Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 125 of 250
Found at i:40211831 original size:28 final size:28
Alignment explanation
Indices: 40211799--40211869 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
40211789 TTGGCAGTAG
40211799 CTAAGACACATTAAAAACATGTACTAAA
1 CTAAGACACATTAAAAACATGTACTAAA
* * *
40211827 CTAAGACACATTAATAACATGTATTAGA
1 CTAAGACACATTAAAAACATGTACTAAA
*
40211855 TTAAGACACATTAAA
1 CTAAGACACATTAAA
40211870 CATTTTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.25
Consensus pattern (28 bp):
CTAAGACACATTAAAAACATGTACTAAA
Found at i:40219255 original size:38 final size:38
Alignment explanation
Indices: 40219209--40219307 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 38
40219199 GAAATCCTTG
*
40219209 TTATAATTATTGTAATTATAATTTACGAT-AGAATATTA
1 TTATAATTATTGTAATTATAATTTACGATCA-AACATTA
* *
40219247 TTATAATTATTGTAATTGA-AATTTTCGGTCAAACATTA
1 TTATAATTATTGTAATT-ATAATTTACGATCAAACATTA
*
40219285 CTATAATTA-TGATAATTATAATT
1 TTATAATTATTG-TAATTATAATT
40219308 ATTATATTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 3 0.06
38 48 0.91
39 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (38 bp):
TTATAATTATTGTAATTATAATTTACGATCAAACATTA
Found at i:40225737 original size:32 final size:32
Alignment explanation
Indices: 40225701--40225761 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
40225691 AATAAAATAA
40225701 TAAATTTACTTTTTAATTTAATATAAATCAAC
1 TAAATTTACTTTTTAATTTAATATAAATCAAC
40225733 TAAATTTACTTTTTAATTTAATATAAATC
1 TAAATTTACTTTTTAATTTAATATAAATC
40225762 TATTACCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (32 bp):
TAAATTTACTTTTTAATTTAATATAAATCAAC
Found at i:40227364 original size:20 final size:20
Alignment explanation
Indices: 40227329--40227381 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40227319 TTATGTTGCT
* *
40227329 TAAAATTTT-ATTTGTTTTA
1 TAAAATTTTCTTTTGTTTAA
**
40227348 TATTATTTTCTTTTGTTTAA
1 TAAAATTTTCTTTTGTTTAA
40227368 TAAAATTTTCTTTT
1 TAAAATTTTCTTTT
40227382 CTTTCGTGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
TAAAATTTTCTTTTGTTTAA
Found at i:40235804 original size:7 final size:7
Alignment explanation
Indices: 40235792--40235822 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
40235782 TTTATTAGGA
40235792 TTATATT
1 TTATATT
40235799 TTATATT
1 TTATATT
40235806 TTATATT
1 TTATATT
*
40235813 TTATCTT
1 TTATATT
40235820 TTA
1 TTA
40235823 CCTTTTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:40239314 original size:23 final size:23
Alignment explanation
Indices: 40239284--40239333 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
40239274 ATTTTTAAAT
40239284 TTTA-AATTATTTAAAAATAATA
1 TTTAGAATTATTTAAAAATAATA
***
40239306 TTTAGAATTATTTAGTGATAATA
1 TTTAGAATTATTTAAAAATAATA
40239329 TTTAG
1 TTTAG
40239334 TGATAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (23 bp):
TTTAGAATTATTTAAAAATAATA
Found at i:40239332 original size:13 final size:13
Alignment explanation
Indices: 40239314--40239346 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40239304 TATTTAGAAT
40239314 TATTTAGTGATAA
1 TATTTAGTGATAA
40239327 TATTTAGTGATAA
1 TATTTAGTGATAA
40239340 TATTTAG
1 TATTTAG
40239347 AAAAAATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:40246668 original size:18 final size:19
Alignment explanation
Indices: 40246635--40246670 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40246625 TCTTAGAGTA
*
40246635 AAATAATGTGTATTAAATC
1 AAATAAAGTGTATTAAATC
40246654 AAATAAAGT-TATTAAAT
1 AAATAAAGTGTATTAAAT
40246671 TTTTGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (19 bp):
AAATAAAGTGTATTAAATC
Found at i:40251983 original size:28 final size:28
Alignment explanation
Indices: 40251908--40252003 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 28
40251898 TATCTAGGAT
* *
40251908 ATGACATTGTGCTAAGTGAAATAAGACC
1 ATGACAATGTGCTAAGTGAAATAAGTCC
* *
40251936 ATGGC-A--T-CTAAATGAAATAAGTCC
1 ATGACAATGTGCTAAGTGAAATAAGTCC
40251960 ATGACAATGTGCTAAGTGAAATAAGTCC
1 ATGACAATGTGCTAAGTGAAATAAGTCC
* *
40251988 ATGGCATTGTGCTAAG
1 ATGACAATGTGCTAAG
40252004 CGAGAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
24 19 0.34
25 2 0.04
27 1 0.02
28 34 0.61
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (28 bp):
ATGACAATGTGCTAAGTGAAATAAGTCC
Found at i:40252106 original size:51 final size:51
Alignment explanation
Indices: 40252030--40252178 Score: 237
Period size: 51 Copynumber: 2.9 Consensus size: 51
40252020 TGAACCTTAA
* *
40252030 GAATAAAATAGCTTTGGACACAAGTGTGTTACTATATGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
40252081 GAATATAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* *
40252132 GAATAAAAGAGCTTTGG-CTACAAGGGTGGTACTATGTGAAGGCCACT
1 GAATAAAATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGGCCACT
40252179 GTGAAACTGT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 1 0.01
51 90 0.99
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:40253159 original size:25 final size:25
Alignment explanation
Indices: 40253125--40253177 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
40253115 ATTATTTACA
40253125 TACCAACTTACTAAGCTATATATCT
1 TACCAACTTACTAAGCTATATATCT
40253150 TACCAACTTACTAAGCTATATATCT
1 TACCAACTTACTAAGCTATATATCT
40253175 TAC
1 TAC
40253178 TCCTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (25 bp):
TACCAACTTACTAAGCTATATATCT
Found at i:40257759 original size:40 final size:40
Alignment explanation
Indices: 40257664--40257892 Score: 331
Period size: 40 Copynumber: 5.8 Consensus size: 40
40257654 TGGATGATAA
* * * **
40257664 CCGGGCTAAGTCCCGAAGGCA--TCTGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
40257702 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
40257741 CCGGGCTAAGTCCAGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
40257781 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
40257821 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
40257861 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
40257893 AGCTATATCC
Statistics
Matches: 175, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
37 14 0.08
38 6 0.03
39 18 0.10
40 135 0.77
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:40262892 original size:528 final size:531
Alignment explanation
Indices: 40261872--40262921 Score: 1990
Period size: 528 Copynumber: 2.0 Consensus size: 531
40261862 TTGGGTCATG
40261872 TGGTATCCGCATCGGGTATTCGAGTTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCT
1 TGGTATCCGCATCGGGTATTCGAGTTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCT
40261937 CCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTGCCGGTTACTACCGACGGTTTGTAAA
66 CCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTGCCGGTTACTACCGACGGTTTGTAAA
40262002 AGGTTTCTCGATGATAGCCACACCAATGACAAAGCTACTTCAAAAAGATGTTAAGTTCGAATGGA
131 AGGTTTCTCGATGATAGCCACACCAATGACAAAGCTACTTCAAAAAGATGTTAAGTTCGAATGGA
40262067 CGGAAAATGTTAGAAAGTTTCGAATGAACTGAAAACTTATATGACTGAAGCTCCAATTCTAGTGC
196 CGGAAAATGTTAGAAAGTTTCGAATGAACTGAAAACTTATATGACTGAAGCTCCAATTCTAGTGC
40262132 AGCCCGAATCAGGCAAAGAGTTTTGTCATTTATAGTGATGCCTCCCTACTTGGGTTGGGTTGCGT
261 AGCCCGAATCAGGCAAAGAGTTTTGTCATTTATAGTGATGCCTCCCTACTTGGGTTGGGTTGCGT
40262197 ATTGATGCAAGAGGGTCGAGTTGTGGCCTATGCGTCGAGACAATTAAAGCACATGAGAAAATTAT
326 ATTGATGCAAGAGGGTCGAGTTGTGGCCTATGCGTCGAGACAATTAAAGCACATGAGAAAATTAT
*
40262262 CCTACCCATGATCTCAAATTAGCTGCCATCGTATTCGCTTTGAAAATATGGCGACATTACTTATT
391 CCGACCCATGATCTCAAATTAGCTGCCATCGTATTCGCTTTGAAAATATGGCGACATTACTTATT
40262327 TGGTGAGAATGCCATGTATTTTCGGATTACAAAAGTCTCAAATATTTGATGACTCAAAGAGACTT
456 TGGTGAGAATGCCATGTATTTTCGGATTACAAAAGTCTCAAATATTTGATGACTCAAAGAGACTT
40262392 GAGAAATATCT
521 GAGAAATATCT
40262403 TGGTATCCGCATC-GGTATTCGAGTTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCT
1 TGGTATCCGCATCGGGTATTCGAGTTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCT
40262467 CCGAG-AATATTACTGAGGTTCGGAGCTTTTTGGGACTTGCCGGTTACTACCGACGGTTTGTAAA
66 CCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTGCCGGTTACTACCGACGGTTTGTAAA
40262531 AGGTTTCTCGATGATAGCCACACCAATGAC-AAGCTACTTCAAAAAGATGTTAAGTTCGAATGGA
131 AGGTTTCTCGATGATAGCCACACCAATGACAAAGCTACTTCAAAAAGATGTTAAGTTCGAATGGA
40262595 CGGAAAAATGTTAGAAAAGTTTCG-ATGAACTGAAAACTTATATGACTGAAGCTCCAATTCTAGT
196 CGG-AAAATGTTAG-AAAGTTTCGAATGAACTGAAAACTTATATGACTGAAGCTCCAATTCTAGT
40262659 GCAGCCCGAATCAGGCAAAGAG-TTTGTCATTTATAGTGATGCCTCCCTACTTGGGTTGGGTTGC
259 GCAGCCCGAATCAGGCAAAGAGTTTTGTCATTTATAGTGATGCCTCCCTACTTGGGTTGGGTTGC
40262723 GTATTGATGCAAGAGGGTCGAGTTGTGGCCTATGCGTCGAGACAATTAAAGCCACATGAGAAAAA
324 GTATTGATGCAAGAGGGTCGAGTTGTGGCCTATGCGTCGAGACAATTAAAG-CACATGAG-AAAA
40262788 TTATCCGA-CCATGATCTC-AATTAGCTGCCATCGTATTCGCTTTG-AAATATGGCGACATTACT
387 TTATCCGACCCATGATCTCAAATTAGCTGCCATCGTATTCGCTTTGAAAATATGGCGACATTACT
40262850 TATTTGGTGAGAAGTGCCATGTATTTTCGGATTACAAAAGTCTCAAATATTTGATGACTCAAAGA
452 TATTTGGTGAGAA-TGCCATGTATTTTCGGATTACAAAAGTCTCAAATATTTGATGACTCAAAGA
40262915 GACTTGA
516 GACTTGA
40262922 ATCTGCGACA
Statistics
Matches: 513, Mismatches: 1, Indels: 13
0.97 0.00 0.02
Matches are distributed among these distances:
527 31 0.06
528 214 0.42
529 179 0.35
530 76 0.15
531 13 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (531 bp):
TGGTATCCGCATCGGGTATTCGAGTTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCT
CCGAGAAATATTACTGAGGTTCGGAGCTTTTTGGGACTTGCCGGTTACTACCGACGGTTTGTAAA
AGGTTTCTCGATGATAGCCACACCAATGACAAAGCTACTTCAAAAAGATGTTAAGTTCGAATGGA
CGGAAAATGTTAGAAAGTTTCGAATGAACTGAAAACTTATATGACTGAAGCTCCAATTCTAGTGC
AGCCCGAATCAGGCAAAGAGTTTTGTCATTTATAGTGATGCCTCCCTACTTGGGTTGGGTTGCGT
ATTGATGCAAGAGGGTCGAGTTGTGGCCTATGCGTCGAGACAATTAAAGCACATGAGAAAATTAT
CCGACCCATGATCTCAAATTAGCTGCCATCGTATTCGCTTTGAAAATATGGCGACATTACTTATT
TGGTGAGAATGCCATGTATTTTCGGATTACAAAAGTCTCAAATATTTGATGACTCAAAGAGACTT
GAGAAATATCT
