Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 44 of 54
Found at i:17527850 original size:27 final size:28
Alignment explanation
Indices: 17527793--17527850 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17527783 NNNNNNNNNT
*
17527793 CCTGGTGGTGGAAAATTACAATTTTGCC
1 CCTGGTGGTGGAAAATTACAATTTTGAC
*
17527821 CCTGG-GGTGGCAAAATTACCATTTT-AC
1 CCTGGTGGTGG-AAAATTACAATTTTGAC
17527848 CCT
1 CCT
17527851 TTTACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTGAC
Found at i:17527921 original size:20 final size:20
Alignment explanation
Indices: 17527904--17527941 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17527894 CCTCAAATCT
*
17527904 TACTCCAATGAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
17527924 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
17527942 GAAGCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:17530522 original size:68 final size:69
Alignment explanation
Indices: 17530440--17530599 Score: 198
Period size: 68 Copynumber: 2.3 Consensus size: 69
17530430 TATAACATCA
* * ** * * *
17530440 ATCATACATGCTTAATCATCTCATGTAG-TATATGGAATCTACATCAAACACACATTCTCATGGC
1 ATCATGCATACTTAATCATCTCATAAAGATATAAGGAATCTACATCAAACACACAATCCCATGGC
17530504 ATTC
66 ATTC
* * * * *
17530508 ATCATGCATACTTAATCACCTC-TAAAGATATAAGGAATTTGCATCATATACACAATCCCATGGC
1 ATCATGCATACTTAATCATCTCATAAAGATATAAGGAATCTACATCAAACACACAATCCCATGGC
17530572 ATTC
66 ATTC
17530576 ATCATGCATACTTAATCATCTCAT
1 ATCATGCATACTTAATCATCTCAT
17530600 TTGGTGTATG
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
67 3 0.04
68 73 0.95
69 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (69 bp):
ATCATGCATACTTAATCATCTCATAAAGATATAAGGAATCTACATCAAACACACAATCCCATGGC
ATTC
Found at i:17530625 original size:68 final size:67
Alignment explanation
Indices: 17530440--17530648 Score: 197
Period size: 68 Copynumber: 3.1 Consensus size: 67
17530430 TATAACATCA
* * * * * * * *
17530440 ATCATACATGCTTAATCATCTCATGTAGTATATGGAATCTACATCAA-ACACACATTCTCATGGC
1 ATCATGCATACTTAATCATCTCATATGGTATATGG-ATTTACAT-AATATACACAATCCCATGGC
17530504 ATTC
64 ATTC
* * * * * *
17530508 ATCATGCATACTTAATCACCTC-TAAAGATATAAGGAATTTGCATCATATACACAATCCCATGGC
1 ATCATGCATACTTAATCATCTCAT-ATGGTATATGG-ATTTACATAATATACACAATCCCATGGC
17530572 ATTC
64 ATTC
* * *
17530576 ATCATGCATACTTAATCATCTCATTTGGTGTATGGATTGTACATAATATACACAATCCTATGGCA
1 ATCATGCATACTTAATCATCTCATATGGTATATGGATT-TACATAATATACACAATCCCATGGCA
*
17530641 TTT
65 TTC
17530644 ATCAT
1 ATCAT
17530649 ACCAAACATG
Statistics
Matches: 113, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
67 5 0.04
68 107 0.95
69 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (67 bp):
ATCATGCATACTTAATCATCTCATATGGTATATGGATTTACATAATATACACAATCCCATGGCAT
TC
Found at i:17531033 original size:21 final size:21
Alignment explanation
Indices: 17531009--17531054 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
17530999 GTGTATCCAT
*
17531009 TCACCTTGATCGAAGACTCAA
1 TCACCTTGATCAAAGACTCAA
*
17531030 TCACCTTGATTAAAGACTCAA
1 TCACCTTGATCAAAGACTCAA
17531051 TCAC
1 TCAC
17531055 AACATTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (21 bp):
TCACCTTGATCAAAGACTCAA
Found at i:17552738 original size:30 final size:30
Alignment explanation
Indices: 17552702--17552761 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17552692 GTGTATCATT
*
17552702 ATTCTTTTTGCATAAGATTTTATGAGGTGA
1 ATTCTTTTCGCATAAGATTTTATGAGGTGA
17552732 ATTCTTTTCGCATAAGATTTTATGAGGTGA
1 ATTCTTTTCGCATAAGATTTTATGAGGTGA
17552762 GTAAAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (30 bp):
ATTCTTTTCGCATAAGATTTTATGAGGTGA
Found at i:17555284 original size:26 final size:26
Alignment explanation
Indices: 17555254--17555314 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
17555244 AACATTGTTC
*
17555254 TGTATCATGTCCATA-TTATTCTTTGT
1 TGTATCATGTACATATTTATTCTTT-T
* *
17555280 TGTATCATTTACATATTTTTTTCTTTT
1 TGTATCATGTACATA-TTTATTCTTTT
17555307 TGTATCAT
1 TGTATCAT
17555315 TTAACAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 13 0.43
27 9 0.30
28 8 0.27
ACGTcount: A:0.20, C:0.13, G:0.08, T:0.59
Consensus pattern (26 bp):
TGTATCATGTACATATTTATTCTTTT
Found at i:17555656 original size:23 final size:23
Alignment explanation
Indices: 17555616--17555680 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
17555606 TGAGTTTTTG
* * *
17555616 ATATGGAATCATGCGACTACTAA
1 ATATAGAATCACGTGACTACTAA
* * * *
17555639 ATTTTGAATCACGTGACTAGTTA
1 ATATAGAATCACGTGACTACTAA
*
17555662 ATATAGAATCGCGTGACTA
1 ATATAGAATCACGTGACTA
17555681 ATCGATTTGG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (23 bp):
ATATAGAATCACGTGACTACTAA
Found at i:17555791 original size:46 final size:46
Alignment explanation
Indices: 17555745--17556018 Score: 140
Period size: 46 Copynumber: 6.0 Consensus size: 46
17555735 ATTGACTCGT
*
17555745 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGT
1 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGC
* * * * *** * * * *
17555791 GTGACTAGTTATTATGGAATCATGTGACTAATTGA-TATTGAGTCGC
1 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTT-ATTATGGAATCGC
* * *
17555837 ATGAGTAGTATATATGGAGTGGCGTTACTAGTTATTATGGAATGGC
1 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGC
* * * ** * * * * ** * *
17555883 GTGAGTATTTATTATAAAATCGCGTGAGTAGGAAATATGGAGTCGC
1 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGC
* * * * * * *
17555929 GTGACTAGTTATTATGGAATTGCGATACTAGTTGA-TA-GTGAGTCGC
1 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTT-ATTATG-GAATCGC
* * * * *
17555975 GTGAGTAATATATATGGAGTGGCGTTACCACTTATTATAGAATC
1 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATC
17556019 ACATGACTAG
Statistics
Matches: 158, Mismatches: 64, Indels: 12
0.68 0.27 0.05
Matches are distributed among these distances:
45 3 0.02
46 153 0.97
47 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.34
Consensus pattern (46 bp):
GTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGC
Found at i:17555797 original size:23 final size:23
Alignment explanation
Indices: 17555715--17555961 Score: 142
Period size: 23 Copynumber: 10.7 Consensus size: 23
17555705 TTAAGATTTA
* *
17555715 GAATCGCGTGAGTAGTTGA-TATT
1 GAATCGCGTGACTAGTT-ATTATG
* * * * *
17555738 GACTCGTGTGAGTAGTAAATATG
1 GAATCGCGTGACTAGTTATTATG
* * *
17555761 GAGTGGCGTTACTAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
*
17555784 GAATCGTGTGACTAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
** * *
17555807 GAATCATGTGACTAATTGA-TATT
1 GAATCGCGTGACTAGTT-ATTATG
* * *
17555830 GAGTCGCATGAGTAG-TATATATG
1 GAATCGCGTGACTAGTTAT-TATG
* * *
17555853 GAGTGGCGTTACTAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
* * * *
17555876 GAATGGCGTGAGTATTTATTATA
1 GAATCGCGTGACTAGTTATTATG
* * ** *
17555899 AAATCGCGTGAGTAGGAAATATG
1 GAATCGCGTGACTAGTTATTATG
*
17555922 GAGTCGCGTGACTAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
*
17555945 GAATTGCGAT-ACTAGTT
1 GAATCGCG-TGACTAGTT
17555962 GATAGTGAGT
Statistics
Matches: 169, Mismatches: 49, Indels: 12
0.73 0.21 0.05
Matches are distributed among these distances:
21 1 0.01
22 2 0.01
23 161 0.95
24 5 0.03
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (23 bp):
GAATCGCGTGACTAGTTATTATG
Found at i:17555842 original size:92 final size:92
Alignment explanation
Indices: 17555730--17555897 Score: 264
Period size: 92 Copynumber: 1.8 Consensus size: 92
17555720 GCGTGAGTAG
** *
17555730 TTGATATTGACTCGTGTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGTGTGA
1 TTGATATTGACTCGCATGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGCGTGA
17555795 CTAGTTATTATGGAATCATGTGACTAA
66 CTAGTTATTATGGAATCATGTGACTAA
* * *
17555822 TTGATATTGAGTCGCATGAGTAGTATATATGGAGTGGCGTTACTAGTTATTATGGAATGGCGTGA
1 TTGATATTGACTCGCATGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGCGTGA
* *
17555887 GTATTTATTAT
66 CTAGTTATTAT
17555898 AAAATCGCGT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 68 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (92 bp):
TTGATATTGACTCGCATGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGCGTGA
CTAGTTATTATGGAATCATGTGACTAA
Found at i:17555875 original size:69 final size:69
Alignment explanation
Indices: 17555794--17556035 Score: 245
Period size: 69 Copynumber: 3.5 Consensus size: 69
17555784 GAATCGTGTG
* *
17555794 ACTAGTTATTATGGAATCATGTGACTAATTGATATTGAGTCGCATGAGTAGTATATATGGAGTGG
1 ACTAGTTATTATGGAATCACGTGACTAATTGATATTGAGTCGCGTGAGTAGTATATATGGAGTGG
17555859 CGTT
66 CGTT
** * * ** * * * *
17555863 ACTAGTTATTATGGAATGGCGTGAGT-ATTTATTATAAAATCGCGTGAGTAGGAAATATGGAGTC
1 ACTAGTTATTATGGAATCACGTGACTAATTGA-TATTGAGTCGCGTGAGTAGTATATATGGAGTG
*
17555927 GCGTG
65 GCGTT
** * * *
17555932 ACTAGTTATTATGGAATTGCGAT-ACTAGTTGATAGTGAGTCGCGTGAGTAATATATATGGAGTG
1 ACTAGTTATTATGGAATCACG-TGACTAATTGATATTGAGTCGCGTGAGTAGTATATATGGAGTG
17555996 GCGTT
65 GCGTT
* * * * *
17556001 ACCACTTATTATAGAATCACATGACTAGTTGATAT
1 ACTAGTTATTATGGAATCACGTGACTAATTGATAT
