Multiple sequence alignment - TraesCS4B01G200900

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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 TraesCS4B01G200900 chr4B 100.000 6006 0 0 1 6006 428971747 428965742 0 11092
1 TraesCS4B01G200900 chr4A 92.203 6118 279 70 1 6006 116470833 116476864 0 8473
2 TraesCS4B01G200900 chr4D 93.896 4980 185 44 1 4914 348803095 348798169 0 7402
3 TraesCS4B01G200900 chr4D 89.935 1073 54 24 4960 6006 348797747 348796703 0 1334


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 TraesCS4B01G200900 chr4B 428965742 428971747 6005 True 11092 11092 100.0000 1 6006 1 chr4B.!!$R1 6005
1 TraesCS4B01G200900 chr4A 116470833 116476864 6031 False 8473 8473 92.2030 1 6006 1 chr4A.!!$F1 6005
2 TraesCS4B01G200900 chr4D 348796703 348803095 6392 True 4368 7402 91.9155 1 6006 2 chr4D.!!$R1 6005

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
248 265 0.391130 TCGATCTTCCGCTGGGTTTG 60.391 55.0 0.00 0.0 33.83 2.93 F
1765 1801 0.170561 CAGCATCAGAAAGCACAGGC 59.829 55.0 1.52 0.0 41.61 4.85 F
2455 2491 0.104671 ACTGGCAAATTGTGTGGTGC 59.895 50.0 0.00 0.0 36.24 5.01 F
3088 3124 0.179089 CATTCAGGTGAGGAGGAGCG 60.179 60.0 0.00 0.0 0.00 5.03 F
4466 4527 0.598065 AAAGGAACATGAAGCGGTGC 59.402 50.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2104 1.202582 CAGAGACTGGTGTAGGAACCG 59.797 57.143 0.0 0.0 43.73 4.44 R
3503 3539 0.033504 GTTGACTGGTCGAAGCTCCA 59.966 55.000 0.0 0.0 0.00 3.86 R
3644 3680 0.608856 TTGCCACATCTCGCCAATGT 60.609 50.000 0.0 0.0 37.85 2.71 R
4533 4594 1.129917 AGCTCAGCCTCTGCATGTAT 58.870 50.000 0.0 0.0 41.13 2.29 R
5675 6167 0.613260 TATCCACAGCTCCACCACAC 59.387 55.000 0.0 0.0 0.00 3.82 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
31 32 0.610687 CGCACCCTCCTCTTCTTCTT 59.389 55.000 0.00 0.00 0.00 2.52
34 35 2.304470 GCACCCTCCTCTTCTTCTTCTT 59.696 50.000 0.00 0.00 0.00 2.52
37 38 4.081697 CACCCTCCTCTTCTTCTTCTTCTC 60.082 50.000 0.00 0.00 0.00 2.87
39 40 3.450817 CCTCCTCTTCTTCTTCTTCTCCC 59.549 52.174 0.00 0.00 0.00 4.30
40 41 4.093011 CTCCTCTTCTTCTTCTTCTCCCA 58.907 47.826 0.00 0.00 0.00 4.37
48 49 4.773149 TCTTCTTCTTCTCCCACTACTTCC 59.227 45.833 0.00 0.00 0.00 3.46
101 115 0.460987 CGGAGGCTTGGAGTGATCAC 60.461 60.000 18.47 18.47 0.00 3.06
109 123 3.370953 GCTTGGAGTGATCACCAGGTAAT 60.371 47.826 22.21 1.35 35.86 1.89
154 171 1.097232 TCCTCGTCTTATTTCGGCGA 58.903 50.000 4.99 4.99 0.00 5.54
169 186 3.123050 TCGGCGATATGAGATGTTGTTG 58.877 45.455 4.99 0.00 0.00 3.33
170 187 2.348872 CGGCGATATGAGATGTTGTTGC 60.349 50.000 0.00 0.00 0.00 4.17
171 188 2.874701 GGCGATATGAGATGTTGTTGCT 59.125 45.455 0.00 0.00 0.00 3.91
172 189 3.303593 GGCGATATGAGATGTTGTTGCTG 60.304 47.826 0.00 0.00 0.00 4.41
173 190 3.310774 GCGATATGAGATGTTGTTGCTGT 59.689 43.478 0.00 0.00 0.00 4.40
174 191 4.201851 GCGATATGAGATGTTGTTGCTGTT 60.202 41.667 0.00 0.00 0.00 3.16
175 192 5.260900 CGATATGAGATGTTGTTGCTGTTG 58.739 41.667 0.00 0.00 0.00 3.33
176 193 5.163824 CGATATGAGATGTTGTTGCTGTTGT 60.164 40.000 0.00 0.00 0.00 3.32
177 194 4.924305 ATGAGATGTTGTTGCTGTTGTT 57.076 36.364 0.00 0.00 0.00 2.83
178 195 4.031418 TGAGATGTTGTTGCTGTTGTTG 57.969 40.909 0.00 0.00 0.00 3.33
179 196 3.443329 TGAGATGTTGTTGCTGTTGTTGT 59.557 39.130 0.00 0.00 0.00 3.32
180 197 4.082300 TGAGATGTTGTTGCTGTTGTTGTT 60.082 37.500 0.00 0.00 0.00 2.83
181 198 4.175516 AGATGTTGTTGCTGTTGTTGTTG 58.824 39.130 0.00 0.00 0.00 3.33
182 199 3.377346 TGTTGTTGCTGTTGTTGTTGT 57.623 38.095 0.00 0.00 0.00 3.32
183 200 3.722147 TGTTGTTGCTGTTGTTGTTGTT 58.278 36.364 0.00 0.00 0.00 2.83
184 201 3.492383 TGTTGTTGCTGTTGTTGTTGTTG 59.508 39.130 0.00 0.00 0.00 3.33
185 202 3.377346 TGTTGCTGTTGTTGTTGTTGT 57.623 38.095 0.00 0.00 0.00 3.32
186 203 3.722147 TGTTGCTGTTGTTGTTGTTGTT 58.278 36.364 0.00 0.00 0.00 2.83
187 204 3.492383 TGTTGCTGTTGTTGTTGTTGTTG 59.508 39.130 0.00 0.00 0.00 3.33
188 205 3.377346 TGCTGTTGTTGTTGTTGTTGT 57.623 38.095 0.00 0.00 0.00 3.32
189 206 3.722147 TGCTGTTGTTGTTGTTGTTGTT 58.278 36.364 0.00 0.00 0.00 2.83
190 207 3.492383 TGCTGTTGTTGTTGTTGTTGTTG 59.508 39.130 0.00 0.00 0.00 3.33
248 265 0.391130 TCGATCTTCCGCTGGGTTTG 60.391 55.000 0.00 0.00 33.83 2.93
276 293 6.689669 CGGTTACTTCGATTGTTTTCTTTTGT 59.310 34.615 0.00 0.00 0.00 2.83
