Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009141.1 Hibiscus syriacus cultivar Beakdansim tig00112649_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: 919200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:393267 original size:81 final size:81
Alignment explanation
Indices: 393106--393273 Score: 239
Period size: 81 Copynumber: 2.1 Consensus size: 81
393096 ACAAGCTAAG
* * *
393106 GTTGAGCAAGTTCTTCTCATTATGAACTTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGA
1 GTTGAGCAAGTTCTTCACATTATGAACGTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGA
* * *
393171 ACCCTATATTGGAAAT
66 ACCCTACACTAGAAAT
*
393187 GTTGAGCCAAGTTCTTCACATTATGAA-GTTCTTCTCCCTCGTTGGATGAGTTCTTTTCATTATG
1 GTTGAG-CAAGTTCTTCACATTATGAACGTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATG
* *
393251 AACTCTCCACTAGAAAT
65 AACCCTACACTAGAAAT
393268 GTTGAG
1 GTTGAG
393274 TGGTTTATCC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 58 0.75
82 19 0.25
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (81 bp):
GTTGAGCAAGTTCTTCACATTATGAACGTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGA
ACCCTACACTAGAAAT
Found at i:394360 original size:21 final size:22
Alignment explanation
Indices: 394322--394382 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
394312 TCTTGAAATC
394322 TCTTTTTTATTTTATTTCTTCT
1 TCTTTTTTATTTTATTTCTTCT
* *
394344 TCTTTTTTGTTTT-TTTCTTTT
1 TCTTTTTTATTTTATTTCTTCT
*
394365 TCATTTTTTTTCTTTATT
1 TC-TTTTTTAT-TTTATT
394383 CATTTTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 9 0.27
22 19 0.58
23 3 0.09
24 2 0.06
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (22 bp):
TCTTTTTTATTTTATTTCTTCT
Found at i:394361 original size:15 final size:15
Alignment explanation
Indices: 394331--394400 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 15
394321 CTCTTTTTTA
*
394331 TTTTATTTCTTCTTCT
1 TTTTATTT-TTTTTCT
394347 TTTT-TGTTTTTTTCT
1 TTTTAT-TTTTTTTCT
394362 TTTTCATTTTTTTTCT
1 TTTT-ATTTTTTTTCT
394378 TTATTCATTTTCATTTTCT
1 TT-TT-ATTTT--TTTTCT
394397 TTTT
1 TTTT
394401 CTTAGGCGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
15 11 0.23
16 17 0.36
17 9 0.19
18 2 0.04
19 8 0.17
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTTTTCT
Found at i:394388 original size:23 final size:21
Alignment explanation
Indices: 394324--394400 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 21
394314 TTGAAATCTC
394324 TTTTTTATTTTATTTC-TTCTTC-
1 TTTTTT-TTTT-TTTCATT-TTCA
*
394346 TTTTTTGTTTTTTTCTTTTTCA
1 TTTTTT-TTTTTTTCATTTTCA
394368 TTTTTTTTCTTTATTCATTTTCA
1 TTTTTTTT-TTT-TTCATTTTCA
*
394391 TTTTCTTTTT
1 TTTTTTTTTT
394401 CTTAGGCGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 9 0.19
22 23 0.48
23 16 0.33
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTTTTTCATTTTCA
Found at i:410020 original size:45 final size:45
Alignment explanation
Indices: 409959--410049 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
409949 TCCTATGACG
409959 CCCCTCCTCGGTTACCGTGTTCTCTGTGCCATTGAGTTTGCCCGC
1 CCCCTCCTCGGTTACCGTGTTCTCTGTGCCATTGAGTTTGCCCGC
*
410004 CCCCTCCTCGGTTACCGTGTTCTCTGTGCCATTGATTTTGCCCGC
1 CCCCTCCTCGGTTACCGTGTTCTCTGTGCCATTGAGTTTGCCCGC
410049 C
1 C
410050 TCTCCTCACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.07, C:0.38, G:0.21, T:0.34
Consensus pattern (45 bp):
CCCCTCCTCGGTTACCGTGTTCTCTGTGCCATTGAGTTTGCCCGC
Found at i:411453 original size:35 final size:35
Alignment explanation
Indices: 411413--411489 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
411403 ATATTAAACT
* *
411413 TATTAAATATTTTGTACTTGATTTTAATTTAAACAA
1 TATTAAATATATTGTACTTGAGTTTAATTTAAA-AA
411449 -ATTAAATATATTGTACTTGAGTTTAATTTAAAAA
1 TATTAAATATATTGTACTTGAGTTTAATTTAAAAA
411483 TATTAAA
1 TATTAAA
411490 CTTAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 2 0.05
35 36 0.95
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (35 bp):
TATTAAATATATTGTACTTGAGTTTAATTTAAAAA
Found at i:421953 original size:55 final size:55
Alignment explanation
Indices: 421894--422248 Score: 433
Period size: 55 Copynumber: 6.5 Consensus size: 55
421884 GAGTCCGCTT
* * *
421894 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAGACGTGTCTGCTC
1 CCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
* *
421949 CCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTC
1 CCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
* *
422004 CCTATTCGTTCAGGGAGTATAAGACTTGAACAATCTTCAACAAACGTGT-TCGCTC
1 CCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCT-GCTC
* * *
422059 CCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCT-CTC
1 CCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGT-CTGCTC
* *
422114 CCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATA-AAACG-GATCCGCTC
1 CCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCA-ACAAACGTG-TCTGCTC
* * *
422169 TCTATTCCTTCAGAGAGTAT-AGAACTCG----ATCTTCAACAAACGTGTCCGCTC
1 CCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCTGCTC
* *
422220 CCTATTCCTTCAGAGAGTATAGGACTCGA
1 CCTATTCCTTCAGGGAGTATAAGACTCGA
422249 TCTTCATAAA
Statistics
Matches: 270, Mismatches: 19, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.00
51 43 0.16
52 2 0.01
54 4 0.01
55 218 0.81
56 1 0.00
57 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (55 bp):
CCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
Found at i:422134 original size:165 final size:161
Alignment explanation
Indices: 421886--422248 Score: 482
Period size: 165 Copynumber: 2.2 Consensus size: 161
421876 CGAATGACGA
* * * * * * *
421886 GTCCGCTTCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAGACGTGTCTGCTCCC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCTGCTCCC
* * *
421951 TATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTG-TCTGCTCCCTATTCGTT
66 TATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCAGAAAACG-GATCCGCTCCCTATTCCTT
*
422014 CAGGGAGTATA-AGACTTGAACAATCTTCAACAAACGT
129 CAGAGAGTATAGA-AC-T---CAATCTTCAACAAACGT
*
422051 GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCT-CTCC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGT-CTGCTCC
* * *
422115 CTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGATCCGCTCTCTATTCCTTC
65 CTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAGAAAACGGATCCGCTCCCTATTCCTTC
*
422180 AGAGAGTATAGAACTCGATCTTCAACAAACGT
130 AGAGAGTATAGAACTCAATCTTCAACAAACGT
422212 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
422249 TCTTCATAAA
Statistics
Matches: 177, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
161 52 0.29
164 2 0.01
165 119 0.67
166 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (161 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCTGCTCCC
TATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAGAAAACGGATCCGCTCCCTATTCCTTCA
GAGAGTATAGAACTCAATCTTCAACAAACGT
Found at i:422551 original size:17 final size:17
Alignment explanation
Indices: 422519--422551 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
422509 TATGTTCATC
422519 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
422536 TCAAT-CTTCAACTATC
1 TCAATGCTTCAA-TATC
422552 CCTGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.39
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:423622 original size:24 final size:24
Alignment explanation
Indices: 423577--423633 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
423567 GAACCCCCTT
*
423577 TTATTTATTTTCTTTTTCTTTTTCA
1 TTATTTATTTTCTTCTTCTTTTT-A
423602 TT-TTTATCTTTCTTCTT-TTTTTA
1 TTATTTAT-TTTCTTCTTCTTTTTA
423625 TTATTTATT
1 TTATTTATT
423634 ATTACTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 4 0.14
24 15 0.52
25 10 0.34
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (24 bp):
TTATTTATTTTCTTCTTCTTTTTA
Found at i:423742 original size:18 final size:19
Alignment explanation
Indices: 423708--423749 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
423698 GTTTTTCTTC
423708 TTTCTCATTTTTATTATTT
1 TTTCTCATTTTTATTATTT
423727 TTTCTCATTTTT-TTATTT
1 TTTCTCATTTTTATTATTT
*
423745 CTTCT
1 TTTCT
423750 TCAAGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCTCATTTTTATTATTT
Found at i:427178 original size:2 final size:2
Alignment explanation
Indices: 427173--427212 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
427163 ATGAAAGAGA
* * *
427173 AT AT AT AT AT AT AT AT AT AC AT AT AT AC AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
427213 GGAAGGATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:427186 original size:8 final size:8
Alignment explanation
Indices: 427177--427212 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
427167 AAGAGAATAT
*
427177 ATATATAT
1 ATATATAC
427185 ATATATAC
1 ATATATAC
427193 ATATATAC
1 ATATATAC
427201 ATATATAC
1 ATATATAC
427209 ATAT
1 ATAT
427213 GGAAGGATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATATAC
Found at i:433437 original size:47 final size:46
Alignment explanation
Indices: 433338--433427 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 46
433328 CCATGCTTTG
* *
433338 TTATTCACAAAAATAAATCCTAACTGCATGATATCTAATTCGTATAC
1 TTATTCA-AAAAATAAATCCTAACTGAATGATATCTAATTCGCATAC
*
433385 TTATTCAAAAAATAAA-CCTAAC-GAAATGATATCTAGTTCGCAT
1 TTATTCAAAAAATAAATCCTAACTG-AATGATATCTAATTCGCAT
433428 GCATTTATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 1 0.03
45 22 0.56
46 9 0.23
47 7 0.18
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACTGAATGATATCTAATTCGCATAC
Found at i:437662 original size:38 final size:38
Alignment explanation
Indices: 437585--437662 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
437575 ATTGAGCATG
* * * *
437585 ATATATTTTTATATAAATTATGTTGAAGTAAAATTTTA
1 ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
**
437623 ATATATTTTTTAAATAAATTATG-TAAAATTTAATATTA
1 ATATA-TTTTTAAATAAATTATGTTAAAATAAAATATTA
437661 AT
1 AT
437663 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (38 bp):
ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
Found at i:437728 original size:21 final size:21
Alignment explanation
Indices: 437704--437771 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
