Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:416703 original size:21 final size:22
Alignment explanation
Indices: 416677--416717 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
416667 GTAGCAGTAC
*
416677 TGTAGC-AGGGTATCGGTTCGT
1 TGTAGCGAGGGAATCGGTTCGT
*
416698 TGTAGCGGGGGAATCGGTTC
1 TGTAGCGAGGGAATCGGTTC
416718 CCCTATGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.29
Consensus pattern (22 bp):
TGTAGCGAGGGAATCGGTTCGT
Found at i:419459 original size:22 final size:22
Alignment explanation
Indices: 419431--419479 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
419421 TTGACAGTCA
*
419431 GTCCTCTAACAGTTCCATACAT
1 GTCCTCTAACAGTTCCAAACAT
419453 GTCCTCTAACAGTTCCAAACAT
1 GTCCTCTAACAGTTCCAAACAT
419475 G-CCTC
1 GTCCTC
419480 CTTGCAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.27, C:0.35, G:0.10, T:0.29
Consensus pattern (22 bp):
GTCCTCTAACAGTTCCAAACAT
Found at i:420969 original size:30 final size:30
Alignment explanation
Indices: 420933--420989 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
420923 GAATGACCTA
* *
420933 TCCATATGTTCC-TAAGAACATAGGTAACTG
1 TCCATATGTCCCAAAAG-ACATAGGTAACTG
420963 TCCATATGTCCCAAAAGACATAGGTAA
1 TCCATATGTCCCAAAAGACATAGGTAA
420990 TGTAACACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCAAAAGACATAGGTAACTG
Found at i:422047 original size:31 final size:30
Alignment explanation
Indices: 422005--422168 Score: 152
Period size: 31 Copynumber: 5.2 Consensus size: 30
421995 CCGAATAACC
*
422005 TAGGTAAATTGTCCATATGTTCCTTAGAACA
1 TAGGT-AATTGTCCATATGTTCCCTAGAACA
* * * *
422036 TATGTATATTGTCCATGTG-TCCCAAAAGACA
1 TAGGTA-ATTGTCCATATGTTCCCTAGA-ACA
*
422067 TAGGTAATTCTGTCCATATGTTCCTTAGAACA
1 TAGGTAA-T-TGTCCATATGTTCCCTAGAACA
* *
422099 TAGGTATATTGTCCATATG-TCCCGAAAGACA
1 TAGGTA-ATTGTCCATATGTTCCCTAGA-ACA
*
422130 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
1 TAGGTAA-T-TGTCCATATGTTCCCTAGAACA
422162 TAGGTAA
1 TAGGTAA
422169 ACCCTCGAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 19
0.75 0.11 0.13
Matches are distributed among these distances:
30 13 0.12
31 44 0.41
32 39 0.36
33 11 0.10
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
TAGGTAATTGTCCATATGTTCCCTAGAACA
Found at i:422082 original size:32 final size:31
Alignment explanation
Indices: 422045--422168 Score: 126
Period size: 32 Copynumber: 3.9 Consensus size: 31
422035 ATATGTATAT
*
422045 TGTCCATGTGTCCCAAAAGACATAGGTAATTC
1 TGTCCATATGTCCC-AAAGACATAGGTAATTC
* **
422077 TGTCCATATGTTCCTTAGAACATAGGT-ATAT-
1 TGTCCATATGTCCCAAAG-ACATAGGTAAT-TC
422108 TGTCCATATGTCCCGAAAGACATAGGTAATTC
1 TGTCCATATGTCCC-AAAGACATAGGTAATTC
* **
422140 TGTCCATATGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTCCCAAAG-ACATAGGTAA
422169 ACCCTCGAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
31 28 0.37
32 48 0.63
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TGTCCATATGTCCCAAAGACATAGGTAATTC
Found at i:422095 original size:63 final size:63
Alignment explanation
Indices: 421983--422167 Score: 275
Period size: 63 Copynumber: 3.0 Consensus size: 63
421973 CCTCGGCAAC
* * * * *
421983 TGTCCATAGGTCCCGAATA-ACCTAGGTAAAT-TGTCCATATGTTCCTTAGAACATATGTATAT
1 TGTCCATATGTCCC-AAAAGACATAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAT
*
422045 TGTCCATGTGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAT
1 TGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAT
* *
422108 TGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 TGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTA
422168 AACCCTCGAA
Statistics
Matches: 112, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
61 3 0.03
62 22 0.20
63 87 0.78
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (63 bp):
TGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAT
Found at i:422364 original size:32 final size:30
Alignment explanation
Indices: 422328--422420 Score: 109
Period size: 29 Copynumber: 3.1 Consensus size: 30
422318 ATATATATAT
422328 ATATGGTTCACTTTCACATATCACATTTAATC
1 ATATGGTTCACTTTCACATATCACATTT--TC
*
422360 ATATGGTTCACTTGT-ACGTA-CACATTTTC
1 ATATGGTTCACTT-TCACATATCACATTTTC
** *
422389 ATATTATTCACTTTCACATATCACATATTC
1 ATATGGTTCACTTTCACATATCACATTTTC
422419 AT
1 AT
422421 TTTCTCCTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 17 0.32
30 10 0.19
31 7 0.13
32 17 0.32
33 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (30 bp):
ATATGGTTCACTTTCACATATCACATTTTC
Found at i:429031 original size:21 final size:21
Alignment explanation
Indices: 429005--429067 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
428995 TTTTGGTGCA
*
429005 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
429026 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
429047 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
429068 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:429075 original size:21 final size:21
Alignment explanation
Indices: 429049--429088 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
429039 CCCCCTTTGA
*
429049 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
429070 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
429089 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:431373 original size:25 final size:25
Alignment explanation
Indices: 431345--431392 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
431335 GTTTTTACAT
431345 AATAAATTGAAGTAGTGTTAAAGTA
1 AATAAATTGAAGTAGTGTTAAAGTA
431370 AATAAATTGAAGTAGTGTTAAAG
1 AATAAATTGAAGTAGTGTTAAAG
431393 AAAGGGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (25 bp):
AATAAATTGAAGTAGTGTTAAAGTA
Found at i:433125 original size:20 final size:20
Alignment explanation
Indices: 433096--433169 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
433086 GCAACCTTCG
* * *
433096 TGCATGGATGCATAGTAGGA
1 TGCATCGATGCACAGCAGGA
433116 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
433136 TGCATCGATGCACAGCATGA
1 TGCATCGATGCACAGCAGGA
433156 TGCATCGATGCACA
1 TGCATCGATGCACA
433170 ACCTTTATGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:433299 original size:21 final size:20
Alignment explanation
Indices: 433230--433328 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
433220 CGGTGTTTGA
**
433230 GTGCATGGATGCACTGCATA
1 GTGCATGGATGCACTGCAGG
*
433250 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
433272 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
433292 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
*
433314 GTACATGGATGCACT
1 GTGCATGGATGCACT
433329 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 30 0.43
22 16 0.23
23 4 0.06
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:433429 original size:29 final size:30
Alignment explanation
Indices: 433397--433459 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
433387 TAAACCTTTT
433397 AAAACAATGAATAAATTCAATT-AAGTCCA
1 AAAACAATGAATAAATTCAATTCAAGTCCA
* ***
433426 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACAATGAATAAATTCAATTCAAGTCCA
433456 AAAA
1 AAAA
433460 TCATTTTGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.27
Consensus pattern (30 bp):
AAAACAATGAATAAATTCAATTCAAGTCCA
Found at i:433455 original size:30 final size:30
Alignment explanation
Indices: 433408--433467 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
433398 AAACAATGAA
433408 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
433437 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
433468 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:433835 original size:32 final size:32
Alignment explanation
Indices: 433790--434021 Score: 347
Period size: 32 Copynumber: 7.2 Consensus size: 32
433780 GGGATGTTAC
* *
433790 AGGTAATCCTGTCCATATGTCCCGAAAGACAG
1 AGGTAATCATGTCCATATGTCCCGAAAGACAT
433822 AGGTAATCATGTCCATATGTCCCGAAAGACAT
1 AGGTAATCATGTCCATATGTCCCGAAAGACAT
* * *
433854 AGGTAATCCTGTTCATATGTCCCGAAATACAT
1 AGGTAATCATGTCCATATGTCCCGAAAGACAT
* **
433886 ATGTAATCATAACCATATGTCCCGAAAGACAT
1 AGGTAATCATGTCCATATGTCCCGAAAGACAT
* * * *
433918 AGATAATCCTGTCCATATATCCCGAAAGGCAT
1 AGGTAATCATGTCCATATGTCCCGAAAGACAT
433950 AGGTAATCATGTCCATATGTCCCGAAAGACAT
1 AGGTAATCATGTCCATATGTCCCGAAAGACAT
*
433982 AGATAATCATGTCCATATGTCCCGAAAGACAT
1 AGGTAATCATGTCCATATGTCCCGAAAGACAT
434014 AGGTAATC
1 AGGTAATC
434022 CTCGACTCTT
Statistics
Matches: 176, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 176 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (32 bp):
AGGTAATCATGTCCATATGTCCCGAAAGACAT
Found at i:436662 original size:17 final size:17
Alignment explanation
Indices: 436640--436684 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
436630 TAAAAATTAT
*
436640 ATTTTAATACTATAATA
1 ATTTTAATAATATAATA
*
436657 ATTTTAATAATTTAATA
1 ATTTTAATAATATAATA
* *
436674 AATTTAGTAAT
1 ATTTTAATAAT
436685 TATTTTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTTAATAATATAATA
Found at i:436792 original size:2 final size:2
Alignment explanation
Indices: 436785--436816 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
436775 AATATACTAA
436785 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
436817 TTGAATAGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:438965 original size:16 final size:17
Alignment explanation
Indices: 438935--438967 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
438925 TTTTTAAATT
*
