Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 15 of 208
Found at i:4595787 original size:54 final size:55
Alignment explanation
Indices: 4595726--4595844 Score: 206
Period size: 54 Copynumber: 2.2 Consensus size: 55
4595716 AGTTTGGATT
4595726 GTTAGTATTTTATGATAAAATCAAATTGAGTCAAATTTAATTACAAATTGATAAG
1 GTTAGTATTTTATGATAAAATCAAATTGAGTCAAATTTAATTACAAATTGATAAG
* *
4595781 G-TAGTATTTTATGATAAAATCAGATTGAGTCAGATTTAATTACAAATTGATAAG
1 GTTAGTATTTTATGATAAAATCAAATTGAGTCAAATTTAATTACAAATTGATAAG
4595835 GTTAG-ATTTT
1 GTTAGTATTTT
4595845 TCAGGTTTGA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
54 57 0.93
55 4 0.07
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.39
Consensus pattern (55 bp):
GTTAGTATTTTATGATAAAATCAAATTGAGTCAAATTTAATTACAAATTGATAAG
Found at i:4601087 original size:6 final size:6
Alignment explanation
Indices: 4601050--4601083 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4601040 ACCATTTCTG
* *
4601050 AACCTT AACCTT AACCTT AACTTT AACCCT AACC
1 AACCTT AACCTT AACCTT AACCTT AACCTT AACC
4601084 CTAATTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (6 bp):
AACCTT
Found at i:4601864 original size:22 final size:20
Alignment explanation
Indices: 4601831--4601879 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
4601821 CAAATACTAT
*
4601831 TTAATTATTGTAATTCTTAA
1 TTAATTATTGTAATTCCTAA
*
4601851 TTAATATAGTTGTACTTCCTAA
1 TTAAT-TA-TTGTAATTCCTAA
4601873 TGTAATT
1 T-TAATT
4601880 TACCAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.21
21 2 0.08
22 13 0.54
23 4 0.17
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (20 bp):
TTAATTATTGTAATTCCTAA
Found at i:4602483 original size:3 final size:3
Alignment explanation
Indices: 4602475--4602526 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
4602465 ATATTTTAAC
4602475 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4602523 ATT A
1 ATT A
4602527 ATTTGAGGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4603539 original size:28 final size:28
Alignment explanation
Indices: 4603495--4603548 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4603485 ATCCGTAATT
* *
4603495 AAGTTCAAGTACTAAAA-TAGATTTAAAA
1 AAGTACAAGTACCAAAATTA-ATTTAAAA
4603523 AAGTACAAGTACCAAAATTAATTTAA
1 AAGTACAAGTACCAAAATTAATTTAA
4603549 TTACCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (28 bp):
AAGTACAAGTACCAAAATTAATTTAAAA
Found at i:4610875 original size:6 final size:6
Alignment explanation
Indices: 4610864--4610898 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4610854 GAGATAAGCT
4610864 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
4610899 TGAATACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:4615209 original size:3 final size:3
Alignment explanation
Indices: 4615201--4615237 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
4615191 TATAAATGAC
4615201 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
4615238 TAAATAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4616856 original size:39 final size:41
Alignment explanation
Indices: 4616768--4616853 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 41
4616758 ACCTACTATA
*
4616768 TTTGATCTACTTCACGCCAATACATGAAGATAAGATCTGTTTTC
1 TTTGATCTACTTCACGCCAATACATGAAGATAAGA--T-TTTGC
*
4616812 TTTGATCTACTTCACGCCCATACATGAAGATAAGA-TTTGC
1 TTTGATCTACTTCACGCCAATACATGAAGATAAGATTTTGC
4616852 TT
1 TT
4616854 GATTCGATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 6 0.15
44 34 0.85
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (41 bp):
TTTGATCTACTTCACGCCAATACATGAAGATAAGATTTTGC
Found at i:4616892 original size:45 final size:44
Alignment explanation
Indices: 4616837--4617430 Score: 376
Period size: 45 Copynumber: 13.3 Consensus size: 44
4616827 GCCCATACAT
* * *
4616837 GAAGATAAGATTTGCTTGATTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTT-CTTCGATCTACTTCGCCACCAGTATGG
* * ***
4616882 GAAGACAAGATCTGCCATCTTCGTTCTACTTCATGCCA--A-TACAT
1 GAAGACAAGATCTG-CTTCTTCGATCTACTTC--GCCACCAGTATGG
* *
4616926 GAAGACAAGATCTGCTTTCTTCGATCT-GTTCCACCACCAGTATGG
1 GAAGACAAGATCTGC-TTCTTCGATCTACTT-CGCCACCAGTATGG
* * * * * * * *
4616971 GGAGATAAGATCTGCTACCTACGATCCACTTCGCTACCAATATAG
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGG
* * * * * *
4617016 CAAGATAGGATTTACTTTCTTCGATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTGC-TTCTTCGATCTACTTCGCCACCAGTATGG
* * * *
4617061 GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGG
* * * * * * * * *
4617106 GGAGATAAGATCTGTTATCTACGATCCACTCCGCTACCAATATAG
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGG
* * *
4617151 GAAGACATGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGC-TTCTTCGATCTACTTCGCCACCAGTATGG
* * ** * ***
4617196 GAAGA-TAGATCTGCTATCTTTGATCTACTT-TACGCCAGTACAT
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGG
* * *
4617239 GAAGACAAGATCTGTTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-CTTCTTCGATCTACTTCGCCACCAGTATGG
* * * * ***
4617284 GAAGGCAAGATCTGCTATCTTTGATCTACTTC-ACGCCAGTACAT
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGG
* *
4617328 AAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-CTTCTTCGATCTACTTCGCCACCAGTATGG
* ** * * ***
4617373 GAAGGCAAGATCTGCTATCTTTAATCTACTTC-ACGCCAGTACAT
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGG
4617417 GAAGACAAGATCTG
1 GAAGACAAGATCTG
4617431 AAATCTACAA
Statistics
Matches: 416, Mismatches: 112, Indels: 43
0.73 0.20 0.08
Matches are distributed among these distances:
42 3 0.01
43 16 0.04
44 124 0.30
45 263 0.63
46 6 0.01
47 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGG
Found at i:4616910 original size:89 final size:89
Alignment explanation
Indices: 4616815--4617074 Score: 290
Period size: 89 Copynumber: 2.9 Consensus size: 89
4616805 TGTTTTCTTT
** *
4616815 GATCTACTTCACGCCCATACATGAAGATAAGATTTGCTTGATTCGATCTACTTCGCCACCAGTAT
1 GATCTACTTCACGCCCATACATGAAGATAAGATTTGCTTTCTTCGATCTACTTCACCACCAGTAT
* *
4616880 GGGAAGACAAGATCTGCCATCTTC
66 GGGAAGACAAGATCTGCCACCTAC
* * * * * *
4616904 GTTCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT-GTTCCACCACCAGTA
1 GATCTACTTCACGCCCATACATGAAGATAAGATTTGCTTTCTTCGATCTACTT-CACCACCAGTA
* * *
4616968 TGGGGAGATAAGATCTGCTACCTAC
65 TGGGAAGACAAGATCTGCCACCTAC
* * ** * * *
4616993 GATCCACTTCGCTACCA-ATATAGCAAGATAGGATTTACTTTCTTCGATCTACTTCACCACCAGT
1 GATCTACTTCACGCCCATACAT-G-AAGATAAGATTTGCTTTCTTCGATCTACTTCACCACCAGT
4617057 ATGGGAAGACAAGATCTG
64 ATGGGAAGACAAGATCTG
4617075 TTATCTTTGA
Statistics
Matches: 138, Mismatches: 29, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
88 5 0.04
89 83 0.60
90 48 0.35
91 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (89 bp):
GATCTACTTCACGCCCATACATGAAGATAAGATTTGCTTTCTTCGATCTACTTCACCACCAGTAT
GGGAAGACAAGATCTGCCACCTAC
Found at i:4617106 original size:135 final size:135
Alignment explanation
Indices: 4616926--4617224 Score: 431
Period size: 135 Copynumber: 2.2 Consensus size: 135
4616916 GCCAATACAT
* **
4616926 GAAGACAAGATCTGCTT-TCTTCGATCTGTTCCACCACCAGTATGGGGAGATAAGATCTGCTACC
1 GAAGACAAGATCTG-TTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATCTGCTACC
* * *
4616990 TACGATCCACTTCGCTACCAATATAGCAAGATAGGATTTACTTTCTTCGATCTACTTCACCACCA
65 TACGATCCACTCCGCTACCAATATAGCAAGACAGGATCTACTTTCTTCGATCTACTTCACCACCA
4617055 GTATGG
130 GTATGG
* *
4617061 GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATCTGTTATCT
1 GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATCTGCTACCT
* * * * * *
4617126 ACGATCCACTCCGCTACCAATATAGGAAGACATGATCTGCTTTCTTTGATCTGCTTCGCCACCAG
66 ACGATCCACTCCGCTACCAATATAGCAAGACAGGATCTACTTTCTTCGATCTACTTCACCACCAG
4617191 TATGG
131 TATGG
* *
4617196 GAAGA-TAGATCTGCTATCTTTGATCTACT
1 GAAGACAAGATCTGTTATCTTTGATCTACT
4617225 TTACGCCAGT
Statistics
Matches: 147, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
134 24 0.16
135 123 0.84
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (135 bp):
GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATCTGCTACCT
ACGATCCACTCCGCTACCAATATAGCAAGACAGGATCTACTTTCTTCGATCTACTTCACCACCAG
TATGG
Found at i:4617333 original size:89 final size:89
Alignment explanation
Indices: 4617033--4617792 Score: 668
Period size: 89 Copynumber: 8.6 Consensus size: 89
4617023 GGATTTACTT
* * *** * * *
4617033 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTCCACCAC
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCAC
* ** *
4617098 CAGTATGGGGAGATAAGATCTGTTA
65 CAGTATGGGAAGGCAAGATCTGCTA
** * * * * * * * * * *
4617123 TCTACGATCCACTCCGCTACCAATATAGGAAGACATGATCTGCTTTCTTTGATCTGCTTCGCCAC
1 TCTTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCAC
4617188 CAGTATGGGAA-G-ATAGATCTGCTA
65 CAGTATGGGAAGGCA-AGATCTGCTA
* *
4617212 TCTTTGATCTACTTTACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTGCTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACC
4617277 AGTATGGGAAGGCAAGATCTGCTA
66 AGTATGGGAAGGCAAGATCTGCTA
* *
4617301 TCTTTGATCTACTTCACGCCAGTACATAAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACC
4617366 AGTATGGGAAGGCAAGATCTGCTA
66 AGTATGGGAAGGCAAGATCTGCTA
* *** ***
4617390 TCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGAAATCTACAATCTA-TT--CCACT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCAC-
* * * *
4617452 GCTGCCCA-GGG-A-G-ATAGAAT-TACTG
65 -CAG--TATGGGAAGGCA-AG-ATCTGCTA
* ** * * * ** * * * *** * *
4617477 GCTTCAATGTACTCCACTGCAACCACGAGGAGGTA-AA-ATCAGCCATCTTTGATCTGCTTCGCT
1 TCTTTGATCTACTTCAC-GCCAGTAC-ATGAAG-ACAAGATCTGTTTTCTTTGATCTACTTCGCC
** *
4617540 GTC--TATGTAGGAAGGAAAGATCTGCTA
63 ACCAGTATG--GGAAGGCAAGATCTGCTA
* * *
4617567 TATTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACC
* *
4617632 AGTATGGGAAGACAAGATCTGGTA
66 AGTATGGGAAGGCAAGATCTGCTA
* * *
4617656 TCTTTGATATACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACC
* *
4617721 AGTATGGGAAGACAAGATCTGGTA
66 AGTATGGGAAGGCAAGATCTGCTA
*
4617745 TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTG-TTTCTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTT
4617793 TCAACCTGCT
Statistics
Matches: 548, Mismatches: 95, Indels: 56
0.78 0.14 0.08
Matches are distributed among these distances:
85 1 0.00
86 6 0.01
87 20 0.04
88 91 0.17
89 343 0.63
90 81 0.15
91 6 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (89 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACC
AGTATGGGAAGGCAAGATCTGCTA
Found at i:4617443 original size:44 final size:44
Alignment explanation
Indices: 4617202--4617785 Score: 209
Period size: 44 Copynumber: 13.2 Consensus size: 44
4617192 ATGGGAAGAT
* ** *
4617202 AGATCTGCTATCTTTGATCTACTTTACGCCAGTACATGAAGACA
1 AGATCTGATATCTTCAATCTACTTCACGCCAGTACATGAAGACA
* * ** * * * *** *
4617246 AGATCTGTTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCA
1 AGATCTGATATCTTCAATCTACTTC-ACGCCAGTACATGAAGACA
* ** *
4617291 AGATCTGCTATCTTTGATCTACTTCACGCCAGTACATAAAGACA
1 AGATCTGATATCTTCAATCTACTTCACGCCAGTACATGAAGACA
* * * * * *** *
4617335 AGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCA
1 AGATCTGATATCTTCAATCTACTTC-ACGCCAGTACATGAAGACA
* *
4617380 AGATCTGCTATCTTTAATCTACTTCACGCCAGTACATGAAGACA
1 AGATCTGATATCTTCAATCTACTTCACGCCAGTACATGAAGACA
* * * ** * * *
4617424 AGATCTGAAATCTACAATCTA-TTCCACTG-CTGCCCAGGGAGA-T
1 AGATCTGATATCTTCAATCTACTT-CAC-GCCAGTACATGAAGACA
** * * * ** * *
4617467 AGAAT-T-ACTGGCTTCAATGTACTCCACTGCAACCACGAGGAGGTA-A
