Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 72 of 141
Found at i:20763967 original size:39 final size:39
Alignment explanation
Indices: 20763924--20764007 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
20763914 TCCCTCTAAA
* *
20763924 AAAAAGATT-AAAATAATATTTAAAAATTC-AAAATTTTAT
1 AAAAA-ATTCAAAATAATA-TAAAAAATTCTAAAAATTTAT
**
20763963 AAAAAATTCAAAATTTTATAAAAAATTCTAAAAATTTAT
1 AAAAAATTCAAAATAATATAAAAAATTCTAAAAATTTAT
20764002 AAAAAA
1 AAAAAA
20764008 AATATTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 12 0.31
39 27 0.69
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (39 bp):
AAAAAATTCAAAATAATATAAAAAATTCTAAAAATTTAT
Found at i:20764000 original size:20 final size:19
Alignment explanation
Indices: 20763945--20764007 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
20763935 AATAATATTT
20763945 AAAAATTCAAAATTTTATA
1 AAAAATTCAAAATTTTATA
20763964 AAAAATTCAAAATTTTATA
1 AAAAATTCAAAATTTTATA
*
20763983 AAAAATTCTAAAAATTTATA
1 AAAAATTC-AAAATTTTATA
20764003 AAAAA
1 AAAAA
20764008 AATATTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 27 0.64
20 15 0.36
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATTTTATA
Found at i:20766730 original size:16 final size:16
Alignment explanation
Indices: 20766706--20766749 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
20766696 TTTGTTATTT
*
20766706 AAAACGAAATAAAAGA
1 AAAAAGAAATAAAAGA
*
20766722 AAAAAGAAAATAAAATA
1 AAAAAG-AAATAAAAGA
20766739 AAAAAGAAATA
1 AAAAAGAAATA
20766750 TATGTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAGAAATAAAAGA
Found at i:20766732 original size:17 final size:17
Alignment explanation
Indices: 20766712--20766747 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20766702 ATTTAAAACG
20766712 AAATAAAAGAAAAAAGA
1 AAATAAAAGAAAAAAGA
*
20766729 AAATAAAATAAAAAAGA
1 AAATAAAAGAAAAAAGA
20766746 AA
1 AA
20766748 TATATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.08
Consensus pattern (17 bp):
AAATAAAAGAAAAAAGA
Found at i:20767630 original size:30 final size:31
Alignment explanation
Indices: 20767580--20767645 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
20767570 TTGTATCTTC
*
20767580 GATCTACTTCACTGCCAATACAGGAAGACAA
1 GATCTACTTCACTACCAATACAGGAAGACAA
*
20767611 GATCTACTTCAC-ACCAATACATGAAGACAA
1 GATCTACTTCACTACCAATACAGGAAGACAA
20767641 GATCT
1 GATCT
20767646 GCTTTCTCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (31 bp):
GATCTACTTCACTACCAATACAGGAAGACAA
Found at i:20767748 original size:44 final size:44
Alignment explanation
Indices: 20767611--20768359 Score: 643
Period size: 44 Copynumber: 16.9 Consensus size: 44
20767601 AGGAAGACAA
* * *
20767611 GATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTCC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* *** * * *
20767655 GATCTACTTCGC-CATCAGTATGGGAAGACAAGATCTGGTATCTTT
1 GATCTACTTCACGC--CAGTACATGAAGACAAGATCTGCTTTCTTC
* *
20767700 GATCTACTTCACGCCAGTACATGAAGATAAGATATGCTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* * *** * * *
20767744 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTT
1 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
*
20767789 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* *** * * *
20767833 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGGTATCTTT
1 GATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* *
20767878 GATCTACTTCAAGCCAGTACATGAAGATAAGATCTGCTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* **
20767922 GATCTACTTCACGCCAATACATGAAGACAAGATCTG-TTGGTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* * * * *
20767965 TGATCCACTTCATGTCAGTACATGAAGACAAGATCTG-TCATCTTT
1 -GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TTCTTC
* * * * * *
20768010 GATCTACTTCATGCCAATACATGAAGATAAGATCTGCTATATTT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* * * *
20768054 GATCAACTTCGCTGCCAGTACAGGAAGACAAGATCTACTTTCTTC
1 GATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGCTTTCTTC
* * * *** *
20768099 AATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTTTCTTC
1 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
*
20768144 GATCTACTTCACGCCAAG-ACAT-AAGGACAAGATGTGCTTTCTTC
1 GATCTACTTCACGCC-AGTACATGAA-GACAAGATCTGCTTTCTTC
* * **
20768188 GATCTACTTCACGCCAATACATGAAGACAAGATCT-ATTGGTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* * * *
20768231 TGATCCACTTCATGTCAGTACATGAAGACAAGATCTG-TCATCTTC
1 -GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TTCTTC
* * * * * *
20768276 GATCTACTTCATGCCAATA-ATGAAGATAAGATCTGCTATATTT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* ** * *
20768319 GATCAACTTCGTTGCCAGTACAGGAAGATAAGATCTG-TTTC
1 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTC
20768360 CTTTTCAACC
Statistics
Matches: 565, Mismatches: 120, Indels: 40
0.78 0.17 0.06
Matches are distributed among these distances:
43 42 0.07
44 322 0.57
45 199 0.35
46 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (44 bp):
GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
Found at i:20767763 original size:89 final size:89
Alignment explanation
Indices: 20767611--20768285 Score: 712
Period size: 89 Copynumber: 7.6 Consensus size: 89
20767601 AGGAAGACAA
* * * *
20767611 GATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTCCGATCTACTTCGCCATCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
20767676 GGGAAGACAAGATCTGGTATCTTT
66 GGGAAGACAAGATCTGGTATCTTT
* *
20767700 GATCTACTTCACGCCAGTACATGAAGATAAGATATGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
20767765 GGGAAGACAAGATCTGGTATCTTT
66 GGGAAGACAAGATCTGGTATCTTT
* *
20767789 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTACTTCACCACCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
20767854 GGGAAGACAAGATCTGGTATCTTT
66 GGGAAGACAAGATCTGGTATCTTT
* * * * * *
20767878 GATCTACTTCAAGCCAGTACATGAAGATAAGATCTGCTTTCTTCGATCTACTTC-ACGCCAATAC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
** *
20767942 ATGAAGACAAGATCT-GT-TGGTTCT
66 GGGAAGACAAGATCTGGTAT-CTT-T
* * * * *
20767966 GATCCACTTCATGTCAGTACATGAAGACAAGATCTG-TCATCTTTGATCTACTTCATGCCA--A-
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TTCTTCGATCTACTTC--GCCACCAG
*** * * *
20768027 TACATGAAGATAAGATCTGCTATATTT
63 TATGGGAAGACAAGATCTGGTATCTTT
* * * * *
20768054 GATCAACTTCGCTGCCAGTACAGGAAGACAAGATCTACTTTCTTCAATCTACTTCGCCACCAGTA
1 GATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
** * *
20768119 TGGGAAGACAAGATCTACTTTCTTC
65 TGGGAAGACAAGATCTGGTATCTTT
* * * *
20768144 GATCTACTTCACGCCAAG-ACAT-AAGGACAAGATGTGCTTTCTTCGATCTACTTC-ACGCCAAT
1 GATCTACTTCACGCC-AGTACATGAA-GACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGT
***
20768206 ACATGAAGACAAGATCTATTGGT-TC--T
64 ATGGGAAGACAAGATC---TGGTATCTTT
* * * *
20768232 GATCCACTTCATGTCAGTACATGAAGACAAGATCTG-TCATCTTCGATCTACTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TTCTTCGATCTACTTC
20768286 ATGCCAATAA
Statistics
Matches: 497, Mismatches: 68, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
86 1 0.00
87 12 0.02
88 154 0.31
89 292 0.59
90 35 0.07
91 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (89 bp):
GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
GGGAAGACAAGATCTGGTATCTTT
Found at i:20768086 original size:266 final size:265
Alignment explanation
Indices: 20767611--20768359 Score: 977
Period size: 266 Copynumber: 2.8 Consensus size: 265
20767601 AGGAAGACAA
* *
20767611 GATCTACTTCACA-CCAATACATGAAGACAAGATCTGCTTTCTCCGATCTACTT--CGCC-ATCA
1 GATCTACTTCA-AGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAAT-A
* * * * * * *
20767672 GTATGGGAAGACAAGATCTGGTAT-CTT-TGATCTACTTCACGCCAGTACATGAAGATAAGATAT
64 -CAT--GAAGACAAGATCT-GT-TGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCT
* * * * *
20767735 G-CTTTCTTCGATCTACTTC--GCCACCAGT-ATGGGAAGACAAGATCTGGTATCTTTGATCTAC
124 GTC-ATCTTCGATCTACTTCATGCCA--A-TAAT--GAAGATAAGATCTGCTATATTTGATCAAC
* * * *
20767796 TTCAC-GCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTACTTCACCACCAGTATGGGAAG
183 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTTTCTTCAATCTACTTCACCACCAGTATGGGAAG
** *
20767860 ACAAGATCTGGTATCTTT
248 ACAAGATCTACTATCTTC
*
20767878 GATCTACTTCAAGCCAGTACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACA
1 GATCTACTTCAAGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACA
20767943 TGAAGACAAGATCTGTTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTGTCATCT
66 TGAAGACAAGATCTGTTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTGTCATCT
*
20768008 TTGATCTACTTCATGCCAATACATGAAGATAAGATCTGCTATATTTGATCAACTTCGCTGCCAGT
131 TCGATCTACTTCATGCCAATA-ATGAAGATAAGATCTGCTATATTTGATCAACTTCGCTGCCAGT
* *
20768073 ACAGGAAGACAAGATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACT
195 ACAGGAAGACAAGATCTGCTTTCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGATCTACT
*
20768138 TTCTTC
260 ATCTTC
* *
20768144 GATCTACTTCACGCCAAG-ACAT-AAGGACAAGATGTGCTTTCTTCGATCTACTTCACGCCAATA
1 GATCTACTTCAAGCC-AGTACATGAA-GACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATA
*
20768207 CATGAAGACAAGATCTATTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTGTCAT
64 CATGAAGACAAGATCTGTTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTGTCAT
*
20768272 CTTCGATCTACTTCATGCCAATAATGAAGATAAGATCTGCTATATTTGATCAACTTCGTTGCCAG
129 CTTCGATCTACTTCATGCCAATAATGAAGATAAGATCTGCTATATTTGATCAACTTCGCTGCCAG
*
20768337 TACAGGAAGATAAGATCTG-TTTC
194 TACAGGAAGACAAGATCTGCTTTC
20768360 CTTTTCAACC
Statistics
Matches: 434, Mismatches: 34, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
264 5 0.01
265 94 0.22
266 269 0.62
267 53 0.12
268 6 0.01
269 5 0.01
270 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (265 bp):
GATCTACTTCAAGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACA
TGAAGACAAGATCTGTTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTGTCATCT
TCGATCTACTTCATGCCAATAATGAAGATAAGATCTGCTATATTTGATCAACTTCGCTGCCAGTA
CAGGAAGACAAGATCTGCTTTCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGATCTACTA
TCTTC
Found at i:20772924 original size:16 final size:16
Alignment explanation
Indices: 20772905--20772939 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20772895 TTTTTACTGC
20772905 TTTTATTTTTATTTTG
1 TTTTATTTTTATTTTG
* *
20772921 TTTTTTTTTTCTTTTG
1 TTTTATTTTTATTTTG
20772937 TTT
1 TTT
20772940 CTTAAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.86
Consensus pattern (16 bp):
TTTTATTTTTATTTTG
Found at i:20773435 original size:3 final size:3
Alignment explanation
Indices: 20773427--20773477 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
20773417 TGTTAAATGG
*
20773427 TTA TTA TTA CTGTA TTA TTA TTA GTA TTTA TTA TTA TTA TGT- TTA TTA
1 TTA TTA TTA -T-TA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA
20773475 TTA
1 TTA
20773478 CCATTTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 1 0.02
3 33 0.80
4 5 0.12
5 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:20773473 original size:19 final size:15
Alignment explanation
Indices: 20773439--20773477 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
20773429 ATTATTACTG
20773439 TATTATTATTAGTATT
1 TATTATTATTAGTA-T
20773455 TATTATTATTATGT-T
1 TATTATTATTA-GTAT
20773470 TATTATTA
1 TATTATTA
20773478 CCATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 11 0.50
