Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 112 of 235
Found at i:38441412 original size:22 final size:23
Alignment explanation
Indices: 38441387--38441429 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
38441377 GACTTAAATT
*
38441387 TTAAAAT-TTGAAAGTAAAAAGA
1 TTAAAATCTTGAAAATAAAAAGA
*
38441409 TTAAATTCTTGAAAATAAAAA
1 TTAAAATCTTGAAAATAAAAA
38441430 TATAAAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (23 bp):
TTAAAATCTTGAAAATAAAAAGA
Found at i:38446206 original size:21 final size:22
Alignment explanation
Indices: 38446158--38446208 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
38446148 TTGAAATACG
* *
38446158 AAAAATAAAATAATTAAACACTT
1 AAAAAT-AAATAATTAAAAAATT
*
38446181 GAAAATAAA-AATTAAAAAATT
1 AAAAATAAATAATTAAAAAATT
38446202 AAAAATA
1 AAAAATA
38446209 TTCGCATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 16 0.67
22 3 0.12
23 5 0.21
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAATAAATAATTAAAAAATT
Found at i:38454983 original size:26 final size:26
Alignment explanation
Indices: 38454954--38455057 Score: 104
Period size: 26 Copynumber: 4.0 Consensus size: 26
38454944 AGAAAAATAG
*
38454954 GCCTTGAGCTGGTGGTTATTTAGCAA
1 GCCTTGAGCCGGTGGTTATTTAGCAA
* *
38454980 GCCTCGAGCCGGTGATTATTTAGC-A
1 GCCTTGAGCCGGTGGTTATTTAGCAA
** *
38455005 GACCTTGAGTTGATGGTTATTTAGCAA
1 G-CCTTGAGCCGGTGGTTATTTAGCAA
* *
38455032 GCTTTGAGCCAGT-GTATATTTAGCAA
1 GCCTTGAGCCGGTGGT-TATTTAGCAA
38455058 TTACTATGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
25 4 0.06
26 56 0.90
27 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (26 bp):
GCCTTGAGCCGGTGGTTATTTAGCAA
Found at i:38455033 original size:52 final size:52
Alignment explanation
Indices: 38454955--38455056 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
38454945 GAAAAATAGG
* *
38454955 CCTTGAGCTGGTGGTTATTTAGCAAGCCTCGAGCCGGTG-ATTATTTAGCAGA
1 CCTTGAGCTGATGGTTATTTAGCAAGCCTCGAGCCAGTGTA-TATTTAGCAGA
* * *
38455007 CCTTGAGTTGATGGTTATTTAGCAAGCTTTGAGCCAGTGTATATTTAGCA
1 CCTTGAGCTGATGGTTATTTAGCAAGCCTCGAGCCAGTGTATATTTAGCA
38455057 ATTACTATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 43 0.98
53 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (52 bp):
CCTTGAGCTGATGGTTATTTAGCAAGCCTCGAGCCAGTGTATATTTAGCAGA
Found at i:38456752 original size:40 final size:40
Alignment explanation
Indices: 38456654--38456916 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
38456644 TCCTCGTTCA
* * * ** *
38456654 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
38456693 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
38456733 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
38456773 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
38456813 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
38456853 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
38456893 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38456917 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:38462801 original size:762 final size:762
Alignment explanation
Indices: 38461338--38462863 Score: 2908
Period size: 762 Copynumber: 2.0 Consensus size: 762
38461328 TTCTTTGTCA
38461338 TCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCTGA
1 TCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCTGA
38461403 TATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCACC
66 TATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCACC
38461468 TCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAACCA
131 TCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAACCA
38461533 AGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGAAT
196 AGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGAAT
38461598 TTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACACCC
261 TTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACACCC
38461663 GAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGTAA
326 GAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGTAA
38461728 GAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCGGT
391 GAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCGGT
38461793 AATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACGGG
456 AATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACGGG
38461858 CTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCA
521 CTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCA
* * *
38461923 GATGGTCTACCTCGAGCAGTGGTAGCACCCGGTTTCCCACTCTGATTTTCATTCTGTTCAAACAA
586 GATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAACAA
* *
38461988 CCTCGGGCAATCTTTAATGAAGTGGTCCACTGATCCGCATTTGTAACAGGAGCGGTCAGGAAATC
651 CCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAATC
*
38462053 TACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTTCTG
716 TACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTCCTG
38462100 TCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCTGA
1 TCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCTGA
38462165 TATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCACC
66 TATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCACC
*
38462230 TCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAACCCA
131 TCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAACCA
38462295 AGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGAAT
196 AGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGAAT
38462360 TTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACACCC
261 TTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACACCC
*
38462425 GAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGTAG
326 GAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGTAA
*
38462490 GAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGGGTGAATGTACCGGT
391 GAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCGGT
38462555 AATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACGGG
456 AATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACGGG
* *
38462620 CTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACTAGCATTGCCCGTATTTCCA
521 CTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCA
**
38462685 GATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCCGACAA
586 GATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAACAA
*
38462750 CCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGGAATC
651 CCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAATC
* *
38462815 TACAACTCCCCGAATGCCATTTACCGCAATATCGGCATTTCGTCCTG
716 TACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTCCTG
38462862 TC
1 TC
38462864 TCGACGTTCA
Statistics
Matches: 748, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
762 748 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.25
Consensus pattern (762 bp):
TCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCTGA
TATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCACC
TCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAACCA
AGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGAAT
TTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACACCC
GAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGTAA
GAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCGGT
AATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACGGG
CTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCA
GATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAACAA
CCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAATC
TACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTCCTG
Found at i:38465461 original size:40 final size:39
Alignment explanation
Indices: 38465363--38465625 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
38465353 TCCTCGTTCA
* * * *
38465363 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
38465402 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
38465441 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
38465481 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
38465521 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
38465561 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
38465602 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38465626 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:38465585 original size:120 final size:119
Alignment explanation
Indices: 38465363--38465625 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
38465353 TCCTCGTTCA
* * *
38465363 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
38465428 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
38465481 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
38465546 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
38465602 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
38465626 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:38465634 original size:41 final size:41
Alignment explanation
Indices: 38465557--38465634 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
38465547 TTTGTATCTC
* * *
38465557 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
38465598 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
38465635 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:38474708 original size:18 final size:16
Alignment explanation
Indices: 38474685--38474718 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
38474675 TGTTCCCCCC
38474685 CCCCCCTCCTTTTTTTT
1 CCCCCCT-CTTTTTTTT
38474702 NCCCCCCTCTTTTTTTT
1 -CCCCCCTCTTTTTTTT
38474719 ATCTATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.53
Consensus pattern (16 bp):
CCCCCCTCTTTTTTTT
