Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008273.1 Hibiscus syriacus cultivar Beakdansim tig00110930_pilon, whole genome shotgun sequence
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: 1042195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:193717 original size:46 final size:46
Alignment explanation
Indices: 193620--193706 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
193610 ATTTTTCTTT
193620 TCATTTTTAACGACGAAATAACATATTTGTAACTTAAAAAAAAAAC
1 TCATTTTTAACGACGAAATAACATATTTGTAACTTAAAAAAAAAAC
* *
193666 TCATTTTTAACGACGAAATGAC-TGTTTGTAACTTAAAAAAA
1 TCATTTTTAACGACGAAATAACATATTTGTAACTTAAAAAAA
193707 TTGACTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (46 bp):
TCATTTTTAACGACGAAATAACATATTTGTAACTTAAAAAAAAAAC
Found at i:212677 original size:93 final size:89
Alignment explanation
Indices: 212580--212763 Score: 305
Period size: 92 Copynumber: 2.0 Consensus size: 89
212570 TGCGTAAATT
* *
212580 GTAAACTTATTCACTGAATTTTATTCTATCTCTTATTTTACTCATTATATTTTTAGTTTTTTTTA
1 GTAAACTTATTCACTGAATTTT-CTCTATCTCTTATTTTACTCATTATACTTTTA--TTTTTTT-
212645 AATTTAATCACTCAACTTTATACATTGA
62 AATTTAATCACTCAACTTTATACATTGA
212673 GTAAACTTATTCACTGAATTTTCTCTATCTCTTATTTTACTCATTATACTTTTATTTTTTTAATT
1 GTAAACTTATTCACTGAATTTTCTCTATCTCTTATTTTACTCATTATACTTTTATTTTTTTAATT
*
212738 TAATCATTCAACTTTATACATTGA
66 TAATCACTCAACTTTATACATTGA
212762 GT
1 GT
212764 TTTTTTGGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
89 29 0.33
90 7 0.08
92 30 0.34
93 22 0.25
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (89 bp):
GTAAACTTATTCACTGAATTTTCTCTATCTCTTATTTTACTCATTATACTTTTATTTTTTTAATT
TAATCACTCAACTTTATACATTGA
Found at i:216882 original size:18 final size:18
Alignment explanation
Indices: 216859--216931 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
216849 ACTGAATATT
216859 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
216877 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
216896 TTATTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
216915 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
216932 GATTATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:216906 original size:38 final size:38
Alignment explanation
Indices: 216863--216937 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
216853 AATATTTGTC
*
216863 CCGAAGGACCACTATGTCCCGAAGGACCACTGATTATT
1 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTATT
216901 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTAT
1 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTAT
216938 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (38 bp):
CCGAAGAACCACTATGTCCCGAAGGACCACTGATTATT
Found at i:217579 original size:19 final size:19
Alignment explanation
Indices: 217555--217604 Score: 77
Period size: 17 Copynumber: 2.7 Consensus size: 19
217545 TTTAAGCAGG
*
217555 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCGTA
217574 TGCATCGA--CACTCCGTA
1 TGCATCGATGCACTCCGTA
217591 TGCATCGATGCACT
1 TGCATCGATGCACT
217605 AATTGCATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 16 0.57
19 12 0.43
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (19 bp):
TGCATCGATGCACTCCGTA
Found at i:218696 original size:30 final size:30
Alignment explanation
Indices: 218633--218689 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
218623 AAAACCGGTA
* * * *
218633 GAACCGGTTGAAAACCGATAAAATCGGGGT
1 GAACCGGCTGAAAACCGACAAAACCGAGGT
218663 GAACCGGCTGAAAACCGACAAAACCGA
1 GAACCGGCTGAAAACCGACAAAACCGA
218690 TTTGAACTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGACAAAACCGAGGT
Found at i:218959 original size:24 final size:25
Alignment explanation
Indices: 218917--218963 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
218907 CGAACTCAAA
*
218917 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAGAAGTTCAATTGAAGCCT
*
218942 AAAATTTG-AGTTCAATTGAAGC
1 AAAATTAGAAGTTCAATTGAAGC
218964 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGTTCAATTGAAGCCT
Found at i:227861 original size:90 final size:90
Alignment explanation
Indices: 227695--227875 Score: 319
Period size: 90 Copynumber: 2.0 Consensus size: 90
227685 AGTTAAGAAG
*
227695 TAACCATAGAAACTATGGAACCCACTATATATTTCCCCCTACTATTTACTCCCTTGTTTTAGTTA
1 TAACCATAGAAACTATGGAACCCACTATATATTTCCCCCTACTATTTACTCCCGTGTTTTAGTTA
227760 CTATGCTTTTATTTTATTAATACCT
66 CTATGCTTTTATTTTATTAATACCT
*
227785 TAACCATAGAAACTATGGAACCCACTATATATTTTCCCCCTTCTATTTACTCCCGTGTTTTAGTT
1 TAACCATAGAAACTATGGAACCCACTATATA-TTTCCCCCTACTATTTACTCCCGTGTTTTAGTT
*
227850 ACTATGC-TTTATTTTTTTAATACCT
65 ACTATGCTTTTATTTTATTAATACCT
227875 T
1 T
227876 TATGAAAAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
90 49 0.56
91 38 0.44
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (90 bp):
TAACCATAGAAACTATGGAACCCACTATATATTTCCCCCTACTATTTACTCCCGTGTTTTAGTTA
CTATGCTTTTATTTTATTAATACCT
Found at i:232730 original size:89 final size:86
Alignment explanation
Indices: 232362--232939 Score: 436
Period size: 85 Copynumber: 6.9 Consensus size: 86
232352 ATTAGAATCA
** * * * *
232362 TCAATTATAAA-GATAAAAAGTATGATT-GAAAAATTAG-GAACCTTAATTATAAAGGTAAAAAG
1 TCAATTATAAAGGA-AAAAAGTGGGATTACAAAAATTAGAG-GCCTCAATTATAAAGGAAAAAAG
* *
232424 TGAGATT-AAAAAATTAGGCGCC
64 TGAGATTGAAAAAAATAGGGGCC
* * * * * *
232446 TCAATTATGAATG--TAGAGTGAGA--A-AAAAATTAGATGCCTC-A--ATAAA-GAAAAAAGT-
1 TCAATTATAAAGGAAAAAAGTGGGATTACAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTG
232501 AGGATTGAAAAAAATAGGGGCC
66 A-GATTGAAAAAAATAGGGGCC
* * *
232523 TTAATTATAAAGGAAAAAAGTGGGTTTACAAAAATTAG-GGCCCTCAATTGTAAAGGAAAAAAGT
1 TCAATTATAAAGGAAAAAAGTGGGATTACAAAAATTAGAGG-CCTCAATTATAAAGGAAAAAAGT
* * *
232587 GAGATT-AAAAAATTAGGGACT
65 GAGATTGAAAAAAATAGGGGCC
* * * ** **
232608 TCAATTATAAATGCATAAAGTGAAATTTTAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTG
1 TCAATTATAAAGGAAAAAAGTGGGATTACAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTG
*
232673 -GAATTGAAAAAAAAAAGAGGGGCC
66 AG-ATTG---AAAAAAATAGGGGCC
* * *
232697 TCAATTATAAAGAAAAAAAGTGGGATTACAAAAATTAGGGGCCTCAATTGTAAAGGAAAAAAGTG
1 TCAATTATAAAGGAAAAAAGTGGGATTACAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTG
*
232762 AGATTGAAAAAAAAATTA-GGGTC
66 AGATTG--AAAAAAA-TAGGGGCC
* * * * *
232785 TCAATTATAAAGGTAAAAAGTGGGATTAC-AAAATTTGAGGCCTCAATTACATA-G-TAAAAGT-
1 TCAATTATAAAGGAAAAAAGTGGGATTACAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTG
* *
232846 -GATT-AAAAAATTAGGGACC
66 AGATTGAAAAAAATAGGGGCC
* * * ** * * * *
232865 T-AATTATAAATGTAGAAAGTGAAATTAAAAAAAGTAGAGGCCTTAATTATAAAGGTAAAAAG-G
1 TCAATTATAAAGGAAAAAAGTGGGATTACAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTG
232928 -GATTGAAAAAAA
66 AGATTGAAAAAAA
232940 ATTAAAGCCT
Statistics
Matches: 392, Mismatches: 72, Indels: 61
0.75 0.14 0.12
Matches are distributed among these distances:
75 1 0.00
76 12 0.03
77 28 0.07
79 31 0.08
80 41 0.10
81 3 0.01
82 28 0.07
83 11 0.03
84 11 0.03
85 78 0.20
86 16 0.04
87 20 0.05
88 40 0.10
89 71 0.18
90 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (86 bp):
TCAATTATAAAGGAAAAAAGTGGGATTACAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTG
AGATTGAAAAAAATAGGGGCC
Found at i:232846 original size:174 final size:173
Alignment explanation
Indices: 232362--232835 Score: 496
Period size: 174 Copynumber: 2.8 Consensus size: 173
232352 ATTAGAATCA
* ** * ** * * *
232362 TCAATTATAAAGATAAAAAGTATGATT-GAAAAATTAGGAACCTTAATTATAAAGGTAAAAAGTG
1 TCAATTATAAAGAAAAAAAGTGGGATTACAAAAATTAGGGCCCTCAATTGTAAAGGAAAAAAGTG
* * * * * *
232426 AGATTAAAAAATTAGGCG-CCTCAATTATGAATG--TAGAGTGAGAA---AAAAATTAGATGCCT
66 AGATTAAAAAATTAGG-GACTTCAATTATAAAGGCAAAAAGTGA-AATTTAAAAATTAGAGGCCT
*
232485 CAA-T--AAA-GAAAAAAGTAGG-ATTG---AAAAAAATAGGGGCC
129 CAATTACAAAGGAAAAAAGT-GGAATTGAAAAAAAAAAGAGGGGCC
* * *
232523 TTAATTATAAAGGAAAAAAGTGGGTTTACAAAAATTAGGGCCCTCAATTGTAAAGGAAAAAAGTG
1 TCAATTATAAAGAAAAAAAGTGGGATTACAAAAATTAGGGCCCTCAATTGTAAAGGAAAAAAGTG
* *
232588 AGATTAAAAAATTAGGGACTTCAATTATAAATGCATAAAGTGAAATTTTAAAAATTAGAGGCCTC
66 AGATTAAAAAATTAGGGACTTCAATTATAAAGGCAAAAAGTGAAA-TTTAAAAATTAGAGGCCTC
*
232653 AATTATAAAGGAAAAAAGTGGAATTGAAAAAAAAAAGAGGGGCC
130 AATTACAAAGGAAAAAAGTGGAATTGAAAAAAAAAAGAGGGGCC
*
232697 TCAATTATAAAGAAAAAAAGTGGGATTACAAAAATTAGGGGCCTCAATTGTAAAGGAAAAAAGTG
1 TCAATTATAAAGAAAAAAAGTGGGATTACAAAAATTAGGGCCCTCAATTGTAAAGGAAAAAAGTG
* * ** *
232762 AGATTGAAAAAAAAATTAGGGTC-TCAATTATAAAGGTAAAAAGTGGGA-TTACAAAATTTGAGG
66 AGATT----AAAAAATTAGGGACTTCAATTATAAAGGCAAAAAGTGAAATTTA-AAAATTAGAGG
232825 CCTCAATTACA
126 CCTCAATTACA
232836 TAGTAAAAGT
Statistics
Matches: 263, Mismatches: 29, Indels: 27
0.82 0.09 0.08
Matches are distributed among these distances:
161 22 0.08
162 60 0.23
163 2 0.01
164 7 0.03
167 17 0.06
168 1 0.00
170 5 0.02
171 13 0.05
174 80 0.30
175 3 0.01
176 20 0.08
177 20 0.08
