Multiple sequence alignment - TraesCS3B01G092500

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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 TraesCS3B01G092500 chr3B 100.000 5716 0 0 1 5716 61565560 61559845 0.000000e+00 10556.0
1 TraesCS3B01G092500 chr3D 94.082 5509 165 80 1 5423 38753574 38748141 0.000000e+00 8218.0
2 TraesCS3B01G092500 chr3D 95.392 217 7 3 5423 5638 38748080 38747866 5.480000e-90 342.0
3 TraesCS3B01G092500 chr3A 92.800 5514 188 77 1 5423 49985779 49980384 0.000000e+00 7790.0
4 TraesCS3B01G092500 chr3A 93.578 218 8 2 5426 5638 49980320 49980104 2.570000e-83 320.0
5 TraesCS3B01G092500 chr1B 100.000 33 0 0 467 499 661058058 661058026 1.720000e-05 62.1


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 TraesCS3B01G092500 chr3B 61559845 61565560 5715 True 10556 10556 100.000 1 5716 1 chr3B.!!$R1 5715
1 TraesCS3B01G092500 chr3D 38747866 38753574 5708 True 4280 8218 94.737 1 5638 2 chr3D.!!$R1 5637
2 TraesCS3B01G092500 chr3A 49980104 49985779 5675 True 4055 7790 93.189 1 5638 2 chr3A.!!$R1 5637

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
376 385 0.998669 TTGACATGTACGCGCATCAG 59.001 50.0 5.73 0.0 0.0 2.90 F
1549 1602 0.467290 TGGTTTCCCACAAGAGGTGC 60.467 55.0 0.00 0.0 46.5 5.01 F
2502 2578 0.035152 TGCAAACTCATGGCCGATCT 60.035 50.0 0.00 0.0 0.0 2.75 F
2805 2891 0.321122 AGGCTGCAACTCACTACTGC 60.321 55.0 0.50 0.0 36.6 4.40 F
2855 2941 0.396435 ACCCAGTTCTGCGATCAACA 59.604 50.0 0.00 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1777 0.465097 AGTGCTATGATGCTGGTGGC 60.465 55.000 0.00 0.00 42.22 5.01 R
2827 2913 0.176680 CAGAACTGGGTCGATCTGGG 59.823 60.000 0.00 0.00 36.50 4.45 R
3317 3428 1.462616 ACACAGCACAACACACACAT 58.537 45.000 0.00 0.00 0.00 3.21 R
4649 4808 1.153823 GACGTAGGATGTGCACGCT 60.154 57.895 13.13 1.21 39.23 5.07 R
4830 4989 0.828022 TACATCCCGTTTCGATGCCT 59.172 50.000 0.00 0.00 40.70 4.75 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
38 39 8.223177 TGGATTTGCATTTGAAAGATGTTTTT 57.777 26.923 0.00 0.00 0.00 1.94
61 63 9.974750 TTTTAAAAATAAACCTTTTGCTGAACG 57.025 25.926 0.00 0.00 0.00 3.95
68 70 2.542595 ACCTTTTGCTGAACGTAACTCG 59.457 45.455 0.00 0.00 46.00 4.18
106 108 2.565391 TCGGTGATCAAAGTTAGGCTCA 59.435 45.455 0.00 0.00 0.00 4.26
111 113 6.456988 CGGTGATCAAAGTTAGGCTCAAATAC 60.457 42.308 0.00 0.00 0.00 1.89
158 161 5.928264 GCGAGGACCTTTAACAGTTTAACTA 59.072 40.000 0.00 0.00 0.00 2.24
186 192 4.081917 ACTTCTAGCTAGTTCTGTTCTGCC 60.082 45.833 20.10 0.00 0.00 4.85
188 194 2.758736 AGCTAGTTCTGTTCTGCCAG 57.241 50.000 0.00 0.00 0.00 4.85
202 209 2.819608 TCTGCCAGGCAATTTCAAGTAC 59.180 45.455 17.03 0.00 38.41 2.73
216 223 8.745837 CAATTTCAAGTACTTTAGTTTGTGCTG 58.254 33.333 5.07 0.00 0.00 4.41
339 348 7.610305 TCAATTATGGACCTTTTCTACTTCCAC 59.390 37.037 0.00 0.00 39.17 4.02
346 355 3.181433 CCTTTTCTACTTCCACCCCAGTT 60.181 47.826 0.00 0.00 0.00 3.16
361 370 3.319755 CCCAGTTGCAACATGATTTGAC 58.680 45.455 30.11 0.63 0.00 3.18
375 384 1.433534 TTTGACATGTACGCGCATCA 58.566 45.000 5.73 3.03 0.00 3.07
376 385 0.998669 TTGACATGTACGCGCATCAG 59.001 50.000 5.73 0.00 0.00 2.90
397 410 6.949715 TCAGCCTGTCATTCATGCATATATA 58.050 36.000 0.00 0.00 39.54 0.86
544 557 8.591072 ACGTACAGCTTATGGGTAATAATACAT 58.409 33.333 0.00 0.00 33.45 2.29
694 709 4.339748 AGTGTATGTGCAAGAGAGAGAGA 58.660 43.478 0.00 0.00 0.00 3.10
695 710 4.398988 AGTGTATGTGCAAGAGAGAGAGAG 59.601 45.833 0.00 0.00 0.00 3.20
696 711 3.698539 TGTATGTGCAAGAGAGAGAGAGG 59.301 47.826 0.00 0.00 0.00 3.69
697 712 1.554836 TGTGCAAGAGAGAGAGAGGG 58.445 55.000 0.00 0.00 0.00 4.30
812 835 5.770685 AGCCTTATGAGAAAGAGAAAGGT 57.229 39.130 0.00 0.00 36.64 3.50
925 949 3.192212 GCTTGACTGGCATTTTCTAAGCT 59.808 43.478 0.00 0.00 37.06 3.74
935 959 4.220602 GCATTTTCTAAGCTTTCCTTCCCA 59.779 41.667 3.20 0.00 34.95 4.37
965 989 6.183360 GGAAGTAGCACATCAAGATCTCCTAA 60.183 42.308 0.00 0.00 0.00 2.69
1210 1244 4.090761 TCAGCAGTTTTCATCTTCACCT 57.909 40.909 0.00 0.00 0.00 4.00
1211 1245 4.464008 TCAGCAGTTTTCATCTTCACCTT 58.536 39.130 0.00 0.00 0.00 3.50
1213 1247 5.360714 TCAGCAGTTTTCATCTTCACCTTTT 59.639 36.000 0.00 0.00 0.00 2.27
1453 1504 1.142474 GGCACAGCAAAATGACAAGC 58.858 50.000 0.00 0.00 0.00 4.01
1500 1551 5.574815 AGAAACAAATTTAATGTGCGTGC 57.425 34.783 0.00 0.00 0.00 5.34
1538 1589 8.349568 AGATCTTACTATTTTGTTGGTTTCCC 57.650 34.615 0.00 0.00 0.00 3.97
