Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:220927 original size:14 final size:13
Alignment explanation
Indices: 220885--220937 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
220875 TTTTCTTCAA
220885 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
220897 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
220909 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
220924 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
220936 TT
1 TT
220938 CTGATTGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.30
13 14 0.38
14 10 0.27
15 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:224053 original size:26 final size:27
Alignment explanation
Indices: 223990--224053 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
223980 TTGTTAGATA
*
223990 AAAAGGTAAGAAATAAATAAATGAAAT
1 AAAAGATAAGAAATAAATAAATGAAAT
* *
224017 TAAA-ATGAAGAAA-AAATAAATTAAAT
1 AAAAGAT-AAGAAATAAATAAATGAAAT
224043 AAAAGATAAGA
1 AAAAGATAAGA
224054 TAAAGAAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (27 bp):
AAAAGATAAGAAATAAATAAATGAAAT
Found at i:224115 original size:9 final size:10
Alignment explanation
Indices: 224082--224235 Score: 61
Period size: 10 Copynumber: 15.2 Consensus size: 10
224072 AATAGTAAGT
*
224082 AAAATAAATAA
1 AAAATATAT-A
224093 AAAATATATA
1 AAAATATATA
224103 AAAATAT-TA
1 AAAATATATA
* *
224112 AAAATAAAGA
1 AAAATATATA
* *
224122 AAAAGA-AGAA
1 AAAATATA-TA
224132 AAAATATATA
1 AAAATATATA
*
224142 TAAATA-A-A
1 AAAATATATA
*
224150 ACAAATAAAT-
1 A-AAATATATA
224160 AAAATAATAATA
1 AAAAT-AT-ATA
*
224172 AAAA-AGTAAA
1 AAAATA-TATA
224182 AATAATATATA
1 AA-AATATATA
* *
224193 TATAATAAATA
1 -AAAATATATA
*
224204 AAAACATA-A
1 AAAATATATA
224213 AAAATAGTATA
1 AAAATA-TATA
* *
224224 TATATATATA
1 AAAATATATA
224234 AA
1 AA
224236 TTAATAAAAC
Statistics
Matches: 107, Mismatches: 21, Indels: 31
0.67 0.13 0.19
Matches are distributed among these distances:
8 1 0.01
9 25 0.23
10 46 0.43
11 29 0.27
12 6 0.06
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.24
Consensus pattern (10 bp):
AAAATATATA
Found at i:224185 original size:94 final size:92
Alignment explanation
Indices: 224087--224261 Score: 203
Period size: 94 Copynumber: 1.9 Consensus size: 92
224077 TAAGTAAAAT
*
224087 AAATAAAAAATATATAA-AAATATTAAAA-ATAAAGAAAAAGAAGA-AAAAATATATATAAATAA
1 AAATAAAAAATATATAATAAATA--AAAACATAAA-AAAAAGAAGATAAAAATATAAATAAATAA
224149 AACAAATAAATAAAATAATAATAAAAAAGTAA
63 AACAAAT-AATAAAA-AATAATAAAAAAGTAA
* * * * * * * *
224181 AAATAATATATATATAATAAATAAAAACATAAAAAATAGTATATATATATATAAATTAATAAAAC
1 AAATAAAAAATATATAATAAATAAAAACATAAAAAAAAGAAGATAAAAATATAAATAAATAAAAC
224246 AAATAATAAAAAATAA
66 AAATAATAAAAAATAA
224262 CATATATATA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
92 5 0.07
93 18 0.26
94 41 0.59
95 5 0.07
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (92 bp):
AAATAAAAAATATATAATAAATAAAAACATAAAAAAAAGAAGATAAAAATATAAATAAATAAAAC
AAATAATAAAAAATAATAAAAAAGTAA
Found at i:224200 original size:43 final size:38
Alignment explanation
Indices: 224152--224272 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 38
224142 TAAATAAAAC
224152 AAATAAATAAAATAATAATAAAAAAGTAAAAATAATATATAT
1 AAATAAATAAAA-AATAATAAAAAAGT--AAAT-ATATATAT
* *
224194 ATAATAAATAAAAACATAA-AAAATAGTATATATATATAT
1 A-AATAAATAAAAA-ATAATAAAAAAGTAAATATATATAT
*
224233 AAATTAATAAAACAAATAATAAAAAA-TAACATATATATAT
1 AAATAAAT-AAA-AAATAATAAAAAAGTAA-ATATATATAT
224273 GTAATCTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
38 6 0.09
39 18 0.26
40 20 0.29
42 9 0.13
43 15 0.22
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (38 bp):
AAATAAATAAAAAATAATAAAAAAGTAAATATATATAT
Found at i:224207 original size:31 final size:34
Alignment explanation
Indices: 224163--224246 Score: 95
Period size: 33 Copynumber: 2.5 Consensus size: 34
224153 AATAAATAAA
*
224163 ATAAT-AATAAAAAA-GT-AAAAATAATATATAT
1 ATAATAAATAAAAAACATAAAAAATAATATATAT
*
224194 ATAATAAAT-AAAAACATAAAAAATAGTATATAT
1 ATAATAAATAAAAAACATAAAAAATAATATATAT
224227 ATATATAAATTAATAAAACA
1 ATA-ATAAA-TAA-AAAACA
224247 AATAATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 10 0.23
32 4 0.09
33 17 0.39
34 5 0.11
35 1 0.02
36 1 0.02
37 6 0.14
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (34 bp):
ATAATAAATAAAAAACATAAAAAATAATATATAT
Found at i:224213 original size:51 final size:49
Alignment explanation
Indices: 224094--224218 Score: 130
Period size: 51 Copynumber: 2.5 Consensus size: 49
224084 AATAAATAAA
* * *
224094 AAATATATAAAAATATTAAAAATAAAGAAAAAGAAGAAAAAATATATAT
1 AAATAAATAAAAAAATAAAAAATAAAGAAAAAGAAGAAAAAATATATAT
*
224143 AAATAAA-ACAAATAAATAAAATAATAATA-AAAAAGTAA-AAATAATATATAT
1 AAATAAATA-AAA-AAATAAAA-AATAA-AGAAAAAG-AAGAAAAAATATATAT
*
224194 ATAATAAATAAAAACATAAAAAATA
1 A-AATAAATAAAAAAATAAAAAATA
224219 GTATATATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
48 1 0.02
49 9 0.14
50 10 0.16
51 31 0.48
52 12 0.19
53 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (49 bp):
AAATAAATAAAAAAATAAAAAATAAAGAAAAAGAAGAAAAAATATATAT
Found at i:224246 original size:37 final size:33
Alignment explanation
Indices: 224163--224236 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
224153 AATAAATAAA
224163 ATAAT-AATAAAAA-AGT-AAAAATAATATATAT
1 ATAATAAATAAAAACA-TAAAAAATAATATATAT
*
224194 ATAATAAATAAAAACATAAAAAATAGTATATAT
1 ATAATAAATAAAAACATAAAAAATAATATATAT
224227 ATATATAAAT
1 ATA-ATAAAT
224237 TAATAAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 5 0.13
32 9 0.24
33 18 0.47
34 6 0.16
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (33 bp):
ATAATAAATAAAAACATAAAAAATAATATATAT
Found at i:224288 original size:38 final size:37
Alignment explanation
Indices: 224154--224289 Score: 105
Period size: 42 Copynumber: 3.4 Consensus size: 37
224144 AATAAAACAA
* *
224154 ATAAATAAAATAATAATAAAAAAGTAAAAATAATATATAT
1 ATAATTAAAAAAATAATAAAAAA-T-AAAAT-ATATATAT
**
224194 ATAA-TAAATAAAA-ACATAAAAAATAGTATATATATAT
1 ATAATTAAA-AAAATA-ATAAAAAATAAAATATATATAT
*
224231 ATAAATTAATAAAACAAATAATAAAAAATAACATATATATAT
1 AT-AA-T--TAAAA-AAATAATAAAAAATAAAATATATATAT
*
224273 GTAATCTAAAAAAATAA
1 ATAAT-TAAAAAAATAA
224290 AAATATATAC
Statistics
Matches: 80, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
37 10 0.12
38 11 0.14
39 11 0.14
40 16 0.20
41 3 0.04
42 28 0.35
43 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (37 bp):
ATAATTAAAAAAATAATAAAAAATAAAATATATATAT
Found at i:224332 original size:22 final size:21
Alignment explanation
Indices: 224283--224337 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 21
224273 GTAATCTAAA
*
224283 AAAATAAAAATATATACTAAAGT
1 AAAA-AAAAA-ATATACAAAAGT
224306 AAAAAAGAAAATATACAAAATGT
1 AAAAAA-AAAATATACAAAA-GT
224329 AAAAAAAAA
1 AAAAAAAAA
224338 TATTACATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAAAAAAAATATACAAAAGT
Found at i:224344 original size:22 final size:22
Alignment explanation
Indices: 224283--224344 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
224273 GTAATCTAAA
*
224283 AAAATAAAAATATATACTAAAGT
1 AAAA-AAAAATATATACAAAAGT
224306 AAAAAAGAAA-ATATACAAAATGT
1 AAAAAA-AAATATATACAAAA-GT
224329 AAAAAAAAATAT-TACA
1 AAAAAAAAATATATACA
224345 TAAAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAAAAAAATATATACAAAAGT
Found at i:224870 original size:37 final size:37
Alignment explanation
Indices: 224825--224936 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
224815 ATGCTTCGGG
* *
224825 ATCCTATTTTTAGGAGTTTGAATCATAATAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAATAAAACTCT
* * *
224862 ATCTTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAATAAAACTCT
*
224899 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAATAAAACTCT
224936 A
1 A
224937 ATGCTATATT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAATAAAACTCT
Found at i:226032 original size:25 final size:25
Alignment explanation
Indices: 225982--226102 Score: 167
Period size: 25 Copynumber: 5.0 Consensus size: 25
225972 AAGGGACAAT
*
225982 ATTTTTCAAAA--C-TTCATCAAAT
1 ATTTTTCAAAATTCTTTCATCAAAC
*
226004 ATTTTTCAAAATTCTTTCATGAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
*
226029 ATTTTTTAAAATTCTTTCATCAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
* *
226054 ATTTTTTAAAATTCTTTCATTAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
*
226079 ATTTCTCAAAATTCTTTCATCAAA
1 ATTTTTCAAAATTCTTTCATCAAA
226103 TTCAATTTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
22 11 0.12
24 1 0.01
25 76 0.86
ACGTcount: A:0.37, C:0.17, G:0.01, T:0.45
Consensus pattern (25 bp):
ATTTTTCAAAATTCTTTCATCAAAC
Found at i:227424 original size:22 final size:22
Alignment explanation
Indices: 227396--227456 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
227386 TTCATCCATG
227396 TGTTATTATTATTTTTATTTAA
1 TGTTATTATTATTTTTATTTAA
* * *
227418 TGTTATTATTAATATTATTTTA
1 TGTTATTATTATTTTTATTTAA
*
227440 TATTATT-TTATTATTTA
1 TGTTATTATTATT-TTTA
227457 CATATTACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (22 bp):
TGTTATTATTATTTTTATTTAA
Found at i:229173 original size:20 final size:21
Alignment explanation
Indices: 229148--229187 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
229138 CTTTGTATAG
229148 TAGTATAGATACCAT-AGGCA
1 TAGTATAGATACCATCAGGCA
*
229168 TAGTATCGATACCATCAGGC
1 TAGTATAGATACCATCAGGC
229188 CCCAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATAGATACCATCAGGCA
Found at i:232245 original size:24 final size:21
Alignment explanation
Indices: 232195--232268 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 21
232185 CCTTGAAGTG
*
232195 CATCGATGCATCCTACCGTGT
1 CATCGATGCATCCTAACGTGT
232216 -ATCGATGCATCCCTTAACGTGT
1 CATCGATGCAT-CC-TAACGTGT
*
232238 ACATCGATGCACTCCTTA--TG-
1 -CATCGATGCA-TCCTAACGTGT
232258 CATCGATGCAT
1 CATCGATGCAT
232269 TAATTGCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
18 1 0.02
19 10 0.22
20 10 0.22
