Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 81 of 199
Found at i:24413858 original size:25 final size:25
Alignment explanation
Indices: 24413810--24413858 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
24413800 AATAAGTGAA
* * *
24413810 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
24413835 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
24413859 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:24414213 original size:18 final size:18
Alignment explanation
Indices: 24414190--24414230 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
24414180 TGGTTGGATT
24414190 CGTGTATCCGTCCGAGTC
1 CGTGTATCCGTCCGAGTC
24414208 CGTGTATCCGTCCGAGTC
1 CGTGTATCCGTCCGAGTC
24414226 CGTGT
1 CGTGT
24414231 CGTGTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.32, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTGTATCCGTCCGAGTC
Found at i:24418363 original size:25 final size:25
Alignment explanation
Indices: 24418325--24418373 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
24418315 AGCACTCTCT
*
24418325 TGAGCCATAAAACAAGATGCTCATG
1 TGAGCCATAAAACAAGAAGCTCATG
** *
24418350 TGAGCCATGTAACAGGAAGCTCAT
1 TGAGCCATAAAACAAGAAGCTCAT
24418374 AAGAGTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (25 bp):
TGAGCCATAAAACAAGAAGCTCATG
Found at i:24420514 original size:24 final size:25
Alignment explanation
Indices: 24420487--24420539 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
24420477 ATATCCCTTG
* *
24420487 ACCTTCCACCTTTCATCTTCTT-TA
1 ACCTTCAACCTTTCATCTCCTTGTA
*
24420511 ACCTTTAACCTTTCATCTCCTTGTA
1 ACCTTCAACCTTTCATCTCCTTGTA
24420536 ACCT
1 ACCT
24420540 CTTTTTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.19, C:0.36, G:0.02, T:0.43
Consensus pattern (25 bp):
ACCTTCAACCTTTCATCTCCTTGTA
Found at i:24423239 original size:19 final size:18
Alignment explanation
Indices: 24423203--24423248 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
24423193 AATATTTAGT
* *
24423203 TTAAGTATTAAATGTGTC
1 TTAAGTATTTAATATGTC
24423221 TTAAGTTATTTAATATGTC
1 TTAAG-TATTTAATATGTC
24423240 -TAAGTATTT
1 TTAAGTATTT
24423249 TCGGCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 9 0.36
19 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (18 bp):
TTAAGTATTTAATATGTC
Found at i:24424783 original size:43 final size:44
Alignment explanation
Indices: 24424670--24424784 Score: 105
Period size: 44 Copynumber: 2.6 Consensus size: 44
24424660 TGAAATTTTG
* * *
24424670 TGTAAAACCACGTCTGGGAT-GTTGGCATCGATTTGAGACTTTCG
1 TGTAAGACCACGTCTGGG-TCGTTGGCATCGATTTGAGACTTACA
* * *
24424714 TGTAAGACC-CTGTCTAGGACAG-TGGCATCGATATT-TGA-TTACA
1 TGTAAGACCAC-GTCTGGGTC-GTTGGCATCGAT-TTGAGACTTACA
24424757 TGTAAGACCACGTCTGGGTCGTTGGCAT
1 TGTAAGACCACGTCTGGGTCGTTGGCAT
24424785 TGTACGAGCT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
42 1 0.02
43 26 0.46
44 27 0.47
45 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGTCGTTGGCATCGATTTGAGACTTACA
Found at i:24427611 original size:16 final size:17
Alignment explanation
Indices: 24427578--24427615 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
24427568 ATTAAAAAAT
*
24427578 AAAAAAATTGAAATTAA
1 AAAAAAATTGAAAGTAA
*
24427595 AAAAAAATT-CAAGTAA
1 AAAAAAATTGAAAGTAA
24427611 AAAAA
1 AAAAA
24427616 TTATGCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAAAATTGAAAGTAA
Found at i:24428656 original size:15 final size:15
Alignment explanation
Indices: 24428628--24428664 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
24428618 CGAGAGGATA
24428628 AAAATG-AA-AAAAG
1 AAAATGAAATAAAAG
*
24428641 AAATTGAAATAAAAG
1 AAAATGAAATAAAAG
24428656 AAAATGAAA
1 AAAATGAAA
24428665 AAGAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 5 0.25
14 2 0.10
15 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAATGAAATAAAAG
Found at i:24428668 original size:12 final size:13
Alignment explanation
Indices: 24428628--24428678 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 13
24428618 CGAGAGGATA
24428628 AAAATGAAAAAAG
1 AAAATGAAAAAAG
*
24428641 AAATTGAAATAAAAG
1 AAAATG-AA-AAAAG
24428656 AAAATG-AAAAAG
1 AAAATGAAAAAAG
*
24428668 AAAAAGAAAAA
1 AAAATGAAAAA
24428679 GAGGAAAGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 10 0.31
13 10 0.31
14 2 0.06
15 10 0.31
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (13 bp):
AAAATGAAAAAAG
Found at i:24428678 original size:6 final size:6
Alignment explanation
Indices: 24428651--24428680 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
24428641 AAATTGAAAT
*
24428651 AAAAGA AAATGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
24428681 GGAAAGCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:24428757 original size:33 final size:32
Alignment explanation
Indices: 24428716--24428836 Score: 125
Period size: 33 Copynumber: 3.7 Consensus size: 32
24428706 AGTGTGAATG
* *
24428716 AAACGAGTGCAAAAGAAAGAGAGCTCGAAAAAA
1 AAACGAGTGAAAAAGAAA-AGAGCTTGAAAAAA
* * *
24428749 AAATGAGTGAAAAAGAAAAAGTGCTTGAAAAGA
1 AAACGAGTGAAAAAG-AAAAGAGCTTGAAAAAA
* *
24428782 AAACAAGTGAAAAAGAGAAAGAGCTTGAAAAAG
1 AAACGAGTGAAAAAGA-AAAGAGCTTGAAAAAA
* * *
24428815 AAACGTGTGAAGAAGAAGAGAG
1 AAACGAGTGAAAAAGAAAAGAG
24428837 TGCTCAAACA
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
32 6 0.08
33 63 0.88
34 3 0.04
ACGTcount: A:0.57, C:0.07, G:0.26, T:0.10
Consensus pattern (32 bp):
AAACGAGTGAAAAAGAAAAGAGCTTGAAAAAA
Found at i:24428777 original size:18 final size:18
Alignment explanation
Indices: 24428726--24428817 Score: 81
Period size: 18 Copynumber: 5.4 Consensus size: 18
24428716 AAACGAGTGC
* *
24428726 AAAAGAAAGAGAGCTCGA
1 AAAAGAAAAAGAGCTTGA
*
24428744 AAAA-AAAATGAG--TGA
1 AAAAGAAAAAGAGCTTGA
*
24428759 AAAAGAAAAAGTGCTTG-
1 AAAAGAAAAAGAGCTTGA
24428776 AAAAGAAAACA-AG--TGA
1 AAAAGAAAA-AGAGCTTGA
*
24428792 AAAAGAGAAAGAGCTTGA
1 AAAAGAAAAAGAGCTTGA
24428810 AAAAGAAA
1 AAAAGAAA
24428818 CGTGTGAAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
15 9 0.16
16 16 0.28
17 16 0.28
18 17 0.29
ACGTcount: A:0.62, C:0.05, G:0.23, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAGCTTGA
Found at i:24428797 original size:66 final size:67
Alignment explanation
Indices: 24428716--24428840 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 67
24428706 AGTGTGAATG
* * *
24428716 AAACGAGTGCAAAAGA-AAGAGAGCTCGAAAAAAAAATGAGTGAAAAAGAA-AAAGTGCTTGAAA
1 AAACAAGTGAAAAAGAGAA-AGAGCTCGAAAAAAAAACGAGTGAAAAAGAAGAAAGTGCTTGAAA
24428779 AGA
65 AGA
* * * * *
24428782 AAACAAGTGAAAAAGAGAAAGAGCTTGAAAAAGAAACGTGTGAAGAAGAAGAGAGTGCT
1 AAACAAGTGAAAAAGAGAAAGAGCTCGAAAAAAAAACGAGTGAAAAAGAAGAAAGTGCT
24428841 CAAACACAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
66 40 0.82
67 9 0.18
ACGTcount: A:0.55, C:0.07, G:0.26, T:0.11
Consensus pattern (67 bp):
AAACAAGTGAAAAAGAGAAAGAGCTCGAAAAAAAAACGAGTGAAAAAGAAGAAAGTGCTTGAAAA
GA
Found at i:24431174 original size:19 final size:18
Alignment explanation
Indices: 24431138--24431183 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
24431128 AATATTTAGT
* *
24431138 TTAAGTATTAAATGTGTC
1 TTAAGTATTTAATATGTC
24431156 TTAAGTTATTTAATATGTC
1 TTAAG-TATTTAATATGTC
24431175 -TAAGTATTT
1 TTAAGTATTT
24431184 TCAGCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 9 0.36
19 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (18 bp):
TTAAGTATTTAATATGTC
Found at i:24433107 original size:7 final size:7
Alignment explanation
Indices: 24433092--24433142 Score: 93
Period size: 7 Copynumber: 7.3 Consensus size: 7
24433082 AAGTAATAAA
*
24433092 TTAATTT
1 TTAAGTT
24433099 TTAAGTT
1 TTAAGTT
24433106 TTAAGTT
1 TTAAGTT
24433113 TTAAGTT
1 TTAAGTT
24433120 TTAAGTT
1 TTAAGTT
24433127 TTAAGTT
1 TTAAGTT
24433134 TTAAGTT
1 TTAAGTT
24433141 TT
1 TT
24433143 TACACATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (7 bp):
TTAAGTT
Found at i:24436684 original size:11 final size:11
Alignment explanation
Indices: 24436668--24436696 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
24436658 CAATATAAAA
24436668 GCATTTAACAT
1 GCATTTAACAT
24436679 GCATTTAACAT
1 GCATTTAACAT
24436690 GCATTTA
1 GCATTTA
24436697 TAATGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (11 bp):
GCATTTAACAT
Found at i:24437071 original size:29 final size:28
Alignment explanation
Indices: 24437024--24437079 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
24437014 ACTTTCATTT
24437024 ATTTCACATTTCAACCCCTCAATTTGCAC
1 ATTTCACATTTCAACCCCT-AATTTGCAC
*
24437053 ATTTCACAATTT-AATCCCTAATTTGCA
1 ATTTCAC-ATTTCAACCCCTAATTTGCA
24437080 TTTTTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 13 0.52
30 4 0.16
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.38
Consensus pattern (28 bp):
ATTTCACATTTCAACCCCTAATTTGCAC
Found at i:24438899 original size:18 final size:19
Alignment explanation
Indices: 24438863--24438899 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
24438853 ATTTGATTCC
*
24438863 TTTTGAATCAACTCGAATA
1 TTTTGAATCAACTCAAATA
24438882 TTTTGAAT-AACTCAAATA
1 TTTTGAATCAACTCAAATA
24438900 ATAAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (19 bp):
TTTTGAATCAACTCAAATA
Found at i:24438986 original size:9 final size:9
Alignment explanation
Indices: 24438974--24439009 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
24438964 AAAAAAATTA
24438974 CAAAATATT
1 CAAAATATT
24438983 CAAAATATT
1 CAAAATATT
24438992 CAAAATATT
1 CAAAATATT
24439001 CAAAATATT
1 CAAAATATT
24439010 TATAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
