Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001989.1 Hibiscus syriacus cultivar Beakdansim tig00004063_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: 499561
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 3
Found at i:218652 original size:118 final size:118
Alignment explanation
Indices: 218359--218697 Score: 421
Period size: 118 Copynumber: 2.8 Consensus size: 118
218349 TATTAAGTGA
* *
218359 CATGATTGAATTGAACTGAATTATGAATTATTGCATGCTGCCATGATTGAATTAAGTCGAATTGT
1 CATGATTGAATTGAACTGAATTGTGAATTATTGCATGCTGCCATGATTGAATTAAGTTGAATTGT
* * * * *
218424 GAATAATTGAATGTTGCCATTATCGAATT-AAGTTGAATTGTGAATTATTGCATGCTAC
66 GAATTATTGCATGTTGCC---A-CG-ATTGAA-TTGAATTATGAATTATTACATGATAC
* * *
218482 CATGATTGAATTGAACTGAATTGTGAATTATTTCATGTTGCCATGGTTGAATTAAGTTGAATTGT
1 CATGATTGAATTGAACTGAATTGTGAATTATTGCATGCTGCCATGATTGAATTAAGTTGAATTGT
* *
218547 GAATTATTGCATGCTGCCACGATTGAATTGAATTATGAATTATTACATGATGC
66 GAATTATTGCATGTTGCCACGATTGAATTGAATTATGAATTATTACATGATAC
* * * * * *
218600 CATGATTGAATTGAA-TCGAATTGTGGATTATTGCATACTGTCATGATCGAATTGAGTTGAATGG
1 CATGATTGAATTGAACT-GAATTGTGAATTATTGCATGCTGCCATGATTGAATTAAGTTGAATTG
* *
218664 TGAATTATTGCATGTTGCCATGATTGAACTGAAT
65 TGAATTATTGCATGTTGCCACGATTGAATTGAAT
218698 CGAATTGTTA
Statistics
Matches: 190, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
117 1 0.01
118 109 0.57
119 4 0.02
120 1 0.01
123 75 0.39
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (118 bp):
CATGATTGAATTGAACTGAATTGTGAATTATTGCATGCTGCCATGATTGAATTAAGTTGAATTGT
GAATTATTGCATGTTGCCACGATTGAATTGAATTATGAATTATTACATGATAC
Found at i:219185 original size:208 final size:209
Alignment explanation
Indices: 218794--219212 Score: 815
Period size: 207 Copynumber: 2.0 Consensus size: 209
218784 CAATTAGGAA
218794 TTAAATGTATAATATTGACATGGAAGAATCCTTTATGGCTATGTTATGGAAAAAATGATTTCTTG
1 TTAAATGTATAATATTGACATGGAAGAATCCTTTATGGCTATGTTATGGAAAAAATGATTTCTTG
218859 GAAAATTAAATTCAAGTCTTTGGTTAATAGTTAGTCCAAGATATAAGGGCATGCCTTAGATTCTA
66 GAAAATTAAATTCAAGTCTTTGGTTAATAGTTAGTCCAAGATATAAGGGCATGCCTTAGATTCTA
218924 GAGCTCAATTGTTTATGGGGAGTACGGTCCAGCACTACGATGCTAATTGATGATAGATGGAGGAT
131 GAGCTCAATTGTTTATGGGGAGTACGGTCCAGCACTACGATGCTAATTGATGATAGATGGAGGAT
218989 ACGTTATGTGGTCT
196 ACGTTATGTGGTCT
219003 TTAAATGTA-AATATTGACATGGAAGAATCC-TTATGGCTATGTTATGGAAAAAATGATTTCTTG
1 TTAAATGTATAATATTGACATGGAAGAATCCTTTATGGCTATGTTATGGAAAAAATGATTTCTTG
219066 GAAAATTAAATTCAAGTCTTTGGTTAATAGTTAGTCCAAGATATAAGGGCATGCCTTAGATTCTA
66 GAAAATTAAATTCAAGTCTTTGGTTAATAGTTAGTCCAAGATATAAGGGCATGCCTTAGATTCTA
219131 GAGCTCAATTGTTTATGGGGGAGTACGGTCCAGCACTACGATGCTAATTGATGATAGATGGAGGA
131 GAGCTCAATTGTTTAT-GGGGAGTACGGTCCAGCACTACGATGCTAATTGATGATAGATGGAGGA
219196 TACGTTATGTGGTCT
195 TACGTTATGTGGTCT
219211 TT
1 TT
219213 GGTGATAGTA
Statistics
Matches: 209, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
207 114 0.55
208 86 0.41
209 9 0.04
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (209 bp):
TTAAATGTATAATATTGACATGGAAGAATCCTTTATGGCTATGTTATGGAAAAAATGATTTCTTG
GAAAATTAAATTCAAGTCTTTGGTTAATAGTTAGTCCAAGATATAAGGGCATGCCTTAGATTCTA
GAGCTCAATTGTTTATGGGGAGTACGGTCCAGCACTACGATGCTAATTGATGATAGATGGAGGAT
ACGTTATGTGGTCT
Found at i:225201 original size:7 final size:7
Alignment explanation
Indices: 225191--225225 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
225181 ATATATCTAA
225191 ACTATAT
1 ACTATAT
225198 ACTATAT
1 ACTATAT
225205 ACTATAT
1 ACTATAT
*
225212 ATTATAT
1 ACTATAT
225219 ACTATAT
1 ACTATAT
225226 TATAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (7 bp):
ACTATAT
Found at i:225834 original size:44 final size:44
Alignment explanation
Indices: 225786--225899 Score: 158
Period size: 44 Copynumber: 2.6 Consensus size: 44
225776 ATTTTCATTT
* **
225786 ATCCAACTCCTTTTGTGAAGGATCAAGTGAA-AAGATTGTTACTG
1 ATCCAACTCCTTCTGTGAAGGATCAAGT-AACAAGATTAATACTG
*
225830 ATCCAACTCCTTCTGTGAAGGATCAAGTAACATGATTAATACTG
1 ATCCAACTCCTTCTGTGAAGGATCAAGTAACAAGATTAATACTG
* *
225874 ATCCAACTCATTCTGTGAAGAATCAA
1 ATCCAACTCCTTCTGTGAAGGATCAA
225900 AGCAATTTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 2 0.03
44 61 0.97
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCCAACTCCTTCTGTGAAGGATCAAGTAACAAGATTAATACTG
Found at i:226229 original size:350 final size:354
Alignment explanation
Indices: 225748--226443 Score: 857
Period size: 350 Copynumber: 2.0 Consensus size: 354
225738 CGCTGATTCA
* * * *
225748 ACTCCTTCTGTGAAGAATCGCACAAAAGATTTTCATTTATCCAACTCCTTTTGTGAAGGATCAAG
1 ACTCCTTCTGTGAAGAACCGCACAAAAGATTTTCACTAATCCAACTCCTTTTATGAAGGATCAAG
** **
225813 TGAAAAGATTGTTACTGATCCAACTCCTTCTGTGAAGGATCAAGTAACATGATTAATACTGATCC
66 TGAAAAGAGCGTTACTGATCCAACTCCTTCTGTGAAGGATCAAGTAACATGACAAATACTGATCC
* * * * * * *
225878 AACTCATTCTGTGAAGAATCAAAGCAATTTCCCAATACCGATTTACCTCCTTCTGTGTTAGAATC
131 AACTCATTCTGTGAAGAACCAAAGCAATTTCACAACACCAATCTACCTCCTTCTGTGATAAAATC
* * * *
225943 GAACAAAATAAGATTATGTTGATTCAACTCCTTATGTGAAGAAT-TGAGCGGAATGA-CACTATT
196 AAACAAAATAAGATTATGCTGATTCAACTCCTTATGTGAAGAATAT-AGCAGAA-GATCACTACT
*** * **
226006 GATCCAACTCCTTCTATGAAGAATCAAAC-AAAATGTTGATGCTGATCTACCTCATTTTGTGATA
259 GATCCAACTCCTTCTATGAAGAATCAAACAAAAATACCGATGCTGATCTACATCATTCCGTGATA
*
226070 GAATCGAGCAAAATAAGATTATTCTGGATCG
324 GAATCGAGCAAAAGAAGATTATTCTGGATCG
226101 ACTCCTTCTGTGAAGAACCG-AGCAAAAGATTTTCACTAAT-CAACT-CTTTTATGAAGGATCAA
1 ACTCCTTCTGTGAAGAACCGCA-CAAAAGATTTTCACTAATCCAACTCCTTTTATGAAGGATCAA
* * ** * **
226163 GTG-AAAGGGCGTTATTGATCTGACTCCTTCTGTGAAGGATCGAGTAACATGACAAATGTTGATC
65 GTGAAAAGAGCGTTACTGATCCAACTCCTTCTGTGAAGGATCAAGTAACATGACAAATACTGATC
* * * * * *
226227 CAACTCCTTCTGTGAAGGACCAAAGTAATTTGACAACGCCAATCTATCTCCTTCTGTGATAAAAT
130 CAACTCATTCTGTGAAGAACCAAAGCAATTTCACAACACCAATCTACCTCCTTCTGTGATAAAAT
* * * ***
226292 CAAACAAAATTAGATTATGCTGTTTCAACTCCTTCTGTGAAGAATATAGCAGAAGATTGGTACTG
195 CAAACAAAATAAGATTATGCTGATTCAACTCCTTATGTGAAGAATATAGCAGAAGATCACTACTG
* * * *
226357 ATCCATCTCCTTCTGTGAAGAATCAAACAAAAAATACCGATGTTGATCTACATCCTTCCGTGATA
260 ATCCAACTCCTTCTATGAAGAATCAAAC-AAAAATACCGATGCTGATCTACATCATTCCGTGATA
*
226422 GAATTGAGCAAAAGAAGATTAT
324 GAATCGAGCAAAAGAAGATTAT
226444 GGTGATCCAA
Statistics
Matches: 288, Mismatches: 50, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
349 2 0.01
350 178 0.62
351 20 0.07
352 53 0.18
353 35 0.12
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (354 bp):
ACTCCTTCTGTGAAGAACCGCACAAAAGATTTTCACTAATCCAACTCCTTTTATGAAGGATCAAG
TGAAAAGAGCGTTACTGATCCAACTCCTTCTGTGAAGGATCAAGTAACATGACAAATACTGATCC
AACTCATTCTGTGAAGAACCAAAGCAATTTCACAACACCAATCTACCTCCTTCTGTGATAAAATC
AAACAAAATAAGATTATGCTGATTCAACTCCTTATGTGAAGAATATAGCAGAAGATCACTACTGA
TCCAACTCCTTCTATGAAGAATCAAACAAAAATACCGATGCTGATCTACATCATTCCGTGATAGA
ATCGAGCAAAAGAAGATTATTCTGGATCG
Found at i:226620 original size:177 final size:179
Alignment explanation
Indices: 226308--226731 Score: 485
Period size: 177 Copynumber: 2.4 Consensus size: 179
226298 AAATTAGATT
* * ** * ***
226308 ATGCTG-TTTCAACTCCTTCTGTGAAGAATATAGCAGAAGATTGGTACTGATCCATCTCCTTCTG
1 ATGCTGATTT-AACTCATTCTATGAAGAATCGAGCAAAAGATTAACACTGATCCATCTCCTTCTG
*
226372 TGAAGAATCAAACAAAAAATACCGATGTTGATCTACATCCTTCCGTGATAGAATTGAGCAAAAGA
65 TGAAGAAT-AAACAAAAAATACCGATGTTGATCTACATCCTTCCGTGATAGAATCGAGCAAAAGA
* *
226437 AGATTATGGTGATCCAACTTCGTATGTTAAGGATTGAGAAAAAGATTGGTA
129 AGATTATGGTGATCCAACTTCGTATGTGAAGGATCGAGAAAAAGATTGGTA
* * * * *
226488 ATGTTGATTTAAGTCCTTCTATGACGAATCGAGCAAAAGATTAACACTGATCCATCTCCTTTTGT
1 ATGCTGATTTAACTCATTCTATGAAGAATCGAGCAAAAGATTAACACTGATCCATCTCCTTCTGT
* *** * * ** * *
226553 GAATAAT-AA-AAAAAATGTTGATGTTGATCTACCTCTTTCTTTGATAGAATCGAGTAAAATAAG
66 GAAGAATAAACAAAAAATACCGATGTTGATCTACATCCTTCCGTGATAGAATCGAGCAAAAGAAG
* * * * *
226616 ATTATGTTGATCCAACTTCTTCTGTGAATGATCGAGAAAAAGATTGGTT
131 ATTATGGTGATCCAACTTCGTATGTGAAGGATCGAGAAAAAGATTGGTA
* * * * *
226665 ATGCTGATTTAACTCATTCTATGAATAATCGAGTAAAATATTAACACTGATCTACCTCCTTCTGT
1 ATGCTGATTTAACTCATTCTATGAAGAATCGAGCAAAAGATTAACACTGATCCATCTCCTTCTGT
226730 GA
66 GA
226732 CGAAATCAAG
Statistics
Matches: 204, Mismatches: 39, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
177 143 0.70
178 2 0.01
180 56 0.27
181 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (179 bp):
ATGCTGATTTAACTCATTCTATGAAGAATCGAGCAAAAGATTAACACTGATCCATCTCCTTCTGT
GAAGAATAAACAAAAAATACCGATGTTGATCTACATCCTTCCGTGATAGAATCGAGCAAAAGAAG
ATTATGGTGATCCAACTTCGTATGTGAAGGATCGAGAAAAAGATTGGTA
Found at i:227982 original size:7 final size:7
Alignment explanation
Indices: 227959--228081 Score: 101
Period size: 7 Copynumber: 17.6 Consensus size: 7
227949 TGAACTCACG
227959 TTTTCTTT
1 TTTTC-TT
227967 TTCTTCTT
1 TT-TTCTT
227975 TTTTC-T
1 TTTTCTT
227981 TTTTC-T
1 TTTTCTT
*
227987 TTCTCTT
1 TTTTCTT
227994 TTTCTCTT
1 TTT-TCTT
228002 TTTTCTT
1 TTTTCTT
*
228009 TCTTCTT
1 TTTTCTT
*
228016 TCTTCTT
1 TTTTCTT
*
228023 TCTTCTT
1 TTTTCTT
*
228030 TCTTCTT
1 TTTTCTT
228037 TTTTCTT
1 TTTTCTT
*
228044 TCTTC-T
1 TTTTCTT
*
228050 TTTTCAT
1 TTTTCTT
*
228057 TTCT-TT
1 TTTTCTT
*
228063 TTTTCCT
1 TTTTCTT
228070 TTTTCTT
1 TTTTCTT
228077 CTTTT
1 -TTTT
228082 TTATTTTTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
6 20 0.20
7 58 0.59
8 17 0.17
9 3 0.03
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:228015 original size:14 final size:14
Alignment explanation
Indices: 227960--228083 Score: 123
Period size: 14 Copynumber: 8.9 Consensus size: 14
227950 GAACTCACGT
*
227960 TTTCTT-TTTCTTC
1 TTTCTTCTTTTTTC
*
227973 TTTTTTC-TTTTTC
1 TTTCTTCTTTTTTC
227986 TTTC-TCTTTTTCTC
1 TTTCTTCTTTTT-TC
* *
228000 TTTTTTCTTTCTTC
1 TTTCTTCTTTTTTC
*
228014 TTTCTTCTTTCTTC
1 TTTCTTCTTTTTTC
228028 TTTCTTCTTTTTTC
1 TTTCTTCTTTTTTC
228042 TTTCTTC-TTTTTC
1 TTTCTTCTTTTTTC
*
228055 ATTTCTT-TTTTTCCTT
1 -TTTCTTCTTTTT--TC
228071 TTTCTTCTTTTTT
1 TTTCTTCTTTTTT
228084 ATTTTTTTCA
Statistics
Matches: 94, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.02
13 23 0.24
14 51 0.54
15 12 0.13
16 6 0.06
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTCTTTTTTC
Found at i:239191 original size:21 final size:21
Alignment explanation
Indices: 239154--239194 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
239144 CTAAAAACCT
*
239154 AAAATCTAAGGCTTAATTAAA
