Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 123 of 172
Found at i:41048328 original size:15 final size:16
Alignment explanation
Indices: 41048286--41048333 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
41048276 TAAAATCTTT
41048286 TTTGAATCCCTAACAATC
1 TTTGAATCCCT-A-AATC
*
41048304 TTTAAATCCCTAAATC
1 TTTGAATCCCTAAATC
41048320 -TTGAATCCCTAAAT
1 TTTGAATCCCTAAAT
41048334 AGTTAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 13 0.46
16 4 0.14
17 1 0.04
18 10 0.36
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (16 bp):
TTTGAATCCCTAAATC
Found at i:41048446 original size:23 final size:24
Alignment explanation
Indices: 41048405--41048450 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
41048395 CCTATAAAAA
*
41048405 TTAGAAACAAAATCGTGAAATCCC
1 TTAGAAACAAAATCATGAAATCCC
*
41048429 TTAG-AACCAAATCATGAAATCC
1 TTAGAAACAAAATCATGAAATCC
41048451 TTATTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (24 bp):
TTAGAAACAAAATCATGAAATCCC
Found at i:41049442 original size:22 final size:22
Alignment explanation
Indices: 41049412--41049453 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41049402 TAAGCATATG
*
41049412 ATTTGGATAAATGTAATTTAAA
1 ATTTCGATAAATGTAATTTAAA
*
41049434 ATTTCGATAAATGTACTTTA
1 ATTTCGATAAATGTAATTTA
41049454 CAAAAGCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTTCGATAAATGTAATTTAAA
Found at i:41060620 original size:40 final size:40
Alignment explanation
Indices: 41060537--41060799 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
41060527 TTGAATGCTG
* * * * * *
41060537 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41060577 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41060617 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41060657 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41060697 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41060737 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41060776 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41060800 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41060819 original size:79 final size:80
Alignment explanation
Indices: 41060576--41060834 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
41060566 AAGTGAATAT
* * * * * *
41060576 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
41060640 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
41060656 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
41060721 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
41060736 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
41060800 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
41060815 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
41060835 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:41068572 original size:40 final size:40
Alignment explanation
Indices: 41068489--41068751 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
41068479 TTGAATGCTG
* * * * * *
41068489 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41068529 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41068569 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41068609 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41068649 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41068689 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41068728 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41068752 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41068771 original size:79 final size:80
Alignment explanation
Indices: 41068528--41068786 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
41068518 AAGTGAATAT
* * * * * *
41068528 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
41068592 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
41068608 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
41068673 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
41068688 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
41068752 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
41068767 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
41068787 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:41070668 original size:48 final size:48
Alignment explanation
Indices: 41070598--41070732 Score: 172
Period size: 48 Copynumber: 2.9 Consensus size: 48
41070588 AGTTCTAGCA
* *
41070598 TATATGTGCCGAAGCCATGTCCCAGACATGGTCTTACGCTGGCACATC
1 TATACGTGCCGAAGCCATGTCCCAGACATGGTCTTACACTGGCACATC
* *
41070646 TATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATC
1 TATACGTGCCGAAGCCATGTCCCAGACATGGTCTTACACTGGCACATC
* *
41070694 --T-CGTAGCCGACG-CATGTCCCGGACAT-GTCTTACACTGGC
1 TATACGT-GCCGAAGCCATGTCCCAGACATGGTCTTACACTGGC
41070733 TTACATCACA
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
44 12 0.15
45 16 0.20
46 7 0.09
48 44 0.56
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (48 bp):
TATACGTGCCGAAGCCATGTCCCAGACATGGTCTTACACTGGCACATC
Found at i:41070814 original size:47 final size:46
Alignment explanation
Indices: 41070652--41070827 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
41070642 CATCTATACG
* * *
41070652 TGCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTC-G
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAA
* * * *
41070697 TAGCCGACGCATGTCCCGGACATGTCTTACACTGGCT-TACATCACAA
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCAA
* * * *
41070744 GGCCAATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAA
1 TGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAA
*
41070790 TGTCGATGCCATGTCCCAGACATGTCTTACACTAGCTC
1 TGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTC
41070828 ACAACAAGTG
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
44 10 0.09
45 15 0.14
46 52 0.49
47 29 0.27
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (46 bp):
TGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAA
Found at i:41071234 original size:29 final size:30
Alignment explanation
Indices: 41071174--41071234 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
41071164 TATTTTTGGC
* ** *
41071174 AAAATGACCATTTTGCCCTTAAATTTTGAA
1 AAAATGACCATTTTACCCTTAAAGCTCGAA
*
41071204 AAAATGACCATTTTACCCTT-AGGCTCGAA
1 AAAATGACCATTTTACCCTTAAAGCTCGAA
41071233 AA
1 AA
41071235 TCAATTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (30 bp):
AAAATGACCATTTTACCCTTAAAGCTCGAA
Found at i:41078344 original size:48 final size:46
Alignment explanation
Indices: 41078228--41078442 Score: 158
Period size: 48 Copynumber: 4.6 Consensus size: 46
41078218 TCAGGTGCCA
* * *
41078228 ATGCCATGTCCCAGACATGGTCTTTCACAAGTTCTAGCATATCTG-T-GCTG
1 ATGCCATGTCCCAGACATGGTC-TT-AC-A-TT-GA-CACATCTGATAGCCG
*
41078278 ATGCCATGTCCCAAACATGGTCTTACATTGACACATCT-ATACGTTCCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGACACATCTGATA-G--CCG
* *
41078326 ATGCCATGTCCCAGACATGGTCTTACACTGACACATCTGGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGACACATCTGATAGCCG
* * * **
41078372 ACG-CATGTCCCGGACAT-GTCTTACATTGGCTTACATCACA-ACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGAC--ACATCTGATA-GCCG
*
41078418 ATG-CATGTCCTAGACAT-GTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
41078443 CTAGCTCTCG
Statistics
Matches: 139, Mismatches: 17, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
44 18 0.13
45 15 0.11
46 39 0.28
47 1 0.01
48 41 0.29
49 4 0.03
50 21 0.15
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
ATGCCATGTCCCAGACATGGTCTTACATTGACACATCTGATAGCCG
Found at i:41078464 original size:46 final size:44
Alignment explanation
Indices: 41078368--41078542 Score: 165
Period size: 46 Copynumber: 3.8 Consensus size: 44
41078358 ACATCTGGTA
* * * * * *
41078368 GCCGACGCATGTCCCGGACATGTCTTACATTGGCTTACATCACAAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTT-C-TCTCAAT
*
41078414 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT-TC-TCTCAAT
*
41078460 GCCGATGTCATGTCCTAGACATGGTCTTACACTAG-TTCTCAT-AATGT
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTCTC-TCAA--T
*
41078507 GGCCAATGCATGTCCCAGACATGTCTTACACTAGCT
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
41078543 CACAACAAGT
Statistics
Matches: 111, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
45 4 0.04
46 58 0.52
47 31 0.28
48 18 0.16
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (44 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTCTCTCAAT
Found at i:41090513 original size:40 final size:40
Alignment explanation
Indices: 41090431--41090612 Score: 217
Period size: 40 Copynumber: 4.6 Consensus size: 40
41090421 TATTCGAAAA
* * * *
41090431 ATATCCGGGCTAAGTCCCGAAGGCTTTTATACTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
* * *
41090471 ATATCCAGACTAAGAT-CCGAAGGCATTTGTTCGAGTTGCT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTGCT
*
41090511 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* * *
41090551 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
*
41090591 ATATCC-GGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
41090613 TACTTGGTTT
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
39 16 0.13
40 104 0.85
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
Found at i:41094570 original size:28 final size:28
Alignment explanation
Indices: 41094538--41094632 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 28
41094528 ACATACATGC
* *
41094538 ATATGGCCCA-CTTGGCCCAATCTCATTT
1 ATATGGCCCATC-AGGCCCAATCACATTT
*
41094566 ATATGGCCCATCAGGCCCAATTCACATTC
1 ATATGGCCCATCAGGCCCAA-TCACATTT
*
41094595 ATATGGCCCATCAGGCCCAAATCACCTTT
1 ATATGGCCCATCAGGCCC-AATCACATTT
41094624 ATATGGCCC
1 ATATGGCCC
41094633 GTTAGGCCGA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.29
29 40 0.68
30 2 0.03
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (28 bp):
ATATGGCCCATCAGGCCCAATCACATTT
Found at i:41094639 original size:29 final size:29
Alignment explanation
Indices: 41094563--41094650 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
41094553 CCCAATCTCA
* * *
41094563 TTTATATGGCCCATCAGGCCCAATTCACA
1 TTTATATGGCCCATCAGGCCCAAATAACC
* *
41094592 TTCATATGGCCCATCAGGCCCAAATCACC
1 TTTATATGGCCCATCAGGCCCAAATAACC
* * *
41094621 TTTATATGGCCCGTTAGGCCGAAATAACC
1 TTTATATGGCCCATCAGGCCCAAATAACC
41094650 T
1 T
41094651 CATATTCATG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (29 bp):
TTTATATGGCCCATCAGGCCCAAATAACC
Found at i:41094892 original size:16 final size:16
Alignment explanation
Indices: 41094866--41094908 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
41094856 GCAGCTAAAC
*
41094866 TTTCAGCTTTTCGGTA
1 TTTCGGCTTTTCGGTA
*
41094882 TTTTGGCTTTTCGGTA
1 TTTCGGCTTTTCGGTA
41094898 TTTCGGCTTTT
1 TTTCGGCTTTT
41094909 GCCGATCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.16, G:0.21, T:0.56
Consensus pattern (16 bp):
TTTCGGCTTTTCGGTA
Found at i:41101802 original size:16 final size:16
Alignment explanation