Found at i:40266300 original size:40 final size:40
Alignment explanation
Indices: 40266200--40266389 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
40266190 TGGATGATAA
* *** * * **
40266200 CCGGGCTAAGTCCCGAAGGCATCTACACTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
40266240 CCGGGC-AAGTCCC-AAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
40266278 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
40266318 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
*
40266359 -CGGGCTATGTCCCGAAGGCATTT-TAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGT-GCGAGT
40266390 AGCTATATCC
Statistics
Matches: 132, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
38 22 0.17
39 15 0.11
40 92 0.70
41 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:40268825 original size:48 final size:47
Alignment explanation
Indices: 40268707--40269221 Score: 408
Period size: 48 Copynumber: 10.7 Consensus size: 47
40268697 GGTAAGATGT
* * * *
40268707 CGATGCCATG-TCCTAGACATGGTCTTACACTGGCTCTCATATATTG-GTGC
1 CGATGCCATGTTCC-AAACATGGTCTTACACTAGC-C-CACA-ATCGAG-GC
*
40268757 CGATACCATGTTCCAAACATGGTCTTACACTAGCCCACAAGTCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACAA-TCGAGGC
* * * * ** *
40268805 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTCTA-TATAAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGC--CCACAATCGAGGC
* * ** *
40268853 CGATGCCATGTTCCAAACATGGTCATACACTGGCTCTCGTATATCG-GTGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGC-C-CACA-ATCGAG-GC
* ** * * * *
40268903 TGATGCCATGTTCCGGACATGGTCTTACACTACCCCACATGTTGAGGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
*
40268951 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* * * * ** *
40268999 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* * * * *
40269047 CGATGCCATATTCCAATCATGGTTTTACACTAGCCCACATGTTGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* *
40269095 CCATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* * * * * ** *
40269143 TGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
*
40269191 CGATGCCATGTCCCAAACATGGTCTTACACT
1 CGATGCCATGTTCCAAACATGGTCTTACACT
40269222 GGCTCACATA
Statistics
Matches: 379, Mismatches: 76, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
47 3 0.01
48 308 0.81
49 5 0.01
50 60 0.16
51 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACAATCGAGGC
Found at i:40269111 original size:144 final size:144
Alignment explanation
Indices: 40268707--40269230 Score: 672
Period size: 144 Copynumber: 3.6 Consensus size: 144
40268697 GGTAAGATGT
* * ** *
40268707 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATTGGTGCCGATACCATGTTCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA--AATGCCGATGCCATGTTCCA
* * * *
40268772 AACATGGTCTTACACTAGCCCACAAGTCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTA
64 AACATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTA
* * * ** *
40268837 GCTTC-TATATAAATGC
129 GC-CCACATGTCGAGGC
* * * * *** ** *
40268853 CGATGCCATGTTCCAAACATGGTCATACACTGGCTCTCGTATATCGGTGTTGATGCCATGTTCCG
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATATAAATGCCGATGCCATGTTCCA
* * *
40268918 GACATGGTCTTACACTACCCCACATGTTGAGGTCGATGCCATGTTCCAAACATGGTCTTACACTA
64 AACATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTA
40268983 GCCCACATGTCGAGGC
129 GCCCACATGTCGAGGC
* *
40268999 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATATTCCAAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
* *
40269064 CATGGTTTTACACTAGCCCACATGTTGAGGCCCATGCCATGTTCCAAACATGGTCTTACACTAGC
66 CATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTAGC
40269129 CCACATGTCGAGGC
131 CCACATGTCGAGGC
* *
40269143 TGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
* *
40269208 CATGGTCTTACACTGGCTCACAT
66 CATGGTCTTACACTAGCCCACAT
40269231 AACCCTACTA
Statistics
Matches: 329, Mismatches: 46, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
144 174 0.53
145 1 0.00
146 150 0.46
148 4 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (144 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
CATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTAGC
CCACATGTCGAGGC
Found at i:40269230 original size:96 final size:96
Alignment explanation
Indices: 40268707--40269231 Score: 545
Period size: 96 Copynumber: 5.4 Consensus size: 96
40268697 GGTAAGATGT
* * * *
40268707 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATTG-GTGCCGATACCATGTTCC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATA--GAG-GCCGATGCCATGTTCC
40268771 AAACATGGTCTTACACTAGCCCACA-AGTCGAGGC
63 AAACATGGTCTTACACTAGCCCACATA-TCGAGGC
* * *
40268805 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTC-TATATAAATGCCGATGCCATGTTCCAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC-TCACATATAGAGGCCGATGCCATGTTCCAA
* * ** *
40268869 ACATGGTCATACACTGGCTCTCGTATATCG-GTGT
65 ACATGGTCTTACACTAGC-C-CACATATCGAG-GC
* * * * * * * *
40268903 TGATGCCATGTTCCGGACATGGTCTTACACTACCCCACATGTTGAGGTCGATGCCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
*
40268968 CATGGTCTTACACTAGCCCACATGTCGAGGC
66 CATGGTCTTACACTAGCCCACATATCGAGGC
* * * * *
40268999 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATATTCCAAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
* * *
40269064 CATGGTTTTACACTAGCCCACATGTTGAGGC
66 CATGGTCTTACACTAGCCCACATATCGAGGC
* * * * * * * * *
40269095 CCATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCGAGGCTGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
* * ** *
40269160 CATGGTCTTACACTAGCTCTCATATAAATGC
66 CATGGTCTTACACTAGCCCACATATCGAGGC
* *
40269191 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
40269232 ACCCTACTAT
Statistics
Matches: 350, Mismatches: 69, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
96 232 0.66
97 5 0.01
98 110 0.31
99 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
CATGGTCTTACACTAGCCCACATATCGAGGC
Found at i:40272429 original size:28 final size:27
Alignment explanation
Indices: 40272362--40272450 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 27
40272352 ATATGACATC
* *
40272362 GTGCTAAGGGAAATAAGACCATGGCA-
1 GTGCTAAGTGAAATAAGTCCATGGCAT
40272388 -T-CTAAGTGAAATAAGTCCATGGCAAT
1 GTGCTAAGTGAAATAAGTCCATGGC-AT
*
40272414 GTGCTAAGTGAAATAAGTCCATGGCTTT
1 GTGCTAAGTGAAATAAGTCCATGGC-AT
40272442 GTGCTAAGT
1 GTGCTAAGT
40272451 CAGAAATTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
24 20 0.36
25 2 0.04
27 1 0.02
28 32 0.58
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (27 bp):
GTGCTAAGTGAAATAAGTCCATGGCAT
Found at i:40272652 original size:51 final size:51
Alignment explanation
Indices: 40272476--40272644 Score: 284
Period size: 51 Copynumber: 3.3 Consensus size: 51
40272466 TGAACCTTAG
*
40272476 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * ** *
40272527 GAATATAATAGCTTTGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
40272578 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
40272629 GAATAAAATAGCTTTG
1 GAATAAAATAGCTTTG
40272645 CCTACAAGGG
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 107 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:40272665 original size:51 final size:51
Alignment explanation
Indices: 40272476--40272673 Score: 274
Period size: 51 Copynumber: 3.9 Consensus size: 51
40272466 TGAACCTTAG
* *
40272476 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGCTACTATGTGAAGGCCACTTTGT
* * *
40272527 GAATATAATAGCTTTGAACACAAGTGTGAC-ACTATGTGAAGGTCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTG-CTACTATGTGAAGGCCACTTTGT
*
40272578 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGCTACTATGTGAAGGCCACTTTGT
* * * *
40272629 GAATAAAATAGCTTT-GCCTACAAGGGTGCTAATATGTGAATGCCA
1 GAATAAAATAGCTTTGGAC-ACAAGTGTGCTACTATGTGAAGGCCA
40272674 TTGTGTATCC
Statistics
Matches: 130, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.02
51 128 0.98
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGCTACTATGTGAAGGCCACTTTGT
Found at i:40272665 original size:102 final size:102
Alignment explanation
Indices: 40272476--40272668 Score: 309
Period size: 102 Copynumber: 1.9 Consensus size: 102
40272466 TGAACCTTAG
*
40272476 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATATAATAGCTT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATAAAATAGCTT
* *
40272541 TGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
66 TGAACACAAGGGTGACAATATGTGAAGGTCACTTTGT
*
40272578 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATAAAATAGCTT
*
40272643 TG-CCTACAAGGGTG-CTAATATGTGAA
66 TGAAC-ACAAGGGTGAC-AATATGTGAA
40272669 TGCCATTGTG
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
101 2 0.02
102 82 0.98
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (102 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATAAAATAGCTT
TGAACACAAGGGTGACAATATGTGAAGGTCACTTTGT
Found at i:40275241 original size:48 final size:43
Alignment explanation
Indices: 40275147--40275292 Score: 143
Period size: 42 Copynumber: 3.3 Consensus size: 43
40275137 AGGAAAATCA
* * * * * * *
40275147 CACACTTAGTGCCAAATAAATAGCTGAAGCTGTATCAATCTCG
1 CACACTAAGTGCCAAATATATAGCAGAAGCTATCTCGATCTTG
40275190 CACACTAAGTGCCAATATGTATATATAGCAGAAGCTATCTCGATCTTG
1 CACACTAAGTGCC-A-A---ATATATAGCAGAAGCTATCTCGATCTTG
* *
40275238 CACACTAAGCG-CAAATATATAGCCGAAGCTATCTCGAT-TTCG
1 CACACTAAGTGCCAAATATATAGCAGAAGCTATCTCGATCTT-G
40275280 CACACTAAGTGCC
1 CACACTAAGTGCC
40275293 CATAAATAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
41 2 0.02
42 34 0.40
43 13 0.15
44 1 0.01
45 2 0.02
46 1 0.01
47 1 0.01
48 32 0.37
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
CACACTAAGTGCCAAATATATAGCAGAAGCTATCTCGATCTTG
Found at i:40275816 original size:21 final size:20
Alignment explanation
Indices: 40275790--40275832 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