178 13 0.05
ACGTcount: A:0.49, C:0.08, G:0.20, T:0.24
Consensus pattern (173 bp):
TCAATTATAAAGAAAAAAAGTGGGATTACAAAAATTAGGGCCCTCAATTGTAAAGGAAAAAAGTG
AGATTAAAAAATTAGGGACTTCAATTATAAAGGCAAAAAGTGAAATTTAAAAATTAGAGGCCTCA
ATTACAAAGGAAAAAAGTGGAATTGAAAAAAAAAAGAGGGGCC
Found at i:232937 original size:42 final size:41
Alignment explanation
Indices: 232362--233000 Score: 370
Period size: 43 Copynumber: 15.3 Consensus size: 41
232352 ATTAGAATCA
* * *
232362 TCAATTATAAA-GATAAAAAGTATGATT-GAAAAATTAGGAACC
1 TCAATTATAAAGGA-AAAAAGT-GGATTAAAAAAATTAGG-GCC
* *
232404 TTAATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGGCGCC
1 TCAATTATAAAGGAAAAAAGTG-GATTAAAAAAATTAGG-GCC
* * * * * *
232446 TCAATTATGAATG--TAGAGT-GA-GAAAAAAATTAGATGCC
1 TCAATTATAAAGGAAAAAAGTGGATTAAAAAAATTAG-GGCC
232484 TC-A--ATAAA-GAAAAAAGTAGGATTGAAAAAAA-TAGGGGCC
1 TCAATTATAAAGGAAAAAAGT-GGATT-AAAAAAATTA-GGGCC
* * *
232523 TTAATTATAAAGGAAAAAAGTGGGTTTACAAAAATTAGGGCCC
1 TCAATTATAAAGGAAAAAAGT-GGATTAAAAAAATTAGGG-CC
* *
232566 TCAATTGTAAAGGAAAAAAGTGAGATT-AAAAAATTAGGGACT
1 TCAATTATAAAGGAAAAAAGTG-GATTAAAAAAATTAGGG-CC
* * * * **
232608 TCAATTATAAATGCATAAAGTGAAATTTTAAAAATTAGAGGCC
1 TCAATTATAAAGGAAAAAAGTG-GATTAAAAAAATTAG-GGCC
**
232651 TCAATTATAAAGGAAAAAAGTGGAATTGAAAAAAAAAAGAGGGGCC
1 TCAATTATAAAGGAAAAAAGTGG-ATT---AAAAAAATTA-GGGCC
* *
232697 TCAATTATAAAGAAAAAAAGTGGGATTACAAAAATTAGGGGCC
1 TCAATTATAAAGGAAAAAAGT-GGATTAAAAAAATTA-GGGCC
* *
232740 TCAATTGTAAAGGAAAAAAGTGAGATTGAAAAAAAAATTAGGGTC
1 TCAATTATAAAGGAAAAAAGTG-GATT---AAAAAAATTAGGGCC
* * *
232785 TCAATTATAAAGGTAAAAAGTGGGATT-ACAAAATTTGAGGCC
1 TCAATTATAAAGGAAAAAAGT-GGATTAAAAAAATTAG-GGCC
* * *
232827 TCAATTACATA-G-TAAAAGT-GATT-AAAAAATTAGGGACC
1 TCAATTATAAAGGAAAAAAGTGGATTAAAAAAATTAGGG-CC
* * * * *
232865 T-AATTATAAATGTAGAAAGTGAAATTAAAAAAAGTAGAGGCC
1 TCAATTATAAAGGAAAAAAGTG-GATTAAAAAAATTAG-GGCC
* * **
232907 TTAATTATAAAGGTAAAAAG-GGATTGAAAAAAAATTAAAGCC
1 TCAATTATAAAGGAAAAAAGTGGATT--AAAAAAATTAGGGCC
* * * * *
232949 TC--TTATAAAGGTAAAAATTGATATTATAAAAA-TAGGAGTC
1 TCAATTATAAAGGAAAAAAGTG-GATTAAAAAAATTAGG-GCC
232989 TCAATTATAAAG
1 TCAATTATAAAG
233001 ATAGAAAATA
Statistics
Matches: 470, Mismatches: 80, Indels: 94
0.73 0.12 0.15
Matches are distributed among these distances:
34 1 0.00
35 4 0.01
36 4 0.01
37 10 0.02
38 35 0.07
39 13 0.03
40 44 0.09
41 16 0.03
42 133 0.28
43 135 0.29
44 2 0.00
45 27 0.06
46 43 0.09
47 3 0.01
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.24
Consensus pattern (41 bp):
TCAATTATAAAGGAAAAAAGTGGATTAAAAAAATTAGGGCC
Found at i:233064 original size:13 final size:13
Alignment explanation
Indices: 233046--233070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233036 TATAATGATA
233046 AAAAAAATAATTG
1 AAAAAAATAATTG
233059 AAAAAAATAATT
1 AAAAAAATAATT
233071 AGGAGATCTA
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAAAATAATTG
Found at i:233898 original size:15 final size:15
Alignment explanation
Indices: 233880--233910 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
233870 TGTTATTATT
233880 TTTTAACAAATTCAG
1 TTTTAACAAATTCAG
233895 TTTTAACAAATTCAG
1 TTTTAACAAATTCAG
233910 T
1 T
233911 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTTAACAAATTCAG
Found at i:234378 original size:12 final size:13
Alignment explanation
Indices: 234342--234385 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
234332 GCCCCGATTA
*
234342 CCCGATTACCAGC
1 CCCGATTACCCGC
234355 CCCGATTACCCGC
1 CCCGATTACCCGC
*
234368 CCCGA-TACCCGA
1 CCCGATTACCCGC
234380 CCCGAT
1 CCCGAT
234386 AAATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.20, C:0.50, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:234467 original size:28 final size:28
Alignment explanation
Indices: 234436--234489 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
234426 TTAATAAATT
*
234436 TTTAAATAAAAAAATATATATTTATATA
1 TTTAAATAAAAAAATATATATATATATA
* * *
234464 TTTAATTAATAATATATATATATATA
1 TTTAAATAAAAAAATATATATATATA
234490 CCCGGCCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTAAATAAAAAAATATATATATATATA
Found at i:234522 original size:12 final size:12
Alignment explanation
Indices: 234507--234541 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
234497 CGATTCTCGG
234507 CCCAATACCCGA
1 CCCAATACCCGA
*
234519 CCCAATACCCGG
1 CCCAATACCCGA
234531 CCCAATACCCG
1 CCCAATACCCG
234542 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:239322 original size:223 final size:225
Alignment explanation
Indices: 239044--239491 Score: 834
Period size: 225 Copynumber: 2.0 Consensus size: 225
239034 TCTATTATCC
239044 GAGACGGGTTCTAAACATAAATCAAAACAATTTAAAACAAAACATAATCGTTTGATCTTATGGGA
1 GAGACGGGTTCTAAACATAAATCAAAACAATTTAAAACAAAACATAATCGTTTGATCTTATGGGA
239109 CGATGTATTAGATTCTTTG-A-AATGTTAGGAGTTCAAATTCTGATATTATGAATAGAGCAAACT
66 CGATGTATTAGATTCTTTGAATAATGTTAGGAGTTCAAATTCTGATATTATGAATAGAGCAAACT
239172 AGATTTAAAATGTTA-CTATAATGAACCTCTATAATACATAATATAAATTAATCTATC-TTAAAT
131 AGATTTAAAATGTTACCTATAATGAACCTCTATAATACATAATATAAATTAATCTATCATTAAAT
239235 T-AATACCTATAATTAAATTAAAGAAAATG
196 TAAATACCTATAATTAAATTAAAGAAAATG
239264 GAGACGGGTTCTAAAACATAAATCAAAATTCAATTTAAAACAAAACATAATCGTTTGATCTTATG
1 GAGACGGGTTCT-AAACATAAATCAAAA--CAATTTAAAACAAAACATAATCGTTTGATCTTATG
239329 GGACGATGTATTAGATTCTTTGAATAATGTTAGGAGTTCAAATTCTGATATTATGAATAGAGCAA
63 GGACGATGTATTAGATTCTTTGAATAATGTTAGGAGTTCAAATTCTGATATTATGAATAGAGCAA
239394 ACTAGATTTAAAATGTTACCTATAATGAACCTCTATAATACATAATATAAATTAATCTATCATTA
128 ACTAGATTTAAAATGTTACCTATAATGAACCTCTATAATACATAATATAAATTAATCTATCATTA
239459 AATTAAATACCTATAATTAAATTAAAGAAAATG
193 AATTAAATACCTATAATTAAATTAAAGAAAATG
239492 TTCAATTTAA
Statistics
Matches: 220, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
220 12 0.05
221 15 0.07
223 57 0.26
224 1 0.00
225 58 0.26
226 42 0.19
227 7 0.03
228 28 0.13
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (225 bp):
GAGACGGGTTCTAAACATAAATCAAAACAATTTAAAACAAAACATAATCGTTTGATCTTATGGGA
CGATGTATTAGATTCTTTGAATAATGTTAGGAGTTCAAATTCTGATATTATGAATAGAGCAAACT
AGATTTAAAATGTTACCTATAATGAACCTCTATAATACATAATATAAATTAATCTATCATTAAAT
TAAATACCTATAATTAAATTAAAGAAAATG
Found at i:247138 original size:19 final size:19
Alignment explanation
Indices: 247116--247157 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
247106 TACCCAACCC
247116 CAAATTCATAATCCATTCT
1 CAAATTCATAATCCATTCT
247135 CAAATTCATAATCCATTCT
1 CAAATTCATAATCCATTCT
247154 CAAA
1 CAAA
247158 ACTACCGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.33
Consensus pattern (19 bp):
CAAATTCATAATCCATTCT
Found at i:251982 original size:28 final size:28
Alignment explanation
Indices: 251949--252004 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
251939 ATCGTCGTTG
* *
251949 CTTTCAAGTATTGAATCGACGGTATAAT
1 CTTTCAAGTACTGAATCGACAGTATAAT
**
251977 CTTTCAAGTACTGGTTCGACAGTATAAT
1 CTTTCAAGTACTGAATCGACAGTATAAT
252005 GTAAACAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (28 bp):
CTTTCAAGTACTGAATCGACAGTATAAT
Found at i:252523 original size:2 final size:2
Alignment explanation
Indices: 252516--252551 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
252506 TTAATTAACA
252516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
252552 TACAAACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255121 original size:16 final size:16
Alignment explanation
Indices: 255097--255133 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
255087 GAAAATTTAA
255097 AATTATTATATATTTT
1 AATTATTATATATTTT
*
255113 AATTTTTATATATTTT
1 AATTATTATATATTTT
*
255129 TATTA
1 AATTA
255134 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTATTATATATTTT
Found at i:259769 original size:15 final size:15
Alignment explanation
Indices: 259745--259780 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
259735 ACACCATTAA
*
259745 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
259760 ATTAAATTATAAAAT
1 ATTAAATTATAAAAC
259775 ATTAAA
1 ATTAAA
259781 CATTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:259830 original size:16 final size:16
Alignment explanation
Indices: 259809--259846 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
259799 TTAAAAATCT
259809 AAATATAAT-TTAATTA
1 AAATATAATATTAA-TA
*
259825 AAATATAATATTTATA
1 AAATATAATATTAATA
259841 AAATAT
1 AAATAT
259847 TAGTTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAATATTAATA
Found at i:261638 original size:16 final size:16
Alignment explanation
Indices: 261617--261647 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
261607 ATAAATTAAT
261617 TTAATGATACTCATCG
1 TTAATGATACTCATCG
*
261633 TTAATGATGCTCATC
1 TTAATGATACTCATC
261648 CACGCTTGAC
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:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (16 bp):
TTAATGATACTCATCG
Found at i:262776 original size:14 final size:14