CAAAATATT
Found at i:24439020 original size:23 final size:23
Alignment explanation
Indices: 24438993--24439038 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
24438983 CAAAATATTC
24438993 AAAATATT-CAAAATATTTATAAA
1 AAAATATTCCAAAAT-TTTATAAA
* *
24439016 AAAATTTTCCACAATTTTATAAA
1 AAAATATTCCAAAATTTTATAAA
24439039 TATATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAATATTCCAAAATTTTATAAA
Found at i:24440595 original size:20 final size:19
Alignment explanation
Indices: 24440538--24440610 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
24440528 ATTATAAAAA
* *
24440538 TATACAAAATTATAATTTTT
1 TATA-AAAATTATAAATATT
*
24440558 TATAAAAA-TATTAATATT
1 TATAAAAATTATAAATATT
24440576 TATAAGAAATTATAAATATT
1 TATAA-AAATTATAAATATT
* * *
24440596 TTTTAAAATTTTAAA
1 TATAAAAATTATAAA
24440611 GAATTAATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 12 0.27
19 16 0.36
20 16 0.36
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (19 bp):
TATAAAAATTATAAATATT
Found at i:24440604 original size:19 final size:19
Alignment explanation
Indices: 24440543--24440610 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 19
24440533 AAAAATATAC
24440543 AAAATTAT-AAT-TTTTTAT
1 AAAATTATAAATATTTTT-T
* * * *
24440561 AAAAATATTAATATTTATA
1 AAAATTATAAATATTTTTT
24440580 AGAAATTATAAATATTTTTT
1 A-AAATTATAAATATTTTTT
*
24440600 AAAATTTTAAA
1 AAAATTATAAA
24440611 GAATTAATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 7 0.18
19 13 0.33
20 19 0.49
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (19 bp):
AAAATTATAAATATTTTTT
Found at i:24440783 original size:19 final size:19
Alignment explanation
Indices: 24440759--24440811 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
24440749 TAAATTCATA
*
24440759 AATAATTTTTATAATATTT
1 AATAATTTTTATAATAATT
* *
24440778 ACTAATTTTTACAA-AATT
1 AATAATTTTTATAATAATT
24440796 AATAATTATTTATAAT
1 AATAATT-TTTATAAT
24440812 TCTCAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATTTTTATAATAATT
Found at i:24442311 original size:29 final size:29
Alignment explanation
Indices: 24442277--24442332 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
24442267 CGCGAAAAAT
24442277 GACCCATTCCGATAAATAATT-AAAAAACC
1 GACCCATTCCGATAAAT-ATTGAAAAAACC
* *
24442306 GACCCATTTCGGTAAATATTGAAAAAA
1 GACCCATTCCGATAAATATTGAAAAAA
24442333 AAGAGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (29 bp):
GACCCATTCCGATAAATATTGAAAAAACC
Found at i:24450200 original size:2 final size:2
Alignment explanation
Indices: 24450193--24450225 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24450183 TGTCCCTTAA
24450193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24450226 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24453523 original size:19 final size:19
Alignment explanation
Indices: 24453490--24453535 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
24453480 AACAGAAAAT
* *
24453490 AAATCAAATATAAAACCAAA
1 AAAT-AAATAAAAAAACAAA
*
24453510 AAATAAATAAAAAAACAAC
1 AAATAAATAAAAAAACAAA
24453529 AAATAAA
1 AAATAAA
24453536 GTCCATTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (19 bp):
AAATAAATAAAAAAACAAA
Found at i:24453916 original size:3 final size:3
Alignment explanation
Indices: 24453908--24453949 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
24453898 GGATTTTTAG
24453908 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24453950 TATTTTGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:24455206 original size:31 final size:31
Alignment explanation
Indices: 24455171--24455235 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
24455161 TTTATATATA
24455171 TTATCATGTCTAACTAATAAATGTATATTGT
1 TTATCATGTCTAACTAATAAATGTATATTGT
24455202 TTATCATGTCTAACTAATAAATGTATATTGT
1 TTATCATGTCTAACTAATAAATGTATATTGT
24455233 TTA
1 TTA
24455236 CTTTAAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (31 bp):
TTATCATGTCTAACTAATAAATGTATATTGT
Found at i:24460316 original size:51 final size:51
Alignment explanation
Indices: 24460144--24460436 Score: 313
Period size: 51 Copynumber: 5.8 Consensus size: 51
24460134 CTTTTATCAT
* * **
24460144 TCGATACACGTAGTAGCCTTCACATGGTACTACACACGTGATCAAGTTTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
* * * **
24460195 -CGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
* * * * *
24460245 -CGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
* * * *
24460295 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA-AGCTTC
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACA-TTTA
* * ** * * * *
24460346 TTGGTACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
*
24460397 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
24460437 TTCATCGATA
Statistics
Matches: 199, Mismatches: 40, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
50 90 0.45
51 108 0.54
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (51 bp):
TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
Found at i:24460387 original size:102 final size:100
Alignment explanation
Indices: 24460148--24460436 Score: 402
Period size: 102 Copynumber: 2.9 Consensus size: 100
24460138 TATCATTCGA
* * * * * *** *
24460148 TACACGTAGTAGCCTTCACATGGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* *
24460212 TTCACATAGTACTACACACGTGATCAAGTTTTACGG
66 TTCACACAGTACTACACACGTGACCAAGTTTTA-GG
24460248 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
24460313 TTCACACAGTACTACACACGTGACCAAAGCTTCTT-GG
66 TTCACACAGTACTACACACGTGACC-AAG-TT-TTAGG
* * *
24460350 TACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATACACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
24460415 TTCACACAGTACTACACACGTG
66 TTCACACAGTACTACACACGTG
24460437 TTCATCGATA
Statistics
Matches: 171, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
100 39 0.23
101 39 0.23
102 89 0.52
103 2 0.01
104 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (100 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
TTCACACAGTACTACACACGTGACCAAGTTTTAGG
Found at i:24472269 original size:21 final size:21
Alignment explanation
Indices: 24472243--24472283 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
24472233 CTCCATGAAC
24472243 AATAAGGATTGGATTACGAGT
1 AATAAGGATTGGATTACGAGT
24472264 AATAAGGATTGGATTACGAG
1 AATAAGGATTGGATTACGAG
24472284 CATTAATGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (21 bp):
AATAAGGATTGGATTACGAGT
Found at i:24478436 original size:18 final size:18
Alignment explanation
Indices: 24478424--24478463 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
24478414 TAAAAGAAAT
24478424 ATAAATACCAAAAAATAA
1 ATAAATACCAAAAAATAA
*
24478442 ATAAATACTAAGAAAAATAA
1 ATAAATAC-CA-AAAAATAA
24478462 AT
1 AT
24478464 TTCACCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (18 bp):
ATAAATACCAAAAAATAA
Found at i:24482942 original size:22 final size:22
Alignment explanation
Indices: 24482880--24482951 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
24482870 GTTCCTCAGA
* **
24482880 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
24482902 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
24482924 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
24482946 CATGAG
1 CATGAG
24482952 GGTTCATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:24486564 original size:16 final size:18
Alignment explanation
Indices: 24486545--24486590 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
24486535 AGTGAGAAGG
24486545 GAAGGAATGA-AGAA-AT
1 GAAGGAATGAGAGAAGAT
*
24486561 GAAGGATTGAGAGAATGAT
1 GAAGGAATGAGAGAA-GAT
24486580 GAAGG-ATGAGA
1 GAAGGAATGAGA
24486591 TGTGAAGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 9 0.36
17 4 0.16
18 5 0.20
19 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.37, T:0.15
Consensus pattern (18 bp):
GAAGGAATGAGAGAAGAT
Found at i:24486806 original size:94 final size:94
Alignment explanation
Indices: 24486645--24486824 Score: 360
Period size: 94 Copynumber: 1.9 Consensus size: 94
24486635 TTATACTTCA
24486645 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
1 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
24486710 ACCATGAATTTTGGAAAGGAGAGGTTGTT
66 ACCATGAATTTTGGAAAGGAGAGGTTGTT
24486739 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
1 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
24486804 ACCATGAATTTTGGAAAGGAG
66 ACCATGAATTTTGGAAAGGAG
24486825 CTAGATGGTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (94 bp):
GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
ACCATGAATTTTGGAAAGGAGAGGTTGTT
Found at i:24488970 original size:110 final size:110
Alignment explanation
Indices: 24488777--24489107 Score: 626
Period size: 110 Copynumber: 3.0 Consensus size: 110
24488767 ATGTCTCTAC
*
24488777 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACGAGAT
1 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACGACAT
24488842 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
66 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
24488887 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACGACAT
1 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACGACAT
24488952 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
66 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
* *
24488997 TCATGGAGTCAACTACTCTTATAGCTAAGACTAGCGATCTCCTCAATTGGAATTGAAGACGACAT
1 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACGACAT
*
24489062 AATAATCCTTCTTAGTATTTGAATCAAATGCTCACTTTGATTCTT
