Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 45 of 103
Found at i:16826898 original size:12 final size:12
Alignment explanation
Indices: 16826860--16826898 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
16826850 AGCAAAAAGG
16826860 AAAGGAAAAGAA
1 AAAGGAAAAGAA
16826872 CAAAGG-AAAGTAA
1 -AAAGGAAAAG-AA
16826885 AAAGGAAAAGAA
1 AAAGGAAAAGAA
16826897 AA
1 AA
16826899 GCTGAGCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (12 bp):
AAAGGAAAAGAA
Found at i:16827319 original size:19 final size:19
Alignment explanation
Indices: 16827295--16827347 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
16827285 TGACCGGCAG
*
16827295 GAGAGAAGAGAAAAAGAAA
1 GAGAGAAAAGAAAAAGAAA
**
16827314 GAGAGAAAAGAACGAGAAA
1 GAGAGAAAAGAAAAAGAAA
16827333 G-GAAGAAAAGAAAAA
1 GAG-AGAAAAGAAAAA
16827348 AAAATGGGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (19 bp):
GAGAGAAAAGAAAAAGAAA
Found at i:16827324 original size:13 final size:12
Alignment explanation
Indices: 16827300--16827347 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
16827290 GGCAGGAGAG
16827300 AAGAGAAAAAGA
1 AAGAGAAAAAGA
16827312 AAGAGAGAAAAGA
1 AAGAGA-AAAAGA
*
16827325 ACGAGAAAGGAAGA
1 AAGAGAAA--AAGA
16827339 AA-AGAAAAA
1 AAGAGAAAAA
16827348 AAAATGGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 8 0.26
13 16 0.52
14 5 0.16
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (12 bp):
AAGAGAAAAAGA
Found at i:16827378 original size:25 final size:25
Alignment explanation
Indices: 16827345--16827392 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
16827335 AAGAAAAGAA
16827345 AAAAAAATGGGCATAGCCCAATAAG
1 AAAAAAATGGGCATAGCCCAATAAG
* *
16827370 AAAAGAATGGGCATGGCCCAATA
1 AAAAAAATGGGCATAGCCCAATA
16827393 GGAAGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (25 bp):
AAAAAAATGGGCATAGCCCAATAAG
Found at i:16827995 original size:63 final size:63
Alignment explanation
Indices: 16827862--16828021 Score: 187
Period size: 63 Copynumber: 2.5 Consensus size: 63
16827852 GGATGTCACC
* * ** * *
16827862 GTGCATGTTCGGAGTGGGCAATGCACATGCCGATTGAATGATGAGGTTTTAATAGTTACAACC
1 GTGCATGTGCGGAGTGGGCAATGCACATGCCGATTGAATGACGAGGTTGCAATAATTACAACA
* * * * *
16827925 GTACATGTGCGGAGTGAGCAATGCACATGCC-AGTTGAATGACGATGTTGCGATAATTACTACA
1 GTGCATGTGCGGAGTGGGCAATGCACATGCCGA-TTGAATGACGAGGTTGCAATAATTACAACA
* *
16827988 GTGCATGTGAGGAGTGGGCAGTGCACATGCCGAT
1 GTGCATGTGCGGAGTGGGCAATGCACATGCCGAT
16828022 AATGATGCAT
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
62 1 0.01
63 78 0.98
64 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.26
Consensus pattern (63 bp):
GTGCATGTGCGGAGTGGGCAATGCACATGCCGATTGAATGACGAGGTTGCAATAATTACAACA
Found at i:16832206 original size:22 final size:22
Alignment explanation
Indices: 16832180--16832221 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16832170 AGTTATTTGG
*
16832180 GCTTAATTTTTATAGTAATTTA
1 GCTTAATTCTTATAGTAATTTA
*
16832202 GCTTAGTTCTTATAGTAATT
1 GCTTAATTCTTATAGTAATT
16832222 CATAGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (22 bp):
GCTTAATTCTTATAGTAATTTA
Found at i:16832386 original size:17 final size:18
Alignment explanation
Indices: 16832364--16832397 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16832354 TTTGTAAGTG
*
16832364 TTTAAT-GAAGGAAGAAT
1 TTTAATGGAAGAAAGAAT
16832381 TTTAATGGAAGAAAGAA
1 TTTAATGGAAGAAAGAA
16832398 AGCAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (18 bp):
TTTAATGGAAGAAAGAAT
Found at i:16838494 original size:31 final size:29
Alignment explanation
Indices: 16838408--16838530 Score: 105
Period size: 29 Copynumber: 4.3 Consensus size: 29
16838398 AAACATTAAA
* * *
16838408 GTGTAACAA-AAT-GTTTTTGAATATGGC
1 GTGTAACAACAATATTTTTTTAACATGGC
*
16838435 GTGTAACAATAATATTTTTTTAACATGGC
1 GTGTAACAACAATATTTTTTTAACATGGC
* *
16838464 GTGTAATAACAGTATTTGTTTTCAACATGGC
1 GTGTAACAACAATATTT-TTTT-AACATGGC
* *
16838495 GTATAACAAC----TTTTTTTAACCATGGT
1 GTGTAACAACAATATTTTTTTAA-CATGGC
16838521 GTGTAACAAC
1 GTGTAACAAC
16838531 TTAACCATAG
Statistics
Matches: 81, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
25 2 0.02
26 18 0.22
27 12 0.15
28 3 0.04
29 26 0.32
30 4 0.05
31 16 0.20
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTTAACATGGC
Found at i:16838661 original size:24 final size:24
Alignment explanation
Indices: 16838540--16838665 Score: 66
Period size: 24 Copynumber: 5.5 Consensus size: 24
16838530 CTTAACCATA
* * * *
16838540 GCGTGTCACATGTTTCTGTACATA
1 GCGTGTAACATATTTTTGTACATG
*
16838564 GCGTGTAACA-ACTTTTT-T-TATG
1 GCGTGTAACATA-TTTTTGTACATG
* * * *
16838586 GAGTGTCACATATTTTTGCACATA
1 GCGTGTAACATATTTTTGTACATG
** **
16838610 GCGTGTAACA-A-CCTAAT-CATG
1 GCGTGTAACATATTTTTGTACATG
* *
16838631 ACATGTAACATATTTTTGTACATG
1 GCGTGTAACATATTTTTGTACATG
16838655 GCGTGTAACAT
1 GCGTGTAACAT
16838666 TATAGCGTGT
Statistics
Matches: 69, Mismatches: 26, Indels: 14
0.63 0.24 0.13
Matches are distributed among these distances:
21 11 0.16
22 17 0.25
23 5 0.07
24 36 0.52
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (24 bp):
GCGTGTAACATATTTTTGTACATG
Found at i:16844612 original size:18 final size:18
Alignment explanation
Indices: 16844583--16844622 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
16844573 AGGGTCCTCA
16844583 CCACATCACACCCGTAGT
1 CCACATCACACCCGTAGT
*
16844601 GCCACA-CACACCCTTAGT
1 -CCACATCACACCCGTAGT
16844619 CCAC
1 CCAC
16844623 TTAAGGGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.28, C:0.47, G:0.10, T:0.15
Consensus pattern (18 bp):
CCACATCACACCCGTAGT
Found at i:16852952 original size:36 final size:36
Alignment explanation
Indices: 16852903--16852971 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
16852893 GGGATTCTTG
16852903 CTTTTTAAAGGGATCAAACGATAACCCTTACACCGA
1 CTTTTTAAAGGGATCAAACGATAACCCTTACACCGA
* * * * *
16852939 CTTTTTTACGGGATCCAGCGATAAGCCTTACAC
1 CTTTTTAAAGGGATCAAACGATAACCCTTACAC
16852972 AATCCACGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (36 bp):
CTTTTTAAAGGGATCAAACGATAACCCTTACACCGA
Found at i:16854640 original size:2 final size:2
Alignment explanation
Indices: 16854628--16854672 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
16854618 NNNNNNNNNN
16854628 TA TA GTA 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
16854671 TA
1 TA
16854673 CATGTACACC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16854740 original size:35 final size:35
Alignment explanation
Indices: 16854701--16854784 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
16854691 CTTACTTAGC
16854701 TCATGTGCACTCCCTACACGCACAACGCAATATCA
1 TCATGTGCACTCCCTACACGCACAACGCAATATCA
* * ***
16854736 TCATGTGCACTCCGTACACTCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACAACGCAATATCA
**
16854771 TCACATGCACTCCC
1 TCATGTGCACTCCC
16854785 ACCCACATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.29, C:0.37, G:0.10, T:0.25
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCACAACGCAATATCA
Found at i:16854792 original size:32 final size:33
Alignment explanation
Indices: 16854728--16854792 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
16854718 ACGCACAACG
** *
16854728 CAATATCATCATGTGCACTCCGTACACTCACATTT
1 CAATATCATCACATGCACTCC--ACACCCACATTT
16854763 CAATATCATCACATGCACTCC-CACCCACAT
1 CAATATCATCACATGCACTCCACACCCACAT
16854793 CATTATCGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 8 0.30
35 19 0.70
ACGTcount: A:0.31, C:0.37, G:0.06, T:0.26
Consensus pattern (33 bp):
CAATATCATCACATGCACTCCACACCCACATTT
Found at i:16854862 original size:19 final size:19
Alignment explanation
Indices: 16854838--16854883 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
16854828 CCGGCACCAT
*
16854838 CACGTGCACTCCTACACCG
1 CACGTGCACTCCCACACCG
16854857 CACGTGCACTCCCACACCG
1 CACGTGCACTCCCACACCG
*
16854876 CATGTGCA
1 CACGTGCA
16854884 TGGTTATAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.46, G:0.17, T:0.15
Consensus pattern (19 bp):
CACGTGCACTCCCACACCG
Found at i:16856889 original size:18 final size:18
Alignment explanation
Indices: 16856866--16856923 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
16856856 TTAAATTATT
16856866 TAATTAAGTCATTGGGCC
1 TAATTAAGTCATTGGGCC
* * **
16856884 TAATTAATTAAATT--GTT
1 TAATTAAGT-CATTGGGCC
16856901 TAATTAAGTCATTGGGCC
1 TAATTAAGTCATTGGGCC
16856919 TAATT
1 TAATT
16856924 GATTAAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 3 0.10
17 9 0.31
18 14 0.48
19 3 0.10
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (18 bp):
TAATTAAGTCATTGGGCC
Found at i:16856892 original size:35 final size:35
Alignment explanation
Indices: 16856826--16857001 Score: 232
Period size: 35 Copynumber: 5.1 Consensus size: 35
16856816 CACTTGATTA
*
16856826 AAATTGTTTAATTAAG---TTGTGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
16856858 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
16856893 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * * *
16856928 AAAATTGTTTAATTAAATTATTGAGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
16856964 AAATTATTTAATTAAGTTATTAGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
16856999 AAA
1 AAA
16857002 CTAAACAATT
Statistics
Matches: 126, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.12
35 81 0.64
36 30 0.24
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:16856965 original size:71 final size:70
Alignment explanation
