Multiple sequence alignment - TraesCS2A01G513600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G513600 chr2A 100.000 2306 0 0 1 2306 738212691 738214996 0.000000e+00 4259.0
1 TraesCS2A01G513600 chr2A 95.205 730 29 2 763 1489 738205888 738206614 0.000000e+00 1149.0
2 TraesCS2A01G513600 chr2A 85.274 584 52 19 1488 2041 738206938 738207517 2.570000e-159 571.0
3 TraesCS2A01G513600 chr2A 89.355 310 33 0 456 765 745560855 745560546 7.720000e-105 390.0
4 TraesCS2A01G513600 chr2A 87.937 315 38 0 452 766 765803724 765804038 2.800000e-99 372.0
5 TraesCS2A01G513600 chr2A 87.829 304 37 0 458 761 161366248 161365945 7.830000e-95 357.0
6 TraesCS2A01G513600 chr2A 97.159 176 2 1 1 176 738205456 738205628 6.230000e-76 294.0
7 TraesCS2A01G513600 chr2A 90.686 204 8 4 266 458 738205687 738205890 6.320000e-66 261.0
8 TraesCS2A01G513600 chr2A 92.857 42 1 2 1881 1922 159097021 159096982 2.470000e-05 60.2
9 TraesCS2A01G513600 chr2D 93.257 1053 50 5 763 1801 606648225 606649270 0.000000e+00 1531.0
10 TraesCS2A01G513600 chr2D 92.179 179 10 2 1 178 606647772 606647947 1.370000e-62 250.0
11 TraesCS2A01G513600 chr2B 89.239 920 71 16 763 1676 738178838 738179735 0.000000e+00 1125.0
12 TraesCS2A01G513600 chr2B 88.235 306 36 0 458 763 304004905 304004600 1.300000e-97 366.0
13 TraesCS2A01G513600 chr2B 92.829 251 18 0 2056 2306 236800754 236800504 4.680000e-97 364.0
14 TraesCS2A01G513600 chr2B 81.356 472 39 27 1 458 738178404 738178840 2.840000e-89 339.0
15 TraesCS2A01G513600 chr2B 96.212 132 5 0 1670 1801 738233103 738233234 1.390000e-52 217.0
16 TraesCS2A01G513600 chr1D 93.962 265 15 1 2042 2306 46359875 46359612 1.280000e-107 399.0
17 TraesCS2A01G513600 chr1D 92.578 256 19 0 2051 2306 202952558 202952303 3.620000e-98 368.0
18 TraesCS2A01G513600 chr5A 89.274 317 34 0 449 765 681937561 681937245 4.620000e-107 398.0
19 TraesCS2A01G513600 chr5A 88.136 59 4 3 1869 1926 528908672 528908616 1.480000e-07 67.6
20 TraesCS2A01G513600 chr1A 89.644 309 32 0 458 766 232326426 232326118 5.970000e-106 394.0
21 TraesCS2A01G513600 chr5D 93.798 258 16 0 2049 2306 39061846 39062103 2.780000e-104 388.0
22 TraesCS2A01G513600 chr5D 92.157 255 20 0 2052 2306 118067769 118067515 6.060000e-96 361.0
23 TraesCS2A01G513600 chrUn 89.251 307 31 2 458 763 33308344 33308039 1.290000e-102 383.0
24 TraesCS2A01G513600 chr3D 94.094 254 12 1 2056 2306 587533331 587533078 1.290000e-102 383.0
25 TraesCS2A01G513600 chr6D 93.227 251 17 0 2056 2306 358092374 358092124 1.010000e-98 370.0
26 TraesCS2A01G513600 chr6D 92.549 255 19 0 2052 2306 346460939 346460685 1.300000e-97 366.0
27 TraesCS2A01G513600 chr1B 92.105 266 15 5 2042 2306 65704667 65704927 1.010000e-98 370.0
28 TraesCS2A01G513600 chr1B 90.909 44 3 1 1876 1918 70501521 70501564 8.900000e-05 58.4
29 TraesCS2A01G513600 chr4A 87.702 309 38 0 458 766 66892566 66892258 6.060000e-96 361.0
30 TraesCS2A01G513600 chr7A 86.452 310 42 0 456 765 149308605 149308914 7.890000e-90 340.0
31 TraesCS2A01G513600 chr5B 90.385 52 4 1 1877 1927 503081293 503081242 1.480000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G513600 chr2A 738212691 738214996 2305 False 4259.00 4259 100.0000 1 2306 1 chr2A.!!$F1 2305
1 TraesCS2A01G513600 chr2A 738205456 738207517 2061 False 568.75 1149 92.0810 1 2041 4 chr2A.!!$F3 2040
2 TraesCS2A01G513600 chr2D 606647772 606649270 1498 False 890.50 1531 92.7180 1 1801 2 chr2D.!!$F1 1800
3 TraesCS2A01G513600 chr2B 738178404 738179735 1331 False 732.00 1125 85.2975 1 1676 2 chr2B.!!$F2 1675

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
209 215 0.02811 CCTTCGTACTACGTACCGGC 59.972 60.0 0.0 0.0 43.14 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1389 0.107945 AGAAGAGCACCGCCAGAATC 60.108 55.0 0.0 0.0 0.0 2.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 6.515035 GCTTTTAGTTTTGCTACAGTCCACAT 60.515 38.462 0.00 0.00 0.00 3.21
64 66 7.308348 GCTTTTAGTTTTGCTACAGTCCACATA 60.308 37.037 0.00 0.00 0.00 2.29
65 67 7.429636 TTTAGTTTTGCTACAGTCCACATAC 57.570 36.000 0.00 0.00 0.00 2.39
101 103 5.818336 TCTTTTGGTTCGAGTTGTGATTGTA 59.182 36.000 0.00 0.00 0.00 2.41
178 180 0.459237 CGCAGAACTGGCTGGAGTAG 60.459 60.000 3.99 0.00 36.41 2.57
179 181 0.610687 GCAGAACTGGCTGGAGTAGT 59.389 55.000 3.99 0.00 36.41 2.73
180 182 1.674221 GCAGAACTGGCTGGAGTAGTG 60.674 57.143 3.99 0.00 36.41 2.74
181 183 1.066573 CAGAACTGGCTGGAGTAGTGG 60.067 57.143 0.00 0.00 32.26 4.00
182 184 1.203187 AGAACTGGCTGGAGTAGTGGA 60.203 52.381 0.00 0.00 0.00 4.02
183 185 0.977395 AACTGGCTGGAGTAGTGGAC 59.023 55.000 0.00 0.00 0.00 4.02
184 186 0.115349 ACTGGCTGGAGTAGTGGACT 59.885 55.000 0.00 0.00 42.90 3.85
185 187 1.358103 ACTGGCTGGAGTAGTGGACTA 59.642 52.381 0.00 0.00 39.06 2.59
199 205 3.265479 AGTGGACTACCTACCTTCGTACT 59.735 47.826 0.00 0.00 37.04 2.73
200 206 4.471386 AGTGGACTACCTACCTTCGTACTA 59.529 45.833 0.00 0.00 37.04 1.82
201 207 4.572795 GTGGACTACCTACCTTCGTACTAC 59.427 50.000 0.00 0.00 37.04 2.73
202 208 3.804873 GGACTACCTACCTTCGTACTACG 59.195 52.174 1.93 1.93 44.19 3.51
203 209 4.434520 GACTACCTACCTTCGTACTACGT 58.565 47.826 8.42 0.00 43.14 3.57
204 210 5.451520 GGACTACCTACCTTCGTACTACGTA 60.452 48.000 8.42 0.00 43.14 3.57
205 211 5.349809 ACTACCTACCTTCGTACTACGTAC 58.650 45.833 8.42 0.00 43.14 3.67
206 212 3.532542 ACCTACCTTCGTACTACGTACC 58.467 50.000 8.42 0.00 43.14 3.34