437694 TAATAAAATA
437704 ATATATTATCGATGAATTTTT
1 ATATATTATCGATGAATTTTT
* * **
437725 ATATA-AAT-AAT-TTTTATTT
1 ATATATTATCGATGAATT-TTT
437744 AAATATATTATCGATGAATTTTT
1 -A-TATATTATCGATGAATTTTT
437767 ATATA
1 ATATA
437772 AATAATTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 3 0.09
21 13 0.39
22 3 0.09
23 5 0.15
24 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (21 bp):
ATATATTATCGATGAATTTTT
Found at i:437729 original size:42 final size:42
Alignment explanation
Indices: 437692--437777 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
437682 GATATATTTA
437692 AATAATAAAAT-AATATATTATCGATGAATTTTTATATAAAT
1 AATAATAAAATAAATATATTATCGATGAATTTTTATATAAAT
** * **
437733 AATTTTTATTTAAATATATTATCGATGAATTTTTATATAAAT
1 AATAATAAAATAAATATATTATCGATGAATTTTTATATAAAT
437775 AAT
1 AAT
437778 TTTTATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 6 0.15
42 33 0.85
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (42 bp):
AATAATAAAATAAATATATTATCGATGAATTTTTATATAAAT
Found at i:437738 original size:15 final size:15
Alignment explanation
Indices: 437718--437793 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
437708 ATTATCGATG
437718 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
437733 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* **
437748 -A--TAT-TATCGAT
1 AATTTTTATATAAAT
437759 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
437775 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
437790 AATT
1 AATT
437794 AGAATTTCAC
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
11 4 0.09
12 2 0.04
13 1 0.02
14 1 0.02
15 34 0.72
16 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:437778 original size:42 final size:42
Alignment explanation
Indices: 437703--437794 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
437693 ATAATAAAAT
437703 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
437745 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
437787 AATA-ATTA
1 AATATATTA
437795 GAATTTCACT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.08
42 46 0.92
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
Found at i:441254 original size:27 final size:29
Alignment explanation
Indices: 441224--441301 Score: 106
Period size: 27 Copynumber: 2.8 Consensus size: 29
441214 ATATGTACGT
441224 ATGTATGTATAATTTATTAATGC-TCG-C
1 ATGTATGTATAATTTATTAATGCATCGAC
* *
441251 ATGTATGTATAATTTATTAATGCATGGAT
1 ATGTATGTATAATTTATTAATGCATCGAC
* *
441280 ATATATATATAATTTATTAATG
1 ATGTATGTATAATTTATTAATG
441302 TATGCATCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 23 0.51
28 2 0.04
29 20 0.44
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (29 bp):
ATGTATGTATAATTTATTAATGCATCGAC
Found at i:441339 original size:39 final size:39
Alignment explanation
Indices: 441290--441366 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
441280 ATATATATAT
* *
441290 AATTTATTAATGTATG-CATCATATATGTATGATATGTAG
1 AATTTATTAATGCATGTC-TCATATATATATGATATGTAG
* *
441329 AATTTGTTAATGCATGTCTCATGTATATATGATATGTA
1 AATTTATTAATGCATGTCTCATATATATATGATATGTA
441367 TGTATTAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (39 bp):
AATTTATTAATGCATGTCTCATATATATATGATATGTAG
Found at i:445069 original size:18 final size:17
Alignment explanation
Indices: 445030--445073 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
445020 ATTATATGGA
445030 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
445046 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
445064 TATTATTATT
1 TATTATTATT
445074 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:446787 original size:5 final size:5
Alignment explanation
Indices: 446777--446804 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
446767 TCTTTTCATC
446777 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
446805 CATCACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:449407 original size:9 final size:9
Alignment explanation
Indices: 449395--449436 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
449385 ATAAAAGGGC
449395 AAAAAGAAAA
1 AAAAAG-AAA
*
449405 AAAAAGCAA
1 AAAAAGAAA
*
449414 AAAAAGAAC
1 AAAAAGAAA
449423 AAAAAGAAA
1 AAAAAGAAA
449432 AAAAA
1 AAAAA
449437 AAGGGACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 22 0.79
10 6 0.21
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:449436 original size:19 final size:18
Alignment explanation
Indices: 449395--449439 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
449385 ATAAAAGGGC
449395 AAAAAGAAAAAAAAAGCAA
1 AAAAAGAAAAAAAAA-CAA
*
449414 AAAAAGAACAAAAAGAAAAA
1 AAAAAGAA-AAAAA-AACAA
449434 AAAAAG
1 AAAAAG
449440 GGACAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 13 0.57
21 2 0.09
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAACAA
Found at i:450059 original size:21 final size:22
Alignment explanation
Indices: 450033--450075 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
450023 AGCTACCCCA
450033 TCAAACC-TTGAGCATCAAATG
1 TCAAACCATTGAGCATCAAATG
*
450054 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTGAGCATCAAATG
450076 AACAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (22 bp):
TCAAACCATTGAGCATCAAATG
Found at i:451207 original size:36 final size:36
Alignment explanation
Indices: 451109--451266 Score: 262
Period size: 36 Copynumber: 4.3 Consensus size: 36
451099 ATTGAAAACA
* *
451109 TTTCCCTTAAAATAAATTTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAG
*
451146 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAG
451183 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
*
451219 TTTCACTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
451255 TTTCCCTTGAAA
1 TTTCCCTTGAAA
451267 CAAAATATTT
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
36 69 0.61
37 38 0.33
38 7 0.06
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:451355 original size:138 final size:137
Alignment explanation
Indices: 451146--451471 Score: 445
Period size: 138 Copynumber: 2.4 Consensus size: 137
451136 CTTGAGATAG
* * * * *
451146 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
1 TTTCCCCTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTATCT
* * *
451211 TGAGACAGTTTCACTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATT
65 TGAGACAGTTTCACTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATT
*
451276 TGAATATG
130 TGAATATA
* * * * **
451284 TTTTCTCTGAAACAAATTTCGTCCCCCTTGAGACAGTTTCTTTTGGAAACAAATTTCGTCTATCT
1 TTTCCCCTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTT-GAAACAAATTTCGTCTATCT
* *
451349 TGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTT
65 TGAGACAGTTTCACTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATT
*
451414 TGAATTTA
130 TGAATATA
* * *
451422 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCCTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
451472 CAAAATCTTC
Statistics
Matches: 162, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
137 32 0.20
138 130 0.80
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (137 bp):
TTTCCCCTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCACTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:451366 original size:102 final size:101
Alignment explanation
Indices: 451190--451372 Score: 267
Period size: 102 Copynumber: 1.8 Consensus size: 101
451180 CAGTTTCCCT
* * * * * * *
451190 TGAAATAAATTTTGTCTCTCTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TGAAACAAATTTCGTCCCCCTTGAGACAGTTTCACTTGAAACAAATTTCGTCTATCTTGAGACAG
451255 TTTCCCTTGAAACAAAATATTTGAATATGTTTTCTC
66 TTTCCCTTGAAACAAAATATTTGAATATGTTTTCTC
**
451291 TGAAACAAATTTCGTCCCCCTTGAGACAGTTTCTTTTGGAAACAAATTTCGTCTATCTTGAGACA
1 TGAAACAAATTTCGTCCCCCTTGAGACAGTTTCACTT-GAAACAAATTTCGTCTATCTTGAGACA
*
451356 GTTTCTCTTGAAACAAA
65 GTTTCCCTTGAAACAAA
451373 TTTCGTCTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 31 0.44
102 40 0.56
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (101 bp):
TGAAACAAATTTCGTCCCCCTTGAGACAGTTTCACTTGAAACAAATTTCGTCTATCTTGAGACAG
TTTCCCTTGAAACAAAATATTTGAATATGTTTTCTC
Found at i:451376 original size:36 final size:36
Alignment explanation
Indices: 451285--451408 Score: 187
Period size: 36 Copynumber: 3.4 Consensus size: 36
451275 TTGAATATGT
***
451285 TTTCTC-TGAAACAAATTTCGTCCCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
*
451320 TTTCTTTTGGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCTCTT-GAAACAAATTTCGTCTATCTTGAGACAG
451357 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
*
451393 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
451409 ATCTTTGAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
35 5 0.06
36 44 0.54
37 32 0.40
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
Found at i:451387 original size:21 final size:21
Alignment explanation
Indices: 451329--451387 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
451319 GTTTCTTTTG
451329 GAAACAAATTTCGTCTATCTT
1 GAAACAAATTTCGTCTATCTT
* *
451350 GAGAC--AGTT--TC--TCTT
1 GAAACAAATTTCGTCTATCTT
451365 GAAACAAATTTCGTCTATCTT
1 GAAACAAATTTCGTCTATCTT
451386 GA
1 GA
451388 GACAGTTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
15 8 0.29
17 5 0.18
19 5 0.18
21 10 0.36
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (21 bp):
GAAACAAATTTCGTCTATCTT
Found at i:451388 original size:174 final size:173
Alignment explanation
Indices: 451030--451408 Score: 478
Period size: 174 Copynumber: 2.2 Consensus size: 173
451020 GAAGAGTTTT
* *
451030 GTCTCTCTTGAGACAGTTTCCCTTTAAACAAATTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTGTCTCCCTTGAGACAGTTTCCCTTGAAACAT
* * * *
451095 AAACATTGAAAACATTTCCCTTAAAATAAATTTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACA
66 AAACATTGAAAACATTTCCCTTAAAACAAATTTTCGTCCCCCTTGAGACAGTTTCCCTTGAAACA
* * * *
451160 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTT
131 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTC
* * *
451203 GTCTCTCTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA--TTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * ** * * **
451268 A-AAATATTTGAATATGTTT-TCTCTGAAACAAA-TTTCGTCCCCCTTGAGACAGTTTCTTTTGG
