Multiple sequence alignment - TraesCS1B01G109100

Loading Multiple Alignment...

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 TraesCS1B01G109100 chr1B 100.000 3894 0 0 1 3894 121012101 121008208 0.000000e+00 7191.0
1 TraesCS1B01G109100 chr1D 92.192 3266 163 50 681 3894 77393243 77390018 0.000000e+00 4534.0
2 TraesCS1B01G109100 chr1A 92.623 2833 118 47 1106 3894 108775698 108772913 0.000000e+00 3989.0
3 TraesCS1B01G109100 chr1A 81.556 450 60 10 173 618 108778346 108777916 2.230000e-92 350.0
4 TraesCS1B01G109100 chr1A 77.899 276 19 18 731 990 108775987 108775738 2.440000e-27 134.0
5 TraesCS1B01G109100 chr1A 89.744 78 8 0 2 79 108778480 108778403 2.480000e-17 100.0
6 TraesCS1B01G109100 chr7A 87.403 770 76 11 1895 2657 477173444 477172689 0.000000e+00 865.0
7 TraesCS1B01G109100 chr7A 83.974 312 29 8 1583 1885 477182080 477181781 2.960000e-71 279.0
8 TraesCS1B01G109100 chr2D 80.347 173 22 7 1 165 610756922 610757090 1.900000e-23 121.0
9 TraesCS1B01G109100 chr2A 81.290 155 24 4 1 151 750424642 750424795 1.900000e-23 121.0
10 TraesCS1B01G109100 chr2B 92.647 68 5 0 11 78 757015500 757015567 8.900000e-17 99.0
11 TraesCS1B01G109100 chr2B 88.235 85 7 2 1 82 757452645 757452729 8.900000e-17 99.0
12 TraesCS1B01G109100 chr2B 83.516 91 11 2 3 89 757394046 757394136 8.970000e-12 82.4
13 TraesCS1B01G109100 chr7D 87.059 85 8 1 1 82 498284754 498284838 4.140000e-15 93.5


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 TraesCS1B01G109100 chr1B 121008208 121012101 3893 True 7191.00 7191 100.0000 1 3894 1 chr1B.!!$R1 3893
1 TraesCS1B01G109100 chr1D 77390018 77393243 3225 True 4534.00 4534 92.1920 681 3894 1 chr1D.!!$R1 3213
2 TraesCS1B01G109100 chr1A 108772913 108778480 5567 True 1143.25 3989 85.4555 2 3894 4 chr1A.!!$R1 3892
3 TraesCS1B01G109100 chr7A 477172689 477173444 755 True 865.00 865 87.4030 1895 2657 1 chr7A.!!$R1 762

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
324 325 0.530744 TCAGCACCGTACCACATCTC 59.469 55.0 0.00 0.0 0.00 2.75 F
506 511 0.658897 CCAAACAGGTTGTACGCGTT 59.341 50.0 20.78 0.8 35.23 4.84 F
1697 3576 0.107654 AGCTTGTTCTATCCGGGTGC 60.108 55.0 0.00 0.0 0.00 5.01 F
2500 4403 0.109723 CGGGGAAGAAACCACCTTGA 59.890 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 3296 0.100682 GCAGCTCCTCGTTGTCGATA 59.899 55.000 0.00 0.00 45.21 2.92 R
2462 4365 0.039798 GTCTCAGTTACGTGGCACGA 60.040 55.000 42.65 24.75 46.05 4.35 R
2661 4564 0.248215 ACGTCTTTACCCGTATCGCG 60.248 55.000 0.00 0.00 35.16 5.87 R
3694 5612 3.516586 TGTACCAGAACTTCATCTCCCA 58.483 45.455 0.00 0.00 0.00 4.37 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
21 22 3.356529 AAGAACGGATCAAGGCAGAAT 57.643 42.857 0.00 0.00 0.00 2.40
28 29 3.242543 CGGATCAAGGCAGAATTCTTTCG 60.243 47.826 4.86 0.00 36.93 3.46
40 41 7.641802 GGCAGAATTCTTTCGATCAAATACTTC 59.358 37.037 4.86 0.00 36.93 3.01
79 80 9.777008 AAAGAATGAAGGTATAATTTTGGGGTA 57.223 29.630 0.00 0.00 0.00 3.69
80 81 9.951866 AAGAATGAAGGTATAATTTTGGGGTAT 57.048 29.630 0.00 0.00 0.00 2.73
83 84 9.822727 AATGAAGGTATAATTTTGGGGTATAGG 57.177 33.333 0.00 0.00 0.00 2.57
84 85 7.235804 TGAAGGTATAATTTTGGGGTATAGGC 58.764 38.462 0.00 0.00 0.00 3.93
85 86 7.074494 TGAAGGTATAATTTTGGGGTATAGGCT 59.926 37.037 0.00 0.00 0.00 4.58
86 87 8.528543 AAGGTATAATTTTGGGGTATAGGCTA 57.471 34.615 0.00 0.00 0.00 3.93
89 90 7.609146 GGTATAATTTTGGGGTATAGGCTACAC 59.391 40.741 0.00 0.00 0.00 2.90
91 92 4.497291 TTTTGGGGTATAGGCTACACTG 57.503 45.455 2.55 0.00 0.00 3.66
94 95 4.480777 TGGGGTATAGGCTACACTGTAT 57.519 45.455 2.55 0.00 0.00 2.29
95 96 4.157246 TGGGGTATAGGCTACACTGTATG 58.843 47.826 2.55 0.00 0.00 2.39
96 97 4.158015 GGGGTATAGGCTACACTGTATGT 58.842 47.826 2.55 0.00 46.06 2.29
97 98 4.591924 GGGGTATAGGCTACACTGTATGTT 59.408 45.833 2.55 0.00 43.19 2.71
98 99 5.279356 GGGGTATAGGCTACACTGTATGTTC 60.279 48.000 2.55 0.00 43.19 3.18
99 100 5.458891 GGTATAGGCTACACTGTATGTTCG 58.541 45.833 2.55 0.00 43.19 3.95
100 101 5.009410 GGTATAGGCTACACTGTATGTTCGT 59.991 44.000 2.55 0.00 43.19 3.85
101 102 3.955650 AGGCTACACTGTATGTTCGTT 57.044 42.857 0.00 0.00 43.19 3.85
102 103 4.267349 AGGCTACACTGTATGTTCGTTT 57.733 40.909 0.00 0.00 43.19 3.60
103 104 4.243270 AGGCTACACTGTATGTTCGTTTC 58.757 43.478 0.00 0.00 43.19 2.78
104 105 3.370061 GGCTACACTGTATGTTCGTTTCC 59.630 47.826 0.00 0.00 43.19 3.13
105 106 3.370061 GCTACACTGTATGTTCGTTTCCC 59.630 47.826 0.00 0.00 43.19 3.97
106 107 3.764237 ACACTGTATGTTCGTTTCCCT 57.236 42.857 0.00 0.00 38.98 4.20
107 108 3.660865 ACACTGTATGTTCGTTTCCCTC 58.339 45.455 0.00 0.00 38.98 4.30
108 109 3.323979 ACACTGTATGTTCGTTTCCCTCT 59.676 43.478 0.00 0.00 38.98 3.69
109 110 3.927142 CACTGTATGTTCGTTTCCCTCTC 59.073 47.826 0.00 0.00 0.00 3.20
110 111 3.833070 ACTGTATGTTCGTTTCCCTCTCT 59.167 43.478 0.00 0.00 0.00 3.10
111 112 5.014858 ACTGTATGTTCGTTTCCCTCTCTA 58.985 41.667 0.00 0.00 0.00 2.43
112 113 5.479375 ACTGTATGTTCGTTTCCCTCTCTAA 59.521 40.000 0.00 0.00 0.00 2.10
113 114 6.154706 ACTGTATGTTCGTTTCCCTCTCTAAT 59.845 38.462 0.00 0.00 0.00 1.73
114 115 7.341256 ACTGTATGTTCGTTTCCCTCTCTAATA 59.659 37.037 0.00 0.00 0.00 0.98
115 116 8.246430 TGTATGTTCGTTTCCCTCTCTAATAT 57.754 34.615 0.00 0.00 0.00 1.28
116 117 8.358148 TGTATGTTCGTTTCCCTCTCTAATATC 58.642 37.037 0.00 0.00 0.00 1.63
