Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold446
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: 3567220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 22
Found at i:2206023 original size:15 final size:15
Alignment explanation
Indices: 2206003--2206033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2205993 ATTTCGTTTG
*
2206003 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2206018 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2206033 G
1 G
2206034 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2207866 original size:21 final size:21
Alignment explanation
Indices: 2207837--2207881 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2207827 AAGTTTTCAT
*
2207837 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2207857 TTTTCGTTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2207879 TTT
1 TTT
2207882 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2212748 original size:15 final size:15
Alignment explanation
Indices: 2212728--2212757 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2212718 TGGCGAGGTT
*
2212728 ATGACCGAATTATTA
1 ATGACCGAAATATTA
2212743 ATGACCGAAATATTA
1 ATGACCGAAATATTA
2212758 GGCGGAAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
ATGACCGAAATATTA
Found at i:2216547 original size:11 final size:11
Alignment explanation
Indices: 2216531--2216558 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2216521 ATGATCATTA
2216531 TTTGCTTAGTT
1 TTTGCTTAGTT
2216542 TTTGCTTAGTT
1 TTTGCTTAGTT
2216553 TTTGCT
1 TTTGCT
2216559 AACTAAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.11, G:0.18, T:0.64
Consensus pattern (11 bp):
TTTGCTTAGTT
Found at i:2226227 original size:1 final size:1
Alignment explanation
Indices: 2226223--2226317 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
2226213 CCAAATAAAC
* * * * * ** * *
2226223 AAAAAAAAGAAGAAAAAAAACAAAAAACAAAAAACAAAAAACCAAAAAAAAAAGAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
2226288 GAAAAAAAAACAAAAAACAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2226318 GGGTCCGGAT
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:2226240 original size:12 final size:11
Alignment explanation
Indices: 2226223--2226317 Score: 84
Period size: 12 Copynumber: 8.3 Consensus size: 11
2226213 CCAAATAAAC
2226223 AAAAAAAAGAA
1 AAAAAAAAGAA
*
2226234 GAAAAAAAACAA
1 -AAAAAAAAGAA
2226246 AAAACAAAA-AA
1 AAAA-AAAAGAA
* **
2226257 CAAAAAACCAA
1 AAAAAAAAGAA
2226268 AAAAAAAAGAA
1 AAAAAAAAGAA
2226279 AAAAAAGAAGAA
1 AAAAAA-AAGAA
*
2226291 AAAAAAACAAAA
1 AAAAAAA-AGAA
*
2226303 AACAAAAAACAA
1 AA-AAAAAAGAA
2226315 AAA
1 AAA
2226318 GGGTCCGGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
10 3 0.04
11 27 0.39
12 35 0.50
13 5 0.07
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:2226249 original size:7 final size:7
Alignment explanation
Indices: 2226207--2226317 Score: 115
Period size: 7 Copynumber: 15.7 Consensus size: 7
2226197 TCCTCCACAA
2226207 AAAAAACC
1 AAAAAA-C
2226215 AAATAAAC
1 AAA-AAAC
2226223 AAAAAA-
1 AAAAAAC
2226229 AAGAAGAA-
1 AA-AA-AAC
2226237 AAAAAAC
1 AAAAAAC
2226244 AAAAAAC
1 AAAAAAC
2226251 AAAAAAC
1 AAAAAAC
2226258 AAAAAACC
1 AAAAAA-C
2226266 AAAAAA-
1 AAAAAAC
2226272 AAAAGAA-
1 AAAA-AAC
*
2226279 AAAAAAG
1 AAAAAAC
*
2226286 AAGAAA-
1 AAAAAAC
2226292 AAAAAAC
1 AAAAAAC
2226299 AAAAAAC
1 AAAAAAC
2226306 AAAAAAC
1 AAAAAAC
2226313 AAAAA
1 AAAAA
2226318 GGGTCCGGAT
Statistics
Matches: 93, Mismatches: 2, Indels: 17
0.83 0.02 0.15
Matches are distributed among these distances:
6 15 0.16
7 57 0.61
8 18 0.19
9 3 0.03
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.01
Consensus pattern (7 bp):
AAAAAAC
Found at i:2227783 original size:29 final size:29
Alignment explanation
Indices: 2227744--2228063 Score: 225
Period size: 29 Copynumber: 10.7 Consensus size: 29
2227734 TCACCCTTCA
2227744 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
2227773 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2227802 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * * *
2227829 AAAGCCTACAAATCAATGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
2227859 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
2227888 AAAGTCCACAACTCCGTGACACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
2227918 TTTTGTAAGCTCACAACTCTGTAGCATTCTTTTTCC
1 -----AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
2227954 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2227986 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2228015 AAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
2228043 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
2228064 ACCTTCAAAA
Statistics
Matches: 238, Mismatches: 43, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
27 20 0.08
28 50 0.21
29 76 0.32
30 45 0.19
32 1 0.00
33 5 0.02
34 18 0.08
35 22 0.09
36 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:2227864 original size:86 final size:86
Alignment explanation
Indices: 2227738--2227898 Score: 234
Period size: 86 Copynumber: 1.9 Consensus size: 86
2227728 CATTCCTCAC
* * * * *
2227738 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCA
1 CCTTCAAAAGCCCACAAATCAATGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
2227803 AAGTCCACAAGTCAGTGGCAA
66 AAGTCCACAAGTCAGTGGCAA
* * *
2227824 CCTTC-AAAGCCTACAAATCAATGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCATCTTTTCC
1 CCTTCAAAAGCCCACAAATCAATGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
2227888 AAAGTCCACAA
65 AAAGTCCACAA
2227899 CTCCGTGACA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
85 18 0.27
86 48 0.73
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (86 bp):
CCTTCAAAAGCCCACAAATCAATGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
AAGTCCACAAGTCAGTGGCAA
Found at i:2227878 original size:57 final size:57
Alignment explanation
Indices: 2227744--2227898 Score: 159
Period size: 57 Copynumber: 2.7 Consensus size: 57
2227734 TCACCCTTCA
* * * * * *
2227744 AAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCCACAAATCAATGGCACCTTTTCC
* *
2227802 AAAGTCCACAAGTCAGTGGCAAC-CTTCAAAGCCTACAAATCAATGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAATGGCA-CCTTTTCC
* * * * *
2227859 GAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAA
1 AAAGCCCACAAGTCAGTGGCAACTCTT-CAAAGCCCACAA
2227899 CTCCGTGACA
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
56 21 0.27
57 25 0.32
58 23 0.29
59 10 0.13
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAATGGCACCTTTTCC
Found at i:2227967 original size:34 final size:35
Alignment explanation
Indices: 2227893--2227967 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
2227883 TTTCCAAAGT
*
2227893 CCACAACTCCGTGACACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTGACACTCTTTTTCCTTTGTAAGC
* * *
2227928 TCACAACTCTGT-AGCATTCTTTTTCCTTT-TAAGC
1 CCACAACTCCGTGA-CACTCTTTTTCCTTTGTAAGC
2227962 CCACAA
1 CCACAA
2227968 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 11 0.32
35 23 0.68
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (35 bp):
CCACAACTCCGTGACACTCTTTTTCCTTTGTAAGC
Found at i:2228026 original size:28 final size:28
Alignment explanation
Indices: 2227958--2228109 Score: 200
Period size: 28 Copynumber: 5.3 Consensus size: 28
2227948 TTTTCCTTTT
* *
2227958 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
2227988 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
2228016 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
2228044 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* *
2228072 AAGCACACAAGT-TGAT-GCAAACCTTTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTT-AA
2228101 AAGCCCACA
1 AAGCCCACA
2228110 CAAGTTGGTG
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
27 3 0.03
28 75 0.67
29 13 0.12
30 21 0.19
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:2228398 original size:149 final size:148
Alignment explanation
Indices: 2228129--2228411 Score: 467
Period size: 149 Copynumber: 1.9 Consensus size: 148
2228119 GGCGTCTTCT
*
2228129 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTAGC
1 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGTCCAATGTAGC
* ** * *