207 213 2.540101 CCTACCTTCGTACTACGTACCG 59.460 54.545 8.42 0.00 43.14 4.02
208 214 1.369625 ACCTTCGTACTACGTACCGG 58.630 55.000 0.00 0.00 43.14 5.28
209 215 0.028110 CCTTCGTACTACGTACCGGC 59.972 60.000 0.00 0.00 43.14 6.13
210 216 1.009829 CTTCGTACTACGTACCGGCT 58.990 55.000 0.00 0.00 43.14 5.52
211 217 0.726827 TTCGTACTACGTACCGGCTG 59.273 55.000 0.00 0.00 43.14 4.85
212 218 1.089481 TCGTACTACGTACCGGCTGG 61.089 60.000 11.02 11.02 43.14 4.85
213 219 1.089481 CGTACTACGTACCGGCTGGA 61.089 60.000 21.41 0.00 35.81 3.86
214 220 0.659957 GTACTACGTACCGGCTGGAG 59.340 60.000 21.41 11.68 39.21 3.86
215 221 0.253044 TACTACGTACCGGCTGGAGT 59.747 55.000 21.41 16.98 39.21 3.85
216 222 0.253044 ACTACGTACCGGCTGGAGTA 59.747 55.000 21.41 17.20 39.21 2.59
217 223 0.942962 CTACGTACCGGCTGGAGTAG 59.057 60.000 21.41 21.98 39.21 2.57
218 224 0.253044 TACGTACCGGCTGGAGTAGT 59.747 55.000 21.41 14.46 39.21 2.73
219 225 1.310933 ACGTACCGGCTGGAGTAGTG 61.311 60.000 21.41 4.03 39.21 2.74
220 226 1.028330 CGTACCGGCTGGAGTAGTGA 61.028 60.000 21.41 0.00 39.21 3.41
221 227 1.180029 GTACCGGCTGGAGTAGTGAA 58.820 55.000 21.41 0.00 39.21 3.18
222 228 1.135170 GTACCGGCTGGAGTAGTGAAC 60.135 57.143 21.41 0.00 39.21 3.18
223 229 0.542232 ACCGGCTGGAGTAGTGAACT 60.542 55.000 21.41 0.00 42.80 3.01
224 230 0.108615 CCGGCTGGAGTAGTGAACTG 60.109 60.000 5.28 0.00 39.07 3.16
225 231 0.108615 CGGCTGGAGTAGTGAACTGG 60.109 60.000 0.00 0.00 39.07 4.00
226 232 0.391793 GGCTGGAGTAGTGAACTGGC 60.392 60.000 0.00 0.00 39.07 4.85
227 233 0.610687 GCTGGAGTAGTGAACTGGCT 59.389 55.000 0.00 0.00 39.07 4.75
228 234 1.674221 GCTGGAGTAGTGAACTGGCTG 60.674 57.143 0.00 0.00 39.07 4.85
229 235 0.976641 TGGAGTAGTGAACTGGCTGG 59.023 55.000 0.00 0.00 39.07 4.85
230 236 1.267121 GGAGTAGTGAACTGGCTGGA 58.733 55.000 0.00 0.00 39.07 3.86
231 237 1.205893 GGAGTAGTGAACTGGCTGGAG 59.794 57.143 0.00 0.00 39.07 3.86
232 238 1.205893 GAGTAGTGAACTGGCTGGAGG 59.794 57.143 0.00 0.00 39.07 4.30
233 239 1.203187 AGTAGTGAACTGGCTGGAGGA 60.203 52.381 0.00 0.00 36.93 3.71
234 240 1.623811 GTAGTGAACTGGCTGGAGGAA 59.376 52.381 0.00 0.00 0.00 3.36
235 241 0.689623 AGTGAACTGGCTGGAGGAAG 59.310 55.000 0.00 0.00 0.00 3.46
236 242 0.398318 GTGAACTGGCTGGAGGAAGT 59.602 55.000 0.00 0.00 0.00 3.01
237 243 1.623811 GTGAACTGGCTGGAGGAAGTA 59.376 52.381 0.00 0.00 0.00 2.24
238 244 1.623811 TGAACTGGCTGGAGGAAGTAC 59.376 52.381 0.00 0.00 0.00 2.73
256 262 5.344743 AGTACTATTCTGTGGACACCATG 57.655 43.478 0.00 0.00 35.28 3.66
257 263 5.023452 AGTACTATTCTGTGGACACCATGA 58.977 41.667 0.00 0.00 35.28 3.07
258 264 4.207891 ACTATTCTGTGGACACCATGAC 57.792 45.455 0.00 0.00 35.28 3.06
259 265 2.496899 ATTCTGTGGACACCATGACC 57.503 50.000 0.00 0.00 35.28 4.02
261 267 1.361204 TCTGTGGACACCATGACCAT 58.639 50.000 3.41 0.00 43.44 3.55
262 268 1.278985 TCTGTGGACACCATGACCATC 59.721 52.381 3.41 0.00 43.44 3.51
332 360 0.173481 ACGGAGGACATGTGTCGATG 59.827 55.000 1.15 0.00 45.65 3.84
366 417 0.250124 TCGTCGCCACACCTCAATTT 60.250 50.000 0.00 0.00 0.00 1.82
369 420 0.537143 TCGCCACACCTCAATTTGCT 60.537 50.000 0.00 0.00 0.00 3.91
397 448 4.254709 TCAGCAGGCCGCACTGTT 62.255 61.111 19.30 0.00 46.13 3.16
411 464 2.469826 CACTGTTAAGCTGTGTCGTGA 58.530 47.619 0.00 0.00 40.68 4.35
455 508 2.505407 TGAGTCCATTCCGTTCCATGAT 59.495 45.455 0.00 0.00 0.00 2.45
456 509 3.709141 TGAGTCCATTCCGTTCCATGATA 59.291 43.478 0.00 0.00 0.00 2.15
457 510 4.163268 TGAGTCCATTCCGTTCCATGATAA 59.837 41.667 0.00 0.00 0.00 1.75
458 511 4.708177 AGTCCATTCCGTTCCATGATAAG 58.292 43.478 0.00 0.00 0.00 1.73
459 512 3.815401 GTCCATTCCGTTCCATGATAAGG 59.185 47.826 0.00 0.00 0.00 2.69
460 513 3.149196 CCATTCCGTTCCATGATAAGGG 58.851 50.000 11.25 11.25 34.01 3.95
461 514 2.341846 TTCCGTTCCATGATAAGGGC 57.658 50.000 12.19 0.00 33.00 5.19
462 515 1.507140 TCCGTTCCATGATAAGGGCT 58.493 50.000 12.19 0.00 33.00 5.19
463 516 1.843851 TCCGTTCCATGATAAGGGCTT 59.156 47.619 12.19 0.00 33.00 4.35
464 517 2.241176 TCCGTTCCATGATAAGGGCTTT 59.759 45.455 12.19 0.00 33.00 3.51
465 518 3.023832 CCGTTCCATGATAAGGGCTTTT 58.976 45.455 0.00 0.00 0.00 2.27
466 519 3.447229 CCGTTCCATGATAAGGGCTTTTT 59.553 43.478 0.00 0.00 0.00 1.94
500 553 9.695155 AAGAAATTTTATAGGATTTTCGGAGGA 57.305 29.630 0.00 0.00 0.00 3.71
501 554 9.868160 AGAAATTTTATAGGATTTTCGGAGGAT 57.132 29.630 0.00 0.00 0.00 3.24
504 557 9.640952 AATTTTATAGGATTTTCGGAGGATTGA 57.359 29.630 0.00 0.00 0.00 2.57
505 558 9.640952 ATTTTATAGGATTTTCGGAGGATTGAA 57.359 29.630 0.00 0.00 0.00 2.69
506 559 9.469097 TTTTATAGGATTTTCGGAGGATTGAAA 57.531 29.630 0.00 0.00 32.57 2.69
507 560 9.640952 TTTATAGGATTTTCGGAGGATTGAAAT 57.359 29.630 0.00 0.00 34.35 2.17
508 561 9.640952 TTATAGGATTTTCGGAGGATTGAAATT 57.359 29.630 0.00 0.00 34.35 1.82
509 562 6.857437 AGGATTTTCGGAGGATTGAAATTT 57.143 33.333 0.00 0.00 34.35 1.82
510 563 7.244886 AGGATTTTCGGAGGATTGAAATTTT 57.755 32.000 0.00 0.00 34.35 1.82
511 564 7.679783 AGGATTTTCGGAGGATTGAAATTTTT 58.320 30.769 0.00 0.00 34.35 1.94
512 565 8.811994 AGGATTTTCGGAGGATTGAAATTTTTA 58.188 29.630 0.00 0.00 34.35 1.52
513 566 9.430623 GGATTTTCGGAGGATTGAAATTTTTAA 57.569 29.630 0.00 0.00 34.35 1.52
556 609 9.878737 AATCTTTTGATTCATAGGATTGGATCT 57.121 29.630 11.73 0.00 45.26 2.75
557 610 8.915057 TCTTTTGATTCATAGGATTGGATCTC 57.085 34.615 0.00 0.00 33.45 2.75
558 611 8.496916 TCTTTTGATTCATAGGATTGGATCTCA 58.503 33.333 0.00 0.00 33.45 3.27
559 612 9.298250 CTTTTGATTCATAGGATTGGATCTCAT 57.702 33.333 0.00 0.00 33.45 2.90