438935 TTATATGTTTTATATGA
1 TTATATGTTTAATATGA
438952 TTATAT-TTTAATATGA
1 TTATATGTTTAATATGA
438968 ATAATCACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (17 bp):
TTATATGTTTAATATGA
Found at i:440231 original size:2 final size:2
Alignment explanation
Indices: 440224--440257 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
440214 GCACATCCCT
440224 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
440258 AAATAAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:444075 original size:2 final size:2
Alignment explanation
Indices: 444068--444117 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
444058 TTGCTGCCTG
444068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
444110 AT AT AT AT
1 AT AT AT AT
444118 GCTCCCACGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:454137 original size:2 final size:2
Alignment explanation
Indices: 454130--454157 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
454120 GTGTCTTATC
454130 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
454158 TCACATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:454733 original size:64 final size:63
Alignment explanation
Indices: 454624--454785 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
454614 TTCCCTTGAA
* * *
454624 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTT-TAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTCTAA-GGG
* * *** *
454688 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGTATTCGATGTTTCCATTTCTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTCTAAGGG
*
454752 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
454786 CTGAACAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 75 0.90
65 6 0.07
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTCTAAGGG
Found at i:456419 original size:29 final size:29
Alignment explanation
Indices: 456377--456486 Score: 204
Period size: 29 Copynumber: 3.8 Consensus size: 29
456367 TTTTATATGT
456377 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
456405 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
456434 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
456463 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
456487 ATATCACATA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.09
29 68 0.85
30 5 0.06
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:456932 original size:64 final size:63
Alignment explanation
Indices: 456863--457019 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
456853 TAATGAAGGT
* **
456863 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
456926 G
63 G
* * * *
456927 ATGCATCGATGCA-TGCCTTATGCATAGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
*
456990 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
457020 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 65 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
Found at i:463375 original size:29 final size:29
Alignment explanation
Indices: 463332--463470 Score: 235
Period size: 29 Copynumber: 4.8 Consensus size: 29
463322 TTTTATATGT
463332 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
463360 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
463389 TCATGCAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
463418 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
463447 TCATGTAGCTTATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
463471 ATATCACATT
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
28 7 0.07
29 92 0.88
30 5 0.05
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:463916 original size:64 final size:63
Alignment explanation
Indices: 463847--464000 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 63
463837 TAATGAAGGT
* * **
463847 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
463910 G
63 G
* *
463911 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
*
463974 AGTGCATCGATGCACTACCTATGCATC
1 A-TGCATCGATGCACTACTTATGCATC
464001 AATACACCTT
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
63 3 0.04
64 65 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
Found at i:468419 original size:64 final size:63
Alignment explanation
Indices: 468310--468471 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
468300 TTCCCTTTAA
* * *
468310 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * ** **
468374 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATTG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
*
468438 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
468472 CTGAACAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 72 0.87
65 9 0.11
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:471549 original size:2 final size:2
Alignment explanation
Indices: 471544--471603 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
471534 ATGAGAGAAT
* * * * * *
471544 GA GA GA GA GT GG GA GA GA GA GA GC GT GA GA GA GA GA GC GT GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
471586 GA GA GA GA GC GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
471604 ACTTGAAAAG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.38, C:0.05, G:0.52, T:0.05
Consensus pattern (2 bp):
GA
Found at i:471562 original size:10 final size:10
Alignment explanation
Indices: 471536--471602 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
471526 GTCATATTAT
*
471536 GAGAGAATGA
1 GAGAGAGTGA
*
471546 GAGAGAGTGG
1 GAGAGAGTGA
*
471556 GAGAGAGAGA
1 GAGAGAGTGA
* * *
471566 GCGTGAGAGA
1 GAGAGAGTGA
*
471576 GAGAGCGTGA
1 GAGAGAGTGA
* *
471586 GAGAGAGAGC
1 GAGAGAGTGA
471596 GAGAGAG
1 GAGAGAG
471603 AACTTGAAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 44 1.00
ACGTcount: A:0.39, C:0.04, G:0.51, T:0.06
Consensus pattern (10 bp):
GAGAGAGTGA
Found at i:471563 original size:14 final size:14
Alignment explanation
Indices: 471544--471603 Score: 93
Period size: 14 Copynumber: 4.3 Consensus size: 14
471534 ATGAGAGAAT
* *
471544 GAGAGAGAGTGGGA
1 GAGAGAGAGCGTGA
471558 GAGAGAGAGCGTGA
1 GAGAGAGAGCGTGA
471572 GAGAGAGAGCGTGA
1 GAGAGAGAGCGTGA
*
471586 GAGAGAGAGCGAGA
1 GAGAGAGAGCGTGA
471600 GAGA
1 GAGA
471604 ACTTGAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.38, C:0.05, G:0.52, T:0.05
Consensus pattern (14 bp):
GAGAGAGAGCGTGA
Found at i:472570 original size:38 final size:38
Alignment explanation
Indices: 472528--472602 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
472518 TGAGTTTGAG
472528 ACAGATTCATCATTTGCTTCATTAAAAAGAAATGGAGT
1 ACAGATTCATCATTTGCTTCATTAAAAAGAAATGGAGT
472566 ACAGATTCATCATTTGCTTCATTAAAAAGAAATGGAG
1 ACAGATTCATCATTTGCTTCATTAAAAAGAAATGGAG
472603 GGGCACAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (38 bp):
ACAGATTCATCATTTGCTTCATTAAAAAGAAATGGAGT
Found at i:473405 original size:186 final size:186
Alignment explanation
Indices: 473030--473408 Score: 688
Period size: 186 Copynumber: 2.0 Consensus size: 186
473020 ATTAAATTTT
*
473030 AAATATTAAATATATTATATATAACATATGGGCTTAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* *
473095 TTTAAGATTCAATAATTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
*
473160 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTGAATTAAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAAA
*
473216 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACTATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
473281 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATTT
473346 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATT-AAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAAA
473402 AAATATT
1 AAATATT
473409 TAATTTGTAT
Statistics
Matches: 186, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
186 121 0.65
187 65 0.35
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAAA
Found at i:477013 original size:27 final size:27
Alignment explanation
Indices: 476983--477042 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
476973 TAAAGAACGC
476983 ATGCCAAACCATGGTA-ATCAACAACCT
1 ATGCCAAACCATGG-AGATCAACAACCT
* *
477010 ATGCCAACCCATGGAGATCAACTACCT
1 ATGCCAAACCATGGAGATCAACAACCT
477037 ATGCCA
1 ATGCCA
477043 CCAAACCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (27 bp):
ATGCCAAACCATGGAGATCAACAACCT
Found at i:480293 original size:228 final size:227
Alignment explanation
Indices: 479867--480753 Score: 828
Period size: 228 Copynumber: 3.9 Consensus size: 227
479857 GTAGTCGAAT
* * * * * * * * * * * *
479867 ATGCAGATCTTTGTGAAGACCCTCACCGGAAAAACAATCACCCTCGAGGTGGAAAGCTCAGACAC
1 ATGCAGATCTTTGTTAA-AACCTAACAGGCAAGACAATTACTCTCGAAGTCGAGAGCTCCGACAC
* * * *
479932 CATCGATAATGTTAAGGCCAAGATTCAAGATAAAGAAGGCATCCCTCCGGACCAGCAGCGATTGA
65 CATTGACAATGTCAAGGCCAAGATTCAAGATAAAGAAGGCATCCCTCCGGACCAGCAGAGATTGA
* *
479997 TCTTCGCCGGAAAACAGCTTGAGGATGGTC-GCACAT-TGGCGGATTACAACATCCAGAAGGAAT
130 TCTTCGCCGGAAAACAGCTGGAGGATGG-CAGCAC-TCTGGCGGATTACAATATCCAGAAGGAAT
*
480060 CGACTCTCCATCTGGTCCTCCGTCTACGCGGTGGC
193 CGACTCTCCATCTGGTCCTCCGTCTACGCGGCGGC
* * *
480095 ATGCAGATCTTTGTTAAAATCCTAACGGGCAAGACAATTACTATTGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTTGTTAAAA-CCTAACAGGCAAGACAATTACTCTCGAAGTCGAGAGCTCCGACAC
* * * * * * *
480160 AATTGACAATGTCAAGGCCAAGATTCAGGATAAGGAGGGGATTCCTCCGGACCAGCAGAGGTTGA
65 CATTGACAATGTCAAGGCCAAGATTCAAGATAAAGAAGGCATCCCTCCGGACCAGCAGAGATTGA
* * * * * * * * * * *
