Multiple sequence alignment - TraesCS7A01G365400

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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 TraesCS7A01G365400 chr7A 100.000 5168 0 0 1 5168 539407172 539402005 0.000000e+00 9544.0
1 TraesCS7A01G365400 chr7A 91.098 2786 238 8 1 2782 539449533 539446754 0.000000e+00 3762.0
2 TraesCS7A01G365400 chr7A 96.651 866 17 2 4046 4903 539445661 539444800 0.000000e+00 1428.0
3 TraesCS7A01G365400 chr7A 89.767 860 75 10 3491 4346 539446761 539445911 0.000000e+00 1088.0
4 TraesCS7A01G365400 chr7A 83.040 908 131 14 3497 4390 539323076 539322178 0.000000e+00 802.0
5 TraesCS7A01G365400 chr7A 98.000 150 3 0 4500 4649 539445813 539445664 1.430000e-65 261.0
6 TraesCS7A01G365400 chr7B 92.101 2785 213 6 1 2782 482486595 482489375 0.000000e+00 3917.0
7 TraesCS7A01G365400 chr7B 90.695 935 74 8 3491 4417 482489368 482490297 0.000000e+00 1232.0
8 TraesCS7A01G365400 chr7B 75.011 2261 530 33 537 2778 482685017 482687261 0.000000e+00 1013.0
9 TraesCS7A01G365400 chr7B 84.589 584 79 8 3739 4315 482687597 482688176 2.090000e-158 569.0
10 TraesCS7A01G365400 chr7B 90.024 411 30 3 4501 4903 482490299 482490706 5.930000e-144 521.0
11 TraesCS7A01G365400 chr7B 90.335 269 13 3 4905 5168 482490837 482491097 1.780000e-89 340.0
12 TraesCS7A01G365400 chr7B 81.853 259 37 5 3491 3740 482687258 482687515 5.240000e-50 209.0
13 TraesCS7A01G365400 chr7B 83.908 87 10 4 4421 4505 594035317 594035401 4.290000e-11 80.5
14 TraesCS7A01G365400 chr7D 94.306 1809 100 3 1 1807 460079726 460081533 0.000000e+00 2767.0
15 TraesCS7A01G365400 chr7D 93.712 986 61 1 1798 2782 460108941 460109926 0.000000e+00 1476.0
16 TraesCS7A01G365400 chr7D 90.958 929 76 7 3491 4417 460109919 460110841 0.000000e+00 1243.0
17 TraesCS7A01G365400 chr7D 83.669 845 119 11 3497 4328 460282618 460283456 0.000000e+00 778.0
18 TraesCS7A01G365400 chr7D 86.595 373 30 6 4501 4860 460110843 460111208 1.350000e-105 394.0
19 TraesCS7A01G365400 chr2B 76.590 2012 419 44 794 2775 784189532 784191521 0.000000e+00 1059.0
20 TraesCS7A01G365400 chr2B 75.674 2002 436 42 811 2782 798129191 798131171 0.000000e+00 952.0
21 TraesCS7A01G365400 chr2B 79.599 799 120 27 3489 4251 784191516 784192307 2.740000e-147 532.0
22 TraesCS7A01G365400 chr2B 81.020 706 99 22 3491 4169 798131164 798131861 3.540000e-146 529.0
23 TraesCS7A01G365400 chr2A 76.179 2015 431 47 794 2782 764309896 764311887 0.000000e+00 1016.0
24 TraesCS7A01G365400 chr2A 94.915 118 6 0 3373 3490 20864299 20864416 8.840000e-43 185.0
25 TraesCS7A01G365400 chr2A 94.366 71 1 2 2783 2851 20862518 20862587 7.080000e-19 106.0
26 TraesCS7A01G365400 chr2D 75.786 2003 432 42 811 2782 638725088 638727068 0.000000e+00 963.0
27 TraesCS7A01G365400 chr2D 75.210 2025 438 54 794 2782 638805216 638807212 0.000000e+00 900.0
28 TraesCS7A01G365400 chr2D 80.939 703 85 29 3491 4169 638727061 638727738 1.280000e-140 510.0
29 TraesCS7A01G365400 chr2D 80.797 703 86 29 3491 4169 638807205 638807882 5.970000e-139 505.0
30 TraesCS7A01G365400 chr2D 100.000 28 0 0 4479 4506 516440329 516440356 9.000000e-03 52.8
31 TraesCS7A01G365400 chr4A 94.135 341 18 2 2783 3121 706948492 706948152 7.670000e-143 518.0
32 TraesCS7A01G365400 chr4A 93.255 341 21 2 2783 3121 706972727 706972387 7.730000e-138 501.0
33 TraesCS7A01G365400 chr4A 92.962 341 22 2 2783 3121 456451252 456450912 3.590000e-136 496.0
34 TraesCS7A01G365400 chr4A 96.648 179 5 1 3312 3490 456450597 456450420 3.910000e-76 296.0
35 TraesCS7A01G365400 chr4A 96.648 179 5 1 3312 3490 706947837 706947660 3.910000e-76 296.0
36 TraesCS7A01G365400 chr4A 96.648 179 5 1 3312 3490 706972073 706971896 3.910000e-76 296.0
37 TraesCS7A01G365400 chr4A 92.308 91 5 2 3119 3208 456450786 456450697 1.510000e-25 128.0
38 TraesCS7A01G365400 chr4A 92.308 91 5 2 3119 3208 706948026 706947937 1.510000e-25 128.0
39 TraesCS7A01G365400 chr4A 100.000 33 0 0 3279 3311 456450652 456450620 1.550000e-05 62.1
40 TraesCS7A01G365400 chr4A 100.000 33 0 0 3279 3311 706947892 706947860 1.550000e-05 62.1
41 TraesCS7A01G365400 chr4A 100.000 33 0 0 3279 3311 706972128 706972096 1.550000e-05 62.1
42 TraesCS7A01G365400 chr1B 93.255 341 20 3 2783 3121 1952251 1952590 2.780000e-137 499.0
43 TraesCS7A01G365400 chr1B 96.089 179 5 1 3312 3490 1952881 1953057 1.820000e-74 291.0
44 TraesCS7A01G365400 chr1B 90.345 145 12 2 2782 2926 667977594 667977452 6.830000e-44 189.0
45 TraesCS7A01G365400 chr1B 91.209 91 6 2 3119 3208 1952716 1952805 7.030000e-24 122.0
46 TraesCS7A01G365400 chr1B 92.982 57 4 0 4413 4469 116255475 116255419 3.320000e-12 84.2
47 TraesCS7A01G365400 chr1B 92.982 57 4 0 4413 4469 146942770 146942826 3.320000e-12 84.2
48 TraesCS7A01G365400 chr1A 92.733 344 23 2 2780 3121 592803213 592803556 3.590000e-136 496.0
49 TraesCS7A01G365400 chr1A 92.375 341 24 2 2783 3121 174049711 174050051 7.780000e-133 484.0
