Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 33 of 47
Found at i:5414208 original size:101 final size:101
Alignment explanation
Indices: 5414033--5414235 Score: 334
Period size: 101 Copynumber: 2.0 Consensus size: 101
5414023 TTACATCAGG
*
5414033 CTAGTCATGATAACACCTATTCATGTTGATACTAAGTCATGATACTAATCCCTATTTACTATGCC
1 CTAGTCATGACAACACCTATTCATGTTGATACTAAGTCATGATACTAATCCCTATTTACTATGCC
* *
5414098 AATGCCCTCATTGATAGCAAGACCACACCCGAGTGT
66 AATGCCCTCATCGACAGCAAGACCACACCCGAGTGT
* * *
5414134 CTAGTCATGACAACACCTATTTATGTTGATACTAGGTCATGATACTATTCCCTATTTACTATGCC
1 CTAGTCATGACAACACCTATTCATGTTGATACTAAGTCATGATACTAATCCCTATTTACTATGCC
* *
5414199 AATGCCCTCATCGACAGCAAGATCACATCCGAGTGT
66 AATGCCCTCATCGACAGCAAGACCACACCCGAGTGT
5414235 C
1 C
5414236 CTTATTGCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (101 bp):
CTAGTCATGACAACACCTATTCATGTTGATACTAAGTCATGATACTAATCCCTATTTACTATGCC
AATGCCCTCATCGACAGCAAGACCACACCCGAGTGT
Found at i:5417167 original size:27 final size:26
Alignment explanation
Indices: 5417123--5417173 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
5417113 TGCACCGAAA
* *
5417123 AATATCTTTTTTAAATTTTAAATTCG
1 AATATCTTTTTAAAATTTAAAATTCG
5417149 AATATCATTTTTAAAATTTAAAATT
1 AATATC-TTTTTAAAATTTAAAATT
5417174 ATATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
AATATCTTTTTAAAATTTAAAATTCG
Found at i:5417270 original size:17 final size:17
Alignment explanation
Indices: 5417248--5417280 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5417238 AAGATAAGAC
5417248 TTACTTTACTTTTAATA
1 TTACTTTACTTTTAATA
5417265 TTACTTTACTTTTAAT
1 TTACTTTACTTTTAAT
5417281 CTTAATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (17 bp):
TTACTTTACTTTTAATA
Found at i:5419654 original size:42 final size:42
Alignment explanation
Indices: 5419595--5419753 Score: 176
Period size: 42 Copynumber: 4.0 Consensus size: 42
5419585 ATCGAGCAAT
*
5419595 TAGTTTTGATGGCATTTTGCCTTCTTGATCATTCCAAATAAA
1 TAGTTTTGATAGCATTTTGCCTTCTTGATCATTCCAAATAAA
*** *
5419637 TAGTTTTGATAGCATTTTG----AGGGATCGA--GC-AAT---
1 TAGTTTTGATAGCATTTTGCCTTCTTGATC-ATTCCAAATAAA
*
5419670 TAGTTTTGATGGCATTTTGCCTTCTTGATCATTCCAAATAAA
1 TAGTTTTGATAGCATTTTGCCTTCTTGATCATTCCAAATAAA
*
5419712 TAGTTTTGATAGCATTTTGCCTTTTTGATCATTCCAAATAAA
1 TAGTTTTGATAGCATTTTGCCTTCTTGATCATTCCAAATAAA
5419754 CTTGGATCAT
Statistics
Matches: 94, Mismatches: 12, Indels: 22
0.73 0.09 0.17
Matches are distributed among these distances:
33 18 0.19
36 4 0.04
37 5 0.05
38 5 0.05
39 4 0.04
42 58 0.62
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (42 bp):
TAGTTTTGATAGCATTTTGCCTTCTTGATCATTCCAAATAAA
Found at i:5419698 original size:75 final size:75
Alignment explanation
Indices: 5419575--5419730 Score: 312
Period size: 75 Copynumber: 2.1 Consensus size: 75
5419565 CTAAAAATGA
5419575 ATTTTGAGGGATCGAGCAATTAGTTTTGATGGCATTTTGCCTTCTTGATCATTCCAAATAAATAG
1 ATTTTGAGGGATCGAGCAATTAGTTTTGATGGCATTTTGCCTTCTTGATCATTCCAAATAAATAG
5419640 TTTTGATAGC
66 TTTTGATAGC
5419650 ATTTTGAGGGATCGAGCAATTAGTTTTGATGGCATTTTGCCTTCTTGATCATTCCAAATAAATAG
1 ATTTTGAGGGATCGAGCAATTAGTTTTGATGGCATTTTGCCTTCTTGATCATTCCAAATAAATAG
5419715 TTTTGATAGC
66 TTTTGATAGC
5419725 ATTTTG
1 ATTTTG
5419731 CCTTTTTGAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (75 bp):
ATTTTGAGGGATCGAGCAATTAGTTTTGATGGCATTTTGCCTTCTTGATCATTCCAAATAAATAG
TTTTGATAGC
Found at i:5432445 original size:25 final size:26
Alignment explanation
Indices: 5432410--5432458 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5432400 CCAAAAGATA
*
5432410 TTTTTTCCACCCAAATGTGTGAATAC
1 TTTTTTCCACCCAAATATGTGAATAC
5432436 TTTTTT-CACCCAAATATGTGAAT
1 TTTTTTCCACCCAAATATGTGAAT
5432459 CTTCAAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (26 bp):
TTTTTTCCACCCAAATATGTGAATAC
Found at i:5433803 original size:90 final size:90
Alignment explanation
Indices: 5433649--5433820 Score: 238
Period size: 90 Copynumber: 1.9 Consensus size: 90
5433639 TCATAATAAA
* * * * *
5433649 TAGCATCTAAAACCATGCTCCTATATAGATTTATATCATCTATCCTATTTAAATATTCATTTTCA
1 TAGCATCTAAAACCATGCTCCTATATAAATTCATATCATCTATCCTACTTAAAGATTCACTTTCA
*
5433714 ACTAGACTTT-TAATAAATGGCTAAG
66 ACCAGA-TTTCTAATAAATGGCTAAG
* * * *
5433739 TAGCATCTATAACCATGCTCCTATATAAATTCATATCTTCTATCCTACTTGAAGATTTACTTTCA
1 TAGCATCTAAAACCATGCTCCTATATAAATTCATATCATCTATCCTACTTAAAGATTCACTTTCA
5433804 ACCAGATTTCTAATAAA
66 ACCAGATTTCTAATAAA
5433821 AGACTCTCTA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 3 0.04
90 68 0.96
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (90 bp):
TAGCATCTAAAACCATGCTCCTATATAAATTCATATCATCTATCCTACTTAAAGATTCACTTTCA
ACCAGATTTCTAATAAATGGCTAAG
Found at i:5435629 original size:24 final size:24
Alignment explanation
Indices: 5435597--5435645 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5435587 TTTTGTTTCA
5435597 ATTAATTGTTTTTCAAATTATGGT
1 ATTAATTGTTTTTCAAATTATGGT
5435621 ATTAATTGTTTTTCAAATTATGGT
1 ATTAATTGTTTTTCAAATTATGGT
5435645 A
1 A
5435646 CACTGCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (24 bp):
ATTAATTGTTTTTCAAATTATGGT
Found at i:5439621 original size:28 final size:26
Alignment explanation
Indices: 5439578--5439642 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
5439568 ATTCACAAAT
*
5439578 GTGTCTAACTTATTGGACAAGGAAAAAA
1 GTGTCTAATTTATTGGACAA--AAAAAA
* *
5439606 GTGTCTAATTTGTTGGCCAAAAAAAA
1 GTGTCTAATTTATTGGACAAAAAAAA
*
5439632 TTGTCTAATTT
1 GTGTCTAATTT
5439643 TTATTAGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 16 0.48
28 17 0.52
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (26 bp):
GTGTCTAATTTATTGGACAAAAAAAA
Found at i:5440624 original size:19 final size:19
Alignment explanation
Indices: 5440583--5440621 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5440573 AATTTAAATG
*
5440583 AATAATTAATTTTTTAATA
1 AATAATTAATTTTTTAAAA
5440602 AATAATT-ATTTTTTAAAA
1 AATAATTAATTTTTTAAAA
5440620 AA
1 AA
5440622 ATATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATAATTAATTTTTTAAAA
Found at i:5445076 original size:2 final size:2
Alignment explanation
Indices: 5445069--5445098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5445059 AAAGGCCCAT
5445069 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
5445099 GGATTGTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5445132 original size:2 final size:2
Alignment explanation
Indices: 5445125--5445162 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5445115 CTCAGCCTTC
5445125 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
5445163 GTATGTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5447057 original size:31 final size:30
Alignment explanation
Indices: 5447016--5447073 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
5447006 TTTTCTTTTA
*
5447016 TAATTTTTATATCATTTATA-TTTATTTAATT
1 TAATTATTATAT--TTTATATTTTATTTAATT
5447047 TAATTATTATATTTTATATTTTATTTA
1 TAATTATTATATTTTATATTTTATTTA
5447074 CATAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 8 0.32
31 11 0.44
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (30 bp):
TAATTATTATATTTTATATTTTATTTAATT
Found at i:5447475 original size:24 final size:23
Alignment explanation
Indices: 5447444--5447496 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
5447434 TTTTTAATGT
*
5447444 ATTT-AAAAGATCAAAAT-TTATA
1 ATTTAAAAAAATCAAAATATTA-A
*
5447466 ATTATAAAAAAATTAAAATATTAA
1 ATT-TAAAAAAATCAAAATATTAA
5447490 ATTTAAA
1 ATTTAAA
5447497 TTTAAGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.12
23 5 0.19
24 15 0.58
25 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTTAAAAAAATCAAAATATTAA
Found at i:5450310 original size:5 final size:5
Alignment explanation
Indices: 5450291--5450324 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
5450281 TTGAGTCATC
5450291 AAAAG AAAA- AGAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG AAAA
5450325 AAAGAAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5452824 original size:19 final size:19
Alignment explanation
Indices: 5452788--5452842 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
5452778 AATATTAAGA
5452788 AAATAAT-TAAAATA--CT
1 AAATAATATAAAATAGCCT
*
5452804 AATTAATA-ATAAATAGCCT
1 AAATAATATA-AAATAGCCT
*
5452823 AAATAATCTAAAATAGCCT
1 AAATAATATAAAATAGCCT
5452842 A
1 A
5452843 GTCAATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 7 0.23
17 5 0.16
19 18 0.58
20 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (19 bp):
AAATAATATAAAATAGCCT
Found at i:5454855 original size:19 final size:19
Alignment explanation
Indices: 5454831--5454870 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5454821 ACTTTTTTCA
*
5454831 TTCTACTCTACGATATTAG
1 TTCTACTCTACGATATAAG
*
5454850 TTCTACTCTAGGATATAAG
1 TTCTACTCTACGATATAAG
5454869 TT
1 TT
5454871 AATTGGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (19 bp):
TTCTACTCTACGATATAAG
Found at i:5456316 original size:2 final size:2
Alignment explanation
Indices: 5456309--5456341 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5456299 AAAGATAGGA
5456309 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5456342 TAAAAAGGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5457384 original size:28 final size:27
Alignment explanation
Indices: 5457353--5457411 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
5457343 AAACTTAAAG
5457353 TTTGTCGT-TTTAAATAAAATTTTATATT
1 TTTGTC-TATTTAAATAAAATTTTA-ATT
* *
5457381 TTTGTCTCATTTAGATAAACTTTTAATT
1 TTTGTCT-ATTTAAATAAAATTTTAATT
5457409 TTT
1 TTT
5457412 AATTTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
29 14 0.52
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTGTCTATTTAAATAAAATTTTAATT
Found at i:5457436 original size:30 final size:30
Alignment explanation
Indices: 5457402--5457483 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
5457392 TAGATAAACT
*
5457402 TTTAATTTTTAATTTATATTTAAATAAGTA
1 TTTAATTTTTAATTTATATTTAAATAAGCA
* *
5457432 TTTAATTTTTAATTTATATTTTAATAAGCG
1 TTTAATTTTTAATTTATATTTAAATAAGCA
* *
5457462 TTTAGTTTTTAATTTGTATTTA
1 TTTAATTTTTAATTTATATTTA
5457484 TTTAAATTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (30 bp):
TTTAATTTTTAATTTATATTTAAATAAGCA
Found at i:5458173 original size:21 final size:21
Alignment explanation
Indices: 5458131--5458174 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5458121 ATTTGTTTTA
* *
5458131 AAATTATATTTAAATACTATT
1 AAATTAAATTTAAATACAATT
5458152 AAATTAAATTTAAATTA-AATT
1 AAATTAAATTTAAA-TACAATT
5458173 AA
1 AA
5458175 GATTCAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTAAATTTAAATACAATT
Found at i:5461232 original size:6 final size:6
Alignment explanation
Indices: 5461221--5461247 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5461211 GAGTCTGCAA
5461221 CAAAAG CAAAAG CAAAAG CAAAAG CAA
1 CAAAAG CAAAAG CAAAAG CAAAAG CAA
5461248 GAGCGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.19, G:0.15, T:0.00
Consensus pattern (6 bp):
CAAAAG
Found at i:5461436 original size:4 final size:4
Alignment explanation
Indices: 5461427--5461451 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5461417 ATTGAACTGG
5461427 GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
5461452 GGACAGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:5461474 original size:13 final size:13
Alignment explanation
