Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold231
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: 1009718
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 7
Found at i:524331 original size:27 final size:26
Alignment explanation
Indices: 524296--524347 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
524286 AAAATATTCC
524296 TATCCAATTTTAAATTTTAAAAAGGT
1 TATCCAATTTTAAATTTTAAAAAGGT
**
524322 TATCGCAATTTTTTATTTTAAAAAGG
1 TATC-CAATTTTAAATTTTAAAAAGG
524348 AAATATGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (26 bp):
TATCCAATTTTAAATTTTAAAAAGGT
Found at i:524910 original size:2 final size:2
Alignment explanation
Indices: 524903--524930 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
524893 TATTTGATAC
524903 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
524931 AGTGAAATAA
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):
TA
Found at i:528504 original size:10 final size:10
Alignment explanation
Indices: 528479--528525 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
528469 GAAGGCCTCT
528479 CCCTCTC-CC
1 CCCTCTCTCC
528488 CCTCTCTCTCC
1 CC-CTCTCTCC
*
528499 CCCTCTCTCT
1 CCCTCTCTCC
* *
528509 TCCTCTCTAC
1 CCCTCTCTCC
528519 CCCTCTC
1 CCCTCTC
528526 GCCCTCGCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 2 0.06
10 25 0.81
11 4 0.13
ACGTcount: A:0.02, C:0.64, G:0.00, T:0.34
Consensus pattern (10 bp):
CCCTCTCTCC
Found at i:528516 original size:12 final size:12
Alignment explanation
Indices: 528481--528508 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
528471 AGGCCTCTCC
528481 CTCTCCCCCTCT
1 CTCTCCCCCTCT
528493 CTCTCCCCCTCT
1 CTCTCCCCCTCT
528505 CTCT
1 CTCT
528509 TCCTCTCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (12 bp):
CTCTCCCCCTCT
Found at i:528532 original size:6 final size:6
Alignment explanation
Indices: 528523--528549 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
528513 CTCTACCCCT
528523 CTCGCC CTCGCC CTCGCC CTCGCC CTC
1 CTCGCC CTCGCC CTCGCC CTCGCC CTC
528550 TCTCTCAAAG
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:0.00, C:0.67, G:0.15, T:0.19
Consensus pattern (6 bp):
CTCGCC
Found at i:539966 original size:2 final size:2
Alignment explanation
Indices: 539959--539989 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
539949 TCACCCCTCC
539959 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
539990 CAAAAATAAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:552639 original size:72 final size:72
Alignment explanation
Indices: 552517--552792 Score: 311
Period size: 72 Copynumber: 3.8 Consensus size: 72
552507 AAGAATTTAC
* * * * * **
552517 TCGATATTTCA-ACATATAAGCAAGTAACATAATCACCATGCATAGATGCTAAAAACAACCTTAA
1 TCGACATTTCAGA-ATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAAAATGACCTTAA
552581 AAGTCTAA
65 AAGTCTAA
* * * *
552589 TCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCATAGATGCTAAGAATGACATCAAA
1 TCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAAAATGACCTTAAA
* *
552654 AGTTTGA
66 AGTCTAA
** * * * * *
552661 TTAATATTTCAGCATATAAGTGAGTGACACAGTCACCATACACAGATGCTAAAAATGACCTTAAA
1 TCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAAAATGACCTTAAA
*
552726 GGTCTAA
66 AGTCTAA
* * * *
552733 TCGACATTTCAGTATATAAGTGAGTGACATAGTCACCATGTACAGATGCTAAAATTGACC
1 TCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAAAATGACC
552793 CCAAAGACCT
Statistics
Matches: 170, Mismatches: 33, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
72 169 0.99
73 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (72 bp):
TCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAAAATGACCTTAAA
AGTCTAA
Found at i:552780 original size:144 final size:144
Alignment explanation
Indices: 552520--552784 Score: 395
Period size: 144 Copynumber: 1.8 Consensus size: 144
552510 AATTTACTCG
* * *
552520 ATATTTCAACATATAAGCAAGTAACATAATCACCATGCATAGATGCTAAAAACAACCTTAAAAGT
1 ATATTTCAACATATAAGCAAGTAACACAATCACCATACACAGATGCTAAAAACAACCTTAAAAGT
*
552585 CTAATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCATAGATGCTAAGAATGACAT
66 CTAATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAGAATGACAT
552650 CAAAAGTTTGATTA
131 CAAAAGTTTGATTA
* ** * * ** *
552664 ATATTTCAGCATATAAGTGAGTGACACAGTCACCATACACAGATGCTAAAAATGACCTTAAAGGT
1 ATATTTCAACATATAAGCAAGTAACACAATCACCATACACAGATGCTAAAAACAACCTTAAAAGT
* * *
552729 CTAATCGACATTTCAGTATATAAGTGAGTGACATAGTCACCATGTACAGATGCTAA
66 CTAATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAA
552785 AATTGACCCC
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
144 106 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (144 bp):
ATATTTCAACATATAAGCAAGTAACACAATCACCATACACAGATGCTAAAAACAACCTTAAAAGT
CTAATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAGAATGACAT
CAAAAGTTTGATTA
Found at i:552820 original size:144 final size:144
Alignment explanation
Indices: 552522--552823 Score: 360
Period size: 144 Copynumber: 2.1 Consensus size: 144
552512 TTTACTCGAT
* ** * * * * *
552522 ATTTCAACATATAAGCAAGTAACATAATCACCATGCATAGATGCTAAAAACAACCTTAAAAGTCT
1 ATTTCAGCATATAAGTGAGTGACACAGTCACCATACACAGATGCTAAAAACAACCTTAAAAGTCT
* *
552587 AATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCATAGATGCTAAGAATGACATCA
66 AATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAGAATGACACCA
** *
552652 AAAGTTTGATTAAT
131 AAAGCCTGATTAAC
** *
552666 ATTTCAGCATATAAGTGAGTGACACAGTCACCATACACAGATGCTAAAAATGACCTTAAAGGTCT
1 ATTTCAGCATATAAGTGAGTGACACAGTCACCATACACAGATGCTAAAAACAACCTTAAAAGTCT
* * *
552731 AATCGACATTTCAGTATATAAGTGAGTGACATAGTCACCATGTACAGATGCTAA-AATTGAC-CC
66 AATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAGAA-TGACACC
*
552794 CAAAGACCT-ACTTAAC
130 AAAAG-CCTGA-TTAAC
552810 ATTT-AGGCATATAA
1 ATTTCA-GCATATAA
552824 ACAAATAATA
Statistics
Matches: 134, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
143 9 0.07
144 125 0.93
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (144 bp):
ATTTCAGCATATAAGTGAGTGACACAGTCACCATACACAGATGCTAAAAACAACCTTAAAAGTCT
AATCGACATTTCAGAATATAAGCGAGTGACATAGTCACCATGCACAGATGCTAAGAATGACACCA
AAAGCCTGATTAAC
Found at i:552822 original size:72 final size:70
Alignment explanation
Indices: 552522--552823 Score: 241
Period size: 72 Copynumber: 4.2 Consensus size: 70
552512 TTTACTCGAT
* ** * * * ** *
552522 ATTTCAACATATAAGCAAGTAACATAATCACCATGCATAGATGCTAAAAACAACCTTAAA-AGTC
1 ATTTCAGCATATAAGTGAGTGACATAGTCACCATGCACAGATGCT-AAAATGACCTCAAAGA-TC
**
552586 TAATCGAC
64 T-ATTAAC
* * * * *
552594 ATTTCAGAATATAAGCGAGTGACATAGTCACCATGCATAGATGCTAAGAATGACATCAAA-AGTT
1 ATTTCAGCATATAAGTGAGTGACATAGTCACCATGCACAGATGCTAA-AATGACCTCAAAGA-TC
*
552658 TGATTAAT
64 T-ATTAAC
* * * *
552666 ATTTCAGCATATAAGTGAGTGACACAGTCACCATACACAGATGCTAAAAATGACCTTAAAGGTCT
1 ATTTCAGCATATAAGTGAGTGACATAGTCACCATGCACAGATGCT-AAAATGACCTCAAAGATCT
**
552731 AATCGAC
65 -ATTAAC
* * * *
552738 ATTTCAGTATATAAGTGAGTGACATAGTCACCATGTACAGATGCTAAAATTGACCCCAAAGACCT
1 ATTTCAGCATATAAGTGAGTGACATAGTCACCATGCACAGATGCTAAAA-TGACCTCAAAGATCT
552803 ACTTAAC
65 A-TTAAC
552810 ATTT-AGGCATATAA
1 ATTTCA-GCATATAA
552824 ACAAATAATA
Statistics
Matches: 186, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
71 8 0.04
72 176 0.95
73 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (70 bp):
ATTTCAGCATATAAGTGAGTGACATAGTCACCATGCACAGATGCTAAAATGACCTCAAAGATCTA
TTAAC
Found at i:557887 original size:26 final size:27
Alignment explanation
Indices: 557858--557926 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
557848 TTTCTTTGGT
557858 TATTTATTTATTTAAAAAAT-TATTAC
1 TATTTATTTATTTAAAAAATATATTAC
*
557884 TATTTATTTATTTTAAAAAATATATTAT
1 TATTTATTTA-TTTAAAAAATATATTAC
557912 TATTTTATTTATTTA
1 TA-TTTATTTATTTA
557927 TTCACTTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 10 0.26
27 10 0.26
28 11 0.28
29 8 0.21
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTTATTTATTTAAAAAATATATTAC
Found at i:557912 original size:25 final size:27
Alignment explanation
Indices: 557857--557925 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 27
557847 TTTTCTTTGG
557857 TTATTTATTTA-TTTAAAAAATTATTA
1 TTATTTATTTATTTTAAAAAATTATTA
*
557883 CTATTTATTTATTTTAAAAAATATATTA
1 TTATTTATTTATTTTAAAAAAT-TATTA
557911 TTATTTTATTTATTT
1 TTA-TTTATTTATTT
557926 ATTCACTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 10 0.26
27 10 0.26
28 7 0.18
29 11 0.29
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATTTATTTATTTTAAAAAATTATTA
Found at i:564800 original size:49 final size:48
Alignment explanation
Indices: 564717--564812 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 48
564707 GATAGTAACT
* *
564717 ATAGATGAGAATGAAATGAGAAGTTGATCAGGGGAATCGACGAAAACC
1 ATAGATGAGAATGAAATGAGAAGTTGATCAGGGGAATAGACAAAAACC
**
564765 ATAGATGAGAATGAAAATGAGAAGTTGATTGGGGGAATAGACAAAAAC
1 ATAGATGAGAATG-AAATGAGAAGTTGATCAGGGGAATAGACAAAAAC
564813 ATACTGATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 13 0.30
49 30 0.70
ACGTcount: A:0.46, C:0.07, G:0.29, T:0.18
Consensus pattern (48 bp):
ATAGATGAGAATGAAATGAGAAGTTGATCAGGGGAATAGACAAAAACC
Found at i:567418 original size:5 final size:5
Alignment explanation
Indices: 567408--567452 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
567398 ATGAAAATGA
* *
