Multiple sequence alignment - TraesCS5A01G515000

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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 TraesCS5A01G515000 chr5A 100.000 5996 0 0 610 6605 678274024 678268029 0.000000e+00 11073.0
1 TraesCS5A01G515000 chr5A 88.528 523 40 10 1000 1509 649696130 649695615 3.380000e-172 616.0
2 TraesCS5A01G515000 chr5A 100.000 295 0 0 1 295 678274633 678274339 4.500000e-151 545.0
3 TraesCS5A01G515000 chr4B 89.731 3827 228 93 685 4428 639852388 639848644 0.000000e+00 4737.0
4 TraesCS5A01G515000 chr4B 90.360 1473 63 32 4819 6234 639848272 639846822 0.000000e+00 1860.0
5 TraesCS5A01G515000 chr4B 91.098 337 29 1 6270 6605 639846822 639846486 7.810000e-124 455.0
6 TraesCS5A01G515000 chr4B 92.282 298 11 4 1 295 639852747 639852459 4.770000e-111 412.0
7 TraesCS5A01G515000 chr4B 91.700 253 17 2 975 1223 154978918 154978666 1.360000e-91 348.0
8 TraesCS5A01G515000 chr4B 98.000 50 1 0 610 659 639852434 639852385 3.280000e-13 87.9
9 TraesCS5A01G515000 chr4D 91.889 2059 130 20 2471 4504 497947998 497945952 0.000000e+00 2843.0
10 TraesCS5A01G515000 chr4D 93.550 1752 68 26 610 2343 497949733 497948009 0.000000e+00 2567.0
11 TraesCS5A01G515000 chr4D 90.974 1828 92 30 4818 6605 497945708 497943914 0.000000e+00 2394.0
12 TraesCS5A01G515000 chr4D 92.000 300 12 4 1 295 497950040 497949748 1.710000e-110 411.0
13 TraesCS5A01G515000 chr7A 90.631 523 36 7 988 1509 652373172 652373682 0.000000e+00 682.0
14 TraesCS5A01G515000 chr7A 88.419 544 39 12 983 1509 107669179 107668643 9.340000e-178 634.0
15 TraesCS5A01G515000 chr7A 94.253 87 5 0 4506 4592 652487197 652487111 4.160000e-27 134.0
16 TraesCS5A01G515000 chr6B 86.239 545 61 8 977 1516 608273851 608274386 4.440000e-161 579.0
17 TraesCS5A01G515000 chr4A 91.304 253 18 2 975 1223 660155136 660154884 6.340000e-90 342.0
18 TraesCS5A01G515000 chr4A 92.135 89 7 0 4503 4591 9380763 9380675 6.950000e-25 126.0
19 TraesCS5A01G515000 chrUn 90.514 253 20 2 975 1223 471169934 471170186 1.370000e-86 331.0
20 TraesCS5A01G515000 chrUn 84.012 344 32 12 1006 1333 205346676 205346340 6.430000e-80 309.0
21 TraesCS5A01G515000 chrUn 83.721 344 33 13 1006 1333 349933070 349933406 2.990000e-78 303.0
22 TraesCS5A01G515000 chr3B 84.302 344 32 11 1006 1333 35682656 35682993 3.840000e-82 316.0
23 TraesCS5A01G515000 chr2A 96.552 87 3 0 4505 4591 4139217 4139303 1.920000e-30 145.0
24 TraesCS5A01G515000 chr2A 94.382 89 5 0 4503 4591 539325666 539325578 3.210000e-28 137.0
25 TraesCS5A01G515000 chr2A 95.349 86 4 0 4507 4592 745552763 745552848 3.210000e-28 137.0
26 TraesCS5A01G515000 chr5D 94.253 87 5 0 4501 4587 494775534 494775448 4.160000e-27 134.0
27 TraesCS5A01G515000 chr3D 93.258 89 6 0 4504 4592 206978599 206978511 1.490000e-26 132.0
28 TraesCS5A01G515000 chr7D 92.308 91 7 0 4501 4591 1261040 1260950 5.380000e-26 130.0
29 TraesCS5A01G515000 chr1B 93.103 87 6 0 4505 4591 563777945 563778031 1.930000e-25 128.0
30 TraesCS5A01G515000 chr5B 92.754 69 2 2 1442 1509 531180140 531180074 5.450000e-16 97.1


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 TraesCS5A01G515000 chr5A 678268029 678274633 6604 True 5809.00 11073 100.00000 1 6605 2 chr5A.!!$R2 6604
1 TraesCS5A01G515000 chr5A 649695615 649696130 515 True 616.00 616 88.52800 1000 1509 1 chr5A.!!$R1 509
2 TraesCS5A01G515000 chr4B 639846486 639852747 6261 True 1510.38 4737 92.29420 1 6605 5 chr4B.!!$R2 6604
3 TraesCS5A01G515000 chr4D 497943914 497950040 6126 True 2053.75 2843 92.10325 1 6605 4 chr4D.!!$R1 6604
4 TraesCS5A01G515000 chr7A 652373172 652373682 510 False 682.00 682 90.63100 988 1509 1 chr7A.!!$F1 521
5 TraesCS5A01G515000 chr7A 107668643 107669179 536 True 634.00 634 88.41900 983 1509 1 chr7A.!!$R1 526
6 TraesCS5A01G515000 chr6B 608273851 608274386 535 False 579.00 579 86.23900 977 1516 1 chr6B.!!$F1 539

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
254 261 0.414629 TTTTCCCCTACCCTCCTCGA 59.585 55.000 0.00 0.0 0.0 4.04 F
1354 1372 0.373024 CGACTCCTTCCTCGTACGTC 59.627 60.000 16.05 0.8 0.0 4.34 F
2018 2112 0.901114 ACATTTGGGCCGGGGTTTAC 60.901 55.000 2.18 0.0 0.0 2.01 F
2537 2642 0.252742 TCCCTTCCTCCTCCTTCCAC 60.253 60.000 0.00 0.0 0.0 4.02 F
2538 2643 0.547712 CCCTTCCTCCTCCTTCCACA 60.548 60.000 0.00 0.0 0.0 4.17 F
3009 3131 1.071642 GCTCCCTATCGGAAAGGCC 59.928 63.158 0.00 0.0 41.4 5.19 F
4703 4920 0.322816 TCAAGGGAAGATGCTGGCAC 60.323 55.000 0.00 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2235 0.099436 CAAGGCTTGCGGCAATCTAC 59.901 55.000 16.80 6.89 44.01 2.59 R
2418 2514 0.179065 GGCAGTTGGACGGGTATACC 60.179 60.000 13.99 13.99 0.00 2.73 R
3035 3158 0.332632 CCTTGGGATCAGGGCTTTCA 59.667 55.000 0.00 0.00 33.27 2.69 R
4302 4481 0.528017 TCGAGCTCATATCCATCGGC 59.472 55.000 15.40 0.00 34.29 5.54 R
4305 4484 4.180057 GTCCATTCGAGCTCATATCCATC 58.820 47.826 15.40 0.00 0.00 3.51 R
4831 5093 0.234884 GAAACCCTGCAACGAACGAG 59.765 55.000 0.14 0.00 0.00 4.18 R
6120 6445 0.802494 GATACAACAAGGCCCACACG 59.198 55.000 0.00 0.00 0.00 4.49 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
50 51 1.315690 GGACACATGATCCATGCTGG 58.684 55.000 13.77 0.00 44.80 4.85
53 54 0.753848 CACATGATCCATGCTGGCCA 60.754 55.000 4.71 4.71 44.80 5.36
64 65 1.105457 TGCTGGCCAATAGATGCAAC 58.895 50.000 12.29 0.00 0.00 4.17
86 87 7.600065 CAACTAAGTTGCTACTTGAGGTAGTA 58.400 38.462 21.56 0.00 46.99 1.82
