Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold375
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: 465583
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 2 of 3
Found at i:211547 original size:3 final size:3
Alignment explanation
Indices: 211539--211583 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
211529 ATATATACTT
211539 TTA TTA 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 TTA TTA
211584 ATTGTTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:212794 original size:20 final size:20
Alignment explanation
Indices: 212753--212794 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
212743 AAAATTGGAA
***
212753 AATGATTTTCAAAATGTTAC
1 AATGATTTTCAAAATAAAAC
212773 AATGATTTTCAAAATAAAAC
1 AATGATTTTCAAAATAAAAC
212793 AA
1 AA
212795 ATGCTTGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
AATGATTTTCAAAATAAAAC
Found at i:216621 original size:2 final size:2
Alignment explanation
Indices: 216614--216640 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
216604 ACACAGTAAC
216614 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
216641 AACCTAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219730 original size:2 final size:2
Alignment explanation
Indices: 219725--219749 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
219715 ATATAGACAA
219725 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
219750 ATGTTAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:221200 original size:24 final size:24
Alignment explanation
Indices: 221152--221201 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
221142 TCTTGAAAAT
*
221152 TTTTATTTATTAAATCTTAATTAA
1 TTTTATTTATTAAATCTTAAATAA
221176 TTTTATTT-TTAAAGT-TATAAATAA
1 TTTTATTTATTAAA-TCT-TAAATAA
221200 TT
1 TT
221202 AATCATACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTATTTATTAAATCTTAAATAA
Found at i:222210 original size:32 final size:32
Alignment explanation
Indices: 222174--222240 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
222164 AATAGCTACG
222174 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
222206 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
222238 AAC
1 AAC
222241 GATGAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (32 bp):
AACTACTTTGATATGATAGAAAGCTAAAATCA
Found at i:225717 original size:34 final size:34
Alignment explanation
Indices: 225650--225866 Score: 310
Period size: 34 Copynumber: 6.4 Consensus size: 34
225640 AACTTAGCCC
* * *
225650 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
225683 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
225717 TGTTGATTAAATGAGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
225751 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
225785 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
225819 TGTTGACTAAATGGGAGATTTGGTAGGTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
225853 TGTTGATTAAATGG
1 TGTTGATTAAATGG
225867 TGGTTTTTAC
Statistics
Matches: 165, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
33 12 0.07
34 153 0.93
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:225830 original size:102 final size:101
Alignment explanation
Indices: 225650--225868 Score: 350
Period size: 102 Copynumber: 2.2 Consensus size: 101
225640 AACTTAGCCC
* * *
225650 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
*
225715 ATTGTTGATTAAATGAGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGAGAGATTTGGTAGCTTACCAT
*
225751 TGTTGATTAAATGG-GAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
1 TGTTGATTAAATGGTG--ATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
* *
225815 CCATTGTTGACTAAATGGGAGATTTGGTAGGTTACCAT
64 CCATTGTTGACTAAATGAGAGATTTGGTAGCTTACCAT
225853 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
225869 GTTTTTACCA
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
100 1 0.01
101 14 0.13
102 92 0.85
103 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGAGAGATTTGGTAGCTTACCAT
Found at i:226199 original size:19 final size:19
Alignment explanation
Indices: 226175--226235 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
226165 GTTATCGAGA
*
226175 TACTATTCACGTATATAGG
1 TACTATTCACGTATACAGG
*
226194 TACTATTCACGTATACGGG
1 TACTATTCACGTATACAGG
* *
226213 TACTATTCAAGTATACAGT
1 TACTATTCACGTATACAGG
226232 TACT
1 TACT
226236 GTACACATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (19 bp):
TACTATTCACGTATACAGG
Found at i:230367 original size:34 final size:34
Alignment explanation
Indices: 230298--230520 Score: 313
Period size: 34 Copynumber: 6.6 Consensus size: 34
230288 AAGTGGGAGA
* * *
230298 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
230331 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
230365 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
230399 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
230433 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
230467 ATTGTTGACTAAATGGGAGATTTGGTAGGTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
230501 ATTGTTGATTAAATGGGAGA
1 ATTGTTGATTAAATGGGAGA
230521 AAGTTACAAT
Statistics
Matches: 169, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
33 14 0.08
34 155 0.92
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:230473 original size:102 final size:101
Alignment explanation
Indices: 230298--230518 Score: 363
Period size: 102 Copynumber: 2.2 Consensus size: 101
230288 AAGTGGGAGA
* *
230298 ATTGTTGATTAAATGGTG-ATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGATTAAATGG-GAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
*
230362 GCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
230399 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGGG-AATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
* *
230464 ACTATTGTTGACTAAATGGGAGATTTGGTAGGTTACC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
230501 ATTGTTGATTAAATGGGA
1 ATTGTTGATTAAATGGGA
230519 GAAAGTTACA
Statistics
Matches: 112, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
100 1 0.01
101 17 0.15
102 94 0.84
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGGAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:230968 original size:18 final size:16
Alignment explanation
Indices: 230947--230990 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
230937 ATTTTAATTA
230947 TTCTTTACTTTTTTCCAT
1 TTCTTT-CTTTTTTCC-T
*
230965 TTCTTTTTTTTTTCCT
1 TTCTTTCTTTTTTCCT
230981 TT-TTTCTTTT
1 TTCTTTCTTTT
230991 ATTTTTTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 8 0.33
18 6 0.25
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTCTTTTTTCCT
Found at i:232653 original size:96 final size:92
Alignment explanation
Indices: 232442--232656 Score: 238
Period size: 93 Copynumber: 2.3 Consensus size: 92
232432 TGTAGTATTA
* * * *
232442 TCAAATGCATGCGACGGGATTTACATCAAAGTATAATCTAATAAATAAGTGATTTTTTTATGAAT
1 TCAAA-GCATGCGACGGGATTTACATCAAAATATAATCTAACAAATAAGTAATTTTTTTATAAAT
*
232507 TTTTTGAAAAAAAAATTATTGCATTTTG
65 TTCTTGAAAAAAAAATTATTGCATTTTG
* * * *
232535 TCAAAGACGTGTGACGGGATTTATATTAAAATATAATCTAACAAATAAGTAACTTTTTTTAATAA
1 TCAAAG-CATGCGACGGGATTTACATCAAAATATAATCTAACAAATAAGTAA-TTTTTTT-ATAA
*
232600 ATTTCTT-AAAAAAAAA-TATGGGTGGATTTTG
63 ATTTCTTGAAAAAAAAATTAT---TGCATTTTG
232631 TCAAACGCATGC-AGCGGGATTTACAT
1 TCAAA-GCATGCGA-CGGGATTTACAT
232657 AAGACTTCCT
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
92 1 0.01
93 46 0.46
94 16 0.16
95 10 0.10
96 27 0.27
97 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (92 bp):
TCAAAGCATGCGACGGGATTTACATCAAAATATAATCTAACAAATAAGTAATTTTTTTATAAATT
TCTTGAAAAAAAAATTATTGCATTTTG
Found at i:234141 original size:36 final size:36
Alignment explanation
Indices: 234101--234172 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
234091 GATTACAAAG
*
234101 CCTACTTCCGCGTCTGAATGGTCCCATTCTTTATTA
1 CCTACTTCCGCGCCTGAATGGTCCCATTCTTTATTA
234137 CCTACTTCCGCGCCTGAATGGTCCCATTCTTTATTA
1 CCTACTTCCGCGCCTGAATGGTCCCATTCTTTATTA
234173 GCTTTGTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.17, C:0.32, G:0.14, T:0.38
Consensus pattern (36 bp):
CCTACTTCCGCGCCTGAATGGTCCCATTCTTTATTA
Found at i:235255 original size:27 final size:28
Alignment explanation
Indices: 235222--235292 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
235212 GCCACCCATT
235222 TATTTGTCAAAAATGGTGG-TTATTTTG
1 TATTTGTCAAAAATGGTGGTTTATTTTG
* *
235249 TGTTTGTCAAAAATGGTGGTTTCTTTTG
1 TATTTGTCAAAAATGGTGGTTTATTTTG
*
235277 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
235293 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TATTTGTCAAAAATGGTGGTTTATTTTG
Found at i:235276 original size:28 final size:27