64 ATAAACA-TTGAAAACATTTCCCT-TAAAACAAATTTTCGTCCCCCTTGAGACAGTTTCCCTT-G
*
451330 AAAC-AAATTTCGTCTATCTTGAGACAGTTTCTCTTGAAACAAATTTC
126 AAACAAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTC
*
451377 GTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
451409 ATCTTTGAAT
Statistics
Matches: 176, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
173 29 0.16
174 96 0.55
175 51 0.29
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (173 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTGTCTCCCTTGAGACAGTTTCCCTTGAAACAT
AAACATTGAAAACATTTCCCTTAAAACAAATTTTCGTCCCCCTTGAGACAGTTTCCCTTGAAACA
AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTC
Found at i:451454 original size:65 final size:65
Alignment explanation
Indices: 451366--451540 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
451356 GTTTCTCTTG
* ** * **
451366 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
451431 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
451496 TA
64 TA
* * *
451498 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
451541 CAGATATCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 31 0.33
66 6 0.06
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:452368 original size:105 final size:105
Alignment explanation
Indices: 452183--452804 Score: 903
Period size: 105 Copynumber: 6.0 Consensus size: 105
452173 GCACTCGAGG
* *** * * *
452183 CAACACAAGTTCAACTTCACAACGAAGGGATAACTGGTTGTCAACAAACAACTTCTCAATTTTAG
1 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAG
*
452248 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
452289 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGA
*
452354 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
452394 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGA
452459 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
452499 AAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGA
452564 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
452604 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGA
** * *
452664 TTCAATTTTAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * ** *
452704 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAG
* *
452769 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
452805 TGGAACAATG
Statistics
Matches: 474, Mismatches: 36, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
100 82 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 305 0.64
106 74 0.16
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:453877 original size:18 final size:17
Alignment explanation
Indices: 453837--453879 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
453827 ATTATATGGA
453837 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
453853 T-TCTATTATTCATGTTAT
1 TAT-TATTATTCAT-TTAT
453871 TATTATTAT
1 TATTATTAT
453880 ATGTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 2 0.09
17 8 0.35
18 11 0.48
19 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:455241 original size:21 final size:23
Alignment explanation
Indices: 455198--455251 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
455188 ATAGCCTTTA
455198 AAATCCTAAAAAAAAAGGTAAAA-
1 AAATCCT-AAAAAAAAGGTAAAAT
*
455221 ATAATCCTAAAATAAA-G-AAAAT
1 A-AATCCTAAAAAAAAGGTAAAAT
455243 AAATCCTAA
1 AAATCCTAA
455252 TTAAAATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 12 0.43
22 2 0.07
23 8 0.29
24 6 0.21
ACGTcount: A:0.65, C:0.11, G:0.06, T:0.19
Consensus pattern (23 bp):
AAATCCTAAAAAAAAGGTAAAAT
Found at i:455309 original size:12 final size:12
Alignment explanation
Indices: 455292--455316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
455282 TACCTAAAAC
455292 AAATATAATATA
1 AAATATAATATA
455304 AAATATAATATA
1 AAATATAATATA
455316 A
1 A
455317 TATTTAAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATAATATA
Found at i:456267 original size:40 final size:42
Alignment explanation
Indices: 456203--456282 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 42
456193 TTCCTTATTC
*
456203 TTTTCTTTTTTTCTCTGTTCGAAACAATGAAC-ATTTTTTCT
1 TTTTCTTTTTTTCTCTGTTAGAAACAATGAACAATTTTTTCT
*
456244 TTTTCTTTTTTTGT-TGTTAGAAACAATGAACAATTTTTT
1 TTTTCTTTTTTTCTCTGTTAGAAACAATGAACAATTTTTT
456283 TCGTAGAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 16 0.44
41 20 0.56
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (42 bp):
TTTTCTTTTTTTCTCTGTTAGAAACAATGAACAATTTTTTCT
Found at i:457536 original size:16 final size:16
Alignment explanation
Indices: 457515--457548 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
457505 ACTCAAAGAC
457515 TAACCATGGTCTATGA
1 TAACCATGGTCTATGA
*
457531 TAACCATGGTCTGTGA
1 TAACCATGGTCTATGA
457547 TA
1 TA
457549 TCAGTATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (16 bp):
TAACCATGGTCTATGA
Found at i:460466 original size:498 final size:496
Alignment explanation
Indices: 459484--460479 Score: 1823
Period size: 498 Copynumber: 2.0 Consensus size: 496
459474 GACTTGGTTT
459484 TTTTTCAGACTTCAGGTTCCTCTAAATTAATTTCTTCTATTAGACCAACAGGAGCATTGTCATAA
1 TTTTTCAGACTTCAGGTTCCTCTAAATTAATTTCTTCTATTAGACCAACAGGAGCATTGTCATAA
*
459549 TACGGTTTCAACCTTTGACCGTTAACTTTAAATCGAACTCCTGAGTTATCTTCAACTTGAATATC
66 TACGGTTTCAACCTTTGACCGTTAACTTTAAATCGAACTCCTGAGTTATCTTCAACTTCAATATC
*
459614 ACCATGAGGAAATACTTGAGTTACTGTAAACGGTCCGAGCCATTTTGATATGAGTTTTCTTGTAA
131 ACCATGAGGAAATACTTGAGTTACTGTAAACGGTCCGAGCCATTTTGATATGAGTTTTCCTGTAA
459679 AAAGTTTAAATTTGGAGTTAAATAACAAAACCTTTAGACCGACAGAAAAAGTTTTAAAAGAAATT
196 AAAGTTTAAATTTGGAGTTAAATAACAAAACCTTTAGACCGACAGAAAAAGTTTTAAAAGAAATT
*
459744 CTACTAGCGTGAAATTATTTTTTTTTCTTTAAATATCCGAGAACTGTCATAGGCATTTCTTTGGA
261 CTACTAGCGTGAAATTATTTTTTTTTCTTTAAATATCCGAGAACTATCATAGGCATTTCTTTGGA
459809 TTTCCTCAAGTTCTTGAATGTGTAATTTCTAAGCTTCACTAACCGCATCCATGTCCATGTTACAA
326 TTTCCTCAAGTTCTTGAATGTGTAATTTCTAAGCTTCACTAACCGCATCCATGTCCATGTTACAA
*
459874 TGTTTAAAATCCCAATAAGCCTGATGTTGTAACTCAACCGGTAAATGGTATGGTTTATCGAAAAC
391 TGTTTAAAAGCCCAATAAGCCTGATGTTGTAACTCAACCGGTAAATGGTATGGTTTATCGAAAAC
459939 AAGCTGGTATGGTGACATCCCAATGGGACCTTTATAAGCTGG
456 AAGCTGGTATGGTGACATCCCAATGGGACCTTTATAAGC-GG
*
459981 TTTTTCAGACTTCAGGTTCCTCTAAATTAATTTCTTCTATTAGACCAACATGAGCATTGTCATAA
1 TTTTTCAGACTTCAGGTTCCTCTAAATTAATTTCTTCTATTAGACCAACAGGAGCATTGTCATAA
*
460046 TACGGTTTTAACCTTTGACCGTTAACTTTAAATCGAACTCCTGAGTTATCTTCAACTTCAATATC
66 TACGGTTTCAACCTTTGACCGTTAACTTTAAATCGAACTCCTGAGTTATCTTCAACTTCAATATC
*
460111 ACCATGAGGAAATACTTGAGTTACTGTAAACGGTCTGAGCCATTTTGATATGAGTTTTCCTGT-A
131 ACCATGAGGAAATACTTGAGTTACTGTAAACGGTCCGAGCCATTTTGATATGAGTTTTCCTGTAA
* *
460175 AAAGTTTAAATTTGGAGTTAAATAACAAAACCTTTTGACCGACAGAAAATGTTTTAAAAGAAATT
196 AAAGTTTAAATTTGGAGTTAAATAACAAAACCTTTAGACCGACAGAAAAAGTTTTAAAAGAAATT
* * * *
460240 CTACTATCGTGAAATTCTTTTGTTTTTTCTTTAAATATTCGAGCACTATCATAGGCATTTCTTTG
261 CTACTAGCGTGAAATT-ATTT-TTTTTTCTTTAAATATCCGAGAACTATCATAGGCATTTCTTTG
460305 GATTTCCTCAAGTTCTTGAATGTGTAATTTCTAAGCTTCACTAACCGCATCCATGTCCATGTTAC
324 GATTTCCTCAAGTTCTTGAATGTGTAATTTCTAAGCTTCACTAACCGCATCCATGTCCATGTTAC
* *
460370 AATGTTTAAAAGCCCAATAAGCCTGATGTTGTAACTCAATCGGTAAATGGTATGGTTTATTGAAA
389 AATGTTTAAAAGCCCAATAAGCCTGATGTTGTAACTCAACCGGTAAATGGTATGGTTTATCGAAA
460435 ACAAGCTGGTATGGTGACATCCCAATGGGACCTTTATAAGCGG
454 ACAAGCTGGTATGGTGACATCCCAATGGGACCTTTATAAGCGG
460478 TT
1 TT
460480 CGATATGCCC
Statistics
Matches: 482, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
496 79 0.16
497 195 0.40
498 208 0.43
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (496 bp):
TTTTTCAGACTTCAGGTTCCTCTAAATTAATTTCTTCTATTAGACCAACAGGAGCATTGTCATAA
TACGGTTTCAACCTTTGACCGTTAACTTTAAATCGAACTCCTGAGTTATCTTCAACTTCAATATC
ACCATGAGGAAATACTTGAGTTACTGTAAACGGTCCGAGCCATTTTGATATGAGTTTTCCTGTAA
AAAGTTTAAATTTGGAGTTAAATAACAAAACCTTTAGACCGACAGAAAAAGTTTTAAAAGAAATT
CTACTAGCGTGAAATTATTTTTTTTTCTTTAAATATCCGAGAACTATCATAGGCATTTCTTTGGA
TTTCCTCAAGTTCTTGAATGTGTAATTTCTAAGCTTCACTAACCGCATCCATGTCCATGTTACAA
TGTTTAAAAGCCCAATAAGCCTGATGTTGTAACTCAACCGGTAAATGGTATGGTTTATCGAAAAC
AAGCTGGTATGGTGACATCCCAATGGGACCTTTATAAGCGG
Found at i:463617 original size:15 final size:16
Alignment explanation
Indices: 463580--463612 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
463570 CCTGTTAACA
463580 TCCTAAAAAGGCTACT
1 TCCTAAAAAGGCTACT
463596 TCCTAAAAAGGCTACT
1 TCCTAAAAAGGCTACT
463612 T
1 T
463613 TTAAAGCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (16 bp):
TCCTAAAAAGGCTACT
Found at i:464963 original size:17 final size:16
Alignment explanation
Indices: 464932--464965 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
464922 CACGTGAGGA
464932 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
464948 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
464965 T
1 T
464966 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:471354 original size:19 final size:21
Alignment explanation
Indices: 471317--471359 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
471307 TAACTTTTTC
471317 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
471337 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
471357 TTT
1 TTT
471360 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:471365 original size:19 final size:20
Alignment explanation
Indices: 471316--471365 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
471306 TTAACTTTTT
*
471316 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
471336 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
471355 CTTTTACCTTT
1 CTTTTACCTTT
471366 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:475211 original size:17 final size:16
Alignment explanation
Indices: 475180--475213 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
475170 CACGTGAGGA
475180 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
475196 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
475213 T
1 T
475214 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:475656 original size:28 final size:28
Alignment explanation
Indices: 475624--475679 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
475614 AGAGGTATGT
475624 TAACTTGAACTTTTTGGAACACCTCTAA
1 TAACTTGAACTTTTTGGAACACCTCTAA