Indices: 16856826--16857001 Score: 232
Period size: 71 Copynumber: 2.5 Consensus size: 70
16856816 CACTTGATTA
* * *
16856826 AAATTGTTTAATTAAG--TTGTGCCTAATTAATT-AAATTATTTAATTAAGTCATTGGGCCTAAT
1 AAATTGTTTAATTAAGTATTGGGCCTAATTAATTAAAATTATTTAATTAAATCATTGAGCCTAAT
16856888 TAATT
66 TAATT
* * * *
16856893 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATTATTGAGCTTAA
1 AAATTGTTTAATTAAGT-ATTGGGCCTAATTAATTAAAATTATTTAATTAAATCATTGAGCCTAA
16856958 TTAATT
65 TTAATT
* *
16856964 AAATTATTTAATTAAGTTATTAGGCCTAATTAATTAAA
1 AAATTGTTTAATTAAG-TATTGGGCCTAATTAATTAAA
16857002 CTAAACAATT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
67 16 0.17
70 14 0.15
71 63 0.67
72 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (70 bp):
AAATTGTTTAATTAAGTATTGGGCCTAATTAATTAAAATTATTTAATTAAATCATTGAGCCTAAT
TAATT
Found at i:16857012 original size:106 final size:103
Alignment explanation
Indices: 16856819--16857015 Score: 277
Period size: 106 Copynumber: 1.9 Consensus size: 103
16856809 TCTCAAGCAC
* * *
16856819 TTGATTAAAATTGTTTAATTAAGTTGTGCCTAATTAATTAAATTATTTAATTAAGTCATTGGGCC
1 TTGATTAAAATTGTTTAATTAAATTGAGCCTAATTAATTAAATTATTTAATTAAGTCATTAGGCC
* ****
16856884 TAATTAATTAAATTGTTTAATTAAGTCATTGGGCCTAA
66 TAATTAATTAAACTAAACAATTAAGTCATTGGGCCTAA
* *
16856922 TTGATTAAAATTGTTTAATTAAATTATTGAGCTTAATTAATTAAATTATTTAATTAAGTTATTAG
1 TTGATTAAAATTGTTTAATT-AA--ATTGAGCCTAATTAATTAAATTATTTAATTAAGTCATTAG
16856987 GCCTAATTAATTAAACTAAACAATTAAGT
63 GCCTAATTAATTAAACTAAACAATTAAGT
16857016 TAACTGGACT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
103 20 0.25
104 2 0.02
106 59 0.73
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (103 bp):
TTGATTAAAATTGTTTAATTAAATTGAGCCTAATTAATTAAATTATTTAATTAAGTCATTAGGCC
TAATTAATTAAACTAAACAATTAAGTCATTGGGCCTAA
Found at i:16864903 original size:35 final size:35
Alignment explanation
Indices: 16864830--16865012 Score: 180
Period size: 35 Copynumber: 5.3 Consensus size: 35
16864820 CAAGCACTTG
* *
16864830 ATTAAACTTGTTTAATTAAGTT-GTA--CCTAATTA
1 ATTAAA-TTATTTAATTAAGTTATTAGGCCTAATTA
16864863 ATTAAATTATTTAATTAAGTTATTAGGCCTAATTA
1 ATTAAATTATTTAATTAAGTTATTAGGCCTAATTA
* * *
16864898 GTTAAATTGTTTAATTAAGTCATT-GAGCCTAATTGA
1 ATTAAATTATTTAATTAAGTTATTAG-GCCTAATT-A
* * **
16864934 ATAAAATTATTTAATTGAA-TTGTT-GGATTTAATTA
1 ATTAAATTATTTAATT-AAGTTATTAGG-CCTAATTA
* *
16864969 ATTAAATTATTTAATTAAGTTATCAAGCCTAATTA
1 ATTAAATTATTTAATTAAGTTATTAGGCCTAATTA
16865004 ATTAAATTA
1 ATTAAATTA
16865013 AACAATTAAG
Statistics
Matches: 123, Mismatches: 18, Indels: 16
0.78 0.11 0.10
Matches are distributed among these distances:
32 14 0.11
33 8 0.07
34 3 0.02
35 72 0.59
36 24 0.20
37 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (35 bp):
ATTAAATTATTTAATTAAGTTATTAGGCCTAATTA
Found at i:16864967 original size:71 final size:69
Alignment explanation
Indices: 16864830--16865012 Score: 196
Period size: 71 Copynumber: 2.6 Consensus size: 69
16864820 CAAGCACTTG
16864830 ATTAAACTTGTTTAATTAAG--TTGTA-CCTAATTAATTAAATTATTTAATTAAGTTATTAGGCC
1 ATTAAA-TTGTTTAATTAAGTATTG-AGCCTAATTAATTAAATTATTTAATTAAGTTATTAGGCC
16864892 TAATTA
64 TAATTA
* * *
16864898 GTTAAATTGTTTAATTAAGTCATTGAGCCTAATTGAATAAAATTATTTAATTGAA-TTGTT-GGA
1 ATTAAATTGTTTAATTAAGT-ATTGAGCCTAATT-AATTAAATTATTTAATT-AAGTTATTAGG-
**
16864961 TTTAATTA
62 CCTAATTA
* **
16864969 ATTAAATTATTTAATTAAGTTATCAAGCCTAATTAATTAAATTA
1 ATTAAATTGTTTAATTAAG-TATTGAGCCTAATTAATTAAATTA
16865013 AACAATTAAG
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
67 13 0.13
68 5 0.05
69 1 0.01
70 21 0.22
71 54 0.56
72 3 0.03
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (69 bp):
ATTAAATTGTTTAATTAAGTATTGAGCCTAATTAATTAAATTATTTAATTAAGTTATTAGGCCTA
ATTA
Found at i:16872733 original size:58 final size:57
Alignment explanation
Indices: 16872643--16872752 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
16872633 CATAATAATC
* * *
16872643 CAAAGTAGAATGCATGCAATAGATTTATTTTATGCCATTTAGTAAATGCTATGTGAGG
1 CAAAGTAGAATGCATGCAATAGATTTATTTTATG-CAATTAATAAATACTATGTGAGG
* *
16872701 CAAAGTAGTATGCATG-AGGTAGATTTATTTTATGCAATTAATAAATACTATG
1 CAAAGTAGAATGCATGCA-ATAGATTTATTTTATGCAATTAATAAATACTATG
16872753 CATGCAAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 16 0.35
58 30 0.65
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (57 bp):
CAAAGTAGAATGCATGCAATAGATTTATTTTATGCAATTAATAAATACTATGTGAGG
Found at i:16875207 original size:72 final size:72
Alignment explanation
Indices: 16875086--16875273 Score: 297
Period size: 72 Copynumber: 2.6 Consensus size: 72
16875076 AAGCTGAAAA
* * *
16875086 ACAAAACCAACTTAGTCAACCAAGATAA-GGGTTAGTCGACTAAAAAGCTACTGCCAAAATCTGA
1 ACAAAACCAACTTAGTCGACTAAGA-AATGGGTTAGTCGACTAAGAAGCTACTGCCAAAATCTGA
*
16875150 ACTTGAAG
65 ACTTCAAG
* *
16875158 ACAGAACCAACTTAGTCGACTAAGAAATGGGTTAGTTGACTAAGAAGCTACTGCCAAAATCTGAA
1 ACAAAACCAACTTAGTCGACTAAGAAATGGGTTAGTCGACTAAGAAGCTACTGCCAAAATCTGAA
16875223 CTTCAAG
66 CTTCAAG
*
16875230 ACAAAACCAACTTAGTCGACTACGAAATGGGTTAGTCGACTAAG
1 ACAAAACCAACTTAGTCGACTAAGAAATGGGTTAGTCGACTAAG
16875274 TGCACACTGC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
71 2 0.02
72 104 0.98
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (72 bp):
ACAAAACCAACTTAGTCGACTAAGAAATGGGTTAGTCGACTAAGAAGCTACTGCCAAAATCTGAA
CTTCAAG
Found at i:16876738 original size:20 final size:20
Alignment explanation
Indices: 16876713--16876758 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
16876703 TTTTGACCCC
*
16876713 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
16876733 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
16876753 ATTTGA
1 ATTTGA
16876759 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:16880414 original size:2 final size:2
Alignment explanation
Indices: 16880409--16880461 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
16880399 NNTAACACAC
16880409 AT AT AT AT AT 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 AT AT AT AT AT
16880451 AT AT AT AT AT A
1 AT AT AT AT AT A
16880462 CCCATCATCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16880530 original size:43 final size:43
Alignment explanation
Indices: 16880483--16880597 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 43
16880473 CAGCTCATGT
* * *
16880483 GCACTCCCTACTCGCACATGGCTGAGTCATCACCGGTTTATGC
1 GCACTCCCTACTCGCACATAGCCGAGTCATCACCGGCTTATGC
* * * **
16880526 GCACTCCCTACGCGCACATAACCGGGTCATCATTGGCTTATGC
1 GCACTCCCTACTCGCACATAGCCGAGTCATCACCGGCTTATGC
*
16880569 GCACTCCCTACTCTCACATAGCCGAGTCA
1 GCACTCCCTACTCGCACATAGCCGAGTCA
16880598 ATATCATTAC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAGCCGAGTCATCACCGGCTTATGC
Found at i:16884625 original size:42 final size:43
Alignment explanation
Indices: 16884537--16884669 Score: 227
Period size: 42 Copynumber: 3.1 Consensus size: 43
16884527 ACCATCCCAC
16884537 CATCATCAGCTCATGTGCACTCCC-CACTCGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACT-GCACATAGTTGGGT
16884580 CATCATCAGCTCATGTGCAC-CCCACACTGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGGT
*
16884622 CATCATCAGCTCATGTGCACTCCCACAC-GCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGGT
16884664 CATCAT
1 CATCAT
16884670 TATCACATAA
Statistics
Matches: 87, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
42 56 0.64
43 31 0.36
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (43 bp):
CATCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGGT
Found at i:16892049 original size:16 final size:17
Alignment explanation
Indices: 16892016--16892051 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16892006 AGCTAAATAT
16892016 GCACACATTAAGGGGGA
1 GCACACATTAAGGGGGA
*
16892033 GCACACATTTA-GGGGA
1 GCACACATTAAGGGGGA
16892049 GCA
1 GCA
16892052 ATCCTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.14
Consensus pattern (17 bp):
GCACACATTAAGGGGGA
Found at i:16892632 original size:20 final size:21
Alignment explanation
Indices: 16892609--16892659 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
16892599 TTACTTTTAA
*
16892609 GTTAGTTATTTTAATTT-TTT
1 GTTATTTATTTTAATTTGTTT
*
16892629 GTTATTTCTTTTAATTTGTTT
1 GTTATTTATTTTAATTTGTTT
*
16892650 ATTATTTATT
1 GTTATTTATT
16892660 AGTTTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (21 bp):
GTTATTTATTTTAATTTGTTT
Found at i:16899064 original size:9 final size:9
Alignment explanation
Indices: 16899036--16899070 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
16899026 TGGATTCAAA
16899036 AAAAAAATT
1 AAAAAAATT
*
16899045 AAATTAAATT
1 AAA-AAAATT
16899055 AAAAAAATT
1 AAAAAAATT
16899064 AAAAAAA
1 AAAAAAA
16899071 AGTCAAAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAAAATT
Found at i:16901409 original size:19 final size:20
Alignment explanation
Indices: 16901375--16901412 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
16901365 ATATATCTTG
*
16901375 CATGTTTTATTTGTGTTTTA
1 CATGTTTTAGTTGTGTTTTA
16901395 CATGTTTT-GTTGTGTTTT
1 CATGTTTTAGTTGTGTTTT
16901413 CGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.11, C:0.05, G:0.18, T:0.66
Consensus pattern (20 bp):
CATGTTTTAGTTGTGTTTTA
Found at i:16908132 original size:17 final size:17
Alignment explanation
Indices: 16908110--16908144 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16908100 TAGGAGGCAT
16908110 AATTTTTATT-TTATTTC
1 AATTTTT-TTGTTATTTC
16908127 AATTTTTTTGTTATTTC
1 AATTTTTTTGTTATTTC
16908144 A
1 A