1 AAAATCTAAGACTTAATTAAA
239175 AAAATCTAAAGAC-TAATTAA
1 AAAATCT-AAGACTTAATTAA
239195 TATTTAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAATCTAAGACTTAATTAAA
Found at i:245095 original size:16 final size:16
Alignment explanation
Indices: 245074--245108 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
245064 CCCTTAATTT
245074 TCTTCATTTCTCTTAC
1 TCTTCATTTCTCTTAC
245090 TCTTCATTTCTCTTAC
1 TCTTCATTTCTCTTAC
245106 TCT
1 TCT
245109 CCGAGCTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.31, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTTCATTTCTCTTAC
Found at i:254263 original size:20 final size:21
Alignment explanation
Indices: 254206--254268 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
254196 TCGGAGGACT
*
254206 GGTATCCATACCGAATGAGTT-
1 GGTATCCATACCGAA-GACTTG
**
254227 GGTATCCATACTAAAGA-TTG
1 GGTATCCATACCGAAGACTTG
*
254247 GGTACCCATACCGAAGACTTG
1 GGTATCCATACCGAAGACTTG
254268 G
1 G
254269 TATTAATACC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 17 0.49
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (21 bp):
GGTATCCATACCGAAGACTTG
Found at i:254270 original size:20 final size:19
Alignment explanation
Indices: 254185--254271 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 19
254175 CTAGATAAAC
* * *
254185 TGGTATCCATATCGGAGGAC
1 TGGTATCCATA-CCGAAGAT
254205 TGGTATCCATACCGAATGAGT
1 TGGTATCCATACCGAA-GA-T
**
254226 TGGTATCCATACTAAAGAT
1 TGGTATCCATACCGAAGAT
*
254245 TGGGTACCCATACCGAAGACT
1 T-GGTATCCATACCGAAGA-T
254266 TGGTAT
1 TGGTAT
254272 TAATACCCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.09
20 33 0.61
21 16 0.30
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (19 bp):
TGGTATCCATACCGAAGAT
Found at i:262032 original size:106 final size:106
Alignment explanation
Indices: 261880--262088 Score: 330
Period size: 106 Copynumber: 2.0 Consensus size: 106
261870 GAGTGTACAT
* * *
261880 GTGGGTGTATGGTTTTAGGGAACCTACACATTCTGGTGATAGGATGGGGGTAGTGTTCATATTTT
1 GTGGGTGTATGATTCTAGGGAACCTACACATTCTGGTGATAGGATGGGGATAGTGTTCATATTTT
* *
261945 TAAAACATGTTTGATAAATTGATTTTTACTGAAGTATTCAA
66 TAAAAAATGTTTGATAAATTGATTTTTACTAAAGTATTCAA
* *
261986 GTGGGTGTATGATTCTGGGGAACCTACACGTTCTGGTGATCA-GATGGGGATAGTGTTCATATTT
1 GTGGGTGTATGATTCTAGGGAACCTACACATTCTGGTGAT-AGGATGGGGATAGTGTTCATATTT
*
262050 TTAAAAAATGTTTTATAAATTGATTTTTACTAAAGTATT
65 TTAAAAAATGTTTGATAAATTGATTTTTACTAAAGTATT
262089 TTATTTATAT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 93 0.99
107 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (106 bp):
GTGGGTGTATGATTCTAGGGAACCTACACATTCTGGTGATAGGATGGGGATAGTGTTCATATTTT
TAAAAAATGTTTGATAAATTGATTTTTACTAAAGTATTCAA
Found at i:266309 original size:21 final size:21
Alignment explanation
Indices: 266279--266411 Score: 110
Period size: 21 Copynumber: 6.4 Consensus size: 21
266269 TGGAGGATTA
*
266279 GTATCCATACCGAATGAGTTG
1 GTATCCATACCGAATGAATTG
* *
266300 GTATCTATACCGAATGAATTA
1 GTATCCATACCGAATGAATTG
** * * *
266321 GTATCTGTATCGAA-GGACTG
1 GTATCCATACCGAATGAATTG
*
266341 GTATCCATACCGAATGAGTTG
1 GTATCCATACCGAATGAATTG
* ** *
266362 GTATCTATATTGAACGAATTG
1 GTATCCATACCGAATGAATTG
*
266383 GTATCCATATCGAAT--ATTGG
1 GTATCCATACCGAATGAATT-G
266403 GTATCCATA
1 GTATCCATA
266412 TTGAAGGATT
Statistics
Matches: 88, Mismatches: 22, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
19 3 0.03
20 24 0.27
21 61 0.69
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (21 bp):
GTATCCATACCGAATGAATTG
Found at i:266411 original size:62 final size:62
Alignment explanation
Indices: 266259--266396 Score: 186
Period size: 62 Copynumber: 2.2 Consensus size: 62
266249 GAAAACACTG
* * * * *
266259 GTATCCATATTGGAGGATTAGTATCCATACCGAATGAGTTGGTATCTATACCGAATGAATTA
1 GTATCCATATCGAAGGACTGGTATCCATACCGAATGAGTTGGTATCTATACCGAACGAATTA
** ** *
266321 GTATCTGTATCGAAGGACTGGTATCCATACCGAATGAGTTGGTATCTATATTGAACGAATTG
1 GTATCCATATCGAAGGACTGGTATCCATACCGAATGAGTTGGTATCTATACCGAACGAATTA
266383 GTATCCATATCGAA
1 GTATCCATATCGAA
266397 TATTGGGTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (62 bp):
GTATCCATATCGAAGGACTGGTATCCATACCGAATGAGTTGGTATCTATACCGAACGAATTA
Found at i:268664 original size:3 final size:3
Alignment explanation
Indices: 268656--268718 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
268646 AAAGAAAAAG
* * *
268656 GAA GAA GAA G-A GAA GAA AAA GAA GAA G-A GAA GAA AAA GAA CAA G-A
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
268701 GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA
268719 TGGGGTAGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.70, C:0.02, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:268679 original size:17 final size:17
Alignment explanation
Indices: 268657--268717 Score: 113
Period size: 17 Copynumber: 3.6 Consensus size: 17
268647 AAGAAAAAGG
268657 AAGAAGAAGAGAAGAAA
1 AAGAAGAAGAGAAGAAA
268674 AAGAAGAAGAGAAGAAA
1 AAGAAGAAGAGAAGAAA
*
268691 AAGAACAAGAGAAGAAA
1 AAGAAGAAGAGAAGAAA
268708 AAGAAGAAGA
1 AAGAAGAAGA
268718 ATGGGGTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (17 bp):
AAGAAGAAGAGAAGAAA
Found at i:269217 original size:19 final size:21
Alignment explanation
Indices: 269190--269232 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
269180 AAGAAAATGA
*
269190 TTTAGTTTTG-AAAGCAAAAT
1 TTTAGTTTTGAAAAACAAAAT
269210 TTTA-TTTTGAAAAACAAAAT
1 TTTAGTTTTGAAAAACAAAAT
269230 TTT
1 TTT
269233 GAAAATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (21 bp):
TTTAGTTTTGAAAAACAAAAT
Found at i:270740 original size:22 final size:22
Alignment explanation
Indices: 270686--270740 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
270676 TTTACACTAT
*
270686 AGTATCGATACCATGAACCCCG
1 AGTATCGATATCATGAACCCCG
*
270708 AGTATTGATATCATGAACCCCG
1 AGTATCGATATCATGAACCCCG
270730 AGTATCGATAT
1 AGTATCGATAT
270741 TGTTTTAGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (22 bp):
AGTATCGATATCATGAACCCCG
Found at i:272565 original size:34 final size:34
Alignment explanation
Indices: 272522--272589 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
272512 TCCACTTTCC
272522 TTTCTCTTTTAGGGGCTCTCTTTTTACACCTCTT
1 TTTCTCTTTTAGGGGCTCTCTTTTTACACCTCTT
*
272556 TTTCTCTTTTCGGGGCTCTCTTTTTACACCTCTT
1 TTTCTCTTTTAGGGGCTCTCTTTTTACACCTCTT
272590 CACCTTCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.07, C:0.28, G:0.12, T:0.53
Consensus pattern (34 bp):
TTTCTCTTTTAGGGGCTCTCTTTTTACACCTCTT
Found at i:272631 original size:41 final size:42
Alignment explanation
Indices: 272556--272637 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 42
272546 TACACCTCTT
* *
272556 TTTCTCTTTTCGGGGCTCTCTTTTTACACCTCTTCACCTTCC
1 TTTCTCTTTTCAGGGCTCTCTTTCTACACCTCTTCACCTTCC
* *
272598 TTTCTCTTTT-AGGGCAT-TCTTTCTATACCTCTTCTCCTTC
1 TTTCTCTTTTCAGGGC-TCTCTTTCTACACCTCTTCACCTTC
272638 TAAATTTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 24 0.69
42 11 0.31
ACGTcount: A:0.09, C:0.33, G:0.09, T:0.50
Consensus pattern (42 bp):
TTTCTCTTTTCAGGGCTCTCTTTCTACACCTCTTCACCTTCC
Found at i:276301 original size:2 final size:2
Alignment explanation
Indices: 276294--276334 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
276284 TGACCACTCA
*
276294 AT AT AT AT AT AT AT AT AT AT AT GT AT -T AT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276333 AT
1 AT
276335 TCTTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:277539 original size:18 final size:19
Alignment explanation
Indices: 277496--277541 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
277486 CAATGTTTTT
* *
277496 GTGATAAATTATATTTGTA
1 GTGATAAATTATAGTTATA
*
277515 GTTATAAATT-TAGTTATA
1 GTGATAAATTATAGTTATA
277533 GTGATAAAT
1 GTGATAAAT
277542 ATATTGTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
GTGATAAATTATAGTTATA
Found at i:278882 original size:22 final size:22
Alignment explanation
Indices: 278845--278912 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
278835 TTAAATATAT
*
278845 TTTTAGTTATCATAACCAATTA
1 TTTTAGTTATCATAACAAATTA
278867 TTTTAGTTAT-ATTAACAAATTCTA
1 TTTTAGTTATCA-TAACAAA-T-TA
*
278891 TTTT-G-TAGCATCAACAAATTA
1 TTTTAGTTATCAT-AACAAATTA
278912 T
1 T
278913 CATAAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
21 4 0.10
22 20 0.51
23 9 0.23
24 6 0.15
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTTAGTTATCATAACAAATTA
Found at i:279048 original size:44 final size:42
Alignment explanation
Indices: 278955--279054 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 42
278945 GATTTAGTCA
*
278955 AAATAAAAATTATGTAAAATTTATTTAGTCAAAATATTTTAT
1 AAATAAAAATTATGTAAAATTTATTTAGTCAAAATAATTTAT
278997 CAAAATAAAAATTATG-ACAAATTTATTTAGTTACAATAATAATTTAT
1 --AAATAAAAATTATGTA-AAATTTATTTAG-T-CAA-AATAATTTAT
*
279044 -AATAAATATTA
1 AAATAAAAATTA
279055 ATTTATCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
43 1 0.02
44 36 0.72
45 1 0.02
46 3 0.06
47 9 0.18
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (42 bp):
AAATAAAAATTATGTAAAATTTATTTAGTCAAAATAATTTAT
Found at i:279358 original size:54 final size:52
Alignment explanation
Indices: 279281--279381 Score: 130
Period size: 54 Copynumber: 1.9 Consensus size: 52
279271 AAAAAAAACA
* * *
279281 ATATTTTTCATAATAATAAATTATAACATATTTATTTAGTCACAATAACATT
1 ATATTTTTCAAAATAAAAAATTATAACAAATTTATTTAGTCACAATAACATT
** *
279333 ATATTTTATCAAAATAAAAAAATTATGTCAAATTTATTTTGTCACAATA
1 ATATTTT-TCAAAAT-AAAAAATTATAACAAATTTATTTAGTCACAATA
279382 TTTTCTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 7 0.17
53 6 0.15
54 28 0.68
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (52 bp):
ATATTTTTCAAAATAAAAAATTATAACAAATTTATTTAGTCACAATAACATT
Found at i:279630 original size:392 final size:389
Alignment explanation
Indices: 278903--279716 Score: 930
Period size: 392 Copynumber: 2.1 Consensus size: 389
278893 TTGTAGCATC
* *
278903 AACAAATTATCATAAATTTATTTAGTCACAATTAAAAAAATAGATTTAGTCAAAATAAAAATTAT
1 AACAAATTATAACAAATTTATTTAGTCACAATTAAAAAAATAGATTTAGTCAAAATAAAAATTAT
*
278968 GTAAAATTTATTTAGTCAAAATATTTTATCAAAATAAAAATTATGACAAATTTATTTAGTTACAA
66 GTAAAATTTATTTAGTCAAAATATTTTATCAAAATAAAAATTATGACAAATTTATTTAATT--AA
* * * * *