117 118 6.785337 TGTTCGTTTCCCTCTCTAATATCA 57.215 37.500 0.00 0.00 0.00 2.15
118 119 6.806751 TGTTCGTTTCCCTCTCTAATATCAG 58.193 40.000 0.00 0.00 0.00 2.90
119 120 5.455056 TCGTTTCCCTCTCTAATATCAGC 57.545 43.478 0.00 0.00 0.00 4.26
120 121 5.141182 TCGTTTCCCTCTCTAATATCAGCT 58.859 41.667 0.00 0.00 0.00 4.24
124 125 4.085733 TCCCTCTCTAATATCAGCTCTGC 58.914 47.826 0.00 0.00 0.00 4.26
126 127 4.467082 CCCTCTCTAATATCAGCTCTGCAT 59.533 45.833 0.00 0.00 0.00 3.96
143 144 6.677781 TCTGCATAAGTATTTTGTACTGCC 57.322 37.500 0.00 0.00 29.32 4.85
145 146 6.316140 TCTGCATAAGTATTTTGTACTGCCAG 59.684 38.462 0.00 0.00 29.32 4.85
166 167 1.825474 ACAGACTGAACCATCTACCCG 59.175 52.381 10.08 0.00 0.00 5.28
167 168 1.825474 CAGACTGAACCATCTACCCGT 59.175 52.381 0.00 0.00 0.00 5.28
168 169 1.825474 AGACTGAACCATCTACCCGTG 59.175 52.381 0.00 0.00 0.00 4.94
169 170 1.822990 GACTGAACCATCTACCCGTGA 59.177 52.381 0.00 0.00 0.00 4.35
170 171 2.232941 GACTGAACCATCTACCCGTGAA 59.767 50.000 0.00 0.00 0.00 3.18
171 172 2.028385 ACTGAACCATCTACCCGTGAAC 60.028 50.000 0.00 0.00 0.00 3.18
172 173 1.067425 TGAACCATCTACCCGTGAACG 60.067 52.381 0.00 0.00 39.44 3.95
173 174 0.971386 AACCATCTACCCGTGAACGT 59.029 50.000 1.75 0.00 37.74 3.99
174 175 1.838112 ACCATCTACCCGTGAACGTA 58.162 50.000 1.75 0.00 37.74 3.57
175 176 2.381911 ACCATCTACCCGTGAACGTAT 58.618 47.619 1.75 0.00 37.74 3.06
176 177 3.554934 ACCATCTACCCGTGAACGTATA 58.445 45.455 1.75 0.00 37.74 1.47
177 178 4.147321 ACCATCTACCCGTGAACGTATAT 58.853 43.478 1.75 0.00 37.74 0.86
178 179 5.316167 ACCATCTACCCGTGAACGTATATA 58.684 41.667 1.75 0.00 37.74 0.86
179 180 5.948162 ACCATCTACCCGTGAACGTATATAT 59.052 40.000 1.75 0.00 37.74 0.86
180 181 6.094603 ACCATCTACCCGTGAACGTATATATC 59.905 42.308 1.75 0.00 37.74 1.63
181 182 6.318144 CCATCTACCCGTGAACGTATATATCT 59.682 42.308 1.75 0.00 37.74 1.98
182 183 6.732531 TCTACCCGTGAACGTATATATCTG 57.267 41.667 1.75 0.00 37.74 2.90
183 184 6.466812 TCTACCCGTGAACGTATATATCTGA 58.533 40.000 1.75 0.00 37.74 3.27
184 185 5.368256 ACCCGTGAACGTATATATCTGAC 57.632 43.478 1.75 0.00 37.74 3.51
196 197 9.627395 ACGTATATATCTGACACTATTTTGCTC 57.373 33.333 0.00 0.00 0.00 4.26
203 204 4.385825 TGACACTATTTTGCTCGTTTCCT 58.614 39.130 0.00 0.00 0.00 3.36
246 247 4.553678 TCGATAGAATTCCCAGGGTTACT 58.446 43.478 5.01 4.10 46.15 2.24
255 256 3.600433 TCCCAGGGTTACTTTCTGGTTA 58.400 45.455 5.01 4.71 44.78 2.85
264 265 7.447545 AGGGTTACTTTCTGGTTAACAATCTTC 59.552 37.037 8.10 0.00 0.00 2.87
267 268 8.553696 GTTACTTTCTGGTTAACAATCTTCGAA 58.446 33.333 8.10 0.00 0.00 3.71
268 269 7.562454 ACTTTCTGGTTAACAATCTTCGAAA 57.438 32.000 8.10 1.53 0.00 3.46
270 271 8.076178 ACTTTCTGGTTAACAATCTTCGAAATG 58.924 33.333 8.10 1.49 0.00 2.32
275 276 6.149633 GGTTAACAATCTTCGAAATGCTGTT 58.850 36.000 8.10 14.92 0.00 3.16
279 280 5.830912 ACAATCTTCGAAATGCTGTTTCAA 58.169 33.333 0.00 7.43 0.00 2.69
287 288 4.676924 CGAAATGCTGTTTCAAAGAAGACC 59.323 41.667 13.15 0.00 0.00 3.85
297 298 3.554934 TCAAAGAAGACCTGTGCAATGT 58.445 40.909 0.00 0.00 29.89 2.71
309 310 1.445582 GCAATGTGCAGCCTTCAGC 60.446 57.895 0.00 0.00 44.26 4.26
323 324 0.973632 TTCAGCACCGTACCACATCT 59.026 50.000 0.00 0.00 0.00 2.90
324 325 0.530744 TCAGCACCGTACCACATCTC 59.469 55.000 0.00 0.00 0.00 2.75
328 329 1.406887 GCACCGTACCACATCTCCATT 60.407 52.381 0.00 0.00 0.00 3.16
377 379 5.522456 CGTATAGTGTTTACGGCTTCCATA 58.478 41.667 0.00 0.00 38.94 2.74
379 381 7.307694 CGTATAGTGTTTACGGCTTCCATATA 58.692 38.462 0.00 0.00 38.94 0.86
394 396 9.686683 GGCTTCCATATAAATACTGGATTATGT 57.313 33.333 0.00 0.00 38.79 2.29
409 411 8.349983 ACTGGATTATGTATTTTTGCCGTATTC 58.650 33.333 0.00 0.00 0.00 1.75
410 412 7.653647 TGGATTATGTATTTTTGCCGTATTCC 58.346 34.615 0.00 0.00 0.00 3.01
411 413 7.504238 TGGATTATGTATTTTTGCCGTATTCCT 59.496 33.333 0.00 0.00 0.00 3.36
412 414 7.807907 GGATTATGTATTTTTGCCGTATTCCTG 59.192 37.037 0.00 0.00 0.00 3.86
413 415 4.364415 TGTATTTTTGCCGTATTCCTGC 57.636 40.909 0.00 0.00 0.00 4.85
414 416 4.013728 TGTATTTTTGCCGTATTCCTGCT 58.986 39.130 0.00 0.00 0.00 4.24
415 417 3.782889 ATTTTTGCCGTATTCCTGCTC 57.217 42.857 0.00 0.00 0.00 4.26
416 418 2.489938 TTTTGCCGTATTCCTGCTCT 57.510 45.000 0.00 0.00 0.00 4.09
417 419 3.620427 TTTTGCCGTATTCCTGCTCTA 57.380 42.857 0.00 0.00 0.00 2.43
418 420 3.620427 TTTGCCGTATTCCTGCTCTAA 57.380 42.857 0.00 0.00 0.00 2.10
419 421 3.838244 TTGCCGTATTCCTGCTCTAAT 57.162 42.857 0.00 0.00 0.00 1.73
420 422 3.838244 TGCCGTATTCCTGCTCTAATT 57.162 42.857 0.00 0.00 0.00 1.40
421 423 4.948341 TGCCGTATTCCTGCTCTAATTA 57.052 40.909 0.00 0.00 0.00 1.40
458 462 8.924511 ATATCCTGTTGTAATATTGGGTTGAG 57.075 34.615 0.00 0.00 0.00 3.02
459 463 6.134535 TCCTGTTGTAATATTGGGTTGAGT 57.865 37.500 0.00 0.00 0.00 3.41
471 475 2.081462 GGGTTGAGTGGGTTTATGTCG 58.919 52.381 0.00 0.00 0.00 4.35
477 481 1.073284 AGTGGGTTTATGTCGGTTGCT 59.927 47.619 0.00 0.00 0.00 3.91
485 489 5.051307 GGTTTATGTCGGTTGCTTGTTTTTC 60.051 40.000 0.00 0.00 0.00 2.29
486 490 3.791973 ATGTCGGTTGCTTGTTTTTCA 57.208 38.095 0.00 0.00 0.00 2.69
487 491 2.869897 TGTCGGTTGCTTGTTTTTCAC 58.130 42.857 0.00 0.00 0.00 3.18
489 493 1.819288 TCGGTTGCTTGTTTTTCACCA 59.181 42.857 0.00 0.00 0.00 4.17
492 497 3.181525 CGGTTGCTTGTTTTTCACCAAAC 60.182 43.478 0.00 0.00 37.20 2.93