567408 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAC AAAAT AGAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
567453 TAACCCAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:568635 original size:24 final size:25
Alignment explanation
Indices: 568608--568659 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
568598 TTATTATTGC
*
568608 TTAATATAAATAT-ATATTT-ATTAT
1 TTAATACAAATATAAT-TTTAATTAT
*
568632 TTAATACAAATGTAATTTTAATTAT
1 TTAATACAAATATAATTTTAATTAT
568657 TTA
1 TTA
568660 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAATACAAATATAATTTTAATTAT
Found at i:568703 original size:36 final size:34
Alignment explanation
Indices: 568616--568733 Score: 127
Period size: 36 Copynumber: 3.5 Consensus size: 34
568606 GCTTAATATA
* * *
568616 AATATATATTTATTATTTAATACAAATGTAATTTT
1 AATATAT-TTTATTATTTAATATAAATATAACTTT
568651 AAT-TA-TTTATT-TTTAATATAAATATAACTTT
1 AATATATTTTATTATTTAATATAAATATAACTTT
*
568682 AATTTATATTTTATTATTTAATATAAATATAATTTT
1 AA--TATATTTTATTATTTAATATAAATATAACTTT
*
568718 GATAT-TTTTAATTATT
1 AATATATTTT-ATTATT
568734 CATTGCATAC
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
31 19 0.26
32 6 0.08
33 5 0.07
34 13 0.18
35 9 0.12
36 20 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (34 bp):
AATATATTTTATTATTTAATATAAATATAACTTT
Found at i:568705 original size:30 final size:29
Alignment explanation
Indices: 568610--568725 Score: 81
Period size: 30 Copynumber: 3.8 Consensus size: 29
568600 ATTATTGCTT
*
568610 AATATAAATATATATTTAT-TATTTAATACA
1 AATATAAATATA-ATTTATAT-TTTAATATA
* * * *
568640 AATGTAATTTTAATTATTTATTTTTAATATA
1 AATATAAATATAATT-TATA-TTTTAATATA
* * * *
568671 AATATAACTTTAATTTATATTTTATTATTT
1 AATATAAATATAATTTATATTTTAATA-TA
568701 AATATAAATATAATTTTGATATTTT
1 AATATAAATATAA-TTT-ATATTTT
568726 TAATTATTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
29 10 0.15
30 26 0.38
31 24 0.35
32 8 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
AATATAAATATAATTTATATTTTAATATA
Found at i:568854 original size:24 final size:24
Alignment explanation
Indices: 568827--568877 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
568817 AAATATATAT
568827 TTATTACTGATTTTAATTTTATTA
1 TTATTACTGATTTTAATTTTATTA
* **
568851 TTATTATTTTTTTTAATTTTATTA
1 TTATTACTGATTTTAATTTTATTA
568875 TTA
1 TTA
568878 ATCCAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (24 bp):
TTATTACTGATTTTAATTTTATTA
Found at i:569568 original size:2 final size:2
Alignment explanation
Indices: 569561--569597 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
569551 AGTTAACTTT
569561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
569598 CGTTTGTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:570940 original size:2 final size:2
Alignment explanation
Indices: 570933--570970 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
570923 AGATAGCTTT
570933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
570971 AAAGAGTTGG
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):
TA
Found at i:571318 original size:93 final size:93
Alignment explanation
Indices: 571190--571367 Score: 275
Period size: 93 Copynumber: 1.9 Consensus size: 93
571180 TATTTTATTG
* * * * *
571190 TTTTAATTTTGTTTTAACTTTTAAGTAATTTTTTTAATTGAGTTGATAATATTTAAGTTATGATA
1 TTTTAATTTTATTTTAACTTTTAAATAATTTTTTTAATTGAATTGATAAAATTTAAGTTATAATA
* *
571255 TTAATTTAGTCACATACTTTATATTTTA
66 TCAATTTAATCACATACTTTATATTTTA
* *
571283 TTTTAATTTTATTTTGACTTTTAAATAATTTTTTTAATTGAATTGATAAAATTTAATTTATAATA
1 TTTTAATTTTATTTTAACTTTTAAATAATTTTTTTAATTGAATTGATAAAATTTAAGTTATAATA
571348 TCAATTTAATCACATACTTT
66 TCAATTTAATCACATACTTT
571368 TTATATATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (93 bp):
TTTTAATTTTATTTTAACTTTTAAATAATTTTTTTAATTGAATTGATAAAATTTAAGTTATAATA
TCAATTTAATCACATACTTTATATTTTA
Found at i:572004 original size:14 final size:14
Alignment explanation
Indices: 571985--572025 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
571975 CTTGTCTTTC
*
571985 ATATATGTATATGT
1 ATATATGTATATAT
*
571999 ATATATGTATACAT
1 ATATATGTATATAT
*
572013 ATATATATATATA
1 ATATATGTATATA
572026 CACATATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:572019 original size:18 final size:18
Alignment explanation
Indices: 571993--572033 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
571983 TCATATATGT
* * *
571993 ATATGTATATATGTATAC
1 ATATATATATATATACAC
572011 ATATATATATATATACAC
1 ATATATATATATATACAC
572029 ATATA
1 ATATA
572034 CACATCCTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATATATATATATACAC
Found at i:572586 original size:14 final size:14
Alignment explanation
Indices: 572569--572616 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
572559 TATTTTTATT
* *
572569 TAAATTTAATTATA
1 TAAATATAAATATA
572583 TAAATATAAATATA
1 TAAATATAAATATA
572597 TAAATATAAATATA
1 TAAATATAAATATA
*
572611 AAAATA
1 TAAATA
572617 ATATTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATATAAATATA
Found at i:572788 original size:22 final size:23
Alignment explanation
Indices: 572760--572802 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
572750 TTTTAATTTA
572760 AAAAAAGGATA-AAATATTACTT
1 AAAAAAGGATATAAATATTACTT
*
572782 AAAAAAGGATATAATTATTAC
1 AAAAAAGGATATAAATATTAC
572803 ATAGAATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (23 bp):
AAAAAAGGATATAAATATTACTT
Found at i:573533 original size:20 final size:19
Alignment explanation
Indices: 573510--573547 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
573500 ATTTAATTAT
573510 AAAATATAATTATTAATATA
1 AAAATAT-ATTATTAATATA
*
573530 AAAATATATTTTTAATAT
1 AAAATATATTATTAATAT
573548 TTTAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATATATTATTAATATA
Found at i:573830 original size:14 final size:13
Alignment explanation
Indices: 573811--573849 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
573801 GATCATATAA
573811 AAAAATTAAATATT
1 AAAAA-TAAATATT
573825 AAAAATATAATATT
1 AAAAATA-AATATT
*
573839 AATAATAAATA
1 AAAAATAAATA
573850 ATTATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATAAATATT
Found at i:573853 original size:14 final size:13
Alignment explanation
Indices: 573817--573859 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
573807 ATAAAAAAAT
*
573817 TAAATATTAAAAA
1 TAAATATTAATAA
573830 TATAATATTAATAA
1 TA-AATATTAATAA
*
573844 TAAATAATTATTAA
1 TAAAT-ATTAATAA
573858 TA
1 TA
573860 TAACAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATATTAATAA
Found at i:574627 original size:25 final size:26
Alignment explanation
Indices: 574580--574663 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
574570 ATATTAATAA
* * *
574580 TTTATTATCAAAATATATTAAATACTT
1 TTTATT-TTAAAATTTATAAAATACTT
*
574607 TTTATTTTAAAATTT-TAAAATATTT
1 TTTATTTTAAAATTTATAAAATACTT
* *
574632 TTTA-ATTAAAATTTAATAAAATAGTT
1 TTTATTTTAAAATTT-ATAAAATACTT
574658 TTTATT
1 TTTATT
574664 GAACTTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 9 0.19
25 12 0.26
26 20 0.43
27 6 0.13
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (26 bp):
TTTATTTTAAAATTTATAAAATACTT
Found at i:583034 original size:23 final size:24
Alignment explanation
Indices: 583008--583065 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
582998 ATAGAAAATA
583008 AATATATAA-A-TTTATTATTATAT
1 AATATATAATACTTTATT-TTATAT
*
583031 AATA-AAAATACTTTATTTTATAT
1 AATATATAATACTTTATTTTATAT
583054 AATAATATAATA
1 AAT-ATATAATA
583066 AATATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 3 0.10
23 14 0.48
24 7 0.24
25 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AATATATAATACTTTATTTTATAT
Found at i:583086 original size:31 final size:31
Alignment explanation
Indices: 583004--583094 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
582994 TTAAATAGAA
583004 AATAAATATATAAA-TTTATTAT--T-ATAT
1 AATAAATATATAAATTTTATTATAATAATAT
* **
583031 AATAAAAATACTTTATTTTA-TATAATAATAT
1 AATAAATATA-TAAATTTTATTATAATAATAT
583062 AATAAATATATAAATTTTATTATAA-AAT-T
1 AATAAATATATAAATTTTATTATAATAATAT
583091 AATA
1 AATA
583095 TGAATTAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
27 9 0.17
28 5 0.10
29 9 0.17
30 11 0.21
31 18 0.35
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
AATAAATATATAAATTTTATTATAATAATAT
Found at i:585984 original size:4 final size:4
Alignment explanation
Indices: 585975--586009 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
585965 AAACTACTTA
585975 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
586010 TATATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:587882 original size:13 final size:13
Alignment explanation
Indices: 587864--587888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
587854 ATTAAAATAT
587864 AAATAAATTACTA
1 AAATAAATTACTA
587877 AAATAAATTACT
1 AAATAAATTACT
587889 TTTTAAACTA
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAATTACTA
Found at i:588041 original size:32 final size:32
Alignment explanation
Indices: 587996--588065 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
587986 CATTAGCTCA
*
587996 TCCTACGTAGACGCGCCATGTAGAACAACAAG
1 TCCTACATAGACGCGCCATGTAGAACAACAAG
* * *
588028 TCCTACATGGACGCGCCATGTAGGACAACGAG
1 TCCTACATAGACGCGCCATGTAGAACAACAAG
588060 TCCTAC
1 TCCTAC
588066 GTAAATGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (32 bp):