283 300 7.045126 TCGATTGTTTTCTTTTGTGGGTTAT 57.955 32.000 0.00 0.00 0.00 1.89
284 301 8.167605 TCGATTGTTTTCTTTTGTGGGTTATA 57.832 30.769 0.00 0.00 0.00 0.98
285 302 8.630917 TCGATTGTTTTCTTTTGTGGGTTATAA 58.369 29.630 0.00 0.00 0.00 0.98
286 303 8.911662 CGATTGTTTTCTTTTGTGGGTTATAAG 58.088 33.333 0.00 0.00 0.00 1.73
293 311 6.535540 TCTTTTGTGGGTTATAAGTGCTGTA 58.464 36.000 0.00 0.00 0.00 2.74
297 315 5.969423 TGTGGGTTATAAGTGCTGTAGTAC 58.031 41.667 0.00 0.00 0.00 2.73
317 335 2.301583 ACTTCTCTTCTCCTTGGTGAGC 59.698 50.000 0.00 0.00 32.22 4.26
330 348 1.071542 TGGTGAGCTTCGTGAATTCCA 59.928 47.619 2.27 0.00 0.00 3.53
331 349 2.151202 GGTGAGCTTCGTGAATTCCAA 58.849 47.619 2.27 0.00 0.00 3.53
332 350 2.160417 GGTGAGCTTCGTGAATTCCAAG 59.840 50.000 2.27 4.00 0.00 3.61
369 388 2.734673 CTTCGCTCTCACGCAAGCC 61.735 63.158 0.00 0.00 45.62 4.35
376 395 1.299014 CTCACGCAAGCCGCAAAAA 60.299 52.632 0.00 0.00 42.60 1.94
390 409 2.472488 CGCAAAAAGCCTGTGTGAATTC 59.528 45.455 0.00 0.00 41.38 2.17
392 411 3.052036 CAAAAAGCCTGTGTGAATTCCG 58.948 45.455 2.27 0.00 0.00 4.30
393 412 2.270352 AAAGCCTGTGTGAATTCCGA 57.730 45.000 2.27 0.00 0.00 4.55
395 414 0.687354 AGCCTGTGTGAATTCCGAGT 59.313 50.000 2.27 0.00 0.00 4.18
396 415 1.072331 AGCCTGTGTGAATTCCGAGTT 59.928 47.619 2.27 0.00 0.00 3.01
403 434 4.750098 TGTGTGAATTCCGAGTTTCTCTTC 59.250 41.667 2.27 0.00 0.00 2.87
407 438 0.677288 TTCCGAGTTTCTCTTCGGCA 59.323 50.000 7.98 0.00 44.53 5.69
463 494 2.878406 TCTGCTGCGCTTTTACTTTCTT 59.122 40.909 9.73 0.00 0.00 2.52
464 495 3.058914 TCTGCTGCGCTTTTACTTTCTTC 60.059 43.478 9.73 0.00 0.00 2.87
481 512 2.036217 TCTTCTTTTCCGCCGACAGTTA 59.964 45.455 0.00 0.00 0.00 2.24
553 584 3.257469 GATGTGCTCATCCTGTCTTGA 57.743 47.619 16.27 0.00 43.15 3.02
554 585 3.806380 GATGTGCTCATCCTGTCTTGAT 58.194 45.455 16.27 0.00 43.15 2.57
555 586 3.708403 TGTGCTCATCCTGTCTTGATT 57.292 42.857 0.00 0.00 0.00 2.57
556 587 3.603532 TGTGCTCATCCTGTCTTGATTC 58.396 45.455 0.00 0.00 0.00 2.52
558 589 4.260170 GTGCTCATCCTGTCTTGATTCTT 58.740 43.478 0.00 0.00 0.00 2.52
560 591 4.019950 TGCTCATCCTGTCTTGATTCTTGA 60.020 41.667 0.00 0.00 0.00 3.02
561 592 4.940046 GCTCATCCTGTCTTGATTCTTGAA 59.060 41.667 0.00 0.00 0.00 2.69
562 593 5.589452 GCTCATCCTGTCTTGATTCTTGAAT 59.411 40.000 0.00 0.00 0.00 2.57
564 595 6.714278 TCATCCTGTCTTGATTCTTGAATGA 58.286 36.000 0.09 0.00 0.00 2.57
573 604 4.220533 GATTCTTGAATGAATCGGCCTG 57.779 45.455 0.00 0.00 41.62 4.85
574 605 3.348647 TTCTTGAATGAATCGGCCTGA 57.651 42.857 0.00 0.00 0.00 3.86
575 606 2.632377 TCTTGAATGAATCGGCCTGAC 58.368 47.619 0.00 0.00 0.00 3.51
576 607 1.672881 CTTGAATGAATCGGCCTGACC 59.327 52.381 0.00 0.00 0.00 4.02
577 608 0.911769 TGAATGAATCGGCCTGACCT 59.088 50.000 0.00 0.00 35.61 3.85
578 609 1.303309 GAATGAATCGGCCTGACCTG 58.697 55.000 0.00 0.00 35.61 4.00
581 612 0.824109 TGAATCGGCCTGACCTGTAG 59.176 55.000 0.00 0.00 35.61 2.74
584 615 1.693627 ATCGGCCTGACCTGTAGTAG 58.306 55.000 0.00 0.00 35.61 2.57
586 617 1.561076 TCGGCCTGACCTGTAGTAGTA 59.439 52.381 0.00 0.00 35.61 1.82
604 635 6.733509 AGTAGTACTCCTTGGAAGATACTGT 58.266 40.000 0.00 0.00 0.00 3.55
607 638 9.134055 GTAGTACTCCTTGGAAGATACTGTTAT 57.866 37.037 0.00 0.00 0.00 1.89
630 661 2.238942 TGCAGTAAGTATGCCATCGG 57.761 50.000 0.00 0.00 43.18 4.18
716 747 2.047465 CGTGCCTTCTGCTCAGCT 60.047 61.111 0.00 0.00 42.00 4.24
724 755 3.465871 CCTTCTGCTCAGCTAATTCTCC 58.534 50.000 0.00 0.00 0.00 3.71
730 761 2.544903 GCTCAGCTAATTCTCCGACTCC 60.545 54.545 0.00 0.00 0.00 3.85
811 844 7.226523 GTGTTGCAAATAGACAAAGGGATTTTT 59.773 33.333 0.00 0.00 0.00 1.94
817 850 9.243105 CAAATAGACAAAGGGATTTTTCTCCTA 57.757 33.333 0.00 0.00 35.50 2.94
874 910 0.604780 CCATCTGCCTGGCTATTCCG 60.605 60.000 21.03 3.48 37.80 4.30
881 917 1.823899 CTGGCTATTCCGGGTTGGC 60.824 63.158 0.00 2.61 37.58 4.52
907 943 4.669197 GCATTACTTGTGCCTTTCTGTACG 60.669 45.833 0.00 0.00 36.61 3.67
982 1018 4.469657 AGAAAACAGGTTATTGTCTGCCA 58.530 39.130 0.00 0.00 34.57 4.92
984 1020 4.853924 AAACAGGTTATTGTCTGCCAAG 57.146 40.909 0.00 0.00 36.25 3.61
1096 1132 7.434307 ACACGTCTTTCCATTTCTATATGTACG 59.566 37.037 0.00 0.00 0.00 3.67
1148 1184 3.204827 CATCCGCTTGGGCTTCGG 61.205 66.667 0.00 0.00 44.16 4.30
1268 1304 0.465824 CTACTCCGACGGGGATGTCT 60.466 60.000 23.53 0.00 46.04 3.41