16908145 CTACATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (17 bp):
AATTTTTTTGTTATTTC
Found at i:16911790 original size:22 final size:22
Alignment explanation
Indices: 16911762--16911813 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
16911752 TTGTAGCGTA
*
16911762 GCTGCAGCTAGAATGAATTTTC
1 GCTGCAGCTAAAATGAATTTTC
16911784 GCTGCAGCTAAAATGAATTTTC
1 GCTGCAGCTAAAATGAATTTTC
*
16911806 ACTGCAGC
1 GCTGCAGC
16911814 GATGTTGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (22 bp):
GCTGCAGCTAAAATGAATTTTC
Found at i:16912090 original size:39 final size:40
Alignment explanation
Indices: 16912035--16912112 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
16912025 CACTGTAGTG
* *
16912035 AAATTTCAACCCAG-AAACAGAATGTTTCTCGCTGCAGCA
1 AAATTGCAACCCAGAAAACAGAAAGTTTCTCGCTGCAGCA
*
16912074 AAATTGCAACCTAGAAAACAGAAAGTTTCTCGCTGCAGC
1 AAATTGCAACCCAGAAAACAGAAAGTTTCTCGCTGCAGC
16912113 GAGAAGCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 12 0.34
40 23 0.66
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (40 bp):
AAATTGCAACCCAGAAAACAGAAAGTTTCTCGCTGCAGCA
Found at i:16912504 original size:42 final size:43
Alignment explanation
Indices: 16912445--16912562 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 43
16912435 TCACCAGCTC
** *
16912445 ATGCGCACTCCCTACTCGCACATGTCTGGGTCATCACT-GAG-TT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCG-GCTT
16912488 ATGCG-ACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* * *
16912530 ATGAGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
16912563 ATATAATTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.05
42 33 0.50
43 30 0.45
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:16913415 original size:19 final size:20
Alignment explanation
Indices: 16913381--16913418 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
16913371 GAAGAAGACC
16913381 AGCTGCTAGAAAATTCAAGA
1 AGCTGCTAGAAAATTCAAGA
16913401 AGCTGCTAG-AAATTCAAG
1 AGCTGCTAGAAAATTCAAG
16913419 GTATTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (20 bp):
AGCTGCTAGAAAATTCAAGA
Found at i:16920031 original size:74 final size:74
Alignment explanation
Indices: 16919835--16920031 Score: 220
Period size: 74 Copynumber: 2.7 Consensus size: 74
16919825 AGACATAGTA
* * *
16919835 CTCTTAGTTGACTAACTATG-TTTCTCAGTCGATTAAGTCTTCTCTATCTTGAATTTGAAATTTC
1 CTCTTAGTTGACTAACCATGCTTT-TTAGTCGATTAAGTCTTCTCTGTCTTGAATTTGAAATTTC
*
16919899 TGGCAGTGAG
65 TAGCAGTGAG
* * * * *
16919909 CTTTTAGTTGAATAACCGTGCTTTTTAGTCGATTAAGT-TGTCTTTGTCTTGTAA-TTGAGATTT
1 CTCTTAGTTGACTAACCATGCTTTTTAGTCGATTAAGTCT-TCTCTGTCTTG-AATTTGAAATTT
* *
16919972 CTAGCATTGTG
64 CTAGCAGTGAG
* * *
16919983 CTCTTAGTTGACTAACCATGCTTTTTGGTTGACTAAGTCTTCTCTGTCT
1 CTCTTAGTTGACTAACCATGCTTTTTAGTCGATTAAGTCTTCTCTGTCT
16920032 CACAATCTGC
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
73 1 0.01
74 94 0.93
75 6 0.06
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (74 bp):
CTCTTAGTTGACTAACCATGCTTTTTAGTCGATTAAGTCTTCTCTGTCTTGAATTTGAAATTTCT
AGCAGTGAG
Found at i:16931893 original size:60 final size:60
Alignment explanation
Indices: 16931791--16931972 Score: 233
Period size: 60 Copynumber: 3.0 Consensus size: 60
16931781 AGACATCATC
* *
16931791 ACCTACTCGTGGGAATTGCCCACGCCA-CCATATAT-AAGTCAGGGCTTCAAGTCCCTCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCCA-ATATGAA-TCAGGGCTTCAAGTCCCCCTTT
* * *
16931851 ACCTTCTTGTGGGAACTGCCCATGCCACCCAATATGAATCAGGGCTTCAAGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCCAATATGAATCAGGGCTTCAAGTCCCCCTTT
* ** * * *
16931911 ACCTACTCATGAAAACTACCCACGCCACCCAATATGAATCGGGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCCAATATGAATCAGGGCTTCAAGTCCCCCTTT
16931971 AC
1 AC
16931973 AATCAAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
60 101 0.95
61 5 0.05
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTGCCCACGCCACCCAATATGAATCAGGGCTTCAAGTCCCCCTTT
Found at i:16932707 original size:16 final size:16
Alignment explanation
Indices: 16932682--16932719 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16932672 CCAGCTGACA
*
16932682 TTTCTCTTTTTTTTTC
1 TTTCTCTTTTTTTTCC
*
16932698 TTTCTTTTTTTTTTCC
1 TTTCTCTTTTTTTTCC
16932714 TTTCTC
1 TTTCTC
16932720 CTCCAGCACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTCTTTTTTTTCC
Found at i:16932829 original size:13 final size:13
Alignment explanation
Indices: 16932793--16932836 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
16932783 TCGTTGCTCT
16932793 TTCTCTCTTTTTC
1 TTCTCTCTTTTTC
*
16932806 GTT-T-TCCTTTTC
1 -TTCTCTCTTTTTC
16932818 TTCTCTCTTTTTC
1 TTCTCTCTTTTTC
16932831 TTCTCT
1 TTCTCT
16932837 TCTAATCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 14 0.54
14 2 0.08
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (13 bp):
TTCTCTCTTTTTC
Found at i:16938565 original size:23 final size:21
Alignment explanation
Indices: 16938530--16938581 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
16938520 GCTATAAATA
* *
16938530 CTTTCTTCTAGCAGCTTCTTCTT
1 CTTT-TTCCAGCAGCTT-GTCTT
16938553 CTATTTTCCAGCAGCTTGTCTT
1 CT-TTTTCCAGCAGCTTGTCTT
16938575 CTTTTTC
1 CTTTTTC
16938582 TTCTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 5 0.19
22 6 0.23
23 13 0.50
24 2 0.08
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.52
Consensus pattern (21 bp):
CTTTTTCCAGCAGCTTGTCTT
Found at i:16939482 original size:43 final size:43
Alignment explanation
Indices: 16939364--16939485 Score: 183
Period size: 43 Copynumber: 2.8 Consensus size: 43
16939354 TGACTCGGCT
**
16939364 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCAGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
16939407 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
16939450 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
16939486 TGATGATGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 71 0.99
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:16944903 original size:60 final size:60
Alignment explanation
Indices: 16944795--16944976 Score: 251
Period size: 60 Copynumber: 3.0 Consensus size: 60
16944785 AAACATCATC
* * *
16944795 ACCTACTCGTGGGAACTGCCCACGCCA-CCATATAT-AAGTCAGGCCTTCAAGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCCA-ATATGAA-TCGGGACTTCAGGTCCCCCTTT
* *
16944855 ACCTACTTGTGGGAACTACCCACGCCACCCAATATGAATCGGGACTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCCAATATGAATCGGGACTTCAGGTCCCCCTTT
* * * *
16944915 ACCTACTCATGGGAACTGCCCACACCACCCAATATGAATCGGGGCTTCAGGTCCCCATTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCCAATATGAATCGGGACTTCAGGTCCCCCTTT
16944975 AC
1 AC
16944977 AATCAAATAT
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
60 104 0.95
61 5 0.05
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTGCCCACGCCACCCAATATGAATCGGGACTTCAGGTCCCCCTTT
Found at i:16945901 original size:24 final size:23
Alignment explanation
Indices: 16945856--16945902 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
16945846 TTCTAATCGA
* *
16945856 CCTTCCTTTTTCCTTTTTCTTCT
1 CCTTCCTTTTTCCCTTTCCTTCT
*
16945879 CCTTTCTTCTTTCCCTTTCCTTCT
1 CCTTCCTT-TTTCCCTTTCCTTCT
16945903 TTCTCCTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (23 bp):
CCTTCCTTTTTCCCTTTCCTTCT
Found at i:16945903 original size:14 final size:14
Alignment explanation
Indices: 16945879--16945935 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
16945869 TTTTTCTTCT
16945879 CCTTT-CTTCTTTC
1 CCTTTCCTTCTTTC
16945892 CCTTTCCTTCTTTC
1 CCTTTCCTTCTTTC
16945906 TCC-TTCCTTTCTTTTC
1 -CCTTTCC-TTC-TTTC
* *
16945922 TCTTTTCTTCTTTC
1 CCTTTCCTTCTTTC
16945936 TTTTCTTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 5 0.14
14 16 0.43
15 9 0.24
16 7 0.19
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
CCTTTCCTTCTTTC
Found at i:16946151 original size:13 final size:13
Alignment explanation
Indices: 16946133--16946167 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
16946123 CGACCCCCTC
16946133 TTTTTCTTCTCTT
1 TTTTTCTTCTCTT
*
16946146 TTTTTCTTGTCTT
1 TTTTTCTTCTCTT
16946159 TTCTTTCTT
1 TT-TTTCTT
16946168 TTTTCCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTCTTCTCTT
Found at i:16947252 original size:37 final size:37
Alignment explanation
Indices: 16947182--16947267 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
16947172 TAAAATATAC
* *
16947182 CATATAGTTTT---ATTGTTATTATCATGAAGTATGT
1 CATATAGTTTTAGGATTATTATCATCATGAAGTATGT
16947216 CATATAGTTTTAGGATTATTATCATCATGTAA-TATGT
1 CATATAGTTTTAGGATTATTATCATCATG-AAGTATGT
* *
16947253 CATGTAGCTTTAGGA
1 CATATAGTTTTAGGA
16947268 GCATTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
34 11 0.25
37 31 0.70
38 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.45
Consensus pattern (37 bp):
CATATAGTTTTAGGATTATTATCATCATGAAGTATGT
Found at i:16980974 original size:2 final size:2
Alignment explanation
Indices: 16980967--16981011 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16980957 GATACACAAC
16980967 AT AT AT AT AT 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 AT AT AT AT AT
16981009 AT A
1 AT A
16981012 AGCATCCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16983444 original size:104 final size:104
Alignment explanation
Indices: 16983311--16983533 Score: 331
Period size: 104 Copynumber: 2.2 Consensus size: 104
16983301 GGAGTCATCG
** * * ** *
16983311 TGTGCA-CCCCCACATTGTGCACAATTAATGCTATTGTGTGCAACCCCCACATTGCGCATAACAA