Indices: 41101781--41101823 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
41101771 GCCGCCAAAC
41101781 TTTCGACTTTTCGGCA
1 TTTCGACTTTTCGGCA
*
41101797 TTTCGACTTTTTGGCA
1 TTTCGACTTTTCGGCA
41101813 TTTCGACTTTT
1 TTTCGACTTTT
41101824 GCCGATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.12, C:0.21, G:0.16, T:0.51
Consensus pattern (16 bp):
TTTCGACTTTTCGGCA
Found at i:41103083 original size:16 final size:16
Alignment explanation
Indices: 41103062--41103093 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41103052 AAATTCAAAA
41103062 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
41103078 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
41103094 GCGCTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
TTTCAAGATTTTTGGG
Found at i:41111492 original size:44 final size:46
Alignment explanation
Indices: 41111380--41111493 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 46
41111370 CTAAAAGTCA
* *
41111380 TATAACCTCTAAAACCTTAAACCCCAAAAAAATTATGAACACTAATC
1 TATAACCTCTAAAACCTTAAACCCCAAAAAAACTA-GAACACTAAAC
* * * **
41111427 TATAACCCCTAAAATAC-TAAACCCC-TAAACCCTA-AACACTAAAC
1 TATAACCTCTAAAA-CCTTAAACCCCAAAAAAACTAGAACACTAAAC
*
41111471 TATAACTTCTAAAACCTTAAACC
1 TATAACCTCTAAAACCTTAAACC
41111494 AAAAAACATC
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.02
44 27 0.49
46 5 0.09
47 21 0.38
48 1 0.02
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (46 bp):
TATAACCTCTAAAACCTTAAACCCCAAAAAAACTAGAACACTAAAC
Found at i:41112281 original size:7 final size:7
Alignment explanation
Indices: 41112271--41112372 Score: 95
Period size: 7 Copynumber: 14.3 Consensus size: 7
41112261 ACTCAAAAAA
41112271 TAAAATT
1 TAAAATT
41112278 TAAAAATT
1 T-AAAATT
41112286 TAAAAATT
1 T-AAAATT
41112294 TAAAATT
1 TAAAATT
41112301 TAAAATTT
1 TAAAA-TT
41112309 TAAAATT
1 TAAAATT
41112316 TAAAATT
1 TAAAATT
*
41112323 TAAAAATA
1 T-AAAATT
*
41112331 AAAAATT
1 TAAAATT
41112338 TAAAA--
1 TAAAATT
41112343 -AAAA-T
1 TAAAATT
41112348 TAAATATT
1 TAAA-ATT
*
41112356 TAATATT
1 TAAAATT
41112363 TAATAATT
1 TAA-AATT
41112371 TA
1 TA
41112373 GTCCATATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
4 4 0.05
6 3 0.04
7 38 0.47
8 36 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:41112283 original size:15 final size:15
Alignment explanation
Indices: 41112265--41112345 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 15
41112255 AAATAAACTC
41112265 AAAAAATAAAATTTA
1 AAAAAATAAAATTTA
**
41112280 AAAATTTAAAAATTT-
1 AAAAAAT-AAAATTTA
** *
41112295 AAAATTTAAAATTTT
1 AAAAAATAAAATTTA
**
41112310 AAAATTTAAAATTTA
1 AAAAAATAAAATTTA
41112325 AAAATAA-AAAATTTA
1 AAAA-AATAAAATTTA
41112340 AAAAAA
1 AAAAAA
41112346 ATTAAATATT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.16
15 42 0.72
16 7 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATAAAATTTA
Found at i:41112285 original size:8 final size:8
Alignment explanation
Indices: 41112272--41112343 Score: 98
Period size: 8 Copynumber: 9.5 Consensus size: 8
41112262 CTCAAAAAAT
41112272 AAAATTTA
1 AAAATTTA
41112280 AAAATTTA
1 AAAATTTA
41112288 AAAATTT-
1 AAAATTTA
41112295 AAAATTT-
1 AAAATTTA
*
41112302 AAAATTTT
1 AAAATTTA
41112310 AAAATTT-
1 AAAATTTA
41112317 AAAATTTA
1 AAAATTTA
*
41112325 AAAA-TAA
1 AAAATTTA
41112332 AAAATTTA
1 AAAATTTA
41112340 AAAA
1 AAAA
41112344 AAATTAAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
7 27 0.46
8 32 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATTTA
Found at i:41112347 original size:18 final size:18
Alignment explanation
Indices: 41112324--41112358 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41112314 TTTAAAATTT
41112324 AAAAATAAAAAATTTAAA
1 AAAAATAAAAAATTTAAA
* *
41112342 AAAAATTAAATATTTAA
1 AAAAATAAAAAATTTAA
41112359 TATTTAATAA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAAAAAATTTAAA
Found at i:41112443 original size:18 final size:18
Alignment explanation
Indices: 41112422--41112461 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41112412 AATAAATTTC
41112422 AAAAAGAGAAAAATAAAA
1 AAAAAGAGAAAAATAAAA
* **
41112440 AAAATGTTAAAAATAAAA
1 AAAAAGAGAAAAATAAAA
41112458 AAAA
1 AAAA
41112462 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAGAGAAAAATAAAA
Found at i:41112459 original size:26 final size:26
Alignment explanation
Indices: 41112404--41112460 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
41112394 TTAAATATTC
* * *
41112404 AAAATTAAAATAAATTTCAAAAAGAG
1 AAAAATAAAAAAAATTTCAAAAAGAA
*
41112430 AAAAATAAAAAAAATGTT-AAAAATAA
1 AAAAATAAAAAAAAT-TTCAAAAAGAA
41112456 AAAAA
1 AAAAA
41112461 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (26 bp):
AAAAATAAAAAAAATTTCAAAAAGAA
Found at i:41112462 original size:18 final size:17
Alignment explanation
Indices: 41112430--41112468 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
41112420 TCAAAAAGAG
41112430 AAAAATAAAAAAAATGTT
1 AAAAATAAAAAAAAT-TT
41112448 AAAAATAAAAAAAATTT
1 AAAAATAAAAAAAATTT
41112465 AAAA
1 AAAA
41112469 TTAATCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAAAAATTT
Found at i:41117383 original size:19 final size:19
Alignment explanation
Indices: 41117361--41117401 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41117351 TTTATTGATA
41117361 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
41117379 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
41117398 TTTT
1 TTTT
41117402 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:41117672 original size:21 final size:21
Alignment explanation
Indices: 41117646--41117689 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
41117636 TGAATTTCAT
41117646 GACCTTTAGCGGCGTTTGTGG
1 GACCTTTAGCGGCGTTTGTGG
*
41117667 GACCTTTAGCGGCGTTTTTGG
1 GACCTTTAGCGGCGTTTGTGG
41117688 GA
1 GA
41117690 TCAGCGCCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.36, T:0.34
Consensus pattern (21 bp):
GACCTTTAGCGGCGTTTGTGG
Found at i:41118386 original size:16 final size:16
Alignment explanation
Indices: 41118365--41118410 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
41118355 AAATGCTAAC
41118365 GATTTAGGGATTTCAA
1 GATTTAGGGATTTCAA
* *
41118381 GATTTAAGGATTTGAA
1 GATTTAGGGATTTCAA
41118397 GATTGTTAGGGATT
1 GA-T-TTAGGGATT
41118411 CAATGAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 16 0.64
17 1 0.04
18 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.39
Consensus pattern (16 bp):
GATTTAGGGATTTCAA
Found at i:41126276 original size:18 final size:20
Alignment explanation
Indices: 41126253--41126289 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41126243 AATTATATTC
41126253 ATTTA-TTG-ATTTTTATAT
1 ATTTATTTGTATTTTTATAT
41126271 ATTTATTTGTATTTTTATA
1 ATTTATTTGTATTTTTATA
41126290 AAAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTATTTGTATTTTTATAT
Found at i:41137568 original size:32 final size:33
Alignment explanation
Indices: 41137532--41137593 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
41137522 AATATTCCTT
*
41137532 TCAAAAATCTATCAAATTTC-ATTAAAATTTTC
1 TCAAAAATCTATCAAATTTCTATCAAAATTTTC
*
41137564 TCAAAATTCTATCAAATTTCTATCAAAATT
1 TCAAAAATCTATCAAATTTCTATCAAAATT
41137594 CTTTGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (33 bp):
TCAAAAATCTATCAAATTTCTATCAAAATTTTC
Found at i:41137589 original size:22 final size:23
Alignment explanation
Indices: 41137539--41137595 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
41137529 CTTTCAAAAA
*
41137539 TCTATCAAATTTC-ATTAAAATT
1 TCTATCAAAATTCTATTAAAATT
* *
41137561 T-TCTCAAAATTCTA-TCAAATT
1 TCTATCAAAATTCTATTAAAATT
41137582 TCTATCAAAATTCT
1 TCTATCAAAATTCT
41137596 TTGTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.44
Consensus pattern (23 bp):
TCTATCAAAATTCTATTAAAATT
Found at i:41137595 original size:11 final size:11
Alignment explanation
Indices: 41137509--41137595 Score: 68
Period size: 11 Copynumber: 7.9 Consensus size: 11
41137499 CTCATAATTC
* *
41137509 TCAACATTCTT
1 TCAAAATTCTA
* *
41137520 TCAATATTCCTT
1 TCAAAATT-CTA
*
41137532 TCAAAAATCTA
1 TCAAAATTCTA
*
41137543 TCAAATTTC-A
1 TCAAAATTCTA
* * *
41137553 TTAAAATTTTC
1 TCAAAATTCTA
41137564 TCAAAATTCTA
1 TCAAAATTCTA
*
41137575 TCAAATTTCTA
1 TCAAAATTCTA
41137586 TCAAAATTCT
1 TCAAAATTCT
41137596 TTGTTTAAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
10 7 0.12
11 43 0.73
12 9 0.15
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.43
Consensus pattern (11 bp):
TCAAAATTCTA
Found at i:41143540 original size:20 final size:20
Alignment explanation
Indices: 41143515--41143587 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
41143505 TCTTGTATGT
41143515 ATCAATTAACCTTAAATTTA
1 ATCAATTAACCTTAAATTTA
* * *
41143535 ATCAATTAACCCTAAACCCTAA
1 ATCAATTAACCTTAAA--TTTA
*
41143557 ATCAA-T--CCAT-AATTTA
1 ATCAATTAACCTTAAATTTA
41143573 ATCAATTAACCTTAA
1 ATCAATTAACCTTAA
41143588 TACTCTAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
16 7 0.17
17 1 0.03
18 2 0.05
19 6 0.15
20 16 0.40
21 1 0.03
22 7 0.17
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (20 bp):
ATCAATTAACCTTAAATTTA
Found at i:41144444 original size:120 final size:120
Alignment explanation
Indices: 41144320--41144549 Score: 284
Period size: 120 Copynumber: 1.9 Consensus size: 120
41144310 ATAATTTTTT
* * *
41144320 AAAAATTATTTATAACAAATTTT-AAAATAATTATCCTTTAAATTAGACAATTTATCTATTAATC
1 AAAAATCATTTATAAC-AATTTTCAAAAGAATTATCCTTTAAATTAAACAATTTATCTATTAATC
* * *
41144384 AAATTTTAATA-TCATTTTTAAATAACTTCACAATAACTATTATATATTTTTTCAAA
65 AAATTTTAACACTAATTTCT-AATAACTTCACAATAACTATTATATATTTTTTCAAA
* * * ** * *
41144440 AAAAATCATTTATTACAGTTTTCAGAAGAATTATTTTTTAAATTAAATAATTTATCTATTAATTA
1 AAAAATCATTTATAACAATTTTCAAAAGAATTATCCTTTAAATTAAACAATTTATCTATTAATCA
* * *
41144505 AATTTTAACACTAATTTCTAATCACTTCATAATAATTATTATATA
66 AATTTTAACACTAATTTCTAATAACTTCACAATAACTATTATATA
41144550 CTTAAATAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
119 5 0.05
120 81 0.88
121 6 0.07
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.45
Consensus pattern (120 bp):
AAAAATCATTTATAACAATTTTCAAAAGAATTATCCTTTAAATTAAACAATTTATCTATTAATCA
AATTTTAACACTAATTTCTAATAACTTCACAATAACTATTATATATTTTTTCAAA
Found at i:41147216 original size:46 final size:44
Alignment explanation
Indices: 41147157--41147271 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
41147147 ACAGGACAGA
* *
41147157 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
41147203 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
41147247 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
41147272 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:41147252 original size:44 final size:45
Alignment explanation
Indices: 41147157--41147290 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
41147147 ACAGGACAGA
* *
41147157 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
41147203 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
41147247 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