40275780 AAACTTATTT
* *
40275790 ATCTATTATCAACCATTCAAA
1 ATCTATCATCAAACA-TCAAA
40275811 ATCTATCATCAAACATCAAA
1 ATCTATCATCAAACATCAAA
40275831 AT
1 AT
40275833 ACATACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (20 bp):
ATCTATCATCAAACATCAAA
Found at i:40277263 original size:17 final size:17
Alignment explanation
Indices: 40277241--40277275 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40277231 CGTGTGGTTG
40277241 GCTGTGTGCGAGACACA
1 GCTGTGTGCGAGACACA
40277258 GCTGTGTGCGAGACACA
1 GCTGTGTGCGAGACACA
40277275 G
1 G
40277276 GCATGGCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.17
Consensus pattern (17 bp):
GCTGTGTGCGAGACACA
Found at i:40288556 original size:27 final size:27
Alignment explanation
Indices: 40288526--40288578 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
40288516 CTGAAATAAA
*
40288526 AAGGGGTTGCTATGTGCTGATTCCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCCC
40288553 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
40288579 GATTAAGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (27 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:40288590 original size:102 final size:103
Alignment explanation
Indices: 40288347--40288611 Score: 408
Period size: 102 Copynumber: 2.6 Consensus size: 103
40288337 GTTGTACATA
** *
40288347 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* * *
40288412 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAA-GTAAAAAGGGGTTGCTATGTGCTGATTCCCCC
*
40288451 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
40288515 TCTGAAA-TAAAAAGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAAGTAAAAAGGGGTTGCTATGTGCTGATTCCCCC
* * *
40288553 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
40288612 AATAACGGTT
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
102 82 0.55
103 2 0.01
104 64 0.43
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAAGTAAAAAGGGGTTGCTATGTGCTGATTCCCCC
Found at i:40290638 original size:29 final size:29
Alignment explanation
Indices: 40290575--40290676 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 29
40290565 ATACCTTATC
* * * *
40290575 TGGCCCATTAAGCCC-ATTCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTAATA
* *
40290603 TGGCCCATTAGGCTCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TAATA
*
40290632 TGGCCCATTAGGCCCAAATTACATTAATA
1 TGGCCCATTAGGCCCAAATCACATTAATA
*
40290661 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
40290677 GTCATATTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
28 14 0.23
29 47 0.76
30 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTAATA
Found at i:40301503 original size:80 final size:79
Alignment explanation
Indices: 40301371--40301551 Score: 292
Period size: 80 Copynumber: 2.3 Consensus size: 79
40301361 TATTCGGATG
* *
40301371 ATATCCGGGCTAAGTCCCGAAGGCATGGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCGT
1 ATATCCGGGCTAAGTCCCGAAGGCATGGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCAT
40301436 TTGTGCGAGTTGCT
66 TTGTGCGAGTTGCT
* * *
40301450 ATATCCGGGCTAAGTCCCAAAGGCTTTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGC-ATGGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
40301515 TTTGTGCGAGTTGCT
65 TTTGTGCGAGTTGCT
*
40301530 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
40301552 TACTTGGGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 37 0.39
80 57 0.61
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCATGGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCAT
TTGTGCGAGTTGCT
Found at i:40301551 original size:39 final size:40
Alignment explanation
Indices: 40301371--40301551 Score: 244
Period size: 40 Copynumber: 4.6 Consensus size: 40
40301361 TATTCGGATG
* *
40301371 ATATCCGGGCTAAGTCCCGAAGGCA-TGGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
*
40301410 ATATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACT
* * *
40301450 ATATCCGGGCTAAGTCCCAAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
*
40301490 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACT
*
40301530 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
40301552 TACTTGGGTT
Statistics
Matches: 126, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
39 40 0.32
40 82 0.65
41 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
Found at i:40304922 original size:33 final size:32
Alignment explanation
Indices: 40304867--40304947 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
40304857 TTTTTTACAT
*
40304867 ATATATATTATATA-AAACATGA-CCTTGAAATGC
1 ATATATATTATATATAAACATGACCCAT-AAA--C
**
40304900 ATATATATTATATATTTA-ATGACCCATAAAC
1 ATATATATTATATATAAACATGACCCATAAAC
40304931 ATATATATTATATATAA
1 ATATATATTATATATAA
40304948 CAAATATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
31 16 0.39
33 21 0.51
34 4 0.10
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (32 bp):
ATATATATTATATATAAACATGACCCATAAAC
Found at i:40304954 original size:18 final size:18
Alignment explanation
Indices: 40304928--40304968 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
40304918 ATGACCCATA
*
40304928 AACATATATATTATATAT
1 AACAAATATATTATATAT
*
40304946 AACAAATATTTTATATAT
1 AACAAATATATTATATAT
40304964 AACAA
1 AACAA
40304969 GATGCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
AACAAATATATTATATAT
Found at i:40305223 original size:31 final size:30
Alignment explanation
Indices: 40305124--40305223 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 30
40305114 CTACACGCAT
* *
40305124 ATATATATTGTATATATAACATAACCATGACGC
1 ATATATATTATATATATAACA-AA-C-TCACGC
* * *
40305157 ATATATTTTATATATATAACAAAATC-CAC
1 ATATATATTATATATATAACAAACTCACGC
*
40305186 ACATATATTATATATATAACGAAACTCACGC
1 ATATATATTATATATATAAC-AAACTCACGC
40305217 ATATATA
1 ATATATA
40305224 GGTATTATGT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
29 20 0.36
30 6 0.11
31 8 0.15
32 2 0.04
33 19 0.35
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (30 bp):
ATATATATTATATATATAACAAACTCACGC
Found at i:40308713 original size:40 final size:40
Alignment explanation
Indices: 40308629--40308853 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
40308619 TCGAATGATG
* * * *
40308629 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40308669 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40308709 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40308748 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40308788 TCCGGGTTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40308829 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40308854 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 35 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40313827 original size:16 final size:18
Alignment explanation
Indices: 40313808--40313840 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40313798 CATACAAATT
40313808 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
40313824 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
40313841 GTGACAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:40314475 original size:43 final size:43
Alignment explanation
Indices: 40314402--40314523 Score: 210
Period size: 43 Copynumber: 2.8 Consensus size: 43
40314392 CTGAACTCAT
*
40314402 TCACCGGCATTAT-GCCTGCTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTACTAGGCTCGAAGCCCGATATTAAC
40314444 TCACCGGCATTATAGCCTACTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTACTAGGCTCGAAGCCCGATATTAAC
*
40314487 TCACCGACATTATAGCCTACTAGGCTCGAAGTCCCGA
1 TCACCGGCATTATAGCCTACTAGGCTCGAAG-CCCGA
40314524 ATAGTACCGT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
42 13 0.17
43 58 0.76
44 5 0.07
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTACTAGGCTCGAAGCCCGATATTAAC
Found at i:40316931 original size:14 final size:14
Alignment explanation
Indices: 40316914--40316941 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40316904 TCACGAAAAT
40316914 TTCACACATATAAA
1 TTCACACATATAAA
40316928 TTCACACATATAAA
1 TTCACACATATAAA
40316942 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TTCACACATATAAA
Found at i:40324953 original size:14 final size:15
Alignment explanation
Indices: 40324934--40324962 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40324924 TTACGAAAGT
40324934 TTCACACAT-ATAAA
1 TTCACACATAATAAA
40324948 TTCACACATAATAAA
1 TTCACACATAATAAA
40324963 AAAAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:40325599 original size:13 final size:13
Alignment explanation
Indices: 40325581--40325609 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40325571 TATTAAAAAC
40325581 CCTAATATTTAAA
1 CCTAATATTTAAA
40325594 CCTAATATTTAAA
1 CCTAATATTTAAA
40325607 CCT
1 CCT
40325610 TAAAAGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (13 bp):
CCTAATATTTAAA
Found at i:40330120 original size:15 final size:16
Alignment explanation
Indices: 40330100--40330129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40330090 CACAATTTAA
40330100 TTATAC-GATATGGAT
1 TTATACGGATATGGAT
40330115 TTATACGGATATGGA
1 TTATACGGATATGGA
40330130 GGCGATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (16 bp):
TTATACGGATATGGAT
Found at i:40352501 original size:22 final size:22
Alignment explanation
Indices: 40352471--40352518 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40352461 CAAAGTTAAC
* * *
40352471 AAATCAACCGAATAGAAATTTT
1 AAATCAACCAAACAAAAATTTT
*
40352493 AAATTAACCAAACAAAAATTTT
1 AAATCAACCAAACAAAAATTTT
40352515 AAAT
1 AAAT
40352519 AGCTTGAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (22 bp):
AAATCAACCAAACAAAAATTTT
Found at i:40354781 original size:17 final size:17
Alignment explanation
Indices: 40354759--40354794 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40354749 GCATCATCAC