66 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
24489107 T
1 T
24489108 TATGAGATTA
Statistics
Matches: 217, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 217 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (110 bp):
TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACGACAT
AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
Found at i:24499137 original size:26 final size:26
Alignment explanation
Indices: 24499100--24499157 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
24499090 CCTAACAATT
*
24499100 TTTTGACAATTTTACCCTTGGTAAAA
1 TTTTGACAATTTTACCCCTGGTAAAA
* *
24499126 TTTTGACGATTTTTCCCCTGGTAAAA
1 TTTTGACAATTTTACCCCTGGTAAAA
24499152 TTTTGA
1 TTTTGA
24499158 GAAGATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (26 bp):
TTTTGACAATTTTACCCCTGGTAAAA
Found at i:24501224 original size:10 final size:11
Alignment explanation
Indices: 24501202--24501250 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
24501192 ACAATTTGTT
*
24501202 ATAAGTTTAT-
1 ATAATTTTATA
24501212 ATAATATTT-T-
1 ATAAT-TTTATA
24501222 ATAATTTTATA
1 ATAATTTTATA
24501233 ATAATTTT-TA
1 ATAATTTTATA
24501243 ATAATTTT
1 ATAATTTT
24501251 TTATTTACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
9 3 0.09
10 21 0.60
11 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
ATAATTTTATA
Found at i:24501246 original size:21 final size:19
Alignment explanation
Indices: 24501169--24501250 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 19
24501159 TCTGCCTAAT
*
24501169 TATAATTTTTATAATTTTTTTC
1 TATAATTTTTATAA---TTTTA
* *
24501191 TACAATTTGTTATAAGTTTA
1 TATAATTT-TTATAATTTTA
24501211 TATAATATTTTATAATTTTA
1 TATAAT-TTTTATAATTTTA
24501231 TAATAATTTTTAATAATTTT
1 T-ATAATTTTT-ATAATTTT
24501251 TTATTTACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 23 0.45
21 15 0.29
22 7 0.14
23 6 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TATAATTTTTATAATTTTA
Found at i:24501251 original size:10 final size:10
Alignment explanation
Indices: 24501207--24501251 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
24501197 TTGTTATAAG
24501207 TTTATATAATAT
1 TTTA-ATAAT-T
24501219 TTT-ATAATT
1 TTTAATAATT
24501228 TTATAATAATT
1 TT-TAATAATT
24501239 TTTAATAATT
1 TTTAATAATT
24501249 TTT
1 TTT
24501252 TATTTACATC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.10
10 17 0.55
11 8 0.26
12 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTAATAATT
Found at i:24502072 original size:22 final size:21
Alignment explanation
Indices: 24502005--24502074 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 21
24501995 TTTATTTTTT
24502005 TGTTTACGTACTAAGCTCTCA
1 TGTTTACGTACTAAGCTCTCA
* *
24502026 TGGCTAACGTACTAAGCTCTCA
1 T-GTTTACGTACTAAGCTCTCA
24502048 TGTTTCACGTACTAAGCTCTCA
1 TGTTT-ACGTACTAAGCTCTCA
24502070 TGTTT
1 TGTTT
24502075 GAACAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.07
22 40 0.93
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (21 bp):
TGTTTACGTACTAAGCTCTCA
Found at i:24502315 original size:18 final size:18
Alignment explanation
Indices: 24502278--24502313 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
24502268 CTTCAATATG
*
24502278 TAATTAAATTTTATTATT
1 TAATTAAATTTCATTATT
24502296 TAATT-AATTTCATTATT
1 TAATTAAATTTCATTATT
24502313 T
1 T
24502314 TATAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTAAATTTCATTATT
Found at i:24502721 original size:33 final size:32
Alignment explanation
Indices: 24502663--24502731 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
24502653 TCCAGAATCG
* * *
24502663 TGAATCTAAACCCGAACCTTGAACCCTAACTT
1 TGAATCTAAACCCGAACCTTAAACCCGAACCT
24502695 TGAATGCTAAACCCTGAACC-TAAACCCGAACCT
1 TGAAT-CTAAACCC-GAACCTTAAACCCGAACCT
24502728 TGAA
1 TGAA
24502732 CATTGGATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 5 0.16
33 22 0.69
34 5 0.16
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (32 bp):
TGAATCTAAACCCGAACCTTAAACCCGAACCT
Found at i:24502791 original size:7 final size:7
Alignment explanation
Indices: 24502779--24502848 Score: 61
Period size: 7 Copynumber: 10.1 Consensus size: 7
24502769 CATACTCAAA
24502779 CTTGAAC
1 CTTGAAC
*
24502786 CTTGAAT
1 CTTGAAC
*
24502793 C-TAAAC
1 CTTGAAC
24502799 CTTGAAC
1 CTTGAAC
* *
24502806 TTTAAAC
1 CTTGAAC
*
24502813 CTTAAAC
1 CTTGAAC
*
24502820 CTCGAAC
1 CTTGAAC
*
24502827 CTCGAAC
1 CTTGAAC
*
24502834 CTCGAAC
1 CTTGAAC
24502841 CTTGAAC
1 CTTGAAC
24502848 C
1 C
24502849 CCAAATCCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
6 4 0.08
7 48 0.92
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (7 bp):
CTTGAAC
Found at i:24502801 original size:13 final size:14
Alignment explanation
Indices: 24502783--24502815 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
24502773 CTCAAACTTG
24502783 AACCTTGAA-TCTA
1 AACCTTGAACTCTA
*
24502796 AACCTTGAACTTTA
1 AACCTTGAACTCTA
24502810 AACCTT
1 AACCTT
24502816 AAACCTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (14 bp):
AACCTTGAACTCTA
Found at i:24507831 original size:97 final size:98
Alignment explanation
Indices: 24507687--24507876 Score: 328
Period size: 97 Copynumber: 1.9 Consensus size: 98
24507677 TACAATAAAA
*
24507687 CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACGATTC
1 CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATTC
*
24507752 CTCTAGAATCCCAAACTCGAAATATTTCCTTTT
66 CTCTAAAATCCCAAACTCGAAATATTTCCTTTT
*
24507785 CTTTAAAA-AACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
1 CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATTC
* *
24507849 CTTTAAAATCCCAAACTCGGAATATTTC
66 CTCTAAAATCCCAAACTCGAAATATTTC
24507877 ATTTATTATT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 79 0.91
98 8 0.09
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (98 bp):
CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATTC
CTCTAAAATCCCAAACTCGAAATATTTCCTTTT
Found at i:24508569 original size:22 final size:23
Alignment explanation
Indices: 24508544--24508596 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
24508534 ATATACATAT
**
24508544 AAATAT-GAAAATATTCTTTAAA
1 AAATATAGAAAATATTAGTTAAA
24508566 AAATATAGGAAAATATTAGTTAAA
1 AAATATA-GAAAATATTAGTTAAA
24508590 AAATATA
1 AAATATA
24508597 CATGTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 6 0.22
24 21 0.78
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (23 bp):
AAATATAGAAAATATTAGTTAAA
Found at i:24508579 original size:24 final size:24
Alignment explanation
Indices: 24508550--24508596 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
24508540 ATATAAATAT
**
24508550 GAAAATATTCTTTAAAAAATATAG
1 GAAAATATTAGTTAAAAAATATAG
24508574 GAAAATATTAGTTAAAAAATATA
1 GAAAATATTAGTTAAAAAATATA
24508597 CATGTACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (24 bp):
GAAAATATTAGTTAAAAAATATAG
Found at i:24510050 original size:44 final size:42
Alignment explanation
Indices: 24509800--24510089 Score: 202
Period size: 44 Copynumber: 6.8 Consensus size: 42
24509790 CTAATGCTTC
* * * *
24509800 AATCTACTCCTCTGCAACTTCAGGGAGATAAGATTTGATGC--
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TTCTT
* * * *
24509841 GATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTT-TT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT--TGTTCTT
* * * *
24509884 AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT--TC-TT
*
24509928 AATTTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATCTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT--TCTT
* *
24509972 CAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTT
1 -AATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTG-TT-CTT
* * *
24510017 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC--
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TTCTT
* * *
24510058 GATCTGCT-CTCTGCAACTTCAGAGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
24510090 TCNNNNNNNN
Statistics
Matches: 202, Mismatches: 31, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
40 46 0.23
41 13 0.06
42 2 0.01
43 8 0.04
44 91 0.45
45 41 0.20
46 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (42 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTCTT
Found at i:24515611 original size:25 final size:26
Alignment explanation
Indices: 24515581--24515630 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
24515571 ATATAAATAT
*
24515581 GAAAATATTC-TTTAAAAAAATATAG
1 GAAAATATTCGTTAAAAAAAATATAG
24515606 GAAAATATTCGTTAAAAAAAATATA
1 GAAAATATTCGTTAAAAAAAATATA
24515631 CATGTACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (26 bp):
GAAAATATTCGTTAAAAAAAATATAG
Found at i:24515728 original size:10 final size:10
Alignment explanation
Indices: 24515713--24515743 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
24515703 AAAAAAATAA
*
24515713 ATATACGTAT
1 ATATACATAT
24515723 ATATACATAT
1 ATATACATAT
24515733 ATATACATAT
1 ATATACATAT
24515743 A
1 A
24515744 AATATGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (10 bp):
ATATACATAT
Found at i:24518063 original size:22 final size:22
Alignment explanation
Indices: 24518038--24518117 Score: 54
Period size: 27 Copynumber: 3.3 Consensus size: 22
24518028 TTATTTGAAA
24518038 TTAAATTAAAATTTATTTTTAT
1 TTAAATTAAAATTTATTTTTAT
24518060 TTAATATATAATTAATTTTATTTTT-T
1 TTAA-AT-TAA--AA-TTTATTTTTAT
* *
24518086 ATTATATAAAAATATGTATTTTATAT
1 -TTAAATTAAAAT-T-TATTTT-TAT
24518112 TTAAAT
1 TTAAAT
24518118 AGTGAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 17