41147291 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:41151909 original size:13 final size:14
Alignment explanation
Indices: 41151881--41151910 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41151871 ACATCTTAAA
41151881 AATCGAGTTAGTAG
1 AATCGAGTTAGTAG
41151895 AATCGAGTT-GTAG
1 AATCGAGTTAGTAG
41151908 AAT
1 AAT
41151911 TGGGCTGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (14 bp):
AATCGAGTTAGTAG
Found at i:41153286 original size:18 final size:18
Alignment explanation
Indices: 41153260--41153294 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41153250 CTTAGGGGAT
* *
41153260 TTACCAAATTCTCTAAGA
1 TTACAAAATACTCTAAGA
41153278 TTACAAAATACTCTAAG
1 TTACAAAATACTCTAAG
41153295 GTTATAGAAT
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:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (18 bp):
TTACAAAATACTCTAAGA
Found at i:41154460 original size:17 final size:17
Alignment explanation
Indices: 41154438--41154470 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41154428 TTAGGAAATA
41154438 TTTATTTTAATGTTTTT
1 TTTATTTTAATGTTTTT
*
41154455 TTTATTTTGATGTTTT
1 TTTATTTTAATGTTTT
41154471 ATATATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTATTTTAATGTTTTT
Found at i:41158553 original size:3 final size:3
Alignment explanation
Indices: 41158547--41158580 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
41158537 ATTAATAATA
41158547 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
41158581 ATGCGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:41160274 original size:15 final size:14
Alignment explanation
Indices: 41160256--41160293 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
41160246 CCTATCTTAT
41160256 TTCCTTCTTTCTTTC
1 TTCCTTCTTTC-TTC
41160271 TTCCTTCCTTTCTTC
1 TTCCTT-CTTTCTTC
41160286 TT-CTTCTT
1 TTCCTTCTT
41160294 GCTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 3 0.14
15 11 0.50
16 5 0.23
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCCTTCTTTCTTC
Found at i:41174134 original size:232 final size:234
Alignment explanation
Indices: 41173789--41174236 Score: 593
Period size: 232 Copynumber: 1.9 Consensus size: 234
41173779 TAACCGTGAA
* * *
41173789 TAAACCTCACAGCAGCTAGGAAGCTCACTCGAATTAAGTAATTCAATTGAACTTCAAAACAAAAG
1 TAAACCTCACAG-AGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAACTTCAAAAAAAAAG
* * * * * *
41173854 ACTAAAACCTGCATAGTTTCTTGTACAGATACCTTAATTCAACCAAATTTC-TAGAACCTCGCAT
65 ACGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCAT-GAAACTCGCAT
* * *
41173918 CTAATTACGAACTAACTTCCTCTAAGAAAGC-GATTTCAT-G-AAAGAGGTTTATGACGCCCTAT
129 CTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTT-ATAGAAAAGAGGTTCATGACACCCTAT
*
41173980 TAAAACCCAAAATCCTAAGGAAAGAAAAGGCTTAAGTGCAAG
193 TAAAACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
*
41174022 TAAACCTCACAG-GCTAGGAAGCTCGCTCAAATGAAGTAATTCAATTGAACTTTCAAAAAACAAA
1 TAAACCTCACAGAGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAAC-TTCAAAAAA-AAA
* * *
41174086 TACGGAAACTTACAAAG-TTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCGCAT
64 GACGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCGCAT
* * ** * *
41174150 CTAATTAGGAACTAGCTTCCTCTGGGAAAGCAAATTTATAGAAAAGAGGTTCATGATACCCTTTT
129 CTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTTATAGAAAAGAGGTTCATGACACCCTATT
*
41174215 AAAACCTAAAATACTAAGGAAA
194 AAAACCCAAAATACTAAGGAAA
41174237 CACAGAAAAA
Statistics
Matches: 185, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
231 35 0.19
232 79 0.43
233 32 0.17
234 39 0.21
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (234 bp):
TAAACCTCACAGAGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAACTTCAAAAAAAAAGA
CGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCGCATCT
AATTACGAACTAACTTCCTCTAAGAAAGCAAATTTATAGAAAAGAGGTTCATGACACCCTATTAA
AACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
Found at i:41175408 original size:168 final size:168
Alignment explanation
Indices: 41175207--41175511 Score: 540
Period size: 168 Copynumber: 1.8 Consensus size: 168
41175197 ACTTAATGAA
* *
41175207 TTAACAATTACCGTTTCGTAAGGATCAAAATTTTAAATTTTGAAAAGTACAGGGACTAAATATAA
1 TTAAAAATTACCGTTTCGTAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATAA
41175272 CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
66 CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
41175337 ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
131 ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
41175375 TTAAAAATTACCGTTT-GATAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATA
1 TTAAAAATTACCGTTTCG-TAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATA
* * * *
41175439 ACCAAATTGAAGTAGAGAGATTAAATCAATAACTTTTGCAAAGTATAGGGACTGTGGTAGAGTTT
65 ACCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTT
41175504 AACCTTTT
130 AACCTTTT
41175512 CTTTTATATT
Statistics
Matches: 130, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
167 1 0.01
168 129 0.99
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (168 bp):
TTAAAAATTACCGTTTCGTAAGGATCAAAATTTTAAATTCTGAAAAGTACAGGGACTAAATATAA
CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
Found at i:41177000 original size:24 final size:25
Alignment explanation
Indices: 41176965--41177040 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
41176955 TAAATATTTA
41176965 TTGGTAGAAAAAACTAATTAAATAT
1 TTGGTAGAAAAAACTAATTAAATAT
41176990 TTGGTAGAAAAAACTAATTAAATAT
1 TTGGTAGAAAAAACTAATTAAATAT
*
41177015 TTGGTAGAAAAAACTAATTAACTAT
1 TTGGTAGAAAAAACTAATTAAATAT
41177040 T
1 T
41177041 AAATGCGCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (25 bp):
TTGGTAGAAAAAACTAATTAAATAT
Found at i:41179450 original size:47 final size:48
Alignment explanation
Indices: 41179377--41179641 Score: 246
Period size: 47 Copynumber: 5.7 Consensus size: 48
41179367 AAGGTGACCA
*
41179377 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
* * *
41179424 ATGCCATGTCCCAGACATGGTTTTACACTGACT-ATCATCTCGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTC-AAGCCG
* * * *
41179472 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTTA-CGTCTCGAGGCAG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTC-AAGCCG
* * * *
41179518 ATG-CATGTCCTAGACAT-GTCTTACACTAGCAC-TCGTCTCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA-GCCG
* * * ***
41179564 ATGCCATGTCCTAGACATGGTCTTACACTAGCTC-TCATAATGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAT-CTCAAGCCG
*
41179612 ATG-CATGTCCTAGACAT-GTCTTACACTGGC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGC
41179642 CAAAAATAAC
Statistics
Matches: 187, Mismatches: 23, Indels: 17
0.82 0.10 0.07
Matches are distributed among these distances:
45 1 0.01
46 75 0.40
47 79 0.42
48 31 0.17
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
Found at i:41179633 original size:140 final size:140
Alignment explanation
Indices: 41179381--41179641 Score: 359
Period size: 140 Copynumber: 1.9 Consensus size: 140
41179371 TGACCAATGC
* * * *
41179381 CATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTT
1 CATGTCCCAGACATGGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAGACATGGTC
*
41179446 TTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
66 TTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
41179511 GAGGCAGATG
131 GAGGCAGATG
* * *
41179521 CATGTCCTAGACAT-GTCTTACACTAGCAC-TCGTCTCAATGCCGATGCCATGTCCTAGACATGG
1 CATGTCCCAGACATGGTCTTACACTAGCACAT-ATCTCAA-GCCGATGCCATGTCCCAGACATGG
* * *
41179584 TCTTACACT-AGCTCTCATAAT-GTGGCCGATGCATGTCCTAGACATGTCTTACACTGGC
64 TCTTACACTGA-CTATCAT-ATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGC
41179642 CAAAAATAAC
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
138 1 0.01
139 20 0.19
140 84 0.79
141 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAGACATGGTC
TTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
GAGGCAGATG
Found at i:41186903 original size:201 final size:201
Alignment explanation
Indices: 41186558--41186974 Score: 825
Period size: 201 Copynumber: 2.1 Consensus size: 201
41186548 AGCAACAGAG
*
41186558 AATGTGCTTTATTAATCAAATGGGTAATTACAATGCTTCATCAGAGTCTCTATCTATAGGCATAA
1 AATGTGCCTTATTAATCAAATGGGTAATTACAATGCTTCATCAGAGTCTCTATCTATAGGCATAA
41186623 GAAATATTAAAGAAGTAGAGATCTAATTCTAATAACTATTACAATCTAAAGTATATTAAAACTTT
66 GAAATATTAAAGAAGTAGAGATCTAATTCTAATAACTATTACAATCTAAAGTATATTAAAACTTT
41186688 ATCTTGATCATGATGGACATCCACTTAATAAGATATTCATAACACTCCCCCTTGGATGTCTATTG
131 ATCTTGATCATGATGGACATCCACTTAATAAGATATTCATAACACTCCCCCTTGGATGTCTATTG
41186753 GTAGAT
196 GTAGAT
41186759 AATGTGCCTTATTAATCAAATGGGTAATTACAATGCTTCATCAGAGTCTCTATCTATAGGCATAA
1 AATGTGCCTTATTAATCAAATGGGTAATTACAATGCTTCATCAGAGTCTCTATCTATAGGCATAA
41186824 GAAATATTAAAGAAGTAGAGATCTAATTCTAATAACTATTACAATCTAAAGTATATTAAAACTTT
66 GAAATATTAAAGAAGTAGAGATCTAATTCTAATAACTATTACAATCTAAAGTATATTAAAACTTT
41186889 ATCTTGATCATGATGGACATCCACTTAATAAGATATTCATAACACTCCCCCTTGGATGTCTATTG
131 ATCTTGATCATGATGGACATCCACTTAATAAGATATTCATAACACTCCCCCTTGGATGTCTATTG
41186954 GTAGAT
196 GTAGAT
41186960 AATGTGCCTTATTAA
1 AATGTGCCTTATTAA
41186975 AACTTTACTA
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 215 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (201 bp):
AATGTGCCTTATTAATCAAATGGGTAATTACAATGCTTCATCAGAGTCTCTATCTATAGGCATAA
GAAATATTAAAGAAGTAGAGATCTAATTCTAATAACTATTACAATCTAAAGTATATTAAAACTTT
ATCTTGATCATGATGGACATCCACTTAATAAGATATTCATAACACTCCCCCTTGGATGTCTATTG
GTAGAT
Found at i:41189935 original size:30 final size:31
Alignment explanation
Indices: 41189899--41189960 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
41189889 ATTTTTTTTA
41189899 GGTTTTATA-T-ATTATAATGATTATTATAAT
1 GGTTTTATATTAATTATAATGATTATT-TAAT
*
41189929 GGTTTTATATTAAATTATTATGATTATTTAAT
1 GGTTTTATATT-AATTATAATGATTATTTAAT
41189961 TGATAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.32
31 1 0.04
32 4 0.14
33 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (31 bp):
GGTTTTATATTAATTATAATGATTATTTAAT
Found at i:41190314 original size:14 final size:14
Alignment explanation
Indices: 41190290--41190322 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41190280 AAGAATTAAG
41190290 GAAACAAAGAAACA
1 GAAACAAAGAAACA
41190304 -AAACAAAAGAAACA
1 GAAAC-AAAGAAACA
41190318 GAAAC
1 GAAAC
41190323 GAAGTAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (14 bp):
GAAACAAAGAAACA
Found at i:41197131 original size:26 final size:26
Alignment explanation
Indices: 41197041--41197139 Score: 128
Period size: 26 Copynumber: 3.8 Consensus size: 26
41197031 TCCCCATTTT
41197041 AGATAGTCCTGACGGACTTCCACAAA
1 AGATAGTCCTGACGGACTTCCACAAA
* * * * *
41197067 GGATAGTCCTCAC-AAGCTTCTACCAA
1 AGATAGTCCTGACGGA-CTTCCACAAA
41197093 AGATAGTCCTGACGGACTTCCACAAA
1 AGATAGTCCTGACGGACTTCCACAAA
*
41197119 AGATAGTCTTGACGGACTTCC
1 AGATAGTCCTGACGGACTTCC
41197140 CACATAATAG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.02
26 58 0.97