1 AG-ATCTGA-TATCTTCAATCTACTTCAC-GCCAGTAC-ATGAAG-ACA
* ** ** * * * *
4617513 A-ATCAGCCATCTTTGATCTGCTTCGCTGTCTATGT--AGGAAGGA-A
1 AGATCTGATATCTTCAATCTACTTCAC-G-CCA-GTACATGAA-GACA
* * **
4617557 AGATCTGCTATATTTGATCTACTTCACGCCAGTACATGAAGACA
1 AGATCTGATATCTTCAATCTACTTCACGCCAGTACATGAAGACA
* * * * ***
4617601 AGATCT-ATTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACA
1 AGATCTGA-TATCTTCAATCTACTTC-ACGCCAGTACATGAAGACA
* ** *
4617646 AGATCTGGTATCTTTGATATACTTCACGCCAGTACATGAAGACA
1 AGATCTGATATCTTCAATCTACTTCACGCCAGTACATGAAGACA
* * * * ***
4617690 AGATCTGTTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACA
1 AGATCTGATATCTTCAATCTACTTCA-CGCCAGTACATGAAGACA
* ** *
4617735 AGATCTGGTATCTTTGATCTACTTCACACCAGTACATGAAGACA
1 AGATCTGATATCTTCAATCTACTTCACGCCAGTACATGAAGACA
4617779 AGATCTG
1 AGATCTG
4617786 TTTCTTTTCA
Statistics
Matches: 400, Mismatches: 117, Indels: 46
0.71 0.21 0.08
Matches are distributed among these distances:
42 3 0.01
43 22 0.05
44 194 0.49
45 177 0.44
46 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
AGATCTGATATCTTCAATCTACTTCACGCCAGTACATGAAGACA
Found at i:4617644 original size:45 final size:44
Alignment explanation
Indices: 4617548--4617785 Score: 253
Period size: 44 Copynumber: 5.4 Consensus size: 44
4617538 CTGTCTATGT
* * * *
4617548 AGGAAGGA-AAGATCTGCTATATTTGATCTACTTCACGCCAGTAC
1 AGGAA-GACAAGATCTGGTATCTTCGATCTACTTCACACCAGTAC
* ** * * *
4617592 ATGAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGGTATCTTCGATCTACTTC-ACACCAGTAC
* * * *
4617637 GGGAAGACAAGATCTGGTATCTTTGATATACTTCACGCCAGTAC
1 AGGAAGACAAGATCTGGTATCTTCGATCTACTTCACACCAGTAC
* * * *
4617681 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACCACCAGTAT
1 AGGAAGACAAGATCTGGTATCTTCGATCTACTTCA-CACCAGTAC
* *
4617726 GGGAAGACAAGATCTGGTATCTTTGATCTACTTCACACCAGTAC
1 AGGAAGACAAGATCTGGTATCTTCGATCTACTTCACACCAGTAC
*
4617770 ATGAAGACAAGATCTG
1 AGGAAGACAAGATCTG
4617786 TTTCTTTTCA
Statistics
Matches: 156, Mismatches: 35, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
43 2 0.01
44 83 0.53
45 71 0.46
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (44 bp):
AGGAAGACAAGATCTGGTATCTTCGATCTACTTCACACCAGTAC
Found at i:4619110 original size:52 final size:48
Alignment explanation
Indices: 4619033--4619169 Score: 163
Period size: 52 Copynumber: 2.8 Consensus size: 48
4619023 AGCCTCTCCA
**
4619033 TTTTTTTTT-ACTC-AAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTCTTT
1 TTTTTTTTTGACTCAAAGGC-CCCTTTGTAGGGTTTCACCCTGG-C-CCCT
*
4619082 TTTGTTTTTTGACTCAAAGAGCCCCTTTGTAGGGTTTCACCTTGGCCCCT
1 TTT-TTTTTTGACTCAAAG-GCCCCTTTGTAGGGTTTCACCCTGGCCCCT
*
4619132 TTTTTTTTTGACTCAAA-GCGCCCTTTGTAGGCTTTCAC
1 TTTTTTTTTGACTCAAAGGC-CCCTTTGTAGGGTTTCAC
4619170 ATTGGTCCCA
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
47 2 0.03
48 17 0.22
49 17 0.22
50 11 0.14
51 5 0.06
52 25 0.32
53 2 0.03
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.45
Consensus pattern (48 bp):
TTTTTTTTTGACTCAAAGGCCCCTTTGTAGGGTTTCACCCTGGCCCCT
Found at i:4623911 original size:2 final size:2
Alignment explanation
Indices: 4623904--4623929 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4623894 AATGTACATG
4623904 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
4623930 ATTTAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4633923 original size:31 final size:30
Alignment explanation
Indices: 4633887--4633971 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
4633877 AGTTAAATCA
*
4633887 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * *
4633917 ACAATTAGAA-TTTCACGTGTATAATTGCACC
1 A-AATTA-AAGTTTCAAGTATACAATTGAACC
*
4633948 AAATTAAAG-TTCATGTATACAATT
1 AAATTAAAGTTTCAAGTATACAATT
4633972 ACGCATTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
29 14 0.32
30 6 0.14
31 22 0.50
32 2 0.05
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:4636123 original size:14 final size:14
Alignment explanation
Indices: 4636106--4636135 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4636096 CTCTTTTAAC
4636106 TCTTCTTTCCTTTT
1 TCTTCTTTCCTTTT
*
4636120 TCTTCTTTCTTTTT
1 TCTTCTTTCCTTTT
4636134 TC
1 TC
4636136 CATTCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TCTTCTTTCCTTTT
Found at i:4648374 original size:24 final size:23
Alignment explanation
Indices: 4648347--4648397 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
4648337 ATTTTTTTAA
4648347 TTAT-AATTATAATTATAATAAAAT
1 TTATAAATTATAA-TATAA-AAAAT
* *
4648371 TTATAAATTCTTATATAAAAAAT
1 TTATAAATTATAATATAAAAAAT
4648394 TTAT
1 TTAT
4648398 CCTACTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 9 0.38
25 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATAAATTATAATATAAAAAAT
Found at i:4648812 original size:37 final size:38
Alignment explanation
Indices: 4648742--4648815 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
4648732 GTCCACATTT
*
4648742 ATAAAAAAAAAATTCACTACCCAAATATTCAAGCCCAAA
1 ATAAAAAAAAAATTCAC-ACCCAAAAATTCAAGCCCAAA
*
4648781 ATAAAAAAAAAATT-A-GCCCAAAAATTACAAGCCCA
1 ATAAAAAAAAAATTCACACCCAAAAATT-CAAGCCCA
4648816 CATGATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 9 0.28
37 8 0.25
38 1 0.03
39 14 0.44
ACGTcount: A:0.58, C:0.22, G:0.04, T:0.16
Consensus pattern (38 bp):
ATAAAAAAAAAATTCACACCCAAAAATTCAAGCCCAAA
Found at i:4650074 original size:4 final size:4
Alignment explanation
Indices: 4650065--4650134 Score: 54
Period size: 4 Copynumber: 17.8 Consensus size: 4
4650055 TTTTCGCTTG
* * * * *
4650065 TTTA TTTA TTCA TTTTA TTTA TTCA TTTA CTTA TTTA -TGA ATTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
4650113 TTCA TTTA TCTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
4650135 TAATCCTTCT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
3 5 0.10
4 42 0.84
5 3 0.06
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:4656595 original size:90 final size:90
Alignment explanation
Indices: 4656303--4656979 Score: 485
Period size: 90 Copynumber: 7.4 Consensus size: 90
4656293 TTGTGATAAG
* * *
4656303 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCA-CATACCCTACCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCA-ACCTTATCTCCCTAAAGTTGC
* * * *
4656367 ATTGGAGTAGATTGAAGACAGAT-AGCAAA
65 AGTGGAGCAGGTT-AA-A-A-ATAAACAAA
* * * * * * *
4656396 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTCT-TCTCCCTGAAGTTG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCT-TATCTCCCTAAAGTTGC
* *
4656459 AGTGGAGTAGGTTAAAAATAAACGAA
65 AGTGGAGCAGGTTAAAAATAAACAAA
* * * * * *
4656485 TCTTATCTCCCTAAATTTGCAGTGGAGTAGATTGAAGCTATTAATCTTATCTCCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCTTATCTCCCTAAAGTTGCA
*
4656550 GTGGAGCAGGTTAAAAATAAACGAA
66 GTGGAGCAGGTTAAAAATAAACAAA
* * * * * *
4656575 TATTATCTCCCTGAAGTTGCAATAGAGCAGATTGAAGCCATCAATCTAATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCTTATCTCCCTAAAGTTGCA
*
4656640 GTAGAGCAGGTTAAAAATAAACAAA
66 GTGGAGCAGGTTAAAAATAAACAAA
* * * ** * * * *
4656665 TCTTATCTCCTTGAAGTTGTAGTGGAGGAGATTGAAGATAACGAATCTTATTTCCCTGAAA-TTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATC-AACCTTATCTCCCT-AAAGTTG
* * * *
4656729 TAGTGGAACAGATTAAAGCTATAAGTTACAAA
64 CAGTGGAGCAGGTTAAA--AATAA---ACAAA
* * * * * * *
4656761 TCTTATTTCCCTGAAGTTACAATGGTGCGGATTGAA-CTCATCATGACAAATCTTATAC-CCTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-CATCA--AC----CTTAT-CTCCCTA
* * ** * *
4656824 AAGTTGTAGTGGGGCAAATTGAATAT-AACAAA
58 AAGTTGCAGTGGAGCAGGTTAAAAATAAACAAA
* * * *
4656856 TCTTATCTCCCTGAAGTTACAGTTGAGCAGATTAAAGCCA-CAAACCTTATCTCCCTAAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATC-AACCTTATCTCCCTAAAGTTGC
* * * *
4656920 AGTGGAACAGGTT-AAAGT-TACAAG
65 AGTGGAGCAGGTTAAAAATAAACAAA
* *
4656944 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
4656980 AATAGCAAAT
Statistics
Matches: 466, Mismatches: 94, Indels: 53
0.76 0.15 0.09
Matches are distributed among these distances:
88 42 0.09
89 82 0.18
90 137 0.29
91 29 0.06
92 13 0.03
93 55 0.12
94 3 0.01
95 39 0.08
96 36 0.08
97 1 0.00
98 1 0.00
99 3 0.01
100 2 0.00
101 23 0.05
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (90 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAACCTTATCTCCCTAAAGTTGCA
GTGGAGCAGGTTAAAAATAAACAAA
Found at i:4656871 original size:45 final size:45
Alignment explanation
Indices: 4656303--4657155 Score: 415
Period size: 44 Copynumber: 18.6 Consensus size: 45
4656293 TTGTGATAAG
* *** *
4656303 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTG-AAGCCACATA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * * * * *
4656347 CCCTACCTCCCTAAAGTTGCATTGGAGTAGATTGAAGACAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-A-A-A-ATAACAAA
* * * * *
4656396 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGATT-AAAGCT-ATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-ATAACAAA
* * * * *
4656440 CCTCT-TCTCCCTGAAGTTG-AGTGGAGTAGGTTAAAAATAAACGAA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAT-AACAAA
* * * ** **
4656485 TCTTATCTCCCTAAATTTGCAGTGGAGTAGATTGAAGCT-ATTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * *
4656529 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAAATAAACGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAT-AACAAA
* * * *** *
4656575 TATTATCTCCCTGAAGTTGCAATAGAGCAGATTGAAGCCATC-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * *
4656619 TCTAATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAAATAAACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAT-AACAAA
* * * * *
4656665 TCTTATCTCCTTGAAGTTGTAGTGGAGGAGATTGAAGATAACGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * ** *
4656710 TCTTATTTCCCTGAAATTATAGTGGAACAGATT-AAAGCTATAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AT-A---ACAAA
* * * * * *
4656761 TCTTATTTCCCTGAAGTTACAATGGTGCGGATTGAACTCATCATGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA---A--ATAACAAA
* * * * *
4656811 TCTTATAC-CCTTGAAGTTGTAGTGGGGCAAATTGAATATAACAAA
1 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * ***
4656856 TCTTATCTCCCTGAAGTTACAGTTGAGCAGATT-AAAGCCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * * * * * * *
4656900 CCTTATCTCCCTAAAGTTGTAGTGGAACAGGTT-AAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* * *
4656944 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAAATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
** * * *
4656989 TCTTATCTCTTTGAAGTTGCAGTAGAGCATATT-AAAGCT-ACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-ATAACAAA
* * *
4657033 -CATTATCTCCCTGAAGTTAGAGTGGAACAGTGGAGCACATTGAAACT-ACAAG
1 TC-TTATCTCCCTGAAG-T----T-G--CAGTGGAGCAGATTGAAAATAACAAA
** * * * ** *
4657085 TCCCATCTCCCTGAAGTTGCAGCGAAGCAGATGGAAGCT-ACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
* *
4657129 TCTTATCTTCCTGAAATTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
4657156 TGGATCGAGG
Statistics
Matches: 610, Mismatches: 158, Indels: 82
0.72 0.19 0.10
Matches are distributed among these distances:
43 12 0.02
44 249 0.41
45 125 0.20
46 83 0.14
47 5 0.01
48 2 0.00
49 30 0.05
50 33 0.05
51 32 0.05
52 32 0.05
53 4 0.01
54 2 0.00
55 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAATAACAAA
Found at i:4657004 original size:133 final size:133
Alignment explanation
Indices: 4656529--4657062 Score: 351
Period size: 133 Copynumber: 3.9 Consensus size: 133