17556036 GGAATCACAT
Statistics
Matches: 136, Mismatches: 33, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
68 5 0.04
69 127 0.93
70 4 0.03
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (69 bp):
ACTAGTTATTATGGAATCACGTGACTAATTGATATTGAGTCGCGTGAGTAGTATATATGGAGTGG
CGTT
Found at i:17555926 original size:92 final size:92
Alignment explanation
Indices: 17555746--17555961 Score: 236
Period size: 92 Copynumber: 2.3 Consensus size: 92
17555736 TTGACTCGTG
* * **
17555746 TGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGTGTGACTAGTTATTATGGAAT
1 TGAGTAGTATATATGGAGTGGCGTTACTAGTTATTATGGAATCGCGTGACTAGTTATTATAAAAT
* *** *
17555811 CATGTGACTAATTGATATTGAGTCGCA
66 CACGTGACTAAGAAATATGGAGTCGCA
* * *
17555838 TGAGTAGTATATATGGAGTGGCGTTACTAGTTATTATGGAATGGCGTGAGTATTTATTATAAAAT
1 TGAGTAGTATATATGGAGTGGCGTTACTAGTTATTATGGAATCGCGTGACTAGTTATTATAAAAT
* * * *
17555903 CGCGTGAGTAGGAAATATGGAGTCGCG
66 CACGTGACTAAGAAATATGGAGTCGCA
* * * *
17555930 TGACTAGT-TATTATGGAATTGCGATACTAGTT
1 TGAGTAGTATA-TATGGAGTGGCGTTACTAGTT
17555962 GATAGTGAGT
Statistics
Matches: 103, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
91 2 0.02
92 101 0.98
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (92 bp):
TGAGTAGTATATATGGAGTGGCGTTACTAGTTATTATGGAATCGCGTGACTAGTTATTATAAAAT
CACGTGACTAAGAAATATGGAGTCGCA
Found at i:17561876 original size:37 final size:37
Alignment explanation
Indices: 17561814--17561886 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
17561804 GGAGTGCACA
*
17561814 TGAGTTGATCATGACCCAGCCATGTGCAGTGTAGGAG
1 TGAGCTGATCATGACCCAGCCATGTGCAGTGTAGGAG
* ** *
17561851 TGAGCTGATGATGACCCAGGTATGTGCGGTGTAGGA
1 TGAGCTGATCATGACCCAGCCATGTGCAGTGTAGGA
17561887 TTGCACATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.25
Consensus pattern (37 bp):
TGAGCTGATCATGACCCAGCCATGTGCAGTGTAGGAG
Found at i:17566139 original size:43 final size:43
Alignment explanation
Indices: 17566078--17566180 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
17566068 GGCGATGTGT
* * * * ***
17566078 GAGTAGGGAATGCGCATAAGCCGAGGATGACCTAGTTATATGC
1 GAGTAGGGAGTGCGCATAACCCAAGGATGACCCAACCATATGC
* *
17566121 GAGTAGGGAGTGCGCATAACCCAATGATGACCCAACCATGTGC
1 GAGTAGGGAGTGCGCATAACCCAAGGATGACCCAACCATATGC
17566164 GAGTAGGGAGTGCGCAT
1 GAGTAGGGAGTGCGCAT
17566181 GAGCTGGTGA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.33, T:0.18
Consensus pattern (43 bp):
GAGTAGGGAGTGCGCATAACCCAAGGATGACCCAACCATATGC
Found at i:17566445 original size:21 final size:21
Alignment explanation
Indices: 17566420--17566479 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
17566410 GGTGCCCTAT
17566420 TTTTCGCTACAGCGAGAATCA
1 TTTTCGCTACAGCGAGAATCA
17566441 TTTTCGCTACAGCGAGAATCA
1 TTTTCGCTACAGCGAGAATCA
17566462 TTTTCGCTACAGCGAGAA
1 TTTTCGCTACAGCGAGAA
17566480 ACTCTCGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
TTTTCGCTACAGCGAGAATCA
Found at i:17566658 original size:60 final size:59
Alignment explanation
Indices: 17566564--17566714 Score: 185
Period size: 60 Copynumber: 2.5 Consensus size: 59
17566554 ACACTGTAGC
* * * **
17566564 TTCTCGCTGCAGGGAGAAACTTTTTGCTTTTGGGTTGCAATTTTGCTGCAGCAAAATTCA
1 TTCTCGCTGCAGCGAGAAACTTTCTG-TTTTGGGTTACAATTTCACTGCAGCAAAATTCA
* ** *
17566624 TTCTCGCTGCAACGAGAAACTTTCTGTTTCTGGGTTACAATTTCACTGCAGTGAGATTCA
1 TTCTCGCTGCAGCGAGAAACTTTCTGTTT-TGGGTTACAATTTCACTGCAGCAAAATTCA
* *
17566684 ATCTCGCTGCAGCGAAAAACTTTCTGTTTTG
1 TTCTCGCTGCAGCGAGAAACTTTCTGTTTTG
17566715 TCTCCTATCT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 5 0.06
60 73 0.94
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (59 bp):
TTCTCGCTGCAGCGAGAAACTTTCTGTTTTGGGTTACAATTTCACTGCAGCAAAATTCA
Found at i:17572409 original size:191 final size:191
Alignment explanation
Indices: 17572085--17572466 Score: 748
Period size: 191 Copynumber: 2.0 Consensus size: 191
17572075 ACTAGACCTA
17572085 TATCCATACCCCCATATAGAATGGCACCGACAGAGCTTAAAGAGCTTAAGGATTAATTAGAGGAT
1 TATCCATACCCCCATATAGAATGGCACCGACAGAGCTTAAAGAGCTTAAGGATTAATTAGAGGAT
17572150 TTGTTGGATAAAGGCTTCATCTGTCCTAGTGTATCCCCATGGGGAGCACCGGTGTTATTTGCAAA
66 TTGTTGGATAAAGGCTTCATCTGTCCTAGTGTATCCCCATGGGGAGCACCGGTGTTATTTGCAAA
17572215 GAAGAAGGATGGGTCACTTAGGCTGTGCATTGATTATCGACAGCTTAAT-AAGTGACGGTG
131 GAAGAAGGATGGGTCACTTAGGCTGTGCATTGATTATCGACAGCTTAATAAAGTGACGGTG
17572275 NTATCCATACCCCCATATAGAATGGCACCGACAGAGCTTAAAGAGCTTAAGGATTAATTAGAGGA
1 -TATCCATACCCCCATATAGAATGGCACCGACAGAGCTTAAAGAGCTTAAGGATTAATTAGAGGA
17572340 TTTGTTGGATAAAGGCTTCATCTGTCCTAGTGTATCCCCATGGGGAGCACCGGTGTTATTTGCAA
65 TTTGTTGGATAAAGGCTTCATCTGTCCTAGTGTATCCCCATGGGGAGCACCGGTGTTATTTGCAA
17572405 AGAAGAAGGATGGGTCACTTAGGCTGTGCATTGATTATCGACAGCTTAATAAAGTGACGGTG
130 AGAAGAAGGATGGGTCACTTAGGCTGTGCATTGATTATCGACAGCTTAATAAAGTGACGGTG
17572467 AAGAATAAGT
Statistics
Matches: 190, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
191 179 0.94
192 11 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (191 bp):
TATCCATACCCCCATATAGAATGGCACCGACAGAGCTTAAAGAGCTTAAGGATTAATTAGAGGAT
TTGTTGGATAAAGGCTTCATCTGTCCTAGTGTATCCCCATGGGGAGCACCGGTGTTATTTGCAAA
GAAGAAGGATGGGTCACTTAGGCTGTGCATTGATTATCGACAGCTTAATAAAGTGACGGTG
Found at i:17576175 original size:9 final size:9
Alignment explanation
Indices: 17576161--17576190 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
17576151 TCTAGTTTCC
17576161 CTTTGTTTT
1 CTTTGTTTT
17576170 CTTTGTTTT
1 CTTTGTTTT
17576179 CTTTGTTTT
1 CTTTGTTTT
17576188 CTT
1 CTT
17576191 CCTTTCCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (9 bp):
CTTTGTTTT
Found at i:17576367 original size:21 final size:22
Alignment explanation
Indices: 17576327--17576367 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17576317 CCATTGGTCC
*
17576327 GTTTTTAAAATTTCATCCATTT
1 GTTTTCAAAATTTCATCCATTT
*
17576349 GTTTTCAAATTTTCA-CCAT
1 GTTTTCAAAATTTCATCCAT
17576368 ACAGTTGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (22 bp):
GTTTTCAAAATTTCATCCATTT
Found at i:17583800 original size:21 final size:21
Alignment explanation
Indices: 17583776--17583817 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17583766 CACATTTAAC
17583776 CATTTT-TCATCATTTTCTCTT
1 CATTTTCTCATCA-TTTCTCTT
*
17583797 CATTTTCTCTTCATTTCTCTT
1 CATTTTCTCATCATTTCTCTT
17583818 AGAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (21 bp):
CATTTTCTCATCATTTCTCTT
Found at i:17583815 original size:10 final size:11
Alignment explanation
Indices: 17583776--17583817 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
17583766 CACATTTAAC
*
17583776 CATTTT-TCAT
1 CATTTTCTCTT
17583786 CATTTTCTCTT
1 CATTTTCTCTT
17583797 CATTTTCTCTT
1 CATTTTCTCTT
17583808 CA-TTTCTCTT
1 CATTTTCTCTT
17583818 AGAATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 14 0.47
11 16 0.53
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (11 bp):
CATTTTCTCTT
Found at i:17587494 original size:43 final size:43
Alignment explanation
Indices: 17587446--17587688 Score: 318
Period size: 43 Copynumber: 5.8 Consensus size: 43
17587436 TGTGATAATT
17587446 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
* * * *
17587489 ATGACCTAGCTTTGTGCGGTGTAGGAGTGAACATGAGCTAATG
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
* * * *
17587532 ATGACCCAGTTGTGTGTGGTGTA--A--G-A-GTGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
*
17587569 ATGACCCAGCTATGTGTGGTGTAGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
* *
17587612 ATGACCCAGCTATGTGCGGTATAGGAGTGCACATGAGTTGATG
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
* * *
17587655 ATGACCTAGCTATGTGCAGTGTGGGAGTGCACAT
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACAT
17587689 AAGTTGAGAG
Statistics
Matches: 174, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
37 30 0.17
38 1 0.01
39 2 0.01
41 2 0.01
42 1 0.01
43 138 0.79
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (43 bp):
ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
Found at i:17587563 original size:37 final size:37
Alignment explanation
Indices: 17587522--17587597 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
17587512 GGAGTGAACA
* *
17587522 TGAGCTAATGATGACCCAGTTGTGTGTGGTGTAAGAG
1 TGAGCTAATGATGACCCAGCTATGTGTGGTGTAAGAG
* *
17587559 TGAGCTGATGATGACCCAGCTATGTGTGGTGTAGGAG
1 TGAGCTAATGATGACCCAGCTATGTGTGGTGTAAGAG
17587596 TG
1 TG
17587598 CACATGAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.29
Consensus pattern (37 bp):
TGAGCTAATGATGACCCAGCTATGTGTGGTGTAAGAG
Found at i:17587640 original size:80 final size:80
Alignment explanation
Indices: 17587441--17587640 Score: 247
Period size: 80 Copynumber: 2.4 Consensus size: 80
17587431 TATTGTGTGA
* * *
17587441 TAATTATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATGATGACCTAGCTTTGTGC
1 TAATGATGACCCAGCTATGTGCGGTGTAGGA--G----TGAGCTGATGATGACCCAGCTATGTGC
17587506 GGTGTAGGAGTGAACATGAGC
60 GGTGTAGGAGTGAACATGAGC
* * * * *
17587527 TAATGATGACCCAGTTGTGTGTGGTGTAAGAGTGAGCTGATGATGACCCAGCTATGTGTGGTGTA
1 TAATGATGACCCAGCTATGTGCGGTGTAGGAGTGAGCTGATGATGACCCAGCTATGTGCGGTGTA
