Multiple sequence alignment - TraesCS3A01G474300

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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 TraesCS3A01G474300 chr3A 100.000 5929 0 0 1 5929 705601743 705595815 0.000000e+00 10949.0
1 TraesCS3A01G474300 chr3A 89.214 751 51 16 5194 5921 705554332 705553589 0.000000e+00 911.0
2 TraesCS3A01G474300 chr3A 84.629 553 66 12 4957 5493 705343323 705342774 3.150000e-147 532.0
3 TraesCS3A01G474300 chr3A 88.264 409 46 2 2 408 705894255 705893847 6.910000e-134 488.0
4 TraesCS3A01G474300 chr3A 88.056 360 21 5 4812 5168 705577478 705577138 1.990000e-109 407.0
5 TraesCS3A01G474300 chr3A 82.114 492 47 21 462 931 705642501 705642029 3.350000e-102 383.0
6 TraesCS3A01G474300 chr3A 83.010 412 62 7 3 408 705902183 705901774 3.380000e-97 366.0
7 TraesCS3A01G474300 chr3A 82.642 265 38 6 4031 4292 705582140 705581881 1.660000e-55 228.0
8 TraesCS3A01G474300 chr3D 91.137 3791 164 62 484 4194 572739204 572742902 0.000000e+00 4981.0
9 TraesCS3A01G474300 chr3D 86.885 1342 121 36 4624 5924 572762903 572764230 0.000000e+00 1452.0
10 TraesCS3A01G474300 chr3D 86.500 1237 87 38 1100 2294 419551393 419550195 0.000000e+00 1286.0
11 TraesCS3A01G474300 chr3D 95.116 819 30 5 4620 5429 572743407 572744224 0.000000e+00 1282.0
12 TraesCS3A01G474300 chr3D 88.835 412 42 3 1 408 572718583 572718994 2.470000e-138 503.0
13 TraesCS3A01G474300 chr3D 82.940 551 82 9 3749 4292 572788216 572788761 2.480000e-133 486.0
14 TraesCS3A01G474300 chr3D 79.900 602 79 20 3884 4470 572794317 572794891 2.570000e-108 403.0
15 TraesCS3A01G474300 chr3D 78.957 537 70 17 3749 4275 572762185 572762688 5.730000e-85 326.0
16 TraesCS3A01G474300 chr3D 83.578 341 34 10 5605 5928 572744057 572744392 3.470000e-77 300.0
17 TraesCS3A01G474300 chr3D 86.063 287 31 6 3515 3800 572793529 572793807 3.470000e-77 300.0
18 TraesCS3A01G474300 chr3D 95.035 141 6 1 4157 4297 572743004 572743143 2.780000e-53 220.0
19 TraesCS3A01G474300 chr3D 89.677 155 11 2 4829 4979 572796766 572796919 6.060000e-45 193.0
20 TraesCS3A01G474300 chr3D 87.681 138 17 0 271 408 572722457 572722594 1.710000e-35 161.0
21 TraesCS3A01G474300 chr3B 90.429 2121 109 42 750 2811 760713865 760711780 0.000000e+00 2706.0
22 TraesCS3A01G474300 chr3B 95.063 952 35 6 3256 4197 760711061 760710112 0.000000e+00 1487.0
23 TraesCS3A01G474300 chr3B 93.026 717 27 15 4769 5465 760603941 760603228 0.000000e+00 1026.0
24 TraesCS3A01G474300 chr3B 94.276 594 29 5 4736 5326 760709606 760709015 0.000000e+00 904.0
25 TraesCS3A01G474300 chr3B 88.321 411 42 6 2 408 760743524 760743116 6.910000e-134 488.0
26 TraesCS3A01G474300 chr3B 88.293 410 44 4 2 408 760781522 760781114 6.910000e-134 488.0
27 TraesCS3A01G474300 chr3B 82.832 565 70 21 3914 4470 760604676 760604131 1.160000e-131 481.0
28 TraesCS3A01G474300 chr3B 90.511 274 24 2 3228 3499 760575815 760575542 1.570000e-95 361.0
29 TraesCS3A01G474300 chr3B 87.584 298 30 6 98 394 760767386 760767095 7.360000e-89 339.0
30 TraesCS3A01G474300 chr3B 84.661 339 35 12 5605 5929 760603441 760603106 7.410000e-84 322.0
31 TraesCS3A01G474300 chr3B 77.930 512 44 32 479 960 760778329 760777857 7.630000e-64 255.0
32 TraesCS3A01G474300 chr3B 84.977 213 27 2 3652 3859 760604889 760604677 1.670000e-50 211.0
33 TraesCS3A01G474300 chr3B 75.922 515 56 28 479 960 760784325 760783846 1.010000e-47 202.0
34 TraesCS3A01G474300 chr3B 90.840 131 12 0 278 408 760716597 760716467 6.110000e-40 176.0
35 TraesCS3A01G474300 chr3B 90.152 132 13 0 277 408 760719151 760719020 7.900000e-39 172.0
36 TraesCS3A01G474300 chr3B 91.589 107 8 1 4804 4910 760575539 760575434 4.790000e-31 147.0
37 TraesCS3A01G474300 chr3B 94.382 89 4 1 4622 4709 760709692 760709604 1.040000e-27 135.0
38 TraesCS3A01G474300 chr3B 91.304 46 4 0 2621 2666 760595628 760595583 4.960000e-06 63.9
39 TraesCS3A01G474300 chr5D 86.570 1236 90 38 1100 2294 438277328 438276128 0.000000e+00 1293.0
40 TraesCS3A01G474300 chr2D 86.570 1236 88 37 1100 2294 574801499 574800301 0.000000e+00 1291.0
41 TraesCS3A01G474300 chr2D 86.397 1235 93 39 1100 2294 488418451 488417252 0.000000e+00 1280.0
42 TraesCS3A01G474300 chr2D 91.765 85 5 1 4543 4625 627266215 627266299 3.750000e-22 117.0
43 TraesCS3A01G474300 chr4D 86.037 1239 88 39 1100 2294 487242240 487243437 0.000000e+00 1251.0
44 TraesCS3A01G474300 chr1A 90.566 689 44 9 1622 2294 242070133 242069450 0.000000e+00 893.0
45 TraesCS3A01G474300 chr1A 89.680 688 49 10 1622 2294 240953416 240952736 0.000000e+00 857.0
46 TraesCS3A01G474300 chr2A 88.792 687 50 12 1622 2294 22436102 22436775 0.000000e+00 817.0
47 TraesCS3A01G474300 chr2A 86.517 89 10 1 4543 4629 757965849 757965937 4.890000e-16 97.1
48 TraesCS3A01G474300 chr7B 82.942 979 88 44 1100 2053 64605936 64605012 0.000000e+00 809.0
49 TraesCS3A01G474300 chr1D 92.671 423 17 7 1886 2294 425476357 425476779 1.100000e-166 597.0
50 TraesCS3A01G474300 chr1D 82.353 85 13 2 4543 4625 479523219 479523135 8.240000e-09 73.1
51 TraesCS3A01G474300 chrUn 79.144 724 95 35 4796 5493 132017539 132018232 3.260000e-122 449.0
52 TraesCS3A01G474300 chr6D 84.615 91 10 4 4538 4625 441969734 441969823 2.940000e-13 87.9
53 TraesCS3A01G474300 chr6B 80.612 98 13 5 4512 4608 454750355 454750447 2.960000e-08 71.3
54 TraesCS3A01G474300 chr6B 80.612 98 13 5 4512 4608 454753000 454753092 2.960000e-08 71.3
55 TraesCS3A01G474300 chr6B 80.612 98 13 5 4512 4608 454755561 454755653 2.960000e-08 71.3