1549 1602 0.467290 TGGTTTCCCACAAGAGGTGC 60.467 55.000 0.00 0.00 46.50 5.01
1560 1613 2.104792 ACAAGAGGTGCTGTGTGTATGT 59.895 45.455 0.00 0.00 0.00 2.29
1735 1794 1.152902 GGCCACCAGCATCATAGCA 60.153 57.895 0.00 0.00 46.50 3.49
1736 1795 1.450531 GGCCACCAGCATCATAGCAC 61.451 60.000 0.00 0.00 46.50 4.40
1738 1797 1.590932 CCACCAGCATCATAGCACTC 58.409 55.000 0.00 0.00 36.85 3.51
1739 1798 1.134310 CCACCAGCATCATAGCACTCA 60.134 52.381 0.00 0.00 36.85 3.41
1740 1799 1.938577 CACCAGCATCATAGCACTCAC 59.061 52.381 0.00 0.00 36.85 3.51
1843 1902 1.556373 ATGGAGTAGCAGCTGTGGCA 61.556 55.000 16.64 0.00 41.70 4.92
2016 2084 2.817423 GCGGCTGCAGAAGATTCCG 61.817 63.158 20.43 20.11 42.15 4.30
2142 2210 0.530650 CGACGGTGCTGCTCCATAAT 60.531 55.000 19.58 2.97 0.00 1.28
2226 2294 1.734465 CCTGTTCATCGTCTTCAAGGC 59.266 52.381 0.00 0.00 0.00 4.35
2297 2367 4.519730 ACCGTCCTCCTCGATCTAATTAAG 59.480 45.833 0.00 0.00 0.00 1.85
2316 2386 6.976934 TTAAGGAGATGGGGAATTAATTGC 57.023 37.500 10.99 10.99 0.00 3.56
2320 2390 4.389374 GAGATGGGGAATTAATTGCGAGA 58.611 43.478 12.83 0.87 0.00 4.04
2321 2391 4.990526 AGATGGGGAATTAATTGCGAGAT 58.009 39.130 12.83 5.30 0.00 2.75
2502 2578 0.035152 TGCAAACTCATGGCCGATCT 60.035 50.000 0.00 0.00 0.00 2.75
2503 2579 1.209261 TGCAAACTCATGGCCGATCTA 59.791 47.619 0.00 0.00 0.00 1.98
2525 2601 1.488393 AGCCTAGCTTAGCTGAAAGGG 59.512 52.381 17.97 11.39 40.10 3.95
2689 2775 1.657822 GGTCATCTTTTCTCTCGCCC 58.342 55.000 0.00 0.00 0.00 6.13
2731 2817 3.209410 CATATGACCCTCTTGCAGTTCC 58.791 50.000 0.00 0.00 0.00 3.62
2732 2818 1.067295 ATGACCCTCTTGCAGTTCCA 58.933 50.000 0.00 0.00 0.00 3.53
2744 2830 2.291735 TGCAGTTCCACATCCATCCATT 60.292 45.455 0.00 0.00 0.00 3.16
2749 2835 6.407299 GCAGTTCCACATCCATCCATTTTAAT 60.407 38.462 0.00 0.00 0.00 1.40
2805 2891 0.321122 AGGCTGCAACTCACTACTGC 60.321 55.000 0.50 0.00 36.60 4.40
2819 2905 2.422479 ACTACTGCTGAGCAATTGCATG 59.578 45.455 30.89 20.11 45.16 4.06
2827 2913 1.634225 GCAATTGCATGCATGTCGC 59.366 52.632 26.79 17.56 45.70 5.19
2845 2931 1.617947 GCCCAGATCGACCCAGTTCT 61.618 60.000 0.00 0.00 0.00 3.01
2855 2941 0.396435 ACCCAGTTCTGCGATCAACA 59.604 50.000 0.00 0.00 0.00 3.33
2868 2954 7.811653 TCTGCGATCAACACAATTATTACAAA 58.188 30.769 0.00 0.00 0.00 2.83
2869 2955 8.458052 TCTGCGATCAACACAATTATTACAAAT 58.542 29.630 0.00 0.00 0.00 2.32
2870 2956 8.978564 TGCGATCAACACAATTATTACAAATT 57.021 26.923 0.00 0.00 0.00 1.82
2947 3035 6.491394 TGCAAAAATGTGTGTACAAGACTAC 58.509 36.000 0.00 0.00 40.84 2.73
3019 3111 1.589716 GGGTGTGCCTGCTGCTTTAG 61.590 60.000 0.00 0.00 42.00 1.85
3046 3138 3.649986 ACGGAAGTGCGCTGCAAC 61.650 61.111 9.73 0.00 46.97 4.17
3219 3311 4.780021 ACTCCTGACTACATCTCCAACATT 59.220 41.667 0.00 0.00 0.00 2.71
3220 3312 5.249393 ACTCCTGACTACATCTCCAACATTT 59.751 40.000 0.00 0.00 0.00 2.32
3221 3313 6.126863 TCCTGACTACATCTCCAACATTTT 57.873 37.500 0.00 0.00 0.00 1.82
3222 3314 6.173339 TCCTGACTACATCTCCAACATTTTC 58.827 40.000 0.00 0.00 0.00 2.29
3223 3315 6.013379 TCCTGACTACATCTCCAACATTTTCT 60.013 38.462 0.00 0.00 0.00 2.52
3224 3316 6.314896 CCTGACTACATCTCCAACATTTTCTC 59.685 42.308 0.00 0.00 0.00 2.87
3225 3317 7.009179 TGACTACATCTCCAACATTTTCTCT 57.991 36.000 0.00 0.00 0.00 3.10
3226 3318 8.134202 TGACTACATCTCCAACATTTTCTCTA 57.866 34.615 0.00 0.00 0.00 2.43
3227 3319 8.762645 TGACTACATCTCCAACATTTTCTCTAT 58.237 33.333 0.00 0.00 0.00 1.98
3228 3320 9.255304 GACTACATCTCCAACATTTTCTCTATC 57.745 37.037 0.00 0.00 0.00 2.08
3229 3321 8.986991 ACTACATCTCCAACATTTTCTCTATCT 58.013 33.333 0.00 0.00 0.00 1.98
3232 3324 8.762645 ACATCTCCAACATTTTCTCTATCTACA 58.237 33.333 0.00 0.00 0.00 2.74
3233 3325 9.039870 CATCTCCAACATTTTCTCTATCTACAC 57.960 37.037 0.00 0.00 0.00 2.90
3234 3326 8.134202 TCTCCAACATTTTCTCTATCTACACA 57.866 34.615 0.00 0.00 0.00 3.72
3235 3327 8.762645 TCTCCAACATTTTCTCTATCTACACAT 58.237 33.333 0.00 0.00 0.00 3.21
3236 3328 8.722480 TCCAACATTTTCTCTATCTACACATG 57.278 34.615 0.00 0.00 0.00 3.21
3237 3329 7.280876 TCCAACATTTTCTCTATCTACACATGC 59.719 37.037 0.00 0.00 0.00 4.06
3238 3330 7.066163 CCAACATTTTCTCTATCTACACATGCA 59.934 37.037 0.00 0.00 0.00 3.96
3239 3331 8.618677 CAACATTTTCTCTATCTACACATGCAT 58.381 33.333 0.00 0.00 0.00 3.96
3240 3332 8.743085 ACATTTTCTCTATCTACACATGCATT 57.257 30.769 0.00 0.00 0.00 3.56