*
17587592 GGAGTGCACATGAGC
66 GGAGTGAACATGAGC
* *
17587607 TGATGATGACCCAGCTATGTGCGGTATAGGAGTG
1 TAATGATGACCCAGCTATGTGCGGTGTAGGAGTG
17587641 CACATGAGTT
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
80 72 0.73
84 1 0.01
86 26 0.26
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (80 bp):
TAATGATGACCCAGCTATGTGCGGTGTAGGAGTGAGCTGATGATGACCCAGCTATGTGCGGTGTA
GGAGTGAACATGAGC
Found at i:17587683 original size:123 final size:123
Alignment explanation
Indices: 17587446--17587676 Score: 354
Period size: 123 Copynumber: 1.9 Consensus size: 123
17587436 TGTGATAATT
* * *
17587446 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATGATGACCTAGCTTTGTGCGGTGT
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGGTAT
* * **
17587511 AGGAGTGAACATGAGCTAATGATGACCCAGTTGTGTGTGGTGTAAGAGTGAGCTGATG
66 AGGAGTGAACATGAGCTAATGATGACCCAGCTATGTGCAGTGTAAGAGTGAGCTGATG
*
17587569 ATGACCCAGCTATGTGTGGTGTAGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGGTAT
1 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGGTAT
* * * *
17587634 AGGAGTGCACATGAGTTGATGATGACCTAGCTATGTGCAGTGT
66 AGGAGTGAACATGAGCTAATGATGACCCAGCTATGTGCAGTGT
17587677 GGGAGTGCAC
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
123 96 1.00
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.27
Consensus pattern (123 bp):
ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGGTAT
AGGAGTGAACATGAGCTAATGATGACCCAGCTATGTGCAGTGTAAGAGTGAGCTGATG
Found at i:17590667 original size:22 final size:21
Alignment explanation
Indices: 17590623--17590667 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
17590613 GCAGAAACAA
* *
17590623 AATGTTTCTCGCTACAGCGAG
1 AATGTTTCTCACTACAGCAAG
*
17590644 AATGATTTCTCACTACAGTAAG
1 AATG-TTTCTCACTACAGCAAG
17590666 AA
1 AA
17590668 GCAGGGCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (21 bp):
AATGTTTCTCACTACAGCAAG
Found at i:17590975 original size:42 final size:41
Alignment explanation
Indices: 17590904--17591050 Score: 168
Period size: 42 Copynumber: 3.5 Consensus size: 41
17590894 AAGCCCATAT
* * * *
17590904 GCACTCCCACTAGCATATGGCTAGGTCAGCATCGGCTTATGC
1 GCACTCCTACTCGCACATAGCT-GGTCAGCATCGGCTTATGC
* *
17590946 ACACTTCTACTCGCACATAGTCTGGTCAGCATCGGCTTATGC
1 GCACTCCTACTCGCACATAG-CTGGTCAGCATCGGCTTATGC
* * * *
17590988 GCACTCCCACTAGCACATAGCTGAGTTAGCATTGGCTTATGC
1 GCACTCCTACTCGCACATAGCTG-GTCAGCATCGGCTTATGC
*
17591030 GTACTCCTACTCGCACATAGC
1 GCACTCCTACTCGCACATAGC
17591051 CAGGTCAATA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 3 0.03
42 83 0.94
43 2 0.02
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26
Consensus pattern (41 bp):
GCACTCCTACTCGCACATAGCTGGTCAGCATCGGCTTATGC
Found at i:17591057 original size:84 final size:84
Alignment explanation
Indices: 17590904--17591057 Score: 211
Period size: 84 Copynumber: 1.8 Consensus size: 84
17590894 AAGCCCATAT
* * * * *
17590904 GCACTCCCACTAGCATATGGCTAGGTCAGCATCGGCTTATGCACACTTCTACTCGCACATAGTCT
1 GCACTCCCACTAGCACATAGCTAGGTCAGCATCGGCTTATGCACACTCCTACTCGCACATAGCCA
17590969 GGTCAGCATCGGCTTATGC
66 GGTCAGCATCGGCTTATGC
* * **
17590988 GCACTCCCACTAGCACATAGCT-GAGTTAGCATTGGCTTATGCGTACTCCTACTCGCACATAGCC
1 GCACTCCCACTAGCACATAGCTAG-GTCAGCATCGGCTTATGCACACTCCTACTCGCACATAGCC
17591052 AGGTCA
65 AGGTCA
17591058 ATATCATTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
83 1 0.02
84 59 0.98
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (84 bp):
GCACTCCCACTAGCACATAGCTAGGTCAGCATCGGCTTATGCACACTCCTACTCGCACATAGCCA
GGTCAGCATCGGCTTATGC
Found at i:17599637 original size:22 final size:22
Alignment explanation
Indices: 17599590--17599653 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
17599580 ATGGCCCAAT
*
17599590 GTCACGCAATACATAACAACAG
1 GTCACGCAATACATAAAAACAG
*
17599612 GTCACGCAATATATAAAAACCA-
1 GTCACGCAATACATAAAAA-CAG
* * *
17599634 GTCACACAATGCCTAAAAAC
1 GTCACGCAATACATAAAAAC
17599654 TAGTGAACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.47, C:0.27, G:0.11, T:0.16
Consensus pattern (22 bp):
GTCACGCAATACATAAAAACAG
Found at i:17599794 original size:207 final size:203
Alignment explanation
Indices: 17599437--17599937 Score: 662
Period size: 207 Copynumber: 2.4 Consensus size: 203
17599427 CATATTCATG
*
17599437 CAATGCCTAAAAACTAGTGAACAAAAGCCTCAAAACAAGAGGTGAATTGCACAAGTCACGCACCA
1 CAATGCCTAAAAACTAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACGCACCA
* * * * * * * * *
17599502 CTAGTCTCGCAATACCTAATATTAAGTCACTCAATGCGTAATATCCACTCACTTTATGCGAACAT
66 CCAATATCGCAATACCTAAGAATAAGTCACTCAATGCCTAATACCCACTCACATTATGCCAACAT
* * *
17599567 AACTAGTCACATAATGGCCCAATGTCACGCAATACATAACAACAGGTCACGCAATATATAAAAAC
131 AACCAGTCACATAATGGCCCAATGTCACACAATACATAACAACAGGTCACGCAATACATAAAAAC
17599632 CAGTCACA
196 CAGTCACA
*
17599640 CAATGCCTAAAAACTAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCATAAGTCA-GTCACG
1 CAATGCCTAAAAACTAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACG-CAC-
* * *
17599704 AATCGCCAATATTGCAATACCTAAGAATAAGTCACTCAATGCCTTATACCCACTCACATTATGCC
64 ---CACCAATATCGCAATACCTAAGAATAAGTCACTCAATGCCTAATACCCACTCACATTATGCC
** * * *
17599769 AACATAACCAGTCATGTACTGGCCCAATGTCACATAATACATAACAACAGGTCATGCAATACATA
126 AACATAACCAGTCACATAATGGCCCAATGTCACACAATACATAACAACAGGTCACGCAATACATA
*
17599834 AAAACCAGTCACG
191 AAAACCAGTCACA
* * * * *
17599847 CAATGCCTAAAAAAACTAGTGAACAAAAGCCTTAAAACAAGAGGTTAATTACACAAGTCATGCAC
1 CAATGCCT--AAAAACTAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACGCAC
* *
17599912 CACCAATCTCGCAATACCTAATAATA
64 CACCAATATCGCAATACCTAAGAATA
17599938 NGCCTTAAAA
Statistics
Matches: 258, Mismatches: 32, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
202 1 0.00
203 59 0.23
205 22 0.09
207 127 0.49
209 48 0.19
210 1 0.00
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.21
Consensus pattern (203 bp):
CAATGCCTAAAAACTAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACGCACCA
CCAATATCGCAATACCTAAGAATAAGTCACTCAATGCCTAATACCCACTCACATTATGCCAACAT
AACCAGTCACATAATGGCCCAATGTCACACAATACATAACAACAGGTCACGCAATACATAAAAAC
CAGTCACA
Found at i:17599844 original size:22 final size:22
Alignment explanation
Indices: 17599804--17599859 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
17599794 AATGTCACAT
* *
17599804 AATACATAACAACAGGTCATGC
1 AATACATAAAAACAGGTCACGC
17599826 AATACATAAAAACCA-GTCACGC
1 AATACATAAAAA-CAGGTCACGC
* *
17599848 AATGCCTAAAAA
1 AATACATAAAAA
17599860 AACTAGTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.50, C:0.23, G:0.11, T:0.16
Consensus pattern (22 bp):
AATACATAAAAACAGGTCACGC
Found at i:17599954 original size:64 final size:63
Alignment explanation
Indices: 17599874--17600001 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 63
17599864 AGTGAACAAA
*
17599874 AGCCTTAAAACAAGAGGTTAATTACACAAGTCATGCACCACCAATCTCGCAATACCTAATAAT
1 AGCCTTAAAACAAGAGGTTAATTACACAAGTCATGCACCACCAATCTCACAATACCTAATAAT
*
17599937 ANGCCTTAAAACAAGAGGTTAATTACACAAGTCATGCACCACCACTCTCACAATACCTAATAAT
1 A-GCCTTAAAACAAGAGGTTAATTACACAAGTCATGCACCACCAATCTCACAATACCTAATAAT
17600001 A
1 A
17600002 AGCCACTCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 1 0.02
64 61 0.98
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.22
Consensus pattern (63 bp):
AGCCTTAAAACAAGAGGTTAATTACACAAGTCATGCACCACCAATCTCACAATACCTAATAAT
Found at i:17601778 original size:22 final size:22
Alignment explanation
Indices: 17601744--17601801 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
17601734 TTGGTAGATA
*
17601744 AAGTAACGCAATGCCTACAAAC
1 AAGTCACGCAATGCCTACAAAC
* **
17601766 AAGTCACGTAATGCCTATGAAC
1 AAGTCACGCAATGCCTACAAAC
17601788 AAGTCACGCAATGC
1 AAGTCACGCAATGC
17601802 TCAACAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (22 bp):
AAGTCACGCAATGCCTACAAAC
Found at i:17603428 original size:21 final size:21
Alignment explanation
Indices: 17603390--17603429 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17603380 AGTGTTTAAC
**
17603390 AAGAAGGAAGCTTATTGGTGA
1 AAGAAGGAAGAATATTGGTGA
*
17603411 AAGAAGGAAGAATGTTGGT
1 AAGAAGGAAGAATATTGGT
17603430 TGACCAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.35, T:0.23
Consensus pattern (21 bp):
AAGAAGGAAGAATATTGGTGA
Found at i:17610238 original size:18 final size:18
Alignment explanation
Indices: 17610215--17610251 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17610205 AATTTGCTCT
*
17610215 TGAGGATTGGTGGTAAGC
1 TGAGGATTGATGGTAAGC
17610233 TGAGGATTGATGGTAAGC
1 TGAGGATTGATGGTAAGC
17610251 T
1 T
17610252 AACTGACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.41, T:0.30
Consensus pattern (18 bp):
TGAGGATTGATGGTAAGC
Found at i:17611793 original size:17 final size:17
Alignment explanation
Indices: 17611771--17611803 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17611761 AAATATGCAC
17611771 ATACTTAGGGGGAGCAT
1 ATACTTAGGGGGAGCAT
17611788 ATACTTAGGGGGAGCA
1 ATACTTAGGGGGAGCA
17611804 ATCCTCATTT
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:0.30, C:0.12, G:0.36, T:0.21