17 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
TATTATTATTAGTAT
Found at i:20776677 original size:29 final size:30
Alignment explanation
Indices: 20776626--20776683 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
20776616 ATGTTGGTTG
*
20776626 TGATTTTGATTTTTGCTGTTAATGGTGTTC
1 TGATTTTGATTTTTGCTGTTAATGCTGTTC
20776656 TGATTTTGA-TTTTGCTGTTAATGCTGTT
1 TGATTTTGATTTTTGCTGTTAATGCTGTT
20776684 AATGGTTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.14, C:0.07, G:0.22, T:0.57
Consensus pattern (30 bp):
TGATTTTGATTTTTGCTGTTAATGCTGTTC
Found at i:20776697 original size:29 final size:29
Alignment explanation
Indices: 20776626--20776698 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
20776616 ATGTTGGTTG
* * *
20776626 TGATTTTGATTTTTGCTGTTAATGGTGTTC
1 TGATTGTGA-TTTTGCTGTTAATGCTGTTA
*
20776656 TGATTTTGATTTTGCTGTTAATGCTGTTAA
1 TGATTGTGATTTTGCTGTTAATGCTGTT-A
* *
20776686 TGGTTGTGTTTTT
1 TGATTGTGATTTT
20776699 TATTTTTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.14, C:0.05, G:0.23, T:0.58
Consensus pattern (29 bp):
TGATTGTGATTTTGCTGTTAATGCTGTTA
Found at i:20776714 original size:37 final size:38
Alignment explanation
Indices: 20776639--20776720 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
20776629 TTTTGATTTT
20776639 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
1 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
* * *
20776677 TGCTGTTAAT-G-GTTGTGTTTTTTATTTTTGCTGTTAA
1 TGCTGTTAATGGTGTTCTGATTTTGA-TTTTGCTGTTAA
*
20776714 TGGTGTT
1 TGCTGTT
20776721 CTGTTAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 10 0.26
37 19 0.49
38 10 0.26
ACGTcount: A:0.13, C:0.06, G:0.24, T:0.56
Consensus pattern (38 bp):
TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
Found at i:20777391 original size:96 final size:96
Alignment explanation
Indices: 20777227--20777487 Score: 513
Period size: 96 Copynumber: 2.7 Consensus size: 96
20777217 AGGTCCGAAA
20777227 TTGAGGGTCTGTAATTTATACATGCTGTAGTGGGTCTGTAATTTGTTTTCATTAGTTTGATACAG
1 TTGAGGGTCTGTAATTTATACATGCTGTAGTGGGTCTGTAATTTGTTTTCATTAGTTTGATACAG
20777292 TAGTCGTATTAGTTTGACCATGTCTAAGAAG
66 TAGTCGTATTAGTTTGACCATGTCTAAGAAG
20777323 TTGAGGGTCTGTAATTTATACATGCTGTAGTGGGTCTGTAATTTGTTTTCATTAGTTTGATACAG
1 TTGAGGGTCTGTAATTTATACATGCTGTAGTGGGTCTGTAATTTGTTTTCATTAGTTTGATACAG
20777388 TAGTCGTATTAGTTTGACCATGTCTAAGAAG
66 TAGTCGTATTAGTTTGACCATGTCTAAGAAG
*
20777419 TTGAGGGTCTGTAATTTATACATGCTGTAGTGGGTCTGTAATTTGTTTTCATTAGTTTGATATAG
1 TTGAGGGTCTGTAATTTATACATGCTGTAGTGGGTCTGTAATTTGTTTTCATTAGTTTGATACAG
20777484 TAGT
66 TAGT
20777488 TGTGTTTGCT
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 164 1.00
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.43
Consensus pattern (96 bp):
TTGAGGGTCTGTAATTTATACATGCTGTAGTGGGTCTGTAATTTGTTTTCATTAGTTTGATACAG
TAGTCGTATTAGTTTGACCATGTCTAAGAAG
Found at i:20778059 original size:13 final size:13
Alignment explanation
Indices: 20778041--20778149 Score: 128
Period size: 13 Copynumber: 8.2 Consensus size: 13
20778031 ATAAAATTTG
20778041 TAATATACTGTTT
1 TAATATACTGTTT
20778054 TAATATACTGTTT
1 TAATATACTGTTT
*
20778067 TAATATACTATTAT
1 TAATATACTGTT-T
* *
20778081 AAATATACTTTTT
1 TAATATACTGTTT
*
20778094 TAATATATTGTTT
1 TAATATACTGTTT
* *
20778107 TAATATACTATTA
1 TAATATACTGTTT
*
20778120 TAATTATATTGTTT
1 TAA-TATACTGTTT
*
20778134 TAATATAATGTTT
1 TAATATACTGTTT
20778147 TAA
1 TAA
20778150 CTTTTAACTT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
13 60 0.74
14 21 0.26
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:20778060 original size:27 final size:26
Alignment explanation
Indices: 20778030--20778149 Score: 105
Period size: 27 Copynumber: 4.5 Consensus size: 26
20778020 AATATACTGT
*
20778030 TATAAAATTTGTAATATACTGTTTTAA
1 TATAATATTT-TAATATACTGTTTTAA
* * * *
20778057 TATACTGTTTTAATATACTATTATAAA
1 TATAATATTTTAATATACTGTT-TTAA
* * *
20778084 TATACTTTTTTAATATATTGTTTTAA
1 TATAATATTTTAATATACTGTTTTAA
* * *
20778110 TATACTATTATAATTATATTGTTTTAA
1 TATAATATTTTAA-TATACTGTTTTAA
*
20778137 TATAATGTTTTAA
1 TATAATATTTTAA
20778150 CTTTTAACTT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
26 25 0.32
27 52 0.68
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (26 bp):
TATAATATTTTAATATACTGTTTTAA
Found at i:20778086 original size:40 final size:40
Alignment explanation
Indices: 20778042--20778149 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 40
20778032 TAAAATTTGT
*
20778042 AATATACTGTTTTAATATACTGTTTTAATATACTATTATA
1 AATATACTGTTTTAATATAATGTTTTAATATACTATTATA
* *
20778082 AATATACTTTTTTAATATATTGTTTTAATATACTATTATA
1 AATATACTGTTTTAATATAATGTTTTAATATACTATTATA
* *
20778122 ATTATATTGTTTTAATATAATGTTTTAA
1 AATATACTGTTTTAATATAATGTTTTAA
20778150 CTTTTAACTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (40 bp):
AATATACTGTTTTAATATAATGTTTTAATATACTATTATA
Found at i:20789404 original size:116 final size:116
Alignment explanation
Indices: 20789200--20789428 Score: 386
Period size: 116 Copynumber: 2.0 Consensus size: 116
20789190 GCAGGCTGGG
* *
20789200 GTTAATCCTTTGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGTTTATTTTTCAGGTTT
1 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGGTTATTTTTCAGGTTT
* *
20789265 AATTAAATTTTGTTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTATGAT
66 AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTATGAT
* * * *
20789316 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTATTTTAGATTGTATGGTTATTTTTCATGTTT
1 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGGTTATTTTTCAGGTTT
20789381 AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTAT
66 AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTAT
20789429 CTAGCTTATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (116 bp):
GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGGTTATTTTTCAGGTTT
AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTATGAT
Found at i:20799506 original size:30 final size:31
Alignment explanation
Indices: 20799472--20799555 Score: 152
Period size: 30 Copynumber: 2.7 Consensus size: 31
20799462 GAGACCCAAG
20799472 GACCCAATCTACCCAAACAGCCCCGTTAC-A
1 GACCCAATCTACCCAAACAGCCCCGTTACAA
20799502 GACCCAATCTACCCAAACAGCCCCGTTACAA
1 GACCCAATCTACCCAAACAGCCCCGTTACAA
*
20799533 GCCCCAATCTACCCAAACAGCCC
1 GACCCAATCTACCCAAACAGCCC
20799556 ACTACAGCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 29 0.56
31 23 0.44
ACGTcount: A:0.33, C:0.45, G:0.10, T:0.12
Consensus pattern (31 bp):
GACCCAATCTACCCAAACAGCCCCGTTACAA
Found at i:20800449 original size:3 final size:3
Alignment explanation
Indices: 20800443--20800484 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
20800433 TGTTGTTTAG
20800443 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20800485 CCTTACTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20800744 original size:15 final size:15
Alignment explanation
Indices: 20800721--20800752 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20800711 TGTTTATATA
*
20800721 TTATGTTATTTTATT
1 TTATCTTATTTTATT
20800736 TTATCTTATTTTATT
1 TTATCTTATTTTATT
20800751 TT
1 TT
20800753 CCATATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (15 bp):
TTATCTTATTTTATT
Found at i:20815549 original size:19 final size:18
Alignment explanation
Indices: 20815508--20815620 Score: 56
Period size: 19 Copynumber: 6.3 Consensus size: 18
20815498 AAATTACAAA
20815508 AAAATTAAAAAAATTATG
1 AAAATTAAAAAAATTATG
*
20815526 GAAATATAAAAAAATT-TAG
1 AAAAT-TAAAAAAATTAT-G
* *
20815545 AAAATTTAGAAAATTTAT-
1 AAAA-TTAAAAAAATTATG
**
20815563 AATTTTATAAAAAA-TA-G
1 AAAATTA-AAAAAATTATG
*
20815580 AAAAAT-AAAAAATTATAG
1 AAAATTAAAAAAATTAT-G
* ** *
20815598 AAAACTATTAAAATTATA
1 AAAATTAAAAAAATTATG
20815616 AAAAT
1 AAAAT
20815621 AACAACAATA
Statistics
Matches: 69, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
15 6 0.09
16 2 0.03
17 8 0.12
18 21 0.30
19 30 0.43
20 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATTAAAAAAATTATG
Found at i:20815599 original size:18 final size:19
Alignment explanation
Indices: 20815497--20815708 Score: 63
Period size: 18 Copynumber: 11.3 Consensus size: 19
20815487 AAAAAAATGT
* * *
20815497 AAAATTACAAAAAAATTAAA
1 AAAATTATAGAAAAA-TATA
* * *
20815517 AAAATTATGGAAATATAAA
1 AAAATTATAGAAAAATATA
*
20815536 AAAATT-TAG-AAAATTTA
1 AAAATTATAGAAAAATATA
* ***
20815553 GAAAATT-TATAATTTTATA
1 -AAAATTATAGAAAAATATA
20815572 AAAA--ATAGAAAAATA-A
1 AAAATTATAGAAAAATATA
* *
20815588 AAAATTATAGAAAACTATT
1 AAAATTATAGAAAAATATA
* *
20815607 AAAATTATAAAAATAACAACAATA
1 AAAATTAT--AGA-AA-AA-TATA
*
20815631 AAAATCATA-AAAAAT-TA
1 AAAATTATAGAAAAATATA
20815648 AAAATTAT--AAAAATCATA
1 AAAATTATAGAAAAAT-ATA
20815666 GAAAAGTTAT--AAAAATA-A
1 -AAAA-TTATAGAAAAATATA
** *
20815684 AATTTTATAAAAAAATCATA
1 AAAATTATAGAAAAAT-ATA
20815704 AAAAT
1 AAAAT
20815709 CCCCTTAAAA
Statistics
Matches: 143, Mismatches: 30, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
16 15 0.10
17 22 0.15
18 33 0.23
19 30 0.21
20 27 0.19
21 3 0.02
22 3 0.02
23 1 0.01
24 9 0.06
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAATTATAGAAAAATATA
Found at i:20815619 original size:9 final size:9
Alignment explanation
Indices: 20815507--20815681 Score: 82
Period size: 9 Copynumber: 19.7 Consensus size: 9
20815497 AAAATTACAA
*
20815507 AAAAATTAA
1 AAAAATTAT
20815516 AAAAATTAT
1 AAAAATTAT
** *
20815525 GGAAATATAA
1 AAAAAT-TAT
20815535 AAAAATT-T
1 AAAAATTAT
20815543 AGAAAATT-T
1 A-AAAATTAT
20815552 AGAAAATT-T
1 A-AAAATTAT
**
20815561 ATAATTTTAT
1 A-AAAATTAT
* *
20815571 AAAAAATAG
1 AAAAATTAT
20815580 AAAAA-TA-
1 AAAAATTAT
20815587 AAAAATTAT
1 AAAAATTAT
*
20815596 AGAAAACTAT
1 A-AAAATTAT
*
20815606 TAAAATTAT
1 AAAAATTAT
20815615 AAAAA-TA-
1 AAAAATTAT
*
20815622 ACAACA--AT
1 A-AAAATTAT
*
20815630 AAAAATCAT
1 AAAAATTAT
*
20815639 AAAAAAT-T
1 AAAAATTAT
20815647 AAAAATTAT
1 AAAAATTAT
*
20815656 AAAAATCAT
1 AAAAATTAT
20815665 AGAAAAGTTAT
1 A-AAAA-TTAT
20815676 AAAAAT
1 AAAAAT
20815682 AAAATTTTAT
Statistics
Matches: 128, Mismatches: 25, Indels: 26
0.72 0.14 0.15
Matches are distributed among these distances:
7 10 0.08
8 18 0.14
9 73 0.57
10 23 0.18
11 4 0.03
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20815657 original size:26 final size:28
Alignment explanation
Indices: 20815628--20815679 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
20815618 AATAACAACA
20815628 ATAAAAATCATA-AAAAATTA-AAAATT
1 ATAAAAATCATAGAAAAATTATAAAATT
*
20815654 ATAAAAATCATAGAAAAGTTATAAAA
1 ATAAAAATCATAGAAAAATTATAAAA
20815680 ATAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
27 7 0.30
28 4 0.17
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (28 bp):
ATAAAAATCATAGAAAAATTATAAAATT
Found at i:20816192 original size:19 final size:20
Alignment explanation
Indices: 20816168--20816218 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
20816158 TTTTATACTT
*
20816168 TTTTTATAAGTTTTTTAT-A
1 TTTTTATAAGTTTTATATCA
*
20816187 TTTTTAATAA-TTTTATATCT
1 TTTTT-ATAAGTTTTATATCA
20816207 TTTTTATAAGTT
1 TTTTTATAAGTT
20816219 GTATTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTATAAGTTTTATATCA
Found at i:20816302 original size:18 final size:17
Alignment explanation
Indices: 20816279--20816491 Score: 130
Period size: 18 Copynumber: 11.8 Consensus size: 17
20816269 GTTCTATATT
*
20816279 TTTTTAGAATTTTTAATA