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 TraesCS3A01G474300 chr3A 705595815 705601743 5928 True 10949.000000 10949 100.000000 1 5929 1 chr3A.!!$R5 5928
1 TraesCS3A01G474300 chr3A 705553589 705554332 743 True 911.000000 911 89.214000 5194 5921 1 chr3A.!!$R2 727
2 TraesCS3A01G474300 chr3A 705342774 705343323 549 True 532.000000 532 84.629000 4957 5493 1 chr3A.!!$R1 536
3 TraesCS3A01G474300 chr3D 572739204 572744392 5188 False 1695.750000 4981 91.216500 484 5928 4 chr3D.!!$F3 5444
4 TraesCS3A01G474300 chr3D 419550195 419551393 1198 True 1286.000000 1286 86.500000 1100 2294 1 chr3D.!!$R1 1194
5 TraesCS3A01G474300 chr3D 572762185 572764230 2045 False 889.000000 1452 82.921000 3749 5924 2 chr3D.!!$F4 2175
6 TraesCS3A01G474300 chr3D 572788216 572788761 545 False 486.000000 486 82.940000 3749 4292 1 chr3D.!!$F1 543
7 TraesCS3A01G474300 chr3D 572718583 572722594 4011 False 332.000000 503 88.258000 1 408 2 chr3D.!!$F2 407
8 TraesCS3A01G474300 chr3D 572793529 572796919 3390 False 298.666667 403 85.213333 3515 4979 3 chr3D.!!$F5 1464
9 TraesCS3A01G474300 chr3B 760709015 760719151 10136 True 930.000000 2706 92.523667 277 5326 6 chr3B.!!$R6 5049
10 TraesCS3A01G474300 chr3B 760603106 760604889 1783 True 510.000000 1026 86.374000 3652 5929 4 chr3B.!!$R5 2277
11 TraesCS3A01G474300 chr3B 760777857 760784325 6468 True 315.000000 488 80.715000 2 960 3 chr3B.!!$R7 958
12 TraesCS3A01G474300 chr5D 438276128 438277328 1200 True 1293.000000 1293 86.570000 1100 2294 1 chr5D.!!$R1 1194
13 TraesCS3A01G474300 chr2D 574800301 574801499 1198 True 1291.000000 1291 86.570000 1100 2294 1 chr2D.!!$R2 1194
14 TraesCS3A01G474300 chr2D 488417252 488418451 1199 True 1280.000000 1280 86.397000 1100 2294 1 chr2D.!!$R1 1194
15 TraesCS3A01G474300 chr4D 487242240 487243437 1197 False 1251.000000 1251 86.037000 1100 2294 1 chr4D.!!$F1 1194
16 TraesCS3A01G474300 chr1A 242069450 242070133 683 True 893.000000 893 90.566000 1622 2294 1 chr1A.!!$R2 672
17 TraesCS3A01G474300 chr1A 240952736 240953416 680 True 857.000000 857 89.680000 1622 2294 1 chr1A.!!$R1 672
18 TraesCS3A01G474300 chr2A 22436102 22436775 673 False 817.000000 817 88.792000 1622 2294 1 chr2A.!!$F1 672
19 TraesCS3A01G474300 chr7B 64605012 64605936 924 True 809.000000 809 82.942000 1100 2053 1 chr7B.!!$R1 953
20 TraesCS3A01G474300 chrUn 132017539 132018232 693 False 449.000000 449 79.144000 4796 5493 1 chrUn.!!$F1 697

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
606 8831 0.035820 TTGCCCCACTAAGCTAACCG 60.036 55.0 0.00 0.0 0.00 4.44 F
1436 9830 0.105964 TGCTGGCGTGACTTGTTAGT 59.894 50.0 0.00 0.0 37.31 2.24 F
1999 10576 0.107508 AGGTGCGATCATGGTTCCAG 60.108 55.0 0.00 0.0 0.00 3.86 F
3248 12838 0.644843 GTGCAAAAAGTTGGTGTGCG 59.355 50.0 0.00 0.0 38.05 5.34 F
4548 14811 0.643820 CGTCCGGAATTACTTGACGC 59.356 55.0 5.23 0.0 41.71 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 10376 0.107508 CTGGAACCATGATCGCACCT 60.108 55.000 0.00 0.0 0.00 4.00 R
3248 12838 1.025041 GCAGGGCAATGTAAGCTACC 58.975 55.000 0.00 0.0 0.00 3.18 R
3747 13346 2.501723 AGAACGGTGATCATTGGCTACT 59.498 45.455 0.00 0.0 0.00 2.57 R
4596 14859 0.638746 CGTCTGGAATTACGTGACGC 59.361 55.000 18.56 0.0 42.63 5.19 R
5902 18370 0.040425 ACCATTTCGTGCAAACGAGC 60.040 50.000 0.93 0.0 43.33 5.03 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
18 2822 1.676303 GCCCCGTCCGGAATTCAAA 60.676 57.895 5.23 0.00 37.50 2.69
20 2824 1.470051 CCCCGTCCGGAATTCAAATT 58.530 50.000 5.23 0.00 37.50 1.82
27 2831 5.167845 CGTCCGGAATTCAAATTTCCAAAT 58.832 37.500 5.23 0.00 0.00 2.32
31 2835 6.817641 TCCGGAATTCAAATTTCCAAATCATG 59.182 34.615 0.00 0.00 0.00 3.07
70 2874 6.294675 CCATATCAGGCAGAAGAAACAAAACA 60.295 38.462 0.00 0.00 0.00 2.83
148 2952 3.428862 GCAAACAATTAGCCCGCACTAAT 60.429 43.478 3.15 3.15 43.17 1.73
201 3005 1.427368 TCACCCATTTGCCCACTAGTT 59.573 47.619 0.00 0.00 0.00 2.24
215 3019 1.628846 ACTAGTTGGGCCACACTAAGG 59.371 52.381 21.11 15.71 0.00 2.69
221 3025 0.326927 GGGCCACACTAAGGTAAGCA 59.673 55.000 4.39 0.00 0.00 3.91
247 3051 4.753233 TCACACTAGAGAGTAGTACCGTC 58.247 47.826 0.00 0.00 33.32 4.79
337 3143 6.378661 TGGATGGATAGCTAATGCACTTAT 57.621 37.500 0.00 0.00 38.92 1.73
355 3161 5.643777 CACTTATCAACCTTCCTTGGTGTAG 59.356 44.000 0.00 0.00 40.73 2.74
356 3162 5.546499 ACTTATCAACCTTCCTTGGTGTAGA 59.454 40.000 0.00 0.00 40.73 2.59
375 3181 4.608948 AGACAAGATCGGCCCTTATAAG 57.391 45.455 5.43 5.43 0.00 1.73
381 3187 1.525077 CGGCCCTTATAAGCGGCAA 60.525 57.895 30.11 0.00 41.36 4.52
393 3199 4.016706 CGGCAAACTCCTCCGGGT 62.017 66.667 0.00 0.00 39.52 5.28
395 3201 2.747686 GCAAACTCCTCCGGGTCA 59.252 61.111 0.00 0.00 0.00 4.02
397 3203 0.322546 GCAAACTCCTCCGGGTCATT 60.323 55.000 0.00 0.00 0.00 2.57
409 3215 1.931172 CGGGTCATTTACTTGTAGCGG 59.069 52.381 0.00 0.00 0.00 5.52
411 3217 3.602483 GGGTCATTTACTTGTAGCGGAA 58.398 45.455 0.00 0.00 0.00 4.30
413 3219 4.094442 GGGTCATTTACTTGTAGCGGAAAG 59.906 45.833 0.00 0.00 0.00 2.62
419 4085 2.140717 ACTTGTAGCGGAAAGGAAACG 58.859 47.619 0.00 0.00 0.00 3.60
435 4111 3.239712 GGAAACGCAGAAGAAACAAAACG 59.760 43.478 0.00 0.00 0.00 3.60
436 4112 3.481112 AACGCAGAAGAAACAAAACGT 57.519 38.095 0.00 0.00 0.00 3.99
438 4114 3.931824 ACGCAGAAGAAACAAAACGTAC 58.068 40.909 0.00 0.00 0.00 3.67
439 4115 3.619929 ACGCAGAAGAAACAAAACGTACT 59.380 39.130 0.00 0.00 0.00 2.73
440 4116 4.093850 ACGCAGAAGAAACAAAACGTACTT 59.906 37.500 0.00 0.00 0.00 2.24