495 500 3.594134 TGCTTGTTTTTCACCAAACAGG 58.406 40.909 4.53 4.53 45.21 4.00
506 511 0.658897 CCAAACAGGTTGTACGCGTT 59.341 50.000 20.78 0.80 35.23 4.84
512 517 4.439305 ACAGGTTGTACGCGTTATCTTA 57.561 40.909 20.78 0.00 0.00 2.10
513 518 5.002464 ACAGGTTGTACGCGTTATCTTAT 57.998 39.130 20.78 0.00 0.00 1.73
521 526 4.252971 ACGCGTTATCTTATACTGCCAT 57.747 40.909 5.58 0.00 0.00 4.40
529 534 7.334421 CGTTATCTTATACTGCCATTTATGCCT 59.666 37.037 0.00 0.00 0.00 4.75
534 539 2.659428 ACTGCCATTTATGCCTTCCTC 58.341 47.619 0.00 0.00 0.00 3.71
541 546 2.961526 TTATGCCTTCCTCGTGACTC 57.038 50.000 0.00 0.00 0.00 3.36
542 547 1.847328 TATGCCTTCCTCGTGACTCA 58.153 50.000 0.00 0.00 0.00 3.41
543 548 0.976641 ATGCCTTCCTCGTGACTCAA 59.023 50.000 0.00 0.00 0.00 3.02
544 549 0.756294 TGCCTTCCTCGTGACTCAAA 59.244 50.000 0.00 0.00 0.00 2.69
551 556 1.613925 CCTCGTGACTCAAAGACCAGA 59.386 52.381 0.00 0.00 0.00 3.86
555 560 3.069586 TCGTGACTCAAAGACCAGAATGT 59.930 43.478 0.00 0.00 0.00 2.71
560 565 3.181451 ACTCAAAGACCAGAATGTGCTCA 60.181 43.478 0.00 0.00 0.00 4.26
562 567 4.401022 TCAAAGACCAGAATGTGCTCATT 58.599 39.130 13.57 13.57 45.57 2.57
565 570 6.660521 TCAAAGACCAGAATGTGCTCATTATT 59.339 34.615 13.66 3.49 43.33 1.40
586 591 4.093472 TCTTTTTCCTTGGACAATCCGA 57.907 40.909 0.00 0.00 40.17 4.55
590 595 7.570132 TCTTTTTCCTTGGACAATCCGATATA 58.430 34.615 0.00 0.00 40.17 0.86
598 603 5.422145 TGGACAATCCGATATATGCTCATG 58.578 41.667 0.00 0.00 40.17 3.07
600 605 5.877012 GGACAATCCGATATATGCTCATGTT 59.123 40.000 0.00 0.00 0.00 2.71
607 612 5.007039 CCGATATATGCTCATGTTGGTATGC 59.993 44.000 0.00 0.00 0.00 3.14
609 614 1.311859 ATGCTCATGTTGGTATGCGG 58.688 50.000 0.00 0.00 0.00 5.69
612 617 0.930310 CTCATGTTGGTATGCGGACG 59.070 55.000 0.00 0.00 0.00 4.79
615 620 1.466950 CATGTTGGTATGCGGACGTTT 59.533 47.619 0.00 0.00 0.00 3.60
616 621 1.149987 TGTTGGTATGCGGACGTTTC 58.850 50.000 0.00 0.00 0.00 2.78
617 622 1.270412 TGTTGGTATGCGGACGTTTCT 60.270 47.619 0.00 0.00 0.00 2.52
618 623 1.802365 GTTGGTATGCGGACGTTTCTT 59.198 47.619 0.00 0.00 0.00 2.52
619 624 1.434555 TGGTATGCGGACGTTTCTTG 58.565 50.000 0.00 0.00 0.00 3.02
623 670 2.386661 ATGCGGACGTTTCTTGAGAT 57.613 45.000 0.00 0.00 0.00 2.75
631 678 5.120830 CGGACGTTTCTTGAGATTCTTGAAT 59.879 40.000 0.00 0.00 0.00 2.57
636 683 8.499162 ACGTTTCTTGAGATTCTTGAATAACAG 58.501 33.333 0.00 0.00 0.00 3.16
650 697 5.500234 TGAATAACAGAATCCCTTGTGAGG 58.500 41.667 0.00 0.00 43.15 3.86
651 698 5.014123 TGAATAACAGAATCCCTTGTGAGGT 59.986 40.000 0.00 0.00 41.85 3.85
653 700 3.884037 ACAGAATCCCTTGTGAGGTTT 57.116 42.857 0.00 0.00 41.85 3.27
654 701 4.184649 ACAGAATCCCTTGTGAGGTTTT 57.815 40.909 0.00 0.00 41.85 2.43
655 702 3.891366 ACAGAATCCCTTGTGAGGTTTTG 59.109 43.478 0.00 0.00 41.85 2.44
657 704 4.217118 CAGAATCCCTTGTGAGGTTTTGAG 59.783 45.833 0.00 0.00 41.85 3.02
659 2443 1.494721 TCCCTTGTGAGGTTTTGAGCT 59.505 47.619 0.00 0.00 41.85 4.09
666 2450 7.255801 CCCTTGTGAGGTTTTGAGCTAAAATAA 60.256 37.037 0.00 0.00 41.85 1.40
668 2452 6.664515 TGTGAGGTTTTGAGCTAAAATAACG 58.335 36.000 0.00 0.00 40.17 3.18
674 2458 8.021396 AGGTTTTGAGCTAAAATAACGTTGATC 58.979 33.333 11.99 1.44 40.17 2.92
675 2459 7.806014 GGTTTTGAGCTAAAATAACGTTGATCA 59.194 33.333 11.99 4.39 40.17 2.92
679 2463 8.039603 TGAGCTAAAATAACGTTGATCAATGT 57.960 30.769 24.54 24.54 41.91 2.71
703 2526 2.862541 AGAAAAAGGGCAAAATTGGGC 58.137 42.857 0.00 0.00 0.00 5.36
907 2737 1.539929 CCAGGTCGATGGAGATTGCTC 60.540 57.143 0.00 0.00 43.57 4.26
963 2806 2.288152 CCCACATCAACAAAAACCCTCG 60.288 50.000 0.00 0.00 0.00 4.63
1049 2897 2.009774 CGACATGTGAACCTCCATTCC 58.990 52.381 1.15 0.00 0.00 3.01
1390 3257 7.213216 TCAGAGTTTGCATGCATTAAAAGTA 57.787 32.000 23.37 0.00 0.00 2.24
1406 3273 4.773323 AAAGTATGAGGCTTGCAACTTC 57.227 40.909 0.00 0.00 0.00 3.01
1429 3296 2.203596 ACGGACTCCAACGGGACT 60.204 61.111 0.00 0.00 38.64 3.85
1452 3319 2.811317 CAACGAGGAGCTGCGGAC 60.811 66.667 0.00 0.00 0.00 4.79
1516 3383 2.049433 GACGTGCACCGCTACTGT 60.049 61.111 12.15 0.43 41.42 3.55
1620 3487 3.784719 GCGCCGGGTAAGGGGTAA 61.785 66.667 2.18 0.00 44.96 2.85
1621 3488 2.187685 CGCCGGGTAAGGGGTAAC 59.812 66.667 2.18 0.00 39.15 2.50
1622 3489 2.361567 CGCCGGGTAAGGGGTAACT 61.362 63.158 2.18 0.00 39.15 2.24
1623 3490 1.042559 CGCCGGGTAAGGGGTAACTA 61.043 60.000 2.18 0.00 39.15 2.24
1624 3491 0.755079 GCCGGGTAAGGGGTAACTAG 59.245 60.000 2.18 0.00 0.00 2.57
1626 3493 2.968271 CCGGGTAAGGGGTAACTAGAT 58.032 52.381 0.00 0.00 0.00 1.98
1627 3494 2.631545 CCGGGTAAGGGGTAACTAGATG 59.368 54.545 0.00 0.00 0.00 2.90
1628 3495 3.569491 CGGGTAAGGGGTAACTAGATGA 58.431 50.000 0.00 0.00 0.00 2.92
1629 3496 4.158015 CGGGTAAGGGGTAACTAGATGAT 58.842 47.826 0.00 0.00 0.00 2.45
1630 3497 4.021368 CGGGTAAGGGGTAACTAGATGATG 60.021 50.000 0.00 0.00 0.00 3.07
1631 3498 4.262938 GGGTAAGGGGTAACTAGATGATGC 60.263 50.000 0.00 0.00 0.00 3.91
1633 3500 5.071923 GGTAAGGGGTAACTAGATGATGCTT 59.928 44.000 0.00 0.00 0.00 3.91
1634 3501 4.965200 AGGGGTAACTAGATGATGCTTC 57.035 45.455 0.00 0.00 0.00 3.86
1636 3503 4.971924 AGGGGTAACTAGATGATGCTTCTT 59.028 41.667 0.00 0.00 0.00 2.52
1639 3506 5.988561 GGGTAACTAGATGATGCTTCTTCTG 59.011 44.000 21.46 15.42 37.08 3.02
1640 3507 6.407525 GGGTAACTAGATGATGCTTCTTCTGT 60.408 42.308 21.46 15.87 37.08 3.41