1 TTTTTATAATTTTT-ATA
*
20816297 TTTTTATAAGTGTTTATA
1 TTTTTATAA-TTTTTATA
20816315 TTTTTATAATATTTT-TA
1 TTTTTATAAT-TTTTATA
20816332 TTTTTATAATTTTCTAT-
1 TTTTTATAATTTT-TATA
*
20816349 TTTTTTTAATTTTCTAATA
1 TTTTTATAATTTT-T-ATA
* * *
20816368 TATTCTAAAAATTTTA-A
1 T-TTTTATAATTTTTATA
*
20816385 TTTTAATAA-TTTTATAA
1 TTTTTATAATTTTTAT-A
* * *
20816402 TTTCTAATATTTTTTTAAAA
1 TTT-TTATA-ATTTTT-ATA
20816422 TTTTTCTATAATTTTTCTATAA
1 -TTTT-TATAA-TTTT-TAT-A
20816444 TTTTTATAATATTTT-TA
1 TTTTTATAAT-TTTTATA
20816461 TTTTTATAATTTTCTATA
1 TTTTTATAATTTT-TATA
*
20816479 TTTTTTTAATTTT
1 TTTTTATAATTTT
20816492 CTAATATATT
Statistics
Matches: 157, Mismatches: 17, Indels: 42
0.73 0.08 0.19
Matches are distributed among these distances:
15 5 0.03
16 11 0.07
17 46 0.29
18 47 0.30
19 8 0.05
20 22 0.14
21 16 0.10
22 2 0.01
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (17 bp):
TTTTTATAATTTTTATA
Found at i:20816322 original size:8 final size:8
Alignment explanation
Indices: 20816287--20816352 Score: 53
Period size: 8 Copynumber: 7.8 Consensus size: 8
20816277 TTTTTTTAGA
20816287 ATTTTTAAT
1 ATTTTT-AT
20816296 ATTTTTAT
1 ATTTTTAT
*
20816304 AAGTGTTTAT
1 -A-TTTTTAT
20816314 ATTTTTAT
1 ATTTTTAT
20816322 AATATTTT-T
1 -AT-TTTTAT
20816331 ATTTTTAT
1 ATTTTTAT
* *
20816339 AATTTTCT
1 ATTTTTAT
20816347 ATTTTT
1 ATTTTT
20816353 TTTAATTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.09
8 22 0.47
9 11 0.23
10 10 0.21
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (8 bp):
ATTTTTAT
Found at i:20816333 original size:17 final size:16
Alignment explanation
Indices: 20816279--20816491 Score: 86
Period size: 17 Copynumber: 11.8 Consensus size: 16
20816269 GTTCTATATT
*
20816279 TTTTTAGAATTTTTAATA
1 TTTTTATAA-TTTT-ATA
20816297 TTTTTATAAGTGTTTATA
1 TTTTTATAA-T-TTTATA
*
20816315 TTTTTATAATATTTTTA
1 TTTTTATAAT-TTTATA
*
20816332 TTTTTATAATTTTCTA
1 TTTTTATAATTTTATA
*
20816348 TTTTTTTTAATTTTCTAATA
1 -TTTTTATAA-TTT-T-ATA
* *
20816368 TATTCTAAAAATTTTA-A
1 T-TT-TTATAATTTTATA
*
20816385 TTTTAATAATTTTATAA
1 TTTTTATAATTTTAT-A
** *
20816402 TTTCTAATATTTTTTTAAAA
1 TTT-T--TATAATTTT-ATA
20816422 TTTTTCTATAATTTTTCTATAA
1 -TTTT-TATAA--TTT-TAT-A
*
20816444 TTTTTATAATATTTTTA
1 TTTTTATAAT-TTTATA
20816461 TTTTTATAATTTTCTATA
1 TTTTTATAA-TTT-TATA
*
20816479 TTTTTTTAATTTT
1 TTTTTATAATTTT
20816492 CTAATATATT
Statistics
Matches: 152, Mismatches: 22, Indels: 44
0.70 0.10 0.20
Matches are distributed among these distances:
15 10 0.07
16 8 0.05
17 45 0.30
18 41 0.27
19 11 0.07
20 20 0.13
21 15 0.10
22 2 0.01
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (16 bp):
TTTTTATAATTTTATA
Found at i:20816426 original size:11 final size:11
Alignment explanation
Indices: 20816402--20816459 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
20816392 AATTTTATAA
*
20816402 TTTCTAATATT
1 TTTCTAAAATT
*
20816413 TTTTTAAAATT
1 TTTCTAAAATT
*
20816424 TTTCTATAATT
1 TTTCTAAAATT
*
20816435 TTTCTATAATT
1 TTTCTAAAATT
* *
20816446 TTTATAATATT
1 TTTCTAAAATT
20816457 TTT
1 TTT
20816460 ATTTTTATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTCTAAAATT
Found at i:20816453 original size:9 final size:9
Alignment explanation
Indices: 20816279--20816491 Score: 101
Period size: 9 Copynumber: 23.4 Consensus size: 9
20816269 GTTCTATATT
*
20816279 TTTTTAGAA
1 TTTTTATAA
20816288 TTTTTA-ATA
1 TTTTTATA-A
20816297 TTTTTATAA
1 TTTTTATAA
*
20816306 GTGTTTAT-A
1 -TTTTTATAA
20816315 TTTTTATAA
1 TTTTTATAA
20816324 TATTTT-T-A
1 T-TTTTATAA
20816332 TTTTTATAA
1 TTTTTATAA
20816341 TTTTCTAT--
1 TTTT-TATAA
*
20816349 TTTTTTTAA
1 TTTTTATAA
20816358 TTTTCTA-ATA
1 TTTT-TATA-A
*
20816368 TATTCTA-AA
1 T-TTTTATAA
**
20816377 AATTT-TAA
1 TTTTTATAA
*
20816385 TTTTAATAA
1 TTTTTATAA
20816394 -TTTTATAA
1 TTTTTATAA
* *
20816402 TTTCTAATATT
1 TTT-TTATA-A
*
20816413 TTTTTAAAA
1 TTTTTATAA
20816422 TTTTTCTATAA
1 -TTTT-TATAA
20816433 TTTTTCTATAA
1 -TTTT-TATAA
20816444 TTTTTATAA
1 TTTTTATAA
20816453 TATTTT-T-A
1 T-TTTTATAA
20816461 TTTTTATAA
1 TTTTTATAA
20816470 TTTTCTAT-A
1 TTTT-TATAA
*
20816479 TTTTTTTAA
1 TTTTTATAA
20816488 TTTT
1 TTTT
20816492 CTAATATATT
Statistics
Matches: 160, Mismatches: 19, Indels: 50
0.70 0.08 0.22
Matches are distributed among these distances:
7 10 0.06
8 32 0.20
9 56 0.35
10 42 0.26
11 20 0.12
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:20816467 original size:129 final size:129
Alignment explanation
Indices: 20816314--20816566 Score: 490
Period size: 129 Copynumber: 2.0 Consensus size: 129
20816304 AAGTGTTTAT
20816314 ATTTTTATAATATTTTTATTTTTATAATTTTCTAT-TTTTTTTAATTTTCTAATATATTCTAAAA
1 ATTTTTATAATATTTTTATTTTTATAATTTTCTATATTTTTTTAATTTTCTAATATATTCTAAAA
20816378 ATTTTAATTTTAATAATTTTATAATTTCTAATATTTTTTTAAAATTTTTCTATAATTTTTCTATA
66 A-TTTAATTTTAATAATTTTATAATTTCTAATATTTTTTTAAAATTTTTCTATAATTTTTCTATA
20816443 ATTTTTATAATATTTTTATTTTTATAATTTTCTATATTTTTTTAATTTTCTAATATATTCTAAAA
1 ATTTTTATAATATTTTTATTTTTATAATTTTCTATATTTTTTTAATTTTCTAATATATTCTAAAA
20816508 ATTTAATTTTAATAATTTTATAATTTCTAATATTTTTTTAAAATTTTTCTATAATTTTT
66 ATTTAATTTTAATAATTTTATAATTTCTAATATTTTTTTAAAATTTTTCTATAATTTTT
20816567 ATTGATTTCA
Statistics
Matches: 123, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
129 93 0.76
130 30 0.24
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (129 bp):
ATTTTTATAATATTTTTATTTTTATAATTTTCTATATTTTTTTAATTTTCTAATATATTCTAAAA
ATTTAATTTTAATAATTTTATAATTTCTAATATTTTTTTAAAATTTTTCTATAATTTTTCTATA
Found at i:20816471 original size:26 final size:26
Alignment explanation
Indices: 20816434--20816531 Score: 74
Period size: 26 Copynumber: 3.7 Consensus size: 26
20816424 TTTCTATAAT
20816434 TTTTCTATAATTTTTATAATATTTTTA
1 TTTT-TATAATTTTTATAATATTTTTA
*
20816461 TTTTTATAATTTTCTAT-ATTTTTTTA
1 TTTTTATAATTTT-TATAATATTTTTA
* * * * * * *
20816487 ATTTTCTAATATATTCTAAAAATTTAA
1 TTTTTATAAT-TTTTATAATATTTTTA
*
20816514 TTTTAATAA-TTTTATAAT
1 TTTTTATAATTTTTATAAT
20816532 TTCTAATATT
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
25 6 0.11
26 27 0.51
27 20 0.38
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTATAATTTTTATAATATTTTTA
Found at i:20817510 original size:19 final size:17
Alignment explanation
Indices: 20817486--20817529 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
20817476 CAATGCATCT
*
20817486 AATAATTATACAAATTACC
1 AATAATAATAC-AATT-CC
*
20817505 AATAATAATTCAATTCC
1 AATAATAATACAATTCC
20817522 AATAATAA
1 AATAATAA
20817530 AACACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
19 9 0.39
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATAATACAATTCC
Found at i:20820171 original size:22 final size:21
Alignment explanation
Indices: 20820114--20820174 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
20820104 TATATGAACA
* *
20820114 AATAAATAATGAATGACATAT
1 AATATATAATAAATGACATAT
20820135 AATATATCAAATAAATGAGCAATAT
1 AATATAT--AATAAATGA-C-ATAT
20820160 AA-ATATAATAAATGA
1 AATATATAATAAATGA
20820175 AATTACGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.18
22 9 0.26
23 8 0.24
24 5 0.15
25 6 0.18
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (21 bp):
AATATATAATAAATGACATAT
Found at i:20821161 original size:44 final size:43
Alignment explanation
Indices: 20821103--20821219 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 43
20821093 ACTAGATGCG
* * *
20821103 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGA-GGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-ATGGCTTTA
* *
20821146 ATTCT-CTCCACTGCAAGTTCAGGGAGATAGGATTATTGGCTTTA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGATTA-TGGCTTTA
20821190 ATCTGCTCCACTGCAACTTCAGGGAGATAA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAA
20821220 AACTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.02
43 7 0.11
44 54 0.87
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGGCTTTA
Found at i:20822819 original size:44 final size:43
Alignment explanation
Indices: 20822325--20823312 Score: 395
Period size: 44 Copynumber: 22.7 Consensus size: 43
20822315 TTGATCCACC
* * * * * *
20822325 ATCTGCTCCACTACAACTTTAGGGGGATAAGATCGGAGGTTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGA-GCTTTA
* * * * * *
20822369 ATCCGCTCCACTGCAACTTCAGAGTGATATGAT-TGTCGACTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTG-AG-CTTTA
* * * * *
20822413 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCACCTTCA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTG--AGCTTTA
**
20822458 ATCTGC-CTCACTG-AAGCTTCA-GGAGGATAAGACTTGCTTTGC-TTA
1 ATCTGCTCT-ACTGCAA-CTTCAGGGA-GATAAGA--T-CTGAGCTTTA
* * * ***
20822503 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-AGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGAGCTTTA
* * * **
20822544 ATCTACTCT-CTGCATCTTCAGAGAGATAAGATCTGATATTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGA-GCTTTA
** * * * * *
20822587 ATCCACTCCACTGTAACTTCAGGGAAATAGGAT-TGTCGGCTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTG--AGCTTTA
* * * *
20822631 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTG--AGCTTTA
* * *
20822676 GTCTGC-CTCACTGTAACTTCA-GGAGGATAAGA-CT-TGCTTACATA
1 ATCTGCTCT-ACTGCAACTTCAGGGA-GATAAGATCTGAGCTT---TA
* * * * * * ***
20822720 TTCGGCTCCACTGCAACCTCAGGGAGATATGA-CT-AGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGAGCTTTA
* * *
20822761 ATCTGTTCT-CTGCAACTTCAGAGAGATAAGATCTGAGGTTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGA-GCTTTA
* *
20822804 ATCCGCTCTACTGCAACTTCAGGGAGATAGGAT-TGTCAGCTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTG--AGCTTTA
* * *
20822848 ATCTGCTCTACTACAACTTCAGGGAGATAAGA-CTTGCCACCTTCA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATC-TG--AGCTTTA
* * **
20822893 GTCTGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTTGC-TTA
1 ATCTGCTCT-ACTGCAACTTCAGGGA-GATAAGA--T-CTGAGCTTTA
* * * ***
20822938 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-AGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGAGCTTTA
* * * *
20822979 ATCTACTCT-CTGCATCTTCAGAGAGATAAGATCTGAGATTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGAG-CTTTA
** * * * *
20823022 ATCCACTCCACTGTAACTTCAGGGAGATAGGAT-TGTCGGCTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTG--AGCTTTA
* * * *
20823066 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTG--AGCTTTA
* * *
20823111 GTCTGC-CTCACTGTAACTTCA-GGAGGATAAGA-CT-TGCTTACATA
1 ATCTGCTCT-ACTGCAACTTCAGGGA-GATAAGATCTGAGCTT---TA
* * * * * ***
20823155 TTCTGCTCCACTGCAACCTCAGGGAGATATGA-CT-AGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGAGCTTTA
* * * *
20823196 ATCTGCTCT-CTGCAACTTCAGAGAGCTAAGATTTGAGGTTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGA-GCTTTA
* * * *
20823239 ATCTGCTCTACTGCAATTTTAGGGAGATAGGATTATTG-GCTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGA-T-CTGAGCTTTA
*
20823283 ATCTGCTCCACTGCAACTTCAGGGAGATAA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAA
20823313 AACTCAATTT
Statistics
Matches: 701, Mismatches: 178, Indels: 130
0.69 0.18 0.13
Matches are distributed among these distances:
40 79 0.11
41 41 0.06
42 5 0.01
43 44 0.06
44 336 0.48
45 177 0.25
46 15 0.02
47 1 0.00
48 2 0.00
49 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTGAGCTTTA
Found at i:20822826 original size:217 final size:218
Alignment explanation
Indices: 20822350--20823312 Score: 1464