3241 3333 8.618677 ACATTTTCTCTATCTACACATGCATTG 58.381 33.333 0.00 1.69 0.00 2.82
3242 3334 6.609237 TTTCTCTATCTACACATGCATTGC 57.391 37.500 0.00 0.46 0.00 3.56
3243 3335 5.280654 TCTCTATCTACACATGCATTGCA 57.719 39.130 14.72 14.72 44.86 4.08
3317 3428 5.952347 AGTCTATTCTCCTCATGTGTGTGTA 59.048 40.000 0.00 0.00 0.00 2.90
3358 3475 2.791347 TGTTGGGTAGTGTGTGTGTT 57.209 45.000 0.00 0.00 0.00 3.32
3360 3477 3.422796 TGTTGGGTAGTGTGTGTGTTTT 58.577 40.909 0.00 0.00 0.00 2.43
3361 3478 3.191581 TGTTGGGTAGTGTGTGTGTTTTG 59.808 43.478 0.00 0.00 0.00 2.44
3362 3479 1.746220 TGGGTAGTGTGTGTGTTTTGC 59.254 47.619 0.00 0.00 0.00 3.68
3410 3535 5.299028 TCATGTGTTACTGAGCATGTGTTTT 59.701 36.000 0.00 0.00 39.54 2.43
3413 3538 5.124617 TGTGTTACTGAGCATGTGTTTTTCA 59.875 36.000 0.00 0.00 0.00 2.69
3414 3539 5.455525 GTGTTACTGAGCATGTGTTTTTCAC 59.544 40.000 0.00 0.00 46.31 3.18
3415 3540 5.356751 TGTTACTGAGCATGTGTTTTTCACT 59.643 36.000 0.00 0.00 46.27 3.41
3416 3541 4.989279 ACTGAGCATGTGTTTTTCACTT 57.011 36.364 0.00 0.00 46.27 3.16
3418 3543 6.449635 ACTGAGCATGTGTTTTTCACTTTA 57.550 33.333 0.00 0.00 46.27 1.85
3419 3544 7.042797 ACTGAGCATGTGTTTTTCACTTTAT 57.957 32.000 0.00 0.00 46.27 1.40
3420 3545 7.141363 ACTGAGCATGTGTTTTTCACTTTATC 58.859 34.615 0.00 0.00 46.27 1.75
3421 3546 7.013655 ACTGAGCATGTGTTTTTCACTTTATCT 59.986 33.333 0.00 0.00 46.27 1.98
3422 3547 7.715657 TGAGCATGTGTTTTTCACTTTATCTT 58.284 30.769 0.00 0.00 46.27 2.40
3423 3548 8.196771 TGAGCATGTGTTTTTCACTTTATCTTT 58.803 29.630 0.00 0.00 46.27 2.52
3424 3549 9.677567 GAGCATGTGTTTTTCACTTTATCTTTA 57.322 29.630 0.00 0.00 46.27 1.85
3429 3554 9.677567 TGTGTTTTTCACTTTATCTTTATCTGC 57.322 29.630 0.00 0.00 46.27 4.26
3430 3555 9.677567 GTGTTTTTCACTTTATCTTTATCTGCA 57.322 29.630 0.00 0.00 43.13 4.41
3599 3743 8.781196 GCTAGCTTAACTAATTACCATTTACCC 58.219 37.037 7.70 0.00 0.00 3.69
3607 3751 8.688222 ACTAATTACCATTTACCCCCAAAAAT 57.312 30.769 0.00 0.00 0.00 1.82
3635 3779 7.206981 ACATGTAATTTGGTTCAGAGTTCAG 57.793 36.000 0.00 0.00 0.00 3.02
3665 3809 7.225931 GTGAGAATTGTGTTGTACTGGACTTAA 59.774 37.037 0.00 0.00 0.00 1.85
3805 3949 2.020720 CGGCCTTATGGTAATTGCACA 58.979 47.619 0.00 0.00 35.27 4.57
3806 3950 2.622942 CGGCCTTATGGTAATTGCACAT 59.377 45.455 0.00 0.00 35.27 3.21
3811 3955 5.394005 GCCTTATGGTAATTGCACATTCACA 60.394 40.000 0.00 0.00 35.27 3.58
3896 4040 3.545703 ACTACCAAGCATATGAACCTGC 58.454 45.455 6.97 0.00 38.69 4.85
3901 4045 3.057736 CCAAGCATATGAACCTGCATAGC 60.058 47.826 6.97 0.00 40.88 2.97
3902 4046 2.787994 AGCATATGAACCTGCATAGCC 58.212 47.619 6.97 0.00 40.88 3.93
3903 4047 1.815003 GCATATGAACCTGCATAGCCC 59.185 52.381 6.97 0.00 38.28 5.19
3904 4048 2.815215 GCATATGAACCTGCATAGCCCA 60.815 50.000 6.97 0.00 38.28 5.36
3905 4049 3.489355 CATATGAACCTGCATAGCCCAA 58.511 45.455 0.00 0.00 34.50 4.12
3906 4050 2.530460 ATGAACCTGCATAGCCCAAA 57.470 45.000 0.00 0.00 0.00 3.28
3907 4051 1.544724 TGAACCTGCATAGCCCAAAC 58.455 50.000 0.00 0.00 0.00 2.93
3938 4082 7.981142 AGAACAATGTTTTCAGACTTAAACGA 58.019 30.769 0.00 0.00 37.12 3.85
3953 4097 7.876068 AGACTTAAACGATATTTCAGGTCAACA 59.124 33.333 0.00 0.00 0.00 3.33
3962 4106 8.088365 CGATATTTCAGGTCAACATGTCCTATA 58.912 37.037 0.00 0.00 33.68 1.31
4281 4437 9.167311 CTTAGTCAGGTCAAACTAATTAATGCT 57.833 33.333 0.00 0.00 37.35 3.79
4328 4487 3.496130 CCTGACCATCATCGCTCATTTAC 59.504 47.826 0.00 0.00 0.00 2.01
4407 4566 1.069296 CAACACAACAGCGGGTACATG 60.069 52.381 0.00 0.00 0.00 3.21
4649 4808 1.003355 GCTGTGCTTGGTGCCTCTA 60.003 57.895 0.00 0.00 42.00 2.43
4830 4989 9.784531 AAAAATATGTTCTCTTTCTCTCTCACA 57.215 29.630 0.00 0.00 0.00 3.58
4963 5126 2.294979 GCAGATCATGGAAGCATGACA 58.705 47.619 0.00 0.00 43.42 3.58
5000 5163 0.906775 TGGAGATGTCATGCTGCTGA 59.093 50.000 0.00 0.00 0.00 4.26
5022 5185 9.974750 GCTGATTACTCTGAATTTGTAACTTAC 57.025 33.333 0.00 0.00 0.00 2.34
5177 5341 1.601430 GCTTACCTGAGCATTAGCAGC 59.399 52.381 0.00 0.00 45.49 5.25
5322 5488 8.733458 TGAACAGAAAGATGAATAATGTTCAGG 58.267 33.333 12.38 0.00 45.87 3.86
5483 5710 2.129555 AATGCACCCACCGAGCTTCT 62.130 55.000 0.00 0.00 0.00 2.85
5524 5751 6.233434 ACATGTACACTTGATCTCACATTGT 58.767 36.000 0.00 0.00 0.00 2.71
5593 5820 4.620567 CGTTGTTGATGGATCAGTGTCCTA 60.621 45.833 11.48 1.80 39.12 2.94
5594 5821 4.471904 TGTTGATGGATCAGTGTCCTAC 57.528 45.455 11.48 7.23 39.12 3.18