Found at i:38488364 original size:131 final size:131
Alignment explanation
Indices: 38488130--38488391 Score: 506
Period size: 131 Copynumber: 2.0 Consensus size: 131
38488120 TTGATAATTG
*
38488130 ATATTAACACACGTTGTTTCCACGAAGCTGCTCTGCTTTGGGCTCAAGCGGTTTAATCTTCTCTG
1 ATATTAACACACGTTGTTTCCACGAAGCTGCTCTGCTTTGGGCTCAAGCAGTTTAATCTTCTCTG
38488195 TAAGCAGGGTCAAGAGTATACCTGTTTACTTTGACCAGACATTGTCTGTCACTAGTATATATGTA
66 TAAGCAGGGTCAAGAGTATACCTGTTTACTTTGACCAGACATTGTCTGTCACTAGTATATATGTA
38488260 T
131 T
*
38488261 ATATTAACACACGTTGTTTCCAGGAAGCTGCTCTGCTTTGGGCTCAAGCAGTTTAATCTTCTCTG
1 ATATTAACACACGTTGTTTCCACGAAGCTGCTCTGCTTTGGGCTCAAGCAGTTTAATCTTCTCTG
38488326 TAAGCAGGGTCAAGAGTATACCTGTTTACTTTGACCAGACATTGTCTGTCACTAGTATATATGTA
66 TAAGCAGGGTCAAGAGTATACCTGTTTACTTTGACCAGACATTGTCTGTCACTAGTATATATGTA
38488391 T
131 T
38488392 GAACAAATCG
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (131 bp):
ATATTAACACACGTTGTTTCCACGAAGCTGCTCTGCTTTGGGCTCAAGCAGTTTAATCTTCTCTG
TAAGCAGGGTCAAGAGTATACCTGTTTACTTTGACCAGACATTGTCTGTCACTAGTATATATGTA
T
Found at i:38489895 original size:14 final size:13
Alignment explanation
Indices: 38489878--38489929 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
38489868 TATACAGAAT
38489878 TTTTTATAATATTA
1 TTTTTATAAT-TTA
*
38489892 TTTTATATAATCTA
1 TTTT-TATAATTTA
*
38489906 TATATTATAATTTTA
1 T-TTTTATAA-TTTA
38489921 TTTTTATAA
1 TTTTTATAA
38489930 ATCTTTCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTATAATTTA
Found at i:38490198 original size:19 final size:20
Alignment explanation
Indices: 38490169--38490206 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38490159 ATAGAGGTGT
38490169 ACAGCTTAATTGTTTTAAAC
1 ACAGCTTAATTGTTTTAAAC
*
38490189 ACAG-TTAATTTTTTTAAA
1 ACAGCTTAATTGTTTTAAA
38490207 AATAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
ACAGCTTAATTGTTTTAAAC
Found at i:38493841 original size:14 final size:14
Alignment explanation
Indices: 38493822--38493859 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
38493812 CAAGATGGTT
38493822 TATGCAAATGGATG
1 TATGCAAATGGATG
*
38493836 TATGCAAATGTATG
1 TATGCAAATGGATG
*
38493850 AATGCAAATG
1 TATGCAAATG
38493860 CACCAACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (14 bp):
TATGCAAATGGATG
Found at i:38503057 original size:73 final size:73
Alignment explanation
Indices: 38502969--38503218 Score: 455
Period size: 73 Copynumber: 3.4 Consensus size: 73
38502959 TTTAATAGAT
* *
38502969 TTAATATTAAATTAAATTTAATATTTATCTTAGTAGTATTTTATTAATTTAATATTAAAGTGATT
1 TTAATATTAAATTAAATTTAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAAATGATT
*
38503034 ATCTTATC
66 ATCTTATA
*
38503042 TTAATATTAAATTAAATTTAATATTTATCTTAATATTATTTTATTAATTTAATATTAAAATGATT
1 TTAATATTAAATTAAATTTAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAAATGATT
38503107 ATCTTATA
66 ATCTTATA
*
38503115 TTAATATTAAATTAAATTTAATATTTATCTTAATATTATTTTATTAATTTAATATTAAAATGATT
1 TTAATATTAAATTAAATTTAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAAATGATT
38503180 ATCTTATA
66 ATCTTATA
38503188 TTAATATTAAATTAAATTTAATATTTATCTT
1 TTAATATTAAATTAAATTTAATATTTATCTT
38503219 GTAGATAAAT
Statistics
Matches: 173, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 173 1.00
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (73 bp):
TTAATATTAAATTAAATTTAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAAATGATT
ATCTTATA
Found at i:38503076 original size:29 final size:30
Alignment explanation
Indices: 38503037--38503097 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
38503027 AGTGATTATC
38503037 TTATCTTAATATTAAATTA-AATTTAATAT
1 TTATCTTAATATTAAATTATAATTTAATAT
**
38503066 TTATCTTAATATTATTTTATTAATTTAATAT
1 TTATCTTAATATTAAATTA-TAATTTAATAT
38503097 T
1 T
38503098 AAAATGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATCTTAATATTAAATTATAATTTAATAT
Found at i:38503093 original size:5 final size:6
Alignment explanation
Indices: 38503042--38503212 Score: 79
Period size: 6 Copynumber: 28.3 Consensus size: 6
38503032 TTATCTTATC
* * *
38503042 TTAATA TTAA-A TTAA-A TTTAATA TTTATC TTAATA TTATTTTA TTAAT-
1 TTAATA TTAATA TTAATA -TTAATA TTAATA TTAATA TTA--ATA TTAATA
* * * *
38503090 TTAATA TTAAAA TGATTA TCTTATA TTAATA TTAA-A TTAA-A TTTAATA
1 TTAATA TTAATA TTAATA T-TAATA TTAATA TTAATA TTAATA -TTAATA
* * * * * * *
38503138 TTTATC TTAATA TTATTTTA TTAAT- TTAATA TTAAAA TGATTA TCTTATA
1 TTAATA TTAATA TTA--ATA TTAATA TTAATA TTAATA TTAATA T-TAATA
38503188 TTAATA TTAA-A TTAA-A TTTAATA TT
1 TTAATA TTAATA TTAATA -TTAATA TT
38503213 TATCTTGTAG
Statistics
Matches: 123, Mismatches: 28, Indels: 28
0.69 0.16 0.16
Matches are distributed among these distances:
5 28 0.23
6 76 0.62
7 9 0.07
8 10 0.08
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:38503147 original size:29 final size:30
Alignment explanation
Indices: 38503110--38503170 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
38503100 AATGATTATC
38503110 TTATATTAATATTAAATTA-AATTTAATAT
1 TTATATTAATATTAAATTATAATTTAATAT
* **
38503139 TTATCTTAATATTATTTTATTAATTTAATAT
1 TTATATTAATATTAAATTA-TAATTTAATAT
38503170 T
1 T
38503171 AAAATGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 16 0.59
31 11 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATATTAATATTAAATTATAATTTAATAT
Found at i:38503172 original size:11 final size:11
Alignment explanation
Indices: 38503042--38503212 Score: 83
Period size: 11 Copynumber: 16.2 Consensus size: 11
38503032 TTATCTTATC
38503042 TTAATATTAA-A
1 TTAAT-TTAATA
38503053 TTAAATTTAATA
1 TT-AATTTAATA
*
38503065 TTTATCTTAATA
1 TTAAT-TTAATA
38503077 TT-ATTT--TA
1 TTAATTTAATA
38503085 TTAATTTAATA
1 TTAATTTAATA
38503096 TTAA---AATGA
1 TTAATTTAAT-A
38503105 TT-ATCTT-ATA
1 TTAAT-TTAATA
38503115 TTAATATTAA-A
1 TTAAT-TTAATA
38503126 TTAAATTTAATA
1 TT-AATTTAATA
*
38503138 TTTATCTTAATA
1 TTAAT-TTAATA
38503150 TT-ATTT--TA
1 TTAATTTAATA
38503158 TTAATTTAATA
1 TTAATTTAATA
38503169 TTAA---AATGA
1 TTAATTTAAT-A
38503178 TT-ATCTT-ATA
1 TTAAT-TTAATA
38503188 TTAATATTAA-A
1 TTAAT-TTAATA
38503199 TTAAATTTAATA
1 TT-AATTTAATA
38503211 TT
1 TT
38503213 TATCTTGTAG
Statistics
Matches: 128, Mismatches: 4, Indels: 55
0.68 0.02 0.29
Matches are distributed among these distances:
8 16 0.12
9 14 0.11
10 10 0.08
11 52 0.41
12 36 0.28
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:38503191 original size:25 final size:25
Alignment explanation
Indices: 38503017--38503198 Score: 119
Period size: 25 Copynumber: 7.4 Consensus size: 25
38503007 TTTTATTAAT
* * *
38503017 TTAATATTAAAGTGATTATCTTATC
1 TTAATATTAAAATTATTATCTTATA
*
38503042 TTAATATT-AAATTA-AAT-TTAATA
1 TTAATATTAAAATTATTATCTT-ATA
* * * * *
38503065 TTTATCTTAATATTATTTTATTA-A
1 TTAATATTAAAATTATTATCTTATA
*
38503089 TTTAATATTAAAATGATTATCTTATA
1 -TTAATATTAAAATTATTATCTTATA
*
38503115 TTAATATT-AAATTA-AAT-TTAATA
1 TTAATATTAAAATTATTATCTT-ATA
* * * * *
38503138 TTTATCTTAATATTATTTTATTA-A
1 TTAATATTAAAATTATTATCTTATA
*
38503162 TTTAATATTAAAATGATTATCTTATA
1 -TTAATATTAAAATTATTATCTTATA
38503188 TTAATATTAAA
1 TTAATATTAAA
38503199 TTAAATTTAA
Statistics
Matches: 117, Mismatches: 28, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
22 4 0.03
23 21 0.18
24 21 0.18
25 65 0.56
26 6 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAATATTAAAATTATTATCTTATA
Found at i:38503262 original size:62 final size:59
Alignment explanation
Indices: 38503188--38503304 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
38503178 TTATCTTATA
* * * *
38503188 TTAATATTAAATTAAATTTAATATTTATCTTGTAGATAAATGTTCTATTAATTTAATAAGAT
1 TTAATATGAAATTAAATCTAATATTTATCTT-T--ATAAATATTATATTAATTTAATAAGAT
*
38503250 TTAATATGAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
1 TTAATATGAAATTAAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
38503305 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
61 1 0.02
62 28 0.56
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (59 bp):
TTAATATGAAATTAAATCTAATATTTATCTTTATAAATATTATATTAATTTAATAAGAT
Found at i:38505122 original size:40 final size:40
Alignment explanation
Indices: 38505069--38505165 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 40
38505059 CTATCTTGGT
*
38505069 ATCGCACACTTAGTGCCTCA-TATAGCCGAAGCTATTCCAA
1 ATCGCACACTTAGTGCCT-ATTATAGCCGAAGCAATTCCAA
* *
38505109 TTCGCACACTTAGTG-CTATTTATAGCCGAAGCAATTTCAA
1 ATCGCACACTTAGTGCCTA-TTATAGCCGAAGCAATTCCAA
*
38505149 ATCTCACACTTAGTGCC
1 ATCGCACACTTAGTGCC
38505166 GAACATAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 2 0.04
40 45 0.92
41 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (40 bp):
ATCGCACACTTAGTGCCTATTATAGCCGAAGCAATTCCAA
Found at i:38508504 original size:16 final size:17
Alignment explanation
Indices: 38508468--38508505 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
38508458 TAAAAAAAGG
*
38508468 AAAACAAATGAATCTTA
1 AAAAAAAATGAATCTTA
*
38508485 AAAAAAAATGAGTCTTA
1 AAAAAAAATGAATCTTA
38508502 AAAA
1 AAAA
38508506 CTTAATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAAAAAATGAATCTTA
Found at i:38510260 original size:96 final size:96
Alignment explanation
Indices: 38510096--38510289 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
38510086 TTCACATGAA
38510096 GTAACATACTTGATAGCGTCTTTGAATAATGAAGGCCAATAAAAACCTGATTCAAGTATTTTGTG
1 GTAACATACTTGATAGCGTCTTTGAATAATGAAGGCCAATAAAAACCTGATTCAAGTATTTTGTG
38510161 TGCGGTCTTAGTTCCACTATAGTGTCCTCCG
66 TGCGGTCTTAGTTCCACTATAGTGTCCTCCG
38510192 GTAACATACTTGATAGCGTCTTTGAATAATGAAGGCCAATAAAAACCTGATTCAAGTATTTTGTG
1 GTAACATACTTGATAGCGTCTTTGAATAATGAAGGCCAATAAAAACCTGATTCAAGTATTTTGTG
38510257 TGCGGTCTTAGTTCCACTATAGTGTCCTCCG
