267 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
772321 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
772386 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
772451 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
772505 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
772570 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
772635 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
772689 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGT-TTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
**
772753 GGTCTACAACCGGTATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
772807 CCATTTAAAA
Statistics
Matches: 478, Mismatches: 7, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
182 32 0.07
183 40 0.08
184 406 0.85
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:774111 original size:23 final size:23
Alignment explanation
Indices: 774080--774142 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
774070 ATAGGTAAAC
*
774080 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
774103 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
774126 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
774143 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:774150 original size:23 final size:23
Alignment explanation
Indices: 774080--774152 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
774070 ATAGGTAAAC
* * **
774080 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
774103 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
774126 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
774149 ATAT
1 ATAT
774153 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:774744 original size:3 final size:3
Alignment explanation
Indices: 774736--774788 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
774726 TTCAATAAAC
*
774736 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
774784 CAT TA
1 TAT TA
774789 GGATAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:775805 original size:161 final size:160
Alignment explanation
Indices: 775632--775964 Score: 594
Period size: 161 Copynumber: 2.1 Consensus size: 160
775622 CTCGTTCTAA
* *
775632 ATAAAAAATTAAAATTAAATCTCGAAATCTCACGAGCTTACAAATTTTAAATTCGATTGGAGCTT
1 ATAAAAAATTAAAATTAAATCTCGAAATCTCACGAGCTTAAAAATTTTAAATTCGACTGGAGCTT
*
775697 GAAAAAACATGACGCTCAAATTTAAACTCGAACATAAACTTTAAATACATGAAAATCTTCTATTA
66 GAAAAAACATGACGCTCAAATTTAAACTCGAACATAAACCTTAAATACATGAAAATCTTCTATTA
*
775762 TATTTTATTTAAAAAAACTACGTATGAATT
131 TATTTTATTTAAAAAAACAACGTATGAATT
775792 ATAAAAAAATTAAAATTAAATCTCGAAATCTCACGAGCTTAAAAATTTTAAATTCGACTGGAGCT
1 AT-AAAAAATTAAAATTAAATCTCGAAATCTCACGAGCTTAAAAATTTTAAATTCGACTGGAGCT
* *
775857 TGAAAAAACATGACGCTTAAATTTAAACTCGAACATGAACCTTAAATACATGAAAATCTTCTATT
65 TGAAAAAACATGACGCTCAAATTTAAACTCGAACATAAACCTTAAATACATGAAAATCTTCTATT
*
775922 ATATTTTATTTAAAAAAACAATGTATGAATT
130 ATATTTTATTTAAAAAAACAACGTATGAATT
775953 ATAAAAAATTAA
1 ATAAAAAATTAA
775965 TTTAAAAATC
Statistics
Matches: 165, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
160 12 0.07
161 153 0.93
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.32
Consensus pattern (160 bp):
ATAAAAAATTAAAATTAAATCTCGAAATCTCACGAGCTTAAAAATTTTAAATTCGACTGGAGCTT
GAAAAAACATGACGCTCAAATTTAAACTCGAACATAAACCTTAAATACATGAAAATCTTCTATTA
TATTTTATTTAAAAAAACAACGTATGAATT
Found at i:783414 original size:14 final size:14
Alignment explanation
Indices: 783395--783428 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
783385 AAATGAAACT