5595 5822 4.096681 TGTTGATGGATCAGTGTCCTACT 58.903 43.478 11.48 0.00 41.36 2.57
5596 5823 5.269189 TGTTGATGGATCAGTGTCCTACTA 58.731 41.667 11.48 2.95 37.60 1.82
5599 5826 7.092891 TGTTGATGGATCAGTGTCCTACTAAAT 60.093 37.037 11.48 0.00 37.60 1.40
5600 5827 8.421784 GTTGATGGATCAGTGTCCTACTAAATA 58.578 37.037 11.48 0.00 37.60 1.40
5601 5828 7.952671 TGATGGATCAGTGTCCTACTAAATAC 58.047 38.462 11.48 0.00 37.60 1.89
5602 5829 7.785028 TGATGGATCAGTGTCCTACTAAATACT 59.215 37.037 11.48 0.00 37.60 2.12
5603 5830 7.348080 TGGATCAGTGTCCTACTAAATACTG 57.652 40.000 11.48 0.00 37.60 2.74
5628 5860 0.972883 TTTTGGTGCTATGCAACCCC 59.027 50.000 5.09 0.00 46.96 4.95
5629 5861 0.178950 TTTGGTGCTATGCAACCCCA 60.179 50.000 5.09 1.01 46.96 4.96
5632 5864 1.194218 GGTGCTATGCAACCCCATTT 58.806 50.000 0.00 0.00 40.86 2.32
5634 5866 1.136891 GTGCTATGCAACCCCATTTCC 59.863 52.381 0.00 0.00 41.47 3.13
5635 5867 1.006998 TGCTATGCAACCCCATTTCCT 59.993 47.619 0.00 0.00 34.76 3.36
5636 5868 1.410153 GCTATGCAACCCCATTTCCTG 59.590 52.381 0.00 0.00 0.00 3.86
5637 5869 1.410153 CTATGCAACCCCATTTCCTGC 59.590 52.381 0.00 0.00 0.00 4.85
5638 5870 0.544833 ATGCAACCCCATTTCCTGCA 60.545 50.000 0.00 0.00 46.20 4.41
5639 5871 1.186917 TGCAACCCCATTTCCTGCAG 61.187 55.000 6.78 6.78 38.06 4.41
5640 5872 1.187567 GCAACCCCATTTCCTGCAGT 61.188 55.000 13.81 0.00 33.19 4.40
5641 5873 0.890683 CAACCCCATTTCCTGCAGTC 59.109 55.000 13.81 0.00 0.00 3.51
5642 5874 0.482446 AACCCCATTTCCTGCAGTCA 59.518 50.000 13.81 0.00 0.00 3.41
5643 5875 0.706433 ACCCCATTTCCTGCAGTCAT 59.294 50.000 13.81 0.00 0.00 3.06
5644 5876 1.077663 ACCCCATTTCCTGCAGTCATT 59.922 47.619 13.81 0.00 0.00 2.57
5645 5877 2.311542 ACCCCATTTCCTGCAGTCATTA 59.688 45.455 13.81 0.00 0.00 1.90
5646 5878 3.245586 ACCCCATTTCCTGCAGTCATTAA 60.246 43.478 13.81 0.00 0.00 1.40
5647 5879 3.131046 CCCCATTTCCTGCAGTCATTAAC 59.869 47.826 13.81 0.00 0.00 2.01
5648 5880 4.019174 CCCATTTCCTGCAGTCATTAACT 58.981 43.478 13.81 0.00 39.44 2.24
5649 5881 5.192927 CCCATTTCCTGCAGTCATTAACTA 58.807 41.667 13.81 0.00 36.07 2.24
5650 5882 5.066505 CCCATTTCCTGCAGTCATTAACTAC 59.933 44.000 13.81 0.00 36.07 2.73
5651 5883 5.647658 CCATTTCCTGCAGTCATTAACTACA 59.352 40.000 13.81 0.00 36.07 2.74
5652 5884 6.150976 CCATTTCCTGCAGTCATTAACTACAA 59.849 38.462 13.81 0.00 36.07 2.41
5653 5885 7.148018 CCATTTCCTGCAGTCATTAACTACAAT 60.148 37.037 13.81 0.00 36.07 2.71
5654 5886 7.759489 TTTCCTGCAGTCATTAACTACAATT 57.241 32.000 13.81 0.00 36.07 2.32
5655 5887 6.741992 TCCTGCAGTCATTAACTACAATTG 57.258 37.500 13.81 3.24 36.07 2.32
5656 5888 5.647658 TCCTGCAGTCATTAACTACAATTGG 59.352 40.000 13.81 0.00 36.07 3.16
5657 5889 5.647658 CCTGCAGTCATTAACTACAATTGGA 59.352 40.000 13.81 0.00 36.07 3.53
5658 5890 6.150976 CCTGCAGTCATTAACTACAATTGGAA 59.849 38.462 13.81 0.00 36.07 3.53
5659 5891 7.144722 TGCAGTCATTAACTACAATTGGAAG 57.855 36.000 10.83 9.28 36.07 3.46
5660 5892 6.030228 GCAGTCATTAACTACAATTGGAAGC 58.970 40.000 10.83 0.00 36.07 3.86
5661 5893 6.349280 GCAGTCATTAACTACAATTGGAAGCA 60.349 38.462 10.83 0.00 36.07 3.91
5662 5894 7.023575 CAGTCATTAACTACAATTGGAAGCAC 58.976 38.462 10.83 0.00 36.07 4.40
5663 5895 6.151144 AGTCATTAACTACAATTGGAAGCACC 59.849 38.462 10.83 0.00 36.07 5.01
5664 5896 6.151144 GTCATTAACTACAATTGGAAGCACCT 59.849 38.462 10.83 0.00 39.86 4.00
5665 5897 6.374333 TCATTAACTACAATTGGAAGCACCTC 59.626 38.462 10.83 0.00 39.86 3.85
5666 5898 3.073274 ACTACAATTGGAAGCACCTCC 57.927 47.619 10.83 0.00 39.86 4.30
5667 5899 2.290960 ACTACAATTGGAAGCACCTCCC 60.291 50.000 10.83 0.00 39.86 4.30
5668 5900 0.779997 ACAATTGGAAGCACCTCCCT 59.220 50.000 10.83 0.00 39.86 4.20
5669 5901 1.147817 ACAATTGGAAGCACCTCCCTT 59.852 47.619 10.83 0.00 39.86 3.95
5670 5902 2.250924 CAATTGGAAGCACCTCCCTTT 58.749 47.619 0.00 0.00 39.86 3.11
5671 5903 3.181423 ACAATTGGAAGCACCTCCCTTTA 60.181 43.478 10.83 0.00 39.86 1.85
5672 5904 2.579410 TTGGAAGCACCTCCCTTTAC 57.421 50.000 1.91 0.00 39.86 2.01
5673 5905 0.696501 TGGAAGCACCTCCCTTTACC 59.303 55.000 1.91 0.00 39.86 2.85
5674 5906 0.696501 GGAAGCACCTCCCTTTACCA 59.303 55.000 0.00 0.00 35.41 3.25
5675 5907 1.074889 GGAAGCACCTCCCTTTACCAA 59.925 52.381 0.00 0.00 35.41 3.67
5676 5908 2.291605 GGAAGCACCTCCCTTTACCAAT 60.292 50.000 0.00 0.00 35.41 3.16
5677 5909 3.431415 GAAGCACCTCCCTTTACCAATT 58.569 45.455 0.00 0.00 0.00 2.32
5678 5910 4.569015 GGAAGCACCTCCCTTTACCAATTA 60.569 45.833 0.00 0.00 35.41 1.40