TCCTACATAGACGCGCCATGTAGAACAACAAG
Found at i:588390 original size:21 final size:22
Alignment explanation
Indices: 588366--588416 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
588356 TATAAAGTAA
588366 TTTAATATTTATTT-TTTT-GTT
1 TTTAATATTT-TTTATTTTAGTT
* *
588387 TTTAAAATTTTTTATTTTATTT
1 TTTAATATTTTTTATTTTAGTT
588409 TTTAATAT
1 TTTAATAT
588417 GTTAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTAATATTTTTTATTTTAGTT
Found at i:588583 original size:15 final size:15
Alignment explanation
Indices: 588563--588602 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
588553 TATTATGTTG
588563 AATTAGGTTTA-GGGT
1 AATTA-GTTTAGGGGT
588578 AATTAGTTTAGGGGT
1 AATTAGTTTAGGGGT
*
588593 AATTAATTTA
1 AATTAGTTTA
588603 TGGTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (15 bp):
AATTAGTTTAGGGGT
Found at i:588588 original size:14 final size:14
Alignment explanation
Indices: 588563--588607 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
588553 TATTATGTTG
588563 AATTAGGTTTAGGGT
1 AATTA-GTTTAGGGT
588578 AATTAGTTTAGGGGT
1 AATTAGTTTA-GGGT
* *
588593 AATTAATTTATGGT
1 AATTAGTTTAGGGT
588607 A
1 A
588608 TAAAAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (14 bp):
AATTAGTTTAGGGT
Found at i:588777 original size:63 final size:62
Alignment explanation
Indices: 588699--588822 Score: 221
Period size: 63 Copynumber: 2.0 Consensus size: 62
588689 ATTTAGTATA
* *
588699 TGGAAATGAAATGGAAATATGTGTGAAAGGGTAAATGGTATTAGTATTGAAGGTGAAGATCT
1 TGGAAATGAAATGGAAATATGTGTGAAAGGGTAAATAGTATTAGTATTGAAAGTGAAGATCT
588761 TGGAAATGGAAATGGAAATATGTGTGAAAGGGTAAATAGTATTAGTATTGAAAGTGAAGATC
1 TGGAAAT-GAAATGGAAATATGTGTGAAAGGGTAAATAGTATTAGTATTGAAAGTGAAGATC
588823 CTGATATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 7 0.12
63 52 0.88
ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28
Consensus pattern (62 bp):
TGGAAATGAAATGGAAATATGTGTGAAAGGGTAAATAGTATTAGTATTGAAAGTGAAGATCT
Found at i:593724 original size:63 final size:63
Alignment explanation
Indices: 593646--593784 Score: 260
Period size: 63 Copynumber: 2.2 Consensus size: 63
593636 TATATGTTCT
*
593646 CTCGTCATATCCTGTACAGCAATTTTATGCTTACCCACCATATTTTCCTATTCAACCTTCATA
1 CTCGTCATATCCTGTACAGCAATTTTATGCTTACCCACCATATTTTCCTATTCAACCTCCATA
*
593709 CTCGTCATATCCTGTACAGCAATTTTATGCTTACCCACTATATTTTCCTATTCAACCTCCATA
1 CTCGTCATATCCTGTACAGCAATTTTATGCTTACCCACCATATTTTCCTATTCAACCTCCATA
593772 CTCGTCATATCCT
1 CTCGTCATATCCT
593785 ACTAAACCTC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 74 1.00
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.38
Consensus pattern (63 bp):
CTCGTCATATCCTGTACAGCAATTTTATGCTTACCCACCATATTTTCCTATTCAACCTCCATA
Found at i:593792 original size:27 final size:27
Alignment explanation
Indices: 593762--593813 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
593752 TTTCCTATTC
* *
593762 AACCTCCATACTCGTCATATCCTACTA
1 AACCTCCATACCCATCATATCCTACTA
593789 AACCTCCATACCCATCATATCCTAC
1 AACCTCCATACCCATCATATCCTAC
593814 CACGACCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.40, G:0.02, T:0.27
Consensus pattern (27 bp):
AACCTCCATACCCATCATATCCTACTA
Found at i:594194 original size:72 final size:72
Alignment explanation
Indices: 594077--594327 Score: 321
Period size: 72 Copynumber: 3.5 Consensus size: 72
594067 GCACATAAAA
* * * *
594077 TTGTTGATTGTAGTTATCGTGCAGATTATCTCAAATTAATTGTTGATAGTAGTTTTAAATATACA
1 TTGTTGATTGTATTTATCGTGCAGATTATCTCGAATTAGTTGTTGATAGTAGTTTTAAATATGCA
594142 AAAATAG
66 AAAATAG
* * * * *
594149 TTGTTGATTATATATATCGTGTAGATTATCTCGCATTAGTTGTTGATAGTAATTTTAAATATGCA
1 TTGTTGATTGTATTTATCGTGCAGATTATCTCGAATTAGTTGTTGATAGTAGTTTTAAATATGCA
594214 AAAAT-G
66 AAAATAG
* * * *
594220 --ATTGATTGTATTTATCGTGCAGATTATCTCGGATTAGTTATTGATATTAGTTTTAAATATGCA
1 TTGTTGATTGTATTTATCGTGCAGATTATCTCGAATTAGTTGTTGATAGTAGTTTTAAATATGCA
594283 AAAATTA-
66 AAAA-TAG
* * *
594290 TTGTTAATTGTATTTATTGTGTAGATTATCTCGAATTA
1 TTGTTGATTGTATTTATCGTGCAGATTATCTCGAATTA
594328 TCGTTTCATC
Statistics
Matches: 153, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
69 59 0.39
70 1 0.01
71 1 0.01
72 92 0.60
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (72 bp):
TTGTTGATTGTATTTATCGTGCAGATTATCTCGAATTAGTTGTTGATAGTAGTTTTAAATATGCA
AAAATAG
Found at i:594676 original size:12 final size:12
Alignment explanation
Indices: 594659--594688 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
594649 TCATAACAAT
*
594659 AATAATTTAATA
1 AATAATTTAAAA
594671 AATAATTTAAAA
1 AATAATTTAAAA
594683 AATAAT
1 AATAAT
594689 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATAATTTAAAA
Found at i:595520 original size:15 final size:15
Alignment explanation
Indices: 595500--595538 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
595490 TTTAAGTTTA
595500 TTAAGTTT-TGTCATT
1 TTAAGTTTATGTCA-T
*
595515 TTAAGTTTATGTTAT
1 TTAAGTTTATGTCAT
595530 TTAAGTTTA
1 TTAAGTTTA
595539 GGTTAATTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.59
Consensus pattern (15 bp):
TTAAGTTTATGTCAT
Found at i:595543 original size:15 final size:15
Alignment explanation
Indices: 595514--595543 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
595504 GTTTTGTCAT
*
595514 TTTAAGTTTATGTTA
1 TTTAAGTTTAGGTTA
595529 TTTAAGTTTAGGTTA
1 TTTAAGTTTAGGTTA
595544 ATTCGACTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTAAGTTTAGGTTA
Found at i:596303 original size:52 final size:52
Alignment explanation
Indices: 596193--596810 Score: 644
Period size: 52 Copynumber: 11.9 Consensus size: 52
596183 AGATAATAAA
* * * *
596193 AATTACAATTTAAAAAATAATAAAACTTAAAAATATATTTTATATTAAATTTTA
1 AATTACTATTT-AAAAATAATAAAAATTAAAAA-ATATTTTATATTAAATCTTG
* * * * *
596247 AATTATTATTTAAAAATAATAAAAATGAAATAATATTTTATATTATATTTTG
1 AATTACTATTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
* * *
596299 AATTAC-ATTTTAAGAAATAATAAAAATTAAATAATATTTTATATTAAATTTTA
1 AATTACTA-TTTAA-AAATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
* * **
596352 AATTA-T-TTTAAAAAATAATAAAAATTTTAAAAAA-A-ATTATAATAAATCTCA
1 AATTACTATTT-AAAAATAATAAAAA--TTAAAAAATATTTTATATTAAATCTTG
* *
596403 AATTATTATTTAAAAATAATTAAAATTAAAAAATA-TTTATATTAAATCTTG
1 AATTACTATTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
*
596454 AATTACTATTT--AAA-AAT---AATT-AAAAA-ATTTTATAATAAATCTTG
1 AATTACTATTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
* *
596498 AATTACTATTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCCTA
1 AATTACTATTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
* * * * *
596550 AATTACTATTTAAGAATAATAAGAATAAAAATAAAAATACTTATATTAAATCTTG
1 AATTACTATTTAAAAATAATAAAAAT-TAAA-AAATAT-TTTATATTAAATCTTG
* * *
596605 ATTTACTATTTAAAAAATAATAAAAATTAAAAAATATATTTTATATTAAATCCTA
1 AATTACTATTT-AAAAATAATAAAAATT-AAAAA-ATATTTTATATTAAATCTTG
*
596660 AATTACTATATGAAAAATAATAAAAATT-AAAAATATTTTATATT-AATCTTG
1 AATTACTAT-TTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
* *
596711 AATCACTATTTAAATAATAATAAAAA-T-AAAAATATTTTATATTAAATCTCG
1 AATTACTATTTAAA-AATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
* **
596762 AATTA-AATTTTTTAAATAATAAAAATTAAAAAATATTTTATATTAAATC
1 AATTACTA-TTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATC
596811 CAAAATTATT
Statistics
Matches: 482, Mismatches: 52, Indels: 62
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.00
44 31 0.06
45 4 0.01
46 3 0.01
47 3 0.01
48 3 0.01
49 3 0.01
50 45 0.09
51 100 0.21
52 117 0.24
53 76 0.16
54 14 0.03
55 62 0.13
56 20 0.04
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (52 bp):
AATTACTATTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTTG
Found at i:596392 original size:51 final size:50
Alignment explanation
Indices: 596201--596809 Score: 404
Period size: 51 Copynumber: 11.8 Consensus size: 50
596191 AAAATTACAA
*
596201 TTTAAAAAATAATAAAACTTAAAAATATATTTTATATTAAATTTTAAATTAT
1 TTTAAAAAATAATAAAAATTAAAAATA-A-TTTATATTAAATTTTAAATTAT
* * * * *
596253 TATTTAAAAATAATAAAAATGAAATAATATTTTATATTATATTTTGAATTACAT
1 T-TTAAAAAATAATAAAAATTAAA-AATAATTTATATTAAATTTTAAATT--AT
* *
596307 TTTAAGAAATAATAAAAATTAAATAATATTTTATATTAAATTTTAAATTAT
1 TTTAAAAAATAATAAAAATTAAA-AATAATTTATATTAAATTTTAAATTAT
* * * *
596358 TTTAAAAAATAATAAAAATTTTAAAAA-AAATTATAATAAATCTCAAATTAT
1 TTTAAAAAATAATAAAAA--TTAAAAATAATTTATATTAAATTTTAAATTAT
* * * *
596409 TATTTAAAAATAATTAAAATTAAAAA-ATATTTATATTAAATCTTGAATTACT
1 T-TTAAAAAATAATAAAAATTAAAAATA-ATTTATATTAAATTTTAAATTA-T
* * * *
596461 ATTT---AAA-AAT---AATTAAAAA-ATTTTATAATAAATCTTGAATTACT
1 -TTTAAAAAATAATAAAAATTAAAAATAATTTATATTAAATTTTAAATTA-T
* **
596505 ATTT-AAAAATAATAAAAATTAAAAAATATTTTATATTAAATCCTAAATTACT
1 -TTTAAAAAATAATAAAAATT-AAAAATAATTTATATTAAATTTTAAATTA-T
* * * *
596557 ATTTAAGAATAATAAGAATAAAAA-TAAAAAT-ACTTATATTAAATCTTGATTTACT
1 -TTTAA-AA-AAT---AATAAAAATTAAAAATAATTTATATTAAATTTTAAATTA-T
**
596612 ATTTAAAAAATAATAAAAATTAAAAAATATATTTTATATTAAATCCTAAATTACT
1 -TTTAAAAAATAATAAAAATT-AAAAATA-A-TTTATATTAAATTTTAAATTA-T
* * * * * *
596667 ATATGAAAAATAATAAAAATTAAAAATATTTTATATT-AATCTTGAATCACT
1 -TTTAAAAAATAATAAAAATTAAAAATAATTTATATTAAATTTTAAATTA-T
* * * **
596718 ATTTAAATAATAATAAAAA-TAAAAATATTTTATATTAAATCTCGAATTAAAT
1 -TTTAAAAAATAATAAAAATTAAAAATAATTTATATTAAATTTTAAATT--AT
** *
596770 TTT-TTAAATAATAAAAATTAAAAAATATTTTATATTAAAT
1 TTTAAAAAATAATAAAAATT-AAAAATAATTTATATTAAAT