87 88 7.393841 ACTAAGTTGCTACTTGAGGTAGTAG 57.606 40.000 21.56 11.54 46.99 2.57
90 91 6.270156 AGTTGCTACTTGAGGTAGTAGTTC 57.730 41.667 11.25 4.32 46.05 3.01
91 92 6.011481 AGTTGCTACTTGAGGTAGTAGTTCT 58.989 40.000 11.25 5.99 46.05 3.01
92 93 6.494146 AGTTGCTACTTGAGGTAGTAGTTCTT 59.506 38.462 11.25 0.00 46.05 2.52
225 232 5.510520 CCATCTCTCTTACCAGCCTTATCAC 60.511 48.000 0.00 0.00 0.00 3.06
251 258 0.501468 ACCTTTTCCCCTACCCTCCT 59.499 55.000 0.00 0.00 0.00 3.69
252 259 1.214217 CCTTTTCCCCTACCCTCCTC 58.786 60.000 0.00 0.00 0.00 3.71
253 260 0.831307 CTTTTCCCCTACCCTCCTCG 59.169 60.000 0.00 0.00 0.00 4.63
254 261 0.414629 TTTTCCCCTACCCTCCTCGA 59.585 55.000 0.00 0.00 0.00 4.04
664 671 3.322191 AGTTTAGCTAGGAGGAGGAGG 57.678 52.381 0.00 0.00 0.00 4.30
665 672 2.860041 AGTTTAGCTAGGAGGAGGAGGA 59.140 50.000 0.00 0.00 0.00 3.71
696 704 1.338769 ACTTGGTTGAGGTGATACGGC 60.339 52.381 0.00 0.00 0.00 5.68
698 706 1.153229 GGTTGAGGTGATACGGCCC 60.153 63.158 0.00 0.00 0.00 5.80
821 835 0.859760 CTCTCCTCCCTCCTCTCCAT 59.140 60.000 0.00 0.00 0.00 3.41
962 976 1.379176 GAAAAGCTCCTCTGGCCCC 60.379 63.158 0.00 0.00 0.00 5.80
992 1010 2.278857 CGGCGAACAGGAGATCGG 60.279 66.667 0.00 0.00 40.01 4.18
1354 1372 0.373024 CGACTCCTTCCTCGTACGTC 59.627 60.000 16.05 0.80 0.00 4.34
1360 1378 1.020437 CTTCCTCGTACGTCCTACCC 58.980 60.000 16.05 0.00 0.00 3.69
1364 1382 1.134401 CCTCGTACGTCCTACCCTACA 60.134 57.143 16.05 0.00 0.00 2.74
1372 1390 3.294214 CGTCCTACCCTACATACCACTT 58.706 50.000 0.00 0.00 0.00 3.16
1373 1391 3.317430 CGTCCTACCCTACATACCACTTC 59.683 52.174 0.00 0.00 0.00 3.01
1374 1392 4.544683 GTCCTACCCTACATACCACTTCT 58.455 47.826 0.00 0.00 0.00 2.85
1375 1393 4.961099 GTCCTACCCTACATACCACTTCTT 59.039 45.833 0.00 0.00 0.00 2.52
1723 1786 7.064609 TGGACTAAAAAGAAAGTGCTATCATCG 59.935 37.037 0.00 0.00 35.33 3.84
1775 1839 6.206829 ACCCTTTGCTTGTTAGTTAGTGAATC 59.793 38.462 0.00 0.00 0.00 2.52
2011 2105 1.318576 GGAGAATACATTTGGGCCGG 58.681 55.000 0.00 0.00 0.00 6.13
2018 2112 0.901114 ACATTTGGGCCGGGGTTTAC 60.901 55.000 2.18 0.00 0.00 2.01
2098 2193 3.552684 GGCCGGTTAAAACCCTAACAAAC 60.553 47.826 1.90 0.00 46.53 2.93
2190 2286 6.150474 GGCATGCTAGGTAAAGTTAACAAGAA 59.850 38.462 18.92 0.00 0.00 2.52
2195 2291 6.090493 GCTAGGTAAAGTTAACAAGAAGGACG 59.910 42.308 8.61 0.00 0.00 4.79
2232 2328 2.633481 GTTCGAGCCCTACTCCCAATAT 59.367 50.000 0.00 0.00 43.01 1.28
2237 2333 3.432378 AGCCCTACTCCCAATATCTACG 58.568 50.000 0.00 0.00 0.00 3.51
2283 2379 1.742768 CCGCCTAATCTTCCTCGCT 59.257 57.895 0.00 0.00 0.00 4.93
2298 2394 1.978617 CGCTGCACCTCCCCATTTT 60.979 57.895 0.00 0.00 0.00 1.82
2318 2414 1.153429 GCACCCCGTCTACCATCAC 60.153 63.158 0.00 0.00 0.00 3.06
2319 2415 1.614241 GCACCCCGTCTACCATCACT 61.614 60.000 0.00 0.00 0.00 3.41
2324 2420 1.191535 CCGTCTACCATCACTCCCAA 58.808 55.000 0.00 0.00 0.00 4.12
2376 2472 3.947834 CTCCTCCATGAACCACCAATTAC 59.052 47.826 0.00 0.00 0.00 1.89
2380 2476 4.340617 TCCATGAACCACCAATTACCTTC 58.659 43.478 0.00 0.00 0.00 3.46
2390 2486 3.526430 ACCAATTACCTTCTCCTAACCCC 59.474 47.826 0.00 0.00 0.00 4.95
2417 2513 7.155655 TCAGATGATCCATTCTAATCTCGAG 57.844 40.000 5.93 5.93 0.00 4.04
2418 2514 6.152492 TCAGATGATCCATTCTAATCTCGAGG 59.848 42.308 13.56 0.00 0.00 4.63
2420 2516 4.483950 TGATCCATTCTAATCTCGAGGGT 58.516 43.478 13.56 3.16 0.00 4.34
2450 2551 0.675522 AACTGCCGATTAACACCGGG 60.676 55.000 6.32 0.00 45.42 5.73
2451 2552 1.219664 CTGCCGATTAACACCGGGA 59.780 57.895 6.32 9.80 45.42 5.14
2461 2562 3.625897 CACCGGGAGTGCCAGTCA 61.626 66.667 6.32 0.00 40.28 3.41
2537 2642 0.252742 TCCCTTCCTCCTCCTTCCAC 60.253 60.000 0.00 0.00 0.00 4.02
2538 2643 0.547712 CCCTTCCTCCTCCTTCCACA 60.548 60.000 0.00 0.00 0.00 4.17
2560 2665 1.402259 CACGGCGAGTTCTCTATGACT 59.598 52.381 16.62 0.00 0.00 3.41
2564 2669 3.478509 GGCGAGTTCTCTATGACTAGGA 58.521 50.000 0.00 0.00 0.00 2.94
2578 2683 8.540388 TCTATGACTAGGAAGCAAAATTACACT 58.460 33.333 0.00 0.00 0.00 3.55
2580 2685 5.637810 TGACTAGGAAGCAAAATTACACTCG 59.362 40.000 0.00 0.00 0.00 4.18
2587 2693 8.398665 AGGAAGCAAAATTACACTCGATATTTC 58.601 33.333 0.00 0.00 0.00 2.17
2588 2694 8.181573 GGAAGCAAAATTACACTCGATATTTCA 58.818 33.333 0.00 0.00 0.00 2.69
2658 2764 8.786826 TGGTAAATGAAATCTAGTAACTGGTG 57.213 34.615 0.00 0.00 0.00 4.17
2659 2765 8.598916 TGGTAAATGAAATCTAGTAACTGGTGA 58.401 33.333 0.00 0.00 0.00 4.02
2701 2810 8.251750 TCAAACTTATAACATGGAAGACTTCG 57.748 34.615 9.08 0.00 0.00 3.79
2715 2824 5.411669 GGAAGACTTCGGTAACAATGTGAAT 59.588 40.000 9.08 0.00 0.00 2.57
2746 2856 2.685380 CCCCCTCTCACGCTCCTT 60.685 66.667 0.00 0.00 0.00 3.36
2784 2894 7.047271 GGGGCAATATTGTTCATGTTGTTTAT 58.953 34.615 16.61 0.00 36.57 1.40
2801 2911 7.500892 TGTTGTTTATACATAATCCCAAGCGAT 59.499 33.333 0.00 0.00 33.44 4.58
2802 2912 8.995220 GTTGTTTATACATAATCCCAAGCGATA 58.005 33.333 0.00 0.00 33.44 2.92
2803 2913 9.733556 TTGTTTATACATAATCCCAAGCGATAT 57.266 29.630 0.00 0.00 33.44 1.63
2866 2985 6.929049 GGTTTTCGGAAAAATCCAGAAATCTT 59.071 34.615 16.83 0.00 36.77 2.40
2872 2991 5.363868 GGAAAAATCCAGAAATCTTAGGGGG 59.636 44.000 0.00 0.00 0.00 5.40
2964 3086 6.418946 AGGAAAGTTTGCCAAAACCATAAAA 58.581 32.000 3.17 0.00 45.75 1.52
2966 3088 7.559533 AGGAAAGTTTGCCAAAACCATAAAATT 59.440 29.630 3.17 0.00 45.75 1.82
2967 3089 7.860373 GGAAAGTTTGCCAAAACCATAAAATTC 59.140 33.333 0.00 0.00 45.75 2.17
2968 3090 7.872113 AAGTTTGCCAAAACCATAAAATTCA 57.128 28.000 0.00 0.00 45.75 2.57
