Multiple sequence alignment - TraesCS1A01G302600

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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 TraesCS1A01G302600 chr1A 100.000 8981 0 0 1 8981 496303580 496312560 0.000000e+00 16585.0
1 TraesCS1A01G302600 chr1A 100.000 47 0 0 8640 8686 496312174 496312220 4.470000e-13 87.9
2 TraesCS1A01G302600 chr1A 100.000 47 0 0 8595 8641 496312219 496312265 4.470000e-13 87.9
3 TraesCS1A01G302600 chr1A 86.441 59 7 1 4119 4176 253380945 253381003 7.530000e-06 63.9
4 TraesCS1A01G302600 chr1D 96.543 5728 170 15 1721 7441 399941002 399946708 0.000000e+00 9455.0
5 TraesCS1A01G302600 chr1D 93.744 1119 60 5 7531 8641 399946697 399947813 0.000000e+00 1670.0
6 TraesCS1A01G302600 chr1D 95.556 720 26 3 994 1707 399940297 399941016 0.000000e+00 1147.0
7 TraesCS1A01G302600 chr1D 86.627 1017 53 37 1 973 399936566 399937543 0.000000e+00 1048.0
8 TraesCS1A01G302600 chr1D 97.196 321 8 1 8640 8960 399947767 399948086 7.930000e-150 542.0
9 TraesCS1A01G302600 chr1D 90.566 53 5 0 1653 1705 433198518 433198466 4.500000e-08 71.3
10 TraesCS1A01G302600 chr1D 86.441 59 7 1 4119 4176 200218983 200219041 7.530000e-06 63.9
11 TraesCS1A01G302600 chr1B 93.596 3092 138 32 1529 4602 536657845 536660894 0.000000e+00 4558.0
12 TraesCS1A01G302600 chr1B 92.435 3014 179 33 5645 8641 536662186 536665167 0.000000e+00 4257.0
13 TraesCS1A01G302600 chr1B 95.211 877 40 2 4764 5638 536661205 536662081 0.000000e+00 1386.0
14 TraesCS1A01G302600 chr1B 87.219 579 40 20 686 1251 536654413 536654970 5.920000e-176 628.0
15 TraesCS1A01G302600 chr1B 94.904 314 15 1 8640 8953 536665121 536665433 2.910000e-134 490.0
16 TraesCS1A01G302600 chr1B 94.697 264 14 0 1245 1508 536657590 536657853 2.330000e-110 411.0
17 TraesCS1A01G302600 chr1B 100.000 29 0 0 4141 4169 330198486 330198458 5.000000e-03 54.7
18 TraesCS1A01G302600 chr3D 84.513 226 35 0 6965 7190 447579726 447579501 3.260000e-54 224.0
19 TraesCS1A01G302600 chr3D 84.694 196 24 3 1923 2115 87395882 87395690 3.310000e-44 191.0
20 TraesCS1A01G302600 chr3D 85.890 163 21 2 2287 2448 87395354 87395193 1.200000e-38 172.0
21 TraesCS1A01G302600 chr5A 78.834 326 45 18 2048 2358 54730386 54730702 1.980000e-46 198.0
22 TraesCS1A01G302600 chr5A 92.453 53 4 0 1653 1705 303641023 303640971 9.670000e-10 76.8
23 TraesCS1A01G302600 chr5A 92.453 53 4 0 1653 1705 303720064 303720012 9.670000e-10 76.8
24 TraesCS1A01G302600 chr5A 90.566 53 5 0 1653 1705 696917115 696917063 4.500000e-08 71.3
25 TraesCS1A01G302600 chr2A 83.732 209 19 11 1346 1544 34166647 34166444 5.540000e-42 183.0
26 TraesCS1A01G302600 chr2D 92.453 53 4 0 1653 1705 42028462 42028410 9.670000e-10 76.8
27 TraesCS1A01G302600 chr4D 90.566 53 5 0 1653 1705 365085382 365085330 4.500000e-08 71.3
28 TraesCS1A01G302600 chr3B 90.566 53 5 0 1653 1705 793155278 793155226 4.500000e-08 71.3
29 TraesCS1A01G302600 chr6B 100.000 32 0 0 4142 4173 506725785 506725754 9.740000e-05 60.2
30 TraesCS1A01G302600 chr7B 94.286 35 0 2 4137 4169 109926787 109926821 1.600000e-02 52.8
31 TraesCS1A01G302600 chr7A 94.286 35 0 2 4137 4169 148481480 148481514 1.600000e-02 52.8


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 TraesCS1A01G302600 chr1A 496303580 496312560 8980 False 5586.933333 16585 100.000000 1 8981 3 chr1A.!!$F2 8980
1 TraesCS1A01G302600 chr1D 399936566 399948086 11520 False 2772.400000 9455 93.933200 1 8960 5 chr1D.!!$F2 8959
2 TraesCS1A01G302600 chr1B 536654413 536665433 11020 False 1955.000000 4558 93.010333 686 8953 6 chr1B.!!$F1 8267

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
334 352 0.036388 TGGTTCGATTGCTCCAGTCC 60.036 55.000 0.00 0.00 0.00 3.85 F
343 361 0.112995 TGCTCCAGTCCAGGCATTTT 59.887 50.000 0.00 0.00 0.00 1.82 F
1796 7226 0.393537 CTGTGCATCTCCCTTGTCCC 60.394 60.000 0.00 0.00 0.00 4.46 F
1802 7232 2.928334 CATCTCCCTTGTCCCTTGATG 58.072 52.381 0.00 0.00 0.00 3.07 F
3755 9195 1.343465 ACTCCACCGGTGTCTAAACTG 59.657 52.381 31.80 14.75 0.00 3.16 F
3930 9370 2.358898 GGCAGTGATTTGTCACACAACT 59.641 45.455 10.76 0.00 42.68 3.16 F
5104 10704 1.002544 ACAGCAACAAGACTCTAGCCC 59.997 52.381 0.00 0.00 0.00 5.19 F
5895 11595 0.037790 TAAGCAAAACCGCAATGGGC 60.038 50.000 0.00 0.00 44.64 5.36 F
6707 12408 0.112218 CAGTTGGGTTGGGTGATCCA 59.888 55.000 0.00 0.00 45.43 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 7204 1.808945 GACAAGGGAGATGCACAGTTG 59.191 52.381 0.00 0.00 0.00 3.16 R
1880 7310 2.289133 TGACAGGTTGCACATTACGCTA 60.289 45.455 0.00 0.00 0.00 4.26 R
3121 8559 2.346766 TGCTAATGGGGCACATACAG 57.653 50.000 0.84 4.66 39.40 2.74 R
3765 9205 4.340381 GCTAAGATCCCTGAAAATGCATGT 59.660 41.667 0.00 0.00 0.00 3.21 R
4659 10148 0.548510 GGGGAGGACTAAATGCAGCT 59.451 55.000 0.00 0.00 0.00 4.24 R
5311 10911 1.304282 CTTGGACCCACCTCCCATG 59.696 63.158 0.00 0.00 39.86 3.66 R
6703 12404 1.151943 ATCAGCCGGGATCCTGGAT 60.152 57.895 39.43 32.99 45.10 3.41 R
7509 13215 0.178981 AACATGTTGAGCCACTGCCT 60.179 50.000 11.07 0.00 38.69 4.75 R