Alignment explanation
Indices: 262757--262787 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
262747 AACTTATGGC
262757 AAATCCATTTTATT
1 AAATCCATTTTATT
262771 AAATCCATTTTATT
1 AAATCCATTTTATT
262785 AAA
1 AAA
262788 CACATACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATCCATTTTATT
Found at i:267488 original size:180 final size:180
Alignment explanation
Indices: 267186--267521 Score: 654
Period size: 180 Copynumber: 1.9 Consensus size: 180
267176 ATAAATATTT
267186 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
1 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
267251 CAAAAATAATTTTTATAAAATGAAATAAAACTATGTAATACTTTAAATAAATTGATACATTACAC
66 CAAAAATAATTTTTATAAAATGAAATAAAACTATGTAATACTTTAAATAAATTGATACATTACAC
267316 AAATACCATATAAGAATGATAATTACCCCAAAACAATAAATATTTACTCC
131 AAATACCATATAAGAATGATAATTACCCCAAAACAATAAATATTTACTCC
267366 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
1 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
* *
267431 CAAAATTAATTTTTCTAAAATGAAATAAAACTATGTAATACTTTAAATAAATTGATACATTACAC
66 CAAAAATAATTTTTATAAAATGAAATAAAACTATGTAATACTTTAAATAAATTGATACATTACAC
267496 AAATACCATATAAGAATGATAATTAC
131 AAATACCATATAAGAATGATAATTAC
267522 ATAGAATATA
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 154 1.00
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (180 bp):
AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
CAAAAATAATTTTTATAAAATGAAATAAAACTATGTAATACTTTAAATAAATTGATACATTACAC
AAATACCATATAAGAATGATAATTACCCCAAAACAATAAATATTTACTCC
Found at i:269038 original size:21 final size:21
Alignment explanation
Indices: 269010--269068 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
269000 GTCTGAGTTA
*
269010 CCCGCGACGGCCACAATAGCG
1 CCCGCGACGGCCGCAATAGCG
** * *
269031 TTCGCGACGACCGTAATAGCG
1 CCCGCGACGGCCGCAATAGCG
269052 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCCGCAAT
269069 CACGGAAAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.39, G:0.29, T:0.10
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:276188 original size:9 final size:9
Alignment explanation
Indices: 276172--276246 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
276162 TTGATCCTTT
276172 TTTA-TTTA
1 TTTATTTTA
276180 TTTATTTTA
1 TTTATTTTA
276189 TTTATTTT-
1 TTTATTTTA
*
276197 TCTTTTTTTA
1 T-TTATTTTA
* *
276207 CTAACTTTTA
1 TTTA-TTTTA
276217 TTTATTTT-
1 TTTATTTTA
276225 TGTTA-TTTA
1 T-TTATTTTA
276234 TTTTATTATTA
1 -TTTATT-TTA
276245 TT
1 TT
276247 ATTATATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
8 9 0.17
9 29 0.56
10 11 0.21
11 3 0.06
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:276240 original size:18 final size:18
Alignment explanation
Indices: 276213--276254 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
276203 TTTACTAACT
* *
276213 TTTA-TTTATTTTTGTTA
1 TTTATTTTATTATTATTA
276230 TTTATTTTATTATTATTA
1 TTTATTTTATTATTATTA
276248 TTATATT
1 TT-TATT
276255 AATATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTTATTATTATTA
Found at i:276345 original size:13 final size:13
Alignment explanation
Indices: 276329--276365 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
276319 CAAATCGGAT
276329 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
276342 TTTTAATTTTTAA
1 TTTTAAATTTTAA
*
276355 TTTTTAATTTT
1 TTTTAAATTTT
276366 CGCAATTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:276352 original size:20 final size:20
Alignment explanation
Indices: 276327--276365 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
276317 ATCAAATCGG
276327 ATTTTTAAATTTTAATTTTA
1 ATTTTTAAATTTTAATTTTA
*
276347 ATTTTTAATTTTTAATTTT
1 ATTTTTAAATTTTAATTTT
276366 CGCAATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTAAATTTTAATTTTA
Found at i:288970 original size:3 final size:3
Alignment explanation
Indices: 288934--288959 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
288924 CAGTTAACAT
288934 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
288960 GCTTGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:293277 original size:11 final size:10
Alignment explanation
Indices: 293261--293296 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
293251 TTTGCCTCTT
293261 TTCTTTGAGG
1 TTCTTTGAGG
293271 ATTCTTTGAGG
1 -TTCTTTGAGG
*
293282 TTCTTGGAGG
1 TTCTTTGAGG
293292 TTCTT
1 TTCTT
293297 GAAGATGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.11, C:0.11, G:0.28, T:0.50
Consensus pattern (10 bp):
TTCTTTGAGG
Found at i:294432 original size:265 final size:265
Alignment explanation
Indices: 293959--294488 Score: 1033
Period size: 265 Copynumber: 2.0 Consensus size: 265
293949 CTCTGATACC
*
293959 ATGTAAAGATTATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
1 ATGTAAAGATCATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
294024 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAACAATTCTCAAGGAGAGTATTTATAGCTAG
66 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAACAATTCTCAAGGAGAGTATTTATAGCTAG
* *
294089 TACTATAGCTGAAACTGATGTAACTAATTTCACAACAAACTAACTGCTTCAATTGATCAGCTGCA
131 TACTATAGCTGAAACTGATGCAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCA
294154 GTGAACCAATCCTTAGCTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACAC
196 GTGAACCAATCCTTAGCTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACAC
294219 TAACA
261 TAACA
294224 ATGTAAAGATCATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
1 ATGTAAAGATCATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
294289 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAACAATTCTCAAGGAGAGTATTTATAGCTAG
66 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAACAATTCTCAAGGAGAGTATTTATAGCTAG
294354 TACTATAGCTGAAACTGATGCAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCA
131 TACTATAGCTGAAACTGATGCAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCA
294419 GTGAACCAATCCTTAGCTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACAC
196 GTGAACCAATCCTTAGCTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACAC
294484 TAACA
261 TAACA
294489 TTCCCCTTGC
Statistics
Matches: 262, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
265 262 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (265 bp):
ATGTAAAGATCATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAACAATTCTCAAGGAGAGTATTTATAGCTAG
TACTATAGCTGAAACTGATGCAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCA
GTGAACCAATCCTTAGCTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACAC
TAACA
Found at i:296850 original size:8 final size:7
Alignment explanation
Indices: 296821--296854 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
296811 AAATTATGGA
296821 TTAAATT
1 TTAAATT
296828 TTAAATT
1 TTAAATT
296835 TTAAATT
1 TTAAATT
*
296842 TTAAAAT
1 TTAAATT
296849 TTAAAT
1 TTAAAT
296855 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TTAAATT
Found at i:299324 original size:19 final size:19
Alignment explanation
Indices: 299300--299338 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
299290 AATCCCTTAT
*
299300 CATAATTGTAAGTTTAATC
1 CATAATGGTAAGTTTAATC
299319 CATAATGGTAAGTTTAATC
1 CATAATGGTAAGTTTAATC
299338 C
1 C
299339 TCACTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (19 bp):
CATAATGGTAAGTTTAATC
Found at i:299854 original size:56 final size:57
Alignment explanation
Indices: 299774--299937 Score: 163
Period size: 60 Copynumber: 2.8 Consensus size: 57
299764 AACTATAACT
* * * *
299774 CTCATTTTAAAATTAGTCCTTAAACTTTTGATATTTCAATTTCATCCTAGACTATGA-
1 CTCATTCT-AAATTAGTCCTTAAACTTTTGATAATTCAATTTCATCCTAAACCATGAC
299831 CTCATTCTAAATTAGTCCTTAAACTTTTGA-ACATTCTAATTTCATCCCTAAACCATGACC
1 CTCATTCTAAATTAGTCCTTAAACTTTTGATA-ATTC-AATTTCAT-CCTAAACCATGA-C
* * * * *
299891 CTCTTTCTAAATTGGTTCC-CAAACTTTTGAATACTCCAATTTCATCC
1 CTCATTCTAAATTAG-TCCTTAAACTTTTG-ATAATTCAATTTCATCC
299938 CCAAATTCAT
Statistics
Matches: 90, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
55 1 0.01
56 25 0.28
57 15 0.17
58 10 0.11
59 2 0.02
60 30 0.33
61 6 0.07
62 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (57 bp):
CTCATTCTAAATTAGTCCTTAAACTTTTGATAATTCAATTTCATCCTAAACCATGAC
Found at i:304895 original size:37 final size:37
Alignment explanation
Indices: 304845--304918 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
304835 ATTTATGGAT
304845 ATGTATTCAATATAACAATCTCATGCACTTTGAAGAA
1 ATGTATTCAATATAACAATCTCATGCACTTTGAAGAA
304882 ATGTATTCAATATAACAATCTCATGCACTTTGAAGAA
1 ATGTATTCAATATAACAATCTCATGCACTTTGAAGAA
304919 GTAACAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (37 bp):
ATGTATTCAATATAACAATCTCATGCACTTTGAAGAA
Found at i:310523 original size:20 final size:20
Alignment explanation
Indices: 310500--310551 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
310490 AACGCGATCC
310500 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