27 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (26 bp):
AGATAGTCCTGACGGACTTCCACAAA
Found at i:41198063 original size:23 final size:23
Alignment explanation
Indices: 41198011--41198056 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41198001 ACAAGATTTC
41198011 CAATTTCTAAGACTTAGATCTTA
1 CAATTTCTAAGACTTAGATCTTA
41198034 CAATTTCTAAGACTTAGATCTTA
1 CAATTTCTAAGACTTAGATCTTA
41198057 GTCTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (23 bp):
CAATTTCTAAGACTTAGATCTTA
Found at i:41201072 original size:46 final size:46
Alignment explanation
Indices: 41200895--41201077 Score: 224
Period size: 46 Copynumber: 4.0 Consensus size: 46
41200885 TTTGACGTGA
* * * * * *
41200895 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * **
41200941 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACCT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
41200987 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
41201033 TTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG
41201078 GAGCACACTC
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 4 0.03
46 116 0.97
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:41204540 original size:28 final size:28
Alignment explanation
Indices: 41204500--41204564 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
41204490 ATGTACTAGA
*
41204500 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
41204528 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41204556 ATACCCCTA
1 ATACCCCTA
41204565 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41204728 original size:27 final size:27
Alignment explanation
Indices: 41204670--41204759 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
41204660 AGGAAGCGTC
41204670 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
41204698 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
41204725 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
41204754 CTGGTG
1 CTGGTG
41204760 ACTTTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:41204770 original size:29 final size:28
Alignment explanation
Indices: 41204680--41204761 Score: 103
Period size: 27 Copynumber: 2.9 Consensus size: 28
41204670 CTGGTGGCTA
* * *
41204680 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* *
41204708 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
41204735 TGCCACAAAATATCTGTATCTGGTGAC
1 TGCCACAAAATATCTGT-TCTGGTGAC
41204762 TTTGTCACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
27 24 0.51
28 15 0.32
29 8 0.17
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:41204778 original size:55 final size:56
Alignment explanation
Indices: 41204670--41204784 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
41204660 AGGAAGCGTC
* *
41204670 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
** * *
41204725 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTTTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
41204781 CTGG
1 CTGG
41204785 CTGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:41205247 original size:19 final size:19
Alignment explanation
Indices: 41205223--41205261 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41205213 TTTTAATTAT
* *
41205223 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
41205242 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
41205261 T
1 T
41205262 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:41212435 original size:28 final size:28
Alignment explanation
Indices: 41212403--41212464 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
41212393 ATTTACTAGA
*
41212403 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
41212431 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41212459 ATACCC
1 ATACCC
41212465 TTAGGGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41212631 original size:27 final size:27
Alignment explanation
Indices: 41212573--41212662 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
41212563 AGGAAGCGTC
41212573 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
41212601 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
41212628 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
41212657 CTGGTG
1 CTGGTG
41212663 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:41212681 original size:55 final size:56
Alignment explanation
Indices: 41212573--41212687 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
41212563 AGGAAGCGTC
* *
41212573 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
41212628 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
41212684 CTGG
1 CTGG
41212688 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:41220574 original size:25 final size:26
Alignment explanation
Indices: 41220539--41220596 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
41220529 CACTTTTATC
41220539 TTTA-TTTATCTTC-TTTAAGTACT-T
1 TTTATTTTATCTTCATTTAA-TACTAT
41220563 TTTATTTTATCTTCATTTAATACTAT
1 TTTATTTTATCTTCATTTAATACTAT
*
41220589 TTCATTTT
1 TTTATTTT
41220597 TAGGTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 13 0.43
26 13 0.43
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTATTTTATCTTCATTTAATACTAT
Found at i:41222683 original size:13 final size:13
Alignment explanation
Indices: 41222665--41222691 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41222655 GAAGAAATCG
41222665 CATACGGGCATGT
1 CATACGGGCATGT
41222678 CATACGGGCATGT
1 CATACGGGCATGT
41222691 C
1 C
41222692 CTTGTTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (13 bp):
CATACGGGCATGT
Found at i:41230215 original size:47 final size:47
Alignment explanation
Indices: 41230160--41230290 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
41230150 CTCAACTGAA
*
41230160 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
* * * * *
41230207 GAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCCTCTCT
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
* * **
41230254 AAATACCTATACCATGACCCGTATTCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
41230291 TTATTTGCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
Found at i:41244329 original size:13 final size:13
Alignment explanation
Indices: 41244311--41244335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41244301 AACGAAGACA
41244311 GACACGGCCGTGC
1 GACACGGCCGTGC
41244324 GACACGGCCGTG
1 GACACGGCCGTG
41244336 TGCACCAACA
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:0.36, G:0.40, T:0.08
Consensus pattern (13 bp):
GACACGGCCGTGC
Found at i:41244863 original size:23 final size:23
Alignment explanation
Indices: 41244837--41244883 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41244827 CATTCTATTG
*
41244837 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
41244860 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
41244883 T
1 T
41244884 AATGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:41246169 original size:23 final size:23
Alignment explanation
Indices: 41246118--41246170 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
41246108 ATGATGATGT
*
41246118 TTAA-TTTTATTTTATCTTTATT
1 TTAATTTTTATTTTATCTTTATA
* * *
41246140 TTTATTTTTATTTTATGTTTGTA
1 TTAATTTTTATTTTATCTTTATA
41246163 TTAATTTT
1 TTAATTTT
41246171 ACCTTTAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.74
Consensus pattern (23 bp):
TTAATTTTTATTTTATCTTTATA
Found at i:41252802 original size:48 final size:49
Alignment explanation
Indices: 41252733--41252860 Score: 143
Period size: 48 Copynumber: 2.6 Consensus size: 49
41252723 ATTAAAGTCG
* * * *
41252733 ATGCCGTGTCCCAGACGGGTCTTACATTGACTTTCATATATCGAG-GCCA
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCG-GTGCCA
* * ***
41252782 ATGCCATGT-CCAGACAGGTCTTACACTGGCTCTCATCTATCGGTGTTG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGCCA
*
41252830 ATGCCATGTCCCAGACAGGTCTTAAACTGAC
1 ATGCCATGTCCCAGACAGGTCTTACACTGAC
41252861 ACACAACAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 1 0.02
48 38 0.58
49 27 0.41
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGCCA
Found at i:41252950 original size:48 final size:49
Alignment explanation
Indices: 41252879--41253042 Score: 151
Period size: 49 Copynumber: 3.4 Consensus size: 49
41252869 AGCTAACACT
* * *
41252879 ATGTCCCA-AGCAGGTCTTACACTAGCT-TGTAT-ATCCCGAGGCCGATGC
1 ATGTCCCAGA-CATGTCTTACACTAGCTCT-CATCATCCCAAGGCCGATGC
* * * *
41252927 ATGTCTCAGACATGTCTTACACTAGCTCTCATCGTCTCAATGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
* * ** *
41252976 ATGTCCCAGACATGTCTTACACTGGCTCTCATAAT---GTGGCTGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
*
41253022 ATGTCCTAGACATGTCTTACA
1 ATGTCCCAGACATGTCTTACA
41253043 TTGGCTCACA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
46 27 0.28
48 25 0.26
49 45 0.46
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
Found at i:41253038 original size:46 final size:47
Alignment explanation
Indices: 41252917--41253054 Score: 154
Period size: 49 Copynumber: 2.9 Consensus size: 47
41252907 GTATATCCCG
* **
41252917 AGGCCGATGCATGT-CTCAGACATGTCTTACACTAGCTCTCATCGTCT
1 AGGCCGATGCATGTCCT-AGACATGTCTTACACTGGCTCTCATAATCT
* * *
41252964 CAATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGT
1 --AGGCCGATGCATGTCCTAGACATGTCTTACACTGGCTCTCATAATCT
* * *
41253013 -GGCTGATGCATGTCCTAGACATGTCTTACATTGGCTCACATA
1 AGGCCGATGCATGTCCTAGACATGTCTTACACTGGCTCTCATA
41253055 CCACCCAATG
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
46 37 0.48
49 39 0.51
50 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (47 bp):
AGGCCGATGCATGTCCTAGACATGTCTTACACTGGCTCTCATAATCT
Found at i:41255461 original size:17 final size:16
Alignment explanation
Indices: 41255434--41255468 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
41255424 TTACAATCAA
41255434 ACAAAACGTATATTCC
1 ACAAAACGTATATTCC
41255450 ACAAATACGTATATTCC
1 ACAAA-ACGTATATTCC
41255467 AC
1 AC
41255469 TTATTCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
ACAAAACGTATATTCC
Found at i:41257507 original size:1000 final size:999
Alignment explanation
Indices: 41255469--41257909 Score: 4614
Period size: 1000 Copynumber: 2.4 Consensus size: 999
41255459 TATATTCCAC
**
41255469 TTATTCTATCTATCATCTAGTCTCTTGGTGTTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
1 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
* *
41255534 ATTTTTGTAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
66 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
*
41255599 TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCTAACTTATTGCTAGATCTTCTCCTAAAT
131 TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAAT
41255664 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
196 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
41255729 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
261 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
41255794 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