441 4117 5.025826 CGCAGAAGAAACAAAACGTACTTT 58.974 37.500 0.00 0.00 0.00 2.66
442 4118 5.510323 CGCAGAAGAAACAAAACGTACTTTT 59.490 36.000 0.00 0.00 31.77 2.27
443 4119 6.683708 CGCAGAAGAAACAAAACGTACTTTTA 59.316 34.615 0.00 0.00 30.39 1.52
445 4121 7.044510 GCAGAAGAAACAAAACGTACTTTTACC 60.045 37.037 0.00 0.00 30.39 2.85
446 4122 7.430211 CAGAAGAAACAAAACGTACTTTTACCC 59.570 37.037 0.00 0.00 30.39 3.69
447 4123 7.337689 AGAAGAAACAAAACGTACTTTTACCCT 59.662 33.333 0.00 0.00 30.39 4.34
452 5785 7.155655 ACAAAACGTACTTTTACCCTCAAAA 57.844 32.000 0.00 0.00 30.39 2.44
475 5808 6.869315 AAAGAAAGAAAAGCAGACCTACTC 57.131 37.500 0.00 0.00 0.00 2.59
477 5810 5.789521 AGAAAGAAAAGCAGACCTACTCTC 58.210 41.667 0.00 0.00 0.00 3.20
482 6834 2.128507 GCAGACCTACTCTCGGGGG 61.129 68.421 0.00 0.00 0.00 5.40
487 6839 0.838987 ACCTACTCTCGGGGGCAAAA 60.839 55.000 0.00 0.00 0.00 2.44
488 6840 0.326927 CCTACTCTCGGGGGCAAAAA 59.673 55.000 0.00 0.00 0.00 1.94
580 8784 3.436496 GAACGATAATCCGATCCGATCC 58.564 50.000 2.69 0.00 0.00 3.36
584 8788 0.412244 TAATCCGATCCGATCCCCCT 59.588 55.000 2.69 0.00 0.00 4.79
586 8790 1.805609 ATCCGATCCGATCCCCCTCT 61.806 60.000 2.69 0.00 0.00 3.69
588 8792 1.122019 CCGATCCGATCCCCCTCTTT 61.122 60.000 2.69 0.00 0.00 2.52
606 8831 0.035820 TTGCCCCACTAAGCTAACCG 60.036 55.000 0.00 0.00 0.00 4.44
678 8922 1.872679 CGAGTAAAGTCGCTCGCCC 60.873 63.158 1.06 0.00 46.01 6.13
1359 9750 1.043673 GGATCTGGCTGTACGGACCT 61.044 60.000 4.71 0.00 0.00 3.85
1360 9751 0.824759 GATCTGGCTGTACGGACCTT 59.175 55.000 4.71 0.00 0.00 3.50
1361 9752 0.537188 ATCTGGCTGTACGGACCTTG 59.463 55.000 4.71 4.24 0.00 3.61
1362 9753 1.741770 CTGGCTGTACGGACCTTGC 60.742 63.158 4.71 0.00 0.00 4.01
1388 9781 1.860078 CGCTGTCGGTGGAGTTTTC 59.140 57.895 0.00 0.00 0.00 2.29
1435 9829 0.792640 CTGCTGGCGTGACTTGTTAG 59.207 55.000 0.00 0.00 0.00 2.34
1436 9830 0.105964 TGCTGGCGTGACTTGTTAGT 59.894 50.000 0.00 0.00 37.31 2.24
1456 9850 7.173218 TGTTAGTCTTCTCACCTGCTAATTTTG 59.827 37.037 0.00 0.00 0.00 2.44
1509 9903 0.108186 TTAGGCATCTGTCGGTGCTG 60.108 55.000 0.00 0.00 41.04 4.41
1510 9904 2.578163 TAGGCATCTGTCGGTGCTGC 62.578 60.000 0.00 0.00 41.04 5.25
1511 9905 2.435586 GCATCTGTCGGTGCTGCT 60.436 61.111 0.00 0.00 38.30 4.24
1514 9908 0.877071 CATCTGTCGGTGCTGCTTTT 59.123 50.000 0.00 0.00 0.00 2.27
1515 9909 0.877071 ATCTGTCGGTGCTGCTTTTG 59.123 50.000 0.00 0.00 0.00 2.44
1516 9910 1.165907 TCTGTCGGTGCTGCTTTTGG 61.166 55.000 0.00 0.00 0.00 3.28
1517 9911 1.153066 TGTCGGTGCTGCTTTTGGA 60.153 52.632 0.00 0.00 0.00 3.53
1518 9912 0.749818 TGTCGGTGCTGCTTTTGGAA 60.750 50.000 0.00 0.00 0.00 3.53
1519 9913 0.383949 GTCGGTGCTGCTTTTGGAAA 59.616 50.000 0.00 0.00 0.00 3.13
1552 9947 0.249911 AGGCTGAGAAACGTCCACAC 60.250 55.000 0.00 0.00 0.00 3.82
1613 10008 0.825840 TCCCCAAAAGCTTTGACCGG 60.826 55.000 13.54 10.88 0.00 5.28
1667 10063 1.434555 TGATTTTGCGTGGTAGTCCG 58.565 50.000 0.00 0.00 36.30 4.79
1672 10068 2.585247 GCGTGGTAGTCCGGCATC 60.585 66.667 0.00 0.00 36.32 3.91
1675 10071 0.597637 CGTGGTAGTCCGGCATCATC 60.598 60.000 0.00 0.00 36.30 2.92
1785 10181 1.202698 AGTTGCTGTCACCTCCTGTTC 60.203 52.381 0.00 0.00 0.00 3.18
1813 10209 6.039159 TGTTATTGCAACAGTTGTGATGAAGA 59.961 34.615 14.88 0.13 0.00 2.87
1856 10252 6.970484 ACTGTTCATCAATTTTAGGTGTGAC 58.030 36.000 0.00 0.00 0.00 3.67
1860 10256 9.072375 TGTTCATCAATTTTAGGTGTGACATAA 57.928 29.630 0.00 0.00 0.00 1.90
1905 10301 5.758296 TCCATGAATTTTAGGTGCGATCTAC 59.242 40.000 0.00 0.00 0.00 2.59
1912 10308 0.824759 AGGTGCGATCTACTCCCAAC 59.175 55.000 0.00 0.00 0.00 3.77
1980 10376 5.129155 CCTCCAATGAATCCTTGCCAATTTA 59.871 40.000 0.00 0.00 0.00 1.40
1981 10377 6.224665 TCCAATGAATCCTTGCCAATTTAG 57.775 37.500 0.00 0.00 0.00 1.85
1984 10380 5.603170 ATGAATCCTTGCCAATTTAGGTG 57.397 39.130 0.00 0.00 0.00 4.00
1985 10381 3.195396 TGAATCCTTGCCAATTTAGGTGC 59.805 43.478 0.00 0.00 0.00 5.01
1987 10383 1.173043 CCTTGCCAATTTAGGTGCGA 58.827 50.000 0.00 0.00 0.00 5.10
1999 10576 0.107508 AGGTGCGATCATGGTTCCAG 60.108 55.000 0.00 0.00 0.00 3.86
2322 11250 3.007635 GGTGGCTGTGGATTTACTACAC 58.992 50.000 0.00 0.00 35.15 2.90
2384 11312 5.567423 GCATTGTGCCTTATCCAAAGAACTT 60.567 40.000 0.00 0.00 37.42 2.66
2834 12362 4.887071 AGTCCACACATGCAAACTTTTAGA 59.113 37.500 0.00 0.00 0.00 2.10
2841 12369 6.183360 ACACATGCAAACTTTTAGATGTGTGA 60.183 34.615 20.07 0.00 43.36 3.58
2842 12370 6.864685 CACATGCAAACTTTTAGATGTGTGAT 59.135 34.615 12.82 0.00 35.88 3.06
2942 12531 2.896685 GCAGCCCTATGAGTATGAGAGT 59.103 50.000 0.00 0.00 0.00 3.24
2943 12532 3.305950 GCAGCCCTATGAGTATGAGAGTG 60.306 52.174 0.00 0.00 0.00 3.51
2945 12534 2.896685 GCCCTATGAGTATGAGAGTGCT 59.103 50.000 0.00 0.00 0.00 4.40
2968 12557 6.203723 GCTTTCATGCAGTAGAACTTATAGGG 59.796 42.308 0.00 0.00 0.00 3.53
2976 12565 6.698380 CAGTAGAACTTATAGGGTTGTGTGT 58.302 40.000 0.00 0.00 0.00 3.72
3020 12609 0.804364 GCAAGCATCACGTGGATTGA 59.196 50.000 21.69 1.86 32.57 2.57
3114 12704 6.499172 TCTGATCTTAACACAAGCTATCTCG 58.501 40.000 0.00 0.00 0.00 4.04
3140 12730 8.394121 GTTCTCTAATCTTCGAATGCATTTCTT 58.606 33.333 14.33 4.25 31.73 2.52
3145 12735 7.572523 AATCTTCGAATGCATTTCTTCCATA 57.427 32.000 14.33 0.00 31.73 2.74
3149 12739 6.757897 TCGAATGCATTTCTTCCATACTTT 57.242 33.333 14.33 0.00 31.73 2.66
3173 12763 4.705507 TGTCCCACTCTACTAGACACAATC 59.294 45.833 0.00 0.00 32.75 2.67
3174 12764 4.951094 GTCCCACTCTACTAGACACAATCT 59.049 45.833 0.00 0.00 41.95 2.40
3175 12765 4.950475 TCCCACTCTACTAGACACAATCTG 59.050 45.833 0.00 0.00 38.49 2.90
