Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 43 of 54
Found at i:17213525 original size:2 final size:2
Alignment explanation
Indices: 17213484--17213515 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17213474 CTATGCAACC
17213484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17213516 TCCATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17214009 original size:14 final size:15
Alignment explanation
Indices: 17213977--17214009 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17213967 CCTCTGAATC
*
17213977 TAAAAACATGAAGTT
1 TAAAAACATGAAGTA
17213992 TAAAAACATG-AGTA
1 TAAAAACATGAAGTA
17214006 TAAA
1 TAAA
17214010 CTCAGTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (15 bp):
TAAAAACATGAAGTA
Found at i:17215012 original size:19 final size:20
Alignment explanation
Indices: 17214985--17215030 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
17214975 AGGAGACAAG
*
17214985 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
17215004 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
17215023 ATAATATT
1 ATAATATT
17215031 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:17215477 original size:20 final size:20
Alignment explanation
Indices: 17215432--17215469 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17215422 TTTTGGCCCC
17215432 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
17215452 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
17215470 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:17215553 original size:27 final size:27
Alignment explanation
Indices: 17215523--17215580 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
17215513 TTGGAGTAAA
*
17215523 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
17215550 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
17215578 AGG
1 AGG
17215581 ACATTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:17216733 original size:13 final size:13
Alignment explanation
Indices: 17216715--17216739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17216705 AGGGAAATTG
17216715 TGATTTTATAAAA
1 TGATTTTATAAAA
17216728 TGATTTTATAAA
1 TGATTTTATAAA
17216740 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17218206 original size:43 final size:43
Alignment explanation
Indices: 17218174--17218255 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
17218164 CACATGGCTG
* * *
17218174 GGTCGTCACCGGTTTATGCGCACACCATACTCGTACATAACCA
1 GGTCATCACCGGCTTATGCGCACACCATACTCGCACATAACCA
* * *
17218217 GGTCATCACCGGCTTATGCGTACTCCCTACTCGCACATA
1 GGTCATCACCGGCTTATGCGCACACCATACTCGCACATA
17218256 GCCGAGTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.24
Consensus pattern (43 bp):
GGTCATCACCGGCTTATGCGCACACCATACTCGCACATAACCA
Found at i:17223040 original size:15 final size:15
Alignment explanation
Indices: 17223000--17223045 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
17222990 TAGTTTTAGT
* * *
17223000 ATTTAACTTTGTTAA
1 ATTTAAATTTTTTTA
17223015 ATTTAAATTTTTTTA
1 ATTTAAATTTTTTTA
*
17223030 ATTTAATTTTTTTTA
1 ATTTAAATTTTTTTA
17223045 A
1 A
17223046 CAAAATTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTTAAATTTTTTTA
Found at i:17224858 original size:13 final size:13
Alignment explanation
Indices: 17224840--17224864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17224830 TTTCAGAAAA
17224840 TTTATAAAATCAT
1 TTTATAAAATCAT
17224853 TTTATAAAATCA
1 TTTATAAAATCA
17224865 CAATTTCCCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17226055 original size:27 final size:28
Alignment explanation
Indices: 17225998--17226055 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17225988 GGAAAAATGT
*
17225998 CCTGGTGGTGGAAAATTACAATTTTGCC
1 CCTGGTGGTGGAAAATTACAATTTTGAC
*
17226026 CCTGG-GGTGGTAAAATTACCATTTT-AC
1 CCTGGTGGTGG-AAAATTACAATTTTGAC
17226053 CCT
1 CCT
17226056 TTTACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTGAC
Found at i:17226131 original size:20 final size:20
Alignment explanation
Indices: 17226108--17226145 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17226098 CCTCAAATCT
17226108 TACTCCAATAAGTAAAATTA
1 TACTCCAATAAGTAAAATTA
*
17226128 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTAAAAT
17226146 GGGGCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTAAAATTA
Found at i:17230789 original size:21 final size:21
Alignment explanation
Indices: 17230763--17230821 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
17230753 TGAAGTTTCG
**
17230763 GCCTTGAGGATCGGCTACCAA
1 GCCTTGAGGATCAACTACCAA
*
17230784 GCCTTGAAGATCAACTACCAA
1 GCCTTGAGGATCAACTACCAA
* *
17230805 GCCATGGGGATCAACTA
1 GCCTTGAGGATCAACTA
17230822 AAGCATCTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.19
Consensus pattern (21 bp):
GCCTTGAGGATCAACTACCAA
Found at i:17245108 original size:13 final size:13
Alignment explanation
Indices: 17245075--17245109 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17245065 TAAACAAAAT
*
17245075 ATGATTTAATAAA
1 ATGATTTTATAAA
17245088 ATGATTTTATAAA
1 ATGATTTTATAAA
*
17245101 ATTATTTTA
1 ATGATTTTA
17245110 AAATTGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:17249499 original size:2 final size:2
Alignment explanation
Indices: 17249492--17249519 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17249482 AAACCAAGTG
17249492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17249520 NTCATGACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17249564 original size:2 final size:2
Alignment explanation
Indices: 17249557--17249586 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17249547 TTTCAAGTAG
17249557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17249587 ACATTCCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17251567 original size:19 final size:20
Alignment explanation
Indices: 17251543--17251603 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
17251533 GGTGGTAAAG
*
17251543 TGAAAATGGCAG-GGGAGCA
1 TGAAAATGGCAGTGAGAGCA
17251562 TGAAAAT-G-ATGTGAGAGCA
1 TGAAAATGGCA-GTGAGAGCA
17251581 TGAAAATGGC-GTGAGAGCA
1 TGAAAATGGCAGTGAGAGCA
17251600 TGAA
1 TGAA
17251604 GAAGAAGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
17 1 0.03
18 2 0.05
19 33 0.89
20 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.36, T:0.16
Consensus pattern (20 bp):
TGAAAATGGCAGTGAGAGCA
Found at i:17252575 original size:80 final size:80
Alignment explanation
Indices: 17252401--17252580 Score: 272
Period size: 80 Copynumber: 2.2 Consensus size: 80
17252391 ATTACATTTC
* * * * *
17252401 CATAAATCA-TCATCATACTTAGCCCATAGTGTTTATGACTATCTCAATACATACATCTCGTGGC
1 CATAAATCACTTA-CATGCTTAGCCCATAGTGTGTATGACTATCTCAACACATACATCTCATGGC
17252465 ATACATTTCATAACCT
65 ATACATTTCATAACCT
*
17252481 CATAAATCACTTACATGCTTAGCCCATGGTGTGTATGACTATCTCAACACATACATCTCATGGCA
1 CATAAATCACTTACATGCTTAGCCCATAGTGTGTATGACTATCTCAACACATACATCTCATGGCA
17252546 TACATTTCATAACCT
66 TACATTTCATAACCT
* *
17252561 TATAAATCATTTACATGCTT
1 CATAAATCACTTACATGCTT
17252581 TGTCACAACC
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
80 89 0.98
81 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.34
Consensus pattern (80 bp):
CATAAATCACTTACATGCTTAGCCCATAGTGTGTATGACTATCTCAACACATACATCTCATGGCA
TACATTTCATAACCT
Found at i:17253028 original size:13 final size:13
Alignment explanation
Indices: 17253010--17253035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17253000 CTCAGTGAGT
17253010 GAACATAGGAAGG
1 GAACATAGGAAGG
17253023 GAACATAGGAAGG
1 GAACATAGGAAGG
17253036 CAATTTAACT
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:0.46, C:0.08, G:0.38, T:0.08
Consensus pattern (13 bp):
GAACATAGGAAGG
Found at i:17254424 original size:24 final size:25
Alignment explanation
Indices: 17254397--17254450 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
17254387 ATGAGCTCTT
17254397 CCCATT-TCTTCCTATTGAGCCATG
1 CCCATTCTCTTCCTATTGAGCCATG
* * * *
17254421 CCCATTCTTTTCTTATTGGGCTATG
1 CCCATTCTCTTCCTATTGAGCCATG
17254446 CCCAT
1 CCCAT
17254451 ATTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.15, C:0.31, G:0.13, T:0.41
Consensus pattern (25 bp):
CCCATTCTCTTCCTATTGAGCCATG
Found at i:17254456 original size:25 final size:25
Alignment explanation
Indices: 17254400--17254456 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
17254390 AGCTCTTCCC
17254400 ATTTCTTCCTATTGAGCCATGCCCAT
1 ATTT-TTCCTATTGAGCCATGCCCAT
* * *
17254426 -TCTTTTCTTATTGGGCTATGCCCAT
1 AT-TTTTCCTATTGAGCCATGCCCAT
17254451 ATTTTT
1 ATTTTT
17254457 TTTTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.16, C:0.25, G:0.12, T:0.47
Consensus pattern (25 bp):
ATTTTTCCTATTGAGCCATGCCCAT
Found at i:17254963 original size:20 final size:20
Alignment explanation
Indices: 17254940--17254980 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
17254930 GCTTTTCTTT
*
17254940 TTTTTTCTTTCCTTTCGCTC
1 TTTTTGCTTTCCTTTCGCTC
*
17254960 TTTTTGCTTTCCTTTTGCTC
1 TTTTTGCTTTCCTTTCGCTC
17254980 T
1 T
17254981 CTTATGCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTTGCTTTCCTTTCGCTC
Found at i:17258328 original size:60 final size:60
Alignment explanation
Indices: 17258233--17258371 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
17258223 TAAGAGACCA
* * * * * *
17258233 AAACAGAAAGTCTTTCGTTGCAGCGAGATTGAATCTCGCTGCAGCGAAATTATAACCCAG
1 AAACAGAAAGTTTTTCGCTACAGCGAAATTCAATCTCGCTGCAGCGAAATTACAACCCAG
* * * *
17258293 AAACAGAATGTTTTTCGCTACAGCGAAATTCAATCTCGCTGTAGTGAAATTGCAACCCAG
1 AAACAGAAAGTTTTTCGCTACAGCGAAATTCAATCTCGCTGCAGCGAAATTACAACCCAG
* *
17258353 AAACAAAAAGTTTCTCGCT
1 AAACAGAAAGTTTTTCGCT
17258372 GCAACGAGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (60 bp):
AAACAGAAAGTTTTTCGCTACAGCGAAATTCAATCTCGCTGCAGCGAAATTACAACCCAG
Found at i:17258797 original size:41 final size:41
Alignment explanation
Indices: 17258725--17258833 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
17258715 TCACCAGCTC
* ** * * *
17258725 ATGCGCACTCCCTACTCGTACATGGCTGGGTCAT-TGGGGTT
1 ATGCGCACTCCCTACTC-AACATAACCGGGTCATCTCGGCTT
*
17258766 ATGCGCACTCCCTACTCACACATAACCGGGTCATCCTCTGCTT
1 ATGCGCACTCCCTACTCA-ACATAACCGGGTCAT-CTCGGCTT
17258809 ATGCGCACTCCCTACTCGAACATAA
1 ATGCGCACTCCCTACTC-AACATAA
17258834 TCGAGTCAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 29 0.51
43 27 0.47
44 1 0.02
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (41 bp):
ATGCGCACTCCCTACTCAACATAACCGGGTCATCTCGGCTT
Found at i:17262583 original size:19 final size:19
Alignment explanation
Indices: 17262559--17262596 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17262549 ACTTTTAAAC
17262559 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17262578 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17262597 AATCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:17265428 original size:27 final size:27
Alignment explanation
Indices: 17265377--17265428 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
17265367 ATATCCTGGT
*
17265377 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
17265404 GGTGGCAAAATTATC-ATTTT-ACCCT
1 GGTGG-AAAATTA-CAATTTTGACCCT
17265429 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.41
28 12 0.55
29 1 0.05
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:17266931 original size:18 final size:17
Alignment explanation
Indices: 17266908--17266943 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
17266898 TATATTCTTT
17266908 TCTTTTCTTTTCTTTCTC
1 TCTTTTCTTTTC-TTCTC
*
17266926 TCTTTTTTTTTCTTCTC
1 TCTTTTCTTTTCTTCTC
17266943 T
1 T
17266944 TTCCCGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTTTTCTTTTCTTCTC
Found at i:17266936 original size:23 final size:23
Alignment explanation
Indices: 17266903--17266946 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17266893 ATATATATAT
*
17266903 TCTTTTCTTTTCTTTTCTTTCTC
1 TCTTTTCTTTTCTTCTCTTTCTC
*
17266926 TCTTTTTTTTTCTTCTCTTTC
1 TCTTTTCTTTTCTTCTCTTTC
17266947 CCGTCGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (23 bp):
TCTTTTCTTTTCTTCTCTTTCTC
Found at i:17267179 original size:35 final size:34
Alignment explanation
Indices: 17267104--17267194 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 34
17267094 TATCAACATC
* ** * *
17267104 AAAATCAGCAGCCAAACTGCTCTATTTTTCCTCA
1 AAAATCAACAGCCAAGTTGCTCTATTCTCCCTCA
*
17267138 AAAATCAACAGCTAAGTTGCTCTATTCTCCCTCCA
1 AAAATCAACAGCCAAGTTGCTCTATTCTCCCT-CA
17267173 AAAATCAACAGCCAAGTTGCTC
1 AAAATCAACAGCCAAGTTGCTC
17267195 CTTCCTCCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 26 0.53
35 23 0.47
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (34 bp):
AAAATCAACAGCCAAGTTGCTCTATTCTCCCTCA
Found at i:17268694 original size:16 final size:16
Alignment explanation
Indices: 17268675--17268705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17268665 ATATAAATAT
17268675 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
17268691 AAAACAATCAAAATC
1 AAAAAAATCAAAATC
17268706 TAAATTTTGG
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:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:17275762 original size:25 final size:25
Alignment explanation
Indices: 17275726--17275774 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
17275716 CCGTTAGACG
*
17275726 TGGCTAGACCACGGGTTGATATACA
1 TGGCTAGACCACGAGTTGATATACA
*
17275751 TGGCTAGGCCACGAGTTGATATAC
1 TGGCTAGACCACGAGTTGATATAC
17275775 GTGGTTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (25 bp):
TGGCTAGACCACGAGTTGATATACA
Found at i:17278392 original size:10 final size:11
Alignment explanation
Indices: 17278374--17278410 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
17278364 GTGGCTGAAA
17278374 TTGATGATATT
1 TTGATGATATT
17278385 TT-ATGATATT
1 TTGATGATATT
*
17278395 TTGGTGATA-T
1 TTGATGATATT
17278405 TTGATG
1 TTGATG
17278411 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (11 bp):
TTGATGATATT
Found at i:17282919 original size:34 final size:34
Alignment explanation
Indices: 17282881--17282963 Score: 116
Period size: 34 Copynumber: 2.4 Consensus size: 34
17282871 GCACTTTTTG
17282881 GCCTCCAAAACCAGCAAAAAAATGG-TAC-TTTCTA
1 GCCTCCAAAACCAGCAAAAAAATGGCT-CTTTTC-A
*
17282915 GCCTCCAAAACTAGCAAAAAAATGGCTCTTTTCA
1 GCCTCCAAAACCAGCAAAAAAATGGCTCTTTTCA
*
17282949 GCCTCCAAAATCAGC
1 GCCTCCAAAACCAGC
17282964 CCTTAAATGG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 39 0.89
35 5 0.11
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (34 bp):
GCCTCCAAAACCAGCAAAAAAATGGCTCTTTTCA
Found at i:17288089 original size:20 final size:21
Alignment explanation
Indices: 17288064--17288102 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17288054 CCATGCTTTC
17288064 TTTTTCAT-TTTCCATGGTTA
1 TTTTTCATATTTCCATGGTTA
*
17288084 TTTTTCATATTTGCATGGT
1 TTTTTCATATTTCCATGGT
17288103 GAATTCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.59
Consensus pattern (21 bp):
TTTTTCATATTTCCATGGTTA
Found at i:17288301 original size:10 final size:11
Alignment explanation
Indices: 17288283--17288319 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
17288273 GTGGCTGAAA
17288283 TTGATGATATT
1 TTGATGATATT
17288294 TT-ATGATATT
1 TTGATGATATT
*
17288304 TTGGTGATA-T
1 TTGATGATATT
17288314 TTGATG
1 TTGATG
17288320 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (11 bp):
TTGATGATATT
Found at i:17294462 original size:17 final size:17
Alignment explanation
Indices: 17294415--17294463 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
17294405 AGCTAGGACT
17294415 TTTGATTGGTCTATTGG
1 TTTGATTGGTCTATTGG
* * *
17294432 GTTGTTTAGTCTATTGG
1 TTTGATTGGTCTATTGG
*
17294449 TTTGATTGGGCTATT
1 TTTGATTGGTCTATT
17294464 TGGCCTACCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (17 bp):
TTTGATTGGTCTATTGG
Found at i:17298615 original size:8 final size:10
Alignment explanation
Indices: 17298586--17298624 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
17298576 TATTATTAAT
17298586 TATATTAAAAA
1 TATA-TAAAAA
17298597 TATATAAAAA
1 TATATAAAAA
17298607 T-TA-AAAAA
1 TATATAAAAA
17298615 TATATAAAAA
1 TATATAAAAA
17298625 AATTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.23
9 4 0.15
10 12 0.46
11 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TATATAAAAA
Found at i:17298642 original size:19 final size:20
Alignment explanation
Indices: 17298592--17298630 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
17298582 TAATTATATT
17298592 AAAAATATAT--AAAAATTA
1 AAAAATATATAAAAAAATTA
17298610 AAAAATATATAAAAAAATTA
1 AAAAATATATAAAAAAATTA
17298630 A
1 A
17298631 TAATTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATATATAAAAAAATTA
Found at i:17308427 original size:13 final size:13
Alignment explanation
Indices: 17308411--17308435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17308401 TTCTAGAAAA
17308411 TTTATAAAATCAT
1 TTTATAAAATCAT
17308424 TTTATAAAATCA
1 TTTATAAAATCA
17308436 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17310750 original size:20 final size:20
Alignment explanation
Indices: 17310693--17310755 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
17310683 TATATACCCA
*
17310693 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
17310712 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
17310732 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
17310752 TCAT
1 TCAT
17310756 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:17310802 original size:43 final size:43
Alignment explanation
Indices: 17310754--17310872 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
17310744 TCACCAGCTC
** * *
17310754 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
17310797 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
17310840 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
17310873 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:17321161 original size:22 final size:22
Alignment explanation
Indices: 17321136--17321179 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17321126 GAGCAAGTAG
17321136 AATAAAAATGAA-AACATAAATA
1 AATAAAAAT-AATAACATAAATA
* *
17321158 AATATAAATAATAATATAAATA
1 AATAAAAATAATAACATAAATA
17321180 GAACAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AATAAAAATAATAACATAAATA