0.69 0.05 0.26
Matches are distributed among these distances:
22 5 0.11
23 5 0.11
24 9 0.20
25 8 0.18
26 6 0.13
27 12 0.27
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (22 bp):
TTAAATTAAAATTTATTTTTAT
Found at i:24529668 original size:95 final size:96
Alignment explanation
Indices: 24529492--24529669 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 96
24529482 TCTTCTCTTG
*** *
24529492 TTGGATATTTAATTGGACATTGGAAACCCTTATGATATTTTGAACTATACCAATAACATTGCACA
1 TTGGATATTTAATTGGACATCAAAAACCCTTATGATATTTTGAACTACACCAATAACATTGCACA
*
24529557 AAAGGTGATAACTCAATCTTATTCTCTCTAT
66 AAAGGTGAGAACTCAATCTTATTCTCTCTAT
* * *
24529588 TTGGAT-TTTAATTGGACATCAAAAACCCTTATGATCTTTTGAACTACACCAATAACATTTCATA
1 TTGGATATTTAATTGGACATCAAAAACCCTTATGATATTTTGAACTACACCAATAACATTGCACA
*
24529652 ACAGGTGAGAGA-TCAATC
66 AAAGGTGAGA-ACTCAATC
24529670 GTACTCCTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
95 65 0.90
96 7 0.10
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (96 bp):
TTGGATATTTAATTGGACATCAAAAACCCTTATGATATTTTGAACTACACCAATAACATTGCACA
AAAGGTGAGAACTCAATCTTATTCTCTCTAT
Found at i:24533751 original size:113 final size:112
Alignment explanation
Indices: 24533580--24534136 Score: 430
Period size: 114 Copynumber: 4.9 Consensus size: 112
24533570 TACCACGCAG
* * *
24533580 CGCCGCAAAATATC-AAGACCAACACGCAGCGTTCTGGTCTTGATGTATATTGGC-ATTAGTGGC
1 CGCCGCAAAAGATCTTA-ACCAAAACGCAGCGTT-TGGTCTTGATGTATATT-GCAATTAGTGGC
* * *
24533643 GCTTATGAACAAACGCCGGTAATGTATAGTATTAGCGGCGCTTAGCGGAAG
63 GCTTATGAA-AAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCGGAAA
* * * *
24533694 CGTCGCAAAAGATGTTAACCAAAACGCAGAGTTTAGTCTTGATGTATATTGCAATTAGTGGCGCT
1 CGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCT
* * * ** *
24533759 TATAAAGAAAACGCTGCTAATGTATAGTATTAGCGGCGCAGAGCGTTAAA
66 TAT-GA-AAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCG-GAAA
* * * * * ** *
24533809 CGCCGCAAGATATCTTAATCAAAACGCACCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGT
1 CGCCGCAAAAGATCTTAACCAAAACGCAGCG-TTTGGTCTTGATGTATATTGCAATTAGTGGCGC
* * * * * * * *
24533874 TTAAGGAAAACGCCAG-TAAAGGATAGT-TATAGCAGCGTTTTGTGGTAAG
65 TTATGAAAAACGCC-GCTAAAGTATAGTAT-TAGCGGCGCTTAGCGG-AAA
* * * * *
24533923 CGCCTCCAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGA-GGAGTATTAG-AATTAGTGGCG
1 CGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTA-TATT-GCAATTAGTGGCG
* * *
24533986 CTTGATGAAAAACGCCGCTAAAGTATA-TCATTAGCGGCG-TTTGTGTAACA
64 CTT-ATGAAAAACGCCGCTAAAGTATAGT-ATTAGCGGCGCTTAGCGGAA-A
* * * * * *
24534036 CGCCGC-AAAGTATCTTAACCAGAACACAGCGTTAGTTCTTGATGTATACTGGAATTAGTGGCGC
1 CGCCGCAAAAG-ATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGC
** * * *
24534100 ACATGAGACAACGCCGCTGAAGCATAGTATTAGCGGC
65 TTATGA-AAAACGCCGCTAAAGTATAGTATTAGCGGC
24534137 ACTTTTACCG
Statistics
Matches: 352, Mismatches: 70, Indels: 43
0.76 0.15 0.09
Matches are distributed among these distances:
112 14 0.04
113 138 0.39
114 139 0.39
115 30 0.09
116 31 0.09
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (112 bp):
CGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCT
TATGAAAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCGGAAA
Found at i:24534264 original size:18 final size:18
Alignment explanation
Indices: 24534243--24534278 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
24534233 TCATTTTATA
24534243 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
24534261 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
24534279 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:24534762 original size:81 final size:81
Alignment explanation
Indices: 24534655--24534805 Score: 198
Period size: 81 Copynumber: 1.9 Consensus size: 81
24534645 GGATTCGGTG
* * * * *
24534655 TCAGGTTAGGCTTTAGTGTTTAGATTAATTAATGTGTTTTAATTT-T-TATAAAATATGGTTTAA
1 TCAGGTTAGGATTTAGGGTTTAGATTAATTAATAT-TTTTAATTTATGTATAAAACAAGGTTT-A
24534718 GGGTTAGGGGTTAGGGAT
64 GGGTTAGGGGTTAGGGAT
* * *
24534736 TCAGGTTATGATTTAGGGTTTTGATTAATTAATATTTTTAATTTATGTATTAAACAAGGTTTAGG
1 TCAGGTTAGGATTTAGGGTTTAGATTAATTAATATTTTTAATTTATGTATAAAACAAGGTTTAGG
24534801 GTTAG
66 GTTAG
24534806 TACAAGTTAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
80 9 0.15
81 39 0.65
82 12 0.20
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.46
Consensus pattern (81 bp):
TCAGGTTAGGATTTAGGGTTTAGATTAATTAATATTTTTAATTTATGTATAAAACAAGGTTTAGG
GTTAGGGGTTAGGGAT
Found at i:24535232 original size:28 final size:27
Alignment explanation
Indices: 24535205--24535264 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
24535195 TGGGGTTTGG
* *
24535205 GGTTTAGGGTTTAGTGTTTAGGGTTTGG
1 GGTTTAGGGGTTAG-GGTTAGGGTTTGG
* *
24535233 GGTTTGGGGGTTAGGGTTGGGGTTTGG
1 GGTTTAGGGGTTAGGGTTAGGGTTTGG
24535260 GGTTT
1 GGTTT
24535265 GGTTTTTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (27 bp):
GGTTTAGGGGTTAGGGTTAGGGTTTGG
Found at i:24535244 original size:8 final size:7
Alignment explanation
Indices: 24535188--24535266 Score: 88
Period size: 7 Copynumber: 11.3 Consensus size: 7
24535178 TTTACTGTTC
24535188 GGGGTTTT
1 GGGG-TTT
24535196 GGGGTTT
1 GGGGTTT
24535203 GGGGTTT
1 GGGGTTT
*
24535210 AGGGTTT
1 GGGGTTT
* *
24535217 AGTGTTT
1 GGGGTTT
*
24535224 AGGGTTT
1 GGGGTTT
24535231 GGGGTTT
1 GGGGTTT
*
24535238 GGGGGTT
1 GGGGTTT
*
24535245 AGGG-TT
1 GGGGTTT
24535251 GGGGTTT
1 GGGGTTT
24535258 GGGGTTT
1 GGGGTTT
24535265 GG
1 GG
24535267 TTTTTGAGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
6 5 0.08
7 54 0.86
8 4 0.06
ACGTcount: A:0.05, C:0.00, G:0.53, T:0.42
Consensus pattern (7 bp):
GGGGTTT
Found at i:24537737 original size:67 final size:67
Alignment explanation
Indices: 24537664--24537802 Score: 253
Period size: 67 Copynumber: 2.1 Consensus size: 67
24537654 ATTAATTGAT
*
24537664 TGAATGTCAATGAATTATCAATTTTGGTTA-TCTAATTGATTGAATGTTTTATAAATTCATTATA
1 TGAATGTCAATGAATTATCAATTTTGGTTAGT-TAATTGATTGAATGTTTAATAAATTCATTATA
24537728 TAA
65 TAA
24537731 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
24537796 AA
66 AA
24537798 TGAAT
1 TGAAT
24537803 TCTCAACAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (67 bp):
TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
AA
Found at i:24537977 original size:34 final size:34
Alignment explanation
Indices: 24537939--24538052 Score: 113
Period size: 34 Copynumber: 3.2 Consensus size: 34
24537929 TTATTAATAT
24537939 ATATATTTTAAAATTGATATCTTACATTACTTAA
1 ATATATTTTAAAATTGATATCTTACATTACTTAA
** * * *
24537973 ATATATATTTTTAAGT-ATATTTTACATGACTTATTAATA
1 ATATAT-TTTAAAATTGATATCTTACATTAC---TT-A-A
24538012 TATATATTTTAAAATTGATATCTTACATTACTTAA
1 -ATATATTTTAAAATTGATATCTTACATTACTTAA
24538047 ATATAT
1 ATATAT
24538053 ATGATACGAG
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
34 24 0.39
35 7 0.11
36 1 0.02
37 4 0.06
38 1 0.02
39 7 0.11
40 18 0.29
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (34 bp):
ATATATTTTAAAATTGATATCTTACATTACTTAA
Found at i:24537983 original size:36 final size:36
Alignment explanation
Indices: 24537900--24538054 Score: 153
Period size: 36 Copynumber: 4.3 Consensus size: 36
24537890 TATTATATTT
* *
24537900 TTAAATATAT-TTTTACAATTTA-AT-TTA-ACTTA-
1 TTAAATATATATTTTAAAATTGATATCTTACA-TTAC
24537932 TTAATATATATATTTTAAAATTGATATCTTACATTAC
1 TTAA-ATATATATTTTAAAATTGATATCTTACATTAC
* * * *
24537969 TTAAATATATATTTT-TAAGT-ATATTTTACATGAC
1 TTAAATATATATTTTAAAATTGATATCTTACATTAC
24538003 TTATTAATATATATATTTTAAAATTGATATCTTACATTAC
1 ---TTAA-ATATATATTTTAAAATTGATATCTTACATTAC
24538043 TTAAATATATAT
1 TTAAATATATAT
24538055 GATACGAGCC
Statistics
Matches: 101, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
32 4 0.04
33 6 0.06
34 22 0.22
35 5 0.05
36 25 0.25
37 13 0.13
38 11 0.11
39 3 0.03
40 12 0.12
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (36 bp):
TTAAATATATATTTTAAAATTGATATCTTACATTAC
Found at i:24538050 original size:38 final size:38
Alignment explanation
Indices: 24537934--24538054 Score: 169
Period size: 38 Copynumber: 3.2 Consensus size: 38
24537924 TTAACTTATT
24537934 AATATATATATTTTAAAATTGATATCTTACATTACTTA
1 AATATATATATTTTAAAATTGATATCTTACATTACTTA
* * *
24537972 AATATATAT-TTTT--AAGT-ATATTTTACATGACTTA
1 AATATATATATTTTAAAATTGATATCTTACATTACTTA
24538006 TTAATATATATATTTTAAAATTGATATCTTACATTACTTA
1 --AATATATATATTTTAAAATTGATATCTTACATTACTTA
24538046 AATATATAT
1 AATATATAT
24538055 GATACGAGCC
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
34 15 0.21
35 3 0.04
36 9 0.13
37 8 0.11
38 18 0.25
39 3 0.04
40 15 0.21
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (38 bp):
AATATATATATTTTAAAATTGATATCTTACATTACTTA
Found at i:24538434 original size:32 final size:31
Alignment explanation
Indices: 24538389--24538484 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
24538379 CTTAGATAAT
24538389 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24538420 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
24538452 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24538483 TT
1 TT
24538485 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:24538834 original size:4 final size:4
Alignment explanation
Indices: 24538788--24538818 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
24538778 ATCTATTATT
24538788 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
24538819 ACTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:24539103 original size:6 final size:7
Alignment explanation
Indices: 24539086--24539111 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