783395 AAAATATAATGTTA
1 AAAATATAATGTTA
**
783409 AAAATATTTTGTTA
1 AAAATATAATGTTA
783423 AAAATA
1 AAAATA
783429 ATTAAATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
AAAATATAATGTTA
Found at i:787979 original size:15 final size:15
Alignment explanation
Indices: 787961--788017 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
787951 TAACCGGTTT
787961 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
787976 CGGTTTTTTTTAAAAAAC
1 CGG---TTTTAAAAAAAC
*
787994 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
788009 CGATTTTAA
1 CGGTTTTAA
788018 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 20 0.59
18 14 0.41
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:787990 original size:18 final size:18
Alignment explanation
Indices: 787964--787998 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
787954 CCGGTTTCGG
787964 TTTTAAAAAAACCGGTTT
1 TTTTAAAAAAACCGGTTT
*
787982 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
787999 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (18 bp):
TTTTAAAAAAACCGGTTT
Found at i:788434 original size:13 final size:13
Alignment explanation
Indices: 788413--788467 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
788403 AAGTTCGATA
*
788413 AATTCAAATACTT
1 AATTGAAATACTT
788426 AATTGAAATACTT
1 AATTGAAATACTT
* *
788439 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
788453 AATTGAAATACTT
1 AATTGAAATACTT
788466 AA
1 AA
788468 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:788549 original size:32 final size:33
Alignment explanation
Indices: 788453--788551 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
788443 AACTCAACAT
* * *
788453 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
788486 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
788519 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
788551 A
1 A
788552 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:788570 original size:21 final size:21
Alignment explanation
Indices: 788546--788585 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
788536 ACTTCAAGTT
788546 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
788567 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
788586 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:796388 original size:23 final size:23
Alignment explanation
Indices: 796342--796395 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
796332 AGCGAGCAAT
* * *
796342 GAAACACAAATTTAGCAAGAAAC
1 GAAACATAAACTTAGCAACAAAC
* *
796365 GGAACATAAACTTAGCAACCAAC
1 GAAACATAAACTTAGCAACAAAC
796388 GAAACATA
1 GAAACATA
796396 TCTAAAACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.20, G:0.13, T:0.13
Consensus pattern (23 bp):
GAAACATAAACTTAGCAACAAAC
Found at i:796666 original size:20 final size:20
Alignment explanation
Indices: 796643--796712 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
796633 GAACTCCAAT
796643 TTCGCAACACAGTTTTCAAA
1 TTCGCAACACAGTTTTCAAA
* * * *
796663 TTCGCAACGCTAATTTCCTAGA
1 TTCGCAACAC-AGTTTTC-AAA
* *
796685 TTCGCAACTCAGTTTTGAAA
1 TTCGCAACACAGTTTTCAAA
796705 TTCGCAAC
1 TTCGCAAC
796713 TCGAATTTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 19 0.49
21 9 0.23
22 11 0.28
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
TTCGCAACACAGTTTTCAAA
Found at i:796698 original size:42 final size:39
Alignment explanation
Indices: 796643--796760 Score: 119
Period size: 42 Copynumber: 2.9 Consensus size: 39
796633 GAACTCCAAT
796643 TTCGCAACACAGTTTTCAAATTCGCAACGCTAATTTCCTAGA