8630 14350 0.038890 AAGAAAGCTCCCTTCCAGCC 59.961 55.000 0.00 0.00 37.63 4.85 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
40 41 0.741221 GTGGGAGCGAACTAAGCAGG 60.741 60.000 0.00 0.00 37.01 4.85
56 57 0.179089 CAGGGAGGACAGAAGCATCG 60.179 60.000 0.00 0.00 0.00 3.84
138 139 0.911525 TTCTTGCAGGGAGGGAGGAG 60.912 60.000 0.00 0.00 0.00 3.69
209 210 1.913778 TTACAGTCTACCAGCGGACA 58.086 50.000 1.50 0.00 35.18 4.02
232 233 1.129998 CCTGCGAATCTTGTTCTGCTG 59.870 52.381 0.00 0.00 0.00 4.41
252 257 0.813821 GCCAGGTTTGATTCTGCTCC 59.186 55.000 0.00 0.00 0.00 4.70
285 290 4.234574 CCGCAGAAAATTACTGGTTTTCC 58.765 43.478 12.38 0.00 43.29 3.13
286 291 3.911964 CGCAGAAAATTACTGGTTTTCCG 59.088 43.478 12.38 2.92 43.29 4.30
287 292 4.319911 CGCAGAAAATTACTGGTTTTCCGA 60.320 41.667 12.38 0.00 43.29 4.55
288 293 5.154222 GCAGAAAATTACTGGTTTTCCGAG 58.846 41.667 12.38 1.57 43.29 4.63
289 294 5.278315 GCAGAAAATTACTGGTTTTCCGAGT 60.278 40.000 12.38 0.00 43.29 4.18
291 296 7.200455 CAGAAAATTACTGGTTTTCCGAGTTT 58.800 34.615 7.49 0.00 43.29 2.66
292 297 8.347035 CAGAAAATTACTGGTTTTCCGAGTTTA 58.653 33.333 7.49 0.00 43.29 2.01
297 302 4.773013 ACTGGTTTTCCGAGTTTAGTTGA 58.227 39.130 0.00 0.00 44.36 3.18
299 304 6.527423 ACTGGTTTTCCGAGTTTAGTTGATA 58.473 36.000 0.00 0.00 44.36 2.15
300 305 6.993902 ACTGGTTTTCCGAGTTTAGTTGATAA 59.006 34.615 0.00 0.00 44.36 1.75
332 350 1.880027 GTTTGGTTCGATTGCTCCAGT 59.120 47.619 0.00 0.00 0.00 4.00
333 351 1.808411 TTGGTTCGATTGCTCCAGTC 58.192 50.000 0.00 0.00 0.00 3.51
334 352 0.036388 TGGTTCGATTGCTCCAGTCC 60.036 55.000 0.00 0.00 0.00 3.85
335 353 0.036388 GGTTCGATTGCTCCAGTCCA 60.036 55.000 0.00 0.00 0.00 4.02
336 354 1.363744 GTTCGATTGCTCCAGTCCAG 58.636 55.000 0.00 0.00 0.00 3.86
337 355 0.250234 TTCGATTGCTCCAGTCCAGG 59.750 55.000 0.00 0.00 0.00 4.45
343 361 0.112995 TGCTCCAGTCCAGGCATTTT 59.887 50.000 0.00 0.00 0.00 1.82
353 371 1.134946 CCAGGCATTTTCATCGGTTCC 59.865 52.381 0.00 0.00 0.00 3.62
356 374 2.091541 GGCATTTTCATCGGTTCCTCA 58.908 47.619 0.00 0.00 0.00 3.86
365 383 2.797278 CGGTTCCTCATCCCCTCCG 61.797 68.421 0.00 0.00 0.00 4.63
366 384 2.444256 GGTTCCTCATCCCCTCCGG 61.444 68.421 0.00 0.00 0.00 5.14
374 392 4.534824 TCCCCTCCGGATCCCGTC 62.535 72.222 3.57 0.00 46.80 4.79
382 400 4.587189 GGATCCCGTCCCGAAGCG 62.587 72.222 0.00 0.00 41.50 4.68
383 401 3.834799 GATCCCGTCCCGAAGCGT 61.835 66.667 0.00 0.00 0.00 5.07
384 402 3.769875 GATCCCGTCCCGAAGCGTC 62.770 68.421 0.00 0.00 0.00 5.19
386 404 4.493747 CCCGTCCCGAAGCGTCTC 62.494 72.222 0.00 0.00 0.00 3.36
387 405 3.744719 CCGTCCCGAAGCGTCTCA 61.745 66.667 0.00 0.00 0.00 3.27
403 421 4.857037 GCGTCTCAAAACATTTTACCCATC 59.143 41.667 0.00 0.00 0.00 3.51
404 422 5.399013 CGTCTCAAAACATTTTACCCATCC 58.601 41.667 0.00 0.00 0.00 3.51
405 423 5.048364 CGTCTCAAAACATTTTACCCATCCA 60.048 40.000 0.00 0.00 0.00 3.41
406 424 6.350110 CGTCTCAAAACATTTTACCCATCCAT 60.350 38.462 0.00 0.00 0.00 3.41
448 466 1.154413 CCTGCAACATCGTTGTCGC 60.154 57.895 2.55 2.55 36.28 5.19
451 469 2.202171 CAACATCGTTGTCGCGGC 60.202 61.111 2.29 2.29 34.06 6.53
456 474 2.667318 ATCGTTGTCGCGGCACTTG 61.667 57.895 15.66 6.24 36.96 3.16
479 497 0.948678 GTGGCTTTGTCCGCACTTTA 59.051 50.000 0.00 0.00 36.65 1.85
550 568 1.277495 GCATGTCGTGGCTGCAAAAC 61.277 55.000 0.50 0.00 35.96 2.43
616 634 3.465403 CCTGGGCTGGGAGACGAG 61.465 72.222 0.00 0.00 39.50 4.18
626 644 3.535561 CTGGGAGACGAGCAAAATATGT 58.464 45.455 0.00 0.00 0.00 2.29
627 645 3.941483 CTGGGAGACGAGCAAAATATGTT 59.059 43.478 0.00 0.00 0.00 2.71
628 646 4.331968 TGGGAGACGAGCAAAATATGTTT 58.668 39.130 0.00 0.00 0.00 2.83
664 696 2.368655 AAATGGTTTGGCTTGATCGC 57.631 45.000 0.00 0.00 0.00 4.58
667 699 0.960364 TGGTTTGGCTTGATCGCTCC 60.960 55.000 0.00 0.00 0.00 4.70
674 706 1.298713 CTTGATCGCTCCGAGTCCG 60.299 63.158 0.00 0.00 39.91 4.79
678 710 1.853114 GATCGCTCCGAGTCCGCATA 61.853 60.000 0.00 0.00 39.91 3.14
706 738 1.531602 GCTTGTGCAAAGGAGGGGT 60.532 57.895 9.63 0.00 39.41 4.95
707 739 1.115326 GCTTGTGCAAAGGAGGGGTT 61.115 55.000 9.63 0.00 39.41 4.11
709 741 0.758685 TTGTGCAAAGGAGGGGTTGG 60.759 55.000 0.00 0.00 0.00 3.77
710 742 1.152546 GTGCAAAGGAGGGGTTGGT 60.153 57.895 0.00 0.00 0.00 3.67
712 744 2.574018 GCAAAGGAGGGGTTGGTGC 61.574 63.158 0.00 0.00 0.00 5.01
713 745 1.152567 CAAAGGAGGGGTTGGTGCA 60.153 57.895 0.00 0.00 0.00 4.57
714 746 1.152546 AAAGGAGGGGTTGGTGCAC 60.153 57.895 8.80 8.80 0.00 4.57
715 747 1.943730 AAAGGAGGGGTTGGTGCACA 61.944 55.000 20.43 1.62 0.00 4.57
767 802 3.285215 GCCTGGCCATCATCAGCG 61.285 66.667 5.51 0.00 0.00 5.18
808 843 9.507329 AAATCGTGCAAGGATGAATAATATACT 57.493 29.630 0.00 0.00 41.20 2.12
841 878 3.709880 TTAGCGTCGGCATCACGGG 62.710 63.158 0.00 0.00 43.41 5.28
924 967 2.567615 TCTTGTTTAGGACCCAGAGCTC 59.432 50.000 5.27 5.27 0.00 4.09
936 979 3.885901 ACCCAGAGCTCTTGAAAAAGAAC 59.114 43.478 15.27 0.00 0.00 3.01
952 995 7.288852 TGAAAAAGAACAATATTCCTGTTGGGA 59.711 33.333 0.00 0.00 43.41 4.37
983 3768 7.534239 CAGAAGTTTCTGCTTAATTAAACGGTC 59.466 37.037 8.78 3.74 46.97 4.79
1068 3853 2.703798 CCCCTGCTTGGATGTTGCG 61.704 63.158 0.00 0.00 38.35 4.85