1 TGTGCATCCCCCACATTGCACACAACTAATGCCATTGTGTGCAACCCCCACATCACGCACAACAA
* *
16983375 TGTGATCTTCCACACTCCCACACCTTGTCATCACAGGCA
66 TGTCATCTTCCACACTCCCACACCCTGTCATCACAGGCA
* *
16983414 TGTGCATCCCCCACATTGCACACAACTAATGCCATTGTGTGCAACCCCCACATCACGGACAATAA
1 TGTGCATCCCCCACATTGCACACAACTAATGCCATTGTGTGCAACCCCCACATCACGCACAACAA
*
16983479 TGTCATCTTCCACACTCCCACACCCTGTCATCACCGGCA
66 TGTCATCTTCCACACTCCCACACCCTGTCATCACAGGCA
16983518 TGTGCATCCCCCACAT
1 TGTGCATCCCCCACAT
16983534 CGCGCACACG
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
103 6 0.06
104 101 0.94
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.23
Consensus pattern (104 bp):
TGTGCATCCCCCACATTGCACACAACTAATGCCATTGTGTGCAACCCCCACATCACGCACAACAA
TGTCATCTTCCACACTCCCACACCCTGTCATCACAGGCA
Found at i:16990962 original size:23 final size:23
Alignment explanation
Indices: 16990932--16990985 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
16990922 TGAGCTGGTG
* *
16990932 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGGTGTGC
16990955 ATGATGATGATGGGATGGTGTGC
1 ATGATGATGATGGGATGGTGTGC
16990978 ATGATGAT
1 ATGATGAT
16990986 AATAGGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.35
Consensus pattern (23 bp):
ATGATGATGATGGGATGGTGTGC
Found at i:16998495 original size:20 final size:20
Alignment explanation
Indices: 16998470--16998507 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16998460 TTTATTTGAC
*
16998470 ATTTTAATCAATTAAAATGG
1 ATTTTAACCAATTAAAATGG
16998490 ATTTTAACCAATTAAAAT
1 ATTTTAACCAATTAAAAT
16998508 CTTTTTGTTT
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:0.08, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTTTAACCAATTAAAATGG
Found at i:16998871 original size:20 final size:20
Alignment explanation
Indices: 16998843--16998881 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16998833 CATTTCAGTA
*
16998843 TTGTTTTAATTGATTAAAAT
1 TTGTGTTAATTGATTAAAAT
16998863 TTGTGTTAATTGATTAAAA
1 TTGTGTTAATTGATTAAAA
16998882 CCTCTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
TTGTGTTAATTGATTAAAAT
Found at i:16999420 original size:27 final size:27
Alignment explanation
Indices: 16999383--16999474 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
16999373 TAACTATTTA
*
16999383 CAATATTTACAGTAATTTCAAGATATT
1 CAATATCTACAGTAATTTCAAGATATT
* *
16999410 CAATATCTACAATAA--TCAAAATCAATTT
1 CAATATCTACAGTAATTTCAAGAT--A-TT
* *
16999438 ACAATATTTACAGTAATTTGAAGATATT
1 -CAATATCTACAGTAATTTCAAGATATT
16999466 CAATATCTA
1 CAATATCTA
16999475 TAATAATCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
25 6 0.12
27 22 0.43
28 4 0.08
29 14 0.27
31 5 0.10
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (27 bp):
CAATATCTACAGTAATTTCAAGATATT
Found at i:16999464 original size:56 final size:56
Alignment explanation
Indices: 16999378--16999487 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
16999368 GCAAGTAACT
16999378 ATTTACAATATTTACAGTAATTTCAAGATATTCAATATCTACAATAATCAAAATCA
1 ATTTACAATATTTACAGTAATTTCAAGATATTCAATATCTACAATAATCAAAATCA
* *
16999434 ATTTACAATATTTACAGTAATTTGAAGATATTCAATATCTATAATAATCAAAAT
1 ATTTACAATATTTACAGTAATTTCAAGATATTCAATATCTACAATAATCAAAAT
16999488 ATACCCAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (56 bp):
ATTTACAATATTTACAGTAATTTCAAGATATTCAATATCTACAATAATCAAAATCA
Found at i:16999721 original size:18 final size:18
Alignment explanation
Indices: 16999682--16999725 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
16999672 TGATTAGTCC
*
16999682 TAAAACATTTAAATGCAC
1 TAAAACATTTAAATGCAA
16999700 TAAAACATTTAAATAG-AA
1 TAAAACATTTAAAT-GCAA
16999718 TAAAACAT
1 TAAAACAT
16999726 AGTTTTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (18 bp):
TAAAACATTTAAATGCAA
Found at i:17001831 original size:71 final size:72
Alignment explanation
Indices: 17001750--17001894 Score: 195
Period size: 71 Copynumber: 2.0 Consensus size: 72
17001740 CATAAAGCCC
* * *
17001750 TAGTCGACTACAAAGGAAGCATAGTTGACCCTGTTCCCA-AAAAATCAAGAAAATCAAGTTCAG-
1 TAGTCAACTACAAAGGAAGCATAGTCGACCCTATT-CCAGAAAAATCAAGAAAATCAAGTTCAGT
17001813 AATAGACA
65 AATAGACA
* * * *
17001821 TAGTCAACTACAGAGGAAGCATAGTCGACCCTATTCTAGAAAGATCAAGAAAATCAAGTTGAGTA
1 TAGTCAACTACAAAGGAAGCATAGTCGACCCTATTCCAGAAAAATCAAGAAAATCAAGTTCAGTA
*
17001886 ATAGCCA
66 ATAGACA
17001893 TA
1 TA
17001895 ATCGACTATA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
70 2 0.03
71 53 0.83
72 9 0.14
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.21
Consensus pattern (72 bp):
TAGTCAACTACAAAGGAAGCATAGTCGACCCTATTCCAGAAAAATCAAGAAAATCAAGTTCAGTA
ATAGACA
Found at i:17004498 original size:38 final size:40
Alignment explanation
Indices: 17004417--17004515 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 40
17004407 GACTCATGTA
*
17004417 CATCCCCCCACATCGTGCAC-ATAGCTGGCACCATCGTGTG
1 CATCCCCCCACATCGTGCACAATAGATGG-ACCATCGTGTG
17004457 CATCCCCCCACATCGTGCACAATCA-AT-G-CCATCGTGTG
1 CATCCCCCCACATCGTGCACAAT-AGATGGACCATCGTGTG
*
17004495 CATCCCCTCACATCGTGCACA
1 CATCCCCCCACATCGTGCACA
17004516 CGGTCACTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
38 30 0.55
40 21 0.38
41 3 0.05
42 1 0.02
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.20
Consensus pattern (40 bp):
CATCCCCCCACATCGTGCACAATAGATGGACCATCGTGTG
Found at i:17004824 original size:20 final size:20
Alignment explanation
Indices: 17004800--17004844 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
17004790 CACCCGCAGA
*
17004800 CAGCACAGGCAGCACGCACC
1 CAGCACAGACAGCACGCACC
* *
17004820 TAGCACAGATAGCACGCACC
1 CAGCACAGACAGCACGCACC
17004840 CAGCA
1 CAGCA
17004845 GAGGGTAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.22, T:0.04
Consensus pattern (20 bp):
CAGCACAGACAGCACGCACC
Found at i:17012090 original size:28 final size:29
Alignment explanation
Indices: 17012058--17012145 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 29
17012048 TTACAGTTTT
*
17012058 AACATTTTTGTCTTAATTCAGACAAGA-A
1 AACATTTTTGTCTTAATTTAGACAAGATA
* *
17012086 AACATATTTGTCTCAATTTAGACAAGATA
1 AACATTTTTGTCTTAATTTAGACAAGATA
*
17012115 AGATATTTTTTTGTCTTAATTATAGACAAGA
1 A-ACA--TTTTTGTCTTAATT-TAGACAAGA
17012146 GTTGTCTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
28 24 0.49
29 2 0.04
30 2 0.04
32 12 0.24
33 9 0.18
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
AACATTTTTGTCTTAATTTAGACAAGATA
Found at i:17012308 original size:17 final size:17
Alignment explanation
Indices: 17012286--17012318 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17012276 ATAATAATGA
17012286 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
17012303 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
17012319 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:17016027 original size:26 final size:28
Alignment explanation
Indices: 17015998--17016056 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
17015988 AAATGATACG
*
17015998 GATGTCCTT-GAA-AGACAAATGGAAGA
1 GATGACCTTAGAAGAGACAAATGGAAGA
**
17016024 GATGAGTTTAGAAGAGACAAATGGAAGA
1 GATGACCTTAGAAGAGACAAATGGAAGA
17016052 GATGA
1 GATGA
17016057 TAAGAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 3 0.11
28 19 0.68
ACGTcount: A:0.44, C:0.07, G:0.31, T:0.19
Consensus pattern (28 bp):
GATGACCTTAGAAGAGACAAATGGAAGA
Found at i:17022458 original size:21 final size:20
Alignment explanation
Indices: 17022423--17022463 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17022413 TTTGGCTAGC
17022423 CATGAATTTACCAT-GAAAA
1 CATGAATTTACCATGGAAAA
17022442 CATGAAATTTAACCATGGAAAA
1 CATG-AATTT-ACCATGGAAAA
17022464 TAAGGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 5 0.26
22 5 0.26
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (20 bp):
CATGAATTTACCATGGAAAA
Found at i:17026802 original size:31 final size:31
Alignment explanation
Indices: 17026767--17026832 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
17026757 TATAACTCCA
17026767 CCAAATGAATAAATTATTACAGCCTATTAGT
1 CCAAATGAATAAATTATTACAGCCTATTAGT
17026798 CCAAATGAATAAATTATTACAGCCTATTAGT
1 CCAAATGAATAAATTATTACAGCCTATTAGT
17026829 CCAA
1 CCAA
17026833 CTCTAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (31 bp):
CCAAATGAATAAATTATTACAGCCTATTAGT
Found at i:17048465 original size:42 final size:42
Alignment explanation
Indices: 17048413--17048595 Score: 181
Period size: 42 Copynumber: 4.4 Consensus size: 42
17048403 GTAATTATAT
* * * * *
17048413 TGACCTAGCTATGTGCGAGTAAGAGTGTGCATACA-CCAAAGA
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATA-AGCCGATGA
* * *
17048455 TGACCCAGCTATGTGCGAGTGGGAGTACGCATAAGCTGATGA
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGA
* * ** * *
17048497 TGACCCGGCTATGTGTGAGTAGGAGTGTACATAAGTCGATCA
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGA
* * *
17048539 TGACTCAGCTATGTGCGAGTAGGAGTGCGCATAAGCAG-TGT
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGA
*
17048580 TGACCCAGCCATGTGC
1 TGACCCAGCTATGTGC
17048596 TAATGGGGAG
Statistics
Matches: 112, Mismatches: 28, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
41 16 0.14
42 96 0.86
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (42 bp):
TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGA
Found at i:17051259 original size:38 final size:38
Alignment explanation
Indices: 17051185--17051289 Score: 97
Period size: 38 Copynumber: 2.6 Consensus size: 38
17051175 CACACTTAGC