623 676 7.855784 AGAAAATTTAACATCCCCTTCAACT 57.144 32.000 0.00 0.00 0.00 3.16
624 677 8.262601 AGAAAATTTAACATCCCCTTCAACTT 57.737 30.769 0.00 0.00 0.00 2.66
625 678 8.367911 AGAAAATTTAACATCCCCTTCAACTTC 58.632 33.333 0.00 0.00 0.00 3.01
626 679 7.855784 AAATTTAACATCCCCTTCAACTTCT 57.144 32.000 0.00 0.00 0.00 2.85
627 680 7.855784 AATTTAACATCCCCTTCAACTTCTT 57.144 32.000 0.00 0.00 0.00 2.52
628 681 7.855784 ATTTAACATCCCCTTCAACTTCTTT 57.144 32.000 0.00 0.00 0.00 2.52
629 682 7.669089 TTTAACATCCCCTTCAACTTCTTTT 57.331 32.000 0.00 0.00 0.00 2.27
630 683 7.669089 TTAACATCCCCTTCAACTTCTTTTT 57.331 32.000 0.00 0.00 0.00 1.94
631 684 8.770010 TTAACATCCCCTTCAACTTCTTTTTA 57.230 30.769 0.00 0.00 0.00 1.52
632 685 6.650427 ACATCCCCTTCAACTTCTTTTTAC 57.350 37.500 0.00 0.00 0.00 2.01
633 686 6.133356 ACATCCCCTTCAACTTCTTTTTACA 58.867 36.000 0.00 0.00 0.00 2.41
634 687 6.609616 ACATCCCCTTCAACTTCTTTTTACAA 59.390 34.615 0.00 0.00 0.00 2.41
635 688 7.290014 ACATCCCCTTCAACTTCTTTTTACAAT 59.710 33.333 0.00 0.00 0.00 2.71
636 689 7.669089 TCCCCTTCAACTTCTTTTTACAATT 57.331 32.000 0.00 0.00 0.00 2.32
637 690 7.722363 TCCCCTTCAACTTCTTTTTACAATTC 58.278 34.615 0.00 0.00 0.00 2.17
638 691 6.929049 CCCCTTCAACTTCTTTTTACAATTCC 59.071 38.462 0.00 0.00 0.00 3.01
639 692 7.202001 CCCCTTCAACTTCTTTTTACAATTCCT 60.202 37.037 0.00 0.00 0.00 3.36
640 693 8.204160 CCCTTCAACTTCTTTTTACAATTCCTT 58.796 33.333 0.00 0.00 0.00 3.36
641 694 9.599866 CCTTCAACTTCTTTTTACAATTCCTTT 57.400 29.630 0.00 0.00 0.00 3.11
652 705 9.833917 TTTTTACAATTCCTTTATTTTTCCGGT 57.166 25.926 0.00 0.00 0.00 5.28
653 706 8.819643 TTTACAATTCCTTTATTTTTCCGGTG 57.180 30.769 0.00 0.00 0.00 4.94
654 707 5.789521 ACAATTCCTTTATTTTTCCGGTGG 58.210 37.500 0.00 0.00 0.00 4.61
655 708 3.945981 TTCCTTTATTTTTCCGGTGGC 57.054 42.857 0.00 0.00 0.00 5.01
656 709 2.877866 TCCTTTATTTTTCCGGTGGCA 58.122 42.857 0.00 0.00 0.00 4.92
657 710 3.436243 TCCTTTATTTTTCCGGTGGCAT 58.564 40.909 0.00 0.00 0.00 4.40
658 711 3.445805 TCCTTTATTTTTCCGGTGGCATC 59.554 43.478 0.00 0.00 0.00 3.91
659 712 3.194542 CCTTTATTTTTCCGGTGGCATCA 59.805 43.478 0.00 0.00 0.00 3.07
660 713 4.322349 CCTTTATTTTTCCGGTGGCATCAA 60.322 41.667 0.00 0.00 0.00 2.57
661 714 4.873746 TTATTTTTCCGGTGGCATCAAA 57.126 36.364 0.00 0.00 0.00 2.69
662 715 2.517650 TTTTTCCGGTGGCATCAAAC 57.482 45.000 0.00 0.00 0.00 2.93
663 716 1.403814 TTTTCCGGTGGCATCAAACA 58.596 45.000 0.00 0.00 0.00 2.83
664 717 1.403814 TTTCCGGTGGCATCAAACAA 58.596 45.000 0.00 0.00 0.00 2.83
665 718 1.626686 TTCCGGTGGCATCAAACAAT 58.373 45.000 0.00 0.00 0.00 2.71
666 719 1.173043 TCCGGTGGCATCAAACAATC 58.827 50.000 0.00 0.00 0.00 2.67
667 720 0.887247 CCGGTGGCATCAAACAATCA 59.113 50.000 0.00 0.00 0.00 2.57
668 721 1.477700 CCGGTGGCATCAAACAATCAT 59.522 47.619 0.00 0.00 0.00 2.45
669 722 2.094078 CCGGTGGCATCAAACAATCATT 60.094 45.455 0.00 0.00 0.00 2.57
670 723 3.130164 CCGGTGGCATCAAACAATCATTA 59.870 43.478 0.00 0.00 0.00 1.90
671 724 4.104776 CGGTGGCATCAAACAATCATTAC 58.895 43.478 0.00 0.00 0.00 1.89
672 725 4.142403 CGGTGGCATCAAACAATCATTACT 60.142 41.667 0.00 0.00 0.00 2.24
673 726 5.065859 CGGTGGCATCAAACAATCATTACTA 59.934 40.000 0.00 0.00 0.00 1.82
674 727 6.404184 CGGTGGCATCAAACAATCATTACTAA 60.404 38.462 0.00 0.00 0.00 2.24
675 728 7.491682 GGTGGCATCAAACAATCATTACTAAT 58.508 34.615 0.00 0.00 0.00 1.73
676 729 7.981225 GGTGGCATCAAACAATCATTACTAATT 59.019 33.333 0.00 0.00 0.00 1.40
677 730 9.023967 GTGGCATCAAACAATCATTACTAATTC 57.976 33.333 0.00 0.00 0.00 2.17
678 731 8.970020 TGGCATCAAACAATCATTACTAATTCT 58.030 29.630 0.00 0.00 0.00 2.40
700 753 7.750229 TCTATAGAATTCAAATGGACATGCC 57.250 36.000 8.44 0.00 37.10 4.40
708 761 4.819783 TGGACATGCCACTCCAAC 57.180 55.556 4.93 0.00 43.33 3.77
709 762 1.074775 TGGACATGCCACTCCAACC 59.925 57.895 4.93 0.00 43.33 3.77
710 763 1.678970 GGACATGCCACTCCAACCC 60.679 63.158 0.00 0.00 36.34 4.11
711 764 1.380302 GACATGCCACTCCAACCCT 59.620 57.895 0.00 0.00 0.00 4.34
712 765 0.618458 GACATGCCACTCCAACCCTA 59.382 55.000 0.00 0.00 0.00 3.53
713 766 0.328258 ACATGCCACTCCAACCCTAC 59.672 55.000 0.00 0.00 0.00 3.18
714 767 0.327924 CATGCCACTCCAACCCTACA 59.672 55.000 0.00 0.00 0.00 2.74
715 768 0.328258 ATGCCACTCCAACCCTACAC 59.672 55.000 0.00 0.00 0.00 2.90
716 769 0.766674 TGCCACTCCAACCCTACACT 60.767 55.000 0.00 0.00 0.00 3.55
717 770 0.400594 GCCACTCCAACCCTACACTT 59.599 55.000 0.00 0.00 0.00 3.16
718 771 1.202891 GCCACTCCAACCCTACACTTT 60.203 52.381 0.00 0.00 0.00 2.66
719 772 2.751816 GCCACTCCAACCCTACACTTTT 60.752 50.000 0.00 0.00 0.00 2.27
720 773 3.562182 CCACTCCAACCCTACACTTTTT 58.438 45.455 0.00 0.00 0.00 1.94
721 774 3.568430 CCACTCCAACCCTACACTTTTTC 59.432 47.826 0.00 0.00 0.00 2.29
722 775 4.461198 CACTCCAACCCTACACTTTTTCT 58.539 43.478 0.00 0.00 0.00 2.52
723 776 5.455612 CCACTCCAACCCTACACTTTTTCTA 60.456 44.000 0.00 0.00 0.00 2.10
724 777 6.238648 CACTCCAACCCTACACTTTTTCTAT 58.761 40.000 0.00 0.00 0.00 1.98
725 778 6.715264 CACTCCAACCCTACACTTTTTCTATT 59.285 38.462 0.00 0.00 0.00 1.73
726 779 6.940867 ACTCCAACCCTACACTTTTTCTATTC 59.059 38.462 0.00 0.00 0.00 1.75
727 780 6.243148 TCCAACCCTACACTTTTTCTATTCC 58.757 40.000 0.00 0.00 0.00 3.01
728 781 6.045106 TCCAACCCTACACTTTTTCTATTCCT 59.955 38.462 0.00 0.00 0.00 3.36
729 782 7.238096 TCCAACCCTACACTTTTTCTATTCCTA 59.762 37.037 0.00 0.00 0.00 2.94