326 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
41255859 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
391 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
41255924 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
456 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
41255989 ACGGCTCTAATTGGATTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACTA
521 ACGGCTCTAATTGGATTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACTA
41256054 CTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAAA
586 CTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAAA
41256119 TGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTAT
651 TGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTAT
41256184 TTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGAA
716 TTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGAA
*
41256249 TTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATTCCTATTGGTGTTGAATT
781 TTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAATT
41256314 TGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTTG
846 TGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTTG
41256379 TATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTTA
911 TATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTTA
41256444 CAGGTTTTAAAGTACTAGCACCAG
976 CAGGTTTTAAAGTACTAGCACCAG
41256468 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
1 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
41256533 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
66 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
* *
41256598 TACTTCTGCAGTATTTGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTTTCCTAAAT
131 TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAAT
41256663 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
196 CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
41256728 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
261 ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
41256793 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
326 ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
41256858 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
391 ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
41256923 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
456 TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
41256988 ACGGCTCTAATTGGATTTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACT
521 ACGGCTCTAATTGGA-TTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACT
41257053 ACTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAA
585 ACTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAA
41257118 ATGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTA
650 ATGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTA
41257183 TTTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGA
715 TTTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGA
41257248 ATTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAAT
780 ATTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAAT
41257313 TTGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTT
845 TTGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTT
41257378 GTATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTT
910 GTATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTT
41257443 ACAGGTTTTAAAGTACTAGCACCAG
975 ACAGGTTTTAAAGTACTAGCACCAG
41257468 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
1 TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
41257533 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
66 ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
* * *
41257598 TACCTT-TGCAGTATTAGTATATTCATTAATAGAAGTCCAACTTATTCCTAGATCTTCTGCTAAA
131 TA-CTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAA
* * * * *
41257662 TCATTTATTTCAGAATTTTTTATCTGAATTCTCAAACATAAACACTTTTCTATTAAAGGGTCTGT
195 TCATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGT
* * * * *
41257727 GATAGGTATAAAGTAATTTTGTTTAACTTTAAAACTTATTACACCGGTATGTAAATTAGACTAAA
260 GATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAA
* * *
41257792 TACCTCCAATAAGTGATTTTATTGTATTTTCAAATCTTTTATCTAATAAAATTGCTATTATAGGT
325 TACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATA-GT
* *
41257857 ATATCATGACCTTTTCTAAATAAAGTTCTAATTGTTATCATAATTATACCTAA
389 ATATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAA
41257910 ATGTATATAT
Statistics
Matches: 1411, Mismatches: 28, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
999 528 0.37
1000 827 0.59
1001 56 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (999 bp):
TTATTCTATCTATCATCTAGTCTCTTGGCATTGATAGATCCTTTAAATGTAATAATTTTGGTTGT
ATTTCTATAGTAAATTTATTAGGTTCAAAAAGCTCAATAATTTTATTATTTATTTCTTTAATTTC
TACTTCTGCAGTATTAGTATATTCATTAATAGAATTCCAACTTATTGCTAGATCTTCTCCTAAAT
CATTTATTTCAGAATTTTTTCTCTGAATTCTTAAACATAAACGCTCTTCTATTAGAGGGTCTGTG
ATAGATATAAAGTAATTTGGTTTAACTTTAAAACCTATTACACCAGTATGTAAATTAGACTGAAT
ACCTCCAATAAGTGCTTTTATTGGATTTTCAAATCTTTTATCTAATAAAACTGCTATTATAGTAT
ATCATGTCCTTTTCTAAATAAAGCTCTAATTGTTATCATAATTATACCTAATTGTTATCTAACAT
TATTTATGTAGATTGGTATATTTCTAGCCTTAAATCCTGTTATGGTTTCATTACCATCTATTCCT
ACGGCTCTAATTGGATTTTCATTGGTTCCCATTTTTCTACAGGAATGGCATTTTTTCTACAACTA
CTAGTGGTAGCTCCAGTATCTAATAAAGCTTGTAAAGAATATGTTTTATATTCTCTAAATTGAAA
TGTAATTTCAATATATGTATAATATTTTCTTGGTTGAAAATTTAAAAATGTAATAACATCACTAT
TTCCAATTTTCATTTGTTGCATAATTGTTGAAGTTTGAATTTCTTCCATTCTAGTGTTTCTAGAA
TTTCTATTAGGTTCAGTTAGAAAAATAGGTACTTGAACTGTTTTCATACCTATTGGTGTTGAATT
TGTACTTATATTATCCTCGTCTTCCTCTGTTTGAGTATTTGAGGGTAAAACTAAATTATCATTTG
TATTTTTTATAGCATTATTTTTAAAATATAATCTATCTCCTGACGACATATATTCTATAGTCTTA
CAGGTTTTAAAGTACTAGCACCAG
Found at i:41260514 original size:15 final size:14
Alignment explanation
Indices: 41260486--41260529 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
41260476 ATTAATACTA
41260486 TTACAAAG-AAAGT
1 TTACAAAGAAAAGT
41260499 TTACAAATGAAAAGT
1 TTACAAA-GAAAAGT
41260514 TTAC-AAGAAAAGT
1 TTACAAAGAAAAGT
41260527 TTA
1 TTA
41260530 AAAAAAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 17 0.59
14 3 0.10
15 9 0.31
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (14 bp):
TTACAAAGAAAAGT
Found at i:41261404 original size:22 final size:21
Alignment explanation
Indices: 41261376--41261420 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
41261366 TAATATAGTA
* *
41261376 TTAATAATTGCAGGAAAATCTT
1 TTAATAATTGAAAGAAAAT-TT
41261398 TTAATAATTGAAAGAAAATTT
1 TTAATAATTGAAAGAAAATTT
41261419 TT
1 TT
41261421 GAACTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (21 bp):
TTAATAATTGAAAGAAAATTT
Found at i:41264515 original size:23 final size:23
Alignment explanation
Indices: 41264489--41264816 Score: 109
Period size: 23 Copynumber: 14.3 Consensus size: 23
41264479 ATAAAACATC
* *
41264489 TCAATTTTCAGCAACTAAACAAT
1 TCAATTTACAGCAACTAAACACT
* *
41264512 TCAATTTGCAG-TACTTAAAACACT
1 TCAATTTACAGCAAC-T-AAACACT
* **
41264536 TCAATTTACAACATTTAAACACT
1 TCAATTTACAGCAACTAAACACT
** * *
41264559 TCAATTTACAGCATTTTAACGCT
1 TCAATTTACAGCAACTAAACACT
* * ** *
41264582 TCAATTCACATCATTTAAACGCT
1 TCAATTTACAGCAACTAAACACT
* * * *
41264605 TCAATTTGCAAC-ACTTTAGCACT
1 TCAATTTACAGCAAC-TAAACACT
* *
41264628 TCAATTTACAGC-ATTTAACACT
1 TCAATTTACAGCAACTAAACACT
* *
41264650 TCAATTTGCAGC-ACTTTAACA-T
1 TCAATTTACAGCAAC-TAAACACT
* * ** * *
41264672 CTCAATTAACAACATTTATACACC
1 -TCAATTTACAGCAACTAAACACT
* *
41264696 TCAA-TTATAGCGA-TAAA-ACAT
1 TCAATTTACAGCAACTAAACAC-T
* *
41264717 CTCAATTTCCAGCAACTAAACAAT
1 -TCAATTTACAGCAACTAAACACT
* * *
41264741 TCAACTTGCAG-TACTTAAAACACT
1 TCAATTTACAGCAAC-T-AAACACT
* * **
41264765 TCAATTTATAACATTTAAACACT
1 TCAATTTACAGCAACTAAACACT
* *
41264788 TCAATTTGCAGC-ACTTTAACACT
1 TCAATTTACAGCAAC-TAAACACT
41264811 TCAATT
1 TCAATT
41264817 CACAACATTT
Statistics
Matches: 224, Mismatches: 64, Indels: 34
0.70 0.20 0.11
Matches are distributed among these distances:
20 2 0.01
21 3 0.01
22 32 0.14
23 151 0.67
24 35 0.16
25 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
TCAATTTACAGCAACTAAACACT
Found at i:41264598 original size:46 final size:46
Alignment explanation
Indices: 41264504--41264927 Score: 364
Period size: 46 Copynumber: 9.2 Consensus size: 46
41264494 TTTCAGCAAC
* * * *
41264504 TAAACAATTCAATTTGCAGTACTTAAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTGCAGCACTT-TAACACTTCAATTCACAACATT
* * * *
41264551 TAAACACTTCAATTTACAGCATTTTAACGCTTCAATTCACATCATT
1 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
* * * * *
41264597 TAAACGCTTCAATTTGCAACACTTTAGCACTTCAATTTACAGCATT
1 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
*
41264643 T-AACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACATT
1 TAAACACTTCAATTTGCAGCACTTTAACACT-TCAATTCACAACATT
* * ** * **
41264688 TATACACCTCAATTAT--AGCGA-TAAAACA-TCTCAATTTC-CAGCAAC
1 TAAACACTTCAATT-TGCAGC-ACTTTAACACT-TCAA-TTCACAACATT
* * * * * *
41264733 TAAACAATTCAACTTGCAGTACTTAAAACACTTCAATTTATAACATT
1 TAAACACTTCAATTTGCAGCACTT-TAACACTTCAATTCACAACATT
41264780 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
1 TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
* ** *
41264826 TAAACAGTACTTCAATGTGCAATACTTTAACACTTCAAATT-AAAACATT
1 TAAAC---ACTTCAATTTGCAGCACTTTAACACTTC-AATTCACAACATT
*
41264875 TAAACACTTCAATTTGTAGCACTTTAACATCTT-AATT-AGCAACATT
1 TAAACACTTCAATTTGCAGCACTTTAACA-CTTCAATTCA-CAACATT
*
41264921 TATACAC
1 TAAACAC
41264928 CTGAATTACA
Statistics
Matches: 304, Mismatches: 56, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
44 2 0.01
45 72 0.24
46 131 0.43
47 57 0.19
48 1 0.00
49 37 0.12
50 4 0.01
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.33
Consensus pattern (46 bp):
TAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATT
Found at i:41264831 original size:23 final size:23
Alignment explanation
Indices: 41264529--41265052 Score: 247
Period size: 23 Copynumber: 22.7 Consensus size: 23
41264519 GCAGTACTTA
41264529 AAACACTTCAATTTACAACATTT
1 AAACACTTCAATTTACAACATTT
*
41264552 AAACACTTCAATTTACAGCATTT
1 AAACACTTCAATTTACAACATTT
* * * *
41264575 TAACGCTTCAATTCACATCATTT
1 AAACACTTCAATTTACAACATTT
* *
41264598 AAACGCTTCAATTTGCAACACTTT
1 AAACACTTCAATTTACAACA-TTT
* *
41264622 -AGCACTTCAATTTACAGCATTT
1 AAACACTTCAATTTACAACATTT
* *
41264644 -AACACTTCAATTTGCAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
*
41264667 -AACA-TCTCAATTAACAACATTT
1 AAACACT-TCAATTTACAACATTT
* * * * *
41264689 ATACACCTCAA-TTATAGCGA-TA
1 AAACACTTCAATTTACAAC-ATTT
* * **
41264711 AAACA-TCTCAATTTCCAGCAACT
1 AAACACT-TCAATTTACAACATTT
* * * *
41264734 AAACAATTCAACTTGCAGTAC-TTA
1 AAACACTTCAATTTACA--ACATTT
*
41264758 AAACACTTCAATTTATAACATTT
1 AAACACTTCAATTTACAACATTT
* *
41264781 AAACACTTCAATTTGCAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
*
41264805 -AACACTTCAATTCACAACATTT
1 AAACACTTCAATTTACAACATTT
* * *
41264827 AAACAGTACTTCAATGTGCAATACTTT