24539076 AAGTGTAAAA
24539086 AAAAAGC
1 AAAAAGC
24539093 AAAAAGC
1 AAAAAGC
24539100 AAAAAGC
1 AAAAAGC
24539107 AAAAA
1 AAAAA
24539112 AAGCGCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.12, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGC
Found at i:24542813 original size:17 final size:18
Alignment explanation
Indices: 24542781--24542815 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24542771 CTTTAGTTTT
24542781 TATAATAAAATTAAAATA
1 TATAATAAAATTAAAATA
*
24542799 TATAA-AAACTTAAAATA
1 TATAATAAAATTAAAATA
24542816 AAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAATAAAATTAAAATA
Found at i:24545353 original size:60 final size:59
Alignment explanation
Indices: 24545237--24545354 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
24545227 AAGGAGGAAG
* * *
24545237 TACTGGTAGTTTATCTGCATACTGGTGGCTTGTCCACAATACTGGCAACTTGTCTGCAT
1 TACTGGCAGTTTATCTGCATACTGGTGGCTTATCCACAATACTGGCAACTTATCTGCAT
* * *
24545296 TACTGGCAGTTTATCTGTACTACTGGTGGCTTATCCATAATATTGGCAA-TCTATCTGCA
1 TACTGGCAGTTTATCTGCA-TACTGGTGGCTTATCCACAATACTGGCAACT-TATCTGCA
24545355 CTATTGGTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 18 0.35
60 33 0.65
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (59 bp):
TACTGGCAGTTTATCTGCATACTGGTGGCTTATCCACAATACTGGCAACTTATCTGCAT
Found at i:24552537 original size:13 final size:13
Alignment explanation
Indices: 24552519--24552544 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24552509 TCGAAAATAA
24552519 GTATATATATAGT
1 GTATATATATAGT
24552532 GTATATATATAGT
1 GTATATATATAGT
24552545 TTAGGGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
GTATATATATAGT
Found at i:24552682 original size:16 final size:16
Alignment explanation
Indices: 24552663--24552693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24552653 ATATTAATGT
*
24552663 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
24552679 TATTTAATATTAAAA
1 TATTTAATATTAAAA
24552694 CAATGCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:24553265 original size:19 final size:19
Alignment explanation
Indices: 24553241--24553310 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 19
24553231 TTGCACAAAA
24553241 AATAAAATTACAATAAATT
1 AATAAAATTACAATAAATT
* *
24553260 AATAAAACTAAAAATGAAATCT
1 AATAAAA-TTACAAT-AAAT-T
24553282 AAAAATAAAATTACAATAAATT
1 ---AATAAAATTACAATAAATT
24553304 AATAAAA
1 AATAAAA
24553311 CTAAAAATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 14 0.34
20 5 0.12
21 4 0.10
22 2 0.05
23 4 0.10
24 5 0.12
25 7 0.17
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (19 bp):
AATAAAATTACAATAAATT
Found at i:24553266 original size:25 final size:25
Alignment explanation
Indices: 24553238--24553316 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
24553228 CAGTTGCACA
24553238 AAAAATAAAATTACAATAAATTAAT
1 AAAAATAAAATTACAATAAATTAAT
* *
24553263 AAAACT--AA--A-AATGAAA-T-CT
1 AAAAATAAAATTACAAT-AAATTAAT
24553282 AAAAATAAAATTACAATAAATTAAT
1 AAAAATAAAATTACAATAAATTAAT
*
24553307 AAAACTAAAA
1 AAAAATAAAA
24553317 ATGAAATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
19 6 0.15
20 4 0.10
21 6 0.15
23 6 0.15
24 4 0.10
25 15 0.37
ACGTcount: A:0.68, C:0.06, G:0.01, T:0.24
Consensus pattern (25 bp):
AAAAATAAAATTACAATAAATTAAT
Found at i:24553285 original size:13 final size:13
Alignment explanation
Indices: 24553260--24553292 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
24553250 ACAATAAATT
24553260 AATAAAA-CTAAA
1 AATAAAATCTAAA
*
24553272 AATGAAATCTAAA
1 AATAAAATCTAAA
24553285 AATAAAAT
1 AATAAAAT
24553293 TACAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (13 bp):
AATAAAATCTAAA
Found at i:24553287 original size:44 final size:44
Alignment explanation
Indices: 24553238--24553327 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
24553228 CAGTTGCACA
24553238 AAAAATAAAATTACAATAAATTAATAAAACTAAAAATGAAATCT
1 AAAAATAAAATTACAATAAATTAATAAAACTAAAAATGAAATCT
24553282 AAAAATAAAATTACAATAAATTAATAAAACTAAAAATGAAATCT
1 AAAAATAAAATTACAATAAATTAATAAAACTAAAAATGAAATCT
24553326 AA
1 AA
24553328 CTTATTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (44 bp):
AAAAATAAAATTACAATAAATTAATAAAACTAAAAATGAAATCT
Found at i:24553833 original size:32 final size:31
Alignment explanation
Indices: 24553797--24553859 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
24553787 TGGAGGGCTA
*
24553797 AATTAGCCATATATGCCACTGTTTTTTTTTTT
1 AATTAGCCATATAAGCCACT-TTTTTTTTTTT
* * *
24553829 AATTAGGCTTATAAGCCTCTTTTTTTTTTTT
1 AATTAGCCATATAAGCCACTTTTTTTTTTTT
24553860 GAAAATTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.56
Consensus pattern (31 bp):
AATTAGCCATATAAGCCACTTTTTTTTTTTT
Found at i:24554332 original size:20 final size:20
Alignment explanation
Indices: 24554285--24554334 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
24554275 TAATTTTCGT
**
24554285 TATTTTTTATTAAGTTAAATT
1 TATTTTTT-TTAAGTTAAAAA
* *
24554306 TAATTTTTTTAATTTAAAAA
1 TATTTTTTTTAAGTTAAAAA
24554326 TATTTTTTT
1 TATTTTTTT
24554335 GTCGTTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTTTTTTAAGTTAAAAA
Found at i:24567794 original size:29 final size:31
Alignment explanation
Indices: 24567747--24567808 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
24567737 TTGATTTAAT
** *
24567747 GTGCAATTATTTACATG-AACTTTAATT-TG
1 GTGCAATTATACACATGAAACTCTAATTGTG
*
24567776 GTGCAATTATACACGTGAAACTCTAATTGTG
1 GTGCAATTATACACATGAAACTCTAATTGTG
24567807 GT
1 GT
24567809 TTAAATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.52
30 9 0.33
31 4 0.15
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.39
Consensus pattern (31 bp):
GTGCAATTATACACATGAAACTCTAATTGTG
Found at i:24569689 original size:26 final size:26
Alignment explanation
Indices: 24569659--24569708 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
24569649 AATGCCCCAT
24569659 AATTCTGCGTCAAAAACTGAACAAAC
1 AATTCTGCGTCAAAAACTGAACAAAC
24569685 AATTCTGCGTCAAAAACTGAACAA
1 AATTCTGCGTCAAAAACTGAACAA
24569709 CTTCACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.20
Consensus pattern (26 bp):
AATTCTGCGTCAAAAACTGAACAAAC
Found at i:24572867 original size:1 final size:1
Alignment explanation
Indices: 24572861--24572921 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
24572851 ACTTTGTACC
* * * * * * *
24572861 AAAAAAAAAAAAAAGAAAAAAGAAAAAAAAGAAAAGAAAAAAAGAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24572922 CAGTAGACAT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:24572881 original size:14 final size:14
Alignment explanation
Indices: 24572861--24572921 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
24572851 ACTTTGTACC
24572861 AAAAAAAA-AAAAA
1 AAAAAAAAGAAAAA
*
24572874 AGAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
*
24572888 AAAGAAAAGAAAAA
1 AAAAAAAAGAAAAA
*
24572902 AAGAAAAAGAAAAA
1 AAAAAAAAGAAAAA
24572916 GAAAAA
1 -AAAAA
24572922 CAGTAGACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
13 7 0.17
14 29 0.73
15 4 0.10
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:24573279 original size:56 final size:55
Alignment explanation
Indices: 24573125--24573281 Score: 215
Period size: 56 Copynumber: 2.8 Consensus size: 55
24573115 GTAAAAGTGT
* * * *
24573125 TAGGATATAATTATGAGATATTATCTTTTAGCAATTTGATTCCTAATGGGATGTTA
1 TAGGATATTATTATGAGATATTATC-TTTAGCAATTTGATTCTTAATGAGATATTA
*
24573181 TAAGATATTATTATGAGATATTATCTCTTAGCAATTTGATTCTTAATGAGATATTA
1 TAGGATATTATTATGAGATATTATCT-TTAGCAATTTGATTCTTAATGAGATATTA
* * *
24573237 TAGGATATTATGATGGGATATTATCTTTAAACAATTTGATTCTTA
1 TAGGATATTATTATGAGATATTATCTTT-AGCAATTTGATTCTTA
24573282 TGTAACTTTA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
55 3 0.03
56 87 0.97
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (55 bp):
TAGGATATTATTATGAGATATTATCTTTAGCAATTTGATTCTTAATGAGATATTA
Found at i:24579091 original size:17 final size:16
Alignment explanation
Indices: 24579054--24579101 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
24579044 CGCACTTTTT
*
24579054 TTTTTGTGAGCTTACA
1 TTTTTGTGAGCTTGCA
*
24579070 GTTTTGTAGAGCTTGCA
1 TTTTTGT-GAGCTTGCA
24579087 TTTTTGGTGAGCTTG
1 TTTTT-GTGAGCTTG
24579102 TGGTTTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 6 0.22
17 19 0.70
18 2 0.07
ACGTcount: A:0.15, C:0.10, G:0.27, T:0.48
Consensus pattern (16 bp):
TTTTTGTGAGCTTGCA
Found at i:24582741 original size:20 final size:20
Alignment explanation
Indices: 24582677--24582743 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 20
24582667 TAAGGGAAAA
*
24582677 GTACAAGTACAACTAGAGAT
1 GTACAAGTACATCTAGAGAT
*
24582697 GTA-AATGTACATATTAGGGGAGAT
1 GTACAA-GTACAT-CTA---GAGAT
24582721 GTACAAGTACATCTAGAGAT
1 GTACAAGTACATCTAGAGAT
24582741 GTA
1 GTA
24582744 TAGATAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
19 2 0.05
20 16 0.42
21 2 0.05
23 2 0.05
24 14 0.37
25 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.25
Consensus pattern (20 bp):
GTACAAGTACATCTAGAGAT
Found at i:24587561 original size:27 final size:27
Alignment explanation
Indices: 24587491--24587561 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
24587481 TTAACGCACA
*
24587491 ATAAAA-TGAAAGCCCTTGTGGCAATCT
1 ATAAAATTG-AAGCCTTTGTGGCAATCT
* * * *
24587518 ATGAAATGGATGTCTTTGTGGCAATCT
1 ATAAAATTGAAGCCTTTGTGGCAATCT
24587545 ATAAAATTGAAGCCTTT
1 ATAAAATTGAAGCCTTT
24587562 TTGGTGTATC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (27 bp):
ATAAAATTGAAGCCTTTGTGGCAATCT
