Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008722.1 Hibiscus syriacus cultivar Beakdansim tig00111780_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: 447499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:219226 original size:73 final size:75
Alignment explanation
Indices: 219062--219244 Score: 203
Period size: 74 Copynumber: 2.5 Consensus size: 75
219052 TTAAATAAGG
* * * * ** *
219062 AGGTACCGATACCCCTCCTAGAGGTACTGATACTCC-TATGCCAATTTTGGCTCCCGAGAAAAAC
1 AGGTACCGATACCCC-CTTAAAGGTACCGATAC-CCTTGTGTTAATTTTAGCTCCCGAGAAAAAC
219126 AGAATGCTCAAT
64 AGAATGCTCAAT
* * *
219138 AGGTACCGATACCCCC-TAGAGGTATCGATACCCTTGTGTTAATTTTAGCT-CCGAGAAAAATAG
1 AGGTACCGATACCCCCTTAAAGGTACCGATACCCTTGTGTTAATTTTAGCTCCCGAGAAAAACAG
219201 AATG-TCTAAT
66 AATGCTC-AAT
* *
219211 GGGTATCGATACCCCCTTAAAGGTACCGATACCC
1 AGGTACCGATACCCCCTTAAAGGTACCGATACCC
219245 CTAATCATTT
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
72 2 0.02
73 35 0.38
74 40 0.43
75 1 0.01
76 15 0.16
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (75 bp):
AGGTACCGATACCCCCTTAAAGGTACCGATACCCTTGTGTTAATTTTAGCTCCCGAGAAAAACAG
AATGCTCAAT
Found at i:221950 original size:37 final size:37
Alignment explanation
Indices: 221900--222059 Score: 208
Period size: 37 Copynumber: 4.4 Consensus size: 37
221890 TATATATATA
*
221900 TTGAAAACT-TATATAATATATGGTTTTTAAAAACATT
1 TTGAAAA-TATATATAATATATGGTTTTAAAAAACATT
221937 TTGAAAATATATATAATATATGGTTTTAAAAAACATT
1 TTGAAAATATATATAATATATGGTTTTAAAAAACATT
*
221974 TTGAAAACT-TATATAATATAT-GTTTTTAAAAACATTT
1 TTGAAAA-TATATATAATATATGGTTTTAAAAAACA-TT
*
222011 TTGAAAA-A-ATAT-AT-TATGGTTTTAAAAAACTTT
1 TTGAAAATATATATAATATATGGTTTTAAAAAACATT
222044 TTGAAAATATAATATA
1 TTGAAAATAT-ATATA
222060 TAGTTTGAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
33 12 0.11
34 14 0.13
35 4 0.04
36 17 0.15
37 62 0.56
38 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (37 bp):
TTGAAAATATATATAATATATGGTTTTAAAAAACATT
Found at i:221984 original size:74 final size:70
Alignment explanation
Indices: 221900--222050 Score: 241
Period size: 74 Copynumber: 2.1 Consensus size: 70
221890 TATATATATA
221900 TTGAAAACTTATATAATATATGGTTTTTAAAAACA-TTTTGAAAATATATATAATATATGGTTTT
1 TTGAAAACTTATATAATATAT-GTTTTTAAAAACATTTTTGAAAA-A-ATAT-AT-TATGGTTTT
221964 AAAAAACATT
61 AAAAAACATT
221974 TTGAAAACTTATATAATATATGTTTTTAAAAACATTTTTGAAAAAATATATTATGGTTTTAAAAA
1 TTGAAAACTTATATAATATATGTTTTTAAAAACATTTTTGAAAAAATATATTATGGTTTTAAAAA
*
222039 ACTTT
66 ACATT
222044 TTGAAAA
1 TTGAAAA
222051 TATAATATAT
Statistics
Matches: 75, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
70 25 0.33
71 2 0.03
72 4 0.05
73 14 0.19
74 30 0.40
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (70 bp):
TTGAAAACTTATATAATATATGTTTTTAAAAACATTTTTGAAAAAATATATTATGGTTTTAAAAA
ACATT
Found at i:222071 original size:31 final size:32
Alignment explanation
Indices: 221910--222092 Score: 140
Period size: 37 Copynumber: 5.4 Consensus size: 32
221900 TTGAAAACTT
* *
221910 ATATAATATATGGTTTTTAAAAACATTTTGAAA
1 ATATAATATATAG-TTTTAAAAACTTTTTGAAA
*
221943 ATATATATAATATATGGTTTTAAAAAACATTTTGAAA
1 ATATA-AT-ATATA--GTTTT-AAAAACTTTTTGAAA
221980 ACT-TATATAATATATGTTTTTAAAAACATTTTTGAAA
1 A-TATA-AT-ATATA-G-TTTTAAAAAC-TTTTTGAAA
* *
222017 AAAT-ATATTATGGTTTTAAAAAACTTTTTGAAA
1 ATATAATA-TATAGTTTT-AAAAACTTTTTGAAA
* *
222050 ATATAATATATAG-TTTGAAAACTTTTT-AAT
1 ATATAATATATAGTTTTAAAAACTTTTTGAAA
222080 ATATATATATATA
1 ATATA-ATATATA
222093 TATATATATA
Statistics
Matches: 128, Mismatches: 9, Indels: 28
0.78 0.05 0.17
Matches are distributed among these distances:
30 7 0.05
31 17 0.13
32 3 0.02
33 25 0.20
34 13 0.10
35 9 0.07
36 11 0.09
37 42 0.33
38 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (32 bp):
ATATAATATATAGTTTTAAAAACTTTTTGAAA
Found at i:222085 original size:2 final size:2
Alignment explanation
Indices: 222078--222130 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
222068 AAACTTTTTA
* *
222078 AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AA AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
222118 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
222131 AAAAGTTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:222155 original size:34 final size:34
Alignment explanation
Indices: 222078--222194 Score: 100
Period size: 34 Copynumber: 3.4 Consensus size: 34
222068 AAACTTTTTA
* * *
222078 ATATATATATATATATATATATA-TATTTAAAATT
1 ATATATATATATATATATAAAAAGT-TTTAAAACT
222112 ATATATATATATATATATAAAAAGTTTTCAAAACT
1 ATATATATATATATATATAAAAAGTTTT-AAAACT
* *
222147 ATAT-TATATA-AT-TTTCAAAAAGTTTTTTAAAAACC
1 ATATATATATATATATAT-AAAAAG--TTTT-AAAACT
222182 ATATAT-TATATAT
1 ATATATATATATAT
222195 TTTTTTCCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
32 2 0.03
33 8 0.11
34 30 0.43
35 27 0.39
36 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (34 bp):
ATATATATATATATATATAAAAAGTTTTAAAACT
Found at i:222231 original size:75 final size:74
Alignment explanation
Indices: 222136--222467 Score: 444
Period size: 75 Copynumber: 4.4 Consensus size: 74
222126 ATATAAAAAG
*
222136 TTTTCAAAACTATAT-T-ATATAA-TTTTCAAAAAGTTTTTTAAAAACCATATATTATATATTTT
1 TTTTAAAAAC-ATATATTATATAAGTTTTCAAAAAGTTTTTTAAAAACCATATATTATATA-TTT
222198 TTTCCAAAATGT
64 TTT-CAAAATGT
* * *
222210 TTTTAAAAACATATGTTATATAAGTTTTCAAAATGTTTTTTAAAAACCATATATTATATATATTT
1 TTTTAAAAACATATATTATATAAGTTTTCAAAAAGTTTTTTAAAAACCATATATTATATATTTTT
222275 TCAAAATGT
66 TCAAAATGT
*
222284 TTTTAAAAACCATATATTATATAAGTTTTCAAAATA-TTTTTTAAAAACCACATATTATATATAT
1 TTTTAAAAA-CATATATTATATAAGTTTTCAAAA-AGTTTTTTAAAAACCATATATTATATAT-T
222348 TTTT-AAAATGT
63 TTTTCAAAATGT
* *
222359 TTTTAAAAATCATATATTATATAAGTTTTCAAAATGTTTTTTAAAAAACCATATATTATATATGT
1 TTTTAAAAA-CATATATTATATAAGTTTTCAAAAAGTTTTTT-AAAAACCATATATTATATATTT
222424 TTTCAAAATGT
64 TTTCAAAATGT
* *
222435 TTTCAAAAA-ACTATATAATATACA-TTTTCAAAA
1 TTTTAAAAACA-TATATTATATA-AGTTTTCAAAA
222468 CTATATATTA
Statistics
Matches: 234, Mismatches: 13, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
73 4 0.02
74 28 0.12
75 128 0.55
76 74 0.32
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (74 bp):
TTTTAAAAACATATATTATATAAGTTTTCAAAAAGTTTTTTAAAAACCATATATTATATATTTTT
TCAAAATGT
Found at i:222261 original size:38 final size:38
Alignment explanation
Indices: 222146--222467 Score: 412
Period size: 37 Copynumber: 8.6 Consensus size: 38
222136 TTTTCAAAAC
*
222146 TATATTATATAA-TTTTCAAAAAGTTTTTTAAAAACCA
1 TATATTATATAAGTTTTCAAAATGTTTTTTAAAAACCA
**
222183 TATATTATATATTTTTTTCCAAAATG-TTTTTAAAAA-CA
1 TATATTATATA-AGTTTT-CAAAATGTTTTTTAAAAACCA
*
222221 TATGTTATATAAGTTTTCAAAATGTTTTTTAAAAACCA
1 TATATTATATAAGTTTTCAAAATGTTTTTTAAAAACCA
222259 TATATTATATATA-TTTTCAAAATG-TTTTTAAAAACCA
1 TATATTATATA-AGTTTTCAAAATGTTTTTTAAAAACCA
*
222296 TATATTATATAAGTTTTCAAAATATTTTTTAAAAACCA
1 TATATTATATAAGTTTTCAAAATGTTTTTTAAAAACCA
* * *
222334 CATATTATATATA-TTTTTAAAATG-TTTTTAAAAATCA
1 TATATTATATA-AGTTTTCAAAATGTTTTTTAAAAACCA
222371 TATATTATATAAGTTTTCAAAATGTTTTTTAAAAAACCA
1 TATATTATATAAGTTTTCAAAATGTTTTTT-AAAAACCA
* * *
222410 TATATTATATATGTTTTCAAAATG-TTTTCAAAAAAC-
1 TATATTATATAAGTTTTCAAAATGTTTTTTAAAAACCA
*
222446 TATATAATATACA-TTTTCAAAA
1 TATATTATATA-AGTTTTCAAAA
222468 CTATATATTA
Statistics
Matches: 253, Mismatches: 19, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
36 28 0.11
37 97 0.38
38 76 0.30
39 46 0.18
40 6 0.02
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (38 bp):
TATATTATATAAGTTTTCAAAATGTTTTTTAAAAACCA
Found at i:222474 original size:61 final size:59
Alignment explanation
Indices: 222403--222515 Score: 181
Period size: 61 Copynumber: 1.9 Consensus size: 59
222393 TGTTTTTTAA
*
222403 AAAACCATATATTATATATGTTTTCAAAATGTTTTCAAAAAACTATATAATATACATTTTC
1 AAAACCATATATTATATATATTTTCAAAATGTTTTC--AAAACTATATAATATACATTTTC
* *
222464 AAAACTATATATTATATATATTTTTAAAATGTTTTCAAAACTATATAATATA
1 AAAACCATATATTATATATATTTTCAAAATGTTTTCAAAACTATATAATATA
222516 TACATTTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
59 16 0.33
61 33 0.67
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (59 bp):
AAAACCATATATTATATATATTTTCAAAATGTTTTCAAAACTATATAATATACATTTTC
Found at i:222499 original size:36 final size:37
Alignment explanation
Indices: 222458--222540 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 37
222448 TATAATATAC
* * **
222458 ATTTTCAAAACTATATATTATATATATTTTTAAAATG
1 ATTTTCAAAACTATATAATATATACATTTCAAAAATG
222495 -TTTTCAAAACTATATAATATATACATTTCAAAAATG
1 ATTTTCAAAACTATATAATATATACATTTCAAAAATG
*
222531 ATTTTTAAAA
1 ATTTTCAAAA
222541 AACAAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 32 0.80
37 8 0.20
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (37 bp):
ATTTTCAAAACTATATAATATATACATTTCAAAAATG
Found at i:224293 original size:106 final size:107
Alignment explanation
Indices: 224108--224316 Score: 411
Period size: 106 Copynumber: 2.0 Consensus size: 107