66 TGCGGTCTTAGTTCCACTATAGTGTCCTCCG
38510288 GT
1 GT
38510290 TGGCCCTGAG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (96 bp):
GTAACATACTTGATAGCGTCTTTGAATAATGAAGGCCAATAAAAACCTGATTCAAGTATTTTGTG
TGCGGTCTTAGTTCCACTATAGTGTCCTCCG
Found at i:38521003 original size:30 final size:30
Alignment explanation
Indices: 38520949--38521006 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38520939 TTGGGTATTT
* *
38520949 CCACACGGGCTGGCCACAGGCCCATGTGAG
1 CCACACGAGCTGGCCACAGACCCATGTGAG
* *
38520979 CCACACGAGCTGGCCATATACCCATGTG
1 CCACACGAGCTGGCCACAGACCCATGTG
38521007 CCAGTCCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.36, G:0.28, T:0.14
Consensus pattern (30 bp):
CCACACGAGCTGGCCACAGACCCATGTGAG
Found at i:38521384 original size:34 final size:34
Alignment explanation
Indices: 38521341--38521415 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
38521331 AATCTTATTA
38521341 TTTGATTTTTCTGAATTACATGATAAATATTTGT
1 TTTGATTTTTCTGAATTACATGATAAATATTTGT
38521375 TTTGATTTTTCTGAATTACATGATAAATATTTGT
1 TTTGATTTTTCTGAATTACATGATAAATATTTGT
38521409 TCTTGAT
1 T-TTGAT
38521416 CTCAATTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 35 0.88
35 5 0.12
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (34 bp):
TTTGATTTTTCTGAATTACATGATAAATATTTGT
Found at i:38524538 original size:262 final size:262
Alignment explanation
Indices: 38524061--38524586 Score: 944
Period size: 262 Copynumber: 2.0 Consensus size: 262
38524051 AGTATTAACG
38524061 TCATGCCCTATAAAATGTTTAAGCAACTAGGTTTTGGGAAACCTAAACACATTAGGATGAGCATT
1 TCATGCCCTATAAAATGTTTAAGCAACTAGGTTTTGGGAAACCTAAACACATTAGGATGAGCATT
* *
38524126 CAATTGGCAGATAGAACAATTAGATTTTCTATAGGTATTGTTGAAGACGTACTTGTGAAAATAGA
66 CAATTGGCAGATAGAACAATTAGATTTCCTAGAGGTATTGTTGAAGACGTACTTGTGAAAATAGA
* *
38524191 TAAATTTATATTCCTAGTAGATTTTGTTGTTTTAGACATGGATGAGGATAGTGACGTTCCTTTAA
131 TAAATTTATATTCCCAGTAGATTTTGTTGTTTTAGACATGGATGAGGATAGCGACGTTCCTTTAA
* * * *
38524256 TTTTAGGATGACCTTTTTTAGTGACTGCTAGGACCATTATAGATGTTGGTATAGGTGAGTTGATA
196 TTTTAGGACGACCCTTTTTAGCGACTGCTAGAACCATTATAGATGTTGGTATAGGTGAGTTGATA
38524321 CT
261 CT
* *
38524323 TCATGCCCTATAAAATGTTTAAGCAACTAGGTTTTGGGAAACTTAAACATATTAGGATGAGCATT
1 TCATGCCCTATAAAATGTTTAAGCAACTAGGTTTTGGGAAACCTAAACACATTAGGATGAGCATT
*
38524388 CAATTGGCAGATAGAATAATTAGATTTCCTAGAGGTATTGTTGAAGACGTACTTGTGAAAATAGA
66 CAATTGGCAGATAGAACAATTAGATTTCCTAGAGGTATTGTTGAAGACGTACTTGTGAAAATAGA
*
38524453 TAAATTTATATTCCCAGTGGATTTTGTTGTTTTAGACATGGATGAGGATAGCGACGTTCCTTTAA
131 TAAATTTATATTCCCAGTAGATTTTGTTGTTTTAGACATGGATGAGGATAGCGACGTTCCTTTAA
38524518 TTTTAGGACGACCCTTTTTAGCGACTGCTAGAACCATTATAGATGTTGGTATAGGTGAGTTGATA
196 TTTTAGGACGACCCTTTTTAGCGACTGCTAGAACCATTATAGATGTTGGTATAGGTGAGTTGATA
38524583 CT
261 CT
38524585 TC
1 TC
38524587 GTGTAGGTGA
Statistics
Matches: 252, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
262 252 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (262 bp):
TCATGCCCTATAAAATGTTTAAGCAACTAGGTTTTGGGAAACCTAAACACATTAGGATGAGCATT
CAATTGGCAGATAGAACAATTAGATTTCCTAGAGGTATTGTTGAAGACGTACTTGTGAAAATAGA
TAAATTTATATTCCCAGTAGATTTTGTTGTTTTAGACATGGATGAGGATAGCGACGTTCCTTTAA
TTTTAGGACGACCCTTTTTAGCGACTGCTAGAACCATTATAGATGTTGGTATAGGTGAGTTGATA
CT
Found at i:38525258 original size:64 final size:64
Alignment explanation
Indices: 38525157--38525284 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
38525147 GTAAGTCAAG
38525157 CTTAGACTATAAATAAGCACTTCTCGGGAGGCAACCCGAGTACTAACACTGCTAATTTCCTCAT
1 CTTAGACTATAAATAAGCACTTCTCGGGAGGCAACCCGAGTACTAACACTGCTAATTTCCTCAT
* * *
38525221 CTTAGACTCTAAATAAG-AGCTTTTCGGGAGGCAACCCGAGTACTAACATTGCTAATTTCCTCAT
1 CTTAGACTATAAATAAGCA-CTTCTCGGGAGGCAACCCGAGTACTAACACTGCTAATTTCCTCAT
38525285 TTTTATTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.02
64 59 0.98
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
CTTAGACTATAAATAAGCACTTCTCGGGAGGCAACCCGAGTACTAACACTGCTAATTTCCTCAT
Found at i:38526396 original size:16 final size:16
Alignment explanation
Indices: 38526361--38526418 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
38526351 TCAGTTTCCC
*
38526361 TTTTTATTTATTTATTTA
1 TTTTTCTTTA-TT-TTTA
38526379 TTTTTCTTTATTTTTA
1 TTTTTCTTTATTTTTA
*
38526395 TTTTTCTTTATTATTA
1 TTTTTCTTTATTTTTA
*
38526411 TTATTCTT
1 TTTTTCTT
38526419 ATCTGTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 26 0.70
17 2 0.05
18 9 0.24
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTTATTTTTA
Found at i:38526449 original size:11 final size:11
Alignment explanation
Indices: 38526435--38526464 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38526425 TATTGGTCAA
38526435 TTATTATTTCT
1 TTATTATTTCT
*
38526446 TTATTGTTTCT
1 TTATTATTTCT
38526457 TTATTATT
1 TTATTATT
38526465 ATTATGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (11 bp):
TTATTATTTCT
Found at i:38528157 original size:18 final size:17
Alignment explanation
Indices: 38528131--38528181 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
38528121 CCATTTGTCT
*
38528131 TTATGTTTATTGTTATTG
1 TTATGTTTATT-TTATTC
* *
38528149 TTATTTTTATTTTTCTTC
1 TTATGTTTA-TTTTATTC
38528167 TTATGTTTATTTTAT
1 TTATGTTTATTTTAT
38528182 CTTTATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 5 0.19
18 20 0.74
19 2 0.07
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.73
Consensus pattern (17 bp):
TTATGTTTATTTTATTC
Found at i:38529157 original size:10 final size:10
Alignment explanation
Indices: 38529142--38529171 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
38529132 ATTGTTCTTT
38529142 AAAAAAAATG
1 AAAAAAAATG
38529152 AAAAAAAAGTG
1 AAAAAAAA-TG
38529163 AAAAAAAAT
1 AAAAAAAAT
38529172 TCATTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:38536176 original size:47 final size:46
Alignment explanation
Indices: 38536082--38536176 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 46
38536072 ATCAGATATA
* * * *
38536082 TGTGGTCAAGCCACTATATTGTAGCTAAGCTGCCAAAACATATATG
1 TGTGGTCAAGCCACTATAATGTAGCTAAGCTACCAAAACAGAAATG
* *
38536128 TGTGGTCAAGCCACTATAAATGTAG-TCAAGCTACCATAATAGAAATG
1 TGTGGTCAAGCCACTAT-AATGTAGCT-AAGCTACCAAAACAGAAATG
38536175 TG
1 TG
38536177 GTTAAACCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
46 18 0.44
47 23 0.56
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (46 bp):
TGTGGTCAAGCCACTATAATGTAGCTAAGCTACCAAAACAGAAATG
Found at i:38539763 original size:33 final size:32
Alignment explanation
Indices: 38539719--38539804 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 32
38539709 AAACTAAAAA
*
38539719 TAGCCCTATACAGTATCAGTACAGTCTGGGCCT
1 TAGCCCAATACAGTATCA-TACAGTCTGGGCCT
* *
38539752 TAGCCCCATACA-T-T-A-ACAGTGTGGGCCT
1 TAGCCCAATACAGTATCATACAGTCTGGGCCT
*
38539780 AAGCCCAATACAGTATCACTACAGT
1 TAGCCCAATACAGTATCA-TACAGT
38539805 GTAATGCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
28 22 0.50
29 1 0.02
30 2 0.05
31 2 0.05
32 1 0.02
33 16 0.36
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (32 bp):
TAGCCCAATACAGTATCATACAGTCTGGGCCT
Found at i:38539931 original size:59 final size:59
Alignment explanation
Indices: 38539837--38539965 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
38539827 CCAAATTCAT
* *
38539837 CTAGCACACCACCCGTACCAACCAACACACTATGTGGGAATATAAACCAACCCACCCAG
1 CTAGCACACCACCCATACCAACCAACACACCATGTGGGAATATAAACCAACCCACCCAG
* * * *
38539896 CTAGCACACCACCCATACTAACCAACACACCATGTGGGGATATAAATCAACCCACTCAG
1 CTAGCACACCACCCATACCAACCAACACACCATGTGGGAATATAAACCAACCCACCCAG
* *
38539955 CCAGCATACCA
1 CTAGCACACCA
38539966 ATATCGCAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.37, C:0.38, G:0.12, T:0.13
Consensus pattern (59 bp):
CTAGCACACCACCCATACCAACCAACACACCATGTGGGAATATAAACCAACCCACCCAG
Found at i:38540226 original size:27 final size:27
Alignment explanation
Indices: 38540181--38540353 Score: 202
Period size: 27 Copynumber: 6.4 Consensus size: 27
38540171 AGGGCATATC
* * * *
38540181 GTCATTTTAACATATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
38540208 GTCATCTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
38540235 GTTATTTTACCTTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
38540262 GTTATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
38540289 ATCATTTTACCTTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
38540316 GCCAATTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
38540343 GTTATTTTACC
1 GTCATTTTACC
38540354 TATTTTAGGG
Statistics
Matches: 123, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 123 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:38540243 original size:54 final size:53
Alignment explanation
Indices: 38540184--38540354 Score: 225
Period size: 54 Copynumber: 3.2 Consensus size: 53
38540174 GCATATCGTC
* * *
38540184 ATTTTAACATATAGGGGTATTACGGTCATCTTACCCTACAGGGGCATTACGGTT
1 ATTTTACCTTATAGGGGCATTACGGTCAT-TTACCCTACAGGGGCATTACGGTT
* * *
38540238 ATTTTACCTTATAGGGGCATTACGGTTATTTTACCCTACAGGGGCATTACGATC
1 ATTTTACCTTATAGGGGCATTACGGTCA-TTTACCCTACAGGGGCATTACGGTT
* * * *
38540292 ATTTTACCTTACAGGGGCATTACGGCCAATTTACCCTATAGGGGTATTACGGTT
1 ATTTTACCTTATAGGGGCATTACGGTC-ATTTACCCTACAGGGGCATTACGGTT
38540346 ATTTTACCT
1 ATTTTACCT
38540355 ATTTTAGGGT
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
54 100 0.98
55 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (53 bp):
ATTTTACCTTATAGGGGCATTACGGTCATTTACCCTACAGGGGCATTACGGTT
Found at i:38540325 original size:81 final size:81
Alignment explanation
Indices: 38540196--38540353 Score: 235
Period size: 81 Copynumber: 2.0 Consensus size: 81
38540186 TTTAACATAT
* * ** * *
38540196 AGGGGTATTACGGTCATCTTACCCTACAGGGGCATTACGGTTATTTTACCTTATAGGGGCATTAC