279033 TAATAATTTATAATAAATATTAATTTATCAGTATAAAAAATTATGAAAAATAATATTCTTTCATA
129 TAACAATTCATAACAAATATTAATTTATCAATATAAAAAAATATGAAAAATAATATTCTTTCATA
* ** * * * * *
279098 TAAAATTATCACAAATTTATTATTCTCAATAACATGTTAGATTTAGTCAAGATAAGAAATTATGT
194 TAAAATTATCACAAATTTATTATTCACAATAACACATTAAATTTAATCAAAATAAAAAATTATAT
* * *
279163 CAAATTGTTTTAATCACAGTATTTTCTTAAAATATAAAATGATAAAAAAATTATTTAGTCACAAT
259 CAAATTGTTTTAATCACAATATTTTCTCAAAATATAAAATGATAAAAAAATTATTTAATCACAAT
* * * *
279228 AAATATTTATAACAAATATTAATTTCTCAATATAAAAATTTATAAAAAAAACAATATT-TTTCAT
324 AAAAATTTATAAAAAATATTAATTTCTCAATATAAAAAATTAT--AAAAAACAATATTATTTCAC
279292 AAT
387 AAT
* * * ** *
279295 AATAAATTATAACATATTTATTTAGTCACAA-TAACATTATA-TTTTA-TCAAAATAAAAAAATT
1 AACAAATTATAACAAATTTATTTAGTCACAATTAAAAAAATAGATTTAGTCAAAAT--AAAAATT
* * * * * * *
279357 ATGTCAAATTTATTTTGTCACAATATTTTCTTAAAATAATAATTTTTGA-AAATTTTATTTAATT
64 ATGTAAAATTTATTTAGTCAAAATATTTTATCAAAATAA-AAATTATGACAAA-TTTATTTAATT
* *
279421 -ATAACAATTCATAACAAATATTAATTTCTCAATATAAAAAAATATGACAAATAATATTCTTTCA
127 AATAACAATTCATAACAAATATTAATTTATCAATATAAAAAAATATGAAAAATAATATTCTTTCA
*
279485 TAATAACAAATTGT-AGCAAATTTATTTAGTT-ACAATAACACATTAAATTTAATCAAAATAAAA
192 T-AT-A-AAATTATCA-CAAATTTA-TTA-TTCACAATAACACATTAAATTTAATCAAAATAAAA
* ** * * * * *
279548 AGATTATATTAAATT-TATTTCGTCACAATATTTTCTCAAAATA-AAAGT-TTGACAAATTTATT
251 A-ATTATATCAAATTGT-TTTAATCACAATATTTTCTCAAAATATAAAATGATAAAAAAATTATT
* * *
279610 TAATCATAATAAAAATTTATAAAAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATAT
314 TAATCACAATAAAAATTTATAAAAAATATTAATTTCTCAATATAAAAAATTATAAAAAACAATAT
279675 TATTTCACAAT
379 TATTTCACAAT
* * *
279686 AACAAATTGTGACAAATTTATTTATTCACAA
1 AACAAATTATAACAAATTTATTTAGTCACAA
279717 AAAAATATAA
Statistics
Matches: 354, Mismatches: 55, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
389 65 0.18
390 17 0.05
391 87 0.25
392 116 0.33
393 34 0.10
394 35 0.10
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (389 bp):
AACAAATTATAACAAATTTATTTAGTCACAATTAAAAAAATAGATTTAGTCAAAATAAAAATTAT
GTAAAATTTATTTAGTCAAAATATTTTATCAAAATAAAAATTATGACAAATTTATTTAATTAATA
ACAATTCATAACAAATATTAATTTATCAATATAAAAAAATATGAAAAATAATATTCTTTCATATA
AAATTATCACAAATTTATTATTCACAATAACACATTAAATTTAATCAAAATAAAAAATTATATCA
AATTGTTTTAATCACAATATTTTCTCAAAATATAAAATGATAAAAAAATTATTTAATCACAATAA
AAATTTATAAAAAATATTAATTTCTCAATATAAAAAATTATAAAAAACAATATTATTTCACAAT
Found at i:279704 original size:197 final size:195
Alignment explanation
Indices: 278903--279716 Score: 862
Period size: 194 Copynumber: 4.2 Consensus size: 195
278893 TTGTAGCATC
* * * * *
278903 AACAAATTATCATAAATTTATTTAGTCACAATTAAAAAAATAGATTTAGTCAAAAT-AAAAATTA
1 AACAAATTAT-ACAAATTTATTTAGTCACAA-TAACACATTAGATTTAATCAAAATAAAAAATTA
* * * * *
278967 TGTAAAATTTATTTAGTCAAAATATTTTATCAAAATAAAAATTATGACAAATTTATTTAGTTACA
64 TGTCAAATTTATTTAGTCACAATATTTTCTCAAAATAAAAATT-TGACAAATTTATTTAATCACA
* * * *
279032 ATAATAATTTATAATAAATATTAATTTATCAGTATAAAAAATTATGAAAAATAATATTCTTTCAT
128 ATAAAAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTCTTTCAT
279097 -AT
193 AAT
* * ** * * *
279099 -A-AAATTATCACAAATTTA-TTATTCTCAATAACATGTTAGATTTAGTCAAGATAAGAAATTAT
1 AACAAATTAT-ACAAATTTATTTAGTCACAATAACACATTAGATTTAATCAAAATAAAAAATTAT
* * * * * * * *
279161 GTCAAATTGT-TTTAATCACAGTATTTTCTTAAAATATAAAATGATAAAAAAATTATTTAGTCAC
65 GTCAAATT-TATTTAGTCACAATATTTTCTCAAAATA-AAAAT-TTGACAAATTTATTTAATCAC
* * * *
279225 AATAAATATTTATAACAAATATTAATTTCTCAATATAAAAATTTATAAAAAAAACAATATT-TTT
127 AATAAAAATTTATAACAAATATTAATTTCTCAATATAAAAAATTAT--GAAAAATAATATTCTTT
279289 CATAAT
190 CATAAT
* * * *
279295 AATAAATTATAACATATTTATTTAGTCACAAT-A-ACATTATATTTTATCAAAATAAAAAAATTA
1 AACAAATTAT-ACAAATTTATTTAGTCACAATAACACATTAGATTTAATCAAAAT-AAAAAATTA
* * *
279358 TGTCAAATTTATTTTGTCACAATATTTTCTTAAAATAATAATTTTTGA-AAATTTTATTTAAT--
64 TGTCAAATTTATTTAGTCACAATATTTTCTCAAAATAA-AA-ATTTGACAAA-TTTATTTAATCA
* * * * *
279420 -TATAACAATTCATAACAAATATTAATTTCTCAATATAAAAAAATATGACAAATAATATTCTTTC
126 CAATAAAAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTCTTTC
279484 ATAAT
191 ATAAT
* * *
279489 AACAAATTGTAGCAAATTTATTTAGTTACAATAACACATTAAATTTAATCAAAATAAAAAGATTA
1 AACAAATTATA-CAAATTTATTTAGTCACAATAACACATTAGATTTAATCAAAATAAAAA-ATTA
* * * * *
279554 TATTAAATTTATTTCGTCACAATATTTTCTCAAAATAAAAGTTTGACAAATTTATTTAATCATAA
64 TGTCAAATTTATTTAGTCACAATATTTTCTCAAAATAAAAATTTGACAAATTTATTTAATCACAA
* * *
279619 TAAAAATTTATAAAAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTATTTCACA
129 TAAAAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTCTTTCATA
279684 AT
194 AT
* *
279686 AACAAATTGTGACAAATTTATTTATTCACAA
1 AACAAATTAT-ACAAATTTATTTAGTCACAA
279717 AAAAATATAA
Statistics
Matches: 516, Mismatches: 77, Indels: 49
0.80 0.12 0.08
Matches are distributed among these distances:
192 19 0.04
193 55 0.11
194 128 0.25
195 58 0.11
196 69 0.13
197 108 0.21
198 69 0.13
199 10 0.02
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (195 bp):
AACAAATTATACAAATTTATTTAGTCACAATAACACATTAGATTTAATCAAAATAAAAAATTATG
TCAAATTTATTTAGTCACAATATTTTCTCAAAATAAAAATTTGACAAATTTATTTAATCACAATA
AAAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTCTTTCATAAT
Found at i:280042 original size:21 final size:22
Alignment explanation
Indices: 280011--280051 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
280001 TGTACTTCTC
280011 GTGACGAAATAGTTAATTGATT
1 GTGACGAAATAGTTAATTGATT
* *
280033 GTGAC-AAATATTTTATTGA
1 GTGACGAAATAGTTAATTGA
280052 GATAGGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (22 bp):
GTGACGAAATAGTTAATTGATT
Found at i:280754 original size:20 final size:21
Alignment explanation
Indices: 280712--280764 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
280702 TTATAAGGTA
280712 GTATCGATACCTTGTCAATGGG
1 GTATCGATA-CTTGTCAATGGG
*
280734 GTATCGATACTTTTC-ATGGG
1 GTATCGATACTTGTCAATGGG
280754 GTATCGATACT
1 GTATCGATACT
280765 CGAGACTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 16 0.53
21 5 0.17
22 9 0.30
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (21 bp):
GTATCGATACTTGTCAATGGG
Found at i:283309 original size:17 final size:16
Alignment explanation
Indices: 283284--283315 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
283274 ATCATTATCA
283284 TAAAAATATTAATTAT
1 TAAAAATATTAATTAT
283300 TAAAATATATTAATTA
1 TAAAA-ATATTAATTA
283316 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAATATTAATTAT
Found at i:283682 original size:20 final size:20
Alignment explanation
Indices: 283638--283684 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
283628 TATTGACATA
*
283638 AATAATATTTAATAGATTAT
1 AATAATATTTAATAGATAAT
*
283658 TATAATATTTTAATA-ATAAT
1 AATAATA-TTTAATAGATAAT
283678 AATAATA
1 AATAATA
283685 AGTTTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATAATATTTAATAGATAAT
Found at i:283850 original size:14 final size:14
Alignment explanation
Indices: 283833--283859 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
283823 TTCATTTTAC
283833 GAAAAATATTTTCT
1 GAAAAATATTTTCT
283847 GAAAAATATTTTC
1 GAAAAATATTTTC
283860 AGTGAAACAA
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:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
GAAAAATATTTTCT
Found at i:284876 original size:19 final size:19
Alignment explanation
Indices: 284849--284901 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
284839 CAATGTTTTT
*
284849 GTGATAAATTATATTTGTA
1 GTGATAAATTATATTTATA
* * *
284868 GTTATAAATTTTAGTTATA
1 GTGATAAATTATATTTATA
*
284887 GTGATAAAATATATT
1 GTGATAAATTATATT
284902 GTTAGAATTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
GTGATAAATTATATTTATA
Found at i:290120 original size:58 final size:58
Alignment explanation
Indices: 290042--290328 Score: 321
Period size: 58 Copynumber: 4.9 Consensus size: 58
290032 TTTGTGTAGA
** *
290042 TCTAACTTTGTAAGGGAAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGAT
1 TCTAACTTTGTAAGAAAAATAAATTATTGAATTTATTTTCTTGAGAATCTTGAATGAT
* * *
290100 TCTAACTTTGTCAGGAAAATAAA-TAGTTGAATTTATTTCCTTGAGAATCTTGAATGAT
1 TCTAACTTTGTAAGAAAAATAAATTA-TTGAATTTATTTTCTTGAGAATCTTGAATGAT
* * * * *
290158 TCTAAATTTATAAGAAAAATAAATTGTTGAATTTATTTTCTTGAGAATCATGACTGAT
1 TCTAACTTTGTAAGAAAAATAAATTATTGAATTTATTTTCTTGAGAATCTTGAATGAT
* * * * *
290216 TATATCTTT-TAAAAAGAAATAAATTATTAAATTTATTTTCTTGAGAATCTTAAATGAT
1 TCTAACTTTGTAAGAA-AAATAAATTATTGAATTTATTTTCTTGAGAATCTTGAATGAT
* * * * *
290274 TCT-ATTTTGTTAA-ATGAAATAAATTTTTAAATTTATTTTCTCGAGAATCTTGAAT
1 TCTAACTTTG-TAAGA-AAAATAAATTATTGAATTTATTTTCTTGAGAATCTTGAAT
290329 AAAGAATTAA
Statistics
Matches: 197, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
57 10 0.05
58 183 0.93
59 4 0.02
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (58 bp):
TCTAACTTTGTAAGAAAAATAAATTATTGAATTTATTTTCTTGAGAATCTTGAATGAT
Found at i:290409 original size:101 final size:101
Alignment explanation
Indices: 290228--290413 Score: 241
Period size: 101 Copynumber: 1.8 Consensus size: 101
290218 TATCTTTTAA
* *
290228 AAAGAAATAAATTATTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAATGAAA
1 AAAGAAATAAATTATTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTAAAAGGAAA
***
290293 TAAATTTTTAAATTTATTTTCTCGAGAATCTTGAAT
66 TAAATCGCTAAATTTATTTTCTCGAGAATCTTGAAT
* * * *
290329 AAAGAATTAAATTGTTGAATTTATTTTCTT-ATGAATCTTTAATGATTCTATCTTT-TAAAAGGA
1 AAAGAAATAAATTATTAAATTTATTTTCTTGA-GAATCTTAAATGATTCTAT-TTTGTAAAAGGA
* *
290392 ATTAAATCGCTAGATTTATTTT
64 AATAAATCGCTAAATTTATTTT
290414 TCCTGGTTTG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
100 1 0.01
101 68 0.94
102 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (101 bp):
AAAGAAATAAATTATTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTAAAAGGAAA
TAAATCGCTAAATTTATTTTCTCGAGAATCTTGAAT
Found at i:293635 original size:28 final size:28
Alignment explanation
Indices: 293548--293623 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
293538 TGGAAGCTTG
*
293548 GGAATA-TTATGTGGCATTTGATTCGCT
1 GGAATATTTATGTGGCGTTTGATTCGCT
* *
293575 GGAATGTTTAGGTGGCGTTTGATTCGCT
1 GGAATATTTATGTGGCGTTTGATTCGCT
293603 GGAATATTTATGTGGCGTTTG
1 GGAATATTTATGTGGCGTTTG
293624 GTTTGTTCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 5 0.12
28 38 0.88
ACGTcount: A:0.18, C:0.09, G:0.32, T:0.41