480225 TTTTCGCCGGGAAGCAGCTGGAAGATGGAAGGACTCTCGCCGACTATAATATCCAGAAGGAGTCG
130 TCTTCGCCGGAAAACAGCTGGAGGATGGCAGCACTCTGGCGGATTACAATATCCAGAAGGAATCG
* *
480290 ACTCTCCATCTGGTCCTCCGTCTCCGCGGCGGT
195 ACTCTCCATCTGGTCCTCCGTCTACGCGGCGGC
** * * * *
480323 ATGCAGATCTTTGTTAAAACCCTAACCTGCAAGACTATCACTCTCGATGTCGAAAGCTCCGACAC
1 ATGCAGATCTTTGTTAAAA-CCTAACAGGCAAGACAATTACTCTCGAAGTCGAGAGCTCCGACAC
* * * * * * *
480388 CATAGATAATGTCAAAGCTAAGATTCAAGATAAAGAAGGCATCCCTCAGGATCAGCAGCGATTGA
65 CATTGACAATGTCAAGGCCAAGATTCAAGATAAAGAAGGCATCCCTCCGGACCAGCAGAGATTGA
* * * *
480453 TCTTCGCCGGAAAACAACTCGAGGATGGCCGCAC-CTTGGCGGATTACAATATCCAAAAGGAATC
130 TCTTCGCCGGAAAACAGCTGGAGGATGGCAGCACTC-TGGCGGATTACAATATCCAGAAGGAATC
* * * *
480517 GACTCTCCATCTGGTCCTCAGGCTTCGTGGCGGC
194 GACTCTCCATCTGGTCCTCCGTCTACGCGGCGGC
* * * * * * * * * *
480551 ATGCAGAT-TTTCGTCAAAACCTTGACAGGAAAAACAATTACCCTGGAGGTAGAGAGCTCGGATA
1 ATGCAGATCTTT-GTTAAAACC-TAACAGGCAAGACAATTACTCTCGAAGTCGAGAGCTCCGACA
* * * * * * * * * * * *
480615 CGATTGACAACGTGAAGGCTAAAATTCAGGACAAAGAAGGGATCCCACCGGGCCAACAGAGGTTG
64 CCATTGACAATGTCAAGGCCAAGATTCAAGATAAAGAAGGCATCCCTCCGGACCAGCAGAGATTG
* * * * * * * *
480680 ATCTTCGCCGGCAAGCAGCTGGAGGACGGCAGGACCCTTGCGGATTACAATATCCAGAAAGAGTC
129 ATCTTCGCCGGAAAACAGCTGGAGGATGGCAGCACTCTGGCGGATTACAATATCCAGAAGGAATC
*
480745 TACTCTCCA
194 GACTCTCCA
480754 CCTTGTGCTG
Statistics
Matches: 524, Mismatches: 128, Indels: 14
0.79 0.19 0.02
Matches are distributed among these distances:
227 8 0.02
228 515 0.98
229 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (227 bp):
ATGCAGATCTTTGTTAAAACCTAACAGGCAAGACAATTACTCTCGAAGTCGAGAGCTCCGACACC
ATTGACAATGTCAAGGCCAAGATTCAAGATAAAGAAGGCATCCCTCCGGACCAGCAGAGATTGAT
CTTCGCCGGAAAACAGCTGGAGGATGGCAGCACTCTGGCGGATTACAATATCCAGAAGGAATCGA
CTCTCCATCTGGTCCTCCGTCTACGCGGCGGC
Found at i:480734 original size:456 final size:456
Alignment explanation
Indices: 479866--480753 Score: 1168
Period size: 456 Copynumber: 1.9 Consensus size: 456
479856 CGTAGTCGAA
* * *
479866 TATGCAGATCTTTGTGAAGACCCTCACCGGAAAAACAATCACCCTCGAGGTGGAAAGCTCAGACA
1 TATGCAGATCTTTGTGAAAACCCTAACCGGAAAAACAATCACCCTCGAGGTCGAAAGCTCAGACA
* * * *
479931 CCATCGATAATGTTAAGGCCAAGATTCAAGATAAAGAAGGCATCCCTCCGGACCAGCAGCGATTG
66 CCATAGATAATGTCAAAGCCAAGATTCAAGATAAAGAAGGCATCCCTCAGGACCAGCAGCGATTG
* * * *
479996 ATCTTCGCCGGAAAACAGCTTGAGGATGGTCGCACATTGGCGGATTACAACATCCAGAAGGAATC
131 ATCTTCGCCGGAAAACAACTCGAGGATGGCCGCACATTGGCGGATTACAACATCCAAAAGGAATC
* * * * * *
480061 GACTCTCCATCTGGTCCTCCGTCTACGCGGTGGCATGCAGATCTTTGTTAAAATCCTAACGGGCA
196 GACTCTCCATCTGGTCCTCAGGCTACGCGGCGGCATGCAGATCTTTGTCAAAATCCTAACAGGAA
* * * * * * *
480126 AGACAATTACTATTGAAGTCGAGAGCTCCGACACAATTGACAATGTCAAGGCCAAGATTCAGGAT
261 AAACAATTACCATGGAAGTAGAGAGCTCCGACACAATTGACAACGTCAAGGCCAAAATTCAGGAC
* * * * * * * *
480191 AAGGAGGGGATTCCTCCGGACCAGCAGAGGTTGATTTTCGCCGGGAAGCAGCTGGAAGATGGAAG
326 AAAGAAGGGATCCCACCGGACCAACAGAGGTTGATCTTCGCCGGCAAGCAGCTGGAAGACGGAAG
* * *
480256 GACTCTCGCCGACTATAATATCCAGAAGGAGTCGACTCTCCATCTGGTCCTCCGTCTCCGCGGCG
391 GACCCTCGCCGACTACAATATCCAGAAAGAGTCGACTCTCCATCTGGTCCTCCGTCTCCGCGGCG
480321 G
456 G
* * * * * * * *
480322 TATGCAGATCTTTGTTAAAACCCTAACCTGCAAGACTATCACTCTCGATGTCGAAAGCTCCGACA
1 TATGCAGATCTTTGTGAAAACCCTAACCGGAAAAACAATCACCCTCGAGGTCGAAAGCTCAGACA
* *
480387 CCATAGATAATGTCAAAGCTAAGATTCAAGATAAAGAAGGCATCCCTCAGGATCAGCAGCGATTG
66 CCATAGATAATGTCAAAGCCAAGATTCAAGATAAAGAAGGCATCCCTCAGGACCAGCAGCGATTG
* *
480452 ATCTTCGCCGGAAAACAACTCGAGGATGGCCGCACCTTGGCGGATTACAATATCCAAAAGGAATC
131 ATCTTCGCCGGAAAACAACTCGAGGATGGCCGCACATTGGCGGATTACAACATCCAAAAGGAATC
* * *
480517 GACTCTCCATCTGGTCCTCAGGCTTCGTGGCGGCATGCAGAT-TTTCGTCAAAA-CCTTGACAGG
196 GACTCTCCATCTGGTCCTCAGGCTACGCGGCGGCATGCAGATCTTT-GTCAAAATCC-TAACAGG
* * * * * * *
480580 AAAAACAATTACCCTGGAGGTAGAGAGCTCGGATACGATTGACAACGTGAAGGCTAAAATTCAGG
259 AAAAACAATTACCATGGAAGTAGAGAGCTCCGACACAATTGACAACGTCAAGGCCAAAATTCAGG
* * *
480645 ACAAAGAAGGGATCCCACCGGGCCAACAGAGGTTGATCTTCGCCGGCAAGCAGCTGGAGGACGGC
324 ACAAAGAAGGGATCCCACCGGACCAACAGAGGTTGATCTTCGCCGGCAAGCAGCTGGAAGACGGA
* * * *
480710 AGGACCCTTGCGGATTACAATATCCAGAAAGAGTCTACTCTCCA
389 AGGACCCTCGCCGACTACAATATCCAGAAAGAGTCGACTCTCCA
480754 CCTTGTGCTG
Statistics
Matches: 366, Mismatches: 64, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
455 5 0.01
456 361 0.99
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (456 bp):
TATGCAGATCTTTGTGAAAACCCTAACCGGAAAAACAATCACCCTCGAGGTCGAAAGCTCAGACA
CCATAGATAATGTCAAAGCCAAGATTCAAGATAAAGAAGGCATCCCTCAGGACCAGCAGCGATTG
ATCTTCGCCGGAAAACAACTCGAGGATGGCCGCACATTGGCGGATTACAACATCCAAAAGGAATC
GACTCTCCATCTGGTCCTCAGGCTACGCGGCGGCATGCAGATCTTTGTCAAAATCCTAACAGGAA
AAACAATTACCATGGAAGTAGAGAGCTCCGACACAATTGACAACGTCAAGGCCAAAATTCAGGAC
AAAGAAGGGATCCCACCGGACCAACAGAGGTTGATCTTCGCCGGCAAGCAGCTGGAAGACGGAAG
GACCCTCGCCGACTACAATATCCAGAAAGAGTCGACTCTCCATCTGGTCCTCCGTCTCCGCGGCG
G
Found at i:482010 original size:23 final size:24
Alignment explanation
Indices: 481984--482029 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
481974 CTATTTATCA
*
481984 TGAAA-ACT-TAATACTATTATTTT
1 TGAAATACTATAATAAT-TTATTTT
482007 TGAAATACTATAATAATTTATTT
1 TGAAATACTATAATAATTTATTT
482030 ATTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 9 0.45
25 6 0.30
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
TGAAATACTATAATAATTTATTTT
Found at i:482518 original size:30 final size:30
Alignment explanation
Indices: 482465--482543 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
482455 CTTTTAAAAC
* *
482465 TTGCAATACAATCCCCTAACATTTAGT-TCAT
1 TTGCAATATAGTCCCC-AACATTTAGTCT-AT
*
482496 TTGCAATATAGTCCCCAACATTTAGTCTGT
1 TTGCAATATAGTCCCCAACATTTAGTCTAT
*
482526 TTGCAATATGGTCCCCAA
1 TTGCAATATAGTCCCCAA
482544 TGTAACCGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 28 0.65
31 15 0.35
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (30 bp):
TTGCAATATAGTCCCCAACATTTAGTCTAT
Found at i:486092 original size:19 final size:19
Alignment explanation
Indices: 486064--486129 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
486054 TAATAATGAG
* *
486064 TTATTGTAATTATGTATTT
1 TTATTATAATTATATATTT
486083 TTATTATAATTATATA-TT
1 TTATTATAATTATATATTT
* * *
486101 TTATTTTTATTTTTTATATTT
1 TTA-TTATA-ATTATATATTT
486122 TTATTATA
1 TTATTATA
486130 GTTTAAATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 5 0.13
19 18 0.47
20 10 0.26
21 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTATAATTATATATTT
Found at i:486893 original size:7 final size:6
Alignment explanation
Indices: 486871--486926 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
486861 TTTAAACTAT
* * *
486871 AATAAA AAT-AT AA-AAA AGTAAA AATAAA AATAAA AATAAA AA-ATAT
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATA-AA
486917 AATAAA AATA
1 AATAAA AATA
486927 TATTTTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 6 0.15
6 33 0.82
7 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:487217 original size:19 final size:19
Alignment explanation
Indices: 487193--487278 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
487183 GCGATTTTGA
*
487193 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
487212 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
487233 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
* *
487256 AAAAAGTGTTACGATAGTG
1 AAAATGTGTTGCGATAGTG
487275 AAAA
1 AAAA
487279 ATCTAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 32 0.57
20 1 0.02
21 1 0.02
22 8 0.14
23 2 0.04
24 2 0.04
25 10 0.18
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:487582 original size:6 final size:6
Alignment explanation
Indices: 487573--487597 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
487563 CCGCCCCGTC
487573 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
487598 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:487737 original size:19 final size:20
Alignment explanation
Indices: 487691--487739 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
487681 GCGATTTTCC
487691 AAAATCGCAACGCGAACTTGG
1 AAAATCGCAAC-CGAACTTGG
** *
487712 ACTATCGCAA-CGAATTTGG
1 AAAATCGCAACCGAACTTGG
487731 AAAATCGCA
1 AAAATCGCA
487740 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 15 0.65
21 8 0.35
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACCGAACTTGG
Found at i:487784 original size:20 final size:20
Alignment explanation
Indices: 487755--487828 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
487745 ATTTTGTATT
*
487755 ATCGCATTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
487775 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
*
487796 ATCGCGTTACGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
487816 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
487829 TTACATAGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 3 0.07
20 24 0.57
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:487785 original size:41 final size:41
Alignment explanation
Indices: 487733--487830 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
487723 GAATTTGGAA
* *
487733 AATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCATTACGATAGTCAG
*
487774 AATCGCGTTGCGATTTTGTATTATCGCGTTACGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCATTACGATAGTCAG
487815 AATCGCGTTGCGATTT
1 AATCGCGTTGCGATTT
487831 ACATAGGTCG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTGTATTATCGCATTACGATAGTCAG
Found at i:487803 original size:21 final size:21