5679 5911 4.881157 AGCACCTCCCTTTACCAATTAT 57.119 40.909 0.00 0.00 0.00 1.28
5680 5912 5.206905 AGCACCTCCCTTTACCAATTATT 57.793 39.130 0.00 0.00 0.00 1.40
5681 5913 5.589831 AGCACCTCCCTTTACCAATTATTT 58.410 37.500 0.00 0.00 0.00 1.40
5682 5914 6.737608 AGCACCTCCCTTTACCAATTATTTA 58.262 36.000 0.00 0.00 0.00 1.40
5683 5915 7.362234 AGCACCTCCCTTTACCAATTATTTAT 58.638 34.615 0.00 0.00 0.00 1.40
5684 5916 8.507761 AGCACCTCCCTTTACCAATTATTTATA 58.492 33.333 0.00 0.00 0.00 0.98
5685 5917 9.138596 GCACCTCCCTTTACCAATTATTTATAA 57.861 33.333 0.00 0.00 0.00 0.98
5687 5919 9.346005 ACCTCCCTTTACCAATTATTTATAACG 57.654 33.333 0.00 0.00 0.00 3.18
5688 5920 9.563748 CCTCCCTTTACCAATTATTTATAACGA 57.436 33.333 0.00 0.00 0.00 3.85
5699 5931 9.651718 CAATTATTTATAACGAAGAGACAAGGC 57.348 33.333 0.00 0.00 0.00 4.35
5700 5932 9.614792 AATTATTTATAACGAAGAGACAAGGCT 57.385 29.630 0.00 0.00 0.00 4.58
5701 5933 6.910536 ATTTATAACGAAGAGACAAGGCTG 57.089 37.500 0.00 0.00 0.00 4.85
5702 5934 3.963428 ATAACGAAGAGACAAGGCTGT 57.037 42.857 0.00 0.00 38.98 4.40
5703 5935 1.871080 AACGAAGAGACAAGGCTGTG 58.129 50.000 0.00 0.00 35.30 3.66
5704 5936 0.034059 ACGAAGAGACAAGGCTGTGG 59.966 55.000 0.00 0.00 35.30 4.17
5705 5937 0.034059 CGAAGAGACAAGGCTGTGGT 59.966 55.000 0.00 0.00 35.30 4.16
5706 5938 1.517242 GAAGAGACAAGGCTGTGGTG 58.483 55.000 0.00 0.00 35.30 4.17
5707 5939 0.839946 AAGAGACAAGGCTGTGGTGT 59.160 50.000 0.00 0.00 35.30 4.16
5708 5940 1.717032 AGAGACAAGGCTGTGGTGTA 58.283 50.000 0.00 0.00 35.30 2.90
5709 5941 2.260822 AGAGACAAGGCTGTGGTGTAT 58.739 47.619 0.00 0.00 35.30 2.29
5710 5942 2.639839 AGAGACAAGGCTGTGGTGTATT 59.360 45.455 0.00 0.00 35.30 1.89
5711 5943 3.073062 AGAGACAAGGCTGTGGTGTATTT 59.927 43.478 0.00 0.00 35.30 1.40
5712 5944 4.286032 AGAGACAAGGCTGTGGTGTATTTA 59.714 41.667 0.00 0.00 35.30 1.40
5713 5945 5.045578 AGAGACAAGGCTGTGGTGTATTTAT 60.046 40.000 0.00 0.00 35.30 1.40
5714 5946 5.570320 AGACAAGGCTGTGGTGTATTTATT 58.430 37.500 0.00 0.00 35.30 1.40
5715 5947 5.648092 AGACAAGGCTGTGGTGTATTTATTC 59.352 40.000 0.00 0.00 35.30 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.603963 TCTTTCAAATGCAAATCCAATGATG 57.396 32.000 0.00 0.00 0.00 3.07
9 10 7.162761 ACATCTTTCAAATGCAAATCCAATGA 58.837 30.769 0.00 0.00 0.00 2.57
38 39 9.798994 TTACGTTCAGCAAAAGGTTTATTTTTA 57.201 25.926 0.00 0.00 30.01 1.52
43 44 6.565247 CGAGTTACGTTCAGCAAAAGGTTTAT 60.565 38.462 0.00 0.00 37.22 1.40
44 45 5.276963 CGAGTTACGTTCAGCAAAAGGTTTA 60.277 40.000 0.00 0.00 37.22 2.01
45 46 4.495184 CGAGTTACGTTCAGCAAAAGGTTT 60.495 41.667 0.00 0.00 37.22 3.27
78 80 7.990886 AGCCTAACTTTGATCACCGATATAAAA 59.009 33.333 0.00 0.00 0.00 1.52
79 81 7.506114 AGCCTAACTTTGATCACCGATATAAA 58.494 34.615 0.00 0.00 0.00 1.40
83 85 4.404394 TGAGCCTAACTTTGATCACCGATA 59.596 41.667 0.00 0.00 0.00 2.92
102 104 0.034089 AGGCCCCACAGTATTTGAGC 60.034 55.000 0.00 0.00 0.00 4.26
106 108 3.631250 CATACAAGGCCCCACAGTATTT 58.369 45.455 0.00 0.00 0.00 1.40
111 113 1.754234 GGCATACAAGGCCCCACAG 60.754 63.158 0.00 0.00 45.87 3.66
135 138 6.925165 TGTAGTTAAACTGTTAAAGGTCCTCG 59.075 38.462 0.00 0.00 31.02 4.63
177 183 1.614903 TGAAATTGCCTGGCAGAACAG 59.385 47.619 22.17 0.00 40.61 3.16
186 192 7.920682 ACAAACTAAAGTACTTGAAATTGCCTG 59.079 33.333 9.34 1.53 0.00 4.85
188 194 7.306574 GCACAAACTAAAGTACTTGAAATTGCC 60.307 37.037 9.34 4.91 0.00 4.52
202 209 6.371809 TGTCCTAAACAGCACAAACTAAAG 57.628 37.500 0.00 0.00 32.81 1.85
216 223 9.021807 TGGAGTAGCTATACATATGTCCTAAAC 57.978 37.037 12.68 5.46 34.07 2.01
281 290 7.890515 ACCATATATGTGAGTGATGACAGTAG 58.109 38.462 11.73 0.00 0.00 2.57
290 299 7.171653 TGAAAACCAACCATATATGTGAGTGA 58.828 34.615 11.73 0.00 0.00 3.41
291 300 7.389803 TGAAAACCAACCATATATGTGAGTG 57.610 36.000 11.73 4.12 0.00 3.51
292 301 8.593945 ATTGAAAACCAACCATATATGTGAGT 57.406 30.769 11.73 0.00 37.63 3.41
320 329 2.374170 GGGTGGAAGTAGAAAAGGTCCA 59.626 50.000 0.00 0.00 36.02 4.02
339 348 2.299582 TCAAATCATGTTGCAACTGGGG 59.700 45.455 28.61 15.58 0.00 4.96
361 370 1.884464 AGGCTGATGCGCGTACATG 60.884 57.895 8.43 0.00 40.82 3.21
369 378 1.002792 CATGAATGACAGGCTGATGCG 60.003 52.381 23.66 0.00 40.82 4.73
370 379 2.776312 CATGAATGACAGGCTGATGC 57.224 50.000 23.66 10.49 38.76 3.91
694 709 0.047176 TCCTCTCTCCTCTCTCCCCT 59.953 60.000 0.00 0.00 0.00 4.79