1298 1334 2.442087 GGGGCGGGCTTTAGCAAT 60.442 61.111 3.88 0.00 44.36 3.56
1381 1417 1.360820 GAGAAGAAAGGCGTGCTACC 58.639 55.000 0.00 0.00 0.00 3.18
1433 1469 2.173996 AGAGAGTGGTAGACTAGGGAGC 59.826 54.545 0.00 0.00 33.83 4.70
1435 1471 0.624785 AGTGGTAGACTAGGGAGCGT 59.375 55.000 0.00 0.00 30.86 5.07
1495 1531 5.761234 TGACTTTGGATTTACAGTTAGCGTT 59.239 36.000 0.00 0.00 0.00 4.84
1506 1542 3.673809 ACAGTTAGCGTTTCGTCAGAATC 59.326 43.478 0.00 0.00 36.09 2.52
1556 1592 6.498651 TCAAGAAAGAGAAACTAGATCAGGGT 59.501 38.462 0.00 0.00 0.00 4.34
1559 1595 7.390823 AGAAAGAGAAACTAGATCAGGGTTTC 58.609 38.462 20.47 20.47 45.04 2.78
1743 1779 7.014230 GCTTTAACATACCCCATCATACAACAT 59.986 37.037 0.00 0.00 0.00 2.71
1765 1801 0.170561 CAGCATCAGAAAGCACAGGC 59.829 55.000 1.52 0.00 41.61 4.85
1827 1863 8.768955 GGCTGAGTCTAAATATTGACAATACTG 58.231 37.037 10.06 2.09 35.81 2.74
1854 1890 3.938963 ACCGTCGAATGCATATCAACTTT 59.061 39.130 0.00 0.00 0.00 2.66
1856 1892 4.033932 CCGTCGAATGCATATCAACTTTCA 59.966 41.667 0.00 0.00 0.00 2.69
1867 1903 8.461222 TGCATATCAACTTTCAAATAAGAGTGG 58.539 33.333 0.00 0.00 0.00 4.00
1872 1908 8.099364 TCAACTTTCAAATAAGAGTGGATCAC 57.901 34.615 0.00 0.00 34.10 3.06
1916 1952 2.512476 ACTTAAACCACCAACCAGACCT 59.488 45.455 0.00 0.00 0.00 3.85
2031 2067 9.056005 TGAATGTTCCTGATGCTATATTTACAC 57.944 33.333 0.00 0.00 0.00 2.90
2065 2101 3.939740 AAGAGCCAATAAGATCAGCCA 57.060 42.857 0.00 0.00 0.00 4.75
2068 2104 0.957362 GCCAATAAGATCAGCCAGGC 59.043 55.000 1.84 1.84 0.00 4.85
2076 2112 1.686325 GATCAGCCAGGCGGTTCCTA 61.686 60.000 11.77 0.00 45.52 2.94
2099 2135 4.080863 ACACCAGTCTCTGATAAATCACCC 60.081 45.833 0.00 0.00 32.44 4.61
2117 2153 1.929836 CCCGCTGAGAAGATTTCGAAG 59.070 52.381 0.00 0.00 34.02 3.79
2150 2186 5.938125 GTGTAATGTAAATCCTCACACCACT 59.062 40.000 0.00 0.00 30.99 4.00
2230 2266 1.541310 CCTGGAGAACCTACACGGCA 61.541 60.000 0.00 0.00 37.04 5.69
2243 2279 2.356135 ACACGGCAACATATCCAGAAC 58.644 47.619 0.00 0.00 0.00 3.01
2277 2313 1.597663 CACCTCTGTTCGTCCAACAAC 59.402 52.381 0.00 0.00 44.71 3.32
2372 2408 5.774690 TGGCTTTGATTTGTACTCTGGAAAT 59.225 36.000 0.00 0.00 0.00 2.17
2392 2428 4.535526 ATTTTCCAAATGGTAGTGGTGC 57.464 40.909 0.00 0.00 36.23 5.01
2440 2476 5.547465 TGATAGTGTTCCTGTACAAACTGG 58.453 41.667 10.86 2.71 44.08 4.00
2444 2480 3.129638 GTGTTCCTGTACAAACTGGCAAA 59.870 43.478 10.86 0.00 42.81 3.68
2455 2491 0.104671 ACTGGCAAATTGTGTGGTGC 59.895 50.000 0.00 0.00 36.24 5.01
2502 2538 1.261619 GTGAAGAAGTGACAACTGCCG 59.738 52.381 0.00 0.00 36.51 5.69
2543 2579 4.800914 GCAACAGTAAGTGGTCAGTCTGAT 60.801 45.833 5.68 0.00 0.00 2.90
2596 2632 0.760189 AATGTTGCCAGCCCTGTTGT 60.760 50.000 0.00 0.00 0.00 3.32
2610 2646 4.160252 GCCCTGTTGTTGGATTATGTGAAT 59.840 41.667 0.00 0.00 0.00 2.57
2656 2692 1.741770 CGGGACCTGCAAGCTGTAC 60.742 63.158 0.00 0.00 0.00 2.90
2700 2736 5.957842 TTGTAAACCAGCAGTTAATCAGG 57.042 39.130 0.00 0.00 37.88 3.86
2762 2798 1.758592 CCGAAGTTCCTCCAACCCA 59.241 57.895 0.00 0.00 35.28 4.51
2798 2834 2.552315 GGTTTTCAATTCTCTGCACCGA 59.448 45.455 0.00 0.00 0.00 4.69
2805 2841 1.186200 TTCTCTGCACCGAGCTGTAT 58.814 50.000 0.00 0.00 45.94 2.29
2853 2889 5.184671 GCTTCAATGGACTTTTCAGAGGATT 59.815 40.000 0.00 0.00 0.00 3.01
2900 2936 5.542779 CCTACTACCAATAAGCCTCATGTC 58.457 45.833 0.00 0.00 0.00 3.06
2965 3001 1.079819 CTGAGCCGCGGAAAGAAGA 60.080 57.895 33.48 3.08 0.00 2.87
3028 3064 0.883833 GTTCACATTCAGGGCACTGG 59.116 55.000 17.80 2.07 44.99 4.00
3088 3124 0.179089 CATTCAGGTGAGGAGGAGCG 60.179 60.000 0.00 0.00 0.00 5.03
3115 3151 4.911390 AGTGAGGTTTCTGTTAATGGGAG 58.089 43.478 0.00 0.00 0.00 4.30
3163 3199 6.069440 ACATCTGATAAGAATTCCCCACTGAA 60.069 38.462 0.65 0.00 0.00 3.02
3167 3203 8.556589 TCTGATAAGAATTCCCCACTGAATAAA 58.443 33.333 0.65 0.00 33.91 1.40
3174 3210 3.670625 TCCCCACTGAATAAAACTGACG 58.329 45.455 0.00 0.00 0.00 4.35
3181 3217 6.347402 CCACTGAATAAAACTGACGTTACCAG 60.347 42.308 1.45 1.45 37.64 4.00
3219 3255 2.195567 GCAGGTGCCAGTTCAGCAA 61.196 57.895 0.00 0.00 43.02 3.91
3231 3267 5.693814 CCAGTTCAGCAAATCTTACAAGAC 58.306 41.667 0.00 0.00 37.98 3.01
3246 3282 4.463050 ACAAGACCACCTATTTTGGGAA 57.537 40.909 0.00 0.00 38.59 3.97
3275 3311 8.437575 TCAGGTTCCCATAAAATAGATTCTACC 58.562 37.037 0.00 0.00 0.00 3.18