Alignment explanation
Indices: 487734--487800 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
487724 AATTTGGAAA
487734 ATCGCATTGCGATTTTGTATT
1 ATCGCATTGCGATTTTGTATT
* **
487755 ATCGCATTGCGA--TAGTCAGA
1 ATCGCATTGCGATTTTGT-ATT
*
487775 ATCGCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTTTGTATT
487796 ATCGC
1 ATCGC
487801 GTTACGATAG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
21 18 0.50
22 3 0.08
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (21 bp):
ATCGCATTGCGATTTTGTATT
Found at i:487965 original size:21 final size:21
Alignment explanation
Indices: 487941--487991 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
487931 ATTTTCCAAA
487941 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
487962 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
487983 ATCGCAACG
1 ATCGCAACG
487992 AATTTGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:488049 original size:247 final size:245
Alignment explanation
Indices: 487589--488050 Score: 696
Period size: 247 Copynumber: 1.9 Consensus size: 245
487579 TCGTGGTCGT
*
487589 GGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCGGATACTATCTTTTTAGAGAAATTTCTTAA
1 GGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCGGATACTATCTTTGTAGAGAAATTTCTTAA
487654 GAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCGAACTTGGACTATCG
66 GAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCGAACTTGGACTATCG
* * * * ** *
487719 CAACGAATTTGGAAAATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTG
131 CAACGAACTTGGAAAATCGCA-TACGAATTTGGAAAATCGCATTGCGATAGTCAGAATCGCATTG
* **
487784 CGATTTTGTATTATCGCGTTACGATAGTCAGAATCGCGTTGCGATTTACATA
195 CGA-TTAGTAGAATCGCGTTACGATAGTCAGAATCGCGTTGCGATTTACATA
487836 GGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCGGATACTATCTTTGTAGAGAAATTTCTTAA
1 GGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCGGATACTATCTTTGTAGAGAAATTTCTTAA
487901 GAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCGAACTTGGACTATCG
66 GAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCGAACTTGGACTATCG
** * **
487966 CAACGTGAACTTGGACTATCGCA-ACGAATTTGGAAAATCGCATTGCGATTTTGT-ATTATCGCA
131 CAAC--GAACTTGGAAAATCGCATACGAATTTGGAAAATCGCATTGCGA--TAGTCAGAATCGCA
488029 TTGCGA-TAGTCAGAATCGCGTT
192 TTGCGATTAGT-AGAATCGCGTT
488051 GCATTGCGAT
Statistics
Matches: 194, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
246 3 0.02
247 162 0.84
248 12 0.06
249 17 0.09
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (245 bp):
GGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCGGATACTATCTTTGTAGAGAAATTTCTTAA
GAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCGAACTTGGACTATCG
CAACGAACTTGGAAAATCGCATACGAATTTGGAAAATCGCATTGCGATAGTCAGAATCGCATTGC
GATTAGTAGAATCGCGTTACGATAGTCAGAATCGCGTTGCGATTTACATA
Found at i:488072 original size:46 final size:46
Alignment explanation
Indices: 488005--488098 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
487995 TTGGAAAATC
* * *
488005 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTT
1 GCATTGCGATTTTGTATTATCGCATTACGATAGACAAAATCGCGTT
*
488051 GCATTGCGATTTTGTATTATCGCGTTACGATAGACAAAATCGCGTT
1 GCATTGCGATTTTGTATTATCGCATTACGATAGACAAAATCGCGTT
488097 GC
1 GC
488099 GATTTACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (46 bp):
GCATTGCGATTTTGTATTATCGCATTACGATAGACAAAATCGCGTT
Found at i:488094 original size:20 final size:20
Alignment explanation
Indices: 488069--488140 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
488059 ATTTTGTATT
*
488069 ATCGCGTTACGATAGACAAA
1 ATCGCGTTGCGATAGACAAA
** *
488089 ATCGCGTTGCGATTTACATA
1 ATCGCGTTGCGATAGACAAA
* * *
488109 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGACAAA
488129 ATCGCGTTGCGA
1 ATCGCGTTGCGA
488141 ATCTGGAAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGATAGACAAA
Found at i:489973 original size:20 final size:20
Alignment explanation
Indices: 489879--490247 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
489869 GATTTTCCAT
* ** *
489879 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
489899 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
489919 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
489939 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
489959 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
489979 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
489999 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
490019 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
490039 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
490059 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
490079 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
490099 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
490119 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
490139 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
490159 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
490179 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
490199 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
490219 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
490239 AATCACAAC
1 AATCGCAAC
490248 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:490950 original size:24 final size:24
Alignment explanation
Indices: 490911--490957 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
490901 AAATTTGGTC
490911 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
490935 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
490958 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:493443 original size:19 final size:19
Alignment explanation
Indices: 493421--493725 Score: 331
Period size: 19 Copynumber: 17.4 Consensus size: 19
493411 CGGAAAATAC
*
493421 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
493440 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
493454 AATCGCAATGCTGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
493474 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
493488 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
493507 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
493526 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
493540 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
493559 AATCGCAATGCGATATGAA
1 AATCGCAATGCGAAATGAA
* *
493578 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
493592 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
493611 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
493630 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
493649 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
493667 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
493681 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
493699 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
493718 AATCGCAA
1 AATCGCAA
493726 CGAGATAATC
Statistics
Matches: 246, Mismatches: 14, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 5 0.02
16 20 0.08
17 10 0.04
18 31 0.13
19 122 0.50
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:493508 original size:33 final size:33
Alignment explanation
Indices: 493421--493747 Score: 237
Period size: 33 Copynumber: 9.5 Consensus size: 33
493411 CGGAAAATAC
* *
493421 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
493454 AATCGCAATGCTGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
493488 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
493526 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* * *
493559 AATCGCAATGCGATATGAAAATCG-AACCGACAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAA
*
493592 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAA
*
493630 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
*
493667 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
*
493699 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
493732 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
493748 TATAAACGCA
Statistics
Matches: 250, Mismatches: 17, Indels: 54
0.78 0.05 0.17
Matches are distributed among these distances:
32 26 0.10
33 94 0.38
34 37 0.15
35 19 0.08
36 7 0.03
37 23 0.09
38 44 0.18
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:493536 original size:52 final size:53
Alignment explanation
Indices: 493449--493725 Score: 347
Period size: 52 Copynumber: 5.2 Consensus size: 53
493439 AAATCCCAAC
493449 ATGAAAATCGCAATGCTGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
493502 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
* * * *
493554 ATGAAAATCGCAATGCGATATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
* * *
493606 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAGAATCGCAATGCGAA
*
493663 ATG-AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAGA-G-AATCGCAATGCGAA
493713 ATGAAAATCGCAA
1 ATGAAAATCGCAA
493726 CGAGATAATC
Statistics
Matches: 203, Mismatches: 12, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
48 1 0.00
49 1 0.00
50 17 0.08
51 23 0.11
52 108 0.53
53 19 0.09
54 7 0.03
56 10 0.05
57 17 0.08
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
Found at i:493577 original size:71 final size:70
Alignment explanation
Indices: 493488--493725 Score: 333
Period size: 71 Copynumber: 3.4 Consensus size: 70
493478 GCAACGAGAG
*
493488 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAAAGAATCGCAATGCGA
493553 AATGAA
65 AATGAA
* * * *
493559 AATCGCAATGCGATATGAAAATCG-AA-CCGACAT--AATCGCAATGCGAAATTAAAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA--CG-AA--AGAATCGCAAT
*
493620 ACGAAATGAA
61 GCGAAATGAA
493630 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
493695 ATG-A
66 ATGAA
493699 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
493726 CGAGATAATC
Statistics
Matches: 147, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 34 0.23
70 19 0.13
71 65 0.44
72 4 0.03
73 7 0.05
75 8 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
ATGAA
Found at i:493863 original size:19 final size:19
Alignment explanation
Indices: 493754--493855 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
493744 AAATTATAAA
493754 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
493773 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
493793 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
493809 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
493826 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
493845 CGCATTGCGAT
1 CGCATTGCGAT
493856 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:493980 original size:14 final size:14
Alignment explanation
Indices: 493961--493997 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
493951 CATCAATTAC
493961 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
493975 ACAAATCATCTTTT
1 ACAAATCAACTTTT
493989 ACAAATCAA
1 ACAAATCAA
493998 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:494047 original size:37 final size:38
Alignment explanation
Indices: 493978--494049 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
493968 AACTTTTACA
*
493978 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
494016 AATCAACTTTTACAAATC-ATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
494050 CAATCAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:495808 original size:14 final size:14
Alignment explanation
Indices: 495789--495845 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
495779 GCGAAATGAA
*
495789 AATCGCAACGACAG
1 AATCGCAACGAAAG
495803 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
495820 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
495836 AATCGCAACG
1 AATCGCAACG
495846 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:495816 original size:33 final size:33
Alignment explanation
Indices: 495770--495862 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
495760 GCGAAACCAA
*
495770 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
495803 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
495836 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
495863 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:495827 original size:19 final size:19
Alignment explanation
Indices: 495733--495867 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
495723 TAGTTTACTT
* *
495733 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
495753 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
495772 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
495791 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
495805 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
495824 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
495838 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
495857 TCGCAATGCGA
1 TCGCAACGCGA
495868 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:495885 original size:19 final size:19
Alignment explanation
Indices: 495863--495991 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
495853 AAAATCGCAA
495863 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
495882 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
495896 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
495915 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
495929 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
495948 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
495967 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
495987 TGCGA
1 TGCGA
495992 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:495905 original size:33 final size:33
Alignment explanation
Indices: 495863--495954 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
495853 AAAATCGCAA
495863 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
495896 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
495929 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
495955 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:496205 original size:92 final size:93
Alignment explanation
Indices: 496035--496320 Score: 558
Period size: 92 Copynumber: 3.1 Consensus size: 93
496025 TTGAATGGAT
496035 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
496100 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
496128 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
496192 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
496220 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
496284 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
496312 AAATTTACT
1 AAATTTACT
496321 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
91 4 0.02
92 149 0.78
93 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:498038 original size:14 final size:14
Alignment explanation
Indices: 498019--498108 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
498009 TTGAAATGAA
498019 AATCGCAACGAGAG
1 AATCGCAACGAGAG
498033 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
498050 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
498066 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
498085 AATCGCAACGAGAG
1 AATCGCAACGAGAG
498099 AATCGCAACG
1 AATCGCAACG
498109 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:498056 original size:33 final size:33
Alignment explanation
Indices: 498011--498125 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
498001 TCTTTTGGTT
498011 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
498044 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
498077 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
498110 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
498126 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:498057 original size:19 final size:18
Alignment explanation
Indices: 498018--498130 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
498008 GTTGAAATGA
498018 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
498033 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
498050 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
498066 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
498083 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
498099 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
498116 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
498131 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:498161 original size:14 final size:14
Alignment explanation
Indices: 498142--498196 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
498132 TTTGGTTTCG
498142 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
498156 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
498175 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
498189 CGTTGCGA
1 CGTTGCGA
498197 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:498359 original size:33 final size:33
Alignment explanation
Indices: 498317--498387 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
498307 AATACTAACT
498317 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
498350 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
498383 TGAAA
1 TGAAA
498388 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:498620 original size:22 final size:22
Alignment explanation
Indices: 498568--498622 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
498558 TGGTTGTGAG
**
498568 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
498590 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
498612 GGATTTCTTCG
1 GGATTTCTTCG
498623 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:498793 original size:20 final size:20
Alignment explanation
Indices: 498768--498961 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
498758 CTTTAAATAT
498768 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
498788 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
498810 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
498829 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
498849 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
498869 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
498889 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
498909 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
498929 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
498949 CGCGTTGCGATTT
1 CGCGTTGCGATTT
498962 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:498955 original size:60 final size:60
Alignment explanation
Indices: 498768--498961 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
498758 CTTTAAATAT
**
498768 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
498829 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
498889 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
498949 CGCGTTGCGATTT
