Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007862.1 Hibiscus syriacus cultivar Beakdansim tig00110229_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: 338149
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:198378 original size:50 final size:50
Alignment explanation
Indices: 198319--198448 Score: 127
Period size: 50 Copynumber: 2.6 Consensus size: 50
198309 GATACCCAGG
* *
198319 TATAACGCGGATCAGGGGGCGCGCTATACTCACGTGGCGCCAGATCACCA
1 TATATCGCGGATCAGGGGGCGCGCTATACTCACGTGGCGCCAAATCACCA
** ** * * * * *
198369 TATATCGCGGGGCAGGGGGCATGCCATACCCACGTGGGGCCAAATCAGCG
1 TATATCGCGGATCAGGGGGCGCGCTATACTCACGTGGCGCCAAATCACCA
* *
198419 TATAGT-GCGGTTCAGGGGGCGCGCTTTACT
1 TATA-TCGCGGATCAGGGGGCGCGCTATACT
198449 GCTACGGGTG
Statistics
Matches: 61, Mismatches: 18, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
50 60 0.98
51 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (50 bp):
TATATCGCGGATCAGGGGGCGCGCTATACTCACGTGGCGCCAAATCACCA
Found at i:202894 original size:23 final size:23
Alignment explanation
Indices: 202863--202946 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
202853 CTCGTATAAA
* *
202863 TGCATCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
202886 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
202909 TGAACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
202932 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
202947 TATAAGATTG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:209807 original size:23 final size:23
Alignment explanation
Indices: 209777--209820 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
209767 ATATAAATCC
209777 ACCGAAGTGCCACGTAGAATTAT
1 ACCGAAGTGCCACGTAGAATTAT
*
209800 ACCGAAGTGCCGCGTAGAATT
1 ACCGAAGTGCCACGTAGAATT
209821 GCACTGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
ACCGAAGTGCCACGTAGAATTAT
Found at i:213145 original size:13 final size:13
Alignment explanation
Indices: 213127--213154 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
213117 TTCAAAGGTT
213127 TCAAAGAAGCAAG
1 TCAAAGAAGCAAG
213140 TCAAAGAAGCAAG
1 TCAAAGAAGCAAG
213153 TC
1 TC
213155 CTAGAGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.11
Consensus pattern (13 bp):
TCAAAGAAGCAAG
Found at i:220935 original size:20 final size:20
Alignment explanation
Indices: 220906--220944 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
220896 ATTCCACCAC
*
220906 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
220926 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
220945 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:227892 original size:40 final size:40
Alignment explanation
Indices: 227832--227941 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
227822 ACTGTAGTGC
227832 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
* *
227872 TACACATAAGGTTGTTCCCACCATATACAACGAAGTGTAT
1 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
* *
227912 TACACATAAGGTCGTGCCCACCATGTACAC
1 TACACATAAGGTTGTGCCCACCATATACAC
227942 TTAGTGTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
Found at i:230117 original size:11 final size:11
Alignment explanation
Indices: 230098--230131 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
230088 ATTTATATAA
*
230098 ATTATTATTTT
1 ATTAATATTTT
230109 ATTAATATTTTT
1 ATTAATA-TTTT
230121 ATTAATATTTT
1 ATTAATATTTT
230132 TGCACTCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:230120 original size:12 final size:12
Alignment explanation
Indices: 230105--230132 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
230095 TAAATTATTA
230105 TTTTATTAATAT
1 TTTTATTAATAT
230117 TTTTATTAATAT
1 TTTTATTAATAT
230129 TTTT
1 TTTT
230133 GCACTCCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTAATAT
Found at i:231666 original size:13 final size:11
Alignment explanation
Indices: 231650--231680 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
231640 ATTTTGGTCC
231650 TTTTTTTTATT
1 TTTTTTTTATT
231661 TTTTTTTTATT
1 TTTTTTTTATT
231672 TTTCTTTTT
1 TTT-TTTTT
231681 TACTAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:231717 original size:22 final size:20
Alignment explanation
Indices: 231689--231743 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
231679 TTTACTAACT
*
231689 TTTATTTATATTTGTTATCTAA
1 TTTATTTATATTTATTAT-T-A
231711 TTTATTTAT-TTTATTATTA
1 TTTATTTATATTTATTATTA
*
231730 TTATATTAATATTT
1 TT-TATTTATATTT
231744 TTCTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 3 0.10
20 7 0.24
21 10 0.34
22 9 0.31
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATTTATATTTATTATTA
Found at i:257704 original size:30 final size:30
Alignment explanation
Indices: 257664--257728 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
257654 AGCCTTGCGT
*
257664 GAGGAGAGGAGAAGAGAAGAGAAGAGAAGA
1 GAGGAAAGGAGAAGAGAAGAGAAGAGAAGA
*
257694 GAGGAAAGGAGAAGAGAAGAGAAGAGAGGA
1 GAGGAAAGGAGAAGAGAAGAGAAGAGAAGA
257724 GAGGA
1 GAGGA
257729 TACAACGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (30 bp):
GAGGAAAGGAGAAGAGAAGAGAAGAGAAGA
Found at i:257705 original size:25 final size:25
Alignment explanation