Period size: 217 Copynumber: 4.4 Consensus size: 218
20822340 ACTTTAGGGG
* * * * *
20822350 GATAAGATCGGAGGTTTTAATCCGCTCCACTGCAACTTCAGAGTGATATGATTGTCGACTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAAT
* *
20822415 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCACCTTCAATCTGCCTCACTG-AAGCTTCA
66 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCACCTTCAGTCTGCCTCACTGTAA-CTTCA
* * *
20822479 GGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
130 GGAGGATAAGACTTGCTTTACATAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACTAGATGCG
*
20822544 ATCTACTCTCTGCATCTTCAGAGA
195 ATCTACTCTCTGCAACTTCAGAGA
** * * *
20822568 GATAAGATCTGATATTTTAATCCACTCCACTGTAACTTCAGGGAAATAGGATTGTCGGCTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAAT
*
20822633 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAG
66 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCACCTTCAGTCTGCCTCACTGTAACTTCAG
* * *
20822698 GAGGATAAGACTTGC-TTACATATTCGGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGA
131 GAGGATAAGACTTGCTTTACATAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACTAGATGCGA
**
20822762 TCTGTTCTCTGCAACTTCAGAGA
196 TCTACTCTCTGCAACTTCAGAGA
* *
20822785 GATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGTCAGCTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAAT
* * * * *
20822850 CTGCTCTACTACAACTTCAGGGAGATAAGACTTGCCACCTTCAGTCTGCCTCACTGCAACTTTAG
66 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCACCTTCAGTCTGCCTCACTGTAACTTCAG
* * *
20822915 GAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
131 GAGGATAAGACTTGCTTTACATAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACTAGATGCGA
*
20822980 TCTACTCTCTGCATCTTCAGAGA
196 TCTACTCTCTGCAACTTCAGAGA
* * *
20823003 GATAAGATCTGAGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTGTCGGCTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAAT
*
20823068 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAG
66 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCACCTTCAGTCTGCCTCACTGTAACTTCAG
* *
20823133 GAGGATAAGACTTGC-TTACATATTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGA
131 GAGGATAAGACTTGCTTTACATAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACTAGATGCGA
*
20823197 TCTGCTCTCTGCAACTTCAGAGA
196 TCTACTCTCTGCAACTTCAGAGA
* * * * * * * *
20823220 GCTAAGATTTGAGGTTTTAATCTGCTCTACTGCAATTTTAGGGAGATAGGATTATTGGCTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAAT
20823285 CTGCTCCACTGCAACTTCAGGGAGATAA
66 CTGCTCCACTGCAACTTCAGGGAGATAA
20823313 AACTCAATTT
Statistics
Matches: 670, Mismatches: 73, Indels: 5
0.90 0.10 0.01
Matches are distributed among these distances:
217 342 0.51
218 326 0.49
219 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (218 bp):
GATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAAT
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCACCTTCAGTCTGCCTCACTGTAACTTCAG
GAGGATAAGACTTGCTTTACATAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACTAGATGCGA
TCTACTCTCTGCAACTTCAGAGA
Found at i:20823165 original size:435 final size:434
Alignment explanation
Indices: 20822350--20823312 Score: 1694
Period size: 435 Copynumber: 2.2 Consensus size: 434
20822340 ACTTTAGGGG
* * * * *
20822350 GATAAGATCGGAGGTTTTAATCCGCTCCACTGCAACTTCAGAGTGATATGATTGTCGACTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGTCG-CTTTAAT
*
20822415 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCACCTTCAATCTGCCTCACTGAAGCTTCAG
65 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGCCACCTTCAATCTGCCTCACTGAAGCTTCAG
20822480 GAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
130 GAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
*
20822545 TCTACTCTCTGCATCTTCAGAGAGATAAGATCTGATATTTTAATCCACTCCACTGTAACTTCAGG
195 TCTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGATTTTAATCCACTCCACTGTAACTTCAGG
20822610 GAAATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTC
260 GAAATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTC
20822675 AGTCTGCCTCACTGTAACTTCAGGAGGATAAGACTTGCTTACATATTCGGCTCCACTGCAACCTC
325 AGTCTGCCTCACTGTAACTTCAGGAGGATAAGACTTGCTTACATATTCGGCTCCACTGCAACCTC
*
20822740 AGGGAGATATGACTAGATGCGATCTGTTCTCTGCAACTTCAGAGA
390 AGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGA
20822785 GATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGTCAGCTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGTC-GCTTTAAT
* * *
20822850 CTGCTCTACTACAACTTCAGGGAGATAAGACTTGCCACCTTCAGTCTGCCTCACTGCAA-CTTTA
65 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGCCACCTTCAATCTGCCTCACTG-AAGCTTCA
20822914 GGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
129 GGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
20822979 ATCTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGATTTTAATCCACTCCACTGTAACTTCAG
194 ATCTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGATTTTAATCCACTCCACTGTAACTTCAG
*
20823044 GGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTT
259 GGAAATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTT
*
20823109 CAGTCTGCCTCACTGTAACTTCAGGAGGATAAGACTTGCTTACATATTCTGCTCCACTGCAACCT
324 CAGTCTGCCTCACTGTAACTTCAGGAGGATAAGACTTGCTTACATATTCGGCTCCACTGCAACCT
20823174 CAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGA
389 CAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGA
* * * * * * *
20823220 GCTAAGATTTGAGGTTTTAATCTGCTCTACTGCAATTTTAGGGAGATAGGATTATTGGCTTTAAT
1 GATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATT-GTCGCTTTAAT
*
20823285 CTGCTCCACTGCAACTTCAGGGAGATAA
65 CTGCTCCACTACAACTTCAGGGAGATAA
20823313 AACTCAATTT
Statistics
Matches: 503, Mismatches: 22, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
435 499 0.99
436 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (434 bp):
GATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGTCGCTTTAATC
TGCTCCACTACAACTTCAGGGAGATAAGACTTGCCACCTTCAATCTGCCTCACTGAAGCTTCAGG
AGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGAT
CTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGATTTTAATCCACTCCACTGTAACTTCAGGG
AAATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
GTCTGCCTCACTGTAACTTCAGGAGGATAAGACTTGCTTACATATTCGGCTCCACTGCAACCTCA
GGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGA
Found at i:20834842 original size:98 final size:98
Alignment explanation
Indices: 20834668--20834858 Score: 346
Period size: 98 Copynumber: 1.9 Consensus size: 98
20834658 GTACAATAAA
* *
20834668 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGTACGATC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
20834733 CCTTTAGAATCCCAAACTCGGAATATTTCCTAT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTAT
*
20834766 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
20834831 CCTTTAAAATCCCAAACTCGGAATATTT
66 CCTTTAAAATCCCAAACTCGGAATATTT
20834859 TCTTTATTAT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAAAATCCCAAACTCGGAATATTTCCTAT
Found at i:20835153 original size:22 final size:21
Alignment explanation
Indices: 20835096--20835156 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
20835086 TATATGAACA
* *
20835096 AATAAATAATGAATGACATAT
1 AATATATAATAAATGACATAT
20835117 AATATATCAAATAAATGAGCAATAT
1 AATATAT--AATAAATGA-C-ATAT
20835142 AA-ATATAATAAATGA
1 AATATATAATAAATGA
20835157 AATTACGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.18
22 9 0.26
23 8 0.24
24 5 0.15
25 6 0.18
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (21 bp):
AATATATAATAAATGACATAT
Found at i:20837124 original size:18 final size:17
Alignment explanation
Indices: 20837091--20837129 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
20837081 TTTTATAAAT
20837091 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
20837109 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
20837126 TGTG
1 TGTG
20837130 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:20837384 original size:23 final size:23
Alignment explanation
Indices: 20837351--20837472 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
20837341 TTATTGATCG
*
20837351 ATCAGTGGTAGCTTCGGCTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
20837374 TTTAGTGGTAGCTACTGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
20837397 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
20837420 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
20837443 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
20837466 ATCAGTG
1 ATCAGTG
20837473 TTGCACTTAT
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:20837427 original size:46 final size:46
Alignment explanation
Indices: 20837351--20837472 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
20837341 TTATTGATCG
* * *
20837351 ATCAGTGGTAGCTTCGGCTATATTTTAGTGGTAGCTACTGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
20837397 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
20837443 ATCAGTGGTAGCTTCAGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
20837473 TTGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:20842075 original size:20 final size:19
Alignment explanation
Indices: 20842050--20842087 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20842040 CAATGGTTTA
20842050 ATAGGAAAAATATGACGANG
1 ATAGGAAAAATATGACGA-G
*
20842070 ATAGGACAAATATGACGA
1 ATAGGAAAAATATGACGA
20842088 TACGAGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.16
Consensus pattern (19 bp):
ATAGGAAAAATATGACGAG
Found at i:20847321 original size:24 final size:24
Alignment explanation
Indices: 20847293--20847344 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
20847283 TTAGTAAGTC
*
20847293 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
20847317 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
20847341 AAAT
1 AAAT
20847345 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:20848139 original size:29 final size:30
Alignment explanation
Indices: 20848085--20848141 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
20848075 TATTATTTTA
**
20848085 ATTTTTTTTAAAATTCTTAACCATAATTCT
1 ATTTTTTTTAAAATTCTTAAAAATAATTCT
*
20848115 ATTTTTTTTTAAA-TCTTAAAAATAATT
1 ATTTTTTTTAAAATTCTTAAAAATAATT
20848142 ATAAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTTTTTTTAAAATTCTTAAAAATAATTCT
Found at i:20851987 original size:11 final size:11
Alignment explanation
Indices: 20851971--20851995 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20851961 ATTGATAAAA
20851971 ATAAGGATGAC
1 ATAAGGATGAC
20851982 ATAAGGATGAC
1 ATAAGGATGAC
20851993 ATA
1 ATA
20851996 GAATGGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (11 bp):
ATAAGGATGAC
Found at i:20871542 original size:18 final size:17
Alignment explanation
Indices: 20871503--20871546 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
20871493 CATTGTGTAA
20871503 TTTGATTTTC--TTTCT
1 TTTGATTTTCTTTTTCT
20871518 TTT--TTTTCTTTTTACT
1 TTTGATTTTCTTTTT-CT
20871534 TTTGATTTTCTTT
1 TTTGATTTTCTTT
20871547 GTGACCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.21
15 6 0.25
16 5 0.21
18 8 0.33
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTGATTTTCTTTTTCT
Found at i:20872446 original size:52 final size:52
Alignment explanation
Indices: 20872386--20872489 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
20872376 ATAAAATAGG
*
20872386 TAATGTGTAAACATCAAGGATTACATTTTTAAAAATTAAGAGTAAATTGACA