1 CGCGTTGCGATTT
498962 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:498978 original size:21 final size:20
Alignment explanation
Indices: 498954--499030 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
498944 ATATTCGCGT
498954 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
498975 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
498995 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
499017 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
499031 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:499041 original size:20 final size:20
Alignment explanation
Indices: 499016--499067 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
499006 AAGAATCGCG
*
499016 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
499036 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
499056 TTGCGATTCTGG
1 TTGCGATTCTGG
499068 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:499404 original size:11 final size:11
Alignment explanation
Indices: 499388--499423 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
499378 TTCGTTGAGA
499388 TTTATTTTATT
1 TTTATTTTATT
499399 TTTATTTTATT
1 TTTATTTTATT
* *
499410 ATTATTTTGTT
1 TTTATTTTATT
499421 TTT
1 TTT
499424 CAGGTTGCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:499617 original size:2 final size:2
Alignment explanation
Indices: 499612--499658 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
499602 TTAAAAAAAT
* * * *
499612 GA GA GA GA GA GA GA GA GA GA GG GA GA GG GA GA GG GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
499654 GA GA G
1 GA GA G
499659 GGGGTAAACG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (2 bp):
GA
Found at i:513087 original size:30 final size:30
Alignment explanation
Indices: 513047--513189 Score: 133
Period size: 30 Copynumber: 4.6 Consensus size: 30
513037 AGATTAGCAT
*
513047 TATAATGTGTAAGGACACTTAGTGCAACAC
1 TATAGTGTGTAAGGACACTTAGTGCAACAC
* *
513077 TATGGTGTGTAAGGACACTTAGTGCATATGGTAC
1 TATAGTGTGTAAGGACACTTAGTGCA-A---CAC
* * *
513111 TATAGTATGTAAGGACACTTAGTACAACAT
1 TATAGTGTGTAAGGACACTTAGTGCAACAC
* ** **
513141 TGTAGTGTGTAAGGATGCCCAGTGCAACAC
1 TATAGTGTGTAAGGACACTTAGTGCAACAC
* *
513171 TGTGGTGTGTAAGGACACT
1 TATAGTGTGTAAGGACACT
513190 CAATGCATAT
Statistics
Matches: 89, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
30 62 0.70
31 1 0.01
33 1 0.01
34 25 0.28
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TATAGTGTGTAAGGACACTTAGTGCAACAC
Found at i:514077 original size:17 final size:17
Alignment explanation
Indices: 514055--514092 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
514045 TATAACCGTT
514055 TATAATATTCATTCATA
1 TATAATATTCATTCATA
514072 TATAATATTCATTCATA
1 TATAATATTCATTCATA
514089 TATA
1 TATA
514093 CGATTATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAATATTCATTCATA
Found at i:520129 original size:48 final size:48
Alignment explanation
Indices: 520065--520159 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
520055 AAGCAAAGAT
* ** *
520065 GGGTCATTTCGGGTTTCGGTTTTATTCGAGTTTATAGTAAGCCGGGTC
1 GGGTCATTTCGAGTTTCAATTTTATTCGAGTCTATAGTAAGCCGGGTC
* * *
520113 GGGTCATTTTGAGTTTCAATTTTATTCGGGTCTATAGTAAGTCGGGT
1 GGGTCATTTCGAGTTTCAATTTTATTCGAGTCTATAGTAAGCCGGGT
520160 TGATTCTTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.17, C:0.13, G:0.29, T:0.41
Consensus pattern (48 bp):
GGGTCATTTCGAGTTTCAATTTTATTCGAGTCTATAGTAAGCCGGGTC
Found at i:520208 original size:30 final size:30
Alignment explanation
Indices: 520174--520263 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
520164 TCTTGTATTA
*
520174 GGTCGGGTCAATATTAGATCAATTATTTTG
1 GGTCGAGTCAATATTAGATCAATTATTTTG
* *
520204 GGTCGAATCAA-ATTAGATCAGTTGATTTTTG
1 GGTCGAGTCAATATTAGATCAATT-A-TTTTG
* *
520235 GGTC-ACGTCGATATTCGATCAATTATTTT
1 GGTCGA-GTCAATATTAGATCAATTATTTT
520264 TCGGTTTGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 11 0.22
30 15 0.31
31 13 0.27
32 10 0.20
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (30 bp):
GGTCGAGTCAATATTAGATCAATTATTTTG
Found at i:520237 original size:31 final size:30
Alignment explanation
Indices: 520181--520263 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
520171 TTAGGTCGGG
520181 TCAATATTAGATCAATTATTTTGGGTCGAA
1 TCAATATTAGATCAATTATTTTGGGTCGAA
* *
520211 TCAA-ATTAGATCAGTTGATTTTTGGGTC-ACG
1 TCAATATTAGATCAATT-A-TTTTGGGTCGA-A
* *
520242 TCGATATTCGATCAATTATTTT
1 TCAATATTAGATCAATTATTTT
520264 TCGGTTTGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 11 0.25
30 10 0.23
31 13 0.30
32 10 0.23
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (30 bp):
TCAATATTAGATCAATTATTTTGGGTCGAA
Found at i:524398 original size:18 final size:19
Alignment explanation
Indices: 524363--524399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
524353 CACGGAATGT
524363 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
524383 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
524400 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:524579 original size:36 final size:36
Alignment explanation
Indices: 524546--524613 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
524536 TACAAATTGT
524546 AAAATATTTATAT-ATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTATAAAATTAAATTC
*
524581 ATAATATTTATATAATTTTTTTATAAAATTAAA
1 AAAATATTTATATAATTTTTTTATAAAATTAAA
524614 AATATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTATAAAATTAAATTC
Found at i:528061 original size:2 final size:2
Alignment explanation
Indices: 528054--528110 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
528044 ATATAAGCCA
528054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
528096 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
528111 AATTTAATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:528492 original size:16 final size:16
Alignment explanation
Indices: 528471--528505 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
528461 CAATAAACAT
*
528471 CAAGCTTAATGATCAA
1 CAAGCTTAACGATCAA
*
528487 CAAGCTTAACGATTAA
1 CAAGCTTAACGATCAA
528503 CAA
1 CAA
528506 CTTTTCTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (16 bp):
CAAGCTTAACGATCAA
Found at i:530113 original size:2 final size:2
Alignment explanation
Indices: 530106--530137 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
530096 ATATTTTAAA
530106 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
530138 TCTTACCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:530173 original size:138 final size:129
Alignment explanation
Indices: 529973--530339 Score: 433
Period size: 138 Copynumber: 2.8 Consensus size: 129
529963 TTTAAACCAA
* * * * * *
529973 ATATATATATATATTTTAAATATATATTCTTAACTTAAATAATAAATTTGGCCAACTTTAAACCA
1 ATATATATATATATTAT-AATATATATTCTTACCTCAAAAAATAAACTTGGCCTACTTTAAACCA
530038 AAAAATATATATTTGATAAATTAAGAAAAAATATATATTTTTATAGTTAAGAATTTAAATATTTT
65 AAAAATATATATTTGATAAATTAAGAAAAAATATATATTTTTATAGTTAAGAATTTAAATA--TT
530103 AAAATAT
128 ----T-T
530110 ATATATATATATATATATATATATATATTCTTACCTCAAAAAATAAACTTGGCCTACTTTAAACC
1 ATATATATATATAT-TATA-ATATATATTCTTACCTCAAAAAATAAACTTGGCCTACTTTAAACC
*
530175 AAAAAATATATATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTT
64 AAAAAATATATATTTGATAAATTAAG-------AA-AAAATATATATTTTTATAGTTAAGAATTT
530240 AAATATTTT
121 AAATATTTT
* *
530249 A-A-A-ATAT-T-TTA-AATATATATTCTTACCTCAAAAAATAAACTTGGCATAATTTAAACCAA
1 ATATATATATATATTATAATATATATTCTTACCTCAAAAAATAAACTTGGCCTACTTTAAACCAA
530308 AAAATATATATTCT-ATAAATTAAGAAAAAATA
66 AAAATATATATT-TGATAAATTAAGAAAAAATA
530340 ATAAAATATA
Statistics
Matches: 209, Mismatches: 10, Indels: 36
0.82 0.04 0.14
Matches are distributed among these distances:
123 6 0.03
124 2 0.01
131 67 0.32
132 1 0.00
133 2 0.01
134 1 0.00
135 1 0.00
136 4 0.02
137 16 0.08
138 68 0.33
139 2 0.01
140 1 0.00
144 2 0.01
145 2 0.01
146 34 0.16
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.38
Consensus pattern (129 bp):
ATATATATATATATTATAATATATATTCTTACCTCAAAAAATAAACTTGGCCTACTTTAAACCAA
AAAATATATATTTGATAAATTAAGAAAAAATATATATTTTTATAGTTAAGAATTTAAATATTTT
Found at i:530307 original size:131 final size:137
Alignment explanation
Indices: 529973--530372 Score: 533
Period size: 131 Copynumber: 3.0 Consensus size: 137
529963 TTTAAACCAA
* * * *
529973 ATATATATATATATTTTAAATATATATTCTTAACTTAAATAATAAATTTGGCCA-ACTTTAAACC
1 ATATATATATATATTTTAAATATATATTCTTACCTCAAAAAATAAACTTGG-CATACTTTAAACC
*
530037 AAAAAATATATATTTGATAAATTAAG-------AA-AAAATATATATTTTTATAGTTAAGAATTT
65 AAAAAATATATATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTT
530094 AAATATTTT
130 AAATA-TTT
*
530103 AAAATATATATATATATATATATATATATATATATTCTTACCTCAAAAAATAAACTTGGCCTACT
1 ---ATATATATATATAT-T-T-TA-A-ATATATATTCTTACCTCAAAAAATAAACTTGGCATACT
530168 TTAAACCAAAAAATATATATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTA
58 TTAAACCAAAAAATATATATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTA
530233 AGAATTTAAATA-TT
123 AGAATTTAAATATTT
*
530247 -T-TA-A-A-ATATTTTAAATATATATTCTTACCTCAAAAAATAAACTTGGCATAATTTAAACCA
1 ATATATATATATATTTTAAATATATATTCTTACCTCAAAAAATAAACTTGGCATACTTTAAACCA
*
530307 AAAAATATATATTCTATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTA
66 AAAAATATATATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTA
530372 A
131 A
530373 GATTATACTA
Statistics
Matches: 244, Mismatches: 9, Indels: 30
0.86 0.03 0.11