Indices: 257667--257728 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
257657 CTTGCGTGAG
257667 GAGAGGAGAA-GAGAAGAGAAGAGAA
1 GAGAGGA-AAGGAGAAGAGAAGAGAA
257692 GAGAGGAAAGGAGAAGAGAAGAGAA
1 GAGAGGAAAGGAGAAGAGAAGAGAA
*
257717 GAGAGGAGAGGA
1 GAGAGGAAAGGA
257729 TACAACGCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (25 bp):
GAGAGGAAAGGAGAAGAGAAGAGAA
Found at i:257728 original size:5 final size:5
Alignment explanation
Indices: 257667--257725 Score: 75
Period size: 5 Copynumber: 11.8 Consensus size: 5
257657 CTTGCGTGAG
* *
257667 GAGAG GAGAA GAGAA GAGAA GAGAA GAGAG GA-AA GGAGAA GAGAA GAGAA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA -GAGAA GAGAA GAGAA
*
257717 GAGAG GAGA
1 GAGAA GAGA
257726 GGATACAACG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
4 1 0.02
5 45 0.94
6 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:265383 original size:22 final size:23
Alignment explanation
Indices: 265358--265406 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
265348 AAAGAATCGA
*
265358 AAAACATGTCA-AAAAGCATAAG
1 AAAACATATCATAAAAGCATAAG
*
265380 AAAACATATCATAAAAGCATATG
1 AAAACATATCATAAAAGCATAAG
265403 AAAA
1 AAAA
265407 TATGCAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.16
Consensus pattern (23 bp):
AAAACATATCATAAAAGCATAAG
Found at i:267948 original size:35 final size:33
Alignment explanation
Indices: 267873--267949 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 33
267863 GTCTAAACCC
*
267873 TAAATTAAATTATTTAGAATTTGGGGTTTAAAA
1 TAAATTGAATTATTTAGAATTTGGGGTTTAAAA
* *
267906 TATAATTGAATTATTTTAGATTTTGGGGTTTAGAA
1 TA-AATTGAATTA-TTTAGAATTTGGGGTTTAAAA
267941 TGAAATTGA
1 T-AAATTGA
267950 GGATTGTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 2 0.05
34 9 0.24
35 26 0.68
36 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (33 bp):
TAAATTGAATTATTTAGAATTTGGGGTTTAAAA
Found at i:269780 original size:21 final size:21
Alignment explanation
Indices: 269755--269795 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
269745 TATTGTTTAT
269755 TATCATTATTTGAAAAAATAA
1 TATCATTATTTGAAAAAATAA
269776 TATCATTATTTGAAAAAATA
1 TATCATTATTTGAAAAAATA
269796 TTATACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
TATCATTATTTGAAAAAATAA
Found at i:273088 original size:38 final size:37
Alignment explanation
Indices: 273055--273127 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 37
273045 TTGGTATTTA
273055 AATACAACAAACTTACAATAA-GA-ATTAAATGGTAAAT
1 AATA-AACAAA-TTACAATAACGATATTAAATGGTAAAT
*
273092 AATAACCAAATTACAATAACTGATATTAAATGGTAA
1 AATAAACAAATTACAATAAC-GATATTAAATGGTAA
273128 TAAACAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 9 0.28
36 5 0.16
37 6 0.19
38 12 0.38
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (37 bp):
AATAAACAAATTACAATAACGATATTAAATGGTAAAT
Found at i:273138 original size:35 final size:34
Alignment explanation
Indices: 273053--273139 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
273043 ATTTGGTATT
*
273053 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
273087 TAAATAATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
273125 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
273140 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:273364 original size:3 final size:3
Alignment explanation
Indices: 273350--273393 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
273340 CTCGCTGTCA
* * * *
273350 TCG TCA TCG TCG TCG TCA TCG TCA TTG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
273394 CTGAGCATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.07, C:0.32, G:0.25, T:0.36
Consensus pattern (3 bp):
TCG
Found at i:273369 original size:18 final size:18
Alignment explanation
Indices: 273346--273390 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
273336 ACTCCTCGCT
273346 GTCATCGTCATCGTCGTC
1 GTCATCGTCATCGTCGTC
*
273364 GTCATCGTCATTGTCGTC
1 GTCATCGTCATCGTCGTC
*
273382 GTCGTCGTC
1 GTCATCGTC
273391 GTCCTGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.09, C:0.31, G:0.24, T:0.36
Consensus pattern (18 bp):
GTCATCGTCATCGTCGTC
Found at i:273764 original size:18 final size:18
Alignment explanation
Indices: 273741--273777 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
273731 AAAGGCGATG
*
273741 GCGGCATCATATATGGTT
1 GCGGCATCATAAATGGTT
273759 GCGGCATCATAAATGGTT
1 GCGGCATCATAAATGGTT
273777 G
1 G
273778 TGGTGGCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (18 bp):
GCGGCATCATAAATGGTT
Found at i:275479 original size:17 final size:18
Alignment explanation
Indices: 275459--275499 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
275449 GAATTATATT
275459 AGTAAAAT-ATTAAATAA
1 AGTAAAATAATTAAATAA
275476 AGTAAAATAATTAAATAA
1 AGTAAAATAATTAAATAA
*
275494 ATTAAA
1 AGTAAA
275500 TACATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATAATTAAATAA
Found at i:275578 original size:10 final size:10
Alignment explanation
Indices: 275547--275581 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
275537 CAAAGATATT
275547 ATTTGAGAGA
1 ATTTGAGAGA
* *
275557 AATTAAGAGA
1 ATTTGAGAGA
275567 ATTTGAGAGA
1 ATTTGAGAGA
275577 ATTTG
1 ATTTG
275582 GTGTGATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (10 bp):