Consensus pattern (28 bp):
GGAATATTTATGTGGCGTTTGATTCGCT
Found at i:293640 original size:28 final size:28
Alignment explanation
Indices: 293554--293642 Score: 106
Period size: 28 Copynumber: 3.2 Consensus size: 28
293544 CTTGGGAATA
* *
293554 TTATGTGGCATTTGATTCGCTGGAATGT
1 TTATGTGGCGTTTGATTCGCTCGAATGT
* * *
293582 TTAGGTGGCGTTTGATTCGCTGGAATAT
1 TTATGTGGCGTTTGATTCGCTCGAATGT
* * *
293610 TTATGTGGCGTTTGGTTTGTTCGAATGT
1 TTATGTGGCGTTTGATTCGCTCGAATGT
293638 TTATG
1 TTATG
293643 AGGGAATTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.45
Consensus pattern (28 bp):
TTATGTGGCGTTTGATTCGCTCGAATGT
Found at i:294301 original size:27 final size:27
Alignment explanation
Indices: 294263--294316 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
294253 AAACCCGAAC
294263 TCGACCCGAATATCACACTTAAAAAAA
1 TCGACCCGAATATCACACTTAAAAAAA
294290 TCGACCCGAATATCACACTTAAAAAAA
1 TCGACCCGAATATCACACTTAAAAAAA
294317 CCCGACCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.07, T:0.19
Consensus pattern (27 bp):
TCGACCCGAATATCACACTTAAAAAAA
Found at i:294329 original size:33 final size:32
Alignment explanation
Indices: 294253--294335 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 32
294243 TTTTTACCCT
294253 AAACCCGAACTCGACCCGAATATCACACTTAAA
1 AAACCCGAACT-GACCCGAATATCACACTTAAA
*
294286 AAA----ATC-GACCCGAATATCACACTTAAAA
1 AAACCCGAACTGACCCGAATATCACACTT-AAA
*
294314 AAACCCGACCTGACCCGAATAT
1 AAACCCGAACTGACCCGAATAT
294336 ATGAATTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
27 18 0.43
28 6 0.14
29 2 0.05
32 2 0.05
33 14 0.33
ACGTcount: A:0.43, C:0.31, G:0.10, T:0.16
Consensus pattern (32 bp):
AAACCCGAACTGACCCGAATATCACACTTAAA
Found at i:294607 original size:21 final size:21
Alignment explanation
Indices: 294583--294630 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
294573 GTTTCATCCG
294583 ACCCGAATATATGAATTAGAA
1 ACCCGAATATATGAATTAGAA
294604 ACCCGAATATATGAATTAGAA
1 ACCCGAATATATGAATTAGAA
294625 ACCCGA
1 ACCCGA
294631 CCTGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.21
Consensus pattern (21 bp):
ACCCGAATATATGAATTAGAA
Found at i:298332 original size:68 final size:68
Alignment explanation
Indices: 298259--298467 Score: 150
Period size: 67 Copynumber: 3.0 Consensus size: 68
298249 TTTTGATATG
298259 ACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTAGATAT
1 ACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTAGATAT
298324 GCT
66 GCT
* * * **
298327 ACTAATCGGATTATG-CTTGTTGGTCT-AGAATAGGGAACAT-TTACATGG---T-GCATTTA-G
1 ACTAAT----TTATGCCTAGTT-G-CTAAGGAT---GAACATGATAGTTGGTTATGGCA--TAGG
** *
298384 ATTCTTTTGATATG--
55 AGAC--TAGATATGCT
298398 ACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTAGGATA
1 ACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTA-GATA
298463 TGCT
65 TGCT
298467 A
1 A
298468 GTATGAGTGT
Statistics
Matches: 101, Mismatches: 16, Indels: 47
0.62 0.10 0.29
Matches are distributed among these distances:
64 6 0.06
65 5 0.05
66 3 0.03
67 18 0.18
68 15 0.15
69 4 0.04
70 3 0.03
71 15 0.15
72 12 0.12
73 9 0.09
74 5 0.05
75 6 0.06
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (68 bp):
ACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTAGATAT
GCT
Found at i:298396 original size:139 final size:138
Alignment explanation
Indices: 298191--298467 Score: 513
Period size: 139 Copynumber: 2.0 Consensus size: 138
298181 GACATTGCAT
298191 CTAATCGGATTATGCTTGTTGGTCATAGAATAGGGAATTACATGGTGCATTTAGATTCTTTTGAT
1 CTAATCGGATTATGCTTGTTGGTCATAGAATAGGGAATTACATGGTGCATTTAGATTCTTTTGAT
298256 ATGACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTA-G
66 ATGACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTAGG
298320 ATATGCTA
131 ATATGCTA
298328 CTAATCGGATTATGCTTGTTGGTC-TAGAATAGGGAACATTTACATGGTGCATTTAGATTCTTTT
1 CTAATCGGATTATGCTTGTTGGTCATAGAATAGGG-A-A-TTACATGGTGCATTTAGATTCTTTT
298392 GATATGACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACT
63 GATATGACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACT
298457 AGGATATGCTA
128 AGGATATGCTA
298468 GTATGAGTGT
Statistics
Matches: 136, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
136 10 0.07
137 25 0.18
138 1 0.01
139 91 0.67
140 9 0.07
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (138 bp):
CTAATCGGATTATGCTTGTTGGTCATAGAATAGGGAATTACATGGTGCATTTAGATTCTTTTGAT
ATGACTAATTTATGCCTAGTTGCTAAGGATGAACATGATAGTTGGTTATGGCATAGGAGACTAGG
ATATGCTA
Found at i:301392 original size:22 final size:22
Alignment explanation
Indices: 301344--301406 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
301334 TTTTGGTGCA
* *
301344 GAGGGAATCGATCCCCCCTCAT
1 GAGGGAACCGATTCCCCCTCAT
*
301366 GAGGGAACCGATTCCCCCT-TT
1 GAGGGAACCGATTCCCCCTCAT
*
301387 GAAGGGGAACCAATTCCCCC
1 G-A-GGGAACCGATTCCCCC
301407 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 18 0.51
23 15 0.43
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCTCAT
Found at i:301836 original size:24 final size:26
Alignment explanation
Indices: 301790--301838 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
301780 AGAATTTTCC
*
301790 AAAAAATTTTAAATTTTCGAAATTAA
1 AAAAAATGTTAAATTTTCGAAATTAA
301816 AAAAAATGTT-AATTTTC-AAATTA
1 AAAAAATGTTAAATTTTCGAAATTA
301839 TTGTGTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 7 0.32
26 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAAAATGTTAAATTTTCGAAATTAA
Found at i:315727 original size:2 final size:2
Alignment explanation
Indices: 315720--315819 Score: 77
Period size: 2 Copynumber: 53.0 Consensus size: 2
315710 TCGGGCTGGG
* * * *
315720 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * * *
315760 TT TA AA TT TA AA T- TA AA TA TA T- TA -A TA T- 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
315798 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
315820 AAGAATTATT
Statistics
Matches: 74, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
1 6 0.08
2 68 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:315828 original size:38 final size:37
Alignment explanation
Indices: 315720--315821 Score: 116
Period size: 38 Copynumber: 2.8 Consensus size: 37
315710 TCGGGCTGGG
* *
315720 TATATATATTTAAAT-TAAATATATAAATATTATATA
1 TATATATATATATATATAAATATATAAATATTATATA
* * * * *
315756 TATATTTAAATTTAAATTAAATATATTAATATTATATA
1 TATATATATATATATA-TAAATATATAAATATTATATA
*
315794 TATATATATATATATATATATATATAAA
1 TATATATATATATATATAAATATATAAA
315822 GAATTATTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
36 9 0.18
37 10 0.20
38 32 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (37 bp):
TATATATATATATATATAAATATATAAATATTATATA
Found at i:318534 original size:1 final size:1
Alignment explanation
Indices: 318530--318630 Score: 130
Period size: 1 Copynumber: 101.0 Consensus size: 1
318520 AAAAACAGAG
* * * * * *
318530 AAAAAATAATAAAATAAAAATAAAAAAAATAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
318595 TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
318631 TAATGGGATT
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.92, C:0.00, G:0.01, T:0.07
Consensus pattern (1 bp):
A
Found at i:318585 original size:36 final size:35
Alignment explanation
Indices: 318530--318633 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 35
318520 AAAAACAGAG
* * * *
318530 AAAAAATAATAAAATAAAAATAAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAA
318565 AATAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAA
1 AA-AAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAA
318601 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAA-AAAAATAA
318634 TGGGATTAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 24 0.38
36 39 0.62
ACGTcount: A:0.91, C:0.00, G:0.01, T:0.08
Consensus pattern (35 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAA
Found at i:318764 original size:28 final size:28
Alignment explanation
Indices: 318711--318764 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
318701 AAACAACACT
* *
318711 AATATATATTATAAAAAATGAAAGAAAA
1 AATATATATAATAAAAAATAAAAGAAAA
318739 AATATATATAAT-AAAAATAAATAGAA
1 AATATATATAATAAAAAATAAA-AGAA
318765 GCGAAAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (28 bp):
AATATATATAATAAAAAATAAAAGAAAA
Found at i:320252 original size:40 final size:43
Alignment explanation
Indices: 320147--320254 Score: 161
Period size: 43 Copynumber: 2.6 Consensus size: 43
320137 TTCTAGCCCA
* *
320147 AGATGACTCATTCGTTGTGAAGTTGGGTCAATCATTGTGTTAC
1 AGATGACTCCTTCGTTGTGAAGTTGGGTCAATCATTGTGGTAC
320190 AGATGACTCCTTCGTTGTGAAGTTGGGTCAATCATT-TGGGTAC
1 AGATGACTCCTTCGTTGTGAAGTTGGGTCAATCATTGT-GGTAC
320233 -GAT-A-TCCTTCGTTGTGAAGTTG
1 AGATGACTCCTTCGTTGTGAAGTTG
320255 AAATCGTAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
40 18 0.29
41 1 0.02
42 4 0.06
43 39 0.63
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (43 bp):
AGATGACTCCTTCGTTGTGAAGTTGGGTCAATCATTGTGGTAC
Found at i:320612 original size:85 final size:85
Alignment explanation
Indices: 320394--320714 Score: 377
Period size: 85 Copynumber: 3.8 Consensus size: 85
320384 CATCTTCTGT
* * * * *
320394 TGAATGGT-ATCGAACTCGACA-GTTCTTGTTAATAGATAACTCC-TCTTGCCTTTGAGTTATGC
1 TGAAT-GTAATCGAACTCGA-AGGTTTTTGTTGACAGATAAC-CCTTCTCGCC-TTGAGTTATGA
*
320456 TATAAATTTGATATGCCCTTGAGC
62 TGTAAATTTGATATGCCCTTGAGC
* *
320480 TGAATGTAATCGAACTCGAAGGTTTTTTATTAACAGATAACCCTTCTCGCCTTGAGTTATGATGT
1 TGAATGTAATCGAACTCGAAGG-TTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGATGT
*
320545 AAATTTGATGTGCCCTTGAGC
65 AAATTTGATATGCCCTTGAGC
** **
320566 TG-ATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGTCCTTCTCGCCTTGAACTAT-ACTG
1 TGAATGTAATCGAACTCGAAGGT-TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGA-TG
*
320629 T-AATTTAATATG-CCTATGAGC
64 TAAATTTGATATGCCCT-TGAGC
* *
320650 TGAATGTAATCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTA
1 TGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTA
320715 CTTGGTTGGG
Statistics
Matches: 204, Mismatches: 21, Indels: 21
0.83 0.09 0.09
Matches are distributed among these distances:
83 3 0.01
84 52 0.25
85 75 0.37
86 53 0.26
87 21 0.10