Indices: 5461456--5461480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5461446 AGAAAGGGAC
5461456 AGCATATATGTAA
1 AGCATATATGTAA
5461469 AGCATATATGTA
1 AGCATATATGTA
5461481 GGTTAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AGCATATATGTAA
Found at i:5463447 original size:3 final size:3
Alignment explanation
Indices: 5463441--5463487 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
5463431 CAACAACAAT
*
5463441 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG ACG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
5463488 AGGAAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5467764 original size:8 final size:8
Alignment explanation
Indices: 5467713--5467767 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
5467703 TATATGAAAT
5467713 AAATATATA
1 AAATAT-TA
5467722 AATATATTA
1 AA-ATATTA
*
5467731 AAATTTTA
1 AAATATTA
* *
5467739 TAATATAA
1 AAATATTA
5467747 AAATTATTA
1 AAA-TATTA
5467756 AAATATTA
1 AAATATTA
5467764 AAAT
1 AAAT
5467768 TTATATAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 21 0.55
9 13 0.34
10 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
AAATATTA
Found at i:5468184 original size:21 final size:20
Alignment explanation
Indices: 5468149--5468196 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
5468139 AAAATATTTA
* *
5468149 TTTAATTAAATAATACAATT
1 TTTAATTAAAAAATAAAATT
5468169 TTTAATATAAAAAATAAAATT
1 TTTAAT-TAAAAAATAAAATT
*
5468190 TTAAATT
1 TTTAATT
5468197 TCATCACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAATTAAAAAATAAAATT
Found at i:5470357 original size:28 final size:27
Alignment explanation
Indices: 5470292--5470365 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
5470282 ACATAATGTT
*
5470292 ATTTT-TTAATTAAATAATTTATAAAA
1 ATTTTATTAAATAAATAATTTATAAAA
*
5470318 ATTTTAATTTAAATAAAT-ATTTATATTATA
1 ATTTT-A-TTAAATAAATAATTTATA--AAA
*
5470348 ATTTTATTAAATATATAA
1 ATTTTATTAAATAAATAA
5470366 ATATTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 5 0.13
28 16 0.41
29 11 0.28
30 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTTATTAAATAAATAATTTATAAAA
Found at i:5470415 original size:18 final size:17
Alignment explanation
Indices: 5470340--5470415 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 17
5470330 ATAAATATTT
5470340 ATATTATAATTTTATTAA
1 ATATTATAA-TTTATTAA
*
5470358 ATA-TATAAATATTTTTAA
1 ATATTAT-AAT-TTATTAA
* *
5470376 A-ATAATAATATATTACA
1 ATATTATAATTTATTA-A
5470393 A-ATTATAATCTTATTAA
1 ATATTATAAT-TTATTAA
5470410 ATATTA
1 ATATTA
5470416 AATATTATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
16 4 0.09
17 19 0.41
18 23 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATAATTTATTAA
Found at i:5470441 original size:22 final size:20
Alignment explanation
Indices: 5470411--5470451 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
5470401 TCTTATTAAA
5470411 TATTAAATATTATATTAATATT
1 TATTAAATA--ATATTAATATT
*
5470433 TATTTAATAATATTAATAT
1 TATTAAATAATATTAATAT
5470452 AAAATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAAATAATATTAATATT
Found at i:5470865 original size:11 final size:11
Alignment explanation
Indices: 5470847--5470934 Score: 67
Period size: 11 Copynumber: 8.1 Consensus size: 11
5470837 TTAATATTTT
5470847 AAAT-ATATAA
1 AAATAATATAA
*
5470857 AAATAATATTA
1 AAATAATATAA
*
5470868 ATATAATATTAA
1 AAATAATA-TAA
*
5470880 AAATTA-ATAA
1 AAATAATATAA
5470890 AAATAAATATAA
1 AAAT-AATATAA
5470902 AAAT-ATA-AA
1 AAATAATATAA
*
5470911 AAATATTTATAA
1 AAATA-ATATAA
* *
5470923 ATATTATATAA
1 AAATAATATAA
5470934 A
1 A
5470935 TTTATAACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
9 6 0.10
10 14 0.23
11 22 0.36
12 19 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATAATATAA
Found at i:5470913 original size:22 final size:24
Alignment explanation
Indices: 5470848--5470913 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
5470838 TAATATTTTA
**
5470848 AATATATAAAAA-TAATATTAATAT
1 AATAT-TAAAAATTAATAAAAATAT
5470872 AATATTAAAAATTAATAAAAATA-
1 AATATTAAAAATTAATAAAAATAT
5470895 AATA-TAAAAATATAA-AAAA
1 AATATTAAAAAT-TAATAAAA
5470914 TATTTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.29
23 13 0.34
24 14 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AATATTAAAAATTAATAAAAATAT
Found at i:5470923 original size:33 final size:33
Alignment explanation
Indices: 5470847--5470923 Score: 79
Period size: 33 Copynumber: 2.3 Consensus size: 33
5470837 TTAATATTTT
* *
5470847 AAATATATAAAAATAATATTAATATAATATTAA
1 AAATTTATAAAAATAATATTAATATAATATAAA
*
5470880 AAATTAATAAAAATAA-ATATAA-A-AATATAAAA
1 AAATTTATAAAAATAATAT-TAATATAATAT-AAA
5470912 AATATTTATAAA
1 AA-ATTTATAAA
5470924 TATTATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
31 5 0.14
32 7 0.19
33 25 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (33 bp):
AAATTTATAAAAATAATATTAATATAATATAAA
Found at i:5471577 original size:7 final size:7
Alignment explanation
Indices: 5471567--5471636 Score: 54
Period size: 7 Copynumber: 10.1 Consensus size: 7
5471557 GTGATATATA
5471567 ATATAAT
1 ATATAAT
*
5471574 ATATCAAC
1 ATAT-AAT
* *
5471582 ATTTTAT
1 ATATAAT
*
5471589 ATA-ATT
1 ATATAAT
*
5471595 ATTTAAT
1 ATATAAT
5471602 ATATAAT
1 ATATAAT
5471609 ATATAAT
1 ATATAAT
* *
5471616 TTAT-TT
1 ATATAAT
5471622 ATATAAT
1 ATATAAT
5471629 ATATAAT
1 ATATAAT
5471636 A
1 A
5471637 GATTTTATGT
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
6 7 0.15
7 34 0.74
8 5 0.11
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (7 bp):
ATATAAT
Found at i:5471610 original size:20 final size:20
Alignment explanation
Indices: 5471560--5471631 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
5471550 GTTTAAAGTG
*
5471560 ATATATAATATAA-TATATCA
1 ATATATAATATAATTAT-TTA
* * *
5471580 ACATTTTATATAATTATTTA
1 ATATATAATATAATTATTTA
*
5471600 ATATATAATAT-ATAATTTA
1 ATATATAATATAATTATTTA
*
5471619 TTTATATAATATA
1 -ATATATAATATA
5471632 TAATAGATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 7 0.17
20 30 0.75
21 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATAATATAATTATTTA
Found at i:5471623 original size:35 final size:34
Alignment explanation
Indices: 5471560--5471636 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 34
5471550 GTTTAAAGTG
5471560 ATATAT-A-ATATAATATATCAACATTTTATATA
1 ATATATAATATATAATATATCAACATTTTATATA
* **
5471592 ATTATTTAATATATAATATAT-AATTTATTTATATA
1 A-TATATAATATATAATATATCAACAT-TTTATATA
5471627 ATATATAATA
1 ATATATAATA
5471637 GATTTTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
32 1 0.03
33 4 0.11
34 12 0.32
35 20 0.54
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (34 bp):
ATATATAATATATAATATATCAACATTTTATATA
Found at i:5471628 original size:27 final size:25
Alignment explanation
Indices: 5471567--5471665 Score: 87
Period size: 27 Copynumber: 3.8 Consensus size: 25
5471557 GTGATATATA
*
5471567 ATATAATATATCAACAT-TTTATATAATT
1 ATATAATATAT-AATATATTT-TAT--TT
*
5471595 ATTTAATATATAATATATAATTTATTT
1 ATATAATATATAATATAT--TTTATTT
* *
5471622 ATATAATATATAATAGATTTTATGT
1 ATATAATATATAATATATTTTATTT
5471647 A-ATAATATA-AATATATTTT
1 ATATAATATATAATATATTTT
5471666 TTTGAATAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
23 9 0.15
24 8 0.13
25 7 0.11
27 22 0.35
28 11 0.18
29 3 0.05
30 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
ATATAATATATAATATATTTTATTT
Found at i:5471641 original size:20 final size:21
Alignment explanation
Indices: 5471601--5471665 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
5471591 AATTATTTAA
**
5471601 TATATAATATATAATTTA-TT
1 TATATAATATATAATAGATTT
5471621 TATATAATATATAATAGATTT
1 TATATAATATATAATAGATTT
* *
5471642 TATGTAATAATATAAATATATTT
1 TATATAAT-ATAT-AATAGATTT
5471665 T
1 T
5471666 TTTGAATAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 9 0.24
22 4 0.11
23 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TATATAATATATAATAGATTT
Found at i:5471664 original size:23 final size:23
Alignment explanation
Indices: 5471593--5471673 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 23
5471583 TTTTATATAA
*
5471593 TTATTTAAT-ATATAATATATAAT
1 TTATTTAATAATATAA-ATATATT
*
5471616 TTATTTATATAATATATAATAGATT
1 TTATTTA-ATAATATA-AATATATT
*
5471641 TTATGTAATAATATAAATATATT
1 TTATTTAATAATATAAATATATT
5471664 TT-TTTGAATA
1 TTATTT-AATA
5471674 GAAAAAATCC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.04
23 20 0.41
24 10 0.20
25 16 0.33
26 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTATTTAATAATATAAATATATT
Found at i:5475361 original size:2 final size:2
Alignment explanation
Indices: 5475356--5475386 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5475346 ACACACACAC
5475356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5475387 GATTTGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5478752 original size:21 final size:22
Alignment explanation
Indices: 5478715--5478762 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
5478705 TAATTACTCA
*
5478715 ATAATTTAACTTAAA-TTATTT
1 ATAATTGAACTTAAATTTATTT
5478736 ATAATTGAA-TTACAATTTTATTT
1 ATAATTGAACTTA-AA-TTTATTT
5478759 ATAA
1 ATAA
5478763 AATATTGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
23 10 0.43
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATTGAACTTAAATTTATTT
Found at i:5490241 original size:21 final size:21
Alignment explanation
Indices: 5490217--5490257 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5490207 ATTGGTTTTT
*
5490217 AATTGA-TATTTTATTAAATTA
1 AATTGATTAATTT-TTAAATTA
5490238 AATTGATTAATTTTTAAATT
1 AATTGATTAATTTTTAAATT
5490258 TTAAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
AATTGATTAATTTTTAAATTA
Found at i:5490348 original size:22 final size:21
Alignment explanation
Indices: 5490323--5490367 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
5490313 TTAAATATAT
*
5490323 CTATATTATATTATAATTAATA
1 CTATATTATA-TATAATAAATA
5490345 C--TATTATATATAATAAATA
1 CTATATTATATATAATAAATA
5490364 -TATA
1 CTATA
5490368 AAATTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
19 10 0.50
20 9 0.45
22 1 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
CTATATTATATATAATAAATA
Found at i:5490728 original size:20 final size:19
Alignment explanation
Indices: 5490669--5490730 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 19
5490659 ACTCCATCTC
*
5490669 ATTTTTTAA-ATTATTATTTT
1 ATTTTTTAATATT-TTA-TAT
5490689 ATTTTTTAGATATTTTATAT
1 ATTTTTTA-ATATTTTATAT
5490709 ATTTTTT-ATACTTTTAATAT
1 ATTTTTTAATA-TTTT-ATAT
5490729 AT
1 AT
5490731 ATATAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 23 0.62
21 4 0.11
22 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTTAATATTTTATAT
Found at i:5491333 original size:114 final size:113
Alignment explanation
Indices: 5491121--5491336 Score: 269
Period size: 113 Copynumber: 1.9 Consensus size: 113
5491111 AGATAAGATT
* * * *
5491121 ATAAATTAATTAATTTAAGATTAAATCTTATAAAAATATATATTAAATAAAAATAAATCTCACGT
1 ATAAATTAATTAATTTAAGATCAAATCTTATAAAAAAATATATTAAATAAAAATAAAGCACACGT
**
5491186 GCTTATTTAATTAATTTATAGGTCTATTTTATTTAATTATAGTAGGTC
66 GCTTATTTAATTAATTTATAAATCTATTTTATTTAATTATAGTAGGTC
* * **
5491234 ATAAATTATTTAATTTAA-AGTCAAATCTTATAAAAAAAATATATTAGAT-AAAATAGGGCACAC
1 ATAAATTAATTAATTTAAGA-TCAAATCTTAT-AAAAAAATATATTAAATAAAAATAAAGCACAC