ATTTGAGAGA
Found at i:278947 original size:2 final size:2
Alignment explanation
Indices: 278942--278984 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
278932 ATATAAGACC
278942 AG AG AG AG AG 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 AG AG AG AG AG
278984 A
1 A
278985 TGTGTATGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:282068 original size:17 final size:17
Alignment explanation
Indices: 282046--282084 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
282036 AGGAGTAAGA
282046 AATTTATGAGAATAAAG
1 AATTTATGAGAATAAAG
282063 AATTTATGAGAATAAAG
1 AATTTATGAGAATAAAG
282080 AATTT
1 AATTT
282085 GCATACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
AATTTATGAGAATAAAG
Found at i:282123 original size:17 final size:18
Alignment explanation
Indices: 282087--282127 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
282077 AAGAATTTGC
282087 ATAC-AATTGTAGTCAAA
1 ATACAAATTGTAGTCAAA
282104 ATATCAAATTG-AGT-AAA
1 ATA-CAAATTGTAGTCAAA
282121 ATACAAA
1 ATACAAA
282128 GTTAATGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 4 0.18
19 5 0.23
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (18 bp):
ATACAAATTGTAGTCAAA
Found at i:286859 original size:13 final size:14
Alignment explanation
Indices: 286798--286861 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
286788 TCGATAATAT
286798 GTTTATTTATGTTC
1 GTTTATTTATGTTC
*
286812 GTTTACTTT-CGTTC
1 GTTTA-TTTATGTTC
286826 GTTTA--TA--TTC
1 GTTTATTTATGTTC
*
286836 GTTTGTTTATGTTC
1 GTTTATTTATGTTC
286850 G-TTATTTATGTT
1 GTTTATTTATGTT
286862 TAATACAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
10 7 0.17
11 1 0.02
12 2 0.05
13 10 0.24
14 18 0.44
15 3 0.07
ACGTcount: A:0.12, C:0.09, G:0.16, T:0.62
Consensus pattern (14 bp):
GTTTATTTATGTTC
Found at i:291396 original size:37 final size:37
Alignment explanation
Indices: 291343--291447 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
291333 CCTTTTCGTC
*
291343 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
291380 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
291417 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
291448 CCACAAGTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:292004 original size:13 final size:13
Alignment explanation
Indices: 291986--292011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
291976 TGTTTACTTA
291986 TTTACTATATTTT
1 TTTACTATATTTT
291999 TTTACTATATTTT
1 TTTACTATATTTT
292012 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:292055 original size:105 final size:105
Alignment explanation
Indices: 291873--292076 Score: 229
Period size: 105 Copynumber: 1.9 Consensus size: 105
291863 TTAATTATAT
* * * * ** * *
291873 TTTATTTATTTATTATATTTTTTTTCATTTTTCTTTGCGTTATATTATATTATTTTCCTATTATT
1 TTTACTTATTTACTATATTTTTTTACATTTTTCCTAACGTTATATTATATTATTTTACTATCATT
*
291938 ATTATATATATATATATTAT-ATTATTATTTTTTATCTATG
66 ATTATATATATAT-TATTATGATTACTATTTTTTATCTATG
291978 TTTACTTATTTACTATATTTTTTTACTATATTTTCCTAACGTTATA-TATATATATTATTACT-T
1 TTTACTTATTTACTATATTTTTTTAC-AT-TTTTCCTAACGTTATATTATAT-TATT-TTACTAT
* *
292041 CATT-TTAT-TTTATATTTTTATGATTACTATTTTTTA
62 CATTATTATATATATATTATTATGATTACTATTTTTTA
292077 GTTAATATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
104 5 0.06
105 42 0.51
106 11 0.13
107 21 0.25
108 4 0.05
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (105 bp):
TTTACTTATTTACTATATTTTTTTACATTTTTCCTAACGTTATATTATATTATTTTACTATCATT
ATTATATATATATTATTATGATTACTATTTTTTATCTATG
Found at i:292322 original size:18 final size:19
Alignment explanation
Indices: 292298--292343 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
292288 TGTATATATA
*
292298 TTTTTTTCTTC-ATTT-AT
1 TTTTTTTATTCAATTTCAT
292315 TTTATTTTATTCAATTTCAT
1 TTT-TTTTATTCAATTTCAT
292335 TTTTTTTAT
1 TTTTTTTAT
292344 ATTTGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 7 0.28
19 10 0.40
20 5 0.20
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTCAATTTCAT
Found at i:293514 original size:19 final size:19
Alignment explanation
Indices: 293490--293526 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
293480 ACCTTACTAA
293490 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
293509 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
293527 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:296951 original size:14 final size:13
Alignment explanation
Indices: 296918--296978 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 13
296908 GGGCAAAAAC
*
296918 AAAAAAGAAAAGA
1 AAAAAAAAAAAGA
* *
296931 AGCAAAAAATAAGA
1 A-AAAAAAAAAAGA
296945 AAAAAAAAGAAAGA
1 AAAAAAAA-AAAGA
296959 ATAAAAATCAAAAAGA
1 A-AAAAA--AAAAAGA
296975 AAAA
1 AAAA
296979 GGGACAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
13 7 0.18
14 15 0.39
15 8 0.21
16 6 0.16
17 2 0.05
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.05
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:296961 original size:20 final size:20
Alignment explanation
Indices: 296919--296976 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
296909 GGCAAAAACA
* *
296919 AAAAAGAAAAGAAGCAAAAAAT
1 AAAAATAAAA-AAG-AAAGAAT