596810 CCAAAATTAT
Statistics
Matches: 472, Mismatches: 51, Indels: 68
0.80 0.09 0.12
Matches are distributed among these distances:
44 26 0.06
45 10 0.02
46 3 0.01
47 3 0.01
48 3 0.01
49 3 0.01
50 48 0.10
51 103 0.22
52 100 0.21
53 73 0.15
54 19 0.04
55 66 0.14
56 6 0.01
57 1 0.00
58 8 0.02
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (50 bp):
TTTAAAAAATAATAAAAATTAAAAATAATTTATATTAAATTTTAAATTAT
Found at i:596426 original size:44 final size:44
Alignment explanation
Indices: 596370--596522 Score: 166
Period size: 44 Copynumber: 3.4 Consensus size: 44
596360 TAAAAAATAA
* ** *
596370 TAAAAAT-TTTAAAAAAAATTATAATAAATCTCAAATTATTATT
1 TAAAAATAATTAAAAAAAATTATAATAAATCTTGAATTACTATT
*
596413 TAAAAATAATTAAAATTAAAAAATATTTATATTAAATCTTGAATTACTATT
1 TAAAAATAATT---A--AAAAAA-A-TTATAATAAATCTTGAATTACTATT
**
596464 TAAAAATAATTAAAAAATTTTATAATAAATCTTGAATTACTATT
1 TAAAAATAATTAAAAAAAATTATAATAAATCTTGAATTACTATT
596508 TAAAAATAA-TAAAAA
1 TAAAAATAATTAAAAA
596523 TTAAAAAATA
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
43 13 0.14
44 35 0.37
46 5 0.05
47 1 0.01
48 1 0.01
49 6 0.06
50 1 0.01
51 32 0.34
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (44 bp):
TAAAAATAATTAAAAAAAATTATAATAAATCTTGAATTACTATT
Found at i:596488 original size:95 final size:96
Alignment explanation
Indices: 596370--596758 Score: 363
Period size: 95 Copynumber: 3.9 Consensus size: 96
596360 TAAAAAATAA
* * *
596370 TAAAAAT-TTTAAAAAAAATTATAATAAATCTCAAATTATTATTTAAAAATAATTAAAATTAAAA
1 TAAAAATAATTAAAAAAAATTATAATAAATCTCAAATTACTATTTAAAAATAATAAAAATTAAAA
* *
596434 AATA-TTTATATTAAATCTTGAATTACTATT
66 AATATTTTATATTAAATCCTAAATTACTATT
** **
596464 TAAAAATAATTAAAAAATTTTATAATAAATCTTGAATTACTATTTAAAAATAATAAAAATTAAAA
1 TAAAAATAATTAAAAAAAATTATAATAAATCTCAAATTACTATTTAAAAATAATAAAAATTAAAA
596529 AATATTTTATATTAAATCCTAAATTACTATT
66 AATATTTTATATTAAATCCTAAATTACTATT
* * ** *
596560 TAAGAATAATAAGAATAAAAATAAAAATACTTATATTAAATCTTGATTTACTATTTAAAAAATAA
1 T-A-AA-AAT---AAT--TAA-AAAAA-A-TTATAATAAATCTCAAATTACTATTT-AAAAATAA
596625 TAAAAATTAAAAAATATATTTTATATTAAATCCTAAATTACTATAT
54 TAAAAATT-AAAAA-ATATTTTATATTAAATCCTAAATTACTAT-T
* * * * ** *
596671 GAAAAATAATAAAAATTAAAAATATTTTATATTAATCTTGAATCACTATTTAAATAATAATAAAA
1 TAAAAATAAT--TAA--AAAAA-ATTATA-ATAAATCTCAAATTACTATTTAAA-AATAATAAAA
596736 A-T-AAAAATATTTTATATTAAATC
59 ATTAAAAAATATTTTATATTAAATC
596759 TCGAATTAAA
Statistics
Matches: 255, Mismatches: 20, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
94 7 0.03
95 54 0.21
96 25 0.10
97 1 0.00
98 2 0.01
99 3 0.01
102 20 0.08
103 4 0.02
104 2 0.01
105 20 0.08
106 36 0.14
107 24 0.09
108 19 0.07
109 7 0.03
110 30 0.12
111 1 0.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (96 bp):
TAAAAATAATTAAAAAAAATTATAATAAATCTCAAATTACTATTTAAAAATAATAAAAATTAAAA
AATATTTTATATTAAATCCTAAATTACTATT
Found at i:596781 original size:264 final size:254
Alignment explanation
Indices: 596200--596834 Score: 702
Period size: 264 Copynumber: 2.4 Consensus size: 254
596190 AAAAATTACA
* *
596200 ATTTAAAAAATAATAAAACTTAAAAATATATTTTATATTAAATTTTAAATT-ATTATTTAAAAAT
1 ATTT-AAAAATAATAAAA--T-AAAA-ATATTTTATATTAAATCTTGAATTAATT-TTT-AAAAT
* * * ** * *
596264 AATAAAAATGAAATAATATTTTATATTATATTTTGAATTACATTTTAAGAAATAATAAAAATTAA
59 AATAAAAATTAAAAAATATTTTATATTAAATCCTAAATTACATTTTAAGAAATAATAAAAATAAA
* * *
596329 ATAATATTTTATATTAAATTTTAAATTATTTTAAAAAATAATAAAAATTTTAAAAAAAATTATAA
124 ATAAAATCTTATATTAAATCTTAAATTATTTTAAAAAATAATAAAAA-TTTAAAAAAAATTATAA
* * * *
596394 TAAATCTCAAATTATTATTTAAAAATAATTAAAATTAAAAAATATTTATATTAAATCTTGAATTA
188 TAAATCTCAAATTACTATTGAAAAATAATAAAAATTAAAAAATATTTATATTAAATCTTGAATCA
596459 CT
253 CT
* * *
596461 ATTTAAAAATAAT----TAAAAA-ATTTTATAATAAATCTTGAATTACTATTTAAAAATAATAAA
1 ATTTAAAAATAATAAAATAAAAATATTTTATATTAAATCTTGAATTAAT-TTTTAAAATAATAAA
*
596521 AATTAAAAAATATTTTATATTAAATCCTAAATTAC-TATTTAAG-AATAATAAGAATAAAAATAA
65 AATTAAAAAATATTTTATATTAAATCCTAAATTACAT-TTTAAGAAATAATAAAAAT-AAAAT-A
* *
596584 AAATACTTATATTAAATCTTGATTTACTATTTAAAAAATAATAAAAA-TTAAAAAATATATTTTA
127 AAAT-CTTATATTAAATCTTAAATTA-T-TTTAAAAAATAATAAAAATTTAAAAAA-A-A--TTA
*
596648 TATTAAATC-CTAAATTACTATATGAAAAATAATAAAAATT-AAAAATATTTTATATT-AATCTT
185 TAATAAATCTC-AAATTACTAT-TGAAAAATAATAAAAATTAAAAAATA-TTTATATTAAATCTT
596710 GAATCACT
247 GAATCACT
* *
596718 ATTTAAATAATAATAAAAATAAAAATATTTTATATTAAATCTCGAATTAAATTTTTTAAATAATA
1 ATTTAAA-AATAAT-AAAATAAAAATATTTTATATTAAATCTTGAATT-AATTTTTAAAATAATA
* *
596783 AAAATTAAAAAATATTTTATATTAAATCCAAAATTA-TTTTTGAAGAAATAAT
63 AAAATTAAAAAATATTTTATATTAAATCCTAAATTACATTTT-AAGAAATAAT
596835 TATGAGATTT
Statistics
Matches: 319, Mismatches: 29, Indels: 48
0.81 0.07 0.12
Matches are distributed among these distances:
250 12 0.04
251 69 0.22
252 8 0.03
253 30 0.09
254 3 0.01
255 19 0.06
256 1 0.00
257 47 0.15
258 30 0.09
260 9 0.03
261 4 0.01
263 9 0.03
264 70 0.22
265 8 0.03
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (254 bp):
ATTTAAAAATAATAAAATAAAAATATTTTATATTAAATCTTGAATTAATTTTTAAAATAATAAAA
ATTAAAAAATATTTTATATTAAATCCTAAATTACATTTTAAGAAATAATAAAAATAAAATAAAAT
CTTATATTAAATCTTAAATTATTTTAAAAAATAATAAAAATTTAAAAAAAATTATAATAAATCTC
AAATTACTATTGAAAAATAATAAAAATTAAAAAATATTTATATTAAATCTTGAATCACT
Found at i:596887 original size:22 final size:22
Alignment explanation
Indices: 596862--596913 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
596852 AAGAGGTTGG
*
596862 TTTAATTAAAGTGATATGTACA
1 TTTAATTAAAGTCATATGTACA
*
596884 TTTAGTTAAAGTCATATGTACA
1 TTTAATTAAAGTCATATGTACA
*
596906 TTCAATTA
1 TTTAATTA
596914 TAATTACATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTAATTAAAGTCATATGTACA
Found at i:597095 original size:22 final size:22
Alignment explanation
Indices: 597059--597115 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
597049 ATATCATTTT
597059 TAATTATATAT--ATTCAATTA
1 TAATTATATATACATTCAATTA
*
597079 TAATTATATATACATTCAGTTA
1 TAATTATATATACATTCAATTA
* *
597101 TAGTCATATATACAT
1 TAATTATATATACAT
597116 ATTCTTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 11 0.34
22 21 0.66
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATTATATATACATTCAATTA
Found at i:597260 original size:2 final size:2
Alignment explanation
Indices: 597253--597299 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
597243 TTAATGTCTC
* * *
597253 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AA AT CAC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
597296 AT AT
1 AT AT
597300 TTAGTTATAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 37 0.97
3 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:597599 original size:53 final size:52
Alignment explanation
Indices: 597469--597599 Score: 167
Period size: 53 Copynumber: 2.5 Consensus size: 52
597459 TAATTATAAA
* *
597469 AATATAAAATATTTTTAAAATTTTTATTATTTTTATATAGTAATTCGAGATTT
1 AATATAAAATATTTTT-ATATTTTTATTATTTTTAAATAGTAATTCGAGATTT
* *
597522 AATATAAAATATTTTTAATTTTTTTATTATTTTTCAAATAGTAATT-TATGATTT
1 AATATAAAATATTTTT-ATATTTTTATTATTTTT-AAATAGTAATTCGA-GATTT
597576 AATATAAAATAATTTTT-TATTTTT
1 AATATAAAAT-ATTTTTATATTTTT
597600 TACTACTTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
53 39 0.56
54 25 0.36
55 6 0.09
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (52 bp):
AATATAAAATATTTTTATATTTTTATTATTTTTAAATAGTAATTCGAGATTT
Found at i:597599 original size:54 final size:52
Alignment explanation
Indices: 597469--597601 Score: 178
Period size: 54 Copynumber: 2.5 Consensus size: 52
597459 TAATTATAAA
* *
597469 AATATAAAATATTTTTAAAATTTTTATTATTTTTATATAGTAATTCGAGATTT
1 AATATAAAATATTTTT-AATTTTTTATTATTTTTAAATAGTAATTCGAGATTT
*
597522 AATATAAAATATTTTTAATTTTTTTATTATTTTTCAAATAGTAATT-TATGATTT
1 AATATAAAATATTTTTAA-TTTTTTATTATTTTT-AAATAGTAATTCGA-GATTT
*
597576 AATATAAAATAATTTTTTATTTTTTA
1 AATATAAAAT-ATTTTTAATTTTTTA
597602 CTACTTTCTA
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
52 2 0.03
53 31 0.43
54 32 0.44
55 7 0.10
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (52 bp):
AATATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTCGAGATTT
Found at i:597689 original size:2 final size:2
Alignment explanation
Indices: 597682--597723 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
597672 TTGGTTTTAA
597682 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
597724 GAGCAAATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:601113 original size:15 final size:16
Alignment explanation
Indices: 601093--601143 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
601083 CCATAGTTTT
601093 ATTATATTAT-TTATA
1 ATTATATTATATTATA
*
601108 ATTATATT-TAATATA
1 ATTATATTATATTATA
* *
601123 TTTATATTATATTTTA
1 ATTATATTATATTATA
601139 ATTAT
1 ATTAT
601144 TTTTTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 1 0.03
15 19 0.66
16 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATATTATATTATA
Found at i:601131 original size:20 final size:21
Alignment explanation
Indices: 601098--601145 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
601088 GTTTTATTAT
601098 ATTATTTATAATTATA-TTTA
1 ATTATTTATAATTATATTTTA
601118 ATATATTTAT-ATTATATTTTA
1 AT-TATTTATAATTATATTTTA
601139 ATTATTT
1 ATTATTT
601146 TTTATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTTATAATTATATTTTA
Found at i:601135 original size:11 final size:11
Alignment explanation
Indices: 601100--601156 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
601090 TTTATTATAT
601100 TATTTATAATTA
1 TATTTAT-ATTA
601112 TATTTA-A-TA
1 TATTTATATTA
601121 TATTTATATTA
1 TATTTATATTA
601132 TATTT-TAATTA
1 TATTTAT-ATTA
*
601143 T-TTTTTATT-
1 TATTTATATTA
601152 TATTT
1 TATTT
601157 TTTTAAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 9 0.22
10 12 0.30
11 13 0.32
12 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATATTA
Found at i:601151 original size:21 final size:21
Alignment explanation
Indices: 601098--601157 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
601088 GTTTTATTAT
* *
601098 ATTATTTATAATTATA-TTTA
1 ATTATTTTTTATTATATTTTA
*
601118 A-TATATTTATATTATATTTTA
1 ATTAT-TTTTTATTATATTTTA
601139 ATTATTTTTTATT-TATTTT
1 ATTATTTTTTATTATATTTT
601158 TTTAAACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 12 0.36
22 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTTTTTATTATATTTTA
Found at i:601155 original size:20 final size:20
Alignment explanation
Indices: 601100--601157 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
601090 TTTATTATAT
*
601100 TATTTATAATTATATTTAATA
1 TATTTATATTTAT-TTTAATA
601121 TATTTATATTATATTTTAAT-
1 TATTTATATT-TATTTTAATA
*
601141 TATTTTTTATTTATTTT
1 TA-TTTATATTTATTTT
601158 TTTAAACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 8 0.24
21 22 0.67
22 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTATATTTATTTTAATA
Found at i:601460 original size:19 final size:18
Alignment explanation
Indices: 601438--601488 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
601428 TTTTATTAAG
601438 ATTTATTATTTAAAAAATA
1 ATTTATTATTTAAAAAA-A
* **
601457 ATTTTTTATTTATATTAAA
1 ATTTATTATTTA-AAAAAA
601476 ATTTATTATTTAA
1 ATTTATTATTTAA
601489 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.04
19 23 0.85
20 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATTATTTAAAAAAA
Found at i:601799 original size:10 final size:10
Alignment explanation
Indices: 601784--601842 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
601774 AATTTTTTTT
601784 ATAATTTAAA
1 ATAATTTAAA
*
601794 ATAATTTAAT
1 ATAATTTAAA
*
601804 TTAATTTAAA
1 ATAATTTAAA
601814 TTATAATTT-AA
1 --ATAATTTAAA
*
601825 ATAATATAAA
1 ATAATTTAAA
601835 AGTAATTT
1 A-TAATTT
601843 TTAAATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
9 6 0.15
10 20 0.51
11 7 0.18
12 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (10 bp):
ATAATTTAAA
Found at i:601805 original size:15 final size:16
Alignment explanation
Indices: 601782--601833 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
601772 TTAATTTTTT
601782 TTATAATTTAAAATAA
1 TTATAATTTAAAATAA
**
601798 TT-TAATTTAATTTAAA
1 TTATAATTTAAAAT-AA
601814 TTATAATTT-AAATAA
1 TTATAATTTAAAATAA
601829 -TATAA
1 TTATAA
601834 AAGTAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.17
15 11 0.37
16 8 0.27
17 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAATTTAAAATAA
Found at i:601841 original size:32 final size:33
Alignment explanation
Indices: 601782--601864 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
601772 TTAATTTTTT
* **
601782 TTATAATTTAAAATAAT-TTAATTTAA-TTTAAA
1 TTATAATTT-AAATAATATAAAAGTAATTTTAAA
601814 TTATAATTTAAATAATATAAAAGTAATTTTTAAA
1 TTATAATTTAAATAATATAAAAGTAA-TTTTAAA
* *
601848 TTTTATTTTAAATAATA
1 TTATAATTTAAATAATA
601865 AAATAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 7 0.16
32 15 0.35
34 21 0.49
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
TTATAATTTAAATAATATAAAAGTAATTTTAAA
Found at i:601858 original size:34 final size:31
Alignment explanation
Indices: 601808--601875 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 31
601798 TTTAATTTAA
601808 TTTAAATTATAATTTAAATAATATAAAAGTAATT
1 TTTAAATTATAATTTAAAT-A-ATAAAA-TAATT
* *
601842 TTTAAATTTTATTTTAAATAATAAAATAATT
1 TTTAAATTATAATTTAAATAATAAAATAATT
601873 TTT
1 TTT
601876 TTAAAAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 8 0.25
32 6 0.19
33 1 0.03
34 17 0.53
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
TTTAAATTATAATTTAAATAATAAAATAATT
Found at i:602653 original size:19 final size:18
Alignment explanation
Indices: 602610--602660 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
602600 GAAGTGAGTG
602610 TCATAAAATTTAATATATT
1 TCATAAAA-TTAATATATT
*
602629 TAATAAAA-TAATTATATT
1 TCATAAAATTAA-TATATT
602647 ATCATAAATATTAA
1 -TCATAAA-ATTAA
602661 AAATTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.12
18 6 0.23
19 13 0.50
20 1 0.04
21 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
TCATAAAATTAATATATT
Found at i:602907 original size:3 final size:3
Alignment explanation
Indices: 602896--602930 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
602886 TATTTTTTTA
*
602896 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
602931 CAAAATACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:606691 original size:26 final size:26
Alignment explanation
Indices: 606662--606714 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
606652 AATTTTAATG
606662 TAAGATTAATACTATAAAAATAAAAA
1 TAAGATTAATACTATAAAAATAAAAA
606688 TAAGATTAATACTATAAAAATAAAAA
1 TAAGATTAATACTATAAAAATAAAAA
606714 T
1 T
606715 GCATATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (26 bp):
TAAGATTAATACTATAAAAATAAAAA
Found at i:607524 original size:2 final size:2
Alignment explanation
Indices: 607517--607553 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
607507 TCTATTGTTT
607517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
607554 CATTATTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:615094 original size:19 final size:19
Alignment explanation
Indices: 615067--615117 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
615057 GAAAACAACA
* *
615067 ATTACTTTAGTAATTACTG
1 ATTAATTTAGTAAATACTG
*
615086 ATTAATTTAGTAAATAGTG
1 ATTAATTTAGTAAATACTG
615105 ATTAATTTAGTAA
1 ATTAATTTAGTAA
615118 GTAGAACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (19 bp):
ATTAATTTAGTAAATACTG
Found at i:617801 original size:14 final size:14
Alignment explanation
Indices: 617762--617794 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
617752 TTATTATAAA
*
617762 AATATAAAAATGTT
1 AATATAAAAATATT
617776 AATATAAAAATATT
1 AATATAAAAATATT
617790 AATAT
1 AATAT
617795 TATAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:618714 original size:2 final size:2
Alignment explanation
Indices: 618707--618740 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
618697 AGTTGTTTGA
618707 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
618741 CCCTGTCTCT
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):
AT
Found at i:618820 original size:26 final size:26
Alignment explanation
Indices: 618784--618836 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
618774 GTTGTTTGAA
* *
618784 TATATATATATATATATATATGTGTG
1 TATATATATATAAAAATATATGTGTG
618810 TATATATATATAAAAATATATGTGTG
1 TATATATATATAAAAATATATGTGTG
618836 T
1 T
618837 GTTTTTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (26 bp):
TATATATATATAAAAATATATGTGTG
Found at i:618830 original size:2 final size:2
Alignment explanation
Indices: 618783--618821 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
618773 AGTTGTTTGA
* * *
618783 AT AT AT AT AT AT AT AT AT AT AT GT GT GT 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
618822 AAAATATATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
AT
Found at i:625197 original size:18 final size:18
Alignment explanation
Indices: 625174--625212 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
625164 AGCAAATTAA
625174 AATACTCATGATTTGAAC
1 AATACTCATGATTTGAAC
625192 AATACTCATGATTTGAAC
1 AATACTCATGATTTGAAC
625210 AAT
1 AAT
625213 CAGCAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (18 bp):
AATACTCATGATTTGAAC
Found at i:627088 original size:27 final size:27
Alignment explanation
Indices: 627028--627088 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
627018 AAATCCAATG
*
627028 ATTAATTTGTTAAAATATAAATCATAT
1 ATTAATTTGTTAAAATATAAATAATAT
* * *
627055 ATAAATTTTTTAAAATATATATAAT-T
1 ATTAATTTGTTAAAATATAAATAATAT
627081 AATTAATT
1 -ATTAATT
627089 AATTTTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTAATTTGTTAAAATATAAATAATAT
Found at i:627307 original size:3 final size:3
Alignment explanation
Indices: 627299--627332 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
627289 ATTTTATAAT
627299 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
627333 AGGGGAAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:628275 original size:20 final size:20
Alignment explanation
Indices: 628236--628271 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
628226 TTTATTTTTT
628236 AAATTATAATAATTTATAAA
1 AAATTATAATAATTTATAAA
628256 AAATTAT-AT-ATTTATA
1 AAATTATAATAATTTATA
628272 TAAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 2 0.12
20 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTATAATAATTTATAAA
Found at i:628286 original size:20 final size:21
Alignment explanation
Indices: 628263--628302 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
628253 AAAAAATTAT
*
628263 ATATTTATA-TAAATTTTAAA