50 TraesCS7A01G365400 chr1A 94.972 179 7 1 3312 3490 174050364 174050540 3.940000e-71 279.0
51 TraesCS7A01G365400 chr1A 94.536 183 4 2 3312 3490 592803872 592804052 1.420000e-70 278.0
52 TraesCS7A01G365400 chr1A 92.308 91 5 2 3119 3208 174050177 174050266 1.510000e-25 128.0
53 TraesCS7A01G365400 chr1A 91.209 91 6 2 3119 3208 592803682 592803771 7.030000e-24 122.0
54 TraesCS7A01G365400 chr1A 100.000 33 0 0 3279 3311 592803817 592803849 1.550000e-05 62.1
55 TraesCS7A01G365400 chr6B 98.701 77 1 0 3415 3491 714777610 714777534 2.510000e-28 137.0
56 TraesCS7A01G365400 chr5D 95.000 60 3 0 3431 3490 5166447 5166506 1.530000e-15 95.3
57 TraesCS7A01G365400 chr5D 86.905 84 9 2 4421 4503 426293901 426293819 5.510000e-15 93.5
58 TraesCS7A01G365400 chr5D 92.857 56 3 1 4422 4477 322389155 322389101 4.290000e-11 80.5
59 TraesCS7A01G365400 chr5B 89.552 67 6 1 4414 4480 89636161 89636096 3.320000e-12 84.2
60 TraesCS7A01G365400 chr3B 86.765 68 7 2 4408 4474 595693924 595693990 2.000000e-09 75.0
61 TraesCS7A01G365400 chr5A 86.567 67 8 1 4414 4480 77093342 77093277 7.180000e-09 73.1


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 TraesCS7A01G365400 chr7A 539402005 539407172 5167 True 9544.000000 9544 100.000000 1 5168 1 chr7A.!!$R2 5167
1 TraesCS7A01G365400 chr7A 539444800 539449533 4733 True 1634.750000 3762 93.879000 1 4903 4 chr7A.!!$R3 4902
2 TraesCS7A01G365400 chr7A 539322178 539323076 898 True 802.000000 802 83.040000 3497 4390 1 chr7A.!!$R1 893
3 TraesCS7A01G365400 chr7B 482486595 482491097 4502 False 1502.500000 3917 90.788750 1 5168 4 chr7B.!!$F2 5167
4 TraesCS7A01G365400 chr7B 482685017 482688176 3159 False 597.000000 1013 80.484333 537 4315 3 chr7B.!!$F3 3778
5 TraesCS7A01G365400 chr7D 460079726 460081533 1807 False 2767.000000 2767 94.306000 1 1807 1 chr7D.!!$F1 1806
6 TraesCS7A01G365400 chr7D 460108941 460111208 2267 False 1037.666667 1476 90.421667 1798 4860 3 chr7D.!!$F3 3062
7 TraesCS7A01G365400 chr7D 460282618 460283456 838 False 778.000000 778 83.669000 3497 4328 1 chr7D.!!$F2 831
8 TraesCS7A01G365400 chr2B 784189532 784192307 2775 False 795.500000 1059 78.094500 794 4251 2 chr2B.!!$F1 3457
9 TraesCS7A01G365400 chr2B 798129191 798131861 2670 False 740.500000 952 78.347000 811 4169 2 chr2B.!!$F2 3358
10 TraesCS7A01G365400 chr2A 764309896 764311887 1991 False 1016.000000 1016 76.179000 794 2782 1 chr2A.!!$F1 1988
11 TraesCS7A01G365400 chr2D 638725088 638727738 2650 False 736.500000 963 78.362500 811 4169 2 chr2D.!!$F2 3358
12 TraesCS7A01G365400 chr2D 638805216 638807882 2666 False 702.500000 900 78.003500 794 4169 2 chr2D.!!$F3 3375
13 TraesCS7A01G365400 chr4A 706971896 706972727 831 True 286.366667 501 96.634333 2783 3490 3 chr4A.!!$R3 707
14 TraesCS7A01G365400 chr4A 706947660 706948492 832 True 251.025000 518 95.772750 2783 3490 4 chr4A.!!$R2 707
15 TraesCS7A01G365400 chr4A 456450420 456451252 832 True 245.525000 496 95.479500 2783 3490 4 chr4A.!!$R1 707
16 TraesCS7A01G365400 chr1B 1952251 1953057 806 False 304.000000 499 93.517667 2783 3490 3 chr1B.!!$F2 707
17 TraesCS7A01G365400 chr1A 174049711 174050540 829 False 297.000000 484 93.218333 2783 3490 3 chr1A.!!$F1 707
18 TraesCS7A01G365400 chr1A 592803213 592804052 839 False 239.525000 496 94.619500 2780 3490 4 chr1A.!!$F2 710

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
768 774 0.807667 CTTTCTCACCCATCTCGCCG 60.808 60.0 0.0 0.0 0.00 6.46 F
2502 2519 0.403271 AATGCCAGGCACTCAGAAGT 59.597 50.0 19.1 0.0 43.04 3.01 F
3419 3609 0.032130 CCAGCGATGCGTATACCTGT 59.968 55.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2601 2618 0.597377 GCCAACTTTCAAGGTTGCCG 60.597 55.0 6.87 0.0 41.64 5.69 R
3481 3671 0.107508 ATCATCCAGAACACAGGCGG 60.108 55.0 0.00 0.0 0.00 6.13 R
5071 6337 0.174845 CTCCGGGTACAGAATGCGAA 59.825 55.0 0.00 0.0 42.53 4.70 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
137 138 1.125021 CATCTCGCGTCACAACACTTC 59.875 52.381 5.77 0.00 0.00 3.01
139 140 1.139989 CTCGCGTCACAACACTTCAT 58.860 50.000 5.77 0.00 0.00 2.57
153 154 6.994496 ACAACACTTCATCTTGAATCTCTTGA 59.006 34.615 0.00 0.00 35.59 3.02
199 200 4.192317 GCATCGGTAATCTCACTTTCCTT 58.808 43.478 0.00 0.00 0.00 3.36
211 212 5.593909 TCTCACTTTCCTTGCAAGAATCAAA 59.406 36.000 28.05 17.32 0.00 2.69
235 236 2.355010 AGGATAACCTGCTGAATGGC 57.645 50.000 0.00 0.00 45.92 4.40
380 381 2.361070 GGGAATAACTACCTCCAGGGGA 60.361 54.545 0.00 0.00 40.27 4.81
441 442 8.333908 CACAGAGATTTATCTTGATAGCAACAC 58.666 37.037 0.00 0.00 37.25 3.32
504 505 6.876257 CCTAAGCTTTCAGTTCTGTATGTTCT 59.124 38.462 3.20 0.00 0.00 3.01
513 515 8.725405 TCAGTTCTGTATGTTCTAACAACAAA 57.275 30.769 0.00 2.49 43.03 2.83
535 537 6.997239 AATTAACGGACAAGATTCCTTACC 57.003 37.500 0.00 0.00 32.88 2.85
625 628 5.814705 CCACCTCTCTTAGCAAATAGTTCAG 59.185 44.000 0.00 0.00 0.00 3.02
669 672 1.137872 AGCAATGACCTCGATGGAGAC 59.862 52.381 6.27 1.08 43.27 3.36