2969 3091 7.495135 AGTTTGCCAAAACCATAAAATTCAG 57.505 32.000 0.00 0.00 45.75 3.02
2970 3092 6.486320 AGTTTGCCAAAACCATAAAATTCAGG 59.514 34.615 0.00 0.00 45.75 3.86
2999 3121 6.731467 TGGTATTTTTCTTTCTGCTCCCTAT 58.269 36.000 0.00 0.00 0.00 2.57
3009 3131 1.071642 GCTCCCTATCGGAAAGGCC 59.928 63.158 0.00 0.00 41.40 5.19
3049 3172 2.692041 CTGGAATTGAAAGCCCTGATCC 59.308 50.000 0.00 0.00 0.00 3.36
3082 3205 1.448985 TTTGCTCCTTCCGTGTATGC 58.551 50.000 0.00 0.00 0.00 3.14
3097 3220 7.860613 TCCGTGTATGCATTACAATTTCATAG 58.139 34.615 3.54 0.00 42.37 2.23
3101 3224 8.908678 GTGTATGCATTACAATTTCATAGCATG 58.091 33.333 3.54 0.00 42.37 4.06
3110 3233 7.534723 ACAATTTCATAGCATGCTCCATATT 57.465 32.000 26.57 15.07 0.00 1.28
3114 3237 8.874744 ATTTCATAGCATGCTCCATATTACTT 57.125 30.769 26.57 0.00 0.00 2.24
3132 3255 4.243007 ACTTGCTTTTACTGGAACATGC 57.757 40.909 0.00 0.00 38.20 4.06
3220 3351 7.951245 ACTTAAAAACTATGGGTGGTGGAAATA 59.049 33.333 0.00 0.00 0.00 1.40
3263 3402 4.322080 TTGAGCTCAACCATATACTCCG 57.678 45.455 25.16 0.00 0.00 4.63
3267 3406 5.773176 TGAGCTCAACCATATACTCCGAATA 59.227 40.000 15.67 0.00 0.00 1.75
3276 3415 5.163591 CCATATACTCCGAATATGCACCGTA 60.164 44.000 0.00 0.00 36.43 4.02
3310 3453 5.432885 ACGAACAAAAGTTGATACCTTGG 57.567 39.130 0.00 0.00 0.00 3.61
3338 3481 7.319646 TGAGCAAACACAAAAGTGAAGTAATT 58.680 30.769 2.22 0.00 0.00 1.40
3387 3530 6.071278 GGAACAGGTGACTCTTGTCTAACTAT 60.071 42.308 0.00 0.00 43.29 2.12
3390 3533 7.403671 ACAGGTGACTCTTGTCTAACTATCTA 58.596 38.462 0.00 0.00 43.29 1.98
3391 3534 7.554835 ACAGGTGACTCTTGTCTAACTATCTAG 59.445 40.741 0.00 0.00 43.29 2.43
3399 3542 6.434652 TCTTGTCTAACTATCTAGCTATGGGC 59.565 42.308 0.00 0.00 42.19 5.36
3489 3634 1.145803 GGTCGCGCCCTTATTATGAC 58.854 55.000 0.00 0.00 0.00 3.06
3494 3639 4.449743 GTCGCGCCCTTATTATGACAAATA 59.550 41.667 0.00 0.00 0.00 1.40
3586 3734 5.546526 GCTAACTAGCTAGCATGGAGAAAT 58.453 41.667 20.91 0.00 45.62 2.17
3692 3844 6.960468 ACTAGCTTTTGTTTCTAACTCAAGC 58.040 36.000 13.68 13.68 42.50 4.01
3837 4003 6.094603 ACTCCACTTGATTAATCTGTTGATGC 59.905 38.462 16.24 0.00 32.44 3.91
3838 4004 5.945191 TCCACTTGATTAATCTGTTGATGCA 59.055 36.000 16.24 0.00 32.44 3.96
3839 4005 6.604396 TCCACTTGATTAATCTGTTGATGCAT 59.396 34.615 16.24 0.00 32.44 3.96
3840 4006 6.695713 CCACTTGATTAATCTGTTGATGCATG 59.304 38.462 16.24 0.00 32.44 4.06
3854 4020 3.264193 TGATGCATGAGTAGTTTCCTGGT 59.736 43.478 2.46 0.00 0.00 4.00
3855 4021 4.469586 TGATGCATGAGTAGTTTCCTGGTA 59.530 41.667 2.46 0.00 0.00 3.25
3856 4022 4.471904 TGCATGAGTAGTTTCCTGGTAG 57.528 45.455 0.00 0.00 0.00 3.18
3857 4023 3.198872 GCATGAGTAGTTTCCTGGTAGC 58.801 50.000 0.00 0.00 0.00 3.58
3858 4024 3.448686 CATGAGTAGTTTCCTGGTAGCG 58.551 50.000 0.00 0.00 0.00 4.26
3942 4115 2.983136 TGCAAAATTCCAAACGCGTATG 59.017 40.909 14.46 3.89 0.00 2.39
4024 4202 1.524621 ATGCTCATGGCTGGTACGC 60.525 57.895 7.54 0.00 42.39 4.42
4198 4377 6.318900 CCCTATCTGAGTTTCATTGTTAACCC 59.681 42.308 2.48 0.00 0.00 4.11
4227 4406 2.126057 TGGATGTATGGATCAGGTGCA 58.874 47.619 0.00 0.00 0.00 4.57
4281 4460 2.764128 GACGAGGATGAGGGGCCA 60.764 66.667 4.39 0.00 0.00 5.36
4302 4481 2.031516 GATGATCATGGAGGCGGCG 61.032 63.158 14.30 0.51 0.00 6.46
4347 4526 0.548031 ATGACATGATGGGCTTCGGT 59.452 50.000 0.00 0.00 0.00 4.69
4350 4529 1.889105 CATGATGGGCTTCGGTCCG 60.889 63.158 4.39 4.39 44.02 4.79
4429 4608 8.474025 TCAAAATTGAACTCAAACAGGTATTGT 58.526 29.630 0.00 0.00 39.55 2.71
4473 4686 9.516314 AGAAAGTGAGTTTGCTACAAAATTTAC 57.484 29.630 0.00 0.00 0.00 2.01
4479 4692 9.593134 TGAGTTTGCTACAAAATTTACATGTTT 57.407 25.926 2.30 0.00 0.00 2.83
4496 4709 6.836242 ACATGTTTTTACCACCATCCAAAAT 58.164 32.000 0.00 0.00 0.00 1.82
4497 4710 6.934083 ACATGTTTTTACCACCATCCAAAATC 59.066 34.615 0.00 0.00 0.00 2.17
4503 4716 4.598036 ACCACCATCCAAAATCAGATCT 57.402 40.909 0.00 0.00 0.00 2.75
4505 4718 5.688807 ACCACCATCCAAAATCAGATCTAG 58.311 41.667 0.00 0.00 0.00 2.43
4506 4719 5.192522 ACCACCATCCAAAATCAGATCTAGT 59.807 40.000 0.00 0.00 0.00 2.57
4507 4720 6.386927 ACCACCATCCAAAATCAGATCTAGTA 59.613 38.462 0.00 0.00 0.00 1.82
4508 4721 6.708054 CCACCATCCAAAATCAGATCTAGTAC 59.292 42.308 0.00 0.00 0.00 2.73
4509 4722 7.419518 CCACCATCCAAAATCAGATCTAGTACT 60.420 40.741 0.00 0.00 0.00 2.73
4510 4723 7.655328 CACCATCCAAAATCAGATCTAGTACTC 59.345 40.741 0.00 0.00 0.00 2.59
4511 4724 7.158021 CCATCCAAAATCAGATCTAGTACTCC 58.842 42.308 0.00 0.00 0.00 3.85
4512 4725 6.732896 TCCAAAATCAGATCTAGTACTCCC 57.267 41.667 0.00 0.00 0.00 4.30
4513 4726 6.444704 TCCAAAATCAGATCTAGTACTCCCT 58.555 40.000 0.00 0.00 0.00 4.20
4514 4727 6.551601 TCCAAAATCAGATCTAGTACTCCCTC 59.448 42.308 0.00 0.00 0.00 4.30
4515 4728 6.553100 CCAAAATCAGATCTAGTACTCCCTCT 59.447 42.308 0.00 0.00 0.00 3.69
4516 4729 7.432869 CAAAATCAGATCTAGTACTCCCTCTG 58.567 42.308 16.65 16.65 33.16 3.35
4517 4730 5.922960 ATCAGATCTAGTACTCCCTCTGT 57.077 43.478 19.73 10.45 33.53 3.41
4518 4731 7.395525 AATCAGATCTAGTACTCCCTCTGTA 57.604 40.000 19.73 11.94 33.53 2.74
4519 4732 6.826632 TCAGATCTAGTACTCCCTCTGTAA 57.173 41.667 19.73 6.92 33.53 2.41
4520 4733 7.209340 TCAGATCTAGTACTCCCTCTGTAAA 57.791 40.000 19.73 6.43 33.53 2.01
4521 4734 7.284074 TCAGATCTAGTACTCCCTCTGTAAAG 58.716 42.308 19.73 3.06 33.53 1.85
4522 4735 7.127493 TCAGATCTAGTACTCCCTCTGTAAAGA 59.873 40.741 19.73 7.46 33.53 2.52
4523 4736 7.776030 CAGATCTAGTACTCCCTCTGTAAAGAA 59.224 40.741 15.36 0.00 0.00 2.52