21 4 0.09
22 7 0.15
23 2 0.04
24 11 0.24
25 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (21 bp):
CATCGATGCATCCTAACGTGT
Found at i:234006 original size:14 final size:14
Alignment explanation
Indices: 233966--233996 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
233956 ATTTACTCTG
233966 ACAGCTAGTCAATA
1 ACAGCTAGTCAATA
233980 ACAGCTAGTCAATA
1 ACAGCTAGTCAATA
233994 ACA
1 ACA
233997 TCTATCCAAT
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:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (14 bp):
ACAGCTAGTCAATA
Found at i:251395 original size:71 final size:71
Alignment explanation
Indices: 251279--251482 Score: 324
Period size: 71 Copynumber: 2.9 Consensus size: 71
251269 CTCCCTGATT
251279 GATATGATGTTTTCAAATGAATTTTTAAAGAA-TCCAAGTTTGATTTTCAAAGGTTTCTTGATTA
1 GATATGATGTTTTCAAATGAATTTTTAAAGAAGT-CAAGTTTGATTTTCAAAGGTTTCTTGATT-
251343 CT-AGACC
64 CTCAGACC
*
251350 GATATGATGTTTTCAAATGAATTTTTAAAGAAGTCAAGTTTGATTTTCAAAGGTTTCTTGATTGT
1 GATATGATGTTTTCAAATGAATTTTTAAAGAAGTCAAGTTTGATTTTCAAAGGTTTCTTGATTCT
*
251415 CCGACC
66 CAGACC
* *
251421 GATATGATGTTATCAAATGAATTTTTAAAGAAGCCAAGTTTGATTCTT-AAAGGTTTCTTGAT
1 GATATGATGTTTTCAAATGAATTTTTAAAGAAGTCAAGTTTGATT-TTCAAAGGTTTCTTGAT
251483 GATACAATCT
Statistics
Matches: 126, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
70 1 0.01
71 122 0.97
72 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (71 bp):
GATATGATGTTTTCAAATGAATTTTTAAAGAAGTCAAGTTTGATTTTCAAAGGTTTCTTGATTCT
CAGACC
Found at i:254252 original size:3 final size:3
Alignment explanation
Indices: 254235--254320 Score: 156
Period size: 3 Copynumber: 29.0 Consensus size: 3
254225 TAATTTCATC
*
254235 TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
254282 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
254321 AATGAACTAA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:258778 original size:17 final size:17
Alignment explanation
Indices: 258756--258789 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
258746 GAAAGTCGTT
258756 TAAATTAAAATCAATTA
1 TAAATTAAAATCAATTA
* *
258773 TAAATTACAATCGATTA
1 TAAATTAAAATCAATTA
258790 GTCTGTATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAATTAAAATCAATTA
Found at i:260841 original size:2 final size:2
Alignment explanation
Indices: 260836--260890 Score: 94
Period size: 2 Copynumber: 27.5 Consensus size: 2
260826 TTTCTGAAAT
260836 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
260878 TC TC -C TC TGC TC T
1 TC TC TC TC T-C TC T
260891 GTTGTTGGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:267230 original size:2 final size:2
Alignment explanation
Indices: 267223--267247 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
267213 ACCCGTGTGC
267223 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
267248 TGGAAATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:267317 original size:41 final size:40
Alignment explanation
Indices: 267272--267349 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
267262 TTTTCAACTG
* * *
267272 AAGCTAATTCCAACAAGTAATTTCGACTTTTCTTCCACACA
1 AAGCTAATTCAAACAAGTAATGTCCACTTTT-TTCCACACA
*
267313 AAGCTAATTCAAACAAGTTATGTCCACTTTTTTCCAC
1 AAGCTAATTCAAACAAGTAATGTCCACTTTTTTCCAC
267350 CACTCAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 6 0.18
41 27 0.82
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (40 bp):
AAGCTAATTCAAACAAGTAATGTCCACTTTTTTCCACACA
Found at i:268495 original size:29 final size:28
Alignment explanation
Indices: 268453--268579 Score: 132
Period size: 29 Copynumber: 4.4 Consensus size: 28
268443 TAGAGGATCC
* *
268453 CATGCAAAATCAGGACGGGGT-TACAGTCT
1 CATGCAAAATCAGGACGAGATATA-A-TCT
268482 CATGCAAAATCAGGACGAGATATAATCT
1 CATGCAAAATCAGGACGAGATATAATCT
*
268510 CATGCAAAATCAAGACGAAGATATAATC-
1 CATGCAAAATCAGGACG-AGATATAATCT
* * *
268538 CTATGCAAAAGCAAGACAATGATATAATCT
1 C-ATGCAAAATCAGGACGA-GATATAATCT
*
268568 CATGCAGAATCA
1 CATGCAAAATCA
268580 AGATGGAGAT
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
28 21 0.24
29 62 0.72
30 3 0.03
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (28 bp):
CATGCAAAATCAGGACGAGATATAATCT
Found at i:268581 original size:29 final size:28
Alignment explanation
Indices: 268479--268582 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 28
268469 GGGGTTACAG
* *
268479 TCTCATGCAAAATCAGGACGAGATATAA
1 TCTCATGCAAAATCAAGACAAGATATAA
268507 TCTCATGCAAAATCAAGACGAAGATATAA
1 TCTCATGCAAAATCAAGAC-AAGATATAA
*
268536 TC-CTATGCAAAAGCAAGACAATGATATAA
1 TCTC-ATGCAAAATCAAGACAA-GATATAA
*
268565 TCTCATGCAGAATCAAGA
1 TCTCATGCAAAATCAAGA
268583 TGGAGATTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
28 21 0.31
29 45 0.67
30 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.21
Consensus pattern (28 bp):
TCTCATGCAAAATCAAGACAAGATATAA
Found at i:272314 original size:24 final size:24
Alignment explanation
Indices: 272283--272364 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
272273 ATTAATGTTT
272283 TATT-TGATTTCTGATTCGGATTC
1 TATTCTGATTTCTGATTCGGATTC
* *
272306 TATTCTGATATCTTATAT-GGATTC
1 TATTCTGATTTCTGAT-TCGGATTC
* *
272330 TGTTCTGATATT-TGA-TCTGAATTC
1 TATTCTGAT-TTCTGATTC-GGATTC
*
272354 TGTTCTGATTT
1 TATTCTGATTT
272365 TTGTTTACCG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.02
23 6 0.12
24 39 0.81
25 2 0.04
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (24 bp):
TATTCTGATTTCTGATTCGGATTC
Found at i:272360 original size:12 final size:13
Alignment explanation
Indices: 272326--272362 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
272316 TCTTATATGG
272326 ATTCTGTTCTGAT
1 ATTCTGTTCTGAT
*
272339 ATT-TGATCTGA-
1 ATTCTGTTCTGAT
272350 ATTCTGTTCTGAT
1 ATTCTGTTCTGAT
272363 TTTTGTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (13 bp):
ATTCTGTTCTGAT
Found at i:272541 original size:31 final size:30
Alignment explanation
Indices: 272503--272577 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 30
272493 AAGACAACCA
* *
272503 TTGGGTAGGCTCTGCGGCCCTGAGATTTTTC
1 TTGGGTAGGCTCCGCGGCCC-GAGAATTTTC
*
272534 TTGGGTAGGCCTCCGTGGCCCGAGAATTTTC
1 TTGGGTAGG-CTCCGCGGCCCGAGAATTTTC
*
272565 TTAGGTAGGCTCC
1 TTGGGTAGGCTCC
272578 AAGGTACTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 4 0.10
31 26 0.67
32 9 0.23
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (30 bp):
TTGGGTAGGCTCCGCGGCCCGAGAATTTTC
Found at i:273456 original size:18 final size:19
Alignment explanation
Indices: 273435--273471 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
273425 TAGATCAAAT
*
273435 ATAATAAATAAA-TAAAAA
1 ATAAAAAATAAATTAAAAA
273453 ATAAAAAATAAATTAAAAA
1 ATAAAAAATAAATTAAAAA
273472 GGGGGAGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAAAAATAAATTAAAAA
Found at i:274317 original size:28 final size:29
Alignment explanation
Indices: 274271--274338 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
274261 TATGAACTTA
* * *
274271 ATTTAAAAATATTTTA-TT-TTTTATTTT
1 ATTTAAAAATATATAATTTATTTTAATTT
274298 CATTTAAAAATATATAATTTATTTTAATTT
1 -ATTTAAAAATATATAATTTATTTTAATTT
274328 A-TTAAAAATAT
1 ATTTAAAAATAT
274339 GACTCGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 24 0.69
29 3 0.09
30 8 0.23
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTTAAAAATATATAATTTATTTTAATTT
Found at i:274462 original size:31 final size:31
Alignment explanation
Indices: 274427--274490 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
274417 ATAACTCGGG
*
274427 GTGATCAAATCTTAATTAAATAAAAACAAAA
1 GTGATCAAACCTTAATTAAATAAAAACAAAA
*
274458 GTGATCATACCTTAATTAAATAAAAACAAAA
1 GTGATCAAACCTTAATTAAATAAAAACAAAA
274489 GT
1 GT
274491 AATTGTATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.27
Consensus pattern (31 bp):
GTGATCAAACCTTAATTAAATAAAAACAAAA
Found at i:274993 original size:13 final size:14
Alignment explanation
Indices: 274964--274996 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
274954 ATCCATAACC
274964 TAAAAAAATTATTAT
1 TAAAAAAATTA-TAT
274979 TAAAAAAATTA-AT
1 TAAAAAAATTATAT
274992 TAAAA
1 TAAAA
274997 CATTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
15 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAAAAATTATAT
Found at i:277474 original size:14 final size:14
Alignment explanation
Indices: 277455--277536 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
277445 TTCTTCGATA
277455 TTAAAAATAAATAT
1 TTAAAAATAAATAT
* *
277469 TTAAAAATTACTAT
1 TTAAAAATAAATAT
* * *
277483 TTATTATATATATAT
1 TTA-AAAATAAATAT
*
277498 TT-ATAA-AAATAT
1 TTAAAAATAAATAT
*
277510 TTAACAATATAAATAA
1 TTAA-AA-ATAAATAT
*
277526 ATAAAAATAAA
1 TTAAAAATAAA
277537 ATACTACTAA
Statistics
Matches: 49, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
12 7 0.14
13 2 0.04
14 21 0.43
15 11 0.22
16 8 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAAATAAATAT
Found at i:278979 original size:3 final size:3
Alignment explanation
Indices: 278971--279074 Score: 190
Period size: 3 Copynumber: 34.7 Consensus size: 3
278961 AATATATATT
*
278971 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
279019 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
279067 TAA TAA TA
1 TAA TAA TA
279075 TGGATAAAAA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:279803 original size:113 final size:113
Alignment explanation
Indices: 279212--279852 Score: 872
Period size: 114 Copynumber: 5.6 Consensus size: 113
279202 ATTGAATAAA
* * * * ** * *
279212 TTCTTCTCTCTCTCCAGATAAGTTCTTCTTATTATGAACTTTCTGCTGGGGATGATGATCCATCA
1 TTCTTC-CT-TCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATAATCCATCA
* * * *
279277 AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTC
63 AATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * * * *
279328 TTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATC
1 TTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCATC
* * * *
279392 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTC
62 AAATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
*
279444 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAA-A
*
279509 TGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
65 TGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
279558 TTCTTCCTTCTTCAGATG-GATTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAT
1 TTCTTCCTTCTTCAGATGAG-TTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAA-
* *
279622 TTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
64 ATGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * *
279672 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
* *
279737 GATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
66 GATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * **
279785 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCTTTCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
279850 GAT
66 GAT
279853 AGATTTGAAT
Statistics
Matches: 486, Mismatches: 31, Indels: 19
0.91 0.06 0.04
Matches are distributed among these distances:
112 3 0.01
113 147 0.30
114 222 0.46
115 3 0.01
116 91 0.19
117 18 0.04
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
GATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
Found at i:280740 original size:82 final size:82
Alignment explanation
Indices: 280526--281095 Score: 946
Period size: 82 Copynumber: 6.9 Consensus size: 82
280516 TAACTCAAAT
*
280526 TCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTA-TG
1 TCAATGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
* * *
280589 AGCACATTCATCTTCCAAAT
64 -GCAAATTCATCTTCTAAAC
*
280609 TCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
1 TCAATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
280674 CAAATTCATCTTCTAAAC
65 CAAATTCATCTTCTAAAC
* *
280692 TCAATGATTGTTCTGTCCAACCAAATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
1 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
280757 AAATTCATCTTCTAAAC
66 AAATTCATCTTCTAAAC
**
280774 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
1 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
280839 AAATTCATCTTCTAAAC
66 AAATTCATCTTCTAAAC
* *
280856 TCAATGATTGTTCTGTCCAACCAAATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
1 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
280921 AAATTCATCTTCTAAAC
66 AAATTCATCTTCTAAAC
**
280938 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
1 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
281003 AAATTCATCTTCTAAAC
66 AAATTCATCTTCTAAAC
**
281020 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
1 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
*
281085 ACATTCATCTT
66 AAATTCATCTT
281096 TCATTTAATT
Statistics
Matches: 464, Mismatches: 21, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
82 379 0.82
83 82 0.18
84 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (82 bp):
TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
AAATTCATCTTCTAAAC
Found at i:281879 original size:19 final size:16
Alignment explanation
Indices: 281857--281902 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
281847 AATAGAAAAG
281857 AATAAATTGAATTTCCAAA
1 AATAAATTGAATTT-C--A
*
281876 AATAAATTGACTTTCA
1 AATAAATTGAATTTCA
281892 AATAAATTGAA
1 AATAAATTGAA
281903 CTTGAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
18 1 0.04
19 13 0.52
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (16 bp):
AATAAATTGAATTTCA
Found at i:282235 original size:1 final size:1
Alignment explanation
Indices: 282231--282302 Score: 72
Period size: 1 Copynumber: 72.0 Consensus size: 1
282221 CTTGACCCCC
* ** * * * * *
282231 TTTTTCTTTTTTCCTTTTTTCTTTTTTTTCTTTTTTTTTTCTTTTTTTTTTCTTTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
282296 TTTTTTT
1 TTTTTTT
282303 CAAGCATAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:282256 original size:21 final size:19
Alignment explanation
Indices: 282230--282302 Score: 92
Period size: 21 Copynumber: 3.6 Consensus size: 19
282220 CCTTGACCCC
*
282230 CTTTTTCTTTTTTCCTTTTTT
1 CTTTTT-TTTTTT-TTTTTTT
282251 CTTTTTTTTCTTTTTTTTTT
1 CTTTTTTTT-TTTTTTTTTT
282271 CTTTTTTTTTTCTTTTTTTTT
1 C-TTTTTTTTT-TTTTTTTTT
282292 CTTTTTTTTTT
1 CTTTTTTTTTT
282303 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
19 1 0.02
20 20 0.42
21 27 0.56
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (19 bp):
CTTTTTTTTTTTTTTTTTT
Found at i:282266 original size:11 final size:11
Alignment explanation
Indices: 282231--282303 Score: 105
Period size: 11 Copynumber: 6.5 Consensus size: 11
282221 CTTGACCCCC
282231 TTTTTCTTTTT
1 TTTTTCTTTTT
282242 TCCTTTT-TTCTTT
1 T--TTTTCTT-TTT
282255 TTTTTCTTTTT
1 TTTTTCTTTTT
282266 TTTTTCTTTTT
1 TTTTTCTTTTT
282277 TTTTTC-TTTT
1 TTTTTCTTTTT
282287 TTTTTCTTTTT
1 TTTTTCTTTTT
282298 TTTTTC
1 TTTTTC
282304 AAGCATAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.18
11 35 0.61
12 4 0.07
13 8 0.14
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:282281 original size:32 final size:34
Alignment explanation
Indices: 282231--282303 Score: 107
Period size: 32 Copynumber: 2.2 Consensus size: 34
282221 CTTGACCCCC
282231 TTTTTCTTTTTTCCTTTTTTC-TTTTTTTTCTTTTT
1 TTTTTC-TTTTT-CTTTTTTCTTTTTTTTTCTTTTT
282266 TTTTTC-TTTT-TTTTTTCTTTTTTTTTCTTTTT
1 TTTTTCTTTTTCTTTTTTCTTTTTTTTTCTTTTT
282298 TTTTTC
1 TTTTTC
282304 AAGCATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 7 0.19
32 20 0.54
33 4 0.11
35 6 0.16
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (34 bp):
TTTTTCTTTTTCTTTTTTCTTTTTTTTTCTTTTT
Found at i:282303 original size:21 final size:21
Alignment explanation
Indices: 282245--282303 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
282235 TCTTTTTTCC
*
282245 TTTTTTCTTTTTTTTCT-TTT
1 TTTTTTCTTTTTTTTTTCTTT
282265 TTTTTTCTTTTTTTTTTCTTT
1 TTTTTTCTTTTTTTTTTCTTT
282286 TTTTTTCTTTTTTTTTTC
1 TTTTTTCTTTTTTTTTTC
282304 AAGCATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTTTCTTT
Found at i:289564 original size:14 final size:15
Alignment explanation
Indices: 289545--289577 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
289535 ATTATTTTTC
289545 AAATTTTA-ATTAAT
1 AAATTTTATATTAAT
*
289559 AAATTTTATCTTAAT
1 AAATTTTATATTAAT
289574 AAAT
1 AAAT
289578 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAT
Found at i:292937 original size:18 final size:18
Alignment explanation
Indices: 292914--292951 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
292904 TGCAAAACAT
* *
292914 ATAAATATTATATAAAAA
1 ATAAATAATAAATAAAAA
292932 ATAAATAATAAATAAAAA
1 ATAAATAATAAATAAAAA
292950 AT
1 AT
292952 TCGAAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAATAAATAAAAA
Found at i:293624 original size:14 final size:14
Alignment explanation
Indices: 293605--293686 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
293595 TTCTTCGATA
293605 TTAAAAATAAATAT
1 TTAAAAATAAATAT
* *
293619 TTAAAAATTACTAT
1 TTAAAAATAAATAT
* * *
293633 TTATTATATATATAT
1 TTA-AAAATAAATAT
*
293648 TT-ATAA-AAATAT
1 TTAAAAATAAATAT
*
293660 TTAACAATATAAATAA
1 TTAA-AA-ATAAATAT
*
293676 ATAAAAATAAA
1 TTAAAAATAAA
293687 ATACTACTAA
Statistics
Matches: 49, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
12 7 0.14
13 2 0.04
14 21 0.43
15 11 0.22
16 8 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAAATAAATAT
Found at i:295130 original size:3 final size:3
Alignment explanation
Indices: 295122--295219 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
295112 AATATATATT
* *
295122 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
295170 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
295218 TA
1 TA
295220 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:295226 original size:15 final size:13
Alignment explanation
Indices: 295111--295216 Score: 127
Period size: 12 Copynumber: 8.6 Consensus size: 13
295101 TATATATGTT
*
295111 TAATATATATTTAA
1 TAATA-ATATATAA
295125 TAATAATA-ATAA
1 TAATAATATATAA
*
295137 TAATGATA-ATAA
1 TAATAATATATAA
295149 TAATAATA-ATAA
1 TAATAATATATAA
*
295161 TAATAATA-GTAA
1 TAATAATATATAA
295173 TAATAATA-ATAA
1 TAATAATATATAA
295185 TAATAATA-ATAA
1 TAATAATATATAA
295197 TAATAATAT-TAA
1 TAATAATATATAA
295209 TAATAATA
1 TAATAATA
295217 ATATGGATAA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
12 78 0.91
13 3 0.03
14 5 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:302960 original size:114 final size:113
Alignment explanation
Indices: 302760--302969 Score: 294
Period size: 114 Copynumber: 1.8 Consensus size: 113
302750 CGCGTTTATT
* * * * ** *
302760 ATTTACGAACATATTCGTTTAATATTAACGAACTTGTTTATTTAATATTTACTAATATGTTCGAT
1 ATTTACGAACATATTCGTTTAATAGTAACGAACATATTTATTTAATATTCAAGAATATATTCGAT
* *
302825 AGCCGACACTCTCTTCTTAACATTTTACTTTGTGTTTAATTCGTCTAAC
66 AACCAACACTCTCTTCTTAACATTTTA-TTTGTGTTTAATTCGTCTAAC
* * *
302874 ATTTACGAACATATTCGTTTAATAGTAACGAACATATTTGTTTAATGTTCAAGAATATATTCGGT
1 ATTTACGAACATATTCGTTTAATAGTAACGAACATATTTATTTAATATTCAAGAATATATTCGAT
*
302939 AACCAACGCTCTCTTCTTAACATTTTATTTG
66 AACCAACACTCTCTTCTTAACATTTTATTTG
302970 CAAACCAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
113 4 0.05
114 79 0.95
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (113 bp):
ATTTACGAACATATTCGTTTAATAGTAACGAACATATTTATTTAATATTCAAGAATATATTCGAT
AACCAACACTCTCTTCTTAACATTTTATTTGTGTTTAATTCGTCTAAC
Found at i:303514 original size:31 final size:31
Alignment explanation
Indices: 303479--303542 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
303469 TAAATATTAT
* *
303479 ATCTTAATCAAATAAAAATGAAAGTGATCAA
1 ATCTTAATCAAATAAAAATAAAAATGATCAA
*
303510 ATCTTAATTAAATAAAAATAAAAATGATCAA
1 ATCTTAATCAAATAAAAATAAAAATGATCAA
303541 AT
1 AT
303543 ATTATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (31 bp):
ATCTTAATCAAATAAAAATAAAAATGATCAA
Found at i:305290 original size:25 final size:25
Alignment explanation