1092 3877 1.073284 GGGCAAAGTACTGACCCTTCA 59.927 52.381 17.11 0.00 38.75 3.02
1183 3984 6.405278 AACAAGGAAAACCGATTGATCTTT 57.595 33.333 0.00 0.00 0.00 2.52
1210 4011 5.583457 TGATGTTATGTCTGATGTTCAGCTG 59.417 40.000 7.63 7.63 43.95 4.24
1221 4022 5.414360 TGATGTTCAGCTGAGACAGTATTC 58.586 41.667 25.31 20.29 33.43 1.75
1517 6947 4.868314 TCTATGAGCTCTGGTCATCATG 57.132 45.455 16.19 7.81 45.91 3.07
1551 6981 7.669427 AGATGAGCTCTCTATTTATCAACAGG 58.331 38.462 16.19 0.00 0.00 4.00
1707 7137 8.893219 TCTCATGGTCATAATAAGCAGTTTAG 57.107 34.615 0.00 0.00 0.00 1.85
1708 7138 8.704668 TCTCATGGTCATAATAAGCAGTTTAGA 58.295 33.333 0.00 0.00 0.00 2.10
1709 7139 8.662781 TCATGGTCATAATAAGCAGTTTAGAC 57.337 34.615 0.00 0.00 0.00 2.59
1710 7140 7.438160 TCATGGTCATAATAAGCAGTTTAGACG 59.562 37.037 0.00 0.00 0.00 4.18
1711 7141 5.522460 TGGTCATAATAAGCAGTTTAGACGC 59.478 40.000 0.00 0.00 0.00 5.19
1712 7142 5.332355 GGTCATAATAAGCAGTTTAGACGCG 60.332 44.000 3.53 3.53 32.91 6.01
1713 7143 5.231568 GTCATAATAAGCAGTTTAGACGCGT 59.768 40.000 13.85 13.85 32.91 6.01
1714 7144 5.457799 TCATAATAAGCAGTTTAGACGCGTC 59.542 40.000 31.30 31.30 32.91 5.19
1715 7145 2.710220 TAAGCAGTTTAGACGCGTCA 57.290 45.000 37.85 22.36 32.91 4.35
1716 7146 1.860676 AAGCAGTTTAGACGCGTCAA 58.139 45.000 37.85 26.26 32.91 3.18
1717 7147 1.860676 AGCAGTTTAGACGCGTCAAA 58.139 45.000 37.85 29.59 32.91 2.69
1718 7148 2.206750 AGCAGTTTAGACGCGTCAAAA 58.793 42.857 37.85 27.97 32.91 2.44
1719 7149 2.610374 AGCAGTTTAGACGCGTCAAAAA 59.390 40.909 37.85 31.26 32.91 1.94
1774 7204 4.564782 ACTACCTTTACTTGTAAGGGGC 57.435 45.455 20.63 0.00 45.23 5.80
1796 7226 0.393537 CTGTGCATCTCCCTTGTCCC 60.394 60.000 0.00 0.00 0.00 4.46
1802 7232 2.928334 CATCTCCCTTGTCCCTTGATG 58.072 52.381 0.00 0.00 0.00 3.07
1813 7243 7.341769 CCCTTGTCCCTTGATGTTGATAATTTA 59.658 37.037 0.00 0.00 0.00 1.40
1852 7282 9.444600 TTCCTGTAGTTTTGATTGTTATAGGTC 57.555 33.333 0.00 0.00 0.00 3.85
2220 7650 6.837312 ACCATAATCCTATTCCGATGTTGAA 58.163 36.000 0.00 0.00 0.00 2.69
2343 7773 4.949856 ACAATTTAACAGGTAGCATCCCAG 59.050 41.667 0.00 0.00 0.00 4.45
3031 8469 9.702726 ATCTGATATTTGTTTTTCGATGTAACG 57.297 29.630 0.00 0.00 0.00 3.18
3042 8480 3.124560 TCGATGTAACGAACACTTGCAA 58.875 40.909 0.00 0.00 42.09 4.08
3103 8541 6.013293 ACCTCTTCCTACAGAATTAGCAAAGT 60.013 38.462 0.00 0.00 32.82 2.66
3110 8548 4.718961 ACAGAATTAGCAAAGTCACCTGT 58.281 39.130 0.00 0.00 32.11 4.00
3121 8559 6.756542 AGCAAAGTCACCTGTTTTGAAAATAC 59.243 34.615 0.00 0.00 34.55 1.89
3165 8604 8.441608 CACATTCTGAGTAGAACTTTTCTCATG 58.558 37.037 0.00 0.00 45.17 3.07
3170 8609 9.784531 TCTGAGTAGAACTTTTCTCATGAAAAT 57.215 29.630 0.00 0.00 46.90 1.82
3337 8776 6.989659 TCTCTATCCTTACACGTTTGTCTTT 58.010 36.000 0.00 0.00 37.15 2.52
3343 8782 5.295045 TCCTTACACGTTTGTCTTTTTCCTC 59.705 40.000 0.00 0.00 37.15 3.71
3435 8874 4.997395 ACATGCCAATGTCTAATATCCGTC 59.003 41.667 0.00 0.00 43.85 4.79
3662 9102 5.347620 TGAACGTGGCATACCTTATACTT 57.652 39.130 0.00 0.00 36.63 2.24
3712 9152 8.579850 AGATAGCAGTTTGACAATCCATTTTA 57.420 30.769 0.00 0.00 0.00 1.52
3742 9182 4.462483 TGCATTTCAGGAAATAACTCCACC 59.538 41.667 6.92 0.00 38.84 4.61
3755 9195 1.343465 ACTCCACCGGTGTCTAAACTG 59.657 52.381 31.80 14.75 0.00 3.16
3765 9205 5.393787 CCGGTGTCTAAACTGCTATTACTCA 60.394 44.000 0.00 0.00 0.00 3.41
3930 9370 2.358898 GGCAGTGATTTGTCACACAACT 59.641 45.455 10.76 0.00 42.68 3.16
3964 9404 3.640029 ACTGTCCCGTTAAACTTCTCAGA 59.360 43.478 0.00 0.00 0.00 3.27
3993 9433 8.773404 TCCTAATCTTCAGCTTTTGTAAGTAC 57.227 34.615 0.00 0.00 33.74 2.73
4075 9515 4.461081 TGTGCCAACTGTAGTCTTTGTTTT 59.539 37.500 0.00 0.00 0.00 2.43
4086 9526 8.205131 TGTAGTCTTTGTTTTAACCACTCTTC 57.795 34.615 0.00 0.00 0.00 2.87
4087 9527 7.825270 TGTAGTCTTTGTTTTAACCACTCTTCA 59.175 33.333 0.00 0.00 0.00 3.02
4360 9809 6.976934 AAATCACCCTGTATGAGTTGTTTT 57.023 33.333 0.00 0.00 33.40 2.43
4403 9852 6.903883 ACAGGCATACGTAAATAGTTTCTG 57.096 37.500 0.00 2.50 0.00 3.02
4629 10118 3.243636 GCATTTTTCGATCATGCAGGGAT 60.244 43.478 15.49 0.15 42.49 3.85
4643 10132 8.316497 TCATGCAGGGATTTCCAAAATAATTA 57.684 30.769 0.00 0.00 38.24 1.40
4670 10159 5.819379 TCAAGACTATTCCAGCTGCATTTAG 59.181 40.000 8.66 8.68 0.00 1.85
4713 10202 9.894783 ACTGTAATGTACGTTCTCATACATATC 57.105 33.333 2.93 0.00 40.36 1.63
4723 10212 8.360390 ACGTTCTCATACATATCTCATGCTTTA 58.640 33.333 0.00 0.00 0.00 1.85
4787 10385 8.242053 CCATATTATCTGTTCAAATGCATCCTC 58.758 37.037 0.00 0.00 0.00 3.71
4803 10401 5.059161 GCATCCTCTGAACATGCAAGTATA 58.941 41.667 13.10 0.00 42.18 1.47
4830 10428 5.954296 AGTTGATCTCTGTTTTGGTGATG 57.046 39.130 0.00 0.00 0.00 3.07
4846 10444 3.146066 GTGATGAGCACCACCTTTGTTA 58.854 45.455 0.00 0.00 41.78 2.41
4851 10449 4.575885 TGAGCACCACCTTTGTTATCTAC 58.424 43.478 0.00 0.00 0.00 2.59
4867 10465 9.856488 TTGTTATCTACTTAGAGTTGCTACAAG 57.144 33.333 0.13 0.00 35.50 3.16
4894 10492 9.586732 TCTCCCTTTCTGAATTTGAGAATAAAA 57.413 29.630 0.00 0.00 29.60 1.52
5104 10704 1.002544 ACAGCAACAAGACTCTAGCCC 59.997 52.381 0.00 0.00 0.00 5.19