3287 3323 3.387962 AGATTCTACCAGGCAATCTCCA 58.612 45.455 3.83 0.00 32.44 3.86
3295 3331 3.094572 CCAGGCAATCTCCAAAGACATT 58.905 45.455 0.00 0.00 33.32 2.71
3446 3482 4.074970 GGACAGAAAAGGAAGAGATTGCA 58.925 43.478 0.00 0.00 0.00 4.08
3488 3524 2.185004 ACGATCCAGTTTTGGGTGAG 57.815 50.000 0.00 0.00 45.10 3.51
3526 3562 1.272769 AGCTTCGACCAGTCAACTACC 59.727 52.381 0.00 0.00 0.00 3.18
3572 3608 4.021104 TCGACAGGTGAAAGATCAGAACAT 60.021 41.667 0.00 0.00 35.88 2.71
3616 3652 5.349061 TGCATGACATCTTCTGTACAGAT 57.651 39.130 25.68 10.99 38.54 2.90
3644 3680 3.189606 AGATGGACAGGTTAATGGGTCA 58.810 45.455 0.00 0.00 32.00 4.02
3711 3772 4.235079 TGTTATTCTTAGCATGGCTGGT 57.765 40.909 0.07 0.00 40.10 4.00
3839 3900 2.323959 CAGTCTGAGCGAGAGAACAAC 58.676 52.381 0.00 0.00 0.00 3.32
3842 3903 1.066914 CTGAGCGAGAGAACAACAGC 58.933 55.000 0.00 0.00 0.00 4.40
3977 4038 4.999950 AGCGATGAGTCTGAAATTGACTTT 59.000 37.500 0.00 0.00 43.88 2.66
4022 4083 2.731572 AGGAGGCCACATGAAAATGAG 58.268 47.619 5.01 0.00 0.00 2.90
4088 4149 4.979657 CATCAGATGCCTGGCTGT 57.020 55.556 21.03 8.62 40.76 4.40
4346 4407 1.131126 GAAACCATGCACAGATCACCG 59.869 52.381 0.00 0.00 0.00 4.94
4350 4411 1.450848 ATGCACAGATCACCGCCAG 60.451 57.895 0.00 0.00 0.00 4.85
4436 4497 1.948145 GACCGAGTAGGACATGACGAT 59.052 52.381 0.00 0.00 45.00 3.73
4466 4527 0.598065 AAAGGAACATGAAGCGGTGC 59.402 50.000 0.00 0.00 0.00 5.01
4637 4698 2.279120 GGCGACGAGGAGATGCTG 60.279 66.667 0.00 0.00 0.00 4.41
4638 4699 2.959071 GCGACGAGGAGATGCTGC 60.959 66.667 0.00 0.00 0.00 5.25
4646 4710 1.220749 GGAGATGCTGCCGTACCAA 59.779 57.895 0.00 0.00 0.00 3.67
4670 4734 3.876300 GGCGACATCGACTTTGCT 58.124 55.556 5.26 0.00 45.57 3.91
4921 4996 3.188460 TCGCTTCTGTTAGCCAAATCAAC 59.812 43.478 0.00 0.00 37.90 3.18
4929 5004 5.971763 TGTTAGCCAAATCAACAAGTGTTT 58.028 33.333 0.00 0.00 35.83 2.83
4938 5013 3.023119 TCAACAAGTGTTTGCTGACCAT 58.977 40.909 0.00 0.00 35.17 3.55
4941 5016 2.884639 ACAAGTGTTTGCTGACCATACC 59.115 45.455 0.00 0.00 37.85 2.73
4942 5017 1.808411 AGTGTTTGCTGACCATACCG 58.192 50.000 0.00 0.00 0.00 4.02
5059 5511 1.437573 GATGAGCGTCATCGGGTGA 59.562 57.895 10.73 0.00 43.11 4.02
5106 5573 3.453916 ATGTCAACATGGTGGCCAA 57.546 47.368 13.89 0.00 36.95 4.52
5107 5574 1.714541 ATGTCAACATGGTGGCCAAA 58.285 45.000 13.89 0.00 36.95 3.28
5108 5575 0.749649 TGTCAACATGGTGGCCAAAC 59.250 50.000 13.89 3.89 36.95 2.93
5110 5577 1.000274 GTCAACATGGTGGCCAAACTC 60.000 52.381 7.24 0.00 36.95 3.01
5111 5578 1.133513 TCAACATGGTGGCCAAACTCT 60.134 47.619 7.24 0.00 36.95 3.24
5112 5579 1.688197 CAACATGGTGGCCAAACTCTT 59.312 47.619 7.24 0.00 36.95 2.85
5113 5580 2.086610 ACATGGTGGCCAAACTCTTT 57.913 45.000 7.24 0.00 36.95 2.52
5114 5581 2.397597 ACATGGTGGCCAAACTCTTTT 58.602 42.857 7.24 0.00 36.95 2.27
5115 5582 2.102925 ACATGGTGGCCAAACTCTTTTG 59.897 45.455 7.24 0.00 41.71 2.44
5116 5583 2.151502 TGGTGGCCAAACTCTTTTGA 57.848 45.000 7.24 0.00 44.38 2.69
5117 5584 1.754226 TGGTGGCCAAACTCTTTTGAC 59.246 47.619 7.24 0.00 44.38 3.18
5118 5585 1.754226 GGTGGCCAAACTCTTTTGACA 59.246 47.619 7.24 0.00 44.38 3.58
5119 5586 2.365293 GGTGGCCAAACTCTTTTGACAT 59.635 45.455 7.24 0.00 44.38 3.06
5163 5630 0.530211 CGAGAGATGGCCTGAAGCTG 60.530 60.000 3.32 0.00 43.05 4.24
5186 5653 3.393089 TGCAGAAGTGTCTCTTTCTCC 57.607 47.619 0.00 0.00 36.40 3.71
5187 5654 2.288457 TGCAGAAGTGTCTCTTTCTCCG 60.288 50.000 0.00 0.00 36.40 4.63
5221 5705 1.817881 CACGGTATTGGTAGGGCGA 59.182 57.895 0.00 0.00 0.00 5.54
5439 5926 2.095213 TGCATCGAATAAAAGTCCGCAC 59.905 45.455 0.00 0.00 0.00 5.34
5470 5959 4.436332 GCATTGCCTTTTTCTTATGGAGG 58.564 43.478 0.00 0.00 0.00 4.30
5492 5981 1.608590 GTGGAAAAGTAAGCAGCAGCA 59.391 47.619 3.17 0.00 45.49 4.41
5521 6010 4.150359 GGGAATTTCTCATGATGGATGCT 58.850 43.478 0.00 0.00 31.32 3.79
5557 6048 1.625315 TCAAGTCCACCTGTGATCTGG 59.375 52.381 0.00 0.00 38.41 3.86
5559 6050 1.448540 GTCCACCTGTGATCTGGCG 60.449 63.158 0.00 0.00 36.34 5.69
5653 6145 3.799755 CTGTTTAGCGCGGGCCAC 61.800 66.667 22.01 15.59 41.24 5.01
5671 6163 2.609350 CACGCCATGGAAATTCTTTGG 58.391 47.619 18.40 9.38 0.00 3.28
5673 6165 2.231235 ACGCCATGGAAATTCTTTGGAC 59.769 45.455 18.40 8.18 0.00 4.02
5674 6166 2.731968 CGCCATGGAAATTCTTTGGACG 60.732 50.000 18.40 13.77 0.00 4.79