310520 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
310540 CCAAAATCGCAA
1 CCAGAATCGCAA
310552 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:310568 original size:21 final size:20
Alignment explanation
Indices: 310541--310639 Score: 63
Period size: 21 Copynumber: 4.8 Consensus size: 20
310531 AATCAGTTTC
310541 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
310562 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
310583 CAAATTCGCATTGCGATTTTT
1 CAAAATCGCAACGCGA-TTTT
* * *
310604 CATAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTT
*
310624 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
310640 ACACATAAAT
Statistics
Matches: 57, Mismatches: 19, Indels: 5
0.70 0.23 0.06
Matches are distributed among these distances:
20 16 0.28
21 40 0.70
22 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:310701 original size:20 final size:20
Alignment explanation
Indices: 310607--310758 Score: 189
Period size: 20 Copynumber: 7.6 Consensus size: 20
310597 GATTTTTCAT
* ** *
310607 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
310627 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
310647 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
310667 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
310687 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
310707 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
310727 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
310747 AATCGCAACGCG
1 AATCGCAACGCG
310759 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 110 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:311177 original size:33 final size:33
Alignment explanation
Indices: 311138--311208 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
311128 TTCACTTAGA
*
311138 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
311171 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
311204 TTTCA
1 TTTCA
311209 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:311348 original size:14 final size:14
Alignment explanation
Indices: 311329--311381 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
311319 AGAATGACTG
311329 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
311343 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
311362 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
311376 TCGCAA
1 TCGCAA
311382 AATCGCATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 16 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.31
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:311365 original size:19 final size:22
Alignment explanation
Indices: 311341--311388 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
311331 GCAACGAGAG
*
311341 AATCGCAACGCGA-AAT-G-AA
1 AATCGCAACGAGAGAATCGCAA
311360 AATCGCAACGAGAGAATCGCAA
1 AATCGCAACGAGAGAATCGCAA
311382 AATCGCA
1 AATCGCA
311389 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 3 0.12
21 1 0.04
22 9 0.36
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (22 bp):
AATCGCAACGAGAGAATCGCAA
Found at i:311411 original size:19 final size:18
Alignment explanation
Indices: 311384--311502 Score: 89
Period size: 19 Copynumber: 7.1 Consensus size: 18
311374 AATCGCAAAA
*
311384 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
311403 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
311417 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
311436 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
311450 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
311468 CTCGCGTTGCGA-TTTC--
1 -TCGCGTTGCGATTTTCAT
*
311484 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
311502 T
1 T
311503 TCAACCAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.25
15 10 0.13
16 9 0.11
17 6 0.08
18 4 0.05
19 30 0.38
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:311431 original size:33 final size:33
Alignment explanation
Indices: 311389--311504 Score: 205
Period size: 33 Copynumber: 3.5 Consensus size: 33
311379 CAAAATCGCA
311389 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
311422 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
311455 TTGCGATTGTCATCTCGCGTTGCGATTTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TTCTCTCG
311489 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
311505 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 56 0.72
34 22 0.28
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:313397 original size:92 final size:93
Alignment explanation
Indices: 313191--313659 Score: 876
Period size: 92 Copynumber: 5.1 Consensus size: 93
313181 TAGATTGCTT
*
313191 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
313256 TTTGTCTTTATTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
313284 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
313348 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
313376 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
313441 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
313469 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-T-
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
313531 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
313559 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
313623 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
313651 AGTAAATTT
1 AGTAAATTT
313660 ATCCATTCAA
Statistics
Matches: 368, Mismatches: 4, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
90 57 0.15
91 33 0.09
92 175 0.48
93 103 0.28
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:313725 original size:19 final size:19
Alignment explanation
Indices: 313701--313798 Score: 84
Period size: 19 Copynumber: 5.4 Consensus size: 19
313691 TAGTTTACTT
* *
313701 TCGCAACACGAACTTAAAA
1 TCGCAACGCGAACTCAAAA
313720 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCG-AACTCAAAA
* *
313739 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAACTCAAAA
*
313758 TCGCAA--CG-A--CAGAA
1 TCGCAACGCGAACTCAAAA
313772 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCG-AACTCAAAA
313791 TCGCAACG
1 TCGCAACG
313799 ACAAGATCGC
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.14
16 3 0.05
17 2 0.03
18 3 0.05
19 45 0.69
20 3 0.05
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAACTCAAAA
Found at i:313779 original size:33 final size:32
Alignment explanation
Indices: 313736--313827 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
313726 CGCGAAACCA
**
313736 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
313768 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
313801 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
313828 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.18
33 46 0.82
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:313850 original size:19 final size:19
Alignment explanation
Indices: 313823--313957 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
313813 CGAAACCAAA
*
313823 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
313842 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
313858 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
313875 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
313891 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
313908 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
313927 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
313947 TCGTGTTGCGA
1 TCGCGTTGCGA
313958 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:313864 original size:14 final size:14
Alignment explanation
Indices: 313845--313901 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
313835 TTTCATTTCG
313845 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
313859 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
313876 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
313892 CGTTGCGATT
1 CGTTGCGATT
313902 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:313870 original size:33 final size:33
Alignment explanation
Indices: 313828--313920 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
313818 CCAAATCGCA
*
313828 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
313861 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
313894 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
313921 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:315360 original size:14 final size:14
Alignment explanation
Indices: 315341--315376 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
315331 ATTGTTTAAT
315341 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
315355 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
315369 TGATTTGT
1 TGATTTGT
315377 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:315569 original size:20 final size:19
Alignment explanation