1 ATATTTATATTAAATATTAAA
628283 ATATTTATATTAAATATTAA
1 ATATTTATATTAAATATTAA
628303 TTTTTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTTATATTAAATATTAAA
Found at i:628299 original size:27 final size:27
Alignment explanation
Indices: 628246--628306 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
628236 AAATTATAAT
*
628246 AATTTATAAAAAATTATATATTTATATA
1 AATTT-TAAAAAATTATATATTAATATA
* *
628274 AATTTTAAAATATT-TATATTAAATATT
1 AATTTTAAAAAATTATATATT-AATATA
628301 AATTTT
1 AATTTT
628307 TATTGTACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 18 0.62
28 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTTAAAAAATTATATATTAATATA
Found at i:628894 original size:19 final size:19
Alignment explanation
Indices: 628870--628916 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 19
628860 TTAATTTGAT
628870 TTAAAATAATAATATTTTA
1 TTAAAATAATAATATTTTA
628889 TT--AA-AATAATATTTTA
1 TTAAAATAATAATATTTTA
628905 TTAAAAT-ATAAT
1 TTAAAATAATAAT
628917 TATAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 14 0.56
17 2 0.08
18 7 0.28
19 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATAATAATATTTTA
Found at i:628896 original size:16 final size:16
Alignment explanation
Indices: 628877--628912 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
628867 GATTTAAAAT
628877 AATAATATTTTATTAA
1 AATAATATTTTATTAA
628893 AATAATATTTTATTAA
1 AATAATATTTTATTAA
628909 AATA
1 AATA
628913 TAATTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAATATTTTATTAA
Found at i:628939 original size:19 final size:21
Alignment explanation
Indices: 628903--628942 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
628893 AATAATATTT
628903 TATTAAAATATAATTATAAAA
1 TATTAAAATATAATTATAAAA
*
628924 TATTAATAT-TAA-TATAAAA
1 TATTAAAATATAATTATAAAA
628943 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAAATATAATTATAAAA
Found at i:629313 original size:2 final size:2
Alignment explanation
Indices: 629301--629330 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
629291 GAATATAAAT
*
629301 TA TA CA 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
629331 AAGTCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:630052 original size:3 final size:3
Alignment explanation
Indices: 630041--630078 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
630031 CATTGTTATT
*
630041 ATC AGC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
630079 TCGTTATCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:631617 original size:16 final size:16
Alignment explanation
Indices: 631598--631629 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
631588 CATCATTAAA
631598 AATAAAATAAAAATTT
1 AATAAAATAAAAATTT
631614 AATAAAATAAAAATTT
1 AATAAAATAAAAATTT
631630 TCTTAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAAATAAAAATTT
Found at i:632589 original size:24 final size:23
Alignment explanation
Indices: 632529--632592 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 23
632519 TTTTTGATAT
*
632529 AAAT-TATTTAAAATAA-AATTA
1 AAATATATTTAAAATAATAATGA
* **
632550 TAATATAATAAAAAATAATAATGA
1 AAATAT-ATTTAAAATAATAATGA
632574 AAATATATTTATAAATAAT
1 AAATATATTTA-AAATAAT
632593 TAAAGTTAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 12 0.38
24 16 0.50
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATATATTTAAAATAATAATGA
Found at i:633041 original size:2 final size:2
Alignment explanation
Indices: 633036--633063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
633026 TGTGTATGTG
633036 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
633064 ACCACAAATT
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):
TA
Found at i:636240 original size:2 final size:2
Alignment explanation
Indices: 636233--636259 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
636223 AAATGAAAGT
636233 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
636260 TGGCATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:636934 original size:21 final size:23
Alignment explanation
Indices: 636909--636962 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
636899 TATTGATGTA
636909 ATAATTAATTTTAATT-AAAT-T
1 ATAATTAATTTTAATTAAAATAT
636930 ATAATGTAA-TTTAATTAAAATAAT
1 ATAAT-TAATTTTAATTAAAAT-AT
636954 ATAATTAAT
1 ATAATTAAT
636963 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
21 12 0.43
22 7 0.25
23 3 0.11
24 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATAATTAATTTTAATTAAAATAT
Found at i:637088 original size:12 final size:12
Alignment explanation
Indices: 637067--637099 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
637057 TTATTTTAAT
637067 ATTT-TTATTAC
1 ATTTATTATTAC
637078 ATTTATTATTAC
1 ATTTATTATTAC
*
637090 TTTTATTATT
1 ATTTATTATT
637100 TTGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTATTATTAC
Found at i:645562 original size:29 final size:30
Alignment explanation
Indices: 645502--645559 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
645492 TTAATGATAA
*
645502 AATATTATATTAATATTAAATACTTAAAAT
1 AATATTATATTAATATTAAATAATTAAAAT
*
645532 AATATTAT-TTATTATTAAAATAATTAAA
1 AATATTATATTAATATT-AAATAATTAAA
645560 TAAAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
AATATTATATTAATATTAAATAATTAAAAT
Found at i:645907 original size:26 final size:25
Alignment explanation
Indices: 645877--645926 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
645867 TCAATCTATA
*
645877 AATATTAAAATTTATATTATTAAAAC
1 AATATTAAAA-TAATATTATTAAAAC
* *
645903 AATATTATAATAATATTTTTAAAA
1 AATATTAAAATAATATTATTAAAA
645927 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATTAAAATAATATTATTAAAAC
Found at i:646182 original size:101 final size:101
Alignment explanation
Indices: 646059--646270 Score: 372
Period size: 101 Copynumber: 2.1 Consensus size: 101
646049 TGAAAAGAGA
* *
646059 AAAACA-TTTTTTAAAAAGAGTATCTTATTTTCCGTTAACCTATAAATCATTTTTTATTGACCAA
1 AAAACATTTTTTTAAAAAAAGTATCTTATTTTCCGCTAACCTATAAATCATTTTTTATTGACCAA
*
646123 ACTATTTTTTCACGAAACAAACACCGAAAAATACAT
66 ACTATTTTTTCACAAAACAAACACCGAAAAATACAT
646159 AAAACATTTTTTTAAAAAAAGTATCTTATTTTCCGCTAACCTATAAATCATTTTTTATTGACCAA
1 AAAACATTTTTTTAAAAAAAGTATCTTATTTTCCGCTAACCTATAAATCATTTTTTATTGACCAA
*
646224 ACTATTTTTTCGCAAAACAAACACCGAAAAATACAT
66 ACTATTTTTTCACAAAACAAACACCGAAAAATACAT
*
646260 AAACCATTTTT
1 AAAACATTTTT
646271 CCCCCAAATA
Statistics
Matches: 106, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
100 6 0.06
101 100 0.94
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (101 bp):
AAAACATTTTTTTAAAAAAAGTATCTTATTTTCCGCTAACCTATAAATCATTTTTTATTGACCAA
ACTATTTTTTCACAAAACAAACACCGAAAAATACAT
Found at i:650397 original size:23 final size:23
Alignment explanation
Indices: 650370--650415 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
650360 TTAATTAGAT
* *
650370 GTGTTCATTAATATGTTCATTTA
1 GTGTTCATCAATAAGTTCATTTA
**
650393 GTGTTTGTCAATAAGTTCATTTA
1 GTGTTCATCAATAAGTTCATTTA
650416 ATTTAAACGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (23 bp):
GTGTTCATCAATAAGTTCATTTA
Found at i:652908 original size:15 final size:15
Alignment explanation
Indices: 652888--652933 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
652878 ATAATTTTTT
*
652888 TATTTTTTTAAATTA
1 TATTTTTTAAAATTA
652903 TATTTTTTAAAATTA
1 TATTTTTTAAAATTA
652918 -A-TTTTTAAAA-TA
1 TATTTTTTAAAATTA
652930 TATT
1 TATT
652934 AAAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.07
13 10 0.36
14 2 0.07
15 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTTTAAAATTA
Found at i:652910 original size:14 final size:14
Alignment explanation
Indices: 652887--652933 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
652877 AATAATTTTT
652887 TTAT-TTTTTTAAA
1 TTATATTTTTTAAA
652900 TTATATTTTTTAAAA
1 TTATATTTTTT-AAA
652915 TTA-A-TTTTTAAA
1 TTATATTTTTTAAA
*
652927 ATATATT
1 TTATATT
652934 AAAAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 5 0.17
13 10 0.34
14 8 0.28
15 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATATTTTTTAAA
Found at i:653068 original size:9 final size:9
Alignment explanation
Indices: 653056--653160 Score: 53
Period size: 9 Copynumber: 11.2 Consensus size: 9
653046 ATGTATAATA
653056 TATTATTAT
1 TATTATTAT
653065 TATTATTAT
1 TATTATTAT
*
653074 TATATATT-C
1 TAT-TATTAT
653083 TATATATATAT
1 TAT-TAT-TAT
653094 TATATATTGCAT
1 TAT-TATT--AT
653106 ATATATATATAT
1 -TAT-TAT-TAT
653118 TA-TATTA-
1 TATTATTAT
653125 TATTATATAT
1 TATTAT-TAT
653135 T-TT-TTA-
1 TATTATTAT
653141 TATTATATAT
1 TATTAT-TAT
653151 TATTA-TAT
1 TATTATTAT
653159 TA
1 TA
653161 ATTTTATACA
Statistics
Matches: 80, Mismatches: 2, Indels: 29
0.72 0.02 0.26
Matches are distributed among these distances:
6 1 0.01
7 6 0.08
8 12 0.15
9 28 0.35
10 12 0.15
11 9 0.11
12 4 0.05
13 7 0.09
14 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (9 bp):
TATTATTAT
Found at i:653086 original size:7 final size:7
Alignment explanation
Indices: 653039--653182 Score: 95
Period size: 7 Copynumber: 20.6 Consensus size: 7
653029 ATTATTTGTA
*
653039 ATATAAT
1 ATATATT
* *
653046 ATGTATA
1 ATATATT
653053 ATATATT
1 ATATATT
653060 AT-TATT
1 ATATATT
653066 ATTATTATT
1 A-TA-TATT
653075 ATATATT
1 ATATATT
*
653082 CTATA-T
1 ATATATT
653088 ATATATT
1 ATATATT
653095 ATATATT
1 ATATATT
653102 GCATATA-T
1 --ATATATT