5491297 -TG-TTATTTAATTAATTTATTTGAAATCTATTTTATTTAAT
64 GTGCTTATTTAATTAATTTA--T-AAATCTATTTTATTTAAT
5491337 ATTTTTAGAC
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
111 16 0.18
112 3 0.03
113 38 0.43
114 31 0.35
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (113 bp):
ATAAATTAATTAATTTAAGATCAAATCTTATAAAAAAATATATTAAATAAAAATAAAGCACACGT
GCTTATTTAATTAATTTATAAATCTATTTTATTTAATTATAGTAGGTC
Found at i:5495361 original size:79 final size:79
Alignment explanation
Indices: 5495257--5495704 Score: 422
Period size: 79 Copynumber: 5.7 Consensus size: 79
5495247 TAAAATACCA
* * * * ** *
5495257 ATTTTCCACCATCAGGGATATTCCAACCCCGTTATTTTCGAAGGGATACTCCAACTTCGATTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGTTTTA
5495322 TTTTCAAAACACTG
66 TTTTCAAAACACTG
* * * * *
5495336 ACTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCCG-AGGAGATACCCCAACCTCGGTTTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAAGG-GATACTCCAACCCCGGTTTT
**
5495400 A-TTTCAAAACACCA
65 ATTTTCAAAACACTG
* * * *
5495414 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCAAAGGGGTACTCCGACCCCGGTTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGTTTTA
*
5495479 TTTCCAAAACA-TCG
66 TTTTCAAAACACT-G
* *** * * * **
5495493 ATTTTTCATAATCAAAGATACTCTAACCCTGTTA-TTTCTGAGGGGGGACTCCAA-CCCGGTTTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTC-GAAGGGATACTCCAACCCCGGTTTT
* * *
5495556 ATTTTTAAAATACCG
65 ATTTTCAAAACACTG
* * * * * * *
5495571 ATTTTTCACCAT-TGGGATACTCCAACTCTGTTATTTTTGAAAGGATACTCTAACCCCGGTTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGTTTTA
* *
5495635 TTTCCAAAACAATG
66 TTTTCAAAACACTG
* * * * *
5495649 ATTTTTCATAATGGGGGATACTCCAATCTCGTTATTTTCAAAGGGATACTCCAACC
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACC
5495705 TCGTTATTTC
Statistics
Matches: 292, Mismatches: 68, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
77 26 0.09
78 131 0.45
79 135 0.46
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGTTTTA
TTTTCAAAACACTG
Found at i:5495547 original size:157 final size:156
Alignment explanation
Indices: 5495238--5495685 Score: 474
Period size: 157 Copynumber: 2.9 Consensus size: 156
5495228 TCATTAATGT
* * *
5495238 TTTTATTTCTAAAATACCAATTTTCCACCATCAGGGATATTCCAACCCCGTTATTTTCGAAGGGA
1 TTTTATTTC-AAAATACCAATTTTTCACCATCAGGGATACTCCAACCCCGTTATTTTCAAAGGGA
** * * * * ***
5495303 TACTCCAACTTCGATTTTATTTTCAAAACA-CTGACTTTTCACAATCGGGGATACTCCAACCTCG
65 TACTCCAACCCCGGTTTTATTTCCAAAACATC-GATTTTTCATAATCAAAGATACTCCAACCTCG
*
5495367 TTATTTCCGAGGAGATACCCCAACCTCGG
129 TTATTTCCGAGGAGAGACCCCAACC-CGG
* * * * *
5495396 TTTTATTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCAAAGGGGT
1 TTTTATTTCAAAATACCAATTTTTCACCATCAGGGATACTCCAACCCCGTTATTTTCAAAGGGAT
* *
5495461 ACTCCGACCCCGGTTTTATTTCCAAAACATCGATTTTTCATAATCAAAGATACTCTAACC-CTGT
66 ACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTCATAATCAAAGATACTCCAACCTC-GT
* * * *
5495525 TATTTCTGAGGGGGGACTCCAACCCGG
130 TATTTCCGAGGAGAGACCCCAACCCGG
* * * * * *
5495552 TTTTATTTTTAAAATACCGATTTTTCACCAT-TGGGATACTCCAACTCTGTTATTTTTGAAA-GG
1 TTTTA-TTTCAAAATACCAATTTTTCACCATCAGGGATACTCCAACCCCGTTA-TTTTCAAAGGG
* **** *
5495615 ATACTCTAACCCCGGTTTTATTTCCAAAACAAT-GATTTTTCATAATGGGGGATACTCCAATCTC
64 ATACTCCAACCCCGGTTTTATTTCCAAAAC-ATCGATTTTTCATAATCAAAGATACTCCAACCTC
5495679 GTTATTT
128 GTTATTT
5495686 TCAAAGGGAT
Statistics
Matches: 242, Mismatches: 42, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
156 85 0.35
157 147 0.61
158 10 0.04
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (156 bp):
TTTTATTTCAAAATACCAATTTTTCACCATCAGGGATACTCCAACCCCGTTATTTTCAAAGGGAT
ACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTCATAATCAAAGATACTCCAACCTCGTT
ATTTCCGAGGAGAGACCCCAACCCGG
Found at i:5495695 original size:28 final size:28
Alignment explanation
Indices: 5495663--5495749 Score: 104
Period size: 28 Copynumber: 3.0 Consensus size: 28
5495653 TTCATAATGG
*
5495663 GGGATACTCCAATCTCGTTATTTTCAAA
1 GGGATACTCCAACCTCGTTATTTTCAAA
* *
5495691 GGGATACTCCAACCTCGTTA-TTTCTGAG
1 GGGATACTCCAACCTCGTTATTTTC-AAA
5495719 GGGATACTCCAACCTCGGTTTTATTTTCAAA
1 GGGATACTCCAACCTC-G--TTATTTTCAAA
5495750 ACACCAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
27 4 0.08
28 36 0.73
29 1 0.02
31 4 0.08
32 4 0.08
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (28 bp):
GGGATACTCCAACCTCGTTATTTTCAAA
Found at i:5495711 original size:107 final size:108
Alignment explanation
Indices: 5495584--5495811 Score: 289
Period size: 107 Copynumber: 2.1 Consensus size: 108
5495574 TTTCACCATT
* * *
5495584 GGGATACTCCAA-CTCTGTTATTTTTGAAAGGATACTCTAACCCCGGTTTTATTTCCAAAACAAT
1 GGGATACTCCAACCTCTGTTATTTCTGAAAGGATACTCCAACCCCGGTTTTATTTCCAAAACAAC
* * * ** * *
5495648 GATTTTTCATAATGGGGGATACTCCAATCTCGTTATTTTCAAA
66 AAATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCAAA
** * * *
5495691 GGGATACTCCAACCTC-GTTATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACC
1 GGGATACTCCAACCTCTGTTATTTCTGAAAGGATACTCCAACCCCGGTTTTATTTCCAAAACAAC
* *
5495755 AAATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAG
66 AAATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCAAA
5495798 GGGATACTCCAACC
1 GGGATACTCCAACC
5495812 ACGATTTTAT
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
107 100 0.97
108 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (108 bp):
GGGATACTCCAACCTCTGTTATTTCTGAAAGGATACTCCAACCCCGGTTTTATTTCCAAAACAAC
AAATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCAAA
Found at i:5495774 original size:79 final size:78
Alignment explanation
Indices: 5495690--5496024 Score: 381
Period size: 79 Copynumber: 4.3 Consensus size: 78
5495680 TTATTTTCAA
* *
5495690 AGGGATACTCCAACCTCGTTA-TTTCTGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACAC
1 AGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCTCGATTTTATTTTCAAAACAC
5495754 CAAATTTTCACAATC
65 C-AATTTTCACAATC
* *
5495769 AGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCACGATTTTATTTTCAAAACATC
1 AGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACC
*
5495834 AATTTTCAATAATC
66 AATTTTC-ACAATC
* * * * * *
5495848 GGGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACC-CTGATTTTATTTTTAAAATAC
1 AGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTC-GATTTTATTTTCAAAACAC
** *
5495912 TGATTTTCACCATC
65 CAATTTTCACAATC
* * * *
5495926 -GGAGATACTCCAACCCCGTTATTTTTGAAGGGTTACTCCAACCTCGGTTTTA-TTTCTAAAACA
1 AGG-GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTTC-AAAACA
* *
5495989 CTGATTTTTCACAATC
64 C-CAATTTTCACAATC
* *
5496005 ATGGATACTTCAACCCCGTT
1 AGGGATACTCCAACCCCGTT
5496025 TTTATCTCTA
Statistics
Matches: 217, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
77 5 0.02
78 58 0.27
79 149 0.69
80 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (78 bp):
AGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACC
AATTTTCACAATC
Found at i:5495822 original size:186 final size:184
Alignment explanation
Indices: 5495509--5495893 Score: 470
Period size: 186 Copynumber: 2.1 Consensus size: 184
5495499 CATAATCAAA
* * * * * *
5495509 GATACTCTAACCCTGTTATTTCTGAGGGGGGACTCCAACCCGGTTTTATTTTTAAAATACCGATT
1 GATACTCCAACCCTGTTATTTCTGAGGGGAGACTCCAACCCGGTTTTATTTTCAAAACACCAAAT
* * * * * * * *
5495574 TTTCACCATTGGGATACTCCAACTCTGTTATTTTTGAAAGGATACTCTAACCCCGGTTTTATTTC
66 TTTCACAATAGGGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCACGATTTTATTTC
* * * * * *
5495639 CAAAACAATGATTTTTC-ATAATGGGGGATACTCCAATCTCGTTATTTTCAA-AGG
131 CAAAAC-ATCAATTTTCAATAATCGGGGATACTCCAACCCCATTATTTTCAAGA-G
*
5495693 GATACTCCAA-CCTCGTTATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAA
1 GATACTCCAACCCT-GTTATTTCTGAGGGGAGACTCCAACC-CGGTTTTATTTTCAAAACACCAA
**
5495757 ATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCACGATTTTAT
64 ATTTTCACAAT-AGGGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCACGATTTTAT
* * *
5495822 TTTCAAAACATCAATTTTCAATAATCGGGGATACTCTAACCCCATTATTTTCGAGAG
128 TTCCAAAACATCAATTTTCAATAATCGGGGATACTCCAACCCCATTATTTTCAAGAG
5495879 GATACTCCAACCCTG
1 GATACTCCAACCCTG
5495894 ATTTTATTTT
Statistics
Matches: 169, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
183 3 0.02
184 33 0.20
185 37 0.22
186 92 0.54
187 4 0.02
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (184 bp):
GATACTCCAACCCTGTTATTTCTGAGGGGAGACTCCAACCCGGTTTTATTTTCAAAACACCAAAT
TTTCACAATAGGGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCACGATTTTATTTC
CAAAACATCAATTTTCAATAATCGGGGATACTCCAACCCCATTATTTTCAAGAG
Found at i:5495921 original size:342 final size:342
Alignment explanation
Indices: 5495350--5495999 Score: 941
Period size: 342 Copynumber: 1.9 Consensus size: 342
5495340 TTCACAATCG
5495350 GGGATACTCCAACCTCGTTATTTCCGAGGAGATACCCCAACCTCGGTTTTATTTCAAAACACCAA
1 GGGATACTCCAACCTCGTTATTTCCGAGGAGATACCCCAACCTCGGTTTTATTTCAAAACACCAA
* * * * *
5495415 TTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCAAAGGGGTACTCCGACCCCGGTTTTAT
66 ATTTTCACAATCAGGGATACTCCAACCCCATTATTTTCAAAGGGGTACTCCAACCACGATTTTAT
* ** * *
5495480 TTCCAAAACATCGATTTTTCATAATCAAAGATACTCTAACCCTGTTATTTCTGAGGGGGGACTCC
131 TTCCAAAACATCGAATTTTCATAATCAAAGATACTCTAACCCCATTATTTCTGAGAGGAGACTCC
* * * *
5495545 AACCCGGTTTTATTTTTAAAATACCGATTTTTCACCATTGG-GATACTCCAACTCTGTTATTTTT
196 AACCCGATTTTATTTTTAAAATACCGATTTTTCACCATCGGAGATACTCCAACCCCGTTATTTTT
*
5495609 GAAAGGATACTCTAACCCCGGTTTTATTTCCAAAACAATGATTTTTCATAATGGGGGATACTCCA
261 GAAAGGATACTCCAACCCCGGTTTTATTTCCAAAACAATGATTTTTCATAATGGGGGATACTCCA
5495674 ATCTCGTTATTTTCAAA
326 ATCTCGTTATTTTCAAA
* * *
5495691 GGGATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCA
1 GGGATACTCCAACCTCGTTATTTCCGAGGAGATACCCCAACCTCGGTTTTA-TTTCAAAACACCA
* *
5495756 AATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCACGATTTT
65 AATTTTCACAATCAGGGATACTCCAACCCCATTATTTTCAAAGGGG-TACTCCAACCACGATTTT
* *** *
5495820 ATTTTCAAAACATC-AATTTTCAATAATCGGGGATACTCTAACCCCATTATTT-TCGAGAGGATA
129 ATTTCCAAAACATCGAATTTTC-ATAATCAAAGATACTCTAACCCCATTATTTCT-GAGAGGAGA
*
5495883 CTCCAACCCTGATTTTATTTTTAAAATACTGA-TTTTCACCATCGGAGATACTCCAACCCCGTTA
192 CTCCAACCC-GATTTTATTTTTAAAATACCGATTTTTCACCATCGGAGATACTCCAACCCCGTTA
* * * * *
5495947 TTTTTGAAGGGTTACTCCAACCTCGGTTTTATTTCTAAAACACTGATTTTTCA
256 TTTTTGAAAGGATACTCCAACCCCGGTTTTATTTCCAAAACAATGATTTTTCA
5496000 CAATCATGGA
Statistics
Matches: 272, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
341 60 0.22
342 129 0.47
343 83 0.31
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (342 bp):
GGGATACTCCAACCTCGTTATTTCCGAGGAGATACCCCAACCTCGGTTTTATTTCAAAACACCAA
ATTTTCACAATCAGGGATACTCCAACCCCATTATTTTCAAAGGGGTACTCCAACCACGATTTTAT
TTCCAAAACATCGAATTTTCATAATCAAAGATACTCTAACCCCATTATTTCTGAGAGGAGACTCC
AACCCGATTTTATTTTTAAAATACCGATTTTTCACCATCGGAGATACTCCAACCCCGTTATTTTT
GAAAGGATACTCCAACCCCGGTTTTATTTCCAAAACAATGATTTTTCATAATGGGGGATACTCCA
ATCTCGTTATTTTCAAA
Found at i:5495996 original size:157 final size:158
Alignment explanation
Indices: 5495691--5495988 Score: 390
Period size: 157 Copynumber: 1.9 Consensus size: 158
5495681 TATTTTCAAA
* * * *
5495691 GGGATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCA
1 GGGATACTCCAACCCCATTATTTCTGAGAGGATACTCCAACCTCGATTTTATTTTCAAAACACCA
*
5495756 AATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCACGATTTTA
66 AATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCACGATTTTA
5495821 TTTTCAAAACATCAATTTTCAATAATCG
131 TTTTCAAAACATCAATTTTCAATAATCG
* * *
5495849 GGGATACTCTAACCCCATTATTT-TCGAGAGGATACTCCAACC-CTGATTTTATTTTTAAAATA-
1 GGGATACTCCAACCCCATTATTTCT-GAGAGGATACTCCAACCTC-GATTTTATTTTCAAAACAC
** * * * * *
5495911 CTGATTTTCACCATC-GGAGATACTCCAACCCCGTTATTTTTGAAGGGTTACTCCAACCTCGGTT
64 CAAATTTTCACAATCAGG-GATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCACGATT
5495975 TTA-TTTCTAAAACA
128 TTATTTTC-AAAACA
5495989 CTGATTTTTC
Statistics
Matches: 121, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
156 6 0.05
157 64 0.53
158 51 0.42
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (158 bp):
GGGATACTCCAACCCCATTATTTCTGAGAGGATACTCCAACCTCGATTTTATTTTCAAAACACCA
AATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCACGATTTTA
TTTTCAAAACATCAATTTTCAATAATCG
Found at i:5496011 original size:157 final size:158
Alignment explanation
Indices: 5495690--5496021 Score: 381
Period size: 157 Copynumber: 2.1 Consensus size: 158
5495680 TTATTTTCAA
* * * * *
5495690 AGGGATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACC
1 AGGGATACTCTAACCCCATTATTTCTGAGAGGATACTCCAACCTCGATTTTATTTTCAAAACACC
*
5495755 AAATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCACGATTTT
66 AAATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCACGATTTT
*
5495820 ATTTTCAAAACATCAATTTTCAATAATC
131 ATTTTCAAAACATCAATTTTCAACAATC
* * *
5495848 GGGGATACTCTAACCCCATTATTT-TCGAGAGGATACTCCAACC-CTGATTTTATTTTTAAAATA
1 AGGGATACTCTAACCCCATTATTTCT-GAGAGGATACTCCAACCTC-GATTTTATTTTCAAAACA
** * * * * *
5495911 -CTGATTTTCACCATC-GGAGATACTCCAACCCCGTTATTTTTGAAGGGTTACTCCAACCTCGGT
64 CCAAATTTTCACAATCAGG-GATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCACGAT
* *
5495974 TTTA-TTTCTAAAACACTGATTTTTC-ACAATC
128 TTTATTTTC-AAAACA-TCAATTTTCAACAATC
*
5496005 ATGGATACT-TCAACCCC
1 AGGGATACTCT-AACCCC
5496022 GTTTTTATCT
Statistics
Matches: 147, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
156 7 0.05
157 82 0.56
158 58 0.39
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (158 bp):
AGGGATACTCTAACCCCATTATTTCTGAGAGGATACTCCAACCTCGATTTTATTTTCAAAACACC
AAATTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCACGATTTT
ATTTTCAAAACATCAATTTTCAACAATC
Found at i:5496308 original size:23 final size:23
Alignment explanation
Indices: 5496257--5496308 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
5496247 ATCGTCCCTC
**
5496257 ATTTTTATGTACTTTTGTGCGTT
1 ATTTTTATGTAAATTTGTGCGTT
5496280 -TATTTTATGTAAATTTGT-CTGTT
1 AT-TTTTATGTAAATTTGTGC-GTT
5496303 ATTTTT
1 ATTTTT
5496309 TTTACTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.08
23 21 0.88
24 1 0.04
ACGTcount: A:0.17, C:0.06, G:0.13, T:0.63
Consensus pattern (23 bp):
ATTTTTATGTAAATTTGTGCGTT
Found at i:5499864 original size:4 final size:4
Alignment explanation
Indices: 5499855--5499906 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
5499845 AATTTTGTAA
5499855 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5499903 AAAT
1 AAAT
5499907 CCAGGTTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:5501696 original size:19 final size:18
Alignment explanation
Indices: 5501658--5501696 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5501648 TGCATGCATT
* *
5501658 TTGACATGGAAAACATGA
1 TTGACATGCAAAAAATGA
5501676 TTGACATGCAAGAAAATGA
1 TTGACATGCAA-AAAATGA
5501695 TT
1 TT
5501697 AGTGACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (18 bp):
TTGACATGCAAAAAATGA
Found at i:5502877 original size:52 final size:50
Alignment explanation
Indices: 5502802--5503040 Score: 282
Period size: 52 Copynumber: 4.7 Consensus size: 50
5502792 ATTTAATTGG
* ** ** * **
5502802 ATGTATCGATACATTGACGAATGTATTAATACATTTGGGTTAAAAACTTAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATTT-GGAT-AAAACCCAGA
** *
5502854 ATGTATCGATACAATGAATAATGTATTAATACATTTAGATCAAAAACCCAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATTTGGAT--AAAACCCAGA
* *
5502906 ATGTATCGATACAATGAATAATGTATCGATTCATTTGGATCAAACCCAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATTTGGATAAAACCCAGA
* * *
5502956 ATGTATCGATATAATGAATAATGTATCGATTCATTTGGATCAAACCCAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATTTGGATAAAACCCAGA
*
5503006 ATGTATCGATACAAT-AAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAATAATGTATCGATACATTT
5503041 TCTTTTCGGA
Statistics
Matches: 170, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
49 18 0.11
50 72 0.42
51 2 0.01
52 78 0.46
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (50 bp):
ATGTATCGATACAATGAATAATGTATCGATACATTTGGATAAAACCCAGA
Found at i:5502961 original size:30 final size:30
Alignment explanation
Indices: 5502925--5503015 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 30
5502915 TACAATGAAT
5502925 AATGTATCGATTCATTTGGATCAAACCCAG
1 AATGTATCGATTCATTTGGATCAAACCCAG
* * *
5502955 AATGTATCGA-T-A--T-AAT--GA---AT
1 AATGTATCGATTCATTTGGATCAAACCCAG
5502975 AATGTATCGATTCATTTGGATCAAACCCAG
1 AATGTATCGATTCATTTGGATCAAACCCAG
5503005 AATGTATCGAT
1 AATGTATCGAT
5503016 ACAATAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 20
0.63 0.08 0.28
Matches are distributed among these distances:
20 11 0.24
21 1 0.02
22 1 0.02
23 1 0.02
24 1 0.02
25 4 0.09
26 1 0.02
27 1 0.02
28 1 0.02
29 1 0.02
30 22 0.49
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (30 bp):
AATGTATCGATTCATTTGGATCAAACCCAG
Found at i:5502972 original size:50 final size:50
Alignment explanation
Indices: 5502851--5503040 Score: 292
Period size: 50 Copynumber: 3.8 Consensus size: 50
5502841 TTAAAAACTT
** *
5502851 AGAATGTATCGATACAATGAATAATGTATTAATACATTTAGATCAAAAACCC
1 AGAATGTATCGATACAATGAATAATGTATCGATACATTTGGATC--AAACCC
*
5502903 AGAATGTATCGATACAATGAATAATGTATCGATTCATTTGGATCAAACCC
1 AGAATGTATCGATACAATGAATAATGTATCGATACATTTGGATCAAACCC
* *
5502953 AGAATGTATCGATATAATGAATAATGTATCGATTCATTTGGATCAAACCC
1 AGAATGTATCGATACAATGAATAATGTATCGATACATTTGGATCAAACCC
*
5503003 AGAATGTATCGATACAAT-AAAAATGTATCGATACATTT
1 AGAATGTATCGATACAATGAATAATGTATCGATACATTT
5503041 TCTTTTCGGA
Statistics
Matches: 130, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
49 18 0.14
50 72 0.55
52 40 0.31
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (50 bp):
AGAATGTATCGATACAATGAATAATGTATCGATACATTTGGATCAAACCC
Found at i:5502980 original size:102 final size:99
Alignment explanation
Indices: 5502851--5503040 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 99
5502841 TTAAAAACTT
*
5502851 AGAATGTATCGATACAATGAATAATGTATTAATACATTTAGATCAAAAACCCAGAATGTATCGAT
1 AGAATGTATCGATACAATGAATAATGTATCAATACATTTAGATC--AAACCCAGAATGTATCGAT
* *
5502916 ACAATGAATAATGTATCGATTCATTTGGATCAAACCC
64 ACAAT-AAAAATGTATCGATACATTTGGATCAAACCC
* * * *
5502953 AGAATGTATCGATATAATGAATAATGTATCGATTCATTTGGATCAAACCCAGAATGTATCGATAC
1 AGAATGTATCGATACAATGAATAATGTATCAATACATTTAGATCAAACCCAGAATGTATCGATAC
5503018 AATAAAAATGTATCGATACATTT
66 AATAAAAATGTATCGATACATTT
5503041 TCTTTTCGGA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
99 18 0.22
100 24 0.30
102 39 0.48
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (99 bp):
AGAATGTATCGATACAATGAATAATGTATCAATACATTTAGATCAAACCCAGAATGTATCGATAC
AATAAAAATGTATCGATACATTTGGATCAAACCC
Found at i:5503120 original size:20 final size:21
Alignment explanation
Indices: 5503097--5503150 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
5503087 CATTTCAGAC
*
5503097 ATGTATTGATACATTCACTT-
1 ATGTATCGATACATTCACTTG
5503117 ATGTATCGATACATTCACTTG
1 ATGTATCGATACATTCACTTG
*
5503138 TTGTATCGATACA
1 ATGTATCGATACA
5503151 CATTGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTG
Found at i:5503282 original size:21 final size:20
Alignment explanation
Indices: 5503258--5503296 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5503248 ATTAGGACCT
5503258 TGTATCGATACATCCTAGGTA
1 TGTATCGATACAT-CTAGGTA
*
5503279 TGTATTGATACATCTAGG
1 TGTATCGATACATCTAGG
5503297 CAAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATCTAGGTA
Found at i:5503290 original size:70 final size:70
Alignment explanation
Indices: 5503118--5503270 Score: 270
Period size: 70 Copynumber: 2.2 Consensus size: 70
5503108 CATTCACTTA
* *
5503118 TGTATCGATACATTCACTTGTTGTATCGATACACATTGTAGAATCTTGAAATCTTTGACCATTAG
1 TGTATCGATACATTCACTTGTTGTATCGATACAAATTATAGAATCTTGAAATCTTTGACCATTAG
5503183 GACCT
66 GACCT
* *
5503188 TGTATCGATACATTCACTTGTTGTATCAATACAAATTATAGAATTTTGAAATCTTTGACCATTAG
1 TGTATCGATACATTCACTTGTTGTATCGATACAAATTATAGAATCTTGAAATCTTTGACCATTAG
5503253 GACCT
66 GACCT
5503258 TGTATCGATACAT
1 TGTATCGATACAT
5503271 CCTAGGTATG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (70 bp):
TGTATCGATACATTCACTTGTTGTATCGATACAAATTATAGAATCTTGAAATCTTTGACCATTAG
GACCT
Found at i:5510126 original size:28 final size:28
Alignment explanation
Indices: 5510094--5510177 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 28
5510084 ACGCCTTTTC
5510094 CTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * **
5510122 CTTTT-TAGTCCTCA-AAG-AGCAGGACA
1 CTTTTAAAGCCCACACAAGTTGGTGG-CA
*
5510148 CCTTTTAAAGCCCACACGAGTTGGTGGCA
1 -CTTTTAAAGCCCACACAAGTTGGTGGCA
5510177 C
1 C
5510178 CCTCCAGTCC
Statistics
Matches: 38, Mismatches: 13, Indels: 10
0.62 0.21 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.13
27 11 0.29
28 12 0.32
29 4 0.11
30 3 0.08
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (28 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:5510256 original size:60 final size:60
Alignment explanation
Indices: 5509880--5510323 Score: 524
Period size: 61 Copynumber: 7.3 Consensus size: 60
5509870 TAGCCCTTCC
* * * *
5509880 AGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCTACACGAGTTAGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
* * * **
5509941 AGTCCTCAAAGAGCAGGACACCTTTTTTTTTTCAAAGCTCACATGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
* *
5510002 AGTCCTCAAAGAGCAGGACACATTTTTTCTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGC-CTTTTTC----TTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
5510067 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTT
* * **
5510128 AGTCCTCAAAGAGCAGGAC-AC-----CTTTTAAAGCCCACACGAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * *
5510183 AGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
5510243 AGTCCTCAAAGAGCATGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--T
*
5510304 AGTCCTCAAAGAACAGGACG
1 AGTCCTCAAAGAGCAGGACG
5510324 TTCTCTCCTT
Statistics
Matches: 333, Mismatches: 35, Indels: 30
0.84 0.09 0.08
Matches are distributed among these distances:
55 47 0.14
56 2 0.01
59 3 0.01
60 81 0.24
61 141 0.42
62 5 0.02
64 5 0.02
65 45 0.14
66 4 0.01
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:5510584 original size:60 final size:60
Alignment explanation
Indices: 5510369--5510724 Score: 406
Period size: 60 Copynumber: 6.0 Consensus size: 60
5510359 GGTGCCTTTT
* * *
5510369 AAAGCCCACATAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCC-TTC
* * * **
5510429 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTT-C
*
5510490 AAAGCCCACACAAGTTGGTGGCACCTTT-AATCCTCAAAGAGCAGGACGCCTTCTCCTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTC
* *
5510549 AAAGCCCACACGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCC-T-T--TT-
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTC
* * * * * * *
5510604 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGATCAAGACACCTTTTTCTTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC-TTCTC-CTTC
* * *
5510666 AAAGCCCGCACAAGTTGGTAGCA-CTTCCTAGTCCTCAAAGAGCAGGACG-CTCTCTCCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCT-TCTCCTT
5510725 TCACCATTTA
Statistics
Matches: 252, Mismatches: 32, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
55 45 0.18
56 2 0.01
57 1 0.00
58 2 0.01
59 29 0.12
60 72 0.29
61 63 0.25
62 38 0.15
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (60 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTC
Found at i:5510714 original size:391 final size:386
Alignment explanation
Indices: 5509969--5511108 Score: 1331
Period size: 391 Copynumber: 2.9 Consensus size: 386
5509959 CACCTTTTTT
* * * * *
5509969 TTTTCAAAGCTCACATGAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACACATTTTTTCTTT
1 TTTT-AAAGCCCACATAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGC-----TTC-TC
* * * *
5510034 TTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
59 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGAAG-C-TTTCTTTTT
*
5510099 AAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACACC-TT--TTAAAGCCC
122 AAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTCCTTAAAGCCC
* * *
5510161 ACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTAAAGCCCACAT
187 ACACGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG-C-----CTTTTAAAGCCCACAC
* * * *
5510226 AAGCTGGTGGCACC-TTTAGTCCTCAAAGAGCATGACGCC-TTCTCCTTTTAAAGCCCACACAAG
246 AAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTCTCTTTTTAAAGCCCACACAAG
* * * *
5510289 TTGGTGGCACTTCCTAGTCCTCAAAGAACAGGACGTTCTCTCCTTTCGCCTTTTTA-TCCTCAAA
311 TTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACC-ATTTAGTCCTCAAA
* *
5510353 GAGCAGGGTGCC
375 GAGCAAGATGCC
*
5510365 TTTTAAAGCCCACATAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTA
1 TTTTAAAGCCCACATAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACG-CTTCTCCTTTTA
*
5510430 AAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAGC
65 AAGCCCACACAAGTTGGTGGCACTTTT-AGTCCTCAAAGAGCAGGAAGCTTTCTTTTT--AAAGC
* *
5510495 CCACACAAGTTGGTGGCAC-CTTTAATCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACA
127 CCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTT-TCCTT-AAAGCCCACA
*
5510559 CGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTG
190 CGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTG
* * * *
5510624 GCACCTTTTAGTCCTCAAAGATCAAGACACCTTTTTCTTTTTAAAGCCCGCACAAGTTGGTAGCA
255 GCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
5510689 CTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCATTTAGTCCTCAAAGAGCAAGATG
320 CTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCATTTAGTCCTCAAAGAGCAAGATG
5510754 CC
385 CC
* * * *
5510756 TTTCAAAGCCCACACAAGTTGCTGGCACTTTTCAGTCCTCAAAGAGCAGGACG-----CCTTTTA
1 TTTTAAAGCCCACATAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCTTCTCCTTTTA
** * *
5510816 AATTCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTTCCCTTTTAA
65 AAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGA-AGC---TTT-CTTTTTAA
*
5510881 AGGCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGC
124 AGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGACGCC-TTTCC--TTAAAGC
* * *
5510946 CCACACAAGTTGGTGGCA-TTTTCTAGTCTTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCA
185 CCACACGAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCC---T--TTT-AAAGCCCA
* * * ** **
5511010 CACAAGTTGGTGGCA-TTTTCTAGTCCTTAAAGAGCAGGA-TGCTTTCTCTTTGCAAAGCCCACA
243 CACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAAGACACCTTTCTCTTTTTAAAGCCCACA
5511073 CAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGG
307 CAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGG
5511109 GCGTCTTTTC
Statistics
Matches: 652, Mismatches: 59, Indels: 65
0.84 0.08 0.08
Matches are distributed among these distances:
386 45 0.07
387 6 0.01
389 59 0.09
390 87 0.13
391 190 0.29
392 68 0.10
393 2 0.00
394 3 0.00
395 90 0.14
396 5 0.01
397 53 0.08
398 44 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (386 bp):
TTTTAAAGCCCACATAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTCTCCTTTTAA
AGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGAAGCTTTCTTTTTAAAGCCCAC
ACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTCCTTAAAGCCCACACGAGTT
GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
TTTAGTCCTCAAAGAGCAAGACACCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT
AGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCATTTAGTCCTCAAAGAGCAAGATGCC
Found at i:5510868 original size:26 final size:27
Alignment explanation
Indices: 5510783--5510869 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 27
5510773 GTTGCTGGCA
* *
5510783 CTTTTCAGTCCTCAAAGAGCAGGACGC
1 CTTTTAAGTCCTCAAAGAGCAGGACAC
* * * **
5510810 CTTTTAAATTCCACACAAGTTGGTGG-CAC
1 CTTTT-AAGTCCTCA-AAG-AGCAGGACAC
5510839 CTTTT-AGTCCTCAAAGAGCAGGACAC
1 CTTTTAAGTCCTCAAAGAGCAGGACAC
5510865 CTTTT
1 CTTTT
5510870 TTCCCTTTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
25 3 0.07
26 11 0.25
27 11 0.25
28 6 0.14
29 10 0.23
30 3 0.07
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCTCAAAGAGCAGGACAC
Found at i:5510992 original size:61 final size:61
Alignment explanation
Indices: 5510754--5511172 Score: 489
Period size: 61 Copynumber: 6.9 Consensus size: 61
5510744 GAGCAAGATG
* *
5510754 CCTTTCAAAGCCCACACAAGTTGCTGGCACTTTTC-AGTCCTCAAAGAGCAGGACG------
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
** * *
5510809 CCTTTTAAATTCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGACACCTTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCC--TTTT
*
5510872 CCCTTTTAAAGGCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 -CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
5510935 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCTTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
5510996 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTTAAAGAGCAGGATG-C-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* ** * * *
5511055 CTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGGCGTCTTTT
1 C-CTTT-TAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
** * *
5511118 CTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTCCTAGTCCTCAAAGAGTAGGA
1 C-C-TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGA
5511173 TGCACTTTAT
Statistics
Matches: 321, Mismatches: 27, Indels: 24
0.86 0.07 0.06
Matches are distributed among these distances:
55 48 0.15
59 4 0.01
60 5 0.02
61 126 0.39
62 29 0.09
63 53 0.17
64 34 0.11
65 22 0.07
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:5511292 original size:43 final size:43
Alignment explanation
Indices: 5511156--5511452 Score: 276
Period size: 43 Copynumber: 6.7 Consensus size: 43
5511146 GCACCTCCTA
* * * * *
5511156 GTCCTCAAAGAGTAGGATGCACTTTATTTTCCTCTTCCCCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTTCT-TTTCTCCTTT
*
5511200 GTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTC-CCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTT--TTCTTTTCTCC-TTT
* *
5511245 GTCCTCAAAGAGCAGGACACACTTTATTTTTCTTTTCTCCTCT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTTCTTTTCTCCTTT
* * *
5511288 GTCCTCAAAAAGCAGGACGCACTTTATTTTCCTTCTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTTCTTTTCTCCTTT
* * * *
5511331 GTCCTCAAAGAGCAGGACACA-TTCCATTCCCTTCTTTTCTCTTTTT
1 GTCCTCAAAGAGCAGGACGCACTT-TATT--TTTCTTTTCTC-CTTT
* * *
5511377 GTCCTCAAAGAGCAGGACACACTTCA-TTTTCTTATTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTTCTT-TTCT-CCTT-T
* * *
5511422 AGTTCTCAAAGAGCATGATGCACTTTATTTT
1 -GTCCTCAAAGAGCAGGACGCACTTTATTTT
5511453 GTCCGGGCCA
Statistics
Matches: 211, Mismatches: 28, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.01
43 75 0.36
44 35 0.17
45 44 0.21
46 50 0.24
47 5 0.02
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.38
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTTCTTTTCTCCTTT
Found at i:5511319 original size:89 final size:89
Alignment explanation
Indices: 5511156--5511452 Score: 318
Period size: 89 Copynumber: 3.3 Consensus size: 89
5511146 GCACCTCCTA
* ** * * *
5511156 GTCCTCAAAGAGTAGGATGCACTTTATTTTCCTCTTCCCCCTTTGTCCTCAAAGAGCAGGACGCA
1 GTCCTCAAAGAGCAGGACACACTTTATTTTTCT-TTTCTCCTTTGTCCTCAAAGAGCAGGACGCA
5511221 CTTCA-TTTCCTTCTTTTCCCTTTT
65 CTTCATTTTCCTTCTTTTCCCTTTT
* *
5511245 GTCCTCAAAGAGCAGGACACACTTTATTTTTCTTTTCTCCTCTGTCCTCAAAAAGCAGGACGCAC
1 GTCCTCAAAGAGCAGGACACACTTTATTTTTCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCAC
* *
5511310 TTTATTTTCCTTC-TCT-CC-TTT
66 TTCATTTTCCTTCTTTTCCCTTTT
* * *
5511331 GTCCTCAAAGAGCAGGACACA-TTCCATTCCCTTCTTTTCTCTTTTTGTCCTCAAAGAGCAGGAC
1 GTCCTCAAAGAGCAGGACACACTT-TATT--TTTCTTTTCTC-CTTTGTCCTCAAAGAGCAGGAC
* * *
5511395 ACACTTCATTTT-CTTATTTTCCCTTCTA
62 GCACTTCATTTTCCTTCTTTTCCCTT-TT
* * **
5511423 GTTCTCAAAGAGCATGATGCACTTTATTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTT
5511453 GTCCGGGCCA
Statistics
Matches: 172, Mismatches: 26, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
85 2 0.01
86 27 0.16
87 2 0.01
88 46 0.27
89 68 0.40
90 3 0.02
91 1 0.01
92 21 0.12
93 2 0.01
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.38
Consensus pattern (89 bp):
GTCCTCAAAGAGCAGGACACACTTTATTTTTCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCAC
TTCATTTTCCTTCTTTTCCCTTTT
Found at i:5511751 original size:20 final size:20
Alignment explanation
Indices: 5511726--5511800 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
5511716 TTTTCACAAT
*
5511726 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGCTCA
*
5511746 TTGTATCAATACATTGCTCA
1 TTGTATCGATACATTGCTCA
5511766 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGCTCA
5511786 TTGTATCGATACATT
1 TTGTATCGATACATT
5511801 TTACAATGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGCTCA
Found at i:5511815 original size:40 final size:40
Alignment explanation
Indices: 5511727--5511820 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
5511717 TTTCACAATT
* *
5511727 TGTATCGATACATTGTTCATTGTATCAATACATTGCTCAT
1 TGTATCGATACATTGCTCATTGTATCAATACATTGCTCAA
* *
5511767 TGTATCGATACATTGCTCATTGTATCGATACATT-TTACAA
1 TGTATCGATACATTGCTCATTGTATCAATACATTGCT-CAA
*
5511807 TGTTTCGATACATT
1 TGTATCGATACATT
5511821 CAGGCATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (40 bp):
TGTATCGATACATTGCTCATTGTATCAATACATTGCTCAA
Found at i:5514164 original size:51 final size:51
Alignment explanation
Indices: 5514103--5514220 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
5514093 GTTATTTTTG
* * * *
5514103 AGGGGATACTCTAACCCCGGTTTTATTTCTAAAATACC-AATTTTCCACAAT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTT-CACAAT
* *
5514154 CGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAAATTTTCACAAT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTTCACAAT
5514205 AGGGGATACTCCAACC
1 AGGGGATACTCCAACC
5514221 TCGTTATTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 52 0.90
52 6 0.10
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (51 bp):
AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTTCACAAT
Found at i:5514387 original size:78 final size:78
Alignment explanation
Indices: 5514155--5514453 Score: 334
Period size: 79 Copynumber: 3.8 Consensus size: 78
5514145 TTCCACAATC
* * *
5514155 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAAATTTTCACAAT-AGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTT-CAAAACATCAATTTTTCACAATCA-GGGATACTCCAA
* *
5514219 CCTCGTTATTTCCAA
64 CCTCGTTATTTTCGA
* * ** * *
5514234 GGGGATACTTCAATCCC-AGCCTTATTTCTAAATCATCAATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGA-TTTTATTTC-AAAACATCAATTTTTCACAATCAGGGATACTCCAA
*
5514298 CCCCGTTATTTTCGA
64 CCTCGTTATTTTCGA
* * * *
5514313 GGGGATACTCCAACCCCGATTTCATTTTCAAAATATCGATTTTT-ATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTA-TTTCAAAACATCAATTTTTCACAATCAGGGATACTCCAAC
*
5514377 CTTGTTATTTTCGA
65 CTCGTTATTTTCGA
* * * *
5514391 GGGGATACTCCAACCCCGATTTTATTTCTGAAACATCGATTTTTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTC-AAAACATCAATTTTTCACAATCAGGGATACTCCA
5514454 GCCCCGTTGT
Statistics
Matches: 185, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
77 4 0.02
78 68 0.37
79 108 0.58
80 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCAAAACATCAATTTTTCACAATCAGGGATACTCCAACC
TCGTTATTTTCGA
Found at i:5514442 original size:157 final size:158
Alignment explanation
Indices: 5514155--5514461 Score: 397
Period size: 157 Copynumber: 1.9 Consensus size: 158
5514145 TTCCACAATC
* *
5514155 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAAATTTTCACAATAGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAAATTTTCACAATAGGGGATACTCCAAC
* *
5514220 CTCGTTATTTCCAAGGGGATACTTCAATCCCAGCCTTATTTCTAAATCATCAATTTTTCACAATC
66 CTCGTTATTTCCAAGGGGATACTCCAACCCCAGCCTTATTTCTAAATCATCAATTTTTCACAATC
5514285 GGGGATACTCCAACCCCGTTATTTTCGA
131 GGGGATACTCCAACCCCGTTATTTTCGA
* * * * * *
5514313 GGGGATACTCCAACCCCGATTTCATTTTCAAAATATC-GATTTTTATAATCA-GGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAAATTTTCACAAT-AGGGGATACTCCAA
* * * ** * *
5514376 CCTTGTTATTTTCGAGGGGATACTCCAACCCC-GATTTTATTTCTGAAA-CATCGATTTTTCATA
65 CCTCGTTATTTCCAAGGGGATACTCCAACCCCAG-CCTTATTTCT-AAATCATCAATTTTTCACA
*
5514439 ATCGGGGATACTCCAGCCCCGTT
128 ATCGGGGATACTCCAACCCCGTT
5514462 GTTATGTCCA
Statistics
Matches: 128, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
156 1 0.01
157 91 0.71
158 36 0.28
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (158 bp):
GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAAATTTTCACAATAGGGGATACTCCAAC
CTCGTTATTTCCAAGGGGATACTCCAACCCCAGCCTTATTTCTAAATCATCAATTTTTCACAATC
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:5515929 original size:32 final size:33
Alignment explanation
Indices: 5515891--5515968 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
5515881 TTCTAAAGCT
5515891 GTTAACTTTGATCACAGAT-TTAAACACATTTG
1 GTTAACTTTGATCACAGATATTAAACACATTTG
* ** * *
5515923 GTTAAC-TTAATCTTAGATATTATACACTTTTG
1 GTTAACTTTGATCACAGATATTAAACACATTTG
5515955 GTTAACTTTGATCA
1 GTTAACTTTGATCA
5515969 AATTTCTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 9 0.24
32 23 0.62
33 5 0.14
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (33 bp):
GTTAACTTTGATCACAGATATTAAACACATTTG
Found at i:5517851 original size:13 final size:13
Alignment explanation
Indices: 5517833--5517860 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5517823 CATTATTCAA
5517833 TGTATCGATACAT
1 TGTATCGATACAT
5517846 TGTATCGATACAT
1 TGTATCGATACAT
5517859 TG
1 TG
5517861 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5517855 original size:33 final size:33
Alignment explanation
Indices: 5517813--5517878 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5517803 GCCAAGGAAA
5517813 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
5517846 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
5517879 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:5523873 original size:16 final size:16
Alignment explanation
Indices: 5523822--5523908 Score: 75
Period size: 16 Copynumber: 5.3 Consensus size: 16
5523812 GGTCATTTTA
* *
5523822 GGTTCAGATTATTTCG
1 GGTTCGGATCATTTCG
* * *
5523838 GATTCGGATAATTTCA
1 GGTTCGGATCATTTCG
5523854 GGTTCGGATCATTTCG
1 GGTTCGGATCATTTCG
* **
5523870 GGTTCTGGGTCATTTTAA
1 GGTTC-GGATCA-TTTCG
*
5523888 GATTCGGATCATTTCG
1 GGTTCGGATCATTTCG
5523904 GGTTC
1 GGTTC
5523909 TAGGTCATTT
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
16 37 0.69
17 10 0.19
18 7 0.13
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.40
Consensus pattern (16 bp):
GGTTCGGATCATTTCG
Found at i:5523896 original size:34 final size:34
Alignment explanation
Indices: 5523856--5523932 Score: 145
Period size: 34 Copynumber: 2.3 Consensus size: 34
5523846 TAATTTCAGG
*
5523856 TTCGGATCATTTCGGGTTCTGGGTCATTTTAAGA
1 TTCGGATCATTTCGGGTTCTAGGTCATTTTAAGA
5523890 TTCGGATCATTTCGGGTTCTAGGTCATTTTAAGA
1 TTCGGATCATTTCGGGTTCTAGGTCATTTTAAGA
5523924 TTCGGATCA
1 TTCGGATCA
5523933 ATCGGTTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (34 bp):
TTCGGATCATTTCGGGTTCTAGGTCATTTTAAGA
Found at i:5524264 original size:14 final size:14
Alignment explanation
Indices: 5524245--5524291 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5524235 ATGTCATGTC
5524245 TTATTTTAATTACT
1 TTATTTTAATTACT
*
5524259 TTATTTGTCA-TA-T
1 TTATTT-TAATTACT
5524272 CTTATTTTAATTACT
1 -TTATTTTAATTACT
5524287 TTATT
1 TTATT
5524292 CATGTAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTTTAATTACT
Found at i:5524268 original size:28 final size:28
Alignment explanation
Indices: 5524236--5524291 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5524226 AATGTATTCA
*
5524236 TGTCATGTCTTATTTTAATTACTTTATT
1 TGTCATATCTTATTTTAATTACTTTATT
5524264 TGTCATATCTTATTTTAATTACTTTATT
1 TGTCATATCTTATTTTAATTACTTTATT
5524292 CATGTAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (28 bp):
TGTCATATCTTATTTTAATTACTTTATT
Found at i:5535824 original size:28 final size:28
Alignment explanation
Indices: 5535768--5535843 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
5535758 GGAATAAAGC
* *** *
5535768 CGGGGTCGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
5535796 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
5535824 CGAGGTTGGAGT-TCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
5535844 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 7 0.17
28 34 0.83
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:5535916 original size:52 final size:52
Alignment explanation
Indices: 5535849--5536160 Score: 174
Period size: 52 Copynumber: 5.9 Consensus size: 52
5535839 TCGATTGTGA
*
5535849 AAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
1 AAAATTGGT-GTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
* * * **
5535902 AAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATT-GTGG
1 AAAATTGGTGTTTTGGAAATAAAATC-GGAGTTGGAGTATCCCCGATTAAAGG
* * ** * * *
5535953 AAAAATTAGTGTTTTAGCGATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGG
1 -AAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTAT-CCC-CG--ATTAAAGG
** * *** * * * *
5536010 --GGTTGGAGTATCCCCGATGAT-TAA-CGGGGTTGGAGTATCCCCGATTGTGAA-G
1 AAAATTGGTGT-T-TTGGA-AATAAAATCGGAGTTGGAGTATCCCCGA-T-TAAAGG
* * *
5536062 -AAATTGATGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATA-G
1 AAAATTG--GTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
* * *
5536114 AAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
1 AAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
5536161 GTGGAGAATT
Statistics
Matches: 194, Mismatches: 46, Indels: 40
0.69 0.16 0.14
Matches are distributed among these distances:
51 42 0.22
52 66 0.34
53 31 0.16
54 29 0.15
55 16 0.08
56 5 0.03
57 5 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
AAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
Found at i:5536015 original size:28 final size:28
Alignment explanation
Indices: 5535970--5536051 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
5535960 AGTGTTTTAG
* *
5535970 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
5535997 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
5536024 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
5536052 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:5538543 original size:13 final size:13
Alignment explanation
Indices: 5538525--5538550 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5538515 ACAAAGATCC
5538525 ATGTATCGATACA
1 ATGTATCGATACA
5538538 ATGTATCGATACA
1 ATGTATCGATACA
5538551 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5538562 original size:33 final size:33
Alignment explanation
Indices: 5538504--5538570 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
5538494 AAAATTTCCA
***
5538504 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
* *
5538537 AATGTATCGATACACAGAAAAATGTATTGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
5538570 A
1 A
5538571 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:5539024 original size:38 final size:38
Alignment explanation
Indices: 5538975--5539060 Score: 145
Period size: 38 Copynumber: 2.3 Consensus size: 38
5538965 AAGGGGGAGA
*
5538975 AGATAATCGTTTAAAGGGGAGAATATTTTTTTAAGAGG
1 AGATAATCGTTTAAAGGGGAAAATATTTTTTTAAGAGG
* *
5539013 AGATAATCGTTTAAGGGGGAAAATATTTTTTTAAGGGG
1 AGATAATCGTTTAAAGGGGAAAATATTTTTTTAAGAGG
5539051 AGATAATCGT
1 AGATAATCGT
5539061 ATACGAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (38 bp):
AGATAATCGTTTAAAGGGGAAAATATTTTTTTAAGAGG
Found at i:5539637 original size:32 final size:33
Alignment explanation
Indices: 5539576--5539638 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
5539566 CACCCAGATG
* *
5539576 TATCGATACATGCTGCTTTGTATCGATACATTA
1 TATCGATACATGCTGCATTGTATCAATACATTA
*
5539609 TATCGATACATG-TTCATTGTATCAATACAT
1 TATCGATACATGCTGCATTGTATCAATACAT
5539639 GGCCAAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (33 bp):
TATCGATACATGCTGCATTGTATCAATACATTA
Found at i:5547048 original size:39 final size:39
Alignment explanation
Indices: 5547005--5547083 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
5546995 TGCATCAGAA
*
5547005 AGGTTTGCA-TTTCTGAAGTATGATCCCCTACACTCTTTG
1 AGGTTTACACTTT-TGAAGTATGATCCCCTACACTCTTTG
* * *
5547044 AGGTTTACACTTTTGGATTATGATCCCTTACACTCTTTG
1 AGGTTTACACTTTTGAAGTATGATCCCCTACACTCTTTG
5547083 A
1 A
5547084 AATTGTTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.91
40 3 0.09
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (39 bp):
AGGTTTACACTTTTGAAGTATGATCCCCTACACTCTTTG
Found at i:5548430 original size:16 final size:17
Alignment explanation
Indices: 5548409--5548442 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5548399 TTGAAGATAT
5548409 AAATATAAAAT-AATAC
1 AAATATAAAATGAATAC
*
5548425 AAATATAATATGAATAC
1 AAATATAAAATGAATAC
5548442 A
1 A
5548443 CAAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATATAAAATGAATAC
Found at i:5548526 original size:6 final size:6
Alignment explanation
Indices: 5548502--5548548 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
5548492 TATAAAAATT
* *
5548502 TATTTA -ATTTA GA-TTA TATTTA TATTCA TCATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA T-ATTTA TATTTA TATTTA
5548549 GATATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
5 9 0.26
6 21 0.60
7 5 0.14