2228194 TGGCCTTGAATCAGCACATTGGCACTTCATGTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
66 TGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAATCAACAT
2228259 ATTGACGCCTTTGGCACC
131 ATTGACGCCTTTGGCACC
* * *
2228277 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGTCCAATGTAG
*
2228342 CTGGCCTTGAATCAGCACATTGGTACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAATCAACA
65 CTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAATCAACA
2228407 TATTG
130 TATTG
2228412 GCACCTTGTC
Statistics
Matches: 124, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
148 42 0.34
149 82 0.66
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (148 bp):
TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAATCAACAT
ATTGACGCCTTTGGCACC
Found at i:2228466 original size:48 final size:49
Alignment explanation
Indices: 2228129--2228451 Score: 393
Period size: 48 Copynumber: 6.6 Consensus size: 49
2228119 GGCGTCTTCT
* * *
2228129 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-GTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
2228177 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
2228225 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGCCTTTGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT--CATC
*
2228277 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
2228326 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGTACC-TCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
2228374 TTTAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTT-GTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
2228422 TTTAAGACCAATGTCGCCGGCCTTGAATCA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCA
2228452 ACACATTGTT
Statistics
Matches: 236, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
47 3 0.01
48 144 0.61
49 43 0.18
50 2 0.01
51 2 0.01
52 42 0.18
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:2229197 original size:13 final size:13
Alignment explanation
Indices: 2229179--2229206 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2229169 TACATAAAAT
2229179 ATTGTATCGATAC
1 ATTGTATCGATAC
2229192 ATTGTATCGATAC
1 ATTGTATCGATAC
2229205 AT
1 AT
2229207 AAGTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:2229197 original size:33 final size:32
Alignment explanation
Indices: 2229160--2229224 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2229150 TTTCAACGAT
2229160 TTGTATCGATACATAAAATATTGTATCGATACA
1 TTGTATCGATACAT-AAATATTGTATCGATACA
* *
2229193 TTGTATCGATACATAAGTTTTGTATCGATACA
1 TTGTATCGATACATAAATATTGTATCGATACA
2229225 ATTTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACATAAATATTGTATCGATACA
Found at i:2229329 original size:52 final size:52
Alignment explanation
Indices: 2229287--2229415 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
2229277 CACTGATCTT
*
2229287 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2229339 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2229391 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2229416 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2232697 original size:13 final size:13
Alignment explanation
Indices: 2232679--2232704 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2232669 CATGGTTCAA
2232679 TGTATCGATACAT
1 TGTATCGATACAT
2232692 TGTATCGATACAT
1 TGTATCGATACAT
2232705 GAAGAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2232700 original size:33 final size:33
Alignment explanation
Indices: 2232658--2232724 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2232648 CTATCACTAT
****
2232658 TTGTATCGATACATGGTTCAATGTATCGATACA
1 TTGTATCGATACATGAAGAAATGTATCGATACA
2232691 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATGAAGAAATGTATCGATACA
2232724 T
1 T
2232725 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGAAGAAATGTATCGATACA
Found at i:2234635 original size:13 final size:13
Alignment explanation
Indices: 2234617--2234642 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2234607 TAGACAAAGT
2234617 ATGTATCGATACA
1 ATGTATCGATACA
2234630 ATGTATCGATACA
1 ATGTATCGATACA
2234643 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2240976 original size:21 final size:20
Alignment explanation
Indices: 2240952--2240998 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
2240942 AAATCTTTTG
*
2240952 CAAAATAC-TTGTTTTTCACTT
1 CAAAATACATCGTTTTTCA--T
*
2240973 CAAATTACATCGTTTTTCAT
1 CAAAATACATCGTTTTTCAT
2240993 CAAAAT
1 CAAAAT
2240999 CACCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACATCGTTTTTCAT
Found at i:2243289 original size:20 final size:18
Alignment explanation
Indices: 2243259--2243300 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
2243249 GATCAAAGTG
2243259 TTTTATATTTTTCAAGAGC
1 TTTTATA-TTTTCAAGAGC
2243278 TTTTATTATTTTCAAGAGC
1 TTTTA-TATTTTCAAGAGC
2243297 TTTT
1 TTTT
2243301 GTTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTTATATTTTCAAGAGC
Found at i:2243564 original size:308 final size:308
Alignment explanation
Indices: 2243006--2243589 Score: 1159
Period size: 308 Copynumber: 1.9 Consensus size: 308
2242996 ATTAGCTTGT
2243006 AACGGCTAGTAACGGCTATATTTTCAAATGCAAGTATCGATACATCAAAAATTGTATCGATACAT
1 AACGGCTAGTAACGGCTATATTTTCAAATGCAAGTATCGATACATCAAAAATTGTATCGATACAT
2243071 TCACACGGGAAATCATTAAAATAAGCTCCAACAAGTCAATAACGGCTATAAAGTCCACCAATCAA
66 TCACACGGGAAATCATTAAAATAAGCTCCAACAAGTCAATAACGGCTATAAAGTCCACCAATCAA
2243136 ACTCCAACGGCTACAACAACATTGAAGCCTATAAATAAGAGCTTCAAGCAGCAAAACACAACAAG
131 ACTCCAACGGCTACAACAACATTGAAGCCTATAAATAAGAGCTTCAAGCAGCAAAACACAACAAG
2243201 AGAGAAGTAGAACCAAGCAAGAAACATCTAGTATTCAAAGTTTTCAAAGATCAAAGTGTTTTATA
196 AGAGAAGTAGAACCAAGCAAGAAACATCTAGTATTCAAAGTTTTCAAAGATCAAAGTGTTTTATA
2243266 TTTTTCAAGAGCTTTTATTATTTTCAAGAGCTTTTGTTTATATTTTTC
261 TTTTTCAAGAGCTTTTATTATTTTCAAGAGCTTTTGTTTATATTTTTC
2243314 AACGGCTAGTAACGGCTATATTTTCAAATGCAAGTATCGATACATCAAAAATTGTATCGATACAT
1 AACGGCTAGTAACGGCTATATTTTCAAATGCAAGTATCGATACATCAAAAATTGTATCGATACAT
*
2243379 TCACCCGGGAAATCATTAAAATAAGCTCCAACAAGTCAATAACGGCTATAAAGTCCACCAATCAA
66 TCACACGGGAAATCATTAAAATAAGCTCCAACAAGTCAATAACGGCTATAAAGTCCACCAATCAA
2243444 ACTCCAACGGCTACAACAACATTGAAGCCTATAAATAAGAGCTTCAAGCAGCAAAACACAACAAG
131 ACTCCAACGGCTACAACAACATTGAAGCCTATAAATAAGAGCTTCAAGCAGCAAAACACAACAAG
2243509 AGAGAAGTAGAACCAAGCAAGAAACATCTAGTATTCAAAGTTTTCAAAGATCAAAGTGTTTTATA
196 AGAGAAGTAGAACCAAGCAAGAAACATCTAGTATTCAAAGTTTTCAAAGATCAAAGTGTTTTATA
2243574 TTTTTCAAGAGCTTTT
261 TTTTTCAAGAGCTTTT
2243590 GTTCATATTG
Statistics
Matches: 275, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 275 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (308 bp):
AACGGCTAGTAACGGCTATATTTTCAAATGCAAGTATCGATACATCAAAAATTGTATCGATACAT
TCACACGGGAAATCATTAAAATAAGCTCCAACAAGTCAATAACGGCTATAAAGTCCACCAATCAA
ACTCCAACGGCTACAACAACATTGAAGCCTATAAATAAGAGCTTCAAGCAGCAAAACACAACAAG
AGAGAAGTAGAACCAAGCAAGAAACATCTAGTATTCAAAGTTTTCAAAGATCAAAGTGTTTTATA
TTTTTCAAGAGCTTTTATTATTTTCAAGAGCTTTTGTTTATATTTTTC
Found at i:2246236 original size:13 final size:13
Alignment explanation
Indices: 2246218--2246253 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2246208 TGCTCTTTGT
2246218 ATCGATACATTGC
1 ATCGATACATTGC
* *
2246231 ATCGATACAATGT
1 ATCGATACATTGC
2246244 ATCGATACAT
1 ATCGATACAT
2246254 CAGTTACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (13 bp):
ATCGATACATTGC
Found at i:2249635 original size:256 final size:256
Alignment explanation
Indices: 2249180--2249694 Score: 1030
Period size: 256 Copynumber: 2.0 Consensus size: 256
2249170 TGTTTTCGAA
2249180 ACAATTCATATGAAACCTTTAAATTTAAAAAAAAAACCAAATCACTCCCCCTTTTGGTTCATCCA
1 ACAATTCATATGAAACCTTTAAATTTAAAAAAAAAACCAAATCACTCCCCCTTTTGGTTCATCCA
2249245 TTCTTGAGCTTACAATGCCTTTACCAATCCCCAAGGAGTCATATCATTTCAAAACCAATATCAAA
66 TTCTTGAGCTTACAATGCCTTTACCAATCCCCAAGGAGTCATATCATTTCAAAACCAATATCAAA
2249310 GTTCATAGTAACTAACACCTATCTGAGGAGGTCAAGCCTTAGAAAATCCTAAAACCTAGCAGGGT
131 GTTCATAGTAACTAACACCTATCTGAGGAGGTCAAGCCTTAGAAAATCCTAAAACCTAGCAGGGT
2249375 GGACAAACCGTACAAACTCATTAAGATTTCCATCAGAACCACCACCAATGCATTCTTCGTT
196 GGACAAACCGTACAAACTCATTAAGATTTCCATCAGAACCACCACCAATGCATTCTTCGTT
2249436 ACAATTCATATGAAACCTTTAAATTTAAAAAAAAAACCAAATCACTCCCCCTTTTGGTTCATCCA
1 ACAATTCATATGAAACCTTTAAATTTAAAAAAAAAACCAAATCACTCCCCCTTTTGGTTCATCCA