5675 6167 2.417243 GCCATGGAAATTCTTTGGACGG 60.417 50.000 18.40 0.30 0.00 4.79
5704 6206 3.319689 GGAGCTGTGGATAAGAGTAGACC 59.680 52.174 0.00 0.00 0.00 3.85
5717 6223 1.002250 GTAGACCACGCAGACACACG 61.002 60.000 0.00 0.00 0.00 4.49
5729 6235 3.865164 GCAGACACACGACATCATTGATA 59.135 43.478 0.00 0.00 0.00 2.15
5890 6396 4.566004 TCTACAAGTGCAAGTACACATCC 58.434 43.478 0.00 0.00 43.23 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.309265 GGAGAGGAAGTAGTGGGAGAAGA 60.309 52.174 0.00 0.00 0.00 2.87
34 35 2.000803 TGGAGAGGAAGTAGTGGGAGA 58.999 52.381 0.00 0.00 0.00 3.71
37 38 0.827368 GCTGGAGAGGAAGTAGTGGG 59.173 60.000 0.00 0.00 0.00 4.61
39 40 0.827368 GGGCTGGAGAGGAAGTAGTG 59.173 60.000 0.00 0.00 0.00 2.74
40 41 0.684805 CGGGCTGGAGAGGAAGTAGT 60.685 60.000 0.00 0.00 0.00 2.73
48 49 2.837291 AGCTAGCGGGCTGGAGAG 60.837 66.667 9.55 0.00 41.43 3.20
101 115 6.981722 ACAAGCTTACTTCAAAATTACCTGG 58.018 36.000 0.00 0.00 32.29 4.45
154 171 6.016024 ACAACAACAGCAACAACATCTCATAT 60.016 34.615 0.00 0.00 0.00 1.78
169 186 3.492756 ACAACAACAACAACAACAACAGC 59.507 39.130 0.00 0.00 0.00 4.40
170 187 5.006165 ACAACAACAACAACAACAACAACAG 59.994 36.000 0.00 0.00 0.00 3.16
171 188 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
172 189 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
173 190 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
174 191 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
175 192 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
176 193 6.128282 ACAAACAACAACAACAACAACAACAA 60.128 30.769 0.00 0.00 0.00 2.83
177 194 5.351465 ACAAACAACAACAACAACAACAACA 59.649 32.000 0.00 0.00 0.00 3.33
178 195 5.674580 CACAAACAACAACAACAACAACAAC 59.325 36.000 0.00 0.00 0.00 3.32
179 196 5.580691 TCACAAACAACAACAACAACAACAA 59.419 32.000 0.00 0.00 0.00 2.83
180 197 5.109210 TCACAAACAACAACAACAACAACA 58.891 33.333 0.00 0.00 0.00 3.33
181 198 5.233263 ACTCACAAACAACAACAACAACAAC 59.767 36.000 0.00 0.00 0.00 3.32
182 199 5.233050 CACTCACAAACAACAACAACAACAA 59.767 36.000 0.00 0.00 0.00 2.83
183 200 4.742167 CACTCACAAACAACAACAACAACA 59.258 37.500 0.00 0.00 0.00 3.33
184 201 4.979197 TCACTCACAAACAACAACAACAAC 59.021 37.500 0.00 0.00 0.00 3.32
185 202 5.009110 TCTCACTCACAAACAACAACAACAA 59.991 36.000 0.00 0.00 0.00 2.83
186 203 4.517075 TCTCACTCACAAACAACAACAACA 59.483 37.500 0.00 0.00 0.00 3.33
187 204 5.041951 TCTCACTCACAAACAACAACAAC 57.958 39.130 0.00 0.00 0.00 3.32
188 205 5.895636 ATCTCACTCACAAACAACAACAA 57.104 34.783 0.00 0.00 0.00 2.83
189 206 5.392919 CCAATCTCACTCACAAACAACAACA 60.393 40.000 0.00 0.00 0.00 3.33
190 207 5.036737 CCAATCTCACTCACAAACAACAAC 58.963 41.667 0.00 0.00 0.00 3.32
248 265 1.445871 AACAATCGAAGTAACCGCCC 58.554 50.000 0.00 0.00 0.00 6.13
276 293 6.666546 AGAAGTACTACAGCACTTATAACCCA 59.333 38.462 0.00 0.00 35.17 4.51
283 300 6.374894 GGAGAAGAGAAGTACTACAGCACTTA 59.625 42.308 0.00 0.00 35.17 2.24
284 301 5.184287 GGAGAAGAGAAGTACTACAGCACTT 59.816 44.000 0.00 0.00 37.69 3.16
285 302 4.703093 GGAGAAGAGAAGTACTACAGCACT 59.297 45.833 0.00 0.00 0.00 4.40
286 303 4.703093 AGGAGAAGAGAAGTACTACAGCAC 59.297 45.833 0.00 0.00 0.00 4.40
293 311 4.742012 TCACCAAGGAGAAGAGAAGTACT 58.258 43.478 0.00 0.00 0.00 2.73
297 315 2.566724 AGCTCACCAAGGAGAAGAGAAG 59.433 50.000 0.00 0.00 37.05 2.85
330 348 2.224450 GCGCCCCATTATACCACTACTT 60.224 50.000 0.00 0.00 0.00 2.24
331 349 1.346722 GCGCCCCATTATACCACTACT 59.653 52.381 0.00 0.00 0.00 2.57
332 350 1.346722 AGCGCCCCATTATACCACTAC 59.653 52.381 2.29 0.00 0.00 2.73
369 388 2.138596 ATTCACACAGGCTTTTTGCG 57.861 45.000 0.00 0.00 44.05 4.85
376 395 0.687354 ACTCGGAATTCACACAGGCT 59.313 50.000 7.93 0.00 0.00 4.58
392 411 2.032808 GTGTTGTGCCGAAGAGAAACTC 60.033 50.000 0.00 0.00 0.00 3.01
393 412 1.940613 GTGTTGTGCCGAAGAGAAACT 59.059 47.619 0.00 0.00 0.00 2.66
395 414 0.934496 CGTGTTGTGCCGAAGAGAAA 59.066 50.000 0.00 0.00 0.00 2.52
396 415 0.878523 CCGTGTTGTGCCGAAGAGAA 60.879 55.000 0.00 0.00 0.00 2.87
403 434 3.773630 CGCTACCGTGTTGTGCCG 61.774 66.667 0.00 0.00 0.00 5.69
429 460 1.933247 CAGCAGAATCCGGAGAACTC 58.067 55.000 11.34 3.84 0.00 3.01
463 494 1.342174 ACTAACTGTCGGCGGAAAAGA 59.658 47.619 7.21 0.00 0.00 2.52
464 495 1.792006 ACTAACTGTCGGCGGAAAAG 58.208 50.000 7.21 2.15 0.00 2.27
