Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 171 of 216
Found at i:53772347 original size:18 final size:18
Alignment explanation
Indices: 53772324--53772360 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53772314 TTTTTTCTCC
53772324 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCCTA
53772342 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCCTA
53772360 A
1 A
53772361 CGTGAGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAACCCTAAAAATCCTA
Found at i:53772809 original size:6 final size:6
Alignment explanation
Indices: 53772798--53772824 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53772788 ATGTATCGCT
53772798 AATCCA AATCCA AATCCA AATCCA AAT
1 AATCCA AATCCA AATCCA AATCCA AAT
53772825 GTACCCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.19
Consensus pattern (6 bp):
AATCCA
Found at i:53775688 original size:22 final size:24
Alignment explanation
Indices: 53775640--53775690 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
53775630 AATTCCCTCA
* *
53775640 AAAAGTAAAAATTTAAGTAATTCT
1 AAAAGTAAAAATTAAAGTAAATCT
*
53775664 AAAA-TAAAAATTAAAG-AAATGT
1 AAAAGTAAAAATTAAAGTAAATCT
53775686 AAAAG
1 AAAAG
53775691 GAGTAGGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.35
23 11 0.48
24 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (24 bp):
AAAAGTAAAAATTAAAGTAAATCT
Found at i:53792949 original size:22 final size:20
Alignment explanation
Indices: 53792894--53792951 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
53792884 TAAATATATA
*
53792894 TTGAATAGTTATGTTTATTG
1 TTGAATAGTTATGTCTATTG
* * *
53792914 TT-AAAAGATGTGTCTATTCG
1 TTGAATAGTTATGTCTATT-G
53792934 TTTGAATAGTTATGTCTA
1 -TTGAATAGTTATGTCTA
53792952 GTAATATGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 2 0.07
22 11 0.39
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.48
Consensus pattern (20 bp):
TTGAATAGTTATGTCTATTG
Found at i:53805262 original size:16 final size:18
Alignment explanation
Indices: 53805230--53805262 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53805220 ATTTCAAAAA
53805230 TTTTAATACATTACTATT
1 TTTTAATACATTACTATT
53805248 TTTTAA-ACATT-CTAT
1 TTTTAATACATTACTAT
53805263 GATATGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAATACATTACTATT
Found at i:53807570 original size:20 final size:20
Alignment explanation
Indices: 53807545--53807583 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
53807535 TTTTCAATGT
53807545 CTCTTTTACACCGAAATTTC
1 CTCTTTTACACCGAAATTTC
53807565 CTCTTTTACACCGAAATTT
1 CTCTTTTACACCGAAATTT
53807584 AACGACCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (20 bp):
CTCTTTTACACCGAAATTTC
Found at i:53808444 original size:44 final size:44
Alignment explanation
Indices: 53808393--53808697 Score: 459
Period size: 44 Copynumber: 6.9 Consensus size: 44
53808383 CAAGATTTGT
*
53808393 TATCTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAA
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
* * *
53808437 TATCTTCGATCTACTTCATGTCAACACATGAAGATAAGATCTAC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
* * *
53808481 TATCTTTGATCTACTTCATGTCAATACATGAAGACAAGATCCAT
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
53808525 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
****
53808569 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATATGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
* *
53808613 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCAA
* *
53808657 TATCTTCGATCCACTTCACGTCAATACATGAAGATAAGATC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATC
53808698 TGCTATATTT
Statistics
Matches: 235, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 2 0.01
44 231 0.98
45 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (44 bp):
TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAA
Found at i:53808712 original size:132 final size:132
Alignment explanation
Indices: 53808392--53808697 Score: 549
Period size: 132 Copynumber: 2.3 Consensus size: 132
53808382 ACAAGATTTG
*
53808392 TTATCTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAATATCTTCGATCTACTTCATG
1 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
* *
53808457 TCAACACATGAAGATAAGATCTACTATCTTTGATCTACTTCATGTCAATACATGAAGACAAGATC
66 TCAACACATGAAGATAAGATATACTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATC
53808522 CA
131 CA
53808524 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
1 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
* *
53808589 TCAATACATGAAGATAAGATATGCTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATC
66 TCAACACATGAAGATAAGATATACTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATC
53808654 CA
131 CA
* *
53808656 TTATCTTCGATCCACTTCACGTCAATACATGAAGATAAGATC
1 TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATC
53808698 TGCTATATTT
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 167 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (132 bp):
TTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCAATATCTTCGATCTACTTCATG
TCAACACATGAAGATAAGATATACTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATC
CA
Found at i:53810004 original size:48 final size:48
Alignment explanation
Indices: 53809944--53810036 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
53809934 CCTTTTGGTC
* * * *
53809944 TCAAGGCTCCCTTTGCGGGTTTTCACCTTGG-CCTCTCCTTTTTTTTAT
1 TCAAGGCGCCCTTTGCAGGCTTTCACCTTGGTCC-CCCCTTTTTTTTAT
*
53809992 TCAAGGCGCCCTTTGTAGGCTTTCACCTTGGTCCCCCCTTTTTTT
1 TCAAGGCGCCCTTTGCAGGCTTTCACCTTGGTCCCCCCTTTTTTT
53810037 AGGAAAAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.09, C:0.31, G:0.17, T:0.43
Consensus pattern (48 bp):
TCAAGGCGCCCTTTGCAGGCTTTCACCTTGGTCCCCCCTTTTTTTTAT
Found at i:53812755 original size:19 final size:20
Alignment explanation
Indices: 53812731--53812777 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53812721 TAGTGGTGTT
* *
53812731 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
53812750 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
53812770 -AATGCAAA
1 TAATGCAAA
53812778 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:53822755 original size:12 final size:12
Alignment explanation
Indices: 53822738--53822765 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53822728 TAAAAATAGA
53822738 TATACTCACAAT
1 TATACTCACAAT
53822750 TATACTCACAAT
1 TATACTCACAAT
53822762 TATA
1 TATA
53822766 ATTCAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (12 bp):
TATACTCACAAT
Found at i:53824789 original size:21 final size:19
Alignment explanation
Indices: 53824756--53824797 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 19
53824746 TTTTGTGTTT
53824756 AATATTTTAATAAATTTGATA
1 AATATTTTAAT-AA-TTGATA
53824777 AATA-TTTATATAATTGATA
1 AATATTTTA-ATAATTGATA
53824796 AA
1 AA
53824798 AATATAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
AATATTTTAATAATTGATA
Found at i:53825584 original size:14 final size:14
Alignment explanation
Indices: 53825551--53825596 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
53825541 AGGAATAGGA
*
53825551 AATTTCATTAGATT
1 AATTTAATTAGATT
*
53825565 ATTTTAAGTTA-ATT
1 AATTTAA-TTAGATT
53825579 AATTTAATTAGATT
1 AATTTAATTAGATT
53825593 AATT
1 AATT
53825597 AATATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (14 bp):
AATTTAATTAGATT
Found at i:53828280 original size:19 final size:20
Alignment explanation
Indices: 53828253--53828304 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
53828243 AATATTATTT
53828253 AAATATTATAATAAATTT-AG
1 AAATATTATAA-AAATTTAAG
53828273 AAAT-TTATAAAAATTTAAG
1 AAATATTATAAAAATTTAAG
*
53828292 AAA-ACTATAAAAA
1 AAATATTATAAAAA
53828305 ATACTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 19 0.66
20 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATATTATAAAAATTTAAG
Found at i:53828364 original size:21 final size:21
Alignment explanation
Indices: 53828330--53828370 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53828320 AAAAATTTAT
53828330 ATTATTAAATATTAT-AAAAG
1 ATTATTAAATATTATGAAAAG
*
53828350 ATTATTGATATATTATGAAAA
1 ATTATT-AAATATTATGAAAA
53828371 AATATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
ATTATTAAATATTATGAAAAG
Found at i:53831389 original size:25 final size:25
Alignment explanation
Indices: 53831355--53831402 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53831345 TGAAGTAAGG
*
53831355 GAAGGTAAAGGAAAGTAAGGGAAGA
1 GAAGGGAAAGGAAAGTAAGGGAAGA
* *
53831380 GAAGGGAAAGGAATGTGAGGGAA
1 GAAGGGAAAGGAAAGTAAGGGAA
53831403 ATTGAGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (25 bp):
GAAGGGAAAGGAAAGTAAGGGAAGA
Found at i:53831706 original size:24 final size:26
Alignment explanation
Indices: 53831664--53831714 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
53831654 TTATTCTATT
*
53831664 ATATTTGTATTTTAATTTAAGT-TAA
1 ATATTTGTATTATAATTTAAGTGTAA
*
53831689 ATATTT-TATTATATTTTAAGTGTAA
1 ATATTTGTATTATAATTTAAGTGTAA
53831714 A
1 A
53831715 ACTAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (26 bp):
ATATTTGTATTATAATTTAAGTGTAA
Found at i:53833007 original size:28 final size:30
Alignment explanation
Indices: 53832944--53833007 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
53832934 AAAGAAAGCC
*
53832944 ATTTTTTAATAAAATTATGGAAATAAGTTA
1 ATTTTTTAATAAAATTATGGAAATAAGCTA
*
53832974 ATTTTTTAA-AAATTTATGGAAAT-AGACTA
1 ATTTTTTAATAAAATTATGGAAATAAG-CTA
53833003 ATTTT
1 ATTTT
53833008 GGTGTCCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 2 0.06
29 20 0.65
30 9 0.29
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (30 bp):
ATTTTTTAATAAAATTATGGAAATAAGCTA
Found at i:53834653 original size:28 final size:28
Alignment explanation
Indices: 53834604--53834661 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
53834594 TGTAACAGTT
* *
53834604 CAGATGTAGATGCAAAACAAATTAGATA
1 CAGATGTAGATACAAAACAAATCAGATA
*
53834632 CAGATGTAGA-ACAAATCAAAATCAGATA
1 CAGATGTAGATACAAAAC-AAATCAGATA
53834660 CA
1 CA
53834662 ATTTCCTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.19
Consensus pattern (28 bp):
CAGATGTAGATACAAAACAAATCAGATA
Found at i:53836063 original size:7 final size:6
Alignment explanation
Indices: 53836040--53836082 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
53836030 AATCAAAAGT
* * *
53836040 AAAGAA AATGAA AAAGAA ATAAGAA AAATAA AAATAA AAAGAA
1 AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA
53836083 GAAGGAACGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:53840786 original size:33 final size:32
Alignment explanation
Indices: 53840749--53840930 Score: 141
Period size: 35 Copynumber: 5.4 Consensus size: 32
53840739 ATAACCCAAT
*
53840749 TATGGTCTTATCATCAGAATGCCATAGTCCAGC
1 TATGGTCTTA-CATCAAAATGCCATAGTCCAGC
* *
53840782 TATGGTCTTACATATAAACACTGCCATAGCCCAGC
1 TATGGTCTTACAT-CAAA-A-TGCCATAGTCCAGC
* * * *
53840817 TATGGTCTTACATATAAACACTGCCCTGGTCCAAC
1 TATGGTCTTACAT-CAAA-A-TGCCATAGTCCAGC
* * * * *
53840852 TATGGTCTTACGTTCATAGTGCCAT-GACCTAGT
1 TATGGTCTTAC-ATCAAAATGCCATAGTCC-AGC
* *
53840885 TATGGTCTTATCATCAGAATGCTATAGTCCAGC
1 TATGGTCTTA-CATCAAAATGCCATAGTCCAGC
53840918 TATGGTCTTACAT
1 TATGGTCTTACAT
53840931 ATAAATACTG
Statistics
Matches: 121, Mismatches: 21, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
32 9 0.07
33 49 0.40
34 5 0.04
35 57 0.47
36 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (32 bp):