Indices: 315483--315583 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
315473 AAAAATGACT
315483 ATCGCAATGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
315501 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
315520 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
315534 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
315553 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
315573 ATCGCAATGCG
1 ATCGCAATGCG
315584 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 28 0.38
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:315636 original size:19 final size:19
Alignment explanation
Indices: 315612--315903 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
315602 GATTATCTCG
315612 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315631 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315650 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
315664 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315683 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315702 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315721 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315740 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315759 TTGCGATTTT-ATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
315777 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
315791 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
315810 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
315829 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
315843 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
315863 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
315877 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
315896 TTGCGATT
1 TTGCGATT
315904 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 6, Indels: 44
0.83 0.02 0.15
Matches are distributed among these distances:
14 29 0.12
16 26 0.11
17 18 0.07
18 17 0.07
19 143 0.58
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:315652 original size:52 final size:52
Alignment explanation
Indices: 315590--315903 Score: 337
Period size: 52 Copynumber: 5.9 Consensus size: 52
315580 TGCGTTTATA
*
315590 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
315642 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
315694 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
315751 ATTTCGCATTGCGATTTTATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TTATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
315802 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
315854 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
315904 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 7, Indels: 27
0.88 0.03 0.10
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 33 0.14
52 100 0.41
53 22 0.09
54 5 0.02
55 5 0.02
56 14 0.06
57 48 0.20
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:318403 original size:24 final size:24
Alignment explanation
Indices: 318369--318415 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
318359 TCTGAACATC
318369 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
318393 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
318416 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:319121 original size:20 final size:20
Alignment explanation
Indices: 319093--319461 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
319083 AAATTTAAGT
* * * *
319093 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
319113 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
319133 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
319153 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
319173 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
319193 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
319213 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
319233 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
319253 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
319273 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
319293 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
319313 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
319333 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
319353 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
319373 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
319393 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
319413 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
319433 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
319453 GTTGCGATT
1 GTTGCGATT
319462 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:324425 original size:37 final size:37
Alignment explanation
Indices: 324352--324426 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
324342 GTTGGAAAAT
*
324352 ATTTATATATTTTCTTTACAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTACAAAAATTAAAATCATAAA
*
324389 ATTTATATAATTTTTTTTAC-AAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTACAAAAATT-AAAATCATAAA
324426 A
1 A
324427 ATGTTTATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTACAAAAATTAAAATCATAAA
Found at i:324428 original size:38 final size:38
Alignment explanation
Indices: 324347--324428 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
324337 AGTAAGTTGG
*
324347 AAAATATTTATATATTTTCTTTACAAAAATTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTACAAAAATTAAAATCAT
*
324386 -AAAATTTATATAATTTTTTTTAC-AAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTACAAAAATT-AAAATCAT
324423 AAAAAT
1 AAAAAT
324429 GTTTATTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
37 16 0.42
38 22 0.58
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTACAAAAATTAAAATCAT
Found at i:329021 original size:41 final size:44
Alignment explanation
Indices: 328956--329038 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 44
328946 TAATTTTATA
*
328956 ACAATTAGTGACTAAAATTAAAAAGT-ATAATA-TTT-ATGAGG
1 ACAATTAGTGACGAAAATTAAAAAGTGATAATAGTTTGATGAGG
*
328997 ACAATTAGTGACG-AAACTATAAAAGTGATAATAGTTTGATGA
1 ACAATTAGTGACGAAAATTA-AAAAGTGATAATAGTTTGATGA
329039 CTAGTGATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
40 5 0.14
41 18 0.50
42 6 0.17
43 3 0.08
44 4 0.11
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (44 bp):
ACAATTAGTGACGAAAATTAAAAAGTGATAATAGTTTGATGAGG
Found at i:330229 original size:16 final size:16
Alignment explanation
Indices: 330203--330253 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
330193 CTTTAGAAAA
*
330203 TTTAAATTATTATATAT
1 TTTAAA-TATTTTATAT
*
330220 TTTAAATATTTTTTAT
1 TTTAAATATTTTATAT
330236 ATTTAAA-ATTTTATAT
1 -TTTAAATATTTTATAT
330252 TT
1 TT
330254 ATATCTCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 16 0.53
17 12 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAAATATTTTATAT
Found at i:333579 original size:23 final size:23
Alignment explanation
Indices: 333535--333579 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
333525 TTTTCAATAA
* *
333535 CTTTATCTTTATGACACGTTTTT
1 CTTTATCTTCATGACACATTTTT
* *
333558 CTTTATCTTCGTGGCACATTTT
1 CTTTATCTTCATGACACATTTT
333580 CCTCTTCCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (23 bp):
CTTTATCTTCATGACACATTTTT
Found at i:336096 original size:2 final size:2
Alignment explanation
Indices: 336089--336116 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
336079 TTGTTCACAA
336089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
336117 CCGATGGCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:352011 original size:6 final size:6
Alignment explanation
Indices: 351944--352007 Score: 114
Period size: 6 Copynumber: 11.0 Consensus size: 6
351934 TATATATTTG
351944 CATTAT CATTAT CATTAT CATTAT CATTAT CATTAT CATTAT CATTAT
1 CATTAT CATTAT CATTAT CATTAT CATTAT CATTAT CATTAT CATTAT
351992 CATTAT -ATTAT -ATTAT
1 CATTAT CATTAT CATTAT
352008 TATTTTGAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.17
6 48 0.83
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (6 bp):
CATTAT
Found at i:353287 original size:16 final size:16
Alignment explanation
Indices: 353266--353298 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
353256 TAATAAATAA
353266 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
353282 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
353298 A
1 A
353299 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:353381 original size:16 final size:16
Alignment explanation
Indices: 353360--353416 Score: 114
Period size: 16 Copynumber: 3.6 Consensus size: 16
353350 CGTTCATTTA
353360 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
353376 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
353392 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