*
17051185 TCATGTGCACTCCCTACACGCACAATGCAATATCATCA
1 TCATGTGCACTCCCTACACGCACAATGCAAGATCATCA
* * *
17051223 TCATGTGCACTCCTTACTCGCAC-ATAGCCAGGTCATCATCA
1 TCATGTGCACTCCCTACACGCACAAT-G-CAAG--ATCATCA
17051264 GCTCATGTGCACTCCC-ACACCGCACA
1 --TCATGTGCACTCCCTACA-CGCACA
17051290 TAGTTGGGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
37 2 0.04
38 22 0.42
39 2 0.04
41 7 0.13
42 2 0.04
43 18 0.34
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (38 bp):
TCATGTGCACTCCCTACACGCACAATGCAAGATCATCA
Found at i:17051275 original size:43 final size:41
Alignment explanation
Indices: 17051182--17051347 Score: 144
Period size: 43 Copynumber: 4.0 Consensus size: 41
17051172 TGCCACACTT
*
17051182 AGCTCATGTGCACTCCCTACACGCACA-ATGCA-AT-ATCATC
1 AGCTCATGTGCACT-CCTACACGCACATA-GCAGGTCATCATC
*
17051222 A--TCATGTGCACTCCTTACTCGCACATAGCCAGGTCATCATC
1 AGCTCATGTGCACTCC-TACACGCACATAG-CAGGTCATCATC
* **
17051263 AGCTCATGTGCACTCCCACACCGCACATAGTTGGGTCATCATC
1 AGCTCATGTGCACTCCTACA-CGCACATAG-CAGGTCATCATC
* * * *
17051306 ATCTCATGTGCACTCCCACACCGCATATAGCTGGGTCATCAT
1 AGCTCATGTGCACTCCTACA-CGCACATAGC-AGGTCATCAT
17051348 TATCACATAA
Statistics
Matches: 107, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
37 2 0.02
38 21 0.20
39 3 0.03
40 2 0.02
41 7 0.07
42 2 0.02
43 70 0.65
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (41 bp):
AGCTCATGTGCACTCCTACACGCACATAGCAGGTCATCATC
Found at i:17056693 original size:20 final size:19
Alignment explanation
Indices: 17056670--17056709 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17056660 AAGAGGAAGA
17056670 AGAAGGAGAAAAGCTACTGG
1 AGAAGGA-AAAAGCTACTGG
* *
17056690 AGAATGAAAAAGTTACTGG
1 AGAAGGAAAAAGCTACTGG
17056709 A
1 A
17056710 AGAACAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.07, G:0.30, T:0.15
Consensus pattern (19 bp):
AGAAGGAAAAAGCTACTGG
Found at i:17060969 original size:71 final size:69
Alignment explanation
Indices: 17060866--17061059 Score: 219
Period size: 71 Copynumber: 2.7 Consensus size: 69
17060856 ATCAAGTTGT
* * * *
17060866 GCCTAACTAACTAAATTGTTTAATTGAA-TCATTGGACCTAATTAATTAAATTTTTTAATTAAAT
1 GCCTAATTAATTAAATTGTTTAATT-AAGTCATTGG-CCTAATTGATTAAATTGTTTAATTAAAT
17060930 CATTGG
64 CATTGG
* * *
17060936 GCCTAATTGATTGAATTTGTTTAATTAAGTCATTAGGCCTACTTGATTAAAATTGTTTAATTAAA
1 GCCTAATTAATT-AAATTGTTTAATTAAGTCATT-GGCCTAATTGATT-AAATTGTTTAATTAAA
**
17061001 TTGTTGG
63 TCATTGG
* * *
17061008 GCTTAATTAATTAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATT
1 GCCTAATTAATTAAATTGTTTAATTAAGTCATT-GGCCTAATTGATTAAATT
17061060 AAACAATTAA
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
70 16 0.15
71 56 0.54
72 32 0.31
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.44
Consensus pattern (69 bp):
GCCTAATTAATTAAATTGTTTAATTAAGTCATTGGCCTAATTGATTAAATTGTTTAATTAAATCA
TTGG
Found at i:17061060 original size:35 final size:35
Alignment explanation
Indices: 17060839--17061059 Score: 207
Period size: 35 Copynumber: 6.3 Consensus size: 35
17060829 TCTCAAGCAC
* *
17060839 TTGATTAAAATTGTTTAATCAAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTCATTGGGCCTAA
* * * *
17060872 CTAACTAAATTGTTTAATTGAA-TCATTGGACCTAA
1 TTGATTAAATTGTTTAATT-AAGTCATTGGGCCTAA
* * *
17060907 TTAATTAAATTTTTTAATTAAATCATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTCATTGGGCCTAA
* * *
17060942 TTGATTGAATTTGTTTAATTAAGTCATTAGGCCTAC
1 TTGATT-AAATTGTTTAATTAAGTCATTGGGCCTAA
* ** *
17060978 TTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAA
1 TTGATT-AAATTGTTTAATTAAGTCATTGGGCCTAA
* * *
17061014 TTAATTAAATTATTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTCATTGGGCCTAA
17061049 TTGATTAAATT
1 TTGATTAAATT
17061060 AAACAATTAA
Statistics
Matches: 152, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
32 12 0.08
33 5 0.03
34 2 0.01
35 76 0.50
36 57 0.38
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.44
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTCATTGGGCCTAA
Found at i:17061068 original size:35 final size:36
Alignment explanation
Indices: 17060878--17061080 Score: 171
Period size: 35 Copynumber: 5.7 Consensus size: 36
17060868 CTAACTAACT
* * * *
17060878 AAATTGTTTAATTGAA-TCATTGGACCTAATTAATT-
1 AAATTATTTAATT-AAGTTATTGGGCCTAATTGATTA
* * * *
17060913 AAATTTTTTAATTAAATCATTGGGCCTAATTGATTG
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTA
* * * * *
17060949 AATTTGTTTAATTAAGTCATTAGGCCTACTTGATTA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTA
* * * * *
17060985 AAATTGTTTAATTAAATTGTTGGGCTTAATTAATT-
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTA
17061020 AAATTATTTAATTAAGTTATTGGGCCTAATTGATT-
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTA
***
17061055 AAATTAAACAATTAAGTTAATTGGGC
1 AAATTATTTAATTAAGTT-ATTGGGC
17061081 TTCTTAAGGA
Statistics
Matches: 140, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
34 2 0.01
35 74 0.53
36 64 0.46
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (36 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTGATTA
Found at i:17061079 original size:71 final size:72
Alignment explanation
Indices: 17060922--17061082 Score: 173
Period size: 71 Copynumber: 2.2 Consensus size: 72
17060912 TAAATTTTTT
* * * * * *
17060922 AATTAAATCATTGGGCCTAATTGATTGAATTTGTTTAATTAAGTCATTAGGCCTACTTGATTAAA
1 AATTAAATTATTGGGCTTAATTAATTGAAATTATTTAATTAAGTCATTAGGCCTAATTGATTAAA
****
17060987 ATTGTTT
66 ATTAAAC
* * *
17060994 AATTAAATTGTTGGGCTTAATTAATT-AAATTATTTAATTAAGTTATTGGGCCTAATTGATT-AA
1 AATTAAATTATTGGGCTTAATTAATTGAAATTATTTAATTAAGTCATTAGGCCTAATTGATTAAA
17061057 ATTAAAC
66 ATTAAAC
*
17061064 AATTAAGTTAATTGGGCTT
1 AATTAAATT-ATTGGGCTT
17061083 CTTAAGGACT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
70 13 0.18
71 38 0.52
72 22 0.30
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (72 bp):
AATTAAATTATTGGGCTTAATTAATTGAAATTATTTAATTAAGTCATTAGGCCTAATTGATTAAA
ATTAAAC
Found at i:17062482 original size:179 final size:181
Alignment explanation
Indices: 17062165--17062532 Score: 562
Period size: 179 Copynumber: 2.0 Consensus size: 181
17062155 GATTGAATAG
*
17062165 GCTGATTTTAAGCAAGAAATTGGAGCAAAAAGTGAAAGCAGTCCAGCTCACTGTTATGACATGAA
1 GCTGATTTCAAGCAAGAAATTGGAGCAAAAAGTGAAAGCAGTCCAGCTCACTGTTATGACATGAA
* *
17062230 TTTCAGTTTTAATTAACAAGAAAGTCTTGGAAATTAATTCTGAAAAATTCCAGGAAAATTATCTT
66 TTTCAGTTTTAATTAACAAGAAACTCTTGGAAATTAATTCTGAAAAATTCCAGAAAAATTATCTT
* *
17062295 TATTAAAATGTTCAATAAGGATTATTTCTGGAAAATATCATGGTCAAACAT
131 TATTAAAATGTTCAATAAGGATTATTTCTGGAAAATATCATGGCCAAACAA
* * * * * *
17062346 GCTGATTTCAAGCAAGAAAATTGGTGCAAATA-T-AAATCTGTCCAGCTCACTGTTCTGGCATGA
1 GCTGATTTCAAGCAAG-AAATTGGAGCAAAAAGTGAAAGCAGTCCAGCTCACTGTTATGACATGA
* *
17062409 ATTTCAGTTTTAATTGACAAGAAACTCTT-GAAATTAATTCTGAAAAATTCCAGAAAAATTATTT
65 ATTTCAGTTTTAATTAACAAGAAACTCTTGGAAATTAATTCTGAAAAATTCCAGAAAAATTATCT
* * *
17062473 TTATTAAAATGTTCAATGAGGATTATTTCTGGAAATTTTCATGGCCAAACAA
130 TTATTAAAATGTTCAATAAGGATTATTTCTGGAAAATATCATGGCCAAACAA
17062525 GCTGATTT
1 GCTGATTT
17062533 AGGCTATTAA
Statistics
Matches: 170, Mismatches: 16, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
179 88 0.52
180 53 0.31
181 16 0.09
182 13 0.08
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (181 bp):
GCTGATTTCAAGCAAGAAATTGGAGCAAAAAGTGAAAGCAGTCCAGCTCACTGTTATGACATGAA
TTTCAGTTTTAATTAACAAGAAACTCTTGGAAATTAATTCTGAAAAATTCCAGAAAAATTATCTT
TATTAAAATGTTCAATAAGGATTATTTCTGGAAAATATCATGGCCAAACAA
Found at i:17067676 original size:29 final size:28
Alignment explanation
Indices: 17067620--17067674 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
17067610 TGACAAGTGC
17067620 TGGGACGAAAAATTTATCGATTTGCCCT
1 TGGGACGAAAAATTTATCGATTTGCCCT
17067648 TGGGACAGAAAAA-TTAT-GATTTTGCCC
1 TGGGAC-GAAAAATTTATCGA-TTTGCCC
17067675 CTATATTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 2 0.08
28 17 0.68
29 6 0.24
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (28 bp):
TGGGACGAAAAATTTATCGATTTGCCCT
Found at i:17073432 original size:106 final size:106
Alignment explanation
Indices: 17073296--17073505 Score: 253
Period size: 106 Copynumber: 2.0 Consensus size: 106
17073286 AACTAAATTG
* * *
17073296 TTTAATTGAATCATTGGGCTTAATTAATT-AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
1 TTTAATTGAATCATTAGGCCTAATTAATTAAAATTATTTAATTAAATCATTGGG-CTAATTAATT
*
17073360 AAATTAAACAATTAAGTTATTGGGCCTAATTGATTGAATTTA
65 AAATTAAACAATTAAGTTATTGGGCCTAATTGATTAAATTTA
* * * ** *
17073402 TTTAATT-AAGTCATTAGGCCTACTTGATTAAAATTGTTTAATTAAATTGTTGGGTTAATTAATT
1 TTTAATTGAA-TCATTAGGCCTAATTAATTAAAATTATTTAATTAAATCATTGGGCTAATTAATT
**** *
17073466 AAATTGTTTAATTAAGTTATTGGGGCTAATTGATTAAATT
65 AAATTAAACAATTAAGTTATTGGGCCTAATTGATTAAATT
17073506 AAACAATTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
105 2 0.02
106 65 0.75
107 20 0.23
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (106 bp):
TTTAATTGAATCATTAGGCCTAATTAATTAAAATTATTTAATTAAATCATTGGGCTAATTAATTA
AATTAAACAATTAAGTTATTGGGCCTAATTGATTAAATTTA
Found at i:17073480 original size:21 final size:21
Alignment explanation
Indices: 17073439--17073480 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17073429 TTAAAATTGT
**
17073439 TTAATTAAATTGTTGGGTTAA
1 TTAATTAAATTGTTGAATTAA
*
17073460 TTAATTAAATTGTTTAATTAA
1 TTAATTAAATTGTTGAATTAA
17073481 GTTATTGGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
TTAATTAAATTGTTGAATTAA
Found at i:17073514 original size:35 final size:35