296941 AAGAAA-AAAAAAGAAAGAAT
1 AA-AAATAAAAAAGAAAGAAT
*
296961 AAAAATCAAAAAGAAA
1 AAAAATAAAAAAGAAA
296977 AAGGGACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 17 0.53
21 3 0.09
22 6 0.19
23 3 0.09
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.05
Consensus pattern (20 bp):
AAAAATAAAAAAGAAAGAAT
Found at i:298709 original size:106 final size:106
Alignment explanation
Indices: 298584--299460 Score: 1421
Period size: 106 Copynumber: 8.3 Consensus size: 106
298574 GTGCCACTTG
* * * ** *
298584 AGACAACACAAGTTCAACTTCACAACAAAGGGATGGCTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
298649 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
298690 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
298755 CAGAGCCAATTTCAACTTCACAACGAATGCTATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * *
298796 AGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTCTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
298861 CAGAGCCAATTTCAACTTCACAGCGAAGGATTTTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * *
298902 AGACAACGCAAGTTCAACTTCATGACGAATGGACCACTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
298967 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
299008 AGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
299073 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
299114 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
299179 CAGAGCCAATTTCAACTTCATAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
299220 AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
299285 CGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
299326 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
** *
299391 TGGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
299432 AGACAACACAAGTTCAACTTCACGACGAA
1 AGACAACGCAAGTTCAACTTCACGACGAA
299461 AACAACTTCT
Statistics
Matches: 716, Mismatches: 55, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 716 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
Found at i:298857 original size:212 final size:212
Alignment explanation
Indices: 298584--299834 Score: 1745
Period size: 212 Copynumber: 6.0 Consensus size: 212
298574 GTGCCACTTG
* * * ** * *
298584 AGACAACACAAGTTCAACTTCACAACAAAGGGATGGCTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
* *
298649 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
298714 ACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
* *
298779 GAATGCTATTGGACTCC
196 GAAGGATATTGGACTCC
* * *
298796 AGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTCTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
* * * *
298861 CAGAGCCAATTTCAACTTCACAGCGAAGGATTTTGGACTCAAGACAACGCAAGTTCAACTTCATG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
298926 ACGAATGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
298991 GAAGGATATTGGACTCC
196 GAAGGATATTGGACTCC
* * *
299008 AGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
299073 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
299138 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCATAGC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
299203 GAAGGATATTGGACTCA
196 GAAGGATATTGGACTCC
* *
299220 AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
* * *
299285 CGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* ** *
299350 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCAATTTCAACTTCACATC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
299415 GAAGGATATTGGACTCC
196 GAAGGATATTGGACTCC
* * ** *
299432 AGACAACACAAGTTCAACTTCACGACGAA--AACAAC----T-T---C--TCAATTT--CAA---
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
* * * *
299480 -AG-CCAATTTT-AACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
299542 ACGAAGGGACCGTTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACCAATTTCAACTTCACAGC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
299607 GAAGGATATTGGACTCG
196 GAAGGATATTGGACTCC
* *
299624 AGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAATTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
* * * * *
299689 CGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
299754 ACGAAGGGA-CGACTGGTTGTCAACAAATAATTTCCCGATTCCAGAGCCAATTTCAACCTCAC-G
131 ACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
299817 ACGGAGGATATTGGACTC
195 -CGAAGGATATTGGACTC
299835 GGAACAATGC
Statistics
Matches: 920, Mismatches: 97, Indels: 44
0.87 0.09 0.04
Matches are distributed among these distances:
192 149 0.16
193 5 0.01
194 4 0.00
198 4 0.00
199 1 0.00
200 6 0.01
202 2 0.00
204 5 0.01
205 1 0.00
206 4 0.00
210 4 0.00
211 8 0.01
212 727 0.79
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (212 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
GAAGGATATTGGACTCC
Found at i:299175 original size:318 final size:317
Alignment explanation
Indices: 298584--299834 Score: 1813
Period size: 318 Copynumber: 4.0 Consensus size: 317
298574 GTGCCACTTG
* **
298584 AGACAACACAAGTTCAACTTCACAACAAAGGGATGGCTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATT
*
298649 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