730 783 7.336176 CCAACCCTACACTTTTTCTATTCCTAC 59.664 40.741 0.00 0.00 0.00 3.18
731 784 6.637657 ACCCTACACTTTTTCTATTCCTACG 58.362 40.000 0.00 0.00 0.00 3.51
732 785 6.212187 ACCCTACACTTTTTCTATTCCTACGT 59.788 38.462 0.00 0.00 0.00 3.57
733 786 7.101700 CCCTACACTTTTTCTATTCCTACGTT 58.898 38.462 0.00 0.00 0.00 3.99
734 787 7.605309 CCCTACACTTTTTCTATTCCTACGTTT 59.395 37.037 0.00 0.00 0.00 3.60
735 788 8.996271 CCTACACTTTTTCTATTCCTACGTTTT 58.004 33.333 0.00 0.00 0.00 2.43
760 813 9.705290 TTTAAAATCCTACAAATCAAAGAAGCC 57.295 29.630 0.00 0.00 0.00 4.35
761 814 5.921962 AATCCTACAAATCAAAGAAGCCC 57.078 39.130 0.00 0.00 0.00 5.19
770 823 7.508687 ACAAATCAAAGAAGCCCTAAAACAAT 58.491 30.769 0.00 0.00 0.00 2.71
839 896 1.134848 AGTGCTCTTCGCTCTGGAATC 60.135 52.381 0.00 0.00 40.69 2.52
840 897 0.176680 TGCTCTTCGCTCTGGAATCC 59.823 55.000 0.00 0.00 40.11 3.01
841 898 0.463620 GCTCTTCGCTCTGGAATCCT 59.536 55.000 0.00 0.00 35.14 3.24
883 943 0.526662 GTCAGGTCCGTGGTGACTAG 59.473 60.000 2.46 0.00 38.06 2.57
1647 2052 2.225491 CCAACCACACGGACTACAAATG 59.775 50.000 0.00 0.00 35.59 2.32
1752 2163 2.296752 TCGTCCGAACAGGTTTCACATA 59.703 45.455 0.00 0.00 41.99 2.29
1806 2253 6.198650 TGAATTCTTCACCTGCATTGTATG 57.801 37.500 7.05 0.00 34.08 2.39
1813 2260 5.675684 TCACCTGCATTGTATGTCTTCTA 57.324 39.130 0.00 0.00 0.00 2.10
1815 2262 5.046663 TCACCTGCATTGTATGTCTTCTACA 60.047 40.000 0.00 0.00 43.86 2.74
1825 2272 2.346803 TGTCTTCTACATGAAAGGCGC 58.653 47.619 0.00 0.00 33.79 6.53
1826 2273 2.289382 TGTCTTCTACATGAAAGGCGCA 60.289 45.455 10.83 0.00 33.79 6.09
1857 2304 5.541953 AGTTTGAGGTCCTACGTTAAACT 57.458 39.130 13.53 13.53 43.28 2.66
1859 2306 5.987953 AGTTTGAGGTCCTACGTTAAACTTC 59.012 40.000 13.53 0.00 44.63 3.01
1879 2326 7.662604 ACTTCGGTAGTTTGTATTACCAAAG 57.337 36.000 1.01 1.01 39.03 2.77
1917 2364 6.778542 TGTCAATTAATATGGATCAGGGGA 57.221 37.500 0.00 0.00 0.00 4.81
1933 2380 5.640147 TCAGGGGAAGTAACATTGTTTGAT 58.360 37.500 7.45 0.00 0.00 2.57
1943 2390 9.844790 AAGTAACATTGTTTGATGTCATATGTG 57.155 29.630 7.45 0.00 39.25 3.21
1944 2391 8.461222 AGTAACATTGTTTGATGTCATATGTGG 58.539 33.333 7.45 0.00 39.25 4.17
1948 2395 5.565592 TGTTTGATGTCATATGTGGAAGC 57.434 39.130 1.90 0.00 0.00 3.86
1949 2396 5.008980 TGTTTGATGTCATATGTGGAAGCA 58.991 37.500 1.90 0.00 0.00 3.91
1963 2410 4.081198 TGTGGAAGCACTTTGTGGATTTTT 60.081 37.500 0.00 0.00 33.64 1.94
1964 2411 5.127845 TGTGGAAGCACTTTGTGGATTTTTA 59.872 36.000 0.00 0.00 33.64 1.52
1969 2416 5.783111 AGCACTTTGTGGATTTTTATGGAC 58.217 37.500 0.00 0.00 33.64 4.02
1973 2420 6.699642 CACTTTGTGGATTTTTATGGACGTTT 59.300 34.615 0.00 0.00 0.00 3.60
1999 2446 6.603095 CGAACCCTTCTTCATTTTTACTCAG 58.397 40.000 0.00 0.00 0.00 3.35
2000 2447 6.204882 CGAACCCTTCTTCATTTTTACTCAGT 59.795 38.462 0.00 0.00 0.00 3.41
2032 2479 8.814038 ATGTTGGAATAAATGAAGAGCTAGTT 57.186 30.769 0.00 0.00 0.00 2.24
2049 2496 9.825109 AGAGCTAGTTAATAAATGAGAAACTCC 57.175 33.333 0.00 0.00 32.85 3.85
2050 2497 9.601217 GAGCTAGTTAATAAATGAGAAACTCCA 57.399 33.333 0.00 0.00 32.85 3.86
2051 2498 9.384764 AGCTAGTTAATAAATGAGAAACTCCAC 57.615 33.333 0.00 0.00 32.85 4.02
2052 2499 8.328864 GCTAGTTAATAAATGAGAAACTCCACG 58.671 37.037 0.00 0.00 32.85 4.94
2053 2500 9.367444 CTAGTTAATAAATGAGAAACTCCACGT 57.633 33.333 0.00 0.00 32.85 4.49
2055 2502 9.148104 AGTTAATAAATGAGAAACTCCACGTAC 57.852 33.333 0.00 0.00 0.00 3.67
2056 2503 6.980051 AATAAATGAGAAACTCCACGTACC 57.020 37.500 0.00 0.00 0.00 3.34
2057 2504 4.618920 AAATGAGAAACTCCACGTACCT 57.381 40.909 0.00 0.00 0.00 3.08
2058 2505 3.870633 ATGAGAAACTCCACGTACCTC 57.129 47.619 0.00 0.00 0.00 3.85
2059 2506 2.872732 TGAGAAACTCCACGTACCTCT 58.127 47.619 0.00 0.00 0.00 3.69
2060 2507 2.818432 TGAGAAACTCCACGTACCTCTC 59.182 50.000 0.00 0.00 31.53 3.20
2061 2508 1.811359 AGAAACTCCACGTACCTCTCG 59.189 52.381 0.00 0.00 0.00 4.04
2062 2509 0.886563 AAACTCCACGTACCTCTCGG 59.113 55.000 0.00 0.00 0.00 4.63
2063 2510 0.964358 AACTCCACGTACCTCTCGGG 60.964 60.000 0.00 0.00 41.89 5.14
2120 2567 3.541713 GCCGCCTAGTCCCTCCAG 61.542 72.222 0.00 0.00 0.00 3.86
2121 2568 3.541713 CCGCCTAGTCCCTCCAGC 61.542 72.222 0.00 0.00 0.00 4.85
2122 2569 3.905678 CGCCTAGTCCCTCCAGCG 61.906 72.222 0.00 0.00 37.39 5.18
2123 2570 4.228567 GCCTAGTCCCTCCAGCGC 62.229 72.222 0.00 0.00 0.00 5.92
2124 2571 3.541713 CCTAGTCCCTCCAGCGCC 61.542 72.222 2.29 0.00 0.00 6.53
2125 2572 3.541713 CTAGTCCCTCCAGCGCCC 61.542 72.222 2.29 0.00 0.00 6.13
2126 2573 4.075793 TAGTCCCTCCAGCGCCCT 62.076 66.667 2.29 0.00 0.00 5.19
2127 2574 3.618855 TAGTCCCTCCAGCGCCCTT 62.619 63.158 2.29 0.00 0.00 3.95
2128 2575 4.475135 GTCCCTCCAGCGCCCTTC 62.475 72.222 2.29 0.00 0.00 3.46
2129 2576 4.722535 TCCCTCCAGCGCCCTTCT 62.723 66.667 2.29 0.00 0.00 2.85
2130 2577 4.168291 CCCTCCAGCGCCCTTCTC 62.168 72.222 2.29 0.00 0.00 2.87
2131 2578 4.168291 CCTCCAGCGCCCTTCTCC 62.168 72.222 2.29 0.00 0.00 3.71
2132 2579 3.080121 CTCCAGCGCCCTTCTCCT 61.080 66.667 2.29 0.00 0.00 3.69
2133 2580 3.077556 TCCAGCGCCCTTCTCCTC 61.078 66.667 2.29 0.00 0.00 3.71
2134 2581 4.168291 CCAGCGCCCTTCTCCTCC 62.168 72.222 2.29 0.00 0.00 4.30
2135 2582 3.080121 CAGCGCCCTTCTCCTCCT 61.080 66.667 2.29 0.00 0.00 3.69
2136 2583 2.762043 AGCGCCCTTCTCCTCCTC 60.762 66.667 2.29 0.00 0.00 3.71
2137 2584 3.855853 GCGCCCTTCTCCTCCTCC 61.856 72.222 0.00 0.00 0.00 4.30
2138 2585 3.532155 CGCCCTTCTCCTCCTCCG 61.532 72.222 0.00 0.00 0.00 4.63