4656519 AAGCTATTAA
* * *** * * * *
4656529 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAAATAAACGAATATTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTGAAAAT-AACAAATCTTATCTCCCTGAAGTTA
* * * * * * * *
4656594 CAATAGAGCAGATTGAAGCCATCAATC-TAATCTCCCTGAAGTT-GCAGTAGAGCAGGTTAAAAA
65 CAGTAGAGCAGATTAAAGCCA-CAAACATTATCTCCCTAAAGTTAG-AGTGGAACAGGTT-AAAG
* *
4656657 TAAACAAA
127 T-TACAAG
* * * * * * * * *
4656665 TCTTATCTCCTTGAAGTTGTAGTGGAGGAGATTGAAGATAACGAATCTTATTTCCCTGAAATTAT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTGAAAATAACAAATCTTATCTCCCTGAAGTTAC
* * * * * * * * **
4656730 AGTGGAACAGATTAAAGCTATAAGTTACAAATCTTATTTCCCTGAAGTTACAATGGTGC-GGATT
66 AGTAGAGCAGATTAAAGCCACAA---AC--A--TTATCTCCCTAAAGTTAGAGTGGAACAGG-TT
*
4656794 GAACTCA-TCATGACAAA
123 -AA---AGT--T-ACAAG
* * * *
4656811 TCTTATAC-CCTTGAAGTTGTAGTGGGGCAAATTGAATATAACAAATCTTATCTCCCTGAAGTTA
1 TCTTAT-CTCCCTGAAGTTGTAGTGGAGCAAACTGAAAATAACAAATCTTATCTCCCTGAAGTTA
* *
4656875 CAGTTGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTT-GTAGTGGAACAGGTTAAAGTT
65 CAGTAGAGCAGATTAAAGCCACAAACATTATCTCCCTAAAGTTAG-AGTGGAACAGGTTAAAGTT
4656939 ACAAG
129 ACAAG
* * ** *
4656944 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAAATAGCAAATCTTATCTCTTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTGAAAATAACAAATCTTATCTCCCTGAAGTTAC
* * *
4657009 AGTAGAGCATATTAAAGCTACAAACATTATCTCCCTGAAGTTAGAGTGGAACAG
66 AGTAGAGCAGATTAAAGCCACAAACATTATCTCCCTAAAGTTAGAGTGGAACAG
4657063 TGGAGCACAT
Statistics
Matches: 316, Mismatches: 61, Indels: 45
0.75 0.14 0.11
Matches are distributed among these distances:
132 1 0.00
133 105 0.33
134 4 0.01
135 37 0.12
136 33 0.10
137 1 0.00
138 2 0.01
139 21 0.07
140 2 0.01
141 2 0.01
142 23 0.07
143 2 0.01
144 1 0.00
145 2 0.01
146 79 0.25
147 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTGAAAATAACAAATCTTATCTCCCTGAAGTTAC
AGTAGAGCAGATTAAAGCCACAAACATTATCTCCCTAAAGTTAGAGTGGAACAGGTTAAAGTTAC
AAG
Found at i:4657006 original size:89 final size:86
Alignment explanation
Indices: 4656854--4657058 Score: 196
Period size: 89 Copynumber: 2.3 Consensus size: 86
4656844 GAATATAACA
* * * *
4656854 AATCTTATCTCCCTGAAGTTACAGTTGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTT-GAGTGGAGCAGATGAAAGACACAAACCTTATCTCCCTAAAGTTG
* * * *
4656919 TAGTGGAACAGGTTAAAGTTAC
65 CAGTAGAACAGATTAAAGCTAC
* * ** *
4656941 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAA-ATAGCAAATCTTATCTCTTTGAAG
1 AA-TCTTATCTCCCTGAAGTTG-AGTGGAGCAGA-TGAAAGACA-CAAACCTTATCTCCCTAAAG
* *
4657005 TTGCAGTAGAGCATATTAAAGCTAC
62 TTGCAGTAGAACAGATTAAAGCTAC
*
4657030 AAACATTATCTCCCTGAAGTTAGAGTGGA
1 AATC-TTATCTCCCTGAAGTT-GAGTGGA
4657059 ACAGTGGAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
87 2 0.02
88 30 0.31
89 63 0.66
90 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (86 bp):
AATCTTATCTCCCTGAAGTTGAGTGGAGCAGATGAAAGACACAAACCTTATCTCCCTAAAGTTGC
AGTAGAACAGATTAAAGCTAC
Found at i:4658722 original size:4 final size:4
Alignment explanation
Indices: 4658713--4658803 Score: 53
Period size: 4 Copynumber: 22.8 Consensus size: 4
4658703 TTTTCGCTTG
* ** * *
4658713 TTTA TTTA TTCA -TTA TTCC TTTTA TTTTA TTCA TTTTA TTTA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT-TA TTTA TT-TA TTTA TTTA TTTA
* * * *
4658763 CTTA TTTA TGTA -TTA TTTA TTCA TTTA TCTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
4658804 TAATCCTTCT
Statistics
Matches: 64, Mismatches: 18, Indels: 10
0.70 0.20 0.11
Matches are distributed among these distances:
3 7 0.11
4 47 0.73
5 10 0.16
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:4658744 original size:14 final size:13
Alignment explanation
Indices: 4658725--4658788 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 13
4658715 TATTTATTCA
*
4658725 TTATTCCTTTTATT
1 TTATTCATTTTA-T
4658739 TTATTCATTTTAT
1 TTATTCATTTTAT
*
4658752 TTATTCA-TTTAC
1 TTATTCATTTTAT
*
4658764 TTATTTATGTATTAT
1 TTATTCAT-T-TTAT
4658779 TTATTCATTT
1 TTATTCATTT
4658789 ATCTATTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 10 0.24
13 9 0.21
14 13 0.31
15 10 0.24
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTCATTTTAT
Found at i:4658778 original size:27 final size:26
Alignment explanation
Indices: 4658740--4658802 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
4658730 CCTTTTATTT
*
4658740 TATTCATT-TTATTTATTCATTTA-C
1 TATTTATTATTATTTATTCATTTATC
4658764 TTATTTATGTATTATTTATTCATTTATC
1 -TATTTAT-TATTATTTATTCATTTATC
4658792 TATTTATTATT
1 TATTTATTATT
4658803 TTAATCCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 6 0.18
26 5 0.15
27 22 0.65
28 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTTATTATTATTTATTCATTTATC
Found at i:4660593 original size:19 final size:20
Alignment explanation
Indices: 4660555--4660597 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4660545 AAATATATAA
*
4660555 ATTTGAAATTTTTAAAAATT
1 ATTTGAAAATTTTAAAAATT
4660575 ATTTGAAAATTTT-AAAATT
1 ATTTGAAAATTTTAAAAATT
4660594 ATTT
1 ATTT
4660598 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTTGAAAATTTTAAAAATT
Found at i:4660606 original size:19 final size:19
Alignment explanation
Indices: 4660555--4660606 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4660545 AAATATATAA
*
4660555 ATTTGAAATTTTTAAAAATT
1 ATTTG-AATTTTTTAAAATT
**
4660575 ATTTGAAAATTTTAAAATT
1 ATTTGAATTTTTTAAAATT
*
4660594 ATTTTAATTTTTT
1 ATTTGAATTTTTT
4660607 TTTGTAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTGAATTTTTTAAAATT
Found at i:4660607 original size:20 final size:20
Alignment explanation
Indices: 4660516--4660607 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 20
4660506 TCTTTAGATT
4660516 TTTTTTTAAAATT-TTTATAA
1 TTTTTTTAAAATTATTT-TAA
*
4660536 TTTTTGTAAAAATATATAAATTTGAA
1 TTTTT-TTAAAAT-TAT---TTT-AA
* * *
4660562 ATTTTTAAAAATTATTTGAA
1 TTTTTTTAAAATTATTTTAA
**
4660582 -AATTTTAAAATTATTTTAA
1 TTTTTTTAAAATTATTTTAA
4660601 TTTTTTT
1 TTTTTTT
4660608 TTGTAATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
19 15 0.27
20 11 0.20
21 8 0.15
22 1 0.02
23 1 0.02
24 3 0.05
25 8 0.15
26 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTTTTAAAATTATTTTAA
Found at i:4664729 original size:52 final size:52
Alignment explanation
Indices: 4664667--4664770 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
4664657 AAACACACTT
4664667 AGTTAAGACTTGTTGCATTGTCCTTTGTAACTAGACAAACAACAAGTTGCAC
1 AGTTAAGACTTGTTGCATTGTCCTTTGTAACTAGACAAACAACAAGTTGCAC
*
4664719 AGTTAAGACTTGTTGCATTGTCCTTTGTAATTAGACAAACAACAAGTTGCAC
1 AGTTAAGACTTGTTGCATTGTCCTTTGTAACTAGACAAACAACAAGTTGCAC
4664771 TAACAATCTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (52 bp):
AGTTAAGACTTGTTGCATTGTCCTTTGTAACTAGACAAACAACAAGTTGCAC
Found at i:4666145 original size:2 final size:2
Alignment explanation
Indices: 4666140--4666165 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4666130 TTCAAAAGAG
4666140 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
4666166 CAATTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4667714 original size:2 final size:2
Alignment explanation
Indices: 4667707--4667746 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4667697 GTATAAGCTA
4667707 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
4667747 TCTTACTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4672266 original size:114 final size:114
Alignment explanation
Indices: 4672133--4672875 Score: 1202
Period size: 114 Copynumber: 6.5 Consensus size: 114
4672123 TATTTGCAAG
* * * *
4672133 CGCCACAAAACATCTTAACCAAAACGCAACGTTAGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * *
4672198 TATGCAAAAACGCCGCT-AA-TACTGTGCTTTAGCGGCGCATTGTAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGT--ATTAGCGGCGCATTATAAAAAA
* *
4672247 CGCCGCAAAATATCTTAACCAAAACACAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
4672312 TATGCAAAAACGCCGCTAAAGCACATTATTAGCGGCGCATTGTAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
4672361 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
**
4672426 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAGG
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* * *
4672475 CGCCGTAAAATATCTTAACCAAAACGAAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGTT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
4672540 TATGGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTGTAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* * *
4672589 CGCCGCAAAATATCTTAACCAAAACTCAGCGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGAT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
4672654 TATGCAAAAACGCTGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAG
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* *
4672703 CGCCACAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
4672768 TATGGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATACAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
4672817 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGT
4672876 TATGAAAAAG
Statistics
Matches: 586, Mismatches: 41, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
114 581 0.99
115 2 0.00
116 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
Found at i:4673450 original size:14 final size:14
Alignment explanation
Indices: 4673433--4673468 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4673423 TTATGATGTA
*
4673433 GGTTTAGTGTTTGG
1 GGTTTAGGGTTTGG
4673447 GGTTTAGGGTTTGG
1 GGTTTAGGGTTTGG
4673461 GGTTTAGG
1 GGTTTAGG
4673469 CCACTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.44
Consensus pattern (14 bp):
GGTTTAGGGTTTGG
Found at i:4675622 original size:14 final size:13
Alignment explanation
Indices: 4675600--4675633 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4675590 AAAGTATTTT
*
4675600 AAAATTAAAAATTA
1 AAAAATAAAAA-TA
4675614 AAAAATAAAAATA
1 AAAAATAAAAATA
4675627 AAAAATA
1 AAAAATA
4675634 TATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:4675960 original size:16 final size:18
Alignment explanation
Indices: 4675939--4675980 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
4675929 ATGTTAAGCT
4675939 ATGTTAA-ACA-TTTTGA
1 ATGTTAACACAGTTTTGA
*
4675955 ATGTTAAGCATAGTTTTGA
1 ATGTTAA-CACAGTTTTGA
4675974 ATGTTAA
1 ATGTTAA
4675981 GCATATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (18 bp):
ATGTTAACACAGTTTTGA
Found at i:4675973 original size:19 final size:19
Alignment explanation
Indices: 4675949--4675985 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4675939 ATGTTAAACA
4675949 TTTTGAATGTTAAGCATAG
1 TTTTGAATGTTAAGCATAG
4675968 TTTTGAATGTTAAGCATA
1 TTTTGAATGTTAAGCATA
4675986 TGAGATTCTG
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:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (19 bp):
TTTTGAATGTTAAGCATAG
Found at i:4676398 original size:21 final size:21
Alignment explanation
Indices: 4676374--4676446 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
4676364 GTTTTGTGAC
4676374 TATTTATTTATATTTTTAGCG
1 TATTTATTTATATTTTTAGCG
* *
4676395 TATTTAATATTATTGATATTATA--T
1 TATTT-AT-TTA-T-AT-TTTTAGCG
*
4676419 TATTTATTTATATTTTCAGCG
1 TATTTATTTATATTTTTAGCG
4676440 TATTTAT
1 TATTTAT
4676447 ATAAACATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 13 0.32
22 5 0.12
23 5 0.12
24 6 0.15
25 2 0.05
26 4 0.10