298714 ACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
* * * * * *
298779 GAATGCTATTGGACTCCAGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTCTCAAT
196 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAAC
* *
298844 AAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATTTTGGACTCA
260 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
** * * * * *
298902 AGACAACGCAAGTTCAACTTCATGACGAATGGACCACTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATT
*
298967 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAATTCACG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
299032 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
*
299097 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
196 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAAC
*
299162 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGGACTCA
260 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
299220 AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATT
* *
299285 CGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* ** *
299350 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCAATTTCAACTTCACATC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
299415 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTT--C-AC-----GA--C-----G---A-A
196 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGCTGGTTGTCAACA
* * * * *
299461 AACAACTTCTCAATTTCAAAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCC
261 AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * * * *
299518 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAAAAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATT
* * *
299583 CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACGCAAGTTCAACTTCACG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
299648 ACGAAGGGACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAAC
131 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
* * *
299713 AAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAC
196 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACG-CTGGTTGTCAAC
* * * * * *
299778 AAATAATTTCCCGATTCCAGAGCCAATTTCAACCTCAC-GACGGAGGATATTGGACTC
260 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
299835 GGAACAATGC
Statistics
Matches: 842, Mismatches: 70, Indels: 42
0.88 0.07 0.04
Matches are distributed among these distances:
298 267 0.32
299 1 0.00
300 1 0.00
301 2 0.00
302 1 0.00
306 2 0.00
307 1 0.00
309 1 0.00
310 2 0.00
314 1 0.00
315 2 0.00
316 1 0.00
317 1 0.00
318 559 0.66
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (317 bp):
AGACAACGCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGCTGGTTGTCAACA
AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:299513 original size:192 final size:193
Alignment explanation
Indices: 299268--299834 Score: 672
Period size: 192 Copynumber: 2.8 Consensus size: 193
299258 GGTTGTCAAC
* * *
299268 AAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAAC
1 AAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
* **
299333 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCC
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAATTTCCCAATTTCAGAGCC
299398 AATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG-A-
131 AATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
* ** * *
299460 AAACAACTTCTCAATTTCAAAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAAT
1 AAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
* * * *
299525 GCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAATTTCCCAATTTCAGAGCC
* * *
299590 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACGCAAGTTCAACTTCACGACGAAGG
131 AATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA--
299655 G
193 G
*
299656 ACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATA
1 A------------AAC-AAC---TTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATA
* * * *
299721 TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAATAAT
50 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAAAAAT
* * * *
299785 TTCCCGATTCCAGAGCCAATTTCAACCTCACGACGGAGGATATTGGACTC
114 TTCCCAATTTCAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTC
299835 GGAACAATGC
Statistics
Matches: 316, Mismatches: 37, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
192 172 0.54
193 1 0.00
196 1 0.00
208 3 0.01
209 3 0.01
211 2 0.01
212 133 0.42
213 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (193 bp):
AAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAATTTCCCAATTTCAGAGCC
AATTTCAACTTCACACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
Found at i:299537 original size:43 final size:43
Alignment explanation
Indices: 299401--299548 Score: 117
Period size: 43 Copynumber: 3.4 Consensus size: 43
299391 TGGAGCCAAT
*
299401 TTCAACTTCACATCGAAGGATATTGGACTCCAGACAACA-CAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAA-AGCAAG
* * * * ** *
299444 TTCAACTTCACGACGAA-AACAACTT---CTCAATTTCAAAGCCAAT
1 TTCAACTTCACAACGAAGGA-TA-TTGGACTCCA-GACAAAG-CAAG
* *
299487 TTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAAAGCAAG
*
299530 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