224098 GTTTGGAATG
224108 TTTTCCTAGTTGATGAATGCTCATGCCTATAAAGCTTTCTCCTTTCTTGTATTACATTATGGAAG
1 TTTTCCTAGTTGATGAATGCTCATGCCTATAAAGCTTTCTCCTTTCTTGTATTACATTATGGAAG
224173 CAGGGCCTGAAAGTT-TATTGATCAGATTTTTGTTATAACAT
66 CAGGGCCTGAAAGTTGTATTGATCAGATTTTTGTTATAACAT
224214 TTTTCCTAGTTGATGAATGCTCATGCCTATAAAGCTTTCTCCTTTCTTGTATTACATTATGGAAG
1 TTTTCCTAGTTGATGAATGCTCATGCCTATAAAGCTTTCTCCTTTCTTGTATTACATTATGGAAG
224279 CAGGGCCTGAAAGTTGTATTGATCAGATTTTTGTTATA
66 CAGGGCCTGAAAGTTGTATTGATCAGATTTTTGTTATA
224317 TAACATGTAT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 80 0.78
107 22 0.22
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (107 bp):
TTTTCCTAGTTGATGAATGCTCATGCCTATAAAGCTTTCTCCTTTCTTGTATTACATTATGGAAG
CAGGGCCTGAAAGTTGTATTGATCAGATTTTTGTTATAACAT
Found at i:231612 original size:15 final size:14
Alignment explanation
Indices: 231585--231626 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
231575 ATAACTAATT
231585 AATATATTTTATTA
1 AATATATTTTATTA
231599 AATATATCTTTATTA
1 AATATAT-TTTATTA
*
231614 AATTTATTTTATT
1 AATATATTTTATT
231627 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
AATATATTTTATTA
Found at i:231713 original size:30 final size:31
Alignment explanation
Indices: 231653--231713 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
231643 ATATATATAT
*
231653 ATATATATTATTTATCTTAACTTTAAAAAAA
1 ATATATATTATTTATCTTAACGTTAAAAAAA
* *
231684 ATATTTATTA-TTATCTTAA-GTTAATAAAA
1 ATATATATTATTTATCTTAACGTTAAAAAAA
231713 A
1 A
231714 GATAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
30 9 0.33
31 9 0.33
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (31 bp):
ATATATATTATTTATCTTAACGTTAAAAAAA
Found at i:231713 original size:31 final size:31
Alignment explanation
Indices: 231653--231713 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
231643 ATATATATAT
*
231653 ATATATATTATTTATCTTAACTTTAAAAAAA
1 ATATATATTATTTATCTTAACTTAAAAAAAA
* * *
231684 ATATTTATTA-TTATCTTAAGTTAATAAAAA
1 ATATATATTATTTATCTTAACTTAAAAAAAA
231714 GATAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (31 bp):
ATATATATTATTTATCTTAACTTAAAAAAAA
Found at i:231727 original size:34 final size:30
Alignment explanation
Indices: 231655--231729 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 30
231645 ATATATATAT
*
231655 ATATATTATTTATCTTAACTTTAAAAAAAAT
1 ATATATTA-TTATCTTAACTTTAAAAAAAAA
* *
231686 ATTTATTATTATCTTAAGTTAATAAAAAGATAAA
1 ATATATTATTATCTTAACTT--TAAAAA-A-AAA
231720 ATATATTATT
1 ATATATTATT
231730 TGAATTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 11 0.31
31 7 0.19
32 6 0.17
33 1 0.03
34 11 0.31
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (30 bp):
ATATATTATTATCTTAACTTTAAAAAAAAA
Found at i:232512 original size:19 final size:18
Alignment explanation
Indices: 232466--232515 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
232456 AATAGTTAAA
*
232466 AATTTAATAAAATATTTAT
1 AATTTAAT-AATTATTTAT
* *
232485 AATTAAATAATTATTTTT
1 AATTTAATAATTATTTAT
232503 AATTTTAATAATT
1 AA-TTTAATAATT
232516 GAGATTGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTTAATAATTATTTAT
Found at i:236798 original size:20 final size:21
Alignment explanation
Indices: 236773--236865 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
236763 TTTTCCCAAT
*
236773 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
236793 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
236814 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
236834 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
236855 TCGCAATGCGA
1 TCGCAATGCGA
236866 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:236818 original size:41 final size:41
Alignment explanation
Indices: 236773--236865 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
236763 TTTTCCCAAT
236773 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
236814 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
236855 TCGCAATGCGA
1 TCGCAATGCGA
236866 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:236878 original size:41 final size:41
Alignment explanation
Indices: 236792--236926 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
236782 GAATAAGTAA
* *
236792 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
236833 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
236874 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
236915 TTCGCAACGCGA
1 ATCGCAACGCGA
236927 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:236879 original size:20 final size:20
Alignment explanation
Indices: 236854--236948 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
236844 AATTGGGAAA
*
236854 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
236874 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
236895 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
236915 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
236935 TTCGCAACGCGATA
1 ATCGCAACGCGATA
236949 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:237164 original size:22 final size:23
Alignment explanation
Indices: 237136--237188 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
237126 CACTCTCTCA
237136 CCCATCTCCGACGAAATCCG-TC
1 CCCATCTCCGACGAAATCCGTTC
*
237158 CCCATCTCCGGCGAAATCCGTTC
1 CCCATCTCCGACGAAATCCGTTC
*
237181 TCCATCTC
1 CCCATCTC
237189 TCAGAGCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.19, C:0.45, G:0.13, T:0.23
Consensus pattern (23 bp):
CCCATCTCCGACGAAATCCGTTC
Found at i:237464 original size:20 final size:20
Alignment explanation
Indices: 237439--237496 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
237429 CGATTCTCTC
237439 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
237459 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
237479 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
237497 AGAACTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.14, C:0.16, G:0.22, T:0.48
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:239663 original size:18 final size:18
Alignment explanation
Indices: 239642--239697 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
239632 GGAAATTACT
239642 ATCGCATGCGAAATGAAA
1 ATCGCATGCGAAATGAAA
* *
239660 ATCGCA-ACG--A-GAGA
1 ATCGCATGCGAAATGAAA
239674 ATCGCATGCGAAATGAAA
1 ATCGCATGCGAAATGAAA
239692 ATCGCA
1 ATCGCA
239698 ACGCTAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 9 0.30
15 3 0.10
17 3 0.10
18 15 0.50
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (18 bp):
ATCGCATGCGAAATGAAA
Found at i:239683 original size:32 final size:33
Alignment explanation
Indices: 239642--239764 Score: 182
Period size: 32 Copynumber: 3.8 Consensus size: 33
239632 GGAAATTACT
239642 ATCGC-ATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
239674 ATCGC-ATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
239705 TTCGCAATGCG-AATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
239737 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
239765 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
31 21 0.26
32 44 0.54
33 16 0.20
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:239742 original size:63 final size:64
Alignment explanation
Indices: 239643--239770 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
239633 GAAATTACTA
*
239643 TCGCATGCGAAATGAAAATCGCAACGAGAGAATCGC-ATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
*
239706 TCGCAATGCG-AATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGC-ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
239770 T
1 T
239771 TAATTTCGCG
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 29 0.48
64 32 0.52
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (64 bp):
TCGCATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
Found at i:239786 original size:19 final size:19
Alignment explanation
Indices: 239764--239805 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
239754 AAATCGCAAC
*
239764 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
239783 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
239802 GCGA
1 GCGA
239806 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:239806 original size:19 final size:19
Alignment explanation
Indices: 239773--239872 Score: 94
Period size: 19 Copynumber: 5.8 Consensus size: 19
239763 CGCGAATTTA
*
239773 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
239792 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
239809 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
239825 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
239842 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
239858 ATTTTGCATTGCGAT
1 ATTTCGCATTGCGAT
239873 AGTACTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 12 0.18
16 14 0.22
17 13 0.20
19 26 0.40
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:239819 original size:14 final size:14
Alignment explanation