Alignment explanation
Indices: 235222--235313 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 27
235212 GCCACCCATT
235222 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
* *
235249 TGTTTGTCAAAAATGGTGGTTTCTTTTG
1 TATTTGTCAAAAATGGTGG-TTATTTTG
* * * *
235277 TATTTGTCAAATATGGAGGCT-TGTT-
1 TATTTGTCAAAAATGGTGGTTATTTTG
235302 TATTTGTCAAAA
1 TATTTGTCAAAA
235314 TTTGTAGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 19 0.34
28 23 0.41
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.47
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:239850 original size:28 final size:27
Alignment explanation
Indices: 239795--239886 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
239785 GCCACCCATT
239795 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
239822 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
* * * *
239850 TATTTGTCAAATATGGAGGCT-TGTT-
1 TATTTGTCAAAAATGGTGGTTATTTTG
239875 TATTTGTCAAAA
1 TATTTGTCAAAA
239887 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 20 0.36
28 22 0.39
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:240734 original size:2 final size:2
Alignment explanation
Indices: 240729--240759 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
240719 ATATATATAT
*
240729 AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
240760 CAAAAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Found at i:248342 original size:25 final size:26
Alignment explanation
Indices: 248309--248365 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
248299 ATTTAAAAAA
* *
248309 TAAATTCGATTA-TAATATTTGACTT
1 TAAATTCGATTATTAATATTCGAATT
*
248334 TAAATTCGATTATTTATATTCGAATT
1 TAAATTCGATTATTAATATTCGAATT
248360 TAAATT
1 TAAATT
248366 AAAATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (26 bp):
TAAATTCGATTATTAATATTCGAATT
Found at i:249520 original size:12 final size:12
Alignment explanation
Indices: 249505--249540 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
249495 TTAAAACTTT
249505 TTATAAAAATAA
1 TTATAAAAATAA
249517 TTATAAAAATAA
1 TTATAAAAATAA
249529 --ATAAAAATAA
1 TTATAAAAATAA
249539 TT
1 TT
249541 GAAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTATAAAAATAA
Found at i:249556 original size:22 final size:22
Alignment explanation
Indices: 249509--249556 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
249499 AACTTTTTAT
* *
249509 AAAAATAATTATAAAAATAAAT
1 AAAAATAATTATAAAAAGAAAC
*
249531 AAAAATAATTGA-AAAAAGGAAC
1 AAAAATAATT-ATAAAAAGAAAC
249553 AAAA
1 AAAA
249557 TGATAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAAATAATTATAAAAAGAAAC
Found at i:252036 original size:18 final size:18
Alignment explanation
Indices: 251989--252036 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
251979 TTATTTAAAT
*
251989 ATAATTATAAATATATAA
1 ATAATTTTAAATATATAA
* * *
252007 AT-ATTTTTAATATTTTA
1 ATAATTTTAAATATATAA
252024 ATAATTTTAAATA
1 ATAATTTTAAATA
252037 GTAAAATGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATTTTAAATATATAA
Found at i:255222 original size:29 final size:28
Alignment explanation
Indices: 255190--255456 Score: 158
Period size: 29 Copynumber: 9.3 Consensus size: 28
255180 CATTAATCAT
* * *
255190 TAAACTTTTCAAAATTATACTTTGACTCC
1 TAAACTTTTCAAAATTACACATT-ACCCC
* *
255219 TAAACTCTTCAAAATTGCACATTAACCCC
1 TAAACTTTTCAAAATTACACATT-ACCCC
* * * *
255248 T-AACATTTCAAAATTCCAGATTATCCCT
1 TAAACTTTTCAAAATTACACATTA-CCCC
* * * *
255276 TAAACTTTTTAAAATTATACCTTGCCCCC
1 TAAACTTTTCAAAATTACACATT-ACCCC
* * * *
255305 TAAACTTTTCACAATTACATATTTATCTC
1 TAAACTTTTCAAAATTACACA-TTACCCC
*
255334 AAAACTTTTCAAAATTACACATTACCCC
1 TAAACTTTTCAAAATTACACATTACCCC
* * **
255362 TAAATTTTTTAAAATTACGGATTAACCCC
1 TAAACTTTTCAAAATTACACATT-ACCCC
* ** * * *
255391 TCAACTTTAAAAAATTACACACTAATCTC
1 TAAACTTTTCAAAATTACACA-TTACCCC
* * * *
255420 TAAATTTTTTAAAATTATAGATTGACCCC
1 TAAACTTTTCAAAATTACACATT-ACCCC
*
255449 AAAACTTT
1 TAAACTTT
255457 AAAATGGTTA
Statistics
Matches: 174, Mismatches: 57, Indels: 14
0.71 0.23 0.06
Matches are distributed among these distances:
27 1 0.01
28 45 0.26
29 125 0.72
30 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (28 bp):
TAAACTTTTCAAAATTACACATTACCCC
Found at i:255448 original size:58 final size:57
Alignment explanation
Indices: 255301--255460 Score: 158
Period size: 57 Copynumber: 2.8 Consensus size: 57
255291 TATACCTTGC
* * * * * * * ** *
255301 CCCCTAAACTTTTCACAATTACATATTTATCTCAAAACTTTTCAAAATTACACATTA
1 CCCCTAAATTTTTTAAAATTACAGATTAACCCCAAAACTTTAAAAAATTACACATAA
* **
255358 CCCCTAAATTTTTTAAAATTACGGATTAACCCCTCAACTTTAAAAAATTACACACTAA
1 CCCCTAAATTTTTTAAAATTACAGATTAACCCCAAAACTTTAAAAAATTACACA-TAA
* * * *
255416 TCTCTAAATTTTTTAAAATTATAGATTGACCCCAAAACTTTAAAA
1 CCCCTAAATTTTTTAAAATTACAGATTAACCCCAAAACTTTAAAA
255461 TGGTTAAAAT
Statistics
Matches: 82, Mismatches: 20, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
57 42 0.51
58 40 0.49
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (57 bp):
CCCCTAAATTTTTTAAAATTACAGATTAACCCCAAAACTTTAAAAAATTACACATAA
Found at i:256873 original size:5 final size:5
Alignment explanation
Indices: 256863--256892 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
256853 CTAAATATCG
256863 AATAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
256893 CGTAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:257602 original size:167 final size:160
Alignment explanation
Indices: 257065--257603 Score: 491
Period size: 166 Copynumber: 3.3 Consensus size: 160
257055 AAATAATTTA
* * * * * * *
257065 AATTTTTTAAAACTAATTTAATGTGAATTTAATGACAATATTAGATGAATTTT-AAAATTTTAAA
1 AATTTTTAAAAATTAATTTAA--TGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAAA
* * *
257129 CCAAGAAAAATCCCTCCGAAAACATA--T--GGAGTAGAAAACTCGATTTTTCAAAAATAGGGAG
64 CAAAGAAAAAT-CCTCC-AAAAAATATTTACGGAGTAGAAAACTCTA-TTTTCAAAAA-A-GGA-
*
257190 ATTTTAA-AGAAAAAATGAAAAACTTATGAAAAT-AAATG
123 ATTTCAAGA-AAAAAATGAAAAACTTATGAAAATGAAA-G
** * * * *
257228 AATTTTTTTAAATTTATTTACTATGAATTAAATAATAATATTTTATGAATTTTAAGAATTAAAAA
1 AATTTTTAAAAATTAATTTA--ATGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAAA
* * * * **
257293 CTAAGAAAAATCCTCCCAAAAACATTTACAGAACAGAAAACTCTATTATTCAGAAATAAGGAAAT
64 CAAAGAAAAATCCTCCAAAAAATATTTACGGAGTAGAAAACTCTATT-TTCA-AAA-AAGG-AAT
*
257358 TTCAAGAAAAAAATGAAAAACTCATGAAAATGAATA-
125 TTCAAGAAAAAAATGAAAAACTTATGAAAATGAA-AG
* *
257394 AATTTTTAAAAACTAATTTAAAATGAATTAAATAATAATATTTGATAAATTTTAAAAATTATAAA
1 AATTTTTAAAAATTAATTT--AATGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAAA
*
257459 CAAAAAAAAATCCTCCAAAAAATATTTACGGAGTAGAAAACTCTATATTTCAAAAGCAAGAGAAT
64 CAAAGAAAAATCCTCCAAAAAATATTTACGGAGTAGAAAACTCTAT-TTTCAAAA--AAG-GAAT
* *
257524 TTGAAGGAAAAAAATGAAAAACTTATAAAAATGAAAG
125 TTCAA-GAAAAAAATGAAAAACTTATGAAAATGAAAG
* * * *
257561 AATTTTTCAAAATTGATTTAATGGTCATTAAAAAATAATATTT
1 AATTTTTAAAAATTAATTTAAT-G-AATTAAATAATAATATTT
257604 AAATTTTTTG
Statistics
Matches: 308, Mismatches: 45, Indels: 42
0.78 0.11 0.11
Matches are distributed among these distances:
162 5 0.02
163 47 0.15
164 19 0.06
165 9 0.03
166 156 0.51
167 69 0.22
168 3 0.01
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.31
Consensus pattern (160 bp):
AATTTTTAAAAATTAATTTAATGAATTAAATAATAATATTTGATGAATTTTAAAAATTATAAACA
AAGAAAAATCCTCCAAAAAATATTTACGGAGTAGAAAACTCTATTTTCAAAAAAGGAATTTCAAG
AAAAAAATGAAAAACTTATGAAAATGAAAG
Found at i:263290 original size:27 final size:27
Alignment explanation
Indices: 263254--263318 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
263244 AGCCATAATT
263254 TTTGACAAACACAAAGTAACCACCATA
1 TTTGACAAACACAAAGTAACCACCATA
263281 TTTGACAAACACAAAGTAACCACCATA
1 TTTGACAAACACAAAGTAACCACCATA
263308 TTTGACAAACA
1 TTTGACAAACA
263319 AATGGTGGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.48, C:0.25, G:0.08, T:0.20
Consensus pattern (27 bp):
TTTGACAAACACAAAGTAACCACCATA
Found at i:269252 original size:13 final size:13
Alignment explanation
Indices: 269236--269267 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
269226 TTTTAAAAAA
269236 CATTTTTTATTTT
1 CATTTTTTATTTT
*
269249 CATTTTTTGTTTT
1 CATTTTTTATTTT
269262 CATTTT
1 CATTTT
269268 CTAAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.75
Consensus pattern (13 bp):
CATTTTTTATTTT
Found at i:269964 original size:23 final size:23
Alignment explanation
Indices: 269937--269981 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
269927 CAACCCTTGA
269937 TGTGATGAACTTGAACTAACATT
1 TGTGATGAACTTGAACTAACATT
269960 TGTGATGAACTTGAACTAACAT
1 TGTGATGAACTTGAACTAACAT
269982 CACCCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (23 bp):
TGTGATGAACTTGAACTAACATT
