Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 88 of 204
Found at i:26996418 original size:50 final size:50
Alignment explanation
Indices: 26996307--26996553 Score: 241
Period size: 50 Copynumber: 4.8 Consensus size: 50
26996297 ATTTGGGTAA
26996307 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
26996363 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
26996413 AGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGATC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
26996463 AGA-ACTCTCATGTAAGACCATATCTGGAATATGACATTGGCA--GTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * * *
26996512 AAACATCCCATGTAAGACCATATCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
26996554 TGTTATTATC
Statistics
Matches: 165, Mismatches: 21, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 78 0.47
51 2 0.01
53 3 0.02
55 2 0.01
56 40 0.24
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:26998981 original size:43 final size:43
Alignment explanation
Indices: 26998907--26998990 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
26998897 CATTGACGTC
* *
26998907 TTATATGATTACGTGTAAGACCCTGTGTGGGACAG-TGGCATCG
1 TTATATGATTACATATAAGACCCTGTGTGGGA-AGTTGGCATCG
* *
26998950 TTATTTGATTACATATAAGACCAC-GTTTGGGAAGTTGGCAT
1 TTATATGATTACATATAAGACC-CTGTGTGGGAAGTTGGCAT
26998991 TGTACGAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
42 2 0.06
43 32 0.91
44 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
TTATATGATTACATATAAGACCCTGTGTGGGAAGTTGGCATCG
Found at i:27005056 original size:11 final size:11
Alignment explanation
Indices: 27005039--27005077 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27005029 TTTTTGGAGT
27005039 TTACAATATAA
1 TTACAATATAA
* *
27005050 ATACAATACAA
1 TTACAATATAA
*
27005061 TTATAATATAA
1 TTACAATATAA
27005072 TTACAA
1 TTACAA
27005078 ATACATGCCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (11 bp):
TTACAATATAA
Found at i:27010692 original size:11 final size:11
Alignment explanation
Indices: 27010673--27010705 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
27010663 TCTAGTATTC
27010673 AATAAAAT-AA
1 AATAAAATAAA
27010683 AATAAAAATAAA
1 AAT-AAAATAAA
27010695 AATAAAATAAA
1 AATAAAATAAA
27010706 GGGCAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 13 0.62
12 5 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:27012315 original size:18 final size:19
Alignment explanation
Indices: 27012294--27012336 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
27012284 TAAATAATTT
27012294 AAAAATTATAAAAATA-AA
1 AAAAATTATAAAAATATAA
*
27012312 AAAAATTATAAAATTATAA
1 AAAAATTATAAAAATATAA
27012331 AAAAAT
1 AAAAAT
27012337 AAAAAAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTATAAAAATATAA
Found at i:27016287 original size:23 final size:25
Alignment explanation
Indices: 27016259--27016317 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 25
27016249 TTAAATATAA
*
27016259 AATATTTTA-TATTAAATTA-ATT-T
1 AATATTTTATTA-TAAATTATATTAG
27016282 AATATTTTATTATAAATTATATTAG
1 AATATTTTATTATAAATTATATTAG
27016307 AATATTTTATT
1 AATATTTTATT
27016318 TCATATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 16 0.50
24 5 0.16
25 11 0.34
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
AATATTTTATTATAAATTATATTAG
Found at i:27016411 original size:64 final size:59
Alignment explanation
Indices: 27016281--27016443 Score: 202
Period size: 64 Copynumber: 2.6 Consensus size: 59
27016271 TAAATTAATT
* *
27016281 TAATATTTTATTATAAATTATATTAGAATATTTTATTTCATATTTTCTGAAATTTGAAAA
1 TAATATTTTATT-TAAATTATATTAAAATATTTTATTTAATATTTTCTGAAATTTGAAAA
*
27016341 TAATATTTTATATTAAATTATATTAAAATGTTTTATTATTATAATATTTTCTGAAATTT-ATAAA
1 TAATATTTTAT-TTAAATTATATTAAAA--TATT-TTATT-TAATATTTTCTGAAATTTGA-AAA
* *
27016405 TAATATTTTATGTTAAATTATATTAAAAGATTTTTTTTA
1 TAATATTTTAT-TTAAATTATATTAAAATATTTTATTTA
27016444 TTTTTATATT
Statistics
Matches: 90, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
60 27 0.30
61 5 0.06
62 5 0.06
63 6 0.07
64 47 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (59 bp):
TAATATTTTATTTAAATTATATTAAAATATTTTATTTAATATTTTCTGAAATTTGAAAA
Found at i:27019373 original size:53 final size:53
Alignment explanation
Indices: 27019294--27019394 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 53
27019284 AATTTTTCCT
* * * *
27019294 ATATGATGCCATAATCCACAAATTACGATTTTACACGGTATAGTCTTCTTTTC
1 ATATGATACCATAACCCACAAATTACGATCTTACACGATATAGTCTTCTTTTC
* * *
27019347 ATATGATACCATAACCCACCAGTTACGATCTTACACGATATGGTCTTC
1 ATATGATACCATAACCCACAAATTACGATCTTACACGATATAGTCTTC
27019395 AACGCTATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (53 bp):
ATATGATACCATAACCCACAAATTACGATCTTACACGATATAGTCTTCTTTTC
Found at i:27022647 original size:13 final size:13
Alignment explanation
Indices: 27022629--27022704 Score: 64
Period size: 13 Copynumber: 5.7 Consensus size: 13
27022619 GTAGTCGTTT
*
27022629 TATGAATTAGTTA
1 TATGAAATAGTTA
* *
27022642 TATGAAAAATGATA
1 TATGAAATA-GTTA
*
27022656 TATGAAATGGTTA
1 TATGAAATAGTTA
*
27022669 TATG-AATCAATTA
1 TATGAAAT-AGTTA
*
27022682 TATGGAAATAGATA
1 TAT-GAAATAGTTA
27022696 TATGAAATA
1 TATGAAATA
27022705 AAACATTGGA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
12 3 0.06
13 26 0.53
14 17 0.35
15 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.16, T:0.36
Consensus pattern (13 bp):
TATGAAATAGTTA
Found at i:27022673 original size:40 final size:40
Alignment explanation
Indices: 27022600--27022703 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
27022590 GATAAATATG
* * * * * * *
27022600 TATATGAAAAATGGTATAGGTAGTCGTTTTATGAATTAGT
1 TATATGAAAAATGATATATGAAATCGTTATATGAATCAAT
*
27022640 TATATGAAAAATGATATATGAAATGGTTATATGAATCAAT
1 TATATGAAAAATGATATATGAAATCGTTATATGAATCAAT
*
27022680 TATATG-GAAATAGATATATGAAAT
1 TATATGAAAAAT-GATATATGAAAT
27022704 AAAACATTGG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 4 0.07
40 50 0.93
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (40 bp):
TATATGAAAAATGATATATGAAATCGTTATATGAATCAAT
Found at i:27022842 original size:40 final size:40
Alignment explanation
Indices: 27022798--27022885 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
27022788 TTATAATGTT
*
27022798 TATGAAAAATAATATAGGTAATGGTTATATAAATCAGTTA
1 TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
* * *
27022838 TATGAAAAATAATATATGAAATTGTTATATGAATCAGTTA
1 TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
*
27022878 TACGAAAA
1 TATGAAAA
27022886 GAGACATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (40 bp):
TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
Found at i:27022895 original size:40 final size:40
Alignment explanation
Indices: 27022801--27022908 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 40
27022791 TAATGTTTAT
* * * *
27022801 GAAAAATAATATAGGTAA-TGGTTATATAAATCAGTTATAT
1 GAAAAATAACATATG-AATTGGTTATATGAATCAGTTATAC
*
27022841 GAAAAATAATATATGAAATT-GTTATATGAATCAGTTATAC
1 GAAAAATAACATATG-AATTGGTTATATGAATCAGTTATAC
*
27022881 GAAAAGA-GACATATGAATTGGTTATATG
1 GAAAA-ATAACATATGAATTGGTTATATG
27022909 GAAATAGATA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 4 0.07
40 53 0.90
41 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (40 bp):
GAAAAATAACATATGAATTGGTTATATGAATCAGTTATAC
Found at i:27022921 original size:27 final size:27
Alignment explanation
Indices: 27022850--27022922 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
27022840 TGAAAAATAA
* *
27022850 TATAT-GAAATTGTTATATGAATCAGT
1 TATATGGAAATAGATATATGAATCAGT
* * * * **
27022876 TATACGAAAAGAGACATATGAATTGGT
1 TATATGGAAATAGATATATGAATCAGT
27022903 TATATGGAAATAGATATATG
1 TATATGGAAATAGATATATG
27022923 GAATAGAACA
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.34
Consensus pattern (27 bp):
TATATGGAAATAGATATATGAATCAGT
Found at i:27024630 original size:16 final size:16
Alignment explanation
Indices: 27024609--27024640 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27024599 GGATAGGAAA
27024609 AAAGAGAGTTTTTTTT
1 AAAGAGAGTTTTTTTT
27024625 AAAGAGAGTTTTTTTT
1 AAAGAGAGTTTTTTTT
27024641 CTTCCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (16 bp):
AAAGAGAGTTTTTTTT
Found at i:27034721 original size:48 final size:48
Alignment explanation
Indices: 27034665--27034760 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
27034655 TTTGTGACAG
*
27034665 TTAGAGTGCTATCTTCCTTACAAAAGATCAAATGTTTCATGAGAGAAC
1 TTAGAGTGCTATCTTCCTTACAAAAGATCAAATGTTTCACGAGAGAAC
27034713 TTAGAGTGCTATCTTCCTTACAAAAGATCAAATGTTTCACGAGAGAAC
1 TTAGAGTGCTATCTTCCTTACAAAAGATCAAATGTTTCACGAGAGAAC
27034761 AAAACATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (48 bp):
TTAGAGTGCTATCTTCCTTACAAAAGATCAAATGTTTCACGAGAGAAC
Found at i:27035988 original size:27 final size:27
Alignment explanation
Indices: 27035937--27035989 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
27035927 ATAATGGTTT
*
27035937 AAAGAAATTGTTGATTGAACGTCTCTC
1 AAAGAAATTGTTGATTGAACATCTCTC
*
27035964 AAAGAAATTGTTGATTGAATATCTCT
1 AAAGAAATTGTTGATTGAACATCTCT
27035990 TATTAATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (27 bp):
AAAGAAATTGTTGATTGAACATCTCTC
Found at i:27048815 original size:24 final size:25
Alignment explanation
Indices: 27048782--27048830 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
27048772 AAGTATATAT
*
27048782 ATGTATATATA-AATTATAAAATAC
1 ATGTACATATAGAATTATAAAATAC
*
27048806 ATGTACATATATGTATTATAAAATA
1 ATGTACATATA-GAATTATAAAATA