Found at i:24587582 original size:26 final size:26
Alignment explanation
Indices: 24587553--24587613 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
24587543 CTATAAAATT
* * *
24587553 GAAGCCTTTTTGGTGTATCTGAAAGG
1 GAAGCCTTTGTGGCGTATCCGAAAGG
*
24587579 GAAGCCTTTGTGGCGTATCCGAAATG
1 GAAGCCTTTGTGGCGTATCCGAAAGG
24587605 GAAGCCTTT
1 GAAGCCTTT
24587614 ATGGAAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (26 bp):
GAAGCCTTTGTGGCGTATCCGAAAGG
Found at i:24590570 original size:19 final size:19
Alignment explanation
Indices: 24590546--24590618 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
24590536 AATCTTCAAG
*
24590546 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
*
24590565 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
24590584 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24590603 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
24590619 AGATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:24590597 original size:38 final size:39
Alignment explanation
Indices: 24590546--24590641 Score: 122
Period size: 38 Copynumber: 2.4 Consensus size: 39
24590536 AATCTTCAAG
* * *
24590546 GATATGCAGTCTTAGATATGATATGTAATCTT-AGATAT
1 GATATGTAATCTTAGATATGATATGCAATCTTAAGATAT
24590584 GATATGTAATCTTAGATATGATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAGATATGATATGCAATCTT--AAGATAT
*
24590625 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
24590642 GATTTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 29 0.58
41 8 0.16
42 13 0.26
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (39 bp):
GATATGTAATCTTAGATATGATATGCAATCTTAAGATAT
Found at i:24590869 original size:23 final size:23
Alignment explanation
Indices: 24590825--24590869 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
24590815 TCTTATTTTG
* *
24590825 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
24590848 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
24590870 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:24591065 original size:23 final size:22
Alignment explanation
Indices: 24591018--24591066 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
24591008 ATTTGTTATT
* *
24591018 TTATTTTTTATTATTAAATTAA
1 TTATTTTATATTATTAAAGTAA
24591040 TTATTTTAATATTATTAATAGT-A
1 TTATTTT-ATATTATTAA-AGTAA
24591063 TTAT
1 TTAT
24591067 GTGGCATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 14 0.61
24 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTTTATATTATTAAAGTAA
Found at i:24591128 original size:17 final size:19
Alignment explanation
Indices: 24591089--24591125 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
24591079 ATCTTGTATC
24591089 ATTATTATTATTTATTATTT
1 ATTATTATTATTTATTA-TT
24591109 ATTATTATTATTT-TTAT
1 ATTATTATTATTTATTAT
24591126 ATTCATGCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 3 0.18
20 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTATTATTATTTATTATT
Found at i:24592220 original size:25 final size:26
Alignment explanation
Indices: 24592192--24592240 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
24592182 AGAGTCTTAA
* *
24592192 TAAGTAACAT-TTTTTAAGTTTTTAT
1 TAAGGAACATATTTTTAAATTTTTAT
*
24592217 TAAGGATCATATTTTTAAATTTTT
1 TAAGGAACATATTTTTAAATTTTT
24592241 GACATTAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (26 bp):
TAAGGAACATATTTTTAAATTTTTAT
Found at i:24598059 original size:14 final size:15
Alignment explanation
Indices: 24598033--24598065 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
24598023 TCCCAAGCTG
24598033 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
24598048 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
24598062 GGAA
1 GGAA
24598066 AAGCGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:24599796 original size:44 final size:44
Alignment explanation
Indices: 24599396--24599803 Score: 162
Period size: 44 Copynumber: 9.3 Consensus size: 44
24599386 GATAACACAT
* * * * *
24599396 CTTGCCTACCTGCACCGAAAGTGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATACCAGC
**** * * * * * * **
24599440 CTTGCCTCCCTGGGTTG-TAGCGGAGCAGGTTAAAAATAGCAAAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATA-CCAGC
* * *
24599484 CTTGCCTTCCTGCACCGACAGCGAAACAGATCGAAGATACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATACCAGC
**** ** * * * * *
24599528 CTTGCCTCCCTGGGTTG-CAATGGAGCAGGTTAAAAATTA-CAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGA-TACCAG-C
* *
24599572 CTTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATACCAGC
**** * * * * * * *
24599616 CTTGCCTCCCTGGGTTG-TAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATACCAG-C
* * * * *
24599660 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAAC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATACCAGC
**** * * * * * *
24599704 CTTGCCTCCCTGGGTTG-TAGC-AGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGA-AGCAGATTGAAGATACCAG-C
* * *
24599748 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATACCAGC
24599792 CTTGCCTCCCTG
1 CTTGCCTCCCTG
24599804 GGTTACAGCA
Statistics
Matches: 240, Mismatches: 112, Indels: 24
0.64 0.30 0.06
Matches are distributed among these distances:
42 1 0.00
43 61 0.25
44 114 0.47
45 63 0.26
46 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (44 bp):
CTTGCCTCCCTGCACCGACAGCGAAGCAGATTGAAGATACCAGC
Found at i:24599840 original size:44 final size:43
Alignment explanation
Indices: 24599616--24599847 Score: 126
Period size: 44 Copynumber: 5.3 Consensus size: 43
24599606 AGACACCAGC
*
24599616 CTTGCCTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTATAGC-GAGCAGGTTAAAAATAGCAGAT
* **** * ** * * * *
24599660 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCA-AC
1 CTTGCCTCCCTG-GGTTATAGCG-AGCAGGTTAAAAATAGCAGAT
*
24599704 CTTGCCTCCCTGGGTTGTAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTATAGC-GAGCAGGTTAAAAATAGCAGAT
* **** * * ** * * * *
24599748 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTG-GGTTATAGCG-AGCAGGTTAAAAATAGCAGAT
*
24599792 CTTGCCTCCCTGGGTTACAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTATAGC-GAGCAGGTTAAAAATAGCAGAT
*
24599836 CTTGCCTTCCTG
1 CTTGCCTCCCTG
24599848 CACCGATAGC
Statistics
Matches: 127, Mismatches: 53, Indels: 16
0.65 0.27 0.08
Matches are distributed among these distances:
43 34 0.27
44 61 0.48
45 32 0.25
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.22
Consensus pattern (43 bp):
CTTGCCTCCCTGGGTTATAGCGAGCAGGTTAAAAATAGCAGAT
Found at i:24599890 original size:88 final size:88
Alignment explanation
Indices: 24599394--24599880 Score: 787
Period size: 88 Copynumber: 5.5 Consensus size: 88
24599384 AAGATAACAC
* * *
24599394 ATCTTGCCTACCTGCACCGAAAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
*
24599459 GCGGAGCAGGTTAAAAATAGCAA
66 GCGGAGCAGGTTAAAAATAGCAG
* * *
24599482 ATCTTGCCTTCCTGCACCGACAGCGAAACAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
**
24599547 ATGGAGCAGGTTAAAAATTA-CAG
66 GCGGAGCAGGTTAAAAA-TAGCAG
*
24599570 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
24599635 GCGGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* *
24599658 ATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
*
24599723 GCAGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
**
24599746 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTACA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
*
24599811 GCAGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* * *
24599834 ATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGATGACCCCAGCC
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
24599881 CTATCTCCCT
Statistics
Matches: 371, Mismatches: 26, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
87 2 0.01
88 367 0.99
89 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTA
GCGGAGCAGGTTAAAAATAGCAG
Found at i:24599976 original size:44 final size:43
Alignment explanation
Indices: 24599880--24600001 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 43
24599870 TGACCCCAGC
*
24599880 CCTATCTCCCTTGGCAGCAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCC-TAGCAGCAGTGGAATAGGTTGAAGATTGTAAGT
** *
24599924 ATTCTCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-T
1 CCTATCTCCCTAG-CAGCAGTGGAATAGGTTGAAGATTGT-AAGT
* *
24599968 CCTATCTCCCTGAGCAACAGTGGAGTAGGTTGAA
1 CCTATCTCCCT-AGCAGCAGTGGAATAGGTTGAA
24600002 AATAGCAGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
43 2 0.03
44 60 0.91
45 4 0.06
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
CCTATCTCCCTAGCAGCAGTGGAATAGGTTGAAGATTGTAAGT
Found at i:24600510 original size:84 final size:84
Alignment explanation
Indices: 24600410--24600693 Score: 272
Period size: 84 Copynumber: 3.3 Consensus size: 84
24600400 AAGCGAATAA
* *
24600410 TCTTATCTCCCTGAAGTCGCAGTGGAGTGGATTAAAATCACACATCTTATCTCTCTAAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACACATCTTATCTCTCTGAAGTTGTA
*
24600475 GAGAGCAGATCGTATCTAG
66 GAGAGCAGATCGCATCTAG
* * ** * *
24600494 TCTTATCTCTCTGAAGTTGTAGTGGAGCAGACTAAGTAAGCA-AGC--CTTATC-CTCCTGAAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAA--AATCACA-CATCTTATCTCT-CTGAAGT
* * * *
24600555 TGTAGTGAGGCAGA-CTGAAGATTGTGAA
62 TGTAGAGA-GCAGATC-G--CA-TCT-AG
* * * * *
24600583 TATTATCTCCCTGAAGTTGCAGTGGAGTGGATTCAAATCACAGATCTTATCTTTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACACATCTTATCTCTCTGAAGTTGTA
*
24600648 GAGAGCAGATCGCATCTGG
66 GAGAGCAGATCGCATCTAG
24600667 TCTTATCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