Found at i:271591 original size:17 final size:17
Alignment explanation
Indices: 271571--271613 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
271561 CTTTTCATAA
271571 AATATAAAAATAAAAAT
1 AATATAAAAATAAAAAT
* * *
271588 AATATAATAATATAATT
1 AATATAAAAATAAAAAT
271605 AAT-TAAAAA
1 AATATAAAAA
271614 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATAAAAATAAAAAT
Found at i:271653 original size:7 final size:7
Alignment explanation
Indices: 271641--271671 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
271631 CTGCATGTGT
271641 CCAAGTG
1 CCAAGTG
271648 CCAAGTG
1 CCAAGTG
271655 CCAAGTG
1 CCAAGTG
271662 CCAAGTG
1 CCAAGTG
271669 CCA
1 CCA
271672 TATAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (7 bp):
CCAAGTG
Found at i:275365 original size:27 final size:27
Alignment explanation
Indices: 275315--275366 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
275305 TAATCTTGTA
* *
275315 ATTTTTCCACTTGGTCAGCAAACTTCT
1 ATTTTACCACTTGGTCAACAAACTTCT
275342 ATTTTACCACTTGGT-AACATAACTT
1 ATTTTACCACTTGGTCAACA-AACTT
275367 TAGATGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (27 bp):
ATTTTACCACTTGGTCAACAAACTTCT
Found at i:277258 original size:2 final size:2
Alignment explanation
Indices: 277251--277295 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
277241 AGTGGTTATC
*
277251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
277293 AT A
1 AT A
277296 ACAAAAAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:281410 original size:2 final size:2
Alignment explanation
Indices: 281403--281433 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
281393 TCAAGGTTCC
281403 TA 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 TA T
281434 TAGAAAAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:282930 original size:2 final size:2
Alignment explanation
Indices: 282923--282949 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
282913 AGATATCTTT
282923 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 T
282950 GAGCAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:283970 original size:2 final size:2
Alignment explanation
Indices: 283924--283951 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
283914 AAGTTCCAAA
283924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283952 GAAAAGCGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284931 original size:36 final size:36
Alignment explanation
Indices: 284872--284940 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
284862 AACTTATTTC
* * *
284872 ATATTAAAATTTTTAAATAAATTAGTTTAAATAAAA
1 ATATGAAAATTTTCAAATAAATTAATTTAAATAAAA
* * *
284908 ATATGAAAATTTTCATATTAATTAATTTCAATA
1 ATATGAAAATTTTCAAATAAATTAATTTAAATA
284941 TTTTGCAAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (36 bp):
ATATGAAAATTTTCAAATAAATTAATTTAAATAAAA
Found at i:290641 original size:2 final size:2
Alignment explanation
Indices: 290636--290660 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
290626 ATAGACAAAA
290636 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
290661 ATGTTAATAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:295340 original size:15 final size:16
Alignment explanation
Indices: 295314--295343 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
295304 GCTTTGATAG
295314 ATAAACAAGAAAGAAA
1 ATAAACAAGAAAGAAA
295330 ATAAA-AAGAAAGAA
1 ATAAACAAGAAAGAA
295344 GAAAGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (16 bp):
ATAAACAAGAAAGAAA
Found at i:297751 original size:15 final size:15
Alignment explanation
Indices: 297706--297756 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
297696 AAATTAAAAT
297706 TAAAAT-TAATAT-A
1 TAAAATATAATATCA
297719 TCAAAA-ATAATTATTCA
1 T-AAAATATAA-TA-TCA
297736 TAAAATATAATATCA
1 TAAAATATAATATCA
297751 TAAAAT
1 TAAAAT
297757 GTATTTATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 7 0.22
15 11 0.34
16 7 0.22
17 6 0.19
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAATATAATATCA
Found at i:298543 original size:17 final size:18
Alignment explanation
Indices: 298521--298554 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
298511 GTAAGTATAT
298521 AATGAT-ATTTTATTATC
1 AATGATAATTTTATTATC
298538 AATGATAATTTTATTAT
1 AATGATAATTTTATTAT
298555 TTGAAGGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
AATGATAATTTTATTATC
Found at i:300005 original size:17 final size:18
Alignment explanation
Indices: 299983--300016 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
299973 GCAAGCATAT
299983 AATGAT-ATTTTATTATC
1 AATGATAATTTTATTATC
*
300000 AATGATAATTTTGTTAT
1 AATGATAATTTTATTAT
300017 TTGAAGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (18 bp):
AATGATAATTTTATTATC
Found at i:300166 original size:14 final size:14
Alignment explanation
Indices: 300147--300179 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
300137 GAGTTTCCTA
300147 TCTTTTT-TTCTTTT
1 TCTTTTTCTT-TTTT
300161 TCTTTTTCTTTTTT
1 TCTTTTTCTTTTTT
300175 TCTTT
1 TCTTT
300180 CTTGTTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:300168 original size:12 final size:11
Alignment explanation
Indices: 300149--300182 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
300139 GTTTCCTATC
300149 TTTTTTTCTTT
1 TTTTTTTCTTT
300160 TTCTTTTTCTTT
1 TT-TTTTTCTTT
300172 TTTTCTTTCTT
1 TTTT-TTTCTT
300183 GTTTATGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:302303 original size:24 final size:24
Alignment explanation
Indices: 302259--302304 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
302249 CATTCTTAGA
* *
302259 ATTATCATTATATTAATATTTACT
1 ATTATCATTATAATAACATTTACT
302283 ATTAT-ATTATTAATAACATTTA
1 ATTATCATTA-TAATAACATTTA
302305 TTTAAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATCATTATAATAACATTTACT
Found at i:302698 original size:14 final size:16
Alignment explanation
Indices: 302671--302703 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
302661 TTAACTTAAA
302671 AAAAAATATATAAC-G
1 AAAAAATATATAACTG
302686 AAAAAATAT-TAACTG
1 AAAAAATATATAACTG
302701 AAA
1 AAA
302704 GGGTTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAAAATATATAACTG
Found at i:304205 original size:2 final size:2
Alignment explanation
Indices: 304198--304235 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
304188 AACTAGATGC
304198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
304236 GAGGTATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:305606 original size:17 final size:17
Alignment explanation
Indices: 305584--305616 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
305574 TAATATGAAT
305584 TATAAATATAAAATTTA
1 TATAAATATAAAATTTA
305601 TATAAATATAAAATTT
1 TATAAATATAAAATTT
305617 TTTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAAATATAAAATTTA
Found at i:305655 original size:11 final size:11
Alignment explanation
Indices: 305629--305664 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
305619 TATATATTAT
305629 TATAATATAAA
1 TATAATATAAA
305640 -A-AATATAAA
1 TATAATATAAA
305649 TATAATATAAA
1 TATAATATAAA
305660 TATAA
1 TATAA
305665 AAATTACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 8 0.35
10 2 0.09
11 13 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAATATAAA
Found at i:305662 original size:17 final size:17
Alignment explanation
Indices: 305508--305665 Score: 65
Period size: 17 Copynumber: 8.8 Consensus size: 17
305498 CAATATGATT
* *
305508 ATATAAATATGAGATAAA
1 ATATAAATAT-AAATATA
305526 ATATATAAT-TAAATATA
1 ATATA-AATATAAATATA
**
305543 ATATACGTATAAATAT-
1 ATATAAATATAAATATA
*
305559 ATCTCAAAATTTATATAATATGA
1 ATAT--AAA--TATA-AATAT-A
*
305582 ATTATAAATATAAA-ATTT
1 A-TATAAATATAAATA-TA
* *
305600 ATATAAATATAAAATTTT
1 ATATAAATAT-AAATATA
* *
305618 TTATATATTATTATAATATA
1 ATATA-AATA-TA-AATATA
305638 A-A-AAATATAAATATA
1 ATATAAATATAAATATA
305653 ATATAAATATAAA
1 ATATAAATATAAA
305666 AATTACCGAG
Statistics
Matches: 106, Mismatches: 16, Indels: 37
0.67 0.10 0.23
Matches are distributed among these distances:
15 7 0.07
16 7 0.07
17 38 0.36
18 19 0.18
19 11 0.10
20 13 0.12
21 5 0.05
22 3 0.03
23 1 0.01
24 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (17 bp):
ATATAAATATAAATATA
Found at i:306106 original size:24 final size:26
Alignment explanation
Indices: 306055--306112 Score: 84
Period size: 24 Copynumber: 2.3 Consensus size: 26
306045 TGGGTGGCTA
* *
306055 GTCAACAAAAGTCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
306081 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
306105 GTCAACAA
1 GTCAACAA
306113 TGATGGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.50
25 2 0.07
26 13 0.43