1 TTCGCAACACAGTTTTCAAATTCGCAACGCTAATTT-CT--A
* * * * *
796685 TTCGCAACTCAGTTTTGAAATTCGCAACTCGAATTTCTT
1 TTCGCAACACAGTTTTCAAATTCGCAACGCTAATTTCTA
* * *
796724 TTCCGCAACGCAATTTTCCAAATTCGCGACGCTAATT
1 TT-CGCAACACAGTTTT-CAAATTCGCAACGCTAATT
796761 CTAAATTCAC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.03
40 12 0.19
41 17 0.27
42 32 0.51
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (39 bp):
TTCGCAACACAGTTTTCAAATTCGCAACGCTAATTTCTA
Found at i:796787 original size:20 final size:20
Alignment explanation
Indices: 796777--796816 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
796767 TCACAATTTG
796777 CGACGCTAATTCCGAATTCC
1 CGACGCTAATTCCGAATTCC
*
796797 CGACGCTAATTTCGAATTCC
1 CGACGCTAATTCCGAATTCC
796817 TAATTCACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.28
Consensus pattern (20 bp):
CGACGCTAATTCCGAATTCC
Found at i:796794 original size:27 final size:27
Alignment explanation
Indices: 796744--796795 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
796734 CAATTTTCCA
*
796744 AATTCGCGACGCTAATTCTAAATTCAC
1 AATTCGCGACGCTAATTCCAAATTCAC
* *
796771 AATTTGCGACGCTAATTCCGAATTC
1 AATTCGCGACGCTAATTCCAAATTC
796796 CCGACGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (27 bp):
AATTCGCGACGCTAATTCCAAATTCAC
Found at i:796841 original size:27 final size:27
Alignment explanation
Indices: 796782--796842 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
796772 ATTTGCGACG
* *
796782 CTAATTCCGAATTCCCGACGCTAATTT
1 CTAATTCCGAATTCACGACGCGAATTT
* *
796809 CGAATTCCTAATTCACGACGCGAA-TT
1 CTAATTCCGAATTCACGACGCGAATTT
796835 CTTAATTC
1 C-TAATTC
796843 GCAACACGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (27 bp):
CTAATTCCGAATTCACGACGCGAATTT
Found at i:796852 original size:20 final size:20
Alignment explanation
Indices: 796809--796853 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
796799 ACGCTAATTT
* *
796809 CGAATTCCTAATTCACGACG
1 CGAATTCCTAATTCACAACA
* *
796829 CGAATTCTTAATTCGCAACA
1 CGAATTCCTAATTCACAACA
796849 CGAAT
1 CGAAT
796854 CCTGCTACGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (20 bp):
CGAATTCCTAATTCACAACA
Found at i:797057 original size:27 final size:27
Alignment explanation
Indices: 797019--797090 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
797009 AAACCATATA
* *
797019 AAATTAGTGTCGTGAATTGTGAATTCG
1 AAATTAGCGTCGCGAATTGTGAATTCG
797046 AAATTAGCGTCGCGAATTGTGAATTCG
1 AAATTAGCGTCGCGAATTGTGAATTCG
*
797073 AAATTCGCGTCGCGAATT
1 AAATTAGCGTCGCGAATT
797091 CAGAAAATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (27 bp):
AAATTAGCGTCGCGAATTGTGAATTCG
Found at i:797143 original size:20 final size:20
Alignment explanation
Indices: 797120--797191 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
797110 AAAGAAATTC
*
797120 GAGTTGCGAATTTCAAAACT
1 GAGTTGCGAATTTGAAAACT
* *
797140 GAGTTGCGAATCTGGAAAATT
1 GAGTTGCGAAT-TTGAAAACT
*
797161 GGTGTTGCGAATTTGAAAACT
1 -GAGTTGCGAATTTGAAAACT
*
797182 GTGTTGCGAA
1 GAGTTGCGAA
797192 ATTGGAGTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 21 0.48
21 13 0.30
22 10 0.23
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (20 bp):
GAGTTGCGAATTTGAAAACT
Found at i:797170 original size:22 final size:20
Alignment explanation
Indices: 797122--797197 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
797112 AGAAATTCGA
** *
797122 GTTGCGAATTTCAAAACTGA
1 GTTGCGAATTGGAAAACTGT
*
797142 GTTGCGAATCTGGAAAATTGGT
1 GTTGCGAAT-TGGAAAACT-GT
*
797164 GTTGCGAATTTGAAAACTGT
1 GTTGCGAATTGGAAAACTGT