735 738 7.526142 ACTTTTGGGAAGAAATAACTTCTCC 57.474 36.000 0.00 0.00 44.00 3.71
768 774 0.807667 CTTTCTCACCCATCTCGCCG 60.808 60.000 0.00 0.00 0.00 6.46
834 840 1.490910 CCTTCCACCATAGGGAACTCC 59.509 57.143 0.00 0.00 43.67 3.85
932 938 5.945784 CCCACTTGGACAAATTAGATCTGAA 59.054 40.000 5.18 0.00 37.39 3.02
1055 1061 5.598005 CAGAAAATATTGGCCATACCCTTCA 59.402 40.000 6.09 0.00 37.83 3.02
1099 1105 5.576563 TCAAGGAAACAGATTTGGAGGTA 57.423 39.130 0.00 0.00 0.00 3.08
1149 1155 7.201803 GCCAGAAATCTTCAGAGCATTAATCTT 60.202 37.037 0.00 0.00 0.00 2.40
1284 1290 3.399330 GCTCACCAGTTGTACAAAGCTA 58.601 45.455 10.51 0.00 0.00 3.32
1369 1375 7.453393 TCTTCCAAAAAGCTTAGAATCTCTGA 58.547 34.615 0.00 0.00 0.00 3.27
1395 1401 8.579850 TCTTGACAGCAAATAAAATATCTGGT 57.420 30.769 0.00 0.00 32.73 4.00
1446 1452 9.871238 CTTAGTAGCCTCAAACTTCTTTACATA 57.129 33.333 0.00 0.00 0.00 2.29
1515 1521 5.468746 CCTTTCCAACATGTTCGTTCTAAGA 59.531 40.000 8.48 0.00 0.00 2.10
1563 1571 6.451393 CCAAATCCCACTTTCAATTCGTAAA 58.549 36.000 0.00 0.00 0.00 2.01
1846 1854 4.104738 TGACTGGAGAAATTCCCTCAACTT 59.895 41.667 9.23 0.00 46.19 2.66
1869 1877 2.024176 GCGACTGCCTCCATTTAGAA 57.976 50.000 0.00 0.00 33.98 2.10
2274 2287 4.837896 AAAGAAGGGAAAGAAAGCGAAG 57.162 40.909 0.00 0.00 0.00 3.79
2430 2447 1.532437 TCTGAAGAACATGCAGTTGCG 59.468 47.619 6.31 0.00 45.83 4.85
2487 2504 2.056094 AAAGCTTCGTTGCTGAATGC 57.944 45.000 0.00 0.00 43.24 3.56
2501 2518 1.093159 GAATGCCAGGCACTCAGAAG 58.907 55.000 19.10 0.00 43.04 2.85
2502 2519 0.403271 AATGCCAGGCACTCAGAAGT 59.597 50.000 19.10 0.00 43.04 3.01
2535 2552 5.186215 TCGTAATCTTGTAAGGGTGATCACA 59.814 40.000 26.47 3.72 0.00 3.58
2601 2618 8.994170 GCTCTTCTCCTTGAATATATGGTTAAC 58.006 37.037 0.00 0.00 33.71 2.01
2691 2716 6.055588 GGGTTCAAGAATAGCAATAGCAGTA 58.944 40.000 0.00 0.00 45.49 2.74
2774 2799 1.074405 TCTGAAGCCAAGCAATGTCCT 59.926 47.619 0.00 0.00 0.00 3.85
2775 2800 1.891150 CTGAAGCCAAGCAATGTCCTT 59.109 47.619 0.00 0.00 0.00 3.36
2776 2801 1.888512 TGAAGCCAAGCAATGTCCTTC 59.111 47.619 10.53 10.53 36.65 3.46
2777 2802 2.165998 GAAGCCAAGCAATGTCCTTCT 58.834 47.619 10.33 0.00 34.85 2.85
2778 2803 1.542492 AGCCAAGCAATGTCCTTCTG 58.458 50.000 0.00 0.00 0.00 3.02
2781 2806 2.731572 CCAAGCAATGTCCTTCTGGAT 58.268 47.619 0.00 0.00 45.29 3.41
2843 2868 9.659830 GGACACTAAGGCGTAAATTAAATTATG 57.340 33.333 0.00 0.00 0.00 1.90
2902 2927 7.984422 AGATCACTGAATTGTACATTGTCAA 57.016 32.000 0.00 0.00 0.00 3.18
2979 3005 5.529800 TGCACCTTTACTCTTACCTTTGTTC 59.470 40.000 0.00 0.00 0.00 3.18
2986 3012 5.741962 ACTCTTACCTTTGTTCTACCCTC 57.258 43.478 0.00 0.00 0.00 4.30
3008 3034 6.183361 CCTCTCTTTTCTTACCCATCTGCTAT 60.183 42.308 0.00 0.00 0.00 2.97
3032 3058 4.610605 TTCTACGTTTCCCATTCACTGA 57.389 40.909 0.00 0.00 0.00 3.41
3035 3061 4.994852 TCTACGTTTCCCATTCACTGAAAG 59.005 41.667 0.00 0.00 42.29 2.62
3037 3063 3.815401 ACGTTTCCCATTCACTGAAAGAG 59.185 43.478 0.00 0.00 37.43 2.85
3042 3069 1.446907 CATTCACTGAAAGAGCGCCT 58.553 50.000 2.29 0.00 37.43 5.52
3046 3073 1.067565 TCACTGAAAGAGCGCCTACAG 60.068 52.381 20.07 20.07 37.43 2.74
3075 3102 5.737290 CGCACAAATTACAGTAATAAGCACC 59.263 40.000 6.22 0.00 0.00 5.01
3082 3109 7.661536 ATTACAGTAATAAGCACCTCTCTCA 57.338 36.000 3.79 0.00 0.00 3.27
3121 3149 8.910351 AATAGCTAATCAGTAGAAATCCCAAC 57.090 34.615 0.00 0.00 30.50 3.77
3143 3299 1.373570 GGGCGGTGAAGAGAAATCAG 58.626 55.000 0.00 0.00 0.00 2.90
3176 3332 1.485066 GAGGGAATCGGGAAACTGCTA 59.515 52.381 0.00 0.00 36.33 3.49
3177 3333 1.209747 AGGGAATCGGGAAACTGCTAC 59.790 52.381 0.00 0.00 36.33 3.58
3179 3335 1.209747 GGAATCGGGAAACTGCTACCT 59.790 52.381 0.00 0.00 36.33 3.08
3184 3340 4.354893 TCGGGAAACTGCTACCTTTTTA 57.645 40.909 0.00 0.00 36.33 1.52
3204 3360 6.732896 TTTAAAGGGTAAAAGAATGCACCA 57.267 33.333 0.00 0.00 32.42 4.17
3208 3364 2.161609 GGGTAAAAGAATGCACCAGTCG 59.838 50.000 0.00 0.00 33.45 4.18
3209 3365 3.071479 GGTAAAAGAATGCACCAGTCGA 58.929 45.455 0.00 0.00 33.45 4.20
3210 3366 3.125316 GGTAAAAGAATGCACCAGTCGAG 59.875 47.826 0.00 0.00 33.45 4.04
3211 3367 1.813513 AAAGAATGCACCAGTCGAGG 58.186 50.000 0.00 0.00 33.45 4.63
3212 3368 0.976641 AAGAATGCACCAGTCGAGGA 59.023 50.000 0.00 0.00 33.45 3.71
3213 3369 0.247736 AGAATGCACCAGTCGAGGAC 59.752 55.000 0.00 0.00 33.45 3.85
3221 3377 4.745116 AGTCGAGGACTGCTGCTA 57.255 55.556 0.00 0.00 41.76 3.49
3222 3378 2.487918 AGTCGAGGACTGCTGCTAG 58.512 57.895 0.00 0.00 41.76 3.42
3223 3379 0.322997 AGTCGAGGACTGCTGCTAGT 60.323 55.000 0.00 2.70 41.76 2.57
3224 3380 0.099791 GTCGAGGACTGCTGCTAGTC 59.900 60.000 18.00 18.00 44.96 2.59
3225 3381 0.034960 TCGAGGACTGCTGCTAGTCT 60.035 55.000 22.34 13.58 45.03 3.24
3226 3382 1.209747 TCGAGGACTGCTGCTAGTCTA 59.790 52.381 22.34 10.22 45.03 2.59
3227 3383 1.601903 CGAGGACTGCTGCTAGTCTAG 59.398 57.143 22.34 2.18 45.03 2.43
3228 3384 2.743510 CGAGGACTGCTGCTAGTCTAGA 60.744 54.545 22.34 0.00 45.03 2.43