Indices: 239800--239854 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
239790 TCATTTCGCA
239800 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
239814 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
239831 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
239847 TTGCGATT
1 TTGCGATT
239855 TTCATTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:239821 original size:33 final size:33
Alignment explanation
Indices: 239779--239872 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
239769 TTTAATTTCG
239779 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
239812 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
239845 CGTTGCGATTTTCATTTTGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
239873 AGTACTTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:239993 original size:14 final size:14
Alignment explanation
Indices: 239976--240011 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
239966 ATCAAATTAA
*
239976 ACAAATCAACTTTT
1 ACAAATCAACCTTT
239990 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
240003 ACAAATCAA
1 ACAAATCAA
240012 TTAAACAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:241444 original size:42 final size:42
Alignment explanation
Indices: 241377--241460 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
241367 CGATGACAGT
* * *
241377 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
241419 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
241461 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:243435 original size:20 final size:20
Alignment explanation
Indices: 243410--243447 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
243400 TCTTTTGGTT
243410 GAAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACGCG
**
243430 GAAATGACTATCGCAACG
1 GAAATGAAAATCGCAACG
243448 AGAGAATCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGCG
Found at i:243472 original size:33 final size:33
Alignment explanation
Indices: 243415--243555 Score: 147
Period size: 33 Copynumber: 4.1 Consensus size: 33
243405 TGGTTGAAAT
**
243415 GAAAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAAAATCGCAACGC-GAAATGAAAATCGCAACGA
* ** * *
243449 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAAAATCGCAACGCGAAATGAAAATCGCAACGA
*
243482 GACAATCGCAACGCGAAATGAAAATCGCAACTGCGA
1 GAAAATCGCAACGCGAAATGAAAATCGCAA---CGA
* *
243518 AATAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GA-AAATCGCAACGCGAAATGAAAATCGCAACGA
243552 GAAA
1 GAAA
243556 TGAAAATCGC
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
33 45 0.49
34 16 0.18
36 3 0.03
37 27 0.30
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:243507 original size:19 final size:19
Alignment explanation
Indices: 243410--243572 Score: 152
Period size: 19 Copynumber: 9.1 Consensus size: 19
243400 TCTTTTGGTT
243410 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
243429 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
243447 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
243463 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
243481 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
243496 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GC
243516 GAAAT--AAATCGCAACGC
1 GAAATGAAAATCGCAACGC
243533 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
243552 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
243571 GA
1 GA
243573 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 11, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 8 0.07
18 14 0.12
19 52 0.44
20 21 0.18
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:243535 original size:37 final size:37
Alignment explanation
Indices: 243485--243572 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
243475 GCGACCAGAC
243485 AATCGCAACGCGAAATGAAAATCGCAACTGCGAAAT-A
1 AATCGCAACGCGAAATGAAAATCGCAAC-GCGAAATAA
243522 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAAT-AA
*
243560 AATCGCAATGCGA
1 AATCGCAACGCGA
243573 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 7 0.15
37 28 0.58
38 13 0.27
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (37 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAA
Found at i:243590 original size:19 final size:19
Alignment explanation
Indices: 243568--243613 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
243558 AAAATCGCAA
*
243568 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
243587 TGCGAATTTTTATTTTGCGT
1 TGCG-ATTTTGATTTCGCGT
243607 TGCGATT
1 TGCGATT
243614 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.11, C:0.13, G:0.26, T:0.50
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:244184 original size:20 final size:20
Alignment explanation
Indices: 244159--244211 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
244149 GCGCTATGTA
244159 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
244179 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
244199 TATCTCGTTGCGA
1 AATCGCGTTGCGA
244212 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:244248 original size:20 final size:20
Alignment explanation
Indices: 244220--244273 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
244210 GATTTTGTAT
244220 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
244240 TATCACATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
244260 TATCGCATTGCGAT
1 TATCGCATTGCGAT
244274 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:244292 original size:61 final size:61
Alignment explanation
Indices: 244160--244294 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
244150 CGCTATGTAA
* * * * * * ** *
244160 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
244221 ATCGCATTGCGATAGTAAGTATCACATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
244283 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
244295 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:245062 original size:21 final size:21
Alignment explanation
Indices: 245038--245090 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
245028 ACACTTAGGG
245038 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
245059 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
245080 TACCGATTCCC
1 AACCGATTCCC
245091 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:245360 original size:33 final size:32
Alignment explanation
Indices: 245315--245412 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
245305 AACTCAACAT
* *
245315 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAA-ACTTCCAAGTTCGATA
245348 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTT-AAAACTTCCAAGTTCGATA
245381 AATTCAAATACTTAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAACTTCCAAGTTCGATA
245412 A
1 A
245413 TTGAAACAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
31 12 0.19
32 7 0.11
33 40 0.65
34 3 0.05
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAACTTCCAAGTTCGATA
Found at i:247704 original size:12 final size:12
Alignment explanation
Indices: 247687--247732 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
247677 TCGGGATAAA
247687 AACCGGTTTTTT
1 AACCGGTTTTTT
247699 AACCGGTTTTTTT
1 AACCGG-TTTTTT
247712 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
247726 ATCCGGT
1 AACCGGT
247733 AAAAAACCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:247717 original size:15 final size:14
Alignment explanation
Indices: 247686--247725 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
247676 TTCGGGATAA
247686 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
247699 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
247712 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
247726 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:251419 original size:38 final size:38
Alignment explanation
Indices: 251337--251449 Score: 131
Period size: 38 Copynumber: 3.0 Consensus size: 38
251327 AGTGACGGTG
* * *
251337 AGGGTGTCTCGGACAAATCCCAAGCTC--AATCTATTC
1 AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
*
251373 AGGCTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
1 AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
** * **
251411 AGGGTGTCTCAGATGAATCCTGAGTTCATTGTCTATTC
1 AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
251449 A
1 A
251450 TTGATTTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 23 0.35
38 42 0.65
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (38 bp):
AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
Found at i:255041 original size:159 final size:154
Alignment explanation
Indices: 254837--255150 Score: 567
Period size: 159 Copynumber: 2.0 Consensus size: 154
254827 ATAATGTAAG
254837 AATCTGTATTATTCTAAATGCTTCTTTTCAATTTCCAAATTTGTTATCTTGCAAAATGTGTTAGA
1 AATCTGTATTATTCTAAATGCTTCTTTTCAATTTCCAAATTTGTTATCTTGCAAAATGTGTTAGA
254902 TATTGAAAGAGAAGTAAATG-AAAACATGTATTTACCGCAGCGTAGTGTAGATAAAAAGTATAAG