1 AAAC---ACTTCAATTTACAACA-TTT
* *
41264854 -AACACTTCAAATTAAAACATTT
1 AAACACTTCAATTTACAACATTT
** *
41264876 AAACACTTCAATTTGTAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
41264900 -AACATCTT-AA-TTAGCAACATTT
1 AAACA-CTTCAATTTA-CAACATTT
* * * * * *
41264922 ATACACCTGAA-TTACAGCAATA
1 AAACACTTCAATTTACAACATTT
* **
41264944 AAACA-TCTCAATTT-CTAGCAACT
1 AAACACT-TCAATTTAC-AACATTT
* *
41264967 AAGCACTTCAATTTACAACATGT
1 AAACACTTCAATTTACAACATTT
** * *
41264990 GTACACTTCAATTTGCAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
* *
41265014 -AACA-TCTCAATTAACAACGTTT
1 AAACACT-TCAATTTACAACATTT
* *
41265036 ATACACCTCAATTTACA
1 AAACACTTCAATTTACA
41265053 GAAATAAAAC
Statistics
Matches: 376, Mismatches: 91, Indels: 68
0.70 0.17 0.13
Matches are distributed among these distances:
22 70 0.19
23 257 0.68
24 30 0.08
25 1 0.00
26 15 0.04
27 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (23 bp):
AAACACTTCAATTTACAACATTT
Found at i:41265613 original size:15 final size:15
Alignment explanation
Indices: 41265593--41265625 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
41265583 GTGTTTTAAG
41265593 ACAACATAAATACTT
1 ACAACATAAATACTT
*
41265608 ACAACATGAATACTT
1 ACAACATAAATACTT
41265623 ACA
1 ACA
41265626 TTTTAATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.21, G:0.03, T:0.24
Consensus pattern (15 bp):
ACAACATAAATACTT
Found at i:41267326 original size:24 final size:24
Alignment explanation
Indices: 41267272--41267337 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
41267262 TGCTCTCTGT
* * *
41267272 GAGCTTCCTGATATGGTTCTTTAT
1 GAGCTTCCCGATATGGCTCTTTAC
*
41267296 GAACTTCCCGATTATGGCTC-TTAC
1 GAGCTTCCCGA-TATGGCTCTTTAC
*
41267320 GAGCTTCTCGATATGGCT
1 GAGCTTCCCGATATGGCT
41267338 ATGTCTGAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 7 0.20
24 21 0.60
25 7 0.20
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
GAGCTTCCCGATATGGCTCTTTAC
Found at i:41271271 original size:40 final size:40
Alignment explanation
Indices: 41271211--41271394 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
41271201 TATTCGAATG
*
41271211 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
41271251 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * *
41271291 ATATCCGGGCTAAGACCCGAAGGAATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
41271331 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
41271371 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
41271395 CTTGTGCGAG
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 120 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:41281431 original size:23 final size:23
Alignment explanation
Indices: 41281364--41281423 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
41281354 ACATCGCTAC
41281364 GTTACTATTAGCAGCTTTGCTGT
1 GTTACTATTAGCAGCTTTGCTGT
*
41281387 GTTACTACTAGCAGCTTTGCTGT
1 GTTACTATTAGCAGCTTTGCTGT
41281410 GTTACTATTAGCAG
1 GTTACTATTAGCAG
41281424 TTACGCTGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (23 bp):
GTTACTATTAGCAGCTTTGCTGT
Found at i:41282408 original size:21 final size:21
Alignment explanation
Indices: 41282367--41282410 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41282357 AAGTTGTTTA
*
41282367 TCTATCAAAAACTTTTCATTT
1 TCTATCAAAAACTTTTAATTT
*
41282388 TCTATCATAAA-TTTTAAATTT
1 TCTATCAAAAACTTTT-AATTT
41282409 TC
1 TC
41282411 AGCATATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (21 bp):
TCTATCAAAAACTTTTAATTT
Found at i:41284149 original size:40 final size:40
Alignment explanation
Indices: 41284087--41284166 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
41284077 CCATGGTAAC
*
41284087 TCTTTCCCATTCCAATTTCGGTATTGTAACTGGCTATAAT
1 TCTTTCCCATTCCAATTCCGGTATTGTAACTGGCTATAAT
41284127 TCTTTCCCATTTCC-ATTCCGGTATTGTAACTGGCTATAAT
1 TCTTTCCCA-TTCCAATTCCGGTATTGTAACTGGCTATAAT
41284167 AATCCCAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (40 bp):
TCTTTCCCATTCCAATTCCGGTATTGTAACTGGCTATAAT
Found at i:41288099 original size:44 final size:44
Alignment explanation
Indices: 41288049--41288206 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 44
41288039 TATGTGTTTT
41288049 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
* *
41288093 CGTGTAAGACCATGTCTAGGACATTGGCATCG-TATATGATTT-
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
* * * * *
41288135 CGTGTAAGACC-CTGCCTAGGGCAGTGTCATCAATATT-TGA-TTA
1 CGTGTAAGACCAC-GTCTAGGACATTGGCATCGAT-TTATGATTTA
* * *
41288178 CATGTAAGACCACGTCTGGGACGTTGGCA
1 CGTGTAAGACCACGTCTAGGACATTGGCA
41288207 CTGTACGAGC
Statistics
Matches: 93, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
42 27 0.29
43 33 0.35
44 33 0.35
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
Found at i:41288176 original size:86 final size:85
Alignment explanation
Indices: 41288046--41288206 Score: 200
Period size: 86 Copynumber: 1.9 Consensus size: 85
41288036 CGATATGTGT
* * * * *
41288046 TTTCGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTACGTGTAAGACCATGTCTA
1 TTTCGTGTAAGACCACGCCTAGGACAGTGGCATCAATTTATGA-TTACATGTAAGACCACGTCTA
41288111 GGACATTGGCATCGTATATGA
65 GGACATTGGCATCGTATATGA
* *
41288132 TTTCGTGTAAGACC-CTGCCTAGGGCAGTGTCATCAATATT-TGATTACATGTAAGACCACGTCT
1 TTTCGTGTAAGACCAC-GCCTAGGACAGTGGCATCAAT-TTATGATTACATGTAAGACCACGTCT
* *
41288195 GGGACGTTGGCA
64 AGGACATTGGCA
41288207 CTGTACGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 29 0.45
86 33 0.52
87 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (85 bp):
TTTCGTGTAAGACCACGCCTAGGACAGTGGCATCAATTTATGATTACATGTAAGACCACGTCTAG
GACATTGGCATCGTATATGA
Found at i:41294802 original size:44 final size:43
Alignment explanation
Indices: 41294739--41294890 Score: 159
Period size: 43 Copynumber: 3.5 Consensus size: 43
41294729 TGTGTTTTCG
* *
41294739 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGATTTAAA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATTT-TGATTTACA
* * *
41294783 TGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGAT-TTTGATTTACA
* * **
41294825 TGTAAGACCCTGTCTAGGAC-TGTGTTATCGATATTTGA-TTACA
1 TGTAAGACCATGTCTGGGACGT-TGGCATCGAT-TTTGATTTACA
41294868 TGTAAGACCATGTCTGGGACGTT
1 TGTAAGACCATGTCTGGGACGTT
41294891 CACATTGTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 26 0.29
43 33 0.37
44 30 0.33
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATTTTGATTTACA
Found at i:41296191 original size:23 final size:23
Alignment explanation
Indices: 41296164--41296209 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
41296154 ATTGAAATTG
41296164 GCTGAAATTA-TAGTGCAATTGTA
1 GCTGAAATTACT-GTGCAATTGTA
41296187 GCTGAAATTACTGTGCAATTGTA
1 GCTGAAATTACTGTGCAATTGTA
41296210 CTTGGTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.35
Consensus pattern (23 bp):
GCTGAAATTACTGTGCAATTGTA
Found at i:41304990 original size:46 final size:47
Alignment explanation
Indices: 41304807--41305112 Score: 167
Period size: 46 Copynumber: 6.6 Consensus size: 47
41304797 TGATATGTGT
* * * *
41304807 GCCAGTGTAAGACATGTCTGGAACATGCATTG-GCTGCATTATG-AGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACATGATGTA-A
* * *
41304853 GCCAGTGTAAGACCATGTTTGGGACATGGCATCG-GCATTGAGACGA-GT--
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGAGC--T-ACATGATGTAA
* * * * * *
41304901 GCTACTATAAGACATGTCTGGGACATGCATTGACCT-CAGGATGTAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACATGATGTAA
41304947 GCCAGTGTAAGACATGTCTGGGACATGCATCGA-CTACGA-GATGT--
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTAC-ATGATGTAA
* * * * **
41304991 GTCAGTGTAAGACCATGTTTGGAACATGGCGTC-AGC-ACGGAT-ATGTGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGAGCTAC--ATGATGTAA
* * * *
41305039 GCTAGTGTAAGACATGTCTAGGACATGCATC-AGCCACATCG-TGAAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACAT-GATGTAA
*
41305085 GCTAGTGTAAGACCATGTCTGGGACATG
1 GCCAGTGTAAGA-CATGTCTGGGACATG
41305113 GCTTGATATG
Statistics
Matches: 204, Mismatches: 33, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
43 3 0.01
44 13 0.06
45 20 0.10
46 84 0.41
47 54 0.26
48 26 0.13
50 2 0.01
51 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGAGCTACATGATGTAA
Found at i:41305057 original size:138 final size:139
Alignment explanation
Indices: 41304855--41305112 Score: 333
Period size: 138 Copynumber: 1.9 Consensus size: 139
41304845 TTATGAGAGC
* * **
41304855 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGAGTGCTACTATAAGACATGTCT
1 CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACATGTCT
* * * * *
41304920 GGGACATGCAT-TGACCTCA-GGATGTAAGCCAGTGTAAGA-CATGTCTGGGACATGCATCGACT
66 AGGACATGCATCAG-CCACATCG-TGAAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACT
41304982 ACGAGATGTGT
129 ACGAGATGTGT
* * * * * *
41304993 CAGTGTAAGACCATGTTTGGAACATGGCGTCAGCACGGATATGTGTGCTAGTGTAAGACATGTCT
1 CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACATGTCT
*
41305058 AGGACATGCATCAGCCACATCGTGAAAGCTAGTGTAAGACCATGTCTGGGACATG
66 AGGACATGCATCAGCCACATCGTGAAAGCCAGTGTAAGACCATGTCTGGGACATG
41305113 GCTTGATATG
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
138 84 0.83
139 17 0.17
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (139 bp):
CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACATGTCT
AGGACATGCATCAGCCACATCGTGAAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTAC
GAGATGTGT
Found at i:41311564 original size:9 final size:9
Alignment explanation
Indices: 41311550--41311574 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41311540 TAAGGTTGCA
41311550 CAAGTCGCC
1 CAAGTCGCC
41311559 CAAGTCGCC
1 CAAGTCGCC
41311568 CAAGTCG
1 CAAGTCG
41311575 ACTGTGGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (9 bp):
CAAGTCGCC
Found at i:41313104 original size:32 final size:32
Alignment explanation
Indices: 41313038--41313104 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
41313028 TTAAAAATCT
* *
41313038 AAAGTTAAAATATGTTATAATATTATTACTTA
1 AAAGTTAAAATATATTATAATATTATTACATA
*
41313070 AAAGTT-AAGTATATTATATATATTATATA-ATA
1 AAAGTTAAAATATATTATA-ATATTAT-TACATA
41313102 AAA
1 AAA
41313105 ACAAACAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 10 0.33
32 18 0.60
33 2 0.07
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (32 bp):
AAAGTTAAAATATATTATAATATTATTACATA
Found at i:41314076 original size:25 final size:25
Alignment explanation
Indices: 41314045--41314128 Score: 114
Period size: 25 Copynumber: 3.4 Consensus size: 25
41314035 GAACTTTAGC
41314045 GCGCTCTCTGATTATTAGCACGTTA
1 GCGCTCTCTGATTATTAGCACGTTA
* *
41314070 GCGCTCTATGATTATTAGCACGCTA
1 GCGCTCTCTGATTATTAGCACGTTA
* * *
41314095 GTGTTCTCCGATTATTAGCACGTTA
1 GCGCTCTCTGATTATTAGCACGTTA
*
41314120 GTGCTCTCT
1 GCGCTCTCT
41314129 ATTTAGCACA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (25 bp):
GCGCTCTCTGATTATTAGCACGTTA
Found at i:41314137 original size:22 final size:22
Alignment explanation