2249501 TTCTTGAGCTTACAATGCCTTTACCAATCCCCAAGGAGTCATATCATTTCAAAACCAATATCAAA
66 TTCTTGAGCTTACAATGCCTTTACCAATCCCCAAGGAGTCATATCATTTCAAAACCAATATCAAA
2249566 GTTCATAGTAACTAACACCTATCTGAGGAGGTCAAGCCTTAGAAAATCCTAAAACCTAGCAGGGT
131 GTTCATAGTAACTAACACCTATCTGAGGAGGTCAAGCCTTAGAAAATCCTAAAACCTAGCAGGGT
2249631 GGACAAACCGTACAAACTCATTAAGATTTCCATCAGAACCACCACCAATGCATTCTTCGTT
196 GGACAAACCGTACAAACTCATTAAGATTTCCATCAGAACCACCACCAATGCATTCTTCGTT
2249692 ACA
1 ACA
2249695 GCGCAGCATT
Statistics
Matches: 259, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
256 259 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.26
Consensus pattern (256 bp):
ACAATTCATATGAAACCTTTAAATTTAAAAAAAAAACCAAATCACTCCCCCTTTTGGTTCATCCA
TTCTTGAGCTTACAATGCCTTTACCAATCCCCAAGGAGTCATATCATTTCAAAACCAATATCAAA
GTTCATAGTAACTAACACCTATCTGAGGAGGTCAAGCCTTAGAAAATCCTAAAACCTAGCAGGGT
GGACAAACCGTACAAACTCATTAAGATTTCCATCAGAACCACCACCAATGCATTCTTCGTT
Found at i:2256370 original size:13 final size:13
Alignment explanation
Indices: 2256352--2256378 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2256342 AAATGCTGCC
2256352 TTGTATCGATACA
1 TTGTATCGATACA
2256365 TTGTATCGATACA
1 TTGTATCGATACA
2256378 T
1 T
2256379 GTTCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2256415 original size:21 final size:20
Alignment explanation
Indices: 2256364--2256419 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
2256354 GTATCGATAC
**
2256364 ATTGTATCGATACATGTTCA
1 ATTGTATCGATACATGGACA
*
2256384 A-TGTATTGATACATGGACAA
1 ATTGTATCGATACATGGAC-A
2256404 ATTGTATCGATACATG
1 ATTGTATCGATACATG
2256420 AAATTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:2256485 original size:13 final size:13
Alignment explanation
Indices: 2256464--2256494 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2256454 CGATATATGG
*
2256464 TACAATGTATCGA
1 TACATTGTATCGA
2256477 TACATTGTATCGA
1 TACATTGTATCGA
2256490 TACAT
1 TACAT
2256495 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:2256490 original size:33 final size:32
Alignment explanation
Indices: 2256448--2256514 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
2256438 CTATCACTAT
*
2256448 TTGTATCGATATATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
2256481 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
2256514 T
1 T
2256515 AGCTTGTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:2262525 original size:19 final size:19
Alignment explanation
Indices: 2262493--2262533 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2262483 TTGACGTTTG
2262493 TTATGTTGTATGAT-TGAA
1 TTATGTTGTATGATATGAA
*
2262511 TTATGGTTGTTTGATATGAA
1 TTAT-GTTGTATGATATGAA
2262531 TTA
1 TTA
2262534 GGGTCTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (19 bp):
TTATGTTGTATGATATGAA
Found at i:2264417 original size:19 final size:19
Alignment explanation
Indices: 2264393--2264451 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
2264383 AAAGGGGGAA
2264393 AAGATAATTGTTTAAGGGG
1 AAGATAATTGTTTAAGGGG
2264412 AAGATAATTGTTTAAGGGG
1 AAGATAATTGTTTAAGGGG
* * *
2264431 GAGATCATCGTTTGAAGGGG
1 AAGATAATTGTTT-AAGGGG
2264451 A
1 A
2264452 GAATTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 29 0.83
20 6 0.17
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (19 bp):
AAGATAATTGTTTAAGGGG
Found at i:2270373 original size:31 final size:31
Alignment explanation
Indices: 2270335--2270398 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
2270325 TATAGATACA
*
2270335 CAATACATAAACACATTGCATAATTGATGTT
1 CAATACATAAACACATTGCATAATTGATATT
* *
2270366 CAATACATAAACATATTGTATAATTGATATT
1 CAATACATAAACACATTGCATAATTGATATT
2270397 CA
1 CA
2270399 CAGTGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (31 bp):
CAATACATAAACACATTGCATAATTGATATT
Found at i:2272582 original size:24 final size:24
Alignment explanation
Indices: 2272540--2272601 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
2272530 TAATTAATAA
2272540 ATTATTTTATATAAATTTTGATATAT
1 ATTA-TTTATATAAATTTT-ATATAT
* * *
2272566 -TTATTTATATTATTTTTATATGT
1 ATTATTTATATAAATTTTATATAT
*
2272589 ATTATTTTTATAA
1 ATTATTTATATAA
2272602 CAAATAACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.17
24 22 0.73
25 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
ATTATTTATATAAATTTTATATAT
Found at i:2280252 original size:33 final size:33
Alignment explanation
Indices: 2280215--2280281 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2280205 TTCAACGATT
2280215 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2280248 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2280281 T
1 T
2280282 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2280253 original size:13 final size:13
Alignment explanation
Indices: 2280235--2280259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2280225 CATAAAATGT
2280235 TGTATCGATACAA
1 TGTATCGATACAA
2280248 TGTATCGATACA
1 TGTATCGATACA
2280260 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2280343 original size:13 final size:13
Alignment explanation
Indices: 2280325--2280349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2280315 ATTACTCACA
2280325 TGTATCGATACAT
1 TGTATCGATACAT
2280338 TGTATCGATACA
1 TGTATCGATACA
2280350 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2280400 original size:52 final size:50
Alignment explanation
Indices: 2280338--2280478 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
2280328 ATCGATACAT
*
2280338 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2280390 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
2280442 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATT--ATGTATCGATACATGCAG
2280479 ATAAATTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2280486 original size:52 final size:52
Alignment explanation
Indices: 2280358--2280478 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2280348 CACTGATCTT
*
2280358 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2280410 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2280462 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
2280479 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2287767 original size:19 final size:19
Alignment explanation
Indices: 2287729--2287768 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2287719 TAATCTTCAC
* *
2287729 AAAAAAAAAAAGATGCAAA
1 AAAAAAAAAAAAAAGCAAA
*
2287748 AAAAAAAAAAAAAAGGAAA
1 AAAAAAAAAAAAAAGCAAA
2287767 AA
1 AA
2287769 CCCCTTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAAAAAGCAAA
Found at i:2288815 original size:35 final size:34
Alignment explanation
Indices: 2288735--2288998 Score: 256
Period size: 33 Copynumber: 7.6 Consensus size: 34
2288725 ATTTTGTCTC
* * *
2288735 AAAGTCCACGACTCAGTGGCA-T-TTTTTC-TTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
2288766 AAAGCCCATAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
* * *
2288802 -AAGTCCACAACTCCGTGGCA-TCTTTCTCCCTTCCT
1 AAAGCCCACAACTCCGTGGCACTCTTT-T-TCTT-TT
*
2288837 AAAGCCCACACAACTCCGTGGCAAC-CTTCTTCTTTT
1 AAAG-CC-CACAACTCCGTGGC-ACTCTTTTTCTTTT
*
2288873 CAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
**
2288907 AAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTT
1 AAAGCCCACAACTCCGTGGCACTC-TTTTT-CTTTT
2288943 CAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
2288977 AAAGCCCACAACTCTGTGGCAC
1 AAAGCCCACAACTCCGTGGCAC
2288999 CGACGACTTT
Statistics
Matches: 197, Mismatches: 18, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
31 17 0.09
32 1 0.01
33 46 0.23
34 27 0.14
35 44 0.22
36 15 0.08
37 28 0.14
38 15 0.08
39 4 0.02
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
Found at i:2288942 original size:70 final size:70
Alignment explanation
Indices: 2288733--2289197 Score: 444
Period size: 70 Copynumber: 6.4 Consensus size: 70
2288723 GCATTTTGTC
* * * * *
2288733 TCAAAGTCCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCATAACTCCGTGGCACTCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
2288796 CCTTT
66 CCTTT
* * * *
2288801 T--AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAACTCCGTGGCAAC-C
1 TCAAAGCCCACAACTCCGTGGCACCTTT-T-TCTT-TTAAAG-CC-CACAACTCCGTGGC-ACTC
*
2288863 TTCTT--CTTT
60 TTTTTCCCTTT
* ** *
2288872 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