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:306243 original size:20 final size:20
Alignment explanation
Indices: 306218--306263 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
306208 AAAAGGGGGC
*
306218 TCCCTCCTTCCTCTCAAGTA
1 TCCCTCATTCCTCTCAAGTA
**
306238 TCCCTCATTCCTCTCTTGTA
1 TCCCTCATTCCTCTCAAGTA
306258 TCCCTC
1 TCCCTC
306264 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.46, G:0.04, T:0.39
Consensus pattern (20 bp):
TCCCTCATTCCTCTCAAGTA
Found at i:308775 original size:21 final size:22
Alignment explanation
Indices: 308746--308791 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
308736 TGTTCAGACA
** *
308746 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
308768 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
308789 AGT
1 AGT
308792 TTCAACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:310706 original size:24 final size:26
Alignment explanation
Indices: 310655--310712 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
310645 TGGGTGGCTA
*
310655 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
310681 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
310705 GTCAACAA
1 GTCAACAA
310713 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:310842 original size:20 final size:20
Alignment explanation
Indices: 310817--310862 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
310807 TAAATGGGGC
*
310817 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
* **
310837 TCCCTCATTCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
310857 TCCCTC
1 TCCCTC
310863 TTTAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.48, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:313023 original size:69 final size:70
Alignment explanation
Indices: 312939--313087 Score: 201
Period size: 69 Copynumber: 2.1 Consensus size: 70
312929 TTTTCAGGAC
* * * *
312939 AAATGTATTTTCAGAAAACTAATTGAAAGAGAGATCTAAATACTTAAAA-GATATTAAACTCATG
1 AAATATATTTCCAGAAAACTAATTGAAAGAGAGATCTAAATACTCAAAAGGATATTAAACTCATA
*
313003 AGGGG
66 AAGGG
* * ** *
313008 GAATATATTTCCAGAAAACTGATTGTTAGAGAGATCTAAATACTCAAAAGGATATTAAACTCTTA
1 AAATATATTTCCAGAAAACTAATTGAAAGAGAGATCTAAATACTCAAAAGGATATTAAACTCATA
313073 AAGGG
66 AAGGG
313078 AAATATATTT
1 AAATATATTT
313088 TCCGAAATCT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
69 42 0.62
70 26 0.38
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (70 bp):
AAATATATTTCCAGAAAACTAATTGAAAGAGAGATCTAAATACTCAAAAGGATATTAAACTCATA
AAGGG
Found at i:313105 original size:70 final size:69
Alignment explanation
Indices: 312939--313121 Score: 206
Period size: 70 Copynumber: 2.6 Consensus size: 69
312929 TTTTCAGGAC
* * * * ** * *
312939 AAATGTATTTTCAGAAAACTAATTGAAAGAGAGATCTAAATACTTAAAAGATATTAAACTCATGA
1 AAATATATTTCCAGAAAACTGACTGTTAGAGAGATCTAAATACTCAAAAGATATTAAACTCATAA
*
313004 GGGG
66 AGGG
* * *
313008 GAATATATTTCCAGAAAACTGATTGTTAGAGAGATCTAAATACTCAAAAGGATATTAAACTCTTA
1 AAATATATTTCCAGAAAACTGACTGTTAGAGAGATCTAAATACTCAAAA-GATATTAAACTCATA
313073 AAGGG
65 AAGGG
* * *
313078 AAATATATTTTCC-GAAATCTGACTGTTAGAGAGATTTGAATACT
1 AAATATA-TTTCCAGAAAACTGACTGTTAGAGAGATCTAAATACT
313122 TAAGATATGT
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
69 42 0.43
70 50 0.52
71 5 0.05
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (69 bp):
AAATATATTTCCAGAAAACTGACTGTTAGAGAGATCTAAATACTCAAAAGATATTAAACTCATAA
AGGG
Found at i:314017 original size:9 final size:9
Alignment explanation
Indices: 313998--314030 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
313988 ATCCTTTCAT
313998 AAAAT-ATA
1 AAAATAATA
314006 AAAATAATA
1 AAAATAATA
314015 AAAATAATA
1 AAAATAATA
*
314024 ATAATAA
1 AAAATAA
314031 AATAATACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:314021 original size:15 final size:16
Alignment explanation
Indices: 313996--314034 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
313986 ATATCCTTTC
313996 ATAAAATATAAAAATA
1 ATAAAATATAAAAATA
*
314012 ATAAAA-ATAATAATA
1 ATAAAATATAAAAATA
314027 ATAAAATA
1 ATAAAATA
314035 ATACAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAATATAAAAATA
Found at i:314055 original size:23 final size:22
Alignment explanation
Indices: 313996--314055 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
313986 ATATCCTTTC
313996 ATAA-AATATAAAAATAATAAAA
1 ATAATAAT-TAAAAATAATAAAA
* *
314018 ATAATAATAATAAAATAATACAA
1 ATAATAATTA-AAAATAATAAAA
*
314041 TTAATTAATTAAAAA
1 ATAA-TAATTAAAAA
314056 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 5 0.16
23 21 0.68
24 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAATAATTAAAAATAATAAAA
Found at i:319283 original size:9 final size:9
Alignment explanation
Indices: 319264--319305 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
319254 ATCATTTCAT
319264 AAAAT-ATA
1 AAAATAATA
319272 AAAATAATA
1 AAAATAATA
319281 AAAATAATA
1 AAAATAATA
319290 AAAATAATA
1 AAAATAATA
*
319299 ATAATAA
1 AAAATAA
319306 AATAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 5 0.16
9 27 0.84
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:319287 original size:15 final size:15
Alignment explanation
Indices: 319262--319307 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
319252 ATATCATTTC
319262 ATAAAATATAA-AAATA
1 ATAAAA-ATAATAAA-A
319278 ATAAAAATAATAAAA
1 ATAAAAATAATAAAA
*
319293 ATAATAATAATAAAA
1 ATAAAAATAATAAAA
319308 TAATATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAAAATAATAAAA
Found at i:319289 original size:3 final size:3
Alignment explanation
Indices: 319269--319316 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
319259 TTCATAAAAT
* * *
319269 ATA AAA ATA ATA AAA ATA ATA AAA ATA ATA ATA ATA A-A ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
319315 AT
1 AT
319317 TAATTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:319694 original size:28 final size:28
Alignment explanation
Indices: 319655--319711 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
319645 AATTACAACT
* *
319655 TTAACAAGTATATAAAATAAATATTTAC
1 TTAACAAGTATAAAAAATAAATATATAC
*
319683 TTAACAATTATAAAAAATAAATATATAC
1 TTAACAAGTATAAAAAATAAATATATAC
319711 T
1 T
319712 GATTCTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (28 bp):
TTAACAAGTATAAAAAATAAATATATAC
Found at i:322114 original size:16 final size:16
Alignment explanation
Indices: 322039--322117 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 16
322029 ATTAAGGTTG
* * *
322039 AAAATCTGTAATTATA
1 AAAATCTGTGATTCTT
*
322055 AAAATCTGTAATTCTT
1 AAAATCTGTGATTCTT
*
322071 AAAAATTTGTGATTCTT
1 -AAAATCTGTGATTCTT
*
322088 AGAAATCTGTGATTCCT
1 A-AAATCTGTGATTCTT
322105 AAAATCTGTGATT
1 AAAATCTGTGATT
322118 GATACTGATC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
16 27 0.49
17 28 0.51
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (16 bp):
AAAATCTGTGATTCTT
Found at i:325819 original size:62 final size:62
Alignment explanation
Indices: 325688--325819 Score: 140
Period size: 62 Copynumber: 2.1 Consensus size: 62
325678 CAATGACGAC
* * * * *
325688 ATGTGGTAGGTGAGGATTGGCTGAAGTGGCGTTGACTGGACAAAAATGCTGACTGGGCGATG
1 ATGTGGTAGGTGAGGATCGACTGAAGTGGCATTGACTGGACAAAAAGGCTGACTGGACGATG
** * * * * *
325750 ACATGGTAGGTGATGG-TCGACTGATGTGGCATTGATTGGATAAAAGGGCTGACTGGATGATG
1 ATGTGGTAGGTGA-GGATCGACTGAAGTGGCATTGACTGGACAAAAAGGCTGACTGGACGATG
325812 ATGTGGTA
1 ATGTGGTA
325820 ATGACGACAT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
62 53 0.96
63 2 0.04
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.27
Consensus pattern (62 bp):
ATGTGGTAGGTGAGGATCGACTGAAGTGGCATTGACTGGACAAAAAGGCTGACTGGACGATG
Found at i:325848 original size:140 final size:140
Alignment explanation
Indices: 325593--325903 Score: 491
Period size: 140 Copynumber: 2.2 Consensus size: 140
325583 AAAGAAAAGT
* * * * *
325593 ATGCTAACTGGGCGATGACATGGCAAGTGATGGTTGGCTGATGTGGCATTGATTAGATAAAAGGG
1 ATGCTGACTGGGCGATGACATGGTAGGTGATGGTCGACTGATGTGGCATTGATTAGATAAAAGGG
325658 ATGACTGGATGATGATGTGGCAATGACGACATGTGGTAGGTGAGGATTGGCTGAAGTGGCGTTGA
66 ATGACTGGATGATGATGTGGCAATGACGACATGTGGTAGGTGAGGATTGGCTGAAGTGGCGTTGA
325723 CTGGACAAAA
131 CTGGACAAAA
*
325733 ATGCTGACTGGGCGATGACATGGTAGGTGATGGTCGACTGATGTGGCATTGATTGGATAAAAGGG
1 ATGCTGACTGGGCGATGACATGGTAGGTGATGGTCGACTGATGTGGCATTGATTAGATAAAAGGG
* *
325798 CTGACTGGATGATGATGTGGTAATGACGACATGTGGTAGGTGAAGG-TTGGCTGAAGTGGCGTTG
66 ATGACTGGATGATGATGTGGCAATGACGACATGTGGTAGGTG-AGGATTGGCTGAAGTGGCGTTG
325862 ACTGGACAAAA
130 ACTGGACAAAA
** * *
325873 ATGCTGACAAGACGATGACATGAT-GGTGATG
1 ATGCTGACTGGGCGATGACATGGTAGGTGATG
325904 ACATGTGACA
Statistics
Matches: 158, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
139 7 0.04
140 148 0.94
141 3 0.02
ACGTcount: A:0.27, C:0.11, G:0.37, T:0.25