Indices: 305259--305315 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
305249 GTAATTATTT
* * *
305259 TATTTTTATTGTTTTTTGTTTTTAC
1 TATTTTTATTATTTGTTGTTTTAAC
*
305284 TATTTTTATTATTTGTTGTTTTAAT
1 TATTTTTATTATTTGTTGTTTTAAC
305309 TATTTTT
1 TATTTTT
305316 TTAGTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (25 bp):
TATTTTTATTATTTGTTGTTTTAAC
Found at i:305618 original size:17 final size:17
Alignment explanation
Indices: 305577--305621 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
305567 ATAATTTGAC
*
305577 ACCTTAAATTAGAAAAA
1 ACCTTAATTTAGAAAAA
*
305594 GCCTTAATTTAGAAAAA
1 ACCTTAATTTAGAAAAA
305611 ACCTTAATTTA
1 ACCTTAATTTA
305622 CCTTAGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (17 bp):
ACCTTAATTTAGAAAAA
Found at i:307118 original size:80 final size:80
Alignment explanation
Indices: 307017--307259 Score: 441
Period size: 80 Copynumber: 3.0 Consensus size: 80
307007 ATATGAATAG
* * * *
307017 TTGAGTGATCATTTTGTAATTTTTATTCTTTTAGCCGTCGGAGACTCAACAAAACAATACCCTAT
1 TTGAGTGATCATTTTGTAATTTTTATTCTTTTAGCCGTCGGAGAATGAACAAAGCAATATCCTAT
307082 AGTTGATAGATTATT
66 AGTTGATAGATTATT
307097 TTGAGTGATCATTTTGTAATTTTTATTCTTTTAGCCGTCGGAGAATGAACAAAGCAATATCCTAT
1 TTGAGTGATCATTTTGTAATTTTTATTCTTTTAGCCGTCGGAGAATGAACAAAGCAATATCCTAT
307162 AGTTGATAGATTATT
66 AGTTGATAGATTATT
*
307177 TTTAGTGATCATTTTGTAATTTTTATTCTTTTAGCCGTCGGAGAATGAACAAAGCAATATCCTAT
1 TTGAGTGATCATTTTGTAATTTTTATTCTTTTAGCCGTCGGAGAATGAACAAAGCAATATCCTAT
307242 AGTTGATAGATTATT
66 AGTTGATAGATTATT
307257 TTG
1 TTG
307260 TAATATGCGC
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 157 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (80 bp):
TTGAGTGATCATTTTGTAATTTTTATTCTTTTAGCCGTCGGAGAATGAACAAAGCAATATCCTAT
AGTTGATAGATTATT
Found at i:308723 original size:23 final size:23
Alignment explanation
Indices: 308693--308745 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
308683 TCGAGACTCG
* *
308693 AGCTCGATTTTGAGCTCAATTGA
1 AGCTCGATTTTGAGCCCAATTCA
308716 AGCTCGATTTTGAGCCCAATTCA
1 AGCTCGATTTTGAGCCCAATTCA
308739 AGCTCGA
1 AGCTCGA
308746 ACTCGATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (23 bp):
AGCTCGATTTTGAGCCCAATTCA
Found at i:308756 original size:17 final size:17
Alignment explanation
Indices: 308734--308785 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
308724 TTTGAGCCCA
308734 ATTCAAGCTCGAACTCG
1 ATTCAAGCTCGAACTCG
308751 ATTCAAGCTCGAACTCG
1 ATTCAAGCTCGAACTCG
308768 ATTCAAGCTCGAACTCG
1 ATTCAAGCTCGAACTCG
308785 A
1 A
308786 ACTCAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (17 bp):
ATTCAAGCTCGAACTCG
Found at i:309608 original size:12 final size:12
Alignment explanation
Indices: 309591--309615 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
309581 TTATTTAAAG
309591 ATAAACAAACTC
1 ATAAACAAACTC
309603 ATAAACAAACTC
1 ATAAACAAACTC
309615 A
1 A
309616 CCAGAGGGGA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAACAAACTC
Found at i:310095 original size:3 final size:3
Alignment explanation
Indices: 310087--310137 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
310077 TCACATTTTG
310087 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
310135 ATA
1 ATA
310138 GGAAAATACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:310878 original size:7 final size:7
Alignment explanation
Indices: 310868--311156 Score: 156
Period size: 7 Copynumber: 41.6 Consensus size: 7
310858 TTAATCATTA
310868 TTTAGGG
1 TTTAGGG
**
310875 TTTAGTA
1 TTTAGGG
**
310882 TTTATAG
1 TTTAGGG
310889 TTTAGGG
1 TTTAGGG
310896 TTTAGGG
1 TTTAGGG
310903 TTTAGGG
1 TTTAGGG
310910 TTTAGGG
1 TTTAGGG
*
310917 TTTTAGGA
1 -TTTAGGG
**
310925 TTTAAAG
1 TTTAGGG
* *
310932 TTCA-TG
1 TTTAGGG
310938 TTTAGGG
1 TTTAGGG
*
310945 TTTAGGA
1 TTTAGGG
**
310952 TTTATAG
1 TTTAGGG
***
310959 TTTATTA
1 TTTAGGG
310966 TTTAGGG
1 TTTAGGG
310973 TTTAGGG
1 TTTAGGG
*
310980 TTTAGTG
1 TTTAGGG
**
310987 TTTATAG
1 TTTAGGG
***
310994 TTTATTA
1 TTTAGGG
311001 TTTAGGG
1 TTTAGGG
*
311008 TTTAGAG
1 TTTAGGG
311015 TTTAGGG
1 TTTAGGG
*
311022 TTTAAGG
1 TTTAGGG
**
311029 TTTATAG
1 TTTAGGG
**
311036 TTTATAG
1 TTTAGGG
311043 TTTAGGG
1 TTTAGGG
311050 TTTAGGG
1 TTTAGGG
*
311057 TTTTA-AG
1 -TTTAGGG
**
311064 TTTA-CA
1 TTTAGGG
*
311070 TTTA-AG
1 TTTAGGG
*
311076 TTTAAGG
1 TTTAGGG
* * *
311083 TTCATGT
1 TTTAGGG
*
311090 TTTAGGC
1 TTTAGGG
*
311097 CTTAGGG
1 TTTAGGG
311104 TTTAGGG
1 TTTAGGG
311111 TTTAGGG
1 TTTAGGG
*
311118 -TTATGGT
1 TTTA-GGG
*
311125 TTTATGG
1 TTTAGGG
*
311132 TTTATGG
1 TTTAGGG
311139 TTTAGGG
1 TTTAGGG
311146 TTTAGGG
1 TTTAGGG
311153 TTTA
1 TTTA
311157 ATGAAAATGA
Statistics
Matches: 218, Mismatches: 58, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
6 19 0.09
7 186 0.85
8 13 0.06
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:311067 original size:35 final size:35
Alignment explanation
Indices: 310868--311156 Score: 181
Period size: 35 Copynumber: 8.3 Consensus size: 35
310858 TTAATCATTA
**
310868 TTTAGGGTTTA--GTATTTATAGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGT-TTTATAGTTTA-TATTTAGGG
* * * *
310903 TTTAGGGTTTAGGGTTTTA-GGATTTAAAGTTCA-TG
1 TTTAGGGTTTAGGGTTTTATAG-TTTATA-TTTAGGG
*
310938 TTTAGGGTTTA-GGATTTATAGTTTATTATTTAGGG
1 TTTAGGGTTTAGGGTTTTATAGTTTA-TATTTAGGG
*
310973 TTTAGGGTTTAGTG-TTTATAGTTTATTATTTAGGG
1 TTTAGGGTTTAGGGTTTTATAGTTTA-TATTTAGGG
* **
311008 TTTAGAGTTTAGGG-TTTA-AGGTTTATAGTTTATAG
1 TTTAGGGTTTAGGGTTTTATA-GTTTATA-TTTAGGG
* *
311043 TTTAGGGTTTAGGGTTTTA-AGTTTACATTTA-AG
1 TTTAGGGTTTAGGGTTTTATAGTTTATATTTAGGG
* * * * * **
311076 TTTAAGGTTCA-TGTTTTA-GGCCTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTTATAG-TTTA-TATTTAGGG
* * *
311111 TTTAGGG-TTATGGTTTTATGGTTTATGGTTTAGGG
1 TTTAGGGTTTAGGGTTTTATAGTTTAT-ATTTAGGG
311146 TTTAGGGTTTA
1 TTTAGGGTTTA
311157 ATGAAAATGA
Statistics
Matches: 206, Mismatches: 30, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
32 7 0.03
33 14 0.07
34 26 0.13
35 135 0.66
36 22 0.11
37 2 0.01
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.49
Consensus pattern (35 bp):
TTTAGGGTTTAGGGTTTTATAGTTTATATTTAGGG
Found at i:311890 original size:18 final size:18
Alignment explanation
Indices: 311869--311932 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
311859 ATACTTGTTT
311869 TTATATATATATTTTAAA
1 TTATATATATATTTTAAA
311887 TTAT-TA-ATA-TTTAAA
1 TTATATATATATTTTAAA
**
311902 TTGA-ATCATAT-TTTTTTA
1 TT-ATAT-ATATATTTTAAA
311920 TTATAT-TATATTT
1 TTATATATATATTT
311933 ATTATCAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
15 8 0.22
16 8 0.22
17 7 0.19
18 14 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATATATATATTTTAAA
Found at i:314241 original size:2 final size:2
Alignment explanation
Indices: 314236--314273 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
314226 AAATAGACTT
* *
314236 TA TA TA CA TA CA 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
314274 ATTAAAAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:317546 original size:19 final size:18
Alignment explanation
Indices: 317510--317558 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
317500 CTCTAAATCA
317510 TTTTTCAAAGATTCATTTT
1 TTTTTCAAA-ATTCATTTT
317529 GTTTTTCAAAA-TCAATTTT
1 -TTTTTCAAAATTC-ATTTT
317548 TTCTTTCAAAA
1 TT-TTTCAAAA
317559 CCAAATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 9 0.33
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTTTCAAAATTCATTTT
Found at i:328346 original size:24 final size:24
Alignment explanation
Indices: 328314--328389 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
328304 TAAGCCTATG
328314 GTATCGATACTACTATGTAAAGTA
1 GTATCGATACTACTATGTAAAGTA
** *
328338 GTATCGATACCCCT-T-T---G-G
1 GTATCGATACTACTATGTAAAGTA
*
328356 GTATCAATACTACTATGTAAAGTA
1 GTATCGATACTACTATGTAAAGTA
328380 GTATCGATAC
1 GTATCGATAC
328390 CCCTTTGTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
18 11 0.29
19 2 0.05
20 1 0.03
22 1 0.03
23 2 0.05
24 21 0.55
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (24 bp):
GTATCGATACTACTATGTAAAGTA
Found at i:328366 original size:42 final size:42
Alignment explanation
Indices: 328313--328407 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
328303 ATAAGCCTAT
*
328313 GGTATCGATACTACTATGTAAAGTAGTATCGATACCCCTTTG
1 GGTATCAATACTACTATGTAAAGTAGTATCGATACCCCTTTG
328355 GGTATCAATACTACTATGTAAAGTAGTATCGATACCCCTTTG
1 GGTATCAATACTACTATGTAAAGTAGTATCGATACCCCTTTG
*
328397 TGTATCAATAC
1 GGTATCAATAC
328408 ATATTTTGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (42 bp):
GGTATCAATACTACTATGTAAAGTAGTATCGATACCCCTTTG
Found at i:328799 original size:22 final size:24
Alignment explanation
Indices: 328754--328800 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
328744 TTAATAAAAC
*
328754 TTTTTATAATATCTAGATATTAAT
1 TTTTTATAATATCTAAATATTAAT
*
328778 TTTTTA-AATATTTAAATA-TAAT
1 TTTTTATAATATCTAAATATTAAT
328800 T
1 T
328801 AGTTAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 10 0.48
24 6 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTTATAATATCTAAATATTAAT
Found at i:332109 original size:23 final size:23
Alignment explanation
Indices: 332053--332111 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
332043 TTCATATTTG
*
332053 AGCTTGAGTTCGAGTTTTAATCA
1 AGCTTGAGTTTGAGTTTTAATCA
332076 AGCTTGAGTTTGAGTTTTAATCA
1 AGCTTGAGTTTGAGTTTTAATCA
*
332099 AGCTTTAGTTTGA
1 AGCTTGAGTTTGA
332112 ACTTAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.42
Consensus pattern (23 bp):
AGCTTGAGTTTGAGTTTTAATCA
Found at i:332120 original size:23 final size:23
Alignment explanation
Indices: 332053--332123 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
332043 TTCATATTTG
* ** *
332053 AGCTTGAGTTCGAGTTTTAATCA
1 AGCTTGAGTTTGAACTTAAATCA
** *
332076 AGCTTGAGTTTGAGTTTTAATCA
1 AGCTTGAGTTTGAACTTAAATCA
*
332099 AGCTTTAGTTTGAACTTAAATCA
1 AGCTTGAGTTTGAACTTAAATCA
332122 AG
1 AG
332124 TTAAGTCCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (23 bp):