66 TATTGAAAGAGAAGTAAATGAAAAACATGTATTTACCGCAGCGTAGTGTAG----AAAGTATAAG
254966 CATGTTACTATCATATTTTCAGAAATGA
127 CATGTTACTATCATATTTTCAGAAATGA
254994 AATCTGTTATTATTTCTAAATGCTTCTTTTCAATTTCCAAATTTGTTATCTTGCAAAATGTGTTA
1 AATCTG-TATTA-TTCTAAATGCTTCTTTTCAATTTCCAAATTTGTTATCTTGCAAAATGTGTTA
255059 GATATTGAAAGAGAAGTAAATGAAAAACATGTATTTACCGCAGCGTAGTGTAGAAAGTATAAGCA
64 GATATTGAAAGAGAAGTAAATGAAAAACATGTATTTACCGCAGCGTAGTGTAGAAAGTATAAGCA
255124 TGTTACTATCATATTTTCAGAAATGA
129 TGTTACTATCATATTTTCAGAAATGA
255150 A
1 A
255151 CACGGTTGCA
Statistics
Matches: 154, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
156 39 0.25
157 6 0.04
158 5 0.03
159 74 0.48
160 30 0.19
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (154 bp):
AATCTGTATTATTCTAAATGCTTCTTTTCAATTTCCAAATTTGTTATCTTGCAAAATGTGTTAGA
TATTGAAAGAGAAGTAAATGAAAAACATGTATTTACCGCAGCGTAGTGTAGAAAGTATAAGCATG
TTACTATCATATTTTCAGAAATGA
Found at i:260689 original size:18 final size:18
Alignment explanation
Indices: 260666--260707 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
260656 ACCATAATTA
260666 CCACCACCATATCCACCG
1 CCACCACCATATCCACCG
260684 CCACCACCATATCCACCG
1 CCACCACCATATCCACCG
260702 CCACCA
1 CCACCA
260708 TAGCCACCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.57, G:0.05, T:0.10
Consensus pattern (18 bp):
CCACCACCATATCCACCG
Found at i:260749 original size:15 final size:15
Alignment explanation
Indices: 260690--260752 Score: 81
Period size: 15 Copynumber: 4.2 Consensus size: 15
260680 ACCGCCACCA
* *
260690 CCATATCCACCGCCA
1 CCATAGCCACCGCCT
*
260705 CCATAGCCACCACCT
1 CCATAGCCACCGCCT
* *
260720 CCATACCCGCCGCCT
1 CCATAGCCACCGCCT
260735 CCATAGCCACCGCCT
1 CCATAGCCACCGCCT
260750 CCA
1 CCA
260753 AAGTTACGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.22, C:0.56, G:0.10, T:0.13
Consensus pattern (15 bp):
CCATAGCCACCGCCT
Found at i:260751 original size:30 final size:30
Alignment explanation
Indices: 260684--260752 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
260674 ATATCCACCG
* *
260684 CCACCACCATATCCACCGCCACCATAGCCA
1 CCACCTCCATACCCACCGCCACCATAGCCA
* *
260714 CCACCTCCATACCCGCCGCCTCCATAGCCA
1 CCACCTCCATACCCACCGCCACCATAGCCA
*
260744 CCGCCTCCA
1 CCACCTCCA
260753 AAGTTACGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.57, G:0.09, T:0.12
Consensus pattern (30 bp):
CCACCTCCATACCCACCGCCACCATAGCCA
Found at i:263341 original size:11 final size:11
Alignment explanation
Indices: 263327--263367 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
263317 ATCATTAAAT
*
263327 TTATTAAACAG
1 TTATTAAACAA
* *
263338 TTATAAAAGAA
1 TTATTAAACAA
263349 TTATTAAACAA
1 TTATTAAACAA
263360 TTATTAAA
1 TTATTAAA
263368 TTTTATCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (11 bp):
TTATTAAACAA
Found at i:268077 original size:23 final size:23
Alignment explanation
Indices: 268051--268102 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
268041 AATATATTCG
* *
268051 TTTAATGTTTGCGAACGTGTTCA
1 TTTAATGTTTACAAACGTGTTCA
* *
268074 TTTATATGTTTATAAACGTGTTCG
1 TTTA-ATGTTTACAAACGTGTTCA
268098 TTTAA
1 TTTAA
268103 CATTCGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (23 bp):
TTTAATGTTTACAAACGTGTTCA
Found at i:271829 original size:2 final size:2
Alignment explanation
Indices: 271814--271849 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
271804 ATTATTTACT
*
271814 TA TA TA TT TA -A 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 TA TA T
271850 TATTAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:272819 original size:12 final size:12
Alignment explanation
Indices: 272786--272821 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
272776 TGAACAGTAA
*
272786 TGAACAGTACCG
1 TGAACAGTATCG
*
272798 TGAATAGTATCG
1 TGAACAGTATCG
272810 TGAACAGTATCG
1 TGAACAGTATCG
272822 AATGCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (12 bp):
TGAACAGTATCG
Found at i:273663 original size:22 final size:20
Alignment explanation
Indices: 273615--273671 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 20
273605 CATATGAAAA
*
273615 TTGTCCCGAATGACCTATGT
1 TTGTCCCGAATGACCTATAT
* *
273635 ATATCCCGAATGATCACTATAT
1 TTGTCCCGAATGA-C-CTATAT
*
273657 TTGTCCCGAAGGACC
1 TTGTCCCGAATGACC
273672 GCGTAGACCC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 12 0.41
21 2 0.07
22 15 0.52
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (20 bp):
TTGTCCCGAATGACCTATAT
Found at i:274483 original size:31 final size:31
Alignment explanation
Indices: 274445--274600 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
274435 CCCGAAGGAC
* * *
274445 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
274476 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
274507 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
274538 CATTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
** *
274569 CAGTCCATATGTCCTAAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
274600 C
1 C
274601 CCTCGACCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:275513 original size:22 final size:21
Alignment explanation
Indices: 275488--275547 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
275478 TTCGCTTGAG
*
275488 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
275510 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
275530 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
275548 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:276488 original size:16 final size:16
Alignment explanation
Indices: 276449--276491 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
276439 ATCATCAGTT
*
276449 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
276465 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
276482 CTTATCAATC
1 CTTATCAATC
276492 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:279315 original size:31 final size:31
Alignment explanation
Indices: 279277--279432 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
279267 CCTGAAGGAC
* * *
279277 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
279308 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
279339 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
279370 CATTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
279401 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
279432 C
1 C
279433 CCTCGACCAT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:280302 original size:20 final size:21
Alignment explanation
Indices: 280261--280316 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
280251 TTCGCTTGAG
*
280261 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATT-CCCATTGAAT
280283 GGGTACCGATTCCC-TTGAAT
1 GGGTACCGATTCCCATTGAAT
*
280303 GGGTACAGATTCCC
1 GGGTACCGATTCCC
280317 CTTGCCCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.59
21 3 0.09
22 10 0.31
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (21 bp):
GGGTACCGATTCCCATTGAAT
Found at i:280320 original size:21 final size:21
Alignment explanation
Indices: 280268--280320 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
280258 GAGGGGTATC
*
280268 GATTCCCCATTGAATGGGTACC
1 GATTCCCC-TTGAATGGGTACA
280290 GATT-CCCTTGAATGGGTACA
1 GATTCCCCTTGAATGGGTACA
280310 GATTCCCCTTG
1 GATTCCCCTTG
280321 CCCAGAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.55
21 9 0.31
22 4 0.14
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (21 bp):
GATTCCCCTTGAATGGGTACA
Found at i:292615 original size:13 final size:13
Alignment explanation
Indices: 292599--292623 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
292589 ATCCGTTAAA
292599 TTTTTATTTTTAC
1 TTTTTATTTTTAC
292612 TTTTTATTTTTA
1 TTTTTATTTTTA
292624 TTCGATCAAG
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:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAC
Found at i:306564 original size:207 final size:208
Alignment explanation
Indices: 306206--306622 Score: 737
Period size: 207 Copynumber: 2.0 Consensus size: 208
306196 GTGTATCCAT
* *
306206 ATTGCCAACTGATGAGCTATCAAATAGTTGACAGGTATTGAGATTCTGCAGCTGCTTTTTGACAA
1 ATTGCCAACTGATGAGCTATCAAATACTTGACAGGTATTGAGATTCTGCAGCTGCTTCTTGACAA
* *
306271 TTCTCATAACTGACAGGATTAGGCGTTTCCTGCTTGTTTTCTAACTACTGTGTTTCAAATAAAGA
66 TTCTCATAACTGACAGGATTAGGCATTTCCTGCTTGTTTTCTAACAACTGTGTTTCAAATAAAGA
*
306336 GGCCGGGATGTCTCTAGATCTATCAGACTTAACCATGTGATACTCATTTGATTGATTATCTTGAA
131 GGCCGGGATGTCTCCAGATCTATCAGACTTAACCATGTGATACTCATTTGATTGATTATCTTGAA
*
306401 AATAAGCACCTAC
196 AATAAGCACATAC
*
306414 ATTGCCAACTGATGCGCTATC-AATACTTGACAGGTATTGAGATTCTGCAGCTGCTTCTTGACAA
1 ATTGCCAACTGATGAGCTATCAAATACTTGACAGGTATTGAGATTCTGCAGCTGCTTCTTGACAA
*
306478 TTCTCATAACTGACAGGATTAGGCATTTCCTGCTTGTTTTCTAACAAGTGTGTTTCAAATAAAGA
66 TTCTCATAACTGACAGGATTAGGCATTTCCTGCTTGTTTTCTAACAACTGTGTTTCAAATAAAGA
*
306543 GGCCGGGATGTCTCCAGATCTATCAGACTTAACCATGTGATACTCATTTGATTGATTTTCTTGAA
131 GGCCGGGATGTCTCCAGATCTATCAGACTTAACCATGTGATACTCATTTGATTGATTATCTTGAA