5126 10726 2.079170 TTTGTTCACCTTGCCCATCA 57.921 45.000 0.00 0.00 0.00 3.07
5311 10911 3.369147 CAGCTACATGTTGAGCACTACAC 59.631 47.826 20.05 0.00 41.36 2.90
5502 11102 7.220741 TCTTATGCAGATGGTATGTACTCTC 57.779 40.000 0.00 0.00 0.00 3.20
5575 11176 3.117888 AGGCCATGTGGGAGTACTAAATG 60.118 47.826 5.01 0.00 40.01 2.32
5653 11352 7.124573 TCCATGCAACACAACTATCTAGTAT 57.875 36.000 0.00 0.00 34.99 2.12
5721 11420 6.491745 TCTGTAGAAGATAGGAAGGCATAGTG 59.508 42.308 0.00 0.00 0.00 2.74
5723 11422 7.295340 TGTAGAAGATAGGAAGGCATAGTGTA 58.705 38.462 0.00 0.00 0.00 2.90
5836 11536 4.956085 ACTAGTAACATGTCTGTTGTGCA 58.044 39.130 0.00 0.00 45.16 4.57
5871 11571 7.076362 CAGAATATCCAAATGAAGCTTCATCG 58.924 38.462 35.67 28.56 46.60 3.84
5895 11595 0.037790 TAAGCAAAACCGCAATGGGC 60.038 50.000 0.00 0.00 44.64 5.36
5992 11692 5.357257 GTTCAAGACACAGAAGTAGAACCA 58.643 41.667 0.00 0.00 0.00 3.67
6204 11904 3.369366 GGGCCACCAATAATTTTGACCTG 60.369 47.826 4.39 0.00 36.50 4.00
6360 12060 4.067192 TGTTATCCAGATTGCATCATCGG 58.933 43.478 0.00 0.00 0.00 4.18
6372 12072 2.291741 GCATCATCGGAATCTGGTTTCC 59.708 50.000 0.00 1.49 41.54 3.13
6423 12123 5.592282 TGAACAGGTGCATCTCTTTTGTTTA 59.408 36.000 0.00 0.00 0.00 2.01
6479 12179 6.540189 ACATTACACTGATAAGAAGATGTGCC 59.460 38.462 0.00 0.00 0.00 5.01
6500 12200 2.584835 AATGCTACACTGAAGGGCAA 57.415 45.000 0.00 0.00 36.49 4.52
6616 12316 7.542477 CGATCATCTTTCTTGTAAGTACACAGT 59.458 37.037 0.00 0.00 35.64 3.55
6623 12323 5.597806 TCTTGTAAGTACACAGTGACCTTG 58.402 41.667 7.81 0.00 35.64 3.61
6707 12408 0.112218 CAGTTGGGTTGGGTGATCCA 59.888 55.000 0.00 0.00 45.43 3.41
6878 12579 2.225727 GGACCATTCGACCTGTTCAAAC 59.774 50.000 0.00 0.00 0.00 2.93
6888 12589 4.495844 CGACCTGTTCAAACTGTTTTCCTC 60.496 45.833 2.41 0.00 0.00 3.71
7120 12821 0.889186 TTGGTCTTTCGAGGCTTGCC 60.889 55.000 2.97 2.97 0.00 4.52
7221 12922 2.464865 CAGAGATACTACAGTTGCCGC 58.535 52.381 0.00 0.00 0.00 6.53
7250 12951 8.729529 TTCTAGCAGAATAACGAGATAATTCG 57.270 34.615 0.00 0.00 45.70 3.34
7385 13086 1.481871 AGCCAATTGAGCATGGGAAG 58.518 50.000 17.54 0.00 37.19 3.46
7448 13150 9.508567 CTGTAATTTTAGCTAGCTTTGGAAATC 57.491 33.333 24.88 12.70 0.00 2.17
7495 13201 5.829924 CAGCATGTTTAACTAATGAGGGGAT 59.170 40.000 0.00 0.00 0.00 3.85
7507 13213 2.032681 GGGGATATCAGCGGGCAC 59.967 66.667 4.83 0.00 0.00 5.01
7530 13236 1.242076 GCAGTGGCTCAACATGTTCT 58.758 50.000 8.48 0.00 36.96 3.01
7535 13241 3.953612 AGTGGCTCAACATGTTCTTTTGA 59.046 39.130 8.48 2.32 0.00 2.69
7536 13242 4.402155 AGTGGCTCAACATGTTCTTTTGAA 59.598 37.500 8.48 0.00 35.84 2.69
7571 13277 4.494350 AAGTGACAACATCATTCAGCAC 57.506 40.909 0.00 0.00 40.28 4.40
7851 13558 1.751924 GTTCTGCTGGAGACTACGGAT 59.248 52.381 0.00 0.00 0.00 4.18
7862 13569 3.207778 AGACTACGGATACAGACTCAGC 58.792 50.000 0.00 0.00 0.00 4.26
7969 13676 1.670590 GTGCTCTCTGAGGTGCTGT 59.329 57.895 18.74 0.00 0.00 4.40
8049 13757 5.994887 TGTACAATTGACTTGTTACGCTT 57.005 34.783 13.59 0.00 45.98 4.68
8161 13872 4.861462 GCTTGAGCTTTCCAGAAATTTAGC 59.139 41.667 0.94 0.94 38.21 3.09
8178 13889 0.742281 AGCAGCTTCATGTACGCAGG 60.742 55.000 0.00 0.00 0.00 4.85
8239 13950 6.475504 TCCAGAATTTCAGAAGCTTCATGTA 58.524 36.000 27.57 13.59 0.00 2.29
8369 14083 6.041069 AGCTAGATTACTGGTACCAGAACATC 59.959 42.308 41.87 33.36 46.30 3.06
8564 14283 8.578151 CCTAAGTACCTATATTTCAGGACTGAC 58.422 40.741 0.67 0.00 39.66 3.51
8605 14325 2.391389 CGCCCACGGAGCTTTCTTC 61.391 63.158 0.00 0.00 34.97 2.87
8606 14326 1.003233 GCCCACGGAGCTTTCTTCT 60.003 57.895 0.00 0.00 0.00 2.85
8607 14327 0.606673 GCCCACGGAGCTTTCTTCTT 60.607 55.000 0.00 0.00 0.00 2.52
8608 14328 1.897560 CCCACGGAGCTTTCTTCTTT 58.102 50.000 0.00 0.00 0.00 2.52
8609 14329 2.230660 CCCACGGAGCTTTCTTCTTTT 58.769 47.619 0.00 0.00 0.00 2.27
8610 14330 3.408634 CCCACGGAGCTTTCTTCTTTTA 58.591 45.455 0.00 0.00 0.00 1.52
8611 14331 3.437049 CCCACGGAGCTTTCTTCTTTTAG 59.563 47.826 0.00 0.00 0.00 1.85
8612 14332 3.120165 CCACGGAGCTTTCTTCTTTTAGC 60.120 47.826 0.00 0.00 0.00 3.09
8613 14333 3.748568 CACGGAGCTTTCTTCTTTTAGCT 59.251 43.478 0.00 0.00 46.02 3.32
8619 14339 6.968263 AGCTTTCTTCTTTTAGCTCCTTTT 57.032 33.333 0.00 0.00 39.67 2.27
8621 14341 8.105097 AGCTTTCTTCTTTTAGCTCCTTTTAG 57.895 34.615 0.00 0.00 39.67 1.85
8622 14342 7.939588 AGCTTTCTTCTTTTAGCTCCTTTTAGA 59.060 33.333 0.00 0.00 39.67 2.10
8623 14343 8.233868 GCTTTCTTCTTTTAGCTCCTTTTAGAG 58.766 37.037 0.00 0.00 36.92 2.43
8625 14345 7.317722 TCTTCTTTTAGCTCCTTTTAGAGGT 57.682 36.000 0.00 0.00 46.39 3.85
8626 14346 7.746703 TCTTCTTTTAGCTCCTTTTAGAGGTT 58.253 34.615 0.00 0.00 46.39 3.50
8627 14347 7.878644 TCTTCTTTTAGCTCCTTTTAGAGGTTC 59.121 37.037 0.00 0.00 46.39 3.62
8628 14348 7.074653 TCTTTTAGCTCCTTTTAGAGGTTCA 57.925 36.000 0.00 0.00 46.39 3.18
8629 14349 7.162082 TCTTTTAGCTCCTTTTAGAGGTTCAG 58.838 38.462 0.00 0.00 46.39 3.02
8630 14350 3.990959 AGCTCCTTTTAGAGGTTCAGG 57.009 47.619 0.00 0.00 46.39 3.86
8631 14351 2.573915 AGCTCCTTTTAGAGGTTCAGGG 59.426 50.000 0.00 0.00 46.39 4.45