40354759 GTGCCCATATGAAATTT
1 GTGCCCATATGAAATTT
40354776 GTGCCCATATGAAATTT
1 GTGCCCATATGAAATTT
40354793 GT
1 GT
40354795 TCATACTACG
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:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (17 bp):
GTGCCCATATGAAATTT
Found at i:40361171 original size:3 final size:3
Alignment explanation
Indices: 40361158--40361187 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
40361148 TTAGGTAAAG
40361158 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40361188 GGTAAGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40364875 original size:35 final size:34
Alignment explanation
Indices: 40364811--40364884 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 34
40364801 AACTTGTCTG
*
40364811 ACTAGTGCTGGGCACACAACCGTTAGTTTATCCA
1 ACTAGCGCTGGGCACACAACCGTTAGTTTATCCA
*
40364845 ACTAGCGCTGGGCACA-ATCACCGTTGGTTTATCCA
1 ACTAGCGCTGGGCACACA--ACCGTTAGTTTATCCA
40364880 ACTAG
1 ACTAG
40364885 AGTTGCGCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 1 0.03
34 15 0.42
35 20 0.56
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (34 bp):
ACTAGCGCTGGGCACACAACCGTTAGTTTATCCA
Found at i:40389398 original size:29 final size:29
Alignment explanation
Indices: 40389349--40389410 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
40389339 TGCCTAGTCG
*
40389349 TGTGGTTGGCCATGCGCGAGACACGGCCA
1 TGTGGTTGGCCATGCACGAGACACGGCCA
* * *
40389378 TGTGGTTGGCCGTGCATGAGACACGGTCA
1 TGTGGTTGGCCATGCACGAGACACGGCCA
40389407 TGTG
1 TGTG
40389411 TTCGACGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.39, T:0.23
Consensus pattern (29 bp):
TGTGGTTGGCCATGCACGAGACACGGCCA
Found at i:40393008 original size:49 final size:49
Alignment explanation
Indices: 40392884--40393383 Score: 758
Period size: 47 Copynumber: 10.4 Consensus size: 49
40392874 TTGTGATGTG
40392884 AGTGTATATATATGTGAT-AGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
40392932 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
40392979 AGTGTATATATATGTGATAAGG-CTGAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCT-AATGGCCGATGTGATGAATGTGAA
40393028 AGTGTATATATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATA--TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
40393079 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
40393128 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
40393175 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
40393224 AGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
40393271 AGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
40393318 AGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
40393365 AGTGTATA-A-ATGTGATAAG
1 AGTGTATATATATGTGATAAG
40393384 TCCCGAAGGG
Statistics
Matches: 420, Mismatches: 21, Indels: 23
0.91 0.05 0.05
Matches are distributed among these distances:
46 12 0.03
47 215 0.51
48 6 0.01
49 139 0.33
51 46 0.11
52 2 0.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:40393033 original size:96 final size:96
Alignment explanation
Indices: 40392884--40393383 Score: 814
Period size: 96 Copynumber: 5.2 Consensus size: 96
40392874 TTGTGATGTG
40392884 AGTGTATATATATGTGAT-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
40392948 AAGGCCGAATGGCCAATGTGATGAATGTGAA
66 AAGGCCGAATGGCCAATGTGATGAATGTGAA
40392979 AGTGTATATATATGTGATAAGG-CTGAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT
1 AGTGTATATATATGTGATAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTG--TATATA--T
* *
40393043 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
61 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
40393079 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
40393144 AAGGCCGAATGGCCAATGTGATGAATGTGAA
66 AAGGCCGAATGGCCAATGTGATGAATGTGAA
40393175 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* * *
40393240 AAGGCCTAATAGCCGATGTGATGAATGTGAA
66 AAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
40393271 AGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* * * *
40393334 AGGGCCGAGTGGCCAACGTGATGGATGTGAA
66 AAGGCCGAATGGCCAATGTGATGAATGTGAA
40393365 AGTGTATA-A-ATGTGATAAG
1 AGTGTATATATATGTGATAAG
40393384 TCCCGAAGGG
Statistics
Matches: 379, Mismatches: 17, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
94 94 0.25
95 21 0.06
96 165 0.44
98 12 0.03
100 85 0.22
101 2 0.01
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
AAGGCCGAATGGCCAATGTGATGAATGTGAA
Found at i:40396014 original size:21 final size:22
Alignment explanation
Indices: 40395988--40396028 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
40395978 CATTAACGAG
40395988 TCAATGTTGTGACA-TCAACAT
1 TCAATGTTGTGACACTCAACAT
40396009 TCAATGTTGTGACACTCAAC
1 TCAATGTTGTGACACTCAAC
40396029 TTTGAGGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (22 bp):
TCAATGTTGTGACACTCAACAT
Found at i:40396627 original size:22 final size:22
Alignment explanation
Indices: 40396602--40396647 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
40396592 TTTAGGTAGA
40396602 TGTGGTCAAAAGAATAGTCTAC
1 TGTGGTCAAAAGAATAGTCTAC
40396624 TGTGGTCAAAAGAATAGTCTAC
1 TGTGGTCAAAAGAATAGTCTAC
40396646 TG
1 TG
40396648 AGCATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (22 bp):
TGTGGTCAAAAGAATAGTCTAC
Found at i:40400369 original size:25 final size:25
Alignment explanation
Indices: 40400303--40400397 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
40400293 AGCTTCTCTT
* * * **
40400303 GAGCCATATAACAAGAAGCTCATGT
1 GAGCTATATAACAGGAAGCTTATCC
*
40400328 GAGCTATATGAA-GGGAAGCTTATCC
1 GAGCTATAT-AACAGGAAGCTTATCC
40400353 GAGCTATATAACAGGAAGCTTATCC
1 GAGCTATATAACAGGAAGCTTATCC
* *
40400378 GGGCTATATAACAGAAAGCT
1 GAGCTATATAACAGGAAGCT
40400398 CATAAGAGCC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 2 0.03
25 55 0.93
26 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (25 bp):
GAGCTATATAACAGGAAGCTTATCC
Found at i:40400384 original size:50 final size:51
Alignment explanation
Indices: 40400289--40400386 Score: 117
Period size: 50 Copynumber: 1.9 Consensus size: 51
40400279 GCACATAATC
* * **
40400289 GGGAAGCTTCTCTTGAGCCATATAACAAGAAGCTCATGTGAGCTATATGAA
1 GGGAAGCTTATCTCGAGCCATATAACAAGAAGCTCATCCGAGCTATATGAA
* * * *
40400340 GGGAAGCTTATC-CGAGCTATATAACAGGAAGCTTATCCGGGCTATAT
1 GGGAAGCTTATCTCGAGCCATATAACAAGAAGCTCATCCGAGCTATAT
40400387 AACAGAAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
50 28 0.72
51 11 0.28
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (51 bp):
GGGAAGCTTATCTCGAGCCATATAACAAGAAGCTCATCCGAGCTATATGAA
Found at i:40400411 original size:25 final size:25
Alignment explanation
Indices: 40400383--40400437 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
40400373 TATCCGGGCT
40400383 ATATAACAGAAAGCTCATAAGAGCC
1 ATATAACAGAAAGCTCATAAGAGCC
** **
40400408 ATAT-TTAGAAAGCTCATGCGAGCC
1 ATATAACAGAAAGCTCATAAGAGCC
40400432 A-ATAAC
1 ATATAAC
40400438 GGGTAGCTCC
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
23 2 0.09
24 17 0.74
25 4 0.17
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (25 bp):
ATATAACAGAAAGCTCATAAGAGCC
Found at i:40400470 original size:73 final size:73
Alignment explanation
Indices: 40400393--40400559 Score: 162
Period size: 73 Copynumber: 2.3 Consensus size: 73
40400383 ATATAACAGA
* * *
40400393 AAGCTCATAAGAGCCATAT-T-TAGAAAGCTCATGCGAGCCAATAACGGGTAGCTCCAAAGAG-C
1 AAGCTCATAAGAGCCATATATCAAG-AAGCTCAAGCGAGCC-ATAACGGGAAGCTCCAAAGAGTC
*
40400455 TATTAATTGGG
64 -ATTAATTAGG
* * * * * *
40400466 AAGCTC-TAGATAGCCATATATCAAGAAGTTCAAGTGAGCCATATCGGGAAGCTTCGAAGAGTCA
1 AAGCTCATA-AGAGCCATATATCAAGAAGCTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGTCA
40400530 TTAATTAGG
65 TTAATTAGG
*
40400539 AAGCTCACAAAGAGCCATATA
1 AAGCTCA-TAAGAGCCATATA
40400560 ATAGGACGCT
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
72 2 0.03
73 47 0.62
74 24 0.32
75 3 0.04
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (73 bp):
AAGCTCATAAGAGCCATATATCAAGAAGCTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGTCAT
TAATTAGG
Found at i:40400564 original size:26 final size:26
Alignment explanation
Indices: 40400522--40400571 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40400512 GGAAGCTTCG
*
40400522 AAGAGTCATTAATTAGGAAGCTCACA
1 AAGAGCCATTAATTAGGAAGCTCACA
*
40400548 AAGAGCCATATAA-TAGGACGCTCA
1 AAGAGCCAT-TAATTAGGAAGCTCA
40400572 TAAGATCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (26 bp):
AAGAGCCATTAATTAGGAAGCTCACA
Found at i:40401040 original size:21 final size:21
Alignment explanation
Indices: 40401016--40401057 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40401006 TAAATTTATC
*
40401016 TCAATTTAATACAATTCATAT
1 TCAATTCAATACAATTCATAT
*
40401037 TCAATTCAATTCAATTCATAT
1 TCAATTCAATACAATTCATAT
40401058 CCTAGGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (21 bp):
TCAATTCAATACAATTCATAT
Found at i:40401045 original size:5 final size:5
Alignment explanation
Indices: 40401016--40401054 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
40401006 TAAATTTATC
* *
40401016 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
40401055 TATCCTAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:40403595 original size:14 final size:14
Alignment explanation
Indices: 40403578--40403606 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40403568 TATTATAATC
40403578 ATTAAGTTTAATTA
1 ATTAAGTTTAATTA
40403592 ATTAAGTTTAATTA
1 ATTAAGTTTAATTA
40403606 A
1 A
40403607 ACCTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTAAGTTTAATTA
Found at i:40403671 original size:20 final size:20
Alignment explanation
Indices: 40403646--40403684 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40403636 GTTACAGGGG
40403646 GAGAGATGAAAGTCATCAAA
1 GAGAGATGAAAGTCATCAAA
40403666 GAGAGATGAAAGTCATCAA
1 GAGAGATGAAAGTCATCAA