299549 GACCGTTGGT
Statistics
Matches: 77, Mismatches: 19, Indels: 18
0.68 0.17 0.16
Matches are distributed among these distances:
41 5 0.06
42 6 0.08
43 55 0.71
44 7 0.09
45 4 0.05
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAAAGCAAG
Found at i:299616 original size:404 final size:404
Alignment explanation
Indices: 299056--299834 Score: 1294
Period size: 404 Copynumber: 1.9 Consensus size: 404
299046 GGTTGTCAAC
*
299056 AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 AAACAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
* * *
299121 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
*
299186 AATTTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACAAAGG
131 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACAAAGG
* *
299251 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAA-GA
196 GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAAC-AAAGGA
* *
299315 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACA
260 TATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACA
*** *
299379 ATTTCCCAATTTTGGAGCCAATTTCAACTTCAC-ATCGAAGGATATTGGACTCCAGACAACACAA
324 ATTTCCCAATTCCAGAGCCAATTTCAACCTCACGA-CGAAGGATATTGGACTCCAGACAACACAA
299443 GTTCAACTTCACGACGA
388 GTTCAACTTCACGACGA
* *
299460 AAACAACTTCTCAATTTCAAAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAAT
1 AAACAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
*
299525 GCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
* * * *
299590 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACGCAAGTTCAACTTCACGACGAAGG
131 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACAAAGG
299655 GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGAT
196 GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGAT
* *
299720 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAAT
261 ATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAAT
* *
299785 TTCCCGATTCCAGAGCCAATTTCAACCTCACGACGGAGGATATTGGACTC
326 TTCCCAATTCCAGAGCCAATTTCAACCTCACGACGAAGGATATTGGACTC
299835 GGAACAATGC
Statistics
Matches: 348, Mismatches: 24, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
403 5 0.01
404 342 0.98
405 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (404 bp):
AAACAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACAAAGG
GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGAT
ATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAAT
TTCCCAATTCCAGAGCCAATTTCAACCTCACGACGAAGGATATTGGACTCCAGACAACACAAGTT
CAACTTCACGACGA
Found at i:299617 original size:298 final size:298
Alignment explanation
Indices: 299162--299758 Score: 978
Period size: 298 Copynumber: 2.0 Consensus size: 298
299152 GGTTGTCAAC
* * *
299162 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGGACTCAAGACAAC
1 AAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAC
* * * * *
299227 GCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCC
66 GCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
299292 AATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
131 AATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
299357 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCAATTTCAACTTCACATCGAAGGAT
196 GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGAT
*
299422 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGA
261 ATTGGACTCCAGACAACACAAGTTCAACTTCACAACGA
* * * *
299460 AAACAACTTCTCAATTTCAAAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAAT
1 AAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAC
* * *
299525 GCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
66 GCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
* * *
299590 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACGCAAGTTCAACTTCACGACGAAGG
131 AATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
299655 GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGAT
196 GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGAT
*
299720 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGA
261 ATTGGACTCCAGACAACACAAGTTCAACTTCACAACGA
299758 A
1 A
299759 GGGACGACTG
Statistics
Matches: 275, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
298 275 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (298 bp):
AAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAC
GCAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAAATTCAGAACC
AATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGAT
ATTGGACTCCAGACAACACAAGTTCAACTTCACAACGA
Found at i:299649 original size:106 final size:106
Alignment explanation
Indices: 299459--299835 Score: 492
Period size: 106 Copynumber: 3.5 Consensus size: 106
299449 CTTCACGACG
* * * *
299459 AAAACAACTTCTCAATTTCA-AAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACA
1 AAAA-AACTTCCCAAATTCAGAA-CCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACA
* *
299523 ATGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAAC
64 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* *
299566 AAAAAACTTCCCAAATTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAAC
1 AAAAAACTTCCCAAATTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAAC
299631 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* * * *
299672 AAACAAA-TTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAA
1 AAA-AAACTTCCCAAATTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAA
* *
299736 CACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAAC
65 CGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAAC
* * * * * * *
299778 AAATAATTTCCC-GATTCCAGAGCCAATTTCAACCTCACGACGGAGGATATTGGACTCG
1 AAAAAACTTCCCAAATT-CAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCG
299836 GAACAATGCT
Statistics
Matches: 241, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
105 6 0.02
106 226 0.94
107 9 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (106 bp):
AAAAAACTTCCCAAATTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
Found at i:300633 original size:37 final size:36
Alignment explanation
Indices: 300583--300686 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 36
300573 CCTTTTCGTC
300583 CTGCTAGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTGCTAGATTCAAACTCCTAAAAATAGGATAGAATT
* *
300619 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTGCTA-GATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
300656 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTGCTA-GATTCAAACTCCTAAAAATAGGAT
300687 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 5 0.08
37 54 0.92
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (36 bp):
CTGCTAGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:301292 original size:29 final size:29
Alignment explanation
Indices: 301248--301358 Score: 80
Period size: 29 Copynumber: 3.6 Consensus size: 29
301238 GTTATATATA
* *
301248 TATATATATATTATTACTTCATTTTATTT
1 TATATTTATATGATTACTTCATTTTATTT
* *
301277 TATATTTCTATGATTACTAT-TTTTTAGTTAATAT
1 TATATTTATATGATTACT-TCATTTTA--T--T-T
* * *
301311 TATATGTATATTTATTTCTTCATTTTATTT
1 TATATTTATA-TGATTACTTCATTTTATTT
*
301341 TATATTTTTATGATTACT
1 TATATTTATATGATTACT
301359 ATTTTTTTAG
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
29 26 0.43
30 10 0.16
31 2 0.03
33 2 0.03
34 10 0.16
35 11 0.18
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (29 bp):
TATATTTATATGATTACTTCATTTTATTT
Found at i:301299 original size:22 final size:22
Alignment explanation
Indices: 301272--301363 Score: 59
Period size: 22 Copynumber: 4.3 Consensus size: 22
301262 TACTTCATTT
301272 TATTTTATATTTCTATGATTAC
1 TATTTTATATTTCTATGATTAC
* * *
301294 TATTTTTTAGTT-AAT-ATTA-
1 TATTTTATATTTCTATGATTAC
* * *
301313 TATGTATATTTATTTCT-TCATT-T
1 TAT-T-T-TATATTTCTATGATTAC
*
301336 TATTTTATATTTTTATGATTAC
1 TATTTTATATTTCTATGATTAC
301358 TATTTT
1 TATTTT
301364 TTTAGTTAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
19 3 0.06
20 12 0.23
21 8 0.15
22 24 0.45
23 6 0.11
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.64
Consensus pattern (22 bp):
TATTTTATATTTCTATGATTAC
Found at i:301337 original size:64 final size:65
Alignment explanation
Indices: 301241--301403 Score: 260
Period size: 65 Copynumber: 2.5 Consensus size: 65
301231 TCCTAACGTT
* *
301241 ATATATATATATATATATTATTACTTCATTTTATTTTATATTTCTATGATTACTA-TTTTTTAGT
1 ATAT-TATATGTATAT-TTATTTCTTCATTTTATTTTATATTTCTATGATTACTATTTTTTTAGT
301305 TA
64 TA
*
301307 ATATTATATGTATATTTATTTCTTCATTTTATTTTATATTTTTATGATTACTATTTTTTTAGTTA
1 ATATTATATGTATATTTATTTCTTCATTTTATTTTATATTTCTATGATTACTATTTTTTTAGTTA
301372 ATATTATATGTATATTTATTT-TTCA-TTTATTT
1 ATATTATATGTATATTTATTTCTTCATTTTATTT
301404 ATTATTATTG
Statistics
Matches: 93, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
63 7 0.08
64 40 0.43
65 42 0.45
66 4 0.04
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.63
Consensus pattern (65 bp):
ATATTATATGTATATTTATTTCTTCATTTTATTTTATATTTCTATGATTACTATTTTTTTAGTTA
Found at i:301471 original size:12 final size:12
Alignment explanation
Indices: 301454--301478 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
301444 TACATTTTTA
301454 TATTTTTATATT
1 TATTTTTATATT
301466 TATTTTTATATT
1 TATTTTTATATT
301478 T
1 T
301479 TTTATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTTATATT
Found at i:301472 original size:20 final size:19
Alignment explanation
Indices: 301447--301507 Score: 81
Period size: 20 Copynumber: 3.3 Consensus size: 19
301437 TTATACATAC
301447 ATTTTTATATTTTTATATTT
1 ATTTTTATATTTTT-TATTT
301467 ATTTTTATATTTTTTA-TT
1 ATTTTTATATTTTTTATTT
* *
301485 -TTTTTATACTATTTATTT
1 ATTTTTATATTTTTTATTT
301503 ATTTT
1 ATTTT
301508 CATTATGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 13 0.35
18 4 0.11
19 6 0.16
20 14 0.38
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTTTATATTTTTTATTT
Found at i:303028 original size:22 final size:21
Alignment explanation
Indices: 302973--303032 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
302963 TGTTGTTGTG
*
302973 GTTTATGTTCGCTTGTTTTGTTC
1 GTTTATGTTCG-TT-TATTGTTC
* *
302996 ATTTATTTTCGTTTATTGTTTC
1 GTTTATGTTCGTTTATTG-TTC
303018 GTTTATGTTCGTTTA
1 GTTTATGTTCGTTTA
303033 CATCCGTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 4 0.13
22 18 0.58
23 9 0.29
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.63
Consensus pattern (21 bp):
GTTTATGTTCGTTTATTGTTC
