Multiple sequence alignment - TraesCS3D01G111700

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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 TraesCS3D01G111700 chr3D 100.000 4003 0 0 1 4003 66141200 66137198 0.000000e+00 7393.0
1 TraesCS3D01G111700 chr3D 89.886 1137 86 15 2032 3141 66310417 66311551 0.000000e+00 1435.0
2 TraesCS3D01G111700 chr3D 86.505 1193 71 36 514 1649 66309267 66310426 0.000000e+00 1229.0
3 TraesCS3D01G111700 chr3D 92.550 698 26 16 2668 3344 66124291 66123599 0.000000e+00 977.0
4 TraesCS3D01G111700 chr3D 90.698 731 54 5 2513 3235 66146993 66146269 0.000000e+00 961.0
5 TraesCS3D01G111700 chr3D 95.602 523 16 5 3426 3943 66306702 66306182 0.000000e+00 832.0
6 TraesCS3D01G111700 chr3D 95.098 510 21 3 3427 3933 66300099 66299591 0.000000e+00 800.0
7 TraesCS3D01G111700 chr3D 97.926 434 7 2 3339 3772 66122065 66121634 0.000000e+00 750.0
8 TraesCS3D01G111700 chr3D 94.848 427 21 1 2154 2580 66124737 66124312 0.000000e+00 665.0
9 TraesCS3D01G111700 chr3D 90.039 512 49 2 2335 2844 66260860 66260349 0.000000e+00 662.0
10 TraesCS3D01G111700 chr3D 86.723 595 33 27 2837 3412 66252766 66252199 1.580000e-173 619.0
11 TraesCS3D01G111700 chr3D 93.235 340 18 4 1 337 66251507 66251844 2.780000e-136 496.0
12 TraesCS3D01G111700 chr3D 88.319 351 28 8 2867 3207 66237494 66237147 3.720000e-110 409.0
13 TraesCS3D01G111700 chr3D 91.781 292 20 4 1 291 66302731 66303019 1.730000e-108 403.0
14 TraesCS3D01G111700 chr3D 95.618 251 10 1 3426 3676 66252087 66251838 6.230000e-108 401.0
15 TraesCS3D01G111700 chr3D 93.651 252 14 2 218 467 66308613 66308864 3.780000e-100 375.0
16 TraesCS3D01G111700 chr3D 93.717 191 12 0 3245 3435 66306914 66306724 1.820000e-73 287.0
17 TraesCS3D01G111700 chr3D 92.670 191 13 1 3245 3435 66300311 66300122 1.420000e-69 274.0
18 TraesCS3D01G111700 chr3D 92.553 188 13 1 3245 3432 66237700 66237514 6.590000e-68 268.0
19 TraesCS3D01G111700 chr3D 95.041 121 5 1 1 120 66308151 66308271 5.280000e-44 189.0
20 TraesCS3D01G111700 chr3D 97.297 37 1 0 750 786 66147049 66147013 3.340000e-06 63.9
21 TraesCS3D01G111700 chr3D 78.512 121 9 7 1207 1324 66261013 66260907 3.340000e-06 63.9
22 TraesCS3D01G111700 chr3D 100.000 28 0 0 468 495 66309253 66309280 7.000000e-03 52.8
23 TraesCS3D01G111700 chr3B 88.304 1445 112 28 2032 3431 109861705 109860273 0.000000e+00 1679.0
24 TraesCS3D01G111700 chr3B 91.105 697 29 12 514 1197 109862803 109862127 0.000000e+00 913.0
25 TraesCS3D01G111700 chr3B 91.388 569 28 6 3426 3990 109797042 109796491 0.000000e+00 760.0
26 TraesCS3D01G111700 chr3B 90.210 429 27 7 1236 1649 109862124 109861696 2.720000e-151 545.0
27 TraesCS3D01G111700 chr3B 87.816 435 31 10 3574 4003 109819355 109818938 1.290000e-134 490.0
28 TraesCS3D01G111700 chr3B 85.455 385 32 15 3058 3431 109797438 109797067 2.920000e-101 379.0
29 TraesCS3D01G111700 chr3B 95.833 120 5 0 3426 3545 109860248 109860129 1.140000e-45 195.0
30 TraesCS3D01G111700 chr3B 100.000 28 0 0 468 495 109862817 109862790 7.000000e-03 52.8
31 TraesCS3D01G111700 chr3A 89.861 1154 78 21 2032 3152 77410983 77409836 0.000000e+00 1447.0
32 TraesCS3D01G111700 chr3A 88.057 1189 72 33 514 1652 77412139 77410971 0.000000e+00 1345.0
33 TraesCS3D01G111700 chr3A 90.501 579 36 6 3431 4003 77409405 77408840 0.000000e+00 747.0
34 TraesCS3D01G111700 chr3A 91.543 473 30 9 1 470 77413064 77412599 0.000000e+00 643.0
35 TraesCS3D01G111700 chr3A 92.440 291 15 4 3149 3435 77409719 77409432 3.720000e-110 409.0
36 TraesCS3D01G111700 chr1A 86.310 336 36 9 1666 1995 513246079 513246410 1.370000e-94 357.0
37 TraesCS3D01G111700 chr1A 74.012 658 144 21 2041 2676 570614984 570615636 4.000000e-60 243.0