24600694 CAGACCCAAG
Statistics
Matches: 156, Mismatches: 29, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
83 2 0.01
84 75 0.48
85 9 0.06
86 6 0.04
87 5 0.03
88 9 0.06
89 49 0.31
90 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACACATCTTATCTCTCTGAAGTTGTA
GAGAGCAGATCGCATCTAG
Found at i:24600789 original size:45 final size:45
Alignment explanation
Indices: 24600492--24600781 Score: 192
Period size: 45 Copynumber: 6.6 Consensus size: 45
24600482 GATCGTATCT
* * *
24600492 AGTCTTATCTCTCTGAAGTTGTAGTGGAGCAGACT-AAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * ** *
24600536 AGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATTGTGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGAAAG-CA
* ** * *
24600582 A-TATTATCTCCCTGAAGTTGCAGTGGAGTGGATTC---AAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
** * * * *
24600623 CAGATCTTATCTTTCTGAAGTTGCAG-AGAGCAGA-TC--G-CATCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * *
24600665 GGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * *
24600710 AGTCTTATCTCCCTTAAGTTGCAGTGGACCAGACTCAAGAAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
*
24600755 AGTCTTATC-CCTCTGAAATTGCAGTGG
1 AGTCTTATCTCC-CTGAAGTTGCAGTGG
24600782 GGTAGACTAA
Statistics
Matches: 189, Mismatches: 41, Indels: 31
0.72 0.16 0.12
Matches are distributed among these distances:
40 20 0.11
41 9 0.05
42 8 0.04
43 8 0.04
44 50 0.26
45 89 0.47
46 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
Found at i:24601363 original size:19 final size:19
Alignment explanation
Indices: 24601339--24601392 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
24601329 AATCTTCAAG
* *
24601339 GATATGCAGTCTTAGTTAT
1 GATATGCAATCTTAGATAT
*
24601358 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
24601377 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
24601393 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:24601418 original size:22 final size:22
Alignment explanation
Indices: 24601355--24601415 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 22
24601345 CAGTCTTAGT
*
24601355 TATGATATGTAATCTT---AGA
1 TATGATATGAAATCTTAGAAGA
*
24601374 TATGATATGCAATCTTAGAAGA
1 TATGATATGAAATCTTAGAAGA
*
24601396 TATGATTGTGAAATCTTAGA
1 TATGA-TATGAAATCTTAGA
24601416 GATTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (22 bp):
TATGATATGAAATCTTAGAAGA
Found at i:24601643 original size:23 final size:23
Alignment explanation
Indices: 24601599--24601643 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
24601589 TTTTATCTTG
* *
24601599 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
24601622 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
24601644 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:24601850 original size:23 final size:23
Alignment explanation
Indices: 24601805--24601851 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
24601795 TTATTTTAGT
* *
24601805 TTTTATTATTATTAAAGTAATTA
1 TTTTAATATTATTAAACTAATTA
24601828 TTTTAATATTATTAATACT-ATTA
1 TTTTAATATTATTAA-ACTAATTA
24601851 T
1 T
24601852 GTGGCATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATATTATTAAACTAATTA
Found at i:24602000 original size:25 final size:24
Alignment explanation
Indices: 24601947--24601997 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
24601937 TAATATATAT
*
24601947 TGTTTTATATATA--ATATACATA
1 TGTTTTATATATATTTTATACATA
*
24601969 TG-CTTATATATATTTTATACATA
1 TGTTTTATATATATTTTATACATA
24601992 TGTTTT
1 TGTTTT
24601998 TATTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 9 0.39
22 2 0.09
23 10 0.43
24 2 0.09
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TGTTTTATATATATTTTATACATA
Found at i:24604174 original size:7 final size:7
Alignment explanation
Indices: 24604164--24604243 Score: 142
Period size: 7 Copynumber: 11.4 Consensus size: 7
24604154 TTAAAGGTTA
*
24604164 AAAGATG
1 AAAGAAG
*
24604171 AAAGATG
1 AAAGAAG
24604178 AAAGAAG
1 AAAGAAG
24604185 AAAGAAG
1 AAAGAAG
24604192 AAAGAAG
1 AAAGAAG
24604199 AAAGAAG
1 AAAGAAG
24604206 AAAGAAG
1 AAAGAAG
24604213 AAAGAAG
1 AAAGAAG
24604220 AAAGAAG
1 AAAGAAG
24604227 AAAGAAG
1 AAAGAAG
24604234 AAAGAAG
1 AAAGAAG
24604241 AAA
1 AAA
24604244 AGAGTTATAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 72 1.00
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (7 bp):
AAAGAAG
Found at i:24604848 original size:112 final size:112
Alignment explanation
Indices: 24604695--24604920 Score: 434
Period size: 112 Copynumber: 2.0 Consensus size: 112
24604685 CAACTAATGC
24604695 TCTTGGTGTGTAAAAGTAGGTGCGTAGCAGGTATTGGATTATTATAAGGAATTGTCATAGAAAGG
1 TCTTGGTGTGTAAAAGTAGGTGCGTAGCAGGTATTGGATTATTATAAGGAATTGTCATAGAAAGG
24604760 ATGAATTGTTAAGGAAATGAGCTTGCTAATGTAGTATGAAAAAGTAA
66 ATGAATTGTTAAGGAAATGAGCTTGCTAATGTAGTATGAAAAAGTAA
24604807 TCTTGGTGTGTAAAAGTAGGTGCGTAGCAGGTATTGGATTATTATAAGGAATTGTCATAGAAAGG
1 TCTTGGTGTGTAAAAGTAGGTGCGTAGCAGGTATTGGATTATTATAAGGAATTGTCATAGAAAGG
* *
24604872 ATGAATTGTTAAGGAAATGAGCTTGGTAATGTATTATGAAAAAGTAA
66 ATGAATTGTTAAGGAAATGAGCTTGCTAATGTAGTATGAAAAAGTAA
24604919 TC
1 TC
24604921 GGGTTAACGC
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (112 bp):
TCTTGGTGTGTAAAAGTAGGTGCGTAGCAGGTATTGGATTATTATAAGGAATTGTCATAGAAAGG
ATGAATTGTTAAGGAAATGAGCTTGCTAATGTAGTATGAAAAAGTAA
Found at i:24605698 original size:27 final size:28
Alignment explanation
Indices: 24605667--24605771 Score: 139
Period size: 27 Copynumber: 3.9 Consensus size: 28
24605657 ACACACCAAA
*
24605667 AAATGGAAGCCCTTGTGGC-TATCTATG
1 AAATGGAAGCCTTTGTGGCATATCTATG
*
24605694 AAATGGATA-TCTTTGTGGCA-ATCTATG
1 AAATGGA-AGCCTTTGTGGCATATCTATG
*
24605721 AAATGAAAGCCTTTGTGGCATATC--TG
1 AAATGGAAGCCTTTGTGGCATATCTATG
24605747 AAATGGAAGCCTTTGTGGCATATCT
1 AAATGGAAGCCTTTGTGGCATATCT
24605772 GAAATGAAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
26 26 0.38
27 38 0.56
28 4 0.06
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (28 bp):
AAATGGAAGCCTTTGTGGCATATCTATG
Found at i:24605793 original size:26 final size:26
Alignment explanation
Indices: 24605704--24605782 Score: 124
Period size: 26 Copynumber: 3.0 Consensus size: 26
24605694 AAATGGATAT
24605704 CTTTGTGGCA-ATCTATGAAATGAAAGC
1 CTTTGTGGCATATC--TGAAATGAAAGC
*
24605731 CTTTGTGGCATATCTGAAATGGAAGC
1 CTTTGTGGCATATCTGAAATGAAAGC
24605757 CTTTGTGGCATATCTGAAATGAAAGC
1 CTTTGTGGCATATCTGAAATGAAAGC
24605783 TTTCATGGCA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
26 36 0.73
27 10 0.20
28 3 0.06
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (26 bp):
CTTTGTGGCATATCTGAAATGAAAGC
Found at i:24608323 original size:8 final size:8
Alignment explanation
Indices: 24608310--24608345 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
24608300 TCCAAGGTTG
24608310 TTTTATAA
1 TTTTATAA
24608318 TTTTATAA
1 TTTTATAA
*
24608326 TTTTGTAA
1 TTTTATAA
*
24608334 TTTTGTAA
1 TTTTATAA
24608342 TTTT
1 TTTT
24608346 TTCATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (8 bp):
TTTTATAA
Found at i:24611295 original size:12 final size:12
Alignment explanation
Indices: 24611278--24611302 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24611268 AATGTTACAC
24611278 GGCCTGGCACAT
1 GGCCTGGCACAT
24611290 GGCCTGGCACAT
1 GGCCTGGCACAT
24611302 G
1 G
24611303 AGCGTGTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (12 bp):
GGCCTGGCACAT
Found at i:24620140 original size:19 final size:21
Alignment explanation
Indices: 24620104--24620142 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
24620094 TTAAATTAAC
24620104 AACTAATATGCAAATGAAATA
1 AACTAATATGCAAATGAAATA
24620125 AACTAA-ATGC-AATGAAAT
1 AACTAATATGCAAATGAAAT
24620143 TGTTTATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
AACTAATATGCAAATGAAATA
Found at i:24631573 original size:322 final size:322
Alignment explanation
Indices: 24630988--24631636 Score: 1262
Period size: 322 Copynumber: 2.0 Consensus size: 322
24630978 TGTCTTAAGC
24630988 ATTGGTGCGGATGACTCCCAAAAGATAGAGACATAGATAAGACTGACGGACTAATAGTACAATGG
1 ATTGGTGCGGATGACTCCCAAAAGATAGAGACATAGATAAGACTGACGGACTAATAGTACAATGG
24631053 ATAGGACCTAAGCAGAATAGATCCTAAATTTTTTTATGGACTTATTCACTTGTGATGTTCATAGT
66 ATAGGACCTAAGCAGAATAGATCCTAAATTTTTTTATGGACTTATTCACTTGTGATGTTCATAGT
24631118 GTGACATACTTAAATCTAGGTGGATGGGGGACCATGTATCGTGACTCAAACAATTTAATTTAAGT
131 GTGACATACTTAAATCTAGGTGGATGGGGGACCATGTATCGTGACTCAAACAATTTAATTTAAGT
24631183 AAAAGCCTGAGTTCTAATAGATAAGGAACCGAAAACTATTGCATTGGGTGTACGACTTCTACAGT
196 AAAAGCCTGAGTTCTAATAGATAAGGAACCGAAAACTATTGCATTGGGTGTACGACTTCTACAGT
*
24631248 ACATAGCTTTATTCATGATACAGGAATCCATAGCATGAGACATGGATAAATGATATCCTCTT
261 ACATAGCTTTATTCATGATACAGAAATCCATAGCATGAGACATGGATAAATGATATCCTCTT
*
24631310 ATTGGTGCGGATGACTCCCAAAAGATAGAGACATAGATAAGACTGACGGACTAATAGTATAATGG
1 ATTGGTGCGGATGACTCCCAAAAGATAGAGACATAGATAAGACTGACGGACTAATAGTACAATGG
24631375 ATAGGACCTAAGCAGAATAGATCCTAAATTTTTTTATGGACTTATTCACTTGTGATGTTCATAGT
66 ATAGGACCTAAGCAGAATAGATCCTAAATTTTTTTATGGACTTATTCACTTGTGATGTTCATAGT
*
24631440 GTGACATACTTAAATCTAGGTGGATGGGGGACCATGTATCGTGACTCATACAATTTAATTTAAGT
131 GTGACATACTTAAATCTAGGTGGATGGGGGACCATGTATCGTGACTCAAACAATTTAATTTAAGT
24631505 AAAAGCCTGAGTTCTAATAGATAAGGAACCGAAAACTATTGCATTGGGTGTACGACTTCTACAGT
196 AAAAGCCTGAGTTCTAATAGATAAGGAACCGAAAACTATTGCATTGGGTGTACGACTTCTACAGT
*
24631570 ACATAGCTTTATTCATGATACCGAAATCCATAGCATGAGACATGGATAAATGATATCCTCTT
261 ACATAGCTTTATTCATGATACAGAAATCCATAGCATGAGACATGGATAAATGATATCCTCTT
24631632 ATTGG
1 ATTGG