1641 3508 6.699642 GGTAACTAGATGATGCTTCTTCTGTC 59.300 42.308 21.46 10.78 37.08 3.51
1642 3509 5.275067 ACTAGATGATGCTTCTTCTGTCC 57.725 43.478 21.46 0.00 37.08 4.02
1643 3510 4.961730 ACTAGATGATGCTTCTTCTGTCCT 59.038 41.667 21.46 4.59 37.08 3.85
1647 3523 2.169352 TGATGCTTCTTCTGTCCTAGGC 59.831 50.000 2.96 0.00 0.00 3.93
1659 3535 4.116238 CTGTCCTAGGCGAATTCTTCTTC 58.884 47.826 2.96 0.00 0.00 2.87
1661 3537 4.162320 TGTCCTAGGCGAATTCTTCTTCAT 59.838 41.667 2.96 0.00 0.00 2.57
1662 3538 4.509600 GTCCTAGGCGAATTCTTCTTCATG 59.490 45.833 2.96 0.00 0.00 3.07
1663 3539 4.405680 TCCTAGGCGAATTCTTCTTCATGA 59.594 41.667 2.96 0.00 0.00 3.07
1664 3540 5.070981 TCCTAGGCGAATTCTTCTTCATGAT 59.929 40.000 2.96 0.00 0.00 2.45
1691 3570 5.423015 TCACTGATGAAGCTTGTTCTATCC 58.577 41.667 2.10 0.00 0.00 2.59
1692 3571 4.269603 CACTGATGAAGCTTGTTCTATCCG 59.730 45.833 2.10 0.00 0.00 4.18
1693 3572 3.797039 TGATGAAGCTTGTTCTATCCGG 58.203 45.455 2.10 0.00 0.00 5.14
1694 3573 2.691409 TGAAGCTTGTTCTATCCGGG 57.309 50.000 2.10 0.00 0.00 5.73
1695 3574 1.906574 TGAAGCTTGTTCTATCCGGGT 59.093 47.619 2.10 0.00 0.00 5.28
1696 3575 2.280628 GAAGCTTGTTCTATCCGGGTG 58.719 52.381 2.10 0.00 0.00 4.61
1697 3576 0.107654 AGCTTGTTCTATCCGGGTGC 60.108 55.000 0.00 0.00 0.00 5.01
1876 3755 2.359850 CCCACCCACATCACCACG 60.360 66.667 0.00 0.00 0.00 4.94
1882 3761 1.079197 CCACATCACCACGCAGCTA 60.079 57.895 0.00 0.00 0.00 3.32
1893 3772 1.657594 CACGCAGCTATTCAGTCAGTG 59.342 52.381 0.00 0.00 0.00 3.66
1903 3786 0.602106 TCAGTCAGTGCTCTTGCTGC 60.602 55.000 10.03 0.00 40.48 5.25
1923 3810 1.681780 CGCTGCCCCCTTTATTTCTCA 60.682 52.381 0.00 0.00 0.00 3.27
2204 4097 5.600908 TTTGCAAGTTAATCCTACGTGTC 57.399 39.130 0.00 0.00 0.00 3.67
2233 4126 2.561478 AGTGTCCGTTTGTTATGGCT 57.439 45.000 0.00 0.00 32.49 4.75
2242 4135 4.156922 CCGTTTGTTATGGCTTCATTGGTA 59.843 41.667 0.00 0.00 32.59 3.25
2269 4162 1.479323 CAAATGTTCAGGGCAGATGGG 59.521 52.381 0.00 0.00 0.00 4.00
2380 4283 6.529125 GGAACACTACAAATTTGCATCATCAG 59.471 38.462 18.12 6.62 0.00 2.90
2387 4290 7.789273 ACAAATTTGCATCATCAGTTCAAAA 57.211 28.000 18.12 0.00 31.55 2.44
2392 4295 7.467557 TTTGCATCATCAGTTCAAAAGAAAC 57.532 32.000 0.00 0.00 0.00 2.78
2395 4298 5.984926 GCATCATCAGTTCAAAAGAAACCAA 59.015 36.000 0.00 0.00 0.00 3.67
2406 4309 6.913170 TCAAAAGAAACCAATCTCATGTAGC 58.087 36.000 0.00 0.00 0.00 3.58
2423 4326 0.584876 AGCGTACAAAAACGACCTGC 59.415 50.000 0.00 0.00 45.68 4.85
2441 4344 3.881688 CCTGCCTACATTTCCTCAGAATG 59.118 47.826 0.00 0.00 39.73 2.67
2443 4346 2.289002 GCCTACATTTCCTCAGAATGCG 59.711 50.000 0.00 0.00 37.89 4.73
2461 4364 1.593196 CGGAACAAAACTGAGAGCCA 58.407 50.000 0.00 0.00 0.00 4.75
2462 4365 2.154462 CGGAACAAAACTGAGAGCCAT 58.846 47.619 0.00 0.00 0.00 4.40
2467 4370 1.135859 CAAAACTGAGAGCCATCGTGC 60.136 52.381 0.00 0.00 0.00 5.34
2476 4379 1.740296 GCCATCGTGCCACGTAACT 60.740 57.895 17.83 0.00 43.14 2.24
2490 4393 1.542915 CGTAACTGAGACGGGGAAGAA 59.457 52.381 0.00 0.00 36.66 2.52
2493 4396 0.685660 ACTGAGACGGGGAAGAAACC 59.314 55.000 0.00 0.00 0.00 3.27
2497 4400 0.767060 AGACGGGGAAGAAACCACCT 60.767 55.000 0.00 0.00 0.00 4.00
2498 4401 0.109913 GACGGGGAAGAAACCACCTT 59.890 55.000 0.00 0.00 0.00 3.50
2499 4402 0.179001 ACGGGGAAGAAACCACCTTG 60.179 55.000 0.00 0.00 0.00 3.61
2500 4403 0.109723 CGGGGAAGAAACCACCTTGA 59.890 55.000 0.00 0.00 0.00 3.02
2501 4404 1.477923 CGGGGAAGAAACCACCTTGAA 60.478 52.381 0.00 0.00 0.00 2.69
2502 4405 2.673258 GGGGAAGAAACCACCTTGAAA 58.327 47.619 0.00 0.00 0.00 2.69
2503 4406 3.035363 GGGGAAGAAACCACCTTGAAAA 58.965 45.455 0.00 0.00 0.00 2.29
2504 4407 3.069586 GGGGAAGAAACCACCTTGAAAAG 59.930 47.826 0.00 0.00 45.69 2.27
2531 4434 5.233083 ACAGATCACATCAAAACTCCAGA 57.767 39.130 0.00 0.00 0.00 3.86
2587 4490 1.770324 CCAGCCAACTCCTTCCCTT 59.230 57.895 0.00 0.00 0.00 3.95
2610 4513 1.063649 CTTGGCGATCACATGCTGC 59.936 57.895 0.00 0.00 0.00 5.25
2616 4519 0.741927 CGATCACATGCTGCCTGACA 60.742 55.000 11.93 0.00 0.00 3.58
2640 4543 4.437239 ACATCACGATTCCATCTCTCAAC 58.563 43.478 0.00 0.00 0.00 3.18
2642 4545 4.743057 TCACGATTCCATCTCTCAACAT 57.257 40.909 0.00 0.00 0.00 2.71
2646 4549 4.202202 ACGATTCCATCTCTCAACATCTCC 60.202 45.833 0.00 0.00 0.00 3.71
2729 4632 3.599343 TCAAGGTCTCAAACATCATCCG 58.401 45.455 0.00 0.00 0.00 4.18
2740 4643 2.934887 ACATCATCCGGAAATGCATGA 58.065 42.857 23.25 15.77 0.00 3.07
2838 4741 3.305629 CGAGCATCTCAGCAACTAGTTTC 59.694 47.826 5.07 0.24 36.85 2.78
2926 4829 6.843069 ACTGCAATGACACCAAAATAAAAC 57.157 33.333 0.00 0.00 0.00 2.43
2938 4841 7.923878 ACACCAAAATAAAACAGGAATACACAC 59.076 33.333 0.00 0.00 0.00 3.82
2949 4852 9.691362 AAACAGGAATACACACATGTTAAATTC 57.309 29.630 0.00 3.71 39.46 2.17
2950 4853 8.402798 ACAGGAATACACACATGTTAAATTCA 57.597 30.769 16.05 0.00 40.48 2.57
2951 4854 9.023962 ACAGGAATACACACATGTTAAATTCAT 57.976 29.630 16.05 9.99 40.48 2.57
2953 4856 8.686334 AGGAATACACACATGTTAAATTCATCC 58.314 33.333 16.05 9.68 40.48 3.51
2954 4857 8.465999 GGAATACACACATGTTAAATTCATCCA 58.534 33.333 16.05 0.00 40.48 3.41
2956 4859 9.638239 AATACACACATGTTAAATTCATCCAAC 57.362 29.630 0.00 0.00 40.48 3.77
2957 4860 7.288810 ACACACATGTTAAATTCATCCAACT 57.711 32.000 0.00 0.00 34.46 3.16
2958 4861 7.370383 ACACACATGTTAAATTCATCCAACTC 58.630 34.615 0.00 0.00 34.46 3.01