38 TraesCS3D01G111700 chr1A 82.143 84 15 0 1393 1476 567719892 567719975 5.550000e-09 73.1
39 TraesCS3D01G111700 chr1A 82.143 84 15 0 1393 1476 567830731 567830814 5.550000e-09 73.1
40 TraesCS3D01G111700 chrUn 85.933 327 41 4 1667 1991 19825865 19826188 1.070000e-90 344.0
41 TraesCS3D01G111700 chrUn 84.431 334 44 6 1664 1995 100188518 100188845 4.990000e-84 322.0
42 TraesCS3D01G111700 chrUn 100.000 28 0 0 3426 3453 35202953 35202926 7.000000e-03 52.8
43 TraesCS3D01G111700 chr5D 84.685 333 45 5 1667 1996 482319151 482319480 1.070000e-85 327.0
44 TraesCS3D01G111700 chr5D 84.337 332 44 7 1667 1995 23170729 23170403 6.460000e-83 318.0
45 TraesCS3D01G111700 chr5D 100.000 32 0 0 3426 3457 521481345 521481376 4.320000e-05 60.2
46 TraesCS3D01G111700 chr4B 84.524 336 44 7 1664 1995 672034941 672034610 3.860000e-85 326.0
47 TraesCS3D01G111700 chr7D 84.639 332 43 7 1667 1995 24028694 24029020 1.390000e-84 324.0
48 TraesCS3D01G111700 chr7D 84.932 73 11 0 98 170 256220869 256220797 1.540000e-09 75.0
49 TraesCS3D01G111700 chr7B 84.366 339 41 10 1667 1998 711532040 711532373 4.990000e-84 322.0
50 TraesCS3D01G111700 chr7B 85.714 70 8 2 102 170 234914742 234914674 5.550000e-09 73.1
51 TraesCS3D01G111700 chr2D 84.337 332 45 7 1669 1998 169594921 169594595 6.460000e-83 318.0
52 TraesCS3D01G111700 chr2D 90.805 87 6 2 81 165 634317951 634317865 9.090000e-22 115.0
53 TraesCS3D01G111700 chr1D 90.000 90 8 1 81 169 415622977 415623066 9.090000e-22 115.0
54 TraesCS3D01G111700 chr1D 81.176 85 16 0 1393 1477 473594304 473594388 7.180000e-08 69.4
55 TraesCS3D01G111700 chr6D 92.105 76 5 1 82 156 27536379 27536304 5.470000e-19 106.0
56 TraesCS3D01G111700 chr1B 82.143 84 15 0 1393 1476 658469226 658469309 5.550000e-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 TraesCS3D01G111700 chr3D 66137198 66141200 4002 True 7393.000000 7393 100.0000 1 4003 1 chr3D.!!$R1 4002
1 TraesCS3D01G111700 chr3D 66121634 66124737 3103 True 797.333333 977 95.1080 2154 3772 3 chr3D.!!$R2 1618
2 TraesCS3D01G111700 chr3D 66308151 66311551 3400 False 656.160000 1435 93.0166 1 3141 5 chr3D.!!$F3 3140
3 TraesCS3D01G111700 chr3D 66306182 66306914 732 True 559.500000 832 94.6595 3245 3943 2 chr3D.!!$R8 698
4 TraesCS3D01G111700 chr3D 66299591 66300311 720 True 537.000000 800 93.8840 3245 3933 2 chr3D.!!$R7 688
5 TraesCS3D01G111700 chr3D 66146269 66147049 780 True 512.450000 961 93.9975 750 3235 2 chr3D.!!$R3 2485
6 TraesCS3D01G111700 chr3D 66251838 66252766 928 True 510.000000 619 91.1705 2837 3676 2 chr3D.!!$R5 839
7 TraesCS3D01G111700 chr3D 66260349 66261013 664 True 362.950000 662 84.2755 1207 2844 2 chr3D.!!$R6 1637
8 TraesCS3D01G111700 chr3D 66237147 66237700 553 True 338.500000 409 90.4360 2867 3432 2 chr3D.!!$R4 565
9 TraesCS3D01G111700 chr3B 109860129 109862817 2688 True 676.960000 1679 93.0904 468 3545 5 chr3B.!!$R3 3077
10 TraesCS3D01G111700 chr3B 109796491 109797438 947 True 569.500000 760 88.4215 3058 3990 2 chr3B.!!$R2 932
11 TraesCS3D01G111700 chr3A 77408840 77413064 4224 True 918.200000 1447 90.4804 1 4003 5 chr3A.!!$R1 4002
12 TraesCS3D01G111700 chr1A 570614984 570615636 652 False 243.000000 243 74.0120 2041 2676 1 chr1A.!!$F4 635

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
124 126 0.322546 CTCCCCACCTGCCTAACAAC 60.323 60.0 0.0 0.0 0.0 3.32 F
1648 2446 0.036671 CCCCTACACGTTCCAGGTTC 60.037 60.0 6.2 0.0 0.0 3.62 F
2009 2807 0.106819 ATGCAGATGTCCAGAAGCCC 60.107 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2788 0.106819 GGGCTTCTGGACATCTGCAT 60.107 55.000 0.0 0.0 0.0 3.96 R