AGCTTGAGTTTGAACTTAAATCA
Found at i:337766 original size:3 final size:3
Alignment explanation
Indices: 337758--337784 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
337748 TTCGATTTAA
337758 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
337785 CAAATAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:338304 original size:49 final size:49
Alignment explanation
Indices: 338245--338393 Score: 271
Period size: 49 Copynumber: 3.0 Consensus size: 49
338235 CGCCTATGAT
338245 ATTGGGCCAATTTTGCCCTATGTTGTGCTATCATGGCCTAACACGTGAA
1 ATTGGGCCAATTTTGCCCTATGTTGTGCTATCATGGCCTAACACGTGAA
* *
338294 ATTGGACCAATTTTGCCCTATATTGTGCTATCATGGCCTAACACGTGAA
1 ATTGGGCCAATTTTGCCCTATGTTGTGCTATCATGGCCTAACACGTGAA
*
338343 ATTGGGCCAATTTTGCCCTATGTTATGCTATCATGGCCTAACACGTGAA
1 ATTGGGCCAATTTTGCCCTATGTTGTGCTATCATGGCCTAACACGTGAA
338392 AT
1 AT
338394 GGCCCATGAG
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 95 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (49 bp):
ATTGGGCCAATTTTGCCCTATGTTGTGCTATCATGGCCTAACACGTGAA
Found at i:338534 original size:40 final size:40
Alignment explanation
Indices: 338475--338591 Score: 170
Period size: 40 Copynumber: 3.0 Consensus size: 40
338465 GTAGTATATT
338475 CATACATGAACACGTAGATGTATGTTAGAGTGTATGCATG
1 CATACATGAACACGTAGATGTATGTTAGAGTGTATGCATG
* *
338515 CATGCATGAACACGTAGATGTAAGTTAGAGTGTAT--A--
1 CATACATGAACACGTAGATGTATGTTAGAGTGTATGCATG
* *
338551 CATAAATGAACACGTAGATGTATGTTAAAGTGTATGCATG
1 CATACATGAACACGTAGATGTATGTTAGAGTGTATGCATG
338591 C
1 C
338592 CTGAGGGAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
36 31 0.46
38 2 0.03
40 34 0.51
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (40 bp):
CATACATGAACACGTAGATGTATGTTAGAGTGTATGCATG
Found at i:338567 original size:36 final size:36
Alignment explanation
Indices: 338446--338585 Score: 160
Period size: 36 Copynumber: 3.9 Consensus size: 36
338436 CTCTCTCTAG
* *
338446 AATGAACACGTAGATGTATG-T--AGTATATTCATA
1 AATGAACACGTAGATGTATGTTAGAGTGTATACATA
* *
338479 CATGAACACGTAGATGTATGTTAGAGTGTATGCATGCATG
1 AATGAACACGTAGATGTATGTTAGAGTGTAT--A--CATA
* *
338519 CATGAACACGTAGATGTAAGTTAGAGTGTATACATA
1 AATGAACACGTAGATGTATGTTAGAGTGTATACATA
*
338555 AATGAACACGTAGATGTATGTTAAAGTGTAT
1 AATGAACACGTAGATGTATGTTAGAGTGTAT
338586 GCATGCCTGA
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
33 19 0.21
34 1 0.01
36 37 0.41
38 1 0.01
40 33 0.36
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (36 bp):
AATGAACACGTAGATGTATGTTAGAGTGTATACATA
Found at i:338572 original size:76 final size:73
Alignment explanation
Indices: 338447--338591 Score: 218
Period size: 76 Copynumber: 1.9 Consensus size: 73
338437 TCTCTCTAGA
* * * *
338447 ATGAACACGTAGATGTATGTAGTATATTCATACATGAACACGTAGATGTATGTTAGAGTGTATGC
1 ATGAACACGTAGATGTAAGTAGTATATACATAAATGAACACGTAGATGTATGTTAAAGTGTATGC
338512 ATGCATGC
66 ATGCATGC
*
338520 ATGAACACGTAGATGTAAGTTAGAGTGTATACATAAATGAACACGTAGATGTATGTTAAAGTGTA
1 ATGAACACGTAGATGTAAG-T--AGTATATACATAAATGAACACGTAGATGTATGTTAAAGTGTA
338585 TGCATGC
63 TGCATGC
338592 CTGAGGGAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 18 0.28
74 1 0.02
76 45 0.70
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (73 bp):
ATGAACACGTAGATGTAAGTAGTATATACATAAATGAACACGTAGATGTATGTTAAAGTGTATGC
ATGCATGC
Found at i:339660 original size:45 final size:45
Alignment explanation
Indices: 339596--339685 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
339586 TGGATGTTCC
*
339596 GATTTTAGGTGACCCTGTAATTGGTCTATTGGGAAAGTCTAGCTT
1 GATTTTAGGTGACCCTGTAAGTGGTCTATTGGGAAAGTCTAGCTT
* *
339641 GATTTTAGGTGATCCTGTAAGTGGTCTATTGGGAATGTCTAGCTT
1 GATTTTAGGTGACCCTGTAAGTGGTCTATTGGGAAAGTCTAGCTT
339686 ATATATTCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (45 bp):
GATTTTAGGTGACCCTGTAAGTGGTCTATTGGGAAAGTCTAGCTT
Found at i:340197 original size:21 final size:21
Alignment explanation
Indices: 340173--340214 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
340163 CTGATCCGTG
*
340173 GTAAGCAGAAACGAATAAGAC
1 GTAAGCAGAAACAAATAAGAC
*
340194 GTAAGCAGAAATAAATAAGAC
1 GTAAGCAGAAACAAATAAGAC
340215 TGTCCTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.12, G:0.21, T:0.12
Consensus pattern (21 bp):
GTAAGCAGAAACAAATAAGAC
Found at i:341620 original size:26 final size:26
Alignment explanation
Indices: 341543--341614 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
341533 GATAGATCCA
341543 CAACA-TACCCTAAAACCTCAAATAAC
1 CAACATTACCCT-AAACCTCAAATAAC
341569 CAACATTACCCTAAACCTCAAATAAC
1 CAACATTACCCTAAACCTCAAATAAC
341595 CAACATTACCCTAAACCTCA
1 CAACATTACCCTAAACCTCA
341615 CTTAACTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 39 0.87
27 6 0.13
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (26 bp):
CAACATTACCCTAAACCTCAAATAAC
Found at i:343569 original size:19 final size:19
Alignment explanation
Indices: 343545--343581 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
343535 TAAGTAGTTG
343545 TATTATAGGATATGTATTA
1 TATTATAGGATATGTATTA
*
343564 TATTATATGATATGTATT
1 TATTATAGGATATGTATT
343582 GTTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (19 bp):
TATTATAGGATATGTATTA
Found at i:350524 original size:21 final size:21
Alignment explanation
Indices: 350459--350531 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
350449 TTTACCATTT
* *
350459 CGGTATTGACATGACAGTTTA
1 CGGTGTTGACATGACAGTCTA
** *
350480 CAATGTTGATATGACAGTCTA
1 CGGTGTTGACATGACAGTCTA
*
350501 CGGTGTTGACATGACAGTCCA
1 CGGTGTTGACATGACAGTCTA
350522 CGGTGATTGA
1 CGGTG-TTGA
350532 TAACTTGACG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 38 0.90
22 4 0.10
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (21 bp):
CGGTGTTGACATGACAGTCTA
Found at i:351433 original size:19 final size:19
Alignment explanation
Indices: 351409--351445 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
351399 TAAGTAGTTG
351409 TATTATAGGATATGTATTA
1 TATTATAGGATATGTATTA
*
351428 TATTATATGATATGTATT
1 TATTATAGGATATGTATT
351446 GTTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (19 bp):
TATTATAGGATATGTATTA
Found at i:357368 original size:27 final size:27
Alignment explanation
Indices: 357319--357386 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
357309 CACTAGTACT
357319 TGTTGAACTACATT-CATTTGACTTAA
1 TGTTGAACTACATTACATTTGACTTAA
* *
357345 TGTTAAACTATATTACATTTGACTTAA
1 TGTTGAACTACATTACATTTGACTTAA
357372 TGTTGAACTACATTA
1 TGTTGAACTACATTA
357387 ATTGAATGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 12 0.32
27 25 0.68
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (27 bp):
TGTTGAACTACATTACATTTGACTTAA
Found at i:357719 original size:43 final size:43
Alignment explanation
Indices: 357578--357720 Score: 126
Period size: 43 Copynumber: 3.3 Consensus size: 43
357568 ACATTTGCGG
* * * * *
357578 CGTTTATATAAAAAACGCCACTAAATATCATAATCTTTTGTAG
1 CGTTTATACAAAAAACGCCGCTAAATATCATAATATTTTGCAA
* * * * * * *
357621 CGTTTATAC-AAAAATGCCGCTAAATGTAAAAACATGTTGCGA
1 CGTTTATACAAAAAACGCCGCTAAATATCATAATATTTTGCAA
** ** *
357663 CGTTTATGTAAAAAACGTTGCTAAATATCATAATTTTTTGCAA
1 CGTTTATACAAAAAACGCCGCTAAATATCATAATATTTTGCAA
357706 CGTTTATACAAAAAA
1 CGTTTATACAAAAAA
357721 ATCCACTGAA
Statistics
Matches: 73, Mismatches: 26, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
42 29 0.40
43 44 0.60
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (43 bp):
CGTTTATACAAAAAACGCCGCTAAATATCATAATATTTTGCAA
Found at i:357747 original size:43 final size:43
Alignment explanation
Indices: 357700--357799 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
357690 TCATAATTTT
* *
357700 TTGCAACGTTTATACAAAAAAAT-CCACTGAATGTCCACACTTA
1 TTGCAACGTTTATAC-AAAAAATGCCACTAAATGTCCACACCTA
*
357743 TTGCAACGTTTATACAAAAAATGCCATTAAATGTCCACACCTA
1 TTGCAACGTTTATACAAAAAATGCCACTAAATGTCCACACCTA
**
357786 TTGCGGCGTTTATA
1 TTGCAACGTTTATA
357800 AAATGAACGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 7 0.14
43 44 0.86
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (43 bp):
TTGCAACGTTTATACAAAAAATGCCACTAAATGTCCACACCTA
Found at i:357762 original size:85 final size:84
Alignment explanation
Indices: 357598--357762 Score: 181
Period size: 85 Copynumber: 1.9 Consensus size: 84
357588 AAAAACGCCA
* * * * *
357598 CTAAATATCATAATCTTTTGTAGCGTTTATACAAAAATGCCGCTAAATGTAAAAACATGTTGCGA
1 CTAAATATCATAATCTTTTGCAACGTTTATACAAAAATGCCACTAAATGTAAAAACATATTGCAA
357663 CGTTTATGTAAAAAACGTTG
66 CGTTTA-GTAAAAAACGTTG
* * ** * *
357683 CTAAATATCATAATTTTTTGCAACGTTTATACAAAAAAAT-CCACTGAATGTCCACACTTATTGC
1 CTAAATATCATAATCTTTTGCAACGTTTATAC--AAAAATGCCACTAAATGTAAAAACATATTGC
357747 AACGTTTA-TACAAAAA
64 AACGTTTAGTA-AAAAA
357763 ATGCCATTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
84 2 0.03
85 34 0.52
86 24 0.36
87 6 0.09
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (84 bp):
CTAAATATCATAATCTTTTGCAACGTTTATACAAAAATGCCACTAAATGTAAAAACATATTGCAA
CGTTTAGTAAAAAACGTTG
Found at i:366341 original size:23 final size:23
Alignment explanation
Indices: 366315--366358 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
366305 CCTTGGTCAG
*
366315 ATTATATTATCATGCCATGTGCC
1 ATTACATTATCATGCCATGTGCC
366338 ATTACATTATCATGCCATGTG
1 ATTACATTATCATGCCATGTG
366359 ATAGAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (23 bp):
ATTACATTATCATGCCATGTGCC
Found at i:368838 original size:2 final size:2
Alignment explanation
Indices: 368831--368864 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
368821 TAACTAGTTA
* *
368831 AT AT AT AT AT AT AT AT AT AT AG AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
368865 GCTTTGTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:372801 original size:2 final size:2
Alignment explanation
Indices: 372794--372822 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
372784 ATATTTAAAT
372794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