40403685 CTTCCCTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGAGATGAAAGTCATCAAA
Found at i:40406150 original size:682 final size:682
Alignment explanation
Indices: 40404838--40406202 Score: 2347
Period size: 682 Copynumber: 2.0 Consensus size: 682
40404828 GTGGTCAGGT
*
40404838 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACTAA
1 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
* *
40404903 TTAAGATCACACGGCCAAGTCACACACCCGTGTGCTAGGCCATGCGGAAAATTAATTTTCATAAA
66 TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
* **
40404968 ATAGGTGCAGACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACATGGCT
131 ATAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACACAGCT
* *
40405033 GAGGCACACTCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
196 GAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
* *
40405098 TGCAGGGGACACATGGCCAACACACATTCCCATGGGACAGGCCATGTGTCACACACAGTCTAGAC
261 TGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAGAC
* *
40405163 ACATGCACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCTTA
326 ACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCCTA
* * **
40405228 ATTCACACATACACTTACACCAATTAAAAGGCACAAAACATAATATACTTAGGCAATGAAACATC
391 ATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACATC
* * * *
40405293 CATAATTATGACCTACACATGCCAATACAATATCAGCATCGATCATACTCACAATATTTATTATG
456 CACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTATA
* * *
40405358 CTCTAACTCAATCATGCAAATTTCCAGTCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
521 CCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
*
40405423 TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGCTATAAA
586 TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATAAA
40405488 TCACTTTCCATCATACACCAAGCATACCATGA
651 TCACTTTCCATCATACACCAAGCATACCATGA
* *
40405520 CGTGTGGTCACACATGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
1 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
* *
40405585 TTAAGATTACACAGCCAAGTCACACACCCGTGTGCTAGGCTATGCGAAAAATTAATTTTCAT-AA
66 TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
40405649 ATAAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGG-CTGTGCCGTCTACACAG
131 AT-AGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTC-GTGCCGTCTACACAG
* * *
40405713 CTGAGACACACGCCCGTGTCTCTGCCCGTGTGCTCAATTCTGAGTATTTTGTTTCTCAAAATTAG
194 CTGAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAA
* *
40405778 GGTGCAGGGGGCACATGGCCAACACACATCCCCATGGGACAGGCCGTGTATCACACACAGTCTAG
259 GGTGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAG
* *
40405843 ACACATACACGTGTGTCTACCCTTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCC
324 ACACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCC
40405908 TAATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACA
389 TAATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACA
40405973 TCCACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTA
454 TCCACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTA
40406038 TACCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTA
519 TACCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTA
* ***
40406103 ATTGTACATAAATTTATCATCTCATCAATCTTTCACATTTCCAAACATTTCACTTTCATGATATA
584 ATTGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATA
40406168 AATCACTTTCCATCATACACCAAGCATACCATGA
649 AATCACTTTCCATCATACACCAAGCATACCATGA
40406202 C
1 C
40406203 TATAACACCA
Statistics
Matches: 642, Mismatches: 39, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
681 5 0.01
682 637 0.99
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (682 bp):
CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
ATAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACACAGCT
GAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
TGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAGAC
ACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCCTA
ATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACATC
CACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTATA
CCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATAAA
TCACTTTCCATCATACACCAAGCATACCATGA
Found at i:40414741 original size:50 final size:50
Alignment explanation
Indices: 40414650--40414988 Score: 439
Period size: 50 Copynumber: 7.0 Consensus size: 50
40414640 TTTGACCACA
**
40414650 TAGGTAAGTACATATGTGATG-TATATTGAACCTTGTGTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* *
40414699 TAGGTAAGTATTTATGTGATGATATATTGAAGCTTGTTTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* * *
40414749 TAGGTAAGAATTTATGTGATGATAAATTGAACCTTCTGTATTCGGCC---
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
*
40414796 -----AAGTATTTATGTGATGATATATTGAACCTTCTGTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
40414841 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* * * *
40414891 TAGGTAAGTATTCATGTGATGATATATTGAACCTTGTATATTTGGCCATA
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* * **
40414941 T-GAGTATGTATTTATGTGATGATATACTTG-ATCTTGCATATTCGGCCA
1 TAG-GTAAGTATTTATGTGATGATATA-TTGAACCTTGTGTATTCGGCCA
40414989 AATGAATGGT
Statistics
Matches: 258, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
42 40 0.16
49 20 0.08
50 195 0.76
51 3 0.01
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (50 bp):
TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
Found at i:40414813 original size:92 final size:92
Alignment explanation
Indices: 40414704--40414964 Score: 344
Period size: 92 Copynumber: 2.8 Consensus size: 92
40414694 CCATGTAGGT
* * *
40414704 AAGTATTTATGTGATGATATATTGAAGCTTGTTTATTCGGCCATGTAGGTAAGAATTTATGTGAT
1 AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
40414769 GATAAATTGAACCTTCTGTATTCGGCC
66 GATAAATTGAACCTTCTGTATTCGGCC
* *
40414796 AAGTATTTATGTGATGATATATTGAACCTTCTGTATTCGGCCATGTAGGTAAGTATTTATGTGAT
1 AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
* *
40414861 GATATATTGAACCTTGTGTATTCGGCC
66 GATAAATTGAACCTTCTGTATTCGGCC
* * *
40414888 ATGTAGGTAAGTATTCATGTGATGATATATTGAACCTTGTATATTTGGCCATAT-GAGTATGTAT
1 A---A-GT-A-T-TT-ATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAG-GTAAGTAT
40414952 TTATGTGATGATA
57 TTATGTGATGATA
40414965 TACTTGATCT
Statistics
Matches: 149, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
92 87 0.58
95 1 0.01
96 2 0.01
97 1 0.01
98 1 0.01
99 3 0.02
100 54 0.36
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (92 bp):
AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
GATAAATTGAACCTTCTGTATTCGGCC
Found at i:40414837 original size:142 final size:141
Alignment explanation
Indices: 40414662--40414925 Score: 465
Period size: 142 Copynumber: 1.9 Consensus size: 141
40414652 GGTAAGTACA
*
40414662 TATGTGATGTATATTGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTTATGTGATGATATATT
1 TATGTGATGTATATTGAACCTTCTGTATTCGGCCATGTAGGTAAGTATTTATGTGATGATATATT
* * *
40414727 GAAGCTTGTTTATTCGGCCATGTAGGTAAGAATTTATGTGATGATAAATTGAACCTTCTGTATTC
66 GAACCTTGTGTATTCGGCCATGTAGGTAAGAATTCATGTGATGATAAATTGAACCTTCTGTATTC
40414792 GGCCAAGTATT
131 GGCCAAGTATT
40414803 TATGTGATGATATATTGAACCTTCTGTATTCGGCCATGTAGGTAAGTATTTATGTGATGATATAT
1 TATGTGATG-TATATTGAACCTTCTGTATTCGGCCATGTAGGTAAGTATTTATGTGATGATATAT
* *
40414868 TGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATATATTGAACCTT
65 TGAACCTTGTGTATTCGGCCATGTAGGTAAGAATTCATGTGATGATAAATTGAACCTT
40414926 GTATATTTGG
Statistics
Matches: 116, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
141 9 0.08
142 107 0.92
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (141 bp):
TATGTGATGTATATTGAACCTTCTGTATTCGGCCATGTAGGTAAGTATTTATGTGATGATATATT
GAACCTTGTGTATTCGGCCATGTAGGTAAGAATTCATGTGATGATAAATTGAACCTTCTGTATTC
GGCCAAGTATT
Found at i:40421070 original size:10 final size:10
Alignment explanation
Indices: 40421051--40421098 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
40421041 GAATCTGTCG
*
40421051 AAAATAAATC
1 AAAATTAATC
40421061 AAAATTAATC
1 AAAATTAATC
*
40421071 AAAATTTAATAT
1 AAAA-TTAAT-C
*
40421083 AAAATTAATT
1 AAAATTAATC
40421093 AAAATT
1 AAAATT
40421099 CAACATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 20 0.59
11 10 0.29
12 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTAATC
Found at i:40421805 original size:15 final size:16
Alignment explanation
Indices: 40421785--40421825 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
40421775 ACATATACTC
40421785 CTTTTTTTTCT-TTTT
1 CTTTTTTTTCTCTTTT
40421800 CTTTTTTTTCTCTTTT
1 CTTTTTTTTCTCTTTT
40421816 -TTTTTCTTTC
1 CTTTTT-TTTC
40421826 AAGATCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
CTTTTTTTTCTCTTTT
Found at i:40421808 original size:17 final size:16
Alignment explanation
Indices: 40421786--40421825 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
40421776 CATATACTCC
*
40421786 TTTTTTTTCT-TTTTC
1 TTTTTTTTCTCTTTTT
40421801 TTTTTTTTCTCTTTTT
1 TTTTTTTTCTCTTTTT
*
40421817 TTTTCTTTC
1 TTTTTTTTC
40421826 AAGATCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTTCTCTTTTT
Found at i:40421813 original size:11 final size:10
Alignment explanation
Indices: 40421786--40421824 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
40421776 CATATACTCC
*
40421786 TTTTT-TTTC
1 TTTTTCTTTT
40421795 TTTTTCTTTT
1 TTTTTCTTTT
40421805 TTTTCTCTTTT
1 TTTT-TCTTTT
40421816 TTTTTCTTT
1 TTTTTCTTT
40421825 CAAGATCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 5 0.19
10 12 0.44
11 10 0.37
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:40424542 original size:77 final size:77
Alignment explanation
Indices: 40424449--40424607 Score: 230
Period size: 77 Copynumber: 2.1 Consensus size: 77
40424439 ACTGGGAGCA
* * * * *
40424449 AGCTGTTGGCTGTTGGCGCACGC-GAGCTGGAGCTAGAAGTAGGCCTGGTGTGTGCGACAGTAGC