1 TAATGTGTAAACATCAAGGATTAAATTTTTAAAAATTAAGAGTAAATTGACA
** *** * *
20872438 TAATGTGTAAGTATTGGGGGTTAAATTTTTAAAAATTAAGATTAAATTGACA
1 TAATGTGTAAACATCAAGGATTAAATTTTTAAAAATTAAGAGTAAATTGACA
20872490 CTATGTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (52 bp):
TAATGTGTAAACATCAAGGATTAAATTTTTAAAAATTAAGAGTAAATTGACA
Found at i:20875662 original size:30 final size:31
Alignment explanation
Indices: 20875594--20875653 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
20875584 GACTTAAATA
* *
20875594 AAAACTTTTGAATAGTTCAATGGCTTGAATG
1 AAAACTTTCGAATAGTTCAATGGATTGAATG
20875625 AAAACTTTCGAATAGTTCAAT-GATTGAAT
1 AAAACTTTCGAATAGTTCAATGGATTGAAT
20875654 TGTAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (31 bp):
AAAACTTTCGAATAGTTCAATGGATTGAATG
Found at i:20881777 original size:23 final size:23
Alignment explanation
Indices: 20881751--20881794 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20881741 ATGATATCTG
20881751 TCAACATCATCAACTATCCACTA
1 TCAACATCATCAACTATCCACTA
*
20881774 TCAACATCATCCACTATCCAC
1 TCAACATCATCAACTATCCAC
20881795 ATTTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.25
Consensus pattern (23 bp):
TCAACATCATCAACTATCCACTA
Found at i:20881787 original size:16 final size:16
Alignment explanation
Indices: 20881766--20881796 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20881756 ATCATCAACT
20881766 ATCCACTATCAACATC
1 ATCCACTATCAACATC
*
20881782 ATCCACTATCCACAT
1 ATCCACTATCAACAT
20881797 TTAATTAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.39, G:0.00, T:0.26
Consensus pattern (16 bp):
ATCCACTATCAACATC
Found at i:20886415 original size:11 final size:11
Alignment explanation
Indices: 20886401--20886427 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20886391 TTATGTGTAA
20886401 ATTATTTATTT
1 ATTATTTATTT
20886412 ATTATTTATTT
1 ATTATTTATTT
20886423 ATTAT
1 ATTAT
20886428 ACTTTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:20890097 original size:5 final size:5
Alignment explanation
Indices: 20890087--20890111 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20890077 TTGCCCCCTC
20890087 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
20890112 TCTCTCTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:20892181 original size:22 final size:21
Alignment explanation
Indices: 20892156--20892201 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
20892146 AAATTGTTGC
* *
20892156 ATTTGTTTTGATATTGGTCTTG
1 ATTTGTTCTGAAATT-GTCTTG
*
20892178 ATTTGTTCTGAAATTGTTTTG
1 ATTTGTTCTGAAATTGTCTTG
20892199 ATT
1 ATT
20892202 GTCTGCTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59
Consensus pattern (21 bp):
ATTTGTTCTGAAATTGTCTTG
Found at i:20892215 original size:23 final size:23
Alignment explanation
Indices: 20892187--20892270 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
20892177 GATTTGTTCT
20892187 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
* * *
20892210 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
20892233 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
*
20892256 GAAATTGTGTTGATT
1 GAAATTGTTTTGATT
20892271 TGTTTATGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.44
Consensus pattern (23 bp):
GAAATTGTTTTGATTGTCTGCTG
Found at i:20895495 original size:17 final size:17
Alignment explanation
Indices: 20895470--20895503 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20895460 ATTATTTTAA
*
20895470 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
20895487 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
20895504 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:20895505 original size:15 final size:16
Alignment explanation
Indices: 20895470--20895508 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
20895460 ATTATTTTAA
*
20895470 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
20895487 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
20895502 ATTTAAT
1 ATTTAAT
20895509 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:20895512 original size:17 final size:18
Alignment explanation
Indices: 20895474--20895513 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
20895464 TTTTAAATTT
*
20895474 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
20895492 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
20895508 TATTAA
1 TATTAA
20895514 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:20895578 original size:66 final size:63
Alignment explanation
Indices: 20895506--20895836 Score: 211
Period size: 66 Copynumber: 5.4 Consensus size: 63
20895496 AATCATATTT
*
20895506 AATATTAATTATTTGAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTAATATAA
1 AATATTAATTATTT-AAATTTTATTTTA-AGTATCATATATTATGATTTGAGTAAATT-ATATAA
20895571 G
63 G
* * * * **
20895572 AATATTAATTATTAAGAATTTTA--TTAA--AT--TATA-TAT--TTTAATTAAAATATAT-TT
1 AATATTAATTATTTA-AATTTTATTTTAAGTATCATATATTATGATTTGAGTAAATTATATAAG
* *
20895626 AATAATAATTATGTT-AATTTATATTTTACTGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TATTTTA-AGTATCATATATTATGATTTGAGTAAATT-ATATA
20895690 AG
62 AG
* * * * * **
20895692 AATATTAATTATTAAGAATTTCA--TTAA--AT--TATA-TAT--TTTAATTAAAATATAT-TT
1 AATATTAATTATTTA-AATTTTATTTTAAGTATCATATATTATGATTTGAGTAAATTATATAAG
* *
20895746 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATA
1 AATATTAATTAT-TTAAATTT-TATTTTA-AGTATCATATATTATGATTTGAGTAAATT-ATATA
20895810 AG
62 AG
*
20895812 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
20895837 AAATTATATA
Statistics
Matches: 198, Mismatches: 34, Indels: 66
0.66 0.11 0.22
Matches are distributed among these distances:
53 10 0.05
54 25 0.13
55 10 0.05
56 24 0.12
57 1 0.01
58 6 0.03
59 12 0.06
61 12 0.06
62 6 0.03
63 1 0.01
64 24 0.12
65 11 0.06
66 46 0.23
67 10 0.05
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTTAAGTATCATATATTATGATTTGAGTAAATTATATAAG
Found at i:20895616 original size:51 final size:51
Alignment explanation
Indices: 20895560--20895736 Score: 129
Period size: 54 Copynumber: 3.1 Consensus size: 51
20895550 GATTTGAGTA
20895560 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTT
1 AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTT
** * * *
20895611 AATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACTGTATCATATATTATGATTTG
1 AATT--AATATA-AGAATATTAATTA--TTAA--GA-ATTTTA-T-TA-AAT-TA-TAT-ATTT-
20895676 AGT
51 --T
* *
20895679 AAATTCATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTT
1 -AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTT
20895731 AATTAA
1 AATTAA
20895737 AATATATTTA
Statistics
Matches: 95, Mismatches: 13, Indels: 36
0.66 0.09 0.25
Matches are distributed among these distances:
51 9 0.09
52 1 0.01
53 6 0.06
54 10 0.11
55 4 0.04
56 7 0.07
57 2 0.02
58 3 0.03
59 8 0.08
60 2 0.02
61 7 0.07
62 3 0.03
63 2 0.02
64 7 0.07
65 4 0.04
66 10 0.11
67 5 0.05
68 1 0.01
69 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (51 bp):
AATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTT
Found at i:20895617 original size:18 final size:17
Alignment explanation
Indices: 20895589--20895623 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20895579 ATTATTAAGA
*
20895589 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20895606 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20895624 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20895670 original size:120 final size:120
Alignment explanation
Indices: 20895469--20895880 Score: 690
Period size: 120 Copynumber: 3.4 Consensus size: 120
20895459 AATTATTTTA
* * *
20895469 AATTTTATTAAATCATATA-TTTAATT-AAATCATATTTAATATTAATTAT-TTGAAATTT-TCT
1 AATTTTATTAAATTATATATTTTAATTAAAAT-ATATTTAATAATAATTATGTT--AATTTATAT
20895530 TTTA-TAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
63 TTTACT-GTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
20895588 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
20895653 ACTGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACTGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
*
20895708 AATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
* *
20895773 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACTGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
20895828 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
20895881 TAAATATGAT
Statistics
Matches: 279, Mismatches: 9, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
119 23 0.08
120 249 0.89
121 7 0.03
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACTGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
Found at i:20895857 original size:18 final size:17
Alignment explanation
Indices: 20895829--20895863 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20895819 ATTATTAAGA
*
20895829 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20895846 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20895864 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20896114 original size:16 final size:16
Alignment explanation
Indices: 20896093--20896128 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
20896083 GATTTGCTAT
20896093 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20896109 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20896125 TACA
1 TACA
20896129 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:20902957 original size:21 final size:21
Alignment explanation
Indices: 20902933--20902973 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20902923 ATCTCACCTC
*
20902933 TACAGTATCCAATCTCACTGT
1 TACAGTAACCAATCTCACTGT
*
20902954 TACAGTAACTAATCTCACTG
1 TACAGTAACCAATCTCACTG
20902974 CCACCGCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (21 bp):
TACAGTAACCAATCTCACTGT
Found at i:20903820 original size:27 final size:27
Alignment explanation
Indices: 20903790--20903841 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20903780 AATTTGACAA
* *
20903790 AAAAAAACGTTAAGGGCCAAAGTGATC
1 AAAAAAACATAAAGGGCCAAAGTGATC
* *
20903817 AAAAAAATATAAAGGGTCAAAGTGA
1 AAAAAAACATAAAGGGCCAAAGTGA
20903842 CCTAACAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (27 bp):
AAAAAAACATAAAGGGCCAAAGTGATC
Found at i:20907905 original size:44 final size:44
Alignment explanation
Indices: 20907839--20907938 Score: 164
Period size: 44 Copynumber: 2.2 Consensus size: 44
20907829 GCCGACTACT
*
20907839 GTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTA-CGATTCAGCACTTTGTGTGTCGAATACTGTTACC
* *
20907884 GTTACTGTTACGATTCAGCACTTTGTGTGTTGAATACTGTTACT
1 GTTACTGTTACGATTCAGCACTTTGTGTGTCGAATACTGTTACC
20907928 GTTACTGTTAC
1 GTTACTGTTAC
20907939 TGTTATCGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 42 0.81
45 10 0.19
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (44 bp):
GTTACTGTTACGATTCAGCACTTTGTGTGTCGAATACTGTTACC
Found at i:20907929 original size:6 final size:6
Alignment explanation
Indices: 20907918--20907966 Score: 64
Period size: 6 Copynumber: 7.8 Consensus size: 6
20907908 GTGTGTTGAA
20907918 TACTGT TACTGT TACTGT TACTGT TA-TCGT TACTGAT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACT-GT TACTG-T TACTG-T TACTG
20907967 GTGTGTTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
5 1 0.03
6 25 0.64
7 13 0.33
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:20910213 original size:33 final size:33
Alignment explanation