2959 4862 7.231317 ACACACATGTTAAATTCATCCAACTCT 59.769 33.333 0.00 0.00 34.46 3.24
2960 4863 8.729756 CACACATGTTAAATTCATCCAACTCTA 58.270 33.333 0.00 0.00 0.00 2.43
2961 4864 8.950210 ACACATGTTAAATTCATCCAACTCTAG 58.050 33.333 0.00 0.00 0.00 2.43
2964 4867 8.616076 CATGTTAAATTCATCCAACTCTAGGAC 58.384 37.037 0.00 0.00 38.13 3.85
2977 4880 8.424918 TCCAACTCTAGGACATCAATTTATCTC 58.575 37.037 0.00 0.00 0.00 2.75
3039 4950 7.199766 TGTTAAGAAAAATATATGCTTGCCCG 58.800 34.615 0.00 0.00 0.00 6.13
3061 4972 3.234386 GCAAACGAAGCAGTAAATCACC 58.766 45.455 0.00 0.00 0.00 4.02
3066 4977 3.498397 ACGAAGCAGTAAATCACCAACTG 59.502 43.478 0.00 0.00 42.80 3.16
3078 4989 3.419793 CCAACTGGTGAGGCAGAAA 57.580 52.632 0.00 0.00 0.00 2.52
3079 4990 1.242076 CCAACTGGTGAGGCAGAAAG 58.758 55.000 0.00 0.00 0.00 2.62
3094 5005 5.957910 GCAGAAAGCAGTACTGTATGTAG 57.042 43.478 23.44 11.42 44.79 2.74
3105 5021 8.765219 GCAGTACTGTATGTAGTATGGAAAATG 58.235 37.037 23.44 0.00 35.75 2.32
3129 5045 8.607441 TGATAAGAATACAATGTCATACCTGC 57.393 34.615 0.00 0.00 0.00 4.85
3174 5090 2.906047 GCTACATAGCTTGGAGGCG 58.094 57.895 3.56 0.00 45.62 5.52
3657 5575 3.684305 AGGCAAGCAAAAACAGAACAAAC 59.316 39.130 0.00 0.00 0.00 2.93
3660 5578 5.220397 GGCAAGCAAAAACAGAACAAACTAC 60.220 40.000 0.00 0.00 0.00 2.73
3694 5612 4.202253 GGAAAAGGTTTCTGTTCAGGCATT 60.202 41.667 0.00 0.00 38.65 3.56
3769 5693 2.363683 CTGTGAAGGATCCTCTTTGGC 58.636 52.381 16.52 3.43 35.26 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.859165 TCTGCCTTGATCCGTTCTTT 57.141 45.000 0.00 0.00 0.00 2.52
6 7 3.242543 CGAAAGAATTCTGCCTTGATCCG 60.243 47.826 9.17 0.00 33.17 4.18
15 16 8.394121 AGAAGTATTTGATCGAAAGAATTCTGC 58.606 33.333 18.27 3.64 44.37 4.26
28 29 7.039882 TCGTTTGTCCCTAGAAGTATTTGATC 58.960 38.462 0.00 0.00 0.00 2.92
40 41 5.122396 CCTTCATTCTTTCGTTTGTCCCTAG 59.878 44.000 0.00 0.00 0.00 3.02
72 73 3.124856 ACAGTGTAGCCTATACCCCAA 57.875 47.619 0.00 0.00 0.00 4.12
79 80 5.593679 AACGAACATACAGTGTAGCCTAT 57.406 39.130 9.25 0.00 41.14 2.57
80 81 5.395682 AAACGAACATACAGTGTAGCCTA 57.604 39.130 9.25 0.00 41.14 3.93
82 83 3.370061 GGAAACGAACATACAGTGTAGCC 59.630 47.826 9.25 0.00 41.14 3.93
83 84 3.370061 GGGAAACGAACATACAGTGTAGC 59.630 47.826 9.25 0.00 41.14 3.58
84 85 4.817517 AGGGAAACGAACATACAGTGTAG 58.182 43.478 9.25 3.98 41.14 2.74
85 86 4.525487 AGAGGGAAACGAACATACAGTGTA 59.475 41.667 5.24 5.24 41.14 2.90
86 87 3.323979 AGAGGGAAACGAACATACAGTGT 59.676 43.478 0.00 0.00 44.84 3.55
89 90 4.457834 AGAGAGGGAAACGAACATACAG 57.542 45.455 0.00 0.00 0.00 2.74
91 92 8.358148 TGATATTAGAGAGGGAAACGAACATAC 58.642 37.037 0.00 0.00 0.00 2.39
94 95 6.683110 GCTGATATTAGAGAGGGAAACGAACA 60.683 42.308 0.00 0.00 0.00 3.18
95 96 5.692654 GCTGATATTAGAGAGGGAAACGAAC 59.307 44.000 0.00 0.00 0.00 3.95
96 97 5.598830 AGCTGATATTAGAGAGGGAAACGAA 59.401 40.000 0.00 0.00 0.00 3.85
97 98 5.141182 AGCTGATATTAGAGAGGGAAACGA 58.859 41.667 0.00 0.00 0.00 3.85
98 99 5.242838 AGAGCTGATATTAGAGAGGGAAACG 59.757 44.000 0.00 0.00 0.00 3.60
99 100 6.454795 CAGAGCTGATATTAGAGAGGGAAAC 58.545 44.000 0.00 0.00 0.00 2.78
100 101 5.011533 GCAGAGCTGATATTAGAGAGGGAAA 59.988 44.000 0.85 0.00 0.00 3.13
101 102 4.526262 GCAGAGCTGATATTAGAGAGGGAA 59.474 45.833 0.85 0.00 0.00 3.97
102 103 4.085733 GCAGAGCTGATATTAGAGAGGGA 58.914 47.826 0.85 0.00 0.00 4.20
103 104 3.831333 TGCAGAGCTGATATTAGAGAGGG 59.169 47.826 0.85 0.00 0.00 4.30
104 105 5.664294 ATGCAGAGCTGATATTAGAGAGG 57.336 43.478 0.85 0.00 0.00 3.69
105 106 7.829725 ACTTATGCAGAGCTGATATTAGAGAG 58.170 38.462 0.85 0.00 0.00 3.20
106 107 7.773489 ACTTATGCAGAGCTGATATTAGAGA 57.227 36.000 0.85 0.00 0.00 3.10
111 112 9.347240 ACAAAATACTTATGCAGAGCTGATATT 57.653 29.630 0.85 0.00 0.00 1.28
112 113 8.915057 ACAAAATACTTATGCAGAGCTGATAT 57.085 30.769 0.85 0.00 0.00 1.63
113 114 9.261180 GTACAAAATACTTATGCAGAGCTGATA 57.739 33.333 0.85 0.00 0.00 2.15
114 115 7.989741 AGTACAAAATACTTATGCAGAGCTGAT 59.010 33.333 0.85 0.00 0.00 2.90
115 116 7.278646 CAGTACAAAATACTTATGCAGAGCTGA 59.721 37.037 0.85 0.00 0.00 4.26
116 117 7.404985 CAGTACAAAATACTTATGCAGAGCTG 58.595 38.462 0.00 0.00 0.00 4.24
117 118 6.037610 GCAGTACAAAATACTTATGCAGAGCT 59.962 38.462 0.00 0.00 0.00 4.09
118 119 6.195165 GCAGTACAAAATACTTATGCAGAGC 58.805 40.000 0.00 0.00 0.00 4.09
119 120 6.316140 TGGCAGTACAAAATACTTATGCAGAG 59.684 38.462 0.00 0.00 0.00 3.35
120 121 6.176896 TGGCAGTACAAAATACTTATGCAGA 58.823 36.000 0.00 0.00 0.00 4.26
124 125 7.549134 TCTGTCTGGCAGTACAAAATACTTATG 59.451 37.037 15.27 2.72 45.23 1.90
126 127 6.872020 GTCTGTCTGGCAGTACAAAATACTTA 59.128 38.462 15.27 0.00 45.23 2.24
143 144 3.118956 GGGTAGATGGTTCAGTCTGTCTG 60.119 52.174 0.00 0.00 44.85 3.51
145 146 2.159226 CGGGTAGATGGTTCAGTCTGTC 60.159 54.545 0.00 0.00 0.00 3.51
152 153 1.067425 CGTTCACGGGTAGATGGTTCA 60.067 52.381 0.00 0.00 35.37 3.18
153 154 1.067354 ACGTTCACGGGTAGATGGTTC 60.067 52.381 4.07 0.00 44.95 3.62
156 157 4.778534 ATATACGTTCACGGGTAGATGG 57.221 45.455 4.07 0.00 44.95 3.51
157 158 7.065443 TCAGATATATACGTTCACGGGTAGATG 59.935 40.741 4.07 0.00 44.95 2.90
160 161 6.148315 TGTCAGATATATACGTTCACGGGTAG 59.852 42.308 4.07 0.00 44.95 3.18
163 164 5.048921 AGTGTCAGATATATACGTTCACGGG 60.049 44.000 4.07 0.00 44.95 5.28
169 170 9.982651 AGCAAAATAGTGTCAGATATATACGTT 57.017 29.630 0.00 0.00 0.00 3.99