2288937 CCTTT
66 CCTTT
* *
2288942 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCGACGACT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGG---C-AC-TCT
*
2289007 TTGTGGCACTCTCTTT
61 TT-T-----TCCCTTT
*
2289023 CTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACT
1 -TC-----AAAGCCCACAACTCCGTGGCACCTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACT
2289088 CTTTTTCCCTTT
59 CTTTTTCCCTTT
* *
2289100 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
2289165 CCTTT
66 CCTTT
* * *
2289170 T--AAGTCCACAACTCTGTGGCATCTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTT
2289198 TCCTTCCCAA
Statistics
Matches: 335, Mismatches: 31, Indels: 62
0.78 0.07 0.14
Matches are distributed among these distances:
66 18 0.05
67 5 0.01
68 42 0.13
69 3 0.01
70 101 0.30
71 40 0.12
72 3 0.01
73 41 0.12
74 4 0.01
75 4 0.01
76 3 0.01
77 6 0.02
81 5 0.01
82 3 0.01
83 4 0.01
84 2 0.01
85 1 0.00
87 28 0.08
88 22 0.07
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (70 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
CCTTT
Found at i:2289154 original size:158 final size:157
Alignment explanation
Indices: 2288867--2289156 Score: 508
Period size: 158 Copynumber: 1.8 Consensus size: 157
2288857 GCAACCTTCT
* **
2288867 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCGTTTAAAGCCCACAACTCCGTGGCACTCT
*
2288932 TTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
66 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
2288997 ACCGACGACTTTGTGGCACTCTCTTTC
131 ACCGACGACTTTGTGGCACTCTCTTTC
* *
2289024 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTC
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTT-CGTTTAAAGCCCACAACTCCGTGGCACTC
*
2289089 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCTGTGG
65 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGG
2289154 CAC
130 CAC
2289157 TCTTTTTCCC
Statistics
Matches: 125, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
157 33 0.26
158 92 0.74
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (157 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCGTTTAAAGCCCACAACTCCGTGGCACTCT
TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
ACCGACGACTTTGTGGCACTCTCTTTC
Found at i:2289236 original size:104 final size:102
Alignment explanation
Indices: 2289027--2289215 Score: 263
Period size: 104 Copynumber: 1.8 Consensus size: 102
2289017 CTCTTTCTCT
*
2289027 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTT
** *
2289092 TTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
66 TTCCCTTCCCAAAGCCCACAACTCCGTGGCAC--TCTTC
* * * *
2289131 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCTGTGGCA-TCTT
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTT
*
2289195 TTTTCCTTCCCAAAGCCCACA
65 TTTCCCTTCCCAAAGCCCACA
2289216 CAAGTCGGTG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
104 47 0.62
105 29 0.38
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.34
Consensus pattern (102 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTT
TTCCCTTCCCAAAGCCCACAACTCCGTGGCACTCTTC
Found at i:2289243 original size:104 final size:102
Alignment explanation
Indices: 2289031--2289248 Score: 251
Period size: 104 Copynumber: 2.1 Consensus size: 102
2289021 TTCTCTTTTT
*
2289031 AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
** * **
2289096 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
66 CTTCCCAAAGCCCACAACTCCGTGGCAC--TCTTCTTCC
* * * * *
2289135 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCTGTGGCA-TCTTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
* *
2289199 CCTTCCCAAAGCCCACACAAGTCGGTGGCAAC-CTTCTTCC
65 CCTTCCCAAAG-CC-CACAACTCCGTGGC-ACTCTTCTTCC
2289239 AAAGCCCACA
1 AAAGCCCACA
2289249 CAAGTCGGTG
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
104 52 0.54
105 31 0.32
106 12 0.12
107 2 0.02
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (102 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
CTTCCCAAAGCCCACAACTCCGTGGCACTCTTCTTCC
Found at i:2289387 original size:49 final size:49
Alignment explanation
Indices: 2289266--2289735 Score: 595
Period size: 49 Copynumber: 9.7 Consensus size: 49
2289256 GTGGCAACCC
* *
2289266 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CAT
* *
2289318 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2289367 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2289416 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2289465 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2289514 CTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2289557 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
2289606 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2289649 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CAT
* *
2289701 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAC
2289736 GTTGACATCC
Statistics
Matches: 366, Mismatches: 37, Indels: 30
0.85 0.09 0.07
Matches are distributed among these distances:
43 77 0.21
45 2 0.01
47 1 0.00
49 211 0.58
50 3 0.01
52 72 0.20
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:2289445 original size:98 final size:98
Alignment explanation
Indices: 2289266--2289801 Score: 745
Period size: 98 Copynumber: 5.5 Consensus size: 98
2289256 GTGGCAACCC
* * *
2289266 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTCCAAT
2289331 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
63 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2289367 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
2289432 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
*
2289465 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
2289530 GCTGGCCTTGACTCAGCACATTGGCA----C--
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2289557 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2289622 GCTGGCCTTGAATCAGCACATTGGCA----C--
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
* * *
2289649 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
* * *
2289714 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
63 GTAGCTGGCCTTGACTCAGCACATTGGCA-CC----T-TCAT
* * * *
2289756 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
2289802 TATCACTTTT
Statistics
Matches: 403, Mismatches: 17, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
92 129 0.32
94 6 0.01
95 42 0.10
98 142 0.35
99 3 0.01
101 40 0.10
105 6 0.01
107 35 0.09
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (98 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
Found at i:2289579 original size:43 final size:44
Alignment explanation
Indices: 2289513--2289691 Score: 236
Period size: 43 Copynumber: 4.0 Consensus size: 44
2289503 GGCATCTTCA
* * * *
2289513 TCTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
2289557 -CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* *
2289604 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 -TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
2289649 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
2289692 ATTTTCCATC
Statistics
Matches: 119, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
43 78 0.66
45 1 0.01
47 1 0.01
49 39 0.33
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:2289585 original size:92 final size:92
Alignment explanation
Indices: 2289465--2289735 Score: 470
Period size: 92 Copynumber: 2.9 Consensus size: 92
2289455 GCACCTTCAT
*
2289465 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2289530 GCTGGCCTTGACTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
2289557 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
2289622 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
2289649 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
2289714 GTAGCTGGCCTTGAATCAGCAC
63 GTAGCTGGCCTTGAATCAGCAC
2289736 GTTGACATCC
Statistics
Matches: 171, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
92 129 0.75
94 5 0.03
95 37 0.22
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2289778 original size:55 final size:55
Alignment explanation
Indices: 2289649--2290032 Score: 282
Period size: 67 Copynumber: 6.7 Consensus size: 55
2289639 ACATTGGCAC
* *