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (6 bp):
TATTTA
Found at i:5549089 original size:16 final size:17
Alignment explanation
Indices: 5549053--5549090 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
5549043 TGATACAAAA
*
5549053 AATAACTAAAACATAAT
1 AATAACTAAAAAATAAT
5549070 -ATAA-TAAAAAATAAT
1 AATAACTAAAAAATAAT
5549085 AATAAC
1 AATAAC
5549091 ATGAGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAACTAAAAAATAAT
Found at i:5549099 original size:26 final size:26
Alignment explanation
Indices: 5549049--5549099 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5549039 TAAATGATAC
*
5549049 AAAAAATAACTAAAACATAATATAAT
1 AAAAAATAACTAAAACATAAGATAAT
*
5549075 AAAAAATAA-TAATAACATGAGATAA
1 AAAAAATAACTAA-AACATAAGATAA
5549100 ATATATGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (26 bp):
AAAAAATAACTAAAACATAAGATAAT
Found at i:5549769 original size:18 final size:18
Alignment explanation
Indices: 5549737--5549772 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5549727 AAAATGCTAT
**
5549737 TAAATTAAATTATATAGC
1 TAAATTAAACCATATAGC
5549755 TAAATTAAACCATATAGC
1 TAAATTAAACCATATAGC
5549773 GACATTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
TAAATTAAACCATATAGC
Found at i:5549812 original size:41 final size:41
Alignment explanation
Indices: 5549755--5549862 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 41
5549745 ATTATATAGC
* ** *
5549755 TAAATTAAACCATATAGCGACA-TTTCAAGATAAAATGCCGT
1 TAAATTAAACCATATAGCAACATTTTCAA-ATAAAACACCAT
* *
5549796 TAAATTAAACCATATAGCAATATTTTCAAATAAAACATCAT
1 TAAATTAAACCATATAGCAACATTTTCAAATAAAACACCAT
* *
5549837 TAAATTAAATCATATAGTAACATTTT
1 TAAATTAAACCATATAGCAACATTTT
5549863 ATCTGTAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 51 0.89
42 6 0.11
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.32
Consensus pattern (41 bp):
TAAATTAAACCATATAGCAACATTTTCAAATAAAACACCAT
Found at i:5553697 original size:30 final size:32
Alignment explanation
Indices: 5553674--5553741 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
5553664 TAAAAATATT
5553674 TAAATATA-TCAAAATTTATATAAAATAAATTA
1 TAAATATACT-AAAATTTATATAAAATAAATTA
* *
5553706 TTAGTATACTAAAATTTATATAAATATAATATTA
1 TAAATATACTAAAATTTATATAAA-ATAA-ATTA
5553740 TA
1 TA
5553742 CTAAATTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 20 0.67
33 5 0.17
34 5 0.17
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (32 bp):
TAAATATACTAAAATTTATATAAAATAAATTA
Found at i:5556833 original size:19 final size:20
Alignment explanation
Indices: 5556789--5556839 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5556779 TACGTAAAAG
* *
5556789 AAATATATATATATATTATA
1 AAATAAATATATATAATATA
5556809 AAATAAATATATA-AATATA
1 AAATAAATATATATAATATA
*
5556828 ACATAAATATAT
1 AAATAAATATAT
5556840 TATCAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAAATATATATAATATA
Found at i:5556833 original size:24 final size:24
Alignment explanation
Indices: 5556783--5556834 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5556773 CGATTCTACG
* **
5556783 TAAAAGAAATATATATATATATTA
1 TAAAAGAAATATATAAATATAACA
*
5556807 TAAAATAAATATATAAATATAACA
1 TAAAAGAAATATATAAATATAACA
5556831 TAAA
1 TAAA
5556835 TATATTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAGAAATATATAAATATAACA
Found at i:5558019 original size:19 final size:20
Alignment explanation
Indices: 5557997--5558043 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5557987 ATATTAAAAT
5557997 TATTAAAAAT-ATATTTTTA
1 TATTAAAAATAATATTTTTA
*
5558016 TATTAATAATAATATTTTTA
1 TATTAAAAATAATATTTTTA
*
5558036 TAATAAAA
1 TATTAAAA
5558044 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAAAAATAATATTTTTA
Found at i:5558020 original size:22 final size:23
Alignment explanation
Indices: 5557995--5558076 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 23
5557985 ATATATTAAA
5557995 ATTATTAAA-AATATATTTTTAT
1 ATTATTAAATAATATATTTTTAT
*
5558017 ATTAAT-AATAATAT-TTTTATAAT
1 ATTATTAAATAATATATTTT-T-AT
** *
5558040 AAAATTTAAATAAAATATTTTTAT
1 ATTA-TTAAATAATATATTTTTAT
5558064 -TTATTAAATAATA
1 ATTATTAAATAATA
5558077 ATTCGAGCTG
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
21 6 0.13
22 20 0.43
23 5 0.11
24 3 0.07
25 8 0.17
26 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATTAAATAATATATTTTTAT
Found at i:5558040 original size:14 final size:14
Alignment explanation
Indices: 5558021--5558063 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5558011 TTTTATATTA
5558021 ATAATAATATTTTT
1 ATAATAATATTTTT
* **
5558035 ATAATAAAATTTAA
1 ATAATAATATTTTT
5558049 ATAA-AATATTTTT
1 ATAATAATATTTTT
5558062 AT
1 AT
5558064 TTATTAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAATAATATTTTT
Found at i:5559854 original size:13 final size:15
Alignment explanation
Indices: 5559836--5559867 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5559826 ATAATAAATT
5559836 ATAAATTA-TA-AAA
1 ATAAATTAGTATAAA
5559849 ATAAATTAGTATAAA
1 ATAAATTAGTATAAA
5559864 ATAA
1 ATAA
5559868 TAATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
ATAAATTAGTATAAA
Found at i:5563672 original size:79 final size:77
Alignment explanation
Indices: 5563531--5563736 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 77
5563521 GAGATAATAA
* * * ** *
5563531 CGGGGTTGGAGTATCCCCTTGAAAATAATGGGGTTGGAGTATCCCCGGTTGTGAAAAATTGATGA
1 CGGGATTGGAGTAT-CCCTCGAAAATAACGGGGTTGGAGTATCCCCGACTATGAAAAATTGAT-A
* *
5563596 -TTAGGAAATAAAAT
64 TTTA-AAAATAAAAC
*
5563610 TGGGATTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCGACTAT-AAAAATTTGATA
1 CGGGATTGGAGTATC-CCTCGAAAATAACGGGGTTGGAGTATCCCCGACTATGAAAAA-TTGATA
*
5563674 TTTTAAAAATAAAGC
64 -TTTAAAAATAAAAC
* * *
5563689 CGGGGTTGGAGTATCCCTTCGGAAATAACGAGGTTGGAGTATCCCCGA
1 CGGGATTGGAGTATCCC-TCGAAAATAACGGGGTTGGAGTATCCCCGA
5563737 TGATGAGTGT
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
78 9 0.08
79 96 0.89
80 3 0.03
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (77 bp):
CGGGATTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCGACTATGAAAAATTGATATT
TAAAAATAAAAC
Found at i:5566102 original size:24 final size:22
Alignment explanation
Indices: 5566046--5566094 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
5566036 TGGACATGTT
5566046 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
5566068 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
5566090 AAAAA
1 AAAAA
5566095 AATGCATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:5567057 original size:20 final size:20
Alignment explanation
Indices: 5567010--5567084 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
5567000 AAAAAGACAT
*
5567010 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
5567029 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
5567050 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
5567070 AATGTATCGATACAT
1 AATGTATCGATACAT
5567085 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:5567078 original size:40 final size:39
Alignment explanation
Indices: 5567007--5567084 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
5566997 GGTAAAAAGA
* *
5567007 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
5567046 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
5567085 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:5567567 original size:32 final size:32
Alignment explanation
Indices: 5567515--5567854 Score: 444
Period size: 32 Copynumber: 10.9 Consensus size: 32
5567505 ATGGTGATTC
* * * **
5567515 GAAAAGGGTCGCCACTGACTTGCATGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* *
5567547 TAAATGGGTTGCCACCGACTTGTGTGGGTTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* ** *
5567579 GAAAAGGGTCACCACTGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* * * *
5567611 GAAATGAGTTGGCACTGACTTATGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* *
5567643 GGAATGGGTTGCCACTGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
5567675 GAAATGGGTTGCCACCGACTTGTGTGGGC---
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
5567704 ---A--GGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
5567731 GGAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
5567763 GGAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
5567795 GAAATGAGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
5567827 GAAATGGGTTGCCACCGACTTGTGTGGG
1 GAAATGGGTTGCCACCGACTTGTGTGGG
5567855 ACTTGTGTGG
Statistics
Matches: 272, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
24 23 0.08
26 1 0.00
30 1 0.00
32 247 0.91
ACGTcount: A:0.17, C:0.18, G:0.34, T:0.31
Consensus pattern (32 bp):
GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
Found at i:5567616 original size:64 final size:64
Alignment explanation
Indices: 5567515--5568267 Score: 1047
Period size: 64 Copynumber: 11.7 Consensus size: 64
5567505 ATGGTGATTC
* * * ** * *
5567515 GAAAAGGGTCGCCACTGACTTGCATGGGCTTTTAAATGGGTTGCCACCGACTTGTGTGGGTTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* ** * * * * *
5567579 GAAAAGGGTCACCACTGACTTGTGTGGGCTTTGAAATGAGTTGGCACTGACTTATGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* *
5567643 GGAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC---
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
5567704 ---A--GGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* *
5567763 GGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
5567827 GAAATGGGTTGCCACCGACTTGTGTGGGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 GAAATGGGTTGCCA-C--C--------GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
5567892 TGTGGGCTTT
55 TGTGGGCTTT
* * ** * *
5567902 GGAATAGGTTGCCACCGACTTGTGTTTGCTTTGGAATGGGTTGCCACAGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
5567966 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
5568030 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
5568094 GGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* * * * *
5568158 GGAATGGGTTGCCATCGACTTGTGTGGGCTTTGGAATGGGTTGCCATCGACTTATGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
5568222 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGG-TGCCAC
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCAC
5568268 AGAGTTGTAG
Statistics
Matches: 624, Mismatches: 46, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
56 53 0.08
58 1 0.00
62 1 0.00
63 5 0.01
64 501 0.80
65 1 0.00
67 1 0.00
72 1 0.00
74 1 0.00
75 59 0.09
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (64 bp):
GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
Found at i:5567695 original size:96 final size:96
Alignment explanation
Indices: 5567525--5568267 Score: 1029
Period size: 96 Copynumber: 7.7 Consensus size: 96
5567515 GAAAAGGGTC
* ** * * * **
5567525 GCCACTGACTTGCATGGGCTTTTAAATGGGTTGCCACCGACTTGTGTGGGTTTTGAAAAGGGTCA
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
*
5567590 CCACTGACTTGTGTGGGCTTTGAAATGAGTT
66 CCACCGACTTGTGTGGGCTTTGAAATGAGTT
* * * * *
5567621 GGCACTGACTTATGTGGGCTTTGGAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTG
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
5567686 CCACCGACTTGTGTGGGC------A-G-GTT
66 CCACCGACTTGTGTGGGCTTTGAAATGAGTT
* *
5567709 GCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTG
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