4524 4737 8.337739 AGATCTAGTACTCCCTCTGTAAAGAAA 58.662 37.037 0.00 0.00 0.00 2.52
4525 4738 9.138596 GATCTAGTACTCCCTCTGTAAAGAAAT 57.861 37.037 0.00 0.00 0.00 2.17
4533 4746 9.397280 ACTCCCTCTGTAAAGAAATATAAAAGC 57.603 33.333 0.00 0.00 0.00 3.51
4534 4747 9.396022 CTCCCTCTGTAAAGAAATATAAAAGCA 57.604 33.333 0.00 0.00 0.00 3.91
4535 4748 9.920946 TCCCTCTGTAAAGAAATATAAAAGCAT 57.079 29.630 0.00 0.00 0.00 3.79
4651 4868 9.887406 ACTAAACTTTGGATACGTACAAAATTG 57.113 29.630 11.21 4.64 37.70 2.32
4703 4920 0.322816 TCAAGGGAAGATGCTGGCAC 60.323 55.000 0.00 0.00 0.00 5.01
4716 4933 2.224018 TGCTGGCACCAAATTTGTCTTC 60.224 45.455 16.73 4.97 0.00 2.87
4740 4957 9.906660 TTCAAAATACTTTCATGACATTACCAC 57.093 29.630 0.00 0.00 0.00 4.16
4742 4959 9.559958 CAAAATACTTTCATGACATTACCACTC 57.440 33.333 0.00 0.00 0.00 3.51
4758 4975 7.905604 TTACCACTCAAAATATCACTCACAG 57.094 36.000 0.00 0.00 0.00 3.66
4760 4977 6.169094 ACCACTCAAAATATCACTCACAGAG 58.831 40.000 0.00 0.00 35.52 3.35
4834 5096 8.765219 CCCTAAATCATATCAGTGTTAAACTCG 58.235 37.037 0.00 0.00 36.83 4.18
5089 5372 4.037208 AGCTGTTCTCCAACTTGTTGATTG 59.963 41.667 14.30 4.98 33.17 2.67
5090 5373 4.036734 GCTGTTCTCCAACTTGTTGATTGA 59.963 41.667 14.30 6.92 33.17 2.57
5091 5374 5.755813 CTGTTCTCCAACTTGTTGATTGAG 58.244 41.667 14.30 11.86 33.17 3.02
5092 5375 4.036734 TGTTCTCCAACTTGTTGATTGAGC 59.963 41.667 14.30 10.85 33.17 4.26
5093 5376 4.090761 TCTCCAACTTGTTGATTGAGCT 57.909 40.909 14.30 0.00 0.00 4.09
5094 5377 4.464008 TCTCCAACTTGTTGATTGAGCTT 58.536 39.130 14.30 0.00 0.00 3.74
5100 5383 5.368256 ACTTGTTGATTGAGCTTAGCTTG 57.632 39.130 8.58 0.00 39.88 4.01
5120 5403 2.223688 TGCACCAAAACTTGTTCCATCG 60.224 45.455 0.00 0.00 0.00 3.84
5155 5443 3.379372 GGTGTGCATGCTTCATACAATCT 59.621 43.478 20.33 0.00 0.00 2.40
5169 5457 7.186570 TCATACAATCTCATTCCTTGTCTGA 57.813 36.000 0.00 0.00 35.16 3.27
5174 5462 7.397221 ACAATCTCATTCCTTGTCTGATGTTA 58.603 34.615 0.00 0.00 0.00 2.41
5224 5512 5.826586 TCAATTGCACGATGTTTACTTTGT 58.173 33.333 0.00 0.00 0.00 2.83
5229 5517 5.403246 TGCACGATGTTTACTTTGTTTTGT 58.597 33.333 0.00 0.00 0.00 2.83
5232 5520 6.892430 GCACGATGTTTACTTTGTTTTGTTTC 59.108 34.615 0.00 0.00 0.00 2.78
5292 5586 1.327292 GCGTGGAATGCGTTTCGTTG 61.327 55.000 0.00 0.00 40.15 4.10
5295 5589 1.018148 TGGAATGCGTTTCGTTGTGT 58.982 45.000 0.00 0.00 34.98 3.72
5297 5591 2.159366 TGGAATGCGTTTCGTTGTGTTT 60.159 40.909 0.00 0.00 34.98 2.83
5449 5743 0.515564 CGTAAAAGGTGAGCCAACCG 59.484 55.000 0.00 0.00 45.53 4.44
5457 5751 2.037772 AGGTGAGCCAACCGATATCATC 59.962 50.000 3.12 0.00 45.53 2.92
5458 5752 2.224281 GGTGAGCCAACCGATATCATCA 60.224 50.000 3.12 0.00 34.09 3.07
5459 5753 3.557898 GGTGAGCCAACCGATATCATCAT 60.558 47.826 3.12 0.00 34.09 2.45
5462 5756 4.772100 TGAGCCAACCGATATCATCATCTA 59.228 41.667 3.12 0.00 0.00 1.98
5487 5784 0.370273 CAAGATTCGTTCGCTTCGGG 59.630 55.000 0.00 0.00 0.00 5.14
5488 5785 0.739813 AAGATTCGTTCGCTTCGGGG 60.740 55.000 0.00 0.00 0.00 5.73
5539 5836 2.988010 TCCATCAGTTAGAGCGCAAT 57.012 45.000 11.47 0.00 0.00 3.56
5551 5848 1.045350 AGCGCAATCTCTGGCCTCTA 61.045 55.000 11.47 0.00 0.00 2.43
5566 5868 6.014242 TCTGGCCTCTACCATATAATGTTCTG 60.014 42.308 3.32 0.00 39.54 3.02
5611 5927 3.104512 TGTATGTGCAGGTAGCTAGGTT 58.895 45.455 0.00 0.00 45.94 3.50
5659 5977 6.802348 GCATATATATACCTGACGCCTAATCG 59.198 42.308 0.00 0.00 0.00 3.34
5681 5999 1.611977 ACGAAAGATCTCGGTGACACA 59.388 47.619 8.08 0.00 43.22 3.72
5682 6000 1.986378 CGAAAGATCTCGGTGACACAC 59.014 52.381 8.08 0.00 35.14 3.82
5713 6031 9.566432 AGAGAGAGAGAGAAATAAGAAGATCTC 57.434 37.037 0.00 0.00 38.84 2.75
5902 6221 7.687941 ACATACGTCTCCAAAAATTCATTCT 57.312 32.000 0.00 0.00 0.00 2.40
5911 6230 8.366401 TCTCCAAAAATTCATTCTTGTGCATAA 58.634 29.630 0.00 0.00 0.00 1.90
5926 6247 8.720562 TCTTGTGCATAAATGTATATTGATCGG 58.279 33.333 0.00 0.00 0.00 4.18
5933 6254 6.500684 AAATGTATATTGATCGGTCCATGC 57.499 37.500 0.00 0.00 0.00 4.06
5960 6281 0.806102 CGGCGTCTCGAATGACCAAT 60.806 55.000 0.00 0.00 33.70 3.16
6053 6377 6.500684 TCAACTTTCAAAGGATGCTACATC 57.499 37.500 1.31 0.00 0.00 3.06
6055 6379 7.394016 TCAACTTTCAAAGGATGCTACATCTA 58.606 34.615 1.31 0.00 0.00 1.98
6056 6380 7.334421 TCAACTTTCAAAGGATGCTACATCTAC 59.666 37.037 1.31 0.00 0.00 2.59
6114 6439 1.134401 TGATGCAGGAACGGAATCTCC 60.134 52.381 0.00 0.00 0.00 3.71
6120 6445 0.744771 GGAACGGAATCTCCAGTGCC 60.745 60.000 0.00 0.00 35.91 5.01
6236 6564 0.035458 AGTCCCAGACTTTTCCAGCG 59.965 55.000 0.00 0.00 40.28 5.18
6237 6565 0.250338 GTCCCAGACTTTTCCAGCGT 60.250 55.000 0.00 0.00 0.00 5.07
6238 6566 1.001633 GTCCCAGACTTTTCCAGCGTA 59.998 52.381 0.00 0.00 0.00 4.42
6239 6567 1.906574 TCCCAGACTTTTCCAGCGTAT 59.093 47.619 0.00 0.00 0.00 3.06
6240 6568 3.101437 TCCCAGACTTTTCCAGCGTATA 58.899 45.455 0.00 0.00 0.00 1.47
6241 6569 3.516300 TCCCAGACTTTTCCAGCGTATAA 59.484 43.478 0.00 0.00 0.00 0.98
6242 6570 4.020039 TCCCAGACTTTTCCAGCGTATAAA 60.020 41.667 0.00 0.00 0.00 1.40
6243 6571 4.332819 CCCAGACTTTTCCAGCGTATAAAG 59.667 45.833 0.00 0.00 34.58 1.85
6244 6572 5.175859 CCAGACTTTTCCAGCGTATAAAGA 58.824 41.667 10.11 0.00 33.12 2.52
6245 6573 5.642063 CCAGACTTTTCCAGCGTATAAAGAA 59.358 40.000 10.11 0.00 33.12 2.52
6246 6574 6.183360 CCAGACTTTTCCAGCGTATAAAGAAG 60.183 42.308 10.11 0.00 33.12 2.85
6247 6575 5.351740 AGACTTTTCCAGCGTATAAAGAAGC 59.648 40.000 10.11 0.00 33.12 3.86
6248 6576 4.395231 ACTTTTCCAGCGTATAAAGAAGCC 59.605 41.667 10.11 0.00 33.12 4.35