27048831 TATATAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
26 11 0.52
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (25 bp):
ATGTACATATAGAATTATAAAATAC
Found at i:27048842 original size:26 final size:26
Alignment explanation
Indices: 27048794--27048847 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
27048784 GTATATATAA
* *
27048794 ATTATAAAATACATGTACATATATGT
1 ATTATAAAATACATATACATATACGT
*
27048820 ATTATAAAATATATATA-AGTATACGT
1 ATTATAAAATACATATACA-TATACGT
27048846 AT
1 AT
27048848 ATTTTAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (26 bp):
ATTATAAAATACATATACATATACGT
Found at i:27048948 original size:58 final size:56
Alignment explanation
Indices: 27048871--27048979 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
27048861 ATATACAAAA
* * *
27048871 AAGAATATATGTATGTATATATATATAGGAGTTATAAAATGTAAAACACATATATTAT
1 AAGAATATATGTATATATATAT-TATA-AAGTTATAAAATATAAAACACATATATTAT
* *
27048929 AAGAAT-TCATGTATATATATATTTTAAAGTTATAGAATATAAAACACATAT
1 AAGAATAT-ATGTATATATATATTATAAAGTTATAAAATATAAAACACATAT
27048980 GTATGTATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
56 22 0.49
57 4 0.09
58 19 0.42
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (56 bp):
AAGAATATATGTATATATATATTATAAAGTTATAAAATATAAAACACATATATTAT
Found at i:27050708 original size:44 final size:43
Alignment explanation
Indices: 27050660--27050989 Score: 155
Period size: 44 Copynumber: 7.7 Consensus size: 43
27050650 ATCATTTTAA
*
27050660 TCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTTTCTTTTG
* ** * *
27050704 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTG-ATC---CG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTTTCTTTTG
* * ** * * **
27050743 ATCTACTCTACTGCAACTTCAAAGAGATAATATCTGTGGT-TTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGT-TTCTTTTG
* * *
27050788 TCCGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTTTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTTTCTTTTG
* * ** * *
27050832 TCTGCTCTACTACTGCTT-AGGGAGATAAGACTTGATGC----G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTTTCTTTTG
* * * * **
27050871 ATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGT-TTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGT-TTCTTTTG
* * *
27050916 TCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTTTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTTTCTTTTG
* **
27050960 TCTGCTCCACTACTGCTT-AGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
27050990 CTTGATGCGA
Statistics
Matches: 205, Mismatches: 59, Indels: 45
0.66 0.19 0.15
Matches are distributed among these distances:
39 2 0.01
40 29 0.14
41 24 0.12
42 2 0.01
43 42 0.20
44 106 0.52
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTTTCTTTTG
Found at i:27050856 original size:128 final size:128
Alignment explanation
Indices: 27050654--27051079 Score: 701
Period size: 128 Copynumber: 3.3 Consensus size: 128
27050644 TGATTCATCA
* *
27050654 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACTG
* * * *
27050719 CTTAGGGAGATAAGACTTGATCCGATCTACTCTACTGCAACTTCAAAGAGATAATATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAATATCTGTGG
** *
27050782 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCTACTACTG
1 TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACTG
*
27050847 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAATATCTGTGG
27050910 TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACTG
* * *
27050975 CTTAGGGAGATAAGACTTGATGCGATATGCTCTACTGTAACTTTAGAGAGATAATATATGT-G
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAATATCTGTGG
* * *
27051037 TTTTAATCTGCTCCACTACAACTTTAGAGAGATAGGATTGGTT
1 TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTT
27051080 CTTCCGATCT
Statistics
Matches: 280, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
127 41 0.15
128 239 0.85
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (128 bp):
TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACTG
CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAATATCTGTGG
Found at i:27051278 original size:45 final size:45
Alignment explanation
Indices: 27051091--27051279 Score: 263
Period size: 45 Copynumber: 4.2 Consensus size: 45
27051081 TTCCGATCTG
* ** * * *
27051091 CTTCACTGCCAGTACAGGAAGGTAAGATCTGCTATCTGCGACCTA
1 CTTCACTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
* *
27051136 CTTCGCTGCCAATATC-GGAAGACAAGATCTACAATCTTTGACCTA
1 CTTCACTGCCAATA-CAGGAAGACAAGATCTACAATCTTCGACCTA
*
27051181 CTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
1 CTTCACTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
*
27051226 CTTCACTGCCAATATAGGAAGACAAGATCTACAATCTTCGACCTA
1 CTTCACTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
*
27051271 CTCCACTGC
1 CTTCACTGC
27051280 TGTTCAGAGA
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.01
45 128 0.98
46 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (45 bp):
CTTCACTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
Found at i:27051996 original size:45 final size:45
Alignment explanation
Indices: 27051898--27051998 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
27051888 GCAAAGCTCG
* *
27051898 AAATGAATAAATCAATCAAGATAGCAAATTTTGCTAGAATACAAA
1 AAATGAATAAATCAATCAAGATAGCAAATTTGGCTAAAATACAAA
* * * **
27051943 ATGA-GAATAAATTAATCAAGATGGCGTATTTGG-TCAAAATACAAA
1 A-AATGAATAAATCAATCAAGATAGCAAATTTGGCT-AAAATACAAA
27051988 AAATGAATAAA
1 AAATGAATAAA
27051999 ATGGAAATAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
44 2 0.04
45 42 0.93
46 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (45 bp):
AAATGAATAAATCAATCAAGATAGCAAATTTGGCTAAAATACAAA
Found at i:27052292 original size:19 final size:19
Alignment explanation
Indices: 27052268--27052317 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
27052258 GGCCTCTCCT
27052268 TTTTCTTTTTTCGTTCTTC
1 TTTTCTTTTTTCGTTCTTC
* *
27052287 TTTTCTTTTCTT-TTTCTTT
1 TTTTCTTTT-TTCGTTCTTC
27052306 TTTTCTTTTTTC
1 TTTTCTTTTTTC
27052318 AAGTGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTTTCGTTCTTC
Found at i:27056864 original size:26 final size:26
Alignment explanation
Indices: 27056831--27056894 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
27056821 AAAAATATAA
**
27056831 AAAATATATATGTATATAT-TAATTAT
1 AAAATATATATACATATATGT-ATTAT
*
27056857 AAAATATATGTACATATATGTATTAT
1 AAAATATATATACATATATGTATTAT
27056883 AAAATATATATA
1 AAAATATATATA
27056895 AGTATACGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (26 bp):
AAAATATATATACATATATGTATTAT
Found at i:27056900 original size:26 final size:26
Alignment explanation
Indices: 27056826--27056905 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
27056816 TTTTCAAAAA
* * *
27056826 TATAAAAAATATATATGTATATATTAAT
1 TATAAAATATATATAAGTATAT-GT-AT
*
27056854 TATAAAATATATGTACA-TATATGTAT
1 TATAAAATATATATA-AGTATATGTAT
*
27056880 TATAAAATATATATAAGTATACGTAT
1 TATAAAATATATATAAGTATATGTAT
27056906 ATTTTAAGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 1 0.02
26 24 0.55
27 1 0.02
28 18 0.41
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (26 bp):
TATAAAATATATATAAGTATATGTAT
Found at i:27056908 original size:28 final size:26
Alignment explanation
Indices: 27056826--27056923 Score: 81
Period size: 28 Copynumber: 3.6 Consensus size: 26
27056816 TTTTCAAAAA
* *
27056826 TATAAAAAATATATATGTATATATTAAT
1 TATAAAATATATATAAGTATATA-T-AT
* *
27056854 TATAAAATATATGTACA-TATATGTAT
1 TATAAAATATATATA-AGTATATATAT
27056880 TATAAAATATATATAAGTATACGTATAT
1 TATAAAATATATATAAGTATA--TATAT
* *
27056908 TTTAAGATAGTATATA
1 TATAAAATA-TATATA
27056924 CAAAAAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
25 1 0.02
26 20 0.35
27 1 0.02
28 29 0.51
29 6 0.11
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (26 bp):
TATAAAATATATATAAGTATATATAT
Found at i:27064668 original size:11 final size:11
Alignment explanation
Indices: 27064652--27064676 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27064642 TACATTTCAT
27064652 AAATTATAATA
1 AAATTATAATA
27064663 AAATTATAATA
1 AAATTATAATA
27064674 AAA
1 AAA
27064677 GCGTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTATAATA
Found at i:27067831 original size:20 final size:20
Alignment explanation
Indices: 27067800--27067859 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
27067790 ATTTTAAAAT
*
27067800 CAAGTGAAAATGATTTTAAC
1 CAAGTTAAAATGATTTTAAC
* *
27067820 CAA-TTCAAAATGATTTCAAT
1 CAAGTT-AAAATGATTTTAAC
*
27067840 CAAGTTAAAATTATTTTAAC
1 CAAGTTAAAATGATTTTAAC
27067860 ACATCAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (20 bp):
CAAGTTAAAATGATTTTAAC
Found at i:27067856 original size:40 final size:40
Alignment explanation
Indices: 27067797--27067891 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
27067787 ATAATTTTAA
* *
27067797 AATCAAGTGAAAATGATTTTAAC-CAATTCAAAATGA-TTTC
1 AATCAAGTTAAAATTATTTTAACAC-A-TCAAAATGATTTTC
*
27067837 AATCAAGTTAAAATTATTTTAACACATCAAAATTATTTTC
1 AATCAAGTTAAAATTATTTTAACACATCAAAATGATTTTC
* *
27067877 AAACAAGTTAGAATT
1 AATCAAGTTAAAATT
27067892 GCTCCAGGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 8 0.17
40 39 0.81
41 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (40 bp):
AATCAAGTTAAAATTATTTTAACACATCAAAATGATTTTC
Found at i:27067891 original size:21 final size:21
Alignment explanation
Indices: 27067785--27067891 Score: 64
Period size: 20 Copynumber: 5.2 Consensus size: 21
27067775 GAAAATTTTG
* * *
27067785 AAATAATTTTAAAATCAAGTGA
1 AAATTATTTTCAAA-CAAGTTA