475652 TAACTTGAACTTTTTGGAACACCTCTAA
1 TAACTTGAACTTTTTGGAACACCTCTAA
475680 GATCCCCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (28 bp):
TAACTTGAACTTTTTGGAACACCTCTAA
Found at i:479894 original size:4 final size:4
Alignment explanation
Indices: 479887--480461 Score: 1071
Period size: 4 Copynumber: 143.8 Consensus size: 4
479877 ATGCATCATA
479887 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
479935 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
479983 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480031 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480079 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480127 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480175 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480223 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480271 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480319 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
480367 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT-
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * *
480414 AATT TATC AATG CATG CATG TATG TATG TGTG TATG ATATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG -TATG TATG TAT
480462 AATTTATTAA
Statistics
Matches: 560, Mismatches: 9, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
3 2 0.00
4 554 0.99
5 4 0.01
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:480513 original size:8 final size:8
Alignment explanation
Indices: 480479--480525 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
480469 TAATGCATGG
480479 ATATATATA
1 ATATAT-TA
480488 TATATATTA
1 -ATATATTA
*
480497 ATTTA-TA
1 ATATATTA
*
480504 ATCTATTA
1 ATATATTA
480512 ATATATTA
1 ATATATTA
480520 ATATAT
1 ATATAT
480526 GCATCATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 6 0.18
8 19 0.58
9 2 0.06
10 6 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (8 bp):
ATATATTA
Found at i:480551 original size:17 final size:17
Alignment explanation
Indices: 480531--480564 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
480521 TATATGCATC
*
480531 ATATATGTATGATTTGT
1 ATATATGTATAATTTGT
480548 ATATATGTATAATTTGT
1 ATATATGTATAATTTGT
480565 TAATACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (17 bp):
ATATATGTATAATTTGT
Found at i:487264 original size:274 final size:280
Alignment explanation
Indices: 486661--487292 Score: 827
Period size: 287 Copynumber: 2.3 Consensus size: 280
486651 GGGTGTGACA
* *
486661 TCTATTCTTT-TAATTTACTCCAAACCCTAAAAATCACATCATAAACTTCATTTCAAAGCCTATA
1 TCTATTTTTTGTAATTTACTCCAAACCCTATAAATCACATCATAAACTTCATTTCAAAGCCTATA
* * *
486725 AATTATATCATAATCTCCAAACCCCATAAACTTTTTGTTCACCAACTTTTTAAATGAATGCAATT
66 AATTATATCATAATCTCCAAACCCCATAAACTTTATGTTCACAAACTTTTCAAATGAATGCAATT
* * * * * *
486790 TAGTCTATTTATATATTAATTTCAGCTTTACATTTTACAATTGTTTCAATTTGATTTTTGTGTTG
131 TAGTCCATTTATATATCAATTCCAACTTTACATTTTACAATTGTTTCAATTTGATATGTGTGTTG
* *
486855 TTTAATTTATTTAAATTTTAGTTTGTAATTTCATGTTTATTCAATTTAGTCCTTAAGATTATATT
196 TTTAATTTATTTAAATTTCA--TTG--A-TT-ATG-TTATTCAATTTAGTCCTTAAAATTATATT
*
486920 TTTATCCGAAATTAACACATAATTATT
254 TTTATCCGAAATTAACAAATAATTATT
* * **
486947 TCTATTTTTTGTAATTTACTCCAACCCCTATAAATAACATCATAAACTTCATTTCAAATTCTATA
1 TCTATTTTTTGTAATTTACTCCAAACCCTATAAATCACATCATAAACTTCATTTCAAAGCCTATA
* *
487012 AATTTTATCATAATCTCCAAACCCCATTAAC-TTATGTTCACAAACTTTTCAAATGAATGCAA-T
66 AATTATATCATAATCTCCAAACCCCATAAACTTTATGTTCACAAACTTTTCAAATGAATGCAATT
*
487075 TAGTCCATTT-TGATATCAATTCCAACTTTACATTTTACAGTTGTTTCAATTTGATCCATGTGTG
131 TAGTCCATTTAT-ATATCAATTCCAACTTTACATTTTACAATTGTTTCAATTTGAT--ATGTGTG
487139 TTGTTTAATTTATTTAAATTTCA-TG-TT-TG-T-TT-AATTTAGTCC-TAAAATTATATTTTTA
193 TTGTTTAATTTATTTAAATTTCATTGATTATGTTATTCAATTTAGTCCTTAAAATTATATTTTTA
* *
487197 TTCGAAATTGACAAATAATTATT
258 TCCGAAATTAACAAATAATTATT
* * * * * *
487220 TCTAATTTTTTGTAATTTACTCCAATCCCTATAAATCTCATCATAAATTTCAATTCAAACCCTCT
1 TCT-ATTTTTTGTAATTTACTCCAAACCCTATAAATCACATCATAAACTTCATTTCAAAGCCTAT
487285 AAATTATA
65 AAATTATA
487293 GGGTAAACTA
Statistics
Matches: 309, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
273 38 0.12
274 70 0.23
275 2 0.01
276 1 0.00
278 2 0.01
280 2 0.01
284 3 0.01
285 49 0.16
286 37 0.12
287 105 0.34
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (280 bp):
TCTATTTTTTGTAATTTACTCCAAACCCTATAAATCACATCATAAACTTCATTTCAAAGCCTATA
AATTATATCATAATCTCCAAACCCCATAAACTTTATGTTCACAAACTTTTCAAATGAATGCAATT
TAGTCCATTTATATATCAATTCCAACTTTACATTTTACAATTGTTTCAATTTGATATGTGTGTTG
TTTAATTTATTTAAATTTCATTGATTATGTTATTCAATTTAGTCCTTAAAATTATATTTTTATCC
GAAATTAACAAATAATTATT
Found at i:494104 original size:41 final size:41
Alignment explanation
Indices: 494059--494154 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
494049 TTATGGATAG
* * *
494059 CCCGAAGGACTTATCATCC-TACTCTAAAGGCTTACGGATGA
1 CCCGAAGGACTTAGCA-CCATACTCGAAAGACTTACGGATGA
* * * *
494100 CCCGAAGGATTTAAGCACCATGCTCGAAAGATTTACTGATGA
1 CCCGAAGGACTT-AGCACCATACTCGAAAGACTTACGGATGA
494142 CCCGAAGGACTTA
1 CCCGAAGGACTTA
494155 CAAATCGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 14 0.31
42 31 0.69
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
CCCGAAGGACTTAGCACCATACTCGAAAGACTTACGGATGA
Found at i:494314 original size:41 final size:41
Alignment explanation
Indices: 494259--494370 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 41
494249 ATCCTACCCG
* * * *
494259 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTA
1 AAGG-CTTACGGATGGCCCGAAGGACTTAGCATCATGCTCGA
* * *
494301 AAGGCTTACGGATGACCCGAAGGATTTAAGCATTATGCTCGA
1 AAGGCTTACGGATGGCCCGAAGGACTT-AGCATCATGCTCGA
* *
494343 AAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGCTTACGGATGGCCCGAAGGACTTA
494371 CAAATCGTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 21 0.36
42 37 0.64
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCCGAAGGACTTAGCATCATGCTCGA
Found at i:494767 original size:214 final size:214
Alignment explanation
Indices: 494028--495551 Score: 2411
Period size: 214 Copynumber: 7.1 Consensus size: 214
494018 ATCCTGGTGA
* * *
494028 AAAACATCCTGCCCGAAGGTCTTATGGATAGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
* * *
494093 CGGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGATTTACTGATGACCCGAAGGACTTACAA
66 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
* *
494158 ATCGTGAAATTTTGAAACTCGCATTCTTTGTTTTAAAAAATTTCATCTTCTTAAAACATCATTTT
131 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCA--TT
*
494223 TTTCATTTTCAAATTCTTGTG
194 TTTCATTTTCAAATTCATGTG
494244 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
*
494309 CGGATGACCCGAAGGATTTAAGCATTATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
66 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
*
494374 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAACATTTCATCTTCTTAAAACATCATTTT
131 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCA--TT
*
494439 TTTCATTTTCAAATTCTTGTG
194 TTTCATTTTCAAATTCATGTG
* * * * *
494460 ATAACATCATACCCGAAGGTTTTATGGATGGCTCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
* *
494525 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
** * * * *
494590 ATTATGAAATTTTGAAAATCACTTTCTTCGTTTTAAAAAATTTCATCTTCTTAAAACATCATTTT
131 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
*
494655 TCATTTTCAAATTAATGTG
196 TCATTTTCAAATTCATGTG
* *
494674 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
* * *
494739 CAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
** * * *
494804 ATTATGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTTCATATTCTTAAAACATCATTTT
131 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
*
494869 TCATTTTCAAATTAATGTG
196 TCATTTTCAAATTCATGTG
* * * *
494888 AAAACATCCTACCCAAAGGTCTTATGGATGGTCCGAAGGACTTATCATCTTGCTCTAAAGACTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
*
494953 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
66 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
*
495018 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
131 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
* *
495083 TCATTTTTAAATTCATTTG
196 TCATTTTCAAATTCATGTG
* * * *
495102 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCCTACTCTAAATGCCTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
*
495167 CGGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
66 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
*
495232 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
131 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
* *
495297 TCATTTTTAAATTCATTTG
196 TCATTTTCAAATTCATGTG
*
495316 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
495381 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
66 CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
*
495446 ATCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAA--T--TC--C----AACATCATTTT
131 ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCA-TTT
*
495501 TTCATTTTCAAATTCTTGTG
195 TTCATTTTCAAATTCATGTG
* *
495521 AAAACATCCTACCTGAAGGTTTTATGGATGG
1 AAAACATCCTACCCGAAGGTCTTATGGATGG
495552 TTTGCTTCAC
Statistics
Matches: 1237, Mismatches: 70, Indels: 13
0.94 0.05 0.01
Matches are distributed among these distances:
204 7 0.01
205 49 0.04
208 1 0.00
210 2 0.00
214 796 0.64
216 382 0.31
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (214 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGCTTA
CGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
ATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
TCATTTTCAAATTCATGTG
Found at i:494776 original size:42 final size:41
Alignment explanation
Indices: 494700--494800 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 41
494690 AGGTCTTATG
* * *
494700 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
1 GATGGCCCGAAGGACTTAACATCATGCTCGAAAGACTTACA
* * *
494741 GATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AACATCATGCTCGAAAGACTTACA
494783 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
494801 TAAATTATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAACATCATGCTCGAAAGACTTACA
Found at i:494990 original size:42 final size:41
Alignment explanation
Indices: 494920--495014 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 41
494910 TATGGATGGT
* * *
494920 CCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGAC
1 CCGAAGGACTTAGCATCATGCTCGAAAGACTTACAGATGAC
* * *
494961 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC
1 CCGAAGGACTT-AGCATCATGCTCGAAAGACTTACAGATGAC
495003 CCGAAGGACTTA
1 CCGAAGGACTTA
495015 CAAATCGTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 11 0.24
42 35 0.76
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (41 bp):
CCGAAGGACTTAGCATCATGCTCGAAAGACTTACAGATGAC
Found at i:495386 original size:41 final size:41
Alignment explanation
Indices: 495331--495442 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 41
495321 ATCCTACCCG
* * * *
495331 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTA
1 AAGG-CTTACGGATGGCCCGAAGGACTTAGCATCATACTCGA
* * *
495373 AAGGCTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGA
1 AAGGCTTACGGATGGCCCGAAGGACTT-AGCATCATACTCGA
* *
495415 AAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGCTTACGGATGGCCCGAAGGACTTA
495443 CAAATCGTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 21 0.36
42 37 0.64
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCCGAAGGACTTAGCATCATACTCGA
Found at i:497654 original size:2 final size:2
Alignment explanation
Indices: 497643--497675 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
497633 TTGTAATCAC
497643 AT AT -T 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
497676 TTTGGGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:501935 original size:20 final size:20
Alignment explanation
Indices: 501910--501955 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
501900 TTGAAGGTAG
501910 TCTTCAATCAACTTGAAACT
1 TCTTCAATCAACTTGAAACT
501930 TCTTCAATCAACTTGAAACT
1 TCTTCAATCAACTTGAAACT
501950 TCTTCA
1 TCTTCA
501956 TTCATCGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (20 bp):
TCTTCAATCAACTTGAAACT
Found at i:510281 original size:3 final size:3
Alignment explanation
Indices: 510275--510304 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
510265 CTCGAAAAAA
*
510275 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
510305 TATTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:511929 original size:4 final size:4
Alignment explanation
Indices: 511922--511951 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
511912 TTATAATTTC
511922 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
511952 ATAAATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:517438 original size:35 final size:36
Alignment explanation
Indices: 517357--517485 Score: 147
Period size: 36 Copynumber: 3.6 Consensus size: 36
517347 ACAAAGTGTC
* *
517357 GTCTCGC-TAGAGACAATTTTTCTAAAAAATAAAAGTTT
1 GTCTCGCTTA-AGAC-ATTTTTCTAAAAAA-CAAATTTT
* *
517395 GTCTCGCTTGAGACAGTTTTCT-AAAAACAAATTTT
1 GTCTCGCTTAAGACATTTTTCTAAAAAACAAATTTT
* *
517430 GTCTCGCTTAAGACA-ATTTCTCACAAAACAAATTTT
1 GTCTCGCTTAAGACATTTTTCT-AAAAAACAAATTTT
517466 GTCTCGCTTAAGACATTTTT
1 GTCTCGCTTAAGACATTTTT
517486 TTCTTCTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
34 5 0.06
35 20 0.25
36 32 0.41
37 10 0.13
38 11 0.14
39 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (36 bp):
GTCTCGCTTAAGACATTTTTCTAAAAAACAAATTTT
Found at i:517483 original size:19 final size:19
Alignment explanation
Indices: 517425--517484 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
517415 CTAAAAACAA
517425 ATTTTGTCTCGCTTAAGAC
1 ATTTTGTCTCGCTTAAGAC
* * ** * *
517444 A-ATT-TCTCACAAAACAA
1 ATTTTGTCTCGCTTAAGAC
517461 ATTTTGTCTCGCTTAAGAC
1 ATTTTGTCTCGCTTAAGAC
517480 ATTTT
1 ATTTT
517485 TTTCTTCTTT
Statistics
Matches: 27, Mismatches: 12, Indels: 4
0.63 0.28 0.09
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
19 14 0.52
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (19 bp):
ATTTTGTCTCGCTTAAGAC
Found at i:517621 original size:66 final size:65
Alignment explanation
Indices: 517541--517678 Score: 206
Period size: 66 Copynumber: 2.1 Consensus size: 65
517531 AATTGCTAAC
* *
517541 CTTTGAGATTGTTTCCCTTTAAAC-AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACTC
1 CTTTGAGATCGTTTCCCTTTAAACGAA-TTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACA-TC
517605 AT
64 AT
* * *
517607 CTTTGAGATCGTTTCCTTTTAAACGAATTTTGTCTCTCTTGAGACAGCTTCTCTTGAAGCATCAT
1 CTTTGAGATCGTTTCCCTTTAAACGAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATCAT
517672 CTTTGAG
1 CTTTGAG
517679 TTTGTTTCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
65 11 0.17
66 53 0.80
67 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (65 bp):
CTTTGAGATCGTTTCCCTTTAAACGAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATCAT
Found at i:517858 original size:40 final size:39
Alignment explanation
Indices: 517813--517948 Score: 123
Period size: 40 Copynumber: 3.3 Consensus size: 39
517803 CATGTCGTCT
*
517813 TCATCATGTAGGAATCATGTCATCCACCGACCAGACCTCC
1 TCATCACGTAGGAA-CATGTCATCCACCGACCAGACCTCC
* * * *
517853 TCATCACGTAGGAGCCGTGTCA-CC-CCTAGATAACCAGTCGTCC
1 TCATCACGTAGGA-ACATGTCATCCACC--G---ACCAGACCTCC
* *
517896 TCATCACGTAAGAACTATGTCATCCACCGACCAGACCTCT
1 TCATCACGTAGGAAC-ATGTCATCCACCGACCAGACCTCC
517936 TCATCACGTAGGA
1 TCATCACGTAGGA
517949 GCTGTGTCAC
Statistics
Matches: 75, Mismatches: 12, Indels: 18
0.71 0.11 0.17
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 39 0.52
42 1 0.01
43 27 0.36
44 2 0.03
45 2 0.03
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.22
Consensus pattern (39 bp):
TCATCACGTAGGAACATGTCATCCACCGACCAGACCTCC
Found at i:517919 original size:83 final size:83
Alignment explanation
Indices: 517806--517985 Score: 272
Period size: 83 Copynumber: 2.2 Consensus size: 83
517796 AAGATGACAT
* * *
517806 GTCGTCTTCATCATGTAGGAATCATGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGT
1 GTCGTCCTCATCACGTAAGAATCATGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGT
517871 GTCACCCCTAGATAACCA
66 GTCACCCCTAGATAACCA
* *
517889 GTCGTCCTCATCACGTAAGAA-CTATGTCATCCACCGACCAGACCTCTTCATCACGTAGGAGCTG
1 GTCGTCCTCATCACGTAAGAATC-ATGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCG
**
517953 TGTCACCCCTAGATAATTA
65 TGTCACCCCTAGATAACCA
*
517972 GTTGTCCTCATCAC
1 GTCGTCCTCATCAC
517986 ATAGGAACCG
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 1 0.01
83 87 0.99
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (83 bp):
GTCGTCCTCATCACGTAAGAATCATGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGT
GTCACCCCTAGATAACCA
Found at i:517957 original size:40 final size:40
Alignment explanation
Indices: 517830--517957 Score: 134
Period size: 40 Copynumber: 3.1 Consensus size: 40
517820 GTAGGAATCA
*
517830 TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCG
1 TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCTG
* * * * *
517870 TGTCA-CC-CCTAGATAACCAGTCGTCCTCATCACGTAAGAACTA
1 TGTCATCCACC--G---ACCAGACCTCCTCATCACGTAGGAGCTG
*
517913 TGTCATCCACCGACCAGACCTCTTCATCACGTAGGAGCTG
1 TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCTG
517953 TGTCA
1 TGTCA
517958 CCCCTAGATA
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 33 0.48
43 28 0.41
44 2 0.03
45 2 0.03
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (40 bp):
TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCTG
Found at i:518079 original size:213 final size:213
Alignment explanation
Indices: 517711--518095 Score: 567
Period size: 213 Copynumber: 1.8 Consensus size: 213
517701 CCCTAAACAT
517711 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCAAGTA
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCAAGTA
* * * *
517776 GGAAATGTGTTATCATCCTAAAGATGACATGTCGTCTTCATCATGTAGGAATCATGTCATCCACC
66 GGAAACGTGTTATCATCCTAAAGATGACATGTCGTCCTCATCACGTAGGAATCATATCATCCACC
517841 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTA
131 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTA
517906 AGAACTATGTCATCCACC
196 AGAACTATGTCATCCACC
* ** *
517924 GACCAGACCTCTTCATCACGTAGGAGCTGTGTCACCCCTAGATAATTAGTTGTCCTCATCACA-T
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCA-AGT
* * * *
517988 AGGAACCGTGTTATCATCCTAAAGATGGC-TAGTTGTCCTCATCGCGTAGGAATCATATCATCCA
65 AGGAAACGTGTTATCATCCTAAAGATGACAT-GTCGTCCTCATCACGTAGGAATCATATCATCCA
* * * * * * *
518052 CTGACCAGATCTCCTCATTATGTAGGAGTCGTGTTACCCTTAGA
129 CCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGA
518096 CGACCAAAAC
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
212 1 0.01
213 149 0.99
214 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (213 bp):
GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCAAGTA
GGAAACGTGTTATCATCCTAAAGATGACATGTCGTCCTCATCACGTAGGAATCATATCATCCACC
GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTA
AGAACTATGTCATCCACC
Found at i:518293 original size:3 final size:3
Alignment explanation
Indices: 518285--518363 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
518275 TCTCAAAAAA
518285 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
518333 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
518364 TATATATATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:519562 original size:39 final size:39
Alignment explanation
Indices: 519513--519587 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
519503 ATGTATTATG
*
519513 TGACACTTCTATTTTTGTCC-TGATGTTTGCATGTTCGTA
1 TGACACTTCTATTTCTG-CCTTGATGTTTGCATGTTCGTA
*
519552 TGACATTTCTATTTCTGCCTTGATGTTTGCATGTTC
1 TGACACTTCTATTTCTGCCTTGATGTTTGCATGTTC
519588 ATTGTTATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (39 bp):
TGACACTTCTATTTCTGCCTTGATGTTTGCATGTTCGTA
Found at i:528103 original size:28 final size:28
Alignment explanation
Indices: 528063--528119 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
528053 CCGCTGTTGC
*
528063 TTTCAAGCACTAGCTCGATGACATAATG
1 TTTCAAGCACTAGCTCGACGACATAATG
* *
528091 TTTCAAGTACTAGCTCGACGGCATAATG
1 TTTCAAGCACTAGCTCGACGACATAATG
528119 T
1 T
528120 AAACAGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACGACATAATG
Found at i:530380 original size:92 final size:89
Alignment explanation