6249 6577 3.906720 TTCCAGCGTATAAAGAAGCCT 57.093 42.857 0.00 0.00 0.00 4.58
6250 6578 3.906720 TCCAGCGTATAAAGAAGCCTT 57.093 42.857 0.00 0.00 0.00 4.35
6251 6579 3.793559 TCCAGCGTATAAAGAAGCCTTC 58.206 45.455 0.00 0.00 0.00 3.46
6252 6580 3.451178 TCCAGCGTATAAAGAAGCCTTCT 59.549 43.478 0.00 0.00 43.15 2.85
6253 6581 4.647853 TCCAGCGTATAAAGAAGCCTTCTA 59.352 41.667 7.53 0.00 39.61 2.10
6254 6582 5.128171 TCCAGCGTATAAAGAAGCCTTCTAA 59.872 40.000 7.53 0.00 39.61 2.10
6255 6583 5.463724 CCAGCGTATAAAGAAGCCTTCTAAG 59.536 44.000 7.53 0.00 39.61 2.18
6281 6649 8.364894 GGTCTCAACCACATACACACATATATA 58.635 37.037 0.00 0.00 45.68 0.86
6311 6679 6.408035 CATCCTCATCATCTAAGCAGCTATT 58.592 40.000 0.00 0.00 0.00 1.73
6316 6684 3.470709 TCATCTAAGCAGCTATTGTGCC 58.529 45.455 0.00 0.00 42.24 5.01
6358 6726 0.324943 GGCCTTACTGGTGCAAGAGA 59.675 55.000 0.00 0.00 38.35 3.10
6370 6738 3.520569 GTGCAAGAGACAAAAGCCAAAA 58.479 40.909 0.00 0.00 0.00 2.44
6398 6766 4.532834 GGTCAAATATCAGGGTAAAGCCA 58.467 43.478 0.36 0.00 39.65 4.75
6413 6781 0.107017 AGCCAAGTTCACACACAGCT 60.107 50.000 0.00 0.00 0.00 4.24
6420 6788 2.017049 GTTCACACACAGCTTTCAGGT 58.983 47.619 0.00 0.00 0.00 4.00
6423 6791 2.016318 CACACACAGCTTTCAGGTTCA 58.984 47.619 0.00 0.00 0.00 3.18
6430 6798 3.385755 ACAGCTTTCAGGTTCAAATTGCT 59.614 39.130 0.00 0.00 0.00 3.91
6435 6803 1.879380 TCAGGTTCAAATTGCTGACCG 59.121 47.619 7.14 4.24 0.00 4.79
6460 6828 7.217070 CGCATACTAGAAACAAGCAAAAATCTC 59.783 37.037 0.00 0.00 0.00 2.75
6465 6833 4.651045 AGAAACAAGCAAAAATCTCCACCT 59.349 37.500 0.00 0.00 0.00 4.00
6467 6835 5.712152 AACAAGCAAAAATCTCCACCTAG 57.288 39.130 0.00 0.00 0.00 3.02
6470 6838 6.012745 ACAAGCAAAAATCTCCACCTAGAAT 58.987 36.000 0.00 0.00 0.00 2.40
6471 6839 6.071728 ACAAGCAAAAATCTCCACCTAGAATG 60.072 38.462 0.00 0.00 0.00 2.67
6472 6840 5.819991 AGCAAAAATCTCCACCTAGAATGA 58.180 37.500 0.00 0.00 0.00 2.57
6478 6846 5.543507 ATCTCCACCTAGAATGACATCAC 57.456 43.478 0.00 0.00 0.00 3.06
6481 6849 3.843619 TCCACCTAGAATGACATCACCAA 59.156 43.478 0.00 0.00 0.00 3.67
6490 6859 7.578310 AGAATGACATCACCAAATTAGATGG 57.422 36.000 0.00 4.59 42.55 3.51
6546 6915 4.574421 CACACCACCGCTCATATTTATTCA 59.426 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 1.143073 GAGAACCCACACCCAAGAACT 59.857 52.381 0.00 0.00 0.00 3.01
87 88 1.605753 GAGAACCCACACCCAAGAAC 58.394 55.000 0.00 0.00 0.00 3.01
90 91 4.821935 GGAGAACCCACACCCAAG 57.178 61.111 0.00 0.00 34.14 3.61
119 120 1.340405 CCATTGTGGTCTCTCCCTTGG 60.340 57.143 0.00 0.00 34.77 3.61
225 232 1.483827 GTAGGGGAAAAGGTAGGGTCG 59.516 57.143 0.00 0.00 0.00 4.79
251 258 5.535406 GGGTTTAAGGTATGAGAGAGATCGA 59.465 44.000 0.00 0.00 0.00 3.59
252 259 5.279056 GGGGTTTAAGGTATGAGAGAGATCG 60.279 48.000 0.00 0.00 0.00 3.69
253 260 5.602978 TGGGGTTTAAGGTATGAGAGAGATC 59.397 44.000 0.00 0.00 0.00 2.75
254 261 5.538877 TGGGGTTTAAGGTATGAGAGAGAT 58.461 41.667 0.00 0.00 0.00 2.75
662 669 1.435959 ACCAAGTACTGTACCCCTCCT 59.564 52.381 14.05 0.00 0.00 3.69
663 670 1.948391 ACCAAGTACTGTACCCCTCC 58.052 55.000 14.05 0.00 0.00 4.30
664 671 2.901839 TCAACCAAGTACTGTACCCCTC 59.098 50.000 14.05 0.00 0.00 4.30
665 672 2.904434 CTCAACCAAGTACTGTACCCCT 59.096 50.000 14.05 0.00 0.00 4.79
696 704 0.039165 GCAAAAGAAAGTGAGCCGGG 60.039 55.000 2.18 0.00 0.00 5.73
698 706 0.385974 CCGCAAAAGAAAGTGAGCCG 60.386 55.000 0.00 0.00 0.00 5.52
889 903 1.610522 GTGGCGTCGGGTATGTATAGT 59.389 52.381 0.00 0.00 0.00 2.12
925 939 1.063038 TCTTGGGCCGGTAGGTGTATA 60.063 52.381 1.90 0.00 40.50 1.47
962 976 0.894184 TTCGCCGGCTAGATAGAGGG 60.894 60.000 26.68 4.37 0.00 4.30
1354 1372 5.163332 GGAAAGAAGTGGTATGTAGGGTAGG 60.163 48.000 0.00 0.00 0.00 3.18
1360 1378 3.195661 GGCGGAAAGAAGTGGTATGTAG 58.804 50.000 0.00 0.00 0.00 2.74
1364 1382 2.643551 CATGGCGGAAAGAAGTGGTAT 58.356 47.619 0.00 0.00 0.00 2.73
1404 1426 1.759293 CGCACGCACATGAGGATGAG 61.759 60.000 0.00 0.00 33.36 2.90
1723 1786 0.609662 ATTGCACCAAAGCATGACCC 59.390 50.000 0.00 0.00 45.19 4.46
1775 1839 9.639601 TGAGACATGACAACAACTAAATACTAG 57.360 33.333 0.00 0.00 0.00 2.57
1782 1846 6.119536 ACCTTTGAGACATGACAACAACTAA 58.880 36.000 0.00 0.00 0.00 2.24
1974 2066 1.559682 TCCCTCACCTGCAACCTTATC 59.440 52.381 0.00 0.00 0.00 1.75
2030 2124 2.044832 CTCCGTCGTACTAGGGCACG 62.045 65.000 1.36 7.29 39.48 5.34
2031 2125 1.722636 CCTCCGTCGTACTAGGGCAC 61.723 65.000 1.36 0.00 0.00 5.01
2032 2126 1.452651 CCTCCGTCGTACTAGGGCA 60.453 63.158 1.36 0.00 0.00 5.36
2033 2127 2.843352 GCCTCCGTCGTACTAGGGC 61.843 68.421 1.36 0.00 0.00 5.19
2098 2193 4.763793 TGCTCAAAGAAGAGGAATTTGGAG 59.236 41.667 0.00 0.00 36.15 3.86
2139 2235 0.099436 CAAGGCTTGCGGCAATCTAC 59.901 55.000 16.80 6.89 44.01 2.59
2144 2240 1.954362 AAACACAAGGCTTGCGGCAA 61.954 50.000 26.45 15.55 44.01 4.52
2147 2243 0.240945 CCTAAACACAAGGCTTGCGG 59.759 55.000 26.45 20.40 0.00 5.69
2190 2286 0.969149 TCATGCTTCAGTGACGTCCT 59.031 50.000 14.12 6.92 0.00 3.85
2195 2291 2.995939 TCGAACATCATGCTTCAGTGAC 59.004 45.455 0.00 0.00 0.00 3.67
2237 2333 2.363925 AGGGCTACGGGTGACTCC 60.364 66.667 0.00 0.00 0.00 3.85
2283 2379 0.762082 TGCAAAAATGGGGAGGTGCA 60.762 50.000 0.00 0.00 39.53 4.57
2294 2390 1.202952 TGGTAGACGGGGTGCAAAAAT 60.203 47.619 0.00 0.00 0.00 1.82
2298 2394 1.195442 TGATGGTAGACGGGGTGCAA 61.195 55.000 0.00 0.00 0.00 4.08
2318 2414 1.839994 TGAGGCATAAGAGGTTGGGAG 59.160 52.381 0.00 0.00 0.00 4.30