353408 ATAAACGAA
1 ATAAACGAA
353417 TATAAACGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.07
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:354386 original size:14 final size:14
Alignment explanation
Indices: 354367--354393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
354357 GAACATAACC
354367 GAACATAACCGAAT
1 GAACATAACCGAAT
354381 GAACATAACCGAA
1 GAACATAACCGAA
354394 CGTTCACGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.22, G:0.15, T:0.11
Consensus pattern (14 bp):
GAACATAACCGAAT
Found at i:354394 original size:10 final size:10
Alignment explanation
Indices: 354347--354379 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
354337 ATAAATGAAT
*
354347 GAACATAAAC
1 GAACATAACC
354357 GAACATAACC
1 GAACATAACC
354367 GAACATAACC
1 GAACATAACC
354377 GAA
1 GAA
354380 TGAACATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.09
Consensus pattern (10 bp):
GAACATAACC
Found at i:357236 original size:2 final size:2
Alignment explanation
Indices: 357229--357285 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
357219 GATCCTAACC
357229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
357271 AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT
357286 TTTCACTCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:357621 original size:2 final size:2
Alignment explanation
Indices: 357614--357657 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
357604 TTCTTTTCTA
357614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
357656 AT
1 AT
357658 TGACATCTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360464 original size:17 final size:17
Alignment explanation
Indices: 360423--360466 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
360413 GATTTGACTG
**
360423 TTAAATATTAAATTATT
1 TTAAATATTAAATTAGA
360440 TTAAATATTAAATTAGA
1 TTAAATATTAAATTAGA
*
360457 TTATATATTA
1 TTAAATATTA
360467 TATGCATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAATATTAAATTAGA
Found at i:361344 original size:14 final size:15
Alignment explanation
Indices: 361313--361345 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
361303 GATAAACGAT
361313 AAATAACAAACCCTA
1 AAATAACAAACCCTA
*
361328 AAATAA-AAATCCTA
1 AAATAACAAACCCTA
361342 AAAT
1 AAAT
361346 CTAAACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAACAAACCCTA
Found at i:371370 original size:297 final size:287
Alignment explanation
Indices: 370817--371471 Score: 753
Period size: 297 Copynumber: 2.2 Consensus size: 287
370807 CATTTATTTA
* * * * * *
370817 TTAGTACTTAAAATTATATTTTT-TGTCGAAATTGACTCATAATTATTTTTATTTTTTGTAATTT
1 TTAGTCCTTAAAATTATATTTTTAT-CCAAAATTAACACATAATTATTTTTATTTTTTATAATTT
*** * * *** * * * *
370881 ACTCC-ATATTATATAAATTACATCATAAACTTCAAACCCTATAACTTATATCAGGA-AT-TCAT
65 ACTCCGA-AACCTATAAATCACATCATAAACTAC-ATTTCAAAAACCTATA--A-AATATATCAT
** * * * ** *
370943 AATCTCTTAACCTATAAACTTTTTTTCACCAATTTTTCAAATGAATGTAATTTAGTTCATTTTGA
125 AATCTCCAAACCTATAAACTTTTGTTCACCAACTTTGCAAATGAAAATAATTTAGTCCATTTTGA
* *
371008 TATTAATTTCAACTTTACATTTTACAATTGTTTTAATTTGATCCTTGCATGTTGTTTAGTTTATT
190 TATTAATTTCAACTTTACATTTTACAATTGTTTCAATTTGATCCATG-ATGTTGTTTA----ATT
* *
371073 TAAATTTAAATTTCAGTTTGTAATTTTATGTTTGTTCAAT
250 T--ATTTAAATTTTAGTTTGTAATTTAATGTTTGTTCAAT
* * *
371113 TTAGTCCTTAAAATTATATTTTTATCCAAAATTAACACATATTTATTTCTTTTTTTTTTGTAATT
1 TTAGTCCTTAAAATTATATTTTTATCCAAAATTAACACATAATTA-TT-TTTATTTTTTATAATT
371178 TACTCCGAAACCTATAAATCACATCATAAACTACATTTCAAAAACCTATAAAATATATCATAATC
64 TACTCCGAAACCTATAAATCACATCATAAACTACATTTCAAAAACCTATAAAATATATCATAATC
*
371243 TCCAAATCCTATAAACTTTTGTTCACCAACTTTGCAAATGAAAATAATTTAGTCCATTTTTATAT
129 TCCAAA-CCTATAAACTTTTGTTCACCAACTTTGCAAATGAAAATAATTTAGTCCATTTTGATAT
* *
371308 TAATTTCAGCTTTACATTTTTACAATTGTTTCAATTTGATCCATG-TGTTTTTTTAATTTATTTA
193 TAATTTCAACTTTACA-TTTTACAATTGTTTCAATTTGATCCATGATG-TTGTTTAATTTATTTA
*
371372 AATTTTAGTTTGTAATTTAATTTTTGTTCAAT
256 AATTTTAGTTTGTAATTTAATGTTTGTTCAAT
* * *
371404 TTAGTCCTTAAAATTATATTTTTATCCAAAATTAGCCCGTAATTATTTTTATTTTTTATAATTTA
1 TTAGTCCTTAAAATTATATTTTTATCCAAAATTAACACATAATTATTTTTATTTTTTATAATTTA
371469 CTC
66 CTC
371472 TAAACCATAT
Statistics
Matches: 309, Mismatches: 41, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
289 19 0.06
290 2 0.01
291 75 0.24
293 4 0.01
294 1 0.00
295 3 0.01
296 51 0.17
297 85 0.28
298 68 0.22
299 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (287 bp):
TTAGTCCTTAAAATTATATTTTTATCCAAAATTAACACATAATTATTTTTATTTTTTATAATTTA
CTCCGAAACCTATAAATCACATCATAAACTACATTTCAAAAACCTATAAAATATATCATAATCTC
CAAACCTATAAACTTTTGTTCACCAACTTTGCAAATGAAAATAATTTAGTCCATTTTGATATTAA
TTTCAACTTTACATTTTACAATTGTTTCAATTTGATCCATGATGTTGTTTAATTTATTTAAATTT
TAGTTTGTAATTTAATGTTTGTTCAAT
Found at i:379615 original size:4 final size:4
Alignment explanation
Indices: 379606--379655 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
379596 ATGGCTTGTA
* *
379606 TCTT TCTT TCTT TCTT TCTT TCCT T-TT T-TT TCTT TCCCTT TTTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T--CTT TCTT TCTT
379654 TC
1 TC
379656 CTTTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 5 0.13
4 30 0.77
6 4 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:379639 original size:14 final size:14
Alignment explanation
Indices: 379608--379664 Score: 82
Period size: 14 Copynumber: 4.2 Consensus size: 14
379598 GGCTTGTATC
*
379608 TTTCTTT-C-TTTC
1 TTTCTTTCCTTTTT
379620 TTTCTTTCCTTTTT
1 TTTCTTTCCTTTTT
*
379634 TTTCTTTCCCTTTT
1 TTTCTTTCCTTTTT
379648 TTTCTTTCCTTTTT
1 TTTCTTTCCTTTTT
379662 TTT
1 TTT
379665 TTGATAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.17
13 1 0.03
14 32 0.80
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTCCTTTTT
Found at i:381576 original size:33 final size:33
Alignment explanation
Indices: 381534--381610 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
381524 ATATACGAAC
381534 GAACACGAACAGAGGTGGGTTTGTTTCATTTAT
1 GAACACGAACAGAGGTGGGTTTGTTTCATTTAT
*
381567 GAACACGAACAGAGGTGTGTTTGTTTCATTTAT
1 GAACACGAACAGAGGTGGGTTTGTTTCATTTAT
**
381600 GTTCACGAACA
1 GAACACGAACA
381611 AACTCGTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (33 bp):
GAACACGAACAGAGGTGGGTTTGTTTCATTTAT
Found at i:381961 original size:30 final size:31
Alignment explanation
Indices: 381904--381961 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
381894 AACACGCTCG
**
381904 CAAACAATAAATAAATAAACATGAACACCTT
1 CAAACAATAAATAAATAAACAAAAACACCTT
* *
381935 CAAA-AATTAATAAATGAACAAAAACAC
1 CAAACAATAAATAAATAAACAAAAACAC
381962 AATATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.62, C:0.17, G:0.03, T:0.17
Consensus pattern (31 bp):
CAAACAATAAATAAATAAACAAAAACACCTT
Found at i:382671 original size:28 final size:28
Alignment explanation
Indices: 382627--382680 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
382617 CCATTTACAA
* *
382627 TATATTGTCGAGTCAATGCTTAAAAGAT
1 TATATTGTCGAGCCAATACTTAAAAGAT
* *
382655 TATATTGTCGGGCCAATACTTGAAAG
1 TATATTGTCGAGCCAATACTTAAAAG
382681 CAACGACGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (28 bp):
TATATTGTCGAGCCAATACTTAAAAGAT
Found at i:383120 original size:15 final size:16
Alignment explanation
Indices: 383100--383133 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
383090 AGGGCTCAAA
*
383100 TTATTAA-TATTTGAT
1 TTATTAATTAGTTGAT
383115 TTATTAATTAGTTGAT
1 TTATTAATTAGTTGAT
383131 TTA
1 TTA
383134 AATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TTATTAATTAGTTGAT
Found at i:390684 original size:32 final size:33
Alignment explanation
Indices: 390627--390688 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
390617 TCATAGTTTT
* *
390627 AATAAATTAAAATAAATTTACCTACAAATATAA
1 AATAAATTAAAATAAAATTAACTACAAATATAA
390660 AATAAATT-AAATAAAATTAACTACAAATA
1 AATAAATTAAAATAAAATTAACTACAAATA
390689 GTCCATGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (33 bp):
AATAAATTAAAATAAAATTAACTACAAATATAA
Found at i:391353 original size:29 final size:27
Alignment explanation
Indices: 391320--391384 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
391310 TATTTTGTTG
391320 TTTAAAAATTAAATAAAT-ATTTAAACTTT
1 TTTAAAAATT-AATAAATCATTT-AA-TTT
*
391349 TTTAAAACA-TAATAAATCCTTTAATTT
1 TTTAAAA-ATTAATAAATCATTTAATTT
391376 TTTAAAAAT
1 TTTAAAAAT
391385 CAATTACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 1 0.03
27 10 0.31
28 9 0.28
29 11 0.34
30 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTAAAAATTAATAAATCATTTAATTT
Found at i:393920 original size:16 final size:16
Alignment explanation
Indices: 393899--393929 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
393889 TTAATTTAGC
393899 CTTACCTCACATCACA
1 CTTACCTCACATCACA
393915 CTTACCTCACATCAC
1 CTTACCTCACATCAC
393930 CCTGGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.45, G:0.00, T:0.26
Consensus pattern (16 bp):