* *
27067807 AAATGATTTT-AACCAA-TTCA
1 AAATTATTTTCAAACAAGTT-A
* *
27067827 AAATGA-TTTCAATCAAGTTA
1 AAATTATTTTCAAACAAGTTA
*
27067847 AAATTATTTT--AACACA-TCA
1 AAATTATTTTCAAACA-AGTTA
27067866 AAATTATTTTCAAACAAGTTA
1 AAATTATTTTCAAACAAGTTA
*
27067887 GAATT
1 AAATT
27067892 GCTCCAGGCC
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 19 0.28
20 23 0.34
21 17 0.25
22 9 0.13
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (21 bp):
AAATTATTTTCAAACAAGTTA
Found at i:27078956 original size:44 final size:44
Alignment explanation
Indices: 27078889--27078982 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
27078879 GTCTCGACTT
*
27078889 TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAC
1 TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAA
* * *
27078933 TCATTTTCATATGCTTATTAAATATAAGTATTGTATTAATCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAA
27078977 TCATTT
1 TCATTT
27078983 ATTGAATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (44 bp):
TCATTTTCATATGCTTATCAAATATAAGTATTATATTAACCAAA
Found at i:27079358 original size:20 final size:19
Alignment explanation
Indices: 27079312--27079358 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
27079302 ACAAATATTT
27079312 AATTTT-TATATTTAAATA
1 AATTTTATATATTTAAATA
* * *
27079330 TAGTTTATATATTCTAATTA
1 AATTTTATATATT-TAAATA
27079350 AATTTTATA
1 AATTTTATA
27079359 AATAATCAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTATATATTTAAATA
Found at i:27079605 original size:13 final size:13
Alignment explanation
Indices: 27079584--27079660 Score: 127
Period size: 13 Copynumber: 5.9 Consensus size: 13
27079574 ACACTCAAAT
27079584 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
27079597 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
27079610 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
27079623 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
*
27079636 TTCTTAAAAGCAC
1 TTCTCAAAAGCAC
27079649 TTCTCAAAAGCA
1 TTCTCAAAAGCA
27079661 ATGAAGAACT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.25
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:27080723 original size:98 final size:98
Alignment explanation
Indices: 27080551--27080747 Score: 333
Period size: 98 Copynumber: 2.0 Consensus size: 98
27080541 TCGTAATAAA
* * * *
27080551 ACTTTAAAAGAACATCCACTTATTCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATATAAAAAATCACACCCAATACGTTAGGGCACAATT
27080616 CTTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CTTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
27080649 ACTTTAAAATAACATCCACTTATCCAAGATATAAAAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATATAAAAAATCACACCCAATACGTTAGGGCACAATT
27080714 CCTTC-AAAATCCCAAACTCGGAATATTTCCTTT
66 -CTTCTAAAATCCCAAACTCGGAATATTTCCTTT
27080747 A
1 A
27080748 TTATTTTTAG
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 89 0.96
99 4 0.04
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATATAAAAAATCACACCCAATACGTTAGGGCACAATT
CTTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:27082843 original size:44 final size:44
Alignment explanation
Indices: 27082792--27083640 Score: 489
Period size: 44 Copynumber: 19.6 Consensus size: 44
27082782 TCTACCTCAT
*
27082792 TGCAACTTCA-GGAGGATAAGACTTACTTACTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTACTTACTTAATCTGCTCCAC
** *
27082836 TGCAACTTCAGGGAGATAAGAC-TA--TA-TGCGATCTGCT-CTC
1 TGCAACTTCAGGGAGATAAGACTTACTTACT-TAATCTGCTCCAC
** * * **
27082876 TGCAACTTCAAAGAGATAAGATCTAAGGTT--TTAATCCACTCCAC
1 TGCAACTTCAGGGAGATAAGA-CTTA-CTTACTTAATCTGCTCCAC
* *
27082920 TGCAACTTCAGGGAGATAGGAC-TA-TCGACTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGACTTACT-TAC-TTAATCTGCTCCAC
* * * * *
27082964 TGCAACTTTAGGGAGATAAGACTTGC-CATCTTCAGTCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGACTTACTTA-CTT-AATCTGCTCCAC
* * *
27083009 TGCAATTTCA-GGAGGATAAGACTTGCTTACTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTACTTACTTAATCTGCTCCAC
** * * * *
27083053 TGCAACTTCAGGGAGATAAGAC-TAGATGC--GATCTGGT-CTC
1 TGCAACTTCAGGGAGATAAGACTTACTTACTTAATCTGCTCCAC
* * * *
27083093 TGCAACTTCAGAGAGATAAGATCTGAGGTT--TTAATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGA-CTTA-CTTACTTAATCTGCTCCAC
* ** *
27083137 TGCAACTTCAGGGAGATAGGAC-TA-TCGGCTTTAATCTGTTCCAC
1 TGCAACTTCAGGGAGATAAGACTTACT-TAC-TTAATCTGCTCCAC
* * * * *
27083181 TGCAACTTTAGGGAGATAAGACTTGC-CATCTTCAGTCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGACTTACTTA-CTT-AATCTGCTCCAC
* * * * *
27083226 TGCAAATTCAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCAT
1 TGCAACTTCAGGGAGATAAGACTTACTTACTTAATCTGCTCCAC
** * * *
27083270 TGCAACTTCAGGGAGATAAGAC-TAGATGC--GATCTGCT-CTC
1 TGCAACTTCAGGGAGATAAGACTTACTTACTTAATCTGCTCCAC
* * * *
27083310 TGCAACTTCAGAGAGATAAGATCTGAGGTT--TTAATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGA-CTTA-CTTACTTAATCTGCTCCAC
* * ** *
27083354 TGCAACTTCAGGGAGGTAGGAC-TA-TCGGCTTTAATCTGCTTCAC
1 TGCAACTTCAGGGAGATAAGACTTACT-TAC-TTAATCTGCTCCAC
* * * * *
27083398 TGCAACTTTAGGGAGATAAGACTTGC-CATCTTCAGTCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGACTTACTTA-CTT-AATCTGCTCCAC
* *
27083443 TGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTACTTACTTAATCTGCTCCAC
** * * * *
27083487 TGCAACTTCAGGGAGATAAGAC-TAGATGC--GATCTGGT-CTC
1 TGCAACTTCAGGGAGATAAGACTTACTTACTTAATCTGCTCCAC
* * * *
27083527 TGCAACTTCAGAGAGGTAAGATCTGAGGTT--TTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGA-CTTA-CTTACTTAATCTGCTCCAC
* **
27083571 TGCAACTTCAGGGAGATAGGAC-TA-TCGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGACTTACT-TAC-TTAATCTGCTCCAC
27083615 TGCAACTTCAGGGAGATAAGACTTAC
1 TGCAACTTCAGGGAGATAAGACTTAC
27083641 CATCTTCGAT
Statistics
Matches: 621, Mismatches: 121, Indels: 124
0.72 0.14 0.14
Matches are distributed among these distances:
40 90 0.14
41 28 0.05
42 8 0.01
43 43 0.07
44 330 0.53
45 119 0.19
46 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGACTTACTTACTTAATCTGCTCCAC
Found at i:27083047 original size:89 final size:88
Alignment explanation
Indices: 27082792--27083638 Score: 492
Period size: 84 Copynumber: 9.8 Consensus size: 88
27082782 TCTACCTCAT
* *
27082792 TGCAACTTCA-GGAGGATAAGACTTAC-TTACTTAGTCTGCTCCACTGCAACTTCAGG-GAGATA
1 TGCAACTTCAGGGA-GATAAGACTTGCATT--TCAGTCTGCTCCACTGCAACTTCAGGAGAGATA
* ** *
27082854 AGAC-T--ATA-TGCGATCTGCT-CTC
63 AGACTTGCTTACTTAG-TCTGCTCCAC
** * * * * ** *
27082876 TGCAACTTCAAAGAGATAAGATCTAAG-GTTTTAATCCACTCCACTGCAACTTCAGG-GAGATAG
1 TGCAACTTCAGGGAGATAAGA-CT-TGCATTTCAGTCTGCTCCACTGCAACTTCAGGAGAGATAA
* *
27082939 GACTAT-C-GACTTTAATCTGCTCCAC
64 GACT-TGCTTAC-TTAGTCTGCTCCAC
* * *
27082964 TGCAACTTTAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAATTTCAGGAG-GATAA
1 TGCAACTTCAGGGAGATAAGACTTG-CAT-TTCAGTCTGCTCCACTGCAACTTCAGGAGAGATAA
27083028 GACTTGCTTACTTAGTCTGCTCCAC
64 GACTTGCTTACTTAGTCTGCTCCAC
* * * *
27083053 TGCAACTTCAGGGAGATAAGACTAG-A-TGC-GATCTGGT-CTCTGCAACTTCA-GAGAGATAAG
1 TGCAACTTCAGGGAGATAAGACTTGCATTTCAG-TCTGCTCCACTGCAACTTCAGGAGAGATAAG
* * * *
27083113 ATCTGAGGTT--TTAATCCGCTCCAC
65 A-CT-TGCTTACTTAGTCTGCTCCAC
* * * *
27083137 TGCAACTTCAGGGAGATAGGACTATCGGC-TTT-AATCTGTTCCACTGCAACTTTAGG-GAGATA
1 TGCAACTTCAGGGAGATAAGACT-T--GCATTTCAGTCTGCTCCACTGCAACTTCAGGAGAGATA
* *
27083199 AGACTTGC-CATCTTCAGTCTGCCCCAC
63 AGACTTGCTTA-CTT-AGTCTGCTCCAC
* * * *
27083226 TGCAAATTCAGGAAGATAAGACTTGC-TTACTTAGTCTGCTCCATTGCAACTTCAGG-GAGATAA
1 TGCAACTTCAGGGAGATAAGACTTGCATT--TCAGTCTGCTCCACTGCAACTTCAGGAGAGATAA
* * * * *
27083289 GACTAG-ATGC-GA-TCTGCT-CTC
64 GACTTGCTTACTTAGTCTGCTCCAC
* * * * *
27083310 TGCAACTTCAGAGAGATAAGA-TCTG-AGGTTTTAATCCGCTCCACTGCAACTTCAGG-GAGGTA
1 TGCAACTTCAGGGAGATAAGACT-TGCA--TTTCAGTCTGCTCCACTGCAACTTCAGGAGAGATA
* * *
27083372 GGACTATCGGC-T--TTAATCTGCTTCAC
63 AGACT-T--GCTTACTTAGTCTGCTCCAC
* *
27083398 TGCAACTTTAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAG-GATAA
1 TGCAACTTCAGGGAGATAAGACTTG-CAT-TTCAGTCTGCTCCACTGCAACTTCAGGAGAGATAA
27083462 GACTTGCTTACTTAGTCTGCTCCAC
64 GACTTGCTTACTTAGTCTGCTCCAC
* * * * *
27083487 TGCAACTTCAGGGAGATAAGACTAG-A-TGC-GATCTGGT-CTCTGCAACTTCA-GAGAGGTAAG
1 TGCAACTTCAGGGAGATAAGACTTGCATTTCAG-TCTGCTCCACTGCAACTTCAGGAGAGATAAG
* * *
27083547 ATCTGAGGTT--TTAATCTGCTCCAC
65 A-CT-TGCTTACTTAGTCTGCTCCAC
* *
27083571 TGCAACTTCAGGGAGATAGGACTATCGGC-TTT-AATCTGCTCCACTGCAACTTCAGG-GAGATA
1 TGCAACTTCAGGGAGATAAGACT-T--GCATTTCAGTCTGCTCCACTGCAACTTCAGGAGAGATA
27083633 AGACTT
63 AGACTT
27083639 ACCATCTTCG
Statistics
Matches: 594, Mismatches: 102, Indels: 132
0.72 0.12 0.16
Matches are distributed among these distances:
83 7 0.01
84 210 0.35
85 25 0.04
86 22 0.04
87 35 0.06
88 95 0.16
89 195 0.33
90 5 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (88 bp):
TGCAACTTCAGGGAGATAAGACTTGCATTTCAGTCTGCTCCACTGCAACTTCAGGAGAGATAAGA
CTTGCTTACTTAGTCTGCTCCAC
Found at i:27083098 original size:173 final size:173
Alignment explanation
Indices: 27082919--27083248 Score: 397
Period size: 173 Copynumber: 1.9 Consensus size: 173
27082909 ATCCACTCCA
* * * *
27082919 CTGCAACTTCAGGGAGATAGGA-CT-ATCGACTTTAATCTGCTCCACTGCAACTTTAGGGAGATA
1 CTGCAACTTCAGAGAGATAAGATCTGA--GACTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
* *
27082982 AGACT-T-GCCATCTTCAGTCTGCCCCACTGCAA-TTTCA-GGAGGATAAGACTTG-CTTACTT-
64 AGACTATCGCC-T-TT-AATCTGCCCCACTGCAACTTT-AGGGA-GATAAGACTTGCCAT-CTTC
* * *
27083041 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGGTCT
123 AGTCTGCCCCACTGCAAATTCAGGAAGATAAGACTAGATGCGATCTGGTCT