*
306608 AATGAGCACATAC
196 AATAAGCACATAC
306621 AT
1 AT
306623 CACCAGAATC
Statistics
Matches: 199, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
207 179 0.90
208 20 0.10
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (208 bp):
ATTGCCAACTGATGAGCTATCAAATACTTGACAGGTATTGAGATTCTGCAGCTGCTTCTTGACAA
TTCTCATAACTGACAGGATTAGGCATTTCCTGCTTGTTTTCTAACAACTGTGTTTCAAATAAAGA
GGCCGGGATGTCTCCAGATCTATCAGACTTAACCATGTGATACTCATTTGATTGATTATCTTGAA
AATAAGCACATAC
Found at i:307363 original size:30 final size:30
Alignment explanation
Indices: 307315--307766 Score: 506
Period size: 30 Copynumber: 15.3 Consensus size: 30
307305 ATTGTTAAAA
*
307315 CTGGGA-ACCTGCTCCTGCTTCTCCAGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* * * * **
307344 CTAGAAGACGTGTTCCTGCTTCTCCGACTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
307374 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
307404 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
*
307434 CT-GGAGACCTGTTCCTGCTTCTCCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
*
307463 CTGGGAGACCTGCTCCTGCTTCTCCTGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* *
307493 CTGGGAGACCTGCTCCTGCTTCTCTGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* * * ** *
307523 CTGGGAGATCTGCTGCTGCTTCTGCAATTA
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* * *
307553 CTGGGAGATCTACTCCTGCTTCTCCAGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* * *
307583 ATGGGAGATCTGCTCCTGCTTCTTCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* * * *
307613 CTCGGACACCAGCTCCTGCTTCTCAGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* * *
307643 CTCGGAGACCTACTCCTGC-TC-CC-ATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* *
307670 CTGGGAGACCTGCTCCTGATTCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
* * ***
307700 CTTGGAGATCTGCTCCTGC-TC-CAATTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
*
307728 AT-GGAGACCTGCTCCTGCTTCTCCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
307757 CTGGGAGACC
1 CTGGGAGACC
307767 AACTAAAAAA
Statistics
Matches: 354, Mismatches: 61, Indels: 15
0.82 0.14 0.03
Matches are distributed among these distances:
27 34 0.10
28 10 0.03
29 43 0.12
30 267 0.75
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.34
Consensus pattern (30 bp):
CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
Found at i:309363 original size:39 final size:39
Alignment explanation
Indices: 309297--309393 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
309287 ACGAAGAGGA
*
309297 AAATGGTGAATTAGGGATTGAGATGCGA-AGGAGAAATGAG-
1 AAATGGGGAATTAGGGATTGAGATGCGAGAGG-GAAA--AGT
*
309337 AAA-GGGGAATTAGGGATTGAGGTGCGAGAGGGAAAAGT
1 AAATGGGGAATTAGGGATTGAGATGCGAGAGGGAAAAGT
309375 AAATGGGGAATTAGGGATT
1 AAATGGGGAATTAGGGATT
309394 CTGGCAATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
37 2 0.04
38 3 0.06
39 41 0.79
40 6 0.12
ACGTcount: A:0.38, C:0.02, G:0.40, T:0.20
Consensus pattern (39 bp):
AAATGGGGAATTAGGGATTGAGATGCGAGAGGGAAAAGT
Found at i:321758 original size:30 final size:30
Alignment explanation
Indices: 321722--321911 Score: 326
Period size: 30 Copynumber: 6.3 Consensus size: 30
321712 ATGCTTAAAA
*
321722 CTGGGAGATCTGCTCCTGCTTCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
* *
321752 CTGGGAGATCTGCTCCTGCTCCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
*
321782 CTGGGAGACCTGCTCCTGCATCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
*
321812 CTGGGAGACCTGCTCCTGCATCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
321842 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
*
321872 CTGGGAGACTTGCTCCTGCTTCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
321902 CTGGGAGACC
1 CTGGGAGACC
321912 AACTAAAACG
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 153 1.00
ACGTcount: A:0.12, C:0.32, G:0.24, T:0.32
Consensus pattern (30 bp):
CTGGGAGACCTGCTCCTGCTTCTCCGATTT
Found at i:325473 original size:2 final size:2
Alignment explanation
Indices: 325466--325533 Score: 69
Period size: 2 Copynumber: 37.5 Consensus size: 2
325456 CCGACCCGAT
*
325466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
325506 TA T- TT TA TA T- TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
325534 TTTTTATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
1 7 0.12
2 50 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:325489 original size:18 final size:17
Alignment explanation
Indices: 325464--325529 Score: 77
Period size: 16 Copynumber: 4.1 Consensus size: 17
325454 TCCCGACCCG
325464 ATTATATATATATATAT
1 ATTATATATATATATAT
325481 A-TATATATATATATAAT
1 ATTATATATATATAT-AT
* *
325498 ATTTTATATAT-TTTAT
1 ATTATATATATATATAT
325514 ATTA-AT-TATATATAT
1 ATTATATATATATATAT
325529 A
1 A
325530 ATATTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.07
15 7 0.17
16 18 0.43
17 6 0.14
18 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATATATATATATAT
Found at i:325524 original size:34 final size:34
Alignment explanation
Indices: 325486--325626 Score: 207
Period size: 34 Copynumber: 4.2 Consensus size: 34
325476 TATATATATA
325486 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
325520 TATATATATAATATTTT-T-TATTTTTTATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
* * *
325552 TATACATATATAATGTTTTATATTTTTTATATTACT
1 TAT--ATATATAATATTTTATATATTTTATATTAAT
325588 TATATATATAATATTTTATAT-TTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
325621 TATATA
1 TATATA
325627 ATACAAACCC
Statistics
Matches: 96, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
32 16 0.17
33 18 0.19
34 47 0.49
35 1 0.01
36 14 0.15
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:325598 original size:68 final size:69
Alignment explanation
Indices: 325484--325624 Score: 230
Period size: 68 Copynumber: 2.1 Consensus size: 69
325474 TATATATATA
* *
325484 TATATATATATAATATTTTATATATTTTATATTAATTATATATATAATATTTTTTATTTTT-TAT
1 TATACATATATAATATTTTATATATTTTATATTAATTATATATATAATATTTTATATTTTTATAT
325548 TAAT
66 TAAT
* * *
325552 TATACATATATAATGTTTTATATTTTTTATATTACTTATATATATAATATTTTATATTTTTATAT
1 TATACATATATAATATTTTATATATTTTATATTAATTATATATATAATATTTTATATTTTTATAT
325617 TAAT
66 TAAT
325621 TATA
1 TATA
325625 TAATACAAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 56 0.84
69 11 0.16
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (69 bp):
TATACATATATAATATTTTATATATTTTATATTAATTATATATATAATATTTTATATTTTTATAT
TAAT
Found at i:325647 original size:7 final size:7
Alignment explanation
Indices: 325637--325662 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
325627 ATACAAACCC
325637 TAAACAT
1 TAAACAT
325644 TAAACAT
1 TAAACAT
325651 TAAACAT
1 TAAACAT
325658 TAAAC
1 TAAAC
325663 CTCTAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACAT
Found at i:326586 original size:23 final size:23
Alignment explanation
Indices: 326560--326604 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
326550 CACCACAGCT
*
326560 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
326583 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
326605 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:326825 original size:149 final size:151
Alignment explanation
Indices: 326572--326888 Score: 516
Period size: 149 Copynumber: 2.1 Consensus size: 151
326562 TATAATTGCA
*
326572 CCGAAGTG-CCGCGTAGAATTGCATCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
* **
326636 TTCCTTAAGAATCATATACATATGCTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
326701 CCACAG-A-ATATATATATATC
130 CCAAAGAATATATATATATATC
*
326721 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
* *
326786 TCCTTAAGAATCATATACATATTCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
326850 CCAAAGAATATATATATATATC
130 CCAAAGAATATATATATATATC
326872 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
326889 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
148 1 0.01
149 123 0.79
150 2 0.01
151 30 0.19
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (151 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATATC
Found at i:327441 original size:2 final size:2
Alignment explanation
Indices: 327434--327505 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
327424 TCTCTTAGAC
327434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327506 CATGTTCAGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327699 original size:2 final size:2
Alignment explanation
Indices: 327692--327747 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
327682 ATTATTTCTT
327692 TA TA TA TA TA TA TA -A 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
327733 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
327748 CTAATCTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:327893 original size:18 final size:18
Alignment explanation