2139 2586 3.855853 GCCCTTCTCCTCCTCCGC 61.856 72.222 0.00 0.00 0.00 5.54
2140 2587 3.157949 CCCTTCTCCTCCTCCGCC 61.158 72.222 0.00 0.00 0.00 6.13
2141 2588 3.532155 CCTTCTCCTCCTCCGCCG 61.532 72.222 0.00 0.00 0.00 6.46
2142 2589 2.756283 CTTCTCCTCCTCCGCCGT 60.756 66.667 0.00 0.00 0.00 5.68
2143 2590 2.283676 TTCTCCTCCTCCGCCGTT 60.284 61.111 0.00 0.00 0.00 4.44
2144 2591 2.564553 CTTCTCCTCCTCCGCCGTTG 62.565 65.000 0.00 0.00 0.00 4.10
2145 2592 4.821589 CTCCTCCTCCGCCGTTGC 62.822 72.222 0.00 0.00 0.00 4.17
2202 2649 3.519930 GGCGACGGAGGGTCTCTC 61.520 72.222 0.00 0.00 43.79 3.20
2211 2658 3.618652 GGGTCTCTCCTCCCGTTC 58.381 66.667 0.00 0.00 33.97 3.95
2212 2659 2.059190 GGGTCTCTCCTCCCGTTCC 61.059 68.421 0.00 0.00 33.97 3.62
2213 2660 2.059190 GGTCTCTCCTCCCGTTCCC 61.059 68.421 0.00 0.00 0.00 3.97
2214 2661 2.044252 TCTCTCCTCCCGTTCCCG 60.044 66.667 0.00 0.00 0.00 5.14
2247 2694 4.570663 GGACGTCCTGATCCGCGG 62.571 72.222 27.64 22.12 0.00 6.46
2248 2695 4.570663 GACGTCCTGATCCGCGGG 62.571 72.222 27.83 8.93 45.07 6.13
2251 2698 4.530857 GTCCTGATCCGCGGGGTG 62.531 72.222 27.83 13.02 43.76 4.61
2270 2717 4.489771 GGCCCTCCCGATGGTGTG 62.490 72.222 0.00 0.00 0.00 3.82
2271 2718 4.489771 GCCCTCCCGATGGTGTGG 62.490 72.222 0.00 0.00 0.00 4.17
2272 2719 4.489771 CCCTCCCGATGGTGTGGC 62.490 72.222 0.00 0.00 0.00 5.01
2273 2720 4.838152 CCTCCCGATGGTGTGGCG 62.838 72.222 0.00 0.00 0.00 5.69
2274 2721 4.838152 CTCCCGATGGTGTGGCGG 62.838 72.222 0.00 0.00 44.42 6.13
2278 2725 2.588877 CGATGGTGTGGCGGATCC 60.589 66.667 0.00 0.00 0.00 3.36
2279 2726 2.203209 GATGGTGTGGCGGATCCC 60.203 66.667 6.06 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 8.632679 TCGAACCAAAAGAAGAAAGTAGTAGTA 58.367 33.333 0.00 0.00 0.00 1.82
64 66 7.495055 TCGAACCAAAAGAAGAAAGTAGTAGT 58.505 34.615 0.00 0.00 0.00 2.73
65 67 7.652507 ACTCGAACCAAAAGAAGAAAGTAGTAG 59.347 37.037 0.00 0.00 0.00 2.57
101 103 4.695455 CCGATTCTGTAGATGGTTGTGTTT 59.305 41.667 0.00 0.00 0.00 2.83
178 180 3.615155 AGTACGAAGGTAGGTAGTCCAC 58.385 50.000 0.00 0.00 35.89 4.02
179 181 4.680708 CGTAGTACGAAGGTAGGTAGTCCA 60.681 50.000 17.85 0.00 46.05 4.02
180 182 3.804873 CGTAGTACGAAGGTAGGTAGTCC 59.195 52.174 17.85 0.00 46.05 3.85
181 183 4.434520 ACGTAGTACGAAGGTAGGTAGTC 58.565 47.826 28.47 0.00 46.05 2.59
182 184 4.473477 ACGTAGTACGAAGGTAGGTAGT 57.527 45.455 28.47 0.00 46.05 2.73
202 208 1.135170 GTTCACTACTCCAGCCGGTAC 60.135 57.143 1.90 0.00 0.00 3.34
203 209 1.180029 GTTCACTACTCCAGCCGGTA 58.820 55.000 1.90 0.00 0.00 4.02
204 210 0.542232 AGTTCACTACTCCAGCCGGT 60.542 55.000 1.90 0.00 28.23 5.28
205 211 0.108615 CAGTTCACTACTCCAGCCGG 60.109 60.000 0.00 0.00 33.85 6.13
206 212 0.108615 CCAGTTCACTACTCCAGCCG 60.109 60.000 0.00 0.00 33.85 5.52
207 213 0.391793 GCCAGTTCACTACTCCAGCC 60.392 60.000 0.00 0.00 33.85 4.85
208 214 0.610687 AGCCAGTTCACTACTCCAGC 59.389 55.000 0.00 0.00 33.85 4.85
209 215 1.066573 CCAGCCAGTTCACTACTCCAG 60.067 57.143 0.00 0.00 33.85 3.86
210 216 0.976641 CCAGCCAGTTCACTACTCCA 59.023 55.000 0.00 0.00 33.85 3.86
211 217 1.205893 CTCCAGCCAGTTCACTACTCC 59.794 57.143 0.00 0.00 33.85 3.85
212 218 1.205893 CCTCCAGCCAGTTCACTACTC 59.794 57.143 0.00 0.00 33.85 2.59
213 219 1.203187 TCCTCCAGCCAGTTCACTACT 60.203 52.381 0.00 0.00 37.68 2.57
214 220 1.267121 TCCTCCAGCCAGTTCACTAC 58.733 55.000 0.00 0.00 0.00 2.73
215 221 1.902508 CTTCCTCCAGCCAGTTCACTA 59.097 52.381 0.00 0.00 0.00 2.74
216 222 0.689623 CTTCCTCCAGCCAGTTCACT 59.310 55.000 0.00 0.00 0.00 3.41
217 223 0.398318 ACTTCCTCCAGCCAGTTCAC 59.602 55.000 0.00 0.00 0.00 3.18
218 224 1.623811 GTACTTCCTCCAGCCAGTTCA 59.376 52.381 0.00 0.00 0.00 3.18
219 225 1.903183 AGTACTTCCTCCAGCCAGTTC 59.097 52.381 0.00 0.00 0.00 3.01
220 226 2.031495 AGTACTTCCTCCAGCCAGTT 57.969 50.000 0.00 0.00 0.00 3.16
221 227 2.921834 TAGTACTTCCTCCAGCCAGT 57.078 50.000 0.00 0.00 0.00 4.00
222 228 3.964031 AGAATAGTACTTCCTCCAGCCAG 59.036 47.826 0.00 0.00 0.00 4.85
223 229 3.706594 CAGAATAGTACTTCCTCCAGCCA 59.293 47.826 0.00 0.00 0.00 4.75
224 230 3.707102 ACAGAATAGTACTTCCTCCAGCC 59.293 47.826 0.00 0.00 0.00 4.85
225 231 4.442192 CCACAGAATAGTACTTCCTCCAGC 60.442 50.000 0.00 0.00 0.00 4.85
226 232 4.956700 TCCACAGAATAGTACTTCCTCCAG 59.043 45.833 0.00 0.00 0.00 3.86
227 233 4.710375 GTCCACAGAATAGTACTTCCTCCA 59.290 45.833 0.00 0.00 0.00 3.86
228 234 4.710375 TGTCCACAGAATAGTACTTCCTCC 59.290 45.833 0.00 0.00 0.00 4.30
229 235 5.394333 GGTGTCCACAGAATAGTACTTCCTC 60.394 48.000 0.00 0.00 0.00 3.71
230 236 4.466726 GGTGTCCACAGAATAGTACTTCCT 59.533 45.833 0.00 0.00 0.00 3.36
231 237 4.222145 TGGTGTCCACAGAATAGTACTTCC 59.778 45.833 0.00 0.00 0.00 3.46
232 238 5.401531 TGGTGTCCACAGAATAGTACTTC 57.598 43.478 0.00 0.00 0.00 3.01
233 239 5.483937 TCATGGTGTCCACAGAATAGTACTT 59.516 40.000 0.00 0.00 35.80 2.24
234 240 5.023452 TCATGGTGTCCACAGAATAGTACT 58.977 41.667 0.00 0.00 35.80 2.73
235 241 5.109903 GTCATGGTGTCCACAGAATAGTAC 58.890 45.833 0.00 0.00 35.80 2.73
236 242 4.161565 GGTCATGGTGTCCACAGAATAGTA 59.838 45.833 0.00 0.00 35.80 1.82
237 243 3.055094 GGTCATGGTGTCCACAGAATAGT 60.055 47.826 0.00 0.00 35.80 2.12
238 244 3.055167 TGGTCATGGTGTCCACAGAATAG 60.055 47.826 0.00 0.00 35.80 1.73
256 262 1.956170 CGCGTATGCCCAGATGGTC 60.956 63.158 0.00 0.00 38.08 4.02
257 263 2.108976 CGCGTATGCCCAGATGGT 59.891 61.111 0.00 0.00 38.08 3.55
258 264 2.666190 CCGCGTATGCCCAGATGG 60.666 66.667 4.92 0.00 38.08 3.51