TATGGTCTTACATCAAAATGCCATAGTCCAGC
Found at i:53840816 original size:35 final size:35
Alignment explanation
Indices: 53840768--53840962 Score: 168
Period size: 35 Copynumber: 5.7 Consensus size: 35
53840758 ATCATCAGAA
53840768 TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
1 TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
*
53840803 TGCCATAGCCCAGCTATGGTCTTACATATAAACAC
1 TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
* * * * * * *
53840838 TGCCCTGGTCCAACTATGGTCTTACGT-T-CATAG
1 TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
* * * *
53840871 TGCCAT-GACCTAGTTATGGTCTTATCAT-CAGA-A-
1 TGCCATAGTCC-AGCTATGGTCTTA-CATATAAACAC
* *
53840904 TGCTATAGTCCAGCTATGGTCTTACATATAAATAC
1 TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
* * * *
53840939 TGCCATGGTCTAACCATGGTCTTA
1 TGCCATAGTCCAGCTATGGTCTTA
53840963 TGTTCATAGT
Statistics
Matches: 127, Mismatches: 26, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
32 6 0.05
33 37 0.29
34 8 0.06
35 76 0.60
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (35 bp):
TGCCATAGTCCAGCTATGGTCTTACATATAAACAC
Found at i:53840941 original size:101 final size:101
Alignment explanation
Indices: 53840807--53840997 Score: 310
Period size: 101 Copynumber: 1.9 Consensus size: 101
53840797 AAACACTGCC
* *
53840807 ATAGCCCAGCTATGGTCTTACATATAAACACTGCCCTGGTCCAACTATGGTCTTACGTTCATAGT
1 ATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
* *
53840872 GCCATGACCTAGTTATGGTCTTATCATCAGAATGCT
66 GCCATAACCCAGTTATGGTCTTATCATCAGAATGCT
* * * *
53840908 ATAGTCCAGCTATGGTCTTACATATAAATACTGCCATGGTCTAACCATGGTCTTATGTTCATAGT
1 ATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
53840973 GCCATAACCCAGTTATGGTCTTATC
66 GCCATAACCCAGTTATGGTCTTATC
53840998 CGTTAATTCA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (101 bp):
ATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
GCCATAACCCAGTTATGGTCTTATCATCAGAATGCT
Found at i:53862788 original size:67 final size:67
Alignment explanation
Indices: 53862705--53862840 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
53862695 ATGCCTCGAG
* *
53862705 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCTAAGATTGGTAACC
1 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
53862770 CA
66 CA
53862772 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
1 ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
53862837 CA
66 CA
53862839 AC
1 AC
53862841 TTTGTATTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (67 bp):
ACATGGCTTCATTATCTCAAGACATAAACTTGCATTTTGCTTGTTTGATCCCAAGATTCGTAACC
CA
Found at i:53863377 original size:34 final size:34
Alignment explanation
Indices: 53863334--53863402 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
53863324 TGTTTTCGAC
53863334 AATGGCTATTAGAAAATTAAGTCAATTTTTGAAA
1 AATGGCTATTAGAAAATTAAGTCAATTTTTGAAA
*
53863368 AATGGCTATTAGGAAATTAAGTCAATTTTTGAAA
1 AATGGCTATTAGAAAATTAAGTCAATTTTTGAAA
53863402 A
1 A
53863403 TGAGTTTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (34 bp):
AATGGCTATTAGAAAATTAAGTCAATTTTTGAAA
Found at i:53876106 original size:124 final size:124
Alignment explanation
Indices: 53875881--53876109 Score: 318
Period size: 124 Copynumber: 1.8 Consensus size: 124
53875871 TATAGCTAAG
* * *
53875881 GGACCTACGCTCCCAGTTGATGTTATAAAGGTTTGCTGATTTATGATTGCAACCTCCAAAAATAA
1 GGACCTACGCTCCCAGCTGATGTTATAAAGGTTTGCTCATTTATGATTACAACCTCCAAAAATAA
* * * **
53875946 CTAATGGACCTACGCTCCCAGCTGATATTCTGAGAGCTCGCAGCTCTAACACAACTAGC
66 CTAACGAACCTACACTCCCAGCTGATATTCCAAGAGCTCGCAGCTCTAACACAACTAGC
53876005 GGACCTACGCTCCCAGCTGATGTTATAAAGGTTTG-TCATTTTATGATTACAACCTCCAAAAATA
1 GGACCTACGCTCCCAGCTGATGTTATAAAGGTTTGCTCA-TTTATGATTACAACCTCCAAAAATA
* * * *
53876069 GCTAGCGAACCTATACTCCTAGCT-AGTATTCCAAGAGCTCG
65 ACTAACGAACCTACACTCCCAGCTGA-TATTCCAAGAGCTCG
53876110 TAGATTTAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
123 3 0.03
124 88 0.97
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (124 bp):
GGACCTACGCTCCCAGCTGATGTTATAAAGGTTTGCTCATTTATGATTACAACCTCCAAAAATAA
CTAACGAACCTACACTCCCAGCTGATATTCCAAGAGCTCGCAGCTCTAACACAACTAGC
Found at i:53876231 original size:262 final size:262
Alignment explanation
Indices: 53875766--53876247 Score: 641
Period size: 262 Copynumber: 1.8 Consensus size: 262
53875756 CTTGGTATTA
* * * * * *
53875766 TATAAAGGTTTGTCGGTTTGTGATCGCAACCTCCAAAAATAGCTAGTGGACCTACGCTTCCATAT
1 TATAAAGGTTTGTCAGTTTATGATCACAACCTCCAAAAATAGCTAGCGAACCTACACTTCCATAT
** * * *
53875831 GATATTCCAAGAGCTCGTAGAGTTAAGCTTGCAACTCCAATATAGCTAAGGGACCTACGCTCCCA
66 GATATTCCAAGAGCTCGTAGAGTTAAGCTCACAACTCCAACACAGCTAAGGAACCTACGCTCCCA
* * *
53875896 GTTGATGTTATAAAGGTTTGCTGATTTATGATTGCAACCTCCAAAAATAACTAATGGACCTACGC
131 ATTGATGTTATAAAGGTTTGCTAATTTATGATTACAACCTCCAAAAATAACTAATGGACCTACGC
53875961 TCCCAGCTGATATTCTGAGAGCTCGCAGCTCTAACACAACTAGCGGACCTACGCTCCCAGCTGAT
196 TCCCAGCTGATATTCTGAGAGCTCGCAGCTCTAACACAACTAGCGGACCTACGCTCCCAGCTGAT
53876026 GT
261 GT
* * *
53876028 TATAAAGGTTTGTCATTTTATGATTACAACCTCCAAAAATAGCTAGCGAACCTATAC-TCC-TA-
1 TATAAAGGTTTGTCAGTTTATGATCACAACCTCCAAAAATAGCTAGCGAACCTACACTTCCATAT
* * * *
53876090 GCTAGTATTCCAAGAGCTCGTAGATTTAAGGTCACAGCTCCAACACAGCT-AGCGAACCTATGCT
66 G--A-TATTCCAAGAGCTCGTAGAGTTAAGCTCACAACTCCAACACAGCTAAG-GAACCTACGCT
* * ** * *
53876154 CTCAATTGATGTTATAAGGGTTTG-TCAATTTATGATTACAACCTTTAAAAATAGCTAGTGGACC
127 CCCAATTGATGTTATAAAGGTTTGCT-AATTTATGATTACAACCTCCAAAAATAACTAATGGACC
53876218 TACGCTCCCAGCTGATATTCTGAGAGCTCG
191 TACGCTCCCAGCTGATATTCTGAGAGCTCG
53876248 TAGAGTTAAG
Statistics
Matches: 188, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
259 1 0.01
260 2 0.01
261 7 0.04
262 178 0.95
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (262 bp):
TATAAAGGTTTGTCAGTTTATGATCACAACCTCCAAAAATAGCTAGCGAACCTACACTTCCATAT
GATATTCCAAGAGCTCGTAGAGTTAAGCTCACAACTCCAACACAGCTAAGGAACCTACGCTCCCA
ATTGATGTTATAAAGGTTTGCTAATTTATGATTACAACCTCCAAAAATAACTAATGGACCTACGC
TCCCAGCTGATATTCTGAGAGCTCGCAGCTCTAACACAACTAGCGGACCTACGCTCCCAGCTGAT
GT
Found at i:53876237 original size:138 final size:138
Alignment explanation
Indices: 53875980--53876298 Score: 379
Period size: 138 Copynumber: 2.3 Consensus size: 138
53875970 ATATTCTGAG
* * * * * *
53875980 AGCTCGCAGCTCTAACACAACTAGCGGACCTACGCTCCCAGCTGATGTTATAAAGGTTTGTCATT
1 AGCTCACAGCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTTATAAAGGTTTGTCAAT
* *
53876045 TTATGATTACAACCTCCAAAAATAGCTAGCGAACCTATACTCCTAGCTAGTATTCCAAGAGCTCG
66 TTATGATTACAACCTCCAAAAATAGCTAGCGAACCTACACTCCCAGCTAGTATTCCAAGAGCTCG
*
53876110 TAGATTTA
131 TAGAGTTA
* * * * *
53876118 AGGTCACAGCTCCAACACAGCTAGCGAACCTATGCTCTCAATTGATGTTATAAGGGTTTGTCAAT
1 AGCTCACAGCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTTATAAAGGTTTGTCAAT
** * * * **
53876183 TTATGATTACAACCTTTAAAAATAGCTAGTGGACCTACGCTCCCAGCT-GATATTCTGAGAGCTC
66 TTATGATTACAACCTCCAAAAATAGCTAGCGAACCTACACTCCCAGCTAG-TATTCCAAGAGCTC
53876247 GTAGAGTTA
130 GTAGAGTTA
** * * * *
53876256 AGCTCGTAGCTCCAACACAGGTGGCGGACCTACGCTACCAACT
1 AGCTCACAGCTCCAACACAGCTAGCGAACCTACGCTCCCAACT
53876299 TACAGTATAA
Statistics
Matches: 149, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
137 1 0.01
138 148 0.99
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (138 bp):
AGCTCACAGCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTTATAAAGGTTTGTCAAT
TTATGATTACAACCTCCAAAAATAGCTAGCGAACCTACACTCCCAGCTAGTATTCCAAGAGCTCG
TAGAGTTA
Found at i:53876427 original size:17 final size:17
Alignment explanation
Indices: 53876407--53876513 Score: 124
Period size: 17 Copynumber: 6.3 Consensus size: 17
53876397 AAGTCTATTC
*
53876407 AAGTTCAGAATTTGCTT
1 AAGTTCAAAATTTGCTT
*
53876424 AAGTTCAAAAATTGCTT
1 AAGTTCAAAATTTGCTT
** *
53876441 AAGCCCAAAATTTGTTT
1 AAGTTCAAAATTTGCTT
*
53876458 AAGTTCAAAATGTGCTT
1 AAGTTCAAAATTTGCTT
* *
53876475 AAGTTCAAGATTTGATT
1 AAGTTCAAAATTTGCTT
*
53876492 AAATTCAAAATTTGCTT
1 AAGTTCAAAATTTGCTT
*
53876509 GAGTT
1 AAGTT
53876514 TACAAAAAGA
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 72 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (17 bp):
AAGTTCAAAATTTGCTT
Found at i:53883154 original size:26 final size:25
Alignment explanation
Indices: 53883102--53883152 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
53883092 TATGATTTGT
53883102 TCTGTTATGTATAAGCATGTGTAATA
1 TCTGTTA-GTATAAGCATGTGTAATA
*
53883128 TCTGTTA-TATAAGCATGTGTGATA
1 TCTGTTAGTATAAGCATGTGTAATA
53883152 T
1 T
53883153 ATTAATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.71
26 7 0.29
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (25 bp):
TCTGTTAGTATAAGCATGTGTAATA
Found at i:53886341 original size:16 final size:16
Alignment explanation
Indices: 53886317--53886349 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53886307 TTCGCTATAT
*
53886317 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
53886333 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
53886349 T
1 T
53886350 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:53886394 original size:45 final size:44
Alignment explanation
Indices: 53886328--53886418 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
53886318 GGATTAGAGG
* *
53886328 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
53886373 TGTAATGAAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
53886417 TG
1 TG
53886419 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGAAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:53886435 original size:39 final size:39
Alignment explanation
Indices: 53886331--53886437 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 39
53886321 TTAGAGGTGT
*
53886331 AATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
1 AATGGAATAGAGGTGTAATAG-TAATCAACTGTTTGGTTG
* ***
53886371 AATGTAATGAAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTG
1 AATG----G-AATAGAGGTGTAATAGTAATCAACTGTTTGGTTG
53886415 AATGGAATAGAGGTGTAATAGTA
1 AATGGAATAGAGGTGTAATAGTA
53886438 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
39 17 0.30
40 5 0.09
44 19 0.34
45 15 0.27
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (39 bp):
AATGGAATAGAGGTGTAATAGTAATCAACTGTTTGGTTG
Found at i:53886663 original size:61 final size:61
Alignment explanation
Indices: 53886595--53886775 Score: 192
Period size: 61 Copynumber: 3.0 Consensus size: 61
53886585 TAATTTAATA
**
53886595 AAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAAATC
1 AAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTAATAAAATC
* * * * * ** *
53886656 ATAATATATAATACT-ATAAAA-T-ATAAT-TTAACATAATTATTAT-TAAATATAATTTAATA
1 AAAATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATTCTTATATAAATTTAATAAAATC
* *
53886715 AAAATATATAATTTAATACAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAATC
1 AAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTAATAAAATC
53886776 TTGTAAAAAG
Statistics
Matches: 92, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 5 0.05
59 32 0.35
60 16 0.17
61 34 0.37
62 5 0.05
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (61 bp):
AAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTAATAAAATC
Found at i:53889659 original size:250 final size:251
Alignment explanation
Indices: 53889213--53889681 Score: 843
Period size: 250 Copynumber: 1.9 Consensus size: 251
53889203 CCAAAATTAC
*
53889213 CCTATTGTTTTTACCGTGTTTATATTGTTTCCTTCCAACAACCAAAAGCATAGCAGAGAAAAAGA