8632 14352 2.941860 GCTCCTTTTAGAGGTTCAGGGC 60.942 54.545 0.00 0.00 46.39 5.19
8633 14353 2.573915 CTCCTTTTAGAGGTTCAGGGCT 59.426 50.000 0.00 0.00 46.39 5.19
8634 14354 2.305927 TCCTTTTAGAGGTTCAGGGCTG 59.694 50.000 0.00 0.00 46.39 4.85
8635 14355 2.619074 CCTTTTAGAGGTTCAGGGCTGG 60.619 54.545 0.00 0.00 40.95 4.85
8636 14356 2.038863 TTTAGAGGTTCAGGGCTGGA 57.961 50.000 0.00 0.00 0.00 3.86
8637 14357 2.038863 TTAGAGGTTCAGGGCTGGAA 57.961 50.000 0.00 0.00 0.00 3.53
8638 14358 1.573108 TAGAGGTTCAGGGCTGGAAG 58.427 55.000 0.00 0.00 0.00 3.46
8639 14359 1.204113 AGAGGTTCAGGGCTGGAAGG 61.204 60.000 0.00 0.00 0.00 3.46
8640 14360 2.203549 GAGGTTCAGGGCTGGAAGGG 62.204 65.000 0.00 0.00 0.00 3.95
8641 14361 2.231380 GGTTCAGGGCTGGAAGGGA 61.231 63.158 0.00 0.00 0.00 4.20
8642 14362 1.301293 GTTCAGGGCTGGAAGGGAG 59.699 63.158 0.00 0.00 0.00 4.30
8643 14363 2.606587 TTCAGGGCTGGAAGGGAGC 61.607 63.158 0.00 0.00 35.57 4.70
8644 14364 3.013932 CAGGGCTGGAAGGGAGCT 61.014 66.667 0.00 0.00 36.63 4.09
8645 14365 2.204213 AGGGCTGGAAGGGAGCTT 60.204 61.111 0.00 0.00 36.63 3.74
8646 14366 1.854507 AGGGCTGGAAGGGAGCTTT 60.855 57.895 0.00 0.00 36.63 3.51
8647 14367 1.379176 GGGCTGGAAGGGAGCTTTC 60.379 63.158 0.00 0.00 36.63 2.62
8648 14368 1.688211 GGCTGGAAGGGAGCTTTCT 59.312 57.895 0.00 0.00 36.63 2.52
8649 14369 0.038890 GGCTGGAAGGGAGCTTTCTT 59.961 55.000 2.68 2.68 36.63 2.52
8750 14470 3.867600 GCTGAATCACTGTCCACATCAGT 60.868 47.826 8.38 0.00 45.43 3.41
8856 14576 4.487282 AGGGCTATAGATGTAGAACCCA 57.513 45.455 3.21 0.00 38.64 4.51
8908 14628 8.353423 ACAAATTGCTAGACCTGATGTTTATT 57.647 30.769 0.00 0.00 0.00 1.40
8936 14656 3.009026 TGAGTATGCATGCAACACGATT 58.991 40.909 26.68 8.86 0.00 3.34
8960 14680 4.457257 CCTCAGCTCGATGATAGTCATACA 59.543 45.833 0.00 0.00 37.20 2.29
8961 14681 5.048434 CCTCAGCTCGATGATAGTCATACAA 60.048 44.000 0.00 0.00 37.20 2.41
8962 14682 6.391227 TCAGCTCGATGATAGTCATACAAA 57.609 37.500 0.00 0.00 37.20 2.83
8963 14683 6.986250 TCAGCTCGATGATAGTCATACAAAT 58.014 36.000 0.00 0.00 37.20 2.32
8964 14684 7.087007 TCAGCTCGATGATAGTCATACAAATC 58.913 38.462 0.00 0.00 37.20 2.17
8965 14685 7.040132 TCAGCTCGATGATAGTCATACAAATCT 60.040 37.037 0.00 0.00 37.20 2.40
8966 14686 7.273164 CAGCTCGATGATAGTCATACAAATCTC 59.727 40.741 0.00 0.00 37.20 2.75
8967 14687 6.529829 GCTCGATGATAGTCATACAAATCTCC 59.470 42.308 0.00 0.00 37.20 3.71
8968 14688 7.576666 GCTCGATGATAGTCATACAAATCTCCT 60.577 40.741 0.00 0.00 37.20 3.69
8969 14689 7.821652 TCGATGATAGTCATACAAATCTCCTC 58.178 38.462 0.00 0.00 37.20 3.71
8970 14690 7.032580 CGATGATAGTCATACAAATCTCCTCC 58.967 42.308 0.00 0.00 37.20 4.30
8971 14691 6.672266 TGATAGTCATACAAATCTCCTCCC 57.328 41.667 0.00 0.00 0.00 4.30
8972 14692 5.544176 TGATAGTCATACAAATCTCCTCCCC 59.456 44.000 0.00 0.00 0.00 4.81
8973 14693 3.736094 AGTCATACAAATCTCCTCCCCA 58.264 45.455 0.00 0.00 0.00 4.96
8974 14694 4.111577 AGTCATACAAATCTCCTCCCCAA 58.888 43.478 0.00 0.00 0.00 4.12
8975 14695 4.728860 AGTCATACAAATCTCCTCCCCAAT 59.271 41.667 0.00 0.00 0.00 3.16
8976 14696 5.194537 AGTCATACAAATCTCCTCCCCAATT 59.805 40.000 0.00 0.00 0.00 2.32
8977 14697 5.893824 GTCATACAAATCTCCTCCCCAATTT 59.106 40.000 0.00 0.00 0.00 1.82
8978 14698 6.381133 GTCATACAAATCTCCTCCCCAATTTT 59.619 38.462 0.00 0.00 0.00 1.82
8979 14699 6.380846 TCATACAAATCTCCTCCCCAATTTTG 59.619 38.462 0.00 0.00 0.00 2.44
8980 14700 4.492646 ACAAATCTCCTCCCCAATTTTGT 58.507 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.895530 TGTCCTCCCTGCTTAGTTCG 59.104 55.000 0.00 0.00 0.00 3.95
40 41 0.103937 CTCCGATGCTTCTGTCCTCC 59.896 60.000 0.00 0.00 0.00 4.30
110 111 3.130160 CTGCAAGAAGAGGGCGGC 61.130 66.667 0.00 0.00 34.07 6.53
111 112 2.437359 CCTGCAAGAAGAGGGCGG 60.437 66.667 0.00 0.00 34.07 6.13
112 113 2.437359 CCCTGCAAGAAGAGGGCG 60.437 66.667 0.00 0.00 42.74 6.13
209 210 2.421424 GCAGAACAAGATTCGCAGGAAT 59.579 45.455 0.00 0.00 45.43 3.01
232 233 0.813821 GAGCAGAATCAAACCTGGCC 59.186 55.000 0.00 0.00 0.00 5.36
269 274 8.229253 ACTAAACTCGGAAAACCAGTAATTTT 57.771 30.769 0.00 0.00 31.96 1.82
307 325 1.202879 AGCAATCGAACCAAACCTGGA 60.203 47.619 0.00 0.00 46.92 3.86
315 333 0.036388 GGACTGGAGCAATCGAACCA 60.036 55.000 0.00 0.00 0.00 3.67
332 350 2.091541 GAACCGATGAAAATGCCTGGA 58.908 47.619 0.00 0.00 0.00 3.86
333 351 1.134946 GGAACCGATGAAAATGCCTGG 59.865 52.381 0.00 0.00 0.00 4.45
334 352 2.094675 AGGAACCGATGAAAATGCCTG 58.905 47.619 0.00 0.00 0.00 4.85
335 353 2.290896 TGAGGAACCGATGAAAATGCCT 60.291 45.455 0.00 0.00 0.00 4.75
336 354 2.091541 TGAGGAACCGATGAAAATGCC 58.908 47.619 0.00 0.00 0.00 4.40
337 355 3.243201 GGATGAGGAACCGATGAAAATGC 60.243 47.826 0.00 0.00 0.00 3.56
343 361 0.031111 AGGGGATGAGGAACCGATGA 60.031 55.000 0.00 0.00 0.00 2.92
372 390 0.511653 GTTTTGAGACGCTTCGGGAC 59.488 55.000 0.00 0.00 0.00 4.46
373 391 0.105224 TGTTTTGAGACGCTTCGGGA 59.895 50.000 0.00 0.00 0.00 5.14
374 392 1.156736 ATGTTTTGAGACGCTTCGGG 58.843 50.000 0.00 0.00 0.00 5.14
375 393 2.969443 AATGTTTTGAGACGCTTCGG 57.031 45.000 0.00 0.00 0.00 4.30
376 394 4.611366 GGTAAAATGTTTTGAGACGCTTCG 59.389 41.667 1.16 0.00 0.00 3.79