3176 12766 4.098654 CCCACTCTACTAGACACAATCTGG 59.901 50.000 0.00 0.00 41.64 3.86
3181 12771 7.872993 CACTCTACTAGACACAATCTGGAAAAA 59.127 37.037 0.00 0.00 38.17 1.94
3247 12837 1.719600 TGTGCAAAAAGTTGGTGTGC 58.280 45.000 0.00 0.00 35.10 4.57
3248 12838 0.644843 GTGCAAAAAGTTGGTGTGCG 59.355 50.000 0.00 0.00 38.05 5.34
3665 13257 3.634448 CCTGCTCCTATCCCGATACATAG 59.366 52.174 0.00 0.00 0.00 2.23
3882 13928 1.900545 CGTCCCCTCCAGTTCTTCCC 61.901 65.000 0.00 0.00 0.00 3.97
3946 13992 0.882042 AAGTGAGCGTGCAACAGGAG 60.882 55.000 0.00 0.00 35.74 3.69
3970 14019 2.290577 GGTCCTTCTGCTGGAATGTCTT 60.291 50.000 0.00 0.00 35.10 3.01
4016 14066 7.722363 TGTGAGTTCTTTTCCCCTTTTTATTC 58.278 34.615 0.00 0.00 0.00 1.75
4110 14164 2.764010 CAAAGGGGTAACTATTTGGCCC 59.236 50.000 0.00 0.00 37.91 5.80
4198 14389 7.715249 TCTGCTCCTGTGGATAATACAATAAAC 59.285 37.037 0.00 0.00 0.00 2.01
4313 14512 7.487484 TGATTTATTTCCTGCGCATTCATTTA 58.513 30.769 12.24 0.00 0.00 1.40
4314 14513 8.143193 TGATTTATTTCCTGCGCATTCATTTAT 58.857 29.630 12.24 0.00 0.00 1.40
4315 14514 8.891671 ATTTATTTCCTGCGCATTCATTTATT 57.108 26.923 12.24 0.00 0.00 1.40
4316 14515 8.715191 TTTATTTCCTGCGCATTCATTTATTT 57.285 26.923 12.24 0.00 0.00 1.40
4317 14516 9.809096 TTTATTTCCTGCGCATTCATTTATTTA 57.191 25.926 12.24 0.00 0.00 1.40
4318 14517 9.979578 TTATTTCCTGCGCATTCATTTATTTAT 57.020 25.926 12.24 0.00 0.00 1.40
4320 14519 9.630098 ATTTCCTGCGCATTCATTTATTTATAG 57.370 29.630 12.24 0.00 0.00 1.31
4321 14520 6.611381 TCCTGCGCATTCATTTATTTATAGC 58.389 36.000 12.24 0.00 0.00 2.97
4322 14521 6.430925 TCCTGCGCATTCATTTATTTATAGCT 59.569 34.615 12.24 0.00 0.00 3.32
4323 14522 6.744537 CCTGCGCATTCATTTATTTATAGCTC 59.255 38.462 12.24 0.00 0.00 4.09
4324 14523 7.361542 CCTGCGCATTCATTTATTTATAGCTCT 60.362 37.037 12.24 0.00 0.00 4.09
4325 14524 7.300320 TGCGCATTCATTTATTTATAGCTCTG 58.700 34.615 5.66 0.00 0.00 3.35
4326 14525 7.041167 TGCGCATTCATTTATTTATAGCTCTGT 60.041 33.333 5.66 0.00 0.00 3.41
4327 14526 7.479916 GCGCATTCATTTATTTATAGCTCTGTC 59.520 37.037 0.30 0.00 0.00 3.51
4328 14527 8.498358 CGCATTCATTTATTTATAGCTCTGTCA 58.502 33.333 0.00 0.00 0.00 3.58
4337 14536 9.555727 TTATTTATAGCTCTGTCAATTGGTACC 57.444 33.333 4.43 4.43 0.00 3.34
4338 14537 6.808321 TTATAGCTCTGTCAATTGGTACCT 57.192 37.500 14.36 0.00 0.00 3.08
4339 14538 5.700402 ATAGCTCTGTCAATTGGTACCTT 57.300 39.130 14.36 0.00 0.00 3.50
4340 14539 3.679389 AGCTCTGTCAATTGGTACCTTG 58.321 45.455 14.36 10.44 0.00 3.61
4341 14540 3.073062 AGCTCTGTCAATTGGTACCTTGT 59.927 43.478 14.36 0.00 0.00 3.16
4342 14541 3.437049 GCTCTGTCAATTGGTACCTTGTC 59.563 47.826 14.36 8.61 0.00 3.18
4343 14542 4.641396 CTCTGTCAATTGGTACCTTGTCA 58.359 43.478 14.36 12.54 0.00 3.58
4344 14543 4.641396 TCTGTCAATTGGTACCTTGTCAG 58.359 43.478 23.39 23.39 37.42 3.51
4396 14630 6.718454 AGTTCCAAGATGTTTGTTGAGATGAT 59.282 34.615 0.00 0.00 0.00 2.45
4399 14633 7.596494 TCCAAGATGTTTGTTGAGATGATTTC 58.404 34.615 0.00 0.00 0.00 2.17
4470 14704 8.980596 ACAATTCATTTCTGGATTATGGCTTTA 58.019 29.630 0.00 0.00 28.95 1.85
4475 14709 7.779326 TCATTTCTGGATTATGGCTTTACATCA 59.221 33.333 0.00 0.00 32.39 3.07
4479 14713 7.977818 TCTGGATTATGGCTTTACATCAGTAT 58.022 34.615 0.00 0.00 32.39 2.12
4482 14716 9.502091 TGGATTATGGCTTTACATCAGTATTAC 57.498 33.333 0.00 0.00 32.39 1.89
4486 14720 9.991906 TTATGGCTTTACATCAGTATTACCTAC 57.008 33.333 0.00 0.00 32.39 3.18
4487 14721 7.426606 TGGCTTTACATCAGTATTACCTACA 57.573 36.000 0.00 0.00 32.34 2.74
4490 14724 6.984474 GCTTTACATCAGTATTACCTACAGCA 59.016 38.462 0.00 0.00 32.34 4.41
4491 14725 7.494625 GCTTTACATCAGTATTACCTACAGCAA 59.505 37.037 0.00 0.00 32.34 3.91
4493 14727 8.942338 TTACATCAGTATTACCTACAGCAAAG 57.058 34.615 0.00 0.00 32.34 2.77
4522 14785 7.985476 CCATTTATGGTTCGTTTCTTCAGTAT 58.015 34.615 0.39 0.00 43.05 2.12
4534 14797 2.947652 TCTTCAGTATTACCTCCGTCCG 59.052 50.000 0.00 0.00 0.00 4.79
4536 14799 1.212688 TCAGTATTACCTCCGTCCGGA 59.787 52.381 0.00 0.00 42.90 5.14
4540 14803 4.279169 CAGTATTACCTCCGTCCGGAATTA 59.721 45.833 5.23 1.25 44.66 1.40
4541 14804 3.740631 ATTACCTCCGTCCGGAATTAC 57.259 47.619 5.23 0.00 44.66 1.89
4542 14805 2.442236 TACCTCCGTCCGGAATTACT 57.558 50.000 5.23 0.00 44.66 2.24
4543 14806 1.565067 ACCTCCGTCCGGAATTACTT 58.435 50.000 5.23 0.00 44.66 2.24
4547 14810 1.135315 TCCGTCCGGAATTACTTGACG 60.135 52.381 17.86 17.86 46.05 4.35
4548 14811 0.643820 CGTCCGGAATTACTTGACGC 59.356 55.000 5.23 0.00 41.71 5.19
4551 14814 3.514645 GTCCGGAATTACTTGACGCTTA 58.485 45.455 5.23 0.00 0.00 3.09
4552 14815 3.928375 GTCCGGAATTACTTGACGCTTAA 59.072 43.478 5.23 0.00 0.00 1.85
4553 14816 4.389687 GTCCGGAATTACTTGACGCTTAAA 59.610 41.667 5.23 0.00 0.00 1.52
4556 14819 5.263185 CGGAATTACTTGACGCTTAAATGG 58.737 41.667 0.00 0.00 0.00 3.16
4558 14821 6.238374 CGGAATTACTTGACGCTTAAATGGAT 60.238 38.462 0.00 0.00 0.00 3.41
4559 14822 6.912591 GGAATTACTTGACGCTTAAATGGATG 59.087 38.462 0.00 0.00 0.00 3.51
4560 14823 7.391148 AATTACTTGACGCTTAAATGGATGT 57.609 32.000 0.00 0.00 0.00 3.06
4561 14824 8.500753 AATTACTTGACGCTTAAATGGATGTA 57.499 30.769 0.00 0.00 0.00 2.29
4562 14825 8.677148 ATTACTTGACGCTTAAATGGATGTAT 57.323 30.769 0.00 0.00 0.00 2.29
4567 14830 7.284919 TGACGCTTAAATGGATGTATCTAGA 57.715 36.000 0.00 0.00 0.00 2.43
4568 14831 7.145985 TGACGCTTAAATGGATGTATCTAGAC 58.854 38.462 0.00 0.00 0.00 2.59
4569 14832 6.456501 ACGCTTAAATGGATGTATCTAGACC 58.543 40.000 0.00 0.00 0.00 3.85