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (21 bp):
TATTTATTTATATTTTTAGCG
Found at i:4677183 original size:9 final size:9
Alignment explanation
Indices: 4677169--4677590 Score: 139
Period size: 9 Copynumber: 49.3 Consensus size: 9
4677159 TAATTATACT
4677169 TAACTTACA
1 TAACTTACA
4677178 TAACTTACA
1 TAACTTACA
*
4677187 TTA--TACA
1 TAACTTACA
*
4677194 CAACTTACA
1 TAACTTACA
*
4677203 TAACTTTCATTA
1 TAAC-TT-A-CA
*
4677215 TACACATACA
1 TA-ACTTACA
*
4677225 TAACCTACA
1 TAACTTACA
*
4677234 TATA-ATACA
1 TA-ACTTACA
* *
4677243 CAACATACA
1 TAACTTACA
4677252 TAACTTACA
1 TAACTTACA
* *
4677261 TAATTTTCA
1 TAACTTACA
*
4677270 T-A-GTACA
1 TAACTTACA
4677277 TAACTTACA
1 TAACTTACA
*
4677286 TAA--TA-T
1 TAACTTACA
4677292 TGAACTTACA
1 T-AACTTACA
* *
4677302 TAATTTTCA
1 TAACTTACA
4677311 TAA--TACA
1 TAACTTACA
*
4677318 TAACTTACT
1 TAACTTACA
* *
4677327 TAATTTTCA
1 TAACTTACA
* *
4677336 TAA--AAAA
1 TAACTTACA
4677343 TAACTTACA
1 TAACTTACA
4677352 TAACTTACA
1 TAACTTACA
* *
4677361 TAATTTTCA
1 TAACTTACA
*
4677370 TAACCTACA
1 TAACTTACA
* *
4677379 TATCTTATA
1 TAACTTACA
*
4677388 CAA--TACA
1 TAACTTACA
*
4677395 CAACTTACA
1 TAACTTACA
* *
4677404 TAATTTTCA
1 TAACTTACA
4677413 TAA--TACA
1 TAACTTACA
4677420 TAACTTACA
1 TAACTTACA
*
4677429 TAA--TA-T
1 TAACTTACA
4677435 TGAACTTACA
1 T-AACTTACA
* * *
4677445 TAATTTTCG
1 TAACTTACA
4677454 TAA--TACA
1 TAACTTACA
4677461 TAACTTACA
1 TAACTTACA
*
4677470 TAA--TA-T
1 TAACTTACA
4677476 TGAACTTACA
1 T-AACTTACA
* *
4677486 TAATTTTCA
1 TAACTTACA
4677495 TAA--TACA
1 TAACTTACA
* *
4677502 TAAGTTACT
1 TAACTTACA
* *
4677511 TAATTTTCA
1 TAACTTACA
4677520 TAA--TACA
1 TAACTTACA
* *
4677527 TAAGTTACT
1 TAACTTACA
* *
4677536 TAATTTTCA
1 TAACTTACA
*
4677545 TAA--TAAA
1 TAACTTACA
*
4677552 AAACTTACA
1 TAACTTACA
4677561 TAACTTACA
1 TAACTTACA
* *
4677570 TAATTTTCA
1 TAACTTACA
4677579 TAACTTACA
1 TAACTTACA
4677588 TAA
1 TAA
4677591 TTTTCATAAT
Statistics
Matches: 299, Mismatches: 76, Indels: 76
0.66 0.17 0.17
Matches are distributed among these distances:
6 3 0.01
7 64 0.21
8 3 0.01
9 212 0.71
10 9 0.03
11 2 0.01
12 4 0.01
13 2 0.01
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (9 bp):
TAACTTACA
Found at i:4677198 original size:25 final size:25
Alignment explanation
Indices: 4677170--4677431 Score: 181
Period size: 25 Copynumber: 10.4 Consensus size: 25
4677160 AATTATACTT
*
4677170 AACTTACATAACTTACATTATACAC
1 AACTTACATAACTTACATAATACAC
* *
4677195 AACTTACATAACTTTCATTATACAC
1 AACTTACATAACTTACATAATACAC
*
4677220 -A--TACATAACCTACATATAATACAC
1 AACTTACATAACTTAC--ATAATACAC
* ***
4677244 AACATACATAACTTACATAATTTTC
1 AACTTACATAACTTACATAATACAC
* ***
4677269 ATA-GTACATAACTTACATAATATTG
1 A-ACTTACATAACTTACATAATACAC
* * *
4677294 AACTTACATAATTTTCATAATACAT
1 AACTTACATAACTTACATAATACAC
* * * * * *
4677319 AACTTACTTAATTTTCATAAAAAAT
1 AACTTACATAACTTACATAATACAC
* *
4677344 AACTTACATAACTTACATAATTTTCAT
1 AACTTACATAACTTACATAA--TACAC
* * * *
4677371 AACCTACATATCTTATACAATACAC
1 AACTTACATAACTTACATAATACAC
* * *
4677396 AACTTACATAATTTTCATAATACAT
1 AACTTACATAACTTACATAATACAC
4677421 AACTTACATAA
1 AACTTACATAA
4677432 TATTGAACTT
Statistics
Matches: 189, Mismatches: 39, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
22 10 0.05
24 10 0.05
25 139 0.74
26 1 0.01
27 29 0.15
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:4677299 original size:41 final size:41
Alignment explanation
Indices: 4677253--4677330 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
4677243 CAACATACAT
*
4677253 AACTTACATAATTTTCATAGTACATAACTTACATAATATTG
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTG
*
4677294 AACTTACATAATTTTCATAATACATAACTTACTTAAT
1 AACTTACATAATTTTCATAATACATAACTTACATAAT
4677331 TTTCATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (41 bp):
AACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:4677354 original size:41 final size:42
Alignment explanation
Indices: 4677309--4677590 Score: 149
Period size: 41 Copynumber: 6.7 Consensus size: 42
4677299 ACATAATTTT
*
4677309 CATAATACATAACTTACTTAATTTTCATAA-AAAAT-A---A
1 CATAATACATAACTTACATAATTTTCATAACAAAATAACTTA
* * *
4677346 C-T--TACATAACTTACATAATTTTCATAACCTACATATCTTA
1 CATAATACATAACTTACATAATTTTCATAA-CAAAATAACTTA
* * * * *
4677386 TACAATACACAACTTACATAATTTTCATAA-TACATAACTTA
1 CATAATACATAACTTACATAATTTTCATAACAAAATAACTTA
* * * *
4677427 CATAATA-TTGAACTTACATAATTTTCGTAA-TACATAACTTA
1 CATAATACAT-AACTTACATAATTTTCATAACAAAATAACTTA
* * *
4677468 CATAATA-TTGAACTTACATAATTTTCATAATACATAAGTTACTTAATTTT
1 CATAATACAT-AACTTACATAATTTTCAT-A-ACA-AA---A--TAACTTA
* * *
4677518 CATAATACATAAGTTACTTAATTTTCATAATAAAA-AACTTA
1 CATAATACATAACTTACATAATTTTCATAACAAAATAACTTA
* * * *
4677559 CATAACTTACATAATTTTCATAACTTACATAA
1 CATAA--TACATAACTTACATAATTTTCATAA
4677591 TTTTCATAAT
Statistics
Matches: 194, Mismatches: 29, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
34 24 0.12
36 4 0.02
37 1 0.01
40 1 0.01
41 81 0.42
42 1 0.01
43 45 0.23
44 1 0.01
45 1 0.01
47 2 0.01
48 3 0.02
49 1 0.01
50 28 0.14
51 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (42 bp):
CATAATACATAACTTACATAATTTTCATAACAAAATAACTTA
Found at i:4677419 original size:16 final size:16
Alignment explanation
Indices: 4677174--4677448 Score: 83
Period size: 16 Copynumber: 17.1 Consensus size: 16
4677164 ATACTTAACT
*
4677174 TACATAACTTACATTA
1 TACATAACTTACATAA
*
4677190 TACACAACTTACATAA
1 TACATAACTTACATAA
* * *
4677206 CTTTCATTA--TACA-CA
1 --TACATAACTTACATAA
*
4677221 TACATAACCTACATATAA
1 TACATAACTTAC--ATAA
* *
4677239 TACACAACATACATAA
1 TACATAACTTACATAA
* * *
4677255 CTTACATAATTTTCATAG
1 --TACATAACTTACATAA
4677273 TACATAACTTACATAA
1 TACATAACTTACATAA
*
4677289 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
*
4677305 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
* * *
4677321 CTTACTTAATTTTCATAA
1 --TACATAACTTACATAA
* *
4677339 AAAATAACTTACATAA
1 TACATAACTTACATAA
* *
4677355 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
* * *
4677373 CCTACATATCTTATACAA
1 --TACATAACTTACATAA
*
4677391 TACACAACTTACATAA
1 TACATAACTTACATAA
4677407 T---T---TT-CATAA
1 TACATAACTTACATAA
4677416 TACATAACTTACATAA
1 TACATAACTTACATAA
*
4677432 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
4677448 T
1 T
4677449 TTTCGTAATA
Statistics
Matches: 187, Mismatches: 47, Indels: 50
0.66 0.17 0.18
Matches are distributed among these distances:
9 6 0.03
10 2 0.01
12 1 0.01
13 5 0.03
15 8 0.04
16 104 0.56
17 1 0.01
18 59 0.32
19 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:4677432 original size:25 final size:25
Alignment explanation
Indices: 4677294--4677601 Score: 217
Period size: 25 Copynumber: 11.9 Consensus size: 25
4677284 CATAATATTG
4677294 AACTTACATAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAT
* * *
4677319 AACTTACTTAATTTTCATAAAAAAT
1 AACTTACATAATTTTCATAATACAT
* * *
4677344 AACTTACATAACTTACATAATTTTCAT
1 AACTTACATAATTTTCATAA--TACAT
* * *
4677371 AACCTACAT-ATCTTAT-ACAATACAC
1 AACTTACATAAT-TT-TCATAATACAT
4677396 AACTTACATAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAT
* * *
4677421 AACTTACATAATATTGA-ACTTACAT
1 AACTTACATAATTTTCATA-ATACAT
* * * ** * *
4677446 AATTTTCGTAATACATAACTTACATAATATT
1 AACTTACATAAT---TTTCATA-AT-ACA-T
4677477 GAACTTACATAATTTTCATAATACAT
1 -AACTTACATAATTTTCATAATACAT
* *
4677503 AAGTTACTTAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAT
* * * *
4677528 AAGTTACTTAATTTTCATAATAAAA
1 AACTTACATAATTTTCATAATACAT
* * *
4677553 AACTTACATAACTTACATAATTTTCAT
1 AACTTACATAATTTTCATAA--TACAT
4677580 AACTTACATAATTTTCATAATA
1 AACTTACATAATTTTCATAATA
4677602 AGCCAAATTT
Statistics
Matches: 215, Mismatches: 52, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
24 2 0.01
25 151 0.70
26 4 0.02
27 37 0.17
28 2 0.01
29 7 0.03
30 2 0.01
31 1 0.00
32 9 0.04
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.39
Consensus pattern (25 bp):
AACTTACATAATTTTCATAATACAT
Found at i:4677586 original size:184 final size:183
Alignment explanation
Indices: 4677253--4677601 Score: 502
Period size: 184 Copynumber: 1.9 Consensus size: 183
4677243 CAACATACAT
*
4677253 AACTTACATAATTTTCATAGTACATAACTTACATAATATTGAACTTACATAATTTTCATAATACA
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTGAACTTACATAATTTTCATAATACA
** * *
4677318 TAACTTACTTAATTTTCATAAAAAATAACTTACATAACTTACATAATTTTCATAACCTACATATC
66 TAACTTACTTAATTTTCATAAAAAATAACTTACATAACTTACATAA-TTAAAAAACCTACATAAC
*
4677383 TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTG
130 TTACACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTG
*
4677437 AACTTACATAATTTTCGTAATACATAACTTACATAATATTGAACTTACATAATTTTCATAATACA
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTGAACTTACATAATTTTCATAATACA
* * * * * * * *
4677502 TAAGTTACTTAATTTTCATAATACATAAGTTACTTAATTTTCATAA-TAAAAAACTTACATAACT
66 TAACTTACTTAATTTTCATAAAAAATAACTTACATAACTTACATAATTAAAAAACCTACATAACT
* * *
4677566 TACATAATTTTCATAACTTACATAATTTTCATAATA
131 TACACAA--TACACAACTTACATAATTTTCATAATA
4677602 AGCCAAATTT
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
182 18 0.12
184 127 0.88
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (183 bp):
AACTTACATAATTTTCATAATACATAACTTACATAATATTGAACTTACATAATTTTCATAATACA
TAACTTACTTAATTTTCATAAAAAATAACTTACATAACTTACATAATTAAAAAACCTACATAACT
TACACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:4692168 original size:44 final size:44
Alignment explanation
Indices: 4692100--4692193 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
4692090 TAGATCACAT
*
4692100 CAGATTGAAACCAGAAATCTTATCTCCCTGA-GATTACAGCGGAG
1 CAGATTGAAACCAGAAATCCTATCTCCCT-ATGATTACAGCGGAG
* * * *
4692144 CAGATTGAAGCTAGTAATCCTATCTCCCTATGATTACAGTGGAG
1 CAGATTGAAACCAGAAATCCTATCTCCCTATGATTACAGCGGAG
4692188 CAGATT
1 CAGATT
4692194 AAAATAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.02
44 43 0.98
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
CAGATTGAAACCAGAAATCCTATCTCCCTATGATTACAGCGGAG
Found at i:4692286 original size:142 final size:143
Alignment explanation
Indices: 4691858--4692291 Score: 748
Period size: 142 Copynumber: 3.1 Consensus size: 143
4691848 AGTGTAAGGA
4691858 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGA-GATTACAGTGGAGCGGATTAAAATAAAGGAT
1 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGATGATTACAGTGGAGCGGATTAAAATAAAGGAT
* *
4691922 ATTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAAATTGAAACCAGAAATCTTATCTCCCT
66 CTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGAAATCTTATCTCCCT
*
4691987 GAGATTACAGCAG
131 GAGATTACAGCGG
*
4692000 AGCAGATTGAAGCTAGTAATTCTATCTCCCTGAT-ATTACAGTGGAGCGGATTAAAATAAAGGAT
1 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGATGATTACAGTGGAGCGGATTAAAATAAAGGAT
*
4692064 CTTATCTCTCTAAAGTTACAGTAGAGTAGATCACATCAGATTGAAACCAGAAATCTTATCTCCCT
66 CTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGAAATCTTATCTCCCT
4692129 GAGATTACAGCGG
131 GAGATTACAGCGG
*
4692142 AGCAGATTGAAGCTAGTAATCCTATCTCCCT-ATGATTACAGTGGAGCAGATTAAAATAAAGGAT
1 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGATGATTACAGTGGAGCGGATTAAAATAAAGGAT
* * *
4692206 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACTAGAAATCTTATTTCCCT
66 CTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGAAATCTTATCTCCCT
*
4692271 GAGATTACAGTGG
131 GAGATTACAGCGG
*