CTTACCTCACATCACA
Found at i:407627 original size:2 final size:2
Alignment explanation
Indices: 407620--407684 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
407610 TATAAAATTT
407620 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
407662 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
407685 TCCTTCTCAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:409528 original size:29 final size:29
Alignment explanation
Indices: 409482--409568 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
409472 AACTCTCACC
409482 TAATTAAATTGATGTAAGCAATGACATCAT
1 TAATTAAA-TGATGTAAGCAATGACATCAT
*
409512 TAATTAAATGATGTAAGCAATGACATCTT
1 TAATTAAATGATGTAAGCAATGACATCAT
*
409541 TAATTAAATGATGTAAGTAATGACATCA
1 TAATTAAATGATGTAAGCAATGACATCA
409569 ATTTAGTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 46 0.85
30 8 0.15
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (29 bp):
TAATTAAATGATGTAAGCAATGACATCAT
Found at i:414295 original size:29 final size:29
Alignment explanation
Indices: 414249--414335 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
414239 AACTCTCACC
414249 TAATTAAATTGATGTAAGCAATGACATCAT
1 TAATTAAA-TGATGTAAGCAATGACATCAT
*
414279 TAATTAAATGATGTAAGCAATGACATCTT
1 TAATTAAATGATGTAAGCAATGACATCAT
*
414308 TAATTAAATGATGTAAGTAATGACATCA
1 TAATTAAATGATGTAAGCAATGACATCA
414336 ATTTAGTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 46 0.85
30 8 0.15
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (29 bp):
TAATTAAATGATGTAAGCAATGACATCAT
Found at i:417300 original size:36 final size:37
Alignment explanation
Indices: 417253--417326 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
417243 GATTACTGTA
417253 GTATTAGATTACTCTAATATG-GACTAACCTTTTTAT
1 GTATTAGATTACTCTAATATGAGACTAACCTTTTTAT
*
417289 GTATTAGATTACTCTAATATGAGACTAATCTTTTTAT
1 GTATTAGATTACTCTAATATGAGACTAACCTTTTTAT
417326 G
1 G
417327 ATAATAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 21 0.58
37 15 0.42
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (37 bp):
GTATTAGATTACTCTAATATGAGACTAACCTTTTTAT
Found at i:426184 original size:2 final size:2
Alignment explanation
Indices: 426177--426218 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
426167 TTGATAATGC
426177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
426219 ATACAGACGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:428395 original size:60 final size:59
Alignment explanation
Indices: 428328--428468 Score: 178
Period size: 59 Copynumber: 2.4 Consensus size: 59
428318 AAAGTATGGC
* * * *
428328 GAATAATTTAGAATGTATGTCATG-GTTTGGGGATGAAATTAAAATATTTAAAAGTTTGAG
1 GAATAATTTAGAATATA-ATCA-GAGTTTAGGGATGAAATTAAAATATTTAAAAGTTTAAG
* *
428388 GACTAATTTAGAATATAATCAGAGTTTAGGGATGAAATTAAAATATTTACAAGTTTAAG
1 GAATAATTTAGAATATAATCAGAGTTTAGGGATGAAATTAAAATATTTAAAAGTTTAAG
428447 GAATAATTT-GCAATGATAATCA
1 GAATAATTTAG-AAT-ATAATCA
428469 TACTTTGAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 2 0.03
59 47 0.66
60 22 0.31
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (59 bp):
GAATAATTTAGAATATAATCAGAGTTTAGGGATGAAATTAAAATATTTAAAAGTTTAAG
Found at i:428444 original size:29 final size:29
Alignment explanation
Indices: 428352--428444 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
428342 GTATGTCATG
* *
428352 GTTTGGGGATGAAATTAAAATATTTAAAA
1 GTTTAGGGATGAAATTAAAATATTTACAA
* * *
428381 GTTT-GAGGACT-AATTTAGAATA-TAATCAGA
1 GTTTAG-GGA-TGAAATTAAAATATTTA-CA-A
428411 GTTTAGGGATGAAATTAAAATATTTACAA
1 GTTTAGGGATGAAATTAAAATATTTACAA
428440 GTTTA
1 GTTTA
428445 AGGAATAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
28 3 0.06
29 24 0.48
30 20 0.40
31 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (29 bp):
GTTTAGGGATGAAATTAAAATATTTACAA
Found at i:429857 original size:16 final size:16
Alignment explanation
Indices: 429810--429857 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
429800 TTAGTTGAAA
*
429810 CGAAAACAACCCGAAT
1 CGAAAACAACTCGAAT
*
429826 CGAAATCAA-TCTGAAT
1 CGAAAACAACTC-GAAT
429842 CGAAAACAACTCGAAT
1 CGAAAACAACTCGAAT
429858 TTAATTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.89
17 2 0.07
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.15
Consensus pattern (16 bp):
CGAAAACAACTCGAAT
Found at i:430666 original size:31 final size:32
Alignment explanation
Indices: 430631--430707 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
430621 AACCGATACA
*
430631 ATATTGA-CTCGACCTGAAAA-CAACTGATCCG
1 ATATTGACCT-GACCCGAAAATCAACTGATCCG
**
430662 ATATTGACCTGACCCGAAAATCAACTGATTTG
1 ATATTGACCTGACCCGAAAATCAACTGATCCG
*
430694 ATATTAACCTGACC
1 ATATTGACCTGACC
430708 TGACTTATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 16 0.40
32 24 0.60
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (32 bp):
ATATTGACCTGACCCGAAAATCAACTGATCCG
Found at i:441121 original size:3 final size:3
Alignment explanation
Indices: 441113--441201 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
441103 TGTTTGATAC
441113 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
441161 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
441202 ACTAAACCGT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:466974 original size:15 final size:15
Alignment explanation
Indices: 466954--466983 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
466944 GATAAAGGAT
466954 TAGTATAAAGATATA
1 TAGTATAAAGATATA
466969 TAGTATAAAGATATA
1 TAGTATAAAGATATA
466984 AGGTGATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (15 bp):
TAGTATAAAGATATA
Found at i:473121 original size:22 final size:22
Alignment explanation
Indices: 473096--473138 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
473086 GAAAGTCAAC
**
473096 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCAAGTCGGGTCG
473118 GGTCAACGGTCAAGTCGGGTC
1 GGTCAACGGTCAAGTCGGGTC
473139 AAACCGGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCAAGTCGGGTCG
Found at i:480397 original size:22 final size:22
Alignment explanation
Indices: 480369--480411 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
480359 AACGGTCAAC
480369 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
480391 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
480412 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:482495 original size:2 final size:2
Alignment explanation
Indices: 482488--482514 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
482478 GGAGAGTAGC
482488 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
482515 CCTGGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:488071 original size:18 final size:18
Alignment explanation
Indices: 488048--488083 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
488038 TTGATCGTTG
488048 CAGATGGATATAACTCTT
1 CAGATGGATATAACTCTT
488066 CAGATGGATATAACTCTT
1 CAGATGGATATAACTCTT
488084 TCTTTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
CAGATGGATATAACTCTT
Found at i:488453 original size:23 final size:23
Alignment explanation
Indices: 488422--488500 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 23
488412 CATTTATGGT
488422 TTTATTTTTTAATTAATATATCG
1 TTTATTTTTTAATTAATATATCG
* * *
488445 TTTACTTTTTAATTAATTTATGG
1 TTTATTTTTTAATTAATATATCG
488468 TTTTATTTTTCTAAATGTAAATATATCG
1 -TTTATTTTT-T-AAT-T-AATATATCG
488496 TTTAT
1 TTTAT
488501 ATGTTACATA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 20 0.44
24 8 0.18
25 1 0.02
26 3 0.07
27 6 0.13
28 7 0.16
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTATTTTTTAATTAATATATCG
Found at i:502510 original size:23 final size:23
Alignment explanation
Indices: 502420--502502 Score: 130
Period size: 23 Copynumber: 3.6 Consensus size: 23
502410 AAGCTTATAT
* *
502420 GGCACTACAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
502443 GGCACTTCGATGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
502466 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
502489 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
502503 TTTATACGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:510373 original size:38 final size:37
Alignment explanation
Indices: 510331--510404 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
510321 TGAAAAATAT
* *
510331 TTATATATTTTCTTTTAAAAAATT-AAATTCATAAAAAA
1 TTATATAATTT-TTTTAAAAAATTGAAAAT-ATAAAAAA
*
510369 TTATATAATTTTTTTACAAAATTGAAAATATAAAAA
1 TTATATAATTTTTTTAAAAAATTGAAAATATAAAAA
510405 TGTTTAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 18 0.56
38 14 0.44
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
TTATATAATTTTTTTAAAAAATTGAAAATATAAAAAA
Found at i:510759 original size:23 final size:23
Alignment explanation
Indices: 510733--510787 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
510723 ATGTAGATTT
510733 CATTCCCATGGGAATGTGAATTC
1 CATTCCCATGGGAATGTGAATTC