2289649 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2289701 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2289756 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
2289820 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2289872 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2289927 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
2289992 AT
54 AT
*
2289994 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2290033 GCTTATCATC
Statistics
Matches: 259, Mismatches: 40, Indels: 52
0.74 0.11 0.15
Matches are distributed among these distances:
49 36 0.14
50 1 0.00
52 42 0.16
54 8 0.03
55 65 0.25
56 2 0.01
57 2 0.01
58 2 0.01
59 1 0.00
61 8 0.03
62 6 0.02
63 5 0.02
64 7 0.03
66 4 0.02
67 70 0.27
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:2289938 original size:171 final size:172
Alignment explanation
Indices: 2289649--2290034 Score: 711
Period size: 171 Copynumber: 2.2 Consensus size: 172
2289639 ACATTGGCAC
*
2289649 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTTCCATCTTTAAGTTCAAT
2289714 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
64 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
2289779 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
129 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
2289823 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT-CATCTTTAAGTTCAATGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCCATCTTTAAGTTCAATGT
2289887 AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
66 AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
2289952 GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
*
2289994 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
2290035 TTATCATCTC
Statistics
Matches: 207, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
171 164 0.79
172 5 0.02
174 38 0.18
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (172 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCCATCTTTAAGTTCAATGT
AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:2290875 original size:33 final size:33
Alignment explanation
Indices: 2290838--2290904 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2290828 TTCAACGATT
2290838 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2290871 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2290904 T
1 T
2290905 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2290876 original size:13 final size:13
Alignment explanation
Indices: 2290858--2290882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2290848 CATAAAATGT
2290858 TGTATCGATACAA
1 TGTATCGATACAA
2290871 TGTATCGATACA
1 TGTATCGATACA
2290883 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2290966 original size:13 final size:13
Alignment explanation
Indices: 2290948--2290972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2290938 ATTACTCACA
2290948 TGTATCGATACAT
1 TGTATCGATACAT
2290961 TGTATCGATACA
1 TGTATCGATACA
2290973 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2291023 original size:52 final size:50
Alignment explanation
Indices: 2290961--2291101 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
2290951 ATCGATACAT
*
2290961 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2291013 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
2291065 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATT--ATGTATCGATACATGCAG
2291102 ATAAATTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2291109 original size:52 final size:52
Alignment explanation
Indices: 2290981--2291101 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2290971 CACTGATCTT
*
2290981 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2291033 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2291085 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
2291102 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2297470 original size:17 final size:17
Alignment explanation
Indices: 2297448--2297484 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2297438 GAGTCAGCCT
* *
2297448 TAACCTTAGCTTGTTTA
1 TAACCTAAGCTTATTTA
2297465 TAACCTAAGCTTATTTA
1 TAACCTAAGCTTATTTA
2297482 TAA
1 TAA
2297485 GTTGGAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (17 bp):
TAACCTAAGCTTATTTA
Found at i:2298520 original size:20 final size:20
Alignment explanation
Indices: 2298479--2298529 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2298469 CCATTGTTTA
* *
2298479 TATCGATACATAGCATAATG
1 TATCGATACATAGAAGAATG
2298499 TATCGATACAT-GAAGAATTG
1 TATCGATACATAGAAGAA-TG
*
2298519 TATCAATACAT
1 TATCGATACAT
2298530 TGTCCCAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (20 bp):
TATCGATACATAGAAGAATG
Found at i:2299874 original size:19 final size:18
Alignment explanation
Indices: 2299839--2299882 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
2299829 AAAAATTAGT
2299839 TAAAAATAACATGAACATGA
1 TAAAAATAACA-GAACAT-A
2299859 TAAAAATACACA-AACATA
1 TAAAAATA-ACAGAACATA
2299877 TAAAAA
1 TAAAAA
2299883 AATAAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 5 0.22
20 8 0.35
21 3 0.13
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (18 bp):
TAAAAATAACAGAACATA
Found at i:2300017 original size:10 final size:11
Alignment explanation
Indices: 2299998--2300041 Score: 65
Period size: 10 Copynumber: 4.2 Consensus size: 11
2299988 TCTTTCGTCC
2299998 TTTTCTTTCTT
1 TTTTCTTTCTT
*
2300009 TTTTC-TTCTC
1 TTTTCTTTCTT
2300019 TTTTCTTT-TT
1 TTTTCTTTCTT
2300029 TTTTCTTTCTT
1 TTTTCTTTCTT
2300040 TT
1 TT
2300042 CCTTCATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 18 0.62
11 11 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:2300023 original size:17 final size:14
Alignment explanation
Indices: 2299998--2300041 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 14
2299988 TCTTTCGTCC
2299998 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
2300012 TCTTCTCTTTTCTTTTT
1 T-TT-TC-TTTCTTTTT
2300029 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
2300042 CCTTCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.33
15 4 0.15
16 4 0.15
17 10 0.37
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:2300023 original size:21 final size:19
Alignment explanation
Indices: 2299997--2300042 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
2299987 TTCTTTCGTC
2299997 CTTTTCTTTCTTTTTTCTTCT
1 CTTTTCTTT-TTTTTTCTT-T
2300018 CTTTTCTTTTTTTTTCTTT
1 CTTTTCTTTTTTTTTCTTT
2300037 CTTTTC
1 CTTTTC
2300043 CTTCATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 7 0.28
20 9 0.36
21 9 0.36
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
CTTTTCTTTTTTTTTCTTT
Found at i:2300087 original size:12 final size:12
Alignment explanation
Indices: 2300070--2300140 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
2300060 CTTTCATTCC
2300070 TCTTTTTCTCTT
1 TCTTTTTCTCTT
2300082 TCTTTTT-TCTTT
1 TCTTTTTCTC-TT
*
2300094 TCATTTTCT-TT
1 TCTTTTTCTCTT
* *
2300105 T-TCTTTCCCTT
1 TCTTTTTCTCTT
2300116 T-TTTTTCTTTCTT
1 TCTTTTTC--TCTT
*
2300129 CCTTTTTCTCTT
1 TCTTTTTCTCTT
2300141 CCAACTAGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
10 4 0.09
11 13 0.28
12 19 0.41
13 4 0.09
14 6 0.13
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTTTTCTCTT
Found at i:2304082 original size:20 final size:21
Alignment explanation
Indices: 2304057--2304110 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
2304047 CATTTTAGGC
2304057 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTGT
*
2304077 ATGTATCGATACATTTACTGT
1 ATGTATCGATACATTCACTGT
* *
2304098 TTGTATCAATACA
1 ATGTATCGATACA
2304111 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTGT
Found at i:2304831 original size:52 final size:52
Alignment explanation
Indices: 2304730--2304862 Score: 167
Period size: 52 Copynumber: 2.5 Consensus size: 52
2304720 CAATGTCCAG
* *
2304730 ATTCAAGGCCTACAACATTGGACTTCAAAGATAAAAAGAGTGCCAATGTGCTA
1 ATTCAAGGCCAACGACATTGGACTT-AAAGATAAAAAGAGTGCCAATGTGCTA
* * * * *
2304783 ATTCATGGCCAGCGACATTGGACTTAAAGATAAGAATAGTGCCAATGTGCTG
1 ATTCAAGGCCAACGACATTGGACTTAAAGATAAAAAGAGTGCCAATGTGCTA
* * *
2304835 ATTGAAGGCCAATGACATTGGGCTTAAA
1 ATTCAAGGCCAACGACATTGGACTTAAA
2304863 AAATGCCAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
52 47 0.69
53 21 0.31