4692284 AGCGGATT
1 AGCAGATT
4692292 AAGATAAATG
Statistics
Matches: 277, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
141 2 0.01
142 275 0.99
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (143 bp):
AGCAGATTGAAGCTAGTAATCCTATCTCCCTGATGATTACAGTGGAGCGGATTAAAATAAAGGAT
CTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGAAATCTTATCTCCCT
GAGATTACAGCGG
Found at i:4692313 original size:98 final size:98
Alignment explanation
Indices: 4692144--4692342 Score: 310
Period size: 98 Copynumber: 2.0 Consensus size: 98
4692134 TACAGCGGAG
* *
4692144 CAGATTGAAGCTAGTAATCCTATCTCCCTATGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
1 CAGATTGAAACTAGAAATCCTATCTCCCTATGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
4692209 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
* * * * * *
4692242 CAGATTGAAACTAGAAATCTTATTTCCCTGA-GATTACAGTGGAGCGGATTAAGATAAATGATTT
1 CAGATTGAAACTAGAAATCCTATCTCCCT-ATGATTACAGTGGAGCAGATTAAAATAAAGGATCT
4692306 TATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
65 TATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
4692340 CAG
1 CAG
4692343 GTCTTATCTC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 91 0.99
99 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (98 bp):
CAGATTGAAACTAGAAATCCTATCTCCCTATGATTACAGTGGAGCAGATTAAAATAAAGGATCTT
ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:4695510 original size:9 final size:9
Alignment explanation
Indices: 4695496--4695607 Score: 82
Period size: 9 Copynumber: 13.2 Consensus size: 9
4695486 GTTTCGACAA
4695496 TACATAACT
1 TACATAACT
4695505 TACATAA-T
1 TACATAACT
4695513 TGATCATAA--
1 T-A-CATAACT
**
4695522 TACAGCACT
1 TACATAACT
4695531 TACATAA-T
1 TACATAACT
*
4695539 T-CACAACT
1 TACATAACT
4695547 TACATAA-T
1 TACATAACT
*
4695555 ATTCATAA--
1 -TACATAACT
4695563 TACATAACT
1 TACATAACT
4695572 TACATAA--
1 TACATAACT
4695579 TACATAACT
1 TACATAACT
4695588 TACATAACT
1 TACATAACT
*
4695597 TACATAGCT
1 TACATAACT
4695606 TA
1 TA
4695608 ATTATACTTA
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
7 20 0.24
8 8 0.10
9 50 0.60
10 5 0.06
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:4695538 original size:16 final size:16
Alignment explanation
Indices: 4695517--4695594 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 16
4695507 CATAATTGAT
4695517 CATAATACAGC-ACTTA
1 CATAATACA-CAACTTA
*
4695533 CATAATTCACAACTTA
1 CATAATACACAACTTA
4695549 CATAAT-----A-TT-
1 CATAATACACAACTTA
*
4695558 CATAATACATAACTTA
1 CATAATACACAACTTA
*
4695574 CATAATACATAACTTA
1 CATAATACACAACTTA
4695590 CATAA
1 CATAA
4695595 CTTACATAGC
Statistics
Matches: 53, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
9 6 0.11
10 2 0.04
11 1 0.02
14 1 0.02
15 3 0.06
16 40 0.75
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (16 bp):
CATAATACACAACTTA
Found at i:4695561 original size:25 final size:23
Alignment explanation
Indices: 4695531--4695602 Score: 90
Period size: 25 Copynumber: 3.0 Consensus size: 23
4695521 ATACAGCACT
*
4695531 TACATAATTCACAACTTACATAA
1 TACATAATTCATAACTTACATAA
*
4695554 TATTCATAATACATAACTTACATAA
1 TA--CATAATTCATAACTTACATAA
4695579 TACATAACTTACATAACTTACATA
1 TACATAA-TT-CATAACTTACATA
4695603 GCTTAATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.17
24 1 0.02
25 34 0.81
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.33
Consensus pattern (23 bp):
TACATAATTCATAACTTACATAA
Found at i:4695573 original size:41 final size:41
Alignment explanation
Indices: 4695494--4695602 Score: 132
Period size: 41 Copynumber: 2.6 Consensus size: 41
4695484 TGGTTTCGAC
* *
4695494 AATACATAACTTACATAATTGATCATAATACAGCACTTACAT
1 AATACACAACTTACATAATT-ATCATAATACAGAACTTACAT
* *
4695536 AATTCACAACTTACATAA-TATTCATAATACATAACTTACAT
1 AATACACAACTTACATAATTA-TCATAATACAGAACTTACAT
*
4695577 AATACATAACTTACATAACTTA-CATA
1 AATACACAACTTACATAA-TTATCATA
4695603 GCTTAATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.02
41 39 0.67
42 16 0.28
43 2 0.03
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (41 bp):
AATACACAACTTACATAATTATCATAATACAGAACTTACAT
Found at i:4696785 original size:21 final size:21
Alignment explanation
Indices: 4696750--4696802 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
4696740 CTGCAACTTA
**
4696750 AAGCAGAGGCGGCAGCGAGG-G
1 AAGCAGAGGTTGCAGCG-GGAG
4696771 AAGCAGAGGTTGCAGCGGGAG
1 AAGCAGAGGTTGCAGCGGGAG
*
4696792 AAGTAGAGGTT
1 AAGCAGAGGTT
4696803 CAAAAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.30, C:0.13, G:0.47, T:0.09
Consensus pattern (21 bp):
AAGCAGAGGTTGCAGCGGGAG
Found at i:4697316 original size:44 final size:44
Alignment explanation
Indices: 4697200--4697317 Score: 100
Period size: 44 Copynumber: 2.7 Consensus size: 44
4697190 GCCGCTAAAA
* ** *
4697200 GCTAAAGAGCATGAC-CATAGCGGCGTTTGTGGAAAAAAACGCC
1 GCTAAAGAACATGACTTGTAGCGACGTTTGTGGAAAAAAACGCC
* * ** *
4697243 GCTAAAGAACATTACTTGTAGC-AGTGTTTGTGG-AAAAGGCTCC
1 GCTAAAGAACATGACTTGTAGCGA-CGTTTGTGGAAAAAAACGCC
4697286 GCTAAAAGAACATGAGCTT-TAGCGACGTTTGT
1 GCT-AAAGAACATGA-CTTGTAGCGACGTTTGT
4697318 TGGTATGCGC
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
43 23 0.39
44 32 0.54
45 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (44 bp):
GCTAAAGAACATGACTTGTAGCGACGTTTGTGGAAAAAAACGCC
Found at i:4697391 original size:43 final size:43
Alignment explanation
Indices: 4697290--4697495 Score: 191
Period size: 43 Copynumber: 4.8 Consensus size: 43
4697280 GGCTCCGCTA
* * ** *
4697290 AAAGAACATGAGCTTTAGCGACGTTTGTTGGT-ATGCGCCACT
1 AAAGAACATGACCTTTAGCGGCGTTTGTTTTTGAAGCGCCACT
* ** ** * *
4697332 AAATG-TCATGTTCTTTAGCGGCGTTTGTCGTAGAATCGCCACT
1 AAA-GAACATGACCTTTAGCGGCGTTTGTTTTTGAAGCGCCACT
* * * *
4697375 AAAGAACATGACCTTTAGCGACGTTTTTTTTTGAAGCCCCGCT
1 AAAGAACATGACCTTTAGCGGCGTTTGTTTTTGAAGCGCCACT
* *
4697418 AAAGAACATGACCTTTAGCGGCGTTTTTTTTTTTGAAGCGCCGCT
1 AAAGAACATGACCTTTAGCGGCG--TTTGTTTTTGAAGCGCCACT
* *
4697463 AAAGAACATGACCTTTAGCAGCGTTTATTTTTG
1 AAAGAACATGACCTTTAGCGGCGTTTGTTTTTG
4697496 TAAACGCTGC
Statistics
Matches: 135, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
42 24 0.18
43 70 0.52
45 41 0.30
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (43 bp):
AAAGAACATGACCTTTAGCGGCGTTTGTTTTTGAAGCGCCACT
Found at i:4697462 original size:45 final size:45
Alignment explanation
Indices: 4697368--4697494 Score: 195
Period size: 45 Copynumber: 2.9 Consensus size: 45
4697358 GTCGTAGAAT
* *
4697368 CGCCACTAAAGAACATGACCTTTAGCGACG--TTTTTTTTTGAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTTGAAG
*
4697411 CCCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTTGAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTTGAAG
* *
4697456 CGCCGCTAAAGAACATGACCTTTAGCAGCGTTTATTTTT
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTT
4697495 GTAAACGCTG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
43 27 0.36
45 49 0.64
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTTGAAG
Found at i:4698420 original size:14 final size:15
Alignment explanation
Indices: 4698389--4698421 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4698379 TTTTAGGGTC
4698389 GAAAATGACTTTTCA
1 GAAAATGACTTTTCA
*
4698404 GAAAATGA-TTTTTA
1 GAAAATGACTTTTCA
4698418 GAAA
1 GAAA
4698422 CAAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (15 bp):
GAAAATGACTTTTCA
Found at i:4699030 original size:20 final size:20
Alignment explanation
Indices: 4699005--4699065 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
4698995 TTAAAATAAA
4699005 ATTAAAATATTAAATAATTT
1 ATTAAAATATTAAATAATTT
* *
4699025 ATTAAAATAATAAAT--TAT
1 ATTAAAATATTAAATAATTT
*
4699043 ATTAATATATT-AATAATTT
1 ATTAAAATATTAAATAATTT
4699062 ATTA
1 ATTA
4699066 TATGACTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 3 0.09
18 11 0.32
19 6 0.18
20 14 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAAATATTAAATAATTT
Found at i:4699037 original size:34 final size:36
Alignment explanation
Indices: 4698986--4699067 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 36
4698976 TCATTTTTAA
*
4698986 AATTTATTATTAAAATAAAATTA-A-AATAT-TAAAT
1 AATTTATTATAAAAAT-AAATTATATAATATATAAAT
*
4699020 AATTTATTA-AAATAATAAATTATATTAATATATTAAT
1 AATTTATTATAAA-AATAAATTATA-TAATATATAAAT
4699057 AATTTATTATA
1 AATTTATTATA
4699068 TGACTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 8 0.20
34 13 0.32
36 5 0.12
37 13 0.32
38 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
AATTTATTATAAAAATAAATTATATAATATATAAAT
Found at i:4702398 original size:17 final size:16
Alignment explanation
Indices: 4702354--4702401 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
4702344 TATGATGTGA
* *
4702354 GATTATTATGTGCATT
1 GATTATTATTTGTATT
4702370 GTATTAATTATTTGTATT
1 G-ATT-ATTATTTGTATT
4702388 GATTGATTATTTGT
1 GATT-ATTATTTGT
4702402 GTTCATTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 1 0.04
17 15 0.56
18 11 0.41
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (16 bp):
GATTATTATTTGTATT
Found at i:4703331 original size:13 final size:13
Alignment explanation
Indices: 4703313--4703337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4703303 ACAAAATAAA
4703313 AAATTAAATATTG
1 AAATTAAATATTG
4703326 AAATTAAATATT
1 AAATTAAATATT
4703338 AACAATAAAT
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATTAAATATTG
Found at i:4715159 original size:12 final size:11
Alignment explanation
Indices: 4715139--4715172 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
4715129 TTGGACTTTA
4715139 ATTTATATTTTT
1 ATTT-TATTTTT
4715151 ATTTCTATTTTT
1 ATTT-TATTTTT
4715163 ATTTTATTTT
1 ATTTTATTTT
4715173 GGGTTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:4716783 original size:17 final size:17
Alignment explanation
Indices: 4716756--4716791 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
4716746 AAAAATTCTC
4716756 AAAAATAATTTTAAGTAA
1 AAAAATAATTTTAAG-AA
4716774 AAAAAT-ATTTTAAGAA
1 AAAAATAATTTTAAGAA
4716790 AA
1 AA
4716792 CAAACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAAATAATTTTAAGAA
Found at i:4717590 original size:7 final size:7
Alignment explanation
Indices: 4717580--4717604 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4717570 TAAATAATTA
4717580 TTAATAT
1 TTAATAT
4717587 TTAATAT
1 TTAATAT
4717594 TTAATAT
1 TTAATAT
4717601 TTAA
1 TTAA
4717605 GATTGTTTGT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAATAT
Found at i:4722021 original size:40 final size:40
Alignment explanation
Indices: 4721950--4722050 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
4721940 GGCATTTGGA
*
4721950 TAAAAAAACACCGCTAAAAATCAATCTTTAGTGGCGCTTC
1 TAAAAAAACACCGCTAAAAATCAATCGTTAGTGGCGCTTC
* * * * *
4721990 TAAAAAAACCCCGCTAAAGATCGAGT-GTTAGTGGCGTTTT
1 TAAAAAAACACCGCTAAAAATC-AATCGTTAGTGGCGCTTC
** *
4722030 TCTAAAAACGCCGCTAAAAAT
1 TAAAAAAACACCGCTAAAAAT
4722051 GAGCATTAGC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 48 0.96
41 2 0.04
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (40 bp):
TAAAAAAACACCGCTAAAAATCAATCGTTAGTGGCGCTTC
Found at i:4722191 original size:41 final size:41
Alignment explanation
Indices: 4722120--4722400 Score: 370
Period size: 41 Copynumber: 6.9 Consensus size: 41
4722110 TTGTGAGTTT
* ** *
4722120 TTGGGACTTTAGCGGCGTTTTTTCAGAAGCGCCACTAATGC
1 TTGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* *