170 171 9.627395 GAGCAAAATAGTGTCAGATATATACGT 57.373 33.333 0.00 0.00 0.00 3.57
171 172 8.789743 CGAGCAAAATAGTGTCAGATATATACG 58.210 37.037 0.00 0.00 0.00 3.06
172 173 9.627395 ACGAGCAAAATAGTGTCAGATATATAC 57.373 33.333 0.00 0.00 0.00 1.47
174 175 9.547753 AAACGAGCAAAATAGTGTCAGATATAT 57.452 29.630 0.00 0.00 0.00 0.86
175 176 8.942338 AAACGAGCAAAATAGTGTCAGATATA 57.058 30.769 0.00 0.00 0.00 0.86
176 177 7.011482 GGAAACGAGCAAAATAGTGTCAGATAT 59.989 37.037 0.00 0.00 0.00 1.63
177 178 6.312918 GGAAACGAGCAAAATAGTGTCAGATA 59.687 38.462 0.00 0.00 0.00 1.98
178 179 5.122396 GGAAACGAGCAAAATAGTGTCAGAT 59.878 40.000 0.00 0.00 0.00 2.90
179 180 4.451096 GGAAACGAGCAAAATAGTGTCAGA 59.549 41.667 0.00 0.00 0.00 3.27
180 181 4.452455 AGGAAACGAGCAAAATAGTGTCAG 59.548 41.667 0.00 0.00 0.00 3.51
181 182 4.385825 AGGAAACGAGCAAAATAGTGTCA 58.614 39.130 0.00 0.00 0.00 3.58
182 183 5.163884 GGTAGGAAACGAGCAAAATAGTGTC 60.164 44.000 0.00 0.00 33.32 3.67
183 184 4.694037 GGTAGGAAACGAGCAAAATAGTGT 59.306 41.667 0.00 0.00 33.32 3.55
184 185 4.693566 TGGTAGGAAACGAGCAAAATAGTG 59.306 41.667 0.00 0.00 40.54 2.74
196 197 1.651987 ATCGCACATGGTAGGAAACG 58.348 50.000 0.00 0.00 0.00 3.60
203 204 4.982295 CGATTTCTAGAATCGCACATGGTA 59.018 41.667 18.00 0.00 42.20 3.25
242 243 8.665643 TTCGAAGATTGTTAACCAGAAAGTAA 57.334 30.769 2.48 0.00 35.04 2.24
243 244 8.665643 TTTCGAAGATTGTTAACCAGAAAGTA 57.334 30.769 2.48 0.00 35.04 2.24
246 247 6.861055 GCATTTCGAAGATTGTTAACCAGAAA 59.139 34.615 2.48 5.22 35.04 2.52
255 256 5.830912 TGAAACAGCATTTCGAAGATTGTT 58.169 33.333 0.00 5.86 35.04 2.83
264 265 4.676924 GGTCTTCTTTGAAACAGCATTTCG 59.323 41.667 8.44 0.00 0.00 3.46
267 268 4.646492 ACAGGTCTTCTTTGAAACAGCATT 59.354 37.500 0.00 0.00 0.00 3.56
268 269 4.037208 CACAGGTCTTCTTTGAAACAGCAT 59.963 41.667 0.00 0.00 0.00 3.79
270 271 3.793465 GCACAGGTCTTCTTTGAAACAGC 60.793 47.826 0.00 0.00 0.00 4.40
275 276 3.953612 ACATTGCACAGGTCTTCTTTGAA 59.046 39.130 0.00 0.00 0.00 2.69
279 280 1.610522 GCACATTGCACAGGTCTTCTT 59.389 47.619 0.00 0.00 44.26 2.52
297 298 2.878089 TACGGTGCTGAAGGCTGCA 61.878 57.895 0.50 0.00 45.14 4.41
300 301 2.214216 TGGTACGGTGCTGAAGGCT 61.214 57.895 0.00 0.00 42.39 4.58
307 308 0.902984 TGGAGATGTGGTACGGTGCT 60.903 55.000 0.00 0.00 0.00 4.40
309 310 2.691409 AATGGAGATGTGGTACGGTG 57.309 50.000 0.00 0.00 0.00 4.94
313 314 8.184192 CACAAATAGAAAATGGAGATGTGGTAC 58.816 37.037 0.00 0.00 33.76 3.34
317 318 6.860080 AGCACAAATAGAAAATGGAGATGTG 58.140 36.000 0.00 0.00 38.82 3.21
323 324 7.229306 CCAGCTATAGCACAAATAGAAAATGGA 59.771 37.037 26.07 0.00 45.16 3.41
324 325 7.013655 ACCAGCTATAGCACAAATAGAAAATGG 59.986 37.037 26.07 19.98 45.16 3.16
328 329 6.183360 GCAACCAGCTATAGCACAAATAGAAA 60.183 38.462 26.07 0.00 45.16 2.52
379 381 8.691797 ACGGCAAAAATACATAATCCAGTATTT 58.308 29.630 0.00 0.00 46.95 1.40
394 396 4.523083 AGAGCAGGAATACGGCAAAAATA 58.477 39.130 0.00 0.00 43.19 1.40
397 399 2.489938 AGAGCAGGAATACGGCAAAA 57.510 45.000 0.00 0.00 43.19 2.44
444 448 7.415086 ACATAAACCCACTCAACCCAATATTA 58.585 34.615 0.00 0.00 0.00 0.98
455 459 2.773487 CAACCGACATAAACCCACTCA 58.227 47.619 0.00 0.00 0.00 3.41
456 460 1.467342 GCAACCGACATAAACCCACTC 59.533 52.381 0.00 0.00 0.00 3.51
457 461 1.073284 AGCAACCGACATAAACCCACT 59.927 47.619 0.00 0.00 0.00 4.00
458 462 1.530323 AGCAACCGACATAAACCCAC 58.470 50.000 0.00 0.00 0.00 4.61
459 463 1.883275 CAAGCAACCGACATAAACCCA 59.117 47.619 0.00 0.00 0.00 4.51
471 475 3.748568 TGTTTGGTGAAAAACAAGCAACC 59.251 39.130 0.23 0.00 44.79 3.77
487 491 0.658897 AACGCGTACAACCTGTTTGG 59.341 50.000 14.46 0.00 39.84 3.28
489 493 3.656559 AGATAACGCGTACAACCTGTTT 58.343 40.909 14.46 0.00 0.00 2.83
492 497 6.141844 CAGTATAAGATAACGCGTACAACCTG 59.858 42.308 14.46 6.47 0.00 4.00
495 500 5.108103 GGCAGTATAAGATAACGCGTACAAC 60.108 44.000 14.46 2.08 0.00 3.32
521 526 2.565391 TGAGTCACGAGGAAGGCATAAA 59.435 45.455 0.00 0.00 0.00 1.40
529 534 2.035961 CTGGTCTTTGAGTCACGAGGAA 59.964 50.000 0.00 0.00 0.00 3.36
534 539 3.185188 CACATTCTGGTCTTTGAGTCACG 59.815 47.826 0.00 0.00 0.00 4.35
541 546 4.778534 AATGAGCACATTCTGGTCTTTG 57.221 40.909 3.28 0.00 46.09 2.77
542 547 6.888632 AGAATAATGAGCACATTCTGGTCTTT 59.111 34.615 12.87 4.12 46.09 2.52
543 548 6.421485 AGAATAATGAGCACATTCTGGTCTT 58.579 36.000 12.87 0.00 46.09 3.01
544 549 5.999044 AGAATAATGAGCACATTCTGGTCT 58.001 37.500 12.87 8.67 46.09 3.85
551 556 7.820872 CCAAGGAAAAAGAATAATGAGCACATT 59.179 33.333 13.95 13.95 46.64 2.71
555 560 6.493115 TGTCCAAGGAAAAAGAATAATGAGCA 59.507 34.615 0.00 0.00 0.00 4.26
560 565 7.396055 TCGGATTGTCCAAGGAAAAAGAATAAT 59.604 33.333 0.00 0.00 35.91 1.28
562 567 6.242396 TCGGATTGTCCAAGGAAAAAGAATA 58.758 36.000 0.00 0.00 35.91 1.75
565 570 4.093472 TCGGATTGTCCAAGGAAAAAGA 57.907 40.909 0.00 0.00 35.91 2.52
586 591 4.877823 CCGCATACCAACATGAGCATATAT 59.122 41.667 0.00 0.00 0.00 0.86
590 595 1.134128 TCCGCATACCAACATGAGCAT 60.134 47.619 0.00 0.00 0.00 3.79
598 603 1.435577 AGAAACGTCCGCATACCAAC 58.564 50.000 0.00 0.00 0.00 3.77
600 605 1.001068 TCAAGAAACGTCCGCATACCA 59.999 47.619 0.00 0.00 0.00 3.25
607 612 3.987868 TCAAGAATCTCAAGAAACGTCCG 59.012 43.478 0.00 0.00 0.00 4.79
609 614 8.495949 TGTTATTCAAGAATCTCAAGAAACGTC 58.504 33.333 0.00 0.00 32.50 4.34