Indices: 41314059--41314175 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 22
41314049 TCTCTGATTA
* *
41314059 TTAGCACGTTAGCGCTCTATGATT
1 TTAGCACGTTAGTGCTCTCT-A-T
* * *
41314083 ATTAGCACGCTAGTGTTCTCCGATT
1 -TTAGCACGTTAGTGCTCT-CTA-T
41314108 ATTAGCACGTTAGTGCTCTCTAT
1 -TTAGCACGTTAGTGCTCTCTAT
* * *
41314131 TTAGCACATTCGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTAT
*
41314153 ATAGCAC-TTCAGTGCTCTCTAT
1 TTAGCACGTT-AGTGCTCTCTAT
41314175 T
1 T
41314176 CATTAGTGCA
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
21 2 0.03
22 35 0.47
23 1 0.01
24 2 0.03
25 35 0.47
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCTAT
Found at i:41314296 original size:31 final size:31
Alignment explanation
Indices: 41314259--41314321 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
41314249 AAGAATATGA
*
41314259 GATAGTGAATTGAAAATAGAAGGTGAAATAT
1 GATAGTGAATTGAAAATAGAAAGTGAAATAT
41314290 GATAGTGAATTGAAAATAGAAAGTGAAATAT
1 GATAGTGAATTGAAAATAGAAAGTGAAATAT
41314321 G
1 G
41314322 TTGTAAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.25
Consensus pattern (31 bp):
GATAGTGAATTGAAAATAGAAAGTGAAATAT
Found at i:41314314 original size:18 final size:18
Alignment explanation
Indices: 41314262--41314316 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
41314252 AATATGAGAT
41314262 AGTGAATTGAAAATAG-A
1 AGTGAATTGAAAATAGAA
*
41314279 AG-G---TG-AAATATGAT
1 AGTGAATTGAAAATA-GAA
41314293 AGTGAATTGAAAATAGAA
1 AGTGAATTGAAAATAGAA
41314311 AGTGAA
1 AGTGAA
41314317 ATATGTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 13
0.66 0.05 0.30
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 10 0.34
19 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (18 bp):
AGTGAATTGAAAATAGAA
Found at i:41314869 original size:18 final size:19
Alignment explanation
Indices: 41314831--41314869 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41314821 GACGATATGA
*
41314831 TTAAATTATGATGTGAATG
1 TTAAATAATGATGTGAATG
*
41314850 TTAAATAATTATGT-AATG
1 TTAAATAATGATGTGAATG
41314868 TT
1 TT
41314870 TGTATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
TTAAATAATGATGTGAATG
Found at i:41315154 original size:29 final size:28
Alignment explanation
Indices: 41315120--41315176 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
41315110 TTTATTTTTC
*
41315120 CTGCTGGTTTCATTGTCTTAGATTTTGA
1 CTGCTGATTTCATTGTCTTAGATTTTGA
41315148 NCTGCTGATTTCATTGTCTTAGATTTTGA
1 -CTGCTGATTTCATTGTCTTAGATTTTGA
41315177 AGCAGATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.49
Consensus pattern (28 bp):
CTGCTGATTTCATTGTCTTAGATTTTGA
Found at i:41318787 original size:183 final size:183
Alignment explanation
Indices: 41318479--41319549 Score: 2115
Period size: 183 Copynumber: 5.9 Consensus size: 183
41318469 TTTCATGAAC
41318479 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
41318544 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
41318609 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
131 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
41318662 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
41318727 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
41318792 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
131 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
41318845 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
41318910 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
41318975 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
131 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
41319028 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
41319093 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
41319158 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
131 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
41319211 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
*
41319276 TCTAAGGAGATTGAAACTTAAGCGGGACTGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
41319341 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
131 AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
41319394 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
1 TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
41319459 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
66 TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
* *
41319524 AATGTAATTTGTTAAGCAGAAATTTT
131 AATGTAATTTGTTAAGAAAAAATTTT
41319550 TAAATTTTTA
Statistics
Matches: 884, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 884 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (183 bp):
TCATTTTTTAAATAAATAAATAATTATAACTTATTTTCTTAACTTATTACATTTAATTAATTCTG
TCTAAGGAGATTGAAACTTAAGCGGGACCGCTGTGACCCCTCCAACCTTTCCTGGAAATTAATTT
AATGTAATTTGTTAAGAAAAAATTTTCTAATTAAGATTTAAAATTTTTAAGTT
Found at i:41321445 original size:183 final size:183
Alignment explanation
Indices: 41321137--41322205 Score: 2075
Period size: 183 Copynumber: 5.8 Consensus size: 183
41321127 TAAAAATTTA
*
41321137 AAAATTTCTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
* * *
41321202 CCTGCTTAAGTTTCAATATCCTTAGATAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
41321267 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
131 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
41321320 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
* * *
41321385 CCTGCTTAAGTTTCAATATCCTTAGATAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
41321450 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
131 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
41321503 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
41321568 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
41321633 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
131 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
41321686 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
41321751 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
41321816 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
131 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
41321869 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
41321934 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
41321999 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
131 TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
41322052 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
1 AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
41322117 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
66 CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
41322182 TAATTATTTATTTATTTAAAAAAT
131 TAATTATTTATTTATTTAAAAAAT
41322206 GAGTTCATGA
Statistics
Matches: 882, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 882 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (183 bp):
AAAATTTTTGCTTAACAAATTACATTAAATTAATTTCCAGGAAAGGTTGGAGGGGTCACAGCGGT
CCCGCTTAAGTTTCAATCTCCTTAGACAGAATTAATTAAATGTAATAAGTTAAGAAAATAAGTTA
TAATTATTTATTTATTTAAAAAATAAAACTTAAAAATTTTAAATCTTAATTAG
Found at i:41324768 original size:39 final size:40
Alignment explanation
Indices: 41324660--41324844 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
41324650 TTGAATGATG
* * *
41324660 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
41324699 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41324740 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41324779 TCCGGGTTAAGTCCCGATGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41324818 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41324845 AACGAGGAGT
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 34 0.28
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:41324804 original size:79 final size:81
Alignment explanation
Indices: 41324660--41324842 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 81
41324650 TTGAATGATG
* * *
41324660 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41324724 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * ** *
41324739 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGATGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
41324801 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
41324819 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41324843 TGAACGAGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.64
80 30 0.34
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:41331937 original size:30 final size:30
Alignment explanation
Indices: 41331901--41331960 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
41331891 AACATGTTTG
41331901 GTGAAGTTATGTACTTA-GCAAATGGCCATA
1 GTGAAGTTATGTAC-TAGGCAAATGGCCATA
41331931 GTGAAGTTATGTACTAGGCAAATGGCCATA
1 GTGAAGTTATGTACTAGGCAAATGGCCATA
41331961 TAGTATTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (30 bp):
GTGAAGTTATGTACTAGGCAAATGGCCATA
Found at i:41332288 original size:16 final size:16
Alignment explanation
Indices: 41332267--41332299 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41332257 TTTATTTTGA
41332267 TTTAATTGAGTTATGT
1 TTTAATTGAGTTATGT
41332283 TTTAATTGAGTTATGT
1 TTTAATTGAGTTATGT
41332299 T
1 T
41332300 AAACATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TTTAATTGAGTTATGT
Found at i:41344096 original size:21 final size:20
Alignment explanation
Indices: 41344069--41344127 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
41344059 TTTTTCACAT
41344069 AAATTTAATATTAAATAATA
1 AAATTTAATATTAAATAATA
*
41344089 ACAATTT-ATATTAGAAGAATA
1 A-AATTTAATATTA-AATAATA
* *
41344110 ATATTTAAATATAAAATA
1 AAATTT-AATATTAAATA
41344128 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 11 0.35
21 15 0.48
22 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATTTAATATTAAATAATA
Found at i:41346798 original size:28 final size:27
Alignment explanation
Indices: 41346719--41346829 Score: 69
Period size: 28 Copynumber: 4.3 Consensus size: 27
41346709 ATATATATAG
*
41346719 AATGA-AATATAT-AATAAAATATAATT
1 AATGATAATATATAAATAAAA-ATAAAT
* * *
41346745 TATAGATAAAATATACAAT-AATATAACAT
1 AAT-GATAATATATA-AATAAAAATAA-AT
41346774 AATGATAATATATAAATAAAAAT-AAT
1 AATGATAATATATAAATAAAAATAAAT
* *
41346800 AA--CTAATAT-T-TATAAAAATAAAT
1 AATGATAATATATAAATAAAAATAAAT
41346823 AAT-ATAA
1 AATGATAA
41346830 AAAATATTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
22 8 0.12
23 6 0.09
24 9 0.13
26 6 0.09
27 6 0.09
28 24 0.36
29 5 0.07
30 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
AATGATAATATATAAATAAAAATAAAT
Found at i:41346801 original size:26 final size:27
Alignment explanation
Indices: 41346719--41346826 Score: 68
Period size: 26 Copynumber: 4.0 Consensus size: 27
41346709 ATATATATAG
41346719 AATGA-AATATAT-AATAA-AATATAATT
1 AATGATAATATATAAATAATAA-ATAA-T
* * *
41346745 TATAGATAAAATATACAATAATATAA-CAT
1 AAT-GATAATATATA-AATAATA-AATAAT
41346774 AATGATAATATATAAATAA-AAATAAT
1 AATGATAATATATAAATAATAAATAAT
* *
41346800 AACTAAT-ATTTATAAA-AATAAATAAT
1 AA-TGATAATATATAAATAATAAATAAT