4722161 TCAGGGT-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 T-TGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* *
4722202 TTGGGTCTTTAGCGGCGTTTTTGAAGAATCGCCGCTAATGA
1 TTGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* *
4722243 TTGGGTCTTTAGCGGCGTTTTTGAGGAAGCGCCTCTAATGC
1 TTGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* *
4722284 TTGTGTCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGC
1 TTGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* * *
4722325 TTGGGTCTTTAGCGGCGGTTTTGAGGAAGCGCTGCTAATGC
1 TTGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
*
4722366 TCAGGG-CTTTAGCGGCGTTTTTAGAA-AAGCGCCGC
1 T-TGGGTCTTTAGCGGCGTTTTT-GAAGAAGCGCCGC
4722401 AAAAAATATT
Statistics
Matches: 213, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
40 4 0.02
41 201 0.94
42 8 0.04
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.32
Consensus pattern (41 bp):
TTGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
Found at i:4725255 original size:43 final size:42
Alignment explanation
Indices: 4725207--4725471 Score: 361
Period size: 43 Copynumber: 6.2 Consensus size: 42
4725197 AAGATTATGT
4725207 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTT-TGGTC
*
4725250 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TTGGTC
* * **
4725293 TATAGCGACGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TTGGTC
* *
4725336 TTTAGCGGTGTTTTTGGGAAAA-CGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TTGGTC
* * * *
4725378 TCTGGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TTGGTC
*
4725421 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGACTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG-TTTGGTC
4725464 TTTAGCGG
1 TTTAGCGG
4725472 TATTTTTTTT
Statistics
Matches: 198, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 39 0.20
43 159 0.80
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTTGGTC
Found at i:4725410 original size:128 final size:129
Alignment explanation
Indices: 4725207--4725478 Score: 422
Period size: 128 Copynumber: 2.1 Consensus size: 129
4725197 AAGATTATGT
* * *
4725207 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGTGTTTTTGGGAAAAGCGCCGCTAAAGGTTGTGGTCTCTAGCGGCGTTTGTGGGAAAA
* *
4725272 GCGCCGCTAAAGGTCATGGTCTATAGCGACGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCATGGTCTATAGCGACGTTTGTGAGAAAAGCGCCGCTAAAGGACTTGGTC
* *
4725336 TTTAGCGGTGTTTTTGGGAAAA-CGCCGCTAAAGGTCT-TGGTCTCTGGCGGCGTTTTTGGGAAA
1 TTTAGCGGTGTTTTTGGGAAAAGCGCCGCTAAAGGT-TGTGGTCTCTAGCGGCGTTTGTGGGAAA
* * *
4725399 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGACTTGGTC
65 AGCGCCGCTAAAGGTCATGGTCTATAGCGACGTTTGTGAGAAAAGCGCCGCTAAAGGACTTGGTC
*
4725464 TTTAGCGGTATTTTT
1 TTTAGCGGTGTTTTT
4725479 TTTTCTAAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 110 0.84
129 21 0.16
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (129 bp):
TTTAGCGGTGTTTTTGGGAAAAGCGCCGCTAAAGGTTGTGGTCTCTAGCGGCGTTTGTGGGAAAA
GCGCCGCTAAAGGTCATGGTCTATAGCGACGTTTGTGAGAAAAGCGCCGCTAAAGGACTTGGTC
Found at i:4728748 original size:3 final size:3
Alignment explanation
Indices: 4728740--4728792 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
4728730 ATTGTACAGT
4728740 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
4728788 GAA GA
1 GAA GA
4728793 TTTATAATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4736075 original size:2 final size:2
Alignment explanation
Indices: 4736070--4736102 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4736060 GGGGAAAAAA
4736070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4736103 AACGTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4736110 original size:16 final size:16
Alignment explanation
Indices: 4736075--4736125 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
4736065 AAAAAATATA
* **
4736075 TATATATATATATATA
1 TATATATATATAAACG
4736091 TATATATATATAAACG
1 TATATATATATAAACG
*
4736107 TATACT-TATAAAAACG
1 TATA-TATATATAAACG
4736123 TAT
1 TAT
4736126 GTACATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 29 0.97
17 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (16 bp):
TATATATATATAAACG
Found at i:4736154 original size:19 final size:21
Alignment explanation
Indices: 4736113--4736155 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4736103 AACGTATACT
*
4736113 TATAAAAACGTATGTACATTA
1 TATAAAAACGTATGCACATTA
*
4736134 TATAAAAAC-TATGCGCA-TA
1 TATAAAAACGTATGCACATTA
4736153 TAT
1 TAT
4736156 GTATGTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (21 bp):
TATAAAAACGTATGCACATTA
Found at i:4736201 original size:2 final size:2
Alignment explanation
Indices: 4736194--4736231 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4736184 TAGTAATAGG
4736194 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
4736232 GGAAAATGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4737859 original size:18 final size:18
Alignment explanation
Indices: 4737805--4737861 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
4737795 CATCCCCATA
4737805 ATGATGGGTATAAATATT
1 ATGATGGGTATAAATATT
* *
4737823 -TGAATCGTGAATCTAAATATT
1 ATG-AT-G-G-GTATAAATATT
4737844 ATGATGGGTATAAATATT
1 ATGATGGGTATAAATATT
4737862 TGAAAGTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
17 2 0.07
18 11 0.37
19 2 0.07
20 2 0.07
21 11 0.37
22 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (18 bp):
ATGATGGGTATAAATATT
Found at i:4740831 original size:18 final size:19
Alignment explanation
Indices: 4740795--4740835 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4740785 ATTATATTAG
*
4740795 GAAAAAAATAAATTTAAAT
1 GAAAAAAATAAATTGAAAT
*
4740814 GAAAAAAATTAA-TGAAAT
1 GAAAAAAATAAATTGAAAT
4740832 GAAA
1 GAAA
4740836 TGTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (19 bp):
GAAAAAAATAAATTGAAAT
Found at i:4740907 original size:28 final size:29
Alignment explanation
Indices: 4740824--4740915 Score: 86
Period size: 28 Copynumber: 3.3 Consensus size: 29
4740814 GAAAAAAATT
*
4740824 AATGAAATGAAATGTTAAATGAATATG-A
1 AATGAAATTAAATGTTAAATGAATATGAA
* * * *
4740852 AATGTAATGT-AAT-TTGTAATAAACATGAA
1 AATGAAAT-TAAATGTT-AAATGAATATGAA
4740881 AAT-AAATTAAATGTTAAATGAATATG-A
1 AATGAAATTAAATGTTAAATGAATATGAA
4740908 AATGAAAT
1 AATGAAAT
4740916 GATGATTATG
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 7 0.14
28 36 0.73
29 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.14, T:0.32
Consensus pattern (29 bp):
AATGAAATTAAATGTTAAATGAATATGAA
Found at i:4740925 original size:19 final size:19
Alignment explanation
Indices: 4740898--4740936 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4740888 TAAATGTTAA
4740898 ATGAATATGAAATGAAATG
1 ATGAATATGAAATGAAATG
* *
4740917 ATGATTATGAAATGGAATG
1 ATGAATATGAAATGAAATG
4740936 A
1 A
4740937 AAGTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (19 bp):
ATGAATATGAAATGAAATG
Found at i:4741012 original size:20 final size:21
Alignment explanation
Indices: 4740978--4741029 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
4740968 ATGAAAGCAA
* * *
4740978 AAATTGAAATGAGAAATAATT
1 AAATTTAAATGAGAAAAAAGT
4740999 AAATTTAAAT-AGAAAAAAGT
1 AAATTTAAATGAGAAAAAAGT
4741019 -AATTTAAATGA
1 AAATTTAAATGA
4741030 ATGGAAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 9 0.33
21 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AAATTTAAATGAGAAAAAAGT
Found at i:4747890 original size:21 final size:22
Alignment explanation
Indices: 4747866--4747913 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
4747856 TATTTAGCAA
*
4747866 CTTTTTAATAATCAC-ATTTTT
1 CTTTTTAACAATCACTATTTTT
* * *
4747887 CTTTATGACAATCACTTTTTTT
1 CTTTTTAACAATCACTATTTTT
4747909 CTTTT
1 CTTTT
4747914 AAATTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.58
Consensus pattern (22 bp):
CTTTTTAACAATCACTATTTTT
Found at i:4764092 original size:31 final size:31
Alignment explanation
Indices: 4764014--4764147 Score: 104
Period size: 31 Copynumber: 4.5 Consensus size: 31
4764004 CCCAAAAAGT
* * *
4764014 TTTAAGTACCAACTTAAGAAAAAGTGTCAAG
1 TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
*
4764045 TTTAGGTACCACATTAGGAAAACA-TGTCAAG
1 TTTAGGTACCAAATTAGGAAAA-AGTGTCAAG
*
4764076 TTTGGGTACCAAATTAGACCGAAAAA-----AA-
1 TTTAGGTACCAAATTAG---GAAAAAGTGTCAAG
* *
4764104 TTTAGGTATCAAATTAGGAAAAAGTGTTAA-
1 TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
*
4764134 TTTAGATACCAAAT
1 TTTAGGTACCAAAT
4764148 GTTATATTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
25 6 0.07
28 15 0.18
29 2 0.02
30 14 0.17
31 40 0.48
32 1 0.01
33 1 0.01
34 5 0.06
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (31 bp):
TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
Found at i:4766890 original size:2 final size:2
Alignment explanation
Indices: 4766883--4766916 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4766873 NNATATACAA
4766883 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
4766917 GATTAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4778385 original size:17 final size:19
Alignment explanation
Indices: 4778363--4778404 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4778353 AACGGTTGTA
4778363 TTCTTTTA-TAAA-ATTAT
1 TTCTTTTACTAAATATTAT
4778380 TTCTTTTACTAAATATTAT
1 TTCTTTTACTAAATATTAT
*
4778399 ATCTTT
1 TTCTTT
4778405 ACATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (19 bp):
TTCTTTTACTAAATATTAT
Found at i:4778405 original size:18 final size:18
Alignment explanation
Indices: 4778364--4778413 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
4778354 ACGGTTGTAT
*
4778364 TCTTTTA-TAAAATTATT
1 TCTTTTACTAAAATTATA
4778381 TCTTTTACTAAATATTATA
1 TCTTTTACTAAA-ATTATA
4778400 TC-TTTACATAAAAT
1 TCTTTTAC-TAAAAT
4778414 AATCATTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.24
18 11 0.38
19 11 0.38
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (18 bp):
TCTTTTACTAAAATTATA
Found at i:4778893 original size:30 final size:30
Alignment explanation
Indices: 4778859--4778934 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 30
4778849 AATATTTTTT
4778859 AAAAATATTAAAAT-TATTACATTTT-AAATA
1 AAAAATATTAAAATATA-TA-ATTTTAAAATA
* *
4778889 AAAAATAATAGAAATATATATTTTTAAAATA
1 AAAAATATTA-AAATATATAATTTTAAAATA
4778920 AAAGAATAATTAAAA
1 AAA-AAT-ATTAAAA
4778935 ACAATTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 13 0.34
31 14 0.37
32 8 0.21
33 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATATTAAAATATATAATTTTAAAATA
Found at i:4783959 original size:81 final size:81
Alignment explanation
Indices: 4783863--4784034 Score: 344
Period size: 81 Copynumber: 2.1 Consensus size: 81
4783853 TTTACAAGAT
4783863 TTGCCATATCAAATCTAATCTAATCTTTACAAGATATGATTCTCTCTATCTTCTAAGATTAGTTA
1 TTGCCATATCAAATCTAATCTAATCTTTACAAGATATGATTCTCTCTATCTTCTAAGATTAGTTA
4783928 CCAAAATTAGCCTAAG
66 CCAAAATTAGCCTAAG
4783944 TTGCCATATCAAATCTAATCTAATCTTTACAAGATATGATTCTCTCTATCTTCTAAGATTAGTTA
1 TTGCCATATCAAATCTAATCTAATCTTTACAAGATATGATTCTCTCTATCTTCTAAGATTAGTTA
4784009 CCAAAATTAGCCTAAG
66 CCAAAATTAGCCTAAG
4784025 TTGCCATATC
1 TTGCCATATC
4784035 TTTATCATCG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 91 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (81 bp):
TTGCCATATCAAATCTAATCTAATCTTTACAAGATATGATTCTCTCTATCTTCTAAGATTAGTTA
CCAAAATTAGCCTAAG