2319 2415 1.965414 TGAGGCATAAGAGGTTGGGA 58.035 50.000 0.00 0.00 0.00 4.37
2376 2472 1.689273 CTGATCGGGGTTAGGAGAAGG 59.311 57.143 0.00 0.00 0.00 3.46
2380 2476 2.598565 TCATCTGATCGGGGTTAGGAG 58.401 52.381 0.62 0.00 0.00 3.69
2418 2514 0.179065 GGCAGTTGGACGGGTATACC 60.179 60.000 13.99 13.99 0.00 2.73
2435 2536 1.087771 CACTCCCGGTGTTAATCGGC 61.088 60.000 0.00 0.00 44.45 5.54
2461 2562 0.541863 GACGGGGGATCTTGATGTGT 59.458 55.000 0.00 0.00 0.00 3.72
2465 2566 0.326618 AGTGGACGGGGGATCTTGAT 60.327 55.000 0.00 0.00 0.00 2.57
2537 2642 0.456221 ATAGAGAACTCGCCGTGGTG 59.544 55.000 0.00 0.00 34.09 4.17
2538 2643 0.456221 CATAGAGAACTCGCCGTGGT 59.544 55.000 0.00 0.00 34.09 4.16
2560 2665 8.958119 AATATCGAGTGTAATTTTGCTTCCTA 57.042 30.769 0.00 0.00 0.00 2.94
2587 2693 6.194967 ACCCCTTGGTTTTCCTCTTATAATG 58.805 40.000 0.00 0.00 44.75 1.90
2588 2694 6.417503 ACCCCTTGGTTTTCCTCTTATAAT 57.582 37.500 0.00 0.00 44.75 1.28
2600 2706 7.269514 CTGAGATACAGTGACCCCTTGGTTT 62.270 48.000 0.00 0.00 42.47 3.27
2701 2810 7.095649 GCCAAGAGAAAAATTCACATTGTTACC 60.096 37.037 0.00 0.00 0.00 2.85
2715 2824 0.560688 AGGGGGTGCCAAGAGAAAAA 59.439 50.000 0.00 0.00 0.00 1.94
2746 2856 2.047769 TTGCCCCTTCTTACCTACCA 57.952 50.000 0.00 0.00 0.00 3.25
2847 2965 5.067805 CCCCTAAGATTTCTGGATTTTTCCG 59.932 44.000 0.00 0.00 0.00 4.30
2848 2966 5.363868 CCCCCTAAGATTTCTGGATTTTTCC 59.636 44.000 0.00 0.00 0.00 3.13
2872 2991 2.195389 GGGTGAAAATAACCGCCCC 58.805 57.895 0.00 0.00 45.12 5.80
2964 3086 4.677182 AGAAAAATACCAGCCACCTGAAT 58.323 39.130 0.00 0.00 41.77 2.57
2966 3088 3.806949 AGAAAAATACCAGCCACCTGA 57.193 42.857 0.00 0.00 41.77 3.86
2967 3089 4.524328 AGAAAGAAAAATACCAGCCACCTG 59.476 41.667 0.00 0.00 38.85 4.00
2968 3090 4.524328 CAGAAAGAAAAATACCAGCCACCT 59.476 41.667 0.00 0.00 0.00 4.00
2969 3091 4.809673 CAGAAAGAAAAATACCAGCCACC 58.190 43.478 0.00 0.00 0.00 4.61
2970 3092 4.021981 AGCAGAAAGAAAAATACCAGCCAC 60.022 41.667 0.00 0.00 0.00 5.01
2999 3121 4.813346 GGAAACAGGCCTTTCCGA 57.187 55.556 18.44 0.00 39.86 4.55
3009 3131 4.517453 TCCAGTTGGAAAATACGGAAACAG 59.483 41.667 0.00 0.00 42.18 3.16
3035 3158 0.332632 CCTTGGGATCAGGGCTTTCA 59.667 55.000 0.00 0.00 33.27 2.69
3049 3172 0.906282 AGCAAAATGGAGGGCCTTGG 60.906 55.000 7.89 0.00 34.31 3.61
3082 3205 6.741109 TGGAGCATGCTATGAAATTGTAATG 58.259 36.000 22.74 0.00 0.00 1.90
3097 3220 4.843220 AAGCAAGTAATATGGAGCATGC 57.157 40.909 10.51 10.51 0.00 4.06
3101 3224 6.542370 TCCAGTAAAAGCAAGTAATATGGAGC 59.458 38.462 0.00 0.00 0.00 4.70
3110 3233 4.824537 TGCATGTTCCAGTAAAAGCAAGTA 59.175 37.500 0.00 0.00 0.00 2.24
3114 3237 3.221771 ACTGCATGTTCCAGTAAAAGCA 58.778 40.909 2.97 0.00 41.47 3.91
3135 3258 7.602644 CCTTGTAAGCTGAATACACAGTTTCTA 59.397 37.037 0.00 0.00 40.58 2.10
3220 3351 1.192428 GGGTGGGAGAGTGAACGTAT 58.808 55.000 0.00 0.00 0.00 3.06
3263 3402 6.159293 TGAGATTGAGATACGGTGCATATTC 58.841 40.000 0.00 0.00 0.00 1.75
3267 3406 4.122776 GTTGAGATTGAGATACGGTGCAT 58.877 43.478 0.00 0.00 0.00 3.96
3276 3415 6.867662 ACTTTTGTTCGTTGAGATTGAGAT 57.132 33.333 0.00 0.00 0.00 2.75
3344 3487 5.304778 TGTTCCATCGACAATCTTTTGAGA 58.695 37.500 0.00 0.00 36.64 3.27
3354 3497 1.691976 AGTCACCTGTTCCATCGACAA 59.308 47.619 0.00 0.00 0.00 3.18
3387 3530 7.695554 ATACTCAAGTAAGAGCCCATAGCTAGA 60.696 40.741 0.00 0.00 42.64 2.43
3390 3533 5.151454 ATACTCAAGTAAGAGCCCATAGCT 58.849 41.667 0.00 0.00 44.24 3.32
3391 3534 3.828875 ACTCAAGTAAGAGCCCATAGC 57.171 47.619 0.00 0.00 39.26 2.97
3399 3542 7.950512 AGGATCATGTGATACTCAAGTAAGAG 58.049 38.462 1.80 0.00 41.82 2.85
3456 3601 1.520787 CGACCACGAAGGGTATGGC 60.521 63.158 0.00 0.00 42.53 4.40
3489 3634 5.341872 TTGAAGGGCAATCCACATATTTG 57.658 39.130 0.00 0.00 38.24 2.32
3494 3639 7.510001 TGAATATAATTGAAGGGCAATCCACAT 59.490 33.333 0.00 0.00 46.25 3.21
3586 3734 2.849942 ACAGCCATTTCAGCGCATATA 58.150 42.857 11.47 0.00 34.64 0.86
3662 3810 9.911138 GAGTTAGAAACAAAAGCTAGTAGTAGT 57.089 33.333 6.47 0.00 0.00 2.73
3666 3814 8.224437 GCTTGAGTTAGAAACAAAAGCTAGTAG 58.776 37.037 16.10 0.00 43.23 2.57
3672 3820 4.740205 GTGGCTTGAGTTAGAAACAAAAGC 59.260 41.667 15.50 15.50 44.56 3.51
3673 3821 4.970003 CGTGGCTTGAGTTAGAAACAAAAG 59.030 41.667 0.00 0.00 32.45 2.27
3692 3844 2.192861 TGGCAAAACCTGAGCGTGG 61.193 57.895 0.00 0.00 40.22 4.94
3801 3967 8.589701 TTAATCAAGTGGAGTAGAGACACATA 57.410 34.615 0.00 0.00 37.58 2.29
3837 4003 3.119101 ACGCTACCAGGAAACTACTCATG 60.119 47.826 0.00 0.00 40.21 3.07
3838 4004 3.097614 ACGCTACCAGGAAACTACTCAT 58.902 45.455 0.00 0.00 40.21 2.90
3839 4005 2.522185 ACGCTACCAGGAAACTACTCA 58.478 47.619 0.00 0.00 40.21 3.41
3840 4006 3.589495 AACGCTACCAGGAAACTACTC 57.411 47.619 0.00 0.00 40.21 2.59
3864 4037 2.481449 GCGCTAGAAAGATCGAGGGAAA 60.481 50.000 0.00 0.00 41.68 3.13
3866 4039 0.669077 GCGCTAGAAAGATCGAGGGA 59.331 55.000 0.00 0.00 41.68 4.20
3868 4041 1.066303 ACAGCGCTAGAAAGATCGAGG 59.934 52.381 10.99 0.00 0.00 4.63
3878 4051 0.926155 CGACGTACTACAGCGCTAGA 59.074 55.000 10.99 0.00 0.00 2.43
3942 4115 2.610833 TGCTGATTTGACGCATGATCTC 59.389 45.455 0.00 0.00 0.00 2.75
4024 4202 4.245660 TGAACCGAATCAAGCTAGACAAG 58.754 43.478 0.00 0.00 0.00 3.16
4198 4377 2.934887 TCCATACATCCACATGGCAAG 58.065 47.619 0.00 0.00 41.33 4.01
4227 4406 1.614241 CCGTCCCTTCCTCCAACGAT 61.614 60.000 0.00 0.00 35.45 3.73
4281 4460 1.368950 CGCCTCCATGATCATCGGT 59.631 57.895 18.08 0.00 0.00 4.69
4302 4481 0.528017 TCGAGCTCATATCCATCGGC 59.472 55.000 15.40 0.00 34.29 5.54