Matches are distributed among these distances:
131 109 0.45
132 1 0.00
133 16 0.07
134 2 0.01
135 2 0.01
136 6 0.02
137 3 0.01
138 64 0.26
139 2 0.01
140 1 0.00
144 2 0.01
145 2 0.01
146 34 0.14
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (137 bp):
ATATATATATATATTTTAAATATATATTCTTACCTCAAAAAATAAACTTGGCATACTTTAAACCA
AAAAATATATATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTA
AATATTT
Found at i:531138 original size:32 final size:30
Alignment explanation
Indices: 531083--531142 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
531073 TTTCGTTATT
* *
531083 TTTTTTATTTTTGGATATTATTTTCATTTCA
1 TTTTTTATTTTTGGACATAATTTT-ATTTCA
*
531114 TTTTTTATTTTTATGACATAATTTTATTT
1 TTTTTTATTTTT-GGACATAATTTTATTT
531143 AAATTTAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (30 bp):
TTTTTTATTTTTGGACATAATTTTATTTCA
Found at i:532347 original size:30 final size:31
Alignment explanation
Indices: 532313--532381 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
532303 CTTTTAAAAC
* *
532313 TTGCAATACAGT-CCCTAACATTTAGTCCGT
1 TTGCAATACAGTCCCCCAACATTTAGTCCAT
** *
532343 TTGCAATATGGTCCCCCAACATTTAGTCTAT
1 TTGCAATACAGTCCCCCAACATTTAGTCCAT
532374 TTGCAATA
1 TTGCAATA
532382 TGGTCTCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (31 bp):
TTGCAATACAGTCCCCCAACATTTAGTCCAT
Found at i:534217 original size:19 final size:20
Alignment explanation
Indices: 534168--534219 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
534158 AGAAGAGAAA
534168 ATCGAAAAAGGAAATTCGAG
1 ATCGAAAAAGGAAATTCGAG
534188 ATCGAAAAAGGAAATTCGAG
1 ATCGAAAAAGGAAATTCGAG
534208 ATCG-AAAAGGAA
1 ATCGAAAAAGGAA
534220 TTTGGGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.52, C:0.10, G:0.25, T:0.13
Consensus pattern (20 bp):
ATCGAAAAAGGAAATTCGAG
Found at i:536865 original size:20 final size:20
Alignment explanation
Indices: 536830--536880 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
536820 TATTGGGTAA
536830 TATCGATATTCTATTCATAAAG
1 TATCGATA--CTATTCATAAAG
* * *
536852 TATCGATACTATTCGTCAGG
1 TATCGATACTATTCATAAAG
536872 TATCGATAC
1 TATCGATAC
536881 CAAAGGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
22 8 0.31
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
TATCGATACTATTCATAAAG
Found at i:537398 original size:22 final size:21
Alignment explanation
Indices: 537365--537436 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
537355 ATTCCCAACG
537365 GTGCTAAGGCACTTTAGTATCA
1 GTGCT-AGGCACTTTAGTATCA
* **
537387 GTGCTACTGCACTTCCGTATCA
1 GTGCTA-GGCACTTTAGTATCA
* * *
537409 ATGTTGAGGCACTTTAGTACCA
1 GTGCT-AGGCACTTTAGTATCA
537431 GTGCTA
1 GTGCTA
537437 TGACGTATTC
Statistics
Matches: 37, Mismatches: 11, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.92
23 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
GTGCTAGGCACTTTAGTATCA
Found at i:554589 original size:23 final size:22
Alignment explanation
Indices: 554518--554578 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
554508 GGGTCTAAGC
* *
554518 GGTCATTCGGGACATATATAGT-
1 GGTCATTCGGGACAAATACA-TA
554540 GGTCATTCGGGACAAATACATA
1 GGTCATTCGGGACAAATACATA
*
554562 GGTCATTCTGGACAAAT
1 GGTCATTCGGGACAAAT
554579 TTCATATGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (22 bp):
GGTCATTCGGGACAAATACATA
Found at i:555702 original size:21 final size:21
Alignment explanation
Indices: 555677--555721 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
555667 ATAGTGTATG
*
555677 TTTTAAA-AGCTTTAAAACCAT
1 TTTTAAATA-CTTTAAAAACAT
555698 TTTTAAATACTTTAAAAACAT
1 TTTTAAATACTTTAAAAACAT
555719 TTT
1 TTT
555722 AATCAACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTTAAATACTTTAAAAACAT
Found at i:560525 original size:12 final size:12
Alignment explanation
Indices: 560510--560563 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
560500 GTTATTTAAA
*
560510 CGGGTATTAGGC
1 CGGGTATTGGGC
*
560522 CGGGTATTGGGT
1 CGGGTATTGGGC
560534 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
560545 CGGGAATCGGGC
1 CGGGTATTGGGC
560557 CGGGTAT
1 CGGGTAT
560564 ATATATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.13, C:0.17, G:0.46, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:560597 original size:23 final size:23
Alignment explanation
Indices: 560561--560642 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
560551 TCGGGCCGGG
560561 TATATATATATATTTAAATTAAA
1 TATATATATATATTTAAATTAAA
* *
560584 TATATATTTTTATTTAAATTAAA
1 TATATATATATATTTAAATTAAA
* * *
560607 TTTAT-TA-ATATTATATATATATA
1 TATATATATATATT-TAAAT-TAAA
560630 TATATATATATAT
1 TATATATATATAT
560643 ATATATATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.09
22 5 0.11
23 32 0.68
24 2 0.04
25 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATATATATATTTAAATTAAA
Found at i:560625 original size:2 final size:2
Alignment explanation
Indices: 560614--560651 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
560604 AAATTTATTA
560614 AT AT -T AT 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 AT AT AT AT A
560652 ATTATTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:568257 original size:23 final size:23
Alignment explanation
Indices: 568231--568278 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
568221 ACTCATACTC
568231 TAAAAAAATATTGA-TTATTGAGT
1 TAAAAAAATATTGATTTA-TGAGT
* *
568254 TAAAGAAATATTTATTTATGAGT
1 TAAAAAAATATTGATTTATGAGT
568277 TA
1 TA
568279 TAAATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (23 bp):
TAAAAAAATATTGATTTATGAGT
Found at i:570980 original size:19 final size:19
Alignment explanation
Indices: 570942--570980 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
570932 TTCATGTTTA
*
570942 ATTTTTTTTTAAATATAAT
1 ATTTTTTTTTAAATAAAAT
570961 ATTTTATTTTTAAA-AAAAT
1 ATTTT-TTTTTAAATAAAAT
570980 A
1 A
570981 AAAATGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTTTTTAAATAAAAT
Found at i:571490 original size:24 final size:24
Alignment explanation
Indices: 571463--571546 Score: 150
Period size: 24 Copynumber: 3.5 Consensus size: 24
571453 CCTTCCTCGC
*
571463 AAATCAATTGCATCGATGCTTCTG
1 AAATCAACTGCATCGATGCTTCTG
571487 AAATCAACTGCATCGATGCTTCTG
1 AAATCAACTGCATCGATGCTTCTG
*
571511 AAATCAACTGCATCGATGCTTCTA
1 AAATCAACTGCATCGATGCTTCTG
571535 AAATCAACTGCA
1 AAATCAACTGCA
571547 GATTCTATCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (24 bp):
AAATCAACTGCATCGATGCTTCTG
Found at i:573853 original size:30 final size:29
Alignment explanation
Indices: 573819--574109 Score: 127
Period size: 30 Copynumber: 9.7 Consensus size: 29
573809 GGAGGTGGCT
* * *
573819 GTGACTTGTACGTGTATGGAGGTGATGGAG
1 GTGACTTGTACATATACGGAGGTGA-GGAG
** * * * * *
573849 GTGACTCATAAACATATGGAGGAGGTGGAG
1 GTGACTTGTACATATACGGAGG-TGAGGAG
* * **
573879 GTGACTTATAAACGTACGGAGGTGGAGGAG
1 GTGACTTGTACATATACGGAGGT-GAGGAG
* *
573909 GTGATTTGTACTTATACGGAGGTGGAGGAG
1 GTGACTTGTACATATACGGAGGT-GAGGAG
* * * * *
573939 GTGATTTGTATATGTACGGAGGAGGAGGTG
1 GTGACTTGTACATATACGGAGG-TGAGGAG
* *
573969 GTGACTTGTAC-TCATATGGAGGAGGAGGAG
1 GTGACTTGTACAT-ATACGGAGG-TGAGGAG
* * * *
573999 GTGATTTGTACTTATAAGGAGGTGGAGGGG
1 GTGACTTGTACATATACGGAGGT-GAGGAG
* * * * * *
574029 GTGACTTGTATACATATGGAGGAGGTGGTG
1 GTGACTTGTACATATACGGAGG-TGAGGAG
* *
574059 GTGACTTGTAC-TCATATGGAGGGGGAGGAG
1 GTGACTTGTACAT-ATACGGA-GGTGAGGAG
* * *
574089 GCGATTTGTACATGTACGGAG
1 GTGACTTGTACATATACGGAG
574110 AAGGTGTTGG
Statistics
Matches: 202, Mismatches: 49, Indels: 21
0.74 0.18 0.08
Matches are distributed among these distances:
29 2 0.01
30 195 0.97
31 5 0.02
ACGTcount: A:0.25, C:0.08, G:0.41, T:0.26
Consensus pattern (29 bp):
GTGACTTGTACATATACGGAGGTGAGGAG
Found at i:573930 original size:60 final size:60
Alignment explanation
Indices: 573861--574099 Score: 210
Period size: 60 Copynumber: 4.0 Consensus size: 60
573851 GACTCATAAA
* * * * *
573861 CATATGGAGGAGGTGGAGGTGACTTATAAACGTACGGAGGTGGAGGAGGTGATTTGTACT
1 CATACGGAGGAGGTGGAGGTGACTTGTACACATACGGAGGTGGAGGAGGTGACTTGTACT
* * * * * ** * *
573921 TATACGGAGGTGGAGGAGGTGATTTGTATATGTACGGAGGAGGAGGTGGTGACTTGTACT
1 CATACGGAGGAGGTGGAGGTGACTTGTACACATACGGAGGTGGAGGAGGTGACTTGTACT
* * * ** * *
573981 CATATGGAGGAGGAGGAGGTGATTTGTACTTATAAGGAGGTGGAGGGGGTGACTTGTA-T
1 CATACGGAGGAGGTGGAGGTGACTTGTACACATACGGAGGTGGAGGAGGTGACTTGTACT
* * * * * * *
574040 ACATATGGAGGAGGTGGTGGTGACTTGTACTCATATGGAGGGGGAGGAGGCGATTTGTAC
1 -CATACGGAGGAGGTGGAGGTGACTTGTACACATACGGAGGTGGAGGAGGTGACTTGTAC
574100 ATGTACGGAG
Statistics
Matches: 148, Mismatches: 29, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
59 1 0.01
60 147 0.99
ACGTcount: A:0.25, C:0.08, G:0.41, T:0.26
Consensus pattern (60 bp):
CATACGGAGGAGGTGGAGGTGACTTGTACACATACGGAGGTGGAGGAGGTGACTTGTACT
Found at i:573932 original size:90 final size:90
Alignment explanation
Indices: 573836--574109 Score: 343
Period size: 90 Copynumber: 3.0 Consensus size: 90
573826 GTACGTGTAT
** * * * ** * *
573836 GGAGGT-GATGGAGGTGACTCATAAACATATGGAGGAGGTGGAGGTGACTTATAAACGTACGGAG
1 GGAGGTGGA-GGAGGTGACTTGTATACATATGGAGGAGGTGGTGGTGACTTGTACTCATATGGAG
*
573900 GTGGAGGAGGTGATTTGTACTTATAC
65 GAGGAGGAGGTGATTTGTACTTATAC
* ** * *
573926 GGAGGTGGAGGAGGTGATTTGTATATGTACGGAGGAGGAGGTGGTGACTTGTACTCATATGGAGG
1 GGAGGTGGAGGAGGTGACTTGTATACATATGGAGGAGGTGGTGGTGACTTGTACTCATATGGAGG
*
573991 AGGAGGAGGTGATTTGTACTTATAA
66 AGGAGGAGGTGATTTGTACTTATAC
*