372823 TAAATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:376881 original size:96 final size:96
Alignment explanation
Indices: 376775--376983 Score: 240
Period size: 96 Copynumber: 2.2 Consensus size: 96
376765 CAAGCTATGT
* * * * * * * *
376775 GTTCTTCTCATCATGATATT-TCTACTGGAAATAATGATCCTTCAAGCAAGGCGTTGCTAATTTG
1 GTTCTTCTCATTATGA-ATTCTCCACTGAAAATAATAATCCCTCAAGCAAGACGTTACTAATTCG
**
376839 AAATATTGTGAATCGAGCAATAGGTCAAACAA
65 AAATATCCTGAATCGAGCAATAGGTCAAACAA
* ** * * *
376871 GTTCTTCTCATTATGAATTCTCCATTGAAAATGTTAATCCCTCAAGCGAGATGTTACTGATTCGA
1 GTTCTTCTCATTATGAATTCTCCACTGAAAATAATAATCCCTCAAGCAAGACGTTACTAATTCGA
* *
376936 AGTGTCCTGAATCGAGCAATAGGTCAAACAA
66 AATATCCTGAATCGAGCAATAGGTCAAACAA
376967 GTTCTTCTCATTATGAA
1 GTTCTTCTCATTATGAA
376984 CTTTTCTCCC
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 3 0.03
96 91 0.97
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (96 bp):
GTTCTTCTCATTATGAATTCTCCACTGAAAATAATAATCCCTCAAGCAAGACGTTACTAATTCGA
AATATCCTGAATCGAGCAATAGGTCAAACAA
Found at i:377112 original size:135 final size:136
Alignment explanation
Indices: 376870--377175 Score: 470
Period size: 135 Copynumber: 2.3 Consensus size: 136
376860 AGGTCAAACA
* * * * *
376870 AGTTCTTCTCATTATGAATTCTCCATTGAAAATGTTAATCCCTCAAGCGAGATGTTACTGATTCG
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGACGTTACTAATTCG
* * *
376935 AAGTGTCCTGAATCGAGCAATAGGTCAAACAAGTTCTTCTCATTATGAACTT-TTCTCCCTCTGT
66 AAGTGTCCTGAATCGAGAAATAGATCAAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCTGT
376999 CAGATG
131 CAGATG
* * *
377005 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTTAAGCGAGGCGTTGCTAATTCG
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGACGTTACTAATTCG
* * *
377070 AAGTGTCGTGAATTGAGAAATAGATCTAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCTGT
66 AAGTGTCCTGAATCGAGAAATAGATCAAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCTGT
*
377135 CGGATG
131 CAGATG
377141 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGT
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGT
377176 TGATCAGTTC
Statistics
Matches: 155, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
135 104 0.67
136 51 0.33
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (136 bp):
AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGACGTTACTAATTCG
AAGTGTCCTGAATCGAGAAATAGATCAAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCTGT
CAGATG
Found at i:378183 original size:7 final size:7
Alignment explanation
Indices: 378173--378264 Score: 96
Period size: 7 Copynumber: 12.6 Consensus size: 7
378163 ACCTCTCATT
378173 TTTTTTC
1 TTTTTTC
378180 -TTTTTC
1 TTTTTTC
*
378186 TTTTCTTT
1 TTTT-TTC
378194 TTTTTTC
1 TTTTTTC
378201 TTTTTTC
1 TTTTTTC
*
378208 CTTTTTC
1 TTTTTTC
*
378215 CTTTTTC
1 TTTTTTC
*
378222 TTTCTTTT
1 TTT-TTTC
378230 TTTTTTC
1 TTTTTTC
378237 TTTTTTC
1 TTTTTTC
378244 ATTCTTTTTC
1 --T-TTTTTC
378254 TTTTTTC
1 TTTTTTC
378261 TTTT
1 TTTT
378265 CTTTCTTAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
6 6 0.08
7 47 0.64
8 13 0.18
9 1 0.01
10 6 0.08
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:378196 original size:22 final size:22
Alignment explanation
Indices: 378171--378271 Score: 118
Period size: 22 Copynumber: 4.5 Consensus size: 22
378161 GAACCTCTCA
378171 TTTTT-TTTCTTTTTCTTTTCT
1 TTTTTCTTTCTTTTTCTTTTCT
*
378192 TTTTT-TTTCTTTTTTCCTTTTTCC
1 TTTTTCTTTC-TTTTT-C-TTTTCT
*
378216 TTTTTCTTTCTTTTTTTTTTCT
1 TTTTTCTTTCTTTTTCTTTTCT
*
378238 TTTTTCATTCTTTTTCTTTT-T
1 TTTTTCTTTCTTTTTCTTTTCT
378259 TCTTTTCTTTCTT
1 T-TTTTCTTTCTT
378272 AGGCGTAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.16
22 38 0.55
23 1 0.01
24 15 0.22
25 4 0.06
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTCTTTCTTTTTCTTTTCT
Found at i:378204 original size:29 final size:28
Alignment explanation
Indices: 378172--378271 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 28
378162 AACCTCTCAT
378172 TTTTTTTCTTTTTCTTTTCTTTTTTTTTC
1 TTTTTTTCTTTTTCTTTT-TTTTTTTTTC
* * *
378201 TTTTTTCCTTTTTCCTTTTTCTTTCTTT-
1 TTTTTTTCTTTTT-CTTTTTTTTTTTTTC
378229 TTTTTTTCTTTTTTCATTCTTTTTCTTTTTTC
1 TTTTTTTC-TTTTTC-TT-TTTTT-TTTTTTC
378261 TTTTCTTTCTT
1 TTTT-TTTCTT
378272 AGGCGTAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.14
29 26 0.45
30 9 0.16
31 5 0.09
32 6 0.10
33 4 0.07
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTTTTTCTTTTTCTTTTTTTTTTTTTC
Found at i:378220 original size:36 final size:37
Alignment explanation
Indices: 378173--378268 Score: 133
Period size: 36 Copynumber: 2.6 Consensus size: 37
378163 ACCTCTCATT
*
378173 TTTTTTCTTTTTCTTTTCTTTTTTTTTCTTTTTTC-C
1 TTTTTCCTTTTTCTTTTCTTTTTTTTTCTTTTTTCTC
378209 TTTTTCCTTTTTC-TTTCTTTTTTTTTTCTTTTTTCATTC
1 TTTTTCCTTTTTCTTTTC-TTTTTTTTTCTTTTTTC--TC
*
378248 TTTTTCTTTTTTCTTTTCTTT
1 TTTTTCCTTTTTCTTTTCTTT
378269 CTTAGGCGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
35 4 0.08
36 29 0.55
39 16 0.30
40 4 0.08
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (37 bp):
TTTTTCCTTTTTCTTTTCTTTTTTTTTCTTTTTTCTC
Found at i:394096 original size:3 final size:3
Alignment explanation
Indices: 394084--394161 Score: 138
Period size: 3 Copynumber: 25.7 Consensus size: 3
394074 TTTTTATCCA
*
394084 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
394130 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
394162 AATATACATT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:394687 original size:17 final size:17
Alignment explanation
Indices: 394665--394699 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
394655 AGAGACAAAG
*
394665 ACAGAGAACGAAAAAAA
1 ACAGAGAAAGAAAAAAA
394682 ACAGAGAAAGAAAAAAA
1 ACAGAGAAAGAAAAAAA
394699 A
1 A
394700 AACAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (17 bp):
ACAGAGAAAGAAAAAAA
Found at i:396239 original size:28 final size:27
Alignment explanation
Indices: 396208--396261 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
396198 TAATTCTTTC
* *
396208 TTTTTAAAATTTTTATATATATTTATTA
1 TTTTCAAAATATTTATATAT-TTTATTA
* *
396236 TTTTCATAATATTTATATGTTTTATT
1 TTTTCAAAATATTTATATATTTTATT
396262 TTATTTGCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATTTTATTA
Found at i:396247 original size:18 final size:19
Alignment explanation
Indices: 396216--396251 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
396206 TCTTTTTAAA
*
396216 ATTTTTATATATATTTATT
1 ATTTTCATATATATTTATT
396235 ATTTTCATA-ATATTTAT
1 ATTTTCATATATATTTAT
396252 ATGTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTCATATATATTTATT
Found at i:406600 original size:17 final size:16
Alignment explanation
Indices: 406580--406665 Score: 63
Period size: 17 Copynumber: 5.2 Consensus size: 16
406570 TATTATGCTT
406580 GAAGAGAAAAGAAAAAA
1 GAAGA-AAAAGAAAAAA
*
406597 GAAG-AAAA-AAAATA
1 GAAGAAAAAGAAAAAA
406611 GAAGAAAAA-AAATAGAA
1 GAAGAAAAAGAAA-A-AA
406628 -AATGAAAAAGAAAAAA
1 GAA-GAAAAAGAAAAAA
*
406644 AAAGGAAAAAAGGAAAAAA
1 GAA-G-AAAAA-GAAAAAA
406663 GAA
1 GAA
406666 AAAGGGGGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
14 9 0.16
15 11 0.19
16 5 0.09
17 15 0.26
18 8 0.14
19 9 0.16
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
GAAGAAAAAGAAAAAA
Found at i:406636 original size:14 final size:14
Alignment explanation
Indices: 406584--406627 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
406574 ATGCTTGAAG
*
406584 AGAAAAGAAAAAAGA
1 AGAAAA-AAAATAGA
406599 AGAAAAAAAATAGA
1 AGAAAAAAAATAGA
406613 AGAAAAAAAATAGA
1 AGAAAAAAAATAGA
406627 A
1 A
406628 AATGAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 22 0.79
15 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (14 bp):
AGAAAAAAAATAGA
Found at i:407004 original size:16 final size:16
Alignment explanation
Indices: 406978--407022 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
406968 TTTGAATACA
*
406978 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
406995 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
407010 ATTCAATTTATTT
1 ATTCAATTTATTT
407023 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:407979 original size:165 final size:165
Alignment explanation
Indices: 407696--408239 Score: 932
Period size: 165 Copynumber: 3.3 Consensus size: 165
407686 AATAGAACAA
407696 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTACAGAATC
407761 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* **
407826 ACCTGGTTTAGCATAACCAATCATTGAATTGGGAAG
131 ACCTGGTTTAGCAGAA-CAATCATTGAATTTAGAAG
* *
407862 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAGCAGAA-
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTA-CAGAAT
* * *
407925 CAATCATTGAATTGGGAAGATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCT
65 CAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
407990 GACCTGGTTTAGCAGAACAATCATTGAATTTAGAAG
130 GACCTGGTTTAGCAGAACAATCATTGAATTTAGAAG
408026 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTACAGAATC
408091 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
** * *
408156 ATTTGG-TTGGACAGAACAATCATTGAGTTTAGAAG
131 ACCTGGTTTAG-CAGAACAATCATTGAATTTAGAAG
408191 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
408240 TTGGTATGAA
Statistics
Matches: 357, Mismatches: 17, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
164 78 0.22
165 221 0.62
166 58 0.16
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (165 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTACAGAATC
AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ACCTGGTTTAGCAGAACAATCATTGAATTTAGAAG
Found at i:407980 original size:82 final size:83
Alignment explanation
Indices: 407696--408288 Score: 865
Period size: 82 Copynumber: 7.1 Consensus size: 83
407686 AATAGAACAA
* *
407696 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTA-CAGAAT
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAGCAGAAT
*
407760 CAAGCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