** *
27083092 CTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGG
1 CTGCAACTTCAGAGAGATAAGATCTGAGACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAG
* **
27083157 ACTATCGGCTTTAATCTGTTCCACTGCAACTTTAGGGAGATAAGACTTGCCATCTTCAGTCTGCC
66 ACTATCGCCTTTAATCTGCCCCACTGCAACTTTAGGGAGATAAGACTTGCCATCTTCAGTCTGCC
27083222 CCACTGCAAATTCAGGAAGATAAGACT
131 CCACTGCAAATTCAGGAAGATAAGACT
27083249 TGCTTACTTA
Statistics
Matches: 134, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
172 29 0.22
173 98 0.73
174 4 0.03
175 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (173 bp):
CTGCAACTTCAGAGAGATAAGATCTGAGACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAG
ACTATCGCCTTTAATCTGCCCCACTGCAACTTTAGGGAGATAAGACTTGCCATCTTCAGTCTGCC
CCACTGCAAATTCAGGAAGATAAGACTAGATGCGATCTGGTCT
Found at i:27083147 original size:217 final size:217
Alignment explanation
Indices: 27082772--27083647 Score: 1554
Period size: 217 Copynumber: 4.0 Consensus size: 217
27082762 GGAATTAGTC
* * * *
27082772 CCATCTTCAGTCTACCTCATTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCTCCACT
1 CCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACT
* * *
27082837 GCAACTTCAGGGAGATAAGACTATATGCGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTAA
66 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGA
* *
27082902 GGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGACTATCGACTTTAATCTGCTCCACTGC
131 GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTATCGGCTTTAATCTGCTCCACTGC
27082967 AACTTTAGGGAGATAAGACTTG
196 AACTTTAGGGAGATAAGACTTG
*
27082989 CCATCTTCAGTCTGCCCCACTGCAATTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACT
1 CCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACT
*
27083054 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGGTCTCTGCAACTTCAGAGAGATAAGATCTGA
66 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGA
*
27083119 GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTATCGGCTTTAATCTGTTCCACTGC
131 GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTATCGGCTTTAATCTGCTCCACTGC
27083184 AACTTTAGGGAGATAAGACTTG
196 AACTTTAGGGAGATAAGACTTG
* * *
27083206 CCATCTTCAGTCTGCCCCACTGCAAATTCAGGAAGATAAGACTTGCTTACTTAGTCTGCTCCATT
1 CCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACT
27083271 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGA
66 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGA
* *
27083336 GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGGTAGGACTATCGGCTTTAATCTGCTTCACTGC
131 GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTATCGGCTTTAATCTGCTCCACTGC
27083401 AACTTTAGGGAGATAAGACTTG
196 AACTTTAGGGAGATAAGACTTG
27083423 CCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACT
1 CCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACT
* *
27083488 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGGTCTCTGCAACTTCAGAGAGGTAAGATCTGA
66 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGA
*
27083553 GGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGACTATCGGCTTTAATCTGCTCCACTGC
131 GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTATCGGCTTTAATCTGCTCCACTGC
* *
27083618 AACTTCAGGGAGATAAGACTTA
196 AACTTTAGGGAGATAAGACTTG
27083640 CCATCTTC
1 CCATCTTC
27083648 GATCTGCTTC
Statistics
Matches: 630, Mismatches: 29, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 630 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (217 bp):
CCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACT
GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGA
GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTATCGGCTTTAATCTGCTCCACTGC
AACTTTAGGGAGATAAGACTTG
Found at i:27099209 original size:15 final size:17
Alignment explanation
Indices: 27099178--27099210 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
27099168 TTCTTTCATC
27099178 TTTTATTATTGATTTAT
1 TTTTATTATTGATTTAT
27099195 TTTTA-TATT-ATTTAT
1 TTTTATTATTGATTTAT
27099210 T
1 T
27099211 GTAAACTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTATTATTGATTTAT
Found at i:27102106 original size:25 final size:25
Alignment explanation
Indices: 27102078--27102126 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
27102068 AAATAATAGG
*
27102078 ATTTGTTAACTCGACTCGACTCAAA
1 ATTTGTTAACTCAACTCGACTCAAA
* * *
27102103 ATTTTTTTACTCAATTCGACTCAA
1 ATTTGTTAACTCAACTCGACTCAA
27102127 TTCAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (25 bp):
ATTTGTTAACTCAACTCGACTCAAA
Found at i:27108921 original size:3 final size:3
Alignment explanation
Indices: 27108913--27108937 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27108903 TCCGACTGCC
27108913 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
27108938 GCGTGTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:27112324 original size:21 final size:21
Alignment explanation
Indices: 27112283--27112325 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
27112273 ACCCCAAACT
* *
27112283 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTATTCC
27112304 CTCAAAAC-TTTTACTCATTCC
1 CTCAAAACTTTTTACT-ATTCC
27112325 C
1 C
27112326 ACTTTCCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTATTCC
Found at i:27112496 original size:30 final size:31
Alignment explanation
Indices: 27112462--27112521 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
27112452 AAACCTTTTA
*
27112462 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
27112492 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
27112522 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:27114590 original size:17 final size:18
Alignment explanation
Indices: 27114568--27114609 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
27114558 GTTCAAGGTG
27114568 TAATTAATTTAAA-TT-TT
1 TAATTAA-TTAAATTTATT
27114585 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
27114603 TAATTAA
1 TAATTAA
27114610 AAACCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:27114605 original size:14 final size:14
Alignment explanation
Indices: 27114568--27114610 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
27114558 GTTCAAGGTG
27114568 TAATTAATTTAAATTTT
1 TAATTAA-TTAAA--TT
27114585 TAATTAATTAAATT
1 TAATTAATTAAATT
*
27114599 TATTTAATTAAA
1 TAATTAATTAAA
27114611 AACCTATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:27114806 original size:31 final size:29
Alignment explanation
Indices: 27114742--27114810 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
27114732 ACAATAACGT
** *
27114742 AAGTGACTAAAACGTAATATTTCAAACAT
1 AAGTGACTAAAACGTAATATGGCAAACAA
*
27114771 AAGTGACTAAAATGTAATATGAGGCAAACAA
1 AAGTGACTAAAACGTAATAT--GGCAAACAA
27114802 AAGTGACTA
1 AAGTGACTA
27114811 TTTTTATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAACGTAATATGGCAAACAA
Found at i:27119148 original size:7 final size:7
Alignment explanation
Indices: 27119138--27119162 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27119128 TAAAAAATTA
27119138 ATTTTAT
1 ATTTTAT
27119145 ATTTTAT
1 ATTTTAT
27119152 ATTTTAT
1 ATTTTAT
27119159 ATTT
1 ATTT
27119163 CAATTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTAT
Found at i:27124448 original size:20 final size:20
Alignment explanation
Indices: 27124434--27124472 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27124424 ATGCTATTAG
*
27124434 AAGCATCGTAGTGCTAACAA
1 AAGCATCGTAGTGCTATCAA
*
27124454 AAGCATCGTAGTACTATCA
1 AAGCATCGTAGTGCTATCA
27124473 GGAGCACTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (20 bp):
AAGCATCGTAGTGCTATCAA
Found at i:27129321 original size:24 final size:24
Alignment explanation
Indices: 27129289--27129337 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
27129279 GACAATGACA
27129289 TAGTTACAGCATGAAAGGGTAGTT
1 TAGTTACAGCATGAAAGGGTAGTT
27129313 TAGTTACAGCATGAAAGGGTAGTT
1 TAGTTACAGCATGAAAGGGTAGTT
27129337 T
1 T
27129338 GGTTCCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.31
Consensus pattern (24 bp):
TAGTTACAGCATGAAAGGGTAGTT
Found at i:27132038 original size:12 final size:11
Alignment explanation
Indices: 27132006--27132032 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27131996 TAAAGAGATG
27132006 AAAAAAGAAAA
1 AAAAAAGAAAA
27132017 AAAAAAGAAAA
1 AAAAAAGAAAA
27132028 AAAAA
1 AAAAA
27132033 GGGAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:27134022 original size:24 final size:22
Alignment explanation
Indices: 27133945--27134019 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
27133935 CAAGTAAAAA
*
27133945 TAATTAACAAATACTATATAATT
1 TAATTAATAAATACTATATAA-T
* * *
27133968 TAATTGAAATTAGTA-TAAATAAT
1 TAATT--AATAAATACTATATAAT
*
27133991 TTA-TAATAAATACTATATAAT
1 TAATTAATAAATACTATATAAT
27134012 GTAATTAA
1 -TAATTAA
27134020 ATATTTAGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
20 6 0.16
21 7 0.18
22 3 0.08
23 11 0.29
24 6 0.16
25 5 0.13
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAATTAATAAATACTATATAAT
Found at i:27151862 original size:20 final size:20
Alignment explanation
Indices: 27151837--27151876 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27151827 CGTAAAATGA
*
27151837 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
27151857 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
27151877 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:27151866 original size:34 final size:34
Alignment explanation
Indices: 27151823--27151888 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
27151813 AGTAAAATGT
*