2609 3426 0.321671 CCAACATCCAGTCCGTGAGT 59.678 55.000 0.0 0.0 0.0 3.41 R
3977 6743 1.944024 CGGTCAAGTAAGTTTGGTGCA 59.056 47.619 0.0 0.0 0.0 4.57 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
124 126 0.322546 CTCCCCACCTGCCTAACAAC 60.323 60.000 0.00 0.00 0.00 3.32
125 127 1.674322 CCCCACCTGCCTAACAACG 60.674 63.158 0.00 0.00 0.00 4.10
156 158 1.681076 GGGAACTCCGCCCTTAACA 59.319 57.895 0.00 0.00 42.56 2.41
159 161 1.209747 GGAACTCCGCCCTTAACATCT 59.790 52.381 0.00 0.00 0.00 2.90
192 194 7.654022 TCCAAAAATATTGGTAATCCCTCAC 57.346 36.000 7.07 0.00 40.40 3.51
194 196 7.676043 TCCAAAAATATTGGTAATCCCTCACAA 59.324 33.333 7.07 0.00 40.40 3.33
195 197 8.317679 CCAAAAATATTGGTAATCCCTCACAAA 58.682 33.333 0.00 0.00 34.92 2.83
196 198 9.369904 CAAAAATATTGGTAATCCCTCACAAAG 57.630 33.333 0.00 0.00 0.00 2.77
208 210 5.450453 TCCCTCACAAAGAAACATGGTTAA 58.550 37.500 0.00 0.00 0.00 2.01
216 218 4.939509 AGAAACATGGTTAACGGATTCG 57.060 40.909 0.00 0.00 43.02 3.34
219 465 2.006888 ACATGGTTAACGGATTCGCTG 58.993 47.619 0.00 0.00 40.63 5.18
236 482 1.668419 CTGGCCCCGTCTAGATTTTG 58.332 55.000 0.00 0.00 0.00 2.44
337 584 4.826733 TCTAGCACACCATGAAACACAAAT 59.173 37.500 0.00 0.00 0.00 2.32
345 592 4.981674 ACCATGAAACACAAATTTACTGCG 59.018 37.500 0.00 0.00 0.00 5.18
365 612 2.597505 CGTTGACGCAGCTATAATGCAC 60.598 50.000 9.55 4.47 44.05 4.57
495 1197 1.400494 CGGGTCAATCCATTTCGTTCC 59.600 52.381 0.00 0.00 38.11 3.62
496 1198 1.400494 GGGTCAATCCATTTCGTTCCG 59.600 52.381 0.00 0.00 38.11 4.30
497 1199 2.081462 GGTCAATCCATTTCGTTCCGT 58.919 47.619 0.00 0.00 35.97 4.69
498 1200 3.264104 GGTCAATCCATTTCGTTCCGTA 58.736 45.455 0.00 0.00 35.97 4.02
499 1201 3.875134 GGTCAATCCATTTCGTTCCGTAT 59.125 43.478 0.00 0.00 35.97 3.06
500 1202 4.334481 GGTCAATCCATTTCGTTCCGTATT 59.666 41.667 0.00 0.00 35.97 1.89
501 1203 5.499047 GTCAATCCATTTCGTTCCGTATTC 58.501 41.667 0.00 0.00 0.00 1.75
502 1204 4.269123 TCAATCCATTTCGTTCCGTATTCG 59.731 41.667 0.00 0.00 0.00 3.34
503 1205 1.928503 TCCATTTCGTTCCGTATTCGC 59.071 47.619 0.00 0.00 35.54 4.70
504 1206 1.331680 CCATTTCGTTCCGTATTCGCG 60.332 52.381 0.00 0.00 35.54 5.87
505 1207 1.584761 CATTTCGTTCCGTATTCGCGA 59.415 47.619 3.71 3.71 35.54 5.87
506 1208 1.695813 TTTCGTTCCGTATTCGCGAA 58.304 45.000 25.66 25.66 37.32 4.70
507 1209 1.695813 TTCGTTCCGTATTCGCGAAA 58.304 45.000 27.23 12.42 36.65 3.46
508 1210 1.695813 TCGTTCCGTATTCGCGAAAA 58.304 45.000 27.23 12.39 35.54 2.29
509 1211 2.057316 TCGTTCCGTATTCGCGAAAAA 58.943 42.857 27.23 14.43 35.54 1.94
593 1299 9.926158 ACAACATTTGAATAAACATAATGCTGA 57.074 25.926 0.00 0.00 30.75 4.26
610 1316 1.133598 CTGATAGCCCAACACGTACGA 59.866 52.381 24.41 0.00 0.00 3.43
621 1327 2.731721 CGTACGAACAGCACGCCA 60.732 61.111 10.44 0.00 32.40 5.69
622 1328 2.716828 CGTACGAACAGCACGCCAG 61.717 63.158 10.44 0.00 32.40 4.85
623 1329 1.663702 GTACGAACAGCACGCCAGT 60.664 57.895 0.00 0.00 0.00 4.00
624 1330 1.372499 TACGAACAGCACGCCAGTC 60.372 57.895 0.00 0.00 0.00 3.51
625 1331 3.767230 CGAACAGCACGCCAGTCG 61.767 66.667 0.00 0.00 45.38 4.18
876 1610 3.997064 CTCTCCGCGTGCCCAGAAG 62.997 68.421 4.92 0.00 0.00 2.85
928 1689 1.198178 ACTTGCTCGTCTTCGTCTCTC 59.802 52.381 0.00 0.00 38.33 3.20
946 1712 1.532794 CCCCTCTCCTCCATCTCCG 60.533 68.421 0.00 0.00 0.00 4.63
950 1716 1.075374 CCTCTCCTCCATCTCCGATCT 59.925 57.143 0.00 0.00 0.00 2.75
1026 1797 1.534476 TGACCAGCCTTACGTGGGA 60.534 57.895 12.59 0.00 38.25 4.37
1093 1864 7.146648 CCTGTCCTACCTCGATTACTATTTTC 58.853 42.308 0.00 0.00 0.00 2.29
1443 2229 2.956964 GGCTCGATTGAGACCGCG 60.957 66.667 14.59 0.00 45.20 6.46
1533 2331 2.042843 GAGAAGGGCGGAGGGAGA 60.043 66.667 0.00 0.00 0.00 3.71