Indices: 327872--327906 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
327862 TCCCATCTAG
327872 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
327890 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
327907 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:328495 original size:64 final size:63
Alignment explanation
Indices: 328397--328557 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
328387 TAATGAAGGT
* *
328397 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
328460 GG
62 GC
*
328462 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
328526 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
328558 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:335314 original size:62 final size:62
Alignment explanation
Indices: 335246--335369 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
335236 AAACTATATT
*
335246 ATATAATAAATATATATTTTTTTATTAATTTGGGTTGTATTTTACATTTATAGGCCCAACAG
1 ATATAATAAATATATATATTTTTATTAATTTGGGTTGTATTTTACATTTATAGGCCCAACAG
335308 ATATAATAAATATATATATTTTTATTAATTTGGGTTGTATTTTACATTTATAGGCCCAACAG
1 ATATAATAAATATATATATTTTTATTAATTTGGGTTGTATTTTACATTTATAGGCCCAACAG
335370 CAATGACCCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (62 bp):
ATATAATAAATATATATATTTTTATTAATTTGGGTTGTATTTTACATTTATAGGCCCAACAG
Found at i:336703 original size:49 final size:54
Alignment explanation
Indices: 336609--336715 Score: 161
Period size: 49 Copynumber: 2.1 Consensus size: 54
336599 TCAATATTTA
336609 TTTATTTTATTTATATGTTATATTATATATATCTATTTATTTTATTTCTTAATAT
1 TTTATTTTATTTATATGTTATATTATATATA-CTATTTATTTTATTTCTTAATAT
*
336664 TTTATTTTATTT-TTTGTTATA-T-TATATA-TA-TTATTTTATTTCTTAATAT
1 TTTATTTTATTTATATGTTATATTATATATACTATTTATTTTATTTCTTAATAT
336713 TTT
1 TTT
336716 TCTATTTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
49 22 0.43
50 2 0.04
52 6 0.12
53 1 0.02
54 8 0.16
55 12 0.24
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (54 bp):
TTTATTTTATTTATATGTTATATTATATATACTATTTATTTTATTTCTTAATAT
Found at i:336721 original size:18 final size:18
Alignment explanation
Indices: 336691--336725 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
336681 TATATTATAT
336691 ATATTATTTTATTTCTTA
1 ATATTATTTTATTTCTTA
336709 ATATT-TTTCTATTTCTT
1 ATATTATTT-TATTTCTT
336726 TTAGTCCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (18 bp):
ATATTATTTTATTTCTTA
Found at i:337694 original size:4 final size:4
Alignment explanation
Indices: 337687--337721 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
337677 TCGTCATTTC
*
337687 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTTT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
337722 CTGACTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:346329 original size:21 final size:21
Alignment explanation
Indices: 346299--346402 Score: 147
Period size: 21 Copynumber: 5.0 Consensus size: 21
346289 ACCGTTATAC
*
346299 AGGGGGAATCGGTACCCCCTG
1 AGGGGGAATCTGTACCCCCTG
* *
346320 AGGGGAAATCTGTTCCCCCTG
1 AGGGGGAATCTGTACCCCCTG
*
346341 -GGGGGAATCGGTACCCCCTG
1 AGGGGGAATCTGTACCCCCTG
* *
346361 GGGGGGAATCTGTTCCCCCTG
1 AGGGGGAATCTGTACCCCCTG
346382 AGGGGGAATCTGTACCCCCTG
1 AGGGGGAATCTGTACCCCCTG
346403 GACAATCTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 17 0.24
21 55 0.76
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.19
Consensus pattern (21 bp):
AGGGGGAATCTGTACCCCCTG
Found at i:346356 original size:41 final size:42
Alignment explanation
Indices: 346299--346402 Score: 174
Period size: 41 Copynumber: 2.5 Consensus size: 42
346289 ACCGTTATAC
346299 AGGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCCCCTG
1 AGGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCCCCTG
* *
346341 -GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
1 AGGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCCCCTG
*
346382 AGGGGGAATCTGTACCCCCTG
1 AGGGGGAATCGGTACCCCCTG
346403 GACAATCTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 39 0.67
42 19 0.33
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.19
Consensus pattern (42 bp):
AGGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCCCCTG
Found at i:349799 original size:21 final size:21
Alignment explanation
Indices: 349775--349836 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
349765 CGTTAGACAA
*
349775 GGGGAATCGGTACCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
*
349796 GGGGAATCTGTACCCCTTGGG
1 GGGGAATCTGTACCCCCTGGG
349817 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
349837 ACAATCTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.39, T:0.19
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:351643 original size:7 final size:7
Alignment explanation
Indices: 351627--351677 Score: 68
Period size: 7 Copynumber: 7.1 Consensus size: 7
351617 CCCTAAATTT
351627 AAAAAA-
1 AAAAAAG
351633 AAAAAAG
1 AAAAAAG
351640 AAAAAAG
1 AAAAAAG
*
351647 AGAAAATG
1 A-AAAAAG
351655 AAAAAAG
1 AAAAAAG
351662 AACAAAAG
1 AA-AAAAG
351670 AAAAAAG
1 AAAAAAG
351677 A
1 A
351678 GGAAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 6 0.15
7 21 0.52
8 13 0.32
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:351652 original size:15 final size:15
Alignment explanation
Indices: 351634--351684 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
351624 TTTAAAAAAA
351634 AAAAAGAAAAAAGAG
1 AAAAAGAAAAAAGAG
*
351649 AAAATGAAAAAAGA-
1 AAAAAGAAAAAAGAG
351663 ACAAAAGAAAAAAGAGG
1 A-AAAAGAAAAAAGA-G
351680 AAAAA
1 AAAAA
351685 ATAAGGTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 1 0.03
15 25 0.81
16 4 0.13
17 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAGAG
Found at i:351671 original size:30 final size:29
Alignment explanation
Indices: 351627--351683 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
351617 CCCTAAATTT
351627 AAAAAAAAAAAAGAAAAAAGA-GAAAATG
1 AAAAAAAAAAAAGAAAAAAGAGGAAAATG
351655 AAAAAAGAACAAAAGAAAAAAGAGGAAAA
1 AAAAAA-AA-AAAAGAAAAAAGAGGAAAA
351684 AATAAGGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 6 0.23
29 2 0.08
30 13 0.50
31 5 0.19
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (29 bp):
AAAAAAAAAAAAGAAAAAAGAGGAAAATG
Found at i:353015 original size:110 final size:110
Alignment explanation
Indices: 352799--353037 Score: 281
Period size: 110 Copynumber: 2.2 Consensus size: 110
352789 GCTTCCTAAT
* * *
352799 TTCAGAGCCAATTTCAACTTCACAGTGAATGATATTGGACTCAAGACAACACAAGCTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* * * * *
352864 CAATGAATGGACGACTGATTGTCAACAAATAACTTTTCAGTTTCA
66 CAACGAAGGGACGACTGACTGTCAACAAACAACTTTCCAGTTTCA
* * *
352909 TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* * * * *
352974 CAGCGAAGGGGCGGCTGACTGTTAATAAACAA-TTTCCCAG-TTC-
66 CAACGAAGGGACGACTGACTGTCAACAAACAACTTT-CCAGTTTCA
*
353017 --CAGAACCAATTTCAACTTCAC
1 TTCAGAGCCAATTTCAACTTCAC
353038 GACGGAGGAT
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
106 19 0.17
109 6 0.05
110 85 0.77
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGACGACTGACTGTCAACAAACAACTTTCCAGTTTCA
Found at i:354544 original size:30 final size:31
Alignment explanation
Indices: 354510--354577 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
354500 TTTGTTTTTT
* * * *
354510 TTAAAAACGTTTTTG-GTTTTTGAAAAAAGA
1 TTAAAAACGCTTTCGAGATTTTGAAAAAAAA
354540 TTAAAAACGCTTTCGAGATTTTGAAAAAAAA
1 TTAAAAACGCTTTCGAGATTTTGAAAAAAAA
354571 TTAAAAA
1 TTAAAAA
354578 TATTATTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (31 bp):
TTAAAAACGCTTTCGAGATTTTGAAAAAAAA
Found at i:354824 original size:27 final size:24
Alignment explanation
Indices: 354746--354831 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 24
354736 TATCCTATTG
*
354746 TATTGATTTATTTT-TTTTATATTT
1 TATTTATTTATTTTGTTTTAT-TTT
354770 TATTTATTTATCTTTGTTTCT-TTGTT
1 TATTTATTTAT-TTTGTTT-TATT-TT
354796 TATCTTATTCTATTTTGTCTTTATTTT
1 TAT-TTATT-TATTTTGT-TTTATTTT
*
354823 TATTCATTT
1 TATTTATTT
354832 CTATTTCACT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
24 10 0.19
25 5 0.10
26 13 0.25
27 17 0.33
28 7 0.13
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72
Consensus pattern (24 bp):
TATTTATTTATTTTGTTTTATTTT
Found at i:357030 original size:17 final size:17
Alignment explanation
Indices: 356992--357030 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
356982 TTTCAAACGT
**
356992 ATTTTTAATAATTTTTA
1 ATTTTTAATAATTTAAA
*
357009 TTTTTTAATAATTTAAA
1 ATTTTTAATAATTTAAA
357026 ATTTT
1 ATTTT
357031 CATAATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTAATAATTTAAA
Found at i:363631 original size:19 final size:19
Alignment explanation
Indices: 363609--363652 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
363599 TGACTTGATC
*
363609 GTTGACCTGCCCATTGACT
1 GTTGACCTACCCATTGACT
* *
363628 GTTGACCTACCCGTTGATT
1 GTTGACCTACCCATTGACT
363647 GTTGAC
1 GTTGAC
363653 TTTGACCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.34