259 265 3.349006 GCCGCGTATGCCCAGATG 61.349 66.667 4.92 0.00 38.08 2.90
332 360 3.508840 CGAATTGGCCAGCGGGAC 61.509 66.667 7.23 3.59 45.44 4.46
334 362 3.508840 GACGAATTGGCCAGCGGG 61.509 66.667 22.86 0.00 37.18 6.13
366 417 3.970721 CTGACATTGTCCGCAGCA 58.029 55.556 14.05 0.00 0.00 4.41
369 420 1.672030 CCTGCTGACATTGTCCGCA 60.672 57.895 27.16 27.16 46.94 5.69
397 448 2.350102 CGTACTGTCACGACACAGCTTA 60.350 50.000 15.53 2.82 46.81 3.09
474 527 9.695155 TCCTCCGAAAATCCTATAAAATTTCTT 57.305 29.630 0.00 0.00 0.00 2.52
475 528 9.868160 ATCCTCCGAAAATCCTATAAAATTTCT 57.132 29.630 0.00 0.00 0.00 2.52
478 531 9.640952 TCAATCCTCCGAAAATCCTATAAAATT 57.359 29.630 0.00 0.00 0.00 1.82
479 532 9.640952 TTCAATCCTCCGAAAATCCTATAAAAT 57.359 29.630 0.00 0.00 0.00 1.82
480 533 9.469097 TTTCAATCCTCCGAAAATCCTATAAAA 57.531 29.630 0.00 0.00 0.00 1.52
481 534 9.640952 ATTTCAATCCTCCGAAAATCCTATAAA 57.359 29.630 0.00 0.00 34.95 1.40
482 535 9.640952 AATTTCAATCCTCCGAAAATCCTATAA 57.359 29.630 0.00 0.00 34.95 0.98
483 536 9.640952 AAATTTCAATCCTCCGAAAATCCTATA 57.359 29.630 0.00 0.00 34.95 1.31
484 537 8.539117 AAATTTCAATCCTCCGAAAATCCTAT 57.461 30.769 0.00 0.00 34.95 2.57
485 538 7.954666 AAATTTCAATCCTCCGAAAATCCTA 57.045 32.000 0.00 0.00 34.95 2.94
486 539 6.857437 AAATTTCAATCCTCCGAAAATCCT 57.143 33.333 0.00 0.00 34.95 3.24
487 540 7.905604 AAAAATTTCAATCCTCCGAAAATCC 57.094 32.000 0.00 0.00 34.95 3.01
530 583 9.878737 AGATCCAATCCTATGAATCAAAAGATT 57.121 29.630 0.00 0.00 0.00 2.40
531 584 9.517868 GAGATCCAATCCTATGAATCAAAAGAT 57.482 33.333 0.00 0.00 0.00 2.40
532 585 8.496916 TGAGATCCAATCCTATGAATCAAAAGA 58.503 33.333 0.00 0.00 0.00 2.52
533 586 8.687292 TGAGATCCAATCCTATGAATCAAAAG 57.313 34.615 0.00 0.00 0.00 2.27
597 650 9.547279 AGTTGAAGGGGATGTTAAATTTTCTAT 57.453 29.630 0.00 0.00 0.00 1.98
598 651 8.950007 AGTTGAAGGGGATGTTAAATTTTCTA 57.050 30.769 0.00 0.00 0.00 2.10
599 652 7.855784 AGTTGAAGGGGATGTTAAATTTTCT 57.144 32.000 0.00 0.00 0.00 2.52
600 653 8.367911 AGAAGTTGAAGGGGATGTTAAATTTTC 58.632 33.333 0.00 0.00 0.00 2.29
601 654 8.262601 AGAAGTTGAAGGGGATGTTAAATTTT 57.737 30.769 0.00 0.00 0.00 1.82
602 655 7.855784 AGAAGTTGAAGGGGATGTTAAATTT 57.144 32.000 0.00 0.00 0.00 1.82
603 656 7.855784 AAGAAGTTGAAGGGGATGTTAAATT 57.144 32.000 0.00 0.00 0.00 1.82
604 657 7.855784 AAAGAAGTTGAAGGGGATGTTAAAT 57.144 32.000 0.00 0.00 0.00 1.40
605 658 7.669089 AAAAGAAGTTGAAGGGGATGTTAAA 57.331 32.000 0.00 0.00 0.00 1.52
606 659 7.669089 AAAAAGAAGTTGAAGGGGATGTTAA 57.331 32.000 0.00 0.00 0.00 2.01
607 660 7.780745 TGTAAAAAGAAGTTGAAGGGGATGTTA 59.219 33.333 0.00 0.00 0.00 2.41
608 661 6.609616 TGTAAAAAGAAGTTGAAGGGGATGTT 59.390 34.615 0.00 0.00 0.00 2.71
609 662 6.133356 TGTAAAAAGAAGTTGAAGGGGATGT 58.867 36.000 0.00 0.00 0.00 3.06
610 663 6.648879 TGTAAAAAGAAGTTGAAGGGGATG 57.351 37.500 0.00 0.00 0.00 3.51
611 664 7.855784 ATTGTAAAAAGAAGTTGAAGGGGAT 57.144 32.000 0.00 0.00 0.00 3.85
612 665 7.201965 GGAATTGTAAAAAGAAGTTGAAGGGGA 60.202 37.037 0.00 0.00 0.00 4.81
613 666 6.929049 GGAATTGTAAAAAGAAGTTGAAGGGG 59.071 38.462 0.00 0.00 0.00 4.79
614 667 7.726216 AGGAATTGTAAAAAGAAGTTGAAGGG 58.274 34.615 0.00 0.00 0.00 3.95
615 668 9.599866 AAAGGAATTGTAAAAAGAAGTTGAAGG 57.400 29.630 0.00 0.00 0.00 3.46
626 679 9.833917 ACCGGAAAAATAAAGGAATTGTAAAAA 57.166 25.926 9.46 0.00 0.00 1.94
627 680 9.262358 CACCGGAAAAATAAAGGAATTGTAAAA 57.738 29.630 9.46 0.00 0.00 1.52
628 681 7.873505 CCACCGGAAAAATAAAGGAATTGTAAA 59.126 33.333 9.46 0.00 0.00 2.01
629 682 7.379750 CCACCGGAAAAATAAAGGAATTGTAA 58.620 34.615 9.46 0.00 0.00 2.41
630 683 6.572703 GCCACCGGAAAAATAAAGGAATTGTA 60.573 38.462 9.46 0.00 0.00 2.41
631 684 5.789521 CCACCGGAAAAATAAAGGAATTGT 58.210 37.500 9.46 0.00 0.00 2.71
632 685 4.629634 GCCACCGGAAAAATAAAGGAATTG 59.370 41.667 9.46 0.00 0.00 2.32
633 686 4.284746 TGCCACCGGAAAAATAAAGGAATT 59.715 37.500 9.46 0.00 0.00 2.17
634 687 3.835395 TGCCACCGGAAAAATAAAGGAAT 59.165 39.130 9.46 0.00 0.00 3.01
635 688 3.231818 TGCCACCGGAAAAATAAAGGAA 58.768 40.909 9.46 0.00 0.00 3.36
636 689 2.877866 TGCCACCGGAAAAATAAAGGA 58.122 42.857 9.46 0.00 0.00 3.36
637 690 3.194542 TGATGCCACCGGAAAAATAAAGG 59.805 43.478 9.46 0.00 0.00 3.11
638 691 4.448537 TGATGCCACCGGAAAAATAAAG 57.551 40.909 9.46 0.00 0.00 1.85
639 692 4.873746 TTGATGCCACCGGAAAAATAAA 57.126 36.364 9.46 0.00 0.00 1.40
640 693 4.039245 TGTTTGATGCCACCGGAAAAATAA 59.961 37.500 9.46 0.00 0.00 1.40
641 694 3.574396 TGTTTGATGCCACCGGAAAAATA 59.426 39.130 9.46 0.00 0.00 1.40
642 695 2.366916 TGTTTGATGCCACCGGAAAAAT 59.633 40.909 9.46 0.00 0.00 1.82
643 696 1.757118 TGTTTGATGCCACCGGAAAAA 59.243 42.857 9.46 0.00 0.00 1.94
644 697 1.403814 TGTTTGATGCCACCGGAAAA 58.596 45.000 9.46 0.00 0.00 2.29
645 698 1.403814 TTGTTTGATGCCACCGGAAA 58.596 45.000 9.46 0.00 0.00 3.13
646 699 1.543802 GATTGTTTGATGCCACCGGAA 59.456 47.619 9.46 0.00 0.00 4.30
647 700 1.173043 GATTGTTTGATGCCACCGGA 58.827 50.000 9.46 0.00 0.00 5.14
648 701 0.887247 TGATTGTTTGATGCCACCGG 59.113 50.000 0.00 0.00 0.00 5.28
649 702 2.945447 ATGATTGTTTGATGCCACCG 57.055 45.000 0.00 0.00 0.00 4.94
650 703 5.329035 AGTAATGATTGTTTGATGCCACC 57.671 39.130 0.00 0.00 0.00 4.61
651 704 8.931385 AATTAGTAATGATTGTTTGATGCCAC 57.069 30.769 0.00 0.00 0.00 5.01
652 705 8.970020 AGAATTAGTAATGATTGTTTGATGCCA 58.030 29.630 0.00 0.00 0.00 4.92
674 727 8.800332 GGCATGTCCATTTGAATTCTATAGAAT 58.200 33.333 20.20 20.20 39.47 2.40