Consensus pattern (140 bp):
ATGCTGACTGGGCGATGACATGGTAGGTGATGGTCGACTGATGTGGCATTGATTAGATAAAAGGG
ATGACTGGATGATGATGTGGCAATGACGACATGTGGTAGGTGAGGATTGGCTGAAGTGGCGTTGA
CTGGACAAAA
Found at i:326583 original size:16 final size:17
Alignment explanation
Indices: 326540--326580 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
326530 TCTATAATTC
* *
326540 TTAAAAATCTGTGATTT
1 TTAAAAATTTATGATTT
326557 TTAGAAAATTTATGATTT
1 TTA-AAAATTTATGATTT
326575 TTAAAA
1 TTAAAA
326581 TTTGTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (17 bp):
TTAAAAATTTATGATTT
Found at i:330509 original size:30 final size:28
Alignment explanation
Indices: 330473--330558 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
330463 ATTTCATTTG
*
330473 AATAAAGATTTATTTGAGTACAAATCAAAA
1 AATAAAGATTTATTTGAATA-AAA-CAAAA
* * *
330503 AATAAAGATATATTTAAATATAACAAAA
1 AATAAAGATTTATTTGAATAAAACAAAA
*
330531 ATATAAAGATTTATTTGAA-AAAATAAAA
1 A-ATAAAGATTTATTTGAATAAAACAAAA
330559 TAGTTCAACG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
28 13 0.28
29 17 0.36
30 17 0.36
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAAAGATTTATTTGAATAAAACAAAA
Found at i:330545 original size:29 final size:30
Alignment explanation
Indices: 330473--330546 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
330463 ATTTCATTTG
* *
330473 AATAAAGATTTATTTGAGTACAAATCAAAA
1 AATAAAGATTTATTTAAATACAAATCAAAA
* *
330503 AATAAAGATATATTTAAATA-TAA-CAAAA
1 AATAAAGATTTATTTAAATACAAATCAAAA
330531 ATATAAAGATTTATTT
1 A-ATAAAGATTTATTT
330547 GAAAAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 6 0.16
29 15 0.39
30 17 0.45
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (30 bp):
AATAAAGATTTATTTAAATACAAATCAAAA
Found at i:333261 original size:19 final size:19
Alignment explanation
Indices: 333237--333275 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
333227 AATATAACTA
333237 TATAGTTTATAATAATAGT
1 TATAGTTTATAATAATAGT
* *
333256 TATAGTTTTTAATACTAGT
1 TATAGTTTATAATAATAGT
333275 T
1 T
333276 GTTAACTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (19 bp):
TATAGTTTATAATAATAGT
Found at i:334519 original size:21 final size:20
Alignment explanation
Indices: 334483--334528 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
334473 CGTAAAGACA
*
334483 TTTTTAAAAAATTATTATGT
1 TTTTTAAAAAATTATTATAT
* *
334503 TTTTTAATAAATGTATTTTAT
1 TTTTTAAAAAAT-TATTATAT
334524 TTTTT
1 TTTTT
334529 TGATGCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTAAAAAATTATTATAT
Found at i:334934 original size:2 final size:2
Alignment explanation
Indices: 334916--334956 Score: 55
Period size: 2 Copynumber: 19.5 Consensus size: 2
334906 ATAATAATGC
*
334916 AT AT AA AT AT GAT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
334957 CAATAATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:338309 original size:20 final size:20
Alignment explanation
Indices: 338281--338329 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
338271 AGAAAGAATT
338281 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* **
338301 GATGAGGGATACTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
338321 GAAGAGGGA
1 GAAGAGGGA
338330 GCCTCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.47, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:338405 original size:25 final size:25
Alignment explanation
Indices: 338372--338422 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
338362 TTGTAATAAA
*
338372 AAATTAGCCACAA-ATTTTGACAAAT
1 AAATAAGCCACAATA-TTTGACAAAT
* *
338397 AAATAAGCCTCCATATTTGACAAAT
1 AAATAAGCCACAATATTTGACAAAT
338422 A
1 A
338423 CAAAGGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (25 bp):
AAATAAGCCACAATATTTGACAAAT
Found at i:338468 original size:27 final size:27
Alignment explanation
Indices: 338397--338477 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
338387 TTTGACAAAT
* * *
338397 AAATAAGCCTCCATATTTGACAAATACA
1 AAATAA-CCACCATTTTTGACAAACACA
338425 AAGGA-AACCACCATTTTTGACAAACACA
1 AA--ATAACCACCATTTTTGACAAACACA
338453 AAATAACCACCATTTTTGACAAACA
1 AAATAACCACCATTTTTGACAAACA
338478 AATGGGTGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 21 0.45
28 22 0.47
29 2 0.04
30 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.22
Consensus pattern (27 bp):
AAATAACCACCATTTTTGACAAACACA
Found at i:340397 original size:21 final size:22
Alignment explanation
Indices: 340359--340404 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
340349 ATCTGTTGAA
**
340359 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGTTGCGGAGTACT
340380 ACTCCACCTGTTGCGGAGTACT
1 ACTCCACCTGTTGCGGAGTACT
340402 ACT
1 ACT
340405 TATCTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGTTGCGGAGTACT
Found at i:342875 original size:20 final size:20
Alignment explanation
Indices: 342847--342895 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
342837 AGAAAGAATT
342847 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* **
342867 GATGAGGGATACTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
342887 GAAGAGGGA
1 GAAGAGGGA
342896 GCTTCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.47, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:342971 original size:25 final size:25
Alignment explanation
Indices: 342938--342988 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
342928 TTGTAATAAA
*
342938 AAATTAGCCACAA-ATTTTGACAAAT
1 AAATAAGCCACAATA-TTTGACAAAT
* *
342963 AAATAAGCCTCCATATTTGACAAAT
1 AAATAAGCCACAATATTTGACAAAT
342988 A
1 A
342989 CAAAGGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (25 bp):
AAATAAGCCACAATATTTGACAAAT
Found at i:343436 original size:110 final size:110
Alignment explanation
Indices: 343243--343465 Score: 437
Period size: 110 Copynumber: 2.0 Consensus size: 110
343233 TTAGAAGCCT
343243 AAAAGGAGGAACCCAATCATATTTTAGGTTAAAAATCAGTGACCTGTTTGAGTGTGTTGTGAGTA
1 AAAAGGAGGAACCCAATCATATTTTAGGTTAAAAATCAGTGACCTGTTTGAGTGTGTTGTGAGTA
343308 TGAAAGAATGTAATTTTGTGAGATTTGCTAAATGGGCTTCTGTCA
66 TGAAAGAATGTAATTTTGTGAGATTTGCTAAATGGGCTTCTGTCA
*
343353 AAAAGGAGGAACCCAATCATATTTTAGGTTAAAAATCAGTGACCTGTTTGAGTGTGTTGTGAGTC
1 AAAAGGAGGAACCCAATCATATTTTAGGTTAAAAATCAGTGACCTGTTTGAGTGTGTTGTGAGTA
343418 TGAAAGAATGTAATTTTGTGAGATTTGCTAAATGGGCTTCTGTCA
66 TGAAAGAATGTAATTTTGTGAGATTTGCTAAATGGGCTTCTGTCA
343463 AAA
1 AAA
343466 CACCTTCCAT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.33
Consensus pattern (110 bp):
AAAAGGAGGAACCCAATCATATTTTAGGTTAAAAATCAGTGACCTGTTTGAGTGTGTTGTGAGTA
TGAAAGAATGTAATTTTGTGAGATTTGCTAAATGGGCTTCTGTCA
Found at i:346837 original size:25 final size:26
Alignment explanation
Indices: 346801--346853 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
346791 AATACAATAC
346801 AAAAAAATAATA-TAAATA-TTATAT
1 AAAAAAATAATATTAAATATTTATAT
* *
346825 AAAAACATCAATATTCAATATTTATAT
1 AAAAAAAT-AATATTAAATATTTATAT
346852 AA
1 AA
346854 TATAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 4 0.17
26 5 0.21
27 8 0.33
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAAAATAATATTAAATATTTATAT
Found at i:346898 original size:20 final size:22
Alignment explanation
Indices: 346847--346900 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 22
346837 ATTCAATATT
346847 TATATAATATAATT-TATTAACA
1 TATATAATA-AATTATATTAACA
346869 TAT-TAA-AAATTATA-TAA-A
1 TATATAATAAATTATATTAACA
346887 TATATAATAAATTA
1 TATATAATAAATTA
346901 AATATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 4 0.14
19 10 0.34
20 9 0.31
21 3 0.10
22 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAATAAATTATATTAACA
Found at i:348694 original size:22 final size:22
Alignment explanation
Indices: 348669--348749 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
348659 TAAATTTAAA
*
348669 TTTAAAACACATAAAATTA-TAT
1 TTTAAAA-ACATAAAATTATTAC
* *
348691 TTTAATAATATAAAATTATTAC
1 TTTAAAAACATAAAATTATTAC
*
348713 TTTAAATA-A-AAAATGTAATTATC
1 TTTAAAAACATAAAAT-T-ATTA-C
*
348736 TTTAAAAAAATAAA
1 TTTAAAAACATAAA
348750 TTTTAAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 5 0.11
21 12 0.26
22 18 0.38
23 8 0.17
24 1 0.02
25 3 0.06
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (22 bp):
TTTAAAAACATAAAATTATTAC
Found at i:348725 original size:20 final size:22
Alignment explanation
Indices: 348697--348751 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
348687 ATATTTTAAT
*
348697 AATATAAAATT-ATTA-CTTTA
1 AATAAAAAATTAATTATCTTTA
348717 AATAAAAAATGTAATTATCTTTA
1 AATAAAAAAT-TAATTATCTTTA
*
348740 AAAAAATAAATT
1 AATAAA-AAATT
348752 TTAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 4 0.14
23 11 0.38
24 4 0.14
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AATAAAAAATTAATTATCTTTA