574016 GGAGGTGGAGGGGGTGACTTGTATACATATGGAGGAGGTGGTGGTGACTTGTACTCATATGGAGG
1 GGAGGTGGAGGAGGTGACTTGTATACATATGGAGGAGGTGGTGGTGACTTGTACTCATATGGAGG
* * * *
574081 GGGAGGAGGCGATTTGTACATGTAC
66 AGGAGGAGGTGATTTGTACTTATAC
574106 GGAG
1 GGAG
574110 AAGGTGTTGG
Statistics
Matches: 156, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
90 154 0.99
91 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.41, T:0.26
Consensus pattern (90 bp):
GGAGGTGGAGGAGGTGACTTGTATACATATGGAGGAGGTGGTGGTGACTTGTACTCATATGGAGG
AGGAGGAGGTGATTTGTACTTATAC
Found at i:574280 original size:78 final size:78
Alignment explanation
Indices: 574181--574345 Score: 269
Period size: 78 Copynumber: 2.1 Consensus size: 78
574171 AGAAGGAGAA
* * * *
574181 GGTGAATAGTACTCGGGAGATGGTGGAGACTCATATTCGTATGGTGCAGGTGCAGGTGATGCATA
1 GGTGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCAGGTGCAAGTGATGCATA
* *
574246 GTAGTACGGTGGT
66 GAAGTACGGAGGT
574259 GGTGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCAGGTGCAAGTGATGCATA
1 GGTGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCAGGTGCAAGTGATGCATA
574324 GAAGTACGGAGGT
66 GAAGTACGGAGGT
574337 GGTG-GTAGT
1 GGTGAGTAGT
574346 GATAGAAGAG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 5 0.06
78 76 0.94
ACGTcount: A:0.25, C:0.11, G:0.38, T:0.26
Consensus pattern (78 bp):
GGTGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCAGGTGCAAGTGATGCATA
GAAGTACGGAGGT
Found at i:577080 original size:16 final size:16
Alignment explanation
Indices: 577059--577100 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
577049 TGAGAAAAAT
577059 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
577075 TTAATTTAATTTTAAA
1 TTAATTTAAATTTAAA
*
577091 ATAACTTTAA
1 TTAA-TTTAA
577101 TAAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:579092 original size:17 final size:17
Alignment explanation
Indices: 579072--579107 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
579062 TGAGTATTAG
579072 GACATGGCGAGTTATAT
1 GACATGGCGAGTTATAT
579089 GACATGGCGAGTTATAT
1 GACATGGCGAGTTATAT
579106 GA
1 GA
579108 TATAAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (17 bp):
GACATGGCGAGTTATAT
Found at i:579285 original size:88 final size:89
Alignment explanation
Indices: 579192--579373 Score: 339
Period size: 88 Copynumber: 2.1 Consensus size: 89
579182 AAAAAGCTCC
*
579192 TATAAGATCGGGTCAAGACCCGGGTTCGAATATTTTGATCATCTCTAATTATACAAGTGGAGTAG
1 TATAAGATCGGGTCAAGACCCGGATTCGAATATTTTGATCATCTCTAATTATACAAGTGGAGTAG
579257 AAATTGAATCGGTTCAAGTATT-A
66 AAATTGAATCGGTTCAAGTATTAA
*
579280 TATAAGATCGGGTCAAGACCTGGATTCGAATATTTTGATCATCTCTAATTATACAAGTGGAGTAG
1 TATAAGATCGGGTCAAGACCCGGATTCGAATATTTTGATCATCTCTAATTATACAAGTGGAGTAG
579345 AAATTGAATCGGTTCAAGTATTAA
66 AAATTGAATCGGTTCAAGTATTAA
579369 TATAA
1 TATAA
579374 AAAGAGTTCA
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 85 0.93
89 6 0.07
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (89 bp):
TATAAGATCGGGTCAAGACCCGGATTCGAATATTTTGATCATCTCTAATTATACAAGTGGAGTAG
AAATTGAATCGGTTCAAGTATTAA
Found at i:584542 original size:22 final size:22
Alignment explanation
Indices: 584514--584556 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
584504 GAAAGTCAAC
*
584514 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGCCGGGTCGGGTCG
584536 GGTCAACGGCCGGGTCGGGTC
1 GGTCAACGGCCGGGTCGGGTC
584557 AAACAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.26, G:0.49, T:0.16
Consensus pattern (22 bp):
GGTCAACGGCCGGGTCGGGTCG
Found at i:584621 original size:20 final size:21
Alignment explanation
Indices: 584566--584623 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
584556 CAAACAGGTC
* *
584566 AAACCGGTTCAGACCGG-T-C
1 AAACCGGTTCAAACCGGTTGA
*
584585 AAACCGGTTCGAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
584606 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCAAACCGGTT
584624 TCCAGCAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.45
20 9 0.27
21 9 0.27
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:584623 original size:9 final size:10
Alignment explanation
Indices: 584555--584623 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
584545 CCGGGTCGGG
*
584555 TCAAACAGG-
1 TCAAACCGGT
584564 TCAAACCGGT
1 TCAAACCGGT
*
584574 TCAGACCGG-
1 TCAAACCGGT
584583 TCAAACCGGT
1 TCAAACCGGT
*
584593 TCGAACCGGT
1 TCAAACCGGT
*
584603 TGAAAACCGGT
1 T-CAAACCGGT
584614 T-AAACCGGT
1 TCAAACCGGT
584623 T
1 T
584624 TCCAGCAGCC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
9 25 0.49
10 18 0.35
11 8 0.16
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:591814 original size:5 final size:5
Alignment explanation
Indices: 591804--591871 Score: 73
Period size: 5 Copynumber: 12.8 Consensus size: 5
591794 AACGGTCAAC
* *
591804 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCG GGTCAAC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC--G
*
591853 GATCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC
591872 AACGGTCAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 46 0.87
7 7 0.13
ACGTcount: A:0.07, C:0.22, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:591822 original size:22 final size:22
Alignment explanation
Indices: 591797--591888 Score: 121
Period size: 22 Copynumber: 4.0 Consensus size: 22
591787 GAAAGTCAAC
591797 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
591819 GGTCAACGGTCGGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCGGGTCG
*
591846 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
591868 GGTCAACGGTCAGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
591889 AGACCGGTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
22 39 0.63
23 1 0.02
26 1 0.02
27 21 0.34
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:591841 original size:27 final size:27
Alignment explanation
Indices: 591804--591871 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
591794 AACGGTCAAC
*
591804 GGTCGGGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCGGGTCAACGATCG
591831 GGTCGGGTCGGGTCGGGTCAACGATCG
1 GGTCGGGTCGGGTCGGGTCAACGATCG
591858 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
591872 AACGGTCAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.07, C:0.22, G:0.51, T:0.19
Consensus pattern (27 bp):
GGTCGGGTCGGGTCGGGTCAACGATCG
Found at i:591885 original size:27 final size:27
Alignment explanation
Indices: 591805--591888 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
591795 ACGGTCAACG
*
591805 GTCGGGTCGGGTCGGGTCAACGGTCGG
1 GTCGGGTCGGGTCGGGTCAACGGTCAG
591832 GTCGGGTCGGGTCGGGTCAAC-G--A-
1 GTCGGGTCGGGTCGGGTCAACGGTCAG
591855 -TCGGGTCGGGTCGGGTCAACGGTCAG
1 GTCGGGTCGGGTCGGGTCAACGGTCAG
591881 GTCGGGTC
1 GTCGGGTC
591889 AGACCGGTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
22 20 0.39
23 1 0.02
25 1 0.02
26 1 0.02
27 28 0.55
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.19
Consensus pattern (27 bp):
GTCGGGTCGGGTCGGGTCAACGGTCAG
Found at i:591903 original size:9 final size:9
Alignment explanation
Indices: 591885--591964 Score: 70
Period size: 9 Copynumber: 8.3 Consensus size: 9
591875 GGTCAGGTCG
*
591885 GGTCAGACC
1 GGTCAAACC
591894 GGTCAAACC
1 GGTCAAACC
*
591903 GGTTCGAACC
1 GG-TCAAACC
*
591913 GGTTGAAACC
1 GG-TCAAACC
591923 GGTCAAACC
1 GGTCAAACC
591932 GGTCAGAACC
1 GGTCA-AACC
*
591942 GGTTGAAAACC
1 GG-T-CAAACC
*
591953 GGTTAAACC
1 GGTCAAACC
591962 GGT
1 GGT
591965 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 29 0.48
10 23 0.38
11 7 0.12
12 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:591925 original size:29 final size:31
Alignment explanation
Indices: 591891--591965 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
591881 GTCGGGTCAG
591891 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
591920 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
591950 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
591966 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:593371 original size:6 final size:6
Alignment explanation
Indices: 593360--593398 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
593350 TATTATATAT
*
593360 TTTTTA TTTTTA TTTTTA TTTTTA TTTTCA TTTTATA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TT
593399 GATTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.90
7 3 0.10
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:593381 original size:18 final size:19
Alignment explanation
Indices: 593355--593398 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
593345 CGATTTATTA
*
593355 TATATTTTTTATTTTTATTT
1 TATA-TTTTTATTTTCATTT
593375 T-TATTTTTATTTTCATTT
1 TATATTTTTATTTTCATTT
593393 TATATT
1 TATATT
593399 GATTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 15 0.68
19 6 0.27
20 1 0.05
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (19 bp):
TATATTTTTATTTTCATTT
Found at i:602863 original size:30 final size:28
Alignment explanation
Indices: 602794--602863 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
602784 TATTTATTCT
*
602794 AATATATTAATTAAGTATTTTGAAATTTA
1 AATATATTAATT-AGTATTTTAAAATTTA
*
602823 AATATGATTAATT-TTATTTTAAAATATATA
1 AATAT-ATTAATTAGTATTTTAAAAT-T-TA
602853 ACATATATTAA
1 A-ATATATTAA
602864 AATAATTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 10 0.29
29 6 0.17
30 15 0.43
31 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (28 bp):
AATATATTAATTAGTATTTTAAAATTTA
Done.