653110 ATATA-T
1 ATATATT
653116 ATTATATT
1 A-TATATT
653124 ATAT-TAT
1 ATATAT-T
*
653131 ATATTTT
1 ATATATT
*
653138 TTATATT
1 ATATATT
653145 ATATATT
1 ATATATT
653152 ATTATATT
1 A-TATATT
*
653160 A-ATTTT
1 ATATATT
*
653166 ATACATT
1 ATATATT
*
653173 -TATATC
1 ATATATT
653179 ATAT
1 ATAT
653183 TCTTTCTAAC
Statistics
Matches: 109, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
6 27 0.25
7 59 0.54
8 13 0.12
9 10 0.09
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (7 bp):
ATATATT
Found at i:653088 original size:2 final size:2
Alignment explanation
Indices: 653039--653158 Score: 60
Period size: 2 Copynumber: 69.0 Consensus size: 2
653029 ATTATTTGTA
*
653039 AT AT A- AT AT GT AT A- AT AT AT -T AT -T AT -T AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* **
653074 -T AT AT AT -T CT AT AT AT AT AT -T AT AT AT -T GC 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
* *
653112 AT AT AT -T AT AT -T AT AT -T AT AT AT -T TT TT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
653149 AT -T AT -T AT AT
1 AT AT AT AT AT AT
653159 TAATTTTATA
Statistics
Matches: 93, Mismatches: 7, Indels: 36
0.68 0.05 0.26
Matches are distributed among these distances:
1 18 0.19
2 75 0.81
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (2 bp):
AT
Found at i:653154 original size:26 final size:26
Alignment explanation
Indices: 653062--653158 Score: 85
Period size: 26 Copynumber: 3.7 Consensus size: 26
653052 AATATATTAT
653062 TATTAT-TATTATTATATATTCTATATATA
1 TATTATATATTATTATATATT-T-T-T-TA
** * *
653091 TATTATATATT-GCATATA-TATATA
1 TATTATATATTATTATATATTTTTTA
653115 TATTATAT-TATATTATATATTTTTTA
1 TATTATATAT-TATTATATATTTTTTA
653141 TATTATATATTATTATAT
1 TATTATATATTATTATAT
653159 TAATTTTATA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
23 1 0.02
24 11 0.20
25 5 0.09
26 21 0.38
27 1 0.02
28 1 0.02
29 11 0.20
30 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (26 bp):
TATTATATATTATTATATATTTTTTA
Found at i:653480 original size:178 final size:175
Alignment explanation
Indices: 653174--653904 Score: 668
Period size: 178 Copynumber: 4.2 Consensus size: 175
653164 TTATACATTT
* * * *** *
653174 ATATCATATTCTTTCTAACATGAC-AAATAATATTTGATTAATATTTAATAAATTTTTTGAAATT
1 ATATCAGATTCTTTCTGATATGACGAAA-AATATTTGATTAATGCCTAATAAATTTTTTGAAA-C
* * * * * * * *
653238 CGAAAGATATAACAAATACATATGGATATCAGATTCTTTTTGATACGACGAAAAATATTTGACTA
64 CGAAAGATGTGACAGATGCATATGGGTATCAGATTCCTTCTGACACGA--AAAAATATTTGACTA
* ** * *
653303 ATGCTTAATAAATTTTTTTGGAACCTGAAAGATGTGACAGATGCATGTGG
127 ATGCCTAATAAA-TTTTTTGGAACCCAAAAGATGTGACAAATGCATATGG
** *
653353 ATA-CAGATTCTTTCTGATATGATAAAAAATATTTGATTAACGCCTAATAAATTTTTTGAAACCG
1 ATATCAGATTCTTTCTGATATGACGAAAAATATTTGATTAATGCCTAATAAATTTTTTGAAACC-
** *
653417 GAAAGATGTGACAGATTTATATGGGTATCAAATTCCTTCTGACACGATAAAAAGTATTTGACTAA
65 GAAAGATGTGACAGATGCATATGGGTATCAGATTCCTTCTGACACGA-AAAAA-TATTTGACTAA
* * * **
653482 TGCTTAGTAAATTTCTTGGAACTTAAAAGATGTGACAAATGCATATGG
128 TGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCATATGG
* * * *
653530 ATATTAGATTCCTTT-GGATACGACGGAAAATATTTGATTAATGCCTAATAAATTTTTTGAAACC
1 ATATCAGATT-CTTTCTGATATGACGAAAAATATTTGATTAATGCCTAATAAATTTTTTGAAACC
* * * *
653594 AGAAAGATGTGATAGATGCATGTGGGTA-C--A------C--A-ACG-AAAAATATTTGATTGAT
65 -GAAAGATGTGACAGATGCATATGGGTATCAGATTCCTTCTGACACGAAAAAATATTTGACTAAT
* * * *
653646 GCCTAATAATTTTTTTTGAACCCGAAAGATGTGACAGATGCATATGG
129 GCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCATATGG
* * * * *
653693 GTATCAGATTCCTTCTGACT-CGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAAAACT
1 ATATCAGATTCTTTCTGA-TATGACGAAAAATATTTGATTAATGCCTAATAAATTTTTTGAAAC-
* * * * * * * *
653757 CAAAAGATGTGACATATGCATGTGAGTATCAGATTTCTTCTTACAGGACGAAAATATTTGACTAA
64 CGAAAGATGTGACAGATGCATATGGGTATCAGATTCCTTCTGACACGA-AAAAATATTTGACTAA
*
653822 TGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCATGTGG
128 TGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCATATGG
* * * * *
653870 GTATTAGATTCATTCTGACATGAGGAAAAATATTT
1 ATATCAGATTCTTTCTGATATGACGAAAAATATTT
653905 AACTAATGAT
Statistics
Matches: 455, Mismatches: 74, Indels: 48
0.79 0.13 0.08
Matches are distributed among these distances:
162 3 0.01
163 121 0.27
164 8 0.02
166 4 0.01
167 1 0.00
169 1 0.00
172 1 0.00
174 1 0.00
175 3 0.01
177 127 0.28
178 175 0.38
179 10 0.02
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (175 bp):
ATATCAGATTCTTTCTGATATGACGAAAAATATTTGATTAATGCCTAATAAATTTTTTGAAACCG
AAAGATGTGACAGATGCATATGGGTATCAGATTCCTTCTGACACGAAAAAATATTTGACTAATGC
CTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCATATGG
Found at i:653602 original size:89 final size:89
Alignment explanation
Indices: 653202--653614 Score: 422
Period size: 89 Copynumber: 4.6 Consensus size: 89
653192 CATGACAAAT
** * * * * *
653202 AATATTTGATTAATATTTAATAAATTTTTTGAAATTC-GAAAGATATAACAAATACATATGGATA
1 AATATTTGATTAATGCTTAATAAATTTTTTGAAA-CCAGAAAGATGTGACAGATGCATATGGATA
*
653266 TCAGATTCTTTTTGATACGACGAAA
65 TCAGATTCCTTTTGATACGACGAAA
* * * *
653291 AATATTTGACTAATGCTTAATAAATTTTTTTGGAACCTGAAAGATGTGACAGATGCATGTGGATA
1 AATATTTGATTAATGCTTAATAAA-TTTTTTGAAACCAGAAAGATGTGACAGATGCATATGGATA
* **
653356 -CAGATT-CTTTCTGATATGATAAAA
65 TCAGATTCCTTT-TGATACGACGAAA
* * * ** *
653380 AATATTTGATTAACGCCTAATAAATTTTTTGAAACCGGAAAGATGTGACAGATTTATATGGGTAT
1 AATATTTGATTAATGCTTAATAAATTTTTTGAAACCAGAAAGATGTGACAGATGCATATGGATAT
* * * *
653445 CAAATTCCTTCTGACACGA-TAAA
66 CAGATTCCTTTTGATACGACGAAA
* * * * * *
653468 AAGTATTTGACTAATGCTTAGTAAATTTCTTGGAACTTA-AAAGATGTGACAAATGCATATGGAT
1 AA-TATTTGATTAATGCTTAATAAATTTTTTGAAAC-CAGAAAGATGTGACAGATGCATATGGAT
* * *
653532 ATTAGATTCCTTTGGATACGACGGAA
64 ATCAGATTCCTTTTGATACGACGAAA
* *
653558 AATATTTGATTAATGCCTAATAAATTTTTTGAAACCAGAAAGATGTGATAGATGCAT
1 AATATTTGATTAATGCTTAATAAATTTTTTGAAACCAGAAAGATGTGACAGATGCAT
653615 GTGGGTACAC
Statistics
Matches: 260, Mismatches: 55, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
88 43 0.17
89 179 0.69
90 38 0.15
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (89 bp):
AATATTTGATTAATGCTTAATAAATTTTTTGAAACCAGAAAGATGTGACAGATGCATATGGATAT
CAGATTCCTTTTGATACGACGAAA
Found at i:653660 original size:74 final size:74
Alignment explanation
Indices: 653556--653695 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 74
653546 GATACGACGG
* *
653556 AAAATATTTGATTAATGCCTAATAA-ATTTTTTGAAACCAGAAAGATGTGATAGATGCATGTGGG
1 AAAATATTTGATTAATGCCTAATAATATTTTTTG-AACCAGAAAGATGTGACAGATGCATATGGG
653620 TACACAACGA
65 TACACAACGA
* * *
653630 AAAATATTTGATTGATGCCTAATAATTTTTTTTGAACCCGAAAGATGTGACAGATGCATATGGGT
1 AAAATATTTGATTAATGCCTAATAATATTTTTTGAACCAGAAAGATGTGACAGATGCATATGGGT
653695 A
66 A
653696 TCAGATTCCT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 53 0.88
75 7 0.12
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (74 bp):
AAAATATTTGATTAATGCCTAATAATATTTTTTGAACCAGAAAGATGTGACAGATGCATATGGGT
ACACAACGA
Found at i:653741 original size:163 final size:169
Alignment explanation
Indices: 653285--653912 Score: 546
Period size: 177 Copynumber: 3.7 Consensus size: 169
653275 TTTTGATACG
* ** *
653285 ACGA-AAAATATTTGACTAATGCTTAATAAATTTTTTTGGAACCTGAAAGATGTGACAGATGCAT
1 ACGACAAAATATTTGACTAATGCCTAATAAA-TTTTTTGGAACCCAAAAGATGTGACAAATGCAT
* * * * * ** * * *
653349 GTGGATA-CAGATTCTTTCTGA-TATGATAAAAAATATTTGATTAACGCCTAATAAATTTTTTGA
65 ATGGGTATTAGATTCCTTCTGACT-CGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAA
* ** * *
653412 AAC-CGGAAAGATGTGACAGATTTATATGGGTATCAAATTCCTTCTGAC
129 AACTC-AAAAGATGTGACAGATGCATGTGAGTATC-AA-----TCT-AC
* * * * **
653460 ACGATAAAAAGTATTTGACTAATGCTTAGTAAATTTCTTGGAACTTAAAAGATGTGACAAATGCA
1 ACGA-CAAAA-TATTTGACTAATGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCA
* * *
653525 TATGGATATTAGATTCCTT-TGGA-TACGACGGAAAATATTTGATTAATGCCTAATAAATTTTTT
64 TATGGGTATTAGATTCCTTCT-GACT-CGACGAAAAATATTTGACTAATGCCTAATAAATTTTTT
* * *
653588 GAAAC-CAGAAAGATGTGATAGATGCATGTGGGTA-C-A-C-A-
127 AAAACTCA-AAAGATGTGACAGATGCATGTGAGTATCAATCTAC
* * * * * *
653626 ACGA-AAAATATTTGATTGATGCCTAATAATTTTTTTTGAACCCGAAAGATGTGACAGATGCATA
1 ACGACAAAATATTTGACTAATGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCATA
*
653690 TGGGTATCAGATTCCTTCTGACTCGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAAAA
66 TGGGTATTAGATTCCTTCTGACTCGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAAAA
*
653755 CTCAAAAGATGTGACATATGCATGTGAGTATCAGATTTCTTCTTAC
131 CTCAAAAGATGTGACAGATGCATGTGAGTATCA-A-----TC-TAC
*
653801 AGGACGAAAATATTTGACTAATGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCAT
1 ACGAC-AAAATATTTGACTAATGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCAT
* * * *
653866 GTGGGTATTAGATTCATTCTGACAT-GAGGAAAAATATTTAACTAATG
65 ATGGGTATTAGATTCCTTCTGAC-TCGACGAAAAATATTTGACTAATG
653913 ATACGACATA
Statistics
Matches: 380, Mismatches: 49, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
163 125 0.33
164 9 0.02
166 5 0.01
167 1 0.00
169 1 0.00
172 1 0.00
174 1 0.00
175 8 0.02
177 134 0.35
178 95 0.25
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (169 bp):
ACGACAAAATATTTGACTAATGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATGCATA
TGGGTATTAGATTCCTTCTGACTCGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAAAA
CTCAAAAGATGTGACAGATGCATGTGAGTATCAATCTAC