Consensus pattern (19 bp):
GTTGACCTACCCATTGACT
Found at i:366033 original size:27 final size:27
Alignment explanation
Indices: 365989--366048 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
365979 TGCTCGGTGT
* *
365989 TCACTGTTGCGACAGTTGGAGAGGTTG
1 TCACTGTTGCGACAGTTGGAAAAGTTG
* *
366016 TCACTGTTGCGGCGGTTGGAAAAGTTG
1 TCACTGTTGCGACAGTTGGAAAAGTTG
366043 TCACTG
1 TCACTG
366049 GCGTTGGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (27 bp):
TCACTGTTGCGACAGTTGGAAAAGTTG
Found at i:370280 original size:37 final size:37
Alignment explanation
Indices: 370230--370375 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
370220 AGACTCGATC
* *
370230 TTGATTTGCTTCACTACTCTTCCGTGAATGCTTAATA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
*
370267 TTGATTTGCTTCACTACTCTTCCTTGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
370304 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* *
370341 TTAATTTGGTTCACTACTCTTCCGTGAAGGCTTAA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAA
370376 AATAGCTCAG
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 103 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.40
Consensus pattern (37 bp):
TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:370442 original size:42 final size:42
Alignment explanation
Indices: 370393--370499 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
370383 CAGAGAACTT
*
370393 ATCATCTTGCTCGAAAGGCTTACAGATAACCCGAAGGATTTA
1 ATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTA
* ** *
370435 ATCATCTTGCTCGAAAGACTGATTGATAACCCGAATGATTTA
1 ATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTA
* * *
370477 ATAATCATGCTCAAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTAC
370500 TGATGGCCCG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (42 bp):
ATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTA
Found at i:370961 original size:220 final size:220
Alignment explanation
Indices: 370567--371016 Score: 654
Period size: 220 Copynumber: 2.0 Consensus size: 220
370557 AAAAATTCCA
** * *
370567 TTTTCAAAAGTCATTAAATGAGAAACTTTGAAAATCGCTCTCATTTTCCAAACTCATGTGAACAC
1 TTTTCAAAAAACATTAAATGAGAAACTTTGAAAATCGCTCTAATTTTCCAAACTCATGTGAAAAC
* * *
370632 ATCTTGCCCGAAGGTCCTATGGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACAGAT
66 ATCCTGCCCAAAGGTCCTATAGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACAGAT
* * * *
370697 GACCCGAAGGATTTAATCATCATGCTCGAAATACTTATTGATGG-CTCGAAGGTCTTACTAAGTA
131 GACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCT-GAAGGACTTACTAAGTA
* * *
370761 AGAAACTTTGGAAATCATTTTCTTGC
195 AGAAAATTTGAAAATCATTTTCTTAC
*
370787 TTTTCAAAAAACATTAAATGAGAAACTTTGAAAATCGCTTTCTAATTTT-CAAATTCATGTGAAA
1 TTTTCAAAAAACATTAAATGAGAAACTTTGAAAATCGC--TCTAATTTTCCAAACTCATGTGAAA
* * * *
370851 ACATCCTG-CCAAAGGTCTTATAGATGGTCCAAAAGACTTATCATCTTGCTTGAAAGATTTACAG
64 ACATCCTGCCCAAAGGTCCTATAGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACAG
*
370915 ATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAATGACTTACTAAGT
129 ATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAAGT
**
370980 AAGAAAATTTGAAAATTGTTTTCTTAC
194 AAGAAAATTTGAAAATCATTTTCTTAC
371007 TTTTCAAAAA
1 TTTTCAAAAA
371017 TTTCATTTTC
Statistics
Matches: 205, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
220 175 0.85
221 22 0.11
222 8 0.04
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (220 bp):
TTTTCAAAAAACATTAAATGAGAAACTTTGAAAATCGCTCTAATTTTCCAAACTCATGTGAAAAC
ATCCTGCCCAAAGGTCCTATAGATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACAGAT
GACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAAGTAA
GAAAATTTGAAAATCATTTTCTTAC
Found at i:376295 original size:125 final size:125
Alignment explanation
Indices: 376073--376323 Score: 502
Period size: 125 Copynumber: 2.0 Consensus size: 125
376063 AGGCTGCCAA
376073 GGTTTCACATAATACGAGGCCACTTCTCAGGCTTCTAACAACTCATCATACAAATCCTTATATGA
1 GGTTTCACATAATACGAGGCCACTTCTCAGGCTTCTAACAACTCATCATACAAATCCTTATATGA
376138 CATTGGGATGTAATCAAAATGAGAGCCATCTCTCAACTTAGATTGAACTGGAGTTTTCAG
66 CATTGGGATGTAATCAAAATGAGAGCCATCTCTCAACTTAGATTGAACTGGAGTTTTCAG
376198 GGTTTCACATAATACGAGGCCACTTCTCAGGCTTCTAACAACTCATCATACAAATCCTTATATGA
1 GGTTTCACATAATACGAGGCCACTTCTCAGGCTTCTAACAACTCATCATACAAATCCTTATATGA
376263 CATTGGGATGTAATCAAAATGAGAGCCATCTCTCAACTTAGATTGAACTGGAGTTTTCAG
66 CATTGGGATGTAATCAAAATGAGAGCCATCTCTCAACTTAGATTGAACTGGAGTTTTCAG
376323 G
1 G
376324 CTTACTTCCC
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (125 bp):
GGTTTCACATAATACGAGGCCACTTCTCAGGCTTCTAACAACTCATCATACAAATCCTTATATGA
CATTGGGATGTAATCAAAATGAGAGCCATCTCTCAACTTAGATTGAACTGGAGTTTTCAG
Found at i:380557 original size:21 final size:22
Alignment explanation
Indices: 380517--380557 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
380507 TTGAGGATTA
*
380517 AAAATAAAAAAAAAGTGAAATT
1 AAAATAAAAAAAAAGAGAAATT
*
380539 AAAAT-AAAAATAAGAGAAA
1 AAAATAAAAAAAAAGAGAAA
380558 AAGGTTTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATAAAAAAAAAGAGAAATT
Found at i:385009 original size:27 final size:25
Alignment explanation
Indices: 384953--385012 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
384943 TCGAAAAGTG
*
384953 ATTTAAAACGTGTTGTAAAAAATTA
1 ATTTAAAAAGTGTTGTAAAAAATTA
* * *
384978 CTTTAAAAAGTGTTTTTGAAAAATATA
1 ATTTAAAAAGTG-TTGTAAAAAAT-TA
385005 ATTTAAAA
1 ATTTAAAA
385013 TTTAACTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 10 0.36
26 9 0.32
27 9 0.32
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (25 bp):
ATTTAAAAAGTGTTGTAAAAAATTA
Found at i:386487 original size:10 final size:10
Alignment explanation
Indices: 386472--386530 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
386462 CATTTAATAA
386472 ATAAACGAAC
1 ATAAACGAAC
386482 ATAAACGAAC
1 ATAAACGAAC
* *
386492 ATGAAC-ATAA
1 ATAAACGA-AC
*
386502 ATGAACACAAAC
1 AT-AA-ACGAAC
386514 ATAAACGAAC
1 ATAAACGAAC
386524 ATAAACG
1 ATAAACG
386531 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
9 1 0.03
10 30 0.75
11 3 0.08
12 5 0.12
13 1 0.03
ACGTcount: A:0.59, C:0.19, G:0.10, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:386529 original size:16 final size:16
Alignment explanation
Indices: 386479--386529 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
386469 TAAATAAACG
*
386479 AACATAAACGAACATG
1 AACATAAACGAACATA
* *
386495 AACATAAATGAACACA
1 AACATAAACGAACATA
386511 AACATAAACGAACATA
1 AACATAAACGAACATA
386527 AAC
1 AAC
386530 GTTGGAGACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.61, C:0.20, G:0.08, T:0.12
Consensus pattern (16 bp):
AACATAAACGAACATA
Found at i:386669 original size:36 final size:35
Alignment explanation
Indices: 386624--386705 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
386614 CTCAAAAAAA
*
386624 ATTAAGAGCTCGATTAAAACTCGAGACTCAAGCTCG
1 ATTATGAGCTCGATTAAAACTCGAGACTCAA-CTCG
* * ** *
386660 ATTATGAGCTCGATTCAAGCTCGATTCTGAACTCG
1 ATTATGAGCTCGATTAAAACTCGAGACTCAACTCG
*
386695 ATTCTGAGCTC
1 ATTATGAGCTC
386706 AATTCAAGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 14 0.36
36 25 0.64
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (35 bp):
ATTATGAGCTCGATTAAAACTCGAGACTCAACTCG
Found at i:386681 original size:23 final size:23
Alignment explanation
Indices: 386651--386698 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
386641 AACTCGAGAC
*
386651 TCAAGCTCGATTATGAGCTCGAT
1 TCAAGCTCGATTATGAACTCGAT
*
386674 TCAAGCTCGATTCTGAACTCGAT
1 TCAAGCTCGATTATGAACTCGAT
386697 TC
1 TC
386699 TGAGCTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (23 bp):
TCAAGCTCGATTATGAACTCGAT
Found at i:386710 original size:12 final size:12
Alignment explanation
Indices: 386654--386723 Score: 81
Period size: 12 Copynumber: 6.0 Consensus size: 12
386644 TCGAGACTCA
*
386654 AGCTCGATTATG
1 AGCTCGATTCTG
*
386666 AGCTCGATTC-A
1 AGCTCGATTCTG
386677 AGCTCGATTCTG
1 AGCTCGATTCTG
*
386689 AACTCGATTCTG
1 AGCTCGATTCTG
* *
386701 AGCTCAATTC-A
1 AGCTCGATTCTG
386712 AGCTCGATTCTG
1 AGCTCGATTCTG
386724 TAACATCCTC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 19 0.40
12 28 0.60
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (12 bp):
AGCTCGATTCTG
Found at i:386717 original size:23 final size:24
Alignment explanation
Indices: 386666--386723 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
386656 CTCGATTATG
* *
386666 AGCTCGATTC-AAGCTCGATTCTGA
1 AGCTCGATTCTGAGCTCAATTC-GA
386690 A-CTCGATTCTGAGCTCAATTC-A
1 AGCTCGATTCTGAGCTCAATTCGA
386712 AGCTCGATTCTG
1 AGCTCGATTCTG
386724 TAACATCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 2 0.07
23 18 0.60
24 10 0.33
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (24 bp):
AGCTCGATTCTGAGCTCAATTCGA
Found at i:387583 original size:19 final size:19
Alignment explanation
Indices: 387559--387609 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
387549 ATGCAATTAG
387559 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