Found at i:4789860 original size:30 final size:30
Alignment explanation
Indices: 4789816--4789909 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
4789806 ATTTCTTATG
*
4789816 CCAATATCTCGATACCCATATCTTTGATTTT
1 CCAATAT-TTGATACCCATATCTTTGATTTT
* * *
4789847 CTAATATTTGATACCTATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGATTTT
* * *
4789877 CCATTATTTGATAACCATATATTTGATTTT
1 CCAATATTTGATACCCATATCTTTGATTTT
4789907 CCA
1 CCA
4789910 TAAATACGGA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
30 47 0.89
31 6 0.11
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGATTTT
Found at i:4789886 original size:15 final size:15
Alignment explanation
Indices: 4789831--4789911 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
4789821 ATCTCGATAC
*
4789831 CCATATCTTTGATTT
1 CCATATATTTGATTT
* *
4789846 TC-TAATATTTGA-TA
1 CCAT-ATATTTGATTT
*
4789860 CCTATATCTTTGACTTT
1 CC-ATATATTTGA-TTT
**
4789877 CCAT-TATTTGATAA
1 CCATATATTTGATTT
4789891 CCATATATTTGATTTT
1 CCATATATTTGA-TTT
4789907 CCATA
1 CCATA
4789912 AATACGGATG
Statistics
Matches: 48, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
14 8 0.17
15 28 0.58
16 9 0.19
17 3 0.06
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.49
Consensus pattern (15 bp):
CCATATATTTGATTT
Found at i:4794311 original size:33 final size:32
Alignment explanation
Indices: 4794240--4794312 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
4794230 TTATATATAC
*
4794240 ATATATATATTTATATACATATTCTTAATTTT
1 ATATATATATATATATACATATTCTTAATTTT
* *
4794272 CATATATATATATATATACGTAATTCTATACTTTT
1 -ATATATATATATATATACAT-ATTCT-TAATTTT
4794307 -TATATA
1 ATATATA
4794313 CTCTTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 24 0.69
34 5 0.14
35 6 0.17
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.52
Consensus pattern (32 bp):
ATATATATATATATATACATATTCTTAATTTT
Found at i:4794358 original size:14 final size:16
Alignment explanation
Indices: 4794321--4794361 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
4794311 TACTCTTTAA
4794321 TTTATATATACATACT
1 TTTATATATACATACT
**
4794337 TTTATATATACATGTT
1 TTTATATATACATACT
4794353 TTTATATAT
1 TTTATATAT
4794362 TTCCATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTATATATACATACT
Found at i:4798236 original size:14 final size:14
Alignment explanation
Indices: 4798217--4798265 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
4798207 ATTTTCTTTT
4798217 AATTTTTTAATTAA
1 AATTTTTTAATTAA
**
4798231 AATTTTTTAAACTTTT
1 AATTTTTT-AA-TTAA
4798247 AA-TTTTTAATTAA
1 AATTTTTTAATTAA
4798260 AATTTT
1 AATTTT
4798266 AATTAGACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 7 0.25
16 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTTTTTAATTAA
Found at i:4804058 original size:20 final size:19
Alignment explanation
Indices: 4804003--4804062 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
4803993 GCCCGAATTA
4804003 TATATTAAATATATATTTT
1 TATATTAAATATATATTTT
* * *
4804022 TATTTTTAATCAAATATACTTT
1 TA-TATTAA--ATATATATTTT
4804044 T-TATTAAATATATATTTT
1 TATATTAAATATATATTTT
4804062 T
1 T
4804063 TGGACTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 10 0.31
19 2 0.06
20 10 0.31
22 10 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTAAATATATATTTT
Found at i:4804060 original size:40 final size:37
Alignment explanation
Indices: 4804001--4804118 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 37
4803991 CGGCCCGAAT
4804001 TATATATTAAATATATATTTTTATTTTTAATCAAATA
1 TATATATTAAATATATATTTTTATTTTTAATCAAATA
* * *
4804038 TACTTTTTATTAAATATATATTTTTTGGACTTTTAATCTGAAT-
1 TA---TATATTAAATATATA-TTTTT--ATTTTTAATC-AAATA
* *
4804081 TATATATTAAATATATTTTTTTATTTTTAATTAAATA
1 TATATATTAAATATATATTTTTATTTTTAATCAAATA
4804118 T
1 T
4804119 GGGCCGGGCC
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
36 3 0.05
37 11 0.17
39 5 0.08
40 27 0.42
41 5 0.08
43 11 0.17
44 3 0.05
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (37 bp):
TATATATTAAATATATATTTTTATTTTTAATCAAATA
Found at i:4804756 original size:20 final size:20
Alignment explanation
Indices: 4804698--4804761 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
4804688 CCGGCTCGAA
*
4804698 TTATATATTAAATATATTTAT
1 TTAT-TATTAAATATATATAT
* *
4804719 TTATT-TTTAATCAAATATACT
1 TTATTATTAAAT-ATATATA-T
*
4804740 TT-TTATTAAATATATATTT
1 TTATTATTAAATATATATAT
4804759 TTA
1 TTA
4804762 GACTTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
19 8 0.24
20 13 0.39
21 12 0.36
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTAAATATATATAT
Found at i:4804759 original size:17 final size:17
Alignment explanation
Indices: 4804720--4804761 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4804710 TATATTTATT
4804720 TATTTTTAATCAAATATA
1 TATTTTT-ATCAAATATA
* *
4804738 -CTTTTTATTAAATATA
1 TATTTTTATCAAATATA
4804754 TATTTTTA
1 TATTTTTA
4804762 GACTTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTTTATCAAATATA
Found at i:4805017 original size:696 final size:693
Alignment explanation
Indices: 4803552--4805628 Score: 3295
Period size: 696 Copynumber: 3.0 Consensus size: 693
4803542 GACACTGTTG
*
4803552 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCTGAATAG
1 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCCGAATAG
4803617 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGGCACCCTCCTCCGCATGGA
66 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGGCACCCTCCTCCGCATGGA
* * *
4803682 TGCTT-GAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTTGAAGTGTCTTGAG
131 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
* *
4803746 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTTAGGTCCAGTAACAGCAAATGATATTGATTTGG
196 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTCAGGTCCAGTAGCAGCAAATGATATTGATTTGG
*
4803811 CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCCA-CT---C-G--G-C--CCGC
261 CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTACCTGGCCGGCCGACGGCCGC
*
4803866 CCAAAAAATGGGAGGGTTCGAGTAAAAATATAGGCTCGAAATATGGGTTTGGGAAAAAAGTGAGG
326 CCAAAAAATGGGAGGGTTCGAGTAAAAATATAGGCTCGAAATATGGGTTTGGGAAAAAA-AGAGG
*
4803931 CCCGTTTAGAAAACAAGCTGGGCCTCGGGTAAGACTTTTTTGGCCAGAGCCGGGCCGTGCCGGCC
390 CCCGTTTAGAAAACAGGCTGGGCCTCGGGTAAGACTTTTTTGGCCAGAGCCGGGCCGTGCCGGCC
4803996 CGAATTATATATTAAATATATATTTTTATTTTTAATCAAATATACTTTTTATTAAATATATATTT
455 CGAATTATATATTAAATATAT-TTTTTATTTTTAATCAAATATACTTTTTATTAAATATATATTT
*
4804061 TTTGGACTTTTAATCTGAATTATATATTAAATATAT-TTTTTTATTTTTAATTAAATATGGGCCG
519 TTTGGACTTTTAATCTGAATTATATATTAAATATATATTTTTTATTTTTAATAAAATATGGGCCG
* *
4804125 GGCCGGCCGGTCGAGCTTAGCAATTTTCTTT-TGGGCCAGGCTTGGACAAATTTTTAGGCCCATA
584 GGTCGG--GCTCG-GCTTAGCAATTTTCTTTCT-GGCC-GGCTTGGACAAATTTTTAGGCCCATA
* * * * *
4804189 TTTCAGGTCAGGCCGGACTCAGACCTATAAAATGGGCCTAAAATTTCATC
644 TTTCGGGTCAGTCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
* *
4804239 TGGATTATATTTGTTTATGATGAATTAATGTTGTAGGAGAAATTTTGGTGGATATGTCCGAATAG
1 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCCGAATAG
* *
4804304 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGGTATGGCACCCTCCTCTGCATGGA
66 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGGCACCCTCCTCCGCATGGA
* *
4804369 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAATGAGGATAGAGCAAGCTGTGGAGGTGTCTTGAG
131 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
4804434 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTCAGGTCCAGTAGCAGCAAATGATATTGATTTGG
196 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTCAGGTCCAGTAGCAGCAAATGATATTGATTTGG
* * *
4804499 CAGAGAGTGGCACGGTGATGGTAGAGGTGATCATGGGTTAGGCTACCTGGCCCGGCCGACGGCCG
261 CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTACCTGG-CCGGCCGACGGCCG
*
4804564 CCCAAAAAATGGGAGGGTTCGAGTAAAAATATAGGCCCGAAATATGGGTTTGGGAAAAAAACGAG
325 CCCAAAAAATGGGAGGGTTCGAGTAAAAATATAGGCTCGAAATATGGGTTTGGGAAAAAAA-GAG
* * * * *
4804629 GCCTGTTTAG-AAACAGGCTGGGCTTTGGGTAATACTTTTTTGGCCTGAGCCGGGCCGTGCCGGC
389 GCCCGTTTAGAAAACAGGCTGGGCCTCGGGTAAGACTTTTTTGGCCAGAGCCGGGCCGTGCCGGC
*
4804693 TCGAATTATATATTAAATATATTTATTTATTTTTAATCAAATATACTTTTTATTAAATATATA-T
454 CCGAATTATATATTAAATATATTT-TTTATTTTTAATCAAATATACTTTTTATTAAATATATATT
* *
4804757 TTTTAGACTTTTAATCTGAATTATATATTAAATATATATTTTTTATTTTTAATCAAATATGGGCC
518 TTTTGGACTTTTAATCTGAATTATATATTAAATATATATTTTTTATTTTTAATAAAATATGGGCC
*
4804822 GGGTCGGGCTCTGGCTTAGTAATTTTCTTTCTGGCCGGACTTGGACAAATTTTTAGGCCCATATT
583 GGGTCGGGCTC-GGCTTAGCAATTTTCTTTCTGGCCGG-CTTGGACAAATTTTTAGGCCCATATT
*
4804887 TCGGGTCAGTCCGGGCTCGGACCTATAAAACGGGTCTAAAATTTCATC
646 TCGGGTCAGTCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
*
4804935 TGGATTATATTTGTTTACGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCCGAATAG
1 TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCCGAATAG
* *
4805000 GTGTAGGATTGATTTAATTAAATTCCAAACCAACTGCATTGATATAGCACCCTCCTCCGCATGGA
66 GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGGCACCCTCCTCCGCATGGA
*
4805065 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGGGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
131 TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
* * *
4805130 AGATAAGGAGGGAGTCGCAAAAGCTTTATTTTCAGGTCCAGTAGCAGCAAACGATACTGATTTGG
196 AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTCAGGTCCAGTAGCAGCAAATGATATTGATTTGG
** * *
4805195 CAGAGATTGGCGCAATGATGGTAGAGGTGATCATGGGTTGGGTTACCCGGCTCGGCCCGACGGCC
261 CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTACCTGGC-CGG-CCGACGGCC
* *
4805260 -CATCCAAAAAATGGAAGGGTTCGGGTAAAAATATAGGCTCGAAATATGGGTTTGGGAAAAAAAG
324 GC--CCAAAAAATGGGAGGGTTCGAGTAAAAATATAGGCTCGAAATATGGGTTTGGGAAAAAAAG
*
4805324 AGGCCCGTTTAGAAAACAGGCTGGGCCTCGGGTAAGACTTTTTTGGCCAGAGCCGGGTCGTGCCG
387 AGGCCCGTTTAGAAAACAGGCTGGGCCTCGGGTAAGACTTTTTTGGCCAGAGCCGGGCCGTGCCG
4805389 GCCCGAATTATATATTAAATATA-TTTTTA-TTTTAATCAAATATACTTTTTATTAAATATATAT
452 GCCCGAATTATATATTAAATATATTTTTTATTTTTAATCAAATATACTTTTTATTAAATATATAT
* *
4805452 TTTTTGGACTTTTAATTTGAATTATATATTAAATATA-A---ATT-TTTTTAATAAAATATGGGC
517 TTTTTGGACTTTTAATCTGAATTATATATTAAATATATATTTTTTATTTTTAATAAAATATGGGC
* *
4805512 CGGGTCGGACTCGGGCTTAGCAATTTTCTTTC-GAGCCGGGCTTGAACAAATTTTTAGGCCCATA
582 CGGGTCGGGCTC-GGCTTAGCAATTTTCTTTCTG-GCC-GGCTTGGACAAATTTTTAGGCCCATA
*
4805576 TTTCGAGTCAGGT-CGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
644 TTTCGGGTCA-GTCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
4805626 TGG
1 TGG
4805629 GCGCAGCCCG
Statistics
Matches: 1287, Mismatches: 76, Indels: 50
0.91 0.05 0.04
Matches are distributed among these distances:
687 130 0.10
688 158 0.12
689 2 0.00
690 1 0.00
691 121 0.09
692 6 0.00
693 1 0.00
694 1 0.00
695 37 0.03
696 425 0.33
697 65 0.05
698 266 0.21
699 74 0.06
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (693 bp):
TGGATTATATTTGTTTATGATGAATTAATGTTGCAGGAGAACTTTTGGTGGATATGTCCGAATAG
GTGTAGGATTGATTTAATTAAATTCCAAACCAGCTGCATTGATATGGCACCCTCCTCCGCATGGA
TGCTTAAAGTTCAATGTTTGTGGGATTGCAAACGAGGATAGAGCAGGCTGTGGAGGTGTCTTGAG
AGATAAGGAGGGAGTCGCAAGAGCTTTATTTTCAGGTCCAGTAGCAGCAAATGATATTGATTTGG
CAGAGATTGGCGCGGTGATGGTAGAGGTGATCATGGGTTGGGCTACCTGGCCGGCCGACGGCCGC
CCAAAAAATGGGAGGGTTCGAGTAAAAATATAGGCTCGAAATATGGGTTTGGGAAAAAAAGAGGC
CCGTTTAGAAAACAGGCTGGGCCTCGGGTAAGACTTTTTTGGCCAGAGCCGGGCCGTGCCGGCCC
GAATTATATATTAAATATATTTTTTATTTTTAATCAAATATACTTTTTATTAAATATATATTTTT