Found at i:653833 original size:88 final size:89
Alignment explanation
Indices: 653621--653912 Score: 372
Period size: 89 Copynumber: 3.3 Consensus size: 89
653611 GCATGTGGGT
* * * * * * *
653621 ACACAACGAAAAATATTTGATTGATGCCTAATAATTTTTTTTGAACCCGAAAGATGTGACAGATG
1 ACACGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAGAACCCAAAAGATGTGACAAATG
* *
653686 CATATGGGTATCAGATTCCTTCTG
66 CATGTGGGTATCAGATTTCTTCTG
* * * *
653710 ACTCGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAAAACTCAAAAGATGTGACATATG
1 ACACGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAGAACCCAAAAGATGTGACAAATG
* *
653775 CATGTGAGTATCAGATTTCTTCTT
66 CATGTGGGTATCAGATTTCTTCTG
* *
653799 ACAGGACG-AAAATATTTGACTAATGCCTAATAAATTTTTTGGAACCCAAAAGATGTGACAAATG
1 ACACGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAGAACCCAAAAGATGTGACAAATG
*
653863 CATGTGGGTATTAGA-TTCATTCTG
66 CATGTGGGTATCAGATTTC-TTCTG
* * *
653887 ACATGAGGAAAAATATTTAACTAATG
1 ACACGACGAAAAATATTTGACTAATG
653913 ATACGACATA
Statistics
Matches: 175, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
87 3 0.02
88 75 0.43
89 97 0.55
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (89 bp):
ACACGACGAAAAATATTTGACTAATGCCTAATAAATTTTTTAGAACCCAAAAGATGTGACAAATG
CATGTGGGTATCAGATTTCTTCTG
Found at i:657394 original size:2 final size:2
Alignment explanation
Indices: 657389--657544 Score: 131
Period size: 2 Copynumber: 89.0 Consensus size: 2
657379 TATTATATGT
657389 TA TA TA TA T- TA TA TA TA -A TA -A TA TA T- TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
657425 T- TA TA TA -A TA TA TA T- TA -A TA TA T- TA TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
657460 TA TA T- TA TA TA TA TC TA T- TA TA TA TA TT TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
657498 TA TA -A TA TA TA -A TA TA TA -A TA TA TA -A CA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
657535 TA TA TA TA TA
1 TA TA TA TA TA
657545 ATAATTATAA
Statistics
Matches: 127, Mismatches: 5, Indels: 44
0.72 0.03 0.25
Matches are distributed among these distances:
1 22 0.17
2 105 0.83
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:657401 original size:5 final size:5
Alignment explanation
Indices: 657378--657521 Score: 58
Period size: 5 Copynumber: 28.8 Consensus size: 5
657368 TTCTCAAAAA
*
657378 ATATT ATATGT -TATAT ATATT ATATAT AATAAT ATATT AT-TAT ATTATT
1 ATATT ATAT-T ATAT-T ATATT ATAT-T -ATATT ATATT ATAT-T A-TATT
*
657427 ATATA ATA-T ATATT A-A-T ATATT ATA-T ATTATT ATA-T AT-TAT ATATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT A-TATT ATATT ATAT-T ATAT-T
* * * *
657474 CTATT ATA-T ATATTT ATATT A-ATAT ATAAT ATATA ATA-T ATAAT ATAT
1 ATATT ATATT ATA-TT ATATT ATAT-T ATATT ATATT ATATT ATATT ATAT
657522 AACATATAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 40
0.67 0.08 0.25
Matches are distributed among these distances:
3 2 0.02
4 20 0.19
5 59 0.55
6 22 0.21
7 4 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (5 bp):
ATATT
Found at i:657401 original size:7 final size:7
Alignment explanation
Indices: 657391--657553 Score: 119
Period size: 7 Copynumber: 23.6 Consensus size: 7
657381 TTATATGTTA
657391 TATATAT
1 TATATAT
657398 TATATA-
1 TATATAT
*
657404 TA-ATAA
1 TATATAT
657410 TATATTAT
1 TATA-TAT
657418 TATATTAT
1 TATA-TAT
*
657426 TATATAA
1 TATATAT
657433 TATATAT
1 TATATAT
657440 TAATATAT
1 T-ATATAT
657448 TATATAT
1 TATATAT
657455 TAT-TA-
1 TATATAT
657460 TATAT-T
1 TATATAT
657466 ATATATAT
1 -TATATAT
657474 CTAT-TA-
1 -TATATAT
657480 TATATAT
1 TATATAT
657487 T-TATAT
1 TATATAT
657493 TAATATAT
1 T-ATATAT
*
657501 AATATAT
1 TATATAT
*
657508 AATATAT
1 TATATAT
*
657515 AATATAT
1 TATATAT
* *
657522 AACATAT
1 TATATAT
*
657529 AATATAT
1 TATATAT
657536 ATATATAT
1 -TATATAT
*
657544 AATA-AT
1 TATATAT
657550 TATA
1 TATA
657554 AAAAAAATTA
Statistics
Matches: 133, Mismatches: 10, Indels: 27
0.78 0.06 0.16
Matches are distributed among these distances:
5 9 0.07
6 20 0.15
7 68 0.51
8 36 0.27
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.50
Consensus pattern (7 bp):
TATATAT
Found at i:657535 original size:43 final size:42
Alignment explanation
Indices: 657390--657547 Score: 110
Period size: 43 Copynumber: 3.6 Consensus size: 42
657380 ATTATATGTT
*
657390 ATATATATTATAT-ATA-ATAATATATTATTATATTATTATA-TA
1 ATATATATTATATAATATATAATATA--A-TATATTAATATATTA
* * *
657432 ATATATATTAATATATTATATATTATTATATATTATATATATCTA
1 ATATATATT-ATATAATATATAATATAATATATTA-ATATAT-TA
657477 TTATATATATTTATATTAATATATAATAT-ATAATATATAATATA-TA
1 --ATATATA-TTATA-TAATATATAATATAAT-ATAT-TAATATATTA
* *
657523 ACATATAATATATATATATATAATA
1 ATATATATTATATA-ATATATAATA
657548 ATTATAAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
42 18 0.19
43 23 0.24
44 8 0.08
45 8 0.08
46 2 0.02
47 12 0.13
48 22 0.23
49 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (42 bp):
ATATATATTATATAATATATAATATAATATATTAATATATTA
Found at i:667616 original size:2 final size:2
Alignment explanation
Indices: 667609--667658 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
667599 CCAAATGCCA
* * *
667609 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT TT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
667650 AT AT A- AT AT
1 AT AT AT AT AT
667659 TTATTTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:668041 original size:3 final size:3
Alignment explanation
Indices: 668033--668062 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
668023 CTCAAATATT
668033 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
668063 TGTTGTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:668148 original size:27 final size:26
Alignment explanation
Indices: 668123--668177 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
668113 AATATATATT
*
668123 TATTTATG--ATAGTTATAGAT-AAA
1 TATTTATGTAATAATTATAGATAAAA
*
668146 TATTTATGTAATAATTATATATAAAA
1 TATTTATGTAATAATTATAGATAAAA
668172 TATTTA
1 TATTTA
668178 AAATTATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
25 10 0.37
26 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (26 bp):
TATTTATGTAATAATTATAGATAAAA
Found at i:669866 original size:14 final size:14
Alignment explanation
Indices: 669829--669871 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
669819 ATATTTAACT
669829 AATTATTAAAAA-A
1 AATTATTAAAAATA
*
669842 TATT-TTAAAAAATA
1 AATTATT-AAAAATA
669856 AATTATTAAAAATA
1 AATTATTAAAAATA
669870 AA
1 AA
669872 ATAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 2 0.08
13 8 0.32
14 13 0.52
15 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTATTAAAAATA
Found at i:669878 original size:20 final size:20
Alignment explanation
Indices: 669850--669891 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
669840 AATATTTTAA
*
669850 AAAATAAATTATTAA-AAAT
1 AAAATAAATAATTAATAAAT
669869 AAAATAAAATAATTAATAAAT
1 AAAAT-AAATAATTAATAAAT
669890 AA
1 AA
669892 TTAGTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 9 0.45
21 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAATAATTAATAAAT
Found at i:670222 original size:46 final size:46
Alignment explanation
Indices: 670158--670245 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
670148 ATTTTTTTTC
* **
670158 TCTTTACTTTCTTATTTTCTCTTCCTTTTTCTTTCCTTCTCTTTCTT
1 TCTTTACTTTCTTATTTTCTCTCCCTTTCCCTTTCC-TCTCTTTCTT
670205 TCTTT-CTTTC-TATTTTTCTCTCCCTTTCCCTTTCCTCTCTT
1 TCTTTACTTTCTTA-TTTTCTCTCCCTTTCCCTTTCCTCTCTT
670246 CCTTCCCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 8 0.22
46 24 0.65
47 5 0.14
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (46 bp):
TCTTTACTTTCTTATTTTCTCTCCCTTTCCCTTTCCTCTCTTTCTT
Found at i:670843 original size:16 final size:17
Alignment explanation
Indices: 670813--670846 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
670803 TTTTTATTAG
670813 TATTTTAATAAATTAAT
1 TATTTTAATAAATTAAT
*
670830 TATTTT-ATATATTAAT
1 TATTTTAATAAATTAAT
670846 T
1 T
670847 TAATTATATT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTAATAAATTAAT
Found at i:671064 original size:10 final size:10
Alignment explanation
Indices: 671051--671083 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
671041 AAATAAATAT
671051 AAATTTTATA
1 AAATTTTATA
671061 AAATTTTATA
1 AAATTTTATA
*
671071 AAATTTTGTA
1 AAATTTTATA
671081 AAA
1 AAA
671084 CTAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (10 bp):
AAATTTTATA
Found at i:672828 original size:12 final size:12
Alignment explanation
Indices: 672803--672839 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
672793 AAAGAAAAAG
*
672803 AAAATCAAAATC
1 AAAATCAAAGTC
672815 AAAATCAAAGTC
1 AAAATCAAAGTC
*
672827 AAAGTCAAAGTC
1 AAAATCAAAGTC
672839 A
1 A
672840 GAGTCAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.59, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCAAAGTC
Found at i:672836 original size:6 final size:6
Alignment explanation
Indices: 672807--672862 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
672797 AAAAAGAAAA
* * * * *
672807 TCAAAA TCAAAA TCAAAG TCAAAG TCAAAG TCAGAG TCAGAG TCAGAG
1 TCAAAG TCAAAG TCAAAG TCAAAG TCAAAG TCAAAG TCAAAG TCAAAG
*
672855 TCAGAG TC
1 TCAAAG TC
672863 GTCGAAGTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (6 bp):
TCAAAG
Done.