* *
407779 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCATAACC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAATC
*
407844 AATCATTGAATTGGGAAG
66 AATCATTGAATTTGGAAG
407862 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAA-C
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAATC
*
407926 AATCATTGAATTGGGAAG
66 AATCATTGAATTTGGAAG
*
407944 ATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAA-C
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAATC
*
408008 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* *
408026 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTA-CAGAAT
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAGCAGAAT
*
408090 CAAGCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
** *
408109 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG-TTGGACAGAA-
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG-CAGAAT
* *
408172 CAATCATTGAGTTTAGAAG
65 CAATCATTGAATTTGGAAG
** * *
408191 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTATGAACCCAAA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGT-T-TA-GC--A
* *
408256 AAACCAATCATTGAATTTGGAAG
61 GAATCAATCATTGAATTTGGAAG
408279 ATGAATTTGC
1 ATGAATTTGC
408289 TCACAGTAAA
Statistics
Matches: 471, Mismatches: 27, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
81 1 0.00
82 227 0.48
83 211 0.45
84 1 0.00
85 1 0.00
87 3 0.01
88 27 0.06
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (83 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAATC
AATCATTGAATTTGGAAG
Found at i:408133 original size:247 final size:248
Alignment explanation
Indices: 407696--408238 Score: 878
Period size: 247 Copynumber: 2.2 Consensus size: 248
407686 AATAGAACAA
*
407696 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGTACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTGTACAGAATC
*
407761 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
66 AAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * *
407826 ACCTGGTTTAGCATAACCAATCATTGAATTGGGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
131 ACCTGATTTAGCAGAACCAAGCATTGAATTGGGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
*
407891 TGTTCTTTGAGTTATCTGACCTGGTTTAG-CAGAACAATCATTGAATTGGGAAG
196 TGTTCTTTGAGTTATCTGACCTGG-TTAGACAGAACAATCATTGAATTGAGAAG
* *
407944 ATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGACCTGGTT-TAGCAGAA-
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTGTA-CAGAAT
*
408007 CAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
65 CAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
* * *
408072 GATCTGATTGTA-CAGAATCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGA
130 GACCTGATT-TAGCAGAACCAAGCATTGAATTGGGAAGATGAATTTGCCAATAGCATCTTCTGGA
** * * *
408136 AGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAACAATCATTGAGTTTAGAAG
194 AGTGTTCTTTGAGTTATCTGACCTGGTTAGACAGAACAATCATTGAATTGAGAAG
408191 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
408239 TTTGGTATGA
Statistics
Matches: 274, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
246 3 0.01
247 212 0.77
248 59 0.22
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (248 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTGTACAGAATC
AAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ACCTGATTTAGCAGAACCAAGCATTGAATTGGGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
TGTTCTTTGAGTTATCTGACCTGGTTAGACAGAACAATCATTGAATTGAGAAG
Found at i:409483 original size:230 final size:226
Alignment explanation
Indices: 409081--409965 Score: 1424
Period size: 230 Copynumber: 3.9 Consensus size: 226
409071 ATTCAAATCT
409081 ATCATTTGATGGATTATCTTTT-CCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAT-TTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
409145 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTGATGGATTA
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCAAATTGATGGATTA
*
409210 GCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCAGCATCTGAAGGAGGAAGAAGAAGTTCATA
130 GCTTTTCCAGAGAAGGTTCATAATGAGAAGAACT---CATCTGAAGAAGGAAGAAGAAGTTCATA
409275 ATGAGAAGAATTTTTTCAACCTTTTATCTGAATTC
192 ATGAGAAGAATTTTTTCAACCTTTTATCTGAATTC
409310 ATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTATTTTTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
409375 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTGATGGATTA
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCAAATTGATGGATTA
*
409440 GCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCATCTGAAGGAGGAAGAAGAAGTTCATA
130 GCTTTTCCAGAGAAGGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATA
409505 ATGAGAAGAATTTTTTCAACCTTTTATCTGAATTC
192 ATGAGAAGAATTTTTTCAACCTTTTATCTGAATTC
409540 ATCATTTGATGGATTATTTTTGCCAGAGAATGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTATTTTTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
409605 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATC-ACTTGATGGATTA
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCAAATTGATGGATTA
*
409669 -TTTTTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
130 GCTTTT-CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
409732 GAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
194 GAGAAGAATTTTTTCAACCTTTTATCTGAATTC
*
409765 ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 ATCATTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
* * * * *
409830 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TGCTCAAATCTAT-TACTTGATGGGTT
66 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAT-CTGAATTC-ATCAAATTGATGGATT
** * * *
409893 ATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG-AGAGAGTTCATAA
129 AGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA-AGTTCATAA
409957 TGAGAAGAA
193 TGAGAAGAA
409966 CTCATCAAAA
Statistics
Matches: 630, Mismatches: 14, Indels: 27
0.94 0.02 0.04
Matches are distributed among these distances:
223 1 0.00
224 78 0.12
225 114 0.18
226 58 0.09
228 25 0.04
229 45 0.07
230 307 0.49
232 1 0.00
233 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (226 bp):
ATCATTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCAAATTGATGGATTAG
CTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAATTTTTTCAACCTTTTATCTGAATTC
Found at i:409709 original size:112 final size:113
Alignment explanation
Indices: 409081--409965 Score: 1372
Period size: 113 Copynumber: 7.8 Consensus size: 113
409071 ATTCAAATCT
*
409081 ATCATTTGATGGATTATCTTTT-CCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
409144 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
* * *
409193 ATCAAATTGATGGATTAGCTTTT-CCAGAGAAGGTTCATAATGAGAAGAACTCAGCATCTGAAGG
1 ATC-ACTTGATGGATTA-TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACT---CATCTGAAGA
*
409257 AGGAAGAAGAAGTTCATAATGAGAAGAATTTTTTCAACCTTTTATCTGAATTC
61 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
*
409310 ATCATTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
409375 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
* * *
409423 ATCAAATTGATGGATTAGCTTTT-CCAGAGAAGGTTCATAATGAGAAGAACTCATCATCTGAAGG
1 ATC-ACTTGATGGATTA-TTTTTGCCAGAGAAGGTTCATAATGAGAAGAA--C-TCATCTGAAGA
*
409487 AGGAAGAAGAAGTTCATAATGAGAAGAATTTTTTCAACCTTTTATCTGAATTC
61 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
* *
409540 ATCATTTGATGGATTATTTTTGCCAGAGAATGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
409605 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
409653 ATCACTTGATGGATTATTTTTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
409717 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
409765 ATCACTTGATGGATTATTTTTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
409829 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TGCTCAAATC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAT-CTGAATTC
* * ** * *
409877 TATTACTTGATGGGTTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 -ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
409942 AG-AGAGAGTTCATAATGAGAAGAA
65 AGAAGA-AGTTCATAATGAGAAGAA
409966 CTCATCAAAA
Statistics
Matches: 727, Mismatches: 29, Indels: 32
0.92 0.04 0.04
Matches are distributed among these distances:
111 1 0.00
112 193 0.27
113 206 0.28
114 110 0.15
115 12 0.02
116 78 0.11
117 127 0.17
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (113 bp):
ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
Found at i:410226 original size:3 final size:3
Alignment explanation
Indices: 410218--410264 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
410208 TTTTTATCCA
410218 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
410265 AATATACATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:410786 original size:16 final size:16
Alignment explanation
Indices: 410765--410797 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
410755 AGAGACAAAG
*
410765 ACAGAGAACGAAAAAA
1 ACAGAGAAAGAAAAAA
410781 ACAGAGAAAGAAAAAA
1 ACAGAGAAAGAAAAAA
410797 A
1 A
410798 AAACAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.00
Consensus pattern (16 bp):
ACAGAGAAAGAAAAAA
Found at i:411621 original size:20 final size:21
Alignment explanation
Indices: 411584--411624 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
411574 GATATTTTTA
**
411584 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
411605 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
411625 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:412348 original size:20 final size:20
Alignment explanation
Indices: 412325--412369 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
412315 TATTTTCCGT
**
412325 TATAAAATATTATTGAAAAA
1 TATAAAATATTATAAAAAAA
*
412345 TATAAAATATTGTAAAAAAA
1 TATAAAATATTATAAAAAAA
412365 TATAA
1 TATAA
412370 TATTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
TATAAAATATTATAAAAAAA
Found at i:412371 original size:18 final size:18