27151823 TTTTCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
27151856 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
27151889 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:27151892 original size:14 final size:15
Alignment explanation
Indices: 27151816--27151892 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
27151806 GATTGCCAGT
* *
27151816 AAAATGTTTTTC-GT
1 AAAATGATTTTCTGG
27151830 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
27151844 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
27151864 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
27151879 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
27151893 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 4 0.08
14 21 0.42
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:27152006 original size:17 final size:16
Alignment explanation
Indices: 27151984--27152017 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27151974 TATATTAATA
27151984 TATATTAATAAATTTTT
1 TATATT-ATAAATTTTT
*
27152001 TATATTTTAAATTTTT
1 TATATTATAAATTTTT
27152017 T
1 T
27152018 TTATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTATAAATTTTT
Found at i:27152010 original size:19 final size:18
Alignment explanation
Indices: 27151982--27152025 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27151972 CATATATTAA
27151982 TATATATTAATAAATTTTT
1 TATATATTAA-AAATTTTT
* **
27152001 TATATTTTAAATTTTTTT
1 TATATATTAAAAATTTTT
27152019 TATATAT
1 TATATAT
27152026 ATTGCAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATATTAAAAATTTTT
Found at i:27154756 original size:20 final size:20
Alignment explanation
Indices: 27154733--27154772 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27154723 AAAAATCTAA
27154733 ATAAACAAA-TTAAAAAATAT
1 ATAAA-AAATTTAAAAAATAT
*
27154753 ATAAAAAATTTAAATAATAT
1 ATAAAAAATTTAAAAAATAT
27154773 GTACAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAAATTTAAAAAATAT
Found at i:27158893 original size:26 final size:26
Alignment explanation
Indices: 27158879--27158931 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
27158869 ACCAAAAATT
*
27158879 TATTTTAAAAATAAAAAATAAAAAAAG
1 TATTTTAAAAAT-AAAAACAAAAAAAG
*
27158906 TATTTTAAAAATAAAAAAATAAAAAA
1 TATTTTAAAAATAAAAACA-AAAAAA
27158932 TAAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
TATTTTAAAAATAAAAACAAAAAAAG
Found at i:27158916 original size:28 final size:28
Alignment explanation
Indices: 27158879--27158931 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
27158869 ACCAAAAATT
27158879 TATTTTAAAAAT-AAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAG
27158906 TATTTTAAAAATAAAAAAATAAAAAA
1 TATTTTAAAAATAAAAAAATAAAAAA
27158932 TAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (28 bp):
TATTTTAAAAATAAAAAAATAAAAAAAG
Found at i:27171205 original size:13 final size:13
Alignment explanation
Indices: 27171187--27171211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27171177 TTTATAATAT
27171187 TATATATGAGATA
1 TATATATGAGATA
27171200 TATATATGAGAT
1 TATATATGAGAT
27171212 GATCCATAGT
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:0.16, T:0.40
Consensus pattern (13 bp):
TATATATGAGATA
Found at i:27171284 original size:43 final size:43
Alignment explanation
Indices: 27171236--27171322 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
27171226 ATATTAATTA
27171236 TCTATCTCATTATGAAATACATGTGTTGTGTCTTTCTATTCAC
1 TCTATCTCATTATGAAATACATGTGTTGTGTCTTTCTATTCAC
27171279 TCTATCTCATTATGAAATACATGTGTTGTGTCTTTCTATTCAC
1 TCTATCTCATTATGAAATACATGTGTTGTGTCTTTCTATTCAC
27171322 T
1 T
27171323 TCTTTAGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.47
Consensus pattern (43 bp):
TCTATCTCATTATGAAATACATGTGTTGTGTCTTTCTATTCAC
Found at i:27173690 original size:42 final size:41
Alignment explanation
Indices: 27173665--27173825 Score: 182
Period size: 42 Copynumber: 3.9 Consensus size: 41
27173655 ATGCTATCAT
27173665 ATATCGATGCCAATAG-CC-AACTATGGTCTTACACGAATCTC
1 ATATCGATGCCAAT-GCCCAAAC-ATGGTCTTACACGAATCTC
* **
27173706 ATATCGATGCCAATGTCCTAGGCATGGTCTTACACGAATCTC
1 ATATCGATGCCAATG-CCCAAACATGGTCTTACACGAATCTC
* * *
27173748 ATATCAATGCCAATTGCCCAAACATGGTCTTACATGAATCAC
1 ATATCGATGCCAA-TGCCCAAACATGGTCTTACACGAATCTC
* * *
27173790 ATAACGATGCCAATGTCCCAGACATGGTTTTACACG
1 ATATCGATGCCAATG-CCCAAACATGGTCTTACACG
27173826 TAGTCACATC
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 16 0.16
42 81 0.80
43 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (41 bp):
ATATCGATGCCAATGCCCAAACATGGTCTTACACGAATCTC
Found at i:27173778 original size:84 final size:83
Alignment explanation
Indices: 27173665--27173825 Score: 225
Period size: 84 Copynumber: 1.9 Consensus size: 83
27173655 ATGCTATCAT
* * * * *
27173665 ATATCGATGCCAATAGCCAACTATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGGCA
1 ATATCAATGCCAATAGCCAACTATGGTCTTACACGAATCACATAACGATGCCAATGTCCCAGACA
27173730 TGGTCTTACACGAATCTC
66 TGGTCTTACACGAATCTC
* *
27173748 ATATCAATGCCAATTGCCCAAAC-ATGGTCTTACATGAATCACATAACGATGCCAATGTCCCAGA
1 ATATCAATGCCAATAG-CC-AACTATGGTCTTACACGAATCACATAACGATGCCAATGTCCCAGA
*
27173812 CATGGTTTTACACG
64 CATGGTCTTACACG
27173826 TAGTCACATC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
83 14 0.21
84 51 0.75
85 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (83 bp):
ATATCAATGCCAATAGCCAACTATGGTCTTACACGAATCACATAACGATGCCAATGTCCCAGACA
TGGTCTTACACGAATCTC
Found at i:27177806 original size:20 final size:21
Alignment explanation
Indices: 27177768--27177806 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
27177758 TTTTTCCCTA
*
27177768 ATTTTTCTCTTCTTTTTCTTT
1 ATTTTTCTCTTCTTCTTCTTT
*
27177789 ATTTTT-TCTTGTTCTTCT
1 ATTTTTCTCTTCTTCTTCT
27177807 CTGTAACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (21 bp):
ATTTTTCTCTTCTTCTTCTTT
Found at i:27178406 original size:31 final size:31
Alignment explanation
Indices: 27178368--27178427 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
27178358 TGTTTGCAAT
27178368 TTCTTATCCACTTTCATATGCAATTTCTTAA
1 TTCTTATCCACTTTCATATGCAATTTCTTAA
27178399 TTCTTATCCACTTTCATATGCAATTTCTT
1 TTCTTATCCACTTTCATATGCAATTTCTT
27178428 CATGCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.50
Consensus pattern (31 bp):
TTCTTATCCACTTTCATATGCAATTTCTTAA
Found at i:27178804 original size:9 final size:9
Alignment explanation
Indices: 27178792--27178850 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
27178782 AAAAATAAAA
27178792 AATTCGGGT
1 AATTCGGGT
27178801 AATTCGGGT
1 AATTCGGGT
* ** *
27178810 ATTTTTTGTT
1 A-ATTCGGGT
*
27178820 AATTCGGTT
1 AATTCGGGT
*
27178829 AATTTGGGT
1 AATTCGGGT
27178838 AATTCGGGT
1 AATTCGGGT
27178847 AATT
1 AATT
27178851 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
9 34 0.87
10 5 0.13
ACGTcount: A:0.22, C:0.07, G:0.25, T:0.46
Consensus pattern (9 bp):
AATTCGGGT
Found at i:27184520 original size:29 final size:29
Alignment explanation
Indices: 27184487--27184564 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
27184477 AAAGAATAAT
* *
27184487 AAATGAAATTGAAAAAGAAAATTTGAGAA
1 AAATGAAAGTGAAAAAGAAAAGTTGAGAA
*
27184516 AAATG-AAGTAAAAGAAGAAAAGTTGAGAA
1 AAATGAAAGTGAAA-AAGAAAAGTTGAGAA
27184545 AAGA-GAAAGTG-AAAAGAAAA
1 AA-ATGAAAGTGAAAAAGAAAA
27184565 CAAAAATTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 13 0.31
29 24 0.57
30 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (29 bp):
AAATGAAAGTGAAAAAGAAAAGTTGAGAA
Found at i:27189108 original size:29 final size:30
Alignment explanation
Indices: 27189073--27189140 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
27189063 TGAAAACTTC
27189073 ATGTATAAAATTACACA-AAATCAAAGTTT
1 ATGTATAAAATTACACATAAATCAAAGTTT
* *
27189102 ATTTATAACATTACACATTAAATCAAAGTTT
1 ATGTATAAAATTACACA-TAAATCAAAGTTT
27189133 ATGTATAA
1 ATGTATAA
27189141 TTTTGAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (30 bp):
ATGTATAAAATTACACATAAATCAAAGTTT
Found at i:27197949 original size:30 final size:30
Alignment explanation
Indices: 27197909--27197967 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
27197899 TATTTTATTG
*
27197909 TTAATGTTTTTATTATTTTAAAGGCATTTA
1 TTAATGTTTTTATTATTTTAAAGCCATTTA
* *
27197939 TTAATTTTTTTATTATTTTAGAGCCATTT
1 TTAATGTTTTTATTATTTTAAAGCCATTT
27197968 GTTTGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.59
Consensus pattern (30 bp):
TTAATGTTTTTATTATTTTAAAGCCATTTA
Found at i:27200856 original size:24 final size:25
Alignment explanation
Indices: 27200794--27200857 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
27200784 AACGATTGAG
* *
27200794 AAAACAGAAAAGAAAAGAAGTGAAA
1 AAAACATAAAAGAAAAGAAGAGAAA
* *
27200819 ATGAA-AT-AAGGAAAAGAA-AGAAA
1 A-AAACATAAAAGAAAAGAAGAGAAA
27200842 AAAACATAAAAGAAAA
1 AAAACATAAAAGAAAA
27200858 AATAAAGTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
22 2 0.07
23 7 0.23
24 17 0.57
25 2 0.07
26 2 0.07
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.06
Consensus pattern (25 bp):
AAAACATAAAAGAAAAGAAGAGAAA
Found at i:27207755 original size:9 final size:9
Alignment explanation
Indices: 27207738--27207774 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
27207728 TAAGTTTTCG
27207738 AATTCGAAT
1 AATTCGAAT
*
27207747 AACTCGAAT
1 AATTCGAAT
*
27207756 AATTTGAAT
1 AATTCGAAT
27207765 AATTCGAAT
1 AATTCGAAT
27207774 A
1 A
27207775 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:27208151 original size:18 final size:17
Alignment explanation
Indices: 27208128--27208187 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