3229 3385 2.616842 GAGGACTGCTGCTAGTCTAGAC 59.383 54.545 15.41 15.41 45.03 2.59
3230 3386 2.025793 AGGACTGCTGCTAGTCTAGACA 60.026 50.000 24.44 9.82 45.03 3.41
3231 3387 2.357637 GGACTGCTGCTAGTCTAGACAG 59.642 54.545 24.44 18.67 45.03 3.51
3232 3388 1.748493 ACTGCTGCTAGTCTAGACAGC 59.252 52.381 29.88 29.88 46.48 4.40
3233 3389 2.023673 CTGCTGCTAGTCTAGACAGCT 58.976 52.381 32.70 15.25 46.46 4.24
3234 3390 1.747924 TGCTGCTAGTCTAGACAGCTG 59.252 52.381 32.70 29.54 46.46 4.24
3235 3391 2.020720 GCTGCTAGTCTAGACAGCTGA 58.979 52.381 32.87 21.16 44.73 4.26
3236 3392 2.033299 GCTGCTAGTCTAGACAGCTGAG 59.967 54.545 32.87 26.23 44.73 3.35
3237 3393 2.618241 CTGCTAGTCTAGACAGCTGAGG 59.382 54.545 30.21 20.22 36.99 3.86
3238 3394 2.239907 TGCTAGTCTAGACAGCTGAGGA 59.760 50.000 30.21 17.55 36.83 3.71
3239 3395 3.283751 GCTAGTCTAGACAGCTGAGGAA 58.716 50.000 26.60 1.54 34.73 3.36
3240 3396 3.066203 GCTAGTCTAGACAGCTGAGGAAC 59.934 52.174 26.60 11.37 34.73 3.62
3241 3397 5.166553 GCTAGTCTAGACAGCTGAGGAACT 61.167 50.000 26.60 17.57 35.80 3.01
3242 3398 3.773560 AGTCTAGACAGCTGAGGAACTT 58.226 45.455 23.35 0.00 41.55 2.66
3243 3399 3.509575 AGTCTAGACAGCTGAGGAACTTG 59.490 47.826 23.35 11.55 41.55 3.16
3244 3400 3.508012 GTCTAGACAGCTGAGGAACTTGA 59.492 47.826 23.35 13.43 41.55 3.02
3245 3401 3.761218 TCTAGACAGCTGAGGAACTTGAG 59.239 47.826 23.35 6.84 41.55 3.02
3246 3402 1.001860 AGACAGCTGAGGAACTTGAGC 59.998 52.381 23.35 0.00 41.55 4.26
3247 3403 0.761187 ACAGCTGAGGAACTTGAGCA 59.239 50.000 23.35 0.00 43.87 4.26
3248 3404 1.141657 ACAGCTGAGGAACTTGAGCAA 59.858 47.619 23.35 0.00 43.87 3.91
3249 3405 2.224719 ACAGCTGAGGAACTTGAGCAAT 60.225 45.455 23.35 0.00 43.87 3.56
3250 3406 2.419324 CAGCTGAGGAACTTGAGCAATC 59.581 50.000 8.42 0.00 43.87 2.67
3251 3407 2.039480 AGCTGAGGAACTTGAGCAATCA 59.961 45.455 0.00 0.00 43.87 2.57
3252 3408 2.419324 GCTGAGGAACTTGAGCAATCAG 59.581 50.000 6.46 6.46 41.55 2.90
3255 3411 1.707427 AGGAACTTGAGCAATCAGGGT 59.293 47.619 0.00 0.00 27.25 4.34
3265 3421 5.324409 TGAGCAATCAGGGTAAAAGAATGT 58.676 37.500 0.00 0.00 0.00 2.71
3267 3423 6.599244 TGAGCAATCAGGGTAAAAGAATGTAG 59.401 38.462 0.00 0.00 0.00 2.74
3272 3428 5.876357 TCAGGGTAAAAGAATGTAGCAGTT 58.124 37.500 0.00 0.00 0.00 3.16
3273 3429 5.938125 TCAGGGTAAAAGAATGTAGCAGTTC 59.062 40.000 0.00 0.00 0.00 3.01
3274 3430 5.123979 CAGGGTAAAAGAATGTAGCAGTTCC 59.876 44.000 0.00 0.00 0.00 3.62
3275 3431 5.014228 AGGGTAAAAGAATGTAGCAGTTCCT 59.986 40.000 0.00 0.00 0.00 3.36
3277 3433 6.882678 GGGTAAAAGAATGTAGCAGTTCCTTA 59.117 38.462 0.00 0.00 0.00 2.69
3334 3519 3.411351 GGCTTGCGTTCGCTCGAA 61.411 61.111 17.63 0.02 0.00 3.71
3354 3539 0.336392 GGCCCATTCCCTTTTCTCCT 59.664 55.000 0.00 0.00 0.00 3.69
3355 3540 1.273267 GGCCCATTCCCTTTTCTCCTT 60.273 52.381 0.00 0.00 0.00 3.36
3402 3592 4.478371 CAGCCAGCCAGCGATCCA 62.478 66.667 0.00 0.00 38.01 3.41
3403 3593 4.172512 AGCCAGCCAGCGATCCAG 62.173 66.667 0.00 0.00 38.01 3.86
3406 3596 4.519437 CAGCCAGCGATCCAGCGA 62.519 66.667 0.00 0.00 43.00 4.93
3407 3597 3.544607 AGCCAGCGATCCAGCGAT 61.545 61.111 0.00 0.00 43.00 4.58
3408 3598 3.344215 GCCAGCGATCCAGCGATG 61.344 66.667 0.00 0.00 46.20 3.84
3409 3599 3.344215 CCAGCGATCCAGCGATGC 61.344 66.667 0.00 0.00 45.38 3.91
3410 3600 3.699484 CAGCGATCCAGCGATGCG 61.699 66.667 0.00 0.00 40.90 4.73
3411 3601 4.212913 AGCGATCCAGCGATGCGT 62.213 61.111 0.00 0.00 43.00 5.24
3412 3602 2.354656 GCGATCCAGCGATGCGTA 60.355 61.111 0.00 0.00 0.00 4.42
3413 3603 1.734477 GCGATCCAGCGATGCGTAT 60.734 57.895 0.00 0.00 0.00 3.06
3414 3604 0.456142 GCGATCCAGCGATGCGTATA 60.456 55.000 0.00 0.00 0.00 1.47
3415 3605 1.260206 CGATCCAGCGATGCGTATAC 58.740 55.000 0.00 0.00 0.00 1.47
3416 3606 1.630148 GATCCAGCGATGCGTATACC 58.370 55.000 0.00 0.00 0.00 2.73
3417 3607 1.202582 GATCCAGCGATGCGTATACCT 59.797 52.381 0.00 0.00 0.00 3.08
3418 3608 0.313987 TCCAGCGATGCGTATACCTG 59.686 55.000 0.00 6.07 0.00 4.00
3419 3609 0.032130 CCAGCGATGCGTATACCTGT 59.968 55.000 0.00 0.00 0.00 4.00
3420 3610 1.268625 CCAGCGATGCGTATACCTGTA 59.731 52.381 0.00 0.00 0.00 2.74
3421 3611 2.316792 CAGCGATGCGTATACCTGTAC 58.683 52.381 0.00 0.00 0.00 2.90
3422 3612 1.951602 AGCGATGCGTATACCTGTACA 59.048 47.619 0.00 0.00 0.00 2.90
3423 3613 2.031069 AGCGATGCGTATACCTGTACAG 60.031 50.000 16.34 16.34 0.00 2.74
3424 3614 2.031420 GCGATGCGTATACCTGTACAGA 60.031 50.000 24.68 5.51 0.00 3.41
3425 3615 3.366070 GCGATGCGTATACCTGTACAGAT 60.366 47.826 24.68 10.24 0.00 2.90
3426 3616 4.795268 CGATGCGTATACCTGTACAGATT 58.205 43.478 24.68 12.77 0.00 2.40
3427 3617 4.617223 CGATGCGTATACCTGTACAGATTG 59.383 45.833 24.68 10.13 0.00 2.67
3428 3618 3.713288 TGCGTATACCTGTACAGATTGC 58.287 45.455 24.68 17.23 0.00 3.56
3429 3619 3.131400 TGCGTATACCTGTACAGATTGCA 59.869 43.478 24.68 19.31 0.00 4.08
3430 3620 4.202212 TGCGTATACCTGTACAGATTGCAT 60.202 41.667 24.68 11.14 0.00 3.96
3431 3621 4.386049 GCGTATACCTGTACAGATTGCATC 59.614 45.833 24.68 7.28 0.00 3.91