1 AGGGGCATTACGATCATCTTACCCTACAGGGGCATTACGGCCAATTTACCCTATAGGGGCATTAC
38540261 GGTTATTTTACCCTAC
66 GGTTATTTTACCCTAC
* * *
38540277 AGGGGCATTACGATCATTTTACCTTACAGGGGCATTACGGCCAATTTACCCTATAGGGGTATTAC
1 AGGGGCATTACGATCATCTTACCCTACAGGGGCATTACGGCCAATTTACCCTATAGGGGCATTAC
38540342 GGTTATTTTACC
66 GGTTATTTTACC
38540354 TATTTTAGGG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (81 bp):
AGGGGCATTACGATCATCTTACCCTACAGGGGCATTACGGCCAATTTACCCTATAGGGGCATTAC
GGTTATTTTACCCTAC
Found at i:38543956 original size:33 final size:33
Alignment explanation
Indices: 38543914--38543984 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
38543904 AATATGTAAA
* * ** *
38543914 ACAGTCTGGGCTTTAGCCTTATAAAGTATCAGT
1 ACAGTCTGGGCCTAAGCCCAATAAAGTATCACT
*
38543947 ACAGTCTGGGCCTAAGCCCAATACAGTATCACT
1 ACAGTCTGGGCCTAAGCCCAATAAAGTATCACT
38543980 ACAGT
1 ACAGT
38543985 GTAATGTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (33 bp):
ACAGTCTGGGCCTAAGCCCAATAAAGTATCACT
Found at i:38544364 original size:27 final size:27
Alignment explanation
Indices: 38544305--38544392 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 27
38544295 ACATAATCGC
* * *
38544305 CATTTTACCATATAGGGGCATTACGGT
1 CATTTTACCCTACAGGGGCATTACGAT
*
38544332 CATTTTACCCTACAGGGGCATTATGAT
1 CATTTTACCCTACAGGGGCATTACGAT
** * * * *
38544359 TGTTTTGCCCTACAGAGGCATTAAGGT
1 CATTTTACCCTACAGGGGCATTACGAT
38544386 CATTTTA
1 CATTTTA
38544393 TTTATTTTGG
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (27 bp):
CATTTTACCCTACAGGGGCATTACGAT
Found at i:38546704 original size:21 final size:21
Alignment explanation
Indices: 38546678--38546892 Score: 148
Period size: 21 Copynumber: 10.3 Consensus size: 21
38546668 ATGTTTTACT
*
38546678 TTCTGTTTAGCTCTTATAAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
38546699 TTCTGTTTAACTCATATGAGT
1 TTCTGTTTAGCTCTTATGAGC
* * *
38546720 TTCTGTTCAGCTCTTTTAAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * *
38546741 TTCTATTAAACTCTTATGAGT
1 TTCTGTTTAGCTCTTATGAGC
*
38546762 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
38546783 TTTTGTTTAACTCATATGAG-
1 TTCTGTTTAGCTCTTATGAGC
* * * *
38546803 TTTTCGTTCAGCTCTTACGAGA
1 TTCT-GTTTAGCTCTTATGAGC
* * * * *
38546825 TTCTGTTCAACACTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
* *
38546846 TTTTGTTTAGCTCTCATGAGC
1 TTCTGTTTAGCTCTTATGAGC
* *
38546867 TTTTGTTCAGCT-TT-TGAGC
1 TTCTGTTTAGCTCTTATGAGC
38546886 TTCTGTT
1 TTCTGTT
38546893 AACAATGTTC
Statistics
Matches: 148, Mismatches: 44, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
19 11 0.07
20 5 0.03
21 129 0.87
22 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:38546724 original size:42 final size:42
Alignment explanation
Indices: 38546677--38546873 Score: 216
Period size: 42 Copynumber: 4.7 Consensus size: 42
38546667 TATGTTTTAC
* *
38546677 TTTCTGTTTAGCTCTTATAAGCTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
* * * * *
38546719 TTTCTGTTCAGCTCTTTTAAGCTTCTATTAAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
*
38546761 TTTCTGTTCAGCTCTTATGAGCTTTTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
* * * * * *
38546803 TTT-TCGTTCAGCTCTTACGAGATTCTGTTCAACACTTATGGG
1 TTTCT-GTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
* * * *
38546845 TTTTTGTTTAGCTCTCATGAGCTTTTGTT
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTT
38546874 CAGCTTTTGA
Statistics
Matches: 130, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
41 1 0.01
42 128 0.98
43 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.48
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
Found at i:38546818 original size:63 final size:63
Alignment explanation
Indices: 38546751--38546896 Score: 167
Period size: 63 Copynumber: 2.4 Consensus size: 63
38546741 TTCTATTAAA
* * *
38546751 CTCTTATGAGTTTCTGTTCAGCTCTTATGAGCTTTTGTTTAACTCAT-ATGAG-TTTTCGTTCAG
1 CTCTTATGAGATTCTGTTCAACACTTATGAGCTTTTGTTTAACTC-TCATGAGCTTTT-GTTCAG
* * * *
38546814 CTCTTACGAGATTCTGTTCAACACTTATGGGTTTTTGTTTAGCTCTCATGAGCTTTTGTTCAG
1 CTCTTATGAGATTCTGTTCAACACTTATGAGCTTTTGTTTAACTCTCATGAGCTTTTGTTCAG
*
38546877 CT-TT-TGAGCTTCTGTT-AACA
1 CTCTTATGAGATTCTGTTCAACA
38546897 ATGTTCTCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
60 4 0.06
61 10 0.14
62 3 0.04
63 51 0.71
64 4 0.06
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (63 bp):
CTCTTATGAGATTCTGTTCAACACTTATGAGCTTTTGTTTAACTCTCATGAGCTTTTGTTCAG
Found at i:38546841 original size:84 final size:84
Alignment explanation
Indices: 38546677--38546873 Score: 261
Period size: 84 Copynumber: 2.3 Consensus size: 84
38546667 TATGTTTTAC
* * ** *
38546677 TTTCTGTTTAGCTCTTATAAGCTTCTGTTTAACTCATATGAGTTTCTGTTCAGCTCTTTTAAGCT
1 TTTCTGTTTAGCTCTTATGAGCTTTTGTTTAACTCATATGAGTTTCTGTTCAGCTCTTACAAGAT
*
38546742 TCTATTAAACTCTTATGAG
66 TCTATTAAACACTTATGAG
* *
38546761 TTTCTGTTCAGCTCTTATGAGCTTTTGTTTAACTCATATGAGTTT-TCGTTCAGCTCTTACGAGA
1 TTTCTGTTTAGCTCTTATGAGCTTTTGTTTAACTCATATGAGTTTCT-GTTCAGCTCTTACAAGA
* * *
38546825 TTCTGTTCAACACTTATGGG
65 TTCTATTAAACACTTATGAG
* *
38546845 TTTTTGTTTAGCTCTCATGAGCTTTTGTT
1 TTTCTGTTTAGCTCTTATGAGCTTTTGTT
38546874 CAGCTTTTGA
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
83 1 0.01
84 97 0.99
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.48
Consensus pattern (84 bp):
TTTCTGTTTAGCTCTTATGAGCTTTTGTTTAACTCATATGAGTTTCTGTTCAGCTCTTACAAGAT
TCTATTAAACACTTATGAG
Found at i:38555823 original size:35 final size:35
Alignment explanation
Indices: 38555784--38555855 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
38555774 CATCTCCAGA
*
38555784 GCTTGGAAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGAAAATATGGAAAGGAATCTTCAAAGATAT
* * *
38555819 GCTTGGCAAATATGGAAGGGGATCTTCAAAGATAT
1 GCTTGGAAAATATGGAAAGGAATCTTCAAAGATAT
38555854 GC
1 GC
38555856 GATCCTAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (35 bp):
GCTTGGAAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:38561759 original size:28 final size:28
Alignment explanation
Indices: 38561726--38561783 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
38561716 GATATATACC
38561726 AAACTAATCATAATTCAACTATCAAAGA
1 AAACTAATCATAATTCAACTATCAAAGA
38561754 AAACTAATCATAATTCAACTATCAAAGA
1 AAACTAATCATAATTCAACTATCAAAGA
38561782 AA
1 AA
38561784 TTAAATAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.24
Consensus pattern (28 bp):
AAACTAATCATAATTCAACTATCAAAGA
Found at i:38561777 original size:14 final size:15
Alignment explanation
Indices: 38561727--38561774 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
38561717 ATATATACCA
38561727 AACTAATCATAATTC
1 AACTAATCATAATTC
***
38561742 AACT-ATCA-AAGAA
1 AACTAATCATAATTC
38561755 AACTAATCATAATTC
1 AACTAATCATAATTC
38561770 AACTA
1 AACTA
38561775 TCAAAGAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 6 0.24
14 8 0.32
15 11 0.44
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (15 bp):
AACTAATCATAATTC
Found at i:38563352 original size:11 final size:9
Alignment explanation
Indices: 38563328--38563400 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 9
38563318 TTGAACTTTA
38563328 ATAAAAAAT
1 ATAAAAAAT
38563337 ATAAAAAAT
1 ATAAAAAAT
**
38563346 ATTTAAAAT
1 ATAAAAAAT
*
38563355 TTACTAAAAAT
1 ATA--AAAAAT
38563366 -TCAAAAAAT
1 AT-AAAAAAT
38563375 AT-AAAAAT
1 ATAAAAAAT
*
38563383 CGTAAAAAAAT
1 -AT-AAAAAAT
38563394 ATAAAAA
1 ATAAAAA
38563401 TTTGTAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
8 6 0.12
9 29 0.58
10 3 0.06
11 12 0.24
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:38563363 original size:29 final size:28
Alignment explanation
Indices: 38563294--38563431 Score: 99
Period size: 28 Copynumber: 4.9 Consensus size: 28
38563284 TGTGTGACAA
* *
38563294 AAAAATTATAAAAA-ATAAAAATTA-TT
1 AAAATTTATAAAAATATAAAAAATATTT
* *
38563320 GAACTTTAATAAAAAATATAAAAAATATTT
1 AAAATTT-AT-AAAAATATAAAAAATATTT
*
38563350 AAAATTTACTAAAAAT-TCAAAAAATA-TA
1 AAAATTTA-TAAAAATAT-AAAAAATATTT
* *
38563378 AAAATCGTAAAAAAATAT-AAAAAT-TTGT
1 AAAAT-TTATAAAAATATAAAAAATATT-T
38563406 AAAATTTTATAAAAATCATAAAAAAT
1 AAAA-TTTATAAAAAT-ATAAAAAAT
38563432 TATAAAGTGC
Statistics
Matches: 87, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.05
27 9 0.10
28 30 0.34
29 30 0.34
30 14 0.16
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATTTATAAAAATATAAAAAATATTT
Found at i:38563390 original size:19 final size:19
Alignment explanation
Indices: 38563368--38563437 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
38563358 CTAAAAATTC
38563368 AAAAAATATAAAAATCGTA
1 AAAAAATATAAAAATCGTA
*
38563387 AAAAAATATAAAAATTTGTA
1 AAAAAATATAAAAA-TCGTA
*** *
38563407 AAATTTTATAAAAATCATA
1 AAAAAATATAAAAATCGTA
*
38563426 AAAAATTATAAA
1 AAAAAATATAAA
38563438 GTGCATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 27 0.64
20 15 0.36
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAAATATAAAAATCGTA
Found at i:38563408 original size:10 final size:10
Alignment explanation
Indices: 38563350--38563437 Score: 53
Period size: 10 Copynumber: 9.2 Consensus size: 10
38563340 AAAAATATTT
38563350 AAAATTTACTA
1 AAAATTTA-TA
*
38563361 AAAATTCA-A
1 AAAATTTATA
38563370 AAAA--TATA
1 AAAATTTATA
*
38563378 AAAATCGTA-A
1 AAAAT-TTATA
*
38563388 AAAA-ATATA
1 AAAATTTATA
*
38563397 AAAATTTGTA
1 AAAATTTATA
*
38563407 AAATTTTATA
1 AAAATTTATA
*
38563417 AAAA-TCATA
1 AAAATTTATA
*
38563426 AAAAATTATA
1 AAAATTTATA
38563436 AA
1 AA
38563438 GTGCATAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
7 1 0.02
8 7 0.12
9 18 0.30
10 25 0.42
11 9 0.15