Indices: 530217--530431 Score: 322
Period size: 92 Copynumber: 2.4 Consensus size: 89
530207 AGTGTGTTAC
* * *
530217 TTTGTTGATTCCCTCAACTATTAAAAGTTATAAAATGATCCAACTATTGGGTAAAGTACACAAAT
1 TTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATGACCCAACTATTGGGTAAAGTACACAAAT
*
530282 AGTCCCCCGGCTATTGGGTGAAGT
66 AGTCCCCCGACTATTGGGTGAAGT
* *
530306 TTTGTTGAGTCCCTCCACTATTAATAGTTACAAAATGGTCACCCAACTATTGGGTAAAGTACACA
1 TTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAAT-G--ACCCAACTATTGGGTAAAGTACACA
*
530371 AATAGTCCCCCGACTATTGGGTGATGT
63 AATAGTCCCCCGACTATTGGGTGAAGT
* *
530398 TTTGTTGAGTCACTCGACTATTAAAAGTTACAAA
1 TTTGTTGAGTCCCTCAACTATTAAAAGTTACAAA
530432 TGATCCTCCG
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
89 32 0.28
90 1 0.01
92 80 0.71
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (89 bp):
TTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATGACCCAACTATTGGGTAAAGTACACAAAT
AGTCCCCCGACTATTGGGTGAAGT
Found at i:535306 original size:17 final size:17
Alignment explanation
Indices: 535284--535328 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
535274 TATAATCACC
535284 TCAAATATATTAGAGAT
1 TCAAATATATTAGAGAT
535301 TCAAATATATTAGAGAT
1 TCAAATATATTAGAGAT
*
535318 TTAAA-ATATTA
1 TCAAATATATTA
535329 AAAACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (17 bp):
TCAAATATATTAGAGAT
Found at i:535820 original size:21 final size:21
Alignment explanation
Indices: 535781--535820 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
535771 CATTGATTAG
* *
535781 AAGATTAAATTTATTAAATTT
1 AAGATTAAATTAATAAAATTT
535802 AAGATTAAATTAATAAAAT
1 AAGATTAAATTAATAAAAT
535821 ATATCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAGATTAAATTAATAAAATTT
Found at i:537598 original size:31 final size:32
Alignment explanation
Indices: 537563--537622 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
537553 ACTTGAATGT
*
537563 AAAATT-AAAGTTCAATGTTATAAATGAAAAG
1 AAAATTAAAAGTTCAATGATATAAATGAAAAG
*
537594 AAAATTAAAAGTTCAGTGATATAAATGAA
1 AAAATTAAAAGTTCAATGATATAAATGAA
537623 TTAGCGAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.28
Consensus pattern (32 bp):
AAAATTAAAAGTTCAATGATATAAATGAAAAG
Found at i:540383 original size:23 final size:23
Alignment explanation
Indices: 540352--540395 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
540342 TACAAAAAGT
540352 AAAGAAAAGCCTACCATAAAGGC
1 AAAGAAAAGCCTACCATAAAGGC
* * *
540375 AAAGGAAAGCGTTCCATAAAG
1 AAAGAAAAGCCTACCATAAAG
540396 ATAAAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAGAAAAGCCTACCATAAAGGC
Found at i:540424 original size:21 final size:19
Alignment explanation
Indices: 540399--540454 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
540389 CATAAAGATA
540399 AAATATTACAAAATAAAAAT
1 AAATATTA-AAAATAAAAAT
*
540419 ACAATATAAGAAAATAAAAAAAT
1 A-AATATTA-AAAAT--AAAAAT
540442 AAATATTAAAAAT
1 AAATATTAAAAAT
540455 CAACAACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 16 0.53
22 6 0.20
23 7 0.23
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATATTAAAAATAAAAAT
Found at i:549172 original size:19 final size:19
Alignment explanation
Indices: 549148--549197 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
549138 ATCGTCGACT
549148 GTTGACTGTTGACCTAAC-C
1 GTTGACTGTTGACCT-ACTC
549167 GTTGACTGTTGACCTACTC
1 GTTGACTGTTGACCTACTC
549186 GTTGACT-TTGAC
1 GTTGACTGTTGAC
549198 TTTGATCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (19 bp):
GTTGACTGTTGACCTACTC
Found at i:550562 original size:20 final size:20
Alignment explanation
Indices: 550526--550563 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
550516 CCTGACTTGT
* *
550526 TTGGAAGACTTGTAAATCGG
1 TTGGAAGACCTGAAAATCGG
550546 TTGGAAGACCTGAAAATC
1 TTGGAAGACCTGAAAATC
550564 AGTTCCTAAT
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:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (20 bp):
TTGGAAGACCTGAAAATCGG
Found at i:550769 original size:2 final size:2
Alignment explanation
Indices: 550762--550827 Score: 116
Period size: 2 Copynumber: 33.0 Consensus size: 2
550752 ACTGGAAATG
550762 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
550804 GA- AT AT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT
550828 TACTGAATCA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 60 0.97
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:553002 original size:2 final size:2
Alignment explanation
Indices: 552995--553020 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
552985 TTGATAATGG
552995 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
553021 GAAATTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:554340 original size:41 final size:41
Alignment explanation
Indices: 554295--554376 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
554285 AAGTGAGTAC
* *
554295 TTATCAGTTCAACTTTGGTACGTTCGTGTATCAATGTTCAG
1 TTATCAGTTCAACTTTGATACCTTCGTGTATCAATGTTCAG
* *
554336 TTATCAGTTCAGCTTTGATACCTTCGTGTATTAATGTTCAG
1 TTATCAGTTCAACTTTGATACCTTCGTGTATCAATGTTCAG
554377 CAGCGTTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (41 bp):
TTATCAGTTCAACTTTGATACCTTCGTGTATCAATGTTCAG
Found at i:558440 original size:31 final size:30
Alignment explanation
Indices: 558399--558469 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
558389 AATTAGAAAA
558399 AAAAATCCATATATTTCTTCTTCTTTTAGAG
1 AAAAATCCATATATTTCTTCTT-TTTTAGAG
* * *
558430 AAAAGTCCATATGTTTCTTCTTTTTTAAATG
1 AAAAATCCATATATTTCTTCTTTTTTAGA-G
558461 AAAAA-CCAT
1 AAAAATCCAT
558470 GACTCCACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (30 bp):
AAAAATCCATATATTTCTTCTTTTTTAGAG
Found at i:562767 original size:11 final size:10
Alignment explanation
Indices: 562734--562759 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
562724 TTTTATTTTT
562734 TAAAAAATTA
1 TAAAAAATTA
562744 TAAAAAATTA
1 TAAAAAATTA
562754 TAAAAA
1 TAAAAA
562760 TTTTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:564788 original size:21 final size:21
Alignment explanation
Indices: 564759--564838 Score: 133
Period size: 21 Copynumber: 3.8 Consensus size: 21
564749 TTGGTAGCGT
564759 AGGTGCATCGGTACACTCTCA
1 AGGTGCATCGGTACACTCTCA
* *
564780 AGATGCATCGATACACTCTCA
1 AGGTGCATCGGTACACTCTCA
564801 AGGTGCATCGGTACACTCTCA
1 AGGTGCATCGGTACACTCTCA
*
564822 AGGTGAATCGGTACACT
1 AGGTGCATCGGTACACT
564839 GTGTGTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (21 bp):
AGGTGCATCGGTACACTCTCA
Found at i:564986 original size:65 final size:63
Alignment explanation
Indices: 564917--565051 Score: 155
Period size: 65 Copynumber: 2.1 Consensus size: 63
564907 TCACTAATTA
* * * * *
564917 CATTCGATGTTTCAA-AAGAGCCCGAAGTGCATCGATGCATGGTCTGTGCATCGGTACATAAAAT
1 CATTCGATGTTTCAATAACA-CCAGAAGTGCATCGATGCA-CGACTGTGCATCGATACA-AAAAT
564981 G
63 G
* * * *
564982 CATTCTATGTTTCAATAACATCAGGAGTGCATCGATGGACGACTGTGCATCGATACAAAAATG
1 CATTCGATGTTTCAATAACACCAGAAGTGCATCGATGCACGACTGTGCATCGATACAAAAATG
565045 CATTCGA
1 CATTCGA
565052 ATTAGGGTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 12 0.20
64 15 0.25
65 29 0.49
66 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (63 bp):
CATTCGATGTTTCAATAACACCAGAAGTGCATCGATGCACGACTGTGCATCGATACAAAAATG
Found at i:567702 original size:44 final size:44
Alignment explanation
Indices: 567639--567739 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
567629 AAACCCGACG
* *
567639 AGTGTATCGATACACATTC-AGGGAATGCATC-GATGCACCTTCAT
1 AGTGTATCGATGCACATTCAAGGG-ATGCATCTG-TACACCTTCAT
* * *
567683 AGTGTATCGATGTATATTCAAGGGATGCATCTGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGGGATGCATCTGTACACCTTCAT
567727 -GTGTATCGATGCA
1 AGTGTATCGATGCA
567740 TAGTGCACAG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 12 0.24
44 32 0.65
45 5 0.10
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGGATGCATCTGTACACCTTCAT
Found at i:576154 original size:32 final size:32
Alignment explanation
Indices: 576118--576212 Score: 123
Period size: 32 Copynumber: 3.2 Consensus size: 32
576108 GATTTTTGTT
* *
576118 AGATGAAAGGAGTTTGTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
576150 AGATGAAAGGAGTGTGTTATGT---A-A--G-
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
576175 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
576207 AGATGA
1 AGATGA
576213 TGTGTACAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
25 22 0.41
26 1 0.02
28 2 0.04
29 2 0.04
31 1 0.02
32 26 0.48
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.28
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
Found at i:576178 original size:25 final size:25
Alignment explanation
Indices: 576150--576203 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
576140 AAGAGATTGA
576150 AGATGAAAGGAGTGTGTTATGTAAG
1 AGATGAAAGGAGTGTGTTATGTAAG
576175 AGATGAAAGGAGTGTGTTATGTAAG
1 AGATGAAAGGAGTGTGTTATGTAAG
576200 AGAT
1 AGAT
576204 TGAAGATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.28
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTATGTAAG
Found at i:580007 original size:3 final size:3
Alignment explanation
Indices: 579999--580037 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
579989 TTGTTATCAA
* * *
579999 AAT AAT AAT AAT AAT AGT AAT AAT AAT AGT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
580038 TAAATAAGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:580014 original size:12 final size:12
Alignment explanation
Indices: 579999--580037 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
579989 TTGTTATCAA
*
579999 AATAATAATAAT
1 AATAGTAATAAT
580011 AATAGTAATAAT
1 AATAGTAATAAT
*
580023 AATAGTAATAGT
1 AATAGTAATAAT
580035 AAT
1 AAT
580038 TAAATAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:580480 original size:137 final size:136
Alignment explanation
Indices: 580221--580630 Score: 475
Period size: 138 Copynumber: 3.0 Consensus size: 136
580211 GGTAAATTTG
* * * * * * *
580221 GAGACAACATGGTTCTTACGTGATGAGGAAATCTAGTTTTCTAAGGGTGACACTGCTCCTACATG
1 GAGATAACATGGTTCTTACGTGATGAGGAAGTCTGGCTATCTAAGGATGACACTGCTCCTACGTG
* * ** *
580286 ATGAGGAGATCTGGTCGGTTGATAACATTAATCCTACGTGATGAGGACATCTCGCCATCTTTAGG