3432 3622 4.617223 CGTATACCTGTACAGATTGCATCG 59.383 45.833 24.68 14.38 0.00 3.84
3433 3623 4.672587 ATACCTGTACAGATTGCATCGT 57.327 40.909 24.68 12.65 0.00 3.73
3434 3624 5.784578 ATACCTGTACAGATTGCATCGTA 57.215 39.130 24.68 14.34 0.00 3.43
3435 3625 3.782046 ACCTGTACAGATTGCATCGTAC 58.218 45.455 24.68 15.46 38.51 3.67
3436 3626 3.194755 ACCTGTACAGATTGCATCGTACA 59.805 43.478 24.68 19.35 41.83 2.90
3437 3627 4.180817 CCTGTACAGATTGCATCGTACAA 58.819 43.478 24.68 0.00 42.57 2.41
3438 3628 4.629634 CCTGTACAGATTGCATCGTACAAA 59.370 41.667 24.68 9.86 42.57 2.83
3439 3629 5.121611 CCTGTACAGATTGCATCGTACAAAA 59.878 40.000 24.68 9.49 42.57 2.44
3440 3630 6.183360 CCTGTACAGATTGCATCGTACAAAAT 60.183 38.462 24.68 0.69 42.57 1.82
3441 3631 6.771076 TGTACAGATTGCATCGTACAAAATC 58.229 36.000 18.85 6.41 41.50 2.17
3442 3632 5.878332 ACAGATTGCATCGTACAAAATCA 57.122 34.783 0.00 0.00 31.15 2.57
3443 3633 6.252967 ACAGATTGCATCGTACAAAATCAA 57.747 33.333 0.00 0.00 31.15 2.57
3444 3634 6.317088 ACAGATTGCATCGTACAAAATCAAG 58.683 36.000 0.00 0.00 31.15 3.02
3445 3635 5.740569 CAGATTGCATCGTACAAAATCAAGG 59.259 40.000 0.00 0.00 31.15 3.61
3446 3636 5.415701 AGATTGCATCGTACAAAATCAAGGT 59.584 36.000 0.00 0.00 31.15 3.50
3447 3637 6.597672 AGATTGCATCGTACAAAATCAAGGTA 59.402 34.615 0.00 0.00 31.15 3.08
3448 3638 5.794687 TGCATCGTACAAAATCAAGGTAG 57.205 39.130 0.00 0.00 0.00 3.18
3449 3639 4.634004 TGCATCGTACAAAATCAAGGTAGG 59.366 41.667 0.00 0.00 0.00 3.18
3450 3640 4.035208 GCATCGTACAAAATCAAGGTAGGG 59.965 45.833 0.00 0.00 0.00 3.53
3451 3641 3.602483 TCGTACAAAATCAAGGTAGGGC 58.398 45.455 0.00 0.00 0.00 5.19
3452 3642 2.350498 CGTACAAAATCAAGGTAGGGCG 59.650 50.000 0.00 0.00 0.00 6.13
3453 3643 1.834188 ACAAAATCAAGGTAGGGCGG 58.166 50.000 0.00 0.00 0.00 6.13
3454 3644 1.102978 CAAAATCAAGGTAGGGCGGG 58.897 55.000 0.00 0.00 0.00 6.13
3455 3645 0.683179 AAAATCAAGGTAGGGCGGGC 60.683 55.000 0.00 0.00 0.00 6.13
3456 3646 2.886730 AAATCAAGGTAGGGCGGGCG 62.887 60.000 0.00 0.00 0.00 6.13
3472 3662 4.832608 CGCCCAACCTCGCCCTAC 62.833 72.222 0.00 0.00 0.00 3.18
3473 3663 4.484872 GCCCAACCTCGCCCTACC 62.485 72.222 0.00 0.00 0.00 3.18
3474 3664 4.157120 CCCAACCTCGCCCTACCG 62.157 72.222 0.00 0.00 0.00 4.02
3475 3665 4.157120 CCAACCTCGCCCTACCGG 62.157 72.222 0.00 0.00 0.00 5.28
3542 3735 4.124970 GTGACTTCGGGTTGACTAAGTTT 58.875 43.478 0.00 0.00 32.51 2.66
3581 3786 6.392625 TCTTCTAGGATTGATGGTTCTACG 57.607 41.667 0.00 0.00 0.00 3.51
3629 3834 3.884895 TGGATACATTGCACCAGGTAAG 58.115 45.455 0.00 0.00 46.17 2.34
3638 3844 5.705609 TTGCACCAGGTAAGAATTTCTTC 57.294 39.130 14.75 7.33 37.89 2.87
3641 3847 5.183713 TGCACCAGGTAAGAATTTCTTCATG 59.816 40.000 14.75 13.24 37.89 3.07
3733 3964 9.729281 AATATTTTGATTCTTGTGCTCCAATTT 57.271 25.926 0.00 0.00 31.20 1.82
3804 4120 4.972514 CTTTGGGAGCAAAATCTCTACC 57.027 45.455 0.00 0.00 33.70 3.18
3814 4130 4.202223 GCAAAATCTCTACCGAGGGTGATA 60.202 45.833 0.00 0.00 36.19 2.15
3983 4512 2.404215 CTATTATGCGGACCAAGACGG 58.596 52.381 0.00 0.00 42.50 4.79
3993 4522 1.743252 CCAAGACGGAGAAGCAGGC 60.743 63.158 0.00 0.00 36.56 4.85
4005 4537 1.277580 AAGCAGGCAGGGCTGTAGAT 61.278 55.000 21.76 5.66 41.66 1.98
4143 4687 2.290260 TGAGGTCACCGCAATCAAAGAT 60.290 45.455 0.00 0.00 28.67 2.40
4430 5533 2.856222 ACTAGTATTACCTCCGTCCCG 58.144 52.381 0.00 0.00 0.00 5.14
4555 5667 5.161943 ACTAATCACACCCTTAACCAGAC 57.838 43.478 0.00 0.00 0.00 3.51
4903 6035 2.897350 CGCCTCTTCCATTCGGCC 60.897 66.667 0.00 0.00 39.34 6.13
4929 6190 1.530283 CCAGCCAGATGATGAGCCA 59.470 57.895 0.00 0.00 0.00 4.75
4936 6197 1.211212 CAGATGATGAGCCACCTCCAA 59.789 52.381 0.00 0.00 37.29 3.53
4940 6201 1.634973 TGATGAGCCACCTCCAATGAA 59.365 47.619 0.00 0.00 37.29 2.57
4947 6208 0.392998 CACCTCCAATGAACCCTCCG 60.393 60.000 0.00 0.00 0.00 4.63
4969 6235 2.286121 ATCGCCTTTCCCCCTCCA 60.286 61.111 0.00 0.00 0.00 3.86
5028 6294 2.446435 ACCTGGAAGCGCAACAATATT 58.554 42.857 11.47 0.00 0.00 1.28
5029 6295 2.164219 ACCTGGAAGCGCAACAATATTG 59.836 45.455 11.47 14.01 0.00 1.90
5031 6297 1.135141 TGGAAGCGCAACAATATTGCC 60.135 47.619 15.48 6.46 42.10 4.52
5032 6298 1.191096 GAAGCGCAACAATATTGCCG 58.809 50.000 15.48 15.39 42.10 5.69
5033 6299 0.179140 AAGCGCAACAATATTGCCGG 60.179 50.000 15.48 0.00 42.10 6.13
5080 6346 0.469917 ATGGATCCGGTTCGCATTCT 59.530 50.000 7.39 0.00 0.00 2.40
5084 6350 1.859080 GATCCGGTTCGCATTCTGTAC 59.141 52.381 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 6.018913 CCGTTCAGATCAAGAGATTCAAGATG 60.019 42.308 0.00 0.00 33.72 2.90
139 140 5.414360 CCGTTCAGATCAAGAGATTCAAGA 58.586 41.667 0.00 0.00 33.72 3.02
153 154 2.365582 GTGGTATTTGGCCGTTCAGAT 58.634 47.619 0.00 0.00 0.00 2.90
199 200 3.507162 TCCTGGAGTTTGATTCTTGCA 57.493 42.857 0.00 0.00 0.00 4.08
380 381 0.251787 GCCAAACCTGTGGGGATCTT 60.252 55.000 0.00 0.00 39.26 2.40
389 390 0.258774 AGACAGTTGGCCAAACCTGT 59.741 50.000 31.35 31.35 39.85 4.00