481 512 7.611467 TCATAAAGCAATTTCACACTGGATACT 59.389 33.333 0.00 0.00 37.61 2.12
552 583 3.879295 TCAGGCCGATTCATTCAAGAATC 59.121 43.478 0.00 6.61 46.56 2.52
553 584 3.629398 GTCAGGCCGATTCATTCAAGAAT 59.371 43.478 0.00 0.00 40.75 2.40
554 585 3.009723 GTCAGGCCGATTCATTCAAGAA 58.990 45.455 0.00 0.00 0.00 2.52
555 586 2.632377 GTCAGGCCGATTCATTCAAGA 58.368 47.619 0.00 0.00 0.00 3.02
556 587 1.672881 GGTCAGGCCGATTCATTCAAG 59.327 52.381 0.00 0.00 0.00 3.02
558 589 0.911769 AGGTCAGGCCGATTCATTCA 59.088 50.000 0.00 0.00 43.70 2.57
560 591 0.620556 ACAGGTCAGGCCGATTCATT 59.379 50.000 0.00 0.00 43.70 2.57
561 592 1.414181 CTACAGGTCAGGCCGATTCAT 59.586 52.381 0.00 0.00 43.70 2.57
562 593 0.824109 CTACAGGTCAGGCCGATTCA 59.176 55.000 0.00 0.00 43.70 2.57
564 595 2.032620 CTACTACAGGTCAGGCCGATT 58.967 52.381 0.00 0.00 43.70 3.34
567 598 1.674962 GTACTACTACAGGTCAGGCCG 59.325 57.143 0.00 0.00 43.70 6.13
568 599 2.950975 GAGTACTACTACAGGTCAGGCC 59.049 54.545 0.00 0.00 37.58 5.19
569 600 2.950975 GGAGTACTACTACAGGTCAGGC 59.049 54.545 0.00 0.00 0.00 4.85
570 601 4.506937 AGGAGTACTACTACAGGTCAGG 57.493 50.000 5.58 0.00 29.09 3.86
571 602 4.641094 CCAAGGAGTACTACTACAGGTCAG 59.359 50.000 8.40 0.00 29.09 3.51
572 603 4.290459 TCCAAGGAGTACTACTACAGGTCA 59.710 45.833 8.40 0.00 29.09 4.02
573 604 4.853007 TCCAAGGAGTACTACTACAGGTC 58.147 47.826 8.40 0.00 29.09 3.85
574 605 4.942363 TCCAAGGAGTACTACTACAGGT 57.058 45.455 8.40 0.00 29.09 4.00
575 606 5.507637 TCTTCCAAGGAGTACTACTACAGG 58.492 45.833 8.40 11.13 29.09 4.00
576 607 7.994334 AGTATCTTCCAAGGAGTACTACTACAG 59.006 40.741 8.40 1.54 29.09 2.74
577 608 7.774157 CAGTATCTTCCAAGGAGTACTACTACA 59.226 40.741 8.40 0.00 29.09 2.74
578 609 7.774625 ACAGTATCTTCCAAGGAGTACTACTAC 59.225 40.741 8.40 0.00 0.00 2.73
581 612 7.407393 AACAGTATCTTCCAAGGAGTACTAC 57.593 40.000 0.00 0.00 0.00 2.73
586 617 9.838339 CAAATATAACAGTATCTTCCAAGGAGT 57.162 33.333 0.00 0.00 0.00 3.85
604 635 7.119116 CCGATGGCATACTTACTGCAAATATAA 59.881 37.037 0.00 0.00 41.47 0.98
607 638 4.754618 CCGATGGCATACTTACTGCAAATA 59.245 41.667 0.00 0.00 41.47 1.40
630 661 5.741011 TCTACCAGGTGTTAATGATGAACC 58.259 41.667 0.76 0.00 0.00 3.62
716 747 5.201243 TCATGAGAAGGAGTCGGAGAATTA 58.799 41.667 0.00 0.00 39.69 1.40
724 755 4.815269 AGTCTTTTCATGAGAAGGAGTCG 58.185 43.478 22.05 1.06 34.71 4.18
730 761 5.235186 ACACGACAAGTCTTTTCATGAGAAG 59.765 40.000 17.75 17.75 34.71 2.85
874 910 1.550072 ACAAGTAATGCATGCCAACCC 59.450 47.619 16.68 0.00 0.00 4.11
881 917 4.171005 CAGAAAGGCACAAGTAATGCATG 58.829 43.478 0.00 0.00 45.27 4.06
982 1018 4.499183 GACATCTTGCTGTGTAGTAGCTT 58.501 43.478 0.00 0.00 41.66 3.74
984 1020 2.854777 CGACATCTTGCTGTGTAGTAGC 59.145 50.000 0.00 0.00 41.49 3.58
1059 1095 3.125316 GGAAAGACGTGTATCCAAGCAAG 59.875 47.826 0.00 0.00 32.08 4.01
1096 1132 4.641954 CTCACAGAACATGCACGATTTAC 58.358 43.478 0.00 0.00 0.00 2.01
1298 1334 7.423844 TTTAGATCTATTCAAGACAGGCTCA 57.576 36.000 2.58 0.00 36.93 4.26
1381 1417 2.411904 GGATCTCGCTTGAGCCATTAG 58.588 52.381 5.42 0.00 41.73 1.73
1433 1469 3.726517 CTGGCAACGGGAGCAACG 61.727 66.667 0.00 0.00 40.24 4.10
1435 1471 1.377202 GATCTGGCAACGGGAGCAA 60.377 57.895 0.00 0.00 45.79 3.91
1495 1531 6.931281 AGAGTTGATTTTGAGATTCTGACGAA 59.069 34.615 0.00 0.00 0.00 3.85
1506 1542 6.660949 ACAGGGGAATTAGAGTTGATTTTGAG 59.339 38.462 0.00 0.00 0.00 3.02
1556 1592 7.770897 GGTCTTGCTGAAGGAAATATAGAGAAA 59.229 37.037 0.00 0.00 0.00 2.52
1559 1595 6.825610 AGGTCTTGCTGAAGGAAATATAGAG 58.174 40.000 0.00 0.00 0.00 2.43
1743 1779 2.555325 CCTGTGCTTTCTGATGCTGAAA 59.445 45.455 0.00 0.00 32.18 2.69
1827 1863 3.308595 TGATATGCATTCGACGGTTTCAC 59.691 43.478 3.54 0.00 0.00 3.18
1854 1890 6.070021 ACATCAGGTGATCCACTCTTATTTGA 60.070 38.462 0.00 0.00 34.40 2.69
1856 1892 6.319048 ACATCAGGTGATCCACTCTTATTT 57.681 37.500 0.00 0.00 34.40 1.40
1867 1903 7.254932 GCAAATCTAAGGTAACATCAGGTGATC 60.255 40.741 0.00 0.00 41.41 2.92
1869 1905 5.880332 GCAAATCTAAGGTAACATCAGGTGA 59.120 40.000 0.00 0.00 41.41 4.02
1872 1908 6.375455 AGTTGCAAATCTAAGGTAACATCAGG 59.625 38.462 0.00 0.00 41.41 3.86
2031 2067 1.882623 GGCTCTTTCAACAGGTTCAGG 59.117 52.381 0.00 0.00 0.00 3.86
2068 2104 1.202582 CAGAGACTGGTGTAGGAACCG 59.797 57.143 0.00 0.00 43.73 4.44