Alignment explanation
Indices: 412335--412378 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
412325 TATAAAATAT
*
412335 TATTG-AAAAATATAAAA
1 TATTGTAAAAAAATAAAA
*
412352 TATTGTAAAAAAATATAA
1 TATTGTAAAAAAATAAAA
*
412370 TATTTTAAA
1 TATTGTAAA
412379 TTATTTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
TATTGTAAAAAAATAAAA
Found at i:419809 original size:182 final size:182
Alignment explanation
Indices: 419502--419955 Score: 712
Period size: 182 Copynumber: 2.5 Consensus size: 182
419492 ACTTTTTTAC
* *
419502 TACCGGTTTTTTCATTTCGAGATCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
419567 TACATTTTTATAAAGTATCGACACTTTATTGACGTTATAATTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
*
419632 TGTCGATACTTATAATAAAGTATAGACACTATCAACATATCCGGTAGCTCTT
131 TGTCGATACTTATAATAAAGTATAGACACTATCAACATATCCGGTAGCGCTT
419684 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
419749 TACATTTTTATAAAGTATCGATACTTTATT-AGCGCTATAACTTCTTCTCTTTTAAATTCCAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTGA-CGCTATAACTTCTTCTCTTTTAAATTCCAAAA
*
419813 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
130 GTGTCGATACTTATAATAAAGTATAGACACTATCAACATATCCGGTAGCGCTT
** ** * * * * * * *
419866 TACCTTTTTTGTCATTTATATACCGGTTTTGTAATTTTTTTACCTATTTTATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
419931 TACATTTTTATAAAGTATCTACACT
66 TACATTTTTATAAAGTATCGACACT
419956 ATCAACATAT
Statistics
Matches: 250, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
181 1 0.00
182 249 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATAGACACTATCAACATATCCGGTAGCGCTT
Found at i:419915 original size:20 final size:20
Alignment explanation
Indices: 419864--419915 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
419854 CCGGTAGCGC
* *
419864 TTTACCTTTTTTGTCATTTA
1 TTTACCTATTTTGTAATTTA
* ** *
419884 TATACCGGTTTTGTAATTTT
1 TTTACCTATTTTGTAATTTA
419904 TTTACCTATTTT
1 TTTACCTATTTT
419916 ATTGTTATGG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTACCTATTTTGTAATTTA
Found at i:419957 original size:112 final size:112
Alignment explanation
Indices: 419828--420401 Score: 844
Period size: 112 Copynumber: 5.1 Consensus size: 112
419818 GATACTTATA
* * * * *
419828 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTTTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
* * *
419893 TTTGTAATTTTTTTACCTATTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * * * * *
419940 ATAAAGTATCTACACTATCAACATATCCGATAGCGTTTTACCTGTTTTGTTATTTATAGATCAGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
* *
420005 TTTTTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
420052 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTCTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
*
420117 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
420163 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
* *
420228 TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * **
420275 ATAAAGTATCGACACTTTCAATATATCCGGTAGTGCTTTACCTGTTTTGTCATTTATAGACCTAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
* * * * *
420340 TTTATCATTTTTTTACTTGTTATATTGTTATAGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
420387 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
420402 AAACCGACAA
Statistics
Matches: 420, Mismatches: 41, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
111 105 0.25
112 315 0.75
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:420205 original size:223 final size:224
Alignment explanation
Indices: 419828--420401 Score: 862
Period size: 223 Copynumber: 2.6 Consensus size: 224
419818 GATACTTATA
* * * *
419828 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTTTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
419893 TTTGTAATTTTTTTACCTATTTTATTGTTATGGATCGATACATTTTTATAAAGTATCTACACTAT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
** * * *
419958 CAACATATCCGATAGCGTTTTACCTGTTTTGTTATTTATAGATCAGTTTTTTCATTTTTTTACTT
131 CAACATATCCGATAGCACTTTACCTGTTTTGTCATTTATAGATCAGTTTTGTCATTTTTTTACAT
*
420023 GTTATATTGTTATGGATCGATACATTTTT
196 GTTATATTGTTATGGATAGATACATTTTT
* * * *
420052 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTCTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
420117 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
* * *
420181 CAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGATCGGTTTTGTCATTTTTTTACAT
131 CAACATATCCGATAGCACTTTACCTGTTTTGTCATTTATAGATCAGTTTTGTCATTTTTTTACAT
420246 GTTATATTGTTATGGATAGATACATTTTT
196 GTTATATTGTTATGGATAGATACATTTTT
* **
420275 ATAAAGTATCGACACTTTCAATATATCCGGTAGTGCTTTACCTGTTTTGTCATTTATAGACCTAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * * *
420340 TTTATCATTTTTTTACTTGTTATATTGTTATAGATCAATATATTTTTATAAAGTATCGACAC
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
420402 AAACCGACAA
Statistics
Matches: 313, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
223 201 0.64
224 112 0.36
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (224 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
CAACATATCCGATAGCACTTTACCTGTTTTGTCATTTATAGATCAGTTTTGTCATTTTTTTACAT
GTTATATTGTTATGGATAGATACATTTTT
Found at i:420749 original size:28 final size:28
Alignment explanation
Indices: 420709--420766 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
420699 AAATTGAATC
420709 AAAATCGAATTAAATATTATAAATAATT
1 AAAATCGAATTAAATATTATAAATAATT
420737 AAAATCGAATTAAATATTATAAATAATT
1 AAAATCGAATTAAATATTATAAATAATT
420765 AA
1 AA
420767 GTTAATTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATCGAATTAAATATTATAAATAATT
Found at i:421998 original size:16 final size:16
Alignment explanation
Indices: 421939--421999 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
421929 AGAAATATCT
*
421939 TCCGAATCGAAAAATAA
1 TCCGAATC-AAAATTAA
*
421956 TCCGAATCAAATTTAA
1 TCCGAATCAAAATTAA
*
421972 CCCG-ATCCAAAATTAA
1 TCCGAAT-CAAAATTAA
*
421988 TTCGAATCAAAA
1 TCCGAATCAAAA
422000 GCAATCTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 24 0.67
17 10 0.28
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (16 bp):
TCCGAATCAAAATTAA
Found at i:424436 original size:122 final size:120
Alignment explanation
Indices: 424179--424486 Score: 293
Period size: 122 Copynumber: 2.5 Consensus size: 120
424169 TATTTAGGGT
* * * * *
424179 AAAC-TAAGTGTTTAGCACTTATACTATTAGTTTTTGTTCAATTTAGTATCTAAACTTTCAATTT
1 AAACTTAA-TGTTTAGTACCTAAACTATCAGTTTTTGTTCAATTTAGTACCTAAACTTTCAATTT
* *
424243 GTTTCAAAATCATATCTAACATTTAGTTGCTATTTCATTTTAGTACCCACCGTTAA
65 GTTTAAAAATCATATCTAACATTTAGTTGCTATTTCATTTTAGTACCCACCATTAA
**
424299 AAACTTAATACGTTTAGTACCTAAACTATCAGTTTTTG-TCCGTTGTAGTACCTAAACTTTCAAT
1 AAACTTAAT--GTTTAGTACCTAAACTATCAGTTTTTGTTCAATT-TAGTACCTAAACTTTCAAT
* * * ** * * * *
424363 TTCTTTTAAAAATCATA-CATAGCGTTTAGTTTTTGTTTCATTTTTTGTATCCACTATT-A
63 TT-GTTTAAAAATCATATC-TAACATTTAGTTGCTATTTCA-TTTTAGTACCCACCATTAA
* * * * *
424422 AAACTTACATGTTTAGTACCTAAATTATCAGTTTTTATTCATTTTTGTA-CTGAAACTTTTAATT
1 AAACTTA-ATGTTTAGTACCTAAACTATCAGTTTTTGTTCAATTTAGTACCT-AAACTTTCAATT
424486 T
64 T
424487 TTTTCCAAAC
Statistics
Matches: 154, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
120 5 0.03
121 9 0.06
122 85 0.55
123 40 0.26
124 15 0.10
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (120 bp):
AAACTTAATGTTTAGTACCTAAACTATCAGTTTTTGTTCAATTTAGTACCTAAACTTTCAATTTG
TTTAAAAATCATATCTAACATTTAGTTGCTATTTCATTTTAGTACCCACCATTAA
Found at i:426431 original size:28 final size:26
Alignment explanation
Indices: 426383--426440 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
426373 AGAGGTGCAC
*
426383 AAAAAATTCGAATATCTGATTTTGCGA
1 AAAAAATTCGAATATCGGA-TTTGCGA
*
426410 AAAAAATATCCGAA-ATCGGATTTGGGA
1 AAAAAAT-T-CGAATATCGGATTTGCGA
426437 AAAA
1 AAAA
426441 TCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 17 0.63
28 6 0.22
29 4 0.15
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAAAATTCGAATATCGGATTTGCGA
Found at i:426469 original size:20 final size:20
Alignment explanation
Indices: 426440--426479 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
426430 TTTGGGAAAA
* *
426440 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
426460 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
426480 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:428864 original size:21 final size:21
Alignment explanation
Indices: 428840--428881 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
428830 AGTTTATTTT
*
428840 TAAATTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
428861 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
428882 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:428929 original size:33 final size:33
Alignment explanation
Indices: 428876--428974 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
428866 TTTGTTTCAA
428876 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
428908 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
428941 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
428974 T
1 T
428975 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:429003 original size:13 final size:13
Alignment explanation
Indices: 428960--429014 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
428950 TTGGAAGTAT
428960 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
428973 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
428987 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
429000 TTAAGTATTTGAA
1 TTAAGTATTTCAA
429013 TT
1 TT
429015 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:429728 original size:17 final size:18
Alignment explanation
Indices: 429708--429741 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
429698 GTTTTTTTAT
429708 AACCG-GTTTTTTAAAAA
1 AACCGAGTTTTTTAAAAA
*
429725 AACCGATTTTTTTAAAA
1 AACCGAGTTTTTTAAAA
429742 TCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGAGTTTTTTAAAAA
Done.