615 620 9.388506 GGATTCTGTTATTCAAGAATCTCAAGA 57.611 33.333 19.38 0.00 43.45 3.02
616 621 8.619546 GGGATTCTGTTATTCAAGAATCTCAAG 58.380 37.037 19.38 0.00 43.79 3.02
617 622 8.331740 AGGGATTCTGTTATTCAAGAATCTCAA 58.668 33.333 21.30 0.00 45.63 3.02
618 623 7.865820 AGGGATTCTGTTATTCAAGAATCTCA 58.134 34.615 21.30 0.22 45.63 3.27
619 624 8.619546 CAAGGGATTCTGTTATTCAAGAATCTC 58.380 37.037 19.38 17.12 44.34 2.75
623 670 7.230747 TCACAAGGGATTCTGTTATTCAAGAA 58.769 34.615 0.00 0.00 0.00 2.52
650 697 8.722342 TGATCAACGTTATTTTAGCTCAAAAC 57.278 30.769 0.00 0.00 38.90 2.43
651 698 9.906660 ATTGATCAACGTTATTTTAGCTCAAAA 57.093 25.926 11.07 0.96 40.34 2.44
653 700 8.511321 ACATTGATCAACGTTATTTTAGCTCAA 58.489 29.630 11.07 1.65 0.00 3.02
654 701 8.039603 ACATTGATCAACGTTATTTTAGCTCA 57.960 30.769 11.07 0.00 0.00 4.26
655 702 8.895932 AACATTGATCAACGTTATTTTAGCTC 57.104 30.769 17.67 0.00 0.00 4.09
666 2450 7.651704 CCCTTTTTCTTAAACATTGATCAACGT 59.348 33.333 11.07 5.66 0.00 3.99
668 2452 7.440856 TGCCCTTTTTCTTAAACATTGATCAAC 59.559 33.333 11.07 0.00 0.00 3.18
674 2458 9.235537 CAATTTTGCCCTTTTTCTTAAACATTG 57.764 29.630 0.00 0.00 0.00 2.82
675 2459 8.412456 CCAATTTTGCCCTTTTTCTTAAACATT 58.588 29.630 0.00 0.00 0.00 2.71
679 2463 5.300539 GCCCAATTTTGCCCTTTTTCTTAAA 59.699 36.000 0.00 0.00 0.00 1.52
684 2507 1.885887 GGCCCAATTTTGCCCTTTTTC 59.114 47.619 3.97 0.00 41.97 2.29
781 2604 2.672961 TATGCATATGCTCCCGCTAC 57.327 50.000 27.13 0.00 42.66 3.58
785 2608 1.959042 GGGATATGCATATGCTCCCG 58.041 55.000 28.33 0.00 41.33 5.14
907 2737 0.468648 GGGGGAATCCGTCTGGTTAG 59.531 60.000 0.00 0.00 36.01 2.34
963 2806 2.115291 GCCCTTGCGAGGTGGAATC 61.115 63.158 19.14 0.00 41.85 2.52
1015 2863 1.737793 CATGTCGTTTACCTGAAGGCC 59.262 52.381 0.00 0.00 39.32 5.19
1016 2864 2.159627 CACATGTCGTTTACCTGAAGGC 59.840 50.000 0.00 0.00 39.32 4.35
1049 2897 4.154737 CGTCAATGGGGTAATATGCATCAG 59.845 45.833 0.19 0.00 0.00 2.90
1363 3228 5.710513 TTAATGCATGCAAACTCTGAAGT 57.289 34.783 26.68 0.00 37.32 3.01
1390 3257 1.074405 TCTGGAAGTTGCAAGCCTCAT 59.926 47.619 0.00 0.00 33.76 2.90
1406 3273 1.372997 CGTTGGAGTCCGTGTCTGG 60.373 63.158 4.30 0.00 0.00 3.86
1429 3296 0.100682 GCAGCTCCTCGTTGTCGATA 59.899 55.000 0.00 0.00 45.21 2.92
1516 3383 4.273257 TTGCGGCTGTCGACGTCA 62.273 61.111 17.16 0.00 45.61 4.35
1613 3480 4.561752 AGAAGCATCATCTAGTTACCCCT 58.438 43.478 0.00 0.00 0.00 4.79
1616 3483 6.578023 ACAGAAGAAGCATCATCTAGTTACC 58.422 40.000 0.00 0.00 32.08 2.85
1617 3484 6.699642 GGACAGAAGAAGCATCATCTAGTTAC 59.300 42.308 0.00 0.00 32.08 2.50
1618 3485 6.609212 AGGACAGAAGAAGCATCATCTAGTTA 59.391 38.462 0.00 0.00 32.08 2.24
1619 3486 5.424895 AGGACAGAAGAAGCATCATCTAGTT 59.575 40.000 0.00 0.00 32.08 2.24
1620 3487 4.961730 AGGACAGAAGAAGCATCATCTAGT 59.038 41.667 0.00 0.00 32.08 2.57
1621 3488 5.534207 AGGACAGAAGAAGCATCATCTAG 57.466 43.478 0.00 0.00 32.08 2.43
1622 3489 5.538053 CCTAGGACAGAAGAAGCATCATCTA 59.462 44.000 1.05 0.00 32.08 1.98
1623 3490 4.344679 CCTAGGACAGAAGAAGCATCATCT 59.655 45.833 1.05 0.00 34.05 2.90
1624 3491 4.630111 CCTAGGACAGAAGAAGCATCATC 58.370 47.826 1.05 0.00 0.00 2.92
1626 3493 2.169352 GCCTAGGACAGAAGAAGCATCA 59.831 50.000 14.75 0.00 0.00 3.07
1627 3494 2.801342 CGCCTAGGACAGAAGAAGCATC 60.801 54.545 14.75 0.00 0.00 3.91
1628 3495 1.137872 CGCCTAGGACAGAAGAAGCAT 59.862 52.381 14.75 0.00 0.00 3.79
1629 3496 0.532573 CGCCTAGGACAGAAGAAGCA 59.467 55.000 14.75 0.00 0.00 3.91
1630 3497 0.818296 TCGCCTAGGACAGAAGAAGC 59.182 55.000 14.75 0.00 0.00 3.86
1631 3498 3.810310 ATTCGCCTAGGACAGAAGAAG 57.190 47.619 14.75 0.00 0.00 2.85
1633 3500 3.366396 AGAATTCGCCTAGGACAGAAGA 58.634 45.455 14.75 0.00 0.00 2.87
1634 3501 3.810310 AGAATTCGCCTAGGACAGAAG 57.190 47.619 14.75 0.00 0.00 2.85
1636 3503 3.802948 GAAGAATTCGCCTAGGACAGA 57.197 47.619 14.75 5.38 34.17 3.41
1647 3523 8.326713 CAGTGAACTATCATGAAGAAGAATTCG 58.673 37.037 0.00 0.00 43.81 3.34
1659 3535 6.315642 ACAAGCTTCATCAGTGAACTATCATG 59.684 38.462 0.00 0.00 39.36 3.07
1661 3537 5.798132 ACAAGCTTCATCAGTGAACTATCA 58.202 37.500 0.00 0.00 39.36 2.15
1662 3538 6.593382 AGAACAAGCTTCATCAGTGAACTATC 59.407 38.462 0.00 0.00 39.36 2.08
1663 3539 6.471146 AGAACAAGCTTCATCAGTGAACTAT 58.529 36.000 0.00 0.00 39.36 2.12
1664 3540 5.858381 AGAACAAGCTTCATCAGTGAACTA 58.142 37.500 0.00 0.00 39.36 2.24
1691 3570 1.278637 GACGACAAACAAGCACCCG 59.721 57.895 0.00 0.00 0.00 5.28
1692 3571 0.307760 CTGACGACAAACAAGCACCC 59.692 55.000 0.00 0.00 0.00 4.61
1693 3572 0.307760 CCTGACGACAAACAAGCACC 59.692 55.000 0.00 0.00 0.00 5.01
1694 3573 1.014352 ACCTGACGACAAACAAGCAC 58.986 50.000 0.00 0.00 0.00 4.40
1695 3574 1.745232 AACCTGACGACAAACAAGCA 58.255 45.000 0.00 0.00 0.00 3.91
1696 3575 2.540973 GGAAACCTGACGACAAACAAGC 60.541 50.000 0.00 0.00 0.00 4.01
1697 3576 2.286184 CGGAAACCTGACGACAAACAAG 60.286 50.000 0.00 0.00 0.00 3.16
1876 3755 1.932511 GAGCACTGACTGAATAGCTGC 59.067 52.381 0.00 0.00 31.61 5.25
1882 3761 2.424557 CAGCAAGAGCACTGACTGAAT 58.575 47.619 7.62 0.00 45.49 2.57
1903 3786 1.025041 GAGAAATAAAGGGGGCAGCG 58.975 55.000 0.00 0.00 0.00 5.18
1923 3810 8.742777 ACATGACTTATCTTGTTTATGTGCATT 58.257 29.630 0.00 0.00 39.54 3.56
2218 4111 3.192422 CCAATGAAGCCATAACAAACGGA 59.808 43.478 0.00 0.00 31.59 4.69