1534 2332 1.686110 GAGAAGGGCGGAGGGAGAA 60.686 63.158 0.00 0.00 0.00 2.87
1642 2440 0.107848 CATGTCCCCCTACACGTTCC 60.108 60.000 0.00 0.00 30.75 3.62
1643 2441 0.545787 ATGTCCCCCTACACGTTCCA 60.546 55.000 0.00 0.00 30.75 3.53
1644 2442 1.189524 TGTCCCCCTACACGTTCCAG 61.190 60.000 0.00 0.00 0.00 3.86
1645 2443 1.611261 TCCCCCTACACGTTCCAGG 60.611 63.158 0.00 0.00 0.00 4.45
1646 2444 1.916777 CCCCCTACACGTTCCAGGT 60.917 63.158 6.20 0.00 0.00 4.00
1647 2445 1.486145 CCCCCTACACGTTCCAGGTT 61.486 60.000 6.20 0.00 0.00 3.50
1648 2446 0.036671 CCCCTACACGTTCCAGGTTC 60.037 60.000 6.20 0.00 0.00 3.62
1649 2447 0.389426 CCCTACACGTTCCAGGTTCG 60.389 60.000 6.20 4.89 0.00 3.95
1650 2448 0.389426 CCTACACGTTCCAGGTTCGG 60.389 60.000 9.90 0.00 0.00 4.30
1651 2449 0.316204 CTACACGTTCCAGGTTCGGT 59.684 55.000 9.90 7.66 0.00 4.69
1652 2450 1.541147 CTACACGTTCCAGGTTCGGTA 59.459 52.381 9.90 8.19 0.00 4.02
1653 2451 0.752054 ACACGTTCCAGGTTCGGTAA 59.248 50.000 9.90 0.00 0.00 2.85
1654 2452 1.138661 ACACGTTCCAGGTTCGGTAAA 59.861 47.619 9.90 0.00 0.00 2.01
1655 2453 1.528161 CACGTTCCAGGTTCGGTAAAC 59.472 52.381 9.90 0.00 37.12 2.01
1656 2454 1.138661 ACGTTCCAGGTTCGGTAAACA 59.861 47.619 9.90 0.00 39.81 2.83
1657 2455 2.224354 ACGTTCCAGGTTCGGTAAACAT 60.224 45.455 9.90 0.00 39.81 2.71
1658 2456 2.809696 CGTTCCAGGTTCGGTAAACATT 59.190 45.455 0.00 0.00 39.81 2.71
1659 2457 3.251487 CGTTCCAGGTTCGGTAAACATTT 59.749 43.478 0.00 0.00 39.81 2.32
1660 2458 4.451774 CGTTCCAGGTTCGGTAAACATTTA 59.548 41.667 0.00 0.00 39.81 1.40
1661 2459 5.615325 CGTTCCAGGTTCGGTAAACATTTAC 60.615 44.000 6.04 6.04 41.68 2.01
1662 2460 3.995705 TCCAGGTTCGGTAAACATTTACG 59.004 43.478 8.11 4.83 42.97 3.18
1663 2461 3.995705 CCAGGTTCGGTAAACATTTACGA 59.004 43.478 8.11 6.67 42.97 3.43
1664 2462 4.451774 CCAGGTTCGGTAAACATTTACGAA 59.548 41.667 8.11 11.04 42.97 3.85
1665 2463 5.376537 CAGGTTCGGTAAACATTTACGAAC 58.623 41.667 24.69 24.69 44.55 3.95
1666 2464 5.050227 CAGGTTCGGTAAACATTTACGAACA 60.050 40.000 28.50 11.51 45.50 3.18
1667 2465 5.050159 AGGTTCGGTAAACATTTACGAACAC 60.050 40.000 28.50 22.98 45.50 3.32
1668 2466 5.050159 GGTTCGGTAAACATTTACGAACACT 60.050 40.000 28.50 0.00 45.50 3.55
1669 2467 6.421405 GTTCGGTAAACATTTACGAACACTT 58.579 36.000 26.03 0.00 44.59 3.16
1670 2468 6.601741 TCGGTAAACATTTACGAACACTTT 57.398 33.333 8.11 0.00 42.97 2.66
1671 2469 7.014092 TCGGTAAACATTTACGAACACTTTT 57.986 32.000 8.11 0.00 42.97 2.27
1672 2470 6.906143 TCGGTAAACATTTACGAACACTTTTG 59.094 34.615 8.11 0.00 42.97 2.44
1673 2471 6.687958 CGGTAAACATTTACGAACACTTTTGT 59.312 34.615 8.11 0.00 42.97 2.83
1674 2472 7.097329 CGGTAAACATTTACGAACACTTTTGTC 60.097 37.037 8.11 0.00 42.97 3.18
1675 2473 7.166307 GGTAAACATTTACGAACACTTTTGTCC 59.834 37.037 8.11 0.00 42.97 4.02
1676 2474 6.445357 AACATTTACGAACACTTTTGTCCT 57.555 33.333 0.00 0.00 33.55 3.85
1677 2475 6.445357 ACATTTACGAACACTTTTGTCCTT 57.555 33.333 0.00 0.00 33.55 3.36
1678 2476 6.859017 ACATTTACGAACACTTTTGTCCTTT 58.141 32.000 0.00 0.00 33.55 3.11
1679 2477 7.317390 ACATTTACGAACACTTTTGTCCTTTT 58.683 30.769 0.00 0.00 33.55 2.27
1680 2478 7.815549 ACATTTACGAACACTTTTGTCCTTTTT 59.184 29.630 0.00 0.00 33.55 1.94
1681 2479 7.569677 TTTACGAACACTTTTGTCCTTTTTG 57.430 32.000 0.00 0.00 33.55 2.44
1682 2480 5.128992 ACGAACACTTTTGTCCTTTTTGT 57.871 34.783 0.00 0.00 33.55 2.83
1683 2481 5.534407 ACGAACACTTTTGTCCTTTTTGTT 58.466 33.333 0.00 0.00 33.55 2.83
1684 2482 5.986741 ACGAACACTTTTGTCCTTTTTGTTT 59.013 32.000 0.00 0.00 33.55 2.83
1685 2483 6.144886 ACGAACACTTTTGTCCTTTTTGTTTC 59.855 34.615 0.00 0.00 33.55 2.78
1686 2484 6.364976 CGAACACTTTTGTCCTTTTTGTTTCT 59.635 34.615 0.00 0.00 33.55 2.52