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
TGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTA
AATTTGATATGCCCTTGAGC
Found at i:320974 original size:109 final size:110
Alignment explanation
Indices: 320778--321240 Score: 419
Period size: 124 Copynumber: 4.0 Consensus size: 110
320768 CAAGTCGATC
* *
320778 TGTTGGGCACAATATCCTTCGTTGTGAAGTTGAAATCGTGGATGGCTTCTTCGTTGTCAAGTTGA
1 TGTTGGGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTCAAGTTGA
320843 GCTTTGAATTGGATATCATTCATTATGAAGTTGAAATCCAAGGAT
66 GCTTTGAATTGGATATCATTCATTATGAAGTTGAAATCCAAGGAT
* *
320888 TGTT-GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGA
1 TGTTGGGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTCAAGTTGA
* *
320952 GCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCTAATCTAAAGATGGAT
66 GCTTTGAATTGGATATCATTCATTATGAAGTTGAAATC----C---A-A-GGAT
* * ** *
321006 GCTGCTTGTGTGCACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCTTATTCGTTGTGAA
1 --TG-TTG-G-GCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTCAA
* *
321071 GTTGAGCTTTGAATTGGATATCATTCGTTGCT-AAGTTGAAATCCAATCTAGAGATGGAT
61 GTTGAGCTTTGAATTGGATATCATTCATT-ATGAAGTTGAAAT-C---C---A-A-GGAT
* * * * *
321130 GCTGCTTGTGGGCACGATATCATTCGTCGTGAAGTTGAAGTCATGGATGGCTCATTCGTTG-CGA
1 --TG--T-TGGGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTC-A
* * * * * *
321194 AATTGAGTTTTGAATTGGATATCCTTCGTTGTGAATTTGAAATCCAA
60 AGTTGAGCTTTGAATTGGATATCATTCATTATGAAGTTGAAATCCAA
321241 TCTTGTGTAA
Statistics
Matches: 307, Mismatches: 25, Indels: 36
0.83 0.07 0.10
Matches are distributed among these distances:
109 92 0.30
110 4 0.01
113 1 0.00
116 2 0.01
117 2 0.01
118 4 0.01
120 3 0.01
121 2 0.01
123 3 0.01
124 188 0.61
125 4 0.01
126 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (110 bp):
TGTTGGGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTCAAGTTGA
GCTTTGAATTGGATATCATTCATTATGAAGTTGAAATCCAAGGAT
Found at i:321113 original size:124 final size:124
Alignment explanation
Indices: 320887--321243 Score: 554
Period size: 124 Copynumber: 2.9 Consensus size: 124
320877 AATCCAAGGA
* *
320887 TTGTTGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGA
1 TTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGA
* *
320952 GCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCTAATCTAAAGATGGATGCTGC
66 GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATGGATGCTGC
* * *
321011 TTGTGTGCACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCTTATTCGTTGTGAAGTTGA
1 TTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGA
* *
321076 GCTTTGAATTGGATATCATTCGTTGCT-AAGTTGAAATCCAATCTAGAGATGGATGCTGC
66 GCTTTGAATTGGATATCCTTCGTTG-TGAAGTTGAAATCCAATCTAAAGATGGATGCTGC
* * * * *
321135 TTGTGGGCACGATATCATTCGTCGTGAAGTTGAAGTCATGGATGGCTCATTCGTTGCGAAATTGA
1 TTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGA
* *
321200 GTTTTGAATTGGATATCCTTCGTTGTGAATTTGAAATCCAATCT
66 GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCT
321244 TGTGTAAGTT
Statistics
Matches: 211, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
123 1 0.00
124 209 0.99
125 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (124 bp):
TTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGA
GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATGGATGCTGC
Found at i:322424 original size:95 final size:94
Alignment explanation
Indices: 322232--322488 Score: 304
Period size: 95 Copynumber: 2.7 Consensus size: 94
322222 AGCTGGATCT
* * * ** *
322232 ATAAAGCCGGAGTATTTAACCAAATGTTCTAGAGGGACAACTCAA--TATAATTGTATAGATATT
1 ATAAAGCTGGAGCATTTAACCAATTACTCTAGAGGGACAACTCAAGCT-TTATTG--T--ATA-T
322295 ATAATCACCTTTATCAGGCTAGCTGAATATTATCC
60 ATAATCACCTTTATCAGGCTAGCTGAATATTATCC
* *
322330 ATAAAG-TCGGAGCGTTTAACCAATTACTCTAGAGGGACAACTTAAGCTTTATTGTATAGTATAA
1 ATAAAGCT-GGAGCATTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATA-TATAA
*
322394 TCACCTTTATCAGGCTAGCTGAATCTTATCC
64 TCACCTTTATCAGGCTAGCTGAATATTATCC
* * * *
322425 ATAAAGCTGGGGCATTTAACTAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATAAT
1 ATAAAGCTGGAGCATTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATATAAT
322489 ATTATAATAT
Statistics
Matches: 139, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
94 6 0.04
95 88 0.63
96 1 0.01
97 1 0.01
98 37 0.27
99 5 0.04
100 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (94 bp):
ATAAAGCTGGAGCATTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATATAATC
ACCTTTATCAGGCTAGCTGAATATTATCC
Found at i:327177 original size:21 final size:21
Alignment explanation
Indices: 327151--327190 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
327141 AATCTTACAT
327151 GGGGGTATCAGTACCCTCTTG
1 GGGGGTATCAGTACCCTCTTG
327172 GGGGGTATCAGTACCCTCT
1 GGGGGTATCAGTACCCTCT
327191 AGGCAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.28
Consensus pattern (21 bp):
GGGGGTATCAGTACCCTCTTG
Found at i:327830 original size:29 final size:29
Alignment explanation
Indices: 327798--327879 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
327788 TAAATATAAG
327798 CATTCAAAGTTAAACAATCAAACCAAAAA
1 CATTCAAAGTTAAACAATCAAACCAAAAA
* *
327827 CATTCAAA-TTCAAACATTCAATCCAAAAA
1 CATTCAAAGTT-AAACAATCAAACCAAAAA
* *
327856 CATTAAAATGTTTAACAAGTCAAA
1 CATTCAAA-GTTAAACAA-TCAAA
327880 GTTCTAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.05
29 31 0.72
30 4 0.09
31 6 0.14
ACGTcount: A:0.54, C:0.20, G:0.04, T:0.23
Consensus pattern (29 bp):
CATTCAAAGTTAAACAATCAAACCAAAAA
Found at i:327833 original size:15 final size:15
Alignment explanation
Indices: 327809--327859 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
327799 ATTCAAAGTT
*
327809 AAACAATCAAACCAA
1 AAACATTCAAACCAA
*
327824 AAACATTCAAATTC--
1 AAACATTCAAA-CCAA
*
327838 AAACATTCAATCCAA
1 AAACATTCAAACCAA
327853 AAACATT
1 AAACATT
327860 AAAATGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 17 0.59
16 1 0.03
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACATTCAAACCAA
Found at i:329896 original size:23 final size:22
Alignment explanation
Indices: 329848--329918 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 22
329838 ACCTCGTAGA
*
329848 GGGTATCGGTA-CC-CTCATGG
1 GGGTATCGGTACCCACTCAAGG
329868 GGGTATCGGTACCCACTCAAAGG
1 GGGTATCGGTACCCACTC-AAGG
* *
329891 GGGTATCAGTACTCA-TGCAAGG
1 GGGTATCGGTACCCACT-CAAGG
329913 GGGTAT
1 GGGTAT
329919 GGATACCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.25
21 2 0.05
22 14 0.32
23 17 0.39
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.23
Consensus pattern (22 bp):
GGGTATCGGTACCCACTCAAGG
Found at i:335701 original size:19 final size:20
Alignment explanation
Indices: 335677--335715 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
335667 CGTTATAAGA
*
335677 TGGGGGTATCGGT-ACCTCC
1 TGGGGGTATCAGTAACCTCC
335696 TGGGGGTATCAGTAACCTCC
1 TGGGGGTATCAGTAACCTCC
335716 GAGCAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.26
Consensus pattern (20 bp):
TGGGGGTATCAGTAACCTCC
Found at i:335780 original size:20 final size:19
Alignment explanation
Indices: 335751--335789 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
335741 AAATCTTACA
335751 TGGGGTATCGGTACCCTCT
1 TGGGGTATCGGTACCCTCT
335770 TGGGCGTATCGGTACCCTCT
1 TGGG-GTATCGGTACCCTCT
335790 GGCCAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.10, C:0.28, G:0.31, T:0.31
Consensus pattern (19 bp):
TGGGGTATCGGTACCCTCT
Found at i:336115 original size:8 final size:7
Alignment explanation
Indices: 336104--336230 Score: 55
Period size: 7 Copynumber: 17.4 Consensus size: 7
336094 AATAATAAAC
336104 AAAATGAA
1 AAAAT-AA
*
336112 AAAAGAGA
1 AAAATA-A
336120 AAAATAA
1 AAAATAA
336127 TAAAATAA
1 -AAAATAA
336135 TAAAAT-A
1 -AAAATAA
336142 AAAATAA
1 AAAATAA
*
336149 AAGACT-A
1 AA-AATAA
* *
336156 ATACTAA
1 AAAATAA
336163 ATAAATAA
1 A-AAATAA
**
336171 AATGGTAAA
1 AA-AAT-AA
336180 ATAAATAA
1 A-AAATAA
336188 AAAATAA
1 AAAATAA
*
336195 AACA-AA
1 AAAATAA
*
336201 AAAATGA
1 AAAATAA
*
336208 ATAA-AA
1 AAAATAA
*
336214 ATAATAA
1 AAAATAA
336221 AAAATAA
1 AAAATAA
336228 AAA
1 AAA
336231 TAAGACATAA
Statistics
Matches: 92, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
6 18 0.20
7 35 0.38
8 34 0.37
9 4 0.04
10 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (7 bp):
AAAATAA
Found at i:336150 original size:28 final size:28
Alignment explanation
Indices: 336083--336229 Score: 79
Period size: 28 Copynumber: 5.0 Consensus size: 28
336073 TAGAAAATGC
* * * *
336083 ATAAATATGAAAATAATAAACAAAATGAA
1 ATAAAAATAAAAATAATAAA-ATAATAAA
* *
336112 A-AAAGAGAAAAATAATAAAATAATAAA
1 ATAAAAATAAAAATAATAAAATAATAAA
336139 ATAAAAATAAAAGACTAATACTAAATAAATAAA
1 ATAAAAATAAAA-A-TAATA--AAAT-AATAAA
* *
336172 ATGGTAAAAT--AAATAA-AAAATAAAACAA
1 AT--AAAAATAAAAATAATAAAATAATA-AA
*
336200 AAAAATGAATAAAAATAATAAAA-AATAAA
1 ATAAA--AATAAAAATAATAAAATAATAAA
336229 A
1 A
336230 ATAAGACATA
Statistics
Matches: 92, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
26 2 0.02
27 10 0.11
28 33 0.36
29 5 0.05
30 15 0.16
31 7 0.08
32 5 0.05
33 10 0.11
35 5 0.05
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.18
Consensus pattern (28 bp):
ATAAAAATAAAAATAATAAAATAATAAA
Found at i:336230 original size:16 final size:16
Alignment explanation
Indices: 336177--336233 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
336167 ATAAAATGGT
336177 AAAATAAATAAAAAATA
1 AAAAT-AATAAAAAATA
336194 AAACA-AA-AAAATGAATA
1 AAA-ATAATAAAA--AATA
336211 AAAATAATAAAAAATA
1 AAAATAATAAAAAATA
336227 AAAATAA
1 AAAATAA
336234 GACATAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
15 4 0.11
16 14 0.40
17 12 0.34
18 5 0.14
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAATAAAAAATA
Found at i:336230 original size:28 final size:27
Alignment explanation
Indices: 336186--336241 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
336176 TAAAATAAAT
* *
336186 AAAA-AATAAAACA-AAAAAATGAATA
1 AAAATAATAAAAAATAAAAAAAGAATA
336211 AAAATAATAAAAAATAAAAATAAGACATA
1 AAAATAATAAAAAATAAAAA-AAGA-ATA
336240 AA
1 AA
336242 TAACAGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 4 0.16
26 8 0.32
27 5 0.20
28 3 0.12
29 5 0.20