Found at i:311776 original size:2 final size:2
Alignment explanation
Indices: 311762--311800 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
311752 CACAAAATTT
311762 GA GA GA G- GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
311801 CAGGCGAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:313526 original size:33 final size:32
Alignment explanation
Indices: 313466--313527 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
313456 GTGGATGGTA
* **
313466 TGGTCATACATAGATTTTTTTGTCTTTTGTTT
1 TGGTCATACATAGAATTTTCAGTCTTTTGTTT
*
313498 TGGTCATATATAGAATTTTCAGTGCTTTTG
1 TGGTCATACATAGAATTTTCAGT-CTTTTG
313528 AAAATGCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (32 bp):
TGGTCATACATAGAATTTTCAGTCTTTTGTTT
Found at i:322250 original size:48 final size:48
Alignment explanation
Indices: 322182--322566 Score: 442
Period size: 48 Copynumber: 8.3 Consensus size: 48
322172 CCGCTGTCAC
* * * *
322182 AGGGAATACCAAACCTTGGAAAAGAGAGACCTGTTCCGCTT-CTTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTAC-TCTGA
* *
322230 AGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* * * *
322277 AGGGAATGTCAGATC-T---G--G-TAGACTTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
*
322318 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* * * **
322366 AGGAAATATCAGATCTTGGAGAAGATAGATTTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* *
322414 AGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* * * *
322462 AGGGAATATCAGATC-T---G--G-CAGACTTGTTCCACTTACTCTAA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
322503 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
*
322551 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
322567 GGGGGAGTTG
Statistics
Matches: 283, Mismatches: 38, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
41 67 0.24
42 3 0.01
44 1 0.00
45 2 0.01
46 1 0.00
47 39 0.14
48 170 0.60
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (48 bp):
AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
Found at i:322368 original size:89 final size:89
Alignment explanation
Indices: 322208--322568 Score: 528
Period size: 89 Copynumber: 4.0 Consensus size: 89
322198 TGGAAAAGAG
* * * *
322208 AGACCTGTTCCGCTT-CTTCTGAAGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTA
1 AGACTTGTTCCACTTAC-TCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTA
*
322271 CTCTGAAGGGAATGTCAGATCTGGT
65 CTCTGAAGGGAATATCAGATCTGGT
*
322296 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTAC
*
322361 TCTGAAGGAAATATCAGATCTTGGAGAAGAT
66 TCTGAAGGGAATATCAGATC-T---G--G-T
* * *
322392 AGATTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTAC
*
322457 TCTGAAGGGAATATCAGATCTGGC
66 TCTGAAGGGAATATCAGATCTGGT
*
322481 AGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTAC
322546 TCTGAAGGGAATATCAGATCTGG
66 TCTGAAGGGAATATCAGATCTGG
322569 GGGAGTTGAT
Statistics
Matches: 249, Mismatches: 15, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
88 37 0.15
89 123 0.49
90 2 0.01
92 1 0.00
93 1 0.00
95 2 0.01
96 83 0.33
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (89 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTAC
TCTGAAGGGAATATCAGATCTGGT
Found at i:322458 original size:185 final size:184
Alignment explanation
Indices: 322225--322566 Score: 594
Period size: 185 Copynumber: 1.9 Consensus size: 184
322215 TTCCGCTTCT
*
322225 TCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATGTCAGA
1 TCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGA
* *
322290 TCTGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCC
66 TCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCC
*
322355 GCTTACTCTGAAGGAAATATCAGATCTTGGAGAAGATAGATTTGTTCCACTTAC
131 ACTTACTCTGAAGGAAATATCAGATCTTGGAGAAGATAGATTTGTTCCACTTAC
* * * *
322409 TCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAG
322474 ATCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTC
65 ATCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTC
*
322539 CACTTACTCTGAAGGGAATATCAGATCT
130 CACTTACTCTGAAGGAAATATCAGATCT
322567 GGGGGAGTTG
Statistics
Matches: 148, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
184 23 0.16
185 125 0.84
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (184 bp):
TCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGA
TCTGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCC
ACTTACTCTGAAGGAAATATCAGATCTTGGAGAAGATAGATTTGTTCCACTTAC
Found at i:323730 original size:17 final size:17
Alignment explanation
Indices: 323710--323753 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
323700 ATTTTTTTTT
323710 TTTTTTTTCATTTTTCA
1 TTTTTTTTCATTTTTCA
*
323727 TTTTTTAGTC-TTTTTCA
1 TTTTTT-TTCATTTTTCA
323744 TTTTTTTTCA
1 TTTTTTTTCA
323754 GGCGAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTTTCATTTTTCA
Found at i:336950 original size:3 final size:3
Alignment explanation
Indices: 336936--336976 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
336926 AAATATGTAA
*
336936 AAT AAT ATT AAT AAT AAT AAT AAT ACAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
336977 GAACGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Done.