377 395 4.915667 GGGTAAAATGTTTTGAGACGCTTC 59.084 41.667 1.16 0.00 0.00 3.86
378 396 4.339814 TGGGTAAAATGTTTTGAGACGCTT 59.660 37.500 1.16 0.00 0.00 4.68
379 397 3.886505 TGGGTAAAATGTTTTGAGACGCT 59.113 39.130 1.16 0.00 0.00 5.07
380 398 4.231718 TGGGTAAAATGTTTTGAGACGC 57.768 40.909 1.16 1.56 0.00 5.19
381 399 5.048364 TGGATGGGTAAAATGTTTTGAGACG 60.048 40.000 1.16 0.00 0.00 4.18
382 400 6.339587 TGGATGGGTAAAATGTTTTGAGAC 57.660 37.500 1.16 0.00 0.00 3.36
383 401 7.552050 AATGGATGGGTAAAATGTTTTGAGA 57.448 32.000 1.16 0.00 0.00 3.27
384 402 9.150348 GTAAATGGATGGGTAAAATGTTTTGAG 57.850 33.333 1.16 0.00 0.00 3.02
385 403 8.097662 GGTAAATGGATGGGTAAAATGTTTTGA 58.902 33.333 1.16 0.00 0.00 2.69
386 404 7.064016 CGGTAAATGGATGGGTAAAATGTTTTG 59.936 37.037 1.16 0.00 0.00 2.44
387 405 7.100409 CGGTAAATGGATGGGTAAAATGTTTT 58.900 34.615 0.00 0.00 0.00 2.43
403 421 2.004733 GGGACTTCGAACGGTAAATGG 58.995 52.381 0.00 0.00 0.00 3.16
404 422 2.671396 CTGGGACTTCGAACGGTAAATG 59.329 50.000 0.00 0.00 0.00 2.32
405 423 2.301009 ACTGGGACTTCGAACGGTAAAT 59.699 45.455 0.00 0.00 0.00 1.40
406 424 1.688197 ACTGGGACTTCGAACGGTAAA 59.312 47.619 0.00 0.00 0.00 2.01
504 522 0.684153 AAATCGGGGGATGCAACAGG 60.684 55.000 0.00 0.00 0.00 4.00
546 564 4.142773 CCGATAATTACGCCACACTGTTTT 60.143 41.667 0.00 0.00 0.00 2.43
550 568 2.284150 CACCGATAATTACGCCACACTG 59.716 50.000 0.00 0.00 0.00 3.66
557 575 0.505655 GACGGCACCGATAATTACGC 59.494 55.000 17.40 0.00 42.83 4.42
607 625 4.662145 CAAACATATTTTGCTCGTCTCCC 58.338 43.478 0.00 0.00 0.00 4.30
617 635 6.616774 AAAACTGGTGGCAAACATATTTTG 57.383 33.333 1.40 6.19 0.00 2.44
643 675 3.509575 AGCGATCAAGCCAAACCATTTTA 59.490 39.130 0.00 0.00 38.01 1.52
664 696 1.198867 CAGATCTATGCGGACTCGGAG 59.801 57.143 2.83 2.83 40.70 4.63
667 699 3.099524 GCAGATCTATGCGGACTCG 57.900 57.895 0.00 0.00 36.28 4.18
674 706 2.541178 GCACAAGCAAGCAGATCTATGC 60.541 50.000 15.77 15.77 42.98 3.14
712 744 0.949397 AACAGTCACATGCAGCTGTG 59.051 50.000 16.64 13.22 46.34 3.66
713 745 2.549064 TAACAGTCACATGCAGCTGT 57.451 45.000 16.64 9.83 43.13 4.40
714 746 3.004862 TGATAACAGTCACATGCAGCTG 58.995 45.455 10.11 10.11 35.31 4.24
715 747 3.005554 GTGATAACAGTCACATGCAGCT 58.994 45.455 0.00 0.00 46.04 4.24
805 840 9.608617 CGACGCTAAGATCAGAAAATAATAGTA 57.391 33.333 0.00 0.00 0.00 1.82
806 841 7.595502 CCGACGCTAAGATCAGAAAATAATAGT 59.404 37.037 0.00 0.00 0.00 2.12
807 842 7.410942 GCCGACGCTAAGATCAGAAAATAATAG 60.411 40.741 0.00 0.00 0.00 1.73
808 843 6.365247 GCCGACGCTAAGATCAGAAAATAATA 59.635 38.462 0.00 0.00 0.00 0.98
809 844 5.177696 GCCGACGCTAAGATCAGAAAATAAT 59.822 40.000 0.00 0.00 0.00 1.28
810 845 4.506654 GCCGACGCTAAGATCAGAAAATAA 59.493 41.667 0.00 0.00 0.00 1.40
841 878 1.298602 CAGCCCAAAAGCCAAAACAC 58.701 50.000 0.00 0.00 0.00 3.32
842 879 0.908198 ACAGCCCAAAAGCCAAAACA 59.092 45.000 0.00 0.00 0.00 2.83
924 967 8.981647 CCAACAGGAATATTGTTCTTTTTCAAG 58.018 33.333 0.00 0.00 36.67 3.02
977 3762 1.883275 CTCTCTCACTGTCTGACCGTT 59.117 52.381 5.17 0.00 0.00 4.44
983 3768 3.355378 ACCATCTCTCTCTCACTGTCTG 58.645 50.000 0.00 0.00 0.00 3.51
1068 3853 0.960861 GGTCAGTACTTTGCCCCAGC 60.961 60.000 0.00 0.00 40.48 4.85
1092 3877 2.419297 CGCAAGCAGGAGATTACCTTCT 60.419 50.000 0.00 0.00 38.32 2.85
1490 6918 5.016051 TGACCAGAGCTCATAGAATGAAC 57.984 43.478 17.77 2.77 39.11 3.18
1551 6981 4.853743 GCTACTGCTTGTAAACAATCTTGC 59.146 41.667 0.00 0.00 35.02 4.01
1637 7067 8.815565 TTAATTAGTTTCTTATGGGTGCATGA 57.184 30.769 0.00 0.00 0.00 3.07
1717 7147 8.182227 GCCTTCGAGTAAACTGCTTATTATTTT 58.818 33.333 0.00 0.00 0.00 1.82
1718 7148 7.335924 TGCCTTCGAGTAAACTGCTTATTATTT 59.664 33.333 0.00 0.00 0.00 1.40
1719 7149 6.821665 TGCCTTCGAGTAAACTGCTTATTATT 59.178 34.615 0.00 0.00 0.00 1.40
1720 7150 6.346096 TGCCTTCGAGTAAACTGCTTATTAT 58.654 36.000 0.00 0.00 0.00 1.28
1721 7151 5.726397 TGCCTTCGAGTAAACTGCTTATTA 58.274 37.500 0.00 0.00 0.00 0.98
1722 7152 4.575885 TGCCTTCGAGTAAACTGCTTATT 58.424 39.130 0.00 0.00 0.00 1.40
1723 7153 4.202245 TGCCTTCGAGTAAACTGCTTAT 57.798 40.909 0.00 0.00 0.00 1.73
1724 7154 3.671008 TGCCTTCGAGTAAACTGCTTA 57.329 42.857 0.00 0.00 0.00 3.09
1725 7155 2.543777 TGCCTTCGAGTAAACTGCTT 57.456 45.000 0.00 0.00 0.00 3.91
1726 7156 2.543777 TTGCCTTCGAGTAAACTGCT 57.456 45.000 0.00 0.00 0.00 4.24
1727 7157 3.242936 TGTTTTGCCTTCGAGTAAACTGC 60.243 43.478 0.00 0.00 31.71 4.40
1728 7158 4.527564 CTGTTTTGCCTTCGAGTAAACTG 58.472 43.478 0.00 0.00 31.71 3.16
1729 7159 3.564225 CCTGTTTTGCCTTCGAGTAAACT 59.436 43.478 0.00 0.00 31.71 2.66
1730 7160 3.562557 TCCTGTTTTGCCTTCGAGTAAAC 59.437 43.478 0.00 0.00 0.00 2.01
1731 7161 3.811083 TCCTGTTTTGCCTTCGAGTAAA 58.189 40.909 0.00 0.00 0.00 2.01
1732 7162 3.478857 TCCTGTTTTGCCTTCGAGTAA 57.521 42.857 0.00 0.00 0.00 2.24
1733 7163 3.135994 GTTCCTGTTTTGCCTTCGAGTA 58.864 45.455 0.00 0.00 0.00 2.59
1774 7204 1.808945 GACAAGGGAGATGCACAGTTG 59.191 52.381 0.00 0.00 0.00 3.16
1796 7226 8.236585 TGGTGGGATAAATTATCAACATCAAG 57.763 34.615 15.62 0.00 34.19 3.02