675 728 7.779326 TGGCATGTCCATTTGAATTCTATAGAA 59.221 33.333 17.32 17.32 40.72 2.10
676 729 7.289310 TGGCATGTCCATTTGAATTCTATAGA 58.711 34.615 7.05 0.00 40.72 1.98
677 730 7.514784 TGGCATGTCCATTTGAATTCTATAG 57.485 36.000 7.05 0.00 40.72 1.31
691 744 1.074775 GGTTGGAGTGGCATGTCCA 59.925 57.895 15.51 15.51 44.18 4.02
692 745 1.678970 GGGTTGGAGTGGCATGTCC 60.679 63.158 11.04 11.04 0.00 4.02
693 746 0.618458 TAGGGTTGGAGTGGCATGTC 59.382 55.000 0.00 0.00 0.00 3.06
694 747 0.328258 GTAGGGTTGGAGTGGCATGT 59.672 55.000 0.00 0.00 0.00 3.21
695 748 0.327924 TGTAGGGTTGGAGTGGCATG 59.672 55.000 0.00 0.00 0.00 4.06
696 749 0.328258 GTGTAGGGTTGGAGTGGCAT 59.672 55.000 0.00 0.00 0.00 4.40
697 750 0.766674 AGTGTAGGGTTGGAGTGGCA 60.767 55.000 0.00 0.00 0.00 4.92
698 751 0.400594 AAGTGTAGGGTTGGAGTGGC 59.599 55.000 0.00 0.00 0.00 5.01
699 752 2.951229 AAAGTGTAGGGTTGGAGTGG 57.049 50.000 0.00 0.00 0.00 4.00
700 753 4.461198 AGAAAAAGTGTAGGGTTGGAGTG 58.539 43.478 0.00 0.00 0.00 3.51
701 754 4.790718 AGAAAAAGTGTAGGGTTGGAGT 57.209 40.909 0.00 0.00 0.00 3.85
702 755 6.374613 GGAATAGAAAAAGTGTAGGGTTGGAG 59.625 42.308 0.00 0.00 0.00 3.86
703 756 6.045106 AGGAATAGAAAAAGTGTAGGGTTGGA 59.955 38.462 0.00 0.00 0.00 3.53
704 757 6.246163 AGGAATAGAAAAAGTGTAGGGTTGG 58.754 40.000 0.00 0.00 0.00 3.77
705 758 7.064253 CGTAGGAATAGAAAAAGTGTAGGGTTG 59.936 40.741 0.00 0.00 0.00 3.77
706 759 7.101700 CGTAGGAATAGAAAAAGTGTAGGGTT 58.898 38.462 0.00 0.00 0.00 4.11
707 760 6.212187 ACGTAGGAATAGAAAAAGTGTAGGGT 59.788 38.462 0.00 0.00 0.00 4.34
708 761 6.637657 ACGTAGGAATAGAAAAAGTGTAGGG 58.362 40.000 0.00 0.00 0.00 3.53
709 762 8.543862 AAACGTAGGAATAGAAAAAGTGTAGG 57.456 34.615 0.00 0.00 0.00 3.18
734 787 9.705290 GGCTTCTTTGATTTGTAGGATTTTAAA 57.295 29.630 0.00 0.00 0.00 1.52
735 788 8.311109 GGGCTTCTTTGATTTGTAGGATTTTAA 58.689 33.333 0.00 0.00 0.00 1.52
736 789 7.673926 AGGGCTTCTTTGATTTGTAGGATTTTA 59.326 33.333 0.00 0.00 0.00 1.52
737 790 6.498303 AGGGCTTCTTTGATTTGTAGGATTTT 59.502 34.615 0.00 0.00 0.00 1.82
738 791 6.019108 AGGGCTTCTTTGATTTGTAGGATTT 58.981 36.000 0.00 0.00 0.00 2.17
739 792 5.583932 AGGGCTTCTTTGATTTGTAGGATT 58.416 37.500 0.00 0.00 0.00 3.01
740 793 5.198602 AGGGCTTCTTTGATTTGTAGGAT 57.801 39.130 0.00 0.00 0.00 3.24
741 794 4.657814 AGGGCTTCTTTGATTTGTAGGA 57.342 40.909 0.00 0.00 0.00 2.94
742 795 6.834168 TTTAGGGCTTCTTTGATTTGTAGG 57.166 37.500 0.00 0.00 0.00 3.18
743 796 7.657336 TGTTTTAGGGCTTCTTTGATTTGTAG 58.343 34.615 0.00 0.00 0.00 2.74
744 797 7.589958 TGTTTTAGGGCTTCTTTGATTTGTA 57.410 32.000 0.00 0.00 0.00 2.41
745 798 6.478512 TGTTTTAGGGCTTCTTTGATTTGT 57.521 33.333 0.00 0.00 0.00 2.83
746 799 7.118245 GGATTGTTTTAGGGCTTCTTTGATTTG 59.882 37.037 0.00 0.00 0.00 2.32
747 800 7.016563 AGGATTGTTTTAGGGCTTCTTTGATTT 59.983 33.333 0.00 0.00 0.00 2.17
748 801 6.498303 AGGATTGTTTTAGGGCTTCTTTGATT 59.502 34.615 0.00 0.00 0.00 2.57
749 802 6.019108 AGGATTGTTTTAGGGCTTCTTTGAT 58.981 36.000 0.00 0.00 0.00 2.57
750 803 5.393866 AGGATTGTTTTAGGGCTTCTTTGA 58.606 37.500 0.00 0.00 0.00 2.69
751 804 5.619981 CGAGGATTGTTTTAGGGCTTCTTTG 60.620 44.000 0.00 0.00 0.00 2.77
752 805 4.459337 CGAGGATTGTTTTAGGGCTTCTTT 59.541 41.667 0.00 0.00 0.00 2.52
753 806 4.010349 CGAGGATTGTTTTAGGGCTTCTT 58.990 43.478 0.00 0.00 0.00 2.52
754 807 3.263425 TCGAGGATTGTTTTAGGGCTTCT 59.737 43.478 0.00 0.00 0.00 2.85
755 808 3.606687 TCGAGGATTGTTTTAGGGCTTC 58.393 45.455 0.00 0.00 0.00 3.86
756 809 3.713826 TCGAGGATTGTTTTAGGGCTT 57.286 42.857 0.00 0.00 0.00 4.35
757 810 3.741388 CGATCGAGGATTGTTTTAGGGCT 60.741 47.826 10.26 0.00 0.00 5.19
758 811 2.544267 CGATCGAGGATTGTTTTAGGGC 59.456 50.000 10.26 0.00 0.00 5.19
759 812 2.544267 GCGATCGAGGATTGTTTTAGGG 59.456 50.000 21.57 0.00 0.00 3.53
760 813 2.544267 GGCGATCGAGGATTGTTTTAGG 59.456 50.000 21.57 0.00 0.00 2.69
761 814 3.194861 TGGCGATCGAGGATTGTTTTAG 58.805 45.455 21.57 0.00 0.00 1.85
796 849 3.691609 GGCTTGGAGTTGGATGAAACTAG 59.308 47.826 0.00 0.00 40.48 2.57
839 896 3.868754 GCCGGCCATTAACTAGGAATAGG 60.869 52.174 18.11 0.00 0.00 2.57
840 897 3.335579 GCCGGCCATTAACTAGGAATAG 58.664 50.000 18.11 0.00 0.00 1.73
841 898 2.289195 CGCCGGCCATTAACTAGGAATA 60.289 50.000 23.46 0.00 0.00 1.75
883 943 1.521681 CTGCTAGCTAACCGGTGGC 60.522 63.158 20.84 20.84 46.36 5.01
889 949 2.174319 GTGGCGCTGCTAGCTAACC 61.174 63.158 17.23 12.38 39.60 2.85
891 951 1.899437 AAGGTGGCGCTGCTAGCTAA 61.899 55.000 17.23 0.00 46.31 3.09
910 970 4.819761 GCCATGGCGACGCTCTCA 62.820 66.667 23.48 9.86 0.00 3.27
1246 1306 2.261052 GAGCTGCTCACGAGTGCT 59.739 61.111 24.02 13.66 40.75 4.40
1325 1385 0.391661 GAGCACCGCCAGAATCAAGA 60.392 55.000 0.00 0.00 0.00 3.02
1329 1389 0.107945 AGAAGAGCACCGCCAGAATC 60.108 55.000 0.00 0.00 0.00 2.52
1531 1928 5.063880 CCGGCTATGTCCTAATTTAAGCTT 58.936 41.667 3.48 3.48 0.00 3.74
1635 2032 6.442952 TCCAATGTTTTTCATTTGTAGTCCG 58.557 36.000 0.00 0.00 43.33 4.79
1752 2163 2.689983 GGATTCAAAATGGACTCGGCAT 59.310 45.455 0.00 0.00 0.00 4.40
1806 2253 2.346803 TGCGCCTTTCATGTAGAAGAC 58.653 47.619 4.18 0.00 37.57 3.01
1813 2260 1.303309 GAGCTATGCGCCTTTCATGT 58.697 50.000 4.18 0.00 40.39 3.21
1815 2262 2.267174 ATGAGCTATGCGCCTTTCAT 57.733 45.000 4.18 4.55 40.39 2.57
1816 2263 2.103094 ACTATGAGCTATGCGCCTTTCA 59.897 45.455 4.18 2.03 40.39 2.69
1817 2264 2.760374 ACTATGAGCTATGCGCCTTTC 58.240 47.619 4.18 0.00 40.39 2.62