TGGACTTTTAATCTGAATTATATATTAAATATATATTTTTTATTTTTAATAAAATATGGGCCGGG
TCGGGCTCGGCTTAGCAATTTTCTTTCTGGCCGGCTTGGACAAATTTTTAGGCCCATATTTCGGG
TCAGTCCGGGCTCGGACCTATAAAACGGGCCTAAAATTTCATC
Found at i:4806262 original size:36 final size:36
Alignment explanation
Indices: 4806215--4806285 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
4806205 TGTAAATTGC
4806215 CTTGGTAGTCCATGATAATCTTGTTGGTGAATACTT
1 CTTGGTAGTCCATGATAATCTTGTTGGTGAATACTT
4806251 CTTGGTAGTCCATGATAATCTTGTTGGTGAATACT
1 CTTGGTAGTCCATGATAATCTTGTTGGTGAATACT
4806286 CCTGTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.41
Consensus pattern (36 bp):
CTTGGTAGTCCATGATAATCTTGTTGGTGAATACTT
Found at i:4811057 original size:2 final size:2
Alignment explanation
Indices: 4811052--4811076 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4811042 ATATATGGTG
4811052 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4811077 TAAAAATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4818682 original size:2 final size:2
Alignment explanation
Indices: 4818675--4818703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4818665 ATTTCTTTTA
4818675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4818704 ATCATTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4819526 original size:17 final size:17
Alignment explanation
Indices: 4819487--4819537 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
4819477 TCCTAAAATG
* *
4819487 AAATTTTTTTATTTATA
1 AAATTTTATAATTTATA
**
4819504 TTATTTTATAATTTATA
1 AAATTTTATAATTTATA
*
4819521 AAATTTTA-AATTAATA
1 AAATTTTATAATTTATA
4819537 A
1 A
4819538 TTGTAAAGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATTTTATAATTTATA
Found at i:4821179 original size:22 final size:21
Alignment explanation
Indices: 4821136--4821181 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
4821126 CAAATAAAAT
*
4821136 AAAATTAATAAATATTTTATA
1 AAAATTAATAAATATTTAATA
4821157 AAAATATAATAAA-ATATTAATA
1 AAAAT-TAATAAATAT-TTAATA
4821179 AAA
1 AAA
4821182 TAAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTAATAAATATTTAATA
Found at i:4821555 original size:23 final size:23
Alignment explanation
Indices: 4821529--4821579 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
4821519 TAATTTTTAA
* * *
4821529 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAATAATAAT
4821552 ATTTAGAATTATTTAATAATAAT
1 ATTTAGAATTATTTAATAATAAT
4821575 ATTTA
1 ATTTA
4821580 AGAAAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (23 bp):
ATTTAGAATTATTTAATAATAAT
Found at i:4826348 original size:32 final size:32
Alignment explanation
Indices: 4826254--4826352 Score: 83
Period size: 36 Copynumber: 3.0 Consensus size: 32
4826244 CCGTGTGGTC
* ** *
4826254 CACACGGTCTACCCACACGGTCTGCATTATTT
1 CACACGGCCTACCCACAAAGTCTGCATGATTT
* * *
4826286 CACACGACCGTGTGACCCAC-ACGATTTGCATGATTT
1 CACACGGCC---T-ACCCACAAAG-TCTGCATGATTT
4826322 CACACGGCCTACCCACAAAGTCTGCATGATT
1 CACACGGCCTACCCACAAAGTCTGCATGATT
4826353 ACAGACGGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
32 23 0.44
33 3 0.06
35 2 0.04
36 24 0.46
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.24
Consensus pattern (32 bp):
CACACGGCCTACCCACAAAGTCTGCATGATTT
Found at i:4828198 original size:15 final size:15
Alignment explanation
Indices: 4828178--4828206 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4828168 CAACCCTTTG
4828178 CAATTATTTTGAATA
1 CAATTATTTTGAATA
4828193 CAATTATTTTGAAT
1 CAATTATTTTGAAT
4828207 TTTAAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
CAATTATTTTGAATA
Found at i:4830148 original size:7 final size:8
Alignment explanation
Indices: 4830124--4830153 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
4830114 TAAAGCAAGT
4830124 ATAAAACAA
1 ATAAAA-AA
4830133 ATAAAAAA
1 ATAAAAAA
4830141 ATAAAAAA
1 ATAAAAAA
4830149 ATAAA
1 ATAAA
4830154 TTGATAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (8 bp):
ATAAAAAA
Found at i:4832824 original size:30 final size:30
Alignment explanation
Indices: 4832790--4832847 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
4832780 CACAGGCTGG
4832790 CACATGGACATGT-GCCTAGCCCCTGTGGCT
1 CACATGGACATGTGGCC-AGCCCCTGTGGCT
* *
4832820 CACATGGGCATGTGGCCAGCCCGTGTGG
1 CACATGGACATGTGGCCAGCCCCTGTGG
4832848 AAATGCCCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.21
Consensus pattern (30 bp):
CACATGGACATGTGGCCAGCCCCTGTGGCT
Found at i:4834678 original size:6 final size:6
Alignment explanation
Indices: 4834667--4834758 Score: 62
Period size: 6 Copynumber: 15.0 Consensus size: 6
4834657 AGAAACAATC
* * * * * *
4834667 ATAAAA ATAAAA ATATAG TTCAAAA GATAAAA AT-GAA ATATAA CTAAGAAA
1 ATAAAA ATAAAA ATAAAA AT-AAAA -ATAAAA ATAAAA ATAAAA ATAA--AA
* *
4834718 ATAACA ATAAAC ATAAAA ATAAAA ATAAAA AT-AAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
4834759 CAAATGGACT
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
5 9 0.14
6 44 0.68
7 6 0.09
8 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (6 bp):
ATAAAA
Found at i:4842160 original size:40 final size:40
Alignment explanation
Indices: 4842115--4842190 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
4842105 GTGTGTCTCA
4842115 TCCACAT-GAGCGTGTAGGCCTCCACACGGCCAGGGCCACG
1 TCCACATAG-GCGTGTAGGCCTCCACACGGCCAGGGCCACG
* *
4842155 TCCACATAGGCGTGTAGGCCTCTACACGGCTAGGGC
1 TCCACATAGGCGTGTAGGCCTCCACACGGCCAGGGC
4842191 AAACGACCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.20, C:0.34, G:0.30, T:0.16
Consensus pattern (40 bp):
TCCACATAGGCGTGTAGGCCTCCACACGGCCAGGGCCACG
Found at i:4842839 original size:21 final size:21
Alignment explanation
Indices: 4842814--4842853 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4842804 TGAATATACG
4842814 TCTGTTTGTCAGAACATTTTA
1 TCTGTTTGTCAGAACATTTTA
**
4842835 TCTGTTTGTGTGAACATTT
1 TCTGTTTGTCAGAACATTT
4842854 GGTTATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.50
Consensus pattern (21 bp):
TCTGTTTGTCAGAACATTTTA
Found at i:4843906 original size:28 final size:28
Alignment explanation
Indices: 4843845--4843906 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
4843835 ATTTAATGCG
4843845 TATAATCTAAATTAATAAAATACAAATA
1 TATAATCTAAATTAATAAAATACAAATA
* *
4843873 TAATAAT-TTAATTAA-ACAAATATAAATAA
1 T-ATAATCTAAATTAATA-AAATACAAAT-A
4843902 TATAA
1 TATAA
4843907 AATATAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 21 0.72
29 7 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (28 bp):
TATAATCTAAATTAATAAAATACAAATA
Found at i:4844201 original size:68 final size:68
Alignment explanation
Indices: 4844092--4844227 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
4844082 TAAATATTAA
*
4844092 TAATGGCGGTAGAATGATTGCAAAGTAATAAGAAAAAGAAAAACAATAAGATCACACAGATTTTA
1 TAATGGCGGTAGAATGATCGCAAAGTAATAAGAAAAAGAAAAACAATAAGATCACACAGATTTTA
4844157 TGT
66 TGT
4844160 TAATGGCGGTAGAATGATCGCAAAGTAATAAGAAAAAGAAAAACAATAAGATCACACAGATTTTA
1 TAATGGCGGTAGAATGATCGCAAAGTAATAAGAAAAAGAAAAACAATAAGATCACACAGATTTTA
4844225 TGT
66 TGT
4844228 AGAAAACCCT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.23
Consensus pattern (68 bp):
TAATGGCGGTAGAATGATCGCAAAGTAATAAGAAAAAGAAAAACAATAAGATCACACAGATTTTA
TGT
Found at i:4846659 original size:21 final size:21
Alignment explanation
Indices: 4846635--4846682 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
4846625 TTTCGAATAG
* *
4846635 TTTAATGATTTAAATGA-TTTT
1 TTTAATAATTT-AATGACATTT
4846656 TTTAAATAATTTAATGACATTT
1 TTT-AATAATTTAATGACATTT
4846678 TTTAA
1 TTTAA
4846683 ACTTTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTAATAATTTAATGACATTT
Found at i:4848159 original size:6 final size:6
Alignment explanation
Indices: 4848150--4848182 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
4848140 GTTATAGTCA
4848150 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
4848183 GCCATGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:4855573 original size:89 final size:89
Alignment explanation
Indices: 4855422--4855599 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
4855412 GTAAGTTAAT
4855422 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTCTGTGAGGCTTTGGGTTTGAATCTTTCCCTTGAA
1 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTCTGTGAGGCTTTGGGTTTGAATCTTTCCCTTGAA
*
4855487 TTTTTGTTATTTTTGTCTTAATCC
66 TTTATGTTATTTTTGTCTTAATCC
*
4855511 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTCTGTGAGGTTTTGGGTTTGAATCTTTCCCTTGAA
1 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTCTGTGAGGCTTTGGGTTTGAATCTTTCCCTTGAA
4855576 TTTATGTTATTTTTGTCTTAATCC
66 TTTATGTTATTTTTGTCTTAATCC
4855600 CTATCCTTGA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.14, C:0.12, G:0.25, T:0.49
Consensus pattern (89 bp):
TTGGTTCAATGGATAGGTGTTGTGCTTGTGTCTGTGAGGCTTTGGGTTTGAATCTTTCCCTTGAA
TTTATGTTATTTTTGTCTTAATCC
Found at i:4856993 original size:24 final size:25
Alignment explanation
Indices: 4856966--4857033 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
4856956 ATGGGGTAGG
*
4856966 ATCTGTGAT-TGCATCTGTATCTGA
1 ATCTGTGATATGCATCTGTATATGA
* * *
4856990 ATCTGTG-TCTGTATTTGTATATGA
1 ATCTGTGATATGCATCTGTATATGA
*
4857014 ATCT-AGATATGCATCTGTAT
1 ATCTGTGATATGCATCTGTAT
4857034 TTGGTTATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (25 bp):
ATCTGTGATATGCATCTGTATATGA
Found at i:4860666 original size:3 final size:3
Alignment explanation
Indices: 4860658--4860710 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
4860648 GTTCGGCCCA
*
4860658 AAG AAG AAG AAG AAG AAG AA- AAG AAG AAA AAG AAAG AAG ACA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG A-AG AAG
*
4860703 AAA AAG AA
1 AAG AAG AA
4860711 AAAAGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 3 0.07
3 35 0.83
4 4 0.10
ACGTcount: A:0.74, C:0.02, G:0.25, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4860695 original size:13 final size:13
Alignment explanation
Indices: 4860664--4860718 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
4860654 CCCAAAGAAG
*
4860664 AAGAAGAAGAAGAA
1 AAGAAGAAAAAG-A
4860678 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
*
4860691 AAGAAGACAAAGA
1 AAGAAGAAAAAGA
4860704 AA-AAGAAAAAAGA
1 AAGAAG-AAAAAGA
4860717 AA
1 AA
4860719 AAAATAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 3 0.08
13 23 0.62
14 11 0.30
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:4860711 original size:6 final size:6
Alignment explanation
Indices: 4860657--4860720 Score: 58
Period size: 6 Copynumber: 10.5 Consensus size: 6
4860647 GGTTCGGCCC
* * * * *
4860657 AAAGAA GAAGAA GAAGAA GAA-AA GAAGAA AAAGAA AGAAGAC AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
4860705 AAAGAAA AAAGAA AAA
1 AAAG-AA AAAGAA AAA
4860721 AATAATATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
5 5 0.10
6 35 0.69
7 11 0.22
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:4860721 original size:33 final size:33
Alignment explanation
Indices: 4860657--4860720 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
4860647 GGTTCGGCCC
*
4860657 AAAGAAGAAGAAGAAGAAGAAAAGAAGAAAAAG
1 AAAGAAGAAGAAGAAAAAGAAAAGAAGAAAAAG
4860690 AAAGAAGACA-AAGAAAAAGAAAA-AAGAAAAA
1 AAAGAAGA-AGAAGAAAAAGAAAAGAAGAAAAA
4860721 AATAATATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.28
33 20 0.69
34 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (33 bp):
AAAGAAGAAGAAGAAAAAGAAAAGAAGAAAAAG
Done.