41346826 A
1 A
41346827 TAAAAAATAT
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
25 4 0.06
26 23 0.35
27 10 0.15
28 16 0.25
29 3 0.05
30 6 0.09
31 2 0.03
32 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
AATGATAATATATAAATAATAAATAAT
Found at i:41348801 original size:206 final size:206
Alignment explanation
Indices: 41348272--41348816 Score: 817
Period size: 204 Copynumber: 2.7 Consensus size: 206
41348262 AATCTGCTTT
* *
41348272 TTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCCTCTTAGATTTGCTTCAGCGTAAGCATG
1 TTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACG
** * * * * *
41348337 CAAAAACCAAATCAGGTATGTCTTCGATTTGCTCCTTGTAAGCACGAGGATACCAAACCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* * * * **
41348402 GATCTGCTTCAGTCTAATCATTTGAAGGTTAGATTTGCTATGTGTCTGCTCTCCGTCGAAAATGG
131 GATCTACTTCAGTATAAACATCTGAAGGCCAGATTTGCTATGTGTCTGCTCTCCGTCGAAAATGG
*
41348467 AGACGCCAAAC
196 AGACACCAAAC
* *
41348478 TTTGATTTGTTCTCTGACAAT--AGAGATGCCAAATCATCTTGGACTTGCTTCAGCGTAAGCACG
1 TTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACG
* * *
41348541 TGAAAGCTAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* *
41348606 GATCTACTTCAGTATAAACATCTGAAGGCCAGATATT-TTATGTGTCTGCTCTCCGTCGAATATG
131 GATCTACTTCAGTATAAACATCTGAAGGCCAGAT-TTGCTATGTGTCTGCTCTCCGTCGAAAATG
41348670 GAGACACCAAAC
195 GAGACACCAAAC
* * *
41348682 TTTGATTTGTTCCCTGACAATACAGATATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACG
1 TTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACG
*
41348747 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAATGATGCCAAACCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
41348812 GATCT
131 GATCT
41348817 TGCTTCAGCC
Statistics
Matches: 304, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
204 177 0.58
205 2 0.01
206 125 0.41
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (206 bp):
TTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACG
TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
GATCTACTTCAGTATAAACATCTGAAGGCCAGATTTGCTATGTGTCTGCTCTCCGTCGAAAATGG
AGACACCAAAC
Found at i:41366228 original size:18 final size:19
Alignment explanation
Indices: 41366205--41366243 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
41366195 CTTGGCCCAT
* *
41366205 TACAGTATCA-ATATTCAG
1 TACAGTAACAGATATACAG
41366223 TACAGTAACAGATATACAG
1 TACAGTAACAGATATACAG
41366242 TA
1 TA
41366244 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (19 bp):
TACAGTAACAGATATACAG
Found at i:41368646 original size:27 final size:27
Alignment explanation
Indices: 41368616--41368905 Score: 323
Period size: 27 Copynumber: 10.7 Consensus size: 27
41368606 TTAGTTTACC
41368616 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
41368643 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
41368670 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
41368697 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
41368724 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
41368751 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
*
41368778 AAATTACTAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
41368805 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
** ***
41368832 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*** **
41368859 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*
41368886 AAATTACCAAAGTACCCCTG
1 AAATTACCAAAATACCCCTG
41368906 ATTTACAGAA
Statistics
Matches: 226, Mismatches: 35, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 4 0.02
27 218 0.96
28 4 0.02
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:41368974 original size:27 final size:27
Alignment explanation
Indices: 41368941--41369136 Score: 257
Period size: 27 Copynumber: 7.3 Consensus size: 27
41368931 CGATTTATAA
* * *
41368941 AATTATCGAAATACCCTTCTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
41368968 AAATATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
41368995 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
41369022 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
41369049 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
41369076 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
41369103 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
41369130 AATTACC
1 AATTACC
41369137 ATTTTGCCCC
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:41369373 original size:27 final size:26
Alignment explanation
Indices: 41369335--41369417 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 26
41369325 CGGAGGAAGC
*
41369335 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
41369362 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* *
41369388 GTATCTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
41369415 GTT
1 GTT
41369418 GACCGATGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 10 0.19
27 42 0.81
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:41369536 original size:22 final size:22
Alignment explanation
Indices: 41369504--41369562 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
41369494 CCCATTATTG
*
41369504 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
41369526 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
41369548 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
41369563 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:41369830 original size:27 final size:26
Alignment explanation
Indices: 41369792--41369878 Score: 120
Period size: 27 Copynumber: 3.3 Consensus size: 26
41369782 CGGAGGAAGC
*
41369792 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
41369819 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
41369845 GTATCTGGTGACTCTGTCACGATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
41369872 GTTCTGG
1 GTTCTGG
41369879 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
26 14 0.25
27 41 0.75
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:41370033 original size:25 final size:24
Alignment explanation
Indices: 41369982--41370038 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
41369972 GGATTGGGTA
* * *
41369982 TGATTCTGTTACTGATTGTGATTC
1 TGATTCTGTCACTAATTCTGATTC
41370006 TGATTCTGTCACCTAATTCTGATTC
1 TGATTCTGTCA-CTAATTCTGATTC
41370031 TGATTCTG
1 TGATTCTG
41370039 ATTCTGTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (24 bp):
TGATTCTGTCACTAATTCTGATTC
Found at i:41370119 original size:85 final size:85
Alignment explanation
Indices: 41369980--41370754 Score: 1523
Period size: 85 Copynumber: 9.1 Consensus size: 85
41369970 CTGGATTGGG
41369980 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370045 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
41370065 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370130 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
41370150 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370215 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
41370235 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370300 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
41370320 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370385 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
41370405 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370470 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
41370490 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370555 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
41370575 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
41370640 TTACTAATACTGATTCTGAT
66 TTACTAATACTGATTCTGAT
*
41370660 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTA
1 TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
*
41370725 TTACTAATATTGATTCTGAT
66 TTACTAATACTGATTCTGAT
*
41370745 TCTGATTCTG
1 TATGATTCTG
41370755 ATTCTGTTTC
Statistics
Matches: 687, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 687 1.00
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.47
Consensus pattern (85 bp):
TATGATTCTGTTACTGATTGTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG
TTACTAATACTGATTCTGAT
Found at i:41370783 original size:36 final size:36
Alignment explanation
Indices: 41370707--41370786 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
41370697 CCTAATTCTG
**
41370707 ATTCTGATTCTGATTCTATTACTAATATTGATTCTG
1 ATTCTGATTCTGATTCTATTACTAATATTGATTCCA
* * * * *
41370743 ATTCTGATTCTGATTCTGTTTCTCATTTTGGTTCCA
1 ATTCTGATTCTGATTCTATTACTAATATTGATTCCA
41370779 ATTCTGAT
1 ATTCTGAT
41370787 AATGTTTCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.51
Consensus pattern (36 bp):
ATTCTGATTCTGATTCTATTACTAATATTGATTCCA
Found at i:41387882 original size:20 final size:20
Alignment explanation
Indices: 41387857--41387897 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41387847 TCAAGTTAGG
*
41387857 AGAATGAGAAAATAGTGTGA
1 AGAATGAGAAAATAGCGTGA
41387877 AGAATGAGAAAATAGCGTGA
1 AGAATGAGAAAATAGCGTGA
41387897 A
1 A
41387898 AAATAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.17
Consensus pattern (20 bp):
AGAATGAGAAAATAGCGTGA
Found at i:41388786 original size:28 final size:28
Alignment explanation
Indices: 41388746--41388827 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
41388736 CTATGTACAT
41388746 CACTTAGTGTGTGAGATATTGAGTATGG
1 CACTTAGTGTGTGAGATATTGAGTATGG
41388774 CACTTAGTGTGTGAGATATTGAGTATGG
1 CACTTAGTGTGTGAGATATTGAGTATGG
* * *
41388802 CTCTTAGTGTGCGAAATATTGAGTAT
1 CACTTAGTGTGTGAGATATTGAGTAT
41388828 TAAGTGGCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.37
Consensus pattern (28 bp):
CACTTAGTGTGTGAGATATTGAGTATGG
Found at i:41404382 original size:55 final size:56
Alignment explanation
Indices: 41404315--41404429 Score: 171
Period size: 56 Copynumber: 2.1 Consensus size: 56
41404305 GTATTTTAGT
* * * *
41404315 TGGTCAATCTAC-AAAATTCAAGAGA-AAGAAATTAACATCTTGCATGTAATTTAAG
1 TGGTCAACCTACAAAAATTAAAGAGAGAA-AAATCAACATCTTGCATATAATTTAAG
41404370 TGGTCAACCTACAAAAATTAAAGAGAGAAAAATCAACATCTTGCATATAATTTAAG
1 TGGTCAACCTACAAAAATTAAAGAGAGAAAAATCAACATCTTGCATATAATTTAAG
41404426 TGGT
1 TGGT
41404430 GTTGTAGTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
55 11 0.20
56 41 0.76
57 2 0.04
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (56 bp):
TGGTCAACCTACAAAAATTAAAGAGAGAAAAATCAACATCTTGCATATAATTTAAG
Found at i:41405861 original size:29 final size:29
Alignment explanation
Indices: 41405794--41405868 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
41405784 TGTTAGTAGT
*
41405794 TGGATTAAATTTTAAAATATGAAAAGTAA
1 TGGATTAAATTCTAAAATATGAAAAGTAA
* *
41405823 AGTGACTAAATTCCTAAAA-AT-AAAAGTACA
1 TG-GATTAAATT-CTAAAATATGAAAAGTA-A
41405853 TGGATTAAATTCTAAA
1 TGGATTAAATTCTAAA
41405869 TTTTTGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 5 0.13
29 16 0.42
30 12 0.32
31 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.31
Consensus pattern (29 bp):
TGGATTAAATTCTAAAATATGAAAAGTAA
Done.