Indices: 20910176--20910319 Score: 138
Period size: 33 Copynumber: 4.5 Consensus size: 33
20910166 AATCTATTGA
*
20910176 GACAATAAACATAGAATAGAGATAGTTCGTTGG
1 GACAATAAACACAGAATAGAGATAGTTCGTTGG
*
20910209 GACAAT-AACACAGAAT--AGATAGTCCGCTT-G
1 GACAATAAACACAGAATAGAGATAGTTCG-TTGG
* * * * *
20910239 GACAGTAAATACAGAACAAAGATAG-TCTGTTAG
1 GACAATAAACACAGAATAGAGATAGTTC-GTTGG
*
20910272 GAAAATAAACACAGAATAGAGATAGTAT-GTTGG
1 GACAATAAACACAGAATAGAGATAGT-TCGTTGG
*
20910305 GACAGTAAACACAGA
1 GACAATAAACACAGA
20910320 TAAAGTCCAC
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
30 15 0.17
31 10 0.11
32 12 0.13
33 51 0.57
35 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.20
Consensus pattern (33 bp):
GACAATAAACACAGAATAGAGATAGTTCGTTGG
Found at i:20910294 original size:96 final size:95
Alignment explanation
Indices: 20910131--20910319 Score: 249
Period size: 96 Copynumber: 2.0 Consensus size: 95
20910121 ACATTCAAAG
* * *
20910131 AGATAGTCCGCTAGAACAGTAAATACAAAAGAGATAATCTATTGAGACAATAAACATAGAATAGA
1 AGATAGTCCGCTAGAACAGTAAATACAAAAAAGATAATCTATTGAGAAAATAAACACAGAATAGA
20910196 GATAGT-TCGTTGGGACAAT-AACACAGAAT
66 GATAGTAT-GTTGGGACAATAAACACAGAAT
* * * *
20910225 AGATAGTCCGCTTGGACAGTAAATACAGAACAAAGATAGTCTGTT-AGGAAAATAAACACAGAAT
1 AGATAGTCCGCTAGAACAGTAAATACA-AA-AAAGATAATCTATTGA-GAAAATAAACACAGAAT
*
20910289 AGAGATAGTATGTTGGGACAGTAAACACAGA
63 AGAGATAGTATGTTGGGACAATAAACACAGA
20910320 TAAAGTCCAC
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
94 25 0.30
95 3 0.04
96 45 0.55
97 9 0.11
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (95 bp):
AGATAGTCCGCTAGAACAGTAAATACAAAAAAGATAATCTATTGAGAAAATAAACACAGAATAGA
GATAGTATGTTGGGACAATAAACACAGAAT
Found at i:20914148 original size:4 final size:4
Alignment explanation
Indices: 20914139--20914183 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
20914129 AACCCCAAAT
* *
20914139 TTTC TTTC TTTC TTTC CTTC TTTT TTTC TTT- TTTC TTTCC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC T
20914184 CCCCTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 3 0.09
4 28 0.80
5 4 0.11
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:20919340 original size:17 final size:18
Alignment explanation
Indices: 20919320--20919384 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 18
20919310 AATAATTGCT
20919320 TTATT-TATATAAAATAA
1 TTATTATATATAAAATAA
* *
20919337 TTATTATTTATTAATAATTA
1 TTATTATATA-TAA-AATAA
20919357 TATATTAAATATATAAAATAA
1 T-TATT--ATATATAAAATAA
20919378 TTATTAT
1 TTATTAT
20919385 TTATTAATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
17 5 0.13
18 5 0.13
19 3 0.08
20 9 0.24
21 9 0.24
22 3 0.08
23 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTATATATAAAATAA
Found at i:20919356 original size:14 final size:14
Alignment explanation
Indices: 20919334--20919412 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
20919324 TTATATAAAA
* *
20919334 TAATTATTATTTAT
1 TAATAATTATATAT
20919348 TAATAATTATATAT
1 TAATAATTATATAT
* *
20919362 T-A-AATATATAAAA
1 TAATAAT-TATATAT
* *
20919375 TAATTATTATTTAT
1 TAATAATTATATAT
*
20919389 TAATAGTTATATAT
1 TAATAATTATATAT
* *
20919403 AAATATTTAT
1 TAATAATTAT
20919413 TTTCTTCACG
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
12 3 0.06
13 7 0.14
14 37 0.76
15 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (14 bp):
TAATAATTATATAT
Found at i:20919363 original size:24 final size:24
Alignment explanation
Indices: 20919336--20919413 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 24
20919326 ATATAAAATA
20919336 ATTATTATTTATTAATAATTATAT
1 ATTATTATTTATTAATAATTATAT
* *
20919360 ATTA--A-ATA-T-ATAA-AATA-
1 ATTATTATTTATTAATAATTATAT
*
20919377 ATTATTATTTATTAATAGTTATAT
1 ATTATTATTTATTAATAATTATAT
* *
20919401 ATAAATATTTATT
1 ATTATTATTTATT
20919414 TTCTTCACGG
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
17 4 0.10
18 3 0.08
19 5 0.12
20 3 0.08
21 3 0.08
22 4 0.10
23 3 0.08
24 15 0.38
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
ATTATTATTTATTAATAATTATAT
Found at i:20919380 original size:41 final size:40
Alignment explanation
Indices: 20919325--20919408 Score: 150
Period size: 41 Copynumber: 2.1 Consensus size: 40
20919315 TTGCTTTATT
20919325 TATATAAAATAATTATTATTTATTAATAATTATATATTAAA
1 TATATAAAATAATTATTATTTATTAATAATTATATA-TAAA
*
20919366 TATATAAAATAATTATTATTTATTAATAGTTATATATAAA
1 TATATAAAATAATTATTATTTATTAATAATTATATATAAA
20919406 TAT
1 TAT
20919409 TTATTTTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 7 0.17
41 35 0.83
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
TATATAAAATAATTATTATTTATTAATAATTATATATAAA
Found at i:20925291 original size:23 final size:24
Alignment explanation
Indices: 20925240--20925286 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
20925230 TTCGAACCAT
*
20925240 GTAACGGGAAGCTCATGTGAGCTAA
1 GTAACGGGAAGCTCATGAGAGC-AA
20925265 GTAACGGGAAGCTCATGAGAGC
1 GTAACGGGAAGCTCATGAGAGC
20925287 CGTAAATCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.34, T:0.17
Consensus pattern (24 bp):
GTAACGGGAAGCTCATGAGAGCAA
Found at i:20925323 original size:50 final size:49
Alignment explanation
Indices: 20925269--20925386 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 49
20925259 AGCTAAGTAA
20925269 CGGGAAGCTCATGAGAGCCGTAAA-TCA-GATAGCT-AAGGAGAG-CTATTAAT
1 CGGGAAGCTCATGAGAGCC--AAAGTCAGGA-AGCTCAA-GAGAGTC-ATTAAT
20925319 CGGGAAGCTCAT-ACGAGCCAAATGTCAGGAAGCTCAAGAGAGTCATTAAT
1 CGGGAAGCTCATGA-GAGCCAAA-GTCAGGAAGCTCAAGAGAGTCATTAAT
*
20925369 CAGGAAGCTCATGAGAGC
1 CGGGAAGCTCATGAGAGC
20925387 TCTGGTGCGT
Statistics
Matches: 60, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
48 3 0.05
49 1 0.02
50 50 0.83
51 6 0.10
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.18
Consensus pattern (49 bp):
CGGGAAGCTCATGAGAGCCAAAGTCAGGAAGCTCAAGAGAGTCATTAAT
Found at i:20928752 original size:19 final size:20
Alignment explanation
Indices: 20928730--20928777 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
20928720 AAAAGTATAT
*
20928730 AAATATAAAAAATT-CAAAA
1 AAATATAAAAAATTGAAAAA
**
20928749 AAATATAAAATTTTGAAAAA
1 AAATATAAAAAATTGAAAAA
20928769 AAATATAAA
1 AAATATAAA
20928778 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAATATAAAAAATTGAAAAA
Found at i:20928770 original size:20 final size:20
Alignment explanation
Indices: 20928745--20928797 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
20928735 TAAAAAATTC
*
20928745 AAAAAAATATAAAATTTTGA
1 AAAAAAATATAAAATTTTAA
20928765 AAAAAAATAT-AAATTTTAA
1 AAAAAAATATAAAATTTTAA
20928784 AAATAAAAT-TAAAA
1 AAA-AAAATATAAAA
20928798 AAATGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAAATATAAAATTTTAA
Found at i:20928778 original size:19 final size:19
Alignment explanation
Indices: 20928745--20928796 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
20928735 TAAAAAATTC
*
20928745 AAAAAAATATAAAATTTTGA
1 AAAAAAATAT-AAATTTTAA
20928765 AAAAAAATATAAATTTTAA
1 AAAAAAATATAAATTTTAA
20928784 AAATAAAAT-TAAA
1 AAA-AAAATATAAA
20928797 AAAATGTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAAATATAAATTTTAA
Found at i:20929150 original size:32 final size:31
Alignment explanation
Indices: 20929116--20929177 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
20929106 TATTTAAATA
*
20929116 TTTAATATTATAATTTTTTATTTTTATTTTTATT
1 TTTAAT-TTA-AATTTTATATTTTTATTTTTA-T
20929150 TTTAATTTAAATTTTATATTTTTATTTT
1 TTTAATTTAAATTTTATATTTTTATTTT
20929178 AAATAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 18 0.67
33 3 0.11
34 6 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTAATTTAAATTTTATATTTTTATTTTTAT
Found at i:20929169 original size:20 final size:19
Alignment explanation
Indices: 20929141--20929181 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
20929131 TTTTATTTTT
20929141 ATTTTTATTTTTAATTTAA
1 ATTTTTATTTTTAATTTAA
*
20929160 ATTTTATATTTTTATTTTAA
1 ATTTT-TATTTTTAATTTAA
20929180 AT
1 AT
20929182 AAACTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTATTTTTAATTTAA
Found at i:20929178 original size:5 final size:6
Alignment explanation
Indices: 20929130--20929177 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
20929120 ATATTATAAT
**
20929130 TTTTTA TTTTTA TTTTTA TTTTTAA TTTAAA TTTTATA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTT-A TTTTTA TTTT-TA TTTTTA TTTT
20929178 AAATAAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 27 0.75
7 9 0.25
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:20929178 original size:13 final size:12
Alignment explanation
Indices: 20929130--20929177 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
20929120 ATATTATAAT
20929130 TTTTTATTTTTA
1 TTTTTATTTTTA
20929142 TTTTTATTTTTAA
1 TTTTTATTTTT-A
**
20929155 TTTAAATTTTATA
1 TTTTTATTTT-TA
20929168 TTTTTATTTT
1 TTTTTATTTT
20929178 AAATAAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 11 0.37
13 18 0.60
14 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:20931032 original size:125 final size:125
Alignment explanation
Indices: 20930760--20931138 Score: 589
Period size: 125 Copynumber: 3.0 Consensus size: 125
20930750 TTAGGGTTTT
* *** * * *
20930760 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTTATCAAATATTATAAAATCACTTCTAGC
1 TAGGTCATGGAAGAAATAATTT-TTTTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAGC
* *
20930825 AGGATGCTATTTGAGAAGAATTTGTG-AAATCGCGCCTTAGTGGACGCGCTTTTGCTACAG
65 AGGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
20930885 TAGGTCATGGAAGAAATAAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTACC
1 TAGGTCATGGAAGAAAT-AATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAGC
* *
20930950 AGAATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
65 AGGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
20931011 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGGA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAGCA
* *
20931076 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCACCCTCGTGGACGCACTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
20931136 TAG
1 TAG
20931139 CATGTTTGAG
Statistics
Matches: 233, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
125 180 0.77
126 53 0.23
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAGCA
GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:20934292 original size:17 final size:17
Alignment explanation
Indices: 20934225--20934292 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
20934215 TATGTGAATG
*
20934225 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
20934241 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
20934260 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
20934279 TAAAATTATTAATT
1 TAAAATTATTAATT
20934293 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:20934388 original size:23 final size:23
Alignment explanation
Indices: 20934360--20934843 Score: 535
Period size: 23 Copynumber: 21.8 Consensus size: 23
20934350 TTAATTTCGT
*
20934360 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934383 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
20934404 TTAGGGTTTTTAATTTAATTAAG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934427 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934450 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
***
20934471 TTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAATTAGG
* **
20934494 TTAAGGTTTTTAAG-TAA-CGGG
1 TTAGGGTTTTTAAGTTAATTAGG
20934515 TTAGGGTTTTTAAG-T--TTAGGG
1 TTAGGGTTTTTAAGTTAATTA-GG
20934536 TTTAGGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AATTAGG
*
20934560 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
20934581 TTAGAG-TTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
20934603 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934626 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
20934647 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
20934670 TTAGAGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
20934691 TTAGGGTTTTTAATTTAATTAAG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934714 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934737 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934758 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
20934781 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
20934802 TTTAAGGTTTTTAA-TTAATTTAGT
1 -TTAGGGTTTTTAAGTTAA-TTAGG
20934826 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAAGTTAA
20934844 GGGTATTAAT
Statistics
Matches: 397, Mismatches: 38, Indels: 51
0.82 0.08 0.10
Matches are distributed among these distances:
20 10 0.03
21 128 0.32
22 36 0.09
23 211 0.53
24 9 0.02
25 3 0.01
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (23 bp):
TTAGGGTTTTTAAGTTAATTAGG
Found at i:20934423 original size:44 final size:44
Alignment explanation
Indices: 20934360--20934847 Score: 573
Period size: 44 Copynumber: 11.0 Consensus size: 44
20934350 TTAATTTCGT
20934360 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
* * *
20934404 TTAGGGTTTTTAATTTAATTAAGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGG
* *
20934450 TTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGG
* * ** *
20934494 TTAAGGTTTTTAA-GTAA-CGGGTTAGGGTTTTTAAGTTTAGGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
*
20934536 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
* *
20934581 TTAGAG-TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGG
* * *
20934626 TTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGG
* * * * **
20934670 TTAGAGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAATTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGG
20934714 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
20934758 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
* *
20934802 TTTAAGGTTTTTAA-TTAATTTAGTTTAGGGTTTTTAAGTTAAGGG
1 -TTAGGGTTTTTAATTTAA-TTAGGTTAGGGTTTTTAAGTTAAGGG
20934847 T
1 T
20934848 ATTAATTGTT
Statistics
Matches: 395, Mismatches: 36, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
42 3 0.01
43 48 0.12
44 230 0.58
45 66 0.17
46 48 0.12
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (44 bp):
TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
Found at i:20934462 original size:67 final size:67
Alignment explanation
Indices: 20934360--20934843 Score: 544
Period size: 67 Copynumber: 7.3 Consensus size: 67
20934350 TTAATTTCGT
*
20934360 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAATTA
*
20934425 AG
66 GG
***
20934427 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAATTA
20934492 GG
66 GG
* * ** *
20934494 TTAAGGTTTTTAA-GTAA-CGGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAA-TTAAAT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTT-AAT
20934556 TAGG
64 TAGG
* * * * *
20934560 TTAGGGTTTTTAAGTTAA--GGGTTAGAG-TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAAT
20934622 TAGG
64 TAGG
* * * *
20934626 TTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAATTAGGTTAGAGTTTTTAAGTTAA-
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAAT
*
20934688 -GGG
64 TAGG
* * *
20934691 TTAGGGTTTTTAATTTAATTAAGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA-
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAAT
*
20934755 -GGG
64 TAGG
*
20934758 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAA-TTAATT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAA-T
*
20934822 TAGT
64 TAGG
*
20934826 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAATTTAA
20934844 GGGTATTAAT
Statistics
Matches: 369, Mismatches: 35, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
65 58 0.16
66 98 0.27
67 195 0.53
68 18 0.05
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (67 bp):
TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAATTA
GG
Found at i:20934933 original size:25 final size:25
Alignment explanation
Indices: 20934904--20934951 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
20934894 ATTCAAAAAT
20934904 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
20934929 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
20934952 TATCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:20936002 original size:7 final size:7
Alignment explanation
Indices: 20935992--20936016 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20935982 TTATATACAT
20935992 AATACTA
1 AATACTA
20935999 AATACTA
1 AATACTA
20936006 AATACTA
1 AATACTA
20936013 AATA
1 AATA
20936017 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:20937806 original size:45 final size:45
Alignment explanation
Indices: 20937756--20937846 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
20937746 TTGTCATGTA
*
20937756 AGTTACCTTGCTTAAAAGATTAACATTTTAATTAATACTCTTATG
1 AGTTACCTTGCTTAAAAAATTAACATTTTAATTAATACTCTTATG
20937801 AGTTACCTTGCTTAAAAAATTAACATTTTAATTAATACTCTTATG
1 AGTTACCTTGCTTAAAAAATTAACATTTTAATTAATACTCTTATG
20937846 A
1 A
20937847 AAAAAATTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (45 bp):
AGTTACCTTGCTTAAAAAATTAACATTTTAATTAATACTCTTATG
Found at i:20943336 original size:28 final size:28
Alignment explanation
Indices: 20943304--20943365 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
20943294 AGTCGGTTTT
* *
20943304 TTTTTTTA-AATTTACCGAAATGGGTCGA
1 TTTTTTGATAATTTACCGAAAT-GGTCCA
*
20943332 TTTTTTGATTATTTACCGAAATGGTCCA
1 TTTTTTGATAATTTACCGAAATGGTCCA
20943360 TTTTTT
1 TTTTTT
20943366 AGGAAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (28 bp):
TTTTTTGATAATTTACCGAAATGGTCCA
Found at i:20943659 original size:126 final size:125
Alignment explanation
Indices: 20943425--20943659 Score: 389
Period size: 126 Copynumber: 1.9 Consensus size: 125
20943415 CCCAACGGTT
*
20943425 AAAAATTATTTCTTACATAACCTACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATT
1 AAAAATTATTTCTTACATAACATACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATT
* * *
20943490 TCTACTCAAATAGCATCCTTGTAGAAGCAATTTTATACTATTTGCTTAGAAACGTCAAAA
66 TCTACTCAAATAACATCCTGGTAGAAGCAATTTTATACAATTTGCTTAGAAACGTCAAAA
* *
20943550 AAAATATTATTTCTTACATGACATACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAAT
1 AAAA-ATTATTTCTTACATAACATACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAAT
* *
20943615 TTCTTCTCAAATAACATCCTGGTAGAAGCGATTTTATACAATTTG
65 TTCTACTCAAATAACATCCTGGTAGAAGCAATTTTATACAATTTG
20943660 ACCAGAAAAC
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
125 4 0.04
126 97 0.96
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (125 bp):
AAAAATTATTTCTTACATAACATACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATT
TCTACTCAAATAACATCCTGGTAGAAGCAATTTTATACAATTTGCTTAGAAACGTCAAAA
Found at i:20945950 original size:295 final size:290
Alignment explanation
Indices: 20945453--20945989 Score: 681
Period size: 295 Copynumber: 1.8 Consensus size: 290
20945443 TTCAAATCAG
* *
20945453 TCTTTTAATTTGTTTTTGTTGTTTTTTCTCGAAAAAGGAGTATATTAGGTTTAAGATTTAACGTT
1 TCTTTTAATTTCTTTTCGTTGTTTTTTCTCGAAAAAGGAGTATATTAGGTTTAAGATTTAACGTT
* * * ** *
20945518 TTAGGTAATGATTGAGTATTTACTAGCGTCTGGACTCTGTAAAGTCTTCTAATTTTATTTTATTG
66 TTAGGTAATGATTGAGTATTTACTAGCGTCTGGACCCTGGAAAGTCTTCTAATTTAATTACATCG
* * * *
20945583 TTTCTGCTAAGCGCTGGCTCCAAAAAGTAATAAAAGCACTTCTTTTTCTACGTTTAAGAGCTTAT
131 TTTCTGCTAAGCACTGGATCCAAAAAGTAATAAAAGCA--TCTTATTCTACGTTTAAGAACTTAT
*
20945648 TGATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCTTCATCTTATATGATGAGAGGAAAA
194 TGATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCTCCATCTTATATGATGAGAGGAAAA
20945713 CCGAATTTGTTTAAGATTTTTTTTTTAAACAA
259 CCGAATTTGTTTAAGATTTTTTTTTTAAACAA
* *
20945745 TCTTTTAAATTTCTTTTCGTT-TTTTTTCTCGTAAAAGG-GATATATTAGGTTTAAGGTTTAACA
1 TCTTTT-AATTTCTTTTCGTTGTTTTTTCTCGAAAAAGGAG-TATATTAGGTTTAAGATTTAAC-
* * *
20945808 TTTTTTAGGTAATGGTTTGAGTATTTACTAGCGTCTGGACCCTGGGAAGTC-TC--ATATTAATT
63 -GTTTTAGGTAAT-GATTGAGTATTTACTAGCGTCTGGACCCTGGAAAGTCTTCTAAT-TTAATT
* * * *
20945870 ACATCGTTTCTGCTAATCATTTGATCCAAACTCAAAAGTAATAAAAGCA-CTTATTCTGCGTTTA
125 ACATCGTTTCTGCTAAGCACTGGATCC--A---AAAAGTAATAAAAGCATCTTATTCTACGTTTA
* * * *
20945934 GGAATTTCTTGATCGATGTATGTTCAAATTTATTGCAGGCATTAGCGTCTCCATCT
185 AGAACTTATTGATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCTCCATCT
20945990 CAGAGACGCA
Statistics
Matches: 208, Mismatches: 26, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
291 1 0.00
292 45 0.22
293 36 0.17
294 13 0.06
295 97 0.47
298 16 0.08
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (290 bp):
TCTTTTAATTTCTTTTCGTTGTTTTTTCTCGAAAAAGGAGTATATTAGGTTTAAGATTTAACGTT
TTAGGTAATGATTGAGTATTTACTAGCGTCTGGACCCTGGAAAGTCTTCTAATTTAATTACATCG
TTTCTGCTAAGCACTGGATCCAAAAAGTAATAAAAGCATCTTATTCTACGTTTAAGAACTTATTG
ATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCTCCATCTTATATGATGAGAGGAAAACC
GAATTTGTTTAAGATTTTTTTTTTAAACAA
Found at i:20955878 original size:45 final size:45
Alignment explanation
Indices: 20955820--20955907 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
20955810 ATAATATTTA
* * *
20955820 ATTATTTTTATATGTGAAATATTTCA-ATTAATTATTTCAAATATC
1 ATTATATTTATATGTGAAATATTTCAGA-TAACTATTTAAAATATC
20955865 ATTATATTTATATGTGAAATATTTCAGATAACTATTTAAAATA
1 ATTATATTTATATGTGAAATATTTCAGATAACTATTTAAAATA
20955908 CACGTATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (45 bp):
ATTATATTTATATGTGAAATATTTCAGATAACTATTTAAAATATC
Found at i:20960398 original size:15 final size:16
Alignment explanation
Indices: 20960372--20960401 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20960362 AATAAATTAT
20960372 TAAAAATACATAAAAA
1 TAAAAATACATAAAAA
20960388 TAAAAAT-CATAAAA
1 TAAAAATACATAAAA
20960402 TTTATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAAATACATAAAAA
Found at i:20960718 original size:29 final size:30
Alignment explanation
Indices: 20960683--20960744 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
20960673 AACTCCCAAA
* * *
20960683 CCTTTTTACTTTTCCCTCAAAACTTTTACT
1 CCTTTTCACTTTCCCCCCAAAACTTTTACT
20960713 CCTTTTCACTTTCCCCCCAAAACTTTTACT
1 CCTTTTCACTTTCCCCCCAAAACTTTTACT
20960743 CC
1 CC
20960745 CCTCCCCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.37, G:0.00, T:0.44
Consensus pattern (30 bp):
CCTTTTCACTTTCCCCCCAAAACTTTTACT
Found at i:20961964 original size:27 final size:28
Alignment explanation
Indices: 20961900--20961964 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 28
20961890 TAAAAAAATC
*
20961900 AATTATC-CATTAATTTATTTATCAATG
1 AATTATCAAATTAATTTATTTATCAATG
* * *
20961927 AATT-GCTAAATTAATTT-TTTATCATTT
1 AATTATC-AAATTAATTTATTTATCAATG
20961954 AATTATCAAAT
1 AATTATCAAAT
20961965 GAATAGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
26 1 0.03
27 20 0.67
28 9 0.30
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.49