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (52 bp):
ATTCAAGGCCAACGACATTGGACTTAAAGATAAAAAGAGTGCCAATGTGCTA
Found at i:2305164 original size:32 final size:32
Alignment explanation
Indices: 2305128--2305223 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 32
2305118 TGGAAGGAGA
2305128 TGCCACCAATTTGTGTGGGCTTTTGA-GAAGGT
1 TGCCACCAATTTGTGTGGGC-TTTGAGGAAGGT
2305160 TGCCACCAATTTGTGTGGGCTTTGAGGAAGGT
1 TGCCACCAATTTGTGTGGGCTTTGAGGAAGGT
* * **
2305192 TACCACTAGCTTGTGTGGGCTTTGAGGAAGGT
1 TGCCACCAATTTGTGTGGGCTTTGAGGAAGGT
2305224 GAAAGCTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 5 0.08
32 54 0.92
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (32 bp):
TGCCACCAATTTGTGTGGGCTTTGAGGAAGGT
Found at i:2305993 original size:33 final size:33
Alignment explanation
Indices: 2305956--2306019 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
2305946 GTTACAAGCT
2305956 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
*
2305989 ATGTATTGATACATTGTACCATGTATCGATA
1 ATGTATCGATACATTGTACCATGTATCGATA
2306020 TAAATAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:2306445 original size:33 final size:33
Alignment explanation
Indices: 2306401--2306552 Score: 207
Period size: 33 Copynumber: 4.6 Consensus size: 33
2306391 CAGAAGGTTA
*
2306401 CCACCAGCTTGTGTGGGCTTTGGAAAAAAG-TTG
1 CCACCAACTTGTGTGGGCTTTGG-AAAAAGCTTG
* * *
2306434 CCACCAACTTGTGTGGGCTTTTGAAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAAAGCTTG
** * * *
2306467 GTACCGACCTGTGTGGGCTTTGGAAAAAGCTTA
1 CCACCAACTTGTGTGGGCTTTGGAAAAAGCTTG
2306500 CCACCAACTTGTGTGGGCTTTGGAAAAAGCTTG
1 CCACCAACTTGTGTGGGCTTTGGAAAAAGCTTG
2306533 CCACCAACTTGTGTGGGCTT
1 CCACCAACTTGTGTGGGCTT
2306553 GTGAAGGAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
32 5 0.05
33 97 0.95
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (33 bp):
CCACCAACTTGTGTGGGCTTTGGAAAAAGCTTG
Found at i:2306680 original size:28 final size:30
Alignment explanation
Indices: 2306620--2306681 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
2306610 CTTGTGGGCT
** *
2306620 TTTGAAGAAGGTTGCCACTGACTTATGGAC
1 TTTGAAGAAGGTTGCCACTGACAAAGGGAC
*
2306650 TTTGAAG-AGG-TGCCACTGACAAAGGGTC
1 TTTGAAGAAGGTTGCCACTGACAAAGGGAC
2306678 TTTG
1 TTTG
2306682 GGAAAGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 18 0.64
29 3 0.11
30 7 0.25
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (30 bp):
TTTGAAGAAGGTTGCCACTGACAAAGGGAC
Found at i:2306715 original size:14 final size:14
Alignment explanation
Indices: 2306696--2306765 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
2306686 AGGATTCATA
2306696 TTGATGAAAATTTC
1 TTGATGAAAATTTC
*
2306710 TTGATG-AAGTTTC
1 TTGATGAAAATTTC
*
2306723 -TGA--CAAATGTTC
1 TTGATGAAAAT-TTC
* *
2306735 TCGAT-AAAAGTTC
1 TTGATGAAAATTTC
*
2306748 TTGATGATAATTTC
1 TTGATGAAAATTTC
2306762 TTGA
1 TTGA
2306766 CAAAGGCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
11 3 0.07
12 6 0.14
13 15 0.35
14 19 0.44
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (14 bp):
TTGATGAAAATTTC
Found at i:2308211 original size:20 final size:19
Alignment explanation
Indices: 2308186--2308267 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 19
2308176 ACTGCCAAGG
*
2308186 AAATGTATCGATACATTAGT
1 AAATGTATCGATACATT-CT
* * *
2308206 AAATGTATTGATCCATGTTT
1 AAATGTATCGATACAT-TCT
2308226 ACAATTGTATCGATACATTTCT
1 A-AA-TGTATCGATACA-TTCT
* *
2308248 CATTGTATCGATACATTCT
1 AAATGTATCGATACATTCT
2308267 A
1 A
2308268 GGCTTTTGAC
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
19 4 0.08
20 28 0.57
21 4 0.08
22 12 0.24
23 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (19 bp):
AAATGTATCGATACATTCT
Found at i:2313327 original size:3 final size:3
Alignment explanation
Indices: 2313313--2313344 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2313303 CATCAAGGAC
*
2313313 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2313345 CTCAGATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:2317909 original size:13 final size:13
Alignment explanation
Indices: 2317891--2317915 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2317881 CATCATTCTC
2317891 TGTATCGATACAT
1 TGTATCGATACAT
2317904 TGTATCGATACA
1 TGTATCGATACA
2317916 CTGTTTCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2318395 original size:20 final size:21
Alignment explanation
Indices: 2318363--2318405 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2318353 CCCCTAGGCA
*
2318363 GCACCCACCAGGTCGCGACCG
1 GCACCCACCAGGTCGCAACCG
2318384 GCACCC-CCAGGTCGCAACCG
1 GCACCCACCAGGTCGCAACCG
2318404 GC
1 GC
2318406 CAGCCCCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.19, C:0.49, G:0.28, T:0.05
Consensus pattern (21 bp):
GCACCCACCAGGTCGCAACCG
Found at i:2319947 original size:19 final size:20
Alignment explanation
Indices: 2319923--2319973 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2319913 TAACCAAACT
**
2319923 TGTATCGATACA-CACAGTA
1 TGTATCGATACACCACAAAA
*
2319942 TGTATCGATACACCATAAAA
1 TGTATCGATACACCACAAAA
2319962 TGTATCGATACA
1 TGTATCGATACA
2319974 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCACAAAA
Found at i:2324621 original size:34 final size:35
Alignment explanation
Indices: 2324583--2324649 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2324573 CCTTACAACA
2324583 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2324617 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2324650 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2325138 original size:13 final size:13
Alignment explanation
Indices: 2325120--2325144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2325110 CTATTTATGA
2325120 TGTATCGATACAC
1 TGTATCGATACAC
2325133 TGTATCGATACA
1 TGTATCGATACA
2325145 TGAATAGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2325225 original size:45 final size:47
Alignment explanation
Indices: 2325117--2325231 Score: 132
Period size: 45 Copynumber: 2.5 Consensus size: 47
2325107 ATACTATTTA
* *
2325117 TGATGTATCGATACACTG--TA-TCGATACATGAATAGTAATGTACAG
1 TGATGTATCGATACA-TGAATAGTCGATACATGAACAGTAATGAACAG
* *
2325162 TGATTTTTATCGATACATGAATAGT-GATACGTGAACAGT-ATGAACAG
1 TGA--TGTATCGATACATGAATAGTCGATACATGAACAGTAATGAACAG
2325209 TGATGTATCGATACATGAATAGT
1 TGATGTATCGATACATGAATAGT
2325232 AATGAACAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
45 22 0.37
46 2 0.03
47 21 0.35
48 14 0.23
49 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (47 bp):
TGATGTATCGATACATGAATAGTCGATACATGAACAGTAATGAACAG
Found at i:2325382 original size:20 final size:20
Alignment explanation
Indices: 2325320--2325389 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
2325310 GCCAATGACA
2325320 TGTATCGATACATATT-ATG
1 TGTATCGATACATATTAATG
* *
2325339 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
2325359 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
2325379 TGTATCGATAC
1 TGTATCGATAC
2325390 TTTTCAGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 28 0.65
21 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:2327475 original size:13 final size:13
Alignment explanation
Indices: 2327457--2327495 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2327447 ACAGCATTCT
2327457 TTGTATCGATACA
1 TTGTATCGATACA
*
2327470 TTGTATTGATACA
1 TTGTATCGATACA
* *
2327483 CTGTATCAATACA
1 TTGTATCGATACA
2327496 GGGGGATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2330058 original size:13 final size:13
Alignment explanation
Indices: 2330040--2330064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2330030 ACACACAGTA
2330040 TGTATCGATACAT
1 TGTATCGATACAT
2330053 TGTATCGATACA
1 TGTATCGATACA
2330065 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2330061 original size:32 final size:33
Alignment explanation
Indices: 2330020--2330086 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
2330010 GTAGCCAAAC
**
2330020 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
2330052 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
2330085 TT
1 TT
2330087 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:2331056 original size:22 final size:21
Alignment explanation
Indices: 2331035--2331074 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2331025 AGTGTTAAAT
*