441 442 2.464459 GGAATGCTTCCGTGGAGCG 61.464 63.158 0.56 0.00 40.59 5.03
504 505 8.077386 GGAATCTTGTCCGTTAATTTGTTGTTA 58.923 33.333 0.00 0.00 0.00 2.41
513 515 5.045432 TGGGTAAGGAATCTTGTCCGTTAAT 60.045 40.000 0.00 0.00 43.03 1.40
535 537 1.093159 GATGAGCTGCTTCCAAGTGG 58.907 55.000 2.53 0.00 0.00 4.00
598 601 6.374417 ACTATTTGCTAAGAGAGGTGGAAA 57.626 37.500 9.51 0.00 0.00 3.13
600 603 5.483937 TGAACTATTTGCTAAGAGAGGTGGA 59.516 40.000 9.51 0.00 0.00 4.02
625 628 1.068055 CAAGTCCAGCCATTCAAGTGC 60.068 52.381 0.00 0.00 0.00 4.40
669 672 2.294074 CTGAAGAGAGAGGGAGGTACG 58.706 57.143 0.00 0.00 0.00 3.67
735 738 2.500098 TGAGAAAGGTGGAATAGACCCG 59.500 50.000 0.00 0.00 33.51 5.28
768 774 2.094182 TGATAGGGACAGAGTTCGCAAC 60.094 50.000 0.00 0.00 0.00 4.17
834 840 3.551659 GCAAAAGCTCAACAAGGGAAGAG 60.552 47.826 0.00 0.00 0.00 2.85
932 938 4.876107 CGGCTCCTATCAAGTTGTTGTAAT 59.124 41.667 2.11 0.00 34.98 1.89
1055 1061 5.244402 TGAACAATGAATGTCTGGATGCTTT 59.756 36.000 0.00 0.00 42.99 3.51
1099 1105 3.992999 TGGCCATTGAAGTGGGAATAAT 58.007 40.909 0.00 0.00 39.73 1.28
1149 1155 2.898612 ACCATGGAATGCATTGTCACAA 59.101 40.909 21.47 0.00 44.97 3.33
1369 1375 9.193806 ACCAGATATTTTATTTGCTGTCAAGAT 57.806 29.630 0.00 0.00 33.12 2.40
1395 1401 3.138839 TCCCTATCTCGTGTGGTATGGTA 59.861 47.826 0.00 0.00 0.00 3.25
1407 1413 3.506844 GGCTACTAAGGTTCCCTATCTCG 59.493 52.174 0.00 0.00 31.13 4.04
1501 1507 9.099454 GTTTCCTGATAATCTTAGAACGAACAT 57.901 33.333 0.00 0.00 0.00 2.71
1515 1521 5.767168 GCCAGATAGCTTGTTTCCTGATAAT 59.233 40.000 0.00 0.00 0.00 1.28
1563 1571 3.643792 AGAGCTCACTTAGTTGACCAAGT 59.356 43.478 17.77 0.00 35.38 3.16
2253 2266 3.004839 GCTTCGCTTTCTTTCCCTTCTTT 59.995 43.478 0.00 0.00 0.00 2.52
2260 2273 3.251004 TCTTCTTGCTTCGCTTTCTTTCC 59.749 43.478 0.00 0.00 0.00 3.13
2271 2284 3.497640 CGGATGGATGATCTTCTTGCTTC 59.502 47.826 8.38 1.23 0.00 3.86
2274 2287 2.805099 GACGGATGGATGATCTTCTTGC 59.195 50.000 8.38 2.18 0.00 4.01
2310 2323 8.133627 GCTTTCACTAAATCAGCATATGTGAAT 58.866 33.333 4.29 0.00 40.84 2.57
2487 2504 1.135257 CGAGTACTTCTGAGTGCCTGG 60.135 57.143 0.00 0.00 39.07 4.45
2501 2518 6.632035 CCTTACAAGATTACGATGACGAGTAC 59.368 42.308 0.00 0.00 42.66 2.73
2502 2519 6.238566 CCCTTACAAGATTACGATGACGAGTA 60.239 42.308 0.00 0.00 42.66 2.59
2535 2552 2.094494 CAGGTCACTTGTCGAGCATACT 60.094 50.000 0.00 0.00 33.29 2.12
2601 2618 0.597377 GCCAACTTTCAAGGTTGCCG 60.597 55.000 6.87 0.00 41.64 5.69
2774 2799 1.617018 CCTCCGCCACTGATCCAGAA 61.617 60.000 0.45 0.00 35.18 3.02
2775 2800 2.060383 CCTCCGCCACTGATCCAGA 61.060 63.158 0.45 0.00 35.18 3.86
2776 2801 2.060383 TCCTCCGCCACTGATCCAG 61.060 63.158 0.00 0.00 37.52 3.86
2777 2802 2.038813 TCCTCCGCCACTGATCCA 59.961 61.111 0.00 0.00 0.00 3.41
2778 2803 2.501610 GTCCTCCGCCACTGATCC 59.498 66.667 0.00 0.00 0.00 3.36
2781 2806 3.371063 GTCGTCCTCCGCCACTGA 61.371 66.667 0.00 0.00 36.19 3.41
2798 2823 1.607767 CCGCCCCACCTCAAATTTTTG 60.608 52.381 0.00 0.00 39.48 2.44
2875 2900 9.500785 TGACAATGTACAATTCAGTGATCTTAA 57.499 29.630 0.00 0.00 35.35 1.85
2979 3005 5.663556 AGATGGGTAAGAAAAGAGAGGGTAG 59.336 44.000 0.00 0.00 0.00 3.18
2986 3012 9.566432 AAATATAGCAGATGGGTAAGAAAAGAG 57.434 33.333 0.00 0.00 32.33 2.85
3008 3034 6.703319 TCAGTGAATGGGAAACGTAGAAATA 58.297 36.000 0.00 0.00 0.00 1.40
3032 3058 0.175989 GGCTACTGTAGGCGCTCTTT 59.824 55.000 23.12 0.00 41.69 2.52
3042 3069 3.927854 TGTAATTTGTGCGGCTACTGTA 58.072 40.909 0.00 0.00 0.00 2.74
3046 3073 4.932268 TTACTGTAATTTGTGCGGCTAC 57.068 40.909 0.00 0.00 0.00 3.58
3136 3292 0.464373 TCATCCGCTGGCCTGATTTC 60.464 55.000 14.77 0.00 0.00 2.17
3143 3299 4.247380 CCCTCTCATCCGCTGGCC 62.247 72.222 0.00 0.00 0.00 5.36
3179 3335 7.565680 TGGTGCATTCTTTTACCCTTTAAAAA 58.434 30.769 0.00 0.00 32.20 1.94
3184 3340 4.223144 ACTGGTGCATTCTTTTACCCTTT 58.777 39.130 0.00 0.00 32.20 3.11
3204 3360 0.322997 ACTAGCAGCAGTCCTCGACT 60.323 55.000 0.00 0.00 44.44 4.18
3208 3364 2.616842 GTCTAGACTAGCAGCAGTCCTC 59.383 54.545 15.91 6.20 45.08 3.71
3209 3365 2.025793 TGTCTAGACTAGCAGCAGTCCT 60.026 50.000 23.01 9.87 45.08 3.85
3210 3366 2.357637 CTGTCTAGACTAGCAGCAGTCC 59.642 54.545 23.01 6.67 45.08 3.85
3211 3367 2.223479 GCTGTCTAGACTAGCAGCAGTC 60.223 54.545 31.95 19.38 46.04 3.51
3212 3368 1.748493 GCTGTCTAGACTAGCAGCAGT 59.252 52.381 31.95 0.00 46.04 4.40
3213 3369 2.490328 GCTGTCTAGACTAGCAGCAG 57.510 55.000 31.95 24.87 46.04 4.24
3215 3371 2.020720 TCAGCTGTCTAGACTAGCAGC 58.979 52.381 30.94 30.94 46.57 5.25
3216 3372 2.618241 CCTCAGCTGTCTAGACTAGCAG 59.382 54.545 31.16 26.76 37.67 4.24
3218 3374 2.925724 TCCTCAGCTGTCTAGACTAGC 58.074 52.381 26.59 26.59 36.45 3.42
3219 3375 4.523083 AGTTCCTCAGCTGTCTAGACTAG 58.477 47.826 23.01 18.10 0.00 2.57
3220 3376 4.577988 AGTTCCTCAGCTGTCTAGACTA 57.422 45.455 23.01 9.26 0.00 2.59
3221 3377 3.449746 AGTTCCTCAGCTGTCTAGACT 57.550 47.619 23.01 9.74 0.00 3.24
3222 3378 3.508012 TCAAGTTCCTCAGCTGTCTAGAC 59.492 47.826 16.32 16.32 0.00 2.59