2076 2112 4.080863 GGGTGATTTATCAGAGACTGGTGT 60.081 45.833 0.00 0.00 37.51 4.16
2099 2135 1.325943 GGCTTCGAAATCTTCTCAGCG 59.674 52.381 0.00 0.00 34.78 5.18
2117 2153 1.444836 TTACATTACACGCCACAGGC 58.555 50.000 0.00 0.00 46.75 4.85
2230 2266 8.960591 CCTTTTCTACATTGTTCTGGATATGTT 58.039 33.333 0.00 0.00 33.58 2.71
2243 2279 4.074970 ACAGAGGTGCCTTTTCTACATTG 58.925 43.478 0.00 0.00 0.00 2.82
2277 2313 1.005037 TGCTAGCCTGTCCAACACG 60.005 57.895 13.29 0.00 0.00 4.49
2346 2382 4.041567 TCCAGAGTACAAATCAAAGCCAGA 59.958 41.667 0.00 0.00 0.00 3.86
2372 2408 2.630580 GGCACCACTACCATTTGGAAAA 59.369 45.455 3.01 0.00 38.94 2.29
2392 2428 0.182537 TACCTCCAATCCATTGCGGG 59.817 55.000 9.40 8.22 36.48 6.13
2440 2476 0.249573 AGCAGCACCACACAATTTGC 60.250 50.000 0.00 0.00 35.08 3.68
2444 2480 1.364901 GCAAGCAGCACCACACAAT 59.635 52.632 0.00 0.00 44.79 2.71
2455 2491 5.946298 TGATAAATTTCTCAGTGCAAGCAG 58.054 37.500 2.34 0.00 0.00 4.24
2502 2538 1.598701 GCAATCACAGGGCTTGGGAC 61.599 60.000 2.71 0.00 43.38 4.46
2543 2579 9.656040 AAATGCAGTGATTTAGCAATTAATGAA 57.344 25.926 0.00 0.00 42.15 2.57
2596 2632 6.888105 TGACTAGCTGATTCACATAATCCAA 58.112 36.000 0.00 0.00 0.00 3.53
2610 2646 1.656587 ATGGTGGGTTGACTAGCTGA 58.343 50.000 0.00 0.00 0.00 4.26
2656 2692 7.324178 ACAATCAGTAGTAGCTTTAACAGGAG 58.676 38.462 0.00 0.00 0.00 3.69
2700 2736 2.409378 CCACATTTTTGCGAGCATGAAC 59.591 45.455 0.00 0.00 0.00 3.18
2762 2798 5.596836 TGAAAACCAAAGATTCAGCTGTT 57.403 34.783 14.67 2.24 0.00 3.16
2798 2834 4.165950 TGGGACATACCATCAAATACAGCT 59.834 41.667 0.00 0.00 41.20 4.24
2805 2841 4.044065 ACTTCCTTGGGACATACCATCAAA 59.956 41.667 0.00 0.00 40.91 2.69
2900 2936 7.553881 AATTTGACTATTACCCAATGACTCG 57.446 36.000 0.00 0.00 0.00 4.18
2937 2973 0.924090 CGCGGCTCAGTGATTAAGTC 59.076 55.000 0.00 0.00 0.00 3.01
2948 2984 0.740868 CATCTTCTTTCCGCGGCTCA 60.741 55.000 23.51 3.33 0.00 4.26
2965 3001 7.606349 ACAGTCGTGATGCATATTACTATCAT 58.394 34.615 0.00 0.00 32.76 2.45
3028 3064 4.565229 CGTATTAACACGCTTCACATCAC 58.435 43.478 0.00 0.00 34.78 3.06
3088 3124 6.438763 CCATTAACAGAAACCTCACTTTCAC 58.561 40.000 0.00 0.00 33.26 3.18
3115 3151 5.005682 GTCAACAATTGTTTGTCTTTGGCTC 59.994 40.000 21.10 1.86 45.30 4.70
3163 3199 4.895668 TCCCTGGTAACGTCAGTTTTAT 57.104 40.909 0.00 0.00 41.49 1.40
3167 3203 2.322658 TCTTCCCTGGTAACGTCAGTT 58.677 47.619 0.00 0.00 43.95 3.16
3174 3210 7.067129 GGAAATCTTAACATCTTCCCTGGTAAC 59.933 40.741 0.00 0.00 31.19 2.50
3181 3217 3.945285 TGCGGAAATCTTAACATCTTCCC 59.055 43.478 0.00 0.00 33.40 3.97
3219 3255 6.663523 CCCAAAATAGGTGGTCTTGTAAGATT 59.336 38.462 0.00 0.00 37.39 2.40
3231 3267 3.763897 CCTGAAGTTCCCAAAATAGGTGG 59.236 47.826 0.00 0.00 35.77 4.61
3275 3311 4.219070 TCAAATGTCTTTGGAGATTGCCTG 59.781 41.667 0.00 0.00 41.74 4.85
3287 3323 6.929049 TCTCGACAGTGTAATCAAATGTCTTT 59.071 34.615 0.00 0.00 38.90 2.52
3488 3524 3.350833 AGCTCCATCAACAAGTGAATCC 58.649 45.455 0.00 0.00 40.50 3.01
3503 3539 0.033504 GTTGACTGGTCGAAGCTCCA 59.966 55.000 0.00 0.00 0.00 3.86
3526 3562 9.967346 TCGATTTTACCTCTGTAGATTCATTAG 57.033 33.333 0.00 0.00 0.00 1.73
3572 3608 5.451798 GCAAGAGTCAGGTTTGGATTTTTCA 60.452 40.000 0.00 0.00 0.00 2.69
3616 3652 6.014669 CCCATTAACCTGTCCATCTTTTTCAA 60.015 38.462 0.00 0.00 0.00 2.69
3644 3680 0.608856 TTGCCACATCTCGCCAATGT 60.609 50.000 0.00 0.00 37.85 2.71
3711 3772 6.458232 AATATAAATACGCACAGGGCAAAA 57.542 33.333 0.00 0.00 45.17 2.44
3839 3900 2.401766 GCCACCATGGAACTCGCTG 61.402 63.158 21.47 3.74 40.96 5.18
3842 3903 0.742281 CTCTGCCACCATGGAACTCG 60.742 60.000 21.47 3.71 40.96 4.18
3977 4038 4.661222 TGCCAACAATAGGTTCATCTTCA 58.339 39.130 0.00 0.00 37.72 3.02
4022 4083 3.419759 CGGTGCAAGTGCCCGTAC 61.420 66.667 19.05 4.50 44.28 3.67
4088 4149 6.111382 GTCATGTTCCATTTCTCTCATGAGA 58.889 40.000 23.75 23.75 46.58 3.27
4106 4167 4.533707 TCTCTCCCAGAAAATCTGTCATGT 59.466 41.667 6.62 0.00 42.80 3.21
4177 4238 4.141756 ACCTCTGTTCCATCATGTCATCTC 60.142 45.833 0.00 0.00 0.00 2.75
4346 4407 3.495001 GTCTGTCACTTCTGTTTACTGGC 59.505 47.826 0.00 0.00 0.00 4.85
4350 4411 6.456501 AGTATGGTCTGTCACTTCTGTTTAC 58.543 40.000 0.00 0.00 0.00 2.01
4436 4497 5.692115 TCATGTTCCTTTGCATACCTCTA 57.308 39.130 0.00 0.00 0.00 2.43
4466 4527 1.138036 CACACCTTGATGCATGCCG 59.862 57.895 16.68 0.00 0.00 5.69