Found at i:17324204 original size:20 final size:20
Alignment explanation
Indices: 17324167--17324212 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
17324157 GAAAAACGCA
17324167 ATTTTCCCTTTGAATTTTCT
1 ATTTTCCCTTTGAATTTTCT
* **
17324187 ATTTTTCCTTTGGTTTTTCT
1 ATTTTCCCTTTGAATTTTCT
*
17324207 CTTTTC
1 ATTTTC
17324213 TTCCTTTCCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.07, T:0.65
Consensus pattern (20 bp):
ATTTTCCCTTTGAATTTTCT
Found at i:17329542 original size:24 final size:24
Alignment explanation
Indices: 17329510--17329568 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
17329500 TTCTAAATCT
17329510 CATTGGAGTCAAATCCATGTGTAA
1 CATTGGAGTCAAATCCATGTGTAA
17329534 CATTGGAGTCAAATCCATGTGTAA
1 CATTGGAGTCAAATCCATGTGTAA
*
17329558 CAATGGAGTCA
1 CATTGGAGTCA
17329569 TGCGAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (24 bp):
CATTGGAGTCAAATCCATGTGTAA
Found at i:17355397 original size:2 final size:2
Alignment explanation
Indices: 17355385--17355415 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17355375 TTTTATGTGT
*
17355385 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17355416 GATTTTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17358363 original size:38 final size:38
Alignment explanation
Indices: 17358320--17358531 Score: 138
Period size: 38 Copynumber: 5.7 Consensus size: 38
17358310 ATAGTGCCCG
17358320 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
* *
17358358 TGTGCACGATGTGGGGGGATG--CAC-ATGCCAGTGA-
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
** * * * *
17358392 TGATG-GTGGTGT-GGGAGATGGATA-ATGATAGTGC-CCG--
1 TG-TGCACGATGTGGGGGGAT-G-TACACGAT-G-GCACTGAT
* *
17358429 TGTGCACAATGTGGGGGGGTGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
* * * *
17358467 TGTGCACGATGTGGGGGGATGCACATGATGGCGCTAGCT
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACT-GAT
** *
17358506 ATGTGCATTATGTAGGGGGATGTACA
1 -TGTGCACGATGTGGGGGGATGTACA
17358532 TGAGTCGAGT
Statistics
Matches: 130, Mismatches: 28, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
33 6 0.05
34 7 0.05
35 12 0.09
36 11 0.08
37 12 0.09
38 58 0.45
39 3 0.02
40 21 0.16
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
Found at i:17358403 original size:109 final size:109
Alignment explanation
Indices: 17358249--17358493 Score: 418
Period size: 109 Copynumber: 2.2 Consensus size: 109
17358239 TAACCGTGTG
* * **
17358249 TGTGCATGATGTGGGGGAATGCACATGCTGGTGATAATGGCGGTGTGGGAGATGGATAATGATAG
1 TGTGCACGATGTGGGGGGATGCACATGCCAGTGATAATGGCGGTGTGGGAGATGGATAATGATAG
*
17358314 TGCCCGTGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
66 TGCCCGTGTGCACAATGTGGGGGGATGTACACGATGGCACTGAT
* *
17358358 TGTGCACGATGTGGGGGGATGCACATGCCAGTGATGATGGTGGTGTGGGAGATGGATAATGATAG
1 TGTGCACGATGTGGGGGGATGCACATGCCAGTGATAATGGCGGTGTGGGAGATGGATAATGATAG
*
17358423 TGCCCGTGTGCACAATGTGGGGGGGTGTACACGATGGCACTGAT
66 TGCCCGTGTGCACAATGTGGGGGGATGTACACGATGGCACTGAT
17358467 TGTGCACGATGTGGGGGGATGCACATG
1 TGTGCACGATGTGGGGGGATGCACATG
17358494 ATGGCGCTAG
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 128 1.00
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.24
Consensus pattern (109 bp):
TGTGCACGATGTGGGGGGATGCACATGCCAGTGATAATGGCGGTGTGGGAGATGGATAATGATAG
TGCCCGTGTGCACAATGTGGGGGGATGTACACGATGGCACTGAT
Found at i:17363847 original size:17 final size:17
Alignment explanation
Indices: 17363814--17363847 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17363804 AATTGAATTA
* *
17363814 TAATTTAATTAATTAAT
1 TAATTTAAATAAATAAT
17363831 TAATTTAAATAAATAAT
1 TAATTTAAATAAATAAT
17363848 ATTCAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTAAATAAATAAT
Found at i:17376716 original size:28 final size:28
Alignment explanation
Indices: 17376638--17376801 Score: 118
Period size: 28 Copynumber: 5.9 Consensus size: 28
17376628 TGATGATTGG
17376638 AATATTTAGATGCCTTAGCAT-TTTCTGA
1 AATATTTAGATGCCTTAGCATCTTT-TGA
* * *
17376666 AAAATTTAGATGCCTCAACATCTTTTGA
1 AATATTTAGATGCCTTAGCATCTTTTGA
* * *
17376694 AATATTTAGATTCCTTAGTATCTTGTGA
1 AATATTTAGATGCCTTAGCATCTTTTGA
* * *** * * *
17376722 AATATCTCGATGTAGTAACACCTTTAGA
1 AATATTTAGATGCCTTAGCATCTTTTGA
* * *
17376750 ATTA-TTAGATGCCTTAGAATCTTTGGA
1 AATATTTAGATGCCTTAGCATCTTTTGA
* *
17376777 AAT-TGTTAGATGCATTAACATCTTT
1 AATAT-TTAGATGCCTTAGCATCTTT
17376802 GGATTTAGTT
Statistics
Matches: 99, Mismatches: 34, Indels: 6
0.71 0.24 0.04
Matches are distributed among these distances:
27 16 0.16
28 80 0.81
29 3 0.03
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (28 bp):
AATATTTAGATGCCTTAGCATCTTTTGA
Found at i:17376812 original size:28 final size:28
Alignment explanation
Indices: 17376737--17376813 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
17376727 CTCGATGTAG
* * *
17376737 TAACACCTTTAGAATTA-TTAGATGCCT
1 TAACATCTTTGGAATTAGTTAGATGCAT
17376764 TAGA-ATCTTTGGAAATT-GTTAGATGCAT
1 TA-ACATCTTTGG-AATTAGTTAGATGCAT
*
17376792 TAACATCTTTGGATTTAGTTAG
1 TAACATCTTTGGAATTAGTTAG
17376814 GTGTGGTAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
27 12 0.29
28 29 0.71
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (28 bp):
TAACATCTTTGGAATTAGTTAGATGCAT
Found at i:17380757 original size:47 final size:47
Alignment explanation
Indices: 17380706--17381003 Score: 373
Period size: 47 Copynumber: 6.4 Consensus size: 47
17380696 CACTGCTCAA
* *
17380706 AGTTGGTGAGACGCCATGGAGGGAATCTGTGAGACGCCAGAGTTAAG
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAG
* * * ** * *
17380753 AGTTGGTGACACTCCATGGTGGGAATGTGTGACACGGTAGCGTTCAG
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAG
* * * *
17380800 AGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACCGGA-TTAAC
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAG
* * * *
17380846 AGTTGGTGACACGTCATGGAGGGATTCTGTGACACGCCAGCGTTTAG
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAG
* * ** *
17380893 AGTTGGTGAGATGCCATGGATTGAATCTGTGAGACGCCAGAGTTAAG
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAG
* *
17380940 AGTTGGTGACACGCCATGGAGGGAATCTATGACACGCCAGAGTTCAG
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAG
17380987 AGTTGGTGACACGCCAT
1 AGTTGGTGACACGCCAT
17381004 TGTCATGTTT
Statistics
Matches: 206, Mismatches: 44, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
46 38 0.18
47 168 0.82
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (47 bp):
AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAG
Found at i:17380818 original size:94 final size:94
Alignment explanation
Indices: 17380679--17381003 Score: 422
Period size: 94 Copynumber: 3.5 Consensus size: 94
17380669 ACGTCATGTT
* * * *
17380679 GGGAATGTGTGACACGACA-CTGCTCAAAGTTGGTGAGACGCCATGGAGGGAATCTGTGAGACGC
1 GGGAATCTGTGACACGCCAGC-GTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGAGACGC
*
17380743 CAGAGTTAAGAGTTGGTGACACTCCATGGT
65 CAGAGTTAAGAGTTGGTGACACTCCATGGA
* ** * *
17380773 GGGAATGTGTGACACGGTAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACC
1 GGGAATCTGTGACACGCCAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGAGACGCC
* *
17380838 GGA-TTAACAGTTGGTGACACGT-CATGGA
66 AGAGTTAAGAGTTGGTGACAC-TCCATGGA
* * * **
17380866 GGGATTCTGTGACACGCCAGCGTTTAGAGTTGGTGAGATGCCATGGATTGAATCTGTGAGACGCC
1 GGGAATCTGTGACACGCCAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGAGACGCC
*
17380931 AGAGTTAAGAGTTGGTGACACGCCATGGA
66 AGAGTTAAGAGTTGGTGACACTCCATGGA
* * *
17380960 GGGAATCTATGACACGCCAGAGTTCAGAGTTGGTGACACGCCAT
1 GGGAATCTGTGACACGCCAGCGTTCAGAGTTGGTGAGACGCCAT
17381004 TGTCATGTTT
Statistics
Matches: 199, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
93 78 0.39
94 120 0.60
95 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (94 bp):
GGGAATCTGTGACACGCCAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGAGACGCC
AGAGTTAAGAGTTGGTGACACTCCATGGA
Found at i:17380900 original size:140 final size:141
Alignment explanation
Indices: 17380706--17381003 Score: 377
Period size: 140 Copynumber: 2.1 Consensus size: 141
17380696 CACTGCTCAA
* *
17380706 AGTTGGTGAGACGCCATGGAGGGAATCTGTGAGACGCCAGAGTTAAGAGTTGGTGACACT-CCAT
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAGAGTTGGTGACA-TGCCAT
* ** * * * *
17380770 GG-TGGGAATGTGTGACACGGTAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACA
65 GGAT-GGAATCTGTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCTATGACA
*
17380834 CACCGGA-TTAAC
129 CACCAGAGTTAAC
* * * * *
17380846 AGTTGGTGACACGTCATGGAGGGATTCTGTGACACGCCAGCGTTTAGAGTTGGTGAGATGCCATG
1 AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAGAGTTGGTGACATGCCATG
* * *
17380911 GATTGAATCTGTGAGACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCTATGACACG
66 GATGGAATCTGTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCTATGACACA
* *
17380976 CCAGAGTTCAG
131 CCAGAGTTAAC
17380987 AGTTGGTGACACGCCAT
1 AGTTGGTGACACGCCAT
17381004 TGTCATGTTT
Statistics
Matches: 134, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
139 1 0.01
140 113 0.84
141 20 0.15
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (141 bp):