27208118 ACTCTCTCTA
27208128 TTTACTTTCCCTCAAACT
1 TTTACTTTCCC-CAAACT
*
27208146 TTTAC-TTCCCAAAACTT
1 TTTACTTTCCCCAAAC-T
*
27208163 TTTATTTTCCCCTAAACT
1 TTTACTTTCCCC-AAACT
27208181 TTTACTT
1 TTTACTT
27208188 CTCACCCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.11
17 10 0.29
18 17 0.49
19 4 0.11
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTACTTTCCCCAAACT
Found at i:27208803 original size:5 final size:5
Alignment explanation
Indices: 27208793--27208818 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27208783 CTCGAAAATT
27208793 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
27208819 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:27210060 original size:21 final size:22
Alignment explanation
Indices: 27210034--27210082 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
27210024 ATTTAAAATA
27210034 TTAAAAAAGTTGTAA-AAATTC
1 TTAAAAAAGTTGTAACAAATTC
* *
27210055 TTAAAAAATTTGTAACAAATTG
1 TTAAAAAAGTTGTAACAAATTC
27210077 TTAAAA
1 TTAAAA
27210083 CTATAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (22 bp):
TTAAAAAAGTTGTAACAAATTC
Found at i:27210199 original size:18 final size:19
Alignment explanation
Indices: 27210160--27210209 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
27210150 TTATTTTTAA
*
27210160 AAAAATGATTAAACATTGT
1 AAAAATGATTAAACATTAT
27210179 AAAAATGA-TAAGA-ATTAT
1 AAAAATGATTAA-ACATTAT
* *
27210197 AAACATTATTAAA
1 AAAAATGATTAAA
27210210 GAATTGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (19 bp):
AAAAATGATTAAACATTAT
Found at i:27210463 original size:18 final size:18
Alignment explanation
Indices: 27210431--27210465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27210421 GTAAAATTAT
**
27210431 TATAATTTTTTCAATTTA
1 TATAATTTTCACAATTTA
27210449 TATAATTTTCACAATTT
1 TATAATTTTCACAATTT
27210466 TTAAATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATTTTCACAATTTA
Found at i:27211650 original size:14 final size:15
Alignment explanation
Indices: 27211621--27211650 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27211611 TGTGAAGAAA
27211621 TATTTTTCTTCTCCT
1 TATTTTTCTTCTCCT
27211636 TATTTTTCTTC-CCT
1 TATTTTTCTTCTCCT
27211650 T
1 T
27211651 GGTCGATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTCTTCTCCT
Found at i:27212665 original size:17 final size:17
Alignment explanation
Indices: 27212638--27212677 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
27212628 GTTATATGAA
27212638 ATTGATATAAT-TATTATG
1 ATTG-TATAATGTA-TATG
27212656 ATTGTATAATGTATATG
1 ATTGTATAATGTATATG
27212673 ATTGT
1 ATTGT
27212678 GTTTATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATTGTATAATGTATATG
Found at i:27215242 original size:4 final size:4
Alignment explanation
Indices: 27215227--27215257 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
27215217 ATTGTAATCA
27215227 AATT ATATT AATT AATT AATT AATT AATT AA
1 AATT A-ATT AATT AATT AATT AATT AATT AA
27215258 ACTTATAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:27215601 original size:63 final size:63
Alignment explanation
Indices: 27215502--27215622 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
27215492 GTTAATTATT
* * *
27215502 CAAATATATTGCATTTAATATATTTTAATCAATTATGTTGCATTTATTTAAAAATTTTCTTTC
1 CAAATATATTGCATTTAATATATTTTAATCAATTATGTTGAATTGATTCAAAAATTTTCTTTC
* * * * *
27215565 CAAATATATTGCATTTGATATTTTTTAGTTAATTATGTTGAATTGATTCATAAATTTT
1 CAAATATATTGCATTTAATATATTTTAATCAATTATGTTGAATTGATTCAAAAATTTT
27215623 AGTTTCACAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (63 bp):
CAAATATATTGCATTTAATATATTTTAATCAATTATGTTGAATTGATTCAAAAATTTTCTTTC
Found at i:27224556 original size:16 final size:17
Alignment explanation
Indices: 27224535--27224566 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27224525 CATGTTAGAG
27224535 CATATAAA-TTTAAAAT
1 CATATAAATTTTAAAAT
27224551 CATATAAATTTTAAAA
1 CATATAAATTTTAAAA
27224567 CTCGTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
CATATAAATTTTAAAAT
Found at i:27224670 original size:9 final size:9
Alignment explanation
Indices: 27224656--27224715 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
27224646 ATTATTCTAG
27224656 AAATTTTTT
1 AAATTTTTT
27224665 AAATTTTTTT
1 AAA-TTTTTT
*
27224675 ATATATTCTTT
1 A-A-ATTTTTT
*
27224686 AGATTTTTT
1 AAATTTTTT
* *
27224695 TAATATTTT
1 AAATTTTTT
27224704 AAATTTTTT
1 AAATTTTTT
27224713 AAA
1 AAA
27224716 AATACAAGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 25 0.62
10 7 0.17
11 7 0.17
12 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
AAATTTTTT
Found at i:27224700 original size:20 final size:21
Alignment explanation
Indices: 27224662--27224712 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
27224652 CTAGAAATTT
27224662 TTTAAATTTTTTTATATATTC
1 TTTAAATTTTTTTATATATTC
*
27224683 TTTAGATTTTTTTA-ATA-T-
1 TTTAAATTTTTTTATATATTC
27224701 TTTAAATTTTTT
1 TTTAAATTTTTT
27224713 AAAAATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.39
19 1 0.04
20 3 0.11
21 13 0.46
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTAAATTTTTTTATATATTC
Found at i:27227992 original size:14 final size:14
Alignment explanation
Indices: 27227973--27228004 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
27227963 GTGATTTACA
*
27227973 TTAAAATTGAAATT
1 TTAAAATTAAAATT
27227987 TTAAAATTAAAATT
1 TTAAAATTAAAATT
27228001 TTAA
1 TTAA
27228005 CCCTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
TTAAAATTAAAATT
Found at i:27243134 original size:20 final size:21
Alignment explanation
Indices: 27243090--27243136 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
27243080 TAATTGTTAT
*
27243090 ATTTTA-ATATTTAAAATATA
1 ATTTTATATATTCAAAATATA
*
27243110 A-TTTATATATTCAAATTA-A
1 ATTTTATATATTCAAAATATA
27243129 ATTTTATA
1 ATTTTATA
27243137 AATAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTATATATTCAAAATATA
Found at i:27244719 original size:16 final size:16
Alignment explanation
Indices: 27244698--27244734 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27244688 TTGGTTCGCT
*
27244698 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
27244714 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
27244730 GTAAT
1 GTAAT
27244735 AGGTAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:27244809 original size:39 final size:44
Alignment explanation
Indices: 27244716--27244825 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 44
27244706 ATAGATGCGT
*
27244716 AATGGAATAGAGGCGTAATAGGTAATTCAATTGTTTGGTTAATAG
1 AATGGAATAGAGGCGTAATAGATAATTCAATTGTTTGGTT-ATAG
* *
27244761 AATGAAATAGAGGCGTAAT-GAT-ATTC-TTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGATAATTCAAT-TGTTTGGTTATAG
*
27244800 AATGGAATAGAGGTGTAATAGCATAA
1 AATGGAATAGAGGCGTAATAG-ATAA
27244826 GGAAAAAAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
39 18 0.32
40 2 0.04
41 2 0.04
42 3 0.05
43 11 0.20
44 2 0.04
45 18 0.32
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGATAATTCAATTGTTTGGTTATAG
Found at i:27245019 original size:31 final size:31
Alignment explanation
Indices: 27244981--27245096 Score: 94
Period size: 31 Copynumber: 3.6 Consensus size: 31
27244971 AATTTAATAA
27244981 AAATATATAATTTAATAAAATTCTTAATATT
1 AAATATATAATTTAATAAAATTCTTAATATT
* *
27245012 AAATATATGAATTTACTAAAA-TCATAATATAT
1 AAATATAT-AATTTAATAAAATTCTTAATAT-T
* * ** *
27245044 AATACTATAAAATATAATTTAAAATAATTATTATT
1 AA-A-TATATAATTTAA--TAAAATTCTTAATATT
27245079 -AA-ATATAATTTAATAAAA
1 AAATATATAATTTAATAAAA
27245097 ATATATAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
29 5 0.07
31 25 0.37
32 14 0.21
33 7 0.10
34 5 0.07
35 6 0.09
36 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (31 bp):
AAATATATAATTTAATAAAATTCTTAATATT
Found at i:27248498 original size:19 final size:20
Alignment explanation
Indices: 27248454--27248498 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
27248444 AACGTCTCTT
*
27248454 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
27248473 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
27248492 TATGCAT
1 TATGCAT
27248499 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:27251367 original size:45 final size:46
Alignment explanation
Indices: 27251303--27251391 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
27251293 AAAGGTGGGA
*
27251303 CCAAGGTGAAAGCCTACAAA-GGGCGCTTTGAGTCAAAAAAAAAGG
1 CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAGG
* *
27251348 CCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTTAAAAAAAAA
1 CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAA
27251392 AAAAAGACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 19 0.47
46 21 0.52
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (46 bp):
CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAGG
Found at i:27251409 original size:51 final size:48
Alignment explanation
Indices: 27251301--27251438 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 48
27251291 TAAAAGGTGG
* * *
27251301 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGT----CAAAAAAAAA
1 GACCAAGGTGAAA-CCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAAA
*
27251346 GGCCAAGGTGAAACCCTACAAAGGG-GCTCTTTGAGTTAAAAAAAAAAAAAA
1 GACCAAGGTGAAA-CCTACAAAGGGAGC-C-TTGAG-TAAAAAAAAAAAAAA
*
27251397 GACCAGGGTGAAACCTACAAAGGGAGCCTTGAGTAAAAAAAA
1 GACCAAGGTGAAACCTACAAAGGGAGCCTTGAGTAAAAAAAA
27251439 TAGAGAGGCT
Statistics
Matches: 79, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
44 2 0.03
45 23 0.29