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.14
Consensus pattern (27 bp):
AAAATAATAAAAAATAAAAAAAGAATA
Found at i:336370 original size:2 final size:2
Alignment explanation
Indices: 336365--336401 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
336355 AAATGAAAGA
336365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
336402 AAATAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:344982 original size:23 final size:22
Alignment explanation
Indices: 344950--344999 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
344940 ATTTTGGCTT
*
344950 TTTTGGCTTTTTTTTGTTTTTTA
1 TTTTGCCTTTTTTTT-TTTTTTA
*
344973 TTTTGCCTTTTTTTTTTTTTTT
1 TTTTGCCTTTTTTTTTTTTTTA
344995 TTTTG
1 TTTTG
345000 AAAAAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.02, C:0.06, G:0.10, T:0.82
Consensus pattern (22 bp):
TTTTGCCTTTTTTTTTTTTTTA
Found at i:344986 original size:22 final size:22
Alignment explanation
Indices: 344958--344999 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
344948 TTTTTTGGCT
344958 TTTTTTTGTTTTTTATTTTGCC
1 TTTTTTTGTTTTTTATTTTGCC
* *
344980 TTTTTTTTTTTTTTTTTTTG
1 TTTTTTTGTTTTTTATTTTG
345000 AAAAAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (22 bp):
TTTTTTTGTTTTTTATTTTGCC
Found at i:346296 original size:34 final size:35
Alignment explanation
Indices: 346242--346310 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
346232 GCATGTATCA
*
346242 AAACTTCAAAGGTAAAAGGAAAGGAGAAGGTGGTG
1 AAACTTCAAAGGTAAAAGGAAAGGAAAAGGTGGTG
346277 AAACTTCAAA-GTAAAAGGAAAGGAAAAGGTGGTG
1 AAACTTCAAAGGTAAAAGGAAAGGAAAAGGTGGTG
346311 GAGAGCTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 23 0.70
35 10 0.30
ACGTcount: A:0.48, C:0.06, G:0.32, T:0.14
Consensus pattern (35 bp):
AAACTTCAAAGGTAAAAGGAAAGGAAAAGGTGGTG
Found at i:354963 original size:31 final size:32
Alignment explanation
Indices: 354885--354969 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 32
354875 GGAATGTCTT
* * * *
354885 GGGGCCTGAGAGCCTACCTAAGAAGGTTACTC
1 GGGGCCTAAGAGCCTACCCAAGAAAGATACTC
* * *
354917 AGGGCCAAAGGGCCTACCCAAGAAAGAT-CTC
1 GGGGCCTAAGAGCCTACCCAAGAAAGATACTC
*
354948 GGGGCCTCAGAGCCTACCCAAG
1 GGGGCCTAAGAGCCTACCCAAG
354970 GGTCACCATA
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 21 0.50
32 21 0.50
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.13
Consensus pattern (32 bp):
GGGGCCTAAGAGCCTACCCAAGAAAGATACTC
Found at i:356263 original size:27 final size:27
Alignment explanation
Indices: 356233--356285 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
356223 GGCTTGGAGA
*
356233 TATTTAGGTCATTTTACACTTTAGGGG
1 TATTTAGGTCATTTTACACTTCAGGGG
* *
356260 TATTTTGGTTATTTTACACTTCAGGG
1 TATTTAGGTCATTTTACACTTCAGGG
356286 CCTTACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (27 bp):
TATTTAGGTCATTTTACACTTCAGGGG
Found at i:356328 original size:44 final size:44
Alignment explanation
Indices: 356278--356366 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
356268 TTATTTTACA
356278 CTTCAGGGCCTTACAATATAGATCCAGAATTTAAATAAATGATT
1 CTTCAGGGCCTTACAATATAGATCCAGAATTTAAATAAATGATT
356322 CTTCAGGGCCTTACAATATAGATCCAGAATTTAAATAAATGATT
1 CTTCAGGGCCTTACAATATAGATCCAGAATTTAAATAAATGATT
356366 C
1 C
356367 CAAGGTTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (44 bp):
CTTCAGGGCCTTACAATATAGATCCAGAATTTAAATAAATGATT
Found at i:356368 original size:21 final size:21
Alignment explanation
Indices: 356300--356368 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
356290 ACAATATAGA
356300 TCCAGAATTTAAATAAATGAT
1 TCCAGAATTTAAATAAATGAT
*** *
356321 TCTTCAGGGCCTTACAATATA-GA-
1 TC--CA-GAATTTA-AATAAATGAT
356344 TCCAGAATTTAAATAAATGAT
1 TCCAGAATTTAAATAAATGAT
356365 TCCA
1 TCCA
356369 AGGTTCAAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 5 0.15
20 6 0.18
21 8 0.24
23 4 0.12
24 6 0.18
25 5 0.15
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (21 bp):
TCCAGAATTTAAATAAATGAT
Found at i:357282 original size:17 final size:18
Alignment explanation
Indices: 357251--357284 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
357241 TCAAAAACAT
357251 AAAATATGACATTTTTGA
1 AAAATATGACATTTTTGA
*
357269 AAAATTTGAC-TTTTTG
1 AAAATATGACATTTTTG
357285 GTCAAAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (18 bp):
AAAATATGACATTTTTGA
Found at i:357303 original size:14 final size:14
Alignment explanation
Indices: 357284--357314 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
357274 TTGACTTTTT
357284 GGTCAAAGTTAACG
1 GGTCAAAGTTAACG
*
357298 GGTCAAAGTTAATG
1 GGTCAAAGTTAACG
357312 GGT
1 GGT
357315 TGACTTGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.26
Consensus pattern (14 bp):
GGTCAAAGTTAACG
Found at i:362078 original size:27 final size:27
Alignment explanation
Indices: 362048--362109 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
362038 TGACTATTTG
** *
362048 GTCAAAGTCAACGGTCAAAGTCAAC-T
1 GTCAAAGTCAACACTCAAAGCCAACAT
362074 AGTCAAAGTCAACACTCAAAGCCAACAT
1 -GTCAAAGTCAACACTCAAAGCCAACAT
362102 GTCAAAGT
1 GTCAAAGT
362110 AAATGGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (27 bp):
GTCAAAGTCAACACTCAAAGCCAACAT
Found at i:362080 original size:14 final size:13
Alignment explanation
Indices: 362048--362109 Score: 79
Period size: 13 Copynumber: 4.6 Consensus size: 13
362038 TGACTATTTG
*
362048 GTCAAAGTCAACG
1 GTCAAAGTCAACA
362061 GTCAAAGTCAACTA
1 GTCAAAGTCAAC-A
362075 GTCAAAGTCAACA
1 GTCAAAGTCAACA
* *
362088 CTCAAAGCCAACA
1 GTCAAAGTCAACA
362101 TGTCAAAGT
1 -GTCAAAGT
362110 AAATGGTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
13 24 0.57
14 18 0.43
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (13 bp):
GTCAAAGTCAACA
Found at i:364260 original size:11 final size:11
Alignment explanation
Indices: 364244--364281 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
364234 TTTTATTATA
364244 ATTATATATTT
1 ATTATATATTT
*
364255 ATTATATATAT
1 ATTATATATTT
*
364266 -TTATATTTTT
1 ATTATATATTT
364276 ATTATA
1 ATTATA
364282 GTTTAATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATATATTT
Found at i:364269 original size:21 final size:21
Alignment explanation
Indices: 364230--364281 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
364220 ATTATAAAAG
364230 ATATTT-TTAT-TATAATTAT
1 ATATTTATTATATATAATTAT
*
364249 ATATTTATTATATATATTTAT
1 ATATTTATTATATATAATTAT
*
364270 ATTTTTATTATA
1 ATATTTATTATA
364282 GTTTAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.21
20 4 0.14
21 19 0.66
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTTATTATATATAATTAT
Found at i:364290 original size:17 final size:17
Alignment explanation
Indices: 364230--364290 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 17
364220 ATTATAAAAG
364230 ATATTTTTATTATAATTAT
1 ATATTTTTATTAT-ATT-T
364249 ATATTTATTATATATATTT
1 ATATTT-TTAT-TATATTT
364268 ATATTTTTATTATAGTTT
1 ATATTTTTATTATA-TTT
364286 A-ATTT
1 ATATTT
364291 GATATAATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.21
18 8 0.21
19 13 0.33
20 7 0.18
21 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
ATATTTTTATTATATTT
Found at i:364296 original size:45 final size:47
Alignment explanation
Indices: 364257--364360 Score: 127
Period size: 49 Copynumber: 2.2 Consensus size: 47
364247 ATATATTTAT
** * *
364257 TATATATATTTATATTTTTATTATAGTTTAATTTGATATAATTCATA
1 TATATATATTTATAAATTTACTATAGTTTAATCTGATATAATTCATA
* * *
364304 TATAATAATATTTTTAAATTTACTATAGTTTAATCTGGTATGATTCATA
1 TAT-AT-ATATTTATAAATTTACTATAGTTTAATCTGATATAATTCATA
364353 TATATATA
1 TATATATA
364361 AGTGTAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 6 0.12
48 4 0.08
49 38 0.79
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (47 bp):
TATATATATTTATAAATTTACTATAGTTTAATCTGATATAATTCATA
Found at i:364766 original size:17 final size:18
Alignment explanation
Indices: 364746--364788 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
364736 TATGTCACAC
364746 ATTTATTTA-TTTTAATT
1 ATTTATTTAGTTTTAATT
364763 ATTT-TTTAGTTTTAATT
1 ATTTATTTAGTTTTAATT
364780 ATTTATTTA
1 ATTTATTTA
364789 ATTTGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTATTTAGTTTTAATT
Found at i:364994 original size:22 final size:24
Alignment explanation
Indices: 364967--365020 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
364957 TTAATTAAAT
364967 TAATTATGATAA-ATTTAT-TTTTC
1 TAATTAT-ATAATATTTATATTTTC
*
364990 T-ATTATATAATTTTTATATTTTC
1 TAATTATATAATATTTATATTTTC
365013 TAATTATA
1 TAATTATA
365021 ATTTCGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.15
22 10 0.37
23 7 0.26
24 6 0.22
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
TAATTATATAATATTTATATTTTC
Found at i:365594 original size:59 final size:60
Alignment explanation
Indices: 365524--365678 Score: 188
Period size: 59 Copynumber: 2.6 Consensus size: 60
365514 TCGAGTAACT
* *
365524 ATTTTGTAACTTTTAATAGTCGAGTGGCTCAATAAAACAACA-CATATTGTTAG-GAGATC
1 ATTTTGTAACTTTTAATAGT-GAGGGGCTCAATAAAACAACATCATATAGTTAGAGAGATC
* * ** *
365583 ATTTTGTAACTTTTAATAATTAGGGGCTCAATAAAGTAACATCCTATAGTTAGAGAGATC
1 ATTTTGTAACTTTTAATAGTGAGGGGCTCAATAAAACAACATCATATAGTTAGAGAGATC
* * *
365643 ATTTTGTAACTTCTAATAGTTGAAGGACTCAATAAA
1 ATTTTGTAACTTTTAATAG-TGAGGGGCTCAATAAA
365679 GTAGTATCCT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 17 0.21
59 28 0.35
60 23 0.28
61 13 0.16
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTGAGGGGCTCAATAAAACAACATCATATAGTTAGAGAGATC
Found at i:365662 original size:30 final size:29
Alignment explanation
Indices: 365572--365663 Score: 78
Period size: 30 Copynumber: 3.1 Consensus size: 29
365562 AACACATATT
*
365572 GTTAGGAGATCATTTTGTAACTTTTAATA
1 GTTAGGAGATCATTTTGTAACTTCTAATA
* * * *** *
365601 ATTAGGGGCTCAATAAAGTAACATCCT-ATA
1 GTTAGGAGATC-ATTTTGTAAC-TTCTAATA
365631 GTTAGAGAGATCATTTTGTAACTTCTAATA
1 GTTAG-GAGATCATTTTGTAACTTCTAATA
365661 GTT
1 GTT
365664 GAAGGACTCA
Statistics
Matches: 44, Mismatches: 15, Indels: 7
0.67 0.23 0.11
Matches are distributed among these distances:
29 11 0.25
30 27 0.61
31 6 0.14
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (29 bp):
GTTAGGAGATCATTTTGTAACTTCTAATA
Found at i:365706 original size:60 final size:59
Alignment explanation