1 AGCTGTTGGCTATTGGCGCACGCGGA-CTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAAC
40424513 AGCGTACATATGG
65 AGCGTACATATGG
*
40424526 AGCTGTTGGCTATTGGCGCACGCGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGGCAGTAACA
1 AGCTGTTGGCTATTGGCGCACGCGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAACA
* *
40424591 GCGTGCATGTGG
66 GCGTACATATGG
40424603 AGCTG
1 AGCTG
40424608 CTAGCCGAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 71 0.97
78 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.39, T:0.21
Consensus pattern (77 bp):
AGCTGTTGGCTATTGGCGCACGCGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAACA
GCGTACATATGG
Found at i:40435558 original size:19 final size:19
Alignment explanation
Indices: 40435536--40435590 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
40435526 TAATAGTATT
40435536 TTATTAATTTAATTTTAAA
1 TTATTAATTTAATTTTAAA
*
40435555 TTATT-ATCTTAATATTAAA
1 TTATTAAT-TTAATTTTAAA
40435574 -T-TTAATTTAATGTTTAA
1 TTATTAATTTAAT-TTTAA
40435591 TAAACATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 7 0.23
18 9 0.29
19 15 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTAATTTAATTTTAAA
Found at i:40437948 original size:43 final size:43
Alignment explanation
Indices: 40437887--40438017 Score: 219
Period size: 43 Copynumber: 3.1 Consensus size: 43
40437877 CATTATATGC
*
40437887 AACACCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTTTAAAA
1 AACACCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
* *
40437930 AACACCGCTAAAGACCAGGACCTTTCGCGGCGCTTTTAT-AAA
1 AACACCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
*
40437972 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
1 AACACCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
40438015 AAC
1 AAC
40438018 GCCATGAATT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 39 0.48
43 42 0.52
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
AACACCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
Found at i:40442702 original size:40 final size:40
Alignment explanation
Indices: 40442566--40442765 Score: 186
Period size: 41 Copynumber: 5.0 Consensus size: 40
40442556 GTTATATGAC
* * * * ***
40442566 TTTTAGCGGCATTTTACCAAAAGCGCCGCCAATGCTCCGGC
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCT-CTAT
* * * * *
40442607 TTTTAGCGGCGTTTTACCAAAAGCGCTGCTAATGCTTTGTT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCT-AT
* * *
40442648 TTTTAGTGGCGTTTTACCAAAAACGCAGCTATTTCTCTAT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTAT
* * **
40442688 TTTTAGCGGCGTTTTAACAAAAAACGCCGGTATTGCTCCGT
1 TTTTAGCGGCGTTTT-ACCAAAAACGCCGCTATTGCTCTAT
*
40442729 TTTTAGCGGCGTTTTA-CTAAAACGCCGCTATTGCTCT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCT
40442766 GTGTTTTACA
Statistics
Matches: 132, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 17 0.13
40 16 0.12
41 99 0.75
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTAT
Found at i:40442732 original size:81 final size:80
Alignment explanation
Indices: 40442607--40442765 Score: 194
Period size: 81 Copynumber: 2.0 Consensus size: 80
40442597 ATGCTCCGGC
* * * ** *
40442607 TTTTAGCGGCGTTTTACCAAAAGCGCTGCTAATGCTTTGTTTTTTAGTGGCGTTTTACCAAAAAC
1 TTTTAGCGGCGTTTTACAAAAAACGCCGCTAATGCTCCGTTTTTTAGCGGCGTTTTA-CAAAAAC
*
40442672 GCAGCTATTTCTCTAT
65 GCAGCTATTGCTCTAT
* * *
40442688 TTTTAGCGGCGTTTTAACAAAAAACGCCGGTATTGCTCCG-TTTTTAGCGGCGTTTTACTAAAAC
1 TTTTAGCGGCGTTTT-ACAAAAAACGCCGCTAATGCTCCGTTTTTTAGCGGCGTTTTACAAAAAC
*
40442752 GCCGCTATTGCTCT
65 GCAGCTATTGCTCT
40442766 GTGTTTTACA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
80 18 0.27
81 31 0.47
82 17 0.26
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (80 bp):
TTTTAGCGGCGTTTTACAAAAAACGCCGCTAATGCTCCGTTTTTTAGCGGCGTTTTACAAAAACG
CAGCTATTGCTCTAT
Found at i:40442773 original size:81 final size:81
Alignment explanation
Indices: 40442566--40442773 Score: 206
Period size: 82 Copynumber: 2.6 Consensus size: 81
40442556 GTTATATGAC
* * * * * * *
40442566 TTTTAGCGGCATTTTACCAAAAGCGCCGCCAATGCTCCG-GCTTTTAGCGGCGTTTTACCAAAAG
1 TTTTAGCGGCGTTTTA-CAAAAACGCCGCTATTGCTCTGTG-TTTTAGCGGCGTTTTACAAAAAA
* **
40442630 CGCTGCTAATGCTTTGTT
64 CGCCGCTAATGCTCCGTT
* * * *
40442648 TTTTAGTGGCGTTTTACCAAAAACGCAGCTATTTCTCTAT-TTTTAGCGGCGTTTTAACAAAAAA
1 TTTTAGCGGCGTTTTA-CAAAAACGCCGCTATTGCTCTGTGTTTTAGCGGCGTTTT-ACAAAAAA
* *
40442712 CGCCGGTATTGCTCCG-T
64 CGCCGCTAATGCTCCGTT
*
40442729 TTTTAGCGGCGTTTTACTAAAACGCCGCTATTGCTCTGTGTTTTA
1 TTTTAGCGGCGTTTTACAAAAACGCCGCTATTGCTCTGTGTTTTA
40442774 CAATTTTTGC
Statistics
Matches: 102, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
80 19 0.19
81 36 0.35
82 47 0.46
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (81 bp):
TTTTAGCGGCGTTTTACAAAAACGCCGCTATTGCTCTGTGTTTTAGCGGCGTTTTACAAAAAACG
CCGCTAATGCTCCGTT
Found at i:40443156 original size:43 final size:42
Alignment explanation
Indices: 40443099--40443218 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 42
40443089 AATGCCAACA
*
40443099 TCCCAGAC-GTGGTCTTACATGTAATCACATATCGATGCC-ACTG
1 TCCCAGACAG-GGTCTTACACG-AATCACATATCGATGCCGA-TG
*
40443142 TCCTAGACAGGGTCTTACACGAATCACATATACGATGCCGATG
1 TCCCAGACAGGGTCTTACACGAATCACATAT-CGATGCCGATG
*
40443185 TCCCAGACATGGTCTTACACGCAATCACATATCG
1 TCCCAGACAGGGTCTTACACG-AATCACATATCG
40443219 TAAATCCTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
42 10 0.14
43 47 0.68
44 12 0.17
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (42 bp):
TCCCAGACAGGGTCTTACACGAATCACATATCGATGCCGATG
Found at i:40447245 original size:67 final size:67
Alignment explanation
Indices: 40447171--40447298 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
40447161 GGTCTATCTA
* * *
40447171 AATCTATACGAGTGAATTTAACATTAATTTATCATTTTTTACATTCATATGGACTAAATTTAACA
1 AATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTTAACA
40447236 TT
66 TT
40447238 AATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTT
1 AATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTT
40447299 TCATCCTAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (67 bp):
AATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTTAACA
TT
Found at i:40450992 original size:18 final size:19
Alignment explanation
Indices: 40450956--40450998 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
40450946 ATTTTTACCC
40450956 TTAAATTAAAAATAAATTA
1 TTAAATTAAAAATAAATTA
**
40450975 TTAAATT-AAAATTTATTA
1 TTAAATTAAAAATAAATTA
40450993 TTAAAT
1 TTAAAT
40450999 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAATTAAAAATAAATTA
Found at i:40451007 original size:18 final size:18
Alignment explanation
Indices: 40450971--40451022 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
40450961 TTAAAAATAA
*
40450971 ATTATTAAATTAA-AATTT
1 ATTATTAAA-TAATATTTT
40450989 ATTATTAAATAATATTTT
1 ATTATTAAATAATATTTT
*
40451007 AATATTATAATAATAT
1 ATTATTA-AATAATAT
40451023 GTAATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 19 0.63
19 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATTAAATAATATTTT
Found at i:40451074 original size:19 final size:21
Alignment explanation
Indices: 40451050--40451105 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
40451040 AATAGTTTTA
*
40451050 AATAACCTAT-TTAA-ATCTT
1 AATAACATATATTAATATCTT
40451069 AATAACATATATTAATATCTT
1 AATAACATATATTAATATCTT
*
40451090 AAAAATCATATATTAA
1 AATAA-CATATATTAA
40451106 AATAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 9 0.28
20 4 0.12
21 9 0.28
22 10 0.31
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAACATATATTAATATCTT
Found at i:40451088 original size:21 final size:20
Alignment explanation
Indices: 40451050--40451106 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
40451040 AATAGTTTTA
*
40451050 AATAACCTAT-TTAAATCTT
1 AATAACATATATTAAATCTT
40451069 AATAACATATATTAATATCTT
1 AATAACATATATTAA-ATCTT
*
40451090 AAAAATCATATATTAAA
1 AATAA-CATATATTAAA
40451107 ATAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.27
20 4 0.12
21 10 0.30
22 10 0.30
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAACATATATTAAATCTT
Found at i:40454328 original size:3 final size:3
Alignment explanation
Indices: 40454320--40454344 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40454310 TATAAATTGA
40454320 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
40454345 GATATAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:40456896 original size:18 final size:18
Alignment explanation
Indices: 40456873--40456936 Score: 128
Period size: 18 Copynumber: 3.6 Consensus size: 18
40456863 CATATAGCCT
40456873 GCCCGTGTGGGTCCACAC
1 GCCCGTGTGGGTCCACAC
40456891 GCCCGTGTGGGTCCACAC
1 GCCCGTGTGGGTCCACAC
40456909 GCCCGTGTGGGTCCACAC
1 GCCCGTGTGGGTCCACAC
40456927 GCCCGTGTGG
1 GCCCGTGTGG
40456937 CTCACACAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.09, C:0.38, G:0.36, T:0.17
Consensus pattern (18 bp):
GCCCGTGTGGGTCCACAC
Found at i:40460215 original size:21 final size:22
Alignment explanation
Indices: 40460161--40460215 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
40460151 TAGGTAAGAC
**
40460161 ATTTTACGGGAATAAGAAAATA
1 ATTTTACGTTAATAAGAAAATA
** *
40460183 ATTTTATATTAATTAGAAAAT-
1 ATTTTACGTTAATAAGAAAATA
40460204 ATTTTACGTTAA
1 ATTTTACGTTAA
40460216 CCATCCTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (22 bp):
ATTTTACGTTAATAAGAAAATA
Found at i:40461662 original size:15 final size:15
Alignment explanation
Indices: 40461629--40461675 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
40461619 CTGAAAATTC
* *
40461629 TAAAATTTATA-AAA
1 TAAAATTAATATATA
40461643 TAAAATTAATATATA
1 TAAAATTAATATATA
*
40461658 TAAAATAAATATATA
1 TAAAATTAATATATA
40461673 TAA
1 TAA
40461676 TTGTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATTAATATATA
Found at i:40461695 original size:28 final size:27