66 ATGAGGAGATCTGGTCGG-TGATGACACTGTTCCTACGTGATGAGGACGTCT-GCCATCTTTAGG
*
580351 GAT-GATA
129 GATAAATA
** *
580358 GAGATAACATGGTTCTTACGT-ATTGAGGAAGTCTGGCTATCTAAGGATGACGTTGCTCCTATGT
1 GAGATAACATGGTTCTTACGTGA-TGAGGAAGTCTGGCTATCTAAGGATGACACTGCTCCTACGT
* * *
580422 GATGAGGAGATCTGATCGGTGAATGACACTGTTCCTACATGATGAGGACGTTTAGCCATCTTTAG
65 GATGAGGAGATCTGGTCGGTG-ATGACACTGTTCCTACGTGATGAGGACGTCT-GCCATCTTTAG
* *
580487 GAATAAATG
128 GGATAAATA
* * *
580496 GAGATAACACT-ATTCCTACGTGATGAGGAAGTCTGACTATCTAAGGATGACACTGCTCCTACGT
1 GAGATAACA-TGGTTCTTACGTGATGAGGAAGTCTGGCTATCTAAGGATGACACTGCTCCTACGT
* * * *
580560 GATGAAGAGACCTGGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGTCTGACCATCTTTAT
65 GATGAGGAGATCTGGTCGGT-GATGACACTGTTCCTACGTGATGAGGACGTCTG-CCATCTTTAG
580625 GGATAA
128 GGATAA
580631 TTTGTTTCAA
Statistics
Matches: 230, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
136 3 0.01
137 109 0.47
138 115 0.50
139 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (136 bp):
GAGATAACATGGTTCTTACGTGATGAGGAAGTCTGGCTATCTAAGGATGACACTGCTCCTACGTG
ATGAGGAGATCTGGTCGGTGATGACACTGTTCCTACGTGATGAGGACGTCTGCCATCTTTAGGGA
TAAATA
Found at i:580792 original size:66 final size:64
Alignment explanation
Indices: 580633--580818 Score: 243
Period size: 66 Copynumber: 2.9 Consensus size: 64
580623 ATGGATAATT
* * *
580633 TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCT---TATTA
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATATTA
* * * *
580694 TATTTCAAGAGAAAATGTATCAAGAGATACAAAATTTGTTTCAAGGGAAAGAATCTCAATATTTT
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATA--TT
580759 A
64 A
* * *
580760 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAA
580819 AGTTTGTGTG
Statistics
Matches: 106, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
61 49 0.46
64 2 0.02
66 55 0.52
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (64 bp):
TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATATTA
Found at i:580926 original size:100 final size:101
Alignment explanation
Indices: 580822--581002 Score: 233
Period size: 99 Copynumber: 1.8 Consensus size: 101
580812 ATCTCAAAGT
* * * * *
580822 TTGTGTGT-TAAGGAAGATTGTCTCAAGTGAGATGAAATTTGTTTTTAAG-AGAACAATCTCAAG
1 TTGTGT-TCTAAGGAA-ATTATCTCAAGCGAGATGAAATTTGTTTTGAAGAAAAACAATATCAAG
*
580885 TGAGAT-AATTTTGTTTCAAACAAAGCATCTTTGAAAC
64 TGAGATCAATCTTGTTTCAAACAAAGCATCTTTGAAAC
* * * *
580922 TTGTGTTCTGAGGGAATTATCTCAAGCGAGATGAAATTTGTTTTGAGGAAAAATAATATCAAGTG
1 TTGTGTTCTAAGGAAATTATCTCAAGCGAGATGAAATTTGTTTTGAAGAAAAACAATATCAAGTG
580987 AGATCAATCTTGTTTC
66 AGATCAATCTTGTTTC
581003 TAGTGAAACA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
99 30 0.44
100 28 0.41
101 10 0.15
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (101 bp):
TTGTGTTCTAAGGAAATTATCTCAAGCGAGATGAAATTTGTTTTGAAGAAAAACAATATCAAGTG
AGATCAATCTTGTTTCAAACAAAGCATCTTTGAAAC
Found at i:582614 original size:2 final size:2
Alignment explanation
Indices: 582609--582661 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
582599 TGTGTGTGTG
582609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
582651 TA TA TA TA TA T
1 TA TA TA TA TA T
582662 TATGGGCATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:584785 original size:15 final size:15
Alignment explanation
Indices: 584755--584784 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
584745 AATGAATGCC
584755 ATGCAGAATGCAAAA
1 ATGCAGAATGCAAAA
584770 ATGCA-AATGCAAAA
1 ATGCAGAATGCAAAA
584784 A
1 A
584785 AAATGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (15 bp):
ATGCAGAATGCAAAA
Found at i:586717 original size:17 final size:17
Alignment explanation
Indices: 586695--586745 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
586685 CCACGATAAA
586695 AAATGCTCATGATGTGT
1 AAATGCTCATGATGTGT
*
586712 AAATGCTCATG-TCATGT
1 AAATGCTCATGAT-GTGT
*
586729 AAATGCTCGTGATGTGT
1 AAATGCTCATGATGTGT
586746 GTGAGGAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 27 0.93
18 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (17 bp):
AAATGCTCATGATGTGT
Found at i:587447 original size:790 final size:790
Alignment explanation
Indices: 585926--587485 Score: 2942
Period size: 790 Copynumber: 2.0 Consensus size: 790
585916 CGAGTCTAGA
585926 GCTCATGTCATGTAAATGCTCGTGATGTGTGTGAGGAGAAACATACAAACCTTTGACTCAAAAGG
1 GCTCATGTCATGTAAATGCTCGTGATGTGTGTGAGGAGAAACATACAAACCTTTGACTCAAAAGG
585991 AAAAAAAAGAAAACTATCAATAGAAAGTTAGGCAAATATGAAAACAAATATTAAACCGTTAGTAA
66 AAAAAAAAGAAAACTATCAATAGAAAGTTAGGCAAATATGAAAACAAATATTAAACCGTTAGTAA
586056 AAAAATAAAATAAAGAAATTAAAAACTTCAATAAATGAATCATAAGTTAACTACAGACTCAAATT
131 AAAAATAAAATAAAGAAATTAAAAACTTCAATAAATGAATCATAAGTTAACTACAGACTCAAATT
*
586121 TATAATTTCCACCATAACGACAATATATAAGCGACCAACAGCCTGATTCTCTAATTCACAGCAGA
196 TATAATTTCCACCATAACGACAATATATAAGCGACCAACAGCCTGATTCTCTAATTCACAACAGA
586186 GTCGCTAAGCTATCATAACTATTTTTTTTGAAAAAAAACAATTAAGTTTAAAAAAACAATTATGA
261 GTCGCTAAGCTATCATAACTATTTTTTTTGAAAAAAAACAATTAAGTTTAAAAAAACAATTATGA
*
586251 CTTTTATTTTGAAAAAATTGGTGATTTTGAATTGATTTGAATAGGAGTCGCCATCGACCTTTGGG
326 CTTTTATTTTGAAAAAATTGGTGATTTTGAATTAATTTGAATAGGAGTCGCCATCGACCTTTGGG
*
586316 TTAGGTAGGTTCAATACTTGAAAACGTATTTTAAAATAATTTTAAGAAAATCGTCTTTTTAAGAC
391 TTAGGTAGGTTCAATACTTGAAAACGTATTTTAAAACAATTTTAAGAAAATCGTCTTTTTAAGAC
586381 AACAATTGGTCCACGTTTACCAAAAATTTGATTTAACGGGTCCGAGAGTCGATTATGTGTAGGGA
456 AACAATTGGTCCACGTTTACCAAAAATTTGATTTAACGGGTCCGAGAGTCGATTATGTGTAGGGA
586446 AGGATAAACACCCCACAACGCCAAAAAATTGGTACTTTGTCGCTTACACATCATCGTAAATGGTG
521 AGGATAAACACCCCACAACGCCAAAAAATTGGTACTTTGTCGCTTACACATCATCGTAAATGGTG
*
586511 GAAAGTATAAATCGAATATAAAGTTAGAATATGATCAATTTATTAAAGTTTAATTAATTTGCTTC
586 GAAAGTATAAATCAAATATAAAGTTAGAATATGATCAATTTATTAAAGTTTAATTAATTTGCTTC
*
586576 GAATTAATTATTAGGAAAATCCTTTTATTCGAAAAGAAATATTGAAATTTGCTCATCCTCCGATG
651 AAATTAATTATTAGGAAAATCCTTTTATTCGAAAAGAAATATTGAAATTTGCTCATCCTCCGATG
586641 GGAAGGCTATCTCTCTTATTCCTTATCTAAAAAGAATATTCCCTCCACGATAAAAAATGCTCATG
716 GGAAGGCTATCTCTCTTATTCCTTATCTAAAAAGAATATTCCCTCCACGATAAAAAATGCTCATG
586706 ATGTGTAAAT
781 ATGTGTAAAT
586716 GCTCATGTCATGTAAATGCTCGTGATGTGTGTGAGGAGAAACATACAAACCTTTGACTCAAAAGG
1 GCTCATGTCATGTAAATGCTCGTGATGTGTGTGAGGAGAAACATACAAACCTTTGACTCAAAAGG
* *
586781 AAAAAAAAGAAAACTCTCAATAGAAAGTTAGGCAAATATTAAAACAAATATTAAACCGTTAGTAA
66 AAAAAAAAGAAAACTATCAATAGAAAGTTAGGCAAATATGAAAACAAATATTAAACCGTTAGTAA
586846 AAAAATAAAATAAAGAAATTAAAAACTTCAATAAATGAATCATAAGTTAACTACAGACTCAAATT
131 AAAAATAAAATAAAGAAATTAAAAACTTCAATAAATGAATCATAAGTTAACTACAGACTCAAATT
* * *
586911 TATAATTTCCACCATAACGACAATATATAAGTGACCGACAGCCTGATTCTCTAATTCCCAACAGA
196 TATAATTTCCACCATAACGACAATATATAAGCGACCAACAGCCTGATTCTCTAATTCACAACAGA
* *
586976 GTCGCTAAGCTGTCATAACTATTTTTTTTGAAAAAAAACAATTAAGTTTAAAAAAACAATTTTGA
261 GTCGCTAAGCTATCATAACTATTTTTTTTGAAAAAAAACAATTAAGTTTAAAAAAACAATTATGA
* *
587041 CTTTTATTTTGAAAAAATTGGTGATTTTGAATTAATTTGAATGGGAGTCTCCATCGACCTTTGGG
326 CTTTTATTTTGAAAAAATTGGTGATTTTGAATTAATTTGAATAGGAGTCGCCATCGACCTTTGGG
*
587106 TTAGGTAGG-TCAAATACTTGAAAACGTCTTTTAAAACAATTTTAAGAAAATCGTCTTTTTAAGA
391 TTAGGTAGGTTC-AATACTTGAAAACGTATTTTAAAACAATTTTAAGAAAATCGTCTTTTTAAGA
*
587170 CAACAATTGGTCCACGTTTACCAAAACTTTGATTTAACGGGTCCGAGAGTCGATTATGTGTAGGG
455 CAACAATTGGTCCACGTTTACCAAAAATTTGATTTAACGGGTCCGAGAGTCGATTATGTGTAGGG
587235 AAGGATAAACACCCCACAACGCCAAAAAATTGGTACTTTGTCGCTTACACATCATCGTAAATGGT
520 AAGGATAAACACCCCACAACGCCAAAAAATTGGTACTTTGTCGCTTACACATCATCGTAAATGGT
587300 GGAAAGTATAAATCAAATATAAAGTTAGAATATGATCAATTTATTAAAGTTTAATTAATTTGCTT
585 GGAAAGTATAAATCAAATATAAAGTTAGAATATGATCAATTTATTAAAGTTTAATTAATTTGCTT
*
587365 CAAATTAATTATTAGGAAAATCCTTTTATTCGAAAAGAAATATTGAAATTTGCTCATCCTTCGAT
650 CAAATTAATTATTAGGAAAATCCTTTTATTCGAAAAGAAATATTGAAATTTGCTCATCCTCCGAT
*
587430 GGGAAGGCTATCTCTCTTATTCCTTGTCTAAAAAGAATATTCCCTCCACGATAAAA
715 GGGAAGGCTATCTCTCTTATTCCTTATCTAAAAAGAATATTCCCTCCACGATAAAA
587486 TTGTGAATCG
Statistics
Matches: 751, Mismatches: 18, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
789 2 0.00
790 749 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (790 bp):
GCTCATGTCATGTAAATGCTCGTGATGTGTGTGAGGAGAAACATACAAACCTTTGACTCAAAAGG
AAAAAAAAGAAAACTATCAATAGAAAGTTAGGCAAATATGAAAACAAATATTAAACCGTTAGTAA
AAAAATAAAATAAAGAAATTAAAAACTTCAATAAATGAATCATAAGTTAACTACAGACTCAAATT
TATAATTTCCACCATAACGACAATATATAAGCGACCAACAGCCTGATTCTCTAATTCACAACAGA
GTCGCTAAGCTATCATAACTATTTTTTTTGAAAAAAAACAATTAAGTTTAAAAAAACAATTATGA
CTTTTATTTTGAAAAAATTGGTGATTTTGAATTAATTTGAATAGGAGTCGCCATCGACCTTTGGG
TTAGGTAGGTTCAATACTTGAAAACGTATTTTAAAACAATTTTAAGAAAATCGTCTTTTTAAGAC
AACAATTGGTCCACGTTTACCAAAAATTTGATTTAACGGGTCCGAGAGTCGATTATGTGTAGGGA
AGGATAAACACCCCACAACGCCAAAAAATTGGTACTTTGTCGCTTACACATCATCGTAAATGGTG
GAAAGTATAAATCAAATATAAAGTTAGAATATGATCAATTTATTAAAGTTTAATTAATTTGCTTC
AAATTAATTATTAGGAAAATCCTTTTATTCGAAAAGAAATATTGAAATTTGCTCATCCTCCGATG
GGAAGGCTATCTCTCTTATTCCTTATCTAAAAAGAATATTCCCTCCACGATAAAAAATGCTCATG
ATGTGTAAAT
Found at i:589334 original size:3 final size:3
Alignment explanation
Indices: 589320--589349 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
589310 GATAAATTGT
589320 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
589350 TAAATTAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:591681 original size:36 final size:37
Alignment explanation
Indices: 591634--591706 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
591624 AGACATGGAT
* * *
591634 AATATTAGGG-AAATGAAGAGTTCAAGTGAGAGGCCA
1 AATATTAGGGAAAAAGAAGAGTCCAAGTGACAGGCCA
591670 AATATTAGGGAAAAAGAAGAGTCCAAGTGACAGGCCA
1 AATATTAGGGAAAAAGAAGAGTCCAAGTGACAGGCCA
591707 TTACCATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (37 bp):
AATATTAGGGAAAAAGAAGAGTCCAAGTGACAGGCCA
Found at i:593589 original size:168 final size:167
Alignment explanation
Indices: 593311--593645 Score: 643
Period size: 168 Copynumber: 2.0 Consensus size: 167
593301 GCACGAATCA
*
593311 AGCGGTTTTAATAATTAAGATATTTGTTGTTATTCTTTAAAGTTTTGAGTTTGACCACCGTGTAT
1 AGCGGTTTCAATAATTAAGATATTTGTTGTTATTCTTTAAAGTTTTGAGTTTGACCACCGTGTAT
*
593376 GCCAAGAGTATGAACATTTATTGTCAAAGAGTTGAGAGTCTTTAAAGAGATACTATATTGTATAT
66 GCCAAGAGTATAAACATTTATTGTCAAAGAGTTGAGAGTCTTTAAAGAGATACTATATTGTATAT
593441 ATAAAAGAAAAAAAAATTATTTAATTTTATATTTATTT