Alignment explanation
Indices: 17073258--17073526 Score: 233
Period size: 35 Copynumber: 7.7 Consensus size: 35
17073248 CACTTGATTA
* * *
17073258 AAATTATTTAATTAAG---TTGTGCCTAACTAACT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * *
17073290 AAATTGTTTAATTGAA-TCATTGGGCTTAATTAATT
1 AAATTATTTAATT-AAGTTATTGGGCCTAATTAATT
*
17073325 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
*** *
17073360 AAATTAAACAATTAAGTTATTGGGCCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * * *
17073395 GAATTTATTTAATTAAGTCATTAGGCCTACTTGATT
1 -AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
17073431 AAAATTGTTTAATTAAATTGTTGGG-TTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * *
17073466 AAATTGTTTAATTAAGTTATTGGGGCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
***
17073501 AAATTAAACAATTAAGTTAATTGGGC
1 AAATTATTTAATTAAGTT-ATTGGGC
17073527 TTCTTAAGGA
Statistics
Matches: 191, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
32 12 0.06
33 2 0.01
34 24 0.13
35 101 0.53
36 52 0.27
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:17079683 original size:68 final size:68
Alignment explanation
Indices: 17079562--17079707 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 68
17079552 CATGTTTGGT
* * * *
17079562 ATGATGAATGCCATAAGATTGTGTACATGATGTAAATTCCATATACCATATGAGGTGATTAAGTA
1 ATGATGAATGCCATAAGATTGTGTACATGATATAAATTCCATATACCACATGAGATGATTAAGAA
*
17079627 TGC
66 AGC
* * * ** * * * *
17079630 ATGACGAATGCCATGAGATTTTGTTTATGATATATATTCCATGTACTACATGAGATGATTGAGAA
1 ATGATGAATGCCATAAGATTGTGTACATGATATAAATTCCATATACCACATGAGATGATTAAGAA
17079695 AGC
66 AGC
17079698 ATGATGAATG
1 ATGATGAATG
17079708 TGAGACCTTG
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (68 bp):
ATGATGAATGCCATAAGATTGTGTACATGATATAAATTCCATATACCACATGAGATGATTAAGAA
AGC
Found at i:17083187 original size:20 final size:21
Alignment explanation
Indices: 17083129--17083187 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
17083119 ACATTTCACT
*
17083129 AATGTATCGATAGATTC-TGG
1 AATGTATCGATAAATTCATGG
* *
17083149 AAAGTATCAATACAA-TCAT-G
1 AATGTATCGATA-AATTCATGG
17083169 AATGTATCGATAAATTCAT
1 AATGTATCGATAAATTCAT
17083188 TGTAGAAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (21 bp):
AATGTATCGATAAATTCATGG
Found at i:17085148 original size:40 final size:40
Alignment explanation
Indices: 17085104--17085231 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
17085094 GAGGTAAAGG
*
17085104 GGTTGTGCTTTAACCTTGAAAAGGTAGAGGCTTTGTGAAA
1 GGTTGTGCTTTAACCTTGAAAAGGTAGAGACTTTGTGAAA
* * * * *
17085144 GGTTGTACTTTAAGCTTGTAAAGATAGAAACTTTGTGAAA
1 GGTTGTGCTTTAACCTTGAAAAGGTAGAGACTTTGTGAAA
* * * *
17085184 GGTCGTGCTTTATCCTTGAAAAGGTCGAGACTTTATG--A
1 GGTTGTGCTTTAACCTTGAAAAGGTAGAGACTTTGTGAAA
17085222 GGTTGTGCTT
1 GGTTGTGCTT
17085232 GTTCCTCTCG
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
38 10 0.14
40 62 0.86
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (40 bp):
GGTTGTGCTTTAACCTTGAAAAGGTAGAGACTTTGTGAAA
Found at i:17092300 original size:38 final size:40
Alignment explanation
Indices: 17092214--17092314 Score: 152
Period size: 38 Copynumber: 2.6 Consensus size: 40
17092204 ACCCGGCTCA
*
17092214 TGTACATCCCCCCACATCGTGCACATAGTCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGTCAGCACCATCG
* **
17092254 TGTGCATCCCCCCACATCGTGCACA-A-TCAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACATAGTCAGCACCATCG
17092292 TGTACATCCCCCCACATCGTGCA
1 TGTACATCCCCCCACATCGTGCA
17092315 TATGAGCACT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 31 0.55
39 1 0.02
40 24 0.43
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.21
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACATAGTCAGCACCATCG
Found at i:17093216 original size:20 final size:20
Alignment explanation
Indices: 17093188--17093233 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
17093178 AGGGAAGAAG
* *
17093188 AAGATAGCTGTTGGAAATTTC
1 AAGATAGCTGCTAG-AATTTC
17093209 AAGA-AGCTGCTAGAATTTC
1 AAGATAGCTGCTAGAATTTC
17093228 AAGATA
1 AAGATA
17093234 TTTATAGGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (20 bp):
AAGATAGCTGCTAGAATTTC
Found at i:17097404 original size:25 final size:24
Alignment explanation
Indices: 17097376--17097423 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17097366 CTCATATGAA
*
17097376 GCAACGAAGGAAGAAAGCCCAAAAG
1 GCAAAGAAGGAA-AAAGCCCAAAAG
* *
17097401 GCAAAGAAGGTAAAATCCCAAAA
1 GCAAAGAAGGAAAAAGCCCAAAA
17097424 TGAGAAGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.54, C:0.19, G:0.23, T:0.04
Consensus pattern (24 bp):
GCAAAGAAGGAAAAAGCCCAAAAG
Found at i:17103164 original size:16 final size:17
Alignment explanation
Indices: 17103139--17103171 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17103129 TTTATTGTGA
*
17103139 TTTAGTTTTATTTAATT
1 TTTAGTTTTAATTAATT
17103156 TTTAG-TTTAATTAATT
1 TTTAGTTTTAATTAATT
17103172 ATTTGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTAGTTTTAATTAATT
Found at i:17104433 original size:23 final size:22
Alignment explanation
Indices: 17104406--17104449 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
17104396 TTTCTAAGAC
17104406 TTTGTGACA-AATTTAGTGATGGA
1 TTTGTGACAGAA-TT-GTGATGGA
17104429 TTTGTGACAGAATTGTGATGG
1 TTTGTGACAGAATTGTGATGG
17104450 TATTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 11 0.55
24 2 0.10
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.39
Consensus pattern (22 bp):
TTTGTGACAGAATTGTGATGGA
Found at i:17105591 original size:21 final size:20
Alignment explanation
Indices: 17105547--17105588 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
17105537 TGTTGAATAG
17105547 TTAATTTAAGTTATTTTAGT
1 TTAATTTAAGTTATTTTAGT
*
17105567 TTAATTTTATGTTATTTT-GT
1 TTAA-TTTAAGTTATTTTAGT
17105587 TT
1 TT
17105589 TAAATTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (20 bp):
TTAATTTAAGTTATTTTAGT
Found at i:17106466 original size:20 final size:19
Alignment explanation
Indices: 17106441--17106478 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
17106431 TTAACAATTA
17106441 GTTTCT-TTCTTTATTTTTGT
1 GTTTCTCTT-TTT-TTTTTGT
17106461 GTTTCTCTTTTTTTTTTG
1 GTTTCTCTTTTTTTTTTG
17106479 ACTTGGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.03, C:0.11, G:0.11, T:0.76
Consensus pattern (19 bp):
GTTTCTCTTTTTTTTTTGT
Found at i:17114173 original size:39 final size:40
Alignment explanation
Indices: 17114104--17114181 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
17114094 AACATATTAG
* *
17114104 AGCAGATTTTGTTTATGACAGTCAACATATCA-AAACATC
1 AGCAGATTTAGTTTATAACAGTCAACATATCATAAACATC
*
17114143 AGCAGACTTTAGTTTATAACAGTTAA-ATATCATAAACAT
1 AGCAGA-TTTAGTTTATAACAGTCAACATATCATAAACAT
17114182 ATCAGCATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 12 0.35
40 22 0.65
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (40 bp):
AGCAGATTTAGTTTATAACAGTCAACATATCATAAACATC
Found at i:17124225 original size:2 final size:2
Alignment explanation
Indices: 17124167--17124217 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
17124157 ATTACTACTA
*
17124167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17124209 AT AT AT AT A
1 AT AT AT AT A
17124218 CGTATATACC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17124236 original size:3 final size:3
Alignment explanation
Indices: 17124228--17124297 Score: 58
Period size: 3 Copynumber: 24.7 Consensus size: 3
17124218 CGTATATACC
* * * *
17124228 CAT CAT CAT C-C CAT CAT CAT CAT CAT C-T CAC CAA CCT -AT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
* *
17124273 CAT CAC CAA C-T CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
17124298 CCAGCTCATG
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 5 0.09
3 48 0.91
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (3 bp):
CAT
Found at i:17124253 original size:20 final size:20
Alignment explanation
Indices: 17124228--17124306 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
17124218 CGTATATACC
*
17124228 CATCATCATC-CCATCATCAT
1 CATCATCATCACCAAC-TCAT
17124248 CATCATC-TCACCAAC-CTAT
1 CATCATCATCACCAACTC-AT
17124267 CATCATCATCACCAACTCAT
1 CATCATCATCACCAACTCAT
*
17124287 CATCATCATCACCAGCTCAT
1 CATCATCATCACCAACTCAT
17124307 GCGCACTCCC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.02
19 11 0.21
20 40 0.75
21 1 0.02
ACGTcount: A:0.32, C:0.41, G:0.01, T:0.27
Consensus pattern (20 bp):
CATCATCATCACCAACTCAT
Found at i:17124357 original size:43 final size:43
Alignment explanation
Indices: 17124305--17124423 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
17124295 TCACCAGCTC
** * *
17124305 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
* *
17124348 ATGCACACTCCCTACTCACACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* * * *
17124391 ATGTGCACTCCATACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
17124424 ACATAATTAC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
42 1 0.02
43 62 0.98
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:17133226 original size:20 final size:21
Alignment explanation
Indices: 17133187--17133231 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
17133177 GCTAGGTGGA
17133187 AAAATTCAAGGGAAAAAAGTG
1 AAAATTCAAGGGAAAAAAGTG
*
17133208 AAAATTCAA-GGAAACAAGTG
1 AAAATTCAAGGGAAAAAAGTG
17133228 AAAA
1 AAAA
17133232 AAAAGTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.13