1813 7243 5.994416 ACTACAGGAAAATATGGTGGGAT 57.006 39.130 0.00 0.00 0.00 3.85
1880 7310 2.289133 TGACAGGTTGCACATTACGCTA 60.289 45.455 0.00 0.00 0.00 4.26
2220 7650 5.931146 GCTACTATAAGCATGAGACAAGCAT 59.069 40.000 0.00 0.00 42.30 3.79
2333 7763 4.749048 TCCTATCTCTTCTGGGATGCTA 57.251 45.455 0.00 0.00 0.00 3.49
2343 7773 7.777095 AGTGTAGTGATGTTTCCTATCTCTTC 58.223 38.462 0.00 0.00 32.49 2.87
2680 8118 4.386413 AAGCTCTGAAGGTTGCCG 57.614 55.556 0.00 0.00 41.55 5.69
2927 8365 5.790593 TCCACATACAGGTGAAGAAGTAAC 58.209 41.667 0.00 0.00 41.32 2.50
3021 8459 2.745102 TGCAAGTGTTCGTTACATCGA 58.255 42.857 0.00 0.00 39.39 3.59
3042 8480 3.197265 GTTGTCAACAAGGCTGCAAATT 58.803 40.909 10.93 0.00 36.39 1.82
3103 8541 8.349245 CACATACAGTATTTTCAAAACAGGTGA 58.651 33.333 0.00 0.00 0.00 4.02
3110 8548 5.540337 TGGGGCACATACAGTATTTTCAAAA 59.460 36.000 0.00 0.00 0.00 2.44
3121 8559 2.346766 TGCTAATGGGGCACATACAG 57.653 50.000 0.84 4.66 39.40 2.74
3259 8698 8.503196 CAGTGTTTTTATGTTGCTGTATGTAGA 58.497 33.333 0.00 0.00 0.00 2.59
3318 8757 5.826208 AGGAAAAAGACAAACGTGTAAGGAT 59.174 36.000 0.00 0.00 38.41 3.24
3320 8759 5.494632 AGGAAAAAGACAAACGTGTAAGG 57.505 39.130 0.00 0.00 38.41 2.69
3384 8823 8.177119 AGATGTTGCTTAATAAAACTGGAACA 57.823 30.769 0.00 0.00 41.57 3.18
3435 8874 6.641314 ACGAACTCAGTGTAAGTGTAAGAATG 59.359 38.462 0.00 0.00 38.75 2.67
3614 9054 5.186409 AGTGCAAGCCATAACATCAAAAGAT 59.814 36.000 0.00 0.00 0.00 2.40
3712 9152 7.899973 AGTTATTTCCTGAAATGCATGAACTT 58.100 30.769 13.92 0.00 40.83 2.66
3742 9182 5.515626 GTGAGTAATAGCAGTTTAGACACCG 59.484 44.000 0.00 0.00 0.00 4.94
3755 9195 6.204359 CCTGAAAATGCATGTGAGTAATAGC 58.796 40.000 0.00 0.00 0.00 2.97
3765 9205 4.340381 GCTAAGATCCCTGAAAATGCATGT 59.660 41.667 0.00 0.00 0.00 3.21
3930 9370 2.224670 ACGGGACAGTTCCATTAAGCAA 60.225 45.455 0.00 0.00 44.98 3.91
3964 9404 5.320277 ACAAAAGCTGAAGATTAGGAAGCT 58.680 37.500 0.00 0.00 45.86 3.74
3993 9433 3.249986 CCAAACATGGCCTAAATGGTG 57.750 47.619 3.32 2.62 38.35 4.17
4075 9515 8.988060 TCCAATAGAATATGTGAAGAGTGGTTA 58.012 33.333 0.00 0.00 0.00 2.85
4136 9576 2.874849 CGGTTGCTGAACTGTGTTTTT 58.125 42.857 0.00 0.00 34.21 1.94
4257 9697 0.468029 CACCTGCAGAAACCCCAAGT 60.468 55.000 17.39 0.00 0.00 3.16
4260 9700 1.072266 ATACACCTGCAGAAACCCCA 58.928 50.000 17.39 0.00 0.00 4.96
4262 9702 4.523083 TCAATATACACCTGCAGAAACCC 58.477 43.478 17.39 0.00 0.00 4.11
4360 9809 8.039538 TGCCTGTATTTGCAATCATGATAAAAA 58.960 29.630 9.04 10.21 33.87 1.94
4482 9931 3.576118 CGAGGGAACATCACCATCTAGAT 59.424 47.826 0.00 0.00 36.28 1.98
4494 9943 2.187958 TCCAGATTGTCGAGGGAACAT 58.812 47.619 0.00 0.00 0.00 2.71
4643 10132 2.093235 GCAGCTGGAATAGTCTTGAGGT 60.093 50.000 17.12 0.00 0.00 3.85
4659 10148 0.548510 GGGGAGGACTAAATGCAGCT 59.451 55.000 0.00 0.00 0.00 4.24
4670 10159 3.763057 ACAGTAACATTTTGGGGAGGAC 58.237 45.455 0.00 0.00 0.00 3.85
4803 10401 8.463930 TCACCAAAACAGAGATCAACTAAAAT 57.536 30.769 0.00 0.00 0.00 1.82
4830 10428 4.833390 AGTAGATAACAAAGGTGGTGCTC 58.167 43.478 0.00 0.00 0.00 4.26
4846 10444 7.067737 GGAGACTTGTAGCAACTCTAAGTAGAT 59.932 40.741 0.00 0.00 0.00 1.98
4851 10449 4.464597 AGGGAGACTTGTAGCAACTCTAAG 59.535 45.833 0.00 0.00 0.00 2.18
4867 10465 8.567285 TTATTCTCAAATTCAGAAAGGGAGAC 57.433 34.615 9.39 0.00 33.57 3.36
4895 10493 9.773328 CATTGCGAAATCAATTTCTAGTTCTTA 57.227 29.630 12.32 0.00 42.96 2.10
4896 10494 7.274250 GCATTGCGAAATCAATTTCTAGTTCTT 59.726 33.333 12.32 0.00 42.96 2.52
4898 10496 6.527722 TGCATTGCGAAATCAATTTCTAGTTC 59.472 34.615 12.32 0.00 42.96 3.01
4920 10520 7.875554 TCAGTTTACAACAGATACAAGTATGCA 59.124 33.333 0.00 0.00 0.00 3.96
5104 10704 2.906691 TGGGCAAGGTGAACAAATTG 57.093 45.000 0.00 0.00 0.00 2.32
5126 10726 9.106070 GATGGGTTGTACTCGTAATTTTTATCT 57.894 33.333 0.00 0.00 0.00 1.98
5311 10911 1.304282 CTTGGACCCACCTCCCATG 59.696 63.158 0.00 0.00 39.86 3.66
5502 11102 2.420628 TTTGCACAATTGAGCTTCGG 57.579 45.000 25.02 2.57 32.76 4.30
5575 11176 3.006859 AGGCTACAAAGAAAATTGCCACC 59.993 43.478 0.00 0.00 41.12 4.61
5653 11352 5.651530 TCAAAATAACTTGCCAACGACAAA 58.348 33.333 0.00 0.00 0.00 2.83
5755 11455 6.974048 CGCCATAGAAACAAATGAATCATGAA 59.026 34.615 0.00 0.00 0.00 2.57
5895 11595 3.272334 GCGCTTGCCAGGATACCG 61.272 66.667 0.00 0.00 37.17 4.02
5953 11653 6.876789 TGTCTTGAACGCCTTCTCATTATAAA 59.123 34.615 0.00 0.00 0.00 1.40
6204 11904 3.740115 TCCTTGACCAACTTGAGCTAAC 58.260 45.455 0.00 0.00 0.00 2.34
6360 12060 4.336280 AGCCAACTAAGGAAACCAGATTC 58.664 43.478 0.00 0.00 0.00 2.52
6372 12072 5.355071 TGCTTCATCACAATAGCCAACTAAG 59.645 40.000 0.00 0.00 32.73 2.18
6479 12179 3.266510 TGCCCTTCAGTGTAGCATTAG 57.733 47.619 0.00 0.00 0.00 1.73
6500 12200 9.584008 AGCATGAATGACAGAAATTAATAGGAT 57.416 29.630 0.00 0.00 0.00 3.24
6532 12232 4.448005 CATCTGCAAAAACACAATTTCGC 58.552 39.130 0.00 0.00 0.00 4.70
6703 12404 1.151943 ATCAGCCGGGATCCTGGAT 60.152 57.895 39.43 32.99 45.10 3.41
6843 12544 4.096231 CGAATGGTCCAATGATTGCACTAA 59.904 41.667 0.00 0.00 0.00 2.24
6878 12579 5.241506 TGAGGTGCTTAATTGAGGAAAACAG 59.758 40.000 0.00 0.00 0.00 3.16