4501 4562 2.119029 GCGGGATGTAAAGGTGGCC 61.119 63.158 0.00 0.00 0.00 5.36
4533 4594 1.129917 AGCTCAGCCTCTGCATGTAT 58.870 50.000 0.00 0.00 41.13 2.29
4637 4698 2.895372 CCATCGCCTTGGTACGGC 60.895 66.667 0.46 0.46 44.11 5.68
4638 4699 2.895372 GCCATCGCCTTGGTACGG 60.895 66.667 1.86 0.00 39.11 4.02
4670 4734 2.297129 TGGACCGCCATCACCATCA 61.297 57.895 0.00 0.00 39.92 3.07
4836 4903 7.040473 AGAAGATTCAGATTCATTCATTGGC 57.960 36.000 0.00 0.00 0.00 4.52
4837 4904 8.566260 GGTAGAAGATTCAGATTCATTCATTGG 58.434 37.037 0.00 0.00 0.00 3.16
4921 4996 2.095768 CGGTATGGTCAGCAAACACTTG 60.096 50.000 0.00 0.00 35.49 3.16
4929 5004 3.792736 GGGGCGGTATGGTCAGCA 61.793 66.667 0.00 0.00 0.00 4.41
5059 5511 3.274288 GCTTCAGCTTATACCAAGCAGT 58.726 45.455 11.24 0.00 45.30 4.40
5088 5555 1.344114 GTTTGGCCACCATGTTGACAT 59.656 47.619 3.88 0.00 36.96 3.06
5089 5556 0.749649 GTTTGGCCACCATGTTGACA 59.250 50.000 3.88 0.00 31.53 3.58
5103 5570 4.676924 GCGAGAAATGTCAAAAGAGTTTGG 59.323 41.667 0.00 0.00 43.70 3.28
5106 5573 3.882888 TGGCGAGAAATGTCAAAAGAGTT 59.117 39.130 0.00 0.00 0.00 3.01
5107 5574 3.476552 TGGCGAGAAATGTCAAAAGAGT 58.523 40.909 0.00 0.00 0.00 3.24
5108 5575 4.488126 TTGGCGAGAAATGTCAAAAGAG 57.512 40.909 0.00 0.00 0.00 2.85
5110 5577 5.464168 AGATTTGGCGAGAAATGTCAAAAG 58.536 37.500 0.00 0.00 43.35 2.27
5111 5578 5.452078 AGATTTGGCGAGAAATGTCAAAA 57.548 34.783 0.00 0.00 43.35 2.44
5112 5579 5.009510 TGAAGATTTGGCGAGAAATGTCAAA 59.990 36.000 0.00 0.00 44.14 2.69
5113 5580 4.518590 TGAAGATTTGGCGAGAAATGTCAA 59.481 37.500 0.00 0.00 0.00 3.18
5114 5581 4.071423 TGAAGATTTGGCGAGAAATGTCA 58.929 39.130 0.00 0.00 0.00 3.58
5115 5582 4.685169 TGAAGATTTGGCGAGAAATGTC 57.315 40.909 0.00 0.00 0.00 3.06
5116 5583 5.010012 AGTTTGAAGATTTGGCGAGAAATGT 59.990 36.000 0.00 0.00 0.00 2.71
5117 5584 5.464168 AGTTTGAAGATTTGGCGAGAAATG 58.536 37.500 0.00 0.00 0.00 2.32
5118 5585 5.712152 AGTTTGAAGATTTGGCGAGAAAT 57.288 34.783 0.00 0.00 0.00 2.17
5119 5586 6.627395 TTAGTTTGAAGATTTGGCGAGAAA 57.373 33.333 0.00 0.00 0.00 2.52
5163 5630 3.137533 AGAAAGAGACACTTCTGCAAGC 58.862 45.455 0.00 0.00 37.93 4.01
5186 5653 1.630148 GTGCAGCAAGTAGGTAGACG 58.370 55.000 0.00 0.00 0.00 4.18
5187 5654 1.630148 CGTGCAGCAAGTAGGTAGAC 58.370 55.000 0.00 0.00 0.00 2.59
5221 5705 5.148651 AGACAAGTCGCTTTAATACAGGT 57.851 39.130 0.00 0.00 34.09 4.00
5470 5959 2.095516 GCTGCTGCTTACTTTTCCACTC 60.096 50.000 8.53 0.00 36.03 3.51
5492 5981 2.025605 TCATGAGAAATTCCCAGCAGCT 60.026 45.455 0.00 0.00 0.00 4.24
5521 6010 2.223641 ACTTGACTAACGCACAAGACGA 60.224 45.455 12.04 0.00 42.12 4.20
5557 6048 2.774439 ACACAGTTTTTCCACATCGC 57.226 45.000 0.00 0.00 0.00 4.58
5559 6050 2.788786 CGCAACACAGTTTTTCCACATC 59.211 45.455 0.00 0.00 0.00 3.06
5610 6101 2.420827 CCAACCAATGGCACCTCGTATA 60.421 50.000 0.00 0.00 43.80 1.47
5653 6145 2.731968 CGTCCAAAGAATTTCCATGGCG 60.732 50.000 6.96 13.06 35.03 5.69
5666 6158 0.884704 CTCCACCACACCGTCCAAAG 60.885 60.000 0.00 0.00 0.00 2.77
5668 6160 2.825982 CTCCACCACACCGTCCAA 59.174 61.111 0.00 0.00 0.00 3.53
5669 6161 3.936203 GCTCCACCACACCGTCCA 61.936 66.667 0.00 0.00 0.00 4.02
5670 6162 3.626924 AGCTCCACCACACCGTCC 61.627 66.667 0.00 0.00 0.00 4.79
5671 6163 2.357517 CAGCTCCACCACACCGTC 60.358 66.667 0.00 0.00 0.00 4.79
5673 6165 2.666190 CACAGCTCCACCACACCG 60.666 66.667 0.00 0.00 0.00 4.94
5674 6166 2.129555 ATCCACAGCTCCACCACACC 62.130 60.000 0.00 0.00 0.00 4.16
5675 6167 0.613260 TATCCACAGCTCCACCACAC 59.387 55.000 0.00 0.00 0.00 3.82
5704 6206 0.939106 TGATGTCGTGTGTCTGCGTG 60.939 55.000 0.00 0.00 0.00 5.34
5717 6223 3.005554 CGCAGGGGATATCAATGATGTC 58.994 50.000 10.95 10.95 30.96 3.06
5890 6396 0.940126 GCATTGCTACCGAGATGTGG 59.060 55.000 0.16 0.00 0.00 4.17
5918 6425 2.621338 CGTGTGTGGCTGTTGAGATAT 58.379 47.619 0.00 0.00 0.00 1.63
5931 6442 4.662961 TCGAGGCTGCCGTGTGTG 62.663 66.667 13.96 0.90 0.00 3.82
5947 6458 3.454375 TGTGTTGAGAAGAAACTCCGTC 58.546 45.455 0.00 0.00 36.22 4.79
5950 6461 3.561725 CCACTGTGTTGAGAAGAAACTCC 59.438 47.826 7.08 0.00 36.22 3.85
5964 6475 1.073923 GATGGAAGTTCCCCACTGTGT 59.926 52.381 19.42 0.00 35.12 3.72
5965 6476 1.614317 GGATGGAAGTTCCCCACTGTG 60.614 57.143 19.42 0.00 35.12 3.66


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

AutoCloner maintained by Alex Coulton.