AGTTGGTGACACGCCATGGAGGGAATCTGTGACACGCCAGAGTTAAGAGTTGGTGACATGCCATG
GATGGAATCTGTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCTATGACACA
CCAGAGTTAAC
Found at i:17380953 original size:24 final size:24
Alignment explanation
Indices: 17380921--17381002 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
17380911 GATTGAATCT
*
17380921 GTGAGACGCCAGAGTTAAGAGTTG
1 GTGACACGCCAGAGTTAAGAGTTG
* *
17380945 GTGACACGCCATG-G--AGGGAATCT-
1 GTGACACGCCA-GAGTTA-AGAGT-TG
* *
17380968 ATGACACGCCAGAGTTCAGAGTTG
1 GTGACACGCCAGAGTTAAGAGTTG
17380992 GTGACACGCCA
1 GTGACACGCCA
17381003 TTGTCATGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
22 2 0.05
23 15 0.35
24 25 0.58
25 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.33, T:0.18
Consensus pattern (24 bp):
GTGACACGCCAGAGTTAAGAGTTG
Found at i:17381053 original size:52 final size:53
Alignment explanation
Indices: 17380993--17381111 Score: 168
Period size: 53 Copynumber: 2.3 Consensus size: 53
17380983 TCAGAGTTGG
* *
17380993 TGACACGCCATTGTCAT-GTTTAGAGTGTATGACACGACATTGCTTGAAAAGC
1 TGACACGCCATGGTCATGGTTTAGAGTGTATGACACGACAGTGCTTGAAAAGC
* * **
17381045 TGACACGCCATGGTCATGGTTTAGAGTGTGTGACACGGCAGTGCTTGAGTAGC
1 TGACACGCCATGGTCATGGTTTAGAGTGTATGACACGACAGTGCTTGAAAAGC
*
17381098 TGACACGTCATGGT
1 TGACACGCCATGGT
17381112 TTGAAATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
52 16 0.27
53 43 0.73
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (53 bp):
TGACACGCCATGGTCATGGTTTAGAGTGTATGACACGACAGTGCTTGAAAAGC
Found at i:17381616 original size:31 final size:31
Alignment explanation
Indices: 17381581--17381670 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
17381571 AGTTATTAGC
*
17381581 GTGTGACAGTATTTTATTTGATATGCATAGA
1 GTGTGACAGTATTTTACTTGATATGCATAGA
* * *
17381612 GTGTGACAGCATTTTACTTGATATGCATGGC
1 GTGTGACAGTATTTTACTTGATATGCATAGA
17381643 GTGTGACA-TCATTTTACTTGATATGCAT
1 GTGTGACAGT-ATTTTACTTGATATGCAT
17381671 GTCATGTCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (31 bp):
GTGTGACAGTATTTTACTTGATATGCATAGA
Found at i:17381671 original size:31 final size:31
Alignment explanation
Indices: 17381591--17381880 Score: 278
Period size: 31 Copynumber: 9.1 Consensus size: 31
17381581 GTGTGACAGT
* * * * *
17381591 ATTTTATTTGATATGCATAGAGTGTGACAGC
1 ATTTTACTTGATATGCATGGCGTGTCACAAC
* *
17381622 ATTTTACTTGATATGCATGGCGTGTGACATC
1 ATTTTACTTGATATGCATGGCGTGTCACAAC
* * *
17381653 ATTTTACTTGATATGCATGTCATGTCACAAA
1 ATTTTACTTGATATGCATGGCGTGTCACAAC
* * * *
17381684 ATTTTACTTGTTATTCATGGCGTTTGACANTTGACAGC
1 ATTTTACTTGATATGCATGGCG--TG-----TCACAAC
* *
17381722 ATTTTACTTCATATGCATGGCGTGTCATAAC
1 ATTTTACTTGATATGCATGGCGTGTCACAAC
* *
17381753 ATTTAACTTGATATGCATGGCGTGTCACGAC
1 ATTTTACTTGATATGCATGGCGTGTCACAAC
* * * *
17381784 GTTTAACTTGTTATGCATGGTGTGTCACAAC
1 ATTTTACTTGATATGCATGGCGTGTCACAAC
*
17381815 ATTTTACTTGTTATGCATGGCGTGTCACAAC
1 ATTTTACTTGATATGCATGGCGTGTCACAAC
17381846 ATTTTGA-TTGCA-ATGCATGGCGTGTCACAAC
1 ATTTT-ACTTG-ATATGCATGGCGTGTCACAAC
17381877 ATTT
1 ATTT
17381881 ATTCCTTATT
Statistics
Matches: 216, Mismatches: 34, Indels: 18
0.81 0.13 0.07
Matches are distributed among these distances:
31 188 0.87
32 1 0.00
33 2 0.01
36 2 0.01
38 23 0.11
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (31 bp):
ATTTTACTTGATATGCATGGCGTGTCACAAC
Found at i:17381725 original size:100 final size:99
Alignment explanation
Indices: 17381615--17381881 Score: 271
Period size: 100 Copynumber: 2.7 Consensus size: 99
17381605 GCATAGAGTG
* * * * *
17381615 TGACAGCATTTTACTTGATATGCATGGCGTGTGACATCATTTTACTTGATATGCATGTCATGTCA
1 TGACAGCATTTTACTTCATATGCATGGCGTGTCACAACATTTAACTTGATATGCATGGCATGTCA
* *
17381680 CAAAATTTTACTTGTTATTCATGGCGTTTGACANT
66 CAAAATTTAACTTGTTATGCATGGCGTTTGACA-T
* *
17381715 TGACAGCATTTTACTTCATATGCATGGCGTGTCATAACATTTAACTTGATATGCATGGCGTGTCA
1 TGACAGCATTTTACTTCATATGCATGGCGTGTCACAACATTTAACTTGATATGCATGGCATGTCA
* ** *
17381780 CGACGTTTAACTTGTTATGCAT-G-GTGTG----
66 CAAAATTTAACTTGTTATGCATGGCGTTTGACAT
* * ** * *
17381808 TCACAACATTTTACTTGTTATGCATGGCGTGTCACAACATTTTGA-TTGCA-ATGCATGGCGTGT
1 TGACAGCATTTTACTTCATATGCATGGCGTGTCACAACA-TTTAACTTG-ATATGCATGGCATGT
*
17381871 CACAACATTTA
64 CACAAAATTTA
17381882 TTCCTTATTT
Statistics
Matches: 144, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
93 59 0.41
94 5 0.03
98 4 0.03
99 1 0.01
100 75 0.52
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (99 bp):
TGACAGCATTTTACTTCATATGCATGGCGTGTCACAACATTTAACTTGATATGCATGGCATGTCA
CAAAATTTAACTTGTTATGCATGGCGTTTGACAT
Found at i:17381762 original size:69 final size:68
Alignment explanation
Indices: 17381646--17381775 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 68
17381636 GCATGGCGTG
* * * * * *
17381646 TGACATCATTTTACTTGATATGCATGTCATGTCACAAAATTTTACTTGTTATTCATGGCGTTTGA
1 TGACAGCATTTTACTTCATATGCATGGCATGTCACAAAATTTAACTTGATATGCATGGCGTTTGA
17381711 CANT
66 CA-T
* * *
17381715 TGACAGCATTTTACTTCATATGCATGGCGTGTCATAACATTTAACTTGATATGCATGGCGT
1 TGACAGCATTTTACTTCATATGCATGGCATGTCACAAAATTTAACTTGATATGCATGGCGT
17381776 GTCACGACGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 52 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (68 bp):
TGACAGCATTTTACTTCATATGCATGGCATGTCACAAAATTTAACTTGATATGCATGGCGTTTGA
CAT
Found at i:17381819 original size:131 final size:130
Alignment explanation
Indices: 17381584--17381837 Score: 323
Period size: 131 Copynumber: 1.9 Consensus size: 130
17381574 TATTAGCGTG
* * * * * * *
17381584 TGACAGTATTTTATTTGATATGCATAGAGTGTGACAGCATTTTACTTGATATGCATGGCGTGTGA
1 TGACAGCATTTTACTTCATATGCATAGAGTGTCACAACATTTAACTTGATATGCATGGCGTGTCA
* *
17381649 CATCATTTTACTTGATATGCATGTCATGTCACAAAATTTTACTTGTTATTCATGGCGTTTGACAN
66 CATCATTTAACTTGATATGCATGTCATGTCACAAAATTTTACTTGTTATGCATGGCGTTTGACA-
17381714 T
130 T
* * *
17381715 TGACAGCATTTTACTTCATATGCATGGCGTGTCATAACATTTAACTTGATATGCATGGCGTGTCA
1 TGACAGCATTTTACTTCATATGCATAGAGTGTCACAACATTTAACTTGATATGCATGGCGTGTCA
* * * *
17381780 CGA-CGTTTAACTTGTTATGCATGGT-GTGTCACAACATTTTACTTGTTATGCATGGCGT
66 C-ATCATTTAACTTGATATGCAT-GTCATGTCACAAAATTTTACTTGTTATGCATGGCGT
17381838 GTCACAACAT
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
131 102 0.97
132 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (130 bp):
TGACAGCATTTTACTTCATATGCATAGAGTGTCACAACATTTAACTTGATATGCATGGCGTGTCA
CATCATTTAACTTGATATGCATGTCATGTCACAAAATTTTACTTGTTATGCATGGCGTTTGACAT
Found at i:17383753 original size:156 final size:154
Alignment explanation
Indices: 17383511--17384006 Score: 537
Period size: 156 Copynumber: 3.2 Consensus size: 154
17383501 GTTTATCGAG
* * * * * * *
17383511 TAACACAGTAATTTATGTAATTACAGTTTACGGAAGTGATGACAAGTCCTCAAGCACCGATCGAT
1 TAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTCAAGCACCGATCGAT
* ** * * *
17383576 CCAGCTTAACCGCAAACAGCTAATAAGCAGACGGTAAGGATATTAAAGTTCTAACGGTTAATGTT
66 CGA-CTCCACCGCAGATAGCTAA-AAGCAGACGGTAAGGATATTAAAGTTGTAACGGTTAATGTT
*
17383641 CAACAATTCCAAACATGATTATTGAA
129 CAACAATTCCATACATGATTATTGAA
* * * *
17383667 TAACACAGTTATATATGTAATTGTAGTTTGCAGAAGCGACGACAGGTCCTTAAGCACCGATCAGT
1 TAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTCAAGCACCGATC-GA
* * ** *
17383732 TCGACTCCACCGCAGATAGCTAACGAGCCGGTGGTAAGGATATTAAAGTTGTAACAGTTAATGTT
65 TCGACTCCACCGCAGATAGCTAA-AAGCAGACGGTAAGGATATTAAAGTTGTAACGGTTAATGTT
* *
17383797 CAACAATTTCATACATGATTATTCAA
129 CAACAATTCCATACATGATTATTGAA
* * * *
17383823 TAACACAGTTAAATATGTAATTGCAGTATGCGGAAGCGACGACAGGTCCTGAAGCATCGATCGAT
1 TAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTCAAGCACCGATCGAT
* ** * ** * *
17383888 CTGGCTCCACTACAGACT-GCTAAAGAGCCA-CCAATTAGGATATTAAAGTTGTAACGATTAATG
66 C-GACTCCACCGCAGA-TAGCTAAA-AG-CAGACGGTAAGGATATTAAAGTTGTAACGGTTAATG
*
17383951 TTCAACAATTCCATATATGATTATTGAA
127 TTCAACAATTCCATACATGATTATTGAA
* * *
17383979 TAACATAGTTATATATGTTATTGTAGTT
1 TAACACAGTTATATATGTAATTGCAGTT
17384007 GACCTAGTCG
Statistics
Matches: 282, Mismatches: 53, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
155 3 0.01
156 273 0.97
157 6 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (154 bp):
TAACACAGTTATATATGTAATTGCAGTTTGCGGAAGCGACGACAGGTCCTCAAGCACCGATCGAT
CGACTCCACCGCAGATAGCTAAAAGCAGACGGTAAGGATATTAAAGTTGTAACGGTTAATGTTCA
ACAATTCCATACATGATTATTGAA
Found at i:17384293 original size:31 final size:31
Alignment explanation
Indices: 17384255--17384614 Score: 314
Period size: 31 Copynumber: 11.6 Consensus size: 31
17384245 TGCTTTACCA
* * *
17384255 GTGTCACAATATTTTACTTGTTATTCATGAC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * * *
17384286 GTGTCACAACGTTTGATTTTGATATGCATGGC
1 GTGTCACAACATTTTA-CTTGTTATGCATGGC
* * * * * *
17384318 ATGTTAGAACATTTTGCTTGTTATCCTTGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * *
17384349 ATGTCACCA-AGTTTATCTTGTTATGCATGGC
1 GTGTCACAACATTTTA-CTTGTTATGCATGGC
* * *
17384380 GTGTCACAACATTTTAATTGTTTTGCATGGA
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * *
17384411 GTGTCACAACATTTTCCTTGTTATCCTTGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
17384442 GTGTCACCA-AGTTTATCTTGTTATGCATGGC