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAAAGTG
Found at i:17133232 original size:21 final size:22
Alignment explanation
Indices: 17133185--17133232 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
17133175 ACGCTAGGTG
17133185 GAAAAATTCAAGGGAAAAAAGT
1 GAAAAATTCAAGGGAAAAAAGT
*
17133207 G-AAAATTCAA-GGAAACAAGT
1 GAAAAATTCAAGGGAAAAAAGT
17133227 GAAAAA
1 GAAAAA
17133233 AAAGTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 13 0.54
22 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.21, T:0.12
Consensus pattern (22 bp):
GAAAAATTCAAGGGAAAAAAGT
Found at i:17135620 original size:20 final size:20
Alignment explanation
Indices: 17135595--17135635 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
17135585 ATAAGCCTTG
* *
17135595 TTGATTTTTATGAAATGAAA
1 TTGATTTATATAAAATGAAA
17135615 TTGATTTATATAAAATGAAA
1 TTGATTTATATAAAATGAAA
17135635 T
1 T
17135636 GAGATTTGAT
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:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (20 bp):
TTGATTTATATAAAATGAAA
Found at i:17138899 original size:2 final size:2
Alignment explanation
Indices: 17138894--17138919 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17138884 TTGTGTTATC
17138894 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
17138920 GTTTGAATTG
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:17160757 original size:42 final size:42
Alignment explanation
Indices: 17160652--17160760 Score: 209
Period size: 42 Copynumber: 2.6 Consensus size: 42
17160642 GAATATTACT
*
17160652 TTTAAATTTAAACAAATTAAACTTAAATGTAATTAATCCTTA
1 TTTAAATTTAAACAAATTAAATTTAAATGTAATTAATCCTTA
17160694 TTTAAATTTAAACAAATTAAATTTAAATGTAATTAATCCTTA
1 TTTAAATTTAAACAAATTAAATTTAAATGTAATTAATCCTTA
17160736 TTTAAATTTAAACAAATTAAATTTA
1 TTTAAATTTAAACAAATTAAATTTA
17160761 GATATAATGG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (42 bp):
TTTAAATTTAAACAAATTAAATTTAAATGTAATTAATCCTTA
Found at i:17160759 original size:21 final size:21
Alignment explanation
Indices: 17160652--17160760 Score: 73
Period size: 21 Copynumber: 5.2 Consensus size: 21
17160642 GAATATTACT
17160652 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
* * ** *
17160673 CTTAAATGT-AATTAATCCT-TA
1 TTTAAATTTAAACAAAT--TAAA
17160694 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
* ** *
17160715 TTTAAATGT-AATTAATCCT-TA
1 TTTAAATTTAAACAAAT--TAAA
17160736 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
17160757 TTTA
1 TTTA
17160761 GATATAATGG
Statistics
Matches: 62, Mismatches: 18, Indels: 16
0.65 0.19 0.17
Matches are distributed among these distances:
20 12 0.19
21 38 0.61
22 12 0.19
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAAATTTAAACAAATTAAA
Found at i:17163423 original size:13 final size:13
Alignment explanation
Indices: 17163405--17163429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17163395 GGAGAAATTG
17163405 TGATTTTATAAAA
1 TGATTTTATAAAA
17163418 TGATTTTATAAA
1 TGATTTTATAAA
17163430 TTTTTGGAAA
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:17165576 original size:42 final size:42
Alignment explanation
Indices: 17165523--17165647 Score: 121
Period size: 42 Copynumber: 3.0 Consensus size: 42
17165513 TCATCTGCTC
* **
17165523 CCCACTAGCACATCGCTAG-GTCATCATCGGCTTATGTGCACT
1 CCCACTAGCACATAGC-AGAGTCATCATCGGCTTATGCACACT
* *
17165565 CCCACTCGCACATAGCCGAGTCATCATCGGCTTATGCACACT
1 CCCACTAGCACATAGCAGAGTCATCATCGGCTTATGCACACT
* * * * *
17165607 CCTACTTGCACATAGTC--AGTCATCATTGGCGTATGTACACT
1 CCCACTAGCACATAG-CAGAGTCATCATCGGCTTATGCACACT
17165648 TTTACTCGCA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
41 22 0.31
42 48 0.68
43 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (42 bp):
CCCACTAGCACATAGCAGAGTCATCATCGGCTTATGCACACT
Found at i:17165647 original size:41 final size:41
Alignment explanation
Indices: 17165542--17165666 Score: 160
Period size: 41 Copynumber: 3.0 Consensus size: 41
17165532 ACATCGCTAG
* * *
17165542 GTCATCATCGGCTTATGTGCACTCCCACTCGCACATAGCCGA
1 GTCATCATCGGCTTATGTACACTCCTACTCGCACATAGTC-A
* *
17165584 GTCATCATCGGCTTATGCACACTCCTACTTGCACATAGTCA
1 GTCATCATCGGCTTATGTACACTCCTACTCGCACATAGTCA
* * **
17165625 GTCATCATTGGCGTATGTACACTTTTACTCGCACATAGTCA
1 GTCATCATCGGCTTATGTACACTCCTACTCGCACATAGTCA
17165666 G
1 G
17165667 GTCCACATCA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 37 0.51
42 35 0.49
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (41 bp):
GTCATCATCGGCTTATGTACACTCCTACTCGCACATAGTCA
Found at i:17170527 original size:25 final size:25
Alignment explanation
Indices: 17170474--17170527 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
17170464 ATAGCTGTGG
*
17170474 TTCCACCATACTTGAATTTCAATTG
1 TTCCACCATACTTGAATTTCAATTA
* *
17170499 TTCCACCATACTTGAATTTTAGTTA
1 TTCCACCATACTTGAATTTCAATTA
17170524 TTCC
1 TTCC
17170528 CACAGCTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (25 bp):
TTCCACCATACTTGAATTTCAATTA
Found at i:17172086 original size:36 final size:36
Alignment explanation
Indices: 17172046--17172136 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
17172036 CAACAAGGTT
* *
17172046 AAGCACAACCTTTATAACATGCCTTTTAACAACATC
1 AAGCACAACCTTCACAACATGCCTTTTAACAACATC
* * *
17172082 AAGCATAACCTTCACAACATGCCTTTTAAGAAGATC
1 AAGCACAACCTTCACAACATGCCTTTTAACAACATC
***
17172118 AAGTGTAACCTTCACAACA
1 AAGCACAACCTTCACAACA
17172137 AGCTTTTTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25
Consensus pattern (36 bp):
AAGCACAACCTTCACAACATGCCTTTTAACAACATC
Found at i:17172154 original size:36 final size:36
Alignment explanation
Indices: 17172052--17172162 Score: 98
Period size: 36 Copynumber: 3.1 Consensus size: 36
17172042 GGTTAAGCAC
* * * * *
17172052 AACCTTTATAACATGCCTTTTAACAACATCAAGCA-T
1 AACCTTCACAACAAGCCTTTTAAGAAGATCAAG-AGT
* *
17172088 AACCTTCACAACATGCCTTTTAAGAAGATCAAGTGT
1 AACCTTCACAACAAGCCTTTTAAGAAGATCAAGAGT
* *** *
17172124 AACCTTCACAACAAGCTTTTTCCTAGGATCAAGAGT
1 AACCTTCACAACAAGCCTTTTAAGAAGATCAAGAGT
17172160 AAC
1 AAC
17172163 TTTTACTAAG
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (36 bp):
AACCTTCACAACAAGCCTTTTAAGAAGATCAAGAGT
Found at i:17186626 original size:35 final size:35
Alignment explanation
Indices: 17186600--17186821 Score: 225
Period size: 35 Copynumber: 6.3 Consensus size: 35
17186590 CTTAATTGTT
*
17186600 TAATTTAATCAATTAGGCCAAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * *
17186635 CAATTTAATTAATTAGGCCCAACAATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
17186670 CAATTTTAATCAATTAGGCCCAATGACTTAATTAAA
1 TAA-TTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * * ***
17186706 CAAATTTAATCAATTGGGCCTAATAATTTAATTGTT
1 -TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
17186742 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
17186777 TAATTTAATTAATTAGG--C-ACAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
*
17186809 CAATTTTAATCAA
1 TAA-TTTAATCAA
17186822 GTCCTTGAGA
Statistics
Matches: 154, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
32 14 0.09
33 9 0.06
35 76 0.49
36 53 0.34
37 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (35 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
Found at i:17186684 original size:71 final size:71
Alignment explanation
Indices: 17186603--17186821 Score: 284
Period size: 71 Copynumber: 3.1 Consensus size: 71
17186593 AATTGTTTAA
* *
17186603 TTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATTAATTAGGCCCAACAATTTAATTA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCCAACAATTTAATTA
17186668 AACAAT
66 AACAAT
* * * *
17186674 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTAATCAATTGGGCCTAATAATTTAATT
1 TTTAATCAATTAGGCCCAATGACTTAATTAAAC-AATTTAATTAATTAGGCCCAACAATTTAATT
****
17186739 GTTTAA-
65 AAACAAT
* * *
17186745 TTTAATTAATTAGGCCCAATGACTTAATTAAATAATTTAATTAATTAGG--C-ACAACTTAATTA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCCAACAATTTAATTA
17186807 AACAAT
66 AACAAT
17186813 TTTAATCAA
1 TTTAATCAA
17186822 GTCCTTGAGA
Statistics
Matches: 124, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
67 11 0.09
68 8 0.06
70 14 0.11
71 62 0.50
72 29 0.23
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (71 bp):
TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCCAACAATTTAATTA
AACAAT
Found at i:17186731 original size:107 final size:103
Alignment explanation
Indices: 17186601--17186821 Score: 280
Period size: 107 Copynumber: 2.1 Consensus size: 103
17186591 TTAATTGTTT
*
17186601 AATTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATTAATTAGGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATTAATTAGGCCCAACAACTTAAT
*
17186666 TAAACAATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
66 TAAACAA-TTTAATCAATTAGGCAC-A--ACTTAATTAAACA
* * * **** **
17186708 AATTTAATCAATTGGGCCTAATAATTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAAT
1 AATTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATTAATTAGGCCCAACAACTTAAT
* *
17186773 TAAATAATTTAATTAATTAGGCACAACTTAATTAAACA
66 TAAACAATTTAATCAATTAGGCACAACTTAATTAAACA
*
17186811 ATTTTAATCAA
1 AATTTAATCAA
17186822 GTCCTTGAGA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
103 23 0.23
105 1 0.01
106 15 0.15
107 61 0.61
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (103 bp):
AATTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATTAATTAGGCCCAACAACTTAAT