4570 14833 6.041637 ACGCTTAAATGGATGTATCTAGACCA 59.958 38.462 0.00 0.00 35.09 4.02
4571 14834 6.929049 CGCTTAAATGGATGTATCTAGACCAA 59.071 38.462 3.35 0.00 34.28 3.67
4572 14835 7.441157 CGCTTAAATGGATGTATCTAGACCAAA 59.559 37.037 3.35 0.00 34.28 3.28
4573 14836 9.289782 GCTTAAATGGATGTATCTAGACCAAAT 57.710 33.333 3.35 0.00 34.28 2.32
4576 14839 8.833231 AAATGGATGTATCTAGACCAAATACG 57.167 34.615 3.35 0.00 34.28 3.06
4577 14840 6.971726 TGGATGTATCTAGACCAAATACGT 57.028 37.500 0.00 0.00 0.00 3.57
4578 14841 6.978338 TGGATGTATCTAGACCAAATACGTC 58.022 40.000 11.72 11.72 39.52 4.34
4579 14842 6.776116 TGGATGTATCTAGACCAAATACGTCT 59.224 38.462 16.64 0.00 43.05 4.18
4580 14843 7.940688 TGGATGTATCTAGACCAAATACGTCTA 59.059 37.037 16.64 11.28 40.93 2.59
4590 14853 8.234136 AGACCAAATACGTCTAGATACATTCA 57.766 34.615 0.00 0.00 38.82 2.57
4591 14854 8.861086 AGACCAAATACGTCTAGATACATTCAT 58.139 33.333 0.00 0.00 38.82 2.57
4592 14855 9.477484 GACCAAATACGTCTAGATACATTCATT 57.523 33.333 0.00 0.00 0.00 2.57
4593 14856 9.832445 ACCAAATACGTCTAGATACATTCATTT 57.168 29.630 0.00 0.00 0.00 2.32
4597 14860 8.749841 ATACGTCTAGATACATTCATTTCAGC 57.250 34.615 0.00 0.00 0.00 4.26
4598 14861 5.687730 ACGTCTAGATACATTCATTTCAGCG 59.312 40.000 0.00 0.00 0.00 5.18
4599 14862 5.687730 CGTCTAGATACATTCATTTCAGCGT 59.312 40.000 0.00 0.00 0.00 5.07
4600 14863 6.129326 CGTCTAGATACATTCATTTCAGCGTC 60.129 42.308 0.00 0.00 0.00 5.19
4601 14864 6.697455 GTCTAGATACATTCATTTCAGCGTCA 59.303 38.462 0.00 0.00 0.00 4.35
4602 14865 5.725110 AGATACATTCATTTCAGCGTCAC 57.275 39.130 0.00 0.00 0.00 3.67
4603 14866 2.880822 ACATTCATTTCAGCGTCACG 57.119 45.000 0.00 0.00 0.00 4.35
4604 14867 2.143122 ACATTCATTTCAGCGTCACGT 58.857 42.857 0.00 0.00 0.00 4.49
4605 14868 3.322369 ACATTCATTTCAGCGTCACGTA 58.678 40.909 0.00 0.00 0.00 3.57
4606 14869 3.743911 ACATTCATTTCAGCGTCACGTAA 59.256 39.130 0.00 0.00 0.00 3.18
4607 14870 4.391830 ACATTCATTTCAGCGTCACGTAAT 59.608 37.500 0.00 0.00 0.00 1.89
4608 14871 5.106712 ACATTCATTTCAGCGTCACGTAATT 60.107 36.000 0.00 0.00 0.00 1.40
4609 14872 4.577687 TCATTTCAGCGTCACGTAATTC 57.422 40.909 0.00 0.00 0.00 2.17
4610 14873 3.369756 TCATTTCAGCGTCACGTAATTCC 59.630 43.478 0.00 0.00 0.00 3.01
4611 14874 2.442212 TTCAGCGTCACGTAATTCCA 57.558 45.000 0.00 0.00 0.00 3.53
4612 14875 1.990799 TCAGCGTCACGTAATTCCAG 58.009 50.000 0.00 0.00 0.00 3.86
4613 14876 1.542472 TCAGCGTCACGTAATTCCAGA 59.458 47.619 0.00 0.00 0.00 3.86
4614 14877 1.654105 CAGCGTCACGTAATTCCAGAC 59.346 52.381 0.00 0.00 0.00 3.51
4616 14879 1.265568 CGTCACGTAATTCCAGACGG 58.734 55.000 12.83 0.00 45.81 4.79
4617 14880 1.135603 CGTCACGTAATTCCAGACGGA 60.136 52.381 12.83 1.92 45.81 4.69
4618 14881 2.527100 GTCACGTAATTCCAGACGGAG 58.473 52.381 3.74 0.00 44.10 4.63
4706 14975 5.758296 TGATAATTCCGTTAAGATGCCACTC 59.242 40.000 0.00 0.00 0.00 3.51
4755 15032 1.059835 GTCGATCAAGCAGTCTTTCGC 59.940 52.381 0.00 0.00 34.34 4.70
5030 16927 4.612264 TCTTTTCCGGTTTACTACAGCT 57.388 40.909 0.00 0.00 0.00 4.24
5102 17010 4.625135 CGCTGTCGTTTGTTATACTTGTC 58.375 43.478 0.00 0.00 0.00 3.18
5351 17691 4.009675 TGGCTTGGTTCTGCTTATAGTTG 58.990 43.478 0.00 0.00 0.00 3.16
5365 17710 2.586258 TAGTTGGCTGCTCGATCTTC 57.414 50.000 0.00 0.00 0.00 2.87
5433 17786 1.020861 TGCTGATGCTGTTGCCTACG 61.021 55.000 0.00 0.00 40.48 3.51
5441 17794 1.148310 CTGTTGCCTACGGAGTTGTG 58.852 55.000 0.00 0.00 37.78 3.33
5444 17797 0.470766 TTGCCTACGGAGTTGTGGTT 59.529 50.000 0.00 0.00 37.78 3.67
5445 17798 0.034337 TGCCTACGGAGTTGTGGTTC 59.966 55.000 0.00 0.00 37.78 3.62
5449 17802 2.485835 CCTACGGAGTTGTGGTTCCAAA 60.486 50.000 0.00 0.00 37.78 3.28
5520 17873 6.381801 GTTCATTGTGATCGAACCTTTCAAT 58.618 36.000 0.00 0.00 34.31 2.57
5559 17912 7.225538 CACTTATCTAATGACCCATGTTCTGAC 59.774 40.741 0.00 0.00 0.00 3.51
5599 17952 2.524569 TTTTGCCTTGCTTGCCTTAC 57.475 45.000 0.00 0.00 0.00 2.34
5628 17981 9.936759 TGTTCTTCAAATGTAAAAACTTCCTTT 57.063 25.926 0.00 0.00 0.00 3.11
5648 18001 2.936919 TGTACATGAGATGGGATGGC 57.063 50.000 0.00 0.00 33.60 4.40
5848 18316 9.100197 ACTTGATAAACCAATTTATTTCAGGGT 57.900 29.630 0.00 0.00 40.42 4.34
5902 18370 1.405821 GTCCCGTCTAGGTCATCACAG 59.594 57.143 0.00 0.00 38.74 3.66
5928 18396 3.624326 TTGCACGAAATGGTTCTTCTG 57.376 42.857 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.411977 TGCGCATGATTTGGAAATTTGAATT 59.588 32.000 5.66 0.00 0.00 2.17
12 13 4.936411 TGCGCATGATTTGGAAATTTGAAT 59.064 33.333 5.66 0.00 0.00 2.57
13 14 4.313282 TGCGCATGATTTGGAAATTTGAA 58.687 34.783 5.66 0.00 0.00 2.69
14 15 3.922910 TGCGCATGATTTGGAAATTTGA 58.077 36.364 5.66 0.00 0.00 2.69
18 2822 2.028294 TGGTTGCGCATGATTTGGAAAT 60.028 40.909 12.75 0.00 0.00 2.17
20 2824 0.964700 TGGTTGCGCATGATTTGGAA 59.035 45.000 12.75 0.00 0.00 3.53
27 2831 0.249657 GGGTTTTTGGTTGCGCATGA 60.250 50.000 12.75 0.00 0.00 3.07
31 2835 2.267426 GATATGGGTTTTTGGTTGCGC 58.733 47.619 0.00 0.00 0.00 6.09
70 2874 3.572642 CCCTAGGTTTTTGGTTGGTCTT 58.427 45.455 8.29 0.00 0.00 3.01
148 2952 0.821301 TCATTTGCTTCGTGTGGGCA 60.821 50.000 0.00 0.00 0.00 5.36
155 2959 3.541632 ACCGGATTATCATTTGCTTCGT 58.458 40.909 9.46 0.00 0.00 3.85
157 2961 3.058914 CGGACCGGATTATCATTTGCTTC 60.059 47.826 9.46 0.00 0.00 3.86
201 3005 0.326927 GCTTACCTTAGTGTGGCCCA 59.673 55.000 0.00 0.00 0.00 5.36
207 3011 4.755123 GTGTGATGTTGCTTACCTTAGTGT 59.245 41.667 0.00 0.00 0.00 3.55
215 3019 5.715070 ACTCTCTAGTGTGATGTTGCTTAC 58.285 41.667 1.16 0.00 33.57 2.34
221 3025 5.585445 CGGTACTACTCTCTAGTGTGATGTT 59.415 44.000 1.16 0.00 36.36 2.71