6888 12589 6.694411 GCAACATAAGATGAGGTGCTTAATTG 59.306 38.462 0.00 0.00 35.12 2.32
7120 12821 1.597742 CTTCAATATCCGGCACTGGG 58.402 55.000 0.00 0.00 0.00 4.45
7250 12951 6.286240 AGATATCCCTGCCAAAAAGAAAAC 57.714 37.500 0.00 0.00 0.00 2.43
7260 12961 2.641321 CTGGATCAAGATATCCCTGCCA 59.359 50.000 0.00 0.86 44.23 4.92
7448 13150 9.669353 GCTGAATCATGTTTATACTTTATGTGG 57.331 33.333 0.00 0.00 0.00 4.17
7470 13173 5.045213 TCCCCTCATTAGTTAAACATGCTGA 60.045 40.000 0.00 0.00 0.00 4.26
7495 13201 4.175337 GCCTGGTGCCCGCTGATA 62.175 66.667 0.00 0.00 0.00 2.15
7507 13213 1.303888 ATGTTGAGCCACTGCCTGG 60.304 57.895 0.00 0.00 44.08 4.45
7508 13214 0.892358 ACATGTTGAGCCACTGCCTG 60.892 55.000 0.00 0.00 38.69 4.85
7509 13215 0.178981 AACATGTTGAGCCACTGCCT 60.179 50.000 11.07 0.00 38.69 4.75
7510 13216 0.242017 GAACATGTTGAGCCACTGCC 59.758 55.000 17.58 0.00 38.69 4.85
7511 13217 1.242076 AGAACATGTTGAGCCACTGC 58.758 50.000 17.58 0.00 37.95 4.40
7512 13218 3.996150 AAAGAACATGTTGAGCCACTG 57.004 42.857 17.58 0.00 0.00 3.66
7513 13219 3.953612 TCAAAAGAACATGTTGAGCCACT 59.046 39.130 17.58 2.31 0.00 4.00
7530 13236 7.968405 GTCACTTTCTCTAAAGCAAGTTCAAAA 59.032 33.333 0.00 0.00 45.06 2.44
7535 13241 6.374333 TGTTGTCACTTTCTCTAAAGCAAGTT 59.626 34.615 0.00 0.00 45.06 2.66
7536 13242 5.880332 TGTTGTCACTTTCTCTAAAGCAAGT 59.120 36.000 0.00 0.00 45.06 3.16
7544 13250 6.369890 GCTGAATGATGTTGTCACTTTCTCTA 59.630 38.462 0.00 0.00 40.28 2.43
7546 13252 5.049198 TGCTGAATGATGTTGTCACTTTCTC 60.049 40.000 0.00 0.00 40.28 2.87
7552 13258 3.003585 TGTGTGCTGAATGATGTTGTCAC 59.996 43.478 0.00 0.00 40.28 3.67
7571 13277 4.793071 TGCGTTCCACTTAAATTCATGTG 58.207 39.130 0.00 0.00 0.00 3.21
7818 13525 0.391661 GCAGAACAAGATCCGCCTCA 60.392 55.000 0.00 0.00 0.00 3.86
7862 13569 8.954950 AGTTGACAAGGATTTACTCATATCAG 57.045 34.615 0.00 0.00 0.00 2.90
7969 13676 0.820226 CACCAAGATCAGCGAGGAGA 59.180 55.000 0.00 0.00 0.00 3.71
8049 13757 6.862711 TTAATGTACAACACAAACGATCCA 57.137 33.333 0.00 0.00 41.55 3.41
8161 13872 0.391661 ACCCTGCGTACATGAAGCTG 60.392 55.000 0.00 5.78 33.09 4.24
8178 13889 1.160137 GAACCACAGCTCATGTCACC 58.840 55.000 0.00 0.00 41.41 4.02
8239 13950 5.737860 TGCTAATCATCACTCATTCTGTGT 58.262 37.500 0.00 0.00 36.83 3.72
8277 13991 5.012239 ACTGCAATATGTTTCTCACCATGT 58.988 37.500 0.00 0.00 0.00 3.21
8344 14058 5.269991 TGTTCTGGTACCAGTAATCTAGCT 58.730 41.667 35.34 0.00 43.96 3.32
8369 14083 5.921408 GTCGGCCTAGATTACATGTAAAGAG 59.079 44.000 21.57 16.92 0.00 2.85
8540 14258 7.994911 TCGTCAGTCCTGAAATATAGGTACTTA 59.005 37.037 0.00 0.00 41.85 2.24
8564 14283 4.741342 ACGGTAGTTCTCTTATTGGTTCG 58.259 43.478 0.00 0.00 0.00 3.95
8615 14335 2.305927 TCCAGCCCTGAACCTCTAAAAG 59.694 50.000 0.00 0.00 0.00 2.27
8616 14336 2.344592 TCCAGCCCTGAACCTCTAAAA 58.655 47.619 0.00 0.00 0.00 1.52
8617 14337 2.038863 TCCAGCCCTGAACCTCTAAA 57.961 50.000 0.00 0.00 0.00 1.85
8618 14338 1.909302 CTTCCAGCCCTGAACCTCTAA 59.091 52.381 0.00 0.00 0.00 2.10
8619 14339 1.573108 CTTCCAGCCCTGAACCTCTA 58.427 55.000 0.00 0.00 0.00 2.43
8620 14340 1.204113 CCTTCCAGCCCTGAACCTCT 61.204 60.000 0.00 0.00 0.00 3.69
8621 14341 1.301293 CCTTCCAGCCCTGAACCTC 59.699 63.158 0.00 0.00 0.00 3.85
8622 14342 2.234296 CCCTTCCAGCCCTGAACCT 61.234 63.158 0.00 0.00 0.00 3.50
8623 14343 2.203549 CTCCCTTCCAGCCCTGAACC 62.204 65.000 0.00 0.00 0.00 3.62
8624 14344 1.301293 CTCCCTTCCAGCCCTGAAC 59.699 63.158 0.00 0.00 0.00 3.18
8625 14345 2.606587 GCTCCCTTCCAGCCCTGAA 61.607 63.158 0.00 0.00 0.00 3.02
8626 14346 3.011517 GCTCCCTTCCAGCCCTGA 61.012 66.667 0.00 0.00 0.00 3.86
8627 14347 2.147433 AAAGCTCCCTTCCAGCCCTG 62.147 60.000 0.00 0.00 37.63 4.45
8628 14348 1.854507 AAAGCTCCCTTCCAGCCCT 60.855 57.895 0.00 0.00 37.63 5.19
8629 14349 1.379176 GAAAGCTCCCTTCCAGCCC 60.379 63.158 0.00 0.00 37.63 5.19
8630 14350 0.038890 AAGAAAGCTCCCTTCCAGCC 59.961 55.000 0.00 0.00 37.63 4.85
8631 14351 1.004161 AGAAGAAAGCTCCCTTCCAGC 59.996 52.381 18.77 0.00 39.54 4.85
8632 14352 3.431673 AAGAAGAAAGCTCCCTTCCAG 57.568 47.619 18.77 0.00 39.54 3.86
8633 14353 3.884037 AAAGAAGAAAGCTCCCTTCCA 57.116 42.857 18.77 0.00 39.54 3.53
8634 14354 4.156922 GCTAAAAGAAGAAAGCTCCCTTCC 59.843 45.833 18.77 6.81 39.54 3.46
8635 14355 5.007034 AGCTAAAAGAAGAAAGCTCCCTTC 58.993 41.667 16.11 16.11 41.35 3.46
8636 14356 4.991776 AGCTAAAAGAAGAAAGCTCCCTT 58.008 39.130 0.73 0.73 41.35 3.95
8637 14357 4.649267 AGCTAAAAGAAGAAAGCTCCCT 57.351 40.909 0.00 0.00 41.35 4.20
8642 14362 8.100508 TCTAAAAGGAGCTAAAAGAAGAAAGC 57.899 34.615 0.00 0.00 35.16 3.51
8750 14470 5.086104 GGCCGAGCCTAATGATAAGAATA 57.914 43.478 7.58 0.00 46.69 1.75
8822 14542 7.180946 ACATCTATAGCCCTTCACATGCTATTA 59.819 37.037 8.36 0.00 43.82 0.98
8879 14599 5.413833 ACATCAGGTCTAGCAATTTGTTCTG 59.586 40.000 0.00 0.00 0.00 3.02
8908 14628 4.759183 TGTTGCATGCATACTCAAACAGTA 59.241 37.500 23.37 0.00 42.09 2.74
8936 14656 3.214696 TGACTATCATCGAGCTGAGGA 57.785 47.619 0.00 0.00 42.40 3.71


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

AutoCloner maintained by Alex Coulton.