Found at i:349101 original size:19 final size:18
Alignment explanation
Indices: 349079--349115 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
349069 TGAATATAAA
*
349079 TAATTTTTTTATATATTTT
1 TAATTTCTTTATA-ATTTT
349098 TAATTTCTTTATAATTTT
1 TAATTTCTTTATAATTTT
349116 AATATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TAATTTCTTTATAATTTT
Found at i:349122 original size:19 final size:19
Alignment explanation
Indices: 349080--349127 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
349070 GAATATAAAT
* *
349080 AATTTTTTTATATATTTTT
1 AATTTATTTATATATTTTA
*
349099 AATTTCTTTATA-ATTTTA
1 AATTTATTTATATATTTTA
349117 ATATTTATTTA
1 A-ATTTATTTA
349128 ATTCATTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
AATTTATTTATATATTTTA
Found at i:349600 original size:50 final size:50
Alignment explanation
Indices: 349541--349828 Score: 495
Period size: 50 Copynumber: 5.8 Consensus size: 50
349531 TATACTTAAA
*
349541 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGTTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** *
349591 GTCAACAATTGCGGCCACCTCTCTCTATTGTCAAAGGTTGGTAAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
349641 GTCAACAATTATAGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
349691 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
349741 GTCAACAATTATGGCCAACTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** *
349791 GTCAACAATTGCGGCCATCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
349829 ACTTTCCACC
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 225 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:358247 original size:12 final size:11
Alignment explanation
Indices: 358224--358277 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
358214 TTGTTATTAA
358224 GATAATTATTT
1 GATAATTATTT
358235 GATAATTATTTT
1 GATAATTA-TTT
*
358247 GATAA--ATTA
1 GATAATTATTT
* *
358256 AATAATCATTT
1 GATAATTATTT
358267 GATAATTATTT
1 GATAATTATTT
358278 AGTTGAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 6 0.17
10 1 0.03
11 20 0.57
12 8 0.23
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (11 bp):
GATAATTATTT
Found at i:359198 original size:18 final size:18
Alignment explanation
Indices: 359175--359245 Score: 72
Period size: 17 Copynumber: 3.9 Consensus size: 18
359165 TTTGTATTAT
*
359175 TTTTTTTTAATTTTTAGA
1 TTTTTTTTAATTTTTAAA
359193 TTTTTTTT-ATTTTTAAA
1 TTTTTTTTAATTTTTAAA
* *
359210 ATTTTTTGAATTATTTTAAA
1 TTTTTTTTAA-T-TTTTAAA
* *
359230 TTTTTATTATTTTTTA
1 TTTTTTTTAATTTTTA
359246 TTTTCTATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 14 0.33
18 14 0.33
19 2 0.05
20 13 0.30
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTTTTAATTTTTAAA
Found at i:359249 original size:16 final size:16
Alignment explanation
Indices: 359162--359242 Score: 53
Period size: 16 Copynumber: 5.0 Consensus size: 16
359152 CATGTTATGA
*
359162 AAATTTGTATTATTTT
1 AAATTTTTATTATTTT
*
359178 ---TTTTTAAT-TTTT
1 AAATTTTTATTATTTT
* *
359190 AGATTTTTTTTATTTTT
1 AAATTTTTATTA-TTTT
359207 AAAATTTTTTGAATTATTTT
1 -AAA-TTTTT--ATTATTTT
359227 AAATTTTTATTATTTT
1 AAATTTTTATTATTTT
359243 TTATTTTCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
12 4 0.08
13 6 0.12
15 6 0.12
16 8 0.16
17 4 0.08
18 7 0.14
19 8 0.16
20 4 0.08
21 3 0.06
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
AAATTTTTATTATTTT
Found at i:359263 original size:44 final size:44
Alignment explanation
Indices: 359178--359264 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
359168 GTATTATTTT
* *
359178 TTTTTAATTTTTAGATTTTTTTTATTTTTAAAATTTTTTGAATTA
1 TTTTAAATTTTTA-ATTTTTTTTATTTTTAAAATTTATTGAATTA
*
359223 TTTTAAATTTTT-ATTATTTTTTATTTTCTATAA-TTATTGAAT
1 TTTTAAATTTTTAATT-TTTTTTATTTT-TAAAATTTATTGAAT
359265 AAAAAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 3 0.08
44 19 0.51
45 15 0.41
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (44 bp):
TTTTAAATTTTTAATTTTTTTTATTTTTAAAATTTATTGAATTA
Found at i:362344 original size:18 final size:20
Alignment explanation
Indices: 362321--362357 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
362311 AAACAAAATA
362321 TATTGCA-TTTTT-TTTTGC
1 TATTGCACTTTTTATTTTGC
362339 TATTGCACTTTTTATTTTG
1 TATTGCACTTTTTATTTTG
362358 TTTTCGCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.65
Consensus pattern (20 bp):
TATTGCACTTTTTATTTTGC
Found at i:363647 original size:23 final size:22
Alignment explanation
Indices: 363604--363657 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
363594 AGTATATATT
*
363604 GTATGTATTATTATCTTTTTACTA
1 GTAT-TATTATTATCTGTTTA-TA
363628 GTATTATTATTAAT-TGTTTATA
1 GTATTATTATT-ATCTGTTTATA
*
363650 ATATTATT
1 GTATTATT
363658 CAATTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.33
23 12 0.44
24 6 0.22
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (22 bp):
GTATTATTATTATCTGTTTATA
Found at i:364820 original size:2 final size:2
Alignment explanation
Indices: 364813--364859 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
364803 GAGATATCTT
364813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
364855 TA TA T
1 TA TA T
364860 GAGCAATGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:366596 original size:2 final size:2
Alignment explanation
Indices: 366589--366618 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
366579 AAGGGTTCCA
366589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
366619 TTGAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367022 original size:3 final size:3
Alignment explanation
Indices: 367014--367043 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
367004 ATATATAGTT
367014 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
367044 ATTGTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:367618 original size:2 final size:2
Alignment explanation
Indices: 367611--367636 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
367601 GAAAGATAAA
367611 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
367637 GAACATGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367831 original size:30 final size:29
Alignment explanation
Indices: 367770--367831 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
367760 TACATTCAAA
* * *
367770 TTTTTCATTGAACAAAAATTGTTGTGCTT
1 TTTTTCATTGAAAAAAAATTCTTGTACTT
*
367799 TTTTTCATCTTAAAAAAAATTCTTGTA-TT
1 TTTTTCAT-TGAAAAAAAATTCTTGTACTT
367828 TTTT
1 TTTT
367832 AATAACTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (29 bp):
TTTTTCATTGAAAAAAAATTCTTGTACTT
Found at i:368927 original size:32 final size:31
Alignment explanation
Indices: 368862--368927 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
368852 ATTTAAATTG
*
368862 ATTTTACTTAAATTATTATTTATTAATAAAAT
1 ATTTTACTTAAATTATTA-TTATAAATAAAAT
*
368894 ATTTTATTTAAATTAATTA-TATAAATAATAAT
1 ATTTTACTTAAATT-ATTATTATAAATAA-AAT
368926 AT
1 AT
368928 AAAAGTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 8 0.27
32 18 0.60
33 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTTTACTTAAATTATTATTATAAATAAAAT
Found at i:374020 original size:30 final size:28
Alignment explanation
Indices: 373965--374029 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 28
373955 CAAATAAGTA
*
373965 TTAACTTATACCTAAATAAGTTCTTAACAT
1 TTAA-TTATACCTAAATAAGCTCTTAA-AT
373995 TTAATTATTACCTAAATTAA-CTCTTAAAT
1 TTAATTA-TACCTAAA-TAAGCTCTTAAAT
374024 TATAAT
1 T-TAAT
374030 CAATATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 6 0.19
30 22 0.71
31 3 0.10
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.43
Consensus pattern (28 bp):
TTAATTATACCTAAATAAGCTCTTAAAT
Found at i:374398 original size:94 final size:94
Alignment explanation
Indices: 374237--374438 Score: 395
Period size: 94 Copynumber: 2.1 Consensus size: 94
374227 TAATAGCGAA
374237 ATTATTTAGGAGACCTTGACTTAGATGTTTCCTATCAAGTTTCGTAGGAAAGTGGAATGTACATT
1 ATTATTTAGGAGACCTTGACTTAGATGTTTCCTATCAAGTTTCGTAGGAAAGTGGAATGTACATT
374302 GTCATGACAGTTGATGCCTAGACTGCATT
66 GTCATGACAGTTGATGCCTAGACTGCATT
374331 ATTATTTAGGAGACCTTGACTTAGATGTTTCCTATCAAGTTTCGTAGGAAAGTGGAATGTACATT
1 ATTATTTAGGAGACCTTGACTTAGATGTTTCCTATCAAGTTTCGTAGGAAAGTGGAATGTACATT
374396 GTCATGACAGTTGATGCCTAGACTGCATT
66 GTCATGACAGTTGATGCCTAGACTGCATT
*
374425 ATTATTTAAGAGAC
1 ATTATTTAGGAGAC
374439 ATCGAACTTA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 107 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (94 bp):
ATTATTTAGGAGACCTTGACTTAGATGTTTCCTATCAAGTTTCGTAGGAAAGTGGAATGTACATT
GTCATGACAGTTGATGCCTAGACTGCATT
Found at i:377200 original size:32 final size:32
Alignment explanation
Indices: 377164--377230 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