Alignment explanation
Indices: 40461664--40461728 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
40461654 TATATAAAAT
*
40461664 AAATATATATAA-TTGTTTAAAAAATTTA
1 AAATATATAGAACTT-TTTAAAAAA-TTA
*
40461692 AAATATGTCAGAACTTTTTAAAAAATTA
1 AAATATAT-AGAACTTTTTAAAAAATTA
*
40461720 AAAAATATA
1 AAATATATA
40461729 AAATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 16 0.52
29 12 0.39
30 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (27 bp):
AAATATATAGAACTTTTTAAAAAATTA
Found at i:40462427 original size:17 final size:17
Alignment explanation
Indices: 40462379--40462453 Score: 53
Period size: 17 Copynumber: 4.2 Consensus size: 17
40462369 TATTAGTAAA
*
40462379 TTTTATGTTTTTATATTGT
1 TTTTAT-TTTTAATATT-T
* *
40462398 TTTGTAATATTAATATTT
1 TTT-TATTTTTAATATTT
*
40462416 TTTTATTTTTAATA-AT
1 TTTTATTTTTAATATTT
* *
40462432 TTATATTTTTTAAGATTT
1 TTTTA-TTTTTAATATTT
40462450 TTTT
1 TTTT
40462454 TTTCAGATGA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
16 5 0.12
17 17 0.40
18 8 0.19
19 11 0.26
20 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATTTTTAATATTT
Found at i:40462443 original size:23 final size:24
Alignment explanation
Indices: 40462397--40462442 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40462387 TTTTATATTG
40462397 TTTTGTAATATTAATATTTTTTTA
1 TTTTGTAATATTAATATTTTTTTA
*
40462421 TTTT-TAATAATTTATATTTTTT
1 TTTTGTAAT-ATTAATATTTTTT
40462443 AAGATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTGTAATATTAATATTTTTTTA
Found at i:40465184 original size:22 final size:23
Alignment explanation
Indices: 40465159--40465204 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
40465149 CAACCAAATC
40465159 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
40465181 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
40465204 A
1 A
40465205 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:40465210 original size:23 final size:23
Alignment explanation
Indices: 40465166--40465210 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40465156 ATCAATTCAA
*
40465166 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
40465189 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
40465211 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:40470075 original size:25 final size:24
Alignment explanation
Indices: 40470041--40470090 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
40470031 TATAACACTA
40470041 ATTATCATATTATTAAATTAATTT
1 ATTATCATATTATTAAATTAATTT
*
40470065 ATTATACATATTATTAATTTAATTT
1 ATTAT-CATATTATTAAATTAATTT
40470090 A
1 A
40470091 AATTTTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATCATATTATTAAATTAATTT
Found at i:40470098 original size:20 final size:20
Alignment explanation
Indices: 40470057--40470098 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
40470047 ATATTATTAA
*
40470057 ATTAATTTATTATACATATT
1 ATTAATTTATTATAAATATT
*
40470077 ATTAATTTAATT-TAAATTTT
1 ATTAATTT-ATTATAAATATT
40470097 AT
1 AT
40470099 AGATTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTAATTTATTATAAATATT
Found at i:40477517 original size:22 final size:20
Alignment explanation
Indices: 40477477--40477525 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
40477467 TAATTTAAAA
40477477 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
40477497 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
40477517 TGTAAAAAT
1 TATAAAAAT
40477526 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:40477638 original size:20 final size:20
Alignment explanation
Indices: 40477613--40477652 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40477603 AAATATTTTC
40477613 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
40477633 AGTAAATCGTTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
40477653 TCATTTTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:40490507 original size:22 final size:23
Alignment explanation
Indices: 40490467--40490530 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
40490457 AATGGCAGCG
* *
40490467 AAACAACATAATAAACAACTA-CA
1 AAACAACACAAAAAACAAC-ACCA
*
40490490 AAACAACA-ATAAAACAACACCA
1 AAACAACACAAAAAACAACACCA
*
40490512 AATCAACACAAAAAACAAC
1 AAACAACACAAAAAACAAC
40490531 CTGCAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 17 0.49
23 17 0.49
ACGTcount: A:0.67, C:0.25, G:0.00, T:0.08
Consensus pattern (23 bp):
AAACAACACAAAAAACAACACCA
Found at i:40498490 original size:22 final size:21
Alignment explanation
Indices: 40498442--40498507 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
40498432 GACTCACCAT
* *
40498442 AGCTCGTATGAGCTTGCCGTTTC
1 AGCTC-TACGAGCTTACCG-TTC
40498465 AGCTCTACAGAGCTTACCGTTC
1 AGCTCTAC-GAGCTTACCGTTC
*
40498487 AGCTCTTCGTAGCTTACCGTT
1 AGCTCTACG-AGCTTACCGTT
40498508 TATCAGCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 1 0.03
22 23 0.61
23 14 0.37
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (21 bp):
AGCTCTACGAGCTTACCGTTC
Found at i:40506181 original size:22 final size:22
Alignment explanation
Indices: 40506129--40506187 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
40506119 TAGCTCGTAT
40506129 GAGCTTACCGTTTCAGCTCTACA
1 GAGCTTACCGTTT-AGCTCTACA
*
40506152 GAGCTTACCGTTTAGCTCTTCA
1 GAGCTTACCGTTTAGCTCTACA
* *
40506174 TAGTTTACCGTTTA
1 GAGCTTACCGTTTA
40506188 TCAGCTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (22 bp):
GAGCTTACCGTTTAGCTCTACA
Found at i:40509799 original size:27 final size:27
Alignment explanation
Indices: 40509769--40509946 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
40509759 ATATTGAGTC
* *
40509769 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40509796 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40509823 CTCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
40509851 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40509878 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
40509905 CGCACACCTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
40509932 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40509947 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40509911 original size:82 final size:81
Alignment explanation
Indices: 40509790--40509945 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
40509780 TGCTATATAA
* * * *
40509790 TCAACTCGCACACTTAGTGCTACGTAATCAAATCTCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACCTAGTGCAACATAGTCAAA-TCGCA
40509855 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40509872 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACCTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACCTAGTGCAACATAGTCAAATCGCA
40509936 CACTTAGTGC
65 CACTTAGTGC
40509946 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 16 0.25
82 49 0.75
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACCTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40509929 original size:54 final size:54
Alignment explanation
Indices: 40509769--40509945 Score: 187
Period size: 54 Copynumber: 3.3 Consensus size: 54
40509759 ATATTGAGTC
* * * *
40509769 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* * ** * *
40509823 CTCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
40509878 CGCACACTTAGTGCATCATATTCATTTCGCACACCTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
40509932 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40509946 TGTACAATTT
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
52 1 0.01
54 55 0.54
55 44 0.44
56 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:40513807 original size:39 final size:41
Alignment explanation
Indices: 40513725--40513807 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 41
40513715 TATGCATATA
** *
40513725 GTATCTGAGATGGGCTAAGGCCCTAATTTATATCTGAGGCT
1 GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
* *
40513766 GTATCTGA-ATGGGCTAAGG-CCTAAACTGTATCTGAATCT
1 GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
40513805 GTA
1 GTA
40513808 ATGGGCTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 18 0.49
40 11 0.30
41 8 0.22
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (41 bp):
GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
Found at i:40520200 original size:7 final size:7
Alignment explanation
Indices: 40520184--40520225 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
40520174 TTTTTAAAAA
40520184 AATTGAG
1 AATTGAG
*
40520191 AATTGGG
1 AATTGAG
40520198 AATTGAG
1 AATTGAG
*
40520205 GATTGAG
1 AATTGAG
40520212 AATTGAG
1 AATTGAG
*
40520219 GATTGAG
1 AATTGAG
40520226 TTAAAAAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (7 bp):
AATTGAG
Found at i:40520203 original size:14 final size:14
Alignment explanation
Indices: 40520184--40520225 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
40520174 TTTTTAAAAA
* *
40520184 AATTGAGAATTGGG
1 AATTGAGGATTGAG
40520198 AATTGAGGATTGAG
1 AATTGAGGATTGAG
40520212 AATTGAGGATTGAG
1 AATTGAGGATTGAG
40520226 TTAAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
AATTGAGGATTGAG
Found at i:40520210 original size:21 final size:21
Alignment explanation
Indices: 40520185--40520225 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40520175 TTTTAAAAAA
40520185 ATTGAGAATTG-GGAATTGAGG
1 ATTGAGAATTGAGG-ATTGAGG
40520206 ATTGAGAATTGAGGATTGAG
1 ATTGAGAATTGAGGATTGAG
40520226 TTAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (21 bp):
ATTGAGAATTGAGGATTGAGG
Found at i:40522860 original size:29 final size:29
Alignment explanation
Indices: 40522804--40522863 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
40522794 CATACAATTT
* **
40522804 TAAATAAATTAAAGGAAACAAATTATATA
1 TAAATAAATTAAAAGAAACAAAAAATATA
40522833 TAAATAAATTTAAAAGAAA-AAAAAATATA
1 TAAATAAA-TTAAAAGAAACAAAAAATATA
40522862 TA
1 TA
40522864 TTATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (29 bp):