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAATTTATA
Found at i:38563437 original size:29 final size:28
Alignment explanation
Indices: 38563299--38563437 Score: 99
Period size: 29 Copynumber: 4.9 Consensus size: 28
38563289 GACAAAAAAA
* *
38563299 TTATAAAAA-AT-AAAAATTATTGAACTT
1 TTATAAAAATATAAAAAATTA-TAAAATT
* *
38563326 TAATAAAAAATATAAAAAATATTTAAAA-T
1 TTAT-AAAAATATAAAAAAT-TATAAAATT
*
38563355 TTACTAAAAAT-TCAAAAAA-TATAAAAATC
1 TTA-TAAAAATAT-AAAAAATTAT-AAAATT
* * * *
38563384 GTAAAAAAATATAAAAATTTGTAAAATT
1 TTATAAAAATATAAAAAATTATAAAATT
38563412 TTATAAAAATCATAAAAAATTATAAA
1 TTATAAAAAT-ATAAAAAATTATAAA
38563438 GTGCATAAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
27 5 0.06
28 34 0.40
29 35 0.41
30 10 0.12
31 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (28 bp):
TTATAAAAATATAAAAAATTATAAAATT
Found at i:38563632 original size:9 final size:9
Alignment explanation
Indices: 38563618--38563858 Score: 75
Period size: 9 Copynumber: 26.0 Consensus size: 9
38563608 TTTTTGTAGG
38563618 ATAATTTTT
1 ATAATTTTT
38563627 ATAATTCTTTT
1 ATAA-T-TTTT
* *
38563638 AAAAATTTT
1 ATAATTTTT
**
38563647 ATGTTTCTTT
1 ATAATT-TTT
* *
38563657 ACATTTTTT
1 ATAATTTTT
*
38563666 ATCATTTTCTT
1 AT-AATTT-TT
*
38563677 ATGAATTTAT
1 AT-AATTTTT
*
38563687 A-AAATTTT
1 ATAATTTTT
38563695 AT-ATTTTT
1 ATAATTTTT
* *
38563703 TTATATTTCT
1 ATA-ATTTTT
*
38563713 ATATATATATT
1 ATA-AT-TTTT
38563724 ATAATTTTT
1 ATAATTTTT
*
38563733 ATGATTTTT
1 ATAATTTTT
38563742 ATGATATTTTT
1 AT-A-ATTTTT
*
38563753 CTAATTTTT
1 ATAATTTTT
****
38563762 AATAAAAAAT
1 -ATAATTTTT
38563772 A-AATATTTT
1 ATAAT-TTTT
*
38563781 TTATATTTTT
1 ATA-ATTTTT
*
38563791 -T-ATTATT
1 ATAATTTTT
* *
38563798 A-AAATTTA
1 ATAATTTTT
38563806 ATAATTTTT
1 ATAATTTTT
38563815 ATAATTTTT
1 ATAATTTTT
*
38563824 ATAACTTTT
1 ATAATTTTT
38563833 ATTAATTTTT
1 A-TAATTTTT
38563843 AT--TTTTT
1 ATAATTTTT
*
38563850 ATCATTTTT
1 ATAATTTTT
38563859 TGCCACATGT
Statistics
Matches: 169, Mismatches: 42, Indels: 42
0.67 0.17 0.17
Matches are distributed among these distances:
7 12 0.07
8 18 0.11
9 65 0.38
10 45 0.27
11 29 0.17
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:38563739 original size:29 final size:28
Alignment explanation
Indices: 38563700--38563762 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
38563690 ATTTTATATT
38563700 TTTTTATATTTCTAT-ATATATATTATAA
1 TTTTTATATTTCTATGATAT-TATTATAA
* * *
38563728 TTTTTATGATTTTTATGATATTTTTCTAA
1 TTTTTAT-ATTTCTATGATATTATTATAA
38563757 TTTTTA
1 TTTTTA
38563763 ATAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 19 0.63
30 4 0.13
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTTATATTTCTATGATATTATTATAA
Found at i:38563823 original size:32 final size:31
Alignment explanation
Indices: 38563747--38563826 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 31
38563737 TTTTTATGAT
*
38563747 ATTTTTCTAATTTTTA-ATAAAAAATAAATA
1 ATTTTTATAATTTTTATATAAAAAATAAATA
* * * * *
38563777 TTTTTTATATTTTTTATTATTAAAATTTAATA
1 ATTTTTATAATTTTTA-TATAAAAAATAAATA
38563809 ATTTTTATAATTTTTATA
1 ATTTTTATAATTTTTATA
38563827 ACTTTTATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 13 0.32
31 2 0.05
32 25 0.62
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
ATTTTTATAATTTTTATATAAAAAATAAATA
Found at i:38564089 original size:84 final size:84
Alignment explanation
Indices: 38563996--38564154 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
38563986 GAGGAACTTA
* * * **
38563996 ATTAATTTTTTGAAAAAATTTTAGGGTATTTTTGATACATTTTGGTAGTTCAAGTACTAAATTGA
1 ATTAATTTTTTGAAAAAATTTAAGGGCATTTTTAATACATTTTGAAAGTTCAAGTACTAAATTGA
38564061 GTGAAAAAAATAGGGGCTT
66 GTGAAAAAAATAGGGGCTT
* ** * * * *
38564080 ATTACTTTTTTTTAAAAATTTAAGGGCCTTTTTAATACATTTTGAAAGTTTAAGTATTTAATTGA
1 ATTAATTTTTTGAAAAAATTTAAGGGCATTTTTAATACATTTTGAAAGTTCAAGTACTAAATTGA
38564145 GTGAAAAAAA
66 GTGAAAAAAA
38564155 GGACTTAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (84 bp):
ATTAATTTTTTGAAAAAATTTAAGGGCATTTTTAATACATTTTGAAAGTTCAAGTACTAAATTGA
GTGAAAAAAATAGGGGCTT
Found at i:38564487 original size:63 final size:63
Alignment explanation
Indices: 38564353--38564488 Score: 157
Period size: 62 Copynumber: 2.2 Consensus size: 63
38564343 TAATTGCCTC
* * *
38564353 ATAAAAATATGCGAGCTATAAAAAGTTGATTATAAAAAAATTAAATAGCATTTAATATCTTTT
1 ATAAAAATATGCGAGCTATAAAAAATTGATTATAAAAAAATTAAATAGCATTTAATATATGTT
* * * * * ** *
38564416 AAAAAAATATGTGAGTTA-AAAAAATTGATTATTAACAGTTTAAATAGTATTTAATATATAGTT
1 ATAAAAATATGCGAGCTATAAAAAATTGATTATAAAAAAATTAAATAGCATTTAATATAT-GTT
38564479 ATAAAAATAT
1 ATAAAAATAT
38564489 AAAATGATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 34 0.57
63 26 0.43
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.36
Consensus pattern (63 bp):
ATAAAAATATGCGAGCTATAAAAAATTGATTATAAAAAAATTAAATAGCATTTAATATATGTT
Found at i:38565061 original size:16 final size:15
Alignment explanation
Indices: 38565031--38565074 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
38565021 TTATATATTG
*
38565031 TTAAAAAAGTTAATT
1 TTAAAAAAATTAATT
38565046 TTAAATAAAATTAATT
1 TTAAA-AAAATTAATT
*
38565062 TTAAGAAAATTAA
1 TTAAAAAAATTAA
38565075 ATATGAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (15 bp):
TTAAAAAAATTAATT
Found at i:38567717 original size:2 final size:2
Alignment explanation
Indices: 38567710--38567752 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
38567700 TTAAAGACAA
38567710 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38567752 A
1 A
38567753 AATTAAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38575064 original size:28 final size:28
Alignment explanation
Indices: 38575032--38575086 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
38575022 AAAAGTCATC
*
38575032 CGCTCTGATGCCCAAGACAAAACATTTT
1 CGCTCCGATGCCCAAGACAAAACATTTT
38575060 CGCTCCGATGCCCAAGACAAAACATTT
1 CGCTCCGATGCCCAAGACAAAACATTT
38575087 CCCAATTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.22
Consensus pattern (28 bp):
CGCTCCGATGCCCAAGACAAAACATTTT
Found at i:38576158 original size:37 final size:37
Alignment explanation
Indices: 38576108--38576184 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
38576098 TGCACAGCCA
*
38576108 ATCCTCTACTATGCTTCTCCTCAATTCCTTCCTCTTC
1 ATCCTCTACTATGCTTCTCCTCAATTCATTCCTCTTC
38576145 ATCCTCTACTATGCTTCTCCTCAATTCATTCCTCTTC
1 ATCCTCTACTATGCTTCTCCTCAATTCATTCCTCTTC
38576182 ATC
1 ATC
38576185 TTCCACTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.16, C:0.39, G:0.03, T:0.43
Consensus pattern (37 bp):
ATCCTCTACTATGCTTCTCCTCAATTCATTCCTCTTC
Found at i:38580588 original size:18 final size:19
Alignment explanation
Indices: 38580557--38580594 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
38580547 TCGACATTTT
*
38580557 ATTTTTATTTTTTATAACA
1 ATTTTTATTATTTATAACA
38580576 ATTTTT-TTATTTATAACA
1 ATTTTTATTATTTATAACA
38580594 A
1 A
38580595 CCATAAAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTATTATTTATAACA
Found at i:38584272 original size:16 final size:16
Alignment explanation
Indices: 38584253--38584285 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38584243 TATTATAGTT
38584253 TTTTAATATATTTTTA
1 TTTTAATATATTTTTA
*
38584269 TTTTTATATATTTTTA
1 TTTTAATATATTTTTA
38584285 T
1 T
38584286 AAATTTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTAATATATTTTTA
Found at i:38585801 original size:14 final size:14
Alignment explanation
Indices: 38585782--38585808 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38585772 TAGAAAAAAA
38585782 ATTTTATTTATTTT
1 ATTTTATTTATTTT
38585796 ATTTTATTTATTT
1 ATTTTATTTATTT
38585809 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTTATTTATTTT
Found at i:38588700 original size:4 final size:4
Alignment explanation
Indices: 38588691--38588724 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
38588681 TTGCTTGTAC
*
38588691 ATAA ATAA ATAA ATAAA ATGA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA A
38588725 GGCTCAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:38593728 original size:17 final size:18
Alignment explanation
Indices: 38593695--38593729 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38593685 CCATATGGTC
*
38593695 TGCCCGTGTGAGCCCACA
1 TGCCCATGTGAGCCCACA
38593713 TGCCCATGTG-GCCCACA
1 TGCCCATGTGAGCCCACA
38593730 CGGTCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (18 bp):
TGCCCATGTGAGCCCACA
Found at i:38595159 original size:60 final size:59
Alignment explanation
Indices: 38595065--38595184 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 59
38595055 ATTCAATAAA
* *
38595065 ACTTCTTATTATACGAGTAACAAGATAAGCTGATTATAGTTTTTTACAATTGTTTCGTTT
1 ACTTCTTATTATACGAGTAACAAGATAAGATGATTATAG-TTTTTACAAATGTTTCGTTT
* *
38595125 ACTTCTTATTATACGAGTAAGAAGATAAGATGATTATAGTTTTTGCAAATGTTTCGTTT
1 ACTTCTTATTATACGAGTAACAAGATAAGATGATTATAGTTTTTACAAATGTTTCGTTT
38595184 A
1 A
38595185 TTAAATATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 19 0.34
60 37 0.66
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (59 bp):
ACTTCTTATTATACGAGTAACAAGATAAGATGATTATAGTTTTTACAAATGTTTCGTTT
Found at i:38615194 original size:60 final size:59
Alignment explanation
Indices: 38615100--38615219 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 59
38615090 ATTCAATAAA
* *
38615100 ACTTCTTATTATACGAGTAACAAGATAAGCTGATTATAGTTTTTTACAATTGTTTCGTTT
1 ACTTCTTATTATACGAGTAACAAGATAAGATGATTATAG-TTTTTACAAATGTTTCGTTT
* *
38615160 ACTTCTTATTATACGAGTAAGAAGATAAGATGATTATAGTTTTTGCAAATGTTTCGTTT
1 ACTTCTTATTATACGAGTAACAAGATAAGATGATTATAGTTTTTACAAATGTTTCGTTT
38615219 A
1 A
38615220 TTAAATATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 19 0.34