1 CCTATTGTTTTTACCGTGTTTATATTGTTTCCTTACAACAACCAAAAGCAT---A-AGAAAAAGA
53889278 TGATCTTCGTTATAAGCAAGAGAAAAAAAATTCAAGAAAAAAGCTTACAACAAGAATGACAACAG
62 TGATCTTCGTTATAAGCAAGAGAAAAAAAATTCAAGAAAAAAGCTTACAACAAGAATGACAACAG
53889343 TGAAGACACCAATTGTAACCAGAAAGGTAACTTGGCAATTATTGCAGCAACTGTTTAGCTCCCAG
127 TGAAGACACCAATTGTAACCAGAAAGGTAACTTGGCAATTATTGCAGCAACTGTTTAGCTCCCAG
53889408 TTCACCATTTTTCTGCCTTTATTTGACTAAGGCAAGTGCACCTATCAATTAGCAAGTGCA
192 TTCACCATTTTTCTGCCTTTATTTGACTAAGGCAAGTGCACCTATCAATTAGCAAGTGCA
53889468 CCTATTGTTTTTACCGTGTTTATATTGTTTCCTTACAACAACCAAAAGCAT-AGAAAAAGATGAT
1 CCTATTGTTTTTACCGTGTTTATATTGTTTCCTTACAACAACCAAAAGCATAAGAAAAAGATGAT
**
53889532 CTTCGTTATAAGCCTGAGAAAAAAAATTCAA-AAAAGAAGCTTACAACAAGAATGACAACAGTGA
66 CTTCGTTATAAGCAAGAGAAAAAAAATTCAAGAAAA-AAGCTTACAACAAGAATGACAACAGTGA
*
53889596 AGACACCAATTGTAACCAGAAAGGTAACTTGGCCATTATTGCAGCAACTGTTTAGCTCCCAGTTC
130 AGACACCAATTGTAACCAGAAAGGTAACTTGGCAATTATTGCAGCAACTGTTTAGCTCCCAGTTC
53889661 ACCATTTTTCTGCCTTTATTT
195 ACCATTTTTCTGCCTTTATTT
53889682 CAAAATATCA
Statistics
Matches: 209, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
249 4 0.02
250 155 0.74
255 50 0.24
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (251 bp):
CCTATTGTTTTTACCGTGTTTATATTGTTTCCTTACAACAACCAAAAGCATAAGAAAAAGATGAT
CTTCGTTATAAGCAAGAGAAAAAAAATTCAAGAAAAAAGCTTACAACAAGAATGACAACAGTGAA
GACACCAATTGTAACCAGAAAGGTAACTTGGCAATTATTGCAGCAACTGTTTAGCTCCCAGTTCA
CCATTTTTCTGCCTTTATTTGACTAAGGCAAGTGCACCTATCAATTAGCAAGTGCA
Found at i:53891199 original size:43 final size:43
Alignment explanation
Indices: 53891135--53891228 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 43
53891125 TAGAATATAA
*
53891135 AACATAACTTACCATTTATTTGCAAAACATAAAGTAAAAGCAT
1 AACATAACTTACCATTCATTTGCAAAACATAAAGTAAAAGCAT
*
53891178 AACATAACTTACCATTCATTTGCATAACATAAAGTAAAAGCAT
1 AACATAACTTACCATTCATTTGCAAAACATAAAGTAAAAGCAT
*
53891221 AATATAAC
1 AACATAAC
53891229 CTAAACCACA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (43 bp):
AACATAACTTACCATTCATTTGCAAAACATAAAGTAAAAGCAT
Found at i:53894366 original size:26 final size:26
Alignment explanation
Indices: 53894336--53894476 Score: 98
Period size: 24 Copynumber: 5.7 Consensus size: 26
53894326 TCCCGTTATG
*
53894336 TGGCTCTTCGTGAGCTTCCCGATTAA
1 TGGCTCTTCGTGAGCTTCCTGATTAA
* * *
53894362 AGGCTTTTTGTGAGCTTCCTG-TTAA
1 TGGCTCTTCGTGAGCTTCCTGATTAA
* * *
53894387 TGGCCCTCCG-AAGCTTCCTGATTAA
1 TGGCTCTTCGTGAGCTTCCTGATTAA
* * * *
53894412 TGGCTCTTCG-GAACTACTTG-TTAT
1 TGGCTCTTCGTGAGCTTCCTGATTAA
* * *
53894436 TGGCTC-GCATGAGCTTCCCGATT-A
1 TGGCTCTTCGTGAGCTTCCTGATTAA
*
53894460 TGGCTCTT-ATGAGCTTC
1 TGGCTCTTCGTGAGCTTC
53894477 TTGTTATACA
Statistics
Matches: 86, Mismatches: 25, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
23 1 0.01
24 39 0.45
25 29 0.34
26 17 0.20
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
TGGCTCTTCGTGAGCTTCCTGATTAA
Found at i:53901018 original size:21 final size:20
Alignment explanation
Indices: 53900976--53901025 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
53900966 TTACATTATC
* *
53900976 ACTATTCATGATTTGACTTT
1 ACTATTCATGACTTGACCTT
*
53900996 ACTGTTCATGGACTTGACCTT
1 ACTATTCAT-GACTTGACCTT
53901017 ACTATTCAT
1 ACTATTCAT
53901026 AAGACTGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (20 bp):
ACTATTCATGACTTGACCTT
Found at i:53904506 original size:210 final size:210
Alignment explanation
Indices: 53904153--53905059 Score: 862
Period size: 210 Copynumber: 4.3 Consensus size: 210
53904143 TGTTAACTGC
* * * * * * * ****
53904153 TTTGGAGGCTGTGATATTAAACCTGCGAGCCTTGAGATTACAGCTGGGAGCTTGACCTCGTGTTA
1 TTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTACAGCTGGGATCTTAAGCTCACACTA
*** * * * * *
53904218 ACTGCTTT-GAAGGCTGC-AGTACTGAACCTGCGAGCCTTAAGAATTTAGGTGGGAGCTTGAACT
66 ACAATTTTAG-AGGCTGCGA-TATTGAACCTACGAGCCTTAAGATTTTAGCTTGGAGCTTGAACT
* * *
53904281 CGCGCTAACTGTTTTGGAGGCTGGGACATTGAACCTACAAGCCTTAAAATTCAAGCTTGGAGCTT
129 CGCGCTAACTGTTTTGGAGGCTGCGACATTAAACCTACAAGCCTTAATATTCAAGCTTGGAGCTT
* *
53904346 AAGCTCACGTTAACTGT
194 AAGCTCACGCTAACTAT
* * * *
53904363 TTTGGAGGTTGCGATATTGAATCTATGAGACTTAAGATTACAGCTGGGATCTTAAGCTCACACTA
1 TTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTACAGCTGGGATCTTAAGCTCACACTA
* *
53904428 ACAATTTTAGAGGCTGCGATATTAAACCTAC-ATGCCTTAAGATTTTAGCTAGGAGCTTGAACTC
66 ACAATTTTAGAGGCTGCGATATTGAACCTACGA-GCCTTAAGATTTTAGCTTGGAGCTTGAACTC
* * * *
53904492 GCGCAAACTGTTTTGGAGGCTGCGACATTAAACCTACAAGCCTTAAGATTCAAGCTTAGAGCTTG
130 GCGCTAACTGTTTTGGAGGCTGCGACATTAAACCTACAAGCCTTAATATTCAAGCTTGGAGCTTA
*
53904557 AGCTCATGCTAACTAT
195 AGCTCACGCTAACTAT
* * * *
53904573 TTTGGAGGTTGTGATATTGAATCTACGAGCCTTAAGACTACAGCTGGGATCTTAAGCTCACACTA
1 TTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTACAGCTGGGATCTTAAGCTCACACTA
* * * * *
53904638 ATAGTTTTAGAGGCTACGGTATTGAACCTACGAGCCTTAAGATTTTAG-TTGAGAGCTTGAGCTC
66 ACAATTTTAGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTTTAGCTTG-GAGCTTGAACTC
* * * * * * * * ***
53904702 GAGTTAATTTTTTTTGAGGCTGCTATATTGAACCTGTGAGCCTTAATATT-ACAG-TTGGGAGCT
130 GCGCTAACTGTTTTGGAGGCTGCGACATTAAACCTACAAGCCTTAATATTCA-AGCTT-GGAGCT
53904765 TAAGCTCGA-GCTAACTAT
193 TAAGCTC-ACGCTAACTAT
* * * * * * *
53904783 TTTAGAGGCTGCAATATTGAACCTGCAAGCCTTAAGATT-CTAGTTGGGAGCTTGAGCTCGAC-C
1 TTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTAC-AGCTGGGATCTTAAGCTC-ACAC
* * * * *
53904846 TAACTATTTTGGAGGCTGC-AGTTTTGAACCTACGAGCCTTAAGACTTTAGCTTGGAGCTTGAGC
64 TAACAATTTTAGAGGCTGCGA-TATTGAACCTACGAGCCTTAAGATTTTAGCTTGGAGCTTGAAC
* * * * * ** ** *
53904910 TCACGCTAACTATTTTGGAGGCTACGATACTAAACCTGTAAGCCTTAATATTTTAGCTAGGAGCT
128 TCGCGCTAACTGTTTTGGAGGCTGCGACATTAAACCTACAAGCCTTAATATTCAAGCTTGGAGCT
* * * * *
53904975 TGAGCTCGCGTTAATTGT
193 TAAGCTCACGCTAACTAT
* * * * * *
53904993 TTTTGAGGCGGCTATATTGAACCTACGAGCCTTAAGATTACAGCTGGGACCTTGAGCTCGCACTA
1 TTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTACAGCTGGGATCTTAAGCTCACACTA
53905058 AC
66 AC
53905060 TTTTTTGAGA
Statistics
Matches: 576, Mismatches: 104, Indels: 34
0.81 0.15 0.05
Matches are distributed among these distances:
209 8 0.01
210 557 0.97
211 11 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (210 bp):
TTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTACAGCTGGGATCTTAAGCTCACACTA
ACAATTTTAGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTTTAGCTTGGAGCTTGAACTCG
CGCTAACTGTTTTGGAGGCTGCGACATTAAACCTACAAGCCTTAATATTCAAGCTTGGAGCTTAA
GCTCACGCTAACTAT
Found at i:53905053 original size:70 final size:69
Alignment explanation
Indices: 53904146--53905071 Score: 728
Period size: 70 Copynumber: 13.2 Consensus size: 69
53904136 AGGCTCGTGT
* * * * * *
53904146 TAACTGCTTTGGAGGCTGTGATATTAAACCTGCGAGCCTTGAGATTACAGCTGGGAGCTTGACCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATT-CAGCTGGGAGCTTGAGCT
* *
53904211 CGTGT
65 CGCGC
* * * * * * *
53904216 TAACTGCTTTGAAGGCTGC-AGTACTGAACCTGCGAGCCTTAAGAATTTAGGTGGGAGCTTGAAC
1 TAACTGTTTTGGAGGCTGCGA-TATTGAACCTACGAGCCTTAAG-ATTCAGCTGGGAGCTTGAGC
53904280 TCGCGC
64 TCGCGC
* * * * * *
53904286 TAACTGTTTTGGAGGCTGGGACATTGAACCTACAAGCCTTAAAATTCAAGCTTGGAGCTTAAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTC-AGCTGGGAGCTTGAGCT
* *
53904351 CACGT
65 CGCGC
* * * * * *
53904356 TAACTGTTTTGGAGGTTGCGATATTGAATCTATGAGACTTAAGATTACAGCTGGGATCTTAAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATT-CAGCTGGGAGCTTGAGCT
* *
53904421 CACAC
65 CGCGC
** * * * * *
53904426 TAACAATTTTAGAGGCTGCGATATTAAACCTAC-ATGCCTTAAGATTTTAGCTAGGAGCTTGAAC
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGA-GCCTTAAGA-TTCAGCTGGGAGCTTGAGC
53904490 TCGCGC
64 TCGCGC
* * * * **
53904496 AAACTGTTTTGGAGGCTGCGACATTAAACCTACAAGCCTTAAGATTCAAGCTTAGAGCTTGAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTC-AGCTGGGAGCTTGAGCT
**
53904561 CATGC
65 CGCGC
* * * * * * *
53904566 TAACTATTTTGGAGGTTGTGATATTGAATCTACGAGCCTTAAGACTACAGCTGGGATCTTAAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGA-TTCAGCTGGGAGCTTGAGCT
* *
53904631 CACAC
65 CGCGC
* * * * * *
53904636 TAA-TAGTTTTAGAGGCTACGGTATTGAACCTACGAGCCTTAAGATTTTAGTTGAGAGCTTGAGC
1 TAACT-GTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGA-TTCAGCTGGGAGCTTGAGC
* *
53904700 TCGAGT
64 TCGCGC
* * * * ** * * *
53904706 TAATTTTTTTTGAGGCTGCTATATTGAACCTGTGAGCCTTAATATTACAGTTGGGAGCTTAAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATT-CAGCTGGGAGCTTGAGCT
*
53904771 CGAGC
65 CGCGC
* * * * * *
53904776 TAACTATTTTAGAGGCTGCAATATTGAACCTGCAAGCCTTAAGATTCTAGTTGGGAGCTTGAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTC-AGCTGGGAGCTTGAGCT
53904841 CGAC-C
65 CG-CGC
* * * *
53904846 TAACTATTTTGGAGGCTGC-AGTTTTGAACCTACGAGCCTTAAGACTTTAGCTTGGAGCTTGAGC
1 TAACTGTTTTGGAGGCTGCGA-TATTGAACCTACGAGCCTTAAGA-TTCAGCTGGGAGCTTGAGC
*
53904910 TCACGC
64 TCGCGC
* * * * *** * * *
53904916 TAACTATTTTGGAGGCTACGATACTAAACCTGTAAGCCTTAATATTTTAGCTAGGAGCTTGAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGA-TTCAGCTGGGAGCTTGAGCT
*
53904981 CGCGT
65 CGCGC
* * * * *
53904986 TAATTGTTTTTGAGGCGGCTATATTGAACCTACGAGCCTTAAGATTACAGCTGGGACCTTGAGCT
1 TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATT-CAGCTGGGAGCTTGAGCT
*
53905051 CGCAC
65 CGCGC
*
53905056 TAACTTTTTTGAGAGG
1 TAACTGTTTTG-GAGG
53905072 GATCATATTA
Statistics
Matches: 678, Mismatches: 157, Indels: 41
0.77 0.18 0.05
Matches are distributed among these distances:
69 15 0.02
70 645 0.95
71 18 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (69 bp):
TAACTGTTTTGGAGGCTGCGATATTGAACCTACGAGCCTTAAGATTCAGCTGGGAGCTTGAGCTC
GCGC
Found at i:53913447 original size:21 final size:20
Alignment explanation
Indices: 53913411--53913467 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
53913401 ATATTATTGT
53913411 TGTTCAT-GATTTGACTCCAC
1 TGTTCATGGA-TTGACTCCAC
53913431 TGTTCATGGACTTGACTCCAC
1 TGTTCATGGA-TTGACTCCAC
53913452 TGTTCATAGGATTGAC
1 TGTTCAT-GGATTGAC
53913468 ATTCAGAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 7 0.21
21 24 0.71
22 3 0.09
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (20 bp):
TGTTCATGGATTGACTCCAC
Found at i:53921666 original size:2 final size:2
Alignment explanation
Indices: 53921659--53921687 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53921649 TACATACGCG
53921659 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
53921688 TAAACCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:53922694 original size:33 final size:33
Alignment explanation
Indices: 53922654--53922724 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
53922644 AGTTGTATTT
* * *
53922654 TTAATTAAATACGGCTTTAGACTGATTTTAAAA
1 TTAATTAAATAAGCCTTTAGACCGATTTTAAAA
* * *
53922687 TTAATTAATTAAGCCTTTAGGCCGGTTTTAAAA
1 TTAATTAAATAAGCCTTTAGACCGATTTTAAAA
53922720 TTAAT
1 TTAAT
53922725 CACACAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (33 bp):
TTAATTAAATAAGCCTTTAGACCGATTTTAAAA
Found at i:53927550 original size:6 final size:6
Alignment explanation
Indices: 53927539--53927568 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53927529 TTTCAGTTCC
53927539 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
53927569 CGCACTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATTGAA
Found at i:53930760 original size:14 final size:15
Alignment explanation
Indices: 53930741--53930779 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
53930731 CAAAACCGAG
53930741 TAAAAAGATTGTTC-
1 TAAAAAGATTGTTCT
53930755 TAAAAAGATTGTTCT