3223 3379 3.761218 CTCAAGTTCCTCAGCTGTCTAGA 59.239 47.826 14.67 3.69 0.00 2.43
3224 3380 3.675775 GCTCAAGTTCCTCAGCTGTCTAG 60.676 52.174 14.67 3.55 0.00 2.43
3225 3381 2.232452 GCTCAAGTTCCTCAGCTGTCTA 59.768 50.000 14.67 0.00 0.00 2.59
3226 3382 1.001860 GCTCAAGTTCCTCAGCTGTCT 59.998 52.381 14.67 3.25 0.00 3.41
3227 3383 1.270518 TGCTCAAGTTCCTCAGCTGTC 60.271 52.381 14.67 0.94 32.76 3.51
3228 3384 0.761187 TGCTCAAGTTCCTCAGCTGT 59.239 50.000 14.67 0.00 32.76 4.40
3229 3385 1.888215 TTGCTCAAGTTCCTCAGCTG 58.112 50.000 7.63 7.63 32.76 4.24
3230 3386 2.039480 TGATTGCTCAAGTTCCTCAGCT 59.961 45.455 0.00 0.00 32.76 4.24
3231 3387 2.419324 CTGATTGCTCAAGTTCCTCAGC 59.581 50.000 0.00 0.00 0.00 4.26
3232 3388 3.008330 CCTGATTGCTCAAGTTCCTCAG 58.992 50.000 4.16 4.16 0.00 3.35
3233 3389 2.290514 CCCTGATTGCTCAAGTTCCTCA 60.291 50.000 0.00 0.00 0.00 3.86
3234 3390 2.290577 ACCCTGATTGCTCAAGTTCCTC 60.291 50.000 0.00 0.00 0.00 3.71
3235 3391 1.707427 ACCCTGATTGCTCAAGTTCCT 59.293 47.619 0.00 0.00 0.00 3.36
3236 3392 2.206576 ACCCTGATTGCTCAAGTTCC 57.793 50.000 0.00 0.00 0.00 3.62
3237 3393 5.473504 TCTTTTACCCTGATTGCTCAAGTTC 59.526 40.000 0.00 0.00 0.00 3.01
3238 3394 5.385198 TCTTTTACCCTGATTGCTCAAGTT 58.615 37.500 0.00 0.00 0.00 2.66
3239 3395 4.985538 TCTTTTACCCTGATTGCTCAAGT 58.014 39.130 0.00 0.00 0.00 3.16
3240 3396 5.964958 TTCTTTTACCCTGATTGCTCAAG 57.035 39.130 0.00 0.00 0.00 3.02
3241 3397 5.774690 ACATTCTTTTACCCTGATTGCTCAA 59.225 36.000 0.00 0.00 0.00 3.02
3242 3398 5.324409 ACATTCTTTTACCCTGATTGCTCA 58.676 37.500 0.00 0.00 0.00 4.26
3243 3399 5.904362 ACATTCTTTTACCCTGATTGCTC 57.096 39.130 0.00 0.00 0.00 4.26
3244 3400 5.358160 GCTACATTCTTTTACCCTGATTGCT 59.642 40.000 0.00 0.00 0.00 3.91
3245 3401 5.125417 TGCTACATTCTTTTACCCTGATTGC 59.875 40.000 0.00 0.00 0.00 3.56
3246 3402 6.375455 ACTGCTACATTCTTTTACCCTGATTG 59.625 38.462 0.00 0.00 0.00 2.67
3247 3403 6.485171 ACTGCTACATTCTTTTACCCTGATT 58.515 36.000 0.00 0.00 0.00 2.57
3248 3404 6.067217 ACTGCTACATTCTTTTACCCTGAT 57.933 37.500 0.00 0.00 0.00 2.90
3249 3405 5.499004 ACTGCTACATTCTTTTACCCTGA 57.501 39.130 0.00 0.00 0.00 3.86
3250 3406 5.123979 GGAACTGCTACATTCTTTTACCCTG 59.876 44.000 0.00 0.00 0.00 4.45
3251 3407 5.014228 AGGAACTGCTACATTCTTTTACCCT 59.986 40.000 0.00 0.00 37.18 4.34
3252 3408 5.254115 AGGAACTGCTACATTCTTTTACCC 58.746 41.667 0.00 0.00 37.18 3.69
3255 3411 7.334421 CAGCTAAGGAACTGCTACATTCTTTTA 59.666 37.037 0.00 0.00 40.86 1.52
3265 3421 2.027192 CCCAACAGCTAAGGAACTGCTA 60.027 50.000 0.00 0.00 40.86 3.49
3267 3423 1.168714 CCCAACAGCTAAGGAACTGC 58.831 55.000 0.00 0.00 40.86 4.40
3272 3428 1.562672 GCTCCCCCAACAGCTAAGGA 61.563 60.000 0.00 0.00 32.48 3.36
3273 3429 1.077429 GCTCCCCCAACAGCTAAGG 60.077 63.158 0.00 0.00 32.48 2.69
3274 3430 0.038166 TTGCTCCCCCAACAGCTAAG 59.962 55.000 0.00 0.00 36.53 2.18
3275 3431 0.704076 ATTGCTCCCCCAACAGCTAA 59.296 50.000 0.00 0.00 36.53 3.09
3277 3433 1.000396 GATTGCTCCCCCAACAGCT 60.000 57.895 0.00 0.00 36.53 4.24
3320 3505 3.411351 GCCTTCGAGCGAACGCAA 61.411 61.111 20.66 6.17 44.88 4.85
3334 3519 0.336392 GGAGAAAAGGGAATGGGCCT 59.664 55.000 4.53 0.00 0.00 5.19
3402 3592 1.951602 TGTACAGGTATACGCATCGCT 59.048 47.619 0.00 0.00 0.00 4.93
3403 3593 2.031420 TCTGTACAGGTATACGCATCGC 60.031 50.000 22.48 0.00 0.00 4.58
3404 3594 3.891056 TCTGTACAGGTATACGCATCG 57.109 47.619 22.48 0.00 0.00 3.84
3405 3595 4.386049 GCAATCTGTACAGGTATACGCATC 59.614 45.833 22.48 0.00 0.00 3.91
3406 3596 4.202212 TGCAATCTGTACAGGTATACGCAT 60.202 41.667 22.48 3.41 0.00 4.73
3407 3597 3.131400 TGCAATCTGTACAGGTATACGCA 59.869 43.478 22.48 18.04 0.00 5.24
3408 3598 3.713288 TGCAATCTGTACAGGTATACGC 58.287 45.455 22.48 15.87 0.00 4.42
3409 3599 4.617223 CGATGCAATCTGTACAGGTATACG 59.383 45.833 22.48 13.22 42.58 3.06
3410 3600 5.529791 ACGATGCAATCTGTACAGGTATAC 58.470 41.667 22.48 9.23 42.58 1.47
3411 3601 5.784578 ACGATGCAATCTGTACAGGTATA 57.215 39.130 22.48 6.22 42.58 1.47
3412 3602 4.672587 ACGATGCAATCTGTACAGGTAT 57.327 40.909 22.48 11.42 42.58 2.73
3413 3603 4.928601 GTACGATGCAATCTGTACAGGTA 58.071 43.478 22.48 10.96 44.71 3.08
3414 3604 3.782046 GTACGATGCAATCTGTACAGGT 58.218 45.455 22.48 13.58 44.71 4.00
3418 3608 6.771076 TGATTTTGTACGATGCAATCTGTAC 58.229 36.000 11.81 11.81 45.12 2.90
3419 3609 6.976636 TGATTTTGTACGATGCAATCTGTA 57.023 33.333 0.00 0.00 42.58 2.74
3420 3610 5.878332 TGATTTTGTACGATGCAATCTGT 57.122 34.783 0.00 0.00 42.58 3.41
3421 3611 5.740569 CCTTGATTTTGTACGATGCAATCTG 59.259 40.000 0.00 2.33 42.58 2.90
3422 3612 5.415701 ACCTTGATTTTGTACGATGCAATCT 59.584 36.000 0.00 0.00 42.58 2.40
3423 3613 5.640732 ACCTTGATTTTGTACGATGCAATC 58.359 37.500 0.00 0.67 40.89 2.67
3424 3614 5.643379 ACCTTGATTTTGTACGATGCAAT 57.357 34.783 0.00 0.00 0.00 3.56
3425 3615 5.123186 CCTACCTTGATTTTGTACGATGCAA 59.877 40.000 0.00 0.00 0.00 4.08