Consensus pattern (28 bp):
AATTATCAAATTAATTTATTTATCAATG
Found at i:20968198 original size:20 final size:22
Alignment explanation
Indices: 20968175--20968217 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
20968165 ACAATATAAT
*
20968175 TATTTTTAT-TATG-TTTTAAA
1 TATTTTTATATAGGTTTTTAAA
20968195 TATTTTTATATAGGTTTTTAAA
1 TATTTTTATATAGGTTTTTAAA
20968217 T
1 T
20968218 TTAAACCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TATTTTTATATAGGTTTTTAAA
Found at i:20968525 original size:31 final size:31
Alignment explanation
Indices: 20968464--20968526 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
20968454 TTAAAATATG
* * *
20968464 TTTGTTAAAAATTTTTAAATTCTTATTTTTT
1 TTTGTGAAAAATTTTAAAATTCTTAATTTTT
* *
20968495 TTTGTGAATAATTTTAAAATT-TTAAATTTT
1 TTTGTGAAAAATTTTAAAATTCTTAATTTTT
20968525 TT
1 TT
20968527 AAACACATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTGTGAAAAATTTTAAAATTCTTAATTTTT
Found at i:20968696 original size:15 final size:15
Alignment explanation
Indices: 20968651--20968697 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
20968641 TGATAAACCA
*
20968651 AAAAATTAAGTACTG
1 AAAAATTAAGTATTG
* *
20968666 AAAAAATAAGTGTTG
1 AAAAATTAAGTATTG
*
20968681 AAAAATTAACTATTG
1 AAAAATTAAGTATTG
20968696 AA
1 AA
20968698 TTTATATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:20971676 original size:24 final size:24
Alignment explanation
Indices: 20971639--20971685 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20971629 GGTGTTTCCC
20971639 GTTAATTGAACTTTGAAGCTACCT
1 GTTAATTGAACTTTGAAGCTACCT
** *
20971663 GTTAATTGCTCTTTGGAGCTACC
1 GTTAATTGAACTTTGAAGCTACC
20971686 CATTATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (24 bp):
GTTAATTGAACTTTGAAGCTACCT
Found at i:20971999 original size:15 final size:16
Alignment explanation
Indices: 20971972--20972002 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
20971962 CCGAGTTACA
20971972 AAATTCATTCAAATTT
1 AAATTCATTCAAATTT
20971988 AAATTC-TTCAAATTT
1 AAATTCATTCAAATTT
20972003 TTAACATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTCATTCAAATTT
Found at i:20973692 original size:16 final size:16
Alignment explanation
Indices: 20973671--20973702 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20973661 GTTTTGTTGC
*
20973671 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
20973687 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
20973703 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:20973990 original size:51 final size:50
Alignment explanation
Indices: 20973930--20974120 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 50
20973920 CCAGTTCACA
* *
20973930 TAGTAGCCTGCACATAGTACTACATATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCG-TACACG
* * * *
20973981 TAGTAGCCTGCACATAGTACTATACACATGATCGA--AGCTATCCCGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT-CCGTACACG
* * *
20974032 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATC-CGTACACG
20974082 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
20974121 TTCACTTTCA
Statistics
Matches: 117, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
49 5 0.04
50 41 0.35
51 65 0.56
52 5 0.04
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGTACACG
Found at i:20974136 original size:101 final size:102
Alignment explanation
Indices: 20973923--20974108 Score: 277
Period size: 102 Copynumber: 1.8 Consensus size: 102
20973913 AATGATACCA
* *
20973923 GTTCACATAGTAGCCTGCACATAGTACTACATATGTGACCATCACTATCCGATACACGTAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGC
* * *
20973988 CTGCACATAGTACTATACACATGATCGAAGCTATCCC
66 CTGCACATAGTACTACACACATGATCCAAGCTATCAC
* * *
20974025 GTACACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAG
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAG
20974088 CCTGCACATAGTACTACACAC
65 CCTGCACATAGTACTACACAC
20974109 GTGACCATCA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 35 0.45
102 38 0.49
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (102 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGC
CTGCACATAGTACTACACACATGATCCAAGCTATCAC
Found at i:20978515 original size:16 final size:16
Alignment explanation
Indices: 20978494--20978525 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20978484 GTTTTGTTGC
*
20978494 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
20978510 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
20978526 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:20978855 original size:37 final size:37
Alignment explanation
Indices: 20978814--20978928 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
20978804 TAGTAGCCTG
20978814 CACATAGTACTACACACGTGATCATCACTTTCACTTT
1 CACATAGTACTACACACGTGATCATCACTTTCACTTT
* * * * ** *
20978851 CACATAGTGGCCTACACAC-AG-T-NT-AGTAGC-C-TA
1 CACATAGT--ACTACACACGTGATCATCACTTTCACTTT
*
20978884 CACATAGTACTACACACGTGACCATCACTTTCACTTT
1 CACATAGTACTACACACGTGATCATCACTTTCACTTT
20978921 CACATAGT
1 CACATAGT
20978929 GGCCTACACA
Statistics
Matches: 55, Mismatches: 15, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
31 8 0.15
32 1 0.02
33 9 0.16
34 2 0.04
35 6 0.11
36 2 0.04
37 18 0.33
38 1 0.02
39 8 0.15
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.28
Consensus pattern (37 bp):
CACATAGTACTACACACGTGATCATCACTTTCACTTT
Found at i:20978869 original size:39 final size:39
Alignment explanation
Indices: 20978823--20978939 Score: 106
Period size: 39 Copynumber: 3.2 Consensus size: 39
20978813 GCACATAGTA
20978823 CTACACACGTGATCATCACTTTCACTTTCACATAGTGGC
1 CTACACACGTGATCATCACTTTCACTTTCACATAGTGGC
* * * ** * *
20978862 CTACACAC-AG-T-NT-AGTAGC-C-TACACATAGT--A
1 CTACACACGTGATCATCACTTTCACTTTCACATAGTGGC
*
20978893 CTACACACGTGACCATCACTTTCACTTTCACATAGTGGC
1 CTACACACGTGATCATCACTTTCACTTTCACATAGTGGC
20978932 CTACACAC
1 CTACACAC
20978940 AGTCCATGCC
Statistics
Matches: 55, Mismatches: 15, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
31 8 0.15
32 1 0.02
33 9 0.16
34 2 0.04
35 6 0.11
36 2 0.04
37 10 0.18
38 1 0.02
39 16 0.29
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (39 bp):
CTACACACGTGATCATCACTTTCACTTTCACATAGTGGC
Found at i:20978917 original size:70 final size:69
Alignment explanation
Indices: 20978804--20978942 Score: 251
Period size: 70 Copynumber: 2.0 Consensus size: 69
20978794 CCGATACACG
* *
20978804 TAGTAGCCTGCACATAGTACTACACACGTGATCATCACTTTCACTTTCACATAGTGGCCTACACA
1 TAGTAGCCTACACATAGTACTACACACGTGACCATCACTTTCACTTTCACATAGTGGCCTACACA
20978869 CAGT
66 CAGT
20978873 NTAGTAGCCTACACATAGTACTACACACGTGACCATCACTTTCACTTTCACATAGTGGCCTACAC
1 -TAGTAGCCTACACATAGTACTACACACGTGACCATCACTTTCACTTTCACATAGTGGCCTACAC
20978938 ACAGT
65 ACAGT
20978943 CCATGCCACA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.27
Consensus pattern (69 bp):
TAGTAGCCTACACATAGTACTACACACGTGACCATCACTTTCACTTTCACATAGTGGCCTACACA
CAGT
Found at i:20996302 original size:14 final size:14
Alignment explanation
Indices: 20996288--20996345 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
20996278 AAAAAAAAAG
20996288 AGAGAAAGGAGAAGA
1 AGAGAAA-GAGAAGA
*
20996303 AGAGAAAGAGAAAA
1 AGAGAAAGAGAAGA
20996317 AGA-AGAAGAGAAGA
1 AGAGA-AAGAGAAGA
20996331 AGAAGAAAGA-AAGA
1 AG-AGAAAGAGAAGA
20996345 A
1 A
20996346 AAAAGGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.03
14 24 0.63
15 12 0.32
16 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAGAAGA
Found at i:20996311 original size:23 final size:20
Alignment explanation
Indices: 20996297--20996341 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
20996287 GAGAGAAAGG
20996297 AGAAGAAGAGAAAGAGAAAA
1 AGAAGAAGAGAAAGAGAAAA
20996317 AGAAGAAGAG-AAGAAGAAGAA
1 AGAAGAAGAGAAAG-AGAA-AA
20996338 AGAA
1 AGAA
20996342 AGAAAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.13
20 14 0.61
21 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAGAAAGAGAAAA
Found at i:20996332 original size:31 final size:30
Alignment explanation
Indices: 20996274--20996350 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 30
20996264 GCCACACGGT
*
20996274 AGAGAAA-AAAAAAGAGAGAAAGGAGAAGA
1 AGAGAAAGAAAAAAGAGAGAAAGAAGAAGA
20996303 AGAGAAAGAGAAAAAGA-AGAAGAGAAGAAGA
1 AGAGAAAGA-AAAAAGAGAGAA-AGAAGAAGA
20996334 AGAAAGAAAGAAAAAAG
1 AG--AGAAAGAAAAAAG
20996351 GTAATGTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 7 0.17
30 5 0.12
31 17 0.40
32 6 0.14
33 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (30 bp):
AGAGAAAGAAAAAAGAGAGAAAGAAGAAGA
Found at i:20996345 original size:17 final size:16
Alignment explanation
Indices: 20996285--20996345 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
20996275 GAGAAAAAAA
*
20996285 AAGAGAGAAAGGAGAAG
1 AAGA-AGAAAGAAGAAG
*
20996302 AAG-AGAAAG-AGAAA
1 AAGAAGAAAGAAGAAG
20996316 AAGAAGAAGAGAAGAAG
1 AAGAAGAA-AGAAGAAG
20996333 AAGAAAGAAAGAA
1 AAG-AAGAAAGAA
20996346 AAAAGGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 7 0.18
15 10 0.26
16 2 0.05
17 14 0.37
18 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAGAAGAAG
Found at i:20996579 original size:61 final size:60
Alignment explanation
Indices: 20996500--20996697 Score: 185
Period size: 61 Copynumber: 3.2 Consensus size: 60
20996490 TATAGTTTAG
* *
20996500 ATTAGAATTTTGTATGAATATTTTAACTTTTTTGTATGAATATTATAATTTTTTTATGAAT
1 ATTATAATTTTGTATGAATATTGTAA-TTTTTTGTATGAATATTATAATTTTTTTATGAAT
* * **
20996561 ATTATAATGTTGTATGAATATTGTAATTATTT-TAT--A-ATTA-AATTTGTATTTATAGTTTT
1 ATTATAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTATAATTT-T-TTTAT-G-AAT
20996620 GGATTAGTAATTTTTTGTATGAATATTGTAA--TTTTGTATGAATATTATAATTTTTTGTATGAA
1 --ATTA-TAA--TTTTGTATGAATATTGTAATTTTTTGTATGAATATTATAATTTTTT-TATGAA
20996683 T
60 T
*
20996684 ATTGTAATTTTGTA
1 ATTATAATTTTGTA
20996698 ATTTTGTATG
Statistics
Matches: 111, Mismatches: 11, Indels: 32
0.72 0.07 0.21
Matches are distributed among these distances:
55 5 0.05
56 5 0.05
57 6 0.05
58 1 0.01
59 11 0.10
60 5 0.05
61 30 0.27
62 9 0.08
63 3 0.03
64 19 0.17
65 4 0.04
66 8 0.07
67 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (60 bp):
ATTATAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTATAATTTTTTTATGAAT
Found at i:20996593 original size:83 final size:83
Alignment explanation
Indices: 20996506--20996739 Score: 228
Period size: 83 Copynumber: 2.8 Consensus size: 83
20996496 TTAGATTAGA
*
20996506 ATTTTGTATGAATATTTTAACTTTTTTGTATGAATATTATAATTTTTT-TATGAATATTATAATG
1 ATTTTGTATGAATATTTTAA-TTTTTTGTATGAATATTATAATTTTTTGTATGAATATTGTAATG
*
20996570 TTGTATGAATATTGTAATT
65 TTGTATGAATATTATAATT
* * * * * *
20996589 ATTTTATAATTAA-ATTTGT-ATTTATAGTTTTG--GATTAGTAATTTTTTGTATGAATATTGTA
1 ATTTTGT-ATGAATATTT-TAATTTTTTG-TATGAATATTA-TAATTTTTTGTATGAATATTGTA
*
20996650 ATTTTGTATGAATATTATAATT
62 ATGTTGTATGAATATTATAATT
* *
20996672 -TTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTG
1 ATTTTGTATGAATATTTTAA---T-T--TTTTGTATGAATATTATAATTTTTTGTATGAATATTG
20996736 TAAT
60 TAAT
20996740 ATTATAATTT
Statistics
Matches: 119, Mismatches: 17, Indels: 25
0.74 0.11 0.16
Matches are distributed among these distances:
81 9 0.08
82 23 0.19
83 46 0.39
84 5 0.04
85 1 0.01
86 1 0.01
87 3 0.03
88 27 0.23
89 4 0.03
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (83 bp):
ATTTTGTATGAATATTTTAATTTTTTGTATGAATATTATAATTTTTTGTATGAATATTGTAATGT
TGTATGAATATTATAATT
Done.