60 37 0.66
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (59 bp):
ACTTCTTATTATACGAGTAACAAGATAAGATGATTATAGTTTTTACAAATGTTTCGTTT
Found at i:38619944 original size:43 final size:42
Alignment explanation
Indices: 38619883--38619971 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 42
38619873 ATGGAACTTG
38619883 GTGAGTTAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA
1 GTGAGTTAATATCGGGCTTCGAGCCTAGCAGGC-ATAATGCCA
* * *
38619926 GTGAGTTAATATTGGGCTTTGAGCCTAGCAGGCATAATGCCG
1 GTGAGTTAATATCGGGCTTCGAGCCTAGCAGGCATAATGCCA
38619968 GTGA
1 GTGA
38619972 ATGAGTTCAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
42 12 0.28
43 31 0.72
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (42 bp):
GTGAGTTAATATCGGGCTTCGAGCCTAGCAGGCATAATGCCA
Found at i:38620569 original size:16 final size:18
Alignment explanation
Indices: 38620538--38620570 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
38620528 AACTCGTCAC
38620538 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
38620556 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
38620571 AATTCGTATG
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:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:38623653 original size:11 final size:11
Alignment explanation
Indices: 38623637--38623667 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
38623627 TTTGAGTGGT
38623637 CAGAAAAGTGC
1 CAGAAAAGTGC
38623648 CAGAAAAGTGC
1 CAGAAAAGTGC
38623659 CAGAAAAGT
1 CAGAAAAGT
38623668 TTTGATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.16, G:0.26, T:0.10
Consensus pattern (11 bp):
CAGAAAAGTGC
Found at i:38629511 original size:16 final size:18
Alignment explanation
Indices: 38629479--38629512 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
38629469 CAACTCGTCA
38629479 TACTATCTATCGTTTTGG
1 TACTATCTATCGTTTTGG
38629497 TACTAT-TAT-GTTTTGG
1 TACTATCTATCGTTTTGG
38629513 AATTCGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (18 bp):
TACTATCTATCGTTTTGG
Found at i:38649779 original size:32 final size:34
Alignment explanation
Indices: 38649743--38649807 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
38649733 TAACAGTGGT
*
38649743 ACTGGGCCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
**
38649775 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATA
38649808 TGGCCTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 13 0.46
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
Found at i:38651683 original size:26 final size:26
Alignment explanation
Indices: 38651653--38651708 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
38651643 TGAAATTCCC
*
38651653 ATCATGGAACCTTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
38651679 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
38651705 ATCA
1 ATCA
38651709 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:38662193 original size:58 final size:58
Alignment explanation
Indices: 38662107--38662223 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
38662097 GCAGGAAAAC
38662107 ACAACCATAAACCAGAGTCAGACATGATGTGACATAAAAGATAAGTAGGGAATAGAAA
1 ACAACCATAAACCAGAGTCAGACATGATGTGACATAAAAGATAAGTAGGGAATAGAAA
*
38662165 ACAACCATACACCAGAGTCAGACATGATGTGACATAAAAGATAAGTAGGGAATAGAAA
1 ACAACCATAAACCAGAGTCAGACATGATGTGACATAAAAGATAAGTAGGGAATAGAAA
38662223 A
1 A
38662224 TTTCCTATTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.15
Consensus pattern (58 bp):
ACAACCATAAACCAGAGTCAGACATGATGTGACATAAAAGATAAGTAGGGAATAGAAA
Found at i:38668891 original size:52 final size:52
Alignment explanation
Indices: 38668813--38668916 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
38668803 AACAGCTACA
*
38668813 ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCTAGAGCTCATTGGC
1 ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCCAGAGCTCATTGGC
*
38668865 ACAAAATATTTTCAGAACTTTTGTTATCCATGGCTATCCAGAGCTCATTGGC
1 ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCCAGAGCTCATTGGC
38668917 TATCTATTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (52 bp):
ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCCAGAGCTCATTGGC
Found at i:38674915 original size:16 final size:17
Alignment explanation
Indices: 38674888--38674928 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
38674878 GCTTGAGATT
38674888 TCAAAATATAAAAAGTA
1 TCAAAATATAAAAAGTA
* *
38674905 T-AAAATTTAAAAATTA
1 TCAAAATATAAAAAGTA
38674921 TCAAAATA
1 TCAAAATA
38674929 AAATATAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (17 bp):
TCAAAATATAAAAAGTA
Found at i:38677627 original size:23 final size:22
Alignment explanation
Indices: 38677563--38677639 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 22
38677553 TGAGCTGATA
38677563 AACAGTAAGCTCTATTGAGCTG
1 AACAGTAAGCTCTATTGAGCTG
38677585 AACAGTAAGCTCT-TTCGAGCTG
1 AACAGTAAGCTCTATT-GAGCTG
* * *
38677607 AATCGGTAAGATCTAATGAGCTG
1 AA-CAGTAAGCTCTATTGAGCTG
38677630 AAACAGTAAG
1 -AACAGTAAG
38677640 TTCTTACGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.04
22 21 0.45
23 21 0.45
24 3 0.06
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (22 bp):
AACAGTAAGCTCTATTGAGCTG
Found at i:38677650 original size:23 final size:23
Alignment explanation
Indices: 38677562--38677651 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 23
38677552 CTGAGCTGAT
*
38677562 AAACAGTAAGCTC-TATTGAGCTG
1 AAACAGTAAGCTCTTA-CGAGCTG
*
38677585 -AACAGTAAGCTCTTTCGAGCTG
1 AAACAGTAAGCTCTTACGAGCTG
* * * * *
38677607 AATCGGTAAGATCTAATGAGCTG
1 AAACAGTAAGCTCTTACGAGCTG
*
38677630 AAACAGTAAGTTCTTACGAGCT
1 AAACAGTAAGCTCTTACGAGCT
38677652 ATGGTGTGTC
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
22 18 0.35
23 34 0.65
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (23 bp):
AAACAGTAAGCTCTTACGAGCTG
Found at i:38678362 original size:73 final size:73
Alignment explanation
Indices: 38678243--38678388 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
38678233 TATAAAACTT
38678243 GTATAACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAAT
1 GTATAACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAAT
38678308 GACATATC
66 GACATATC
38678316 GTATAACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAAT
1 GTATAACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAAT
38678381 GACATATC
66 GACATATC
38678389 TTAAAATCTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (73 bp):
GTATAACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAAT
GACATATC
Found at i:38678403 original size:73 final size:73
Alignment explanation
Indices: 38678247--38678404 Score: 282
Period size: 73 Copynumber: 2.2 Consensus size: 73
38678237 AAACTTGTAT
38678247 AACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAATGACA
1 AACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAATGACA
*
38678312 TATCGTAT
66 TATCGTAA
38678320 AACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAATGACA
1 AACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAATGACA
*
38678385 TATCTTAA
66 TATCGTAA
38678393 AATCTA-TAACAA
1 AA-CTATTAACAA
38678405 TTTCAAAAAC
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
73 79 0.96
74 3 0.04
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.26
Consensus pattern (73 bp):
AACTATTAACAACCATCAATAATCTAACAAGAAACTTCAAAATACCTAAGTATTCAACAATGACA
TATCGTAA
Found at i:38680998 original size:10 final size:10
Alignment explanation
Indices: 38680979--38681028 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
38680969 TTAAATTCTA
38680979 AAAGATAAAT
1 AAAGATAAAT
38680989 ACAA-ATAAAT
1 A-AAGATAAAT
*
38680999 AAAGATAATT
1 AAAGATAAAT
38681009 AAAGATAAAT
1 AAAGATAAAT
38681019 GAAA-ATAAAT
1 -AAAGATAAAT
38681029 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:38685246 original size:22 final size:21
Alignment explanation
Indices: 38685202--38685245 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38685192 ATTTACTACC
*
38685202 AACAAATTATAAATTGTTAAA
1 AACAAATTATAAAATGTTAAA
38685223 AACATAATTA-AAAATGTTAAA
1 AACA-AATTATAAAATGTTAAA
38685244 AA
1 AA
38685246 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (21 bp):
AACAAATTATAAAATGTTAAA
Found at i:38685276 original size:33 final size:30
Alignment explanation
Indices: 38685212--38685291 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 30
38685202 AACAAATTAT
**
38685212 AAATTGTTAAAAACATAATTAAAAATGTTAAAA
1 AAATT-TTAAAAA-ATAATTAAAAACATT-AAA
38685245 AAATTTTAAAAAATAATTATAATAACATTAAA
1 AAATTTTAAAAAATAATTA-AA-AACATTAAA
**
38685277 CTATTTTAAAAAATA
1 AAATTTTAAAAAATA
38685292 CTAACAATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.17
32 25 0.61
33 9 0.22
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATTTTAAAAAATAATTAAAAACATTAAA
Found at i:38695109 original size:46 final size:44
Alignment explanation
Indices: 38695009--38695116 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
38694999 TGTCTTTAAC
** * * * *
38695009 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
*
38695053 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATA--TATAAT
38695099 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
38695117 TTTCTATTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
Found at i:38700173 original size:50 final size:51
Alignment explanation
Indices: 38700096--38700224 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
38700086 GACCATGGCA
38700096 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
38700147 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
38700197 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