1 GTGTCACAACATTTTA-CTTGTTATGCATGGC
* * * *
17384473 GTGTCACAACATTTTCCTCGTTATCCTTGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
17384504 GTGTCACCA-AGTTTATCTTGTTATGCATGGC
1 GTGTCACAACATTTTA-CTTGTTATGCATGGC
* * **
17384535 GTGTCACGACATTTTACTTGTTTTGCATGAT
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * *
17384566 GTGTGACAACATTTTACTTGGTATTCACT-GC
1 GTGTCACAACATTTTACTTGTTATGCA-TGGC
17384597 GTGTCACAACATTTTACT
1 GTGTCACAACATTTTACT
17384615 GTTTATGGTT
Statistics
Matches: 255, Mismatches: 66, Indels: 16
0.76 0.20 0.05
Matches are distributed among these distances:
30 12 0.05
31 207 0.81
32 36 0.14
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGTTATGCATGGC
Found at i:17386836 original size:31 final size:31
Alignment explanation
Indices: 17386798--17386948 Score: 198
Period size: 31 Copynumber: 4.9 Consensus size: 31
17386788 ACACCAGAAC
* * *
17386798 TTGTTATGCATGGCGGGTCAGAACAATTTAA
1 TTGTTATGCATGGCGTGTCACAACATTTTAA
*
17386829 TTGTTATGCATGGCGTGTCACAAC-GTTTAA
1 TTGTTATGCATGGCGTGTCACAACATTTTAA
* *
17386859 CTTGTTATGCATGGCGTGTCACAACCTTTTAC
1 -TTGTTATGCATGGCGTGTCACAACATTTTAA
*
17386891 TTGTTATGCATGGCGTGTCACAACATTTTAC
1 TTGTTATGCATGGCGTGTCACAACATTTTAA
* *
17386922 TTGTTATGCATGGCTTGTCTC-ACATTT
1 TTGTTATGCATGGCGTGTCACAACATTT
17386949 ATTCCTTATA
Statistics
Matches: 110, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
30 11 0.10
31 95 0.86
32 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
TTGTTATGCATGGCGTGTCACAACATTTTAA
Found at i:17386895 original size:62 final size:62
Alignment explanation
Indices: 17386795--17386940 Score: 220
Period size: 62 Copynumber: 2.4 Consensus size: 62
17386785 TACACACCAG
* * *
17386795 AACTTGTTATGCATGGCGGGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACAACGTTT
1 AACTTGTTATGCATGGCGTGTCACAACAATTTAATTGTTATGCATGGCGTGTCACAACATTT
** *
17386857 AACTTGTTATGCATGGCGTGTCACAACCTTTTACTTGTTATGCATGGCGTGTCACAACATTT
1 AACTTGTTATGCATGGCGTGTCACAACAATTTAATTGTTATGCATGGCGTGTCACAACATTT
* *
17386919 TACTTGTTATGCATGGCTTGTC
1 AACTTGTTATGCATGGCGTGTC
17386941 TCACATTTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 76 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (62 bp):
AACTTGTTATGCATGGCGTGTCACAACAATTTAATTGTTATGCATGGCGTGTCACAACATTT
Found at i:17390460 original size:31 final size:31
Alignment explanation
Indices: 17390422--17390503 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
17390412 GTGTCAATCG
*
17390422 TGTTGTAACATGCCATGCATAT-AATGTAAAA
1 TGTTGTAACACGCCATGCATATCAA-GTAAAA
*
17390453 TGTTGTAACACGCCATGCATATCAAGTCAAA
1 TGTTGTAACACGCCATGCATATCAAGTAAAA
* *
17390484 TGTCGTGACACGCCATGCAT
1 TGTTGTAACACGCCATGCAT
17390504 CACTATAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 44 0.96
32 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (31 bp):
TGTTGTAACACGCCATGCATATCAAGTAAAA
Found at i:17390679 original size:55 final size:54
Alignment explanation
Indices: 17390530--17390715 Score: 185
Period size: 55 Copynumber: 3.4 Consensus size: 54
17390520 TGGTTACACC
* * ** *
17390530 AACATCCGTGACACGCTAAAAACTCAAAAAACTAGTTAACCCATGACACGCTAGG
1 AACAGCCGTGACACGCTAAAAAC-CCAAAAACTAGTTAACCCACAACACCCTAGG
* * * * * * *
17390585 AACAACCATGACACGCCAAAAACCCATAAATTCAATTAACCCACCACACCCTAGG
1 AACAGCCGTGACACGCTAAAAACCCAAAAACT-AGTTAACCCACAACACCCTAGG
* **
17390640 AACAGCCGTGACACGCTAACAACCCAAATAACTAGTTAACCCACAACACGCC-AAT
1 AACAGCCGTGACACGCTAAAAACCCAAA-AACTAGTTAACCCACAACAC-CCTAGG
*
17390695 AACAGTCGTGACACGCTAAAA
1 AACAGCCGTGACACGCTAAAA
17390716 TAACTCTTCA
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
54 6 0.06
55 95 0.90
56 5 0.05
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (54 bp):
AACAGCCGTGACACGCTAAAAACCCAAAAACTAGTTAACCCACAACACCCTAGG
Found at i:17395537 original size:42 final size:42
Alignment explanation
Indices: 17395478--17395643 Score: 269
Period size: 42 Copynumber: 4.0 Consensus size: 42
17395468 TGTTGATTTG
*
17395478 AACCCGGCTATGTGCGAGTAGGAGTGCACATAAGTCGTTGCT
1 AACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
*
17395520 AACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTACT
1 AACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
17395562 GACTCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 AACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* * *
17395604 GACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 AACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
17395644 TTGCCTCCGT
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 116 1.00
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.23
Consensus pattern (42 bp):
AACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:17395914 original size:26 final size:26
Alignment explanation
Indices: 17395878--17395939 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
17395868 TTGCATATGA
17395878 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
17395904 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
17395930 GTTGATGATG
1 GATGATGATG
17395940 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:17404588 original size:21 final size:21
Alignment explanation
Indices: 17404564--17404607 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
17404554 TAATATCAAG
*
17404564 TGCACATGATGGTACACATCA
1 TGCACATGATGGTACACACCA
17404585 TGCACATGATGGTACACACCA
1 TGCACATGATGGTACACACCA
17404606 TG
1 TG
17404608 TATTAAACCC
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:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TGCACATGATGGTACACACCA
Found at i:17404846 original size:82 final size:85
Alignment explanation
Indices: 17404687--17404883 Score: 201
Period size: 82 Copynumber: 2.4 Consensus size: 85
17404677 AAAAGTGTTA
* * ** *
17404687 TTGTTACACGCCATGGTT-AAAAAAAA-TATTGTTGTTACACATCATACACAAAAACATATTACA
1 TTGTTACACGTCAT-ATTGAAAAAAAATTATAATTGTTACACACCATACACAAAAACATATTACA
* *
17404750 CTTCATGGTT-AAAAAA-A-G
65 CGTAATGGTTAAAAAAATATG
* ** *
17404768 TTGTTACATG-CTATATTGAAAAAAAATTATAATTGTTACACACCATGTACAAAAACATGTTACA
1 TTGTTACACGTC-ATATTGAAAAAAAATTATAATTGTTACACACCATACACAAAAACATATTACA
17404832 CGTAAT-GTTGAAAAAAATATTG
65 CGTAATGGTT-AAAAAAATA-TG
*
17404854 TTGTTACACGTCATATTGAAAAAATATTAT
1 TTGTTACACGTCATATTGAAAAAAAATTAT
17404884 TGGTACAAGC
Statistics
Matches: 95, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
80 3 0.03
81 22 0.23
82 35 0.37
83 6 0.06
84 1 0.01
86 27 0.28
87 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (85 bp):
TTGTTACACGTCATATTGAAAAAAAATTATAATTGTTACACACCATACACAAAAACATATTACAC
GTAATGGTTAAAAAAATATG
Found at i:17404861 original size:30 final size:29
Alignment explanation
Indices: 17404825--17404890 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
17404815 TACAAAAACA
* *
17404825 TGTTACACGTAATGTTGAAAAAAATATTGT
1 TGTTACACGTAATATTG-AAAAAATATTAT
*
17404855 TGTTACACGTCATATTGAAAAAATATTAT
1 TGTTACACGTAATATTGAAAAAATATTAT
*
17404884 TGGTACA
1 TGTTACA
17404891 AGCTATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (29 bp):
TGTTACACGTAATATTGAAAAAATATTAT
Found at i:17404890 original size:29 final size:30
Alignment explanation
Indices: 17404828--17404907 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
17404818 AAAAACATGT
* * *
17404828 TACACGTAATGTTGAAAAAAATATTGTTGT
1 TACACGTAATATTGAAAAAAATATTATTGG
*
17404858 TACACGTCATATTG-AAAAAATATTATTGG
1 TACACGTAATATTGAAAAAAATATTATTGG
* *
17404887 TACAAGCT-ATATTTAAAAAAA
1 TACACG-TAATATTGAAAAAAA
17404908 ATTTGTTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (30 bp):
TACACGTAATATTGAAAAAAATATTATTGG
Found at i:17405563 original size:10 final size:10
Alignment explanation
Indices: 17405548--17405582 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
17405538 TAAGATGTCC
17405548 ATTTTTCATA
1 ATTTTTCATA
17405558 ATTTTTCATA
1 ATTTTTCATA
17405568 ATTTTCTC-TA
1 ATTTT-TCATA
17405578 ATTTT
1 ATTTT
17405583 CTAAATTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 22 0.92
11 2 0.08
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTTTCATA
Found at i:17406083 original size:15 final size:15
Alignment explanation
Indices: 17406055--17406090 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
17406045 TCGTTCTTTT
*
17406055 TTATATGTTCTTATTA
1 TTAT-TGTTATTATTA
17406071 TTATTGTTATTATTA
1 TTATTGTTATTATTA
17406086 TTATT
1 TTATT
17406091 ATTGGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.67
Consensus pattern (15 bp):
TTATTGTTATTATTA
Found at i:17409873 original size:17 final size:19
Alignment explanation
Indices: 17409832--17409873 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
17409822 ATGTATATAT
17409832 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
17409853 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
17409870 ATGA
1 ATGA
17409874 TGTTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:17409968 original size:2 final size:2
Alignment explanation
Indices: 17409961--17409985 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17409951 GATGATGTAT
17409961 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