387578 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
387597 TGCATCGATGCAT
1 TGCATCGATGCAT
387610 CCCATTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGCA
Found at i:388095 original size:29 final size:29
Alignment explanation
Indices: 388056--388136 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
388046 TATGTGATAT
388056 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
388086 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
388115 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
388137 ACATATAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:388239 original size:15 final size:15
Alignment explanation
Indices: 388221--388254 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
388211 GAGGGTATAA
388221 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
388236 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
388251 TAGT
1 TAGT
388255 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:389844 original size:2 final size:2
Alignment explanation
Indices: 389837--389877 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
389827 GAACATGTGA
389837 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
389878 GTCTAAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:395755 original size:21 final size:21
Alignment explanation
Indices: 395713--395755 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
395703 TTTCTGGGTT
* * *
395713 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
395734 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
395755 A
1 A
395756 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:395816 original size:66 final size:67
Alignment explanation
Indices: 395713--395885 Score: 208
Period size: 67 Copynumber: 2.6 Consensus size: 67
395703 TTTCTGGGTT
* * * *
395713 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACGA-A-ATGAATTTCCAGAAT
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAAC-ATATAAGAAATTCCAGAAT
395775 GCTAG
63 GCTAG
* *
395780 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCATATAAGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACATATAAGAAATTCCAGAATGCT
*
395845 TG
66 AG
* *
395847 AGGGGAATCGATACCCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA-GGGGGGAACCGATACCCCC
395886 ATGAGAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
65 3 0.03
66 22 0.24
67 50 0.54
68 18 0.19
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACATATAAGAAATTCCAGAATGCT
AG
Found at i:396247 original size:27 final size:27
Alignment explanation
Indices: 396177--396255 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
396167 GATCACATTC
396177 CATATTATG-A-TACATGACATG-ATT
1 CATATTATGTATTACATGACATGAATT
*
396201 TATATTAAATGTATTACATGACATGAATT
1 CATATT--ATGTATTACATGACATGAATT
*
396230 CATATTATGTATTGCATGACATGAAT
1 CATATTATGTATTACATGACATGAAT
396256 ATGCAGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 5 0.11
26 3 0.06
27 20 0.43
28 11 0.23
29 8 0.17
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (27 bp):
CATATTATGTATTACATGACATGAATT
Found at i:396711 original size:23 final size:23
Alignment explanation
Indices: 396667--396711 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
396657 ATTATTATAT
*
396667 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
396690 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
396712 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:396745 original size:147 final size:139
Alignment explanation
Indices: 396405--396696 Score: 413
Period size: 142 Copynumber: 2.0 Consensus size: 139
396395 ACGCGGTTCT
* *
396405 TTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGGAAGACACATACTTGATCCATAG
1 TTAGGACATATGTATA-CC--T-GAACCTGTGTGAAGTCTTGAAACACACATACTTGATCCATAG
396470 TATGTTATGATCTTAAGGAATTCTATGTGGTCCTTTGGACATCATTATATGGCACTACGGTGCAA
62 TATGTTATGATCTTAAGGAATTCTATGTGGTCCTTTGGACATCATTATATGGCACTACGGTGCAA
**
396535 TTCTACGCGGTTC
127 TTCTACGCGGCAC
*
396548 TTAGGACATATGTATATCCTTGGAACCTGTGTGAAGTCTTGAAAGACACATACTTGATCCATAGT
1 TTAGGACATATGTATA-CC-T-GAACCTGTGTGAAGTCTTGAAACACACATACTTGATCCATAG-
*
396613 ATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCACTACGGT
62 -TATGT-TATGA-TCTTAAGGAATTCTATGTGGTCCTT-TGGACATCATTATATGGCACTACGGT
*
396678 GCAATTCTACGGGGCAC
123 GCAATTCTACGCGGCAC
396695 TT
1 TT
396697 CGGTGCATTT
Statistics
Matches: 139, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
142 44 0.32
143 19 0.14
144 5 0.04
145 5 0.04
146 25 0.18
147 41 0.29
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (139 bp):
TTAGGACATATGTATACCTGAACCTGTGTGAAGTCTTGAAACACACATACTTGATCCATAGTATG
TTATGATCTTAAGGAATTCTATGTGGTCCTTTGGACATCATTATATGGCACTACGGTGCAATTCT
ACGCGGCAC
Found at i:402782 original size:21 final size:21
Alignment explanation
Indices: 402740--402782 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
402730 TTTCTGGGTT
* * *
402740 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
402761 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
402782 A
1 A
402783 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:402843 original size:66 final size:67
Alignment explanation
Indices: 402740--402911 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
402730 TTTCTGGGTT
* * *
402740 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-A-AATGAATTTCCAGAAT
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTATAA-GAAATTCCAGAAT
402802 GCTAG
63 GCTAG
* * *
402807 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATAAGAAATTCCATATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCT
*
402872 TG
66 AG
* *
402874 AGGGGAATCGATACCCCCAGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCC
402912 ATGAGAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 2 0.02
66 22 0.24
67 67 0.72
68 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCT
AG
Found at i:402900 original size:20 final size:20
Alignment explanation
Indices: 402875--402912 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
402865 TATTGCTTGA
*
402875 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
402895 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
402913 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:403282 original size:34 final size:29
Alignment explanation
Indices: 403214--403285 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
403204 CATATTATGA
*
403214 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
403243 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
403272 TGCATGACATGAAT
1 TACATGACATGAAT
403286 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:403597 original size:2 final size:2
Alignment explanation
Indices: 403590--403665 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
403580 GTCCTTCGGG
403590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
403632 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
403666 TCTGTGGAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:403802 original size:23 final size:23
Alignment explanation
Indices: 403769--403813 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
403759 ATTTTTATAT
*
403769 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
403792 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
403814 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:405074 original size:149 final size:149
Alignment explanation
Indices: 404680--405129 Score: 893
Period size: 149 Copynumber: 3.0 Consensus size: 149
404670 CAAAGTGCCC
404680 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
404745 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAG-ATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
404809 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
404828 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
404893 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
404958 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
404977 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
405042 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
405107 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
405126 CGTA
1 CGTA
405130 TACCCTCGAC
Statistics
Matches: 301, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
148 124 0.41
149 177 0.59
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:405288 original size:31 final size:31
Alignment explanation
Indices: 405243--405317 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
405233 CACTTTCACA
* *
405243 TATCACGTA-TCACGTAGCTT-CTTTTCATAT
1 TATCACATAGTCACGTAG-TTCCTTTCCATAT
405273 TATCACATAGTCACGTAGTTCCTTTCCATAT
1 TATCACATAGTCACGTAGTTCCTTTCCATAT
*
405304 AATTCACAT-GTCAC
1 TA-TCACATAGTCAC
405318 ATATGTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.26
31 23 0.59
32 6 0.15
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (31 bp):
TATCACATAGTCACGTAGTTCCTTTCCATAT
Done.