2223 4116 6.268847 AGGTTTTACCAATGAAGCCATAACAA 59.731 34.615 0.00 0.00 41.95 2.83
2233 4126 7.786030 TGAACATTTGAGGTTTTACCAATGAA 58.214 30.769 11.92 0.00 41.95 2.57
2242 4135 3.037549 TGCCCTGAACATTTGAGGTTTT 58.962 40.909 0.00 0.00 0.00 2.43
2269 4162 5.410924 TGTCTGCTGTGTATACATGAAGTC 58.589 41.667 9.18 7.74 35.97 3.01
2353 4256 5.771469 TGATGCAAATTTGTAGTGTTCCAG 58.229 37.500 19.03 0.00 0.00 3.86
2361 4264 8.523523 TTTGAACTGATGATGCAAATTTGTAG 57.476 30.769 19.03 4.93 0.00 2.74
2380 4283 7.327032 GCTACATGAGATTGGTTTCTTTTGAAC 59.673 37.037 0.00 0.00 38.30 3.18
2387 4290 4.207891 ACGCTACATGAGATTGGTTTCT 57.792 40.909 0.00 0.00 0.00 2.52
2392 4295 5.794687 TTTTGTACGCTACATGAGATTGG 57.205 39.130 0.00 0.00 38.68 3.16
2395 4298 5.061808 GTCGTTTTTGTACGCTACATGAGAT 59.938 40.000 0.00 0.00 41.16 2.75
2406 4309 1.223187 AGGCAGGTCGTTTTTGTACG 58.777 50.000 0.00 0.00 42.68 3.67
2423 4326 2.874701 CCGCATTCTGAGGAAATGTAGG 59.125 50.000 0.00 0.00 39.92 3.18
2441 4344 0.238553 GGCTCTCAGTTTTGTTCCGC 59.761 55.000 0.00 0.00 0.00 5.54
2443 4346 2.160417 CGATGGCTCTCAGTTTTGTTCC 59.840 50.000 0.00 0.00 0.00 3.62
2461 4364 0.885879 TCTCAGTTACGTGGCACGAT 59.114 50.000 42.65 28.44 46.05 3.73
2462 4365 0.039798 GTCTCAGTTACGTGGCACGA 60.040 55.000 42.65 24.75 46.05 4.35
2467 4370 1.214589 CCCCGTCTCAGTTACGTGG 59.785 63.158 0.00 0.00 38.67 4.94
2476 4379 0.395312 GTGGTTTCTTCCCCGTCTCA 59.605 55.000 0.00 0.00 0.00 3.27
2497 4400 2.151202 GTGATCTGTCCGCCTTTTCAA 58.849 47.619 0.00 0.00 0.00 2.69
2498 4401 1.071542 TGTGATCTGTCCGCCTTTTCA 59.928 47.619 0.00 0.00 0.00 2.69
2499 4402 1.808411 TGTGATCTGTCCGCCTTTTC 58.192 50.000 0.00 0.00 0.00 2.29
2500 4403 2.290260 TGATGTGATCTGTCCGCCTTTT 60.290 45.455 0.00 0.00 0.00 2.27
2501 4404 1.278985 TGATGTGATCTGTCCGCCTTT 59.721 47.619 0.00 0.00 0.00 3.11
2502 4405 0.904649 TGATGTGATCTGTCCGCCTT 59.095 50.000 0.00 0.00 0.00 4.35
2503 4406 0.904649 TTGATGTGATCTGTCCGCCT 59.095 50.000 0.00 0.00 0.00 5.52
2504 4407 1.737838 TTTGATGTGATCTGTCCGCC 58.262 50.000 0.00 0.00 0.00 6.13
2505 4408 2.744202 AGTTTTGATGTGATCTGTCCGC 59.256 45.455 0.00 0.00 0.00 5.54
2512 4415 6.419980 CTCTTCTGGAGTTTTGATGTGATC 57.580 41.667 0.00 0.00 37.30 2.92
2531 4434 3.618690 AGAAGGCGCTTGATAACTCTT 57.381 42.857 7.64 0.00 0.00 2.85
2587 4490 0.460109 CATGTGATCGCCAAGGACGA 60.460 55.000 3.31 7.79 44.75 4.20
2610 4513 3.073678 TGGAATCGTGATGTTTGTCAGG 58.926 45.455 0.00 0.00 35.81 3.86
2640 4543 1.144936 GAACCCGGAGCTGGAGATG 59.855 63.158 0.73 0.00 0.00 2.90
2642 4545 2.683933 GGAACCCGGAGCTGGAGA 60.684 66.667 0.73 0.00 0.00 3.71
2661 4564 0.248215 ACGTCTTTACCCGTATCGCG 60.248 55.000 0.00 0.00 35.16 5.87
2729 4632 4.193865 CCCCAAAAAGATCATGCATTTCC 58.806 43.478 0.00 0.00 0.00 3.13
2740 4643 2.654385 TGGAGATGACCCCCAAAAAGAT 59.346 45.455 0.00 0.00 0.00 2.40
2826 4729 2.256117 ACCTTGCGAAACTAGTTGCT 57.744 45.000 9.34 0.00 0.00 3.91
2838 4741 0.744414 ATCGGTCCATGAACCTTGCG 60.744 55.000 0.00 0.00 37.15 4.85
2926 4829 9.507280 GATGAATTTAACATGTGTGTATTCCTG 57.493 33.333 0.00 0.00 37.67 3.86
2938 4841 8.616076 GTCCTAGAGTTGGATGAATTTAACATG 58.384 37.037 0.00 0.00 35.87 3.21
2947 4850 6.566079 ATTGATGTCCTAGAGTTGGATGAA 57.434 37.500 0.00 0.00 35.87 2.57
2949 4852 8.915057 ATAAATTGATGTCCTAGAGTTGGATG 57.085 34.615 0.00 0.00 35.87 3.51
2950 4853 8.943085 AGATAAATTGATGTCCTAGAGTTGGAT 58.057 33.333 0.00 0.00 35.87 3.41
2951 4854 8.324191 AGATAAATTGATGTCCTAGAGTTGGA 57.676 34.615 0.00 0.00 0.00 3.53
2953 4856 8.206867 TGGAGATAAATTGATGTCCTAGAGTTG 58.793 37.037 17.81 0.00 39.49 3.16
2954 4857 8.324191 TGGAGATAAATTGATGTCCTAGAGTT 57.676 34.615 17.81 0.00 39.49 3.01
2956 4859 7.333921 GCATGGAGATAAATTGATGTCCTAGAG 59.666 40.741 17.81 7.88 39.49 2.43
2957 4860 7.164122 GCATGGAGATAAATTGATGTCCTAGA 58.836 38.462 17.81 1.02 39.49 2.43
2958 4861 6.938596 TGCATGGAGATAAATTGATGTCCTAG 59.061 38.462 17.81 11.86 39.49 3.02
2959 4862 6.712095 GTGCATGGAGATAAATTGATGTCCTA 59.288 38.462 17.81 6.96 39.49 2.94
2960 4863 5.533903 GTGCATGGAGATAAATTGATGTCCT 59.466 40.000 17.81 3.55 39.49 3.85
2961 4864 5.300034 TGTGCATGGAGATAAATTGATGTCC 59.700 40.000 11.46 11.46 39.27 4.02
2964 4867 6.139048 TGTGTGCATGGAGATAAATTGATG 57.861 37.500 0.00 0.00 0.00 3.07
3021 4932 2.697751 TGCCGGGCAAGCATATATTTTT 59.302 40.909 21.55 0.00 34.76 1.94
3037 4948 0.589223 TTTACTGCTTCGTTTGCCGG 59.411 50.000 0.00 0.00 37.11 6.13
3039 4950 3.234386 GTGATTTACTGCTTCGTTTGCC 58.766 45.455 0.00 0.00 0.00 4.52
3061 4972 0.595095 GCTTTCTGCCTCACCAGTTG 59.405 55.000 0.00 0.00 34.47 3.16
3066 4977 1.002544 AGTACTGCTTTCTGCCTCACC 59.997 52.381 0.00 0.00 42.00 4.02
3078 4989 7.655521 TTTCCATACTACATACAGTACTGCT 57.344 36.000 22.90 12.27 33.94 4.24
3079 4990 8.765219 CATTTTCCATACTACATACAGTACTGC 58.235 37.037 22.90 0.00 33.94 4.40
3105 5021 8.607441 TGCAGGTATGACATTGTATTCTTATC 57.393 34.615 0.00 0.00 0.00 1.75
3159 5075 0.687757 TCCTCGCCTCCAAGCTATGT 60.688 55.000 0.00 0.00 0.00 2.29
3657 5575 7.391833 AGAAACCTTTTCCTGCTCATTTAGTAG 59.608 37.037 0.00 0.00 37.65 2.57
3660 5578 6.015940 ACAGAAACCTTTTCCTGCTCATTTAG 60.016 38.462 0.00 0.00 0.00 1.85
3694 5612 3.516586 TGTACCAGAACTTCATCTCCCA 58.483 45.455 0.00 0.00 0.00 4.37
3769 5693 7.435192 GTGACATTAAGAACAACAAGAAAAGGG 59.565 37.037 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.