695 710 0.478507 CTCCTCTCTCCTCTCTCCCC 59.521 65.000 0.00 0.00 0.00 4.81
696 711 1.421646 CTCTCCTCTCTCCTCTCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
697 712 2.370189 CTCTCTCCTCTCTCCTCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
812 835 3.710724 TGAAAATGGAGATGCCCATGAA 58.289 40.909 0.00 0.00 45.69 2.57
872 896 5.986135 TCTCTAAGCTTTCTCAAGAACACAC 59.014 40.000 3.20 0.00 33.13 3.82
935 959 5.426689 TCTTGATGTGCTACTTCCAAGAT 57.573 39.130 0.00 0.00 0.00 2.40
1218 1252 7.646922 CCTCTCTTTCAACATTTTCTCAACAAG 59.353 37.037 0.00 0.00 0.00 3.16
1285 1335 1.123077 TGACTGTGAGCACACCTTCT 58.877 50.000 11.92 0.00 45.40 2.85
1453 1504 7.416964 TCCCTTCTTTTATTCTCTCTCTGAG 57.583 40.000 0.00 0.00 43.96 3.35
1549 1602 5.056480 TGACAAGAGGAAACATACACACAG 58.944 41.667 0.00 0.00 0.00 3.66
1560 1613 5.152623 AGATTGACGATGACAAGAGGAAA 57.847 39.130 0.00 0.00 0.00 3.13
1650 1709 7.701445 GCTCACTGCAAAGAGTTCAATTATAT 58.299 34.615 14.45 0.00 42.31 0.86
1651 1710 7.076842 GCTCACTGCAAAGAGTTCAATTATA 57.923 36.000 14.45 0.00 42.31 0.98
1652 1711 5.947443 GCTCACTGCAAAGAGTTCAATTAT 58.053 37.500 14.45 0.00 42.31 1.28
1653 1712 5.362556 GCTCACTGCAAAGAGTTCAATTA 57.637 39.130 14.45 0.00 42.31 1.40
1705 1764 1.827789 GGTGGCCTTGTGCTGACAA 60.828 57.895 3.32 0.00 39.88 3.18
1718 1777 0.465097 AGTGCTATGATGCTGGTGGC 60.465 55.000 0.00 0.00 42.22 5.01
1843 1902 1.541310 TTTGAGTCTCCATCGGCGGT 61.541 55.000 7.21 0.00 0.00 5.68
1920 1979 1.516386 CGACGATGACGGTCTTGGG 60.516 63.158 9.88 0.58 44.46 4.12
1993 2061 2.025767 ATCTTCTGCAGCCGCGAGAT 62.026 55.000 8.23 9.30 42.97 2.75
2061 2129 0.665835 CCGAAGCTAGCATCTCGAGT 59.334 55.000 26.09 0.00 0.00 4.18
2226 2294 1.133976 GTGTGGAGAATGGAGGATGGG 60.134 57.143 0.00 0.00 0.00 4.00
2297 2367 3.486383 TCGCAATTAATTCCCCATCTCC 58.514 45.455 0.00 0.00 0.00 3.71
2439 2512 1.028868 CCTTTCAGCCACCTAGCAGC 61.029 60.000 0.00 0.00 34.23 5.25
2502 2578 4.528596 CCCTTTCAGCTAAGCTAGGCTATA 59.471 45.833 12.10 2.91 38.25 1.31
2503 2579 3.326297 CCCTTTCAGCTAAGCTAGGCTAT 59.674 47.826 12.10 0.00 38.25 2.97
2525 2601 5.296748 TGGGTCAGCAAAATTAAGCTTTTC 58.703 37.500 3.20 0.00 39.50 2.29
2689 2775 4.940463 TGCTATAGTAGTACTTTTGGGCG 58.060 43.478 8.40 0.00 0.00 6.13
2731 2817 5.524646 GCACCAATTAAAATGGATGGATGTG 59.475 40.000 15.47 4.84 40.56 3.21
2732 2818 5.426185 AGCACCAATTAAAATGGATGGATGT 59.574 36.000 15.47 0.00 40.56 3.06
2797 2883 1.808343 TGCAATTGCTCAGCAGTAGTG 59.192 47.619 29.37 0.00 40.61 2.74
2800 2886 1.133598 GCATGCAATTGCTCAGCAGTA 59.866 47.619 29.37 8.59 42.14 2.74
2805 2891 2.193447 GACATGCATGCAATTGCTCAG 58.807 47.619 29.37 19.50 43.18 3.35
2819 2905 2.106938 TCGATCTGGGCGACATGC 59.893 61.111 0.00 0.00 45.38 4.06
2827 2913 0.176680 CAGAACTGGGTCGATCTGGG 59.823 60.000 0.00 0.00 36.50 4.45
2837 2923 0.798776 GTGTTGATCGCAGAACTGGG 59.201 55.000 11.71 11.71 43.58 4.45
2845 2931 8.978564 AATTTGTAATAATTGTGTTGATCGCA 57.021 26.923 0.00 0.00 34.52 5.10
2868 2954 8.804204 GGATACTGGCTAGTAGTACATTGTAAT 58.196 37.037 15.61 2.04 42.36 1.89
2869 2955 7.781219 TGGATACTGGCTAGTAGTACATTGTAA 59.219 37.037 15.61 0.00 42.36 2.41
2870 2956 7.292319 TGGATACTGGCTAGTAGTACATTGTA 58.708 38.462 15.61 0.00 42.36 2.41
2871 2957 6.134055 TGGATACTGGCTAGTAGTACATTGT 58.866 40.000 15.61 0.00 42.36 2.71
2872 2958 6.650427 TGGATACTGGCTAGTAGTACATTG 57.350 41.667 15.61 0.00 42.36 2.82
2873 2959 7.509318 TGAATGGATACTGGCTAGTAGTACATT 59.491 37.037 23.89 23.89 42.36 2.71
2874 2960 7.010771 TGAATGGATACTGGCTAGTAGTACAT 58.989 38.462 15.61 14.81 42.36 2.29
2875 2961 6.370453 TGAATGGATACTGGCTAGTAGTACA 58.630 40.000 15.61 13.36 42.36 2.90
2876 2962 6.896021 TGAATGGATACTGGCTAGTAGTAC 57.104 41.667 15.61 8.51 42.36 2.73
2877 2963 8.367911 CAAATGAATGGATACTGGCTAGTAGTA 58.632 37.037 15.61 10.20 42.36 1.82
2878 2964 7.220030 CAAATGAATGGATACTGGCTAGTAGT 58.780 38.462 15.61 4.26 42.36 2.73
2879 2965 6.148480 GCAAATGAATGGATACTGGCTAGTAG 59.852 42.308 15.61 0.00 42.36 2.57
2880 2966 5.997746 GCAAATGAATGGATACTGGCTAGTA 59.002 40.000 12.75 12.75 43.19 1.82
2881 2967 4.823989 GCAAATGAATGGATACTGGCTAGT 59.176 41.667 8.18 8.18 40.99 2.57
2882 2968 4.823442 TGCAAATGAATGGATACTGGCTAG 59.177 41.667 0.00 0.00 37.61 3.42
2947 3035 3.058016 CAGACAGTAAGCACACAATTGGG 60.058 47.826 6.04 6.04 0.00 4.12
3019 3111 1.860078 CACTTCCGTTTCCGCTCAC 59.140 57.895 0.00 0.00 0.00 3.51