131 ATAAAAG-AAAAAAAATTATTTAATTTTATATTTATTT
593479 AGCGGTTTCAATAATTAAGATATTTGTTGTTATTCTTTAAAGTTTTGAGTTTGACCACCGTGTAT
1 AGCGGTTTCAATAATTAAGATATTTGTTGTTATTCTTTAAAGTTTTGAGTTTGACCACCGTGTAT
593544 GCCAAGAGTATAAACATTTATTGTCAAAGAGTTGAGAGTCTTTAAAGAGATACTATATTGTATAT
66 GCCAAGAGTATAAACATTTATTGTCAAAGAGTTGAGAGTCTTTAAAGAGATACTATATTGTATAT
593609 ATAAAAGAAAAAAAATTATTTAATTTTATATTTATTT
131 ATAAAAGAAAAAAAATTATTTAATTTTATATTTATTT
593646 TGAGTTATAA
Statistics
Matches: 165, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
167 30 0.18
168 135 0.82
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.41
Consensus pattern (167 bp):
AGCGGTTTCAATAATTAAGATATTTGTTGTTATTCTTTAAAGTTTTGAGTTTGACCACCGTGTAT
GCCAAGAGTATAAACATTTATTGTCAAAGAGTTGAGAGTCTTTAAAGAGATACTATATTGTATAT
ATAAAAGAAAAAAAATTATTTAATTTTATATTTATTT
Found at i:600740 original size:20 final size:21
Alignment explanation
Indices: 600715--600807 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
600705 TTTTCCCAAT
*
600715 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
600735 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
600756 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
600776 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
600797 TCGCAATGCGA
1 TCGCAATGCGA
600808 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:600761 original size:41 final size:41
Alignment explanation
Indices: 600715--600807 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
600705 TTTTCCCAAT
600715 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
600756 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
600797 TCGCAATGCGA
1 TCGCAATGCGA
600808 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:600820 original size:41 final size:41
Alignment explanation
Indices: 600734--600868 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
600724 GAATAAGTAA
* *
600734 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
600775 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
600816 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
600857 TTCGCAACGCGA
1 ATCGCAACGCGA
600869 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:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:600821 original size:20 final size:20
Alignment explanation
Indices: 600796--600910 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
600786 AATTGGGAAA
*
600796 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
600816 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
600837 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
600857 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
600877 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
600897 TTCGCAACGCGATA
1 ATCGCAACGCGATA
600911 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:600869 original size:41 final size:41
Alignment explanation
Indices: 600793--600924 Score: 151
Period size: 41 Copynumber: 3.2 Consensus size: 41
600783 GCGAATTGGG
* * *
600793 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
600834 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
600876 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
600915 ATAATCGCAA
1 AAAATCGCAA
600925 TACGATTTTC
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 39 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:601126 original size:22 final size:22
Alignment explanation
Indices: 601098--601141 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
601088 CACTCTCTCA
601098 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
601120 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
601142 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:601458 original size:20 final size:20
Alignment explanation
Indices: 601404--601462 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
601394 GCGATTCTCT
**
601404 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
601424 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
601444 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
601463 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:602803 original size:18 final size:18
Alignment explanation
Indices: 602782--602826 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
602772 TCCACTTCGG
*
602782 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
602800 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
602818 GAGCCATCA
1 GAGCCATCA
602827 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:603362 original size:19 final size:20
Alignment explanation
Indices: 603308--603374 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
603298 TAGTTTACTT
* *
603308 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
603328 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
603348 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
603367 TCGCAACG
1 TCGCAACG
603375 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:603420 original size:19 final size:19
Alignment explanation
Indices: 603308--603428 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
603298 TAGTTTACTT
* **
603308 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
603328 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
603348 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
603367 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
603381 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
603399 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
603418 TCGCAATGCGA
1 TCGCAACGCGA
603429 TTTGTGTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.21
19 26 0.31
20 24 0.29
21 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:603460 original size:14 final size:14
Alignment explanation
Indices: 603441--603497 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
603431 TGTGTTTCGT
603441 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
603455 GTTGCGATTTCATTTCGC
1 GTTGCGATTT--TGT--C
603473 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
603487 GTTGCGATTTT
1 GTTGCGATTTT
603498 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.49
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:603477 original size:32 final size:33
Alignment explanation
Indices: 603435--603513 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
603425 GCGATTTGTG
*
603435 TTTCGTGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
603467 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
603500 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
603514 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:603512 original size:19 final size:17
Alignment explanation
Indices: 603456--603513 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
603446 GATTTTGTCG
603456 TTGCGATTTCATTTCGC
1 TTGCGATTTCATTTCGC
*
603473 GTTGCGATTT--TGTCG-
1 -TTGCGATTTCATTTCGC
603488 TTGCGATTTTCATTTCGC
1 TTGCGA-TTTCATTTCGC
603506 ATTGCGAT
1 -TTGCGAT
603514 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 10 0.30
19 6 0.18
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (17 bp):
TTGCGATTTCATTTCGC
Found at i:603532 original size:20 final size:20
Alignment explanation
Indices: 603507--603553 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
603497 TCATTTCGCA
603507 TTGCGATAGCCATTTCCACG
1 TTGCGATAGCCATTTCCACG
* * *
603527 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCACG
603547 TTGCGAT
1 TTGCGAT
603554 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:605310 original size:14 final size:14
Alignment explanation
Indices: 605291--605326 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
605281 ATTGTTTAAT
605291 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
605305 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
605319 TGATTTGT
1 TGATTTGT
605327 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:605465 original size:19 final size:19
Alignment explanation
Indices: 605443--605510 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
605433 ATCGCAACGA
605443 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
605462 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
605481 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
605495 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
605511 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:605554 original size:20 final size:20
Alignment explanation
Indices: 605529--605586 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
605519 TCGCATTGCG
*
605529 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
605549 ATTTTCGCGTTACGATAGCC
1 ATTTTCGCGTTGCGATAGCC
605569 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
605587 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:606670 original size:24 final size:24
Alignment explanation
Indices: 606643--606696 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
606633 GTATTCGAAA
* *
606643 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
606667 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
606691 TTTGAT
1 TTTGAT
606697 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:606888 original size:12 final size:12
Alignment explanation
Indices: 606871--606895 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
606861 ATATAATCCT
606871 GAAGAAGAAAAA
1 GAAGAAGAAAAA
606883 GAAGAAGAAAAA
1 GAAGAAGAAAAA
606895 G
1 G
606896 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:609201 original size:19 final size:19
Alignment explanation
Indices: 609177--609307 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
609167 ATCGCAACCT
609177 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
609196 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
609210 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
609229 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
609243 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
609262 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
609276 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
609295 ATCGCAACGCGAA
1 ATCGCAATGCGAA
609308 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Done.