TAAACAATTTAATCAATTAGGCACAACTTAATTAAACA
Found at i:17191040 original size:68 final size:68
Alignment explanation
Indices: 17190926--17191193 Score: 277
Period size: 68 Copynumber: 3.9 Consensus size: 68
17190916 CACATACAAG
* * * * *
17190926 CTTACTCATCTCATAAGGTACATGGAAAATGCATCATATACATAATCTCATGGCATTCATCATGC
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
* *
17190991 TTT
66 ATA
* * * * *
17190994 CTCAATCATCTCATGTAGTATATGGAATATACATCATATGCATAATCTCATGGCATTTATCATGC
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
17191059 ATA
66 ATA
* * * * * * * * *
17191062 CTTAATCACCTTATATGGTATATGGAGTTTACATCATATACACAATCTTATAGTATACATCATGC
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
17191127 ATA
66 ATA
* * * * *
17191130 CTTGATCATCTCAAATGGTATATGGATTTTACATCATATACTTAAATC-CTATGGCATTCATCAT
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACAT-AATCTC-ATGGCATTCATCAT
17191194 ACCAAACATA
Statistics
Matches: 161, Mismatches: 37, Indels: 3
0.80 0.18 0.01
Matches are distributed among these distances:
68 146 0.91
69 15 0.09
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (68 bp):
CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
ATA
Found at i:17192433 original size:16 final size:16
Alignment explanation
Indices: 17192408--17192438 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17192398 ATAAAAATAT
17192408 CAAAAAAATCAAAATC
1 CAAAAAAATCAAAATC
*
17192424 CAAAAGAATCAAAAT
1 CAAAAAAATCAAAAT
17192439 TTAATTTTTG
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:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
CAAAAAAATCAAAATC
Found at i:17193829 original size:37 final size:36
Alignment explanation
Indices: 17193787--17193904 Score: 123
Period size: 37 Copynumber: 3.3 Consensus size: 36
17193777 TAAATCAGGT
*
17193787 TCAAGCACAACCATTACAAGCCACTACCTTTTATGGA
1 TCAAGCACAACC-TTACAAGTCACTACCTTTTATGGA
* * * *
17193824 TCAAGCACAA-CTT-TAAGTCATTATCTTTCATGGA
1 TCAAGCACAACCTTACAAGTCACTACCTTTTATGGA
* * * *
17193858 TCAAGCATAACCTTTACAAATCACTGCTTTTTATGGA
1 TCAAGCACAACC-TTACAAGTCACTACCTTTTATGGA
17193895 TCAAGCACAA
1 TCAAGCACAA
17193905 TCTCTCTACT
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
34 25 0.39
35 3 0.05
36 3 0.05
37 33 0.52
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.30
Consensus pattern (36 bp):
TCAAGCACAACCTTACAAGTCACTACCTTTTATGGA
Found at i:17193954 original size:29 final size:29
Alignment explanation
Indices: 17193920--17193991 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
17193910 CTACTTTTCT
* * *
17193920 ATGGAGGTATAAGC-TTTCTACCTTTTCCA
1 ATGGAGGTATAACCATTT-TACCATTTACA
17193949 ATGGAGGTATAACCATTTTACCATTTACA
1 ATGGAGGTATAACCATTTTACCATTTACA
17193978 ATGGAGGTATAACC
1 ATGGAGGTATAACC
17193992 TAACACTACC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 36 0.92
30 3 0.08
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (29 bp):
ATGGAGGTATAACCATTTTACCATTTACA
Found at i:17194019 original size:31 final size:30
Alignment explanation
Indices: 17193920--17194023 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 30
17193910 CTACTTTTCT
* ** *
17193920 ATGGAGGTATAAGCT-TTCTACCTTTTCCA
1 ATGGAGGTATAACCTACACTACCTTTTACA
*** *
17193949 ATGGAGGTATAACC-ATTTTACCATTTACA
1 ATGGAGGTATAACCTACACTACCTTTTACA
*
17193978 ATGGAGGTATAACCTAACACTACCTTTTGCA
1 ATGGAGGTATAACCT-ACACTACCTTTTACA
*
17194009 ATTGAGGTATAACCT
1 ATGGAGGTATAACCT
17194024 TACAACAGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 38 0.61
31 24 0.39
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (30 bp):
ATGGAGGTATAACCTACACTACCTTTTACA
Found at i:17198254 original size:54 final size:54
Alignment explanation
Indices: 17198196--17198363 Score: 273
Period size: 54 Copynumber: 3.1 Consensus size: 54
17198186 GAGATGGATA
* * *
17198196 GGATGTTCGACTATGTGCACAATGTGGTGGGATGCACATGAGCTGGGTGAGATG
1 GGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
17198250 GGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
1 GGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
** * *
17198304 GGACATCCGGCTATGTGCACGATGTGGTGGGATGCACGTGAGTTGGGTGAGATG
1 GGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
17198358 GGATGT
1 GGATGT
17198364 TTGTTGGAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 105 1.00
ACGTcount: A:0.20, C:0.14, G:0.42, T:0.25
Consensus pattern (54 bp):
GGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
Found at i:17201377 original size:22 final size:22
Alignment explanation
Indices: 17201329--17201381 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
17201319 GAATCCTAAC
17201329 TTCGCTGCAACGGAACGGCATT
1 TTCGCTGCAACGGAACGGCATT
* * *
17201351 CTCGCTGCAACGAGAA-TGCCTT
1 TTCGCTGCAACG-GAACGGCATT
17201373 TTCGCTGCA
1 TTCGCTGCA
17201382 GTGAGGACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.25
Consensus pattern (22 bp):
TTCGCTGCAACGGAACGGCATT
Found at i:17208254 original size:54 final size:54
Alignment explanation
Indices: 17208196--17208367 Score: 299
Period size: 54 Copynumber: 3.2 Consensus size: 54
17208186 GAGGGAGATG
*
17208196 GATGGGATGTCCGGCTATGTGCACGATGTGTTGGGATGCACATGAGCTGGGTGA
1 GATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
*
17208250 GATGGGATGTCCGGTTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
1 GATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
** *
17208304 GATGGGACATCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGA
1 GATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
17208358 GATGGGATGT
1 GATGGGATGT
17208368 TTGTTGGAAA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.19, C:0.13, G:0.42, T:0.26
Consensus pattern (54 bp):
GATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
Found at i:17209509 original size:36 final size:36
Alignment explanation
Indices: 17209450--17209590 Score: 151
Period size: 36 Copynumber: 3.9 Consensus size: 36
17209440 TTGTGAGCTT
17209450 GTATAGCCAGATGT-GGGGACAAGATACCACACACTA
1 GTATAGCCAGATGTAGGGG-CAAGATACCACACACTA
* * *
17209486 GTATAGCCAAATGTAGGGGCAAGATACCATACACTT
1 GTATAGCCAGATGTAGGGGCAAGATACCACACACTA
* * * **
17209522 GTGTAGCCAGATGTAGGGACATGATACCACATGCTA
1 GTATAGCCAGATGTAGGGGCAAGATACCACACACTA
* * *
17209558 TTATTA-CCAGATGTGGGGGCAAGATAGCACACA
1 GTA-TAGCCAGATGTAGGGGCAAGATACCACACA
17209591 TCCATATAGC
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
36 78 0.93
37 6 0.07
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (36 bp):
GTATAGCCAGATGTAGGGGCAAGATACCACACACTA
Found at i:17209577 original size:72 final size:72
Alignment explanation
Indices: 17209447--17209583 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 72
17209437 ATTTTGTGAG
*
17209447 CTTGTATAGCCAGATGTGGGGACAAGATACCACACACTAGTATAGCCAAATGTAGGGGCAAGATA
1 CTTGTATAGCCAGATGTAGGGACAAGATACCACACACTAGTATAGCCAAATGTAGGGGCAAGATA
17209512 CCATACA
66 CCATACA
* * ** * * *
17209519 CTTGTGTAGCCAGATGTAGGGACATGATACCACATGCTATTATTA-CCAGATGTGGGGGCAAGAT
1 CTTGTATAGCCAGATGTAGGGACAAGATACCACACACTAGTA-TAGCCAAATGTAGGGGCAAGAT
17209583 A
65 A
17209584 GCACACATCC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 54 0.96
73 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (72 bp):
CTTGTATAGCCAGATGTAGGGACAAGATACCACACACTAGTATAGCCAAATGTAGGGGCAAGATA
CCATACA
Found at i:17212882 original size:77 final size:76
Alignment explanation
Indices: 17212755--17212917 Score: 245
Period size: 77 Copynumber: 2.1 Consensus size: 76
17212745 TATGCCATCT
*
17212755 ATTTTAATTTTGGGTGATTCATAAAAAATAGAAAATTGTTTCCTACTTTAAAAACAATTCCTAAA
1 ATTTTAATTTTGAGTGATTCATAAAAAATAGAAAATTGTTTCCTACTTTAAAAA-AATTCCTAAA
17212820 ATTAAGAATAGA
65 ATTAAGAATAGA
* ** * *
17212832 ATTTTTATTTTGAGTGATTCATAATGAATAGTAAATTGTTTCCTACTTTAAAAAAATTTCTAAAA
1 ATTTTAATTTTGAGTGATTCATAAAAAATAGAAAATTGTTTCCTACTTTAAAAAAATTCCTAAAA
* *
17212897 TTAAGGATAGT
66 TTAAGAATAGA
17212908 ATTTTAATTT
1 ATTTTAATTT
17212918 GGAAAATTCA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 28 0.36
77 49 0.64
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (76 bp):
ATTTTAATTTTGAGTGATTCATAAAAAATAGAAAATTGTTTCCTACTTTAAAAAAATTCCTAAAA
TTAAGAATAGA
Found at i:17213870 original size:2 final size:2
Alignment explanation
Indices: 17213863--17213908 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
17213853 TTATTTTTAG
17213863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
17213906 TA T
1 TA T
17213909 GTGAAATGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 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:17229180 original size:42 final size:42
Alignment explanation
Indices: 17229128--17229252 Score: 196
Period size: 42 Copynumber: 3.0 Consensus size: 42
17229118 CATCTCATAT
* * *
17229128 GCAACAGCTTATGCGCACTCCCACTCGCACATAGCCTGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
17229170 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
** *
17229212 GCAACGGCTTATGTGCACTCTTACTAGCACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
17229253 CACATCAACA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:17255297 original size:8 final size:9
Alignment explanation
Indices: 17255271--17255299 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
17255261 TTTTTAATTA
17255271 TTTATATAT
1 TTTATATAT
17255280 TTTATATAT
1 TTTATATAT
17255289 TTTAT-TAT
1 TTTATATAT
17255297 TTT
1 TTT
17255300 TTAGTGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTATATAT
Done.