24631637 CATTATATGG
Statistics
Matches: 323, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
322 323 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (322 bp):
ATTGGTGCGGATGACTCCCAAAAGATAGAGACATAGATAAGACTGACGGACTAATAGTACAATGG
ATAGGACCTAAGCAGAATAGATCCTAAATTTTTTTATGGACTTATTCACTTGTGATGTTCATAGT
GTGACATACTTAAATCTAGGTGGATGGGGGACCATGTATCGTGACTCAAACAATTTAATTTAAGT
AAAAGCCTGAGTTCTAATAGATAAGGAACCGAAAACTATTGCATTGGGTGTACGACTTCTACAGT
ACATAGCTTTATTCATGATACAGAAATCCATAGCATGAGACATGGATAAATGATATCCTCTT
Found at i:24645658 original size:74 final size:74
Alignment explanation
Indices: 24645574--24645715 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
24645564 GGGTTGCTAA
* * * * *
24645574 GTGCTGATTCCCCAAATTATTGATTCTAAAGGTGGTTGCTAAGTGCTGATTCCACTGTATATTTG
1 GTGCTGATTCCCCAAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTG
24645639 ATTTGCTGT
66 ATTTGCTGT
** *
24645648 GTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATATTTG
1 GTGCTGATTCCCCAAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTG
24645713 ATT
66 ATT
24645716 GTGAAAGGGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (74 bp):
GTGCTGATTCCCCAAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTG
ATTTGCTGT
Found at i:24648228 original size:26 final size:24
Alignment explanation
Indices: 24648183--24648236 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
24648173 TAGTTTATTA
24648183 ATATTTTAATTTGATTTTTA-AAT
1 ATATTTTAATTTGATTTTTAGAAT
24648206 GATATTTTATTATTT-ATTATTTAGAAT
1 -ATATTTTA--ATTTGATT-TTTAGAAT
24648233 ATAT
1 ATAT
24648237 AAGTGGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
24 8 0.31
25 3 0.12
26 12 0.46
27 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (24 bp):
ATATTTTAATTTGATTTTTAGAAT
Found at i:24654629 original size:25 final size:25
Alignment explanation
Indices: 24654546--24654640 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
24654536 GCGAATACTC
24654546 CACAGCTCGTGAGAGCATACCGATT
1 CACAGCTCGTGAGAGCATACCGATT
* * * **
24654571 TATAGCACGTGAGAGCATATTGA-T
1 CACAGCTCGTGAGAGCATACCGATT
* * *
24654595 CTACAACTCGAGTGAGCATACCGATT
1 C-ACAGCTCGTGAGAGCATACCGATT
*
24654621 CACAGCTCGTGTGAGCATAC
1 CACAGCTCGTGAGAGCATAC
24654641 ATGTATATGA
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
24 1 0.02
25 50 0.94
26 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (25 bp):
CACAGCTCGTGAGAGCATACCGATT
Found at i:24666388 original size:17 final size:17
Alignment explanation
Indices: 24666366--24666399 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24666356 TGGATTCCTT
24666366 GCTTTGACACAATCCAC
1 GCTTTGACACAATCCAC
24666383 GCTTTGACACAATCCAC
1 GCTTTGACACAATCCAC
24666400 TTAGAACCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.24
Consensus pattern (17 bp):
GCTTTGACACAATCCAC
Found at i:24680020 original size:29 final size:29
Alignment explanation
Indices: 24679976--24680161 Score: 169
Period size: 29 Copynumber: 6.4 Consensus size: 29
24679966 CCCTCAGATA
*
24679976 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
* * * *
24680005 ATAAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
* * * * *
24680034 ATGAAAATGGATAG-TGACGACCATCAAAC
1 ATGAAAAGGGATAGCT-TCGGCTATCAAAT
* * * * *
24680063 ATGAAAAGGGGT-GGTAACGACCATCAAAT
1 ATGAAAAGGGATAGCT-TCGGCTATCAAAT
24680092 ATGAAAAGGGATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
* * * *
24680121 GTGAAAAGGGATAGCTTCAGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
24680150 ATGAAAAGGGAT
1 ATGAAAAGGGAT
24680162 GGTGACGAAC
Statistics
Matches: 128, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
28 2 0.02
29 124 0.97
30 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAAT
Found at i:24680178 original size:29 final size:29
Alignment explanation
Indices: 24679976--24680248 Score: 144
Period size: 29 Copynumber: 9.4 Consensus size: 29
24679966 CCCTCAGATA
* * *
24679976 ATGAAAAGGGATAGCTTCG-GCTATCGAAT
1 ATGAAAAGGGATGGTTTCGAAC-ATCGAAT
* * * *
24680005 ATAAAAAGGGATAGCTTT-G-GCTATCGATT
1 ATGAAAAGGGAT-GGTTTCGAAC-ATCGAAT
* * ** * * *
24680034 ATGAAAATGGATAGTGACGACCATCAAAC
1 ATGAAAAGGGATGGTTTCGAACATCGAAT
* ** * *
24680063 ATGAAAAGGGGTGGTAACGACCATCAAAT
1 ATGAAAAGGGATGGTTTCGAACATCGAAT
* * * *
24680092 ATGAAAAGGGATAGCTTCG-GCTATCAAAT
1 ATGAAAAGGGATGGTTTCGAAC-ATCGAAT
* * * * *
24680121 GTGAAAAGGGATAGCTTC-AGCTATCGATT
1 ATGAAAAGGGATGGTTTCGAAC-ATCGAAT
** * *
24680150 ATGAAAAGGGATGGTGACGAACATTGATT
1 ATGAAAAGGGATGGTTTCGAACATCGAAT
24680179 AATGAAAAGGGATGGTTTC-AACCATCGAAT
1 -ATGAAAAGGGATGGTTTCGAA-CATCGAAT
*
24680209 ATGAAAAGGGATGGTTTCGACCATCGAAT
1 ATGAAAAGGGATGGTTTCGAACATCGAAT
24680238 ATGAAAAGGGA
1 ATGAAAAGGGA
24680249 AGATTACAAA
Statistics
Matches: 194, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
28 2 0.01
29 164 0.85
30 28 0.14
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATGGTTTCGAACATCGAAT
Found at i:24680263 original size:29 final size:29
Alignment explanation
Indices: 24680143--24680263 Score: 80
Period size: 29 Copynumber: 4.1 Consensus size: 29
24680133 AGCTTCAGCT
* * * * *
24680143 ATCGATTATGAAAAGGGATGGTGACGAAC
1 ATCGAATATGAAAAGGGAAGATTACAAAC
* * * * * *
24680172 ATTGATTAATGAAAAGGGATGGTTTCAACC
1 ATCGAAT-ATGAAAAGGGAAGATTACAAAC
* * * * *
24680202 ATCGAATATGAAAAGGGATGGTTTCGACC
1 ATCGAATATGAAAAGGGAAGATTACAAAC
*
24680231 ATCGAATATGAAAAGGGAAGATTACAAAT
1 ATCGAATATGAAAAGGGAAGATTACAAAC
24680260 ATCG
1 ATCG
24680264 TTTGGCACAC
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 54 0.70
30 23 0.30
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.24
Consensus pattern (29 bp):
ATCGAATATGAAAAGGGAAGATTACAAAC
Found at i:24680263 original size:117 final size:116
Alignment explanation
Indices: 24679962--24680263 Score: 284
Period size: 116 Copynumber: 2.6 Consensus size: 116
24679952 CGACGTATCG
* * * * * * * ****
24679962 ACAACCCTCAGATAATGAAAAGGGATAGCTTCGGCTATCGAATATAAAAAGGGATAGCTTTGGCT
1 ACAACCATCAAAT-ATGAAAAGGGATAGCTTCGACCATCAAATATGAAAAGGGATAGATTCAAAT
* * *
24680027 ATCGATTATGAAAATGGATAGTGACGACCATCAAACATGAAAAGGGGTGGTA
65 ATCGATTATGAAAAGGGATAGTGACGAACATCAAACATGAAAAGGGATGGTA
* * * * * **
24680079 ACGACCATCAAATATGAAAAGGGATAGCTTCGGCTATCAAATGTGAAAAGGGATAGCTTCAGCTA
1 ACAACCATCAAATATGAAAAGGGATAGCTTCGACCATCAAATATGAAAAGGGATAGATTCAAATA
* * * *
24680144 TCGATTATGAAAAGGGATGGTGACGAACATTGATTA-ATGAAAAGGGATGGTT
66 TCGATTATGAAAAGGGATAGTGACGAACA-TCA-AACATGAAAAGGGATGGTA
* * * * *
24680196 TCAACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGA-AGATTACAAAT
1 ACAACCATCAAATATGAAAAGGGATAGCTTCGACCATCAAATATGAAAAGGGATAGATT-CAAAT
24680260 ATCG
65 ATCG
24680264 TTTGGCACAC
Statistics
Matches: 155, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
116 77 0.50
117 77 0.50
118 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (116 bp):
ACAACCATCAAATATGAAAAGGGATAGCTTCGACCATCAAATATGAAAAGGGATAGATTCAAATA
TCGATTATGAAAAGGGATAGTGACGAACATCAAACATGAAAAGGGATGGTA
Found at i:24683917 original size:14 final size:14
Alignment explanation
Indices: 24683898--24683934 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
24683888 ATGAAGACAA
*
24683898 GATCTAGTTTCTTC
1 GATCTACTTTCTTC
24683912 GATCTACTTTCTTC
1 GATCTACTTTCTTC
24683926 GATCTACTT
1 GATCTACTT
24683935 CGCCACCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.49
Consensus pattern (14 bp):
GATCTACTTTCTTC
Found at i:24684159 original size:89 final size:87
Alignment explanation
Indices: 24683912--24684540 Score: 566
Period size: 89 Copynumber: 7.1 Consensus size: 87
24683902 TAGTTTCTTC
* * * *** ** *
24683912 GATCTACTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAACTTCAATCTA
1 GATCTGCTTTCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
* *
24683977 CTCCACCACCAGTATGGGGAGACAA
65 CTTC-CCACCAGTATGGGAAGAC-A
*
24684002 GATCTG-TTGTCTTTGATCTACTTCACGCCCTA-TACATGAAGACAAGATCTGCTTTCTTCGATC
1 GATCTGCTT-TCTTCGATCTACTTCACG-CC-AGTACATGAAGACAAGATCTGCTTTCTTCGATC
24684065 TACTTCGCCACCAGTATGGGAAGACA
63 TACTTC-CCACCAGTATGGGAAGACA
* * *
24684091 GTATCTGCTTTCTTCGATCTACTTTACGCCAATACATGAAGACAAGATCTTCTTTCTTCGATCTA
1 G-ATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
* * * *** *
24684156 CTTCACGCCAATACATGAAGTCAA
65 CTTCCCACCAGTATGGGAAGAC-A
* *** * *
24684180 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTGTCTTTGATCTA
1 GATCTGCTTTCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
* * * ***
24684245 CTTCACGCCAATACATGAAGACAA
65 CTTCCCACCAGTATGGGAAGAC-A
* * *** * *
24684269 GATCTGTTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTA
1 GATCTGCTTTCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
* * ***
24684334 CTTCACGCCAGTACATGAAGACA
65 CTTCCCACCAGTATGGGAAGACA
* *
24684357 GATCTGCTTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCATTT-TTTGATCT
1 GATCTGC-TTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTCTTCGATCT
* *
24684421 ACTTCGCCACTAGTATGGGAAGATAA
64 ACTTC-CCACCAGTATGGGAAGA-CA
* *
24684447 GATCTG-TTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCATTT-TCCGATCT
1 GATCTGCTT-TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTCTTCGATCT
*
24684510 ACTTCGCCACCAATATGGGAAGACAA
64 ACTTC-CCACCAGTATGGGAAGAC-A
24684536 GATCT
1 GATCT
24684541 ACTGCTACTC
Statistics
Matches: 470, Mismatches: 55, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
88 79 0.17
89 292 0.62
90 96 0.20
91 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (87 bp):
GATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTAC
TTCCCACCAGTATGGGAAGACA
Done.