377154 AATAGCTACT
*
377164 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACATTGATATGATAGAAAGCTAAAATCA
377196 AACTACATTGATATGATAGAAAGCTAAAATCA
1 AACTACATTGATATGATAGAAAGCTAAAATCA
377228 AAC
1 AAC
377231 GATGAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (32 bp):
AACTACATTGATATGATAGAAAGCTAAAATCA
Found at i:382953 original size:93 final size:95
Alignment explanation
Indices: 382827--383004 Score: 236
Period size: 93 Copynumber: 1.9 Consensus size: 95
382817 TGCATGCGAC
* * * * *
382827 GGGATTTACATCAAAGTATAATCTAATAAATAAGTGA-TTTTTTT-ATTAATTTTTTGAAAAAAA
1 GGGATTTACATCAAAATATAATCTAACAAATAAGTAACTTTTTTTAATGAATTTCTT-AAAAAAA
*
382890 A-ATGATTGCATTTTGTCAAATACGTGTGAG
65 ATATGAGTGCATTTTGTCAAATACGTGTGAG
* *
382920 GGGATTTATATTAAAATATAATCTAACAAATAAGTAACTTTTTTTAATGAATTTCTTAAAAAAAA
1 GGGATTTACATCAAAATATAATCTAACAAATAAGTAACTTTTTTTAATGAATTTCTTAAAAAAAA
* *
382985 TATGGGTGGATTTTGTCAAA
66 TATGAGTGCATTTTGTCAAA
383005 CGCATGCAGC
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
93 32 0.44
94 15 0.21
95 25 0.35
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.39
Consensus pattern (95 bp):
GGGATTTACATCAAAATATAATCTAACAAATAAGTAACTTTTTTTAATGAATTTCTTAAAAAAAA
TATGAGTGCATTTTGTCAAATACGTGTGAG
Found at i:383020 original size:95 final size:93
Alignment explanation
Indices: 382812--383025 Score: 229
Period size: 93 Copynumber: 2.3 Consensus size: 93
382802 TGTAGTATTA
* * * * *
382812 TCAAATGCATGC-GACGGGATTTACATCAAAGTATAATCTAATAAATAAGTGATTTTTTTATTAA
1 TCAAACGCATGCAG-CGGGATTTACATCAAAATATAATCTAACAAATAAGTAATTTTTTTATGAA
* *
382876 TTTTTTGAAAAAAAAATGATTGCATTTTG
65 TTTCTTGAAAAAAAAATGAGTGCATTTTG
** * *
382905 TCAAATACGTGTG-AG-GGGATTTATATTAAAATATAATCTAACAAATAAGTAACTTTTTTTAAT
1 TC-AA-ACGCATGCAGCGGGATTTACATCAAAATATAATCTAACAAATAAGTAA-TTTTTTT-AT
* *
382968 GAATTTCTT-AAAAAAAATATGGGTGGATTTTG
62 GAATTTCTTGAAAAAAAA-ATGAGTGCATTTTG
383000 TCAAACGCATGCAGCGGGATTTACAT
1 TCAAACGCATGCAGCGGGATTTACAT
383026 AAGACTTCCT
Statistics
Matches: 97, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
93 39 0.40
94 21 0.22
95 37 0.38
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (93 bp):
TCAAACGCATGCAGCGGGATTTACATCAAAATATAATCTAACAAATAAGTAATTTTTTTATGAAT
TTCTTGAAAAAAAAATGAGTGCATTTTG
Found at i:384184 original size:2 final size:2
Alignment explanation
Indices: 384172--384201 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
384162 ATAAATAGAC
*
384172 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
384202 TCTTAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:384697 original size:22 final size:23
Alignment explanation
Indices: 384661--384703 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
384651 CTACACGAAC
**
384661 AAAATTAAATTCAAAT-TTTTCT
1 AAAATTAAACCCAAATGTTTTCT
384683 AAAATTAAACCCAAATGTTTT
1 AAAATTAAACCCAAATGTTTT
384704 GCAACCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAATTAAACCCAAATGTTTTCT
Found at i:385258 original size:95 final size:95
Alignment explanation
Indices: 385052--385661 Score: 658
Period size: 96 Copynumber: 6.4 Consensus size: 95
385042 TACTTGCGAT
* *
385052 AAGTTTTATATTAAAATATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAAATA
1 AAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAA-A
* ***
385117 ATATAGTTGTTTTTTATCAAACGTATGAAGTG-
65 ATATAGCTACCTTTTATCAAACGTATG-AG-GC
* * * *
385149 AAG-TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTATAATGAAATTTTGAAAAAAAA
1 AAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAA
* * *
385213 TATGGCTACCTTTTATCAAACGTGTGCGGC
66 TATAGCTACCTTTTATCAAACGTATGAGGC
* * *
385243 AAGTTTTATATTAAAGTATGATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAACAA
1 AAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAA
* * *
385308 TAT-GATTACCTTTTATCAAACGTATAAGGTG
66 TATAG-CTACCTTTTATCAAACGTATGAGG-C
* * *
385339 GAG-TTTATATTAAAGTATAATTCAATAAATGAGTAATCTTTTTTAATGAAATTTTGAAAAAAAA
1 AAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTG-AAAAAAA
* *
385403 ATATAGCTGCCTTTTATCAAATGCGTGTGA--C
65 ATATAGCTACCTTTTATCAAA--CGTATGAGGC
* *
385434 AAGTTTTATAATAAAGTATAATTCAATAAATGAGTAATCATTTTTAATGAAATTTTGGAAAAAAA
1 AAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTT-GAAAAAAA
* * * **
385499 ATATGGATATCTTTTATCAAACGTATGAGAT
65 ATATAGCTACCTTTTATCAAACGTATGAGGC
** * * * *
385530 GGGATATATATTAAAGTATAATTCAATAAATAAGTAGA-CTTTTTTAATGAAATTTTGGAAAAAA
1 AAGTTTTATATTAAAGTATAATTCAATAAATGAGT-GATCATTTTTAATGAAATTTT-GAAAAAA
* * * *
385594 AATTATAACTGCCTTTTATCAAACGTACGAGGT
64 AA-TATAGCTACCTTTTATCAAACGTATGAGGC
* * * *
385627 AGGATTTATATTAAAATATAATTCAAAAAATGAGT
1 AAGTTTTATATTAAAGTATAATTCAATAAATGAGT
385662 CGTCCTTTTT
Statistics
Matches: 434, Mismatches: 65, Indels: 28
0.82 0.12 0.05
Matches are distributed among these distances:
93 1 0.00
94 11 0.03
95 150 0.35
96 208 0.48
97 59 0.14
98 5 0.01
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.38
Consensus pattern (95 bp):
AAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAA
TATAGCTACCTTTTATCAAACGTATGAGGC
Found at i:385269 original size:191 final size:188
Alignment explanation
Indices: 385052--385678 Score: 789
Period size: 191 Copynumber: 3.3 Consensus size: 188
385042 TACTTGCGAT
385052 AAGTTTTATATTAAAATATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAAATA
1 AAGTTTTATATTAAAATATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAAA-A
* * *
385117 ATATAGTTGTTTTTTATCAAACGTATGAAGTGAAGTTTATATTAAAGTATAATTTAATAAATAAG
65 ATAT-GTTATCTTTTATCAAACGTATGAAGTG-AGTTTATATTAAAGTATAATTCAATAAATAAG
* * * * *
385182 TGATCCTTTATAATGAAATTTTGAAAAAAAATATGGCTACCTTTTATCAAACGTGTGCGGC
128 TGATCTTTTTTAATGAAATTTTGAAAAAAAATATAGCTGCCTTTTATCAAACGTGTGAGGC
* * *
385243 AAGTTTTATATTAAAGTATGATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAACAA
1 AAGTTTTATATTAAAATATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAAAAA
* *
385308 TATGATTACCTTTTATCAAACGTAT-AAGGTGGAGTTTATATTAAAGTATAATTCAATAAATGAG
66 TATG-TTATCTTTTATCAAACGTATGAA-GT-GAGTTTATATTAAAGTATAATTCAATAAATAAG
*
385372 TAATCTTTTTTAATGAAATTTTGAAAAAAAAATATAGCTGCCTTTTATCAAATGCGTGTGA--C
128 TGATCTTTTTTAATGAAATTTTG-AAAAAAAATATAGCTGCCTTTTATCAAA--CGTGTGAGGC
* * * *
385434 AAGTTTTATAATAAAGTATAATTCAATAAATGAGTAATCATTTTTAATGAAATTTTGGAAAAAAA
1 AAGTTTTATATTAAAATATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTT-GAAAAAAA
* * *
385499 ATATGGATATCTTTTATCAAACGTATG-AGATGGGATATATATTAAAGTATAATTCAATAAATAA
65 ATAT-GTTATCTTTTATCAAACGTATGAAG-TGAG-TTTATATTAAAGTATAATTCAATAAATAA
* ** *
385563 GTAGA-CTTTTTTAATGAAATTTTGGAAAAAAAATTATAACTGCCTTTTATCAAACGTACGAGGT
127 GT-GATCTTTTTTAATGAAATTTT-GAAAAAAAA-TATAGCTGCCTTTTATCAAACGTGTGAGGC
* * * * *
385627 AGGATTTATATTAAAATATAATTCAAAAAATGAGTCG-TCCTTTTTAACAAAA
1 AAGTTTTATATTAAAATATAATTCAATAAATGAGT-GATCATTTTTAATAAAA
385679 CTAAGTTTAT
Statistics
Matches: 381, Mismatches: 38, Indels: 32
0.84 0.08 0.07
Matches are distributed among these distances:
189 3 0.01
190 74 0.19
191 148 0.39
192 86 0.23
193 70 0.18
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (188 bp):
AAGTTTTATATTAAAATATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAAAAA
TATGTTATCTTTTATCAAACGTATGAAGTGAGTTTATATTAAAGTATAATTCAATAAATAAGTGA
TCTTTTTTAATGAAATTTTGAAAAAAAATATAGCTGCCTTTTATCAAACGTGTGAGGC
Found at i:390370 original size:26 final size:24
Alignment explanation
Indices: 390341--390402 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
390331 ATTTATTATG
* *
390341 TTAAATAAAATAATAAATTAAAATTT
1 TTAAATAAAATAA-AAAAT-AAATTA
390367 TTAAATTAGAAATAAAAAATAAATTA
1 TTAAA-TA-AAATAAAAAATAAATTA
*
390393 TTAAAAAAAA
1 TTAAATAAAA
390403 AGTTAACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 15 0.48
27 6 0.19
28 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
TTAAATAAAATAAAAAATAAATTA
Found at i:390451 original size:12 final size:12
Alignment explanation
Indices: 390434--390469 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
390424 TAAAACTTTT
390434 TTATAAAAATAA
1 TTATAAAAATAA
390446 TTATAAAAATAA
1 TTATAAAAATAA
390458 --ATAAAAATAA
1 TTATAAAAATAA
390468 TT
1 TT
390470 GAAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTATAAAAATAA
Found at i:390485 original size:22 final size:22
Alignment explanation
Indices: 390438--390485 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
390428 ACTTTTTTAT
* *
390438 AAAAATAATTATAAAAATAAAT
1 AAAAATAATTATAAAAAGAAAC
*
390460 AAAAATAATTGA-AAAAAGGAAC
1 AAAAATAATT-ATAAAAAGAAAC
390482 AAAA
1 AAAA
390486 TGATAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAAATAATTATAAAAAGAAAC
Found at i:394357 original size:95 final size:94
Alignment explanation
Indices: 394120--394976 Score: 816