17409986 TATACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17417648 original size:2 final size:2
Alignment explanation
Indices: 17417641--17417715 Score: 59
Period size: 2 Copynumber: 39.0 Consensus size: 2
17417631 TTAACACATT
* * *
17417641 TA TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA -A TA TT TGA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * *
17417682 GA -A NA CA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17417716 AATTAATATT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
1 4 0.07
2 56 0.93
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:17417693 original size:49 final size:48
Alignment explanation
Indices: 17417640--17417733 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 48
17417630 CTTAACACAT
17417640 TTATATATATATATATATATATATATAAATTAATATTTGAAAGAANACA
1 TTATATATATATATATATATATATATAAATTAATATTTGAAAGAA-ACA
17417689 TTATATATATATATATATATATATATAAATTAATATTTGAAAGAA
1 TTATATATATATATATATATATATATAAATTAATATTTGAAAGAA
17417734 GGTAAAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (48 bp):
TTATATATATATATATATATATATATAAATTAATATTTGAAAGAAACA
Found at i:17418335 original size:22 final size:22
Alignment explanation
Indices: 17418286--17418346 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
17418276 TAACTATTGT
*
17418286 GCAACAATAGTGCAATTACCAT
1 GCAACAATAGTGCAATTACCAC
* * *
17418308 GTAACAACAGTGCAATTACCGC
1 GCAACAATAGTGCAATTACCAC
*
17418330 GCAACAATAATGCAATT
1 GCAACAATAGTGCAATT
17418347 GGTTTGTTCG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (22 bp):
GCAACAATAGTGCAATTACCAC
Found at i:17424026 original size:172 final size:170
Alignment explanation
Indices: 17423637--17424026 Score: 455
Period size: 172 Copynumber: 2.3 Consensus size: 170
17423627 TTAAATGGCT
*
17423637 TTATAATTATATAAATGATTTTAAAATTGAATTTTTCTCTT---TTTTGGTTAAAACAGATAATA
1 TTATAATTATTTAAATGATTTT-AAATTGAATTTTT-T-TTACATTTTGGTTAAAACAGATAATA
* * *
17423699 ATTTGATGTTTGCATTAGGAAACGTGAAGAAAAAGCCATACATTAACAAGAAAAGTTTATTTATA
63 ATTTGATGTTTGCATCAAGAAACGTGAAGAAAAAGCCATACATTAACAAGAAAAGTATATTTATA
* * *
17423764 GTCACTCATATCTTCAAAAGCCTTAATACTTGCTTTAAGTGGA
128 GTCAATCATACCTTCAAAAGCCTTAATACTTGCTTCAAGTGGA
* * * ** * **
17423807 TTGATAACTCTTTAAATGATCTTAAATTGAATTTTTTAAACCATTTTGGTTAAAATAGATTGTAA
1 TT-ATAATTATTTAAATGATTTTAAATTGAATTTTTTTTA-CATTTTGGTTAAAACAGATAATAA
* * *
17423872 TTTGATGTTTGCATCAAGAAACGTGAAGTGAAAA-CCATCCATTGACAAGAAAAGTATATTTATA
64 TTTGATGTTTGCATCAAGAAACGTGAAG-AAAAAGCCATACATTAACAAGAAAAGTATATTTATA
* * * * **
17423936 GTCAATCATGCCTTTATACGCCTTGTTACTTGCTTCAAGTGGA
128 GTCAATCATACCTTCAAAAGCCTTAATACTTGCTTCAAGTGGA
*
17423979 CTTATAATTTTTTAAATGATTTTAAATTGAATTTTTTTTGACATTTTG
1 -TTATAATTATTTAAATGATTTTAAATTGAATTTTTTTT-ACATTTTG
17424027 TAAGGTCTAC
Statistics
Matches: 183, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
169 1 0.01
170 15 0.08
171 16 0.09
172 144 0.79
173 7 0.04
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (170 bp):
TTATAATTATTTAAATGATTTTAAATTGAATTTTTTTTACATTTTGGTTAAAACAGATAATAATT
TGATGTTTGCATCAAGAAACGTGAAGAAAAAGCCATACATTAACAAGAAAAGTATATTTATAGTC
AATCATACCTTCAAAAGCCTTAATACTTGCTTCAAGTGGA
Found at i:17430358 original size:2 final size:2
Alignment explanation
Indices: 17430351--17430398 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
17430341 ATGTATAACT
17430351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17430393 TA TA TA
1 TA TA TA
17430399 CAAAACAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17434864 original size:11 final size:11
Alignment explanation
Indices: 17434848--17434880 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
17434838 AGCCTTCCAC
17434848 TTTTCTCTCTT
1 TTTTCTCTCTT
17434859 TTTTCTCT-TT
1 TTTTCTCTCTT
17434869 TTTTCTTCTCTT
1 TTTTC-TCTCTT
17434881 GGGTGGAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 11 0.55
12 2 0.10
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTCTCTT
Found at i:17452852 original size:20 final size:20
Alignment explanation
Indices: 17452823--17452865 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
17452813 ATTAGGTTAC
17452823 TTTTAAGTTAGTT-ATCTTAA
1 TTTTAAGTTA-TTCATCTTAA
* *
17452843 TTTTATGTTATTCATGTTAA
1 TTTTAAGTTATTCATCTTAA
17452863 TTT
1 TTT
17452866 GGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTTAAGTTATTCATCTTAA
Found at i:17456776 original size:13 final size:13
Alignment explanation
Indices: 17456758--17456782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17456748 TCTAGAAAAC
17456758 TTATAAAATCATT
1 TTATAAAATCATT
17456771 TTATAAAATCAT
1 TTATAAAATCAT
17456783 AATTTCTTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTATAAAATCATT
Found at i:17458488 original size:44 final size:44
Alignment explanation
Indices: 17458439--17458526 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
17458429 ATGTCTTTCA
* * *
17458439 ATGAAAAGACTTATATCCTTTCATAATATGACTCTTCAAATAAT
1 ATGAAAAGACTTATATCCCTCCATAATATAACTCTTCAAATAAT
* *
17458483 ATGAAAAGACTTGTTTCCCTCCATAATATAACTCTTCAAATAAT
1 ATGAAAAGACTTATATCCCTCCATAATATAACTCTTCAAATAAT
17458527 TGTTTTCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (44 bp):
ATGAAAAGACTTATATCCCTCCATAATATAACTCTTCAAATAAT
Found at i:17459698 original size:21 final size:21
Alignment explanation
Indices: 17459655--17459698 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17459645 TTATATCAAG
**
17459655 TGCACATGATGTTACATGCCA
1 TGCACATGATGTTACACACCA
*
17459676 TGCACATGATGTTACACATCA
1 TGCACATGATGTTACACACCA
17459697 TG
1 TG
17459699 TACAAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (21 bp):
TGCACATGATGTTACACACCA
Found at i:17459843 original size:31 final size:31
Alignment explanation
Indices: 17459754--17459847 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 31
17459744 GTGCACATGA
* *
17459754 TGTTACACGCCATGTTGAAAAACAATATT-T
1 TGTTACAAGCCATGTTGAAAAAAAATATTGT
*
17459784 TGTTACATGCCATGGTT---AAAAAA-A--GT
1 TGTTACAAGCCAT-GTTGAAAAAAAATATTGT
*
17459810 TGTTACAAGACATGTTGAAAAAAAATATTGT
1 TGTTACAAGCCATGTTGAAAAAAAATATTGT
17459841 TGTTACA
1 TGTTACA
17459848 CGTCATGTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
25 3 0.06
26 12 0.23
27 1 0.02
28 11 0.21
29 1 0.02
30 12 0.23
31 12 0.23
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (31 bp):
TGTTACAAGCCATGTTGAAAAAAAATATTGT
Found at i:17459855 original size:31 final size:31
Alignment explanation
Indices: 17459754--17459855 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
17459744 GTGCACATGA
*
17459754 TGTTACACGCCATGTTGAAAAACAATATT-T
1 TGTTACACGCCATGTTGAAAAAAAATATTGT
*
17459784 TGTTACATGCCATGGTT---AAAAAA-A--GT
1 TGTTACACGCCAT-GTTGAAAAAAAATATTGT
* *
17459810 TGTTACAAGACATGTTGAAAAAAAATATTGT
1 TGTTACACGCCATGTTGAAAAAAAATATTGT
*
17459841 TGTTACACGTCATGT
1 TGTTACACGCCATGT
17459856 ACGAAAACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
25 3 0.05
26 12 0.21
27 1 0.02
28 11 0.19
29 1 0.02
30 12 0.21
31 18 0.31
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (31 bp):
TGTTACACGCCATGTTGAAAAAAAATATTGT
Found at i:17459895 original size:81 final size:81
Alignment explanation
Indices: 17459784--17459952 Score: 207
Period size: 81 Copynumber: 2.1 Consensus size: 81
17459774 AACAATATTT
* * *
17459784 TGTTACATGCCATGGTTAAAAAAAGTTGTTACAAGAC-ATGTTGAAAAAAAATATTGTTGTTACA
1 TGTTACATGCCATGGTTAAAAAAAGTTGTTA-AACACTATGTTGAAAAAAAATATTATTATTACA
*
17459848 CGTCATGTACGAAAACA
65 CGTCATGTACAAAAACA
* * * *
17459865 TGTTAGATGTCATGGTT-AAAAAAGATTGTTATACACTATGTTGAAAAGAAATATTATTATTACA
1 TGTTACATGCCATGGTTAAAAAAAG-TTGTTAAACACTATGTTGAAAAAAAATATTATTATTACA
* * *
17459929 TGTTATGTATAAAAACA
65 CGTCATGTACAAAAACA
17459946 TGTTACA
1 TGTTACA
17459953 CGTCACATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
80 10 0.14
81 64 0.86
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (81 bp):
TGTTACATGCCATGGTTAAAAAAAGTTGTTAAACACTATGTTGAAAAAAAATATTATTATTACAC
GTCATGTACAAAAACA
Found at i:17461614 original size:30 final size:30
Alignment explanation
Indices: 17461580--17461639 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17461570 GGAGCTAGTT
*
17461580 CCTCTTTCTGAGTTGGATTTAATTTTGATG
1 CCTCTTTCTAAGTTGGATTTAATTTTGATG
17461610 CCTCTTTCTAAGTTGGATTTAATTTTGATG
1 CCTCTTTCTAAGTTGGATTTAATTTTGATG
17461640 ACTGATCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.50
Consensus pattern (30 bp):
CCTCTTTCTAAGTTGGATTTAATTTTGATG
Found at i:17462507 original size:49 final size:49
Alignment explanation
Indices: 17462451--17462549 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
17462441 TTTACTCTAT
* * * *
17462451 AGGAAAAAAAAGGGAAAGAAAAATAGTTCCAAAATTTAGGTAAAAAAGA
1 AGGAAAAAAAAAGAAAAGAAAAATAATTCCAAAATTTAGGAAAAAAAGA
*
17462500 AGGAAAAAAAAAGAAAAGAAAAATAATTCCAAATTTTAGGAAAAAAAGA
1 AGGAAAAAAAAAGAAAAGAAAAATAATTCCAAAATTTAGGAAAAAAAGA
17462549 A
1 A
17462550 AAGAAATACT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.65, C:0.04, G:0.17, T:0.14
Consensus pattern (49 bp):
AGGAAAAAAAAAGAAAAGAAAAATAATTCCAAAATTTAGGAAAAAAAGA
Found at i:17462710 original size:21 final size:21
