Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 58 of 199
Found at i:16847275 original size:21 final size:21
Alignment explanation
Indices: 16847249--16847297 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
16847239 TTCTTTTGAA
* *
16847249 CCTCTGTTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
16847270 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
16847291 CCTCTGC
1 CCTCTGC
16847298 CATAAGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.47, G:0.18, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:16847352 original size:87 final size:87
Alignment explanation
Indices: 16847184--16847345 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 87
16847174 TTCTGCTCTG
* ** *
16847184 CTCTGCTTCTCTCGCTGCAGCCTCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGCTGCAGCCTCTGCCATAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA
** * *
16847249 CCTCTGTTTCTCTCGCTGCAGC
66 CCTCACTGTCGCTCGCTGCAGC
* *
16847271 CTCTGCTTCCCTCGCTGCCGCCTCTGCCATAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGCTGCAGCCTCTGCCATAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA
16847336 CCTCAACTGT
66 CCTC-ACTGT
16847346 GGTCGCTTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
87 63 0.97
88 2 0.03
ACGTcount: A:0.13, C:0.31, G:0.17, T:0.39
Consensus pattern (87 bp):
CTCTGCTTCCCTCGCTGCAGCCTCTGCCATAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA
CCTCACTGTCGCTCGCTGCAGC
Found at i:16848628 original size:9 final size:9
Alignment explanation
Indices: 16848614--16848683 Score: 81
Period size: 9 Copynumber: 8.0 Consensus size: 9
16848604 ACCTCTGCGC
16848614 GTAAGTTAT
1 GTAAGTTAT
16848623 GTAAGTTAT
1 GTAAGTTAT
* *
16848632 TTAATTTAT
1 GTAAGTTAT
16848641 GTAAGTTAT
1 GTAAGTTAT
16848650 GTAAGTTAT
1 GTAAGTTAT
* *
16848659 TTAGGTTAT
1 GTAAGTTAT
16848668 GT-A-TTAT
1 GTAAGTTAT
*
16848675 GTTAGTTAT
1 GTAAGTTAT
16848684 TATGTTATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.12
8 1 0.02
9 44 0.86
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:16848645 original size:27 final size:27
Alignment explanation
Indices: 16848614--16848684 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
16848604 ACCTCTGCGC
*
16848614 GTAAGTTATGTAAGTTATTTAATTTAT
1 GTAAGTTATGTAAGTTATTTAAGTTAT
*
16848641 GTAAGTTATGTAAGTTATTTAGGTTAT
1 GTAAGTTATGTAAGTTATTTAAGTTAT
*
16848668 GT-A-TTATGTTAGTTATT
1 GTAAGTTATGTAAGTTATT
16848685 ATGTTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.32
26 1 0.02
27 27 0.66
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (27 bp):
GTAAGTTATGTAAGTTATTTAAGTTAT
Found at i:16848702 original size:24 final size:25
Alignment explanation
Indices: 16848626--16848702 Score: 59
Period size: 27 Copynumber: 3.0 Consensus size: 25
16848616 AAGTTATGTA
** * *
16848626 AGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATTTAGGTTATGT-A-TTAAGTT
*
16848653 AGTTATTTAGGTTATGTATTATGTT
1 AGTTATTTAGGTTATGTATTAAGTT
*
16848678 AGTTA-TTATGTTAT-TATATAAGTT
1 AGTTATTTAGGTTATGTAT-TAAGTT
16848702 A
1 A
16848703 TGCAAGTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.07
24 14 0.32
25 11 0.25
26 1 0.02
27 15 0.34
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (25 bp):
AGTTATTTAGGTTATGTATTAAGTT
Found at i:16848703 original size:29 final size:29
Alignment explanation
Indices: 16848671--16848858 Score: 98
Period size: 31 Copynumber: 6.6 Consensus size: 29
16848661 AGGTTATGTA
16848671 TTATGTTAGTTATTATGTTATTATATAAG
1 TTATGTTAGTTATTATGTTATTATATAAG
** *
16848700 TTATGCAAGTTTCTATATATG-T-TTATAT-AT
1 TTATGTTAG--T-TAT-TATGTTATTATATAAG
16848730 TGTATGTTAGTTATTATGTTATTATATAAG
1 T-TATGTTAGTTATTATGTTATTATATAAG
* * *
16848760 TTATGCTAGATATATAAGTTA-T-T-TAAG
1 TTATGTTAGTTAT-TATGTTATTATATAAG
*
16848787 TTA--TTATGTTATTA---TA-TAAAGT-A-
1 TTATGTTA-GTTATTATGTTATTATA-TAAG
* *
16848810 TTATGTAATTTATTATGTTATTATATGTAAG
1 TTATGTTAGTTATTATGTTATTATA--TAAG
*
16848841 TTATGTAAGTTATTATGT
1 TTATGTTAGTTATTATGT
16848859 AAGTTATGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
22 3 0.02
23 3 0.02
24 7 0.06
25 7 0.06
26 4 0.03
27 13 0.11
28 8 0.07
29 27 0.22
30 11 0.09
31 30 0.25
32 4 0.03
33 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (29 bp):
TTATGTTAGTTATTATGTTATTATATAAG
Found at i:16848823 original size:12 final size:11
Alignment explanation
Indices: 16848787--16848865 Score: 51
Period size: 12 Copynumber: 7.4 Consensus size: 11
16848777 GTTATTTAAG
*
16848787 TTATTATGTTA
1 TTATTATGTAA
*
16848798 TTA-TAT-AAA
1 TTATTATGTAA
*
16848807 GTATTATGTAA
1 TTATTATGTAA
*
16848818 TTTATTATGTTA
1 -TTATTATGTAA
16848830 TTA-TATGTAA
1 TTATTATGTAA
*
16848840 --GTTATGTAA
1 TTATTATGTAA
16848849 GTTATTATGTAA
1 -TTATTATGTAA
16848861 GTTAT
1 -TTAT
16848866 GCAAGCTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
9 10 0.19
10 12 0.23
11 8 0.15
12 22 0.42
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (11 bp):
TTATTATGTAA
Found at i:16848828 original size:32 final size:31
Alignment explanation
Indices: 16848775--16848858 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 31
16848765 CTAGATATAT
*
16848775 AAGTTATTTAAGTTATTATGTTATTATAT-A
1 AAGTTATGTAAGTTATTATGTTATTATATGA
* *
16848805 AAGTATTATGTAATTTATTATGTTATTATATGT
1 AAG--TTATGTAAGTTATTATGTTATTATATGA
16848838 AAGTTATGTAAGTTATTATGT
1 AAGTTATGTAAGTTATTATGT
16848859 AAGTTATGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.06
31 17 0.36
32 24 0.51
33 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (31 bp):
AAGTTATGTAAGTTATTATGTTATTATATGA
Found at i:16848847 original size:9 final size:9
Alignment explanation
Indices: 16848833--16848915 Score: 62
Period size: 9 Copynumber: 8.8 Consensus size: 9
16848823 TATGTTATTA
16848833 TATGTAAGT
1 TATGTAAGT
16848842 TATGTAAGTTAT
1 TATGTAAG---T
16848854 TATGTAAGT
1 TATGTAAGT
*
16848863 TATGCAAGCT
1 TATGTAAG-T
*
16848873 TAAATATAAGT
1 T--ATGTAAGT
16848884 TATGT-A-T
1 TATGTAAGT
*
16848891 TATATAAGT
1 TATGTAAGT
*
16848900 TTTGTAAGT
1 TATGTAAGT
16848909 TATGTAA
1 TATGTAA
16848916 TGGTGTATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
7 5 0.09
8 2 0.03
9 33 0.57
10 2 0.03
11 2 0.03
12 14 0.24
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (9 bp):
TATGTAAGT
Found at i:16849030 original size:62 final size:62
Alignment explanation
Indices: 16848948--16849067 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
16848938 AAAAAACTTA
* *
16848948 TAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACTTATTTAGAAAACGAAG
1 TAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAACACTTATTTAGAAAACGAAG
* * *
16849010 TAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAAGACTTATTTAGAAAAC
1 TAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAACACTTATTTAGAAAAC
16849068 TTATAAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (62 bp):
TAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAACACTTATTTAGAAAACGAAG
Found at i:16849035 original size:16 final size:16
Alignment explanation
Indices: 16849010--16849047 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
16849000 GAAAACGAAG
*
16849010 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
16849025 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
16849041 TAAATTT
1 TAAATTT
16849048 AGAAGACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:16849079 original size:17 final size:17
Alignment explanation
Indices: 16849057--16849089 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16849047 TAGAAGACTT
16849057 ATTTAGAAAACTTATAA
1 ATTTAGAAAACTTATAA
16849074 ATTTAGAAAACTTATA
1 ATTTAGAAAACTTATA
16849090 TAGATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTTAGAAAACTTATAA
Found at i:16849110 original size:62 final size:57
Alignment explanation
Indices: 16848929--16849136 Score: 152
Period size: 62 Copynumber: 3.5 Consensus size: 57
16848919 TGTATTATGT
* * * * *
16848929 AACTTATGTAAAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAA-ATTTAGA
1 AACTTATTTAGAAAACTTATAAATTTAAAACTAATAAA---TATTA-AAACAATATTTAGA
** * * *
16848989 ACACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGA
1 A-ACTTATTTAGAAAACTTA-TAAATTTAAAACTAATAAATATTAAAAC-AAT--ATTTAGA
* *
16849051 AGACTTATTTAGAAAACTTATAAATTTAGAAAACTTATATAGATATTAAAACAATATTTA-C
1 A-ACTTATTTAGAAAACTTATAAATTT--AAAAC-TA-ATAAATATTAAAACAATATTTAGA
*
16849112 AA-TTATTTAGAAAACTTACAAATTT
1 AACTTATTTAGAAAACTTATAAATTT
16849137 TATAGTAATA
Statistics
Matches: 121, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
58 2 0.02
59 28 0.23
60 2 0.02
61 22 0.18
62 47 0.39
63 4 0.03
64 5 0.04
65 11 0.09
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.36
Consensus pattern (57 bp):
AACTTATTTAGAAAACTTATAAATTTAAAACTAATAAATATTAAAACAATATTTAGA
Found at i:16853350 original size:20 final size:21
Alignment explanation
Indices: 16853296--16853350 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
16853286 CGCTGAAATG
* *
16853296 TAAACTCTAAACCTTAAACCT
1 TAAACTCTAAGCCCTAAACCT
* * *
16853317 CAATCTCCAAGCCCTAAA-CT
1 TAAACTCTAAGCCCTAAACCT
16853337 TAAACTCTAAGCCC
1 TAAACTCTAAGCCC
16853351 AGAACACAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.38, C:0.35, G:0.04, T:0.24
Consensus pattern (21 bp):
TAAACTCTAAGCCCTAAACCT
Found at i:16853885 original size:134 final size:133
Alignment explanation
Indices: 16853720--16854130 Score: 510
Period size: 133 Copynumber: 3.1 Consensus size: 133
16853710 TTAACATTTT
* * * * *
16853720 GCCACTAAAG-CATAAAAGGAAACAACAAAACGATACTGTTTTGCTCAAAATTTTTCCTCAAATT
1 GCCACTAAAGAAATAAAATGAAACAATAAAACGGTACTGTTTTGCTCAAATTTTTTCCTCAAATT
* * * *
16853784 AGATATCATTACCGGCGTTTCTCCAATAACGCCACTATATCCCAATATTTGCGGCGTTTTTTGCA
66 AGATATCTTTACCGGCGTTTCTCCAAAAACGCCGCTATAT-CCAATTTTTGCGGCGTTTTTTGCA
16853849 ATGC
130 ATGC
* *
16853853 GCCACTAAAGAAATAAAATGAAGCAATAAAACGGTAGTGTTTTG-TCCAAATTTTTTCCTCAAAT
1 GCCACTAAAGAAATAAAATGAAACAATAAAACGGTACTGTTTTGCT-CAAATTTTTTCCTCAAAT
* ** * *
16853917 CAGATATCTTTACCGGCGTTTC-CCTAAAAACGCCGCTA-ATTGAATCTTTTCCGGCGTTTTTTA
65 TAGATATCTTTACCGGCGTTTCTCC-AAAAACGCCGCTATATCCAAT-TTTTGCGGCGTTTTTTG
16853980 CAATGC
128 CAATGC
*
16853986 GCCACTAAAGAAATAAAATGAAACAATAAAACGGTACTGTTTTGCTCAGATTTTTTCCTCAAATT
1 GCCACTAAAGAAATAAAATGAAACAATAAAACGGTACTGTTTTGCTCAAATTTTTTCCTCAAATT
* * *
16854051 CGTTATCTTTACCGGTGTTTCT-CAGAAAACGCCGCTATATTCCAATTTTTTGCGGCGTTTTTAT
66 AGATATCTTTACCGGCGTTTCTCCA-AAAACGCCGCTATA-TCCAA-TTTTTGCGGCGTTTTT-T
* *
16854115 GGAA-AC
127 GCAATGC
16854121 GCCACTAAAG
1 GCCACTAAAG
16854131 CCATAAAGTA
Statistics
Matches: 238, Mismatches: 29, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
132 4 0.02
133 125 0.53
134 77 0.32
135 28 0.12
136 4 0.02
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (133 bp):
GCCACTAAAGAAATAAAATGAAACAATAAAACGGTACTGTTTTGCTCAAATTTTTTCCTCAAATT
AGATATCTTTACCGGCGTTTCTCCAAAAACGCCGCTATATCCAATTTTTGCGGCGTTTTTTGCAA
TGC
Found at i:16862680 original size:27 final size:28
Alignment explanation
Indices: 16862603--16862680 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
16862593 AAAACTTAAA
*
16862603 AAAAAGTT-TAAAACAAATTAAAAATACAT
1 AAAAA-TTATAAAAGAAA-TAAAAATACAT
** *
16862632 AAAGTTTATAAAAGAAAT-AAAATATAT
1 AAAAATTATAAAAGAAATAAAAATACAT
*
16862659 AAAAATTAT-AAAGTAATAAAAA
1 AAAAATTATAAAAGAAATAAAAA
16862681 AACTTGAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
26 7 0.17
27 19 0.47
28 3 0.08
29 11 0.28
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (28 bp):
AAAAATTATAAAAGAAATAAAAATACAT
Found at i:16863612 original size:39 final size:39
Alignment explanation
Indices: 16863553--16863640 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
16863543 AAAAATTATA
* * *
16863553 TTTAATACAATAAAATATTTATTATATTTAT-TTATATTT
1 TTTAATATAATAAAAAATTTATTATATTTATGGTA-ATTT
*
16863592 TTTAGTATAATAAAAAATTTATTATATTTATGGTAATTT
1 TTTAATATAATAAAAAATTTATTATATTTATGGTAATTT
16863631 TTTAATATAA
1 TTTAATATAA
16863641 ATATACTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 41 0.95
40 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (39 bp):
TTTAATATAATAAAAAATTTATTATATTTATGGTAATTT
Found at i:16867887 original size:25 final size:25
Alignment explanation
Indices: 16867859--16867926 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
16867849 AGCTGTATAA
* *
16867859 CGGGAAGCTCTTGTGAG-CAAATTAT
1 CGGGAAGCTCTAGAGAGCCAAA-TAT
*
16867884 CGGGAAGCTCAAGAGAGCCAAATAT
1 CGGGAAGCTCTAGAGAGCCAAATAT
* *
16867909 CGGGATGCTCTGGAGAGC
1 CGGGAAGCTCTAGAGAGC
16867927 TATTAATTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 32 0.89
26 4 0.11
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCTAGAGAGCCAAATAT
Found at i:16883357 original size:46 final size:46
Alignment explanation
Indices: 16883281--16883509 Score: 352
Period size: 46 Copynumber: 5.0 Consensus size: 46
16883271 ATTACTATAG
* * *
16883281 CTCAGTATGATTTTCTTCACGGAAATACCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
16883327 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
*
16883373 CTCAGTATGGTTTTCTTCACTGAAACACCATTCCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
* *
16883419 CTCAGTATGGTTTTCTTCACTAAAACACCATACCTATTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
* * * *
16883465 CTCAGTATGGTTTTCTTTA-TCGAAATACCTTACCTACGTTTCACA
1 CTCAGTATGGTTTTCTTCACT-GAAACACCATACCTACTTTTCACA
16883510 CTTTGCCATG
Statistics
Matches: 169, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 168 0.99
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.37
Consensus pattern (46 bp):
CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
Found at i:16892824 original size:22 final size:23
Alignment explanation
Indices: 16892789--16892832 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16892779 AATAAGATTT
16892789 AATATTAAATTTAATCTAATATA
1 AATATTAAATTTAATCTAATATA
* *
16892812 AATATTATA-TTAATTTAATAT
1 AATATTAAATTTAATCTAATAT
16892833 TAAAGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTAAATTTAATCTAATATA
Found at i:16895900 original size:33 final size:33
Alignment explanation
Indices: 16895852--16896084 Score: 129
Period size: 33 Copynumber: 6.7 Consensus size: 33
16895842 TTAACCGTTA
*
16895852 TCGGTGGATTCAGCACTTAGCAACCACCAATGAG
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAG
* * *
16895886 TCGGGGAATAAGCACTTAGCAACCCCTTTCACATTTAAG
1 TCGGGGAATCAGCACTTAGCAACCAC---CA-A--TGAG
** *
16895925 ATACGGTGGGTTCAGCACTTAGCAACCACCAATGAT
1 -T-CGG-GGAATCAGCACTTAGCAACCACCAATGAG
16895961 TCGGGGAATCAGCACTTAGCAACC-CC------
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAG
* *
16895987 TCGGGGAATCAGCACTTAGCAACCCCTTCACATTTAAG
1 TCGGGGAATCAGCACTTAGCAACCAC--CA-A--TGAG
* *
16896025 ATACAGTGGAATCAGCACTTAGCAACCACCAATGAA
1 -T-C-GGGGAATCAGCACTTAGCAACCACCAATGAG
** *
16896061 TAAGGGAATCAACACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
16896085 CCTTTTTTAT
Statistics
Matches: 155, Mismatches: 20, Indels: 49
0.69 0.09 0.22
Matches are distributed among these distances:
26 24 0.15
27 1 0.01
29 1 0.01
32 2 0.01
33 56 0.36
34 7 0.05
35 2 0.01
36 6 0.04
37 1 0.01
38 2 0.01
39 8 0.05
40 2 0.01
41 25 0.16
42 18 0.12
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAG
Found at i:16895990 original size:26 final size:26
Alignment explanation
Indices: 16895961--16896013 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
16895951 CACCAATGAT
16895961 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
16895987 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
16896013 T
1 T
16896014 TCACATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (26 bp):
TCGGGGAATCAGCACTTAGCAACCCC
Found at i:16896041 original size:100 final size:101
Alignment explanation
Indices: 16895886--16896087 Score: 325
Period size: 100 Copynumber: 2.0 Consensus size: 101
16895876 CACCAATGAG
* **
16895886 TCGGGGAATAAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGTTCAGCACTTAGCAAC
1 TCGGGGAATAAGCACTTAGCAACCCCTTTCACATTTAAGATACAGTGGAATCAGCACTTAGCAAC
* ** *
16895951 CACCAATGATTCGGGGAATCAGCACTTAGCAACCCC
66 CACCAATGAATAAGGGAATCAACACTTAGCAACCCC
*
16895987 TCGGGGAATCAGCACTTAGCAACCCC-TTCACATTTAAGATACAGTGGAATCAGCACTTAGCAAC
1 TCGGGGAATAAGCACTTAGCAACCCCTTTCACATTTAAGATACAGTGGAATCAGCACTTAGCAAC
16896051 CACCAATGAATAAGGGAATCAACACTTAGCAACCCC
66 CACCAATGAATAAGGGAATCAACACTTAGCAACCCC
16896087 T
1 T
16896088 TTTTTATTCA
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 68 0.73
101 25 0.27
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (101 bp):
TCGGGGAATAAGCACTTAGCAACCCCTTTCACATTTAAGATACAGTGGAATCAGCACTTAGCAAC
CACCAATGAATAAGGGAATCAACACTTAGCAACCCC
Found at i:16897181 original size:11 final size:12
Alignment explanation
Indices: 16897153--16897186 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
16897143 GCCCAAACGT
16897153 CGAAATTTTTGAA
1 CGAAATTTTT-AA
16897166 CGAAATTTTT-A
1 CGAAATTTTTAA
16897177 CGAAATTTTT
1 CGAAATTTTT
16897187 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:16897302 original size:76 final size:76
Alignment explanation
Indices: 16897217--16897369 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
16897207 AAAATATAAT
*
16897217 AATAATCATATTTTTCCTTGTCAGATTTGTGGTCCCGAAACCACTGTTCCGAGTAGACCCAGAAT
1 AATAATCATATTTTTCCTTGTCAGATTTGTGGTCCCGAAACCACTGTTCCGACTAGACCCAGAAT
16897282 TGGGCTGTTAC
66 TGGGCTGTTAC
* *
16897293 AATAATCATATTTTTCCTTGTCGGATTTGTGGTCCTGAAACCACTGTTCCGACTAGACCCAGAAT
1 AATAATCATATTTTTCCTTGTCAGATTTGTGGTCCCGAAACCACTGTTCCGACTAGACCCAGAAT
16897358 TGGGCTGTTAC
66 TGGGCTGTTAC
16897369 A
1 A
16897370 GCATTGATTC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (76 bp):
AATAATCATATTTTTCCTTGTCAGATTTGTGGTCCCGAAACCACTGTTCCGACTAGACCCAGAAT
TGGGCTGTTAC
Found at i:16912881 original size:44 final size:44
Alignment explanation
Indices: 16912818--16913052 Score: 165
Period size: 44 Copynumber: 5.3 Consensus size: 44
16912808 TGAATATTAT
* *
16912818 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGTCTTAC
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACACTAATCTTAC
* * * * * *
16912862 CTCCCTGAAGTTGCAGTGGAGCAAACTAAAGATATCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACA-CTAATCTTAC
* * * *
16912907 CTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTCACTAAACATATC
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACACTAATCTTA-C
* * * * *
16912952 C-CCCTAAAGTTGTAGTGGGGTA-AGTTGAA-AC-C-AAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGACACTAA-TCTTAC
* * * * * * *
16912993 CTCTCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACA-CTAATCTTAC
*
16913038 TTCCCTGAAGTTGCA
1 CTCCCTGAAGTTGCA
16913053 ATAGAACAGA
Statistics
Matches: 145, Mismatches: 36, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
41 3 0.02
42 24 0.17
43 4 0.03
44 58 0.40
45 54 0.37
46 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACACTAATCTTAC
Found at i:16913199 original size:177 final size:177
Alignment explanation
Indices: 16912958--16913363 Score: 591
Period size: 177 Copynumber: 2.3 Consensus size: 177
16912948 TATCCCCCTA
* * * * *
16912958 AAGTTGTAGTGGGGTAAGTTGAAACCAAGTCTTATCTCTCTAAAGTTACAGTGGAGCAGACTGAA
1 AAGTTGTAGTGGAG-CAGTTTAAACCAA-TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAA
16913023 GATAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACAGA-TTAAAACTATAAATTACCGATCTT
64 GATAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACA-ATTTAAAACTATAAATTACCGATCTT
*
16913087 ATCTCACTGAAGTTGCAGTAGAGCAAATCATAGCAAACCTTATCT-CTCTG
128 ATCTCACTGAAGTTACAGTAGAGCAAATCATAGCAAACCTTATCTCCT-TG
* *
16913137 AAGTTGTAGTGGAGCAGTTTAAACCAATCTTCTCTCTCTGAAGTTGCAGTGGAGTAGACTGAAGA
1 AAGTTGTAGTGGAGCAGTTTAAACCAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGA
* * * * *
16913202 TAGCGAATCTTATTTCTCTGAAGTTGCAGTGGAACAATTTCAAGCTATAAATTACCGATCTTATC
66 TAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACAATTTAAAACTATAAATTACCGATCTTATC
* * * *
16913267 TCGCTGAAGTTATAGTAGAGCATATTATAGCAAACCTTATCTCCTTG
131 TCACTGAAGTTACAGTAGAGCAAATCATAGCAAACCTTATCTCCTTG
* *
16913314 AAGTTGCAGTGGAGCAGTTTAAACCAATCTTATCTCCCTGAAGTTGCAGT
1 AAGTTGTAGTGGAGCAGTTTAAACCAATCTTATCTCTCTGAAGTTGCAGT
16913364 AAAATAGATT
Statistics
Matches: 205, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
176 1 0.00
177 178 0.87
178 13 0.06
179 13 0.06
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (177 bp):
AAGTTGTAGTGGAGCAGTTTAAACCAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGA
TAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACAATTTAAAACTATAAATTACCGATCTTATC
TCACTGAAGTTACAGTAGAGCAAATCATAGCAAACCTTATCTCCTTG
Found at i:16913329 original size:41 final size:39
Alignment explanation
Indices: 16913261--16913364 Score: 102
Period size: 41 Copynumber: 2.6 Consensus size: 39
16913251 AATTACCGAT
** *
16913261 CTTATCTCGCTGAAGTTATAGTAGAGCA-TATTATAGCAAAC
1 CTTATCTC-CTGAAGTTGCAGTAGAGCAGT-TTA-AACAAAC
* * *
16913302 CTTATCTCCTTGAAGTTGCAGTGGAGCAGTTTAAACCAAT
1 CTTATCTCC-TGAAGTTGCAGTAGAGCAGTTTAAACAAAC
16913342 CTTATCTCCCTGAAGTTGCAGTA
1 CTTATCT-CCTGAAGTTGCAGTA
16913365 AAATAGATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
40 24 0.45
41 28 0.53
42 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (39 bp):
CTTATCTCCTGAAGTTGCAGTAGAGCAGTTTAAACAAAC
Found at i:16937473 original size:6 final size:6
Alignment explanation
Indices: 16937462--16937494 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
16937452 CCTTTCCGTT
16937462 CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTT
1 CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTT
16937495 GTGCCCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTAC
Found at i:16945815 original size:20 final size:18
Alignment explanation
Indices: 16945792--16945837 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
16945782 TATTTTTGAT
*
16945792 ATCGATACTTTTTGAAAATA
1 ATCGATACCTTTT-AAAA-A
16945812 ATCGATACCTTTTAAAAA
1 ATCGATACCTTTTAAAAA
16945830 A-CGATACC
1 ATCGATACC
16945838 ACAATTGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 4 0.16
20 12 0.48
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (18 bp):
ATCGATACCTTTTAAAAA
Found at i:16945830 original size:21 final size:20
Alignment explanation
Indices: 16945792--16945830 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16945782 TATTTTTGAT
**
16945792 ATCGATACTTTTTGAAAATA
1 ATCGATACTTTTAAAAAATA
16945812 ATCGATACCTTTTAAAAAA
1 ATCGATA-CTTTTAAAAAA
16945831 CGATACCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (20 bp):
ATCGATACTTTTAAAAAATA
Found at i:16947430 original size:3 final size:3
Alignment explanation
Indices: 16947422--16947447 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16947412 AATAATTATT
16947422 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
16947448 TTATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16949454 original size:10 final size:10
Alignment explanation
Indices: 16949441--16949491 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
16949431 TAAATTTTAA
*
16949441 ATAATTATCT
1 ATAATTATTT
16949451 ATAATT-TTGT
1 ATAATTATT-T
16949461 ATAATT-TTT
1 ATAATTATTT
16949470 ATAATTATTT
1 ATAATTATTT
16949480 AATAATTATTT
1 -ATAATTATTT
16949491 A
1 A
16949492 AGAAACAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 8 0.22
10 19 0.51
11 10 0.27
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
ATAATTATTT
Found at i:16949456 original size:41 final size:40
Alignment explanation
Indices: 16949411--16949488 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
16949401 TCAATTTTAT
16949411 TAATTTCT-TATAATTCTTAATAAATT-TTAAATAATTATCTA
1 TAATTT-TGTATAATT-TTAAT-AATTATTAAATAATTATCTA
* *
16949452 TAATTTTGTATAATTTTTATAATTATTTAATAATTAT
1 TAATTTTGTATAATTTTAATAATTATTAAATAATTAT
16949489 TTAAGAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 4 0.12
40 16 0.48
41 13 0.39
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (40 bp):
TAATTTTGTATAATTTTAATAATTATTAAATAATTATCTA
Found at i:16949484 original size:11 final size:10
Alignment explanation
Indices: 16949405--16949492 Score: 58
Period size: 10 Copynumber: 8.6 Consensus size: 10
16949395 TTGAGCTCAA
*
16949405 TTTTATTAAT
1 TTTTAATAAT
16949415 TTCTT-ATAAT
1 TT-TTAATAAT
*
16949425 TCTTAATAAAT
1 TTTTAAT-AAT
*
16949436 TTTAAATAAT
1 TTTTAATAAT
*
16949446 TATCT-ATAAT
1 T-TTTAATAAT
16949456 TTTGT-ATAAT
1 TTT-TAATAAT
16949466 TTTT-ATAAT
1 TTTTAATAAT
16949475 TATTTAATAAT
1 T-TTTAATAAT
16949486 TATTTAA
1 T-TTTAA
16949493 GAAACAACTC
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
9 10 0.16
10 31 0.48
11 23 0.36
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:16949651 original size:51 final size:53
Alignment explanation
Indices: 16949590--16949689 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
16949580 AAAATAATAA
* *
16949590 TTCTTATAAATTTT-AGT-TTTTTAAATAATTTTCTATAATGTTTTTAATCAT
1 TTCTTATAAATTTTAAGTATTTTTAAACAATTTTCTATAATGTTGTTAATCAT
*
16949641 TTCTTATAAATTTTAATTATTTTTAAACAATTTTCTATAATGTTGTTAA
1 TTCTTATAAATTTTAAGTATTTTTAAACAATTTTCTATAATGTTGTTAA
16949690 AAACCATGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 14 0.32
52 2 0.05
53 28 0.64
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (53 bp):
TTCTTATAAATTTTAAGTATTTTTAAACAATTTTCTATAATGTTGTTAATCAT
Found at i:16949672 original size:20 final size:20
Alignment explanation
Indices: 16949631--16949674 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16949621 TCTATAATGT
*
16949631 TTTTAATCATTTCTTATAAA
1 TTTTAATCATTTCTTAAAAA
*
16949651 TTTTAATTATTT-TTAAACAA
1 TTTTAATCATTTCTTAAA-AA
16949671 TTTT
1 TTTT
16949675 CTATAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAATCATTTCTTAAAAA
Found at i:16950808 original size:17 final size:17
Alignment explanation
Indices: 16950786--16950818 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16950776 ATTCTATCTT
16950786 ATTTTTATT-TTATTTAG
1 ATTTTT-TTATTATTTAG
16950803 ATTTTTTTATTATTTA
1 ATTTTTTTATTATTTA
16950819 ATTAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTTTTTTATTATTTAG
Found at i:16956171 original size:5 final size:5
Alignment explanation
Indices: 16956163--16956190 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16956153 TTAAGTATAA
16956163 ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATA
16956191 AAAGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:16957079 original size:12 final size:12
Alignment explanation
Indices: 16957062--16957088 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16957052 TTCAGCATTA
16957062 ATGCCCAAGTAG
1 ATGCCCAAGTAG
16957074 ATGCCCAAGTAG
1 ATGCCCAAGTAG
16957086 ATG
1 ATG
16957089 GAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (12 bp):
ATGCCCAAGTAG
Found at i:16957167 original size:25 final size:25
Alignment explanation
Indices: 16957139--16957245 Score: 112
Period size: 25 Copynumber: 4.4 Consensus size: 25
16957129 GAACTTTAGC
** * *
16957139 GTGCTCTCAAATTAGTAGCACATCA
1 GTGCTCTCTGATTACTAGCACGTCA
* **
16957164 GTGCTCTCTGATTATTAGCACGTTG
1 GTGCTCTCTGATTACTAGCACGTCA
16957189 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGATTACTAGCACGTCA
* *
16957214 GTGCTCTCTG-TT--TAGCACATCT
1 GTGCTCTCTGATTACTAGCACGTCA
16957236 GTGCTCTCTG
1 GTGCTCTCTG
16957246 TATAGTACTT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
22 18 0.25
24 2 0.03
25 51 0.72
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (25 bp):
GTGCTCTCTGATTACTAGCACGTCA
Found at i:16957239 original size:22 final size:22
Alignment explanation
Indices: 16957154--16957269 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 22
16957144 CTCAAATTAG
*
16957154 TAGCACATCAGTGCTCTCTGATTAT
1 TAGCACATCTGTGCTCTCTG--T-T
*
16957179 TAGCACGT-TGGTGCTCTCTGATT
1 TAGCACATCT-GTGCTCTCTG-TT
* *
16957202 ACTAGCACGTCAGTGCTCTCTGTT
1 --TAGCACATCTGTGCTCTCTGTT
*
16957226 TAGCACATCTGTGCTCTCTGTA
1 TAGCACATCTGTGCTCTCTGTT
* *
16957248 TAGTAC-TTTAGTGCTCTCTGTT
1 TAGCACATCT-GTGCTCTCTGTT
16957270 CATTAGTGCA
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
21 2 0.03
22 35 0.46
23 1 0.01
24 3 0.04
25 35 0.46
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (22 bp):
TAGCACATCTGTGCTCTCTGTT
Found at i:16965134 original size:9 final size:9
Alignment explanation
Indices: 16965120--16965171 Score: 72
Period size: 9 Copynumber: 5.8 Consensus size: 9
16965110 GTTTAGACTA
16965120 AAAAAAATC
1 AAAAAAATC
16965129 AAAAAAATC
1 AAAAAAATC
16965138 AAAAAAAAATC
1 --AAAAAAATC
16965149 AAAAAAATC
1 AAAAAAATC
16965158 -AAAAAAT-
1 AAAAAAATC
16965165 AAAAAAA
1 AAAAAAA
16965172 AAAGACAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 13 0.32
9 18 0.45
11 9 0.22
ACGTcount: A:0.83, C:0.08, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:16965144 original size:20 final size:20
Alignment explanation
Indices: 16965119--16965163 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
16965109 AGTTTAGACT
16965119 AAAAAAAATCAAAAAAATCA
1 AAAAAAAATCAAAAAAATCA
16965139 AAAAAAAATCAAAAAAATCA
1 AAAAAAAATCAAAAAAATCA
16965159 AAAAA
1 AAAAA
16965164 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (20 bp):
AAAAAAAATCAAAAAAATCA
Found at i:16965162 original size:29 final size:29
Alignment explanation
Indices: 16965120--16965206 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
16965110 GTTTAGACTA
16965120 AAAAAAATCAAAAAAATCAAAAAAAAATC
1 AAAAAAATCAAAAAAATCAAAAAAAAATC
* *
16965149 AAAAAAATC-AAAAAATAAAAAAAAAAGAC
1 AAAAAAATCAAAAAAATCAAAAAAAAA-TC
16965178 AAAAATAA--AAAAAAATCAAAGTAAAAAAT
1 AAAAA-AATCAAAAAAATCAAA--AAAAAAT
16965207 AGGAGAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
28 16 0.33
29 25 0.51
30 2 0.04
31 6 0.12
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.10
Consensus pattern (29 bp):
AAAAAAATCAAAAAAATCAAAAAAAAATC
Found at i:16965172 original size:9 final size:9
Alignment explanation
Indices: 16965118--16965191 Score: 71
Period size: 9 Copynumber: 8.0 Consensus size: 9
16965108 GAGTTTAGAC
16965118 TAAAAAAAA
1 TAAAAAAAA
*
16965127 TCAAAAAAA
1 TAAAAAAAA
16965136 TCAAAAAAAAA
1 T--AAAAAAAA
*
16965147 TCAAAAAAA
1 TAAAAAAAA
*
16965156 T-CAAAAAA
1 TAAAAAAAA
16965164 TAAAAAAAA
1 TAAAAAAAA
16965173 -AAGACAAAAA
1 TAA-A-AAAAA
16965183 TAAAAAAAA
1 TAAAAAAAA
16965192 ATCAAAGTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
8 9 0.17
9 29 0.54
10 6 0.11
11 10 0.19
ACGTcount: A:0.82, C:0.07, G:0.01, T:0.09
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:16965172 original size:20 final size:20
Alignment explanation
Indices: 16965129--16965192 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
16965119 AAAAAAAATC
*
16965129 AAAAAAATCAAAAAA-AAATC
1 AAAAAAATCAAAAAATAAA-A
16965149 AAAAAAATCAAAAAATAAAA
1 AAAAAAATCAAAAAATAAAA
16965169 AAAAAAGA-C-AAAAATAAAA
1 AAAAAA-ATCAAAAAATAAAA
16965188 AAAAA
1 AAAAA
16965193 TCAAAGTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 15 0.37
20 22 0.54
21 4 0.10
ACGTcount: A:0.84, C:0.06, G:0.02, T:0.08
Consensus pattern (20 bp):
AAAAAAATCAAAAAATAAAA
Found at i:16965226 original size:21 final size:21
Alignment explanation
Indices: 16965200--16965244 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
16965190 AAATCAAAGT
* *
16965200 AAAAAATAGGAGAAAAAGAAA
1 AAAAAAGAAGAGAAAAAGAAA
16965221 AAAAAAGAAGAGAAAAAGAAA
1 AAAAAAGAAGAGAAAAAGAAA
16965242 AAA
1 AAA
16965245 GAGAGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAGAGAAAAAGAAA
Found at i:16965236 original size:15 final size:15
Alignment explanation
Indices: 16965212--16965248 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
16965202 AAAATAGGAG
16965212 AAAAAGA-AAAAA-A
1 AAAAAGAGAAAAAGA
*
16965225 AAGAAGAGAAAAAGA
1 AAAAAGAGAAAAAGA
16965240 AAAAAGAGA
1 AAAAAGAGA
16965249 GGTCAAGGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 6 0.30
14 5 0.25
15 9 0.45
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAGA
Found at i:16966090 original size:17 final size:18
Alignment explanation
Indices: 16966057--16966097 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
16966047 AAAAACTTAA
16966057 AAAAATGAATGAAAAAATG
1 AAAAATGAA-GAAAAAATG
16966076 AAAAATGAA-AAAAAATG
1 AAAAATGAAGAAAAAATG
16966093 AAAAA
1 AAAAA
16966098 GTAAAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAAATGAAGAAAAAATG
Found at i:16967456 original size:88 final size:88
Alignment explanation
Indices: 16967307--16968603 Score: 2081
Period size: 88 Copynumber: 14.7 Consensus size: 88
16967297 AACAGATCAG
* * ** * *
16967307 TGAAGACAACAGATCTTGCCTTCTTACATTGACAGCGAAGCAGGTCGAAGAAAAAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16967372 CTCTCGATTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * * *
16967395 TGAAGACAGAAGATCTTGTCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACATAGACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16967460 CTCTCGGTTGTGATGAAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * *
16967483 TGAAGACAAAAGATCTTACCTTCCTGTATTGATAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16967548 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * *
16967571 TGAAGATAAAAGATCTTGCCTTCCTGTATTGATAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16967636 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
16967659 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16967724 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
16967747 TGAAGACAAAAGATCTTACCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16967812 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
16967835 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACATAGACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16967900 CTCTCGGTTGTGATGAAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
16967923 TGAAGACAAAAGATCTTGCCTTCCTGTATTGATAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16967988 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
16968011 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGTAGGTCGAAAACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16968076 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * *
16968099 TGAAAACGAAAGATCTTGCCTTCCTGTATTGACAGCGAAACAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16968164 CTCTCGGTTGTGATGAAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
16968187 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGGAGCAGGTTGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16968252 CTCTCGGTTGTGATGGAGCTAGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
16968275 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCAAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16968340 CTCTCAGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* ** * * *
16968363 TGAAGATAAGTGATCTTGCCTTCCTGCATTGACAGCGAAGCAAGTCAAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16968428 CTCTCGGTTGTGATAGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* ** * * *
16968451 TGAAGATAAAAGATCTTGCCTTCCTACATTGTCAGCAAAGCAGGTCGAAGACACAAACCTTGCTT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16968516 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * * *
16968539 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGTGAAGTAGGTCGAAAACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16968604 TCTTGTACTG
Statistics
Matches: 1126, Mismatches: 83, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 1126 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (88 bp):
TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
CTCTCGGTTGTGATGGAGCTGGT
Found at i:16968697 original size:46 final size:46
Alignment explanation
Indices: 16968630--16968789 Score: 221
Period size: 46 Copynumber: 3.5 Consensus size: 46
16968620 GAGCAGACTA
* * * *
16968630 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGAGATCG
1 AAGATAGTAAATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCG
* * *
16968676 AAGATAGTAAATCTTGTCTTCCTGTATTTGGCAACGGAGGAGATTG
1 AAGATAGTAAATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCG
* * *
16968722 AAGATAGTAGATCTTATCTTTCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGTAAATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCG
*
16968768 AAGATGGTAAATCTTATCTTCC
1 AAGATAGTAAATCTTATCTTCC
16968790 CATTACAGTG
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 100 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (46 bp):
AAGATAGTAAATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCG
Found at i:16969010 original size:44 final size:44
Alignment explanation
Indices: 16968826--16969036 Score: 153
Period size: 44 Copynumber: 4.8 Consensus size: 44
16968816 CCATTAGTCT
* * * *
16968826 TATCACCTTAAGCAGTAGTGGAGTAGGTTGAAGGTTGCAGATTC
1 TATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATTC
* * ** *
16968870 TGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAATC
1 TATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATTC
* * * * * * *
16968913 TTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TCC
1 -TATC-ACCCTAA-GCAGTAGTGGAGCAGATTGAAG--ATTGCAGATTC
* * *
16968958 TATCACCCTAAACAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
1 TATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATTC
* *
16969002 TGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGAT
1 TATCACCCTAAGCAGTAGTGGAGCAGATTGAAGAT
16969037 GGTGAATCTT
Statistics
Matches: 124, Mismatches: 33, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
41 3 0.02
43 27 0.22
44 71 0.57
45 20 0.16
46 1 0.01
47 1 0.01
48 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (44 bp):
TATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATTC
Found at i:16969179 original size:132 final size:132
Alignment explanation
Indices: 16968757--16969162 Score: 668
Period size: 132 Copynumber: 3.1 Consensus size: 132
16968747 ATTTGGCAGC
* * * *
16968757 GGAGTAGATCGAAGATGGTAAATCTTATCTTCCCATTACAGTGGAGAAGCGGATTTAAGCCATTA
1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* * *
16968822 GTCTTATCACCTTAAGCAGTAGTGGAGTAGGTTGAAGGTTGCAGATTCTGTCACCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
16968887 GT
131 GT
16968889 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
*
16968954 GTCCTATCACCCTAAACAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
16969019 GT
131 GT
*
16969021 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATATAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* ** * ** *
16969086 GTCCTATCACCCTAAGCAGTAGTGGGGTAGGTCAAAGACTATAGATTCTGTCCCCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
16969151 GT
131 GT
16969153 GGAGCAGATC
1 GGAGCAGATC
16969163 AACAATAACG
Statistics
Matches: 257, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 257 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (132 bp):
GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
GT
Found at i:16978705 original size:44 final size:46
Alignment explanation
Indices: 16978644--16978736 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 46
16978634 TACAACATCT
** * *
16978644 ATTCCATTCAATTAAACACA-AGAA-TATTG-TTACAGCTCTATTCC
1 ATTCCATTCAACCAAACA-ATAGAATTACTGATTACAGATCTATTCC
*
16978688 ATTCCATTCAACCAAACAATTGAATTACTGATTACAGATCTATTCC
1 ATTCCATTCAACCAAACAATAGAATTACTGATTACAGATCTATTCC
16978734 ATT
1 ATT
16978737 ACAACTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 19 0.46
45 4 0.10
46 17 0.41
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAATAGAATTACTGATTACAGATCTATTCC
Found at i:16978739 original size:16 final size:16
Alignment explanation
Indices: 16978726--16978784 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
16978716 TGATTACAGA
16978726 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
*
16978742 TCTATTACATTACAAC
1 TCTATTCCATTACAAC
16978758 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
*
16978774 CCTATTCCATT
1 TCTATTCCATT
16978785 CCCCCCAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.39
Consensus pattern (16 bp):
TCTATTCCATTACAAC
Found at i:16978754 original size:32 final size:32
Alignment explanation
Indices: 16978718--16978784 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
16978708 TGAATTACTG
*
16978718 ATTACAGA-TCTATTCCATTACAACTCTATTAC
1 ATTACA-ACTCTATTCCATTACAACCCTATTAC
*
16978750 ATTACAACTCTATTCCATTACAACCCTATTCC
1 ATTACAACTCTATTCCATTACAACCCTATTAC
16978782 ATT
1 ATT
16978785 CCCCCCAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.33, C:0.28, G:0.01, T:0.37
Consensus pattern (32 bp):
ATTACAACTCTATTCCATTACAACCCTATTAC
Found at i:16982633 original size:29 final size:29
Alignment explanation
Indices: 16982596--16982653 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
16982586 GAAAATATTG
* *
16982596 GAAGAAAAATTCTAGGAGAATTAGAAAAT
1 GAAGAAAAATCCTAGCAGAATTAGAAAAT
* **
16982625 GAAGTAAAATCCTAGCCTAATTAGAAAAT
1 GAAGAAAAATCCTAGCAGAATTAGAAAAT
16982654 TGGTTTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (29 bp):
GAAGAAAAATCCTAGCAGAATTAGAAAAT
Found at i:16985169 original size:37 final size:37
Alignment explanation
Indices: 16985127--16985197 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
16985117 AGTATTACTT
16985127 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
*
16985164 AATAGTTTATTAAATTAAAATAGATTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
16985198 AAAAAATGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:16985175 original size:18 final size:19
Alignment explanation
Indices: 16985127--16985201 Score: 102
Period size: 18 Copynumber: 4.1 Consensus size: 19
16985117 AGTATTACTT
16985127 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
* * *
16985145 AATAGAGTTATTAAATGAG
1 AATAGATTTATTAAATTAA
16985164 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
16985182 AATAGATTTATTAAA-TAA
1 AATAGATTTATTAAATTAA
16985200 AA
1 AA
16985202 AATGAGTTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 25 0.51
19 24 0.49
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (19 bp):
AATAGATTTATTAAATTAA
Found at i:16985352 original size:27 final size:26
Alignment explanation
Indices: 16985275--16985360 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
16985265 TTTTTTTTCC
*
16985275 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCATGGTGCCGCCAATTTA
*
16985300 CTTTGGCACCAATGGTGCCACCAATTTA
1 -TTTGGCACC-ATGGTGCCGCCAATTTA
*
16985328 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-ATGGTGCCGCCAATTTA
*
16985355 ATTGGC
1 TTTGGC
16985361 TGGTGTCAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.17
27 41 0.79
28 2 0.04
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (26 bp):
TTTGGCACCATGGTGCCGCCAATTTA
Found at i:16985428 original size:27 final size:29
Alignment explanation
Indices: 16985394--16985476 Score: 136
Period size: 29 Copynumber: 2.9 Consensus size: 29
16985384 TTTTGTTTTT
16985394 TTTATATATTTTGGTAAATAAAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAAG
16985423 TTTATATATTTTGGTAAAT--AAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAAG
16985450 -TTATAATATTTTGGTAAATAAAAAAAA
1 TTTAT-ATATTTTGGTAAATAAAAAAAA
16985477 TTGTAATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.08
27 22 0.43
29 25 0.49
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (29 bp):
TTTATATATTTTGGTAAATAAAAAAAAAG
Found at i:16985483 original size:27 final size:26
Alignment explanation
Indices: 16985394--16985489 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 26
16985384 TTTTGTTTTT
16985394 TTTATATATTTTGGTAAATAAAAAAAAA
1 TTTA-ATATTTTGGTAAAT-AAAAAAAA
*
16985422 GTTTATATATTTTGGTAAATAAAAAAAG
1 -TTTA-ATATTTTGGTAAATAAAAAAAA
16985450 TTATAATATTTTGGTAAATAAAAAAAA
1 TT-TAATATTTTGGTAAATAAAAAAAA
16985477 TTGTAATATTTTG
1 TT-TAATATTTTG
16985490 ATAATTTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
27 35 0.56
28 9 0.14
29 19 0.30
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (26 bp):
TTTAATATTTTGGTAAATAAAAAAAA
Found at i:16993796 original size:21 final size:21
Alignment explanation
Indices: 16993770--16993809 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16993760 AATCACTTTG
16993770 AAACACTTTTATCTTACAATT
1 AAACACTTTTATCTTACAATT
16993791 AAACACTTTTATCTTACAA
1 AAACACTTTTATCTTACAA
16993810 CATGTGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (21 bp):
AAACACTTTTATCTTACAATT
Found at i:16994391 original size:14 final size:14
Alignment explanation
Indices: 16994372--16994399 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16994362 GAGAAAAACA
16994372 ACCTCCACGACCTC
1 ACCTCCACGACCTC
16994386 ACCTCCACGACCTC
1 ACCTCCACGACCTC
16994400 TTCCATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.57, G:0.07, T:0.14
Consensus pattern (14 bp):
ACCTCCACGACCTC
Found at i:17001667 original size:109 final size:109
Alignment explanation
Indices: 17001509--17001895 Score: 549
Period size: 109 Copynumber: 3.6 Consensus size: 109
17001499 TGGTCAAATC
* * * *
17001509 GAAAAATCGAAACCCAGCGCATTAGGGCACGTTTCCTTAAATTTCCAAACCCAAAATATTATCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
*
17001574 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAATGA
66 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
* *
17001618 GAAAAATCGACACCCAGCGCATTAGGGCACGTTTCCTTAAATTTCCAAACGCAAAATATTATCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
*
17001683 ACTTCGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
66 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
* * * * * * * *
17001727 GAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATGCAAAACACTGTCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
* *
17001792 ATTTTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
66 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
* * * * * * *
17001836 TAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAAAGCTAAATATT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATT
17001896 GCCTCATTTA
Statistics
Matches: 256, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 256 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (109 bp):
GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
Found at i:17002559 original size:3 final size:3
Alignment explanation
Indices: 17002545--17002585 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
17002535 CAAATAAAAC
* *
17002545 TAA TAA TGA TAA TAA TTAA TAA TAA TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA T
17002586 CATGATAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:17002566 original size:16 final size:16
Alignment explanation
Indices: 17002545--17002585 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17002535 CAAATAAAAC
*
17002545 TAATAATGATAATAAT
1 TAATAATAATAATAAT
17002561 TAATAATAATAATAA-
1 TAATAATAATAATAAT
*
17002576 TATTAATAAT
1 TAATAATAAT
17002586 CATGATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TAATAATAATAATAAT
Found at i:17004182 original size:22 final size:23
Alignment explanation
Indices: 17004129--17004184 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
17004119 CCCGTTTTTA
* * *
17004129 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
17004152 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
17004174 ATTAAAATTAA
1 ATTAAAATTAA
17004185 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:17004197 original size:16 final size:16
Alignment explanation
Indices: 17004160--17004199 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
17004150 TTAATAAAAT
* *
17004160 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
17004176 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
17004192 TAAAATTA
1 TAAAATTA
17004200 TCTAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:17004305 original size:9 final size:9
Alignment explanation
Indices: 17004272--17004299 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
17004262 TTTATCAAAT
17004272 TATTAATTG
1 TATTAATTG
17004281 TATTAATTG
1 TATTAATTG
17004290 TATTAATTG
1 TATTAATTG
17004299 T
1 T
17004300 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:17004308 original size:68 final size:68
Alignment explanation
Indices: 17004188--17004397 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
17004178 AAATTAATTG
* *
17004188 TTAGTAAAATTATCTAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
17004251 TGA
66 TGA
17004254 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
17004319 TGA
66 TGA
*
17004322 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
17004387 TGA
66 TGA
*
17004390 TTAATAAA
1 TTAGTAAA
17004398 ACAAACTTGA
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 25 0.18
68 113 0.82
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:17004352 original size:9 final size:9
Alignment explanation
Indices: 17004340--17004367 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
17004330 TTTATCAAAT
17004340 TATTAATTG
1 TATTAATTG
17004349 TATTAATTG
1 TATTAATTG
17004358 TATTAATTG
1 TATTAATTG
17004367 T
1 T
17004368 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:17010410 original size:34 final size:33
Alignment explanation
Indices: 17010341--17010431 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 33
17010331 GACTTGTTGC
* *
17010341 TATGTAAACCCCCATGTTATATAGTATGACGTAG
1 TATGTAAA-CCCCATGTTATGTAGTATCACGTAG
*
17010375 TATGTAAACCCCTATGTTATGTAGTA-CATCTTAG
1 TATGTAAACCCC-ATGTTATGTAGTATCA-CGTAG
* *
17010409 TATATGAACCCACATGTTATGTA
1 TATGTAAACCC-CATGTTATGTA
17010432 CTTTGTGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.10
34 43 0.88
35 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
TATGTAAACCCCATGTTATGTAGTATCACGTAG
Found at i:17010471 original size:15 final size:15
Alignment explanation
Indices: 17010453--17010509 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
17010443 AATATGTTTG
17010453 AACCCTATATGTTCA
1 AACCCTATATGTTCA
* *
17010468 AACCTTGTATGTGT-A
1 AACCCTATATGT-TCA
* *
17010483 AACCCTACATGTACA
1 AACCCTATATGTTCA
*
17010498 AATCCTATATGT
1 AACCCTATATGT
17010510 GTGAACCTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 31 0.97
16 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (15 bp):
AACCCTATATGTTCA
Found at i:17010487 original size:30 final size:30
Alignment explanation
Indices: 17010444--17010524 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
17010434 TTGTGAATTA
* * * *
17010444 ATATGTTTGAACCCTATATGTTCAAA-CCTT
1 ATATGTGTAAACCCTACATGTACAAATCC-T
*
17010474 GTATGTGTAAACCCTACATGTACAAATCCT
1 ATATGTGTAAACCCTACATGTACAAATCCT
* *
17010504 ATATGTGTGAACCTTACATGT
1 ATATGTGTAAACCCTACATGT
17010525 GAGAACCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 40 0.95
31 2 0.05
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (30 bp):
ATATGTGTAAACCCTACATGTACAAATCCT
Found at i:17010603 original size:15 final size:15
Alignment explanation
Indices: 17010563--17010657 Score: 93
Period size: 15 Copynumber: 6.4 Consensus size: 15
17010553 CCCATTACTG
* *
17010563 TATGTGCGAAACCAA
1 TATGTGCGAACCCTA
*
17010578 TATGTGTGAACCCTA
1 TATGTGCGAACCCTA
*
17010593 TATGTGCGAA-CCTG
1 TATGTGCGAACCCTA
* * *
17010607 TATGTGTGAACCATG
1 TATGTGCGAACCCTA
*
17010622 TATGCGCGAACCCTA
1 TATGTGCGAACCCTA
*
17010637 TATGTGTGAACCCTA
1 TATGTGCGAACCCTA
*
17010652 CATGTG
1 TATGTG
17010658 AACCTATAAC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
14 12 0.18
15 53 0.82
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (15 bp):
TATGTGCGAACCCTA
Found at i:17010608 original size:44 final size:44
Alignment explanation
Indices: 17010560--17010648 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
17010550 ATACCCATTA
* *
17010560 CTGTATGTGCGAAACCA-ATATGTGTGAACCCTATATGTGCGAAC
1 CTGTATGTGCG-AACCATATATGCGCGAACCCTATATGTGCGAAC
* * *
17010604 CTGTATGTGTGAACCATGTATGCGCGAACCCTATATGTGTGAAC
1 CTGTATGTGCGAACCATATATGCGCGAACCCTATATGTGCGAAC
17010648 C
1 C
17010649 CTACATGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 5 0.13
44 34 0.87
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (44 bp):
CTGTATGTGCGAACCATATATGCGCGAACCCTATATGTGCGAAC
Found at i:17012863 original size:17 final size:17
Alignment explanation
Indices: 17012843--17012884 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
17012833 TATAAAAGCC
17012843 TATAATATTTTAAAATA
1 TATAATATTTTAAAATA
* * *
17012860 TATAAAAATTTACAATA
1 TATAATATTTTAAAATA
17012877 TATAATAT
1 TATAATAT
17012885 ATAAAAATTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAATATTTTAAAATA
Found at i:17013202 original size:16 final size:18
Alignment explanation
Indices: 17013171--17013203 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
17013161 TAAATATGAG
17013171 CAAACTGTTATCTAGATT
1 CAAACTGTTATCTAGATT
17013189 CAAA-TGTT-TCTAGAT
1 CAAACTGTTATCTAGAT
17013204 AATCATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (18 bp):
CAAACTGTTATCTAGATT
Found at i:17016590 original size:24 final size:24
Alignment explanation
Indices: 17016559--17016712 Score: 114
Period size: 24 Copynumber: 6.3 Consensus size: 24
17016549 AGCCATGTAA
17016559 CGGGAAGCTCGTAAGAGCCATAAT
1 CGGGAAGCTCGTAAGAGCCATAAT
*
17016583 CGGGAAGCTCGTAAAAGCCATAAT
1 CGGGAAGCTCGTAAGAGCCATAAT
* **
17016607 CGGGAAGCTCATGTGAGCCA-ATAT
1 CGGGAAGCTCGTAAGAGCCATA-AT
* * ** * *
17016631 TGAGAAGCTCCAAAGAGCCTTTTAT
1 CGGGAAGCTCGTAAGAGCC-ATAAT
* *
17016656 CGGGAAGCTCCG-GAGAGCCAATTAT
1 CGGGAAGCT-CGTAAGAGCC-ATAAT
* * * *
17016681 CGGGAAGCTCATATGAGCAATAAA
1 CGGGAAGCTCGTAAGAGCCATAAT
17016705 CGGGAAGC
1 CGGGAAGC
17016713 GCAAGAGAGC
Statistics
Matches: 100, Mismatches: 25, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
23 1 0.01
24 66 0.66
25 32 0.32
26 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (24 bp):
CGGGAAGCTCGTAAGAGCCATAAT
Found at i:17020635 original size:21 final size:19
Alignment explanation
Indices: 17020593--17020635 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
17020583 TAAAATGTTA
**
17020593 CTTAAATTATATTAGTTTT
1 CTTAAATTATATTAACTTT
17020612 CTTAAATTGATATTTAACTTT
1 CTTAAATT-ATA-TTAACTTT
17020633 CTT
1 CTT
17020636 TTATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (19 bp):
CTTAAATTATATTAACTTT
Found at i:17021833 original size:7 final size:7
Alignment explanation
Indices: 17021818--17021881 Score: 83
Period size: 7 Copynumber: 8.6 Consensus size: 7
17021808 TAAATTTAAA
*
17021818 TTTATTT
1 TTTAATT
17021825 TTTAATT
1 TTTAATT
17021832 TTTAATT
1 TTTAATT
17021839 TTTAATT
1 TTTAATT
17021846 TTTAATT
1 TTTAATT
17021853 TTTAATAT
1 TTTAAT-T
17021861 AATTTAATT
1 --TTTAATT
17021870 TTTATATT
1 TTTA-ATT
17021878 TTTA
1 TTTA
17021882 TAATGTTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
7 37 0.71
8 8 0.15
9 1 0.02
10 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTAATT
Found at i:17022728 original size:3 final size:3
Alignment explanation
Indices: 17022720--17022750 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17022710 TTTATTCTCT
17022720 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17022751 TGGTTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17025162 original size:25 final size:22
Alignment explanation
Indices: 17025146--17025208 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
17025136 TCTCCGATTA
17025146 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCCGT
* * *
17025168 TTATCACATTCGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCCGT
* **
17025190 ATAGCATTTTAGTGCTCTC
1 TTAGCACATTAGTGCTCTC
17025209 TATTCAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCCGT
Found at i:17025424 original size:16 final size:16
Alignment explanation
Indices: 17025405--17025437 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17025395 GTGTCTAAAT
17025405 ATGTATTAATTGAGTA
1 ATGTATTAATTGAGTA
17025421 ATGTATTAATTGAGTA
1 ATGTATTAATTGAGTA
17025437 A
1 A
17025438 GTTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGTATTAATTGAGTA
Found at i:17033551 original size:25 final size:24
Alignment explanation
Indices: 17033475--17033551 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
17033465 GAACACACGA
* *
17033475 TGGCTCTCACGAGCTTCTCGTTATT
1 TGGCTCTCATGAGCTTCT-GATATT
* * *
17033500 TAGCTCTTATGAGCATTCTAATATT
1 TGGCTCTCATGAGC-TTCTGATATT
17033525 TGGCTCTCATGAGCTTCCTGATATT
1 TGGCTCTCATGAGCTT-CTGATATT
17033550 TG
1 TG
17033552 ACTCGTATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
24 2 0.05
25 36 0.86
26 4 0.10
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (24 bp):
TGGCTCTCATGAGCTTCTGATATT
Found at i:17035340 original size:50 final size:52
Alignment explanation
Indices: 17035197--17035340 Score: 141
Period size: 50 Copynumber: 2.7 Consensus size: 52
17035187 GGTAAAGAGA
* *
17035197 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-CA-TGAG--TATGAAAGG
* * * * *
17035253 TCCCATGTAAGACCATGTTTGGAACGTGGCGTTGGCAC-TGAG-ATGAAAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACATGAGTATGAAAGG
* *
17035303 T-CCACCGTAAGACCATGTCTGGGACATAGCATGGGCAC
1 TCCCA-CGTAAGACCATGTCTGGGACATGGCATTGGCAC
17035341 CGATATAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
49 3 0.04
50 34 0.45
53 4 0.05
55 1 0.01
56 33 0.44
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (52 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACATGAGTATGAAAGG
Found at i:17042473 original size:20 final size:20
Alignment explanation
Indices: 17042435--17042474 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17042425 AGTTCTTTTT
*
17042435 TTTTTTTGCAAGATTTTAGG
1 TTTTTTTGCAAGATATTAGG
* *
17042455 TTTTTTTGCCAGCTATTAGG
1 TTTTTTTGCAAGATATTAGG
17042475 ATTATACAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (20 bp):
TTTTTTTGCAAGATATTAGG
Found at i:17045817 original size:24 final size:25
Alignment explanation
Indices: 17045776--17045823 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
17045766 ATAATAATCT
*
17045776 TAATATTTTATTAAAAAA-ATATAC
1 TAATATTTTAATAAAAAATATATAC
**
17045800 TAATATTTTAATGGAAAATATATA
1 TAATATTTTAATAAAAAATATATA
17045824 TTACAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
TAATATTTTAATAAAAAATATATAC
Found at i:17045817 original size:25 final size:24
Alignment explanation
Indices: 17045776--17045823 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
17045766 ATAATAATCT
*
17045776 TAATATTTTATTAAAAAAATATAC
1 TAATATTTTATGAAAAAAATATAC
* *
17045800 TAATATTTTAATGGAAAATATATA
1 TAATATTTT-ATGAAAAAAATATA
17045824 TTACAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TAATATTTTATGAAAAAAATATAC
Found at i:17046992 original size:17 final size:19
Alignment explanation
Indices: 17046970--17047004 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
17046960 TTATAACACT
17046970 TTCTTT-CAAC-TTTTTTG
1 TTCTTTACAACGTTTTTTG
17046987 TTCTTTACAACGTTTTTT
1 TTCTTTACAACGTTTTTT
17047005 TTTTGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.14, C:0.17, G:0.06, T:0.63
Consensus pattern (19 bp):
TTCTTTACAACGTTTTTTG
Found at i:17047002 original size:18 final size:17
Alignment explanation
Indices: 17046970--17047003 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17046960 TTATAACACT
*
17046970 TTCTTTCAACTTTTTTG
1 TTCTTTCAACGTTTTTG
17046987 TTCTTTACAACGTTTTT
1 TTCTTT-CAACGTTTTT
17047004 TTTTTGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (17 bp):
TTCTTTCAACGTTTTTG
Found at i:17047914 original size:21 final size:21
Alignment explanation
Indices: 17047879--17047919 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17047869 ACCCCAAACC
*
17047879 TCAAGGTTCAAGGTTTAAAGT
1 TCAAGGTTCAAGGTTCAAAGT
**
17047900 TCAAGGTTCGGGGTTCAAAG
1 TCAAGGTTCAAGGTTCAAAG
17047920 CAAAATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (21 bp):
TCAAGGTTCAAGGTTCAAAGT
Found at i:17051164 original size:16 final size:16
Alignment explanation
Indices: 17051139--17051172 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17051129 TCACTTTCTC
*
17051139 AAATATTAATTAAATA
1 AAATAATAATTAAATA
*
17051155 AAATAATAATTTAATA
1 AAATAATAATTAAATA
17051171 AA
1 AA
17051173 GAATGTTAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATAATTAAATA
Found at i:17055700 original size:34 final size:35
Alignment explanation
Indices: 17055656--17055722 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
17055646 CAGTAAAATA
17055656 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* * *
17055690 TTTTCTGTAAAATTATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
17055723 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:17057406 original size:13 final size:13
Alignment explanation
Indices: 17057388--17057434 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
17057378 TTAGAAGGAA
*
17057388 GTTAATGGTATTG
1 GTTAATGGTAATG
17057401 GTTAATGGTAATG
1 GTTAATGGTAATG
17057414 G-TAATGGTAAATG
1 GTTAATGGT-AATG
*
17057427 GTAAATGG
1 GTTAATGG
17057435 GGGTGTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 7 0.23
13 18 0.60
14 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (13 bp):
GTTAATGGTAATG
Found at i:17057414 original size:19 final size:19
Alignment explanation
Indices: 17057390--17057430 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
17057380 AGAAGGAAGT
* *
17057390 TAATGGTATTGGTTAATGG
1 TAATGGTAATGGTAAATGG
17057409 TAATGGTAATGGTAAATGG
1 TAATGGTAATGGTAAATGG
17057428 TAA
1 TAA
17057431 ATGGGGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (19 bp):
TAATGGTAATGGTAAATGG
Found at i:17057434 original size:7 final size:6
Alignment explanation
Indices: 17057390--17057430 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
17057380 AGAAGGAAGT
*
17057390 TAATGG TATTGG TTAATGG TAATGG TAATGG TAAATGG TAA
1 TAATGG TAATGG -TAATGG TAATGG TAATGG T-AATGG TAA
17057431 ATGGGGGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (6 bp):
TAATGG
Found at i:17061896 original size:13 final size:13
Alignment explanation
Indices: 17061878--17061903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17061868 GAGTAGATAC
17061878 ATATATGTTTGGT
1 ATATATGTTTGGT
17061891 ATATATGTTTGGT
1 ATATATGTTTGGT
17061904 GAATACTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
ATATATGTTTGGT
Found at i:17062514 original size:27 final size:27
Alignment explanation
Indices: 17062481--17062577 Score: 122
Period size: 27 Copynumber: 3.6 Consensus size: 27
17062471 ATATAATCAA
17062481 AGTACGCCACAAAGGCAATCCATACAG
1 AGTACGCCACAAAGGCAATCCATACAG
* * * *
17062508 AGCACGCCACAAAGGCTATCTATAGAG
1 AGTACGCCACAAAGGCAATCCATACAG
* * * *
17062535 GGTACGCCACAAAGGCGATTCATTCAG
1 AGTACGCCACAAAGGCAATCCATACAG
17062562 AGTACGCCACAAAGGC
1 AGTACGCCACAAAGGC
17062578 TTACAGGATG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.13
Consensus pattern (27 bp):
AGTACGCCACAAAGGCAATCCATACAG
Found at i:17067454 original size:12 final size:12
Alignment explanation
Indices: 17067423--17067455 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17067413 TATTAATTTA
17067423 ATAATATTTAAT
1 ATAATATTTAAT
17067435 ATAA-ATTTAAT
1 ATAATATTTAAT
*
17067446 CTAATATTTA
1 ATAATATTTA
17067456 TCTTGATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:17069935 original size:17 final size:18
Alignment explanation
Indices: 17069915--17069948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17069905 CATTTTTTTG
17069915 TATAT-ACATTATTTTAC
1 TATATAACATTATTTTAC
*
17069932 TATATAATATTATTTTA
1 TATATAACATTATTTTA
17069949 AGTGTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAACATTATTTTAC
Found at i:17075013 original size:9 final size:9
Alignment explanation
Indices: 17075001--17075043 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 9
17074991 ACTCAAAAGA
17075001 AAAAAAATC
1 AAAAAAATC
17075010 AAAAAAATC
1 AAAAAAATC
17075019 --AAAAATC
1 AAAAAAATC
17075026 --AAAAAT-
1 AAAAAAATC
17075032 AAAAAAATC
1 AAAAAAATC
17075041 AAA
1 AAA
17075044 GTCAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 13 0.42
8 6 0.19
9 12 0.39
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:17075013 original size:15 final size:14
Alignment explanation
Indices: 17074993--17075043 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
17074983 GAGATCAGAC
17074993 TCAAAAGAAAAAAAA
1 TCAAAA-AAAAAAAA
17075008 TCAAAAAAATCAAAAA
1 TCAAAAAAA--AAAAA
17075024 TCAAAAATAAAAAAA
1 TCAAAAA-AAAAAAA
17075039 TCAAA
1 TCAAA
17075044 GTCAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.09
15 16 0.48
16 12 0.36
17 2 0.06
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (14 bp):
TCAAAAAAAAAAAA
Found at i:17075037 original size:21 final size:21
Alignment explanation
Indices: 17075003--17075054 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
17074993 TCAAAAGAAA
17075003 AAAAATCAAAAAAATCAAAAATC
1 AAAAAT-AAAAAAATC-AAAATC
*
17075026 AAAAATAAAAAAATCAAAGTC
1 AAAAATAAAAAAATCAAAATC
17075047 AAAAATAA
1 AAAAATAA
17075055 GAGAAAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 13 0.46
22 9 0.32
23 6 0.21
ACGTcount: A:0.75, C:0.10, G:0.02, T:0.13
Consensus pattern (21 bp):
AAAAATAAAAAAATCAAAATC
Found at i:17075051 original size:15 final size:15
Alignment explanation
Indices: 17075001--17075043 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
17074991 ACTCAAAAGA
17075001 AAAAAAATCAAAAA-
1 AAAAAAATCAAAAAT
17075015 AATCAAAAATCAAAAAT
1 AA--AAAAATCAAAAAT
17075032 AAAAAAATCAAA
1 AAAAAAATCAAA
17075044 GTCAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.08
15 10 0.38
16 12 0.46
17 2 0.08
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAATCAAAAAT
Found at i:17075073 original size:7 final size:6
Alignment explanation
Indices: 17075056--17075093 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
17075046 CAAAAATAAG
17075056 AGAAAA AGAAAGA AGAAAAA AGAAAA AG-AAA AGAAAA A
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA A
17075094 TAGAGAGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 15 0.52
7 6 0.21
8 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:17075074 original size:13 final size:12
Alignment explanation
Indices: 17075056--17075093 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
17075046 CAAAAATAAG
17075056 AGAAAAAGAAAGA
1 AGAAAAAGAAA-A
17075069 AGAAAAAAGAAAA
1 AG-AAAAAGAAAA
17075082 AG-AAAAGAAAA
1 AGAAAAAGAAAA
17075093 A
1 A
17075094 TAGAGAGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.42
13 5 0.21
14 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAAA
Found at i:17077224 original size:48 final size:48
Alignment explanation
Indices: 17077160--17077311 Score: 153
Period size: 48 Copynumber: 3.1 Consensus size: 48
17077150 AAGAATCTTA
* *
17077160 CTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCG
1 CTTCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCG
* ** * * * * ** *
17077208 CTTCCCCGAC-ATTGCAGTTAAAAAGGTTAAAGCTACAACAACGAATCTCA
1 CTTCCCAGACGA-TGCAGTGGAACAGATTAAAGCCACATCAGTGAA--TCG
*
17077258 CTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCG
1 CTTCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCG
17077306 CTTCCC
1 CTTCCC
17077312 TTACACTGTA
Statistics
Matches: 77, Mismatches: 23, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
47 1 0.01
48 40 0.52
50 35 0.45
51 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (48 bp):
CTTCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCG
Found at i:17077325 original size:98 final size:98
Alignment explanation
Indices: 17077152--17077494 Score: 497
Period size: 98 Copynumber: 3.5 Consensus size: 98
17077142 GTGAAATCAA
* *
17077152 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCGA
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCGCTTCCCCAA
17077217 CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
66 CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
* **
17077250 GAATCTCACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCGCTTCCCTTA
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCGCTTCCCCAA
* * *
17077315 CACTGTAGTTAAAAAGGTTAAAGCTACAACAGC
66 CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
* * * * * **
17077348 AAATCTTACTTCCCTGGCGGTGCAATGGAACAGATTAAAGCCATATCAACGAATCTTGCTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATC--GCTTCCCC
**
17077413 AACATTGCAGTTAAAATCGTTAAAGCTACAACAAC
64 AACATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
* *
17077448 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATC
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATC
17077495 GTGGAACAAA
Statistics
Matches: 218, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
98 138 0.63
100 80 0.37
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (98 bp):
GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCGCTTCCCCAA
CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
Found at i:17077337 original size:48 final size:47
Alignment explanation
Indices: 17077186--17077338 Score: 126
Period size: 48 Copynumber: 3.1 Consensus size: 47
17077176 GTGGAACAGA
* *
17077186 TTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAAAGG
1 TTAAAGCCACATCAGTGAATCGCTTCCCAGACA-TGCAGTTAAAAAGG
* * ** * * ** * *
17077234 TTAAAGCTACAACAACGAATCTCACTTCCCAGGCGATGCAGTGGAACAGA
1 TTAAAGCCACATCAGTGAA--TCGCTTCCCAGAC-ATGCAGTTAAAAAGG
** *
17077284 TTAAAGCCACATCAGTGAATCGCTTCCCTTACACTGTAGTTAAAAAGG
1 TTAAAGCCACATCAGTGAATCGCTTCCCAGACA-TGCAGTTAAAAAGG
17077332 TTAAAGC
1 TTAAAGC
17077339 TACAACAGCA
Statistics
Matches: 76, Mismatches: 25, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
47 1 0.01
48 39 0.51
50 35 0.46
51 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (47 bp):
TTAAAGCCACATCAGTGAATCGCTTCCCAGACATGCAGTTAAAAAGG
Found at i:17077486 original size:50 final size:50
Alignment explanation
Indices: 17077152--17077492 Score: 205
Period size: 50 Copynumber: 6.9 Consensus size: 50
17077142 GTGAAATCAA
* * ***
17077152 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAAC
* * * ** * * *
17077202 GAATC--GCTTCCCCGAC-ATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
1 GAATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTAAAGCCACAACAAC
* * * **
17077250 GAATCTCACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGT
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAAC
* ** * ** * * * *
17077300 GAATC--GCTTCCCTTAC-ACTGTAGTTAAAAAGGTTAAAGCTACAACAGC
1 GAATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTAAAGCCACAACAAC
* * * * *
17077348 AAATCTTACTTCCCTGGCGGTGCAATGGAACAGATTAAAGCCATATCAAC
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAAC
* *** * * *
17077398 GAATCTTGCTTCCCCAAC-ATTGCAGT-TAAAATCG-TTAAAGCTACAACAAC
1 GAATCTTACTTCCCTGGCGA-TGCAGTGGAACA--GATTAAAGCCACAACAAC
*
17077448 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACA
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACA
17077493 TCGTGGAACA
Statistics
Matches: 207, Mismatches: 70, Indels: 28
0.68 0.23 0.09
Matches are distributed among these distances:
47 2 0.01
48 67 0.32
49 4 0.02
50 129 0.62
51 5 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (50 bp):
GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAAC
Found at i:17077502 original size:23 final size:23
Alignment explanation
Indices: 17077472--17077518 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
17077462 TGGCGGTGCA
*
17077472 GTGGAACAGATTAAAGCCACATC
1 GTGGAACAAATTAAAGCCACATC
17077495 GTGGAACAAATTAAAGCCACATC
1 GTGGAACAAATTAAAGCCACATC
17077518 G
1 G
17077519 GTGAATCGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (23 bp):
GTGGAACAAATTAAAGCCACATC
Found at i:17077571 original size:48 final size:47
Alignment explanation
Indices: 17077504--17077671 Score: 140
Period size: 48 Copynumber: 3.5 Consensus size: 47
17077494 CGTGGAACAA
*
17077504 ATTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAAAG
1 ATTAAAGCCACAACGGTGAATCGCTTCCCCGACA-TGCAGTTAAAAAG
* * * * ** *
17077552 ATTAAAGCTACAACTGTGAATC-TTACTCCCCAGGCGATGCAGTGGAACAG
1 ATTAAAGCCACAACGGTGAATCGCT--TCCCC-GAC-ATGCAGTTAAAAAG
* * * * *
17077602 ATTAAAGCCACATCGGTAAATCGCTTCTCTGACACTGCAATTAAAAAG
1 ATTAAAGCCACAACGGTGAATCGCTTCCCCGACA-TGCAGTTAAAAAG
* *
17077650 ATTAAAGCTACAACAGTGAATC
1 ATTAAAGCCACAACGGTGAATC
17077672 TTACTTCTCA
Statistics
Matches: 90, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
47 2 0.02
48 48 0.53
49 8 0.09
50 30 0.33
51 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (47 bp):
ATTAAAGCCACAACGGTGAATCGCTTCCCCGACATGCAGTTAAAAAG
Found at i:17077593 original size:121 final size:122
Alignment explanation
Indices: 17077373--17077616 Score: 339
Period size: 121 Copynumber: 2.0 Consensus size: 122
17077363 GGCGGTGCAA
* * *
17077373 TGGAACAGATTAAAGCCATATCAACGAATCTTGCTTCCCCAACATTGCAGTTAAAATCGTTAAAG
1 TGGAACAAATTAAAGCCACATCAACGAATC-TGCTTCCCCAACATTGCAGTTAAAATAGTTAAAG
* * *
17077438 CTACAACAACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCG
65 CTACAACAACGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
*** *
17077496 TGGAACAAATTAAAGCCACATCGGTGAATC-GCTTCCCCGACATTGCAGTTAAAA-AGATTAAAG
1 TGGAACAAATTAAAGCCACATCAACGAATCTGCTTCCCCAACATTGCAGTTAAAATAG-TTAAAG
***
17077559 CTACAACTGTGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
65 CTACAACAACGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
17077617 GTAAATCGCT
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
120 1 0.01
121 81 0.76
123 25 0.23
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (122 bp):
TGGAACAAATTAAAGCCACATCAACGAATCTGCTTCCCCAACATTGCAGTTAAAATAGTTAAAGC
TACAACAACGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
Found at i:17077607 original size:50 final size:50
Alignment explanation
Indices: 17077550--17077723 Score: 165
Period size: 50 Copynumber: 3.5 Consensus size: 50
17077540 GCAGTTAAAA
* *
17077550 AGATTAAAGCTACAACTGTGAATCTTACTCCCCAGGCGATGCAGTGGAAC
1 AGATTAAAGCTACAACTGTGAATCTTACTTCTCAGGCGATGCAGTGGAAC
* * * * * * * * ** *
17077600 AGATTAAAGCCACATCGGTAAATC--GCTTCTCTGAC-ACTGCAATTAAAA
1 AGATTAAAGCTACAACTGTGAATCTTACTTCTCAGGCGA-TGCAGTGGAAC
* * *
17077648 AGATTAAAGCTACAACAGTGAATCTTACTTCTCAGGCGGTGTAGTGGAAC
1 AGATTAAAGCTACAACTGTGAATCTTACTTCTCAGGCGATGCAGTGGAAC
*
17077698 AGATTGAAGCTACAACTGTGAATCTT
1 AGATTAAAGCTACAACTGTGAATCTT
17077724 GCTTTGTCGA
Statistics
Matches: 92, Mismatches: 28, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
47 1 0.01
48 33 0.36
50 58 0.63
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (50 bp):
AGATTAAAGCTACAACTGTGAATCTTACTTCTCAGGCGATGCAGTGGAAC
Found at i:17077669 original size:98 final size:98
Alignment explanation
Indices: 17077495--17077707 Score: 318
Period size: 98 Copynumber: 2.2 Consensus size: 98
17077485 AAGCCACATC
* * * *
17077495 GTGGAACAAATTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
1 GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACACTGCAATTAAAAAGATTAAAGC
*
17077560 TACAACTGTGAATCTTACTCCCCAGGCGATGCA
66 TACAACAGTGAATCTTACTCCCCAGGCGATGCA
* *
17077593 GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCTCTGACACTGCAATTAAAAAGATTAAAGC
1 GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACACTGCAATTAAAAAGATTAAAGC
* * * *
17077658 TACAACAGTGAATCTTACTTCTCAGGCGGTGTA
66 TACAACAGTGAATCTTACTCCCCAGGCGATGCA
*
17077691 GTGGAACAGATTGAAGC
1 GTGGAACAGATTAAAGC
17077708 TACAACTGTG
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 103 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (98 bp):
GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACACTGCAATTAAAAAGATTAAAGC
TACAACAGTGAATCTTACTCCCCAGGCGATGCA
Found at i:17078158 original size:23 final size:23
Alignment explanation
Indices: 17078113--17078160 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
17078103 AATAAAATAC
*
17078113 CCTAACCCGAAATACTAACTAAA
1 CCTAACCCGAAATACCAACTAAA
* * *
17078136 CCTAACCCGAATTACCCATTAAA
1 CCTAACCCGAAATACCAACTAAA
17078159 CC
1 CC
17078161 CTAGCCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.19
Consensus pattern (23 bp):
CCTAACCCGAAATACCAACTAAA
Found at i:17079421 original size:17 final size:18
Alignment explanation
Indices: 17079401--17079434 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17079391 ACATTTTTTG
17079401 TATAT-ACATTATTTTAC
1 TATATAACATTATTTTAC
*
17079418 TATATAATATTATTTTA
1 TATATAACATTATTTTA
17079435 AGTGTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAACATTATTTTAC
Done.