1687 2485 7.095816 CGAACACTTTTGTCCTTTTTGTTTCTT 60.096 33.333 0.00 0.00 33.55 2.52
1688 2486 8.445275 AACACTTTTGTCCTTTTTGTTTCTTT 57.555 26.923 0.00 0.00 33.55 2.52
1689 2487 8.083462 ACACTTTTGTCCTTTTTGTTTCTTTC 57.917 30.769 0.00 0.00 0.00 2.62
1690 2488 7.713073 ACACTTTTGTCCTTTTTGTTTCTTTCA 59.287 29.630 0.00 0.00 0.00 2.69
1691 2489 8.555361 CACTTTTGTCCTTTTTGTTTCTTTCAA 58.445 29.630 0.00 0.00 0.00 2.69
1692 2490 9.114952 ACTTTTGTCCTTTTTGTTTCTTTCAAA 57.885 25.926 0.00 0.00 33.76 2.69
1728 2526 7.833285 ATGAACTCTAAACTTTAAAGGGCAA 57.167 32.000 19.14 1.57 0.00 4.52
1729 2527 7.034685 TGAACTCTAAACTTTAAAGGGCAAC 57.965 36.000 19.14 3.01 0.00 4.17
1730 2528 6.603997 TGAACTCTAAACTTTAAAGGGCAACA 59.396 34.615 19.14 5.23 39.74 3.33
1731 2529 7.122948 TGAACTCTAAACTTTAAAGGGCAACAA 59.877 33.333 19.14 0.00 39.74 2.83
1732 2530 7.412853 ACTCTAAACTTTAAAGGGCAACAAA 57.587 32.000 19.14 0.00 39.74 2.83
1733 2531 7.842982 ACTCTAAACTTTAAAGGGCAACAAAA 58.157 30.769 19.14 0.00 39.74 2.44
1734 2532 7.762615 ACTCTAAACTTTAAAGGGCAACAAAAC 59.237 33.333 19.14 0.00 39.74 2.43
1735 2533 7.612677 TCTAAACTTTAAAGGGCAACAAAACA 58.387 30.769 19.14 0.00 39.74 2.83
1736 2534 8.261522 TCTAAACTTTAAAGGGCAACAAAACAT 58.738 29.630 19.14 0.00 39.74 2.71
1737 2535 7.695480 AAACTTTAAAGGGCAACAAAACATT 57.305 28.000 19.14 0.00 39.74 2.71
1738 2536 6.918892 ACTTTAAAGGGCAACAAAACATTC 57.081 33.333 19.14 0.00 39.74 2.67
1739 2537 6.649155 ACTTTAAAGGGCAACAAAACATTCT 58.351 32.000 19.14 0.00 39.74 2.40
1740 2538 7.787028 ACTTTAAAGGGCAACAAAACATTCTA 58.213 30.769 19.14 0.00 39.74 2.10
1741 2539 8.261522 ACTTTAAAGGGCAACAAAACATTCTAA 58.738 29.630 19.14 0.00 39.74 2.10
1742 2540 8.655651 TTTAAAGGGCAACAAAACATTCTAAG 57.344 30.769 0.00 0.00 39.74 2.18
1743 2541 5.869649 AAGGGCAACAAAACATTCTAAGT 57.130 34.783 0.00 0.00 39.74 2.24
1744 2542 6.969993 AAGGGCAACAAAACATTCTAAGTA 57.030 33.333 0.00 0.00 39.74 2.24
1745 2543 6.575162 AGGGCAACAAAACATTCTAAGTAG 57.425 37.500 0.00 0.00 39.74 2.57
1746 2544 6.303839 AGGGCAACAAAACATTCTAAGTAGA 58.696 36.000 0.00 0.00 39.74 2.59
1747 2545 6.775629 AGGGCAACAAAACATTCTAAGTAGAA 59.224 34.615 3.33 3.33 42.29 2.10
1748 2546 7.451566 AGGGCAACAAAACATTCTAAGTAGAAT 59.548 33.333 7.61 7.61 45.91 2.40
1846 2644 7.103641 ACCATCTTGTATATTTATGTAGGGCG 58.896 38.462 0.00 0.00 0.00 6.13
1847 2645 7.038587 ACCATCTTGTATATTTATGTAGGGCGA 60.039 37.037 0.00 0.00 0.00 5.54
1848 2646 7.822334 CCATCTTGTATATTTATGTAGGGCGAA 59.178 37.037 0.00 0.00 0.00 4.70
1849 2647 9.214957 CATCTTGTATATTTATGTAGGGCGAAA 57.785 33.333 0.00 0.00 0.00 3.46
1850 2648 9.787435 ATCTTGTATATTTATGTAGGGCGAAAA 57.213 29.630 0.00 0.00 0.00 2.29
1851 2649 9.616156 TCTTGTATATTTATGTAGGGCGAAAAA 57.384 29.630 0.00 0.00 0.00 1.94
1882 2680 3.701532 TTTTTCCCACGTTGCAGTAAG 57.298 42.857 0.00 0.00 0.00 2.34
1883 2681 2.623878 TTTCCCACGTTGCAGTAAGA 57.376 45.000 0.00 0.00 0.00 2.10
1884 2682 2.623878 TTCCCACGTTGCAGTAAGAA 57.376 45.000 0.00 0.00 0.00 2.52
1885 2683 2.851263 TCCCACGTTGCAGTAAGAAT 57.149 45.000 0.00 0.00 0.00 2.40
1886 2684 2.422597 TCCCACGTTGCAGTAAGAATG 58.577 47.619 0.00 0.00 0.00 2.67
1887 2685 2.151202 CCCACGTTGCAGTAAGAATGT 58.849 47.619 0.00 0.00 0.00 2.71
1888 2686 2.552315 CCCACGTTGCAGTAAGAATGTT 59.448 45.455 0.00 0.00 0.00 2.71
1889 2687 3.004315 CCCACGTTGCAGTAAGAATGTTT 59.996 43.478 0.00 0.00 0.00 2.83
1890 2688 4.499019 CCCACGTTGCAGTAAGAATGTTTT 60.499 41.667 0.00 0.00 0.00 2.43
1891 2689 4.440758 CCACGTTGCAGTAAGAATGTTTTG 59.559 41.667 0.00 0.00 0.00 2.44
1892 2690 5.034152 CACGTTGCAGTAAGAATGTTTTGT 58.966 37.500 0.00 0.00 0.00 2.83
1893 2691 5.514914 CACGTTGCAGTAAGAATGTTTTGTT 59.485 36.000 0.00 0.00 0.00 2.83