Indices: 365572--365711 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 59
365562 AACACATATT
* * *
365572 GTTAGGAGATCATTTTGTAACTTTTAATAATTAGGGGCTCAATAAAGTAACATCCTATA
1 GTTAGGAGATCATTTTGTAACTTCTAATAATTAAGGACTCAATAAAGTAACATCCTATA
* **
365631 GTTAGAGAGATCATTTTGTAACTTCTAATAGTTGAAGGACTCAATAAAGTAGTATCCTATA
1 GTTAG-GAGATCATTTTGTAACTTCTAATAATT-AAGGACTCAATAAAGTAACATCCTATA
* *
365692 GTTAGGGGACCATTTGTGTA
1 GTTAGGAGATCATTT-TGTA
365712 TTTTACCCAC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 5 0.07
60 33 0.47
61 32 0.46
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (59 bp):
GTTAGGAGATCATTTTGTAACTTCTAATAATTAAGGACTCAATAAAGTAACATCCTATA
Found at i:366635 original size:14 final size:14
Alignment explanation
Indices: 366616--366642 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
366606 CCCCCCCCCC
366616 CCCAAAAAAAAAAA
1 CCCAAAAAAAAAAA
366630 CCCAAAAAAAAAA
1 CCCAAAAAAAAAA
366643 TCTTTAATTC
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:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (14 bp):
CCCAAAAAAAAAAA
Found at i:371535 original size:15 final size:15
Alignment explanation
Indices: 371512--371546 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
371502 ATACACCGCG
*
371512 ACATAAAGTCCAGCA
1 ACATTAAGTCCAGCA
371527 ACATTAAGTCCAGCA
1 ACATTAAGTCCAGCA
371542 ACATT
1 ACATT
371547 CTACTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (15 bp):
ACATTAAGTCCAGCA
Found at i:373476 original size:182 final size:181
Alignment explanation
Indices: 373161--373608 Score: 631
Period size: 182 Copynumber: 2.5 Consensus size: 181
373151 TTTTTACTAC
* * * *
373161 CGGTTTTGTCATTTCGAAATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * * * * * *
373226 ATTTTTATAAAGTATCGACATTTTATTGGTGTTATAATTTCTTTTATTTTAAATTCTAAAATTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGTGTTATAACTTATTCTATTTTAAATTCCAAAAGTGT
* *
373291 CGATACTTATAATAAAGTATCGACACTTTCAACATATAC-GGTAGC-TCTTTA
131 CGATACTTATAATAAAATATCGACACTATCAACATAT-CTGGTAGCGT-TTTA
*
373342 TCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATA
1 -CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
* *
373407 CATTTTTATAAAGTATCGTCACTTTATTAGTGTTATAACTTATTCTCTTTTAAATTCCAAAAGTG
65 CATTTTTATAAAGTATCGACACTTTATTAGTGTTATAACTTATTCTATTTTAAATTCCAAAAGTG
373472 TCGATACTTATAATAAAATATCGACACTATCAACATATCTGGTAGCGTTTTA
130 TCGATACTTATAATAAAATATCGACACTATCAACATATCTGGTAGCGTTTTA
* * *
373524 C----ATGTC-TTTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATA
1 CGGTTTTGTCATTTT-GAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
*
373584 CATTTTTATAAAGTATCGATACTTT
65 CATTTTTATAAAGTATCGACACTTT
373609 CAATATATCC
Statistics
Matches: 241, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
176 4 0.02
177 73 0.30
181 2 0.01
182 161 0.67
183 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (181 bp):
CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTAGTGTTATAACTTATTCTATTTTAAATTCCAAAAGTGT
CGATACTTATAATAAAATATCGACACTATCAACATATCTGGTAGCGTTTTA
Found at i:373809 original size:112 final size:112
Alignment explanation
Indices: 373484--373940 Score: 669
Period size: 112 Copynumber: 4.1 Consensus size: 112
373474 GATACTTATA
* * * * * *
373484 ATAAAATATCGACACTATCAACATATCTGGTAGCGTTTTA-C----ATGTCTTTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
* *
373544 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
* * *
373591 ATAAAGTATCGATACTTTCAATATATCCGGTAGC-TCTTTACCTGCTTT-TCATTTATAGATCGG
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGT-TTTACCTGTTTTGTCATTTATAGACCGG
*
373654 TTTTGTCATTTTTTTACCTGTTATATTGTTATAGATTAATACATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
*
373702 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
*
373767 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
** * *
373814 ATAAAGTATCGACACTTTCAATATATCCAATAGCGTTTTACCTATTTTGTCATTTATAGACCAGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
*
373879 TTTGTCATTTTTTTACCTGTTATATTGTTAT-GAATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAG-ATCAATACATTTTT
373926 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
373941 AAACCGACAA
Statistics
Matches: 319, Mismatches: 22, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
106 1 0.00
107 33 0.10
108 1 0.00
111 103 0.32
112 181 0.57
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
Found at i:374708 original size:17 final size:17
Alignment explanation
Indices: 374668--374750 Score: 96
Period size: 17 Copynumber: 4.8 Consensus size: 17
374658 ATGTTTACGA
*
374668 AGGAATTGAAATCTGTGA
1 AGGAATTGAAATCTGT-C
*
374686 AGGAATTGAAATCTATC
1 AGGAATTGAAATCTGTC
*
374703 AGGAATTGGAATCTGTC
1 AGGAATTGAAATCTGTC
*
374720 AGGAATT-AGAATCTGTT
1 AGGAATTGA-AATCTGTC
*
374737 AGGAATTGTAATCT
1 AGGAATTGAAATCT
374751 AATTCCATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
17 41 0.73
18 15 0.27
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.31
Consensus pattern (17 bp):
AGGAATTGAAATCTGTC
Found at i:375383 original size:32 final size:33
Alignment explanation
Indices: 375309--375392 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
375299 TTTTCACCCT
375309 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCACACTTAAAA
*
375343 AAACCCGACCCGACCCGAATATCATACTT-AAA
1 AAACCCGACCCGACCCGAATATCACACTTAAAA
*
375375 AAATCCGACCCG-CCCGAA
1 AAACCCGACCCGACCCGAA
375393 CAAAATAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
31 6 0.12
32 14 0.29
33 21 0.44
34 7 0.15
ACGTcount: A:0.40, C:0.37, G:0.11, T:0.12
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:375630 original size:5 final size:5
Alignment explanation
Indices: 375620--375645 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
375610 ATAAGGTTTC
375620 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
375646 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:376480 original size:21 final size:21
Alignment explanation
Indices: 376456--376502 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
376446 AAAAAGCTGT
376456 CAATTTACACAACATTGTCGC
1 CAATTTACACAACATTGTCGC
*
376477 CAATTTACACAACATTGTCGT
1 CAATTTACACAACATTGTCGC
376498 CAATT
1 CAATT
376503 CATATACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.32
Consensus pattern (21 bp):
CAATTTACACAACATTGTCGC
Found at i:383880 original size:30 final size:30
Alignment explanation
Indices: 383833--383892 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
383823 AAACTTTGAA
*
383833 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATCAAGTCCAAAAACCATTTTG
383862 TAAATTCAACTCAAGTCCAAAAACCATTTTG
1 TAAATTCAA-TCAAGTCCAAAAACCATTTTG
383893 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 12 0.43
31 7 0.25
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAATTCAATCAAGTCCAAAAACCATTTTG
Found at i:384026 original size:21 final size:21
Alignment explanation
Indices: 384002--384041 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
383992 ATGTTTAATG
384002 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
384023 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
384042 CCAATTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:386746 original size:8 final size:8
Alignment explanation
Indices: 386733--386778 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
386723 TTGCAGCCTT
386733 GATGCATG
1 GATGCATG
386741 GATGCATG
1 GATGCATG
386749 GATGCAT-
1 GATGCATG
386756 G--GCA-G
1 GATGCATG
*
386761 GATGCATC
1 GATGCATG
386769 GATGCATG
1 GATGCATG
386777 GA
1 GA
386779 AAGGATTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
5 4 0.12
7 4 0.12
8 24 0.75
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (8 bp):
GATGCATG
Found at i:386789 original size:21 final size:21
Alignment explanation
Indices: 386740--386858 Score: 204
Period size: 21 Copynumber: 5.7 Consensus size: 21
386730 CTTGATGCAT
*
386740 GGATGCATGGATGCATGGC-A
1 GGATGCATCGATGCATGGCAA
*
386760 GGATGCATCGATGCATGGAAA
1 GGATGCATCGATGCATGGCAA
*
386781 GGATTCATCGATGCATGGCAA
1 GGATGCATCGATGCATGGCAA
386802 GGATGCATCGATGCATGGCAA
1 GGATGCATCGATGCATGGCAA
386823 GGATGCATCGATGCATGGCAA
1 GGATGCATCGATGCATGGCAA
386844 GGATGCATCGATGCA
1 GGATGCATCGATGCA
386859 CTAATTGCAT
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
20 17 0.18
21 76 0.82
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.20
Consensus pattern (21 bp):
GGATGCATCGATGCATGGCAA
Found at i:386808 original size:13 final size:13
Alignment explanation
Indices: 386790--386851 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
386780 AGGATTCATC
386790 GATGCATGGCAAG
1 GATGCATGGCAAG
386803 GATGCAT--C---
1 GATGCATGGCAAG
386811 GATGCATGGCAAG
1 GATGCATGGCAAG
386824 GATGCAT--C---
1 GATGCATGGCAAG
386832 GATGCATGGCAAG
1 GATGCATGGCAAG
386845 GATGCAT
1 GATGCAT
386852 CGATGCACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 20
0.66 0.00 0.34
Matches are distributed among these distances:
8 14 0.36
10 2 0.05
11 2 0.05
13 21 0.54
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (13 bp):
GATGCATGGCAAG
Found at i:386947 original size:21 final size:21
Alignment explanation
Indices: 386921--386978 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
386911 CATTAGTGCA
386921 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
*
386942 GATGCATGGATGCACTGTAGG
1 GATGCATGGATGCACTGCAGG
*
386963 GATACATGGATGCACT
1 GATGCATGGATGCACT
386979 TTGACACCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.22
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:387079 original size:29 final size:29
Alignment explanation
Indices: 387058--387115 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
387048 AAACTTTGAA
*
387058 TAAATTTAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
387087 TAAATTCAATTCAAGTCTAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
387116 TGCCTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:387109 original size:30 final size:30
Alignment explanation
Indices: 387058--387117 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
387048 AAACTTTGAA
*
387058 TAAATTTAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