247 3051 3.680786 TCGCTGGTGGACGAGTGG 61.681 66.667 2.99 0.00 33.78 4.00
337 3143 3.042682 TGTCTACACCAAGGAAGGTTGA 58.957 45.455 0.00 0.00 40.77 3.18
355 3161 3.067833 GCTTATAAGGGCCGATCTTGTC 58.932 50.000 14.28 0.00 0.00 3.18
356 3162 2.548067 CGCTTATAAGGGCCGATCTTGT 60.548 50.000 15.70 0.00 32.04 3.16
393 3199 5.155278 TCCTTTCCGCTACAAGTAAATGA 57.845 39.130 0.00 0.00 0.00 2.57
395 3201 5.106830 CGTTTCCTTTCCGCTACAAGTAAAT 60.107 40.000 0.00 0.00 0.00 1.40
397 3203 3.742369 CGTTTCCTTTCCGCTACAAGTAA 59.258 43.478 0.00 0.00 0.00 2.24
409 3215 4.287238 TGTTTCTTCTGCGTTTCCTTTC 57.713 40.909 0.00 0.00 0.00 2.62
411 3217 4.712122 TTTGTTTCTTCTGCGTTTCCTT 57.288 36.364 0.00 0.00 0.00 3.36
413 3219 3.239712 CGTTTTGTTTCTTCTGCGTTTCC 59.760 43.478 0.00 0.00 0.00 3.13
419 4085 6.864560 AAAAGTACGTTTTGTTTCTTCTGC 57.135 33.333 0.54 0.00 36.96 4.26
452 5785 6.596621 AGAGTAGGTCTGCTTTTCTTTCTTT 58.403 36.000 0.00 0.00 32.57 2.52
464 5797 2.128507 CCCCCGAGAGTAGGTCTGC 61.129 68.421 0.00 0.00 34.71 4.26
465 5798 2.128507 GCCCCCGAGAGTAGGTCTG 61.129 68.421 0.00 0.00 34.71 3.51
466 5799 2.164332 TTGCCCCCGAGAGTAGGTCT 62.164 60.000 0.00 0.00 38.71 3.85
467 5800 1.262640 TTTGCCCCCGAGAGTAGGTC 61.263 60.000 0.00 0.00 0.00 3.85
469 5802 0.326927 TTTTTGCCCCCGAGAGTAGG 59.673 55.000 0.00 0.00 0.00 3.18
470 5803 1.450025 GTTTTTGCCCCCGAGAGTAG 58.550 55.000 0.00 0.00 0.00 2.57
471 5804 0.037160 GGTTTTTGCCCCCGAGAGTA 59.963 55.000 0.00 0.00 0.00 2.59
472 5805 1.228459 GGTTTTTGCCCCCGAGAGT 60.228 57.895 0.00 0.00 0.00 3.24
473 5806 1.228429 TGGTTTTTGCCCCCGAGAG 60.228 57.895 0.00 0.00 0.00 3.20
475 5808 2.570284 GGTGGTTTTTGCCCCCGAG 61.570 63.158 0.00 0.00 0.00 4.63
477 5810 2.840102 TGGTGGTTTTTGCCCCCG 60.840 61.111 0.00 0.00 0.00 5.73
482 6834 0.741915 TCTTCCGTGGTGGTTTTTGC 59.258 50.000 0.00 0.00 39.52 3.68
487 6839 1.029681 GCTTTTCTTCCGTGGTGGTT 58.970 50.000 0.00 0.00 39.52 3.67
488 6840 0.106918 TGCTTTTCTTCCGTGGTGGT 60.107 50.000 0.00 0.00 39.52 4.16
552 8748 3.153676 TCGGATTATCGTTCGCTTTGA 57.846 42.857 0.00 0.00 0.00 2.69
580 8784 0.034089 CTTAGTGGGGCAAAGAGGGG 60.034 60.000 0.00 0.00 0.00 4.79
584 8788 2.290705 GGTTAGCTTAGTGGGGCAAAGA 60.291 50.000 0.00 0.00 0.00 2.52
586 8790 1.612199 CGGTTAGCTTAGTGGGGCAAA 60.612 52.381 0.00 0.00 0.00 3.68
588 8792 0.905809 TCGGTTAGCTTAGTGGGGCA 60.906 55.000 0.00 0.00 0.00 5.36
606 8831 2.096248 ACAGTAGGAGTAGCACTGCTC 58.904 52.381 6.86 7.17 43.78 4.26
707 8951 4.394712 CTGCTGGTGGGACGGGAC 62.395 72.222 0.00 0.00 0.00 4.46
739 8986 1.113517 GTGAATCGGATCGGAGGGGA 61.114 60.000 9.03 0.00 0.00 4.81
740 8987 1.367840 GTGAATCGGATCGGAGGGG 59.632 63.158 9.03 0.00 0.00 4.79
741 8988 1.115930 AGGTGAATCGGATCGGAGGG 61.116 60.000 9.03 0.00 0.00 4.30
742 8989 0.315568 GAGGTGAATCGGATCGGAGG 59.684 60.000 9.03 0.00 0.00 4.30
743 8990 0.039978 CGAGGTGAATCGGATCGGAG 60.040 60.000 9.03 0.00 39.04 4.63
744 8991 2.030551 CGAGGTGAATCGGATCGGA 58.969 57.895 5.34 5.34 39.04 4.55
745 8992 1.661821 GCGAGGTGAATCGGATCGG 60.662 63.158 0.00 0.00 42.94 4.18
746 8993 1.661821 GGCGAGGTGAATCGGATCG 60.662 63.158 0.00 0.00 42.94 3.69
747 8994 0.319125 GAGGCGAGGTGAATCGGATC 60.319 60.000 0.00 0.00 42.94 3.36
748 8995 1.742768 GAGGCGAGGTGAATCGGAT 59.257 57.895 0.00 0.00 42.94 4.18
874 9133 2.045926 CTGCTAGGTGGTGGTGGC 60.046 66.667 0.00 0.00 0.00 5.01
1210 9582 2.063979 TGATGGCGAAGGGATCCGT 61.064 57.895 5.45 2.61 0.00 4.69
1421 9815 2.987821 GAGAAGACTAACAAGTCACGCC 59.012 50.000 8.16 0.00 41.02 5.68
1435 9829 4.762251 ACCAAAATTAGCAGGTGAGAAGAC 59.238 41.667 0.00 0.00 32.04 3.01
1436 9830 4.985538 ACCAAAATTAGCAGGTGAGAAGA 58.014 39.130 0.00 0.00 32.04 2.87
1437 9831 4.142816 CGACCAAAATTAGCAGGTGAGAAG 60.143 45.833 0.00 0.00 33.77 2.85
1509 9903 6.866010 ACTCAATTTCCAATTTCCAAAAGC 57.134 33.333 0.00 0.00 0.00 3.51
1510 9904 7.118245 GCCTACTCAATTTCCAATTTCCAAAAG 59.882 37.037 0.00 0.00 0.00 2.27
1511 9905 6.934083 GCCTACTCAATTTCCAATTTCCAAAA 59.066 34.615 0.00 0.00 0.00 2.44
1514 9908 5.185635 CAGCCTACTCAATTTCCAATTTCCA 59.814 40.000 0.00 0.00 0.00 3.53
1515 9909 5.418840 TCAGCCTACTCAATTTCCAATTTCC 59.581 40.000 0.00 0.00 0.00 3.13
1516 9910 6.375455 TCTCAGCCTACTCAATTTCCAATTTC 59.625 38.462 0.00 0.00 0.00 2.17
1517 9911 6.248433 TCTCAGCCTACTCAATTTCCAATTT 58.752 36.000 0.00 0.00 0.00 1.82
1518 9912 5.819991 TCTCAGCCTACTCAATTTCCAATT 58.180 37.500 0.00 0.00 0.00 2.32
1519 9913 5.441718 TCTCAGCCTACTCAATTTCCAAT 57.558 39.130 0.00 0.00 0.00 3.16
1552 9947 6.108687 TCCATACTGACTGTAGCAAATTCAG 58.891 40.000 0.00 0.00 39.72 3.02
1613 10008 0.669318 TCACTGGCATCGAACCGAAC 60.669 55.000 0.00 0.00 39.99 3.95
1667 10063 3.356290 ACAAGGGTACAAAGATGATGCC 58.644 45.455 0.00 0.00 0.00 4.40
1672 10068 4.630069 CCGACTAACAAGGGTACAAAGATG 59.370 45.833 0.00 0.00 0.00 2.90
1675 10071 2.740447 GCCGACTAACAAGGGTACAAAG 59.260 50.000 0.00 0.00 0.00 2.77
1754 10150 4.065088 GTGACAGCAACTCCATCACTTTA 58.935 43.478 0.00 0.00 37.33 1.85
1785 10181 3.042189 CACAACTGTTGCAATAACACGG 58.958 45.455 19.82 0.00 0.00 4.94
1841 10237 7.403312 TGGGATTATGTCACACCTAAAATTG 57.597 36.000 0.00 0.00 34.61 2.32
1860 10256 6.910191 TGGACAGTCATATATTGTTTGGGAT 58.090 36.000 2.17 0.00 0.00 3.85
1905 10301 5.683876 AGGATTCATATATCGGTTGGGAG 57.316 43.478 0.00 0.00 0.00 4.30
1912 10308 5.877012 CCACTGGAAAGGATTCATATATCGG 59.123 44.000 0.00 0.00 37.29 4.18
1980 10376 0.107508 CTGGAACCATGATCGCACCT 60.108 55.000 0.00 0.00 0.00 4.00