1894 2692 5.514914 ACGTTGCAGTAAGAATGTTTTGTTG 59.485 36.000 0.00 0.00 0.00 3.33
1895 2693 5.514914 CGTTGCAGTAAGAATGTTTTGTTGT 59.485 36.000 0.00 0.00 0.00 3.32
1896 2694 6.291060 CGTTGCAGTAAGAATGTTTTGTTGTC 60.291 38.462 0.00 0.00 0.00 3.18
1897 2695 5.587289 TGCAGTAAGAATGTTTTGTTGTCC 58.413 37.500 0.00 0.00 0.00 4.02
1898 2696 5.359576 TGCAGTAAGAATGTTTTGTTGTCCT 59.640 36.000 0.00 0.00 0.00 3.85
1899 2697 5.687285 GCAGTAAGAATGTTTTGTTGTCCTG 59.313 40.000 0.00 0.00 0.00 3.86
1900 2698 5.687285 CAGTAAGAATGTTTTGTTGTCCTGC 59.313 40.000 0.00 0.00 0.00 4.85
1901 2699 4.734398 AAGAATGTTTTGTTGTCCTGCA 57.266 36.364 0.00 0.00 0.00 4.41
1902 2700 4.734398 AGAATGTTTTGTTGTCCTGCAA 57.266 36.364 0.00 0.00 34.16 4.08
1903 2701 5.083533 AGAATGTTTTGTTGTCCTGCAAA 57.916 34.783 0.00 0.00 39.03 3.68
1904 2702 5.111293 AGAATGTTTTGTTGTCCTGCAAAG 58.889 37.500 0.00 0.00 39.03 2.77
1905 2703 3.951775 TGTTTTGTTGTCCTGCAAAGT 57.048 38.095 0.00 0.00 39.03 2.66
1906 2704 4.264460 TGTTTTGTTGTCCTGCAAAGTT 57.736 36.364 0.00 0.00 39.03 2.66
1907 2705 4.636249 TGTTTTGTTGTCCTGCAAAGTTT 58.364 34.783 0.00 0.00 39.03 2.66
1908 2706 4.450419 TGTTTTGTTGTCCTGCAAAGTTTG 59.550 37.500 11.41 11.41 39.03 2.93
1909 2707 4.527509 TTTGTTGTCCTGCAAAGTTTGA 57.472 36.364 19.82 3.95 39.03 2.69
1910 2708 4.527509 TTGTTGTCCTGCAAAGTTTGAA 57.472 36.364 19.82 8.06 39.03 2.69
1911 2709 4.108699 TGTTGTCCTGCAAAGTTTGAAG 57.891 40.909 19.82 17.73 39.03 3.02
1912 2710 3.509575 TGTTGTCCTGCAAAGTTTGAAGT 59.490 39.130 20.15 0.00 39.03 3.01
1913 2711 4.021544 TGTTGTCCTGCAAAGTTTGAAGTT 60.022 37.500 20.15 0.00 39.03 2.66
1914 2712 4.799564 TGTCCTGCAAAGTTTGAAGTTT 57.200 36.364 20.15 0.00 34.27 2.66
1915 2713 5.906113 TGTCCTGCAAAGTTTGAAGTTTA 57.094 34.783 20.15 4.94 34.27 2.01
1916 2714 6.463995 TGTCCTGCAAAGTTTGAAGTTTAT 57.536 33.333 20.15 0.00 34.27 1.40
1917 2715 7.575414 TGTCCTGCAAAGTTTGAAGTTTATA 57.425 32.000 20.15 3.68 34.27 0.98
1918 2716 8.177119 TGTCCTGCAAAGTTTGAAGTTTATAT 57.823 30.769 20.15 0.00 34.27 0.86
1919 2717 8.081633 TGTCCTGCAAAGTTTGAAGTTTATATG 58.918 33.333 20.15 5.37 34.27 1.78
1920 2718 8.082242 GTCCTGCAAAGTTTGAAGTTTATATGT 58.918 33.333 20.15 0.00 34.27 2.29
1921 2719 8.637986 TCCTGCAAAGTTTGAAGTTTATATGTT 58.362 29.630 20.15 0.00 34.27 2.71
1922 2720 8.702438 CCTGCAAAGTTTGAAGTTTATATGTTG 58.298 33.333 20.15 0.00 34.27 3.33
1923 2721 9.248291 CTGCAAAGTTTGAAGTTTATATGTTGT 57.752 29.630 19.82 0.00 31.28 3.32
1924 2722 9.593134 TGCAAAGTTTGAAGTTTATATGTTGTT 57.407 25.926 19.82 0.00 30.74 2.83
1943 2741 9.921637 ATGTTGTTTAGTTTTGAAGAGACAAAA 57.078 25.926 0.00 0.00 44.08 2.44
1944 2742 9.751542 TGTTGTTTAGTTTTGAAGAGACAAAAA 57.248 25.926 0.00 0.00 46.43 1.94
1990 2788 9.448438 AAATTAGTTGTGTAGCACATATCTCAA 57.552 29.630 2.65 0.00 44.16 3.02
1991 2789 9.618890 AATTAGTTGTGTAGCACATATCTCAAT 57.381 29.630 2.65 0.00 44.16 2.57
1992 2790 6.915544 AGTTGTGTAGCACATATCTCAATG 57.084 37.500 2.65 0.00 44.16 2.82
1993 2791 5.295292 AGTTGTGTAGCACATATCTCAATGC 59.705 40.000 2.65 0.00 44.16 3.56
1994 2792 4.768583 TGTGTAGCACATATCTCAATGCA 58.231 39.130 0.00 0.00 39.62 3.96
1995 2793 4.812626 TGTGTAGCACATATCTCAATGCAG 59.187 41.667 0.00 0.00 39.62 4.41
1996 2794 5.052481 GTGTAGCACATATCTCAATGCAGA 58.948 41.667 0.00 0.00 40.63 4.26
1997 2795 5.699915 GTGTAGCACATATCTCAATGCAGAT 59.300 40.000 0.00 0.00 40.63 2.90
1998 2796 5.699458 TGTAGCACATATCTCAATGCAGATG 59.301 40.000 0.00 0.00 40.63 2.90
1999 2797 4.715713 AGCACATATCTCAATGCAGATGT 58.284 39.130 0.00 0.00 40.63 3.06
2000 2798 4.755629 AGCACATATCTCAATGCAGATGTC 59.244 41.667 0.00 0.00 40.63 3.06
2001 2799 4.083431 GCACATATCTCAATGCAGATGTCC 60.083 45.833 0.00 0.00 38.00 4.02