* *
510756 CATTCCAATGGGAATGTGGATTC
1 CATTCCCATGGGAATGTGAATTC
510779 CATTCCCAT
1 CATTCCCAT
510788 CACATTCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (23 bp):
CATTCCCATGGGAATGTGAATTC
Found at i:513688 original size:2 final size:2
Alignment explanation
Indices: 513681--513753 Score: 102
Period size: 2 Copynumber: 39.0 Consensus size: 2
513671 TCTATAGTCT
*
513681 TA TA TA TA TA TA TA TA TA TA -A TA TA TA T- TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
513721 TA TA TA TA TA TA TA TA TA TA -A TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
513754 AAAAAATACA
Statistics
Matches: 65, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
1 5 0.08
2 60 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:514337 original size:31 final size:31
Alignment explanation
Indices: 514289--514363 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
514279 TTTTTATTAT
* *
514289 TTCGGGTAGGGTAGGGTTTATAATTCAAATA
1 TTCGGGTCGGGTCGGGTTTATAATTCAAATA
* *
514320 TTCGGGTCGGGTCGGGTTTCTAATTCATATA
1 TTCGGGTCGGGTCGGGTTTATAATTCAAATA
*
514351 TTTGGGTCGGGTC
1 TTCGGGTCGGGTC
514364 AGATCGGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.37
Consensus pattern (31 bp):
TTCGGGTCGGGTCGGGTTTATAATTCAAATA
Found at i:515227 original size:16 final size:17
Alignment explanation
Indices: 515202--515249 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
515192 ATATAAAATT
*
515202 AGATTCTAATTTCT-AC
1 AGATTTTAATTTCTGAC
* *
515218 CGATTTTAATTCCTTGAC
1 AGATTTTAATTTC-TGAC
515236 AGATTTTAATTTCT
1 AGATTTTAATTTCT
515250 CATTATAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 10 0.40
17 2 0.08
18 13 0.52
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (17 bp):
AGATTTTAATTTCTGAC
Found at i:515267 original size:12 final size:12
Alignment explanation
Indices: 515250--515274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
515240 TTTAATTTCT
515250 CATTATAATGAA
1 CATTATAATGAA
515262 CATTATAATGAA
1 CATTATAATGAA
515274 C
1 C
515275 CAAAAGGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (12 bp):
CATTATAATGAA
Found at i:520108 original size:17 final size:17
Alignment explanation
Indices: 520064--520120 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
520054 GTTCTATTTG
520064 TAATTAGTTATTATAATAA
1 TAATTA-TTATT-TAATAA
*
520083 -AATTTATTATTTATTAA
1 TAA-TTATTATTTAATAA
*
520100 TAATTATTATATAATAA
1 TAATTATTATTTAATAA
520117 TAAT
1 TAAT
520121 ATAAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 21 0.64
18 9 0.27
19 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAATTATTATTTAATAA
Found at i:520123 original size:13 final size:13
Alignment explanation
Indices: 520097--520136 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
520087 TATTATTTAT
*
520097 TAATAATTATTATA
1 TAATAA-TAATATA
520111 TAATAATAATATA
1 TAATAATAATATA
*
520124 AAATAATAATATA
1 TAATAATAATATA
520137 AAAAGGACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:520137 original size:13 final size:13
Alignment explanation
Indices: 520107--520139 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
520097 TAATAATTAT
*
520107 TATATAATAATAA
1 TATAAAATAATAA
520120 TATAAAATAATAA
1 TATAAAATAATAA
520133 TATAAAA
1 TATAAAA
520140 AGGACGGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TATAAAATAATAA
Found at i:523481 original size:125 final size:126
Alignment explanation
Indices: 523259--523510 Score: 497
Period size: 125 Copynumber: 2.0 Consensus size: 126
523249 ACCTCATTCC
523259 TGGACCATCCTTTTACGCTGTCATTGGGTCCTCATCATGGCCTGTAAGTATTCTGATGAACTGAA
1 TGGACCATCCTTTTACGCTGTCATTGGGTCCTCATCATGGCCTGTAAGTATTCTGATGAACTGAA
523324 GATCTATAAGGTTGATATTGGTTATTTCTAGTTGCAATTTCAATTGTTAGAC-AATGAATT
66 GATCTATAAGGTTGATATTGGTTATTTCTAGTTGCAATTTCAATTGTTAGACAAATGAATT
523384 TGGACCATCCTTTTACGCTGTCATTGGGTCCTCATCATGGCCTGTAAGTATTCTGATGAACTGAA
1 TGGACCATCCTTTTACGCTGTCATTGGGTCCTCATCATGGCCTGTAAGTATTCTGATGAACTGAA
523449 GATCTATAAGGTTGATATTGGTTATTTCTAGTTGCAATTTCAATTGTTAGACAAATGAATT
66 GATCTATAAGGTTGATATTGGTTATTTCTAGTTGCAATTTCAATTGTTAGACAAATGAATT
523510 T
1 T
523511 TAAATGTCCT
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 117 0.93
126 9 0.07
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (126 bp):
TGGACCATCCTTTTACGCTGTCATTGGGTCCTCATCATGGCCTGTAAGTATTCTGATGAACTGAA
GATCTATAAGGTTGATATTGGTTATTTCTAGTTGCAATTTCAATTGTTAGACAAATGAATT
Found at i:525015 original size:2 final size:2
Alignment explanation
Indices: 525010--525052 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
525000 TTGACCTTAC
525010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
525052 T
1 T
525053 GAAATATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:525537 original size:36 final size:36
Alignment explanation
Indices: 525490--525561 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
525480 GTTTGGATCT
525490 CCCAAAATGCAAATTTGTATAGTTGATACGCCCATC
1 CCCAAAATGCAAATTTGTATAGTTGATACGCCCATC
525526 CCCAAAATGCAAATTTGTATAGTTGATACGCCCATC
1 CCCAAAATGCAAATTTGTATAGTTGATACGCCCATC
525562 AGTTTGGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (36 bp):
CCCAAAATGCAAATTTGTATAGTTGATACGCCCATC
Found at i:526788 original size:46 final size:46
Alignment explanation
Indices: 526736--526828 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
526726 AAAGGAAAGA
526736 CAGAGGAGCAGCAAAAGAGCAAGTGATCATTTGTACAATCAATAAC
1 CAGAGGAGCAGCAAAAGAGCAAGTGATCATTTGTACAATCAATAAC
526782 CAGAGGAGCAGCAAAAGAGCAAGTGATCATTTGTACAATCAATAAC
1 CAGAGGAGCAGCAAAAGAGCAAGTGATCATTTGTACAATCAATAAC
526828 C
1 C
526829 CTTCTCAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (46 bp):
CAGAGGAGCAGCAAAAGAGCAAGTGATCATTTGTACAATCAATAAC
Found at i:530956 original size:12 final size:12
Alignment explanation
Indices: 530939--530970 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
530929 GGAGAAGTTT
530939 GAAGATGAGGAA
1 GAAGATGAGGAA
*
530951 GAAGATGAGGAT
1 GAAGATGAGGAA
530963 GAAGATGA
1 GAAGATGA
530971 ATCTGGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.41, T:0.12
Consensus pattern (12 bp):
GAAGATGAGGAA
Found at i:535152 original size:25 final size:24
Alignment explanation
Indices: 535119--535164 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
535109 ATATTATTAT
*
535119 TTTTTAAATTGT-TAAACAAAAAAC
1 TTTTTAAAATGTGTAAA-AAAAAAC
535143 TTTTTAAAATGTGTAAAAAAAA
1 TTTTTAAAATGTGTAAAAAAAA
535165 TATTAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (24 bp):
TTTTTAAAATGTGTAAAAAAAAAC
Found at i:555673 original size:39 final size:39
Alignment explanation
Indices: 555619--555695 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
555609 CATCACTCTT
555619 TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCTA
1 TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCTA
* * *
555658 TAAATCTTAGTTGATTGATTTGAATGTCAGAGATCCCT
1 TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCT
555696 CTTTTGATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (39 bp):
TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCTA
Found at i:556193 original size:20 final size:20
Alignment explanation
Indices: 556168--556208 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
556158 GTAAAACCGT
556168 AAGATTGATTAGCTGTCAAC
1 AAGATTGATTAGCTGTCAAC
556188 AAGATTGATTAGCTGTCAAC
1 AAGATTGATTAGCTGTCAAC
556208 A
1 A
556209 GTCAACATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
AAGATTGATTAGCTGTCAAC
Found at i:556903 original size:31 final size:31
Alignment explanation
Indices: 556848--556934 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
556838 TAGAAGTTAC
556848 AAAATGGTCATTAAACTTTATCAAACTATTAT
1 AAAATGGTCATTAAAC-TTATCAAACTATTAT
*
556880 AAAATGGTCATTAAACTTATCAAACTGTTAT
1 AAAATGGTCATTAAACTTATCAAACTATTAT
* * *
556911 TAGATGGTCCTTAAACTTATCAAA
1 AAAATGGTCATTAAACTTATCAAA
556935 TTTGTCACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 35 0.69
32 16 0.31
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (31 bp):
AAAATGGTCATTAAACTTATCAAACTATTAT
Found at i:559110 original size:17 final size:18
Alignment explanation
Indices: 559078--559111 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
559068 GTTGCACTTA
*
559078 TATTTTTTTGAAAAAATT
1 TATTCTTTTGAAAAAATT
559096 TATTCTTTT-AAAAAAT
1 TATTCTTTTGAAAAAAT
559112 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTCTTTTGAAAAAATT
Found at i:565606 original size:2 final size:2
Alignment explanation
Indices: 565599--565668 Score: 110
Period size: 2 Copynumber: 36.5 Consensus size: 2
565589 AGTTAAGCTT
*
565599 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565640 TA TA TA TA -A TA TA TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
565669 GAGATTAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
1 3 0.05
2 60 0.95
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Done.