1981 10377 0.392998 ACTGGAACCATGATCGCACC 60.393 55.000 0.00 0.00 0.00 5.01
1984 10380 3.270877 ACTAAACTGGAACCATGATCGC 58.729 45.455 0.00 0.00 0.00 4.58
1985 10381 5.880054 AAACTAAACTGGAACCATGATCG 57.120 39.130 0.00 0.00 0.00 3.69
1987 10383 6.719370 TGCTTAAACTAAACTGGAACCATGAT 59.281 34.615 0.00 0.00 0.00 2.45
1999 10576 3.911964 CACCGCATGTGCTTAAACTAAAC 59.088 43.478 0.00 0.00 38.34 2.01
2102 10687 6.769822 ACTTGCCACTATATCATCTGGAAAAG 59.230 38.462 0.00 0.00 0.00 2.27
2384 11312 6.745190 GCTCAACCCCATTGATGATATAGTCA 60.745 42.308 0.00 0.00 46.37 3.41
2547 11475 3.492102 TGGAGTGTTTCAGGAGGAAAG 57.508 47.619 0.00 0.00 45.76 2.62
2822 12350 9.282247 CAAGATATCACACATCTAAAAGTTTGC 57.718 33.333 5.32 0.00 32.40 3.68
2834 12362 7.400599 AAACAGAATGCAAGATATCACACAT 57.599 32.000 5.32 2.25 42.53 3.21
2842 12370 9.414295 CAGAAATCAAAAACAGAATGCAAGATA 57.586 29.630 0.00 0.00 42.53 1.98
2942 12531 6.763135 CCTATAAGTTCTACTGCATGAAAGCA 59.237 38.462 0.00 0.00 43.35 3.91
2943 12532 6.203723 CCCTATAAGTTCTACTGCATGAAAGC 59.796 42.308 0.00 0.00 0.00 3.51
2945 12534 7.195374 ACCCTATAAGTTCTACTGCATGAAA 57.805 36.000 0.00 0.00 0.00 2.69
3020 12609 8.038351 ACAAAACTAAGCATAACAACCAGTTTT 58.962 29.630 0.00 0.00 42.40 2.43
3071 12660 5.793817 TCAGAAACATAGACTTGCTAGCAA 58.206 37.500 27.67 27.67 31.33 3.91
3114 12704 7.914465 AGAAATGCATTCGAAGATTAGAGAAC 58.086 34.615 13.38 0.00 43.15 3.01
3140 12730 5.091552 AGTAGAGTGGGACAAAAGTATGGA 58.908 41.667 0.00 0.00 44.16 3.41
3145 12735 5.010820 GTGTCTAGTAGAGTGGGACAAAAGT 59.989 44.000 0.00 0.00 44.16 2.66
3149 12739 4.108501 TGTGTCTAGTAGAGTGGGACAA 57.891 45.455 0.00 0.00 44.16 3.18
3247 12837 1.299541 CAGGGCAATGTAAGCTACCG 58.700 55.000 0.00 0.00 0.00 4.02
3248 12838 1.025041 GCAGGGCAATGTAAGCTACC 58.975 55.000 0.00 0.00 0.00 3.18
3665 13257 2.565841 GTGGAGCAACATATCTGGGTC 58.434 52.381 0.00 0.00 0.00 4.46
3747 13346 2.501723 AGAACGGTGATCATTGGCTACT 59.498 45.455 0.00 0.00 0.00 2.57
3946 13992 2.543067 ATTCCAGCAGAAGGACCGGC 62.543 60.000 0.00 0.00 38.07 6.13
4016 14066 6.764308 AACAATCACTGACAATTATGGGAG 57.236 37.500 0.00 0.00 0.00 4.30
4081 14135 2.525368 AGTTACCCCTTTGGACAATGC 58.475 47.619 0.00 0.00 38.00 3.56
4107 14161 1.546476 CTCCTCCGAGTATGTATGGGC 59.454 57.143 0.00 0.00 0.00 5.36
4110 14164 5.730296 AAATCCTCCTCCGAGTATGTATG 57.270 43.478 0.00 0.00 33.93 2.39
4198 14389 4.251543 GGTACAAACCAAATGAAGTGGG 57.748 45.455 0.00 0.00 45.98 4.61
4313 14512 7.806180 AGGTACCAATTGACAGAGCTATAAAT 58.194 34.615 15.94 0.00 0.00 1.40
4314 14513 7.195374 AGGTACCAATTGACAGAGCTATAAA 57.805 36.000 15.94 0.00 0.00 1.40
4315 14514 6.808321 AGGTACCAATTGACAGAGCTATAA 57.192 37.500 15.94 0.00 0.00 0.98
4316 14515 6.156256 ACAAGGTACCAATTGACAGAGCTATA 59.844 38.462 18.16 0.00 0.00 1.31
4317 14516 5.045578 ACAAGGTACCAATTGACAGAGCTAT 60.046 40.000 18.16 0.00 0.00 2.97
4318 14517 4.286032 ACAAGGTACCAATTGACAGAGCTA 59.714 41.667 18.16 0.00 0.00 3.32
4319 14518 3.073062 ACAAGGTACCAATTGACAGAGCT 59.927 43.478 18.16 1.15 0.00 4.09
4320 14519 3.412386 ACAAGGTACCAATTGACAGAGC 58.588 45.455 18.16 0.00 0.00 4.09
4321 14520 4.641396 TGACAAGGTACCAATTGACAGAG 58.359 43.478 18.16 0.00 29.90 3.35
4322 14521 4.102524 ACTGACAAGGTACCAATTGACAGA 59.897 41.667 32.74 11.89 45.66 3.41
4324 14523 4.431416 ACTGACAAGGTACCAATTGACA 57.569 40.909 18.16 16.38 31.92 3.58
4325 14524 7.448748 AAATACTGACAAGGTACCAATTGAC 57.551 36.000 18.16 13.22 0.00 3.18
4328 14527 9.623000 GGTATAAATACTGACAAGGTACCAATT 57.377 33.333 15.94 0.00 33.81 2.32
4329 14528 8.999895 AGGTATAAATACTGACAAGGTACCAAT 58.000 33.333 15.94 0.00 33.29 3.16
4330 14529 8.383374 AGGTATAAATACTGACAAGGTACCAA 57.617 34.615 15.94 0.00 33.29 3.67
4331 14530 7.842743 AGAGGTATAAATACTGACAAGGTACCA 59.157 37.037 15.94 0.00 33.29 3.25
4332 14531 8.142551 CAGAGGTATAAATACTGACAAGGTACC 58.857 40.741 2.73 2.73 33.81 3.34
4333 14532 8.693625 ACAGAGGTATAAATACTGACAAGGTAC 58.306 37.037 0.00 0.00 33.81 3.34
4334 14533 8.834004 ACAGAGGTATAAATACTGACAAGGTA 57.166 34.615 0.00 0.00 33.81 3.08
4335 14534 7.399191 TGACAGAGGTATAAATACTGACAAGGT 59.601 37.037 0.00 0.00 32.69 3.50
4336 14535 7.782049 TGACAGAGGTATAAATACTGACAAGG 58.218 38.462 0.00 0.00 32.69 3.61
4337 14536 7.923344 CCTGACAGAGGTATAAATACTGACAAG 59.077 40.741 3.32 0.00 37.02 3.16
4338 14537 7.782049 CCTGACAGAGGTATAAATACTGACAA 58.218 38.462 3.32 0.00 37.02 3.18
4339 14538 7.348080 CCTGACAGAGGTATAAATACTGACA 57.652 40.000 3.32 0.00 37.02 3.58
4396 14630 8.684386 TGTAGGTTATCATGAAACAGTTGAAA 57.316 30.769 17.03 1.09 0.00 2.69
4399 14633 6.149308 TGCTGTAGGTTATCATGAAACAGTTG 59.851 38.462 17.03 8.22 36.20 3.16
4402 14636 6.741992 TTGCTGTAGGTTATCATGAAACAG 57.258 37.500 17.03 15.03 36.74 3.16
4404 14638 7.377766 TCTTTGCTGTAGGTTATCATGAAAC 57.622 36.000 0.00 5.90 0.00 2.78
4470 14704 7.182817 TCTTTGCTGTAGGTAATACTGATGT 57.817 36.000 0.00 0.00 35.84 3.06
4517 14780 1.683943 TCCGGACGGAGGTAATACTG 58.316 55.000 9.76 0.00 39.76 2.74
4522 14785 2.738743 AGTAATTCCGGACGGAGGTAA 58.261 47.619 13.64 0.00 46.06 2.85
4534 14797 6.431198 TCCATTTAAGCGTCAAGTAATTCC 57.569 37.500 0.00 0.00 0.00 3.01
4536 14799 7.391148 ACATCCATTTAAGCGTCAAGTAATT 57.609 32.000 0.00 0.00 0.00 1.40
4540 14803 6.349300 AGATACATCCATTTAAGCGTCAAGT 58.651 36.000 0.00 0.00 0.00 3.16
4541 14804 6.851222 AGATACATCCATTTAAGCGTCAAG 57.149 37.500 0.00 0.00 0.00 3.02
4542 14805 7.652105 GTCTAGATACATCCATTTAAGCGTCAA 59.348 37.037 0.00 0.00 0.00 3.18
4543 14806 7.145985 GTCTAGATACATCCATTTAAGCGTCA 58.854 38.462 0.00 0.00 0.00 4.35