1 TAAAAAGATTGTTCT
*
53930770 TAAAATGATT
1 TAAAAAGATT
53930780 TTTGCCTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (15 bp):
TAAAAAGATTGTTCT
Found at i:53932586 original size:24 final size:24
Alignment explanation
Indices: 53932541--53932586 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53932531 GGACGTTATC
* * *
53932541 TGAAAAGGATATCATTGGAAAGGT
1 TGAAAAGGATAACAATGAAAAGGT
53932565 TGAAAAGGATAACAATGAAAAG
1 TGAAAAGGATAACAATGAAAAG
53932587 TTCGGTATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.04, G:0.26, T:0.20
Consensus pattern (24 bp):
TGAAAAGGATAACAATGAAAAGGT
Found at i:53937031 original size:25 final size:26
Alignment explanation
Indices: 53937003--53937057 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
53936993 AAAATCCTAT
*
53937003 GTGGCGTA-TTACTTAGGAAGCCTTA
1 GTGGCGAAGTTACTTAGGAAGCCTTA
* * *
53937028 GTGGCGAAGTTATTTGGGAAGCCTTT
1 GTGGCGAAGTTACTTAGGAAGCCTTA
53937054 GTGG
1 GTGG
53937058 TGATTTATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.20, C:0.13, G:0.35, T:0.33
Consensus pattern (26 bp):
GTGGCGAAGTTACTTAGGAAGCCTTA
Found at i:53937068 original size:76 final size:75
Alignment explanation
Indices: 53936971--53937112 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 75
53936961 AACCAAGCCG
* * * *
53936971 AGCCTTTGTGGCGAATCATCTGAAAATCCTATGTGGCGTATTACTTAGGAAGCCTTAGTGGCGAA
1 AGCCTTTGTGGCGAATCATCTGAAAAGCCTATGCGACGTATTACTTAGGAAGCCTCAGTGGC-AA
53937036 GTTATTTGGGA
65 GTTATTTGGGA
* * * * * * *
53937047 AGCCTTTGTGGTGATTTATCTGAAAAGCTTATGCGACGTATTATTTGGGCAGCCTCAGTGGCAAG
1 AGCCTTTGTGGCGAATCATCTGAAAAGCCTATGCGACGTATTACTTAGGAAGCCTCAGTGGCAAG
53937112 T
66 T
53937113 GATCTAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
75 4 0.07
76 51 0.93
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (75 bp):
AGCCTTTGTGGCGAATCATCTGAAAAGCCTATGCGACGTATTACTTAGGAAGCCTCAGTGGCAAG
TTATTTGGGA
Found at i:53938325 original size:84 final size:84
Alignment explanation
Indices: 53938184--53938355 Score: 317
Period size: 84 Copynumber: 2.0 Consensus size: 84
53938174 TAAGTTCTAG
53938184 AACTCACTTGGAAGTTGACGCCAAAACCTTCTTCTTAGATTTTTCCCTTGCTACCCGAACCTCCA
1 AACTCACTTGGAAGTTGACGCCAAAACCTTCTTCTTAGATTTTTCCCTTGCTACCCGAACCTCCA
*
53938249 ACAACTTACAAAACATGAC
66 ACAACTTACAAAACATAAC
*
53938268 AACTCACTTGGAAGTTGATGCCAAAACCTTCTTCTTAGATTTTTCCCTTGCTACCCGAACCTCCA
1 AACTCACTTGGAAGTTGACGCCAAAACCTTCTTCTTAGATTTTTCCCTTGCTACCCGAACCTCCA
*
53938333 GCAACTTACAAAACATAAC
66 ACAACTTACAAAACATAAC
53938352 AACT
1 AACT
53938356 ATTTCAGTCT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.31, C:0.30, G:0.10, T:0.28
Consensus pattern (84 bp):
AACTCACTTGGAAGTTGACGCCAAAACCTTCTTCTTAGATTTTTCCCTTGCTACCCGAACCTCCA
ACAACTTACAAAACATAAC
Found at i:53942740 original size:17 final size:17
Alignment explanation
Indices: 53942718--53942750 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53942708 AATTAATATA
53942718 ATTATTAATTTGTTAAT
1 ATTATTAATTTGTTAAT
*
53942735 ATTATTAATTTTTTAA
1 ATTATTAATTTGTTAA
53942751 ATTTTATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTATTAATTTGTTAAT
Found at i:53944922 original size:72 final size:76
Alignment explanation
Indices: 53944837--53945021 Score: 225
Period size: 76 Copynumber: 2.5 Consensus size: 76
53944827 ATTTGTTTAT
* * *
53944837 TATTTTTACATCAATATTATACTTATTTACAATTTACGAAGAAAAT-GAAA-AA-AAATTAT-TT
1 TATTTTTACATCAATAATATACTTATTTACAATTTACAAAAAAAATGGAAACAATAAATTATATT
* *
53944898 GTATTGCATTG
66 GGATTACATTG
* * ***
53944909 TATTTTTACATCAATAATATACTTATTCAAAATTTACAAAAAAAATGGAAACAATTTTTTATATT
1 TATTTTTACATCAATAATATACTTATTTACAATTTACAAAAAAAATGGAAACAATAAATTATATT
*
53944974 GGATTATATTG
66 GGATTACATTG
* *
53944985 TATTTTAACATAAATAATATACTTATTTACAATTTAC
1 TATTTTTACATCAATAATATACTTATTTACAATTTAC
53945022 CCAAAAATGG
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
72 41 0.44
73 4 0.04
74 2 0.02
75 4 0.04
76 43 0.46
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (76 bp):
TATTTTTACATCAATAATATACTTATTTACAATTTACAAAAAAAATGGAAACAATAAATTATATT
GGATTACATTG
Found at i:53946751 original size:85 final size:85
Alignment explanation
Indices: 53946597--53946766 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 85
53946587 TAGATCACAC
* * * * *
53946597 TTTCACCATAGGTAAGATAATGTCAGAGATCATGCCAGAATCCAATTTTGAATGATCTTATAACT
1 TTTCACCATACGTAAGACAATGTCAGAGATCAAGCCAGAATCCAATTTAGAATGATCCTATAACT
*
53946662 TACCTGCAACAACAAAAGTA
66 TACCTACAACAACAAAAGTA
** * * * *
53946682 TTTCACCATACGTAAGACAATGTCAGAGATCAAGTTAGAATCCAATTTAGGATGCTCCTGTGA-T
1 TTTCACCATACGTAAGACAATGTCAGAGATCAAGCCAGAATCCAATTTAGAATGATCCTATAACT
* *
53946746 GTACCTACAATAACACAAGTA
66 -TACCTACAACAACAAAAGTA
53946767 CAAGAAGCAT
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
84 1 0.01
85 69 0.99
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (85 bp):
TTTCACCATACGTAAGACAATGTCAGAGATCAAGCCAGAATCCAATTTAGAATGATCCTATAACT
TACCTACAACAACAAAAGTA
Found at i:53950532 original size:22 final size:22
Alignment explanation
Indices: 53950507--53950549 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53950497 GCATGTTTAT
53950507 TTTTC-ATTTTTAGTTTAGTTTG
1 TTTTCGATTTTTA-TTTAGTTTG
*
53950529 TTTTCGATTTTTATTTGGTTT
1 TTTTCGATTTTTATTTAGTTT
53950550 TTATTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.70
Consensus pattern (22 bp):
TTTTCGATTTTTATTTAGTTTG
Found at i:53950532 original size:23 final size:22
Alignment explanation
Indices: 53950501--53950549 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
53950491 TTTCTTGCAT
53950501 GTTTATTTTTC-ATTTTTAGTTTA
1 GTTTA-TTTTCGATTTTTA-TTTA
* *
53950524 GTTTGTTTTCGATTTTTATTTG
1 GTTTATTTTCGATTTTTATTTA
53950546 GTTT
1 GTTT
53950550 TTATTTAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.12, C:0.04, G:0.14, T:0.69
Consensus pattern (22 bp):
GTTTATTTTCGATTTTTATTTA
Found at i:53955749 original size:28 final size:26
Alignment explanation
Indices: 53955708--53955772 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 26
53955698 GCAATTCGGG
*
53955708 CCTTTTTGTTTTTTTCTTTTCTCTTTTT
1 CCTTTTT-TTTTTTTCTTTTCT-TTTTC
53955736 CCTTTTTTTCTTTTTCTTTTCTTTTTC
1 CCTTTTTTT-TTTTTCTTTTCTTTTTC
53955763 CCTTTTTTTT
1 CCTTTTTTTT
53955773 GCAGATTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 1 0.03
27 15 0.43
28 19 0.54
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (26 bp):
CCTTTTTTTTTTTTCTTTTCTTTTTC
Found at i:53955876 original size:43 final size:44
Alignment explanation
Indices: 53955790--53955881 Score: 150
Period size: 43 Copynumber: 2.1 Consensus size: 44
53955780 GGGCCGTTGG
*
53955790 GCTGGATGCTGGCCTGCTGCTGGAACGGGCCTGGGGCTACTGGA
1 GCTGGATGCTGGCCTGCTGCTGGAACAGGCCTGGGGCTACTGGA
* *
53955834 -CTGGATGCTGGCCTGCTGCTGGAACAGGCCTGGGGTTGCTGGA
1 GCTGGATGCTGGCCTGCTGCTGGAACAGGCCTGGGGCTACTGGA
53955877 GCTGG
1 GCTGG
53955882 CCTGCTGGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (44 bp):
GCTGGATGCTGGCCTGCTGCTGGAACAGGCCTGGGGCTACTGGA
Found at i:53955895 original size:43 final size:42
Alignment explanation
Indices: 53955791--53955898 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 42
53955781 GGCCGTTGGG
* *
53955791 CTGGATGCTGGCCTGCTGCTGGAACGGGCCTGGGGCTACTGGA
1 CTGGATGCTGG-CAGCTGCTGGAACAGGCCTGGGGCTACTGGA
* * *
53955834 CTGGATGCTGGCCTGCTGCTGGAACAGGCCTGGGGTTGCTGGA
1 CTGGATGCTGG-CAGCTGCTGGAACAGGCCTGGGGCTACTGGA
*
53955877 GCTGGCCTGCTGG-AGCTGCTGG
1 -CTGG-ATGCTGGCAGCTGCTGG
53955899 GCGTTGGGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
43 48 0.83
44 4 0.07
45 6 0.10
ACGTcount: A:0.10, C:0.25, G:0.43, T:0.22
Consensus pattern (42 bp):
CTGGATGCTGGCAGCTGCTGGAACAGGCCTGGGGCTACTGGA
Found at i:53956022 original size:18 final size:17
Alignment explanation
Indices: 53955999--53956078 Score: 72
Period size: 19 Copynumber: 4.4 Consensus size: 17
53955989 CCGCTGCTGC
*
53955999 TATTTTTTTATTCTTTAT
1 TATTTTTTTTTTCTTT-T
53956017 TATTTTTTTCTTT-TTCTT
1 TATTTTTTT-TTTCTT-TT
53956035 CTATTTTTTCTTTTCCTTTCT
1 -TATTTTTT-TTTT-CTTT-T
*
53956056 TTTTTTTTTTTTCTTTT
1 TATTTTTTTTTTCTTTT
53956073 TATTTT
1 TATTTT
53956079 CTTTCTTCCC
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
17 6 0.12
18 16 0.31
19 18 0.35
20 9 0.17
21 3 0.06
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (17 bp):
TATTTTTTTTTTCTTTT
Found at i:53956030 original size:24 final size:23
Alignment explanation
Indices: 53956003--53956076 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 23
53955993 TGCTGCTATT
53956003 TTTTTATTCTTTATTATTTTTTTC
1 TTTTTATTCTTTATT-TTTTTTTC
* *
53956027 TTTTTCTTC--TATTTTTTCTT-
1 TTTTTATTCTTTATTTTTTTTTC
** *
53956047 TTCCT-TTCTTTTTTTTTTTTTC
1 TTTTTATTCTTTATTTTTTTTTC
53956069 TTTTTATT
1 TTTTTATT
53956077 TTCTTTCTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 15 0.39
22 7 0.18
23 2 0.05
24 8 0.21
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTATTCTTTATTTTTTTTTC
Found at i:53956063 original size:15 final size:15
Alignment explanation
Indices: 53956009--53956085 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
53955999 TATTTTTTTA
53956009 TTCTTTATTATTTT-T
1 TTCTTT-TTATTTTCT
*
53956024 TTC-TTTT-TCTTCT
1 TTCTTTTTATTTTCT
* *
53956037 AT-TTTTTCTTTTCCT
1 TTCTTTTTATTTT-CT
*
53956052 TTCTTTTT-TTTTTT
1 TTCTTTTTATTTTCT
53956066 TTCTTTTTATTTTCT
1 TTCTTTTTATTTTCT
53956081 TTCTT
1 TTCTT
53956086 CCCCTTCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
12 3 0.06
13 8 0.16
14 14 0.28
15 20 0.40
16 5 0.10
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTTTTTATTTTCT
Found at i:53956078 original size:19 final size:19
Alignment explanation
Indices: 53956001--53956078 Score: 79
Period size: 18 Copynumber: 4.1 Consensus size: 19
53955991 GCTGCTGCTA
* *
53956001 TTTTTTTATTCTTTATTATT
1 TTTTTTTTTTCTTT-CTATT
53956021 TTTTTCTTTTTC-TTCTATT
1 TTTTT-TTTTTCTTTCTATT
* *
53956040 TTTTCTTTTCCTTTCT-TT
1 TTTTTTTTTTCTTTCTATT
*
53956058 TTTTTTTTTTCTTTTTATT
1 TTTTTTTTTTCTTTCTATT
53956077 TT
1 TT
53956079 CTTTCTTCCC
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
18 20 0.42
19 16 0.33
20 7 0.15
21 5 0.10
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTTCTTTCTATT
Found at i:53956464 original size:9 final size:9
Alignment explanation
Indices: 53956440--53956483 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
53956430 GGGTTTTTAG
53956440 GTGGTGGCTT
1 GTGGTGG-TT
53956450 -TGGTGGTT
1 GTGGTGGTT
* *
53956458 GTAGTGGTG
1 GTGGTGGTT
53956467 GTGGTGGTT
1 GTGGTGGTT
53956476 GTGGTGGT
1 GTGGTGGT
53956484 GGTGTTTGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 2 0.07
9 27 0.93
ACGTcount: A:0.02, C:0.02, G:0.55, T:0.41
Consensus pattern (9 bp):
GTGGTGGTT
Found at i:53956470 original size:15 final size:15
Alignment explanation
Indices: 53956450--53956487 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
53956440 GTGGTGGCTT
*
53956450 TGGTGGTTGTAGTGG
1 TGGTGGTGGTAGTGG
*
53956465 TGGTGGTGGTTGTGG
1 TGGTGGTGGTAGTGG
53956480 TGGTGGTG
1 TGGTGGTG
53956488 TTTGCGCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.03, C:0.00, G:0.58, T:0.39
Consensus pattern (15 bp):
TGGTGGTGGTAGTGG
Found at i:53956471 original size:18 final size:18
Alignment explanation
Indices: 53956450--53956487 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
53956440 GTGGTGGCTT
53956450 TGGTGGTTGTAGTGGTGG
1 TGGTGGTTGTAGTGGTGG
*
53956468 TGGTGGTTGTGGTGGTGG
1 TGGTGGTTGTAGTGGTGG
53956486 TG
1 TG
53956488 TTTGCGCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.00, G:0.58, T:0.39
Consensus pattern (18 bp):
TGGTGGTTGTAGTGGTGG
Found at i:53956806 original size:29 final size:30
Alignment explanation
Indices: 53956773--53956902 Score: 92
Period size: 30 Copynumber: 4.4 Consensus size: 30
53956763 GCAAAAATGC
53956773 AATTTTAGAAAAATATA-GGGCTAAAGTGT
1 AATTTTAGAAAAATATAGGGGCTAAAGTGT
* * **
53956802 AATTTCTAG-AAAGTTTAGGGGCCCAAGTGT
1 AATTT-TAGAAAAATATAGGGGCTAAAGTGT
* *
53956832 AA-TTTA-CAAAATATTAGGGG-TTAAGATGT
1 AATTTTAGAAAAATA-TAGGGGCTAAAG-TGT
* * *
53956861 AAATTTAGAAAAAGT-TAGGGGTTAAAATGT
1 AATTTTAGAAAAA-TATAGGGGCTAAAGTGT
*
53956891 AATTTTTGAAAA
1 AATTTTAGAAAA
53956903 GTTTGGGGGC
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
28 9 0.11
29 24 0.30
30 38 0.48
31 7 0.09
32 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.32
Consensus pattern (30 bp):
AATTTTAGAAAAATATAGGGGCTAAAGTGT
Found at i:53956904 original size:29 final size:30
Alignment explanation
Indices: 53956832--53956910 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
53956822 GCCCAAGTGT
* *
53956832 AATTTACAAAATA-TTAGGGGTTAAGATGTA
1 AATTTAGAAAA-AGTTAGGGGTTAAAATGTA
53956862 AATTTAGAAAAAGTTAGGGGTTAAAATGTA
1 AATTTAGAAAAAGTTAGGGGTTAAAATGTA
* * *
53956892 ATTTTTG-AAAAGTTTGGGG
1 AATTTAGAAAAAGTTAGGGG
53956911 GCCAAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.28
30 31 0.72
ACGTcount: A:0.41, C:0.01, G:0.24, T:0.34
Consensus pattern (30 bp):
AATTTAGAAAAAGTTAGGGGTTAAAATGTA
Found at i:53957282 original size:75 final size:73
Alignment explanation
Indices: 53957197--53958055 Score: 1002
Period size: 77 Copynumber: 11.3 Consensus size: 73
53957187 TTTTTATTTG
* * * * * *
53957197 AAAA-ACAGAAACTGAAAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACAGAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGA
53957261 GTTGATTTTTA
63 GTTGATTTTTA
* * ** * *
53957272 AAAA-ACAGAAATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAGACAGAAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTAT
53957336 GAGTTGATTTTTTTGA
61 GAGTTGA--TTTTT-A
* * *
53957352 AAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACTCGAGGCTCAACTCAACTCTCGTATTAT
1 AAAAGACAGAAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTAT
**
53957417 GAGTTGATTTAAA
61 GAGTTGATTTTTA
*
53957430 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGATGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
53957495 GATTTTTAAA
66 GATTTTT--A
* * *
53957505 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTGTATTATAAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
53957570 TATTTTTTTAAA
66 GA--TTTTT--A
*
53957582 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
53957647 GATTTTTTTTAA
66 GA---TTTTT-A
* * *
53957659 AAAAGACATAAATTAAAAATACCTCAGCATGACCCAAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
53957724 GATTTTAAAA
66 GATTTT--TA
* *
53957734 AAAAAACCGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
53957799 GATTTTTTTTAAA
66 GA---TTTTT--A
* *
53957812 AAAAGACATAAATTAAAAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
**
53957877 GATTTAAA
66 GATTTTTA
* *
53957885 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATAAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
53957950 GATTTTAAA
66 GATTTT-TA
*
53957959 AAAAGACCGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGT
*
53958024 TGATATTTGA
65 TGAT-TTTTA
* * *
53958034 AAAAAATAGAAAGTGAAAAATA
1 AAAAGACAGAAA-TTAAAAATA
53958056 TTTCTTGAAA
Statistics
Matches: 705, Mismatches: 55, Indels: 47
0.87 0.07 0.06
Matches are distributed among these distances:
73 86 0.12
74 91 0.13
75 166 0.24
76 12 0.02
77 178 0.25
78 88 0.12
79 20 0.03
80 5 0.01
81 59 0.08
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (73 bp):
AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTTA
Found at i:53957595 original size:152 final size:149
Alignment explanation
Indices: 53957211--53958027 Score: 1104
Period size: 152 Copynumber: 5.4 Consensus size: 149
53957201 ACAGAAACTG
* * * * **
53957211 AAAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTAAAAA
1 AAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
* * ** * *
53957276 -ACAGAAATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGT
63 GACAGAAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGT
* *
53957340 TGATTTTTTTGAAAAAA-ACAGAAATTTAAA
123 TGA-TTTTTTAAAAAAAGACATAAA-TT--A
* *
53957370 AGAAATACCTCAGCGTGACTCGAGGCTCAACTCAACTCTCGTATTATGAGTTGATTTAAAAAAAG
1 A-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAG
*
53957435 ACAGAAATTAAAAATACCTCAGCGTGACCCGATGCTCAACTCACCTCTGTATTATGAGTTGA-TT
64 ACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT
53957499 TTTAAAAAAAGACATAAATTA
129 TTTAAAAAAAGACATAAATTA
* * *
53957520 AAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTGTATTATAAGTTTATTTTTTTAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA----TTTAAAAAA
*
53957585 AGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAT
62 AGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-
*
53957650 TTTTTTTAAAAAAGACATAAATTA
126 TTTTTTAAAAAAAGACATAAATTA
* * *
53957674 AAAATACCTCAGCATGACCCAAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTT-AAAAAAAG
*
53957739 ACCGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT
64 ACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--T
53957804 TTTTTAAAAAAAGACATAAATTA
127 TTTTTAAAAAAAGACATAAATTA
*
53957827 AAAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAGAC
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAGAC
* *
53957892 ATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATAAGTTGA--TTT
66 AGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
**
53957955 TAAAAAAAGACCGAAATTA
131 TAAAAAAAGACATAAATTA
53957974 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGAT
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGAT
53958028 ATTTGAAAAA
Statistics
Matches: 603, Mismatches: 43, Indels: 35
0.89 0.06 0.05
Matches are distributed among these distances:
147 57 0.09
148 27 0.04
149 34 0.06
150 2 0.00
151 70 0.12
152 154 0.26
153 79 0.13
154 83 0.14
155 32 0.05
156 2 0.00
158 44 0.07
159 8 0.01
160 11 0.02
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (149 bp):
AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAGAC
AGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
TAAAAAAAGACATAAATTA
Found at i:53958927 original size:15 final size:14
Alignment explanation
Indices: 53958903--53958950 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 14
53958893 CCTTTTCGGG
*
53958903 TTTTCATCTTGATTT
1 TTTTCTTCTTG-TTT
*
53958918 TTTTCTTCTTCTTT
1 TTTTCTTCTTGTTT
53958932 TTTT-TT-TTGTTT
1 TTTTCTTCTTGTTT
53958944 TTTTCTT
1 TTTTCTT
53958951 GTTTTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 9 0.31
13 4 0.14
14 7 0.24
15 9 0.31
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTGTTT
Found at i:53958944 original size:7 final size:7
Alignment explanation
Indices: 53958929--53959009 Score: 90
Period size: 7 Copynumber: 10.9 Consensus size: 7
53958919 TTTCTTCTTC
*
53958929 TTTTTTT
1 TTTTTTG
*
53958936 TTTTGTTT
1 TTTT-TTG
53958944 TTTTCTTG
1 TTTT-TTG
53958952 TTTTTTG
1 TTTTTTG
53958959 TTTGTTTG
1 TTT-TTTG
53958967 TTTTTTG
1 TTTTTTG
53958974 TTTTTTG
1 TTTTTTG
53958981 TTTTGTTTG
1 -TTT-TTTG
53958990 TTTTTTG
1 TTTTTTG
*
53958997 TTTCTTG
1 TTTTTTG
53959004 TTTTTT
1 TTTTTT
53959010 TAGGCATAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
7 36 0.55
8 26 0.39
9 4 0.06
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (7 bp):
TTTTTTG
Found at i:53958944 original size:11 final size:11
Alignment explanation
Indices: 53958930--53958999 Score: 95
Period size: 11 Copynumber: 6.3 Consensus size: 11
53958920 TTCTTCTTCT
53958930 TTTTTTTTTTG
1 TTTTTTTTTTG
*
53958941 TTTTTTTCTTG
1 TTTTTTTTTTG
*
53958952 TTTTTTGTTTG
1 TTTTTTTTTTG
*
53958963 TTTGTTTTTTG
1 TTTTTTTTTTG
53958974 TTTTTTGTTTTG
1 TTTTTT-TTTTG
*
53958986 TTTGTTTTTTG
1 TTTTTTTTTTG
53958997 TTT
1 TTT
53959000 CTTGTTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
11 41 0.80
12 10 0.20
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:53958944 original size:23 final size:23
Alignment explanation
Indices: 53958918--53959009 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 23
53958908 ATCTTGATTT
53958918 TTTTCTTCTTCTTTTTTTT-TTTG
1 TTTT-TTCTTCTTTTTTTTGTTTG
*
53958941 TTTTTTTCTTGTTTTTTGTTTGTTTG
1 -TTTTTTCTT-CTTTTT-TTTGTTTG
*
53958967 TTTTTTGTT-TTTTGTTTTGTTTG
1 TTTTTTCTTCTTTT-TTTTGTTTG
*
53958990 TTTTTTGTTTCTTGTTTTTT
1 TTTTTT-CTTCTT-TTTTTT
53959010 TAGGCATAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
23 23 0.40
24 12 0.21
25 17 0.29
26 6 0.10
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (23 bp):
TTTTTTCTTCTTTTTTTTGTTTG
Found at i:53959010 original size:15 final size:15
Alignment explanation
Indices: 53958909--53959010 Score: 68
Period size: 15 Copynumber: 6.8 Consensus size: 15
53958899 CGGGTTTTCA
*
53958909 TCTTGATTTTTTT-CT
1 TCTTG-TTTTTTTGTT
* *
53958924 TCTTCTTTTTTTTTT
1 TCTTGTTTTTTTGTT
*
53958939 TGTT-TTTTTCTTGTT
1 TCTTGTTTTT-TTGTT
* *
53958954 TTTTGTTTGTTTGTT
1 TCTTGTTTTTTTGTT
*
53958969 TTTTG-TTTTTTGTT
1 TCTTGTTTTTTTGTT
*
53958983 T-TGTTTGTTTTTTGTT
1 TCT-TGT-TTTTTTGTT
53958999 TCTTGTTTTTTT
1 TCTTGTTTTTTT
53959011 AGGCATAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
13 1 0.01
14 22 0.31
15 31 0.44
16 16 0.23
17 1 0.01
ACGTcount: A:0.01, C:0.06, G:0.12, T:0.81
Consensus pattern (15 bp):
TCTTGTTTTTTTGTT
Found at i:53964581 original size:18 final size:18
Alignment explanation
Indices: 53964558--53964838 Score: 117
Period size: 17 Copynumber: 15.6 Consensus size: 18
53964548 CAACTTTTTC
53964558 TTTTTTGAAAACACGAAT
1 TTTTTTGAAAACACGAAT
* *
53964576 TTTTTTAAAATACAAGAA-
1 TTTTTTGAAA-ACACGAAT
*
53964594 -TTTTAG-AAACACGAAACT
1 TTTTTTGAAAACACG-AA-T
*
53964612 TTTGTTTAAAAAACACGAA-
1 TTT-TTT-GAAAACACGAAT
**
53964631 AATTTTG-AAACACGAGATT
1 TTTTTTGAAAACACGA-A-T
53964650 TTTTTTGAAAACACGAATTT
1 TTTTTTGAAAACACGAA--T
*
53964670 TCTTTTTG-AAACATGAATT
1 T-TTTTTGAAAACACGAA-T
*
53964689 TTTTTTG-AAACACGAAA
1 TTTTTTGAAAACACGAAT
*
53964706 ATTTTT-AAAACACGAGA-
1 TTTTTTGAAAACACGA-AT
* * * *
53964723 ATTTTAG-AGACACGAAA
1 TTTTTTGAAAACACGAAT
* * *
53964740 ATTCTTAAAAACAC-AA-
1 TTTTTTGAAAACACGAAT
*
53964756 ATTTTTGAAAACACGACA-
1 TTTTTTGAAAACACGA-AT
*
53964774 -ATTTTG-AAACACGAGAAT
1 TTTTTTGAAAACAC--GAAT
* *
53964792 TTTTTTGAAAACACTATTT
1 TTTTTTGAAAACACGA-AT
*
53964811 TTTTTTG-AAACACAAAT
1 TTTTTTGAAAACACGAAT
53964828 TTTTTTGAAAA
1 TTTTTTGAAAA
53964839 GACGTATCGT
Statistics
Matches: 205, Mismatches: 30, Indels: 56
0.70 0.10 0.19
Matches are distributed among these distances:
15 4 0.02
16 31 0.15
17 51 0.25
18 46 0.22
19 31 0.15
20 27 0.13
21 8 0.04
22 7 0.03
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (18 bp):
TTTTTTGAAAACACGAAT
Found at i:53964594 original size:19 final size:18
Alignment explanation
Indices: 53964558--53964597 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
53964548 CAACTTTTTC
* *
53964558 TTTTTTGAAAACACGAAT
1 TTTTTTAAAAACAAGAAT
53964576 TTTTTTAAAATACAAGAAT
1 TTTTTTAAAA-ACAAGAAT
53964595 TTT
1 TTT
53964598 AGAAACACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
TTTTTTAAAAACAAGAAT
Found at i:53964663 original size:20 final size:18
Alignment explanation
Indices: 53964633--53964704 Score: 99
Period size: 20 Copynumber: 3.8 Consensus size: 18
53964623 AACACGAAAA
53964633 TTTTGAAACACGAGATTTT
1 TTTTGAAACACGA-ATTTT
53964652 TTTTGAAAACACGAATTTTCT
1 TTTTG-AAACACGAA-TTT-T
*
53964673 TTTTGAAACATGAATTTT
1 TTTTGAAACACGAATTTT
53964691 TTTTGAAACACGAA
1 TTTTGAAACACGAA
53964705 AATTTTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
18 14 0.29
19 9 0.19
20 19 0.40
21 6 0.12
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (18 bp):
TTTTGAAACACGAATTTT
Found at i:53965353 original size:28 final size:26
Alignment explanation
Indices: 53965312--53965377 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 26
53965302 GCAATTCGGG
*
53965312 CCTTTTTGTTTTTTTCTTTTCTCTTTTT
1 CCTTTTT-TTTTTTTCTTTTCT-TTTTC
53965340 CCTTTTTTTCTTTTTCTTTTCTTTTTC
1 CCTTTTTTT-TTTTTCTTTTCTTTTTC
53965367 CCTTTTTTTTT
1 CCTTTTTTTTT
53965378 GCAGATTGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.06
27 15 0.42
28 19 0.53
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (26 bp):
CCTTTTTTTTTTTTCTTTTCTTTTTC
Found at i:53965458 original size:43 final size:44
Alignment explanation
Indices: 53965395--53965486 Score: 150
Period size: 43 Copynumber: 2.1 Consensus size: 44
53965385 GGGCCGTTGG
* *
53965395 GCTGGATGCTGGCCTGCTGCTGGAACGGGCCTGGGGCTGCTGGA
1 GCTGGATGCTGGCCTACTGCTGGAACAGGCCTGGGGCTGCTGGA
*
53965439 -CTGGATGCTGGCCTACTGCTGGAACAGGCCTGGGGTTGCTGGA
1 GCTGGATGCTGGCCTACTGCTGGAACAGGCCTGGGGCTGCTGGA
53965482 GCTGG
1 GCTGG
53965487 CCTGCTGGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (44 bp):
GCTGGATGCTGGCCTACTGCTGGAACAGGCCTGGGGCTGCTGGA
Found at i:53965501 original size:43 final size:42
Alignment explanation
Indices: 53965396--53965501 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 42
53965386 GGCCGTTGGG
* *
53965396 CTGGATGCTGGCCTGCTGCTGGAACGGGCCTGGGGCTGCTGGA
1 CTGGATGCTGG-CAGCTGCTGGAACAGGCCTGGGGCTGCTGGA
*
53965439 CTGGATGCTGGCCTA-CTGCTGGAACAGGCCTGGGGTTGCTGGA
1 CTGGATGCTGG-C-AGCTGCTGGAACAGGCCTGGGGCTGCTGGA
*
53965482 GCTGGCCTGCTGG-AGCTGCT
1 -CTGG-ATGCTGGCAGCTGCT
53965502 TGGCGTTGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
42 1 0.02
43 44 0.80
44 4 0.07
45 6 0.11
ACGTcount: A:0.10, C:0.25, G:0.42, T:0.23
Consensus pattern (42 bp):
CTGGATGCTGGCAGCTGCTGGAACAGGCCTGGGGCTGCTGGA
Found at i:53965638 original size:22 final size:22
Alignment explanation
Indices: 53965613--53965661 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
53965603 TGTTTTTTTA
53965613 TTCTTTATTTTTTTCT-TTTTCT
1 TTCTTT-TTTTTTTCTATTTTCT
53965635 TTCTTTTTTTTTTCTATTTTCT
1 TTCTTTTTTTTTTCTATTTTCT
53965657 TTCTT
1 TTCTT
53965662 CCCCTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (22 bp):
TTCTTTTTTTTTTCTATTTTCT
Found at i:53965648 original size:11 final size:11
Alignment explanation
Indices: 53965605--53965661 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
53965595 GTTGCTGCTG
*
53965605 TTTTTTTATTC
1 TTTTTTTTTTC
53965616 TTTATTTTTTTC
1 TTT-TTTTTTTC
*
53965628 -TTTTTCTTTC
1 TTTTTTTTTTC
53965638 TTTTTTTTTTC
1 TTTTTTTTTTC
* *
53965649 TATTTTCTTTC
1 TTTTTTTTTTC
53965660 TT
1 TT
53965662 CCCCTTCTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
10 7 0.18
11 24 0.63
12 7 0.18
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:53965785 original size:21 final size:21
Alignment explanation
Indices: 53965755--53965806 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
53965745 CGGTATCTCC
* *
53965755 TCTCTTCTTTTCTCTTTT-CTT
1 TCTCTCCTTTCCT-TTTTCCTT
53965776 TCTCTCCTTTCCTTTTTCCTT
1 TCTCTCCTTTCCTTTTTCCTT
53965797 TCTCT-CTTTC
1 TCTCTCCTTTC
53965807 TTTCTCCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (21 bp):
TCTCTCCTTTCCTTTTTCCTT
Found at i:53966043 original size:15 final size:15
Alignment explanation
Indices: 53966023--53966053 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53966013 GTTTTTAGGT
53966023 GGTGGTGGTGGTTGC
1 GGTGGTGGTGGTTGC
*
53966038 GGTGGTGGTGTTTGC
1 GGTGGTGGTGGTTGC
53966053 G
1 G
53966054 CGAGGGTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.58, T:0.35
Consensus pattern (15 bp):
GGTGGTGGTGGTTGC
Found at i:53966408 original size:29 final size:29
Alignment explanation
Indices: 53966376--53966488 Score: 113
Period size: 30 Copynumber: 3.8 Consensus size: 29
53966366 TCTAGAAAGT
* *
53966376 TTAGGGGCCCAAGTGTAATTTATAAAATA
1 TTAGGGGCCAAAATGTAATTTATAAAATA
* * *
53966405 TTAGGGGTCAAGATGTAAATTTAGAAAA-A
1 TTAGGGGCCAAAATGT-AATTTATAAAATA
* *
53966434 GTTAGGGGTCAAAATGTAATTTTTGAAAAGT-
1 -TTAGGGGCCAAAATGTAATTTAT-AAAA-TA
53966465 TTAGGGGCCAAAATGTAATTTATA
1 TTAGGGGCCAAAATGTAATTTATA
53966489 TTTTTTGTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
29 19 0.28
30 50 0.72
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (29 bp):
TTAGGGGCCAAAATGTAATTTATAAAATA
Found at i:53966439 original size:30 final size:30
Alignment explanation
Indices: 53966312--53966486 Score: 114
Period size: 29 Copynumber: 5.9 Consensus size: 30
53966302 TAGAGGGCGC
* * *
53966312 AAAGTTTCTGGGGCAAAAATGCAATTTTAGAA
1 AAAGTTT-AGGGGCCAAAATGTAA-TTTAGAA
* * * *
53966344 AAA-TATA-GGGCTAAAGTGTATTTCTAG--
1 AAAGTTTAGGGGCCAAAATGTAATT-TAGAA
* * *
53966371 AAAGTTTAGGGGCCCAAGTGTAATTTA-TA
1 AAAGTTTAGGGGCCAAAATGTAATTTAGAA
* *
53966400 AAA-TATTAGGGGTCAAGATGTAAATTTAGAA
1 AAAGT-TTAGGGGCCAAAATGT-AATTTAGAA
* *
53966431 AAAG-TTAGGGGTCAAAATGTAATTTTTG-A
1 AAAGTTTAGGGGCCAAAATGTAA-TTTAGAA
53966460 AAAGTTTAGGGGCCAAAATGTAATTTA
1 AAAGTTTAGGGGCCAAAATGTAATTTA
53966487 TATTTTTTGT
Statistics
Matches: 113, Mismatches: 19, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
27 3 0.03
28 8 0.07
29 51 0.45
30 42 0.37
31 6 0.05
32 3 0.03
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
AAAGTTTAGGGGCCAAAATGTAATTTAGAA
Found at i:53966481 original size:60 final size:59
Alignment explanation
Indices: 53966371--53966486 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 59
53966361 GTATTTCTAG
* * * *
53966371 AAAGTTTAGGGGCCCAAGTGTAATTTATAAAATATTAGGGGTCAAGATGTAAATTTAGAA
1 AAAGTTTAGGGGCCAAAATGTAATTTATAAAATATTAGGGGCCAAAATGT-AATTTAGAA
* *
53966431 AAAG-TTAGGGGTCAAAATGTAATTTTTGAAAAGT-TTAGGGGCCAAAATGTAATTTA
1 AAAGTTTAGGGGCCAAAATGTAATTTAT-AAAA-TATTAGGGGCCAAAATGTAATTTA
53966487 TATTTTTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
59 25 0.52
60 22 0.46
61 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (59 bp):
AAAGTTTAGGGGCCAAAATGTAATTTATAAAATATTAGGGGCCAAAATGTAATTTAGAA
Found at i:53967176 original size:17 final size:17
Alignment explanation
Indices: 53967156--53967190 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
53967146 AAAAAATGGC
53967156 TTGCTTTTTTTTTGCTG
1 TTGCTTTTTTTTTGCTG
53967173 TTGCTTTTTTTTTGCTG
1 TTGCTTTTTTTTTGCTG
53967190 T
1 T
53967191 GGGCTGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.17, T:0.71
Consensus pattern (17 bp):
TTGCTTTTTTTTTGCTG
Found at i:53967256 original size:21 final size:21
Alignment explanation
Indices: 53967230--53967270 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
53967220 GTGGCCTGCT
53967230 GGGTTGCACGGGTCGGGTCGC
1 GGGTTGCACGGGTCGGGTCGC
*
53967251 GGGTTGCACTGGTCGGGTCG
1 GGGTTGCACGGGTCGGGTCG
53967271 GTTCAGTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.22, G:0.51, T:0.22
Consensus pattern (21 bp):
GGGTTGCACGGGTCGGGTCGC
Found at i:53967341 original size:20 final size:18
Alignment explanation
Indices: 53967318--53967394 Score: 86
Period size: 20 Copynumber: 4.1 Consensus size: 18
53967308 TTTTTTTATA
53967318 TTTTTTCTTTCCTTTTTCTC
1 TTTTTTCTTT-CTTTTT-TC
*
53967338 TTTTTTCTTTC--TCTTC
1 TTTTTTCTTTCTTTTTTC
53967354 TTTTTTCTTTCTTTTTTTC
1 TTTTTTCTTTC-TTTTTTC
53967373 TCTTTTTCTTTCTTTCTTTC
1 T-TTTTTCTTTCTTT-TTTC
53967393 TT
1 TT
53967395 CTTCCTTCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
16 13 0.26
17 2 0.04
19 10 0.20
20 25 0.50
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCTTTCTTTTTTC
Found at i:53967355 original size:16 final size:16
Alignment explanation
Indices: 53967336--53967394 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
53967326 TTCCTTTTTC
53967336 TCTTTTTTCTTTCTCT
1 TCTTTTTTCTTTCTCT
53967352 TCTTTTTTCTTTCT-T
1 TCTTTTTTCTTTCTCT
* *
53967367 T-TTTTCTCTTTTTCTT
1 TCTTTTTTCTTTCTC-T
53967383 TCTTTCTTTCTT
1 TCTTT-TTTCTT
53967395 CTTCCTTCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 10 0.28
15 2 0.06
16 16 0.44
17 3 0.08
18 5 0.14
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TCTTTTTTCTTTCTCT
Found at i:53967356 original size:24 final size:24
Alignment explanation
Indices: 53967321--53967398 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
53967311 TTTTATATTT
53967321 TTTCT-TTCCTTTTTCTCTTTTTTC
1 TTTCTCTT-CTTTTTCTCTTTTTTC
53967345 TTTCTCTTCTTTTT-TCTTTCTTT-
1 TTTCTCTTCTTTTTCTCTTT-TTTC
*
53967368 TTT-TC-TCTTTTTCT-TTCTTTC
1 TTTCTCTTCTTTTTCTCTTTTTTC
53967389 TTTCTTCTTC
1 TTTC-TCTTC
53967399 CTTCCCTTCG
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
20 3 0.07
21 12 0.26
22 3 0.07
23 10 0.22
24 16 0.35
25 2 0.04
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTCTCTTCTTTTTCTCTTTTTTC
Found at i:53967358 original size:35 final size:36
Alignment explanation
Indices: 53967318--53967401 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 36
53967308 TTTTTTTATA
53967318 TTTTTTCTTTCCTTTTTCTCT-TTTTTCTTTCTCTTC
1 TTTTTTCTTTCCTTTTTCTCTCTTTTTCTTTCT-TTC
*
53967354 TTTTTTCTTT-CTTTTTTTCTCTTTTTCTTTCTTTC
1 TTTTTTCTTTCCTTTTTCTCTCTTTTTCTTTCTTTC
*
53967389 TTTCTTC-TTCCTT
1 TTTTTTCTTTCCTT
53967402 CCCTTCGACT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
34 2 0.05
35 21 0.48
36 21 0.48
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (36 bp):
TTTTTTCTTTCCTTTTTCTCTCTTTTTCTTTCTTTC
Found at i:53967370 original size:36 final size:35
Alignment explanation
Indices: 53967318--53967401 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 35
53967308 TTTTTTTATA
53967318 TTTTTTCTTTCC-TTTTTCTCTTTTTTCTTTCTCTTC
1 TTTTTTCTTTCCTTTTTTCTC-TTTTTCTTTCT-TTC
*
53967354 TTTTTTCTTTCTTTTTTTCTCTTTTTCTTTCTTTC
1 TTTTTTCTTTCCTTTTTTCTCTTTTTCTTTCTTTC
*
53967389 TTTCTTC-TTCCTT
1 TTTTTTCTTTCCTT
53967402 CCCTTCGACT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 5 0.11
35 9 0.20
36 22 0.50
37 8 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (35 bp):
TTTTTTCTTTCCTTTTTTCTCTTTTTCTTTCTTTC
Found at i:53968007 original size:30 final size:30
Alignment explanation
Indices: 53967960--53968016 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53967950 GCCCAAGTGT
*
53967960 AATTTACAAAATATTAGGGGTTAAAATGTA
1 AATTTACAAAATATTAGGGGTCAAAATGTA
*
53967990 AATTTAGAAAA-AGTTAGGGGTCAAAAT
1 AATTTACAAAATA-TTAGGGGTCAAAAT
53968017 AATTTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (30 bp):
AATTTACAAAATATTAGGGGTCAAAATGTA
Found at i:53980398 original size:44 final size:43
Alignment explanation
Indices: 53980330--53981015 Score: 280
Period size: 44 Copynumber: 15.8 Consensus size: 43
53980320 CCTTTGTTTT
* * * * *
53980330 AATCCGCTCCACTGTGATCTCAGGGAAATAGGATTACTAGCATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-CTAGCTTC
* * * *
53980374 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-CCT-GATAC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTCTAGCTTC
* * * * * * *
53980415 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TCTAGCTTC
* * * *
53980459 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-CTAGCTTC
* *
53980503 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-TCT-GAC-AC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTCTAG-CTTC
* * * * * * *
53980544 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TCTAGCTTC
* *
53980588 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-CTAGCTTC
* *
53980632 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TCTGAAAATCATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTCT----AGCTTC
** * * * * *
53980678 GGTCTGTTCCACTGTAATCTTAGGGAAATAAGA-CCT-GAC-GC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTCTAG-CTTC
* * ** * * * *
53980719 GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTCA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTC-T-AGCTTC
** * * *
53980763 AATCCACTCCAATGTAATCTCAGGGAGATAGGATTACTAACTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-CTAGCTTC
* * *
53980807 AATCTGATCCGCTGTAATCTCAGGGAGATAAGA-TCTGAAATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTCT---A-GCTTC
** * * * *
53980853 GGTCTGTTCCACTGTAATCTCAGGGAAATAAGA--CTTGAC-GC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTCTAG-CTTC
* * ** * * * * *
53980894 GATCTACTCTGCTGTAA-CTTTAGAGAGATAAGATCCTTCA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTC-T-AGCTTC
*** * *
53980938 AATCCATTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-CTAGCTTC
*
53980982 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
53981016 CTGACACGAT
Statistics
Matches: 469, Mismatches: 127, Indels: 92
0.68 0.18 0.13
Matches are distributed among these distances:
40 4 0.01
41 102 0.22
42 15 0.03
43 11 0.02
44 262 0.56
45 9 0.02
46 66 0.14
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTCTAGCTTC
Found at i:53980463 original size:129 final size:129
Alignment explanation
Indices: 53980220--53980669 Score: 675
Period size: 129 Copynumber: 3.5 Consensus size: 129
53980210 CTCCGCAACG
* * * * * * * * * *
53980220 TCAGAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAACCTGATG
1 TCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATA
* * * * *
53980285 CGATCTACTCTATTATAACTTCAGTGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTGATC
66 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
* * *
53980349 TCAGGGAAATAGGATTACTAGCATCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATA
1 TCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATA
*
53980414 CGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
66 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
* * * * *
53980478 TCAGGGAGATAGGATTACTATCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACA
1 TCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATA
53980543 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
66 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
*
53980607 TCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA
1 TCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGA
53980670 AAATCATCGG
Statistics
Matches: 292, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 292 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (129 bp):
TCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATA
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
Found at i:53980741 original size:175 final size:175
Alignment explanation
Indices: 53980459--53981019 Score: 874
Period size: 175 Copynumber: 3.2 Consensus size: 175
53980449 CCTTTATTTT
* * ** *** * *
53980459 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTATCTTTAATCTGCTCCGCTGTAATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAATCTTCGGTCTGTTCCACTGTAATC
* * * * *
53980522 TCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTT
66 TCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTT
* *
53980587 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
131 TAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTC
*
53980632 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAATCATCGGTCTGTTCCACTGTAATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAATCTTCGGTCTGTTCCACTGTAATC
*
53980697 TTAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTT
66 TCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTT
*
53980762 TAATCCACTCCAATGTAATCTCAGGGAGATAGGATTACTAACTTC
131 TAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTC
* * *
53980807 AATCTGATCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAATCTTCGGTCTGTTCCACTGTAATC
* *
53980872 TCAGGGAAATAAGACTTGACGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCCTTCATTT
66 TCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTT
*
53980937 TAATCCATTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTC
131 TAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTC
*
53980982 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA
53981020 CACGATCTAC
Statistics
Matches: 357, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
173 32 0.09
174 1 0.00
175 324 0.91
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (175 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAATCTTCGGTCTGTTCCACTGTAATC
TCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTT
TAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTC
Found at i:53980999 original size:304 final size:298
Alignment explanation
Indices: 53980249--53981060 Score: 930
Period size: 304 Copynumber: 2.7 Consensus size: 298
53980239 GGCTTCAATG
* * * * * * *
53980249 TACTCCACTGTAACCACAGGGAGGTAAAACCTGATGCGATCTACTCTATTATAACTTCAGTGAGA
1 TACTCCACTGTAA-CTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGA
** * * *
53980314 TAAGATCCTTTGTTTTAATCCGCTCCACTGTGATCTCAGGGAAATAGGATTACTAGCATCAATCT
65 TAAGATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACATCAATCT
* *
53980379 GCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTTCTCTACTGTAACTTCAGAGAGAT
130 GCTCCGCTGTAATCTCAGGGAGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGAT
* * * * *
53980444 AAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTAATCTG
195 AAGATCCTTCATTTTAATCCACTCCAATGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTG
*
53980509 CTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATC
260 ATCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATC
* * * *** ** * *
53980548 TACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-TCTCAGG
1 TACTCCACTGTAAC-TCAGGGAGATAAGA--CTTGA-TGCGATCTACTCTACTGTAACT-TCAGA
* * * * * * *
53980612 GAGATAGGAT--TACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA-AAAT
61 GAGATAAGATCCTTC-A-TTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTAA-
** * * * * * *
53980674 CATCGGTCTGTTCCACTGTAATCTTAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTT
121 CATCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGACACGATCTACTCTACTGTAACTT
53980739 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCAATGTAATCTCAGGGAGATAGGATTACTAAC
186 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCAATGTAATCTCAGGGAGATAGGATTACTAAC
* *
53980804 TTCAATCTGATCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTC
251 TTCAATCTGATCCGCTGTAATCTCAGGGAGATAAGATCTG--A--C-ACGATC
** * * * *
53980857 TGTTCCACTGTAATCTCAGGGAAATAAGACTTGACGCGATCTACTCTGCTGTAACTTTAGAGAGA
1 TACTCCACTGTAA-CTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGA
** *
53980922 TAAGATCCTTCATTTTAATCCATTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCT
65 TAAGATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACATCAATCT
*
53980987 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGAT
130 GCTCCGCTGTAATCTCAGGGAGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGAT
53981052 AAGATCCTT
195 AAGATCCTT
53981061 TCTTCAATCA
Statistics
Matches: 412, Mismatches: 81, Indels: 35
0.78 0.15 0.07
Matches are distributed among these distances:
298 1 0.00
299 22 0.05
300 1 0.00
301 4 0.01
302 57 0.14
303 2 0.00
304 229 0.56
305 3 0.01
306 57 0.14
307 6 0.01
308 3 0.01
309 26 0.06
310 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (298 bp):
TACTCCACTGTAACTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
AAGATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACATCAATCTG
CTCCGCTGTAATCTCAGGGAGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGATA
AGATCCTTCATTTTAATCCACTCCAATGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGA
TCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATC
Found at i:53982297 original size:21 final size:21
Alignment explanation
Indices: 53982271--53982317 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
53982261 GGTATAGCAG
53982271 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
** *
53982292 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
53982313 GATCA
1 GATCA
53982318 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.38, G:0.11, T:0.26
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:53983298 original size:9 final size:9
Alignment explanation
Indices: 53983286--53983381 Score: 65
Period size: 9 Copynumber: 10.4 Consensus size: 9
53983276 CTTTTTCTTC
53983286 TTTTATTTT
1 TTTTATTTT
*
53983295 TTTTCTTTT
1 TTTTATTTT
53983304 TTTCCTATTTT
1 TTT--TATTTT
53983315 GACTTTTA-TTT
1 ---TTTTATTTT
*
53983326 TTTGA--TT
1 TTTTATTTT
*
53983333 TTTGATTTT
1 TTTTATTTT
*
53983342 TTTGA-TTT
1 TTTTATTTT
53983350 TTTTATTTT
1 TTTTATTTT
53983359 TTTTGATTTT
1 TTTT-ATTTT
*
53983369 TTTGATTTT
1 TTTTATTTT
53983378 TTTT
1 TTTT
53983382 TTAGTCTGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
7 7 0.10
8 11 0.15
9 33 0.46
10 8 0.11
11 8 0.11
12 2 0.03
14 3 0.04
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.79
Consensus pattern (9 bp):
TTTTATTTT
Found at i:53983330 original size:14 final size:15
Alignment explanation
Indices: 53983311--53983343 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53983301 TTTTTTCCTA
53983311 TTTTGACTTTT-ATT
1 TTTTGACTTTTGATT
*
53983325 TTTTGATTTTTGATT
1 TTTTGACTTTTGATT
53983340 TTTT
1 TTTT
53983344 TGATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (15 bp):
TTTTGACTTTTGATT
Found at i:53983352 original size:18 final size:18
Alignment explanation
Indices: 53983323--53983380 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
53983313 TTGACTTTTA
53983323 TTTTTTGA--TTTTTGAT
1 TTTTTTGATTTTTTTGAT
53983339 TTTTTTGATTTTTTT-ATT
1 TTTTTTGATTTTTTTGA-T
53983357 TTTTTTGATTTTTTTGAT
1 TTTTTTGATTTTTTTGAT
53983375 TTTTTT
1 TTTTTT
53983381 TTTAGTCTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.21
17 1 0.03
18 28 0.74
19 1 0.03
ACGTcount: A:0.10, C:0.00, G:0.09, T:0.81
Consensus pattern (18 bp):
TTTTTTGATTTTTTTGAT
Found at i:53983353 original size:27 final size:26
Alignment explanation
Indices: 53983323--53983382 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
53983313 TTGACTTTTA
*
53983323 TTTTTTGATTTTTGATTTTTTTGATT
1 TTTTTTTATTTTTGATTTTTTTGATT
*
53983349 TTTTTATTTTTTTTGATTTTTTTGATT
1 TTTTT-TTATTTTTGATTTTTTTGATT
53983376 TTTTTTT
1 TTTTTTT
53983383 TAGTCTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (26 bp):
TTTTTTTATTTTTGATTTTTTTGATT
Found at i:53985452 original size:19 final size:20
Alignment explanation
Indices: 53985423--53985471 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
53985413 CACTTCGTGA
* *
53985423 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
53985442 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
53985462 AAATG-AATGC
1 AAATGTAATGC
53985472 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:53993551 original size:13 final size:15
Alignment explanation
Indices: 53993514--53993550 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
53993504 AAAGAATAAT
53993514 ATTTTATATTAAAAA
1 ATTTTATATTAAAAA
*
53993529 ATTTTATATTAAAAG
1 ATTTTATATTAAAAA
53993544 ATTTTAT
1 ATTTTAT
53993551 TTTTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTTATATTAAAAA
Found at i:53993605 original size:25 final size:26
Alignment explanation
Indices: 53993577--53993625 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
53993567 ATTTGAAAAT
53993577 AATATTTTATATTAA-ATTATATTAA
1 AATATTTTATATTAAGATTATATTAA
*
53993602 AATATTTTATATTAAGATTTTATT
1 AATATTTTATATTAAGATTATATT
53993626 TTTATATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AATATTTTATATTAAGATTATATTAA
Found at i:53996544 original size:12 final size:12
Alignment explanation
Indices: 53996527--53996557 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53996517 TTGTTTTCTT
53996527 TTTCTTTCCCTA
1 TTTCTTTCCCTA
*
53996539 TTTCTTTCCCTT
1 TTTCTTTCCCTA
53996551 TTTCTTT
1 TTTCTTT
53996558 TTCATCCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCTTTCCCTA
Found at i:53997171 original size:18 final size:18
Alignment explanation
Indices: 53997144--53997179 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53997134 CCACATGGCT
*
53997144 ACAGTTTGTTACACGGCC
1 ACAGTCTGTTACACGGCC
*
53997162 ACAGTCTGTTACATGGCC
1 ACAGTCTGTTACACGGCC
53997180 TAGTCACACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (18 bp):
ACAGTCTGTTACACGGCC
Found at i:53999472 original size:12 final size:12
Alignment explanation
Indices: 53999452--53999481 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53999442 TTTAAATTTT
*
53999452 TTAAAATTTTAA
1 TTAATATTTTAA
53999464 TTAATATTTTAA
1 TTAATATTTTAA
53999476 TTAATA
1 TTAATA
53999482 AATATATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAATATTTTAA
Found at i:53999734 original size:13 final size:14
Alignment explanation
Indices: 53999706--53999735 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53999696 ACCCACAATG
53999706 TATATAAAAAATTA
1 TATATAAAAAATTA
53999720 TATATAAAAAA-TA
1 TATATAAAAAATTA
53999733 TAT
1 TAT
53999736 CAAACAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATAAAAAATTA
Found at i:53999861 original size:100 final size:94
Alignment explanation
Indices: 53999755--53999953 Score: 238
Period size: 94 Copynumber: 2.1 Consensus size: 94
53999745 TAGTTAAAAA
*
53999755 TAAAATATATTTAACATAATGA-TAAATATTAAAAATATACAATTCCATCATATAGTAACATATT
1 TAAAATATATTTAACATAAT-ACT--ATA-T-AAAATATA-AATTCCATCATATAATAACATATT
*
53999819 TATTAATTTATTTATATAAATAAAGGAATTATTAAT
60 T-TTAATTTATTTATATAAATAAAAGAATTATTAAT
* * * ** * * *
53999855 TAAAATATTTTTAACATAATACTATATATAATATATATTTTATTATATAATTACATATTTTTATT
1 TAAAATATATTTAACATAATACTATATAAAATATAAATTCCATCATATAATAACATATTTTTAAT
53999920 TTATTTATATAAATAAAAGAATTATTAAT
66 TTATTTATATAAATAAAAGAATTATTAAT
53999949 TAAAA
1 TAAAA
53999954 AGATGGATTA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
94 37 0.42
95 19 0.22
96 7 0.08
97 1 0.01
98 3 0.03
99 1 0.01
100 20 0.23
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (94 bp):
TAAAATATATTTAACATAATACTATATAAAATATAAATTCCATCATATAATAACATATTTTTAAT
TTATTTATATAAATAAAAGAATTATTAAT
Found at i:54001296 original size:23 final size:23
Alignment explanation
Indices: 54001267--54001311 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
54001257 TTAAAAATTA
54001267 ATTTTAATTAAATAAATATAATC
1 ATTTTAATTAAATAAATATAATC
*
54001290 ATTTTAATTAAATAAATTTAAT
1 ATTTTAATTAAATAAATATAAT
54001312 TTAATTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTTAATTAAATAAATATAATC
Found at i:54002427 original size:43 final size:44
Alignment explanation
Indices: 54002321--54002742 Score: 438
Period size: 43 Copynumber: 9.8 Consensus size: 44
54002311 TTTTTACAAT
* * **
54002321 AAACGCCGCTATAGA-CAATGGTCTTTAGCGGCGCTTATAAAT-
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
* *
54002363 AAACGCCGCTATAGACC-GTGGTCTTTAGGGGCGCTTTTGCATC
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
* **
54002406 AAACGCCGCTATAGA-CTGTGGTCTTTAGCGGCGCTTTGGCATC
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
* * *
54002449 AATCGCCGCCATAGACCA-TGGTCTTTAGCGGCGCTTTTGCATC
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
* ** *
54002492 AAACGCCGCGATAGACCA-TGGAT-TTTAGCGGCGCTTACCCGTC
1 AAACGCCGCTATAGACCAGTGG-TCTTTAGCGGCGCTTTTCCATC
* * *
54002535 AAACGCCGCTATAGACCAG-GATCTTTCGCGGCGCTTTTCCATA
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
* * * * * *
54002578 AAACGCCACTATAGACCAG-GATCTTTCGTGGCGCTTTCCCATA
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
* * ** *
54002621 AAACGCCGCTATAGACCAG-GATCTTTCGCGGCGCTTAACCATA
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
* *
54002664 AAACGCCGCTATAGACC--TGGATCTTTCGCGGCGCTTTCCCATC
1 AAACGCCGCTATAGACCAGTGG-TCTTTAGCGGCGCTTTTCCATC
*
54002707 AAACGCCGCTATAGACC-TTGGTCTTTAGCGGCGCTT
1 AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTT
54002743 AAAAAACAAA
Statistics
Matches: 334, Mismatches: 36, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
42 38 0.11
43 291 0.87
44 5 0.01
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (44 bp):
AAACGCCGCTATAGACCAGTGGTCTTTAGCGGCGCTTTTCCATC
Found at i:54002537 original size:129 final size:129
Alignment explanation
Indices: 54002321--54002742 Score: 512
Period size: 129 Copynumber: 3.3 Consensus size: 129
54002311 TTTTTACAAT
* * * *
54002321 AAACGCCGCTATAGACAATGGTCTTTAGCGGCGCTTATAAATAAACGCCGCTATAGACCGTGG-T
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTTTACATAAACGCCGCTATAGACCATGGAT
* *** * * **
54002385 CTTTAGGGGCGCTTTTGCATCAAACGCCGCTATAGA-CTGTGGTCTTTAGCGGCGCTTTGGCATC
66 CTTTAGCGGCGCTTAACCATCAAACGCCGCTATAGACCTG-GATCTTTCGCGGCGCTTTCCCATC
* * * *
54002449 AATCGCCGCCATAGACCATGGTCTTTAGCGGCGCTTTTGCATCAAACGCCGCGATAGACCATGGA
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTTTACAT-AAACGCCGCTATAGACCATGGA
* * * * *
54002514 T-TTTAGCGGCGCTTACCCGTCAAACGCCGCTATAGACCAGGATCTTTCGCGGCGCTTTTCCATA
65 TCTTTAGCGGCGCTTAACCATCAAACGCCGCTATAGACCTGGATCTTTCGCGGCGCTTTCCCATC
* * * **
54002578 AAACGCCACTATAGACCA-GGATCTTTCGTGGCGCTTTCCCATAAAACGCCGCTATAGACCA-GG
1 AAACGCCGCTATAGACCATGG-TCTTTAGCGGCGCTTTTACAT-AAACGCCGCTATAGACCATGG
* *
54002641 ATCTTTCGCGGCGCTTAACCATAAAACGCCGCTATAGACCTGGATCTTTCGCGGCGCTTTCCCAT
64 ATCTTTAGCGGCGCTTAACCATCAAACGCCGCTATAGACCTGGATCTTTCGCGGCGCTTTCCCAT
54002706 C
129 C
*
54002707 AAACGCCGCTATAGACCTTGGTCTTTAGCGGCGCTT
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTT
54002743 AAAAAACAAA
Statistics
Matches: 249, Mismatches: 39, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
128 42 0.17
129 202 0.81
130 5 0.02
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (129 bp):
AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTTTACATAAACGCCGCTATAGACCATGGAT
CTTTAGCGGCGCTTAACCATCAAACGCCGCTATAGACCTGGATCTTTCGCGGCGCTTTCCCATC
Found at i:54002781 original size:86 final size:85
Alignment explanation
Indices: 54002313--54002786 Score: 421
Period size: 86 Copynumber: 5.5 Consensus size: 85
54002303 CACGGCACTT
* * **
54002313 TTTAC-AATAAACGCCGCTATAGACAATGGTCTTTAGCGGCGCTTAT-AAAT-AAACGCCGCTAT
1 TTTACAAACAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTT-TCCCATCAAACGCCGCTAT
*
54002375 AGACCGTGGTCTTTAGGGGCGC
65 AGACC-TGGTCTTTAGCGGCGC
* * ** ** * *
54002397 TTTTGC-ATCAAACGCCGCTATAGACTGTGGTCTTTAGCGGCGCTTTGGCATCAATCGCCGCCAT
1 -TTTACAAACAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTTCCCATCAAACGCCGCTAT
54002461 AGACCATGGTCTTTAGCGGCGC
65 AGACC-TGGTCTTTAGCGGCGC
* * * * *
54002483 TTTTGC-ATCAAACGCCGCGATAGACCATGGAT-TTTAGCGGCGCTTACCCGTCAAACGCCGCTA
1 -TTTACAAACAAACGCCGCTATAGACCATGG-TCTTTAGCGGCGCTTTCCCATCAAACGCCGCTA
* *
54002546 TAGACCAGGATCTTTCGCGGCGC
64 TAGACCTGG-TCTTTAGCGGCGC
* * * * * *
54002569 TTTTCCATA-AAACGCCACTATAGACCA-GGATCTTTCGTGGCGCTTTCCCATAAAACGCCGCTA
1 -TTTACAAACAAACGCCGCTATAGACCATGG-TCTTTAGCGGCGCTTTCCCATCAAACGCCGCTA
* *
54002632 TAGACCAGGATCTTTCGCGGCGC
64 TAGACCTGG-TCTTTAGCGGCGC
* * *
54002655 TTAACCATA-AAACGCCGCTATAGACC-TGGATCTTTCGCGGCGCTTTCCCATCAAACGCCGCTA
1 TTTA-CAAACAAACGCCGCTATAGACCATGG-TCTTTAGCGGCGCTTTCCCATCAAACGCCGCTA
54002718 TAGACCTTGGTCTTTAGCGGCGC
64 TAGACC-TGGTCTTTAGCGGCGC
* * * * *
54002741 TTAAAAAACAAACGCCGCTATA-CCTCATGGTTTTTAGCGGCACTTT
1 TTTACAAACAAACGCCGCTATAGAC-CATGGTCTTTAGCGGCGCTTT
54002787 TAGAAAAACG
Statistics
Matches: 332, Mismatches: 45, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
84 1 0.00
85 52 0.16
86 273 0.82
87 6 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (85 bp):
TTTACAAACAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTTCCCATCAAACGCCGCTATA
GACCTGGTCTTTAGCGGCGC
Found at i:54002888 original size:14 final size:14
Alignment explanation
Indices: 54002871--54002900 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54002861 AATCAGAAGA
54002871 AACCAAATCTAACC
1 AACCAAATCTAACC
54002885 AACCAAATCTAACC
1 AACCAAATCTAACC
54002899 AA
1 AA
54002901 ATCTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (14 bp):
AACCAAATCTAACC
Found at i:54003157 original size:21 final size:21
Alignment explanation
Indices: 54003109--54003166 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
54003099 TTAAGCTGTT
*
54003109 CTGCTTCCCTCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAGCCG
* **
54003130 CTACTTCCCTCGCTGCATTCG
1 CTGCTTCCCTCGCTGCAGCCG
*
54003151 CTGCTTCTCTCGCTGC
1 CTGCTTCCCTCGCTGC
54003167 CGCATCTGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.05, C:0.45, G:0.17, T:0.33
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCG
Found at i:54003325 original size:87 final size:87
Alignment explanation
Indices: 54003154--54003314 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 87
54003144 GCATTCGCTG
* *
54003154 CTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTTGCTGGAGTTGTTCATACTTTTGTTGAACCTCA
1 CTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATACTTTTGTTGAACCTCA
54003219 GCTTCTCTCATTGCTGCCTCTA
66 GCTTCTCTCATTGCTGCCTCTA
*
54003241 CTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTT-TTGAACCTC
1 CTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATA-CTTTTGTTGAACCTC
54003305 AGCTTCTCTC
65 AGCTTCTCTC
54003315 GATGTTGCCT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
87 65 0.93
88 5 0.07
ACGTcount: A:0.13, C:0.29, G:0.17, T:0.41
Consensus pattern (87 bp):
CTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATACTTTTGTTGAACCTCA
GCTTCTCTCATTGCTGCCTCTA
Found at i:54009266 original size:14 final size:14
Alignment explanation
Indices: 54009247--54009284 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
54009237 GTGTTTAAAA
54009247 TTAAAATTTAATGT
1 TTAAAATTTAATGT
54009261 TTAAAATTTAATGT
1 TTAAAATTTAATGT
54009275 TTAAAATTTA
1 TTAAAATTTA
54009285 TTTGGTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
TTAAAATTTAATGT
Found at i:54011605 original size:23 final size:23
Alignment explanation
Indices: 54011562--54011606 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54011552 TGCTTTTGTA
*
54011562 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
54011585 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
54011607 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Done.