2331035 TATTTTACTAAGGGGGAGAAA
1 TATTTGACTAAGGGGGAGAAA
* *
2331056 TGTTTGATTAAGGGGGAGA
1 TATTTGACTAAGGGGGAGA
2331075 GAAAAGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.30
Consensus pattern (21 bp):
TATTTGACTAAGGGGGAGAAA
Found at i:2331671 original size:20 final size:21
Alignment explanation
Indices: 2331646--2331694 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2331636 ATACATTGTG
**
2331646 TCGATACATGACCA-AATGTA
1 TCGATACATGAAAAGAATGTA
*
2331666 TCGATACTTGAAAAGAATGTA
1 TCGATACATGAAAAGAATGTA
2331687 TCGATACA
1 TCGATACA
2331695 AGTCATTGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
TCGATACATGAAAAGAATGTA
Found at i:2331764 original size:13 final size:13
Alignment explanation
Indices: 2331746--2331771 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2331736 ACACAAAGTA
2331746 TGTATCGATACAT
1 TGTATCGATACAT
2331759 TGTATCGATACAT
1 TGTATCGATACAT
2331772 CATATAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2331787 original size:33 final size:32
Alignment explanation
Indices: 2331729--2331793 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
2331719 GCTAAACTTT
2331729 TATCGATACACAAAGTATGTATCGATACATTG
1 TATCGATACACAAAGTATGTATCGATACATTG
*
2331761 TATCGATACATCATA-TAATGTATCGATACATTG
1 TATCGATACA-CAAAGT-ATGTATCGATACATTG
2331794 GCTTGTAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.37
33 19 0.63
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (32 bp):
TATCGATACACAAAGTATGTATCGATACATTG
Found at i:2332870 original size:18 final size:19
Alignment explanation
Indices: 2332806--2332852 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
2332796 TTTTTTGTTC
2332806 TTGTTTTTTAATTAAATTTT
1 TTGTTTTTTAATT-AATTTT
2332826 TTGTTTTTTAATT-ATTTT
1 TTGTTTTTTAATTAATTTT
2332844 TTGTTTTTT
1 TTGTTTTTT
2332853 GTTTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (19 bp):
TTGTTTTTTAATTAATTTT
Found at i:2332870 original size:25 final size:25
Alignment explanation
Indices: 2332822--2332869 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2332812 TTTAATTAAA
2332822 TTTTTTGTTTTTTAATTATTTTTTG
1 TTTTTTGTTTTTTAATTATTTTTTG
2332847 TTTTTTGTTTTTT-ATTATTTTTT
1 TTTTTTGTTTTTTAATTATTTTTT
2332870 TTGTGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTTTGTTTTTTAATTATTTTTTG
Found at i:2334149 original size:13 final size:13
Alignment explanation
Indices: 2334131--2334161 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2334121 GTTACAAGCT
2334131 ATGTATCGATACA
1 ATGTATCGATACA
2334144 ATGTATCGATACA
1 ATGTATCGATACA
*
2334157 TTGTA
1 ATGTA
2334162 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2334251 original size:19 final size:20
Alignment explanation
Indices: 2334226--2334278 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
2334216 ACAATTTGTC
*
2334226 CATGTATCGATACAATG-AA
1 CATGTATCGATACAAAGCAA
* *
2334245 TATGTATCGATACAAAGCAG
1 CATGTATCGATACAAAGCAA
2334265 CATGTATCGATACA
1 CATGTATCGATACA
2334279 TATGGGAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (20 bp):
CATGTATCGATACAAAGCAA
Found at i:2334945 original size:21 final size:21
Alignment explanation
Indices: 2334912--2334952 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2334902 CTAATTAAAA
2334912 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2334933 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2334953 CACTGTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2335014 original size:13 final size:13
Alignment explanation
Indices: 2334996--2335073 Score: 120
Period size: 13 Copynumber: 6.0 Consensus size: 13
2334986 TCACTATTCA
2334996 TGTATCGATACAT
1 TGTATCGATACAT
2335009 TGTATCGATACAT
1 TGTATCGATACAT
*
2335022 TGTATCGATACAG
1 TGTATCGATACAT
2335035 TGTATCGATACAT
1 TGTATCGATACAT
* * *
2335048 TGTAACGATATAG
1 TGTATCGATACAT
2335061 TGTATCGATACAT
1 TGTATCGATACAT
2335074 CATAAATAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2336029 original size:71 final size:72
Alignment explanation
Indices: 2335913--2336056 Score: 272
Period size: 71 Copynumber: 2.0 Consensus size: 72
2335903 ACACATCTTC
2335913 AAGAAACACATTAGAAAGTTCAAATATCAAAGTTTTCGTTTTTCT-CCCCTTAAACGATTATCTC
1 AAGAAACACATTAGAAAGTTCAAATATCAAAGTTTTCGTTTTTCTCCCCCTTAAACGATTATCTC
2335977 CTCCTTT
66 CTCCTTT
*
2335984 AAGAAACACATTAGAAAGTTCAAATATCAAAGTTTTCGTTTTTCTCCCCCTTAAATGATTATCTC
1 AAGAAACACATTAGAAAGTTCAAATATCAAAGTTTTCGTTTTTCTCCCCCTTAAACGATTATCTC
2336049 CTCCTTT
66 CTCCTTT
2336056 A
1 A
2336057 TAAAAAATTC
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 45 0.63
72 26 0.37
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (72 bp):
AAGAAACACATTAGAAAGTTCAAATATCAAAGTTTTCGTTTTTCTCCCCCTTAAACGATTATCTC
CTCCTTT
Found at i:2344390 original size:13 final size:13
Alignment explanation
Indices: 2344372--2344396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2344362 CATTTTATGG
2344372 TGTATCGATACAA
1 TGTATCGATACAA
2344385 TGTATCGATACA
1 TGTATCGATACA
2344397 TACTATGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2344412 original size:32 final size:33
Alignment explanation
Indices: 2344349--2344416 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
2344339 CGTTACAAGC
**
2344349 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
2344382 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
2344414 CAA
1 CAA
2344417 GTTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:2344495 original size:20 final size:20
Alignment explanation
Indices: 2344470--2344519 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2344460 TGTTTTTCAA
*
2344470 GTATCGATACAATGCAATAT
1 GTATCGATACAATGAAATAT
* *
2344490 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAATAT
2344510 GTATCGATAC
1 GTATCGATAC
2344520 TTTTGAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
GTATCGATACAATGAAATAT
Found at i:2353067 original size:13 final size:13
Alignment explanation
Indices: 2353049--2353073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2353039 CATTTTATGG
2353049 TGTATCGATACAA
1 TGTATCGATACAA
2353062 TGTATCGATACA
1 TGTATCGATACA
2353074 TACTATGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2353089 original size:32 final size:33
Alignment explanation
Indices: 2353031--2353093 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2353021 CAAGCTAATA
**
2353031 TATCGATACATTTTATGGTGTATCGATACAATG
1 TATCGATACATACTATGGTGTATCGATACAATG
2353064 TATCGATACATACTAT-GTGTATCGATACAA
1 TATCGATACATACTATGGTGTATCGATACAA
2353094 GTTTAGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (33 bp):
TATCGATACATACTATGGTGTATCGATACAATG
Found at i:2353189 original size:20 final size:20
Alignment explanation
Indices: 2353147--2353196 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2353137 TGTTTTTCAA
*
2353147 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
2353167 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
2353187 GTATCGATAC
1 GTATCGATAC
2353197 TTTTGAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:2354237 original size:13 final size:13
Alignment explanation
Indices: 2354219--2354244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2354209 CAATTTTTTG
2354219 TGTATCGATACAT
1 TGTATCGATACAT
2354232 TGTATCGATACAT
1 TGTATCGATACAT
2354245 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2354330 original size:20 final size:20
Alignment explanation
Indices: 2354305--2354377 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2354295 ATCTTTTTTT
2354305 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2354325 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2354346 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2354366 ATGTATCGATAC
1 ATGTATCGATAC
2354378 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2354356 original size:41 final size:42
Alignment explanation
Indices: 2354283--2354377 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2354273 CTGCCAAGAA
*
2354283 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
2354325 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
2354366 ATGTATCGATAC
1 ATGTATCGATAC
2354378 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:2355015 original size:16 final size:16
Alignment explanation
Indices: 2354984--2355029 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