Consensus pattern (17 bp):
ATACTTAGGGGGAGCAT
Found at i:17613352 original size:22 final size:22
Alignment explanation
Indices: 17613327--17613370 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
17613317 AAGCAAATAA
17613327 ATTAGTTATTAGGTATTGCATT
1 ATTAGTTATTAGGTATTGCATT
17613349 ATTAGTTATTAGGTATTGCATT
1 ATTAGTTATTAGGTATTGCATT
17613371 GTGTTGGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (22 bp):
ATTAGTTATTAGGTATTGCATT
Found at i:17620046 original size:14 final size:14
Alignment explanation
Indices: 17620027--17620066 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
17620017 TGGTGCATTT
*
17620027 TCTATATTCTTGAA
1 TCTATATTCATGAA
17620041 TCTATATTCATGAA
1 TCTATATTCATGAA
17620055 TCTATATTCATG
1 TCTATATTCATG
17620067 CAGCTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (14 bp):
TCTATATTCATGAA
Found at i:17625826 original size:34 final size:34
Alignment explanation
Indices: 17625788--17625855 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
17625778 TCACCAAGCT
* *
17625788 TTTACAATGGCTTTTCACAGGCTCAGCCAAAACC
1 TTTACAATAGCTTTTCACAGGCTCAACCAAAACC
* * * *
17625822 TTTACACTAGTTTTTCACGGGCTCAACTAAAACC
1 TTTACAATAGCTTTTCACAGGCTCAACCAAAACC
17625856 CAAAGTGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (34 bp):
TTTACAATAGCTTTTCACAGGCTCAACCAAAACC
Found at i:17626670 original size:22 final size:22
Alignment explanation
Indices: 17626642--17626698 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
17626632 CACATTGCTG
17626642 GTTTTTAGGCATTATGTCACTA
1 GTTTTTAGGCATTATGTCACTA
* *
17626664 GTTTTTAGGCATCATGTCACTG
1 GTTTTTAGGCATTATGTCACTA
17626686 GTTTTTAGGCATT
1 GTTTTTAGGCATT
17626699 GCGTGACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.46
Consensus pattern (22 bp):
GTTTTTAGGCATTATGTCACTA
Found at i:17626802 original size:22 final size:23
Alignment explanation
Indices: 17626748--17626804 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
17626738 GTAACTTAAA
*
17626748 CATTGTGTGACT-GGATTTTAGG
1 CATTGTGTGACTAGGATTGTAGG
***
17626770 CATTACATGACTAGG-TTGTAGG
1 CATTGTGTGACTAGGATTGTAGG
17626792 CATTGTGTGACTA
1 CATTGTGTGACTA
17626805 ATTTTTAGGC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (23 bp):
CATTGTGTGACTAGGATTGTAGG
Found at i:17626813 original size:22 final size:21
Alignment explanation
Indices: 17626748--17626815 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
17626738 GTAACTTAAA
*
17626748 CATTGTGTGACTGGATTTTAGG
1 CATTGTGTGACT-AATTTTAGG
*** * *
17626770 CATTACATGACTAGGTTGTAGG
1 CATTGTGTGACTA-ATTTTAGG
17626792 CATTGTGTGACTAATTTTTAGG
1 CATTGTGTGACTAA-TTTTAGG
17626814 CA
1 CA
17626816 ATGCTTAAGT
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (21 bp):
CATTGTGTGACTAATTTTAGG
Found at i:17626871 original size:23 final size:23
Alignment explanation
Indices: 17626841--17626924 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
17626831 AATGCCGAAA
*
17626841 AACTAGTCACGCAATGCCCTATC
1 AACTAGTCATGCAATGCCCTATC
* * *
17626864 AACTAGTCATGCAAT-ACTTAAC
1 AACTAGTCATGCAATGCCCTATC
*
17626886 AA-TCAGTCATGGAATGCCCTATC
1 AACT-AGTCATGCAATGCCCTATC
* *
17626909 AACCAGTCAAGCAATG
1 AACTAGTCATGCAATG
17626925 TTTAAAAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
21 1 0.02
22 16 0.34
23 30 0.64
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (23 bp):
AACTAGTCATGCAATGCCCTATC
Found at i:17626947 original size:45 final size:45
Alignment explanation
Indices: 17626838--17626978 Score: 158
Period size: 45 Copynumber: 3.2 Consensus size: 45
17626828 CACAATGCCG
* * *
17626838 AAAAACTAGTCACGCAATGCCCTATCAACTAGTCATGCAATACTT
1 AAAAATTAGTCACGCAATGCCCTATCAACCAGTCATGCAATGCTT
* * * * * *
17626883 AACAATCAGTCATGGAATGCCCTATCAACCAGTCAAGCAATGTTT
1 AAAAATTAGTCACGCAATGCCCTATCAACCAGTCATGCAATGCTT
* ** *
17626928 AAAAATTAGTAACGCAATG-CCTAAAAACCAGTCATGCAATGCCT
1 AAAAATTAGTCACGCAATGCCCTATCAACCAGTCATGCAATGCTT
17626972 AAAAATT
1 AAAAATT
17626979 GGTTACACGA
Statistics
Matches: 77, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
44 27 0.35
45 50 0.65
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (45 bp):
AAAAATTAGTCACGCAATGCCCTATCAACCAGTCATGCAATGCTT
Found at i:17626952 original size:22 final size:22
Alignment explanation
Indices: 17626927--17626998 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
17626917 AAGCAATGTT
17626927 TAAAAATTAGTAACGCAATGCC
1 TAAAAATTAGTAACGCAATGCC
** * *
17626949 TAAAAACCAGTCATGCAATGCC
1 TAAAAATTAGTAACGCAATGCC
* * * *
17626971 TAAAAATTGGTTACACGATGCC
1 TAAAAATTAGTAACGCAATGCC
17626993 TAAAAA
1 TAAAAA
17626999 CCAACAAAAC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.22
Consensus pattern (22 bp):
TAAAAATTAGTAACGCAATGCC
Found at i:17626967 original size:44 final size:44
Alignment explanation
Indices: 17626909--17627001 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
17626899 ATGCCCTATC
** *
17626909 AACCAGTCAAGCAATGTTTAAAAATTAGTAACGCAATGCCTAAA
1 AACCAGTCAAGCAATGCCTAAAAATTAGTAACACAATGCCTAAA
* * * *
17626953 AACCAGTCATGCAATGCCTAAAAATTGGTTACACGATGCCTAAA
1 AACCAGTCAAGCAATGCCTAAAAATTAGTAACACAATGCCTAAA
17626997 AACCA
1 AACCA
17627002 ACAAAACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (44 bp):
AACCAGTCAAGCAATGCCTAAAAATTAGTAACACAATGCCTAAA
Found at i:17627172 original size:50 final size:51
Alignment explanation
Indices: 17627099--17627229 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 51
17627089 TACTTGGCAA
* *
17627099 AAAATGCTC-AAATGCTCAAAAG-TTTTCTTCGTTTATCAAAAACCACTCC
1 AAAATGCTCAAAATGCTCAAAAGTTTTTCTTCATATATCAAAAACCACTCC
* **
17627148 AAAATGCTCAAAATGTTCAAAAGTTTTTCTTCATATATCAAAAATTACTCC
1 AAAATGCTCAAAATGCTCAAAAGTTTTTCTTCATATATCAAAAACCACTCC
** * *
17627199 AAAATGCTCAAAACACTTAAAGGTTTTTCTT
1 AAAATGCTCAAAATGCTCAAAAGTTTTTCTT
17627230 TCTGACAAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
49 9 0.13
50 12 0.17
51 49 0.70
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.34
Consensus pattern (51 bp):
AAAATGCTCAAAATGCTCAAAAGTTTTTCTTCATATATCAAAAACCACTCC
Found at i:17628681 original size:73 final size:74
Alignment explanation
Indices: 17628600--17628746 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
17628590 GAATAAATTA
*
17628600 TTTTTGACTTGGTGGATACAACAT-TAATCTGATCATGAATGATCATATATAATTGTGTTCCAAT
1 TTTTTGACTTGGTGGATACAACATATAATCTGATCATAAATGATCATATATAATTGTGTTCCAAT
*
17628664 AGTTTTTTT
66 AGTTATTTT
*
17628673 TTTTTGACTTGGTGGATACAACATATAATCTGATCATAAATTATCATATATAATTGTGTTCCAAT
1 TTTTTGACTTGGTGGATACAACATATAATCTGATCATAAATGATCATATATAATTGTGTTCCAAT
17628738 AGTTATTTT
66 AGTTATTTT
17628747 ATATTATGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 24 0.34
74 46 0.66
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (74 bp):
TTTTTGACTTGGTGGATACAACATATAATCTGATCATAAATGATCATATATAATTGTGTTCCAAT
AGTTATTTT
Found at i:17631880 original size:11 final size:11
Alignment explanation
Indices: 17631866--17631902 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
17631856 AATAATATTT
*
17631866 TATTAATAAAA
1 TATTATTAAAA
17631877 TATTATTAAAA
1 TATTATTAAAA
*
17631888 TAGTATTAAAA
1 TATTATTAAAA
17631899 TATT
1 TATT
17631903 TCTACTGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:17637107 original size:25 final size:25
Alignment explanation
Indices: 17637073--17637128 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
17637063 AGTCTGTGAT
*
17637073 ATATACGTGGCAAGGCCACGGGTTG
1 ATATACGTGGCAAGGCCACGAGTTG
* * *
17637098 ATATATGTGGCTAGGCCATGAGTTG
1 ATATACGTGGCAAGGCCACGAGTTG
17637123 ATATAC
1 ATATAC
17637129 ATGGTTGCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCACGAGTTG
Found at i:17638547 original size:21 final size:21
Alignment explanation
Indices: 17638522--17638571 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
17638512 CTAAAGTTTC
17638522 ACTAATTACTAAAATTATAAA
1 ACTAATTACTAAAATTATAAA
17638543 ACTAATTACTAAAATTATAAA
1 ACTAATTACTAAAATTATAAA
*
17638564 ACAAATTA
1 ACTAATTA
17638572 ATCTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (21 bp):
ACTAATTACTAAAATTATAAA
Found at i:17641460 original size:19 final size:20
Alignment explanation
Indices: 17641425--17641463 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
17641415 AATTTAAAAC
17641425 AAAATAACATAAAATTAACT
1 AAAATAACATAAAATTAACT
*
17641445 AAAATAA-ATTAAATTAACT
1 AAAATAACATAAAATTAACT
17641464 GCTCAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAACATAAAATTAACT
Found at i:17641658 original size:41 final size:42
Alignment explanation
Indices: 17641595--17641744 Score: 124
Period size: 44 Copynumber: 3.5 Consensus size: 42
17641585 ACTTATCATC
* *
17641595 TACTCAACCCAC-TCTACCATAAATCATGGGAA-GTGGAGACA
1 TACTCAATCCACTTC-ACAATAAATCATGGGAATGTGGAGACA
* * **
17641636 TACTCAATCCACTTAACAATAAAATTATGGGAATGTGGAGATT
1 TACTCAATCCACTTCACAAT-AAATCATGGGAATGTGGAGACA
* * * * *
17641679 TTCTCAATCCACATCACAACACCCATCATGGGAATGTGGAGACC
1 TACTCAATCCACTTCACAATA--AATCATGGGAATGTGGAGACA
* *
17641723 TTCTTAATCCACATTCACAATA
1 TACTCAATCCAC-TTCACAATA