1818 2265 2.918712 ACTATGAGCTATGCGCCTTT 57.081 45.000 4.18 0.00 40.39 3.11
1819 2266 2.874701 CAAACTATGAGCTATGCGCCTT 59.125 45.455 4.18 0.00 40.39 4.35
1820 2267 2.103094 TCAAACTATGAGCTATGCGCCT 59.897 45.455 4.18 0.00 40.39 5.52
1821 2268 2.483876 TCAAACTATGAGCTATGCGCC 58.516 47.619 4.18 0.00 40.39 6.53
1836 2283 5.107722 CGAAGTTTAACGTAGGACCTCAAAC 60.108 44.000 0.00 2.68 0.00 2.93
1857 2304 7.498570 ACAACTTTGGTAATACAAACTACCGAA 59.501 33.333 0.00 0.00 40.51 4.30
1859 2306 7.193377 ACAACTTTGGTAATACAAACTACCG 57.807 36.000 0.00 0.00 40.51 4.02
1871 2318 8.228035 ACATTGCTTTAGTACAACTTTGGTAA 57.772 30.769 0.00 0.00 0.00 2.85
1894 2341 6.778542 TCCCCTGATCCATATTAATTGACA 57.221 37.500 0.00 0.00 0.00 3.58
1895 2342 7.234355 ACTTCCCCTGATCCATATTAATTGAC 58.766 38.462 0.00 0.00 0.00 3.18
1912 2359 5.393866 ACATCAAACAATGTTACTTCCCCT 58.606 37.500 0.00 0.00 36.47 4.79
1917 2364 9.844790 CACATATGACATCAAACAATGTTACTT 57.155 29.630 10.38 0.00 39.93 2.24
1933 2380 4.216042 CACAAAGTGCTTCCACATATGACA 59.784 41.667 10.38 0.00 44.53 3.58
1943 2390 5.639082 CCATAAAAATCCACAAAGTGCTTCC 59.361 40.000 0.00 0.00 31.34 3.46
1944 2391 6.366061 GTCCATAAAAATCCACAAAGTGCTTC 59.634 38.462 0.00 0.00 31.34 3.86
1948 2395 5.768317 ACGTCCATAAAAATCCACAAAGTG 58.232 37.500 0.00 0.00 0.00 3.16
1949 2396 6.399639 AACGTCCATAAAAATCCACAAAGT 57.600 33.333 0.00 0.00 0.00 2.66
1963 2410 0.322322 AGGGTTCGCAAACGTCCATA 59.678 50.000 0.00 0.00 41.18 2.74
1964 2411 0.536460 AAGGGTTCGCAAACGTCCAT 60.536 50.000 0.00 0.00 41.18 3.41
1969 2416 0.941542 TGAAGAAGGGTTCGCAAACG 59.058 50.000 0.00 0.00 42.01 3.60
1973 2420 4.825085 AGTAAAAATGAAGAAGGGTTCGCA 59.175 37.500 0.00 0.00 34.02 5.10
2023 2470 9.825109 GGAGTTTCTCATTTATTAACTAGCTCT 57.175 33.333 0.00 0.00 31.08 4.09
2032 2479 7.844009 AGGTACGTGGAGTTTCTCATTTATTA 58.156 34.615 0.00 0.00 31.08 0.98
2035 2482 5.479375 AGAGGTACGTGGAGTTTCTCATTTA 59.521 40.000 0.00 0.00 34.97 1.40
2041 2488 1.811359 CGAGAGGTACGTGGAGTTTCT 59.189 52.381 0.00 0.00 0.00 2.52
2042 2489 2.259505 CGAGAGGTACGTGGAGTTTC 57.740 55.000 0.00 0.00 0.00 2.78
2103 2550 3.541713 CTGGAGGGACTAGGCGGC 61.542 72.222 0.00 0.00 41.55 6.53
2104 2551 3.541713 GCTGGAGGGACTAGGCGG 61.542 72.222 0.00 0.00 41.55 6.13
2105 2552 3.905678 CGCTGGAGGGACTAGGCG 61.906 72.222 0.00 0.00 41.55 5.52
2106 2553 4.228567 GCGCTGGAGGGACTAGGC 62.229 72.222 0.00 0.00 41.55 3.93
2107 2554 3.541713 GGCGCTGGAGGGACTAGG 61.542 72.222 7.64 0.00 41.55 3.02
2108 2555 3.541713 GGGCGCTGGAGGGACTAG 61.542 72.222 7.64 0.00 41.55 2.57
2109 2556 3.618855 AAGGGCGCTGGAGGGACTA 62.619 63.158 7.64 0.00 41.55 2.59
2111 2558 4.475135 GAAGGGCGCTGGAGGGAC 62.475 72.222 7.64 0.00 34.90 4.46
2112 2559 4.722535 AGAAGGGCGCTGGAGGGA 62.723 66.667 7.64 0.00 0.00 4.20
2113 2560 4.168291 GAGAAGGGCGCTGGAGGG 62.168 72.222 7.64 0.00 0.00 4.30
2114 2561 4.168291 GGAGAAGGGCGCTGGAGG 62.168 72.222 7.64 0.00 0.00 4.30
2115 2562 3.080121 AGGAGAAGGGCGCTGGAG 61.080 66.667 7.64 0.00 0.00 3.86
2116 2563 3.077556 GAGGAGAAGGGCGCTGGA 61.078 66.667 7.64 0.00 0.00 3.86
2117 2564 4.168291 GGAGGAGAAGGGCGCTGG 62.168 72.222 7.64 0.00 0.00 4.85
2118 2565 3.080121 AGGAGGAGAAGGGCGCTG 61.080 66.667 7.64 0.00 0.00 5.18
2119 2566 2.762043 GAGGAGGAGAAGGGCGCT 60.762 66.667 7.64 0.00 0.00 5.92
2120 2567 3.855853 GGAGGAGGAGAAGGGCGC 61.856 72.222 0.00 0.00 0.00 6.53
2121 2568 3.532155 CGGAGGAGGAGAAGGGCG 61.532 72.222 0.00 0.00 0.00 6.13
2122 2569 3.855853 GCGGAGGAGGAGAAGGGC 61.856 72.222 0.00 0.00 0.00 5.19
2123 2570 3.157949 GGCGGAGGAGGAGAAGGG 61.158 72.222 0.00 0.00 0.00 3.95
2124 2571 3.532155 CGGCGGAGGAGGAGAAGG 61.532 72.222 0.00 0.00 0.00 3.46
2125 2572 2.352032 AACGGCGGAGGAGGAGAAG 61.352 63.158 13.24 0.00 0.00 2.85
2126 2573 2.283676 AACGGCGGAGGAGGAGAA 60.284 61.111 13.24 0.00 0.00 2.87
2127 2574 3.068691 CAACGGCGGAGGAGGAGA 61.069 66.667 13.24 0.00 0.00 3.71
2128 2575 4.821589 GCAACGGCGGAGGAGGAG 62.822 72.222 13.24 0.00 0.00 3.69
2185 2632 3.519930 GAGAGACCCTCCGTCGCC 61.520 72.222 0.00 0.00 46.92 5.54
2193 2640 1.000612 GAACGGGAGGAGAGACCCT 59.999 63.158 0.00 0.00 43.57 4.34
2194 2641 2.059190 GGAACGGGAGGAGAGACCC 61.059 68.421 0.00 0.00 42.43 4.46
2195 2642 2.059190 GGGAACGGGAGGAGAGACC 61.059 68.421 0.00 0.00 39.35 3.85
2196 2643 3.618652 GGGAACGGGAGGAGAGAC 58.381 66.667 0.00 0.00 0.00 3.36
2230 2677 4.570663 CCGCGGATCAGGACGTCC 62.571 72.222 27.67 27.67 0.00 4.79
2231 2678 4.570663 CCCGCGGATCAGGACGTC 62.571 72.222 30.73 7.13 0.00 4.34
2234 2681 4.530857 CACCCCGCGGATCAGGAC 62.531 72.222 30.73 0.00 0.00 3.85
2253 2700 4.489771 CACACCATCGGGAGGGCC 62.490 72.222 0.00 0.00 35.25 5.80
2254 2701 4.489771 CCACACCATCGGGAGGGC 62.490 72.222 0.00 0.00 35.25 5.19
2255 2702 4.489771 GCCACACCATCGGGAGGG 62.490 72.222 0.00 0.00 38.43 4.30
2256 2703 4.838152 CGCCACACCATCGGGAGG 62.838 72.222 0.00 0.00 38.05 4.30
2257 2704 4.838152 CCGCCACACCATCGGGAG 62.838 72.222 0.00 0.00 39.52 4.30
2259 2706 4.175337 ATCCGCCACACCATCGGG 62.175 66.667 0.00 0.00 43.10 5.14
2260 2707 2.588877 GATCCGCCACACCATCGG 60.589 66.667 0.00 0.00 44.16 4.18
2261 2708 2.588877 GGATCCGCCACACCATCG 60.589 66.667 0.00 0.00 36.34 3.84
2262 2709 2.203209 GGGATCCGCCACACCATC 60.203 66.667 5.45 0.00 38.95 3.51
2263 2710 4.175337 CGGGATCCGCCACACCAT 62.175 66.667 5.45 0.00 41.17 3.55
2266 2713 4.530857 CTCCGGGATCCGCCACAC 62.531 72.222 5.45 0.00 46.86 3.82


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.