2002 2800 5.061179 CACATATCTCAATGCAGATGTCCA 58.939 41.667 0.00 0.00 34.75 4.02
2003 2801 5.179555 CACATATCTCAATGCAGATGTCCAG 59.820 44.000 0.00 0.00 34.75 3.86
2004 2802 5.071384 ACATATCTCAATGCAGATGTCCAGA 59.929 40.000 0.00 0.00 34.75 3.86
2005 2803 3.986996 TCTCAATGCAGATGTCCAGAA 57.013 42.857 0.00 0.00 0.00 3.02
2006 2804 3.870274 TCTCAATGCAGATGTCCAGAAG 58.130 45.455 0.00 0.00 0.00 2.85
2007 2805 2.355132 CTCAATGCAGATGTCCAGAAGC 59.645 50.000 0.00 0.00 0.00 3.86
2008 2806 1.404391 CAATGCAGATGTCCAGAAGCC 59.596 52.381 0.00 0.00 0.00 4.35
2009 2807 0.106819 ATGCAGATGTCCAGAAGCCC 60.107 55.000 0.00 0.00 0.00 5.19
2010 2808 1.817099 GCAGATGTCCAGAAGCCCG 60.817 63.158 0.00 0.00 0.00 6.13
2011 2809 1.900351 CAGATGTCCAGAAGCCCGA 59.100 57.895 0.00 0.00 0.00 5.14
2012 2810 0.179089 CAGATGTCCAGAAGCCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
2013 2811 1.522580 GATGTCCAGAAGCCCGAGC 60.523 63.158 0.00 0.00 40.32 5.03
2028 2826 5.500645 GCCCGAGCTTTATAAATCAACTT 57.499 39.130 0.00 0.00 35.50 2.66
2029 2827 5.891451 GCCCGAGCTTTATAAATCAACTTT 58.109 37.500 0.00 0.00 35.50 2.66
2030 2828 5.971792 GCCCGAGCTTTATAAATCAACTTTC 59.028 40.000 0.00 0.00 35.50 2.62
2031 2829 6.183360 GCCCGAGCTTTATAAATCAACTTTCT 60.183 38.462 0.00 0.00 35.50 2.52
2032 2830 7.628580 GCCCGAGCTTTATAAATCAACTTTCTT 60.629 37.037 0.00 0.00 35.50 2.52
2033 2831 7.910683 CCCGAGCTTTATAAATCAACTTTCTTC 59.089 37.037 0.00 0.00 0.00 2.87
2265 3072 1.374947 CCCAACGTCATCCAGTGGT 59.625 57.895 9.54 0.00 0.00 4.16
2270 3077 2.982130 GTCATCCAGTGGTCGGCT 59.018 61.111 9.54 0.00 0.00 5.52
2625 3442 1.544825 CCCACTCACGGACTGGATGT 61.545 60.000 0.00 0.00 0.00 3.06
2656 3473 1.052124 TCCCACCAGAACCTGACGTT 61.052 55.000 0.00 0.00 37.41 3.99
2731 3549 1.000396 CCTTCCAAAGGCTCCAGGG 60.000 63.158 0.00 0.00 42.78 4.45
2793 3611 1.278985 ACGACCTTTCCATCATGCTCA 59.721 47.619 0.00 0.00 0.00 4.26
2819 3637 2.969806 CTGCGCGCTCCACAACATT 61.970 57.895 33.29 0.00 0.00 2.71
2822 3640 1.282570 CGCGCTCCACAACATTTGT 59.717 52.632 5.56 0.00 46.75 2.83
3052 3915 5.940470 GGATCAGCCGATAATACAAGGAATT 59.060 40.000 0.00 0.00 29.66 2.17
3086 3949 4.549458 AGAGCACCAAAATTCATTCGTTG 58.451 39.130 0.00 0.00 0.00 4.10
3125 3994 2.543653 CGGGAAGAGCCAACAAGTTTTG 60.544 50.000 0.00 0.00 38.95 2.44
3142 4016 5.480205 AGTTTTGTTCTCGAGATTAGTCCC 58.520 41.667 17.44 2.33 0.00 4.46
3520 6259 2.971660 TTGAGTTTGTCGTGGACTCA 57.028 45.000 1.60 1.60 45.71 3.41
3977 6743 4.331968 CTCTCTATCAGCGAGGAATAGGT 58.668 47.826 0.00 0.00 0.00 3.08
3980 6746 1.123077 ATCAGCGAGGAATAGGTGCA 58.877 50.000 0.00 0.00 35.99 4.57
3983 6749 1.220749 GCGAGGAATAGGTGCACCA 59.779 57.895 36.39 22.64 38.89 4.17
3990 6756 4.332828 AGGAATAGGTGCACCAAACTTAC 58.667 43.478 36.39 22.55 38.89 2.34
3991 6757 4.042934 AGGAATAGGTGCACCAAACTTACT 59.957 41.667 36.39 24.21 38.89 2.24
3995 6761 2.949644 AGGTGCACCAAACTTACTTGAC 59.050 45.455 36.39 5.24 38.89 3.18
3997 6763 1.944024 TGCACCAAACTTACTTGACCG 59.056 47.619 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 126 3.597255 GAGTTCCCTCCCTTAACTTTCG 58.403 50.000 0.00 0.00 33.72 3.46
165 167 8.536175 TGAGGGATTACCAATATTTTTGGAAAC 58.464 33.333 12.18 2.75 43.89 2.78
167 169 7.676043 TGTGAGGGATTACCAATATTTTTGGAA 59.324 33.333 12.18 3.85 43.89 3.53
169 171 7.416964 TGTGAGGGATTACCAATATTTTTGG 57.583 36.000 4.53 4.53 43.89 3.28
177 179 6.074648 TGTTTCTTTGTGAGGGATTACCAAT 58.925 36.000 0.00 0.00 43.89 3.16
179 181 5.055265 TGTTTCTTTGTGAGGGATTACCA 57.945 39.130 0.00 0.00 43.89 3.25
192 194 5.567534 CGAATCCGTTAACCATGTTTCTTTG 59.432 40.000 0.00 0.00 0.00 2.77
194 196 4.379082 GCGAATCCGTTAACCATGTTTCTT 60.379 41.667 0.00 0.00 38.24 2.52