3426 3616 4.634004 CCTACCTTGATTTTGTACGATGCA 59.366 41.667 0.00 0.00 0.00 3.96
3427 3617 4.035208 CCCTACCTTGATTTTGTACGATGC 59.965 45.833 0.00 0.00 0.00 3.91
3428 3618 4.035208 GCCCTACCTTGATTTTGTACGATG 59.965 45.833 0.00 0.00 0.00 3.84
3429 3619 4.196971 GCCCTACCTTGATTTTGTACGAT 58.803 43.478 0.00 0.00 0.00 3.73
3430 3620 3.602483 GCCCTACCTTGATTTTGTACGA 58.398 45.455 0.00 0.00 0.00 3.43
3431 3621 2.350498 CGCCCTACCTTGATTTTGTACG 59.650 50.000 0.00 0.00 0.00 3.67
3432 3622 2.681344 CCGCCCTACCTTGATTTTGTAC 59.319 50.000 0.00 0.00 0.00 2.90
3433 3623 2.356330 CCCGCCCTACCTTGATTTTGTA 60.356 50.000 0.00 0.00 0.00 2.41
3434 3624 1.615919 CCCGCCCTACCTTGATTTTGT 60.616 52.381 0.00 0.00 0.00 2.83
3435 3625 1.102978 CCCGCCCTACCTTGATTTTG 58.897 55.000 0.00 0.00 0.00 2.44
3436 3626 0.683179 GCCCGCCCTACCTTGATTTT 60.683 55.000 0.00 0.00 0.00 1.82
3437 3627 1.076995 GCCCGCCCTACCTTGATTT 60.077 57.895 0.00 0.00 0.00 2.17
3438 3628 2.595655 GCCCGCCCTACCTTGATT 59.404 61.111 0.00 0.00 0.00 2.57
3439 3629 3.861797 CGCCCGCCCTACCTTGAT 61.862 66.667 0.00 0.00 0.00 2.57
3455 3645 4.832608 GTAGGGCGAGGTTGGGCG 62.833 72.222 0.00 0.00 0.00 6.13
3456 3646 4.484872 GGTAGGGCGAGGTTGGGC 62.485 72.222 0.00 0.00 0.00 5.36
3457 3647 4.157120 CGGTAGGGCGAGGTTGGG 62.157 72.222 0.00 0.00 0.00 4.12
3458 3648 4.157120 CCGGTAGGGCGAGGTTGG 62.157 72.222 0.00 0.00 0.00 3.77
3474 3664 3.607370 GAACACAGGCGGAGGACCC 62.607 68.421 0.00 0.00 0.00 4.46
3475 3665 2.047179 GAACACAGGCGGAGGACC 60.047 66.667 0.00 0.00 0.00 4.46
3476 3666 1.374758 CAGAACACAGGCGGAGGAC 60.375 63.158 0.00 0.00 0.00 3.85
3477 3667 2.583441 CCAGAACACAGGCGGAGGA 61.583 63.158 0.00 0.00 0.00 3.71
3478 3668 1.903877 ATCCAGAACACAGGCGGAGG 61.904 60.000 0.00 0.00 0.00 4.30
3479 3669 0.742281 CATCCAGAACACAGGCGGAG 60.742 60.000 0.00 0.00 0.00 4.63
3480 3670 1.191489 TCATCCAGAACACAGGCGGA 61.191 55.000 0.00 0.00 0.00 5.54
3481 3671 0.107508 ATCATCCAGAACACAGGCGG 60.108 55.000 0.00 0.00 0.00 6.13
3482 3672 1.012086 CATCATCCAGAACACAGGCG 58.988 55.000 0.00 0.00 0.00 5.52
3483 3673 2.012673 GACATCATCCAGAACACAGGC 58.987 52.381 0.00 0.00 0.00 4.85
3484 3674 3.339253 TGACATCATCCAGAACACAGG 57.661 47.619 0.00 0.00 0.00 4.00
3485 3675 3.626217 CCATGACATCATCCAGAACACAG 59.374 47.826 0.00 0.00 33.61 3.66
3486 3676 3.613030 CCATGACATCATCCAGAACACA 58.387 45.455 0.00 0.00 33.61 3.72
3487 3677 2.947652 CCCATGACATCATCCAGAACAC 59.052 50.000 0.00 0.00 33.61 3.32
3488 3678 2.684630 GCCCATGACATCATCCAGAACA 60.685 50.000 0.00 0.00 33.61 3.18
3489 3679 1.952296 GCCCATGACATCATCCAGAAC 59.048 52.381 0.00 0.00 33.61 3.01
3542 3735 9.696572 ATCCTAGAAGAAGTATAACTGTGTACA 57.303 33.333 0.00 0.00 0.00 2.90
3581 3786 1.208293 CCTCTTGGTCCCACTAAGCTC 59.792 57.143 0.00 0.00 36.73 4.09
3679 3885 9.942850 CTGGGGAAAATAAAGTAAAATGTCATT 57.057 29.630 0.00 0.00 0.00 2.57
3710 3941 9.729281 ATAAAATTGGAGCACAAGAATCAAAAT 57.271 25.926 0.49 0.00 43.48 1.82
3801 4117 4.220724 AGCTGTAAATATCACCCTCGGTA 58.779 43.478 0.00 0.00 32.11 4.02
3804 4120 4.273480 CCAAAGCTGTAAATATCACCCTCG 59.727 45.833 0.00 0.00 0.00 4.63
3814 4130 4.579869 ACGATGACTCCAAAGCTGTAAAT 58.420 39.130 0.00 0.00 0.00 1.40
3983 4512 1.903877 TACAGCCCTGCCTGCTTCTC 61.904 60.000 0.00 0.00 36.81 2.87
3993 4522 5.188434 TGATTTTCTTGATCTACAGCCCTG 58.812 41.667 0.00 0.00 0.00 4.45
4005 4537 7.039270 CAGCCATTTGATGATGATTTTCTTGA 58.961 34.615 0.00 0.00 0.00 3.02
4143 4687 0.315886 CCTGCAGTGCTGAAAATGCA 59.684 50.000 22.25 5.91 45.82 3.96
4490 5601 1.823610 GCAGTTTACTACTCCCTCCGT 59.176 52.381 0.00 0.00 33.85 4.69
4583 5695 8.401046 TCGGTTTCAACTTTCAAGTTTATTTG 57.599 30.769 2.01 0.00 46.52 2.32
4903 6035 3.518303 TCATCATCTGGCTGGGATCTATG 59.482 47.826 0.00 0.00 0.00 2.23
4929 6190 0.546747 TCGGAGGGTTCATTGGAGGT 60.547 55.000 0.00 0.00 0.00 3.85
4936 6197 1.735376 CGATCCGTCGGAGGGTTCAT 61.735 60.000 20.50 0.00 44.00 2.57
4947 6208 2.203029 GGGGAAAGGCGATCCGTC 60.203 66.667 5.68 0.00 37.87 4.79
5003 6269 4.697756 TGCGCTTCCAGGTTCCGG 62.698 66.667 9.73 0.00 0.00 5.14
5004 6270 2.668212 TTGCGCTTCCAGGTTCCG 60.668 61.111 9.73 0.00 0.00 4.30
5005 6271 1.452145 TTGTTGCGCTTCCAGGTTCC 61.452 55.000 9.73 0.00 0.00 3.62
5006 6272 0.598065 ATTGTTGCGCTTCCAGGTTC 59.402 50.000 9.73 0.00 0.00 3.62
5007 6273 1.904287 TATTGTTGCGCTTCCAGGTT 58.096 45.000 9.73 0.00 0.00 3.50
5008 6274 2.128771 ATATTGTTGCGCTTCCAGGT 57.871 45.000 9.73 0.00 0.00 4.00
5009 6275 2.801063 CAATATTGTTGCGCTTCCAGG 58.199 47.619 9.73 0.00 0.00 4.45
5017 6283 1.938814 CGCCGGCAATATTGTTGCG 60.939 57.895 28.98 23.55 45.78 4.85
5033 6299 4.509737 GTCTGGTAGGGACGCCGC 62.510 72.222 0.00 0.00 0.00 6.53
5071 6337 0.174845 CTCCGGGTACAGAATGCGAA 59.825 55.000 0.00 0.00 42.53 4.70
5080 6346 2.363795 CTCTGGGCTCCGGGTACA 60.364 66.667 0.00 0.00 0.00 2.90
5084 6350 3.775654 GTCACTCTGGGCTCCGGG 61.776 72.222 0.00 0.00 0.00 5.73
5123 6389 1.366854 GACTTCCGCCGTCCCAATTC 61.367 60.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.