4305 4484 4.180057 GTCCATTCGAGCTCATATCCATC 58.820 47.826 15.40 0.00 0.00 3.51
4437 4616 7.445945 AGCAAACTCACTTTCTAGAACATACT 58.554 34.615 4.18 0.00 0.00 2.12
4438 4617 7.659652 AGCAAACTCACTTTCTAGAACATAC 57.340 36.000 4.18 0.00 0.00 2.39
4444 4623 8.677148 ATTTTGTAGCAAACTCACTTTCTAGA 57.323 30.769 0.00 0.00 0.00 2.43
4452 4631 8.574196 ACATGTAAATTTTGTAGCAAACTCAC 57.426 30.769 0.00 0.00 0.00 3.51
4473 4686 6.933521 TGATTTTGGATGGTGGTAAAAACATG 59.066 34.615 0.00 0.00 0.00 3.21
4479 4692 6.493166 AGATCTGATTTTGGATGGTGGTAAA 58.507 36.000 0.00 0.00 0.00 2.01
4488 4701 7.079048 AGGGAGTACTAGATCTGATTTTGGAT 58.921 38.462 5.18 0.00 0.00 3.41
4496 4709 6.826632 TTACAGAGGGAGTACTAGATCTGA 57.173 41.667 25.82 13.64 38.02 3.27
4497 4710 7.284074 TCTTTACAGAGGGAGTACTAGATCTG 58.716 42.308 20.83 20.83 39.96 2.90
4507 4720 9.397280 GCTTTTATATTTCTTTACAGAGGGAGT 57.603 33.333 0.00 0.00 0.00 3.85
4508 4721 9.396022 TGCTTTTATATTTCTTTACAGAGGGAG 57.604 33.333 0.00 0.00 0.00 4.30
4509 4722 9.920946 ATGCTTTTATATTTCTTTACAGAGGGA 57.079 29.630 0.00 0.00 0.00 4.20
4562 4775 9.976511 CTCCATCCGTAAACAAATATAAGAGTA 57.023 33.333 0.00 0.00 0.00 2.59
4563 4776 8.483758 ACTCCATCCGTAAACAAATATAAGAGT 58.516 33.333 0.00 0.00 0.00 3.24
4564 4777 8.888579 ACTCCATCCGTAAACAAATATAAGAG 57.111 34.615 0.00 0.00 0.00 2.85
4568 4781 9.701098 GACATACTCCATCCGTAAACAAATATA 57.299 33.333 0.00 0.00 0.00 0.86
4569 4782 8.429641 AGACATACTCCATCCGTAAACAAATAT 58.570 33.333 0.00 0.00 0.00 1.28
4570 4783 7.788026 AGACATACTCCATCCGTAAACAAATA 58.212 34.615 0.00 0.00 0.00 1.40
4571 4784 6.650120 AGACATACTCCATCCGTAAACAAAT 58.350 36.000 0.00 0.00 0.00 2.32
4572 4785 6.045072 AGACATACTCCATCCGTAAACAAA 57.955 37.500 0.00 0.00 0.00 2.83
4573 4786 5.670792 AGACATACTCCATCCGTAAACAA 57.329 39.130 0.00 0.00 0.00 2.83
4574 4787 5.670792 AAGACATACTCCATCCGTAAACA 57.329 39.130 0.00 0.00 0.00 2.83
4575 4788 6.803642 ACTAAGACATACTCCATCCGTAAAC 58.196 40.000 0.00 0.00 0.00 2.01
4576 4789 7.994911 TCTACTAAGACATACTCCATCCGTAAA 59.005 37.037 0.00 0.00 0.00 2.01
4577 4790 7.512130 TCTACTAAGACATACTCCATCCGTAA 58.488 38.462 0.00 0.00 0.00 3.18
4578 4791 7.071069 TCTACTAAGACATACTCCATCCGTA 57.929 40.000 0.00 0.00 0.00 4.02
4579 4792 5.938279 TCTACTAAGACATACTCCATCCGT 58.062 41.667 0.00 0.00 0.00 4.69
4580 4793 6.879276 TTCTACTAAGACATACTCCATCCG 57.121 41.667 0.00 0.00 0.00 4.18
4581 4794 9.298250 TGTATTCTACTAAGACATACTCCATCC 57.702 37.037 0.00 0.00 32.60 3.51
4584 4797 8.577296 GCATGTATTCTACTAAGACATACTCCA 58.423 37.037 0.00 0.00 32.60 3.86
4585 4798 8.577296 TGCATGTATTCTACTAAGACATACTCC 58.423 37.037 0.00 0.00 32.60 3.85
4586 4799 9.967346 TTGCATGTATTCTACTAAGACATACTC 57.033 33.333 0.00 0.00 32.60 2.59
4630 4843 7.650104 CCAAACAATTTTGTACGTATCCAAAGT 59.350 33.333 10.21 6.26 41.31 2.66
4631 4844 7.863375 TCCAAACAATTTTGTACGTATCCAAAG 59.137 33.333 10.21 4.15 41.31 2.77
4640 4857 5.986135 TGGGAAATCCAAACAATTTTGTACG 59.014 36.000 1.22 0.00 43.84 3.67
4682 4899 0.750911 GCCAGCATCTTCCCTTGAGG 60.751 60.000 0.00 0.00 0.00 3.86
4696 4913 2.224018 TGAAGACAAATTTGGTGCCAGC 60.224 45.455 21.74 5.61 0.00 4.85
4716 4933 9.559958 GAGTGGTAATGTCATGAAAGTATTTTG 57.440 33.333 0.00 0.00 39.27 2.44
4730 4947 8.391106 GTGAGTGATATTTTGAGTGGTAATGTC 58.609 37.037 0.00 0.00 0.00 3.06
4732 4949 8.267620 TGTGAGTGATATTTTGAGTGGTAATG 57.732 34.615 0.00 0.00 0.00 1.90
4740 4957 9.761504 ATATGACTCTGTGAGTGATATTTTGAG 57.238 33.333 11.84 0.00 43.29 3.02
4750 4967 7.918033 CCTTACTGTTATATGACTCTGTGAGTG 59.082 40.741 4.85 0.00 43.53 3.51
4758 4975 9.614792 ATTTTCACCCTTACTGTTATATGACTC 57.385 33.333 0.00 0.00 0.00 3.36
4793 5013 8.608185 ATGATTTAGGGTTTGATATGGTGTTT 57.392 30.769 0.00 0.00 0.00 2.83
4794 5014 9.881773 ATATGATTTAGGGTTTGATATGGTGTT 57.118 29.630 0.00 0.00 0.00 3.32
4808 5028 8.765219 CGAGTTTAACACTGATATGATTTAGGG 58.235 37.037 0.00 0.00 35.01 3.53
4831 5093 0.234884 GAAACCCTGCAACGAACGAG 59.765 55.000 0.14 0.00 0.00 4.18
4834 5096 1.404035 ACTTGAAACCCTGCAACGAAC 59.596 47.619 0.00 0.00 0.00 3.95
4837 5099 1.021202 TGACTTGAAACCCTGCAACG 58.979 50.000 0.00 0.00 0.00 4.10
5051 5334 0.952280 CAGCTAAGGATGCATGGCAG 59.048 55.000 2.46 0.00 43.65 4.85
5089 5372 2.294512 AGTTTTGGTGCAAGCTAAGCTC 59.705 45.455 11.76 8.28 36.09 4.09
5090 5373 2.310538 AGTTTTGGTGCAAGCTAAGCT 58.689 42.857 11.76 0.00 42.56 3.74
5091 5374 2.796593 CAAGTTTTGGTGCAAGCTAAGC 59.203 45.455 4.23 4.23 29.69 3.09
5092 5375 4.045636 ACAAGTTTTGGTGCAAGCTAAG 57.954 40.909 0.00 0.00 29.69 2.18
5093 5376 4.429108 GAACAAGTTTTGGTGCAAGCTAA 58.571 39.130 0.00 0.00 33.76 3.09
5094 5377 3.181480 GGAACAAGTTTTGGTGCAAGCTA 60.181 43.478 0.00 0.00 38.71 3.32
5120 5403 1.582968 CACACCATGCAAGCTGTCC 59.417 57.895 0.00 0.00 0.00 4.02
5155 5443 6.115446 GGACATAACATCAGACAAGGAATGA 58.885 40.000 0.00 0.00 0.00 2.57
5229 5517 9.171877 TCATGCACATATACACAACATTAGAAA 57.828 29.630 0.00 0.00 0.00 2.52
5232 5520 8.146479 ACTCATGCACATATACACAACATTAG 57.854 34.615 0.00 0.00 0.00 1.73
5288 5582 3.302221 CGTCTTCCTGTACAAACACAACG 60.302 47.826 0.00 0.00 0.00 4.10
5292 5586 5.347907 CCTTATCGTCTTCCTGTACAAACAC 59.652 44.000 0.00 0.00 0.00 3.32
5295 5589 4.501071 GCCTTATCGTCTTCCTGTACAAA 58.499 43.478 0.00 0.00 0.00 2.83
5297 5591 2.429610 GGCCTTATCGTCTTCCTGTACA 59.570 50.000 0.00 0.00 0.00 2.90
5457 5751 7.182761 AGCGAACGAATCTTGATTTTTAGATG 58.817 34.615 0.00 0.00 31.70 2.90