46 5 0.06
47 1 0.01
48 9 0.11
49 5 0.06
50 12 0.15
51 22 0.28
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.14
Consensus pattern (48 bp):
GACCAAGGTGAAACCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAAA
Found at i:27251460 original size:49 final size:45
Alignment explanation
Indices: 27251303--27251469 Score: 140
Period size: 45 Copynumber: 3.5 Consensus size: 45
27251293 AAAGGTGGGA
* * *
27251303 CCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGT-CAAAAAAAAAGG
1 CCAAGGTGAAAACCTACAAAGGG-GCCTTGAGTAAAAAAAAAAAGG
* *
27251348 CCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTTAAAAAAAAAAAAAAGA
1 CCAAGGTGAAAACCTACAAAGGGGC-C-TTGAG-T---AAAAAAAAAAAGG
*
27251399 CCAGGGTG-AAACCTACAAAGGGAGCCTTGAGTAAAAAAAATAGAGAGG
1 CCAAGGTGAAAACCTACAAAGGG-GCCTTGAGTAAAAAAAA-A-A-AGG
* **
27251447 CTAAGGTGAAAACCCGCAAAGGG
1 CCAAGGTGAAAACCTACAAAGGG
27251470 CACCTTAGAC
Statistics
Matches: 99, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
44 2 0.02
45 30 0.30
46 6 0.06
47 2 0.02
48 9 0.09
49 17 0.17
50 14 0.14
51 19 0.19
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (45 bp):
CCAAGGTGAAAACCTACAAAGGGGCCTTGAGTAAAAAAAAAAAGG
Found at i:27252925 original size:75 final size:75
Alignment explanation
Indices: 27252802--27252948 Score: 217
Period size: 75 Copynumber: 2.0 Consensus size: 75
27252792 ATCGAAAGAA
* *
27252802 AGTAGATCTTGTCTTCATGTATCAGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATA
1 AGTAGATCTTGTCTTCATGTATCAGCGTGAAGTAGATCAAAGTCAACAGATCTCGCCTCCCCATA
27252867 CTGGTGGTGG
66 CTGGTGGTGG
* * *
27252877 AGTAGATCTTGTCTTCATGTA-CTGGTGTGAAGTAGATCAAAGAT-AACAGATCTCGCCTTCCCA
1 AGTAGATCTTGTCTTCATGTATC-AGCGTGAAGTAGATCAAAG-TCAACAGATCTCGCCTCCCCA
27252940 TACTGGTGG
64 TACTGGTGG
27252949 CGAAGCAGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
74 1 0.02
75 63 0.97
76 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (75 bp):
AGTAGATCTTGTCTTCATGTATCAGCGTGAAGTAGATCAAAGTCAACAGATCTCGCCTCCCCATA
CTGGTGGTGG
Found at i:27252945 original size:44 final size:45
Alignment explanation
Indices: 27252880--27253049 Score: 150
Period size: 44 Copynumber: 3.8 Consensus size: 45
27252870 GTGGTGGAGT
***
27252880 AGATCTTGTCTTCATGTACTGGT-GTGAAGTAGATCAAAGATAAC
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * * *
27252924 AGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGA-AAGT
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-AAAGATAA-C
*** * *
27252970 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAG-TCAAC
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAT-AAC
* *
27253014 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
27253050 TTGTCTTCAT
Statistics
Matches: 95, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
44 39 0.41
45 35 0.37
46 21 0.22
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (45 bp):
AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGATAAC
Found at i:27253029 original size:165 final size:164
Alignment explanation
Indices: 27252757--27253171 Score: 670
Period size: 165 Copynumber: 2.5 Consensus size: 164
27252747 GATCGAATAT
*
27252757 ACAGATCTCGCATTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAGTAGATCTTGTCTTCATGT
1 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAGTAGATCTTGTCTTCATGT
**
27252822 ATCAGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCTT
66 ATTGGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCTT
*
27252887 GTCTTCATGTACTGGTGTGAAGTAGATCAAAGATA
131 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-A
27252922 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAGTAGATCTTGTCTTCATGT
1 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAGTAGATCTTGTCTTCATGT
27252987 ATTGGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCTT
66 ATTGGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCTT
27253052 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAA
131 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAA
* * * * * * * **
27253086 ACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTCG-AAGAAAACAGATCTTGTCTTCATGT
1 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAGTAGATCTTGTCTTCATGT
* * *
27253150 ACTGGAGTGAAGTAGATTAAAG
66 ATTGGCGTGAAGTAGATCAAAG
27253172 ATAGTAGGTC
Statistics
Matches: 234, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 42 0.18
164 33 0.14
165 159 0.68
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (164 bp):
ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAGTAGATCTTGTCTTCATGT
ATTGGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCTT
GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAA
Found at i:27253153 original size:45 final size:43
Alignment explanation
Indices: 27253045--27253172 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 43
27253035 GTGGTGGAGT
27253045 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAC
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAC
* *** * * * *
27253088 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAGAAAAC
1 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAG-AAAC
* *
27253133 AGATCTTGTCTTCATGTACTGGAGTGAAGTAGATTAAAGA
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
27253173 TAGTAGGTCC
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
43 19 0.29
44 25 0.38
45 22 0.33
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAC
Found at i:27253441 original size:44 final size:45
Alignment explanation
Indices: 27253385--27253474 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 45
27253375 ATCGATTAAA
* * *
27253385 AAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCATATACTGGTAGTGAAGTAGATCGAAG
*
27253429 AAAGCAGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCATATACTGGTAGTGAAGTAGATCGAAG
27253474 A
1 A
27253475 TACAAGTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 24 0.59
45 17 0.41
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (45 bp):
AAAGCAGATCTTGTCTTCATATACTGGTAGTGAAGTAGATCGAAG
Found at i:27259114 original size:25 final size:25
Alignment explanation
Indices: 27259085--27259148 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
27259075 TTTGTCTCGC
*
27259085 ATGGGTTGCTGTTTTTTTCTCTTTT
1 ATGGGTTGTTGTTTTTTTCTCTTTT
* *
27259110 CTGGGTTGTTTTTTTTTTCTCTTTT
1 ATGGGTTGTTGTTTTTTTCTCTTTT
27259135 ATGGGTTGTTGTTT
1 ATGGGTTGTTGTTT
27259149 CTGGTGAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.03, C:0.09, G:0.22, T:0.66
Consensus pattern (25 bp):
ATGGGTTGTTGTTTTTTTCTCTTTT
Found at i:27259301 original size:25 final size:26
Alignment explanation
Indices: 27259262--27259425 Score: 180
Period size: 25 Copynumber: 6.6 Consensus size: 26
27259252 AAACTTACAC
27259262 GGCAATGCAG-CAGAGGACTGTCGAT
1 GGCAATGCAGACAGAGGACTGTCGAT
* *
27259287 GGCAATGTAGA-AGAGGACTATCGAT
1 GGCAATGCAGACAGAGGACTGTCGAT
* *
27259312 GGCAATGC-GACAAAGGACTTTCGAT
1 GGCAATGCAGACAGAGGACTGTCGAT
*
27259337 GGCAATGC-GACAGAGGACTTTCGAT
1 GGCAATGCAGACAGAGGACTGTCGAT
* * *
27259362 GACGATGC-GGCAGAGGACTGTCGAT
1 GGCAATGCAGACAGAGGACTGTCGAT
** *
27259387 GGTGATGCA-ACAGAGGACTGTTGAT
1 GGCAATGCAGACAGAGGACTGTCGAT
27259412 GGCAATGCAG-CAGA
1 GGCAATGCAGACAGA
27259426 CGTTCAGGGA
Statistics
Matches: 119, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.02
25 117 0.98
ACGTcount: A:0.30, C:0.18, G:0.34, T:0.18
Consensus pattern (26 bp):
GGCAATGCAGACAGAGGACTGTCGAT
Found at i:27260091 original size:32 final size:32
Alignment explanation
Indices: 27260048--27260141 Score: 147
Period size: 31 Copynumber: 3.0 Consensus size: 32
27260038 GGCCCATTTT
*
27260048 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAAG
1 TATTTTAAAAATATTT-TAAAATTAAAAAAAAG
*
27260080 TATTTTTAAAATATTTTAAAATT-AAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAAG
27260111 TATTTTAAAAATATTTTAAAATTAAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAAA
27260142 TTAAAAAAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
31 30 0.53
32 24 0.42
33 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (32 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAAG
Found at i:27260128 original size:41 final size:40
Alignment explanation
Indices: 27260074--27260223 Score: 185
Period size: 41 Copynumber: 3.6 Consensus size: 40
27260064 AAAAATTAAA
**
27260074 AAAAAGTATTTTTAAAATATTTTAAAATTAAAAAAAGTATTTT
1 AAAAA-TA-TTTTAAAAT-TTAAAAAATTAAAAAAAGTATTTT
*
27260117 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
1 AAAAATATTTTAAAATT-TAAAAAATTAAAAAAAGTATTTT
* *
27260158 AAAAATATTTTAAAATTTAAAAAAAATT-AAAAAAGTATGTA
1 AAAAATATTTTAAAATTT--AAAAAATTAAAAAAAGTATTTT
*
27260199 AAAAATATTTTAAAATTAAAAAAAT
1 AAAAATATTTTAAAATTTAAAAAAT
27260224 AAATATATTT
Statistics
Matches: 97, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
39 7 0.07
40 1 0.01
41 74 0.76
42 10 0.10
43 5 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
AAAAATATTTTAAAATTTAAAAAATTAAAAAAAGTATTTT
Found at i:27260251 original size:5 final size:5
Alignment explanation
Indices: 27260241--27260273 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
27260231 TTTATTATAT
27260241 CGGGC CGGGC CGGGC CGGGC CGGGCC CGGGC CG
1 CGGGC CGGGC CGGGC CGGGC CGGG-C CGGGC CG
27260274 AAAAAGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.42, G:0.58, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:27260708 original size:39 final size:41
Alignment explanation
Indices: 27260658--27260756 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 41
27260648 TTTCCTTTTT