3103 3195 2.353889 TCTTCGACGATACTGCTACCAC 59.646 50.000 0.00 0.00 0.00 4.16
3219 3311 6.114767 TGCAATGCATGTGTAGATAGAGAAA 58.885 36.000 2.72 0.00 31.71 2.52
3220 3312 5.673514 TGCAATGCATGTGTAGATAGAGAA 58.326 37.500 2.72 0.00 31.71 2.87
3221 3313 5.280654 TGCAATGCATGTGTAGATAGAGA 57.719 39.130 2.72 0.00 31.71 3.10
3235 3327 6.824553 AGAGTAGATAGAGAAATGCAATGCA 58.175 36.000 11.44 11.44 44.86 3.96
3236 3328 8.087750 AGTAGAGTAGATAGAGAAATGCAATGC 58.912 37.037 0.00 0.00 0.00 3.56
3237 3329 9.624697 GAGTAGAGTAGATAGAGAAATGCAATG 57.375 37.037 0.00 0.00 0.00 2.82
3238 3330 8.802267 GGAGTAGAGTAGATAGAGAAATGCAAT 58.198 37.037 0.00 0.00 0.00 3.56
3239 3331 7.231722 GGGAGTAGAGTAGATAGAGAAATGCAA 59.768 40.741 0.00 0.00 0.00 4.08
3240 3332 6.717540 GGGAGTAGAGTAGATAGAGAAATGCA 59.282 42.308 0.00 0.00 0.00 3.96
3241 3333 6.717540 TGGGAGTAGAGTAGATAGAGAAATGC 59.282 42.308 0.00 0.00 0.00 3.56
3242 3334 8.698973 TTGGGAGTAGAGTAGATAGAGAAATG 57.301 38.462 0.00 0.00 0.00 2.32
3243 3335 8.729047 TCTTGGGAGTAGAGTAGATAGAGAAAT 58.271 37.037 0.00 0.00 0.00 2.17
3317 3428 1.462616 ACACAGCACAACACACACAT 58.537 45.000 0.00 0.00 0.00 3.21
3358 3475 7.118245 CAGTAGTGAATTAGTGATCAGTGCAAA 59.882 37.037 13.54 0.00 35.03 3.68
3360 3477 6.101997 CAGTAGTGAATTAGTGATCAGTGCA 58.898 40.000 13.54 3.60 35.03 4.57
3361 3478 5.006165 GCAGTAGTGAATTAGTGATCAGTGC 59.994 44.000 13.54 0.00 33.42 4.40
3362 3479 6.336566 AGCAGTAGTGAATTAGTGATCAGTG 58.663 40.000 13.54 0.00 31.85 3.66
3410 3535 8.712363 GCGATATGCAGATAAAGATAAAGTGAA 58.288 33.333 0.00 0.00 45.45 3.18
3428 3553 8.282592 TCACTCATTAATTAACAAGCGATATGC 58.717 33.333 0.00 0.00 46.98 3.14
3429 3554 9.803130 CTCACTCATTAATTAACAAGCGATATG 57.197 33.333 0.00 0.00 0.00 1.78
3430 3555 9.547753 ACTCACTCATTAATTAACAAGCGATAT 57.452 29.630 0.00 0.00 0.00 1.63
3431 3556 8.942338 ACTCACTCATTAATTAACAAGCGATA 57.058 30.769 0.00 0.00 0.00 2.92
3432 3557 7.849804 ACTCACTCATTAATTAACAAGCGAT 57.150 32.000 0.00 0.00 0.00 4.58
3433 3558 7.277098 GGTACTCACTCATTAATTAACAAGCGA 59.723 37.037 0.00 0.50 0.00 4.93
3434 3559 7.277981 AGGTACTCACTCATTAATTAACAAGCG 59.722 37.037 0.00 0.00 0.00 4.68
3607 3751 9.959749 GAACTCTGAACCAAATTACATGTTAAA 57.040 29.630 2.30 0.00 0.00 1.52
3629 3773 5.028549 ACACAATTCTCACAGTCTGAACT 57.971 39.130 6.91 0.00 35.60 3.01
3635 3779 5.050091 CCAGTACAACACAATTCTCACAGTC 60.050 44.000 0.00 0.00 0.00 3.51
3805 3949 4.826733 TGCTGGTCATGTACTTTTGTGAAT 59.173 37.500 0.00 0.00 0.00 2.57
3806 3950 4.203226 TGCTGGTCATGTACTTTTGTGAA 58.797 39.130 0.00 0.00 0.00 3.18
3877 4021 3.643199 TGCAGGTTCATATGCTTGGTA 57.357 42.857 0.00 0.00 42.98 3.25
3878 4022 2.512692 TGCAGGTTCATATGCTTGGT 57.487 45.000 0.00 0.00 42.98 3.67
3879 4023 3.057736 GCTATGCAGGTTCATATGCTTGG 60.058 47.826 0.00 0.00 42.98 3.61
3896 4040 2.230130 TCTTTGGGGTTTGGGCTATG 57.770 50.000 0.00 0.00 0.00 2.23
3901 4045 2.437651 ACATTGTTCTTTGGGGTTTGGG 59.562 45.455 0.00 0.00 0.00 4.12
3902 4046 3.836365 ACATTGTTCTTTGGGGTTTGG 57.164 42.857 0.00 0.00 0.00 3.28
3903 4047 5.645497 TGAAAACATTGTTCTTTGGGGTTTG 59.355 36.000 1.83 0.00 0.00 2.93
3904 4048 5.810095 TGAAAACATTGTTCTTTGGGGTTT 58.190 33.333 1.83 0.00 0.00 3.27
3905 4049 5.188751 TCTGAAAACATTGTTCTTTGGGGTT 59.811 36.000 1.83 0.00 0.00 4.11
3906 4050 4.714308 TCTGAAAACATTGTTCTTTGGGGT 59.286 37.500 1.83 0.00 0.00 4.95
3907 4051 5.049828 GTCTGAAAACATTGTTCTTTGGGG 58.950 41.667 1.83 0.00 0.00 4.96
3944 4088 9.591792 CATACATATATAGGACATGTTGACCTG 57.408 37.037 13.52 1.21 42.27 4.00
3953 4097 7.147655 GGGTCTGTGCATACATATATAGGACAT 60.148 40.741 0.54 0.00 35.97 3.06
3962 4106 4.410228 ACAAGAGGGTCTGTGCATACATAT 59.590 41.667 0.00 0.00 35.97 1.78
4328 4487 2.096496 CCCGCTTAAAGTCTGCATGAAG 59.904 50.000 0.00 0.00 0.00 3.02
4455 4614 7.784470 ACCCATTGCTTATTAACAGGTTTTA 57.216 32.000 0.00 0.00 0.00 1.52
4509 4668 8.758829 TCAGGCAAGTAGTATTTCTTAGATTGA 58.241 33.333 0.00 0.00 0.00 2.57
4649 4808 1.153823 GACGTAGGATGTGCACGCT 60.154 57.895 13.13 1.21 39.23 5.07
4830 4989 0.828022 TACATCCCGTTTCGATGCCT 59.172 50.000 0.00 0.00 40.70 4.75
5022 5185 4.496840 GGGTTGACACTTCCGTAAACAAAG 60.497 45.833 0.00 0.00 0.00 2.77
5322 5488 0.960861 GCTGTTTGGCCCTGTCTACC 60.961 60.000 0.00 0.00 0.00 3.18
5483 5710 8.946085 GTGTACATGTATTGAAAGGAAGAATCA 58.054 33.333 9.18 0.00 0.00 2.57
5596 5823 9.965824 GCATAGCACCAAAATAATACAGTATTT 57.034 29.630 11.16 0.00 35.62 1.40