5458 5752 7.308782 AGCGAACGAATCTTGATTTTTAGAT 57.691 32.000 0.00 0.00 32.62 1.98
5459 5753 6.721571 AGCGAACGAATCTTGATTTTTAGA 57.278 33.333 0.00 0.00 0.00 2.10
5462 5756 4.846137 CGAAGCGAACGAATCTTGATTTTT 59.154 37.500 0.00 0.00 0.00 1.94
5487 5784 5.582269 TGAGTTGATTGAGAAATCATCGACC 59.418 40.000 2.22 0.00 38.79 4.79
5488 5785 6.653273 TGAGTTGATTGAGAAATCATCGAC 57.347 37.500 2.22 0.00 38.79 4.20
5539 5836 5.655394 ACATTATATGGTAGAGGCCAGAGA 58.345 41.667 5.01 0.00 42.47 3.10
5566 5868 8.495148 ACATATCAAAGCCAAAAACGAAAAATC 58.505 29.630 0.00 0.00 0.00 2.17
5611 5927 5.698089 GCATGTATATACTTTGCAGCTCTGA 59.302 40.000 24.40 1.37 36.62 3.27
5659 5977 0.992802 GTCACCGAGATCTTTCGTGC 59.007 55.000 0.00 0.00 38.88 5.34
5681 5999 6.945435 TCTTATTTCTCTCTCTCTCTGTGTGT 59.055 38.462 0.00 0.00 0.00 3.72
5682 6000 7.389803 TCTTATTTCTCTCTCTCTCTGTGTG 57.610 40.000 0.00 0.00 0.00 3.82
5688 6006 8.499162 CGAGATCTTCTTATTTCTCTCTCTCTC 58.501 40.741 0.00 0.00 33.92 3.20
5692 6010 9.612620 GAATCGAGATCTTCTTATTTCTCTCTC 57.387 37.037 0.00 0.00 33.92 3.20
5694 6012 9.743057 TTGAATCGAGATCTTCTTATTTCTCTC 57.257 33.333 0.00 0.00 33.92 3.20
5841 6160 7.545615 ACAACAGAAAAACCACAAGAAGATTTC 59.454 33.333 0.00 0.00 0.00 2.17
5842 6161 7.331687 CACAACAGAAAAACCACAAGAAGATTT 59.668 33.333 0.00 0.00 0.00 2.17
5843 6162 6.813152 CACAACAGAAAAACCACAAGAAGATT 59.187 34.615 0.00 0.00 0.00 2.40
5844 6163 6.332630 CACAACAGAAAAACCACAAGAAGAT 58.667 36.000 0.00 0.00 0.00 2.40
5845 6164 5.336372 CCACAACAGAAAAACCACAAGAAGA 60.336 40.000 0.00 0.00 0.00 2.87
5846 6165 4.864247 CCACAACAGAAAAACCACAAGAAG 59.136 41.667 0.00 0.00 0.00 2.85
5861 6180 1.942677 TGTACGTTCACCCACAACAG 58.057 50.000 0.00 0.00 0.00 3.16
5886 6205 8.537049 TTATGCACAAGAATGAATTTTTGGAG 57.463 30.769 10.11 4.72 36.51 3.86
5902 6221 8.389779 ACCGATCAATATACATTTATGCACAA 57.610 30.769 0.00 0.00 0.00 3.33
5911 6230 4.943705 GGCATGGACCGATCAATATACATT 59.056 41.667 0.00 0.00 0.00 2.71
5923 6242 1.672854 CGTAGAAGGGCATGGACCGA 61.673 60.000 0.00 0.00 34.63 4.69
5926 6247 4.857251 CCGTAGAAGGGCATGGAC 57.143 61.111 0.00 0.00 0.00 4.02
5933 6254 1.651240 TTCGAGACGCCGTAGAAGGG 61.651 60.000 0.00 0.00 0.00 3.95
5960 6281 1.806542 GAGGTGCGCATCTCTTTTTCA 59.193 47.619 37.33 0.00 35.71 2.69
6009 6330 4.887071 TGAAACAAAACAGCTATGGACAGT 59.113 37.500 0.00 0.00 0.00 3.55
6053 6377 6.410845 CGTTGAATGTTATCACCGATTGTAG 58.589 40.000 0.00 0.00 37.41 2.74
6055 6379 4.094294 CCGTTGAATGTTATCACCGATTGT 59.906 41.667 0.00 0.00 37.41 2.71
6056 6380 4.094294 ACCGTTGAATGTTATCACCGATTG 59.906 41.667 0.00 0.00 37.41 2.67
6120 6445 0.802494 GATACAACAAGGCCCACACG 59.198 55.000 0.00 0.00 0.00 4.49
6233 6561 5.602628 CCTTAGAAGGCTTCTTTATACGCT 58.397 41.667 32.69 9.84 41.14 5.07
6234 6562 5.908916 CCTTAGAAGGCTTCTTTATACGC 57.091 43.478 32.69 1.70 41.14 4.42
6248 6576 5.869888 GTGTATGTGGTTGAGACCTTAGAAG 59.130 44.000 0.00 0.00 46.66 2.85
6249 6577 5.305902 TGTGTATGTGGTTGAGACCTTAGAA 59.694 40.000 0.00 0.00 46.66 2.10
6250 6578 4.836175 TGTGTATGTGGTTGAGACCTTAGA 59.164 41.667 0.00 0.00 46.66 2.10
6251 6579 4.929808 GTGTGTATGTGGTTGAGACCTTAG 59.070 45.833 0.00 0.00 46.66 2.18
6252 6580 4.345547 TGTGTGTATGTGGTTGAGACCTTA 59.654 41.667 0.00 0.00 46.66 2.69
6253 6581 3.135712 TGTGTGTATGTGGTTGAGACCTT 59.864 43.478 0.00 0.00 46.66 3.50
6254 6582 2.703536 TGTGTGTATGTGGTTGAGACCT 59.296 45.455 0.00 0.00 46.66 3.85
6255 6583 3.120321 TGTGTGTATGTGGTTGAGACC 57.880 47.619 0.00 0.00 46.71 3.85
6256 6584 9.929180 ATATATATGTGTGTATGTGGTTGAGAC 57.071 33.333 0.00 0.00 0.00 3.36
6264 6592 9.977762 GATGCACAATATATATGTGTGTATGTG 57.022 33.333 26.52 20.92 44.99 3.21
6265 6593 9.166173 GGATGCACAATATATATGTGTGTATGT 57.834 33.333 26.52 15.96 44.99 2.29
6266 6594 9.387257 AGGATGCACAATATATATGTGTGTATG 57.613 33.333 26.52 12.94 44.99 2.39
6267 6595 9.605275 GAGGATGCACAATATATATGTGTGTAT 57.395 33.333 24.27 24.27 46.78 2.29
6281 6649 4.760715 GCTTAGATGATGAGGATGCACAAT 59.239 41.667 0.00 0.00 0.00 2.71
6302 6670 2.620251 TAATCGGCACAATAGCTGCT 57.380 45.000 7.57 7.57 40.71 4.24
6311 6679 5.820423 AGTTTGCATAACTATAATCGGCACA 59.180 36.000 11.11 0.00 0.00 4.57
6316 6684 7.360101 GGCCTACAGTTTGCATAACTATAATCG 60.360 40.741 12.06 4.44 0.00 3.34
6358 6726 0.836606 CCCTGGGTTTTGGCTTTTGT 59.163 50.000 3.97 0.00 0.00 2.83
6370 6738 1.852965 CCCTGATATTTGACCCTGGGT 59.147 52.381 20.72 20.72 39.44 4.51
6398 6766 2.684881 CCTGAAAGCTGTGTGTGAACTT 59.315 45.455 0.00 0.00 0.00 2.66
6413 6781 3.243367 CGGTCAGCAATTTGAACCTGAAA 60.243 43.478 0.00 0.00 36.23 2.69
6430 6798 3.259064 GCTTGTTTCTAGTATGCGGTCA 58.741 45.455 0.00 0.00 0.00 4.02
6435 6803 7.486232 GGAGATTTTTGCTTGTTTCTAGTATGC 59.514 37.037 0.00 0.00 0.00 3.14
6437 6805 8.515414 GTGGAGATTTTTGCTTGTTTCTAGTAT 58.485 33.333 0.00 0.00 0.00 2.12
6460 6828 3.912496 TGGTGATGTCATTCTAGGTGG 57.088 47.619 0.00 0.00 0.00 4.61
6465 6833 8.493607 TCCATCTAATTTGGTGATGTCATTCTA 58.506 33.333 1.40 0.00 36.72 2.10
6467 6835 7.572523 TCCATCTAATTTGGTGATGTCATTC 57.427 36.000 1.40 0.00 36.72 2.67
6470 6838 5.652014 GGTTCCATCTAATTTGGTGATGTCA 59.348 40.000 1.40 0.00 36.72 3.58
6471 6839 5.888161 AGGTTCCATCTAATTTGGTGATGTC 59.112 40.000 1.40 0.00 36.72 3.06
6472 6840 5.831103 AGGTTCCATCTAATTTGGTGATGT 58.169 37.500 1.40 0.00 36.72 3.06
6490 6859 2.781945 CTTGCAGTGTTGGAAGGTTC 57.218 50.000 1.41 0.00 45.76 3.62
6546 6915 4.184629 GCATTCCGAGTATGTTGTTCTCT 58.815 43.478 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.