17641745 CTTATATGTA
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
41 15 0.17
42 13 0.15
43 23 0.27
44 28 0.33
45 7 0.08
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (42 bp):
TACTCAATCCACTTCACAATAAATCATGGGAATGTGGAGACA
Found at i:17641685 original size:43 final size:44
Alignment explanation
Indices: 17641615--17641745 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 44
17641605 ACTCTACCAT
* *
17641615 AAATCATGGGAA-GTGGAGACATACTCAATCCACTTAACAATA-
1 AAATCATGGGAATGTGGAGACATTCTCAATCCACTTCACAATAC
* ** * *
17641657 AAATTATGGGAATGTGGAGATTTTCTCAATCCACATCACAACAC
1 AAATCATGGGAATGTGGAGACATTCTCAATCCACTTCACAATAC
** * *
17641701 CCATCATGGGAATGTGGAGACCTTCTTAATCCACATTCACAATAC
1 AAATCATGGGAATGTGGAGACATTCTCAATCCAC-TTCACAATAC
17641746 TTATATGTAT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
42 11 0.15
43 24 0.34
44 28 0.39
45 8 0.11
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (44 bp):
AAATCATGGGAATGTGGAGACATTCTCAATCCACTTCACAATAC
Found at i:17646127 original size:30 final size:30
Alignment explanation
Indices: 17646093--17646166 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
17646083 AATAAGGAGA
*
17646093 AAAACAGGAAGTTTTGAAATTTTGGGTTTC
1 AAAACAGAAAGTTTTGAAATTTTGGGTTTC
17646123 AAAACAGAAAGTTTTGAAATTTTGGGTTTC
1 AAAACAGAAAGTTTTGAAATTTTGGGTTTC
17646153 AAAACAGAAAGTTT
1 AAAACAGAAAGTTT
17646167 CTTGCTACAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
AAAACAGAAAGTTTTGAAATTTTGGGTTTC
Found at i:17646418 original size:2 final size:2
Alignment explanation
Indices: 17646411--17646460 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
17646401 ACCATATACC
17646411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17646453 AT AT AT AT
1 AT AT AT AT
17646461 CAATCATCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17646548 original size:42 final size:42
Alignment explanation
Indices: 17646501--17646625 Score: 187
Period size: 42 Copynumber: 3.0 Consensus size: 42
17646491 CATCTCATAT
* * * * *
17646501 GCAACGGTTTATGCGCACTCCCACTCACACATAGTCTGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
*
17646543 GCAACGGCTTATGTGCACTCCCACTCGTACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
*
17646585 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
17646626 CACATCAACA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:17688486 original size:30 final size:30
Alignment explanation
Indices: 17688452--17688607 Score: 99
Period size: 30 Copynumber: 5.2 Consensus size: 30
17688442 AGTAGTGGTT
17688452 AAAGGTTTTATCTTAA-CCTTGAAAAGAAA
1 AAAGGTTTTATCTTAAGCCTTGAAAAGAAA
** * *
17688481 GAAAGGTTCGATC-TAAACCTTGAAAAG-AT
1 -AAAGGTTTTATCTTAAGCCTTGAAAAGAAA
* *
17688510 AAAGAGTTTTGT-TTAAGCCTTTAAAAGATAA
1 AAAG-GTTTTATCTTAAGCCTTGAAAAGA-AA
* *
17688541 AGAGATTTTATC-TAAGCCTTGAAAAGATAA
1 AAAGGTTTTATCTTAAGCCTTGAAAAGA-AA
* ** * *
17688571 AGAGGTCCTAT-ATAAGCCTTAAAAAGATAA
1 AAAGGTTTTATCTTAAGCCTTGAAAAGA-AA
*
17688601 AGAGGTT
1 AAAGGTT
17688608 ATACCTTCGC
Statistics
Matches: 101, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
28 4 0.04
29 20 0.20
30 73 0.72
31 4 0.04
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (30 bp):
AAAGGTTTTATCTTAAGCCTTGAAAAGAAA
Found at i:17688554 original size:59 final size:60
Alignment explanation
Indices: 17688491--17688604 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
17688481 GAAAGGTTCG
** * * *
17688491 ATCTAAACCTTGAAAAGATAAAGA-GTTTTGTTTAAGCCTTTAAAAGATAAAGAGATTTT
1 ATCTAAACCTTGAAAAGATAAAGAGGTCCTATATAAGCCTTAAAAAGATAAAGAGATTTT
*
17688550 ATCTAAGCCTTGAAAAGATAAAGAGGTCCTATATAAGCCTTAAAAAGATAAAGAG
1 ATCTAAACCTTGAAAAGATAAAGAGGTCCTATATAAGCCTTAAAAAGATAAAGAG
17688605 GTTATACCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 23 0.48
60 25 0.52
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.28
Consensus pattern (60 bp):
ATCTAAACCTTGAAAAGATAAAGAGGTCCTATATAAGCCTTAAAAAGATAAAGAGATTTT
Found at i:17688620 original size:30 final size:29
Alignment explanation
Indices: 17688523--17688611 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 29
17688513 GAGTTTTGTT
* * *
17688523 TAAGCCTTTAAAAGATAAAGAGATTTTATC
1 TAAGCCTTAAAAAGATAAAGAGGTTATA-C
*
17688553 TAAGCCTTGAAAAGATAAAGAGGTCCTATA-
1 TAAGCCTTAAAAAGATAAAGAGGT--TATAC
17688583 TAAGCCTTAAAAAGATAAAGAGGTTATAC
1 TAAGCCTTAAAAAGATAAAGAGGTTATAC
17688612 CTTCGCCTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.08
30 45 0.87
32 3 0.06
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (29 bp):
TAAGCCTTAAAAAGATAAAGAGGTTATAC
Found at i:17688620 original size:60 final size:59
Alignment explanation
Indices: 17688493--17688622 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 59
17688483 AAGGTTCGAT
* ** * * * * *
17688493 CTAAACCTTGAAAAGATAAAGAGTTTTGTTTAAGCCTTTAAAAGATAAAGAGATTTTAT
1 CTAAGCCTTGAAAAGATAAAGAGTCCTATATAAGCCTTAAAAAGATAAAGAGATTATAC
*
17688552 CTAAGCCTTGAAAAGATAAAGAGGTCCTATATAAGCCTTAAAAAGATAAAGAGGTTATAC
1 CTAAGCCTTGAAAAGATAAAGA-GTCCTATATAAGCCTTAAAAAGATAAAGAGATTATAC
**
17688612 CTTCGCCTTGA
1 CTAAGCCTTGA
17688623 CAACGGGAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
59 21 0.36
60 38 0.64
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (59 bp):
CTAAGCCTTGAAAAGATAAAGAGTCCTATATAAGCCTTAAAAAGATAAAGAGATTATAC
Found at i:17690434 original size:73 final size:73
Alignment explanation
Indices: 17690314--17690481 Score: 232
Period size: 73 Copynumber: 2.3 Consensus size: 73
17690304 AGAATCATCT
* * * *
17690314 TGTGCACTCCCACACCGCACA-AATCAATATCATCAGTGTGTGCACTCACACAACACACCATTAT
1 TGTGCACTCCCACACCGCACATGATCAATATCATCAGTGTGTACACTCACACAACACACAACTAT
17690378 CACCGTCA
66 CACCGTCA
* * * *
17690386 TGTGCACTCCCACACCACACATGGT-AGATATCATCAGTGTGTACACTCACATAGCACACAACTA
1 TGTGCACTCCCACACCGCACATGATCA-ATATCATCAGTGTGTACACTCACACAACACACAACTA
*
17690450 TCGCCGTCA
65 TCACCGTCA
17690459 TGTGCACTCCCACACCGCACATG
1 TGTGCACTCCCACACCGCACATG
17690482 CATGGTTATA
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
72 21 0.25
73 63 0.75
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.21
Consensus pattern (73 bp):
TGTGCACTCCCACACCGCACATGATCAATATCATCAGTGTGTACACTCACACAACACACAACTAT
CACCGTCA
Found at i:17701996 original size:13 final size:13
Alignment explanation
Indices: 17701978--17702007 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17701968 TTATTTAATG
*
17701978 AAATTTATAAAAA
1 AAATTTAGAAAAA
17701991 AAATTTAGAAAAA
1 AAATTTAGAAAAA
17702004 AAAT
1 AAAT
17702008 AAAAGGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AAATTTAGAAAAA
Found at i:17703823 original size:23 final size:23
Alignment explanation
Indices: 17703712--17703875 Score: 111
Period size: 23 Copynumber: 7.1 Consensus size: 23
17703702 TTGTTGTGGG
* *
17703712 TTACATGCCCTTTAGCATGTTTGGA
1 TTACATG-CC-TTAGCATATTTGGT
* * *
17703737 TTATATGCCTTTGTATATTTGGT
1 TTACATGCCTTAGCATATTTGGT
* * * *
17703760 TTACATGTCTTAGCATGTGT-GA
1 TTACATGCCTTAGCATATTTGGT
* * *
17703782 TTATAT-CTCTTAACGTATTTGGT
1 TTACATGC-CTTAGCATATTTGGT
*
17703805 TTACATGCCTTAGCATATTGGGT
1 TTACATGCCTTAGCATATTTGGT
* *
17703828 TTACATGCCTTATCATGA-ATGG-
1 TTACATGCCTTAGCAT-ATTTGGT
* *
17703850 TTATATACCTTAGCATATTTGGT
1 TTACATGCCTTAGCATATTTGGT
17703873 TTA
1 TTA
17703876 GATAGTGTAA
Statistics
Matches: 103, Mismatches: 30, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
21 1 0.01
22 30 0.29
23 62 0.60
24 4 0.04
25 6 0.06
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.45
Consensus pattern (23 bp):
TTACATGCCTTAGCATATTTGGT
Found at i:17703854 original size:68 final size:68
Alignment explanation
Indices: 17703731--17703875 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 68
17703721 CTTTAGCATG
* * * * * * **
17703731 TTTGGATTATATGCCTTTGTATATTTGGTTTACATGTCTTAGCATGTGTGATTATAT-CTCTTAA
1 TTTGGTTTACATGCCTTAGCATATTGGGTTTACATGCCTTAGCATGAATGATTATATAC-CTTAA
*
17703795 CGTA
65 CATA
* * *
17703799 TTTGGTTTACATGCCTTAGCATATTGGGTTTACATGCCTTATCATGAATGGTTATATACCTTAGC
1 TTTGGTTTACATGCCTTAGCATATTGGGTTTACATGCCTTAGCATGAATGATTATATACCTTAAC
17703864 ATA
66 ATA
17703867 TTTGGTTTA
1 TTTGGTTTA
17703876 GATAGTGTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 63 0.98
69 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (68 bp):
TTTGGTTTACATGCCTTAGCATATTGGGTTTACATGCCTTAGCATGAATGATTATATACCTTAAC
ATA
Found at i:17704587 original size:13 final size:13
Alignment explanation
Indices: 17704569--17704597 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17704559 GCAAGATAAC
17704569 ACTAAGGATTCCA
1 ACTAAGGATTCCA
17704582 ACTAAGGATTCCA
1 ACTAAGGATTCCA
17704595 ACT
1 ACT
17704598 TCGCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (13 bp):
ACTAAGGATTCCA
Found at i:17711399 original size:13 final size:14
Alignment explanation
Indices: 17711381--17711411 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
17711371 TGCCTTGGAT
17711381 AAAATAAAAA-TAA
1 AAAATAAAAAGTAA
17711394 AAAATAAAAAGTAA
1 AAAATAAAAAGTAA
17711408 AAAA
1 AAAA
17711412 AAGGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAATAAAAAGTAA
Found at i:17719914 original size:20 final size:21
Alignment explanation
Indices: 17719889--17719943 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
17719879 GATCAGTTGG
*
17719889 AAGAAAGGAGAAAG-GAAAGA
1 AAGAAAGGAGAAAGAAAAAGA
17719909 AAGAAAGGAGAAAGAAAAAGA
1 AAGAAAGGAGAAAGAAAAAGA
*
17719930 GAGAAAGGAAGAAA
1 AAGAAAGG-AGAAA
17719944 AAGCTTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 14 0.45
21 12 0.39
22 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
AAGAAAGGAGAAAGAAAAAGA
Found at i:17725666 original size:29 final size:29
Alignment explanation
Indices: 17725624--17725693 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
17725614 ATTAATCATA
*
17725624 AAATTAACTAATATTAGATTGTCTCACCT
1 AAATTAACTAATATTAGATTGACTCACCT
17725653 AAATTAACTAATATTAGATTGACTCACCT
1 AAATTAACTAATATTAGATTGACTCACCT
17725682 AAATTAACTAAT
1 AAATTAACTAAT
17725694 TTAAAATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.36
Consensus pattern (29 bp):
AAATTAACTAATATTAGATTGACTCACCT
Found at i:17727139 original size:21 final size:21
Alignment explanation
Indices: 17727115--17727155 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17727105 AATGATAGCA
17727115 TCATACAAAGTCAAACAGCTC
1 TCATACAAAGTCAAACAGCTC
* * *
17727136 TCATTCATAGTCAAGCAGCT
1 TCATACAAAGTCAAACAGCT
17727156 TTACTTTAAT
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:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (21 bp):
TCATACAAAGTCAAACAGCTC
Found at i:17728656 original size:15 final size:16
Alignment explanation
Indices: 17728624--17728656 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17728614 CATTGGCAAC
17728624 TTAAATGCAAATGCTA
1 TTAAATGCAAATGCTA
*
17728640 TTAAATTCAAA-GCTA
1 TTAAATGCAAATGCTA
17728655 TT
1 TT
17728657 TGAAAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (16 bp):
TTAAATGCAAATGCTA
Found at i:17731377 original size:86 final size:86
Alignment explanation
Indices: 17731232--17731399 Score: 255
Period size: 86 Copynumber: 2.0 Consensus size: 86
17731222 TTTAAACATA
* * **
17731232 GCATGTAACTTGATCTCTATCTTTGTATTTTACTAAGACATAAACTCTTGGAGTGAAACACCTTA
1 GCATGTAACATGATCTCTATCTTTGTATTTCACTAAGACATAAACTCTTAAAGTGAAACACCTTA
*
17731297 AACATGGTGTGTAACAATATG
66 AACATGATGTGTAACAATATG
* * * *
17731318 GCATGTAACATGGTCTCTATCTTTGTCTTTCACTAGGACATAAACTCTTAAAGTTAAACACCTTA
1 GCATGTAACATGATCTCTATCTTTGTATTTCACTAAGACATAAACTCTTAAAGTGAAACACCTTA
17731383 AACATGATGTGTAACAA
66 AACATGATGTGTAACAA
17731400 CTATTTTTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (86 bp):
GCATGTAACATGATCTCTATCTTTGTATTTCACTAAGACATAAACTCTTAAAGTGAAACACCTTA
AACATGATGTGTAACAATATG
Found at i:17731461 original size:29 final size:28
Alignment explanation
Indices: 17731381--17731479 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 28
17731371 TTAAACACCT
*
17731381 TAAACATGATGTGTAACAACTATTTTTTC
1 TAAACATGACGTGTAACAAC-ATTTTTTC
* * * *
17731410 --AATATGGCATATAACAAC--TTTTTC
1 TAAACATGACGTGTAACAACATTTTTTC
*
17731434 TAAACATGACGTGTAACAACATTATTTTT
1 TAAACATGACGTGTAACAACATT-TTTTC
*
17731463 TAAACATGGCGTGTAAC
1 TAAACATGACGTGTAAC
17731480 TTGGTCTCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
24 6 0.11
26 14 0.26
27 13 0.24
28 1 0.02
29 20 0.37
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (28 bp):
TAAACATGACGTGTAACAACATTTTTTC
Found at i:17731570 original size:27 final size:27
Alignment explanation
Indices: 17731546--17731618 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
17731536 GTATAACACT
17731546 TTTTTTTCCAACATGGCGTGCAACAACA
1 TTTTTTT-CAACATGGCGTGCAACAACA
* ** *
17731574 TTTTTTTGAACATGGCGTATAATAACA
1 TTTTTTTCAACATGGCGTGCAACAACA
*
17731601 TTATTTTTTAAACATGGC
1 -T-TTTTTTCAACATGGC
17731619 TTGTAACTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 16 0.42
28 8 0.21
29 14 0.37
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (27 bp):
TTTTTTTCAACATGGCGTGCAACAACA
Found at i:17732009 original size:2 final size:2
Alignment explanation
Indices: 17732002--17732031 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17731992 ATGGCTTAAG
17732002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17732032 CTTAACAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17733050 original size:37 final size:37
Alignment explanation
Indices: 17733003--17733121 Score: 195
Period size: 37 Copynumber: 3.2 Consensus size: 37
17732993 AATGCAATAT
* * *
17733003 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAC
1 CATCATCATGTGTGCACTTCCTACTCACACACTTCAA
17733040 CATCATCATGTGTGCACTTCCTACTCACACAC-TCTAA
1 CATCATCATGTGTGCACTTCCTACTCACACACTTC-AA
17733077 CATCATCATGTGTGCACTTCCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTTCCTACTCACACACTTCAA
17733114 CATCATCA
1 CATCATCA
17733122 CACAACATTA
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
36 2 0.03
37 73 0.95
38 2 0.03
ACGTcount: A:0.26, C:0.37, G:0.08, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTTCCTACTCACACACTTCAA
Found at i:17735259 original size:28 final size:27
Alignment explanation
Indices: 17735171--17735336 Score: 134
Period size: 29 Copynumber: 5.8 Consensus size: 27
17735161 TTAAGACAAC
* *
17735171 TTTTGTCTTTAATTGAGACAAAAATATTT
1 TTTTGTC-TAAATTAAGACAAAAA-ATTT
* * **
17735200 TATCTTGTCTAAATTGAGACAATTATGTTT
1 T-T-TTGTCTAAATTAAGACAA-AAAATTT
* *
17735230 TTTTGGCTAGATTAAGACAAAAAATATT
1 TTTTGTCTAAATTAAGACAAAAAAT-TT
*
17735258 TTTTGTCTTAAATTAAGACAAATACATTT
1 TTTTGTC-TAAATTAAGACAAA-AAATTT
* * *
17735287 TCTTGTCTAAATTAAGACCAAATATGTT
1 TTTTGTCTAAATTAAGACAAAAAAT-TT
17735315 TTCTTGTCTAAATTAAGACAAA
1 TT-TTGTCTAAATTAAGACAAA
17735337 TATGTTAAAG
Statistics
Matches: 111, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
27 5 0.05
28 39 0.35
29 41 0.37
30 20 0.18
31 6 0.05
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (27 bp):
TTTTGTCTAAATTAAGACAAAAAATTT
Found at i:17735301 original size:57 final size:56
Alignment explanation
Indices: 17735181--17735338 Score: 174
Period size: 57 Copynumber: 2.8 Consensus size: 56
17735171 TTTTGTCTTT
* * * ** *
17735181 AATTGAGACAAAAATATTTTATCTTGTCTAAATTGAGACAATTATGTTTTTTTGGCTA
1 AATTAAGACAAAAATA-TTT-TCTTGTCTAAATTAAGACAAATACATTTTCTTGGCTA
* *
17735239 GATTAAGACAAAAAATATTTT-TTGTCTTAAATTAAGACAAATACATTTTCTTGTCTA
1 AATTAAGAC-AAAAATATTTTCTTGTC-TAAATTAAGACAAATACATTTTCTTGGCTA
* *
17735296 AATTAAGACCAAATATGTTTTCTTGTCTAAATTAAGACAAATA
1 AATTAAGA-CAAAAATATTTTCTTGTCTAAATTAAGACAAATA
17735339 TGTTAAAGCT
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
56 5 0.06
57 57 0.67
58 16 0.19
59 7 0.08
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (56 bp):
AATTAAGACAAAAATATTTTCTTGTCTAAATTAAGACAAATACATTTTCTTGGCTA
Found at i:17736525 original size:27 final size:27
Alignment explanation
Indices: 17736494--17736545 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
17736484 AAACATCTTA
17736494 AACATGACATGTAACAACATTTTTTTC
1 AACATGACATGTAACAACATTTTTTTC
* *
17736521 AACATGGCGTGTAACAACATTTTTT
1 AACATGACATGTAACAACATTTTTT
17736546 CAATACGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (27 bp):
AACATGACATGTAACAACATTTTTTTC
Found at i:17737547 original size:49 final size:49
Alignment explanation
Indices: 17737475--17737669 Score: 188
Period size: 49 Copynumber: 4.0 Consensus size: 49
17737465 TTTCATGTTG
* *
17737475 CATGATATTCATGAAAAATAGCATTTAATCATCCTCTAAATGACATTGC
1 CATGATGTTCATGAAACATAGCATTTAATCATCCTCTAAATGACATTGC
* * *
17737524 CATGATGTTCATGAAACATAGCATTTAATCATCTTTTAAATAACATTG-
1 CATGATGTTCATGAAACATAGCATTTAATCATCCTCTAAATGACATTGC
* * * *
17737572 CATGGAAAATATCTTTGCATAAAACATAGCATTTAAT--T--T-TAGAT-ACATTAC
1 CAT-G-----AT-GTT-CATGAAACATAGCATTTAATCATCCTCTAAATGACATTGC
17737623 CATGATGTTCATGAAACATAGCATTTAATCATCCTCTAAATGACATT
1 CATGATGTTCATGAAACATAGCATTTAATCATCCTCTAAATGACATT
17737670 ACATGGAAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 30
0.74 0.07 0.19
Matches are distributed among these distances:
43 19 0.16
44 2 0.02
45 3 0.03
47 1 0.01
48 7 0.06
49 49 0.41
50 6 0.05
51 7 0.06
52 1 0.01
54 3 0.03
55 2 0.02
56 19 0.16
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (49 bp):
CATGATGTTCATGAAACATAGCATTTAATCATCCTCTAAATGACATTGC
Found at i:17739541 original size:16 final size:16
Alignment explanation
Indices: 17739516--17739547 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17739506 ATAAATATAT
17739516 CAAAAAAATCAAAATC
1 CAAAAAAATCAAAATC
*
17739532 CAAAAGAATCAAAATC
1 CAAAAAAATCAAAATC
17739548 TAAATTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.19, G:0.03, T:0.12
Consensus pattern (16 bp):
CAAAAAAATCAAAATC
Found at i:17742071 original size:34 final size:35
Alignment explanation
Indices: 17742043--17742149 Score: 153
Period size: 35 Copynumber: 3.1 Consensus size: 35
17742033 GGAGTGCGTG
17742043 TGATGATATTGAAATGTGCGTGTA-GGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTACGGAGTGCACA
* *
17742077 TGATGATATTGAAATATGCGTGTACAGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTACGGAGTGCACA
*** *
17742112 TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTACGGAGTGCACA
17742147 TGA
1 TGA
17742150 GCTAAGTAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
34 23 0.36
35 41 0.64
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGTACGGAGTGCACA
Found at i:17742187 original size:2 final size:2
Alignment explanation
Indices: 17742180--17742226 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
17742170 TGTACATGTT
17742180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17742222 TA TA T
1 TA TA T
17742227 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17751774 original size:15 final size:15
Alignment explanation
Indices: 17751754--17751784 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17751744 AGACTCGGTC
17751754 AATAAAATAAGAAAA
1 AATAAAATAAGAAAA
*
17751769 AATAAAATAATAAAA
1 AATAAAATAAGAAAA
17751784 A
1 A
17751785 GAATGTGTGT
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:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AATAAAATAAGAAAA
Found at i:17754093 original size:21 final size:21
Alignment explanation
Indices: 17754045--17754093 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
17754035 GAATAGGATG
*
17754045 GTAGGAACTAGGGAAGCAGGAA
1 GTAGG-ACCAGGGAAGCAGGAA
** *
17754067 ACAGGACCAGGGAAGTAGGAA
1 GTAGGACCAGGGAAGCAGGAA
17754088 GTAGGA
1 GTAGGA
17754094 ATCAGAAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.41, C:0.10, G:0.41, T:0.08
Consensus pattern (21 bp):
GTAGGACCAGGGAAGCAGGAA
Found at i:17756503 original size:2 final size:2
Alignment explanation
Indices: 17756496--17756562 Score: 98
Period size: 2 Copynumber: 33.0 Consensus size: 2
17756486 ATGTATTCGT
* * *
17756496 TA TA TA TA TA AA TA TA AA TNA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
17756539 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
17756563 AGAGTTACTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 56 0.97
3 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:17758420 original size:29 final size:29
Alignment explanation
Indices: 17758388--17758443 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
17758378 TTTAACTCAA
17758388 AATAAAAATATAAAAACTTAATTAAATAT
1 AATAAAAATATAAAAACTTAATTAAATAT
* *
17758417 AATAAAAATATAAAAATTTATTTAAAT
1 AATAAAAATATAAAAACTTAATTAAAT
17758444 TTTTATGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (29 bp):
AATAAAAATATAAAAACTTAATTAAATAT
Found at i:17771366 original size:2 final size:2
Alignment explanation
Indices: 17771359--17771388 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17771349 ATCACTGGTA
17771359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17771389 TTTGTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17772623 original size:8 final size:8
Alignment explanation
Indices: 17772599--17772637 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
17772589 GGCTAAAAAA
17772599 TTAATAAT
1 TTAATAAT
17772607 TTAATTAAT
1 TTAA-TAAT
17772616 TTAATAAT
1 TTAATAAT
*
17772624 TTTATATAT
1 TTAATA-AT
17772633 TTAAT
1 TTAAT
17772638 TATCAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 13 0.48
9 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTAATAAT
Found at i:17772753 original size:15 final size:17
Alignment explanation
Indices: 17772723--17772762 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
17772713 GAATTAAATT
17772723 ATAAAATAATTTTATTA
1 ATAAAATAATTTTATTA
17772740 ATAAAA-AA-TTTATTA
1 ATAAAATAATTTTATTA
17772755 AGTAAAAT
1 A-TAAAAT
17772763 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
ATAAAATAATTTTATTA
Found at i:17776021 original size:39 final size:40
Alignment explanation
Indices: 17775967--17776056 Score: 137
Period size: 39 Copynumber: 2.2 Consensus size: 40
17775957 TCTTAACGTG
*
17775967 TTTCGTGTCTAATCATGTCTGACACATTAAGACAC-AAAT
1 TTTCGTGTCTAATCATATCTGACACATTAAGACACAAAAT
**
17776006 TTTCGTGTCTAATCATATCTGACATGTTAAGACACGAAAAT
1 TTTCGTGTCTAATCATATCTGACACATTAAGACAC-AAAAT
17776047 TTTCGTGTCT
1 TTTCGTGTCT
17776057 TAACGTGTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 32 0.70
41 14 0.30
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (40 bp):
TTTCGTGTCTAATCATATCTGACACATTAAGACACAAAAT
Found at i:17779027 original size:60 final size:60
Alignment explanation
Indices: 17778934--17779054 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
17778924 TATAGAGTAC
*
17778934 ATATTATAGGACAGAAAATCACTTAATTATTTAGTTTATTATACATAAATTAGCAAATTA
1 ATATTATAGGACAGAAAATCACTTAATTATTTAGTTTAGTATACATAAATTAGCAAATTA
** *
17778994 ATATTATAGGACAGAAAATCGTTTAATTATTTAGTTTAGTATACATGAATTAGCAAATTA
1 ATATTATAGGACAGAAAATCACTTAATTATTTAGTTTAGTATACATAAATTAGCAAATTA
17779054 A
1 A
17779055 GGATAAAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (60 bp):
ATATTATAGGACAGAAAATCACTTAATTATTTAGTTTAGTATACATAAATTAGCAAATTA
Found at i:17790520 original size:12 final size:12
Alignment explanation
Indices: 17790503--17790543 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
17790493 ACTTTCCATA
*
17790503 ATATATATATAT
1 ATATATATTTAT
17790515 ATATATATTTAT
1 ATATATATTTAT
* *
17790527 TTATTTATTTAT
1 ATATATATTTAT
17790539 ATATA
1 ATATA
17790544 AAAAGGTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATATATTTAT
Found at i:17800566 original size:23 final size:24
Alignment explanation
Indices: 17800520--17800570 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
17800510 AAATGTTATG
*
17800520 ATATGTTTTATATGATATACACAT
1 ATATGTTTTATATGATATAAACAT
*
17800544 ATATGTTTT-TATTATATAAACAT
1 ATATGTTTTATATGATATAAACAT
17800567 ATAT
1 ATAT
17800571 AATAATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (24 bp):
ATATGTTTTATATGATATAAACAT
Found at i:17800570 original size:25 final size:24
Alignment explanation
Indices: 17800520--17800571 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
17800510 AAATGTTATG
*
17800520 ATATGTTTTATATGATATACACAT
1 ATATGTTTTATATGATAAACACAT
*
17800544 ATATGTTTTTATTAT-ATAAACATAT
1 ATATG-TTTTA-TATGATAAACACAT
17800569 ATA
1 ATA
17800572 ATAATATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 16 0.67
26 3 0.12
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (24 bp):
ATATGTTTTATATGATAAACACAT
Found at i:17803824 original size:25 final size:25
Alignment explanation
Indices: 17803796--17803848 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
17803786 TAATGTTGGC
17803796 AATTACCACATGAATAACCAAAAGG
1 AATTACCACATGAATAACCAAAAGG
* *
17803821 AATTATCACATGAATAACTAAAAGG
1 AATTACCACATGAATAACCAAAAGG
17803846 AAT
1 AAT
17803849 CATGTAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (25 bp):
AATTACCACATGAATAACCAAAAGG
Found at i:17807590 original size:2 final size:2
Alignment explanation
Indices: 17807583--17807672 Score: 119
Period size: 2 Copynumber: 42.5 Consensus size: 2
17807573 ATTCTAAATG
17807583 AT AT AT AT AT AT AT AT AT AT AT AT ANT ACT -T ACT ACT ACT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT A-T A-T A-T AT A-T
17807628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17807670 AT A
1 AT A
17807673 AAACAAGTTA
Statistics
Matches: 83, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
1 1 0.01
2 69 0.83
3 13 0.16
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17812615 original size:20 final size:20
Alignment explanation
Indices: 17812572--17812629 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
17812562 TTGTCCAAAG
* *
17812572 TAATTATTTGAAATGAAATTA
1 TAATTATTTG-AATAAAATAA
*
17812593 TAATTGTTTGAATAAAATAA
1 TAATTATTTGAATAAAATAA
17812613 TAA-TATTT-AATAAAATA
1 TAATTATTTGAATAAAATA
17812630 TTCTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.27
19 4 0.12
20 11 0.33
21 9 0.27
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (20 bp):
TAATTATTTGAATAAAATAA
Found at i:17812626 original size:18 final size:18
Alignment explanation
Indices: 17812603--17812658 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
17812593 TAATTGTTTG
17812603 AATAAAATAATAATATTT
1 AATAAAATAATAATATTT
* * *
17812621 AATAAAATATTCTATTTTT
1 AATAAAATAAT-AATATTT
* *
17812640 TATAAAAAAATAATATTT
1 AATAAAATAATAATATTT
17812658 A
1 A
17812659 TAGAAAAATT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAAATAATAATATTT
Found at i:17815884 original size:15 final size:15
Alignment explanation
Indices: 17815866--17815898 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17815856 AAAACAATAT
17815866 TTTAAAATCAAAAAC
1 TTTAAAATCAAAAAC
*
17815881 TTTAAAATCAAAATC
1 TTTAAAATCAAAAAC
17815896 TTT
1 TTT
17815899 GATCTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TTTAAAATCAAAAAC
Found at i:17816293 original size:20 final size:20
Alignment explanation
Indices: 17816250--17816307 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
17816240 TTGTCTAAAG
* *
17816250 TAATTATTTGAAATGAAATTA
1 TAATTATTTG-AATAAAATAA
*
17816271 TAATTGTTTGAATAAAATAA
1 TAATTATTTGAATAAAATAA
17816291 TAA-TATTT-AATAAAATA
1 TAATTATTTGAATAAAATA