Period size: 95 Copynumber: 9.0 Consensus size: 94
394110 ATACTTGCGG
* * * * *
394120 TAAGTTTTATATTAAAATATAATTTAATAAATGAGTGATTATTTTTAATAAAATTTTGAAAAAAA
1 TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTG-GAAAAA
* *
394185 TAATATAGTTGCTTTTTATCAAA-CGTATGAA
65 -AATATGGTTGCCTTTTATCAAAGCGTATG-A
* * * * *
394216 GTGAAG-TTTATATTAAAATATAATTTAATAAATAAGTGGTCCTTTTTAATGAAATTTTGGAAAA
1 -T-AAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGGAAAA
* *
394280 AAATATGGTTACCTTTTATCAAACGCGTACGA
64 AAATATGGTTGCCTTTTATCAAA-GCGTATGA
* * *
394312 CAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTT-AAAAAAC
1 TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGGAAAAA-
*
394376 AATATGGTTACCTTTTATCAAA-CGTATGA
65 AATATGGTTGCCTTTTATCAAAGCGTATGA
** * *
394405 GGTGGGATTTATATTAAAATATAATTCAATAAATGAGT-AGTCATTTTTAATGAAATTTTGGAAA
1 --TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGA-TCATTTTTAATGAAATTTTGGAAA
* *
394469 AAAATATGGTTGCCTTTTATCAAACGCATGTGA
63 AAAATATGGTTGCCTTTTATCAAA-GCGTATGA
* * *
394502 TAAGTTTTATAGTAAAGTCTAATTCAATAAATGAGTGACCATTTTTAATGAAATTTTGGAAAAAA
1 TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGGAAAAAA
* * *
394567 ATTATGGATGTCTTTTATTAAA-CGTATGAGA
66 A-TATGGTTGCCTTTTATCAAAGCGTAT--GA
** * * * * * *
394598 TGGGGTTTAGATTAAAGTAAAATTCAATAAATAAGT-AGTCTTTTTTAATGAAATTTTGAAAAAA
1 TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGA-TCATTTTTAATGAAATTTTGGAAAAA
*
394662 AATTATGATTGCCTTTTATCAAA-CGTATGA
65 AA-TATGGTTGCCTTTTATCAAAGCGTATGA
** * * * *
394692 GGTGGGATTTATATTAAAGTATAATTCAAAAAATGAGTGGTCCTTTTTAATGAAATTTTGGAAAA
1 --TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGGAAAA
** * ** *
394757 AAATATGACTGTCTTTTATCAAACGCGTGCGG
64 AAATATGGTTGCCTTTTATCAAA-GCGTATGA
* * * **
394789 CAAGTTTTATATTAAAGTATAATTTAATAAATGAGTGGTCATTTTTAATGAAATGTTTTAAAAAA
1 TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAA--TTTTGGAAAA
* *
394854 AAAGTATGGTTGTCTTTTAT-AAAACGTATGA
64 AAA-TATGGTTGCCTTTTATCAAAGCGTATGA
* * * * * *
394885 GGTGAGATTTATATTAAAATATAATTCAATAAATGAGTGGTC-CTTTGAATGAAATTTTGGAAAA
1 --TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGGAAAA
* **
394949 AAATATGGCTATCTTTTATCAAATGCGT
64 AAATATGGTTGCCTTTTATCAAA-GCGT
394977 GCAGCAAATT
Statistics
Matches: 636, Mismatches: 96, Indels: 57
0.81 0.12 0.07
Matches are distributed among these distances:
93 6 0.01
94 28 0.04
95 293 0.46
96 170 0.27
97 87 0.14
98 52 0.08
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (94 bp):
TAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGGAAAAAA
ATATGGTTGCCTTTTATCAAAGCGTATGA
Found at i:394993 original size:287 final size:282
Alignment explanation
Indices: 394125--394971 Score: 1004
Period size: 287 Copynumber: 3.0 Consensus size: 282
394115 TGCGGTAAGT
* * * *
394125 TTTATATTAAAATATAATTTAATAAATGAGTGATTATTTTTAATAAAATTTT-GAAAAAAATAAT
1 TTTATATTAAAATATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGGAAAAAAAT-AT
* * *
394189 -ATAGTTGCTTTTTATCAAACGTATGAAGTGAAG-TTTATATTAAAATATAATTTAATAAATAAG
65 GAT-G-T-C-TTTTATCAAACGCATG-AG-GAAGTTTTATATTAAAGTATAATTTAATAAATGAG
* ** * * **
394252 TGGTCCTTTTTAATGAAATTTTGGAAAAAAATATGGTTACCTTTTATCAAACGCGTACGA-CAAG
124 TGGTCATTTTTAATGAAATTTTGGAAAAAAATATGGTTGTCTTTTAT-AAA-ACGTATGAGTGAG
* * *
394316 TTTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTT-AAAAAACAATA
187 ATTTATATTAAAGTATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGAAAAAA-AATA
394380 TGGTTACCTTTTATCAAACGTATGAGGTGGGA
251 TGGTTACCTTTTATCAAACGTATGAGGTGGGA
*
394412 TTTATATTAAAATATAATTCAATAAATGAGTAGTCATTTTTAATGAAATTTTGGAAAAAAATATG
1 TTTATATTAAAATATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGGAAAAAAATAT-
* * * * * * * **
394477 GTTGCCTTTTATCAAACGCATGTGATAAGTTTTATAGTAAAGTCTAATTCAATAAATGAGTGACC
65 GATGTCTTTTATCAAACGCATGAG-GAAGTTTTATATTAAAGTATAATTTAATAAATGAGTGGTC
* * * *
394542 ATTTTTAATGAAATTTTGGAAAAAAATTATGGATGTCTTTTATTAAACGTATGAGATGGGGTTTA
129 ATTTTTAATGAAATTTTGGAAAAAAA-TATGGTTGTCTTTTATAAAACGTATGAG-TGAGATTTA
* * * * * *
394607 GATTAAAGTAAAATTCAATAAATAAGTAGTCTTTTTTAATGAAATTTTGAAAAAAAATTATGATT
192 TATTAAAGTATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGAAAAAAAA-TATGGTT
*
394672 GCCTTTTATCAAACGTATGAGGTGGGA
256 ACCTTTTATCAAACGTATGAGGTGGGA
* * *
394699 TTTATATTAAAGTATAATTCAAAAAATGAGTGGTCCTTTTTAATGAAATTTTGGAAAAAAATATG
1 TTTATATTAAAATATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGGAAAAAAATATG
* *
394764 ACTGTCTTTTATCAAACGCGTGCGGCAAGTTTTATATTAAAGTATAATTTAATAAATGAGTGGTC
66 A-TGTCTTTTATCAAACGCATGAGG-AAGTTTTATATTAAAGTATAATTTAATAAATGAGTGGTC
**
394829 ATTTTTAATGAAATGTTTTAAAAAAAAAGTATGGTTGTCTTTTATAAAACGTATGAGGTGAGATT
129 ATTTTTAATGAAA--TTTTGGAAAAAAA-TATGGTTGTCTTTTATAAAACGTATGA-GTGAGATT
* * * * *
394894 TATATTAAAATATAATTCAATAAATGAGTGGTC-CTTTGAATGAAATTTTGGAAAAAAATATGGC
190 TATATTAAAGTATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGAAAAAAAATATGGT
*
394958 TATCTTTTATCAAA
255 TACCTTTTATCAAA
394972 TGCGTGCAGC
Statistics
Matches: 475, Mismatches: 71, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
284 10 0.02
285 70 0.15
286 63 0.13
287 229 0.48
288 32 0.07
289 70 0.15
290 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (282 bp):
TTTATATTAAAATATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGGAAAAAAATATG
ATGTCTTTTATCAAACGCATGAGGAAGTTTTATATTAAAGTATAATTTAATAAATGAGTGGTCAT
TTTTAATGAAATTTTGGAAAAAAATATGGTTGTCTTTTATAAAACGTATGAGTGAGATTTATATT
AAAGTATAATTCAATAAATGAGTGGTCATTTTTAATGAAATTTTGAAAAAAAATATGGTTACCTT
TTATCAAACGTATGAGGTGGGA
Found at i:397764 original size:26 final size:27
Alignment explanation
Indices: 397721--397789 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
397711 AACTATAGCC
*
397721 TTCTTCTATTTTAATTCTTCTTTAC-TTT
1 TTCTTCTATTTT-TTTCTT-TTTACTTTT
* *
397749 TTC-TCTTTTTTTTTCTTTTTTCTTTT
1 TTCTTCTATTTTTTTCTTTTTACTTTT
397775 TTCTTCTATTTTTTT
1 TTCTTCTATTTTTTT
397790 ATCGAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 4 0.11
26 11 0.31
27 17 0.49
28 3 0.09
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (27 bp):
TTCTTCTATTTTTTTCTTTTTACTTTT
Found at i:397767 original size:17 final size:17
Alignment explanation
Indices: 397747--397781 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
397737 CTTCTTTACT
*
397747 TTTTCTCTTTTTTTTTC
1 TTTTCTCTTTTTTCTTC
*
397764 TTTTTTCTTTTTTCTTC
1 TTTTCTCTTTTTTCTTC
397781 T
1 T
397782 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTCTTTTTTCTTC
Found at i:397786 original size:17 final size:17
Alignment explanation
Indices: 397752--397786 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
397742 TTACTTTTTC
* *
397752 TCTTTTTTTTTCTTTTT
1 TCTTTTTTCTTCTATTT
397769 TCTTTTTTCTTCTATTT
1 TCTTTTTTCTTCTATTT
397786 T
1 T
397787 TTTATCGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TCTTTTTTCTTCTATTT
Found at i:397786 original size:19 final size:17
Alignment explanation
Indices: 397741--397788 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
397731 TTAATTCTTC
397741 TTTACTTTTTCTCTTTTTT
1 TTTA-TTTTT-TCTTTTTT
*
397760 TTTCTTTTTTCTTTTTT
1 TTTATTTTTTCTTTTTT
397777 CTTCTATTTTTT
1 -TT-TATTTTTT
397789 TATCGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTTCTTTTTT
Found at i:397788 original size:14 final size:13
Alignment explanation
Indices: 397721--397789 Score: 59
Period size: 14 Copynumber: 5.1 Consensus size: 13
397711 AACTATAGCC
**
397721 TTCTTCTATTTTAA
1 TTCTTCT-TTTTTT
*
397735 TTCTTCTTTACTTT
1 TTCTTCTTT-TTTT
397749 TTC-TCTTTTTTT
1 TTCTTCTTTTTTT
*
397761 TTCTTTTTTCTTTT
1 TTCTTCTTT-TTTT
397775 TTCTTCTATTTTTT
1 TTCTTCT-TTTTTT
397789 T
1 T
397790 ATCGAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
12 6 0.13
13 11 0.24
14 26 0.58
15 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTCTTTTTTT
Found at i:399893 original size:26 final size:24
Alignment explanation
Indices: 399864--399925 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
399854 ATTTATTATG
* *
399864 TTAAATAAAATAATAAATTAAAATTT
1 TTAAATAAAATAA-AAAAT-AAATTA
399890 TTAAATTAGAAATAAAAAATAAATTA
1 TTAAA-TA-AAATAAAAAATAAATTA
*
399916 TTAAAAAAAA
1 TTAAATAAAA
399926 GTTAACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 15 0.48
27 6 0.19
28 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
TTAAATAAAATAAAAAATAAATTA
Found at i:399973 original size:12 final size:12
Alignment explanation
Indices: 399956--399991 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
399946 TAAAACTTTT
399956 TTATAAAAATAA
1 TTATAAAAATAA
399968 TTATAAAAATAA
1 TTATAAAAATAA
399980 --ATAAAAATAA
1 TTATAAAAATAA
399990 TT
1 TT
399992 GAAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTATAAAAATAA
Done.