Alignment explanation
Indices: 17462686--17462725 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
17462676 AAAATTTAGG
17462686 AAAAAAAGAAAA-AAAATAAT
1 AAAAAAAGAAAAGAAAATAAT
*
17462706 AAAAAAGGAAAAGAAAATAA
1 AAAAAAAGAAAAGAAAATAA
17462726 ATTCCAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAAAAGAAAATAAT
Found at i:17462782 original size:15 final size:15
Alignment explanation
Indices: 17462762--17462792 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17462752 AAAAAGAGAA
17462762 AAGAAAAATAATTCC
1 AAGAAAAATAATTCC
17462777 AAGAAAAATAATTCC
1 AAGAAAAATAATTCC
17462792 A
1 A
17462793 CAATTTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AAGAAAAATAATTCC
Found at i:17464173 original size:27 final size:27
Alignment explanation
Indices: 17464143--17464197 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
17464133 CATCATAGTT
*
17464143 TATACCAACCAAAT-TTTCAACATAACG
1 TATAACAACCAAATCTTT-AACATAACG
* *
17464170 TATAACAACTAAATCTTTAATATAACG
1 TATAACAACCAAATCTTTAACATAACG
17464197 T
1 T
17464198 GGTACATGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (27 bp):
TATAACAACCAAATCTTTAACATAACG
Found at i:17465258 original size:2 final size:2
Alignment explanation
Indices: 17465251--17465294 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
17465241 CTTTTAGGAT
17465251 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
17465294 T
1 T
17465295 GTAATTAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17465554 original size:20 final size:22
Alignment explanation
Indices: 17465515--17465555 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17465505 ATTTAAATTA
*
17465515 TTTGAAATACCAATATTTATTT
1 TTTGAAAGACCAATATTTATTT
17465537 TTTGAAAGA-CAA-ATTTATT
1 TTTGAAAGACCAATATTTATT
17465556 GATGAAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTGAAAGACCAATATTTATTT
Found at i:17466430 original size:2 final size:2
Alignment explanation
Indices: 17466423--17466457 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17466413 TGCATGTGNT
17466423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17466458 TGCTAATCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17470400 original size:17 final size:17
Alignment explanation
Indices: 17470378--17470410 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17470368 AAATGAGGAT
17470378 TGCTCCCCCTAAGTATA
1 TGCTCCCCCTAAGTATA
17470395 TGCTCCCCCTAAGTAT
1 TGCTCCCCCTAAGTAT
17470411 GTGCATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.36, G:0.12, T:0.30
Consensus pattern (17 bp):
TGCTCCCCCTAAGTATA
Found at i:17473328 original size:63 final size:63
Alignment explanation
Indices: 17473254--17473379 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
17473244 TTCCCTCTAA
17473254 AATTTTGGTTATTTACCTTTGGCAGTATTTATTCTTTCTCTTTGCACCCGGTAAACCAAATTT
1 AATTTTGGTTATTTACCTTTGGCAGTATTTATTCTTTCTCTTTGCACCCGGTAAACCAAATTT
17473317 AATTTTGGTTATTTACCTTTGGCAGTATTTATTCTTTCTCTTTGCACCCGGTAAACCAAATTT
1 AATTTTGGTTATTTACCTTTGGCAGTATTTATTCTTTCTCTTTGCACCCGGTAAACCAAATTT
17473380 TACCTCATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (63 bp):
AATTTTGGTTATTTACCTTTGGCAGTATTTATTCTTTCTCTTTGCACCCGGTAAACCAAATTT
Found at i:17479843 original size:23 final size:23
Alignment explanation
Indices: 17479817--17479860 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17479807 TATGAAACGG
* *
17479817 CATGGTGGGAATGTGTGACACGT
1 CATGGTGAGAATATGTGACACGT
17479840 CATGGTGAGAATATGTGACAC
1 CATGGTGAGAATATGTGACAC
17479861 AGCTATGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (23 bp):
CATGGTGAGAATATGTGACACGT
Found at i:17479984 original size:23 final size:23
Alignment explanation
Indices: 17479888--17480073 Score: 130
Period size: 23 Copynumber: 8.1 Consensus size: 23
17479878 GTTTAGAGTT
** * *
17479888 TGTGACACACCATGGAGGGAATA
1 TGTGACATGCCATGGTGAGAATA
*
17479911 TGTGACATGGCA-GGCTGAGAATA
1 TGTGACATGCCATGG-TGAGAATA
* * * *
17479934 TGTGACACGAC-TCGGGGGGAAATA
1 TGTGACATGCCAT-GGTGAG-AATA
* *
17479958 TGTGAGATGACATGGTGAGAATA
1 TGTGACATGCCATGGTGAGAATA
*
17479981 TGTGACATGTCA-GTGTGAG-A-A
1 TGTGACATGCCATG-GTGAGAATA
* * *
17480002 TGTGGCATGCCATGGTGTGCATA
1 TGTGACATGCCATGGTGAGAATA
* *
17480025 TGTGACACGCCATAGTGAGAATA
1 TGTGACATGCCATGGTGAGAATA
* *
17480048 TGTGACACGCCATGGTGAGCATA
1 TGTGACATGCCATGGTGAGAATA
17480071 TGT
1 TGT
17480074 AACACGACTG
Statistics
Matches: 129, Mismatches: 25, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
21 15 0.12
22 6 0.05
23 88 0.68
24 19 0.15
25 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.24
Consensus pattern (23 bp):
TGTGACATGCCATGGTGAGAATA
Found at i:17480070 original size:46 final size:46
Alignment explanation
Indices: 17479906--17480079 Score: 151
Period size: 44 Copynumber: 3.8 Consensus size: 46
17479896 ACCATGGAGG
* * * * *
17479906 GAATATGTGACATGGCA-GGCTGAGAATATGTGACACGACTCGGGGGGA
1 GAATATGTGACATGCCATGG-TGAGCATATGTGACACG-C-CAGTGTGA
* * * * *
17479954 -AATATGTGAGATGACATGGTGAGAATATGTGACATGTCAGTGTGA
1 GAATATGTGACATGCCATGGTGAGCATATGTGACACGCCAGTGTGA
* *
17479999 G-A-ATGTGGCATGCCATGGTGTGCATATGTGACACGCCA-TAGTGA
1 GAATATGTGACATGCCATGGTGAGCATATGTGACACGCCAGT-GTGA
* *
17480043 GAATATGTGACACGCCATGGTGAGCATATGTAACACG
1 GAATATGTGACATGCCATGGTGAGCATATGTGACACG
17480080 ACTGTGACAC
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
43 1 0.01
44 34 0.33
45 7 0.07
46 29 0.28
47 30 0.29
48 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (46 bp):
GAATATGTGACATGCCATGGTGAGCATATGTGACACGCCAGTGTGA
Found at i:17480155 original size:47 final size:47
Alignment explanation
Indices: 17480081--17480231 Score: 223
Period size: 47 Copynumber: 3.2 Consensus size: 47
17480071 TGTAACACGA
*
17480081 CTGTGACACGGTAGGGTTCAGAATTTGTGACACGCCATGGAAGGAAT
1 CTGTGACACGGTAGGGTTCAGAGTTTGTGACACGCCATGGAAGGAAT
* * * *
17480128 CTGTGACATGGCAGGGTTCAGAGTTTGTGACACACCATGGAGGGAAT
1 CTGTGACACGGTAGGGTTCAGAGTTTGTGACACGCCATGGAAGGAAT
* *
17480175 TTATGACACGGTA-GGTTCAGAGTTTGTGACACGCCATGGAAGGAAT
1 CTGTGACACGGTAGGGTTCAGAGTTTGTGACACGCCATGGAAGGAAT
*
17480221 CTGTGATACGG
1 CTGTGACACGG
17480232 CAAGTTGATA
Statistics
Matches: 90, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 39 0.43
47 51 0.57
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (47 bp):
CTGTGACACGGTAGGGTTCAGAGTTTGTGACACGCCATGGAAGGAAT
Found at i:17483746 original size:31 final size:31
Alignment explanation
Indices: 17483704--17483872 Score: 266
Period size: 31 Copynumber: 5.5 Consensus size: 31
17483694 CAGCGTTATT
* *
17483704 GTGTGACAACATTTGACTTGATATGCATGGC
1 GTGTAACAACATTTTACTTGATATGCATGGC
* * *
17483735 ATGTAACAACATTTTAATTGATATGCATGGT
1 GTGTAACAACATTTTACTTGATATGCATGGC
17483766 GTGTAACAACATTTTACTTGATATGCATGGC
1 GTGTAACAACATTTTACTTGATATGCATGGC
17483797 GTGTAACAACATTTTACTTGATATGCATGGC
1 GTGTAACAACATTTTACTTGATATGCATGGC
* * *
17483828 GTGTAACGACATTTTACTTGATTTGCATGGT
1 GTGTAACAACATTTTACTTGATATGCATGGC
17483859 GTGTAACAACATTT
1 GTGTAACAACATTT
17483873 ATTTCTTTCT
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 126 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (31 bp):
GTGTAACAACATTTTACTTGATATGCATGGC
Found at i:17490788 original size:31 final size:31
Alignment explanation
Indices: 17490747--17491192 Score: 385
Period size: 31 Copynumber: 14.4 Consensus size: 31
17490737 CTGCAACAAG
* * *
17490747 TCAGCATGTCACGCCATAAATCTGTTTCCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* *
17490778 TCAACGTGTCACGCCATAAATCTGCAACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * *
17490809 TGAGCGTGTCACCCCATAAATCTGCTACCAG
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * * * * *
17490840 TTACCGTGTCATGCCATTAATCTGTTTCCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
*
17490871 TCAGCGTGTCACGCCATAAATCTACTACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * * **
17490902 TCAGCGTGTCACACCATGAATCTACTAAAAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * *
17490933 TCAGCATGTCACGCCATGAATCTGCTTCCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * * *
17490964 TCAGCGTGTCACTCAATGAATCTGCTTCCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
** *
17490995 TCAGCGTGTCACGCCATAAATCTATTGCCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * * *
17491026 TCAGCATGTCAC-CCTATAATTTTGCTAGCAC
1 TCAGCGTGTCACGCC-ATAAATCTGCTACCAC
* * * * *
17491057 TCAGCTTGTCATGCCATGAATCTGTTTCCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * * *
17491088 TCAGCGTGTGACGTCATAAATCTG-TAACAAG
1 TCAGCGTGTCACGCCATAAATCTGCT-ACCAC
* * *
17491119 TCAGAGTGTCAC-CTCATAAATCTGTTACCCC
1 TCAGCGTGTCACGC-CATAAATCTGCTACCAC
* * * *
17491150 TCAGTGTGTCACCCCATAAATCTGTTTCCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
*
17491181 TCAACGTGTCAC
1 TCAGCGTGTCAC
17491193 TAGAAAAGGG
Statistics
Matches: 331, Mismatches: 78, Indels: 12
0.79 0.19 0.03
Matches are distributed among these distances:
30 3 0.01
31 324 0.98
32 4 0.01
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (31 bp):
TCAGCGTGTCACGCCATAAATCTGCTACCAC
Found at i:17491947 original size:24 final size:24
Alignment explanation