4547 14810 8.677148 TTTGGTCTAGATACATCCATTTAAGC 57.323 34.615 0.00 0.00 0.00 3.09
4551 14814 8.429641 ACGTATTTGGTCTAGATACATCCATTT 58.570 33.333 0.00 0.00 0.00 2.32
4552 14815 7.963532 ACGTATTTGGTCTAGATACATCCATT 58.036 34.615 0.00 0.00 0.00 3.16
4553 14816 7.451877 AGACGTATTTGGTCTAGATACATCCAT 59.548 37.037 0.00 0.00 42.69 3.41
4567 14830 9.832445 AAATGAATGTATCTAGACGTATTTGGT 57.168 29.630 0.00 0.00 0.00 3.67
4571 14834 9.197694 GCTGAAATGAATGTATCTAGACGTATT 57.802 33.333 0.00 0.00 0.00 1.89
4572 14835 7.539022 CGCTGAAATGAATGTATCTAGACGTAT 59.461 37.037 0.00 0.00 0.00 3.06
4573 14836 6.856426 CGCTGAAATGAATGTATCTAGACGTA 59.144 38.462 0.00 0.00 0.00 3.57
4574 14837 5.687730 CGCTGAAATGAATGTATCTAGACGT 59.312 40.000 0.00 0.00 0.00 4.34
4575 14838 5.687730 ACGCTGAAATGAATGTATCTAGACG 59.312 40.000 0.00 0.00 0.00 4.18
4576 14839 6.697455 TGACGCTGAAATGAATGTATCTAGAC 59.303 38.462 0.00 0.00 0.00 2.59
4577 14840 6.697455 GTGACGCTGAAATGAATGTATCTAGA 59.303 38.462 0.00 0.00 0.00 2.43
4578 14841 6.345329 CGTGACGCTGAAATGAATGTATCTAG 60.345 42.308 0.00 0.00 0.00 2.43
4579 14842 5.458779 CGTGACGCTGAAATGAATGTATCTA 59.541 40.000 0.00 0.00 0.00 1.98
4580 14843 4.268644 CGTGACGCTGAAATGAATGTATCT 59.731 41.667 0.00 0.00 0.00 1.98
4581 14844 4.032900 ACGTGACGCTGAAATGAATGTATC 59.967 41.667 4.25 0.00 0.00 2.24
4582 14845 3.932710 ACGTGACGCTGAAATGAATGTAT 59.067 39.130 4.25 0.00 0.00 2.29
4583 14846 3.322369 ACGTGACGCTGAAATGAATGTA 58.678 40.909 4.25 0.00 0.00 2.29
4584 14847 2.143122 ACGTGACGCTGAAATGAATGT 58.857 42.857 4.25 0.00 0.00 2.71
4585 14848 2.880822 ACGTGACGCTGAAATGAATG 57.119 45.000 4.25 0.00 0.00 2.67
4586 14849 5.447279 GGAATTACGTGACGCTGAAATGAAT 60.447 40.000 4.25 0.00 0.00 2.57
4587 14850 4.142988 GGAATTACGTGACGCTGAAATGAA 60.143 41.667 4.25 0.00 0.00 2.57
4588 14851 3.369756 GGAATTACGTGACGCTGAAATGA 59.630 43.478 4.25 0.00 0.00 2.57
4589 14852 3.124466 TGGAATTACGTGACGCTGAAATG 59.876 43.478 4.25 0.00 0.00 2.32
4590 14853 3.331150 TGGAATTACGTGACGCTGAAAT 58.669 40.909 4.25 0.00 0.00 2.17
4591 14854 2.734606 CTGGAATTACGTGACGCTGAAA 59.265 45.455 4.25 0.00 0.00 2.69
4592 14855 2.029739 TCTGGAATTACGTGACGCTGAA 60.030 45.455 4.25 0.00 0.00 3.02
4593 14856 1.542472 TCTGGAATTACGTGACGCTGA 59.458 47.619 4.25 0.00 0.00 4.26
4594 14857 1.654105 GTCTGGAATTACGTGACGCTG 59.346 52.381 4.25 0.00 0.00 5.18
4595 14858 1.731424 CGTCTGGAATTACGTGACGCT 60.731 52.381 18.56 0.00 42.63 5.07
4596 14859 0.638746 CGTCTGGAATTACGTGACGC 59.361 55.000 18.56 0.00 42.63 5.19
4597 14860 1.135603 TCCGTCTGGAATTACGTGACG 60.136 52.381 21.71 21.71 42.85 4.35
4598 14861 2.527100 CTCCGTCTGGAATTACGTGAC 58.473 52.381 0.00 4.16 45.87 3.67
4599 14862 1.475280 CCTCCGTCTGGAATTACGTGA 59.525 52.381 0.00 0.00 45.87 4.35
4600 14863 1.470979 CCCTCCGTCTGGAATTACGTG 60.471 57.143 0.00 0.00 45.87 4.49
4601 14864 0.822164 CCCTCCGTCTGGAATTACGT 59.178 55.000 0.00 0.00 45.87 3.57
4602 14865 1.067212 CTCCCTCCGTCTGGAATTACG 59.933 57.143 0.00 0.00 45.87 3.18
4603 14866 2.108970 ACTCCCTCCGTCTGGAATTAC 58.891 52.381 0.00 0.00 45.87 1.89
4604 14867 2.544844 ACTCCCTCCGTCTGGAATTA 57.455 50.000 0.00 0.00 45.87 1.40
4605 14868 2.292323 ACTACTCCCTCCGTCTGGAATT 60.292 50.000 0.00 0.00 45.87 2.17
4606 14869 1.288335 ACTACTCCCTCCGTCTGGAAT 59.712 52.381 0.00 0.00 45.87 3.01
4607 14870 0.702902 ACTACTCCCTCCGTCTGGAA 59.297 55.000 0.00 0.00 45.87 3.53
4608 14871 0.702902 AACTACTCCCTCCGTCTGGA 59.297 55.000 0.00 0.00 43.88 3.86
4609 14872 1.558233 AAACTACTCCCTCCGTCTGG 58.442 55.000 0.00 0.00 0.00 3.86
4610 14873 6.461110 TTAATAAACTACTCCCTCCGTCTG 57.539 41.667 0.00 0.00 0.00 3.51
4611 14874 6.041751 CCATTAATAAACTACTCCCTCCGTCT 59.958 42.308 0.00 0.00 0.00 4.18
4612 14875 6.221659 CCATTAATAAACTACTCCCTCCGTC 58.778 44.000 0.00 0.00 0.00 4.79
4613 14876 5.071384 CCCATTAATAAACTACTCCCTCCGT 59.929 44.000 0.00 0.00 0.00 4.69
4614 14877 5.071384 ACCCATTAATAAACTACTCCCTCCG 59.929 44.000 0.00 0.00 0.00 4.63
4615 14878 6.511017 ACCCATTAATAAACTACTCCCTCC 57.489 41.667 0.00 0.00 0.00 4.30
4706 14975 3.818295 ATACTCTAGGCTAGGTGGGAG 57.182 52.381 20.92 12.99 0.00 4.30
4755 15032 1.812571 ACGAGGTAGGCATGCAAAAAG 59.187 47.619 21.36 6.65 0.00 2.27
4789 15066 3.181482 GCGAGGACATGATTCTTCAGAGA 60.181 47.826 0.00 0.00 34.73 3.10
4793 15070 3.616956 AAGCGAGGACATGATTCTTCA 57.383 42.857 0.00 0.00 36.00 3.02
5102 17010 5.012239 CCCATCCATATTTACATCCCACTG 58.988 45.833 0.00 0.00 0.00 3.66
5351 17691 2.964389 GCGGAAGATCGAGCAGCC 60.964 66.667 2.38 2.24 0.00 4.85
5365 17710 2.329678 TTTCACAGGCAACAACGCGG 62.330 55.000 12.47 0.00 41.41 6.46
5433 17786 4.465632 AACTTTTTGGAACCACAACTCC 57.534 40.909 0.00 0.00 0.00 3.85
5520 17873 9.154632 TCATTAGATAAGTGCCAAGTATAGGAA 57.845 33.333 0.00 0.00 0.00 3.36
5559 17912 7.426456 GCAAAATGTGACGTATCAGTAATTCAG 59.574 37.037 0.00 0.00 34.75 3.02
5628 17981 2.779430 AGCCATCCCATCTCATGTACAA 59.221 45.455 0.00 0.00 0.00 2.41
5630 17983 3.498774 AAGCCATCCCATCTCATGTAC 57.501 47.619 0.00 0.00 0.00 2.90
5632 17985 2.747467 CGAAAGCCATCCCATCTCATGT 60.747 50.000 0.00 0.00 0.00 3.21
5657 18010 2.131067 AAAGCCACCACCAAACCGG 61.131 57.895 0.00 0.00 42.50 5.28
5663 18016 0.754957 CAGAACCAAAGCCACCACCA 60.755 55.000 0.00 0.00 0.00 4.17
5848 18316 4.788925 AGGTATGGCCATGCTAGTTAAA 57.211 40.909 29.67 4.31 40.61 1.52
5902 18370 0.040425 ACCATTTCGTGCAAACGAGC 60.040 50.000 0.93 0.00 43.33 5.03


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

AutoCloner maintained by Alex Coulton.