797184 GTTGCGAAATTGGA
1 GTTGCG-AATTGGA
797198 GTTCGCGTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.37
21 19 0.41
22 10 0.22
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTGGAAAACTGT
Found at i:801264 original size:28 final size:26
Alignment explanation
Indices: 801233--801294 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
801223 TTCGATAAAA
801233 TAATTAATTTTCATCCATATAAATAAT-T
1 TAATTAATTTTCAT-C--ATAAATAATAT
* *
801261 TAATAATATTTTTATCATAAATAATAT
1 TAATTA-ATTTTCATCATAAATAATAT
801288 TAATTAA
1 TAATTAA
801295 ACTATTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 10 0.34
27 6 0.21
28 6 0.21
29 7 0.24
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (26 bp):
TAATTAATTTTCATCATAAATAATAT
Found at i:801854 original size:25 final size:22
Alignment explanation
Indices: 801810--801863 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 22
801800 ATATTTTATT
801810 ATTTTTTAATATTTTGTATTTA
1 ATTTTTTAATATTTTGTATTTA
*
801832 ATTTATTTAATATTTTACTTATTTA
1 ATTT-TTTAATATTTT--GTATTTA
801857 ATTTTTT
1 ATTTTTT
801864 TACAGATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 11 0.39
24 3 0.11
25 10 0.36
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
ATTTTTTAATATTTTGTATTTA
Found at i:801865 original size:25 final size:23
Alignment explanation
Indices: 801811--801865 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
801801 TATTTTATTA
801811 TTTTTTAATATTTTGTATTTAAT
1 TTTTTTAATATTTTGTATTTAAT
* *
801834 TTATTTAATATTTTACTTATTTAAT
1 TTTTTTAATATTTT--GTATTTAAT
801859 TTTTTTA
1 TTTTTTA
801866 CAGATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 13 0.48
25 14 0.52
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTTAATATTTTGTATTTAAT
Found at i:807880 original size:29 final size:30
Alignment explanation
Indices: 807848--807906 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
807838 GATCGAGAAA
* *
807848 TATAGTCTGACCAGTGTTAAATCAA-AAAT
1 TATAATCTGACCAATGTTAAATCAATAAAT
*
807877 TATAATCTGACCAATGTTAGATCAATAAAT
1 TATAATCTGACCAATGTTAAATCAATAAAT
807907 AAATCTATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (30 bp):
TATAATCTGACCAATGTTAAATCAATAAAT
Found at i:808695 original size:24 final size:24
Alignment explanation
Indices: 808637--808696 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
808627 GATGAAAAGA
*
808637 TAAAT-ACTTTCTTTTTTCAATTT
1 TAAATAACTTTCTTTTTTCAAGTT
*
808660 TAAATAAGTTTCTTTTTT-ATAGTT
1 TAAATAACTTTCTTTTTTCA-AGTT
* *
808684 TAAGTCACTTTCT
1 TAAATAACTTTCT
808697 CAAATCTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 6 0.20
24 24 0.80
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.57
Consensus pattern (24 bp):
TAAATAACTTTCTTTTTTCAAGTT
Found at i:824774 original size:33 final size:33
Alignment explanation
Indices: 824731--824797 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
824721 ATCAAACAAC
*
824731 ATACATTTTTAATAGTTAGTTGATTACAAAGGA
1 ATACAATTTTAATAGTTAGTTGATTACAAAGGA
824764 ATACAATTTTAATAGTTAGTTGATTACAAAGGA
1 ATACAATTTTAATAGTTAGTTGATTACAAAGGA
824797 A
1 A
824798 ACTTGTATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (33 bp):
ATACAATTTTAATAGTTAGTTGATTACAAAGGA
Found at i:825063 original size:38 final size:38
Alignment explanation
Indices: 825009--825082 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
824999 TTTGGCAAAC
* * *
825009 TTGACCCGACCCGAAAATTATACACCCTCTACCTGAAT
1 TTGACCAGACCCGAAAAATATACACCCTCCACCTGAAT
* * *
825047 TTGACCAGACCGGAAAAATATATACTCTCCACCTGA
1 TTGACCAGACCCGAAAAATATACACCCTCCACCTGA