2354974 CTCTCCTTTG
2354984 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
2355002 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
2355018 TCTCCCCCTTAA
1 TCTCCCCCTTAA
2355030 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:2356853 original size:13 final size:13
Alignment explanation
Indices: 2356835--2356873 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2356825 ATAATCACCC
*
2356835 TGTATCGATACAG
1 TGTATCGATACAA
2356848 TGTATCGATACAA
1 TGTATCGATACAA
2356861 TGTATCGATACAA
1 TGTATCGATACAA
2356874 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2356884 original size:20 final size:20
Alignment explanation
Indices: 2356859--2356937 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
2356849 GTATCGATAC
2356859 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
2356879 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
2356904 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
2356923 ACATGTATCGATACA
1 A-ATGTATCGATACA
2356938 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:2358986 original size:15 final size:15
Alignment explanation
Indices: 2358950--2358987 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2358940 TACATCAATT
* *
2358950 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
2358965 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
2358980 TCATTTTG
1 TCATTTTG
2358988 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:2363067 original size:13 final size:13
Alignment explanation
Indices: 2363049--2363074 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2363039 CAATTTTTTG
2363049 TGTATCGATACAT
1 TGTATCGATACAT
2363062 TGTATCGATACAT
1 TGTATCGATACAT
2363075 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2363160 original size:20 final size:20
Alignment explanation
Indices: 2363135--2363207 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2363125 ATCTTTTTTT
2363135 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2363155 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2363176 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2363196 ATGTATCGATAC
1 ATGTATCGATAC
2363208 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2363186 original size:41 final size:42
Alignment explanation
Indices: 2363113--2363207 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2363103 CTGCCAAGAA
*
2363113 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
2363155 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
2363196 ATGTATCGATAC
1 ATGTATCGATAC
2363208 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:2364122 original size:21 final size:21
Alignment explanation
Indices: 2364079--2364123 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2364069 CTGCCAGTTT
* *
2364079 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATGTATC
2364100 CATGTATCGATACAATGTATC
1 CATGTATCGATACAATGTATC
2364121 CAT
1 CAT
2364124 ACAAAGCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (21 bp):
CATGTATCGATACAATGTATC
Found at i:2370332 original size:13 final size:13
Alignment explanation
Indices: 2370314--2370347 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2370304 TCGAGTGATT
2370314 ACCCAATTCACTA
1 ACCCAATTCACTA
2370327 ACCCAATTCACTA
1 ACCCAATTCACTA
*
2370340 ACCAAATT
1 ACCCAATT
2370348 GACACAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (13 bp):
ACCCAATTCACTA
Found at i:2372362 original size:21 final size:20
Alignment explanation
Indices: 2372333--2372375 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2372323 GACTAGTGTG
* *
2372333 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTAGCGACCT
*
2372354 GGGAGTGCCGGTAGCGACCT
1 GGGACTGCCGGTAGCGACCT
2372374 GG
1 GG
2372376 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTAGCGACCT
Found at i:2372834 original size:13 final size:13
Alignment explanation
Indices: 2372816--2372854 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2372806 ATAATCCCCC
*
2372816 TGTATCGATACAG
1 TGTATCGATACAA
2372829 TGTATCGATACAA
1 TGTATCGATACAA
2372842 TGTATCGATACAA
1 TGTATCGATACAA
2372855 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2372865 original size:20 final size:20
Alignment explanation
Indices: 2372840--2372918 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
2372830 GTATCGATAC
2372840 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
**
2372860 AATGTATCGATACATTGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
2372885 AATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
2372905 CATGTATCGATACA
1 AATGTATCGATACA
2372919 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 31 0.65
25 17 0.35
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2377054 original size:13 final size:13
Alignment explanation
Indices: 2377036--2377063 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2377026 TCTAATACTA
2377036 ATTCATCAAAAGT
1 ATTCATCAAAAGT
2377049 ATTCATCAAAAGT
1 ATTCATCAAAAGT
2377062 AT
1 AT
2377064 AAGAGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (13 bp):
ATTCATCAAAAGT
Found at i:2379044 original size:13 final size:13
Alignment explanation
Indices: 2379026--2379051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2379016 CAATTTTTTG
2379026 TGTATCGATACAT
1 TGTATCGATACAT
2379039 TGTATCGATACAT
1 TGTATCGATACAT
2379052 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2379048 original size:33 final size:33
Alignment explanation
Indices: 2379006--2379070 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2378996 TACAAGCCAA
* *
2379006 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
2379039 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
2379071 AGTTTGGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:2385217 original size:21 final size:21
Alignment explanation
Indices: 2385191--2385232 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2385181 TGATTTTATT
*
2385191 CATACTTTGTTATATCAAAAC
1 CATACTTTGTCATATCAAAAC
2385212 CATACTTTGTCATATCAAAAC
1 CATACTTTGTCATATCAAAAC
2385233 TAAGATCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (21 bp):
CATACTTTGTCATATCAAAAC
Found at i:2385747 original size:87 final size:86
Alignment explanation
Indices: 2385644--2385815 Score: 251
Period size: 87 Copynumber: 2.0 Consensus size: 86
2385634 TAATATTATC
*
2385644 CCTTAACTCATACTTCTCCTCTTTAATAACTT-T-TCCCTTTTTAGAAAGTGT-TAAAACAAATT
1 CCTTAACTCATACTTCTCCTCTTTAATAACTTCTCCCCCTTTTT--AAAGT-TATAAAACAAA-T
*
2385706 TTTATTGCAAATTATTTCTCCCCTT
62 TTTATTGCAAATTACTTCTCCCCTT
*
2385731 CCTTAACTCATACTTCTCCTTTTTAATAACTTCTCCCCCCTTTTTAAAGTTATAAAACAAATTTT
1 CCTTAACTCATACTTCTCCTCTTTAATAACTTCT-CCCCCTTTTTAAAGTTATAAAACAAATTTT
2385796 ATTGCAAATTACTTCTCCCC
65 ATTGCAAATTACTTCTCCCC
2385816 CTTTTTATTA
Statistics
Matches: 78, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
87 55 0.71
88 15 0.19
90 8 0.10
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.43
Consensus pattern (86 bp):
CCTTAACTCATACTTCTCCTCTTTAATAACTTCTCCCCCTTTTTAAAGTTATAAAACAAATTTTA
TTGCAAATTACTTCTCCCCTT
Found at i:2389795 original size:78 final size:78
Alignment explanation
Indices: 2389707--2389868 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 78
2389697 ATGATCTCAC
* * *
2389707 CTTCTTTAACATAAGTCAACTCCCTTGGATGTTTTCTTTTGGTTTTAGTTGGCTCATGTTCATCA
1 CTTCTTTAACATAAGTCAACTCCCTTGGATGTTTTCTTTCGATTTGAGTTGGCTCATGTTCATCA
2389772 ACTTCCTTTGGAG
66 ACTTCCTTTGGAG
2389785 CTTCTTTAACATAAGTCAACTCCCTTGGATGTTTTCTTTCGATTTGAGTTGGCTCATGTTCATCA
1 CTTCTTTAACATAAGTCAACTCCCTTGGATGTTTTCTTTCGATTTGAGTTGGCTCATGTTCATCA
2389850 ACTTCCTTTGGAG
66 ACTTCCTTTGGAG
*
2389863 GTTCTT
1 CTTCTT
2389869 CGATTTGGAT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (78 bp):
CTTCTTTAACATAAGTCAACTCCCTTGGATGTTTTCTTTCGATTTGAGTTGGCTCATGTTCATCA
ACTTCCTTTGGAG
Found at i:2393428 original size:15 final size:15
Alignment explanation
Indices: 2393408--2393439 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2393398 CAAATCCTAT
*
2393408 GACTCATCATTACTA
1 GACTCATCATCACTA
2393423 GACTCATCATCACTA
1 GACTCATCATCACTA
2393438 GA
1 GA
2393440 AGAAAAGTAA
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:0.34, C:0.28, G:0.09, T:0.28
Consensus pattern (15 bp):
GACTCATCATCACTA
Done.