Indices: 17491889--17491973 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
17491879 CTTGCATCAG
* *
17491889 CAACAGCTTCACTTGGTGCAACAA
1 CAACAACTTCACTTGGTGCACCAA
** *
17491913 CAGTAATTTCACTTGGTGCACCAA
1 CAACAACTTCACTTGGTGCACCAA
* * *
17491937 CAACAGCTTCATTTGGTGCACCAG
1 CAACAACTTCACTTGGTGCACCAA
*
17491961 TAACAACTTCACT
1 CAACAACTTCACT
17491974 CGCTCGACTA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (24 bp):
CAACAACTTCACTTGGTGCACCAA
Found at i:17496946 original size:151 final size:151
Alignment explanation
Indices: 17496776--17497082 Score: 501
Period size: 151 Copynumber: 2.0 Consensus size: 151
17496766 AATTTAAATT
17496776 TAAATTATTAATTTCGAAACCCTTAAAAA-TTATTAATAAAATAAGATGAAACAAATATTTAAAG
1 TAAATTATTAATTTCGAAACCC-TAAAAATTTATTAATAAAATAAGATGAAACAAATATTTAAAG
*
17496840 TTATATTTAACTTTATCAACCATAAATACAATCTTTAATTTAGAAAATTTCAAC-CTAAAAAATA
65 TTATATTTAACTTTATCAACCATAAATACAATCTTTAATTTAGAAAATTTCAACAATAAAAAATA
17496904 TAACCTAAAATATTAAACAAAA
130 TAACCTAAAATATTAAACAAAA
*
17496926 TAAANTTATTAATTTTGAAACCCTAAAAATTTATTAATAAAATAAGATGAAACAAATATTTAAAG
1 TAAA-TTATTAATTTCGAAACCCTAAAAATTTATTAATAAAATAAGATGAAACAAATATTTAAAG
* *
17496991 TTATATTTAACTTTATCAACCATAAATACAATCTTTAATTTAGGATATTTCAACTTAAAATAAAA
65 TTATATTTAACTTTATCAACCATAAATACAATCTTTAATTTAGAAAATTTCAAC----AATAAAA
*
17497056 AATATAACTTAAAATATTAAACAAAA
126 AATATAACCTAAAATATTAAACAAAA
17497082 T
1 T
17497083 CAAAACATAA
Statistics
Matches: 145, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
150 10 0.07
151 104 0.72
156 31 0.21
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (151 bp):
TAAATTATTAATTTCGAAACCCTAAAAATTTATTAATAAAATAAGATGAAACAAATATTTAAAGT
TATATTTAACTTTATCAACCATAAATACAATCTTTAATTTAGAAAATTTCAACAATAAAAAATAT
AACCTAAAATATTAAACAAAA
Found at i:17503069 original size:2 final size:2
Alignment explanation
Indices: 17503064--17503088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17503054 ATATATAGCT
17503064 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17503089 TTCCAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17504014 original size:21 final size:21
Alignment explanation
Indices: 17503990--17504030 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17503980 CTCCAACTTG
17503990 TTTTCTTCTTCCTCCTTTCTC
1 TTTTCTTCTTCCTCCTTTCTC
* *
17504011 TTTTCTTTTTTCTCCTTTCT
1 TTTTCTTCTTCCTCCTTTCT
17504031 TCCCTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTCTTCTTCCTCCTTTCTC
Found at i:17509098 original size:23 final size:23
Alignment explanation
Indices: 17509068--17509243 Score: 117
Period size: 23 Copynumber: 7.7 Consensus size: 23
17509058 TCACTCATGT
*
17509068 TGTTACACTTCAT-TTTCAAAAAA
1 TGTTACACTCCATGTTT-AAAAAA
* *
17509091 TGTTACACGCCATGTTTAAAAAT
1 TGTTACACTCCATGTTTAAAAAA
17509114 TGTTACA-TGCCATGTTTAAAAAA
1 TGTTACACT-CCATGTTTAAAAAA
* * *
17509137 TGTTACACACCATG-CTCAAAAA
1 TGTTACACTCCATGTTTAAAAAA
* * * * *
17509159 TATTACA-TGCAAGTTCAAAAAT
1 TGTTACACTCCATGTTTAAAAAA
* ** *
17509181 TGTTACACGCCATGTTTCCAACA
1 TGTTACACTCCATGTTTAAAAAA
* * *
17509204 TGTTACACGCTATGTTAAATAAATA
1 TGTTACACTCCATGTTTAA-AAA-A
*
17509229 TGTTACACGCCATGT
1 TGTTACACTCCATGT
17509244 GCTAACACAT
Statistics
Matches: 115, Mismatches: 31, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
21 3 0.03
22 22 0.19
23 70 0.61
24 5 0.04
25 15 0.13
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (23 bp):
TGTTACACTCCATGTTTAAAAAA
Found at i:17509120 original size:46 final size:45
Alignment explanation
Indices: 17509067--17509197 Score: 140
Period size: 46 Copynumber: 2.9 Consensus size: 45
17509057 GTCACTCATG
*
17509067 TTGTTACACTTCATTTTCAAAAAATGTTACACGCCATGTTTAAAAA
1 TTGTTACA-TCCATTTTCAAAAAATGTTACACGCCATGTTTAAAAA
* * *
17509113 TTGTTACATGCCATGTTT-AAAAAATGTTACACACCATGCTCAAAAA
1 TTGTTACAT-CCAT-TTTCAAAAAATGTTACACGCCATGTTTAAAAA
* * ** *
17509159 -TATTACATGCAAGTTCAAAAATTGTTACACGCCATGTTT
1 TTGTTACATCCATTTTCAAAAAATGTTACACGCCATGTTT
17509198 CCAACATGTT
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
43 2 0.03
44 21 0.30
45 8 0.11
46 36 0.51
47 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (45 bp):
TTGTTACATCCATTTTCAAAAAATGTTACACGCCATGTTTAAAAA
Found at i:17509977 original size:31 final size:31
Alignment explanation
Indices: 17509942--17510030 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
17509932 CCTTGGGTTG
*
17509942 GTAATATACAGTCTCATTGCACCTTGGACCA
1 GTAATGTACAGTCTCATTGCACCTTGGACCA
* * *
17509973 GTAATGTACA-TTTCCATTGCACCTTAGACCG
1 GTAATGTACAGTCT-CATTGCACCTTGGACCA
* * *
17510004 GCAATGTACAGCCCCATTGCACCTTGG
1 GTAATGTACAGTCTCATTGCACCTTGG
17510031 GTAGCATTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.04
31 45 0.96
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (31 bp):
GTAATGTACAGTCTCATTGCACCTTGGACCA
Found at i:17510709 original size:19 final size:21
Alignment explanation
Indices: 17510680--17510719 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
17510670 CAATTCCATA
17510680 GACATTTATTTTGACA-TTTT
1 GACATTTATTTTGACACTTTT
17510700 GACA-TTATTTTGACACTTTT
1 GACATTTATTTTGACACTTTT
17510720 AGGATAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
GACATTTATTTTGACACTTTT
Found at i:17511514 original size:2 final size:2
Alignment explanation
Indices: 17511507--17511532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17511497 CAAAGTTTAT
17511507 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
17511533 AAAGATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17513553 original size:9 final size:9
Alignment explanation
Indices: 17513541--17513570 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
17513531 TTAAAAATCT
17513541 TTTAAATAA
1 TTTAAATAA
17513550 TTTAAATAA
1 TTTAAATAA
17513559 TTTAAATAA
1 TTTAAATAA
17513568 TTT
1 TTT
17513571 TTTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTTAAATAA
Found at i:17514179 original size:27 final size:27
Alignment explanation
Indices: 17514135--17514189 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17514125 TAAGTGCGAG
* **
17514135 TGTTGAAAAAAATGTTGTTACACATCA
1 TGTTAAAAAAAAAATTGTTACACATCA
* *
17514162 TGTTAAAAAAAAAATTGTTGCACGTCA
1 TGTTAAAAAAAAAATTGTTACACATCA
17514189 T
1 T
17514190 ATTTAAGGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (27 bp):
TGTTAAAAAAAAAATTGTTACACATCA
Found at i:17514291 original size:29 final size:28
Alignment explanation
Indices: 17514258--17514347 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
17514248 AGTTATAAAC
17514258 CATGTTTAAAAAATAATATTATTACAAGT
1 CATGTTTAAAAAA-AATATTATTACAAGT
* *
17514287 CATGTTT-AAAAAAATATTATTGCACGT
1 CATGTTTAAAAAAAATATTATTACAAGT
* ** *
17514314 CATATTTAAAAAAAA-ATGGTTACATGT
1 CATGTTTAAAAAAAATATTATTACAAGT
17514341 CATGTTT
1 CATGTTT
17514348 TAAGTAACTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
27 33 0.63
28 12 0.23
29 7 0.13
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (28 bp):
CATGTTTAAAAAAAATATTATTACAAGT
Found at i:17514555 original size:29 final size:29
Alignment explanation
Indices: 17514499--17514556 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
17514489 AGAGACAAAG
* * *
17514499 TTACACGTCATATTTAAAAAATATTTTTA
1 TTACACGTCATATTAAAAAAAAAATTTTA
*
17514528 TTACACGTCATGTTAAAAAAAAAATTTTA
1 TTACACGTCATATTAAAAAAAAAATTTTA
17514557 CATGCCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (29 bp):
TTACACGTCATATTAAAAAAAAAATTTTA
Found at i:17514584 original size:27 final size:27
Alignment explanation
Indices: 17514525--17514591 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
17514515 AAAAATATTT
* *
17514525 TTATTACACGTCATGTTAAAAAAAAAA
1 TTATTACATGCCATGTTAAAAAAAAAA
* **
17514552 TT-TTACATGCCATGTTGAAAAAAATG
1 TTATTACATGCCATGTTAAAAAAAAAA
*
17514578 TTATTACATACCAT
1 TTATTACATGCCAT
17514592 ATTTAAGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (27 bp):
TTATTACATGCCATGTTAAAAAAAAAA
Found at i:17522790 original size:39 final size:35
Alignment explanation
Indices: 17522664--17522831 Score: 132
Period size: 36 Copynumber: 4.7 Consensus size: 35
17522654 TCTCACCAGC
**
17522664 TCATGTGCACTCCCAGGCCGCACATA-GCTAGA-ATCA
1 TCATGTGCACTCCCACACCGCACA-AGGC-A-ATATCA
17522700 TCATGTGCACTCCCACACCGCACAAGGCAATATCA
1 TCATGTGCACTCCCACACCGCACAAGGCAATATCA
* * *
17522735 TCATGTGCACTTCCACACTGCACATGGCATATATCA
1 TCATGTGCACTCCCACACCGCACAAGGCA-ATATCA
* *
17522771 TCAGTGTGTGCACTCCCACA--GCAC-A-CCACTATCA
1 TCA---TGTGCACTCCCACACCGCACAAGGCAATATCA
*
17522805 TTGTCATGTGCACTCCCACACCACACA
1 ---TCATGTGCACTCCCACACCGCACA
17522832 CGCACGGTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
34 20 0.18
35 34 0.31
36 36 0.33
37 7 0.06
39 13 0.12
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (35 bp):
TCATGTGCACTCCCACACCGCACAAGGCAATATCA
Found at i:17524826 original size:19 final size:15
Alignment explanation
Indices: 17524789--17524818 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17524779 GATATATTCC
17524789 CAACCAATATATATT
1 CAACCAATATATATT
17524804 CAACCAATATATATT
1 CAACCAATATATATT
17524819 AAAGCAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
CAACCAATATATATT
Done.