5567774 CCACCGACTTGTGTGGGCTTTGAAATGAGTT
66 CCACCGACTTGTGTGGGCTTTGAAATGAGTT
5567805 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGACTTGTGTGGGCTTT
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCA-C--C--------GACTTGTGTGGGCTTT
*
5567870 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAAT-AGGTT
55 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGA-GTT
** * *
5567912 GCCACCGACTTGTGTTTGCTTTGGAATGGGTTGCCACAGACTTGTGTGGGCTTTGAAATGGGTTG
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
*
5567977 CCACCGACTTGTGTGGGCTTTGAAATGGGTT
66 CCACCGACTTGTGTGGGCTTTGAAATGAGTT
*
5568008 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTG
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
* *
5568073 CCACCGACTTGTGTGGGCTTTGGAATGGGTT
66 CCACCGACTTGTGTGGGCTTTGAAATGAGTT
*
5568104 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTG
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
* * *
5568169 CCATCGACTTGTGTGGGCTTTGGAATGGGTT
66 CCACCGACTTGTGTGGGCTTTGAAATGAGTT
* *
5568200 GCCATCGACTTATGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGG-TG
1 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
5568264 CCAC
66 CCAC
5568268 AGAGTTGTAG
Statistics
Matches: 589, Mismatches: 37, Indels: 43
0.88 0.06 0.06
Matches are distributed among these distances:
88 81 0.14
89 1 0.00
90 1 0.00
94 1 0.00
95 6 0.01
96 408 0.69
97 1 0.00
99 1 0.00
106 2 0.00
107 87 0.15
ACGTcount: A:0.15, C:0.18, G:0.35, T:0.32
Consensus pattern (96 bp):
GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
CCACCGACTTGTGTGGGCTTTGAAATGAGTT
Found at i:5567713 original size:24 final size:24
Alignment explanation
Indices: 5567681--5567727 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5567671 CTTTGAAATG
5567681 GGTTGCCACCGACTTGTGTGGGCA
1 GGTTGCCACCGACTTGTGTGGGCA
5567705 GGTTGCCACCGACTTGTGTGGGC
1 GGTTGCCACCGACTTGTGTGGGC
5567728 TTTGGAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.11, C:0.26, G:0.38, T:0.26
Consensus pattern (24 bp):
GGTTGCCACCGACTTGTGTGGGCA
Found at i:5567872 original size:43 final size:43
Alignment explanation
Indices: 5567811--5567897 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5567801 AGTTGCCACC
5567811 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
5567854 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
5567897 G
1 G
5567898 CTTTGGAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.14, C:0.16, G:0.38, T:0.32
Consensus pattern (43 bp):
GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
Found at i:5567895 original size:32 final size:32
Alignment explanation
Indices: 5567854--5568267 Score: 704
Period size: 32 Copynumber: 13.0 Consensus size: 32
5567844 ACTTGTGTGG
5567854 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
* *
5567886 GACTTGTGTGGGCTTTGGAATAGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
** * *
5567918 GACTTGTGTTTGCTTTGGAATGGGTTGCCACA
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
5567950 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
5567982 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
5568014 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
*
5568046 GACTTGTGTGGGCTTTGGAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
*
5568078 GACTTGTGTGGGCTTTGGAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
5568110 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
* *
5568142 GACTTGTGTGGGCTTTGGAATGGGTTGCCATC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
* *
5568174 GACTTGTGTGGGCTTTGGAATGGGTTGCCATC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
*
5568206 GACTTATGTGGGCTTTGAAATGGGTTGCCACC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
5568238 GACTTGTGTGGGCTTTGAAATGGG-TGCCAC
1 GACTTGTGTGGGCTTTGAAATGGGTTGCCAC
5568268 AGAGTTGTAG
Statistics
Matches: 364, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
31 6 0.02
32 358 0.98
ACGTcount: A:0.15, C:0.18, G:0.35, T:0.32
Consensus pattern (32 bp):
GACTTGTGTGGGCTTTGAAATGGGTTGCCACC
Found at i:5568300 original size:27 final size:27
Alignment explanation
Indices: 5568259--5569033 Score: 1091
Period size: 27 Copynumber: 28.0 Consensus size: 27
5568249 GCTTTGAAAT
* * *
5568259 GGGTGCCACAGAGTTGTAGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5568286 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5568313 GGGTGCCACGGATTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5568340 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5568367 AGGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
5568395 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
5568422 GAGATGCCATGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
5568450 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5568477 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
5568505 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5568532 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
5568560 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5568587 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5568614 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5568642 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5568669 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5568696 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
5568723 GAATGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5568750 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5568777 GGGATGCCACAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5568805 GGGTGCCACGGAGTTGTGGAGTTGTGGACTTAAAA
1 GGGTGCCAC--------GGAGTTGTGGACTTAAAA
*
5568840 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
5568868 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5568896 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5568923 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5568950 GGATGCCACGGAGTTATGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
5568978 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
5569005 AGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
5569033 G
1 G
5569034 AAAATGCCAC
Statistics
Matches: 675, Mismatches: 55, Indels: 35
0.88 0.07 0.05
Matches are distributed among these distances:
27 426 0.63
28 224 0.33
35 18 0.03
36 7 0.01
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:5568399 original size:55 final size:54
Alignment explanation
Indices: 5568259--5569033 Score: 1091
Period size: 55 Copynumber: 14.0 Consensus size: 54
5568249 GCTTTGAAAT
* * * * *
5568259 GGGTGCCACAGAGTTGTAGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
*
5568313 GGGTGCCACGGATTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
5568367 AGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * * * *
5568422 GAGATGCCATGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
5568477 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * *
5568532 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * *
5568587 GGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAA
*
5568642 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
**
5568696 GGGTGCCACGGAGTTGTGGACTTAAAAGAATGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
*
5568750 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAA
* *
5568805 GGGTGCCACGGAGTTGTGGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCAC--------GGAGTTGTGGACTTAAAAG-GGTGCCACAGAGTTGTGGACTTAAAA
*
5568868 GGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * * *
5568923 GGGTGCCACGGAGTTGTGGACTAAAAAGGATGCCACGGAGTTATGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAA
* * *
5568978 GGGTGCCACAGAGTTGTGGACTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAA
5569033 G
1 G
5569034 AAAATGCCAC
Statistics
Matches: 654, Mismatches: 50, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
54 250 0.38
55 300 0.46
56 53 0.08
63 44 0.07
64 7 0.01
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (54 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
Found at i:5568419 original size:82 final size:82
Alignment explanation
Indices: 5568259--5569033 Score: 1103
Period size: 82 Copynumber: 9.4 Consensus size: 82
5568249 GCTTTGAAAT
* *
5568259 GGGTGCCACAGAGTTGTAGA-TTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
5568323 GATTTGTGGACTTAAAA
66 GAGTTGTGGACTTAAAA
*
5568340 GGGTGCCACAGAGTTGTGGACTTAAAAAGG-TGCCACAGAGTTGTGGACTTTAAAAGGGTGCCAC
1 GGGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC
*
5568404 AGAGTTGTGGACTTAAAA
65 GGAGTTGTGGACTTAAAA
* ** * * *
5568422 GAGATGCCATGGAGTTATGGACTT-AAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCAC
1 G-GGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
5568486 GGAGTTGTGGACTTTAAAA
65 GGAGTTGTGGAC-TTAAAA
*
5568505 GGGTGCCACAGAGTTGTGGACTT-AAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCAC
1 GGGTGCCACAGAGTTGTGGACTTAAAAAG-GATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
5568569 GGAGTTGTGGACTTAAAA
65 GGAGTTGTGGACTTAAAA
* *
5568587 GGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
5568652 GAGTTGTGGACTTAAAA
66 GAGTTGTGGACTTAAAA
* ** *
5568669 GGGTGCCACAGAGTTGTGGAC-TAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAATGCCACA
1 GGGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
5568733 GAGTTGTGGACTTAAAA
66 GAGTTGTGGACTTAAAA
* * * *
5568750 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC-
5568815 GAGTTGTGGAGTTGTGGACTTAAAA
65 -------GGAGTTGTGGACTTAAAA
* * *
5568840 GAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 G-GGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
5568905 GGAGTTGTGGACTTAAAA
65 GGAGTTGTGGACTTAAAA
* *
5568923 GGGTGCCACGGAGTTGTGGAC-TAAAAAGGATGCCACGGAGTTATGGACTTTAAAAGGGTGCCAC
1 GGGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC
*
5568987 AGAGTTGTGGACTTAAAA
65 GGAGTTGTGGACTTAAAA
* * *
5569005 AGATGCCACAGAGTTGTGGACTTTAAAAG
1 GGGTGCCACAGAGTTGTGGACTTAAAAAG
5569034 AAAATGCCAC
Statistics
Matches: 628, Mismatches: 47, Indels: 36
0.88 0.07 0.05
Matches are distributed among these distances:
81 135 0.21
82 301 0.48
83 114 0.18
90 18 0.03
91 60 0.10
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (82 bp):
GGGTGCCACAGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
GAGTTGTGGACTTAAAA
Found at i:5568834 original size:35 final size:36
Alignment explanation
Indices: 5568788--5568860 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 36
5568778 GGATGCCACA
*
5568788 GAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTG
1 GAGTTGTGGACTTAAAAGAGATGCCACGGAGTTGTG
5568823 GAGTTGTGGACTTAAAAGAGATGCCACGGAGTTGTG
1 GAGTTGTGGACTTAAAAGAGATGCCACGGAGTTGTG
5568859 GA
1 GA
5568861 CTTAAAAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 18 0.50
36 18 0.50
ACGTcount: A:0.26, C:0.11, G:0.38, T:0.25
Consensus pattern (36 bp):
GAGTTGTGGACTTAAAAGAGATGCCACGGAGTTGTG
Found at i:5576598 original size:24 final size:22
Alignment explanation
Indices: 5576542--5576590 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
5576532 TGGACATGTT
5576542 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
5576564 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
5576586 AAAAA
1 AAAAA
5576591 AATGCATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Done.