5599 5826 8.402472 GTTGCATAGCACCAAAATAATACAGTA 58.598 33.333 0.00 0.00 38.71 2.74
5600 5827 7.257722 GTTGCATAGCACCAAAATAATACAGT 58.742 34.615 0.00 0.00 38.71 3.55
5601 5828 6.697019 GGTTGCATAGCACCAAAATAATACAG 59.303 38.462 0.21 0.00 38.71 2.74
5602 5829 6.406400 GGGTTGCATAGCACCAAAATAATACA 60.406 38.462 7.57 0.00 38.71 2.29
5603 5830 5.983118 GGGTTGCATAGCACCAAAATAATAC 59.017 40.000 7.57 0.00 38.71 1.89
5628 5860 6.741992 TGTAGTTAATGACTGCAGGAAATG 57.258 37.500 19.93 0.00 44.60 2.32
5636 5868 6.030228 GCTTCCAATTGTAGTTAATGACTGC 58.970 40.000 4.43 0.00 39.48 4.40
5637 5869 7.023575 GTGCTTCCAATTGTAGTTAATGACTG 58.976 38.462 4.43 0.00 39.48 3.51
5638 5870 6.151144 GGTGCTTCCAATTGTAGTTAATGACT 59.849 38.462 4.43 0.00 38.04 3.41
5639 5871 6.151144 AGGTGCTTCCAATTGTAGTTAATGAC 59.849 38.462 4.43 0.00 39.02 3.06
5640 5872 6.245408 AGGTGCTTCCAATTGTAGTTAATGA 58.755 36.000 4.43 0.00 39.02 2.57
5641 5873 6.404734 GGAGGTGCTTCCAATTGTAGTTAATG 60.405 42.308 4.43 0.00 39.02 1.90
5642 5874 5.652452 GGAGGTGCTTCCAATTGTAGTTAAT 59.348 40.000 4.43 0.00 39.02 1.40
5643 5875 5.007682 GGAGGTGCTTCCAATTGTAGTTAA 58.992 41.667 4.43 0.00 39.02 2.01
5644 5876 4.566907 GGGAGGTGCTTCCAATTGTAGTTA 60.567 45.833 4.43 0.00 39.09 2.24
5645 5877 3.421844 GGAGGTGCTTCCAATTGTAGTT 58.578 45.455 4.43 0.00 39.02 2.24
5646 5878 2.290960 GGGAGGTGCTTCCAATTGTAGT 60.291 50.000 4.43 0.00 39.09 2.73
5647 5879 2.025887 AGGGAGGTGCTTCCAATTGTAG 60.026 50.000 4.43 2.73 39.09 2.74
5648 5880 1.992557 AGGGAGGTGCTTCCAATTGTA 59.007 47.619 4.43 0.00 39.09 2.41
5649 5881 0.779997 AGGGAGGTGCTTCCAATTGT 59.220 50.000 4.43 0.00 39.09 2.71
5650 5882 1.928868 AAGGGAGGTGCTTCCAATTG 58.071 50.000 0.00 0.00 39.09 2.32
5651 5883 2.702270 AAAGGGAGGTGCTTCCAATT 57.298 45.000 2.80 0.00 39.09 2.32
5652 5884 2.291605 GGTAAAGGGAGGTGCTTCCAAT 60.292 50.000 2.80 0.00 39.09 3.16
5653 5885 1.074889 GGTAAAGGGAGGTGCTTCCAA 59.925 52.381 2.80 0.00 39.09 3.53
5654 5886 0.696501 GGTAAAGGGAGGTGCTTCCA 59.303 55.000 2.80 0.00 39.09 3.53
5655 5887 0.696501 TGGTAAAGGGAGGTGCTTCC 59.303 55.000 0.00 0.00 36.46 3.46
5656 5888 2.579410 TTGGTAAAGGGAGGTGCTTC 57.421 50.000 0.00 0.00 0.00 3.86
5657 5889 3.542969 AATTGGTAAAGGGAGGTGCTT 57.457 42.857 0.00 0.00 0.00 3.91
5658 5890 4.881157 ATAATTGGTAAAGGGAGGTGCT 57.119 40.909 0.00 0.00 0.00 4.40
5659 5891 5.932619 AAATAATTGGTAAAGGGAGGTGC 57.067 39.130 0.00 0.00 0.00 5.01
5661 5893 9.346005 CGTTATAAATAATTGGTAAAGGGAGGT 57.654 33.333 0.00 0.00 0.00 3.85
5662 5894 9.563748 TCGTTATAAATAATTGGTAAAGGGAGG 57.436 33.333 0.00 0.00 0.00 4.30
5673 5905 9.651718 GCCTTGTCTCTTCGTTATAAATAATTG 57.348 33.333 0.00 0.00 0.00 2.32
5674 5906 9.614792 AGCCTTGTCTCTTCGTTATAAATAATT 57.385 29.630 0.00 0.00 0.00 1.40
5675 5907 9.046296 CAGCCTTGTCTCTTCGTTATAAATAAT 57.954 33.333 0.00 0.00 0.00 1.28
5676 5908 8.038944 ACAGCCTTGTCTCTTCGTTATAAATAA 58.961 33.333 0.00 0.00 29.46 1.40
5677 5909 7.491372 CACAGCCTTGTCTCTTCGTTATAAATA 59.509 37.037 0.00 0.00 34.62 1.40
5678 5910 6.313905 CACAGCCTTGTCTCTTCGTTATAAAT 59.686 38.462 0.00 0.00 34.62 1.40
5679 5911 5.637810 CACAGCCTTGTCTCTTCGTTATAAA 59.362 40.000 0.00 0.00 34.62 1.40
5680 5912 5.168569 CACAGCCTTGTCTCTTCGTTATAA 58.831 41.667 0.00 0.00 34.62 0.98
5681 5913 4.381612 CCACAGCCTTGTCTCTTCGTTATA 60.382 45.833 0.00 0.00 34.62 0.98
5682 5914 3.589988 CACAGCCTTGTCTCTTCGTTAT 58.410 45.455 0.00 0.00 34.62 1.89
5683 5915 2.288825 CCACAGCCTTGTCTCTTCGTTA 60.289 50.000 0.00 0.00 34.62 3.18
5684 5916 1.541233 CCACAGCCTTGTCTCTTCGTT 60.541 52.381 0.00 0.00 34.62 3.85
5685 5917 0.034059 CCACAGCCTTGTCTCTTCGT 59.966 55.000 0.00 0.00 34.62 3.85
5686 5918 0.034059 ACCACAGCCTTGTCTCTTCG 59.966 55.000 0.00 0.00 34.62 3.79
5687 5919 1.202698 ACACCACAGCCTTGTCTCTTC 60.203 52.381 0.00 0.00 34.62 2.87
5688 5920 0.839946 ACACCACAGCCTTGTCTCTT 59.160 50.000 0.00 0.00 34.62 2.85
5689 5921 1.717032 TACACCACAGCCTTGTCTCT 58.283 50.000 0.00 0.00 34.62 3.10
5690 5922 2.770164 ATACACCACAGCCTTGTCTC 57.230 50.000 0.00 0.00 34.62 3.36
5691 5923 3.508845 AAATACACCACAGCCTTGTCT 57.491 42.857 0.00 0.00 34.62 3.41
5692 5924 5.880341 GAATAAATACACCACAGCCTTGTC 58.120 41.667 0.00 0.00 34.62 3.18
5693 5925 5.897377 GAATAAATACACCACAGCCTTGT 57.103 39.130 0.00 0.00 38.31 3.16


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

AutoCloner maintained by Alex Coulton.