TAAATAAATTAAAAGAAACAAAAAATATA
Found at i:40535018 original size:30 final size:30
Alignment explanation
Indices: 40534960--40535032 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
40534950 TTTGTTAATG
* * **
40534960 AATAAGTAATTTAATATATTTATTTTTAAA
1 AATAAATAATTTAAAATATTTAAATTTAAA
* *
40534990 TAAT-ATTAATTTAAAATTTTTAAATTTAAA
1 -AATAAATAATTTAAAATATTTAAATTTAAA
40535020 AATAAATAATTTA
1 AATAAATAATTTA
40535033 TTTCAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 3 0.09
30 29 0.83
31 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
AATAAATAATTTAAAATATTTAAATTTAAA
Found at i:40535357 original size:33 final size:33
Alignment explanation
Indices: 40535309--40535383 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
40535299 GATGTTCATT
* * *
40535309 GATAAATAATGTGCCTCGTTAAAATCTTACTAA
1 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
40535342 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
1 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
40535375 GATAAAAAA
1 GATAAAAAA
40535384 ATCTTAGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (33 bp):
GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
Found at i:40538228 original size:25 final size:26
Alignment explanation
Indices: 40538200--40538249 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
40538190 CAACAAAACT
* *
40538200 AAAATCTAACCTA-AAAAGAAAAGAG
1 AAAACCTAAACTAGAAAAGAAAAGAG
*
40538225 AAAACCTAAACTAGAAATGAAAAGA
1 AAAACCTAAACTAGAAAAGAAAAGA
40538250 ACAAAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (26 bp):
AAAACCTAAACTAGAAAAGAAAAGAG
Found at i:40545251 original size:27 final size:25
Alignment explanation
Indices: 40545209--40545265 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
40545199 AATTATAAAA
*
40545209 AAAATTAATATTTATTTTAAAATAT-
1 AAAATTAATATTTATTATAAAA-ATC
40545234 AAAATTAATATTAATATTATAAAAATC
1 AAAATTAATATT--TATTATAAAAATC
40545261 AAAAT
1 AAAAT
40545266 ATAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 12 0.43
26 2 0.07
27 14 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATTAATATTTATTATAAAAATC
Found at i:40551086 original size:24 final size:24
Alignment explanation
Indices: 40551057--40551105 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40551047 CGGTGCTCAC
40551057 TATAAGAAGAAAGTTCAGGAGCTA
1 TATAAGAAGAAAGTTCAGGAGCTA
40551081 TATAAGAAGAAAGTTCAGGAGCTA
1 TATAAGAAGAAAGTTCAGGAGCTA
40551105 T
1 T
40551106 CGGATGCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.22
Consensus pattern (24 bp):
TATAAGAAGAAAGTTCAGGAGCTA
Found at i:40575974 original size:15 final size:15
Alignment explanation
Indices: 40575950--40576002 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
40575940 GGTTCATAAT
*
40575950 TAGGGCTCGCACATG
1 TAGGGTTCGCACATG
*
40575965 TAGGGTTCGCAC--C
1 TAGGGTTCGCACATG
40575978 TAGGGTTCGCACATG
1 TAGGGTTCGCACATG
*
40575993 TAAGGTTCGC
1 TAGGGTTCGC
40576003 GTATGCGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.38
15 20 0.62
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.25
Consensus pattern (15 bp):
TAGGGTTCGCACATG
Found at i:40575983 original size:13 final size:13
Alignment explanation
Indices: 40575965--40575989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40575955 CTCGCACATG
40575965 TAGGGTTCGCACC
1 TAGGGTTCGCACC
40575978 TAGGGTTCGCAC
1 TAGGGTTCGCAC
40575990 ATGTAAGGTT
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:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (13 bp):
TAGGGTTCGCACC
Found at i:40576065 original size:21 final size:20
Alignment explanation
Indices: 40576039--40576092 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
40576029 GACATATATA
40576039 AGGTTCGCATAAAAAGCACAT
1 AGGTTCGCATAAAAA-CACAT
* * *
40576060 AGGTTCACATAAATACATAT
1 AGGTTCGCATAAAAACACAT
40576080 AGGGTTCGCATAA
1 A-GGTTCGCATAA
40576093 CATGGCTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (20 bp):
AGGTTCGCATAAAAACACAT
Found at i:40576329 original size:25 final size:25
Alignment explanation
Indices: 40576301--40576353 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
40576291 TTATGACTCG
*
40576301 CATGTGACAAACAACAGGTGACACA
1 CATGTAACAAACAACAGGTGACACA
* ** *
40576326 CATGTAATATTCAACAGGTGACTCA
1 CATGTAACAAACAACAGGTGACACA
40576351 CAT
1 CAT
40576354 ATACAACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (25 bp):
CATGTAACAAACAACAGGTGACACA
Found at i:40581094 original size:27 final size:26
Alignment explanation
Indices: 40581059--40581160 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 26
40581049 AGCATGGCTG
* *
40581059 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
40581085 CCAGATACAGATAACCGTGGCAGAGCCA
1 CCAGA-ACAGATAA-TGTGGCAGAGCCA
*
40581113 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
40581140 CCA-AATCAGATAATTGTGGCA
1 CCAGAA-CAGATAA-TGTGGCA
40581161 TAGAAACCAG
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.12
27 41 0.63
28 16 0.25
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40582425 original size:17 final size:18
Alignment explanation
Indices: 40582405--40582438 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40582395 AGAAGTTGAT
*
40582405 AAAGAGAGAA-AAAAAGA
1 AAAGAAAGAAGAAAAAGA
40582422 AAAGAAAGAAGAAAAAG
1 AAAGAAAGAAGAAAAAG
40582439 GAAGAATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAGAAAAAGA
Found at i:40589014 original size:27 final size:26
Alignment explanation
Indices: 40588951--40589062 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
40588941 AACATGGCTG
* * * *
40588951 CCAGAATAGAAAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
40588977 CTAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
40589005 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
40589032 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
40589059 CCAG
1 CCAG
40589063 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 5 0.07
27 53 0.72
28 16 0.22
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40591341 original size:29 final size:29
Alignment explanation
Indices: 40591307--40591377 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
40591297 TGAGAACTTA
40591307 TGATATGTGAGCCTTTATGGCTGAATCTC
1 TGATATGTGAGCCTTTATGGCTGAATCTC
40591336 TGATATGTGAGCCTTTATGGCTGAATCTC
1 TGATATGTGAGCCTTTATGGCTGAATCTC
40591365 TGATATGTGAGCC
1 TGATATGTGAGCC
40591378 CGTCTAGCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (29 bp):
TGATATGTGAGCCTTTATGGCTGAATCTC
Found at i:40591507 original size:65 final size:65
Alignment explanation
Indices: 40591384--40591515 Score: 158
Period size: 65 Copynumber: 2.0 Consensus size: 65
40591374 AGCCCGTCTA
* * * * *
40591384 GCGAAGATTGTTTGAATGCAAGTTGGTGTCTTAACAGTTGTTCCTGTTACATGTGTGCCCTTGTG
1 GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAACAGCTATTCATGATACATGTGTGCCCTTGTG
* ** * *
40591449 GCGAAGATTGTTTGAATGCAGGTGGGTGTCTTAATGGCTATCTGATGATGCATG-GTGCCCTTGT
1 GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAACAGCTAT-TCATGATACATGTGTGCCCTTGT
40591513 G
65 G
40591514 GC
1 GC
40591516 TATATGTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 48 0.86
66 8 0.14
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (65 bp):
GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAACAGCTATTCATGATACATGTGTGCCCTTGTG
Found at i:40607024 original size:30 final size:30
Alignment explanation
Indices: 40606988--40607056 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
40606978 TATATTTGAT
*
40606988 TCGATTCGATTGAATTACATCTCATTCGAC
1 TCGATTCGATTGAATTACATCTCACTCGAC
* *
40607018 TCGATTCGATTGAATTCCATCTCACTCGGC
1 TCGATTCGATTGAATTACATCTCACTCGAC
40607048 TCGATTCGA
1 TCGATTCGA
40607057 GAAAATTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (30 bp):
TCGATTCGATTGAATTACATCTCACTCGAC
Found at i:40607221 original size:17 final size:18
Alignment explanation
Indices: 40607188--40607221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40607178 TAGAAGTATT
40607188 AATAATTATACATTTAAA
1 AATAATTATACATTTAAA
*
40607206 AATATTTATA-ATTTAA
1 AATAATTATACATTTAA
40607222 TATAAGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAATTATACATTTAAA
Found at i:40610698 original size:39 final size:38
Alignment explanation
Indices: 40610643--40610718 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
40610633 AGTATCAATT
40610643 TCACATTTTATCTTTAAGATAATTTTT-ATTTAAAAAA
1 TCACATTTTATCTTTAAGATAATTTTTAATTTAAAAAA
* * * *
40610680 TCACATTTTTTACATTTAATATATTTTTTAATTTCAAAA
1 TCACATTTTAT-C-TTTAAGATAATTTTTAATTTAAAAA
40610719 TACATAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 10 0.31
38 1 0.03
39 13 0.41
40 8 0.25
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (38 bp):
TCACATTTTATCTTTAAGATAATTTTTAATTTAAAAAA
Found at i:40611590 original size:15 final size:15
Alignment explanation
Indices: 40611570--40611601 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40611560 GGTAACGTTG
40611570 TAACTAAGGGTTGAA
1 TAACTAAGGGTTGAA
40611585 TAACTAAGGGTTGAA
1 TAACTAAGGGTTGAA
40611600 TA
1 TA
40611602 CAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (15 bp):
TAACTAAGGGTTGAA
Found at i:40614198 original size:41 final size:40
Alignment explanation
Indices: 40614133--40614227 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
40614123 ATAATAAATC
*
40614133 AAATATATTTAAAACAAATATTAAAATAAGAAACAAATAAA
1 AAATATA-ATAAAACAAATATTAAAATAAGAAACAAATAAA
* * * * * *
40614174 AAATGATACTAAAACAATTCTTAAAATAATACACAAATTAA
1 AAAT-ATAATAAAACAAATATTAAAATAAGAAACAAATAAA
40614215 AAATATAATAAAA
1 AAATATAATAAAA
40614228 AGTGATTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 8 0.17
41 35 0.76
42 3 0.07
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.25
Consensus pattern (40 bp):
AAATATAATAAAACAAATATTAAAATAAGAAACAAATAAA
Done.