387087 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
387118 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:387252 original size:21 final size:21
Alignment explanation
Indices: 387228--387267 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
387218 ATGTTTAATG
387228 AAAAAAATATCAATTGTTAAC
1 AAAAAAATATCAATTGTTAAC
**
387249 AAAATGATATCAATTGTTA
1 AAAAAAATATCAATTGTTA
387268 CCAATTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAAAAATATCAATTGTTAAC
Found at i:390013 original size:30 final size:30
Alignment explanation
Indices: 389966--390025 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
389956 AAACTTTGAA
*
389966 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATCAAGTCCAAAAACCATTTTG
389995 TAAATTCAACTCAAGTCCAAAAACCATTTTG
1 TAAATTCAA-TCAAGTCCAAAAACCATTTTG
390026 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 12 0.43
31 7 0.25
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAATTCAATCAAGTCCAAAAACCATTTTG
Found at i:390160 original size:21 final size:21
Alignment explanation
Indices: 390136--390175 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
390126 ATGTTTAATG
390136 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
390157 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
390176 CCAATTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:391364 original size:19 final size:20
Alignment explanation
Indices: 391321--391368 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
391311 TCTAAATCCT
*
391321 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
391341 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
391360 TTTTCAAAA
1 TTTTCAAAA
391369 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:392729 original size:8 final size:8
Alignment explanation
Indices: 392718--392742 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
392708 ATTCGATGTT
392718 TGGATGCA
1 TGGATGCA
392726 TGGATGCA
1 TGGATGCA
392734 TGGATGCA
1 TGGATGCA
392742 T
1 T
392743 TGCCTGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.28
Consensus pattern (8 bp):
TGGATGCA
Found at i:406526 original size:2 final size:2
Alignment explanation
Indices: 406519--406562 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
406509 TATACCCAGA
406519 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
406561 AT
1 AT
406563 TCAATAAAAC
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:407948 original size:3 final size:3
Alignment explanation
Indices: 407940--407977 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
407930 TAATCAAAAT
*
407940 TAA TAA TAA TAA T-A TAA TTA TAA TAA TACA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
407978 TTTTTGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:407953 original size:24 final size:24
Alignment explanation
Indices: 407926--407978 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
407916 TAGACCACAA
407926 AATATAATCAAAATTAATA-ATAAT
1 AATATAATCAAAA-TAATACATAAT
* *
407950 AATATAATTATAATAATACATAAT
1 AATATAATCAAAATAATACATAAT
407974 AATAT
1 AATAT
407979 TTTTGTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
AATATAATCAAAATAATACATAAT
Found at i:407962 original size:14 final size:14
Alignment explanation
Indices: 407940--407977 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
407930 TAATCAAAAT
407940 TAATAATAATAATA
1 TAATAATAATAATA
*
407954 TAATTATAATAATA
1 TAATAATAATAATA
*
407968 -CATAATAATA
1 TAATAATAATA
407978 TTTTTGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:408233 original size:40 final size:41
Alignment explanation
Indices: 408132--408239 Score: 128
Period size: 43 Copynumber: 2.6 Consensus size: 41
408122 GGTAGGAGAC
* *
408132 GACACGACTCATATGTAATGAAGAGGTCTGGTCGTCTAAGGGT
1 GACACGACTCATATGTGATGAAGAGGTCTGGTCG--TAAGGAT
* * *
408175 GACACGACTCCTATGTGATGAGGAGGTCTGGTCG-ATGGAT
1 GACACGACTCATATGTGATGAAGAGGTCTGGTCGTAAGGAT
* *
408215 GACACAACTCATACGTGATGAAGAG
1 GACACGACTCATATGTGATGAAGAG
408240 TTTTGGCCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
40 25 0.45
43 31 0.55
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.23
Consensus pattern (41 bp):
GACACGACTCATATGTGATGAAGAGGTCTGGTCGTAAGGAT
Found at i:408464 original size:131 final size:131
Alignment explanation
Indices: 408166--408527 Score: 383
Period size: 131 Copynumber: 2.7 Consensus size: 131
408156 GGTCTGGTCG
* * *** * *
408166 TCTAAGGGTGACACGACTCCTATGTGATGAGGAGGTCTGGTCGATGGATGACACAACTCATACGT
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGG
* * * * ** *** *
408231 GATGAAGA-GTTTTGGCCATCTTTAGGAAGGGTGGTAACATGGTTCCTACGCGATGAGGACGACT
66 GATGAGGATG-ATAGACCATCTTTAGGAA---TAATAACACAATTCCTACGCGATAAGGACGACT
408295 GATTA
127 GATTA
* *
408300 TCTAGGGGTGACACAGA-TCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACGCGGTTCCTACG
1 TCTAAGGGTGACAC-GACTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACG
* * * *
408364 GGATGAGGATGATAGACCATCTTTAGGAATAATAACACAATTCCTACGTGATAAGGATG-GTTAG
65 GGATGAGGATGATAGACCATCTTTAGGAATAATAACACAATTCCTACGCGATAAGGACGACTGA-
408428 TTA
129 TTA
*
408431 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCAGG-GGATGACACGGTTCCTACG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTC-GGTGGATGACACGGTTCCTACG
* *
408495 GGATGAGGATGACA-AGCCATCTTTAGGTATAAT
65 GGATGAGGATGATAGA-CCATCTTTAGGAATAAT
408528 GGTTTCAAGA
Statistics
Matches: 194, Mismatches: 28, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
130 5 0.03
131 109 0.56
132 2 0.01
134 75 0.39
135 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (131 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGG
GATGAGGATGATAGACCATCTTTAGGAATAATAACACAATTCCTACGCGATAAGGACGACTGATT
A
Found at i:408697 original size:63 final size:61
Alignment explanation
Indices: 408620--408771 Score: 187
Period size: 63 Copynumber: 2.4 Consensus size: 61
408610 TCTCAAAGAT
* * * *
408620 CTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTCTCATAAGAAATTGTCTCAAGAGACAAAA
1 CTTTGTTTCCAGAGAAACA-ACTCAAAGATTTTTCTCAAAAGAAACTATCTCAAGAGA-AAAA
* **
408683 CTTTGTTTCCAGAGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTATCTTGAGAGAAAAA
1 CTTTGTTTCCAGAGAAAC-AACTCAAAGATTTTTCTCAAAAGAAACTATCTCAAGAGAAAAA
* * *
408745 ATTTGTTTCCAGAAAAACAATTCAAAG
1 CTTTGTTTCCAGAGAAACAACTCAAAG
408772 GATATTGATA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
61 8 0.10
62 20 0.26
63 49 0.63
64 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (61 bp):
CTTTGTTTCCAGAGAAACAACTCAAAGATTTTTCTCAAAAGAAACTATCTCAAGAGAAAAA
Found at i:410813 original size:16 final size:16
Alignment explanation
Indices: 410792--410822 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
410782 GTAGGATTTA
410792 GGGGTCCTTGTTTTGC
1 GGGGTCCTTGTTTTGC
*
410808 GGGGTCTTTGTTTTG
1 GGGGTCCTTGTTTTG
410823 TAAGGTTCAA
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:0.00, C:0.13, G:0.39, T:0.48
Consensus pattern (16 bp):
GGGGTCCTTGTTTTGC
Found at i:411014 original size:17 final size:17
Alignment explanation
Indices: 410992--411026 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
410982 ACAAATATTT
*
410992 AAGAAAAATAAGTACAA
1 AAGAAAAACAAGTACAA
*
411009 AAGAAAAACAAGTTCAA
1 AAGAAAAACAAGTACAA
411026 A
1 A
411027 CAATATGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (17 bp):
AAGAAAAACAAGTACAA
Found at i:413456 original size:29 final size:30
Alignment explanation
Indices: 413372--413536 Score: 115
Period size: 30 Copynumber: 5.6 Consensus size: 30
413362 AAACAGGAAT
* * * *
413372 TTAAAGGACTAAAATGGCAGAAATAGAAAC
1 TTAAAGGGCTAAAATAGTAAAAATAGAAAC
*
413402 TTAAATGGCTAAAATAGTAAAAATAGAAAC
1 TTAAAGGGCTAAAATAGTAAAAATAGAAAC
* * *
413432 TT-AAGGGTCT-AAATA-TCAAATATAGACAT
1 TTAAAGGG-CTAAAATAGT-AAAAATAGAAAC
** * *
413461 TTAAAGCACTAAAATAATAAAAATATAAAC
1 TTAAAGGGCTAAAATAGTAAAAATAGAAAC
* * *
413491 -TCAAGGGACT-AAATAGTAAAAATAAAAAG
1 TTAAAGGG-CTAAAATAGTAAAAATAGAAAC
* *
413520 TTAAAGGACCAAAATAG
1 TTAAAGGGCTAAAATAG
413537 CACTAACCAA
Statistics
Matches: 103, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
28 1 0.01
29 43 0.42
30 58 0.56
31 1 0.01
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.22
Consensus pattern (30 bp):
TTAAAGGGCTAAAATAGTAAAAATAGAAAC
Found at i:413457 original size:59 final size:59
Alignment explanation
Indices: 413394--413505 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
413384 AATGGCAGAA
* * * *
413394 ATAGAAACTTAAATG-GCTAAAATAGTAAAAATAGAAACTTAAGGGTCTAAATATCAAAT
1 ATAGAAACTTAAA-GCACTAAAATAATAAAAATAGAAACTCAAGGGACTAAATATCAAAT
* * *
413453 ATAGACATTTAAAGCACTAAAATAATAAAAATATAAACTCAAGGGACTAAATA
1 ATAGAAACTTAAAGCACTAAAATAATAAAAATAGAAACTCAAGGGACTAAATA
413506 GTAAAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 1 0.02
59 44 0.98
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (59 bp):
ATAGAAACTTAAAGCACTAAAATAATAAAAATAGAAACTCAAGGGACTAAATATCAAAT
Found at i:413524 original size:59 final size:59
Alignment explanation
Indices: 413410--413535 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 59
413400 ACTTAAATGG
* * * * * * *
413410 CTAAAATAGTAAAAATAGAAACTTAAGGGTCTAAATATCAAATATAGACATTTAAAGCA
1 CTAAAATAATAAAAATAGAAACTCAAGGGACTAAATATCAAAAATAAAAAGTTAAAGCA
* *
413469 CTAAAATAATAAAAATATAAACTCAAGGGACTAAATAGT-AAAAATAAAAAGTTAAAGGA
1 CTAAAATAATAAAAATAGAAACTCAAGGGACTAAATA-TCAAAAATAAAAAGTTAAAGCA
*
413528 CCAAAATA
1 CTAAAATA
413536 GCACTAACCA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 55 0.98
60 1 0.02
ACGTcount: A:0.57, C:0.10, G:0.11, T:0.22
Consensus pattern (59 bp):
CTAAAATAATAAAAATAGAAACTCAAGGGACTAAATATCAAAAATAAAAAGTTAAAGCA
Found at i:413579 original size:29 final size:30
Alignment explanation
Indices: 413514--413581 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
413504 TAGTAAAAAT
*
413514 AAAAAGTTAAAGGACCAAAATAGCACTAAC
1 AAAAATTTAAAGGACCAAAATAGCACTAAC
* *
413544 CAAAATTTAAAGGA-CAAAATAGCATTAA-
1 AAAAATTTAAAGGACCAAAATAGCACTAAC
413572 AAATAATTTA
1 AAA-AATTTA
413582 GAGCCCATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.06
29 19 0.58
30 12 0.36
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.21
Consensus pattern (30 bp):
AAAAATTTAAAGGACCAAAATAGCACTAAC
Done.