195 197 3.126343 GCGAATCCGTTAACCATGTTTCT 59.874 43.478 0.00 0.00 38.24 2.52
196 198 3.126343 AGCGAATCCGTTAACCATGTTTC 59.874 43.478 0.00 0.27 38.24 2.78
216 218 0.107165 AAAATCTAGACGGGGCCAGC 60.107 55.000 4.39 0.00 0.00 4.85
219 465 1.101635 GGCAAAATCTAGACGGGGCC 61.102 60.000 10.47 10.47 0.00 5.80
236 482 5.784578 AGGTTTATTTTATCGGATTGGGC 57.215 39.130 0.00 0.00 0.00 5.36
345 592 2.286418 GGTGCATTATAGCTGCGTCAAC 60.286 50.000 0.00 0.00 42.62 3.18
365 612 9.868277 TTTAATTTTGTAGTTAGCATGATTGGG 57.132 29.630 0.00 0.00 0.00 4.12
593 1299 1.273048 TGTTCGTACGTGTTGGGCTAT 59.727 47.619 16.05 0.00 0.00 2.97
621 1327 2.055310 TTGCGTCACGACTCACGACT 62.055 55.000 0.00 0.00 45.77 4.18
622 1328 1.204228 TTTGCGTCACGACTCACGAC 61.204 55.000 0.00 0.00 45.77 4.34
623 1329 0.933047 CTTTGCGTCACGACTCACGA 60.933 55.000 0.00 0.00 45.77 4.35
625 1331 1.201825 GCTTTGCGTCACGACTCAC 59.798 57.895 0.00 0.00 0.00 3.51
626 1332 3.625232 GCTTTGCGTCACGACTCA 58.375 55.556 0.00 0.00 0.00 3.41
876 1610 3.675698 CGCGAGAGAGGGATTTATAAAGC 59.324 47.826 0.00 4.86 0.00 3.51
928 1689 1.532794 CGGAGATGGAGGAGAGGGG 60.533 68.421 0.00 0.00 0.00 4.79
946 1712 3.755378 ACAGCAGAAACAATGGTGAGATC 59.245 43.478 11.65 0.00 46.52 2.75
950 1716 2.622942 GGAACAGCAGAAACAATGGTGA 59.377 45.455 11.65 0.00 46.52 4.02
1026 1797 1.595382 GGCGGAATAGTGCTGCGAT 60.595 57.895 0.00 0.00 38.52 4.58
1106 1877 2.126307 CCGGCACAGACTCAGACG 60.126 66.667 0.00 0.00 0.00 4.18
1193 1964 1.302431 CACAGATTCACCACGCCCA 60.302 57.895 0.00 0.00 0.00 5.36
1233 2007 0.328258 GCCTCTTAAACCCCTGCTGA 59.672 55.000 0.00 0.00 0.00 4.26
1235 2009 0.329596 CTGCCTCTTAAACCCCTGCT 59.670 55.000 0.00 0.00 0.00 4.24
1236 2010 0.328258 TCTGCCTCTTAAACCCCTGC 59.672 55.000 0.00 0.00 0.00 4.85
1237 2011 2.040412 AGTTCTGCCTCTTAAACCCCTG 59.960 50.000 0.00 0.00 0.00 4.45
1238 2012 2.306219 GAGTTCTGCCTCTTAAACCCCT 59.694 50.000 0.00 0.00 0.00 4.79
1443 2229 0.249657 CTTCATAGCTCCCGCCACTC 60.250 60.000 0.00 0.00 36.60 3.51
1456 2245 1.226859 CGCTTCCGCCGTCTTCATA 60.227 57.895 0.00 0.00 0.00 2.15
1478 2267 0.318441 CACCACAGACTCATCCACGT 59.682 55.000 0.00 0.00 0.00 4.49
1533 2331 0.402121 GGTCCTTCTTCCACAGCCTT 59.598 55.000 0.00 0.00 0.00 4.35
1534 2332 1.831652 CGGTCCTTCTTCCACAGCCT 61.832 60.000 0.00 0.00 0.00 4.58
1642 2440 5.050227 TGTTCGTAAATGTTTACCGAACCTG 60.050 40.000 26.87 11.17 44.60 4.00
1643 2441 5.050159 GTGTTCGTAAATGTTTACCGAACCT 60.050 40.000 26.87 0.00 44.60 3.50
1644 2442 5.050159 AGTGTTCGTAAATGTTTACCGAACC 60.050 40.000 26.87 22.27 44.60 3.62
1645 2443 5.977731 AGTGTTCGTAAATGTTTACCGAAC 58.022 37.500 25.36 25.36 44.92 3.95
1646 2444 6.601741 AAGTGTTCGTAAATGTTTACCGAA 57.398 33.333 9.39 11.84 39.81 4.30
1647 2445 6.601741 AAAGTGTTCGTAAATGTTTACCGA 57.398 33.333 9.39 7.66 39.81 4.69
1648 2446 6.687958 ACAAAAGTGTTCGTAAATGTTTACCG 59.312 34.615 9.39 5.88 36.09 4.02
1649 2447 7.166307 GGACAAAAGTGTTCGTAAATGTTTACC 59.834 37.037 9.39 0.00 37.95 2.85
1650 2448 7.911727 AGGACAAAAGTGTTCGTAAATGTTTAC 59.088 33.333 5.73 5.73 38.42 2.01
1651 2449 7.987649 AGGACAAAAGTGTTCGTAAATGTTTA 58.012 30.769 0.00 0.00 38.42 2.01
1652 2450 6.859017 AGGACAAAAGTGTTCGTAAATGTTT 58.141 32.000 0.00 0.00 38.42 2.83
1653 2451 6.445357 AGGACAAAAGTGTTCGTAAATGTT 57.555 33.333 0.00 0.00 38.42 2.71
1654 2452 6.445357 AAGGACAAAAGTGTTCGTAAATGT 57.555 33.333 0.00 0.00 38.42 2.71
1655 2453 7.749539 AAAAGGACAAAAGTGTTCGTAAATG 57.250 32.000 0.00 0.00 38.42 2.32
1656 2454 7.815549 ACAAAAAGGACAAAAGTGTTCGTAAAT 59.184 29.630 0.00 0.00 38.42 1.40
1657 2455 7.146648 ACAAAAAGGACAAAAGTGTTCGTAAA 58.853 30.769 0.00 0.00 38.42 2.01
1658 2456 6.679843 ACAAAAAGGACAAAAGTGTTCGTAA 58.320 32.000 0.00 0.00 38