38700225 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:38700238 original size:31 final size:31
Alignment explanation
Indices: 38700200--38700317 Score: 202
Period size: 31 Copynumber: 3.8 Consensus size: 31
38700190 ACAAATGACA
*
38700200 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
38700231 AGTGAAAAGTGGTAG-TTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
38700262 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
38700293 AGTGAAAAATGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
38700318 AAGTGACAAG
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
30 2 0.02
31 79 0.95
32 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:38700405 original size:47 final size:46
Alignment explanation
Indices: 38700336--38700499 Score: 167
Period size: 47 Copynumber: 3.6 Consensus size: 46
38700326 AGTGATTTCC
* *
38700336 GTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACT
1 GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGAT-CT
* * *
38700383 GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTT
1 GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATCT
* * * *
38700429 GTGTAAGACCATAGCTGGGCTATGGCATC-----GATATATGAATAT
1 GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATG-ATCT
* * *
38700471 GTGTAAGACCATAGCTGGGCTATGGCATC
1 GTATAAGACCATATCTGGGATATGGCATC
38700500 ATTATGTGAA
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
41 7 0.07
42 32 0.30
46 27 0.25
47 40 0.38
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (46 bp):
GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATCT
Found at i:38700487 original size:42 final size:42
Alignment explanation
Indices: 38700386--38700526 Score: 167
Period size: 42 Copynumber: 3.3 Consensus size: 42
38700376 TGCTACTGTA
* * * * *
38700386 TAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTTGTG
1 TAAGACCATAGCTGGGCTATGGCATC---GATATATG-AATATGTG
38700432 TAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
* *
38700474 TAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATATGTG
38700516 TAAGACCATAG
1 TAAGACCATAG
38700527 TTGAATTATG
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
41 1 0.01
42 55 0.63
43 7 0.08
46 24 0.28
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (42 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
Found at i:38702373 original size:51 final size:51
Alignment explanation
Indices: 38702297--38702399 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
38702287 AATACTACCG
* *
38702297 AGTATCGGTATCGACATTCCGTAGAAGATGGTTGACACACATGATTGGGAA
1 AGTATCGGTAACGACATTCCGTAGAAGATGGTTGACACACAAGATTGGGAA
* *
38702348 AGTATCGGTAACGGCATTCCGTAGAAGATGGTTGAGACACAAGATTGGGAA
1 AGTATCGGTAACGACATTCCGTAGAAGATGGTTGACACACAAGATTGGGAA
38702399 A
1 A
38702400 AAGGTCCCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (51 bp):
AGTATCGGTAACGACATTCCGTAGAAGATGGTTGACACACAAGATTGGGAA
Found at i:38710328 original size:18 final size:18
Alignment explanation
Indices: 38710307--38710341 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38710297 CTGAATAATT
*
38710307 GACTGTTACAGAATAAAA
1 GACTGATACAGAATAAAA
*
38710325 GACTGATACGGAATAAA
1 GACTGATACAGAATAAA
38710342 TGAATATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (18 bp):
GACTGATACAGAATAAAA
Found at i:38712578 original size:7 final size:7
Alignment explanation
Indices: 38712566--38712597 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38712556 TCACCATTTT
38712566 ACCCTAA
1 ACCCTAA
38712573 ACCCTAA
1 ACCCTAA
*
38712580 ACCTTAA
1 ACCCTAA
38712587 ACCCTAA
1 ACCCTAA
38712594 ACCC
1 ACCC
38712598 GCATTAGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.16
Consensus pattern (7 bp):
ACCCTAA
Found at i:38713221 original size:24 final size:24
Alignment explanation
Indices: 38713194--38713243 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
38713184 ACAGTCCCGC
*
38713194 AACCTATGGGGACCACTACAAAAG
1 AACCTATGGAGACCACTACAAAAG
*
38713218 AACCTATGTAGACCACTACAAAAG
1 AACCTATGGAGACCACTACAAAAG
38713242 AA
1 AA
38713244 GCACTCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (24 bp):
AACCTATGGAGACCACTACAAAAG
Found at i:38718576 original size:74 final size:74
Alignment explanation
Indices: 38718341--38718550 Score: 381
Period size: 74 Copynumber: 2.9 Consensus size: 74
38718331 TCATGATTAA
38718341 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTCTAAA
1 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTCTAAA
38718406 AGAAAATTT
66 AGAAAATTT
38718415 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTCTAAA
1 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTCTAAA
38718480 AGAAAATTT
66 AGAAAATTT
* *
38718489 ATTATCAAGAATTTTATGAAA-T-TATAT-ATTATTAAATTATATTTAATAATAATTATTTTAAA
1 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTCTAAA
38718551 TTATACAAAT
Statistics
Matches: 134, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
71 33 0.25
72 5 0.04
73 1 0.01
74 95 0.71
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (74 bp):
ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTCTAAA
AGAAAATTT
Found at i:38718745 original size:18 final size:17
Alignment explanation
Indices: 38718717--38718751 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38718707 ATTATTAAGA
*
38718717 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
38718734 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
38718752 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:38718942 original size:39 final size:40
Alignment explanation
Indices: 38718893--38719001 Score: 121
Period size: 44 Copynumber: 2.6 Consensus size: 40
38718883 AGTTTTTTCC
38718893 ATTATGCTATTACACCTCTATTCCATTCAACCAAACACAAG
1 ATTA-GCTATTACACCTCTATTCCATTCAACCAAACACAAG
* **
38718934 ATTA-CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTAG
1 ATTAGCTATTACACCTCTATT-C----CATTCAACCAAACACAAG
*
38718978 ATTAGCTATTACACCTCTAATCCA
1 ATTAGCTATTACACCTCTATTCCA
38719002 ATACACCTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
39 15 0.26
40 3 0.05
41 4 0.07
44 21 0.37
45 14 0.25
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (40 bp):
ATTAGCTATTACACCTCTATTCCATTCAACCAAACACAAG
Found at i:38718980 original size:44 final size:45
Alignment explanation
Indices: 38718916--38719006 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
38718906 ACCTCTATTC
* * *
38718916 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
**
38718960 CATTCAACCAAACAGTAGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
38719005 CA
1 CA
38719007 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 20 0.49
45 21 0.51
ACGTcount: A:0.38, C:0.29, G:0.05, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:38719021 original size:17 final size:16
Alignment explanation
Indices: 38718987--38719039 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
38718977 GATTAGCTAT
38718987 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
38719003 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
38719020 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
38719036 TACA
1 TACA
38719040 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:38728128 original size:31 final size:31
Alignment explanation
Indices: 38728093--38728175 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
38728083 CTTTCTGCAT
* *
38728093 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * *
38728124 TAAAATGCAGCCAAAAACAACAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
*
38728155 TAAAAATTACAACCAAAAACA
1 T-AAAA-TCCAACCAAAAACA
38728176 TTAATTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 27 0.63
32 4 0.09
33 12 0.28
ACGTcount: A:0.61, C:0.19, G:0.02, T:0.17
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:38734046 original size:9 final size:9
Alignment explanation
Indices: 38734032--38734159 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
38734022 ATGTATTAGT
38734032 TAAGTTATG
1 TAAGTTATG
38734041 TAAGTTGTTATG
1 TAA---GTTATG
*
38734053 TACGTTATG
1 TAAGTTATG
*
38734062 TGAGTTATG
1 TAAGTTATG
*
38734071 TAAATTATG
1 TAAGTTATG
38734080 TAAGTTATG
1 TAAGTTATG
*
38734089 TGAGTTATG
1 TAAGTTATG
38734098 TAAGTTGTTATG
1 TAA---GTTATG
*
38734110 TAAATTATG
1 TAAGTTATG
*
38734119 TAAGTTATA
1 TAAGTTATG
*
38734128 TGAGTTATG
1 TAAGTTATG
38734137 TAAGTTATG
1 TAAGTTATG
* *
38734146 TAATTTATT
1 TAAGTTATG
38734155 TAAGT
1 TAAGT
38734160 AATGATCAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 79 0.82
12 17 0.18
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:38734159 original size:57 final size:57
Alignment explanation
Indices: 38734032--38734159 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
38734022 ATGTATTAGT
** * *
38734032 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * *
38734089 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
38734146 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
38734160 AATGATCAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:38736351 original size:5 final size:5
Alignment explanation
Indices: 38736325--38736382 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
38736315 ATGTGTTAAA
* *
38736325 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
38736374 ATATT ATAT
1 ATATT ATAT
38736383 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:38736361 original size:10 final size:9
Alignment explanation
Indices: 38736326--38736383 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
38736316 TGTGTTAAAA
38736326 TATATATAT
1 TATATATAT
*
38736335 TAAAT-TAT
1 TATATATAT