825083 CCCGACATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.23
Consensus pattern (38 bp):
TTGACCAGACCCGAAAAATATACACCCTCCACCTGAAT
Found at i:827370 original size:102 final size:105
Alignment explanation
Indices: 827203--827409 Score: 339
Period size: 102 Copynumber: 2.0 Consensus size: 105
827193 GTTTCATAAG
*
827203 TTAGACATAGAGGTTGATTGCAATATCTGTGTAATATGATATGTGGAATTAGATATAAAAGATT-
1 TTAGACATAGAGGTTGATTGCAATATCTGTGTAATATGATACGTGGAATTAGATATAAAAGATTA
827267 A-C-ATTTCATATGTTTAAGAAAGACCTAGTTTTCATTCT
66 ATCAATTTCATATGTTTAAGAAAGACCTAGTTTTCATTCT
*
827305 TTAGACATAGAGGTTGGTTGCAATATCTGTGTAATATGATACGTGGAATTAGATATAAAAGATTA
1 TTAGACATAGAGGTTGATTGCAATATCTGTGTAATATGATACGTGGAATTAGATATAAAAGATTA
*
827370 CATTTCAATTTCATATGTTTAAGAAAGTCCTAGTTTTCAT
66 -A--TCAATTTCATATGTTTAAGAAAGACCTAGTTTTCAT
827410 CTGTAGAGTT
Statistics
Matches: 96, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
102 62 0.65
104 1 0.01
107 1 0.01
108 32 0.33
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (105 bp):
TTAGACATAGAGGTTGATTGCAATATCTGTGTAATATGATACGTGGAATTAGATATAAAAGATTA
ATCAATTTCATATGTTTAAGAAAGACCTAGTTTTCATTCT
Found at i:828093 original size:19 final size:20
Alignment explanation
Indices: 828069--828108 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
828059 CGGGGGGTGA
828069 TTTAATAA-TGGTTTTCCTC
1 TTTAATAACTGGTTTTCCTC
828088 TTTAATAACTGGTTTTCCTC
1 TTTAATAACTGGTTTTCCTC
828108 T
1 T
828109 AACACAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTAATAACTGGTTTTCCTC
Found at i:829906 original size:14 final size:14
Alignment explanation
Indices: 829887--829913 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
829877 AAACTTTTGC
829887 TTAGACAATGGAAA
1 TTAGACAATGGAAA
829901 TTAGACAATGGAA
1 TTAGACAATGGAA
829914 CCAGCAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (14 bp):
TTAGACAATGGAAA
Found at i:838585 original size:16 final size:16
Alignment explanation
Indices: 838564--838594 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
838554 TAAAAAATAA
838564 ACGAACATAAACGAAT
1 ACGAACATAAACGAAT
838580 ACGAACATAAACGAA
1 ACGAACATAAACGAA
838595 CAAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAT
Found at i:838694 original size:16 final size:16
Alignment explanation
Indices: 838673--838725 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
838663 ACGAACAAAC
838673 GAACACGAACATAAAT
1 GAACACGAACATAAAT
838689 GAACACGAACATAAAT
1 GAACACGAACATAAAT
*
838705 GAACACGAACATAAAC
1 GAACACGAACATAAAT
838721 GAACA
1 GAACA
838726 TAAACGTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.09
Consensus pattern (16 bp):
GAACACGAACATAAAT
Found at i:839487 original size:14 final size:14
Alignment explanation
Indices: 839470--839525 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
839460 AATGAACATA
*
839470 AACGAACATAATCG
1 AACGAACATAACCG
839484 AACGAACAT-A---
1 AACGAACATAACCG
*
839494 AACGAACATAACCA
1 AACGAACATAACCG
839508 AACGAACATAACCG
1 AACGAACATAACCG
839522 AACG
1 AACG
839526 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:839490 original size:24 final size:24
Alignment explanation
Indices: 839449--839524 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
839439 AGATTGTGTT
*
839449 GAACATAAAT-GAATGAACATAAAC
1 GAACAT-AATCGAACGAACATAAAC
839473 GAACATAATCGAACGAACATAAAC
1 GAACATAATCGAACGAACATAAAC
* * *
839497 GAACATAACCAAACGAACATAACC
1 GAACATAATCGAACGAACATAAAC
839521 GAAC
1 GAAC
839525 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
GAACATAATCGAACGAACATAAAC
Done.