27260658 CCCACCATCCCTCCCCCTTAC-CTCGA-T-TCTCTC-CTTCTC
1 CCCACCATCCCT-CCCCTTACTCT-GACTCTCTCTCTCTTCTC
*
27260697 CCCACCGTCCCTCCCCTTACTCTGACTCTCTCTCTCTTCT-
1 CCCACCATCCCTCCCCTTACTCTGACTCTCTCTCTCTTCTC
*
27260737 -CCACCATCCCTCACC-TACTC
1 CCCACCATCCCTCCCCTTACTC
27260757 ATCTTCTCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
38 15 0.28
39 27 0.51
40 6 0.11
41 5 0.09
ACGTcount: A:0.11, C:0.56, G:0.03, T:0.30
Consensus pattern (41 bp):
CCCACCATCCCTCCCCTTACTCTGACTCTCTCTCTCTTCTC
Found at i:27261948 original size:16 final size:16
Alignment explanation
Indices: 27261927--27261996 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
27261917 TTTGGTTCGC
* *
27261927 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
27261943 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
27261959 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
27261975 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
27261991 TGTAAT
1 TGTAAT
27261997 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:27262029 original size:45 final size:44
Alignment explanation
Indices: 27261975--27262069 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
27261965 GGAATAGAGG
*
27261975 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
27262020 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
27262064 TGTAAT
1 TGTAAT
27262070 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:27262250 original size:18 final size:17
Alignment explanation
Indices: 27262229--27262263 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27262219 TTATTATTAA
*
27262229 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
27262247 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
27262264 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:27262393 original size:16 final size:16
Alignment explanation
Indices: 27262356--27262397 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27262346 TTAATCATAT
*
27262356 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
27262372 TT-AAATATATTATAA
1 TTAAAATATATTATAA
27262387 TTAAAATATAT
1 TTAAAATATAT
27262398 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:27262404 original size:14 final size:15
Alignment explanation
Indices: 27262365--27262406 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27262355 TTTAAACATA
*
27262365 ATTATTATTAAATAT
1 ATTATAATTAAATAT
27262380 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
27262394 A-TATAATTTAATA
1 ATTATAATTAAATA
27262407 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:27262417 original size:147 final size:147
Alignment explanation
Indices: 27262150--27262422 Score: 512
Period size: 147 Copynumber: 1.9 Consensus size: 147
27262140 ATGATTATTG
*
27262150 TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTTAAC
1 TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAAC
*
27262215 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
66 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
27262280 AAATTTGTTTTGGTAAA
131 AAATTTGTTTTGGTAAA
27262297 TTATT-TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAA
1 TTATTGTTA-TTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAA
27262361 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
65 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
27262423 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
146 3 0.02
147 120 0.98
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:27266631 original size:31 final size:31
Alignment explanation
Indices: 27266593--27266675 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
27266583 AATCTCAAAG
*
27266593 TTATATATTAATTTTGATTTAAAGT-TAAATT
1 TTATATATAAATTTTGATTTAAAGTATAAA-T
*
27266624 TTATATATAAATTTTGATTT--TGTATAAAT
1 TTATATATAAATTTTGATTTAAAGTATAAAT
27266653 TTATATATAAAATTTTGATTTAA
1 TTATATAT-AAATTTTGATTTAA
27266676 TGCAATTCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
29 11 0.24
30 16 0.35
31 19 0.41
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (31 bp):
TTATATATAAATTTTGATTTAAAGTATAAAT
Found at i:27266682 original size:29 final size:29
Alignment explanation
Indices: 27266593--27266673 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
27266583 AATCTCAAAG
* *
27266593 TTATATATTAATTTTGA-TTTAAAGTTAAATT
1 TTATATATAAATTTTGATTTTGAA--TAAA-T
*
27266624 TTATATATAAATTTTGATTTTGTATAAAT
1 TTATATATAAATTTTGATTTTGAATAAAT
27266653 TTATATATAAAATTTTGATTT
1 TTATATAT-AAATTTTGATTT
27266674 AATGCAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 9 0.20
30 16 0.36
31 16 0.36
32 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (29 bp):
TTATATATAAATTTTGATTTTGAATAAAT
Found at i:27267528 original size:22 final size:22
Alignment explanation
Indices: 27267503--27267579 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
27267493 ATTTTGTATT
* *
27267503 ATATAACATATCAGAGAATATA
1 ATATAACATATCGGAGAATATC
* *
27267525 ATATAACATATTGGAGCATATC
1 ATATAACATATCGGAGAATATC
*
27267547 ATATAACATATCGGAGTATATC
1 ATATAACATATCGGAGAATATC
27267569 ATATAACATAT
1 ATATAACATAT
27267580 TAGAACATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (22 bp):
ATATAACATATCGGAGAATATC
Found at i:27267551 original size:44 final size:44
Alignment explanation
Indices: 27267503--27267590 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
27267493 ATTTTGTATT
* *
27267503 ATATAACATATCAGAGAATATAATATAACATATTGGAGCATATC
1 ATATAACATATCAGAGAATATAATATAACATATTAGAACATATC
* * *
27267547 ATATAACATATCGGAGTATATCATATAACATATTAGAACATATC
1 ATATAACATATCAGAGAATATAATATAACATATTAGAACATATC
27267591 TTACTCCCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (44 bp):
ATATAACATATCAGAGAATATAATATAACATATTAGAACATATC
Found at i:27267589 original size:22 final size:22
Alignment explanation
Indices: 27267503--27267590 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
27267493 ATTTTGTATT
*
27267503 ATATAACATATCAGAGA-ATATA
1 ATATAACATATCAGA-ACATATC
** *
27267525 ATATAACATATTGGAGCATATC
1 ATATAACATATCAGAACATATC
* **
27267547 ATATAACATATCGGAGTATATC
1 ATATAACATATCAGAACATATC
*
27267569 ATATAACATATTAGAACATATC
1 ATATAACATATCAGAACATATC
27267591 TTACTCCCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (22 bp):
ATATAACATATCAGAACATATC
Found at i:27269336 original size:29 final size:28
Alignment explanation
Indices: 27269304--27269374 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
27269294 TAGTTGAAAT
*
27269304 TAAATTTTAAAATCTAAAAGTAGAAGAAC
1 TAAATTTTAAAATC-AAAAGTAAAAGAAC
* * *
27269333 TAAATTCCTAAAAACAAAAGTAAAAGGAC
1 TAAATT-TTAAAATCAAAAGTAAAAGAAC
* *
27269362 AAAATTTCAAAAT
1 TAAATTTTAAAAT
27269375 TACCAAAAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
28 4 0.12
29 23 0.70
30 6 0.18
ACGTcount: A:0.58, C:0.10, G:0.08, T:0.24
Consensus pattern (28 bp):
TAAATTTTAAAATCAAAAGTAAAAGAAC
Found at i:27272166 original size:25 final size:24
Alignment explanation
Indices: 27272132--27272182 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
27272122 ATTTAAAAAA
*
27272132 TTGTCTGCTCTTGGTAACACGTTCT
1 TTGTCTGCTCCTGGTAACACG-TCT
*
27272157 TTGTCTGCTCCTGGTAGCACGTCT
1 TTGTCTGCTCCTGGTAACACGTCT
27272181 TT
1 TT
27272183 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (24 bp):
TTGTCTGCTCCTGGTAACACGTCT
Found at i:27283714 original size:75 final size:76
Alignment explanation
Indices: 27283586--27283730 Score: 222
Period size: 75 Copynumber: 1.9 Consensus size: 76
27283576 ATTGATGTAA
* * *
27283586 AATACAGTAGAATACAATATAAATAAGTTTTCTTTTTTTTTCCGTAGATTGTAAATAAGTATATA
1 AATACAATAGAATACAATACAAATAAG-TTTCTTATTTTTTCCGTAGATTGTAAATAAGTATATA
27283651 TTATTGACATGG
65 TTATTGACATGG
*
27283663 AATACAATAGAATACAATACAAATAA-TTTCTTAATTTTTT-CTTAGATTGTAAATAAGTATATA
1 AATACAATAGAATACAATACAAATAAGTTTCTT-ATTTTTTCCGTAGATTGTAAATAAGTATATA
27283726 TTATT
65 TTATT
27283731 TATGTAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
75 33 0.52
76 6 0.10
77 24 0.38
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (76 bp):
AATACAATAGAATACAATACAAATAAGTTTCTTATTTTTTCCGTAGATTGTAAATAAGTATATAT
TATTGACATGG
Found at i:27283742 original size:75 final size:76
Alignment explanation
Indices: 27283539--27283749 Score: 250
Period size: 77 Copynumber: 2.8 Consensus size: 76
27283529 TTTTCATTGC
* * * * *
27283539 TTCTTATTTTTT-GGTAAATTGTAAGT-ATTGATATATTATTGATGTAAAATACAGTAGAATACA
1 TTCTTATTTTTTCCGTAGATTGTAAATAAGT-ATATATTATTGATGTAAAATACAATAGAATACA
*
27283602 ATATAAATAAGTT
65 ATACAAATAAG-T
* ** **
27283615 TTCTTTTTTTTTCCGTAGATTGTAAATAAGTATATATTATTGACATGGAATACAATAGAATACAA
1 TTCTTATTTTTTCCGTAGATTGTAAATAAGTATATATTATTGATGTAAAATACAATAGAATACAA
27283680 TACAAATAA-T
66 TACAAATAAGT
* *
27283690 TTCTTAATTTTTT-CTTAGATTGTAAATAAGTATATATTATTTATGTAAAATACAATAGAA
1 TTCTT-ATTTTTTCCGTAGATTGTAAATAAGTATATATTATTGATGTAAAATACAATAGAA
27283750 CAATTTTTTT
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
75 47 0.41
76 17 0.15
77 48 0.42
78 2 0.02
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (76 bp):
TTCTTATTTTTTCCGTAGATTGTAAATAAGTATATATTATTGATGTAAAATACAATAGAATACAA
TACAAATAAGT
Found at i:27284844 original size:26 final size:27
Alignment explanation
Indices: 27284809--27284871 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
27284799 AATAAAAATA
27284809 ACCAAAATATTAT-AATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
*
27284835 ATCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
27284862 ACCAAAATAT
1 ACCAAAATAT
27284872 ACCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Done.