38736343 TAT-TATAT
1 TATATATAT
38736351 TATAGTATAT
1 TATA-TATAT
38736361 TATAT-TA-
1 TATATATAT
38736368 TATATTATAT
1 TATA-TATAT
38736378 TATATA
1 TATATA
38736384 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:38736373 original size:12 final size:12
Alignment explanation
Indices: 38736328--38736383 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
38736318 TGTTAAAATA
*
38736328 TATATATTAAAT
1 TATATATTATAT
38736340 TAT-TATTATATT
1 TATATATTATA-T
38736352 ATAGTATATTATAT
1 -TA-TATATTATAT
38736366 TATATATTATAT
1 TATATATTATAT
38736378 TATATA
1 TATATA
38736384 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:38736757 original size:18 final size:19
Alignment explanation
Indices: 38736734--38736772 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
38736724 ATATATAGAT
38736734 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
38736752 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
38736771 AT
1 AT
38736773 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:38737122 original size:39 final size:39
Alignment explanation
Indices: 38737012--38737146 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
38737002 GACCTCGAGT
* * * *
38737012 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
38737053 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
38737091 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
38737130 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
38737147 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:38737282 original size:13 final size:12
Alignment explanation
Indices: 38737259--38737307 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
38737249 GAGCTATTGG
*
38737259 AATGAAATGAGA
1 AATGAATTGAGA
38737271 AATTGAATTGAGA
1 AA-TGAATTGAGA
38737284 AATGAAATTGAGA
1 AATG-AATTGAGA
*
38737297 TATGAGATTGA
1 AATGA-ATTGA
38737308 AAACATGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 5 0.16
13 27 0.84
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (12 bp):
AATGAATTGAGA
Found at i:38740027 original size:11 final size:11
Alignment explanation
Indices: 38740013--38740062 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
38740003 AAAATTTTAA
38740013 AAATTCTTGAC
1 AAATTCTTGAC
* *
38740024 AAATTATTTTGTC
1 AAA-T-TCTTGAC
*
38740037 AAATTCTTGAA
1 AAATTCTTGAC
38740048 AAATTCTTGAC
1 AAATTCTTGAC
38740059 AAAT
1 AAAT
38740063 ATACAAGTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 21 0.68
12 2 0.06
13 8 0.26
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATTCTTGAC
Found at i:38740462 original size:18 final size:19
Alignment explanation
Indices: 38740441--38740476 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38740431 TTTGAAATTC
38740441 TTCATCTCT-CAATTCTAT
1 TTCATCTCTGCAATTCTAT
*
38740459 TTCATCTTTGCAATTCTA
1 TTCATCTCTGCAATTCTA
38740477 CAGAAATAAG
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:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (19 bp):
TTCATCTCTGCAATTCTAT
Found at i:38741111 original size:40 final size:41
Alignment explanation
Indices: 38741060--38741160 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 41
38741050 TTTAGTGGCG
**
38741060 TTTTACAAAAGCTTCACTAATTCTCAATTTTT-GCGGCGTT
1 TTTTACAAAAGCGCCACTAATTCTCAATTTTTAGCGGCGTT
* * *
38741100 TTTTACGAAAGCGCCACTAATTCTCTATTTTTAGTGGCGTT
1 TTTTACAAAAGCGCCACTAATTCTCAATTTTTAGCGGCGTT
*
38741141 TTTGTA-AAAA-CGCCGCTAAT
1 TTT-TACAAAAGCGCCACTAAT
38741161 GCCTCTGCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 37 0.71
41 13 0.25
42 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (41 bp):
TTTTACAAAAGCGCCACTAATTCTCAATTTTTAGCGGCGTT
Found at i:38742299 original size:41 final size:40
Alignment explanation
Indices: 38742226--38742312 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 40
38742216 CCCGGCCCAT
*
38742226 ACCATTAACTTAATATATATACTATACCATTGAACTCGCCTAA
1 ACCATAAACTTAATATATATACTATACCATTGAA--C-CCTAA
* *
38742269 ACCATAAACTTAA-A-ATATATTCTACCATTGAACCCTAA
1 ACCATAAACTTAATATATATACTATACCATTGAACCCTAA
38742307 ACCATA
1 ACCATA
38742313 GGCTTTAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 11 0.27
39 1 0.02
41 16 0.39
42 1 0.02
43 12 0.29
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (40 bp):
ACCATAAACTTAATATATATACTATACCATTGAACCCTAA
Found at i:38742521 original size:28 final size:28
Alignment explanation
Indices: 38742485--38742551 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
38742475 AGTTTATCGA
* *
38742485 TTAGTGTTTATGGTTT-ATGTTTTAAAAT
1 TTAGGGTTTAGGGTTTAATG-TTTAAAAT
*
38742513 TTAGGGTTTAGGGTTTAATGTTTAAGAT
1 TTAGGGTTTAGGGTTTAATGTTTAAAAT
38742541 TTAAGGGTTTA
1 TT-AGGGTTTA
38742552 CAGAAAGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (28 bp):
TTAGGGTTTAGGGTTTAATGTTTAAAAT
Found at i:38742536 original size:21 final size:21
Alignment explanation
Indices: 38742489--38742551 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
38742479 TATCGATTAG
* * *
38742489 TGTTTATGGTTTATGTTTTAA
1 TGTTTAAGGTTTAGGGTTTAA
** *
38742510 AATTTAGGGTTTAGGGTTTAA
1 TGTTTAAGGTTTAGGGTTTAA
*
38742531 TGTTTAAGATTTAAGGGTTTA
1 TGTTTAAGGTTT-AGGGTTTA
38742552 CAGAAAGCCA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (21 bp):
TGTTTAAGGTTTAGGGTTTAA
Found at i:38742886 original size:41 final size:40
Alignment explanation
Indices: 38742841--38743067 Score: 253
Period size: 41 Copynumber: 5.6 Consensus size: 40
38742831 AACTTTTTGC
*
38742841 GGCGTTTGGACCAAAAACGCCGCTATTAATCAGTTTTTAGT
1 GGCGTTTGGA-CAAAAACGCCGCTATTGATCAGTTTTTAGT
* *
38742882 GGCGTTTGGGATAAAAACGCCGCAATTGATCAGTTTTTAGT
1 GGCGTTT-GGACAAAAACGCCGCTATTGATCAGTTTTTAGT
*
38742923 GGCGTTTGGA-ATTAAAACGCCGCTATTGATCAGCTTTTAGT
1 GGCGTTTGGACA--AAAACGCCGCTATTGATCAGTTTTTAGT
** * *
38742964 GGCGTTTGGTGAAAAACGCCACTATTGACCAGTTTTTAGT
1 GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * * * *
38743004 GGCGTTTTGGCCAAAAACACCGTTATAGTTTAGTTTTTAGT
1 GGCG-TTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
38743045 GGCGTTTCGGAC--AAACGCCGCTA
1 GGCGTTT-GGACAAAAACGCCGCTA
38743068 ATGTTTATTA
Statistics
Matches: 159, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
39 10 0.06
40 35 0.22
41 110 0.69
42 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (40 bp):
GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
Found at i:38743042 original size:81 final size:80
Alignment explanation
Indices: 38742841--38743051 Score: 223
Period size: 81 Copynumber: 2.6 Consensus size: 80
38742831 AACTTTTTGC
* *
38742841 GGCGTTTGGACCA-AAAACGCCGCTATTA-ATCAGTTTTTAGTGGCGTTTGGGATAAAAACGCCG
1 GGCGTTTGGA--ATAAAACACCGCTA-TAGATCAGTTTTTAGTGGCGTTTGGGA-AAAAACGCCA
*
38742904 CAATTGATCAGTTTTTAGT
62 CAATTGACCAGTTTTTAGT
* * * *
38742923 GGCGTTTGGAATTAAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTGGTG-AAAAACGCCACT
1 GGCGTTTGGAA-TAAAACACCGCTATAGATCAGTTTTTAGTGGCGTTTGG-GAAAAAACGCCACA
38742987 ATTGACCAGTTTTTAGT
64 ATTGACCAGTTTTTAGT
* * * *
38743004 GGCGTTTTGGCCA-AAAACACCGTTATAGTTTAGTTTTTAGTGGCGTTT
1 GGCG-TTTGG-AATAAAACACCGCTATAGATCAGTTTTTAGTGGCGTTT
38743052 CGGACAAACG
Statistics
Matches: 111, Mismatches: 12, Indels: 13
0.82 0.09 0.10
Matches are distributed among these distances:
80 1 0.01
81 60 0.54
82 48 0.43
83 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (80 bp):
GGCGTTTGGAATAAAACACCGCTATAGATCAGTTTTTAGTGGCGTTTGGGAAAAAACGCCACAAT
TGACCAGTTTTTAGT
Found at i:38746613 original size:55 final size:55
Alignment explanation
Indices: 38746550--38746662 Score: 199
Period size: 55 Copynumber: 2.1 Consensus size: 55
38746540 TCAGTGTATT
*
38746550 TATGCTCGATCAACACTTTGGTGCGTATATTGGAGTGTTGGTGAATTGATCTGAC
1 TATGCTCGATCAACACTTTGATGCGTATATTGGAGTGTTGGTGAATTGATCTGAC
* *
38746605 TATGCTCGATTAACACTTTGATGCGTATATTGGAGTGTTGGTGGATTGATCTGAC
1 TATGCTCGATCAACACTTTGATGCGTATATTGGAGTGTTGGTGAATTGATCTGAC
38746660 TAT
1 TAT
38746663 CTATCCTTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (55 bp):
TATGCTCGATCAACACTTTGATGCGTATATTGGAGTGTTGGTGAATTGATCTGAC
Found at i:38753759 original size:27 final size:27
Alignment explanation
Indices: 38753729--38753782 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
38753719 TCATACAACC
* *
38753729 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
38753756 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
38753783 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:38781404 original size:9 final size:9
Alignment explanation
Indices: 38781387--38781421 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
38781377 TAAGTGATTA
*
38781387 TTATGAAAT
1 TTATCAAAT
38781396 TTATCAAAT
1 TTATCAAAT
38781405 TTATCAAAT
1 TTATCAAAT
38781414 TTATCAAA
1 TTATCAAA
38781422 AGTAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (9 bp):
TTATCAAAT
Found at i:38782831 original size:25 final size:25
Alignment explanation
Indices: 38782797--38782846 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
38782787 AAATAGGTTG
38782797 GAAATTGAATGAAATTATTTTTATT
1 GAAATTGAATGAAATTATTTTTATT
38782822 GAAATTGAATGAAATTATTTTTATT
1 GAAATTGAATGAAATTATTTTTATT
38782847 CTTTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (25 bp):
GAAATTGAATGAAATTATTTTTATT
Found at i:38784382 original size:23 final size:23
Alignment explanation
Indices: 38784356--38784404 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
38784346 AATTAAAATA
*
38784356 AAATAATTAAGTA-ATAATTAATT
1 AAATAATTAAG-AGATAACTAATT
*
38784379 AAATTATTAAGAGATAACTAATT
1 AAATAATTAAGAGATAACTAATT
38784402 AAA
1 AAA
38784405 AAAAAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (23 bp):
AAATAATTAAGAGATAACTAATT
Done.