17816308 TTCTATTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.27
19 4 0.12
20 11 0.33
21 9 0.27
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (20 bp):
TAATTATTTGAATAAAATAA
Found at i:17828350 original size:27 final size:27
Alignment explanation
Indices: 17828299--17828350 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
17828289 ATATCCTGGT
*
17828299 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTGACCCTGA
*
17828326 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
17828351 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGA
Found at i:17828421 original size:20 final size:20
Alignment explanation
Indices: 17828396--17828441 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
17828386 CTTCTAAACC
17828396 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
17828416 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
17828436 TCAAAT
1 TCAAAT
17828442 GAGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:17833495 original size:14 final size:14
Alignment explanation
Indices: 17833476--17833511 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17833466 AATTAGTAGG
*
17833476 TTTTAGTTTAATTA
1 TTTTAGGTTAATTA
17833490 TTTTAGGTTAATTA
1 TTTTAGGTTAATTA
*
17833504 ATTTAGGT
1 TTTTAGGT
17833512 GAGTTAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (14 bp):
TTTTAGGTTAATTA
Found at i:17834661 original size:2 final size:2
Alignment explanation
Indices: 17834654--17834712 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
17834644 AACAAAGTTA
17834654 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17834696 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
17834713 CAATAATTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17835290 original size:54 final size:54
Alignment explanation
Indices: 17835231--17835339 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
17835221 AATAAAATAA
*
17835231 TATTTTATTAATAAAATAATATTAAAATATTAATATTTTATTTAGTGTCGAAAT
1 TATTTTATTAATAAAATAATATTAAAATATTAATATATTATTTAGTGTCGAAAT
*
17835285 TATTTTATTAATAAAATAATTTTAAAATATTAATATATTATTTAGTGTCGAAAT
1 TATTTTATTAATAAAATAATATTAAAATATTAATATATTATTTAGTGTCGAAAT
17835339 T
1 T
17835340 TTTCATGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.49
Consensus pattern (54 bp):
TATTTTATTAATAAAATAATATTAAAATATTAATATATTATTTAGTGTCGAAAT
Found at i:17836048 original size:16 final size:16
Alignment explanation
Indices: 17836043--17836105 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
17836033 AAGGAGAAAG
17836043 GAAA-GAAAGAAAGGA
1 GAAAGGAAAGAAAGGA
17836058 GAAAGGAAA-AGAAGGA
1 GAAAGGAAAGA-AAGGA
*
17836074 GAAGAAGAAAGAAAAAGAGA
1 GAA-AGGAAAG--AAAG-GA
17836094 GAAAGG-AAGAAA
1 GAAAGGAAAGAAA
17836106 AGCTTGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
15 5 0.13
16 15 0.38
17 5 0.13
18 3 0.08
19 5 0.13
20 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAAGGAAAGAAAGGA
Found at i:17836054 original size:20 final size:20
Alignment explanation
Indices: 17836029--17836105 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 20
17836019 GGTCGGTTGG
17836029 AAGAAAGGAGAAAGGAAAGA
1 AAGAAAGGAGAAAGGAAAGA
17836049 AAGAAAGGAGAAAGGAAAAGA
1 AAGAAAGGAGAAAGG-AAAGA
* * *
17836070 AGGAGAAGAAGAAAGAAAAAGA
1 AAGA-AAGGAGAAAG-GAAAGA
*
17836092 GAGAAAGGAAGAAA
1 AAGAAAGG-AGAAA
17836106 AGCTTGGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.32
21 11 0.23
22 21 0.45
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AAGAAAGGAGAAAGGAAAGA
Found at i:17836073 original size:36 final size:36
Alignment explanation
Indices: 17836033--17836101 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
17836023 GGTTGGAAGA
*
17836033 AAGGAGAA-AGGAAAGAAAGAA-AGGAGAAAGGAAAAG
1 AAGGAGAAGAAGAAAGAAA-AAGA-GAGAAAGGAAAAG
17836069 AAGGAGAAGAAGAAAGAAAAAGAGAGAAAGGAA
1 AAGGAGAAGAAGAAAGAAAAAGAGAGAAAGGAA
17836102 GAAAAGCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (36 bp):
AAGGAGAAGAAGAAAGAAAAAGAGAGAAAGGAAAAG
Found at i:17837592 original size:20 final size:20
Alignment explanation
Indices: 17837564--17837603 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17837554 AATAAATATC
* *
17837564 TAAATTTCCAATAGCTTCTT
1 TAAACTTCCAACAGCTTCTT
17837584 TAAACTTCCAACAGCTTCTT
1 TAAACTTCCAACAGCTTCTT
17837604 CTTCTGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAACTTCCAACAGCTTCTT
Found at i:17838556 original size:35 final size:35
Alignment explanation
Indices: 17838517--17838585 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
17838507 GAGTGCGTGG
*
17838517 GATGATATTGAAATGTGCTTGTAGGGAGTGCACAT
1 GATGATATTGAAATGTGCGTGTAGGGAGTGCACAT
***
17838552 GATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
1 GATGATATTGAAATGTGCGTGTAGGGAGTGCACA
17838586 AGAGCTGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.30
Consensus pattern (35 bp):
GATGATATTGAAATGTGCGTGTAGGGAGTGCACAT
Found at i:17838658 original size:21 final size:21
Alignment explanation
Indices: 17838625--17838680 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
17838615 TTTATATATT
* *
17838625 TATACGCTATAGAGATGTTTA
1 TATATGCTATAGAAATGTTTA
*
17838646 TATATGCTGTAGAAATGTTTA
1 TATATGCTATAGAAATGTTTA
17838667 TATATGCTAT-GAAA
1 TATATGCTATAGAAA
17838681 AAGTTAAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (21 bp):
TATATGCTATAGAAATGTTTA
Found at i:17842984 original size:43 final size:42
Alignment explanation
Indices: 17842914--17843041 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 42
17842904 CCCTCCACAC
* * *
17842914 TCAGCTCATGTGCACTCCCTACTCGCACATGGCCGGGTCATCA
1 TCAGCTCATGTGCACT-CCTACACGCACATAGCTGGGTCATCA
*
17842957 TCAGCTCATGTGCACTCCTACACCGCACATAACTGGGTCATCA
1 TCAGCTCATGTGCACTCCTACA-CGCACATAGCTGGGTCATCA
* * *
17843000 TAACCTCATGTGCACTCCCACACGCACATAG-TGGGTCATCA
1 TCAGCTCATGTGCACTCCTACACGCACATAGCTGGGTCATCA
17843041 T
1 T
17843042 TATCACACAA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 11 0.14
42 13 0.17
43 52 0.68
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.23
Consensus pattern (42 bp):
TCAGCTCATGTGCACTCCTACACGCACATAGCTGGGTCATCA
Found at i:17844317 original size:42 final size:42
Alignment explanation
Indices: 17844265--17844390 Score: 207
Period size: 42 Copynumber: 3.0 Consensus size: 42
17844255 GTAATGATAT
*
17844265 TGACCTGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
*
17844307 TGACCCGGCTATGTGCAAGTGGGAGTGCACATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
* * *
17844349 TGACCCGACTATGTGCGAGTGGGAGTACGCATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
17844391 ATATGAGATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.22
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
Found at i:17844697 original size:21 final size:21
Alignment explanation
Indices: 17844663--17844725 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
17844653 TTGTCCAGCT
*
17844663 AAATTTCACTGCAGCGAGAAA
1 AAATCTCACTGCAGCGAGAAA
* * *
17844684 GAATCTCGCTGCAGCTAGAAA
1 AAATCTCACTGCAGCGAGAAA
17844705 AAATCTCACTGCAGCGAGAAA
1 AAATCTCACTGCAGCGAGAAA
17844726 CCTTATGTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (21 bp):
AAATCTCACTGCAGCGAGAAA
Found at i:17844875 original size:19 final size:19
Alignment explanation
Indices: 17844853--17844889 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17844843 GGTTTGGTGA
17844853 GAAACCCTCGGTTAGTTGG
1 GAAACCCTCGGTTAGTTGG
17844872 GAAACCCTCGGTTAGTTG
1 GAAACCCTCGGTTAGTTG
17844890 ATAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (19 bp):
GAAACCCTCGGTTAGTTGG
Found at i:17851985 original size:42 final size:41
Alignment explanation
Indices: 17851926--17852035 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 41
17851916 TATTGACACG
17851926 GCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTGACCC
1 GCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTGACCC
*
17851967 AGCTATGTGCAAGTGGGAGTGCACATAAGCCGTTGCTGACCC
1 -GCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTGACCC
* *
17852009 GACTATGTGTGAGTGGGAGTGCGCATA
1 G-CTATGTGCGAGTGGGAGTGCACATA
17852036 TGAGATGATG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 62 0.98
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.23
Consensus pattern (41 bp):
GCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTGACCC
Found at i:17854287 original size:19 final size:19
Alignment explanation
Indices: 17854263--17854300 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17854253 CCATTTAACT
17854263 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
17854282 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
17854301 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:17855555 original size:13 final size:13
Alignment explanation
Indices: 17855537--17855561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17855527 GGAGAAATTG
17855537 TGATTTTATAAAA
1 TGATTTTATAAAA
17855550 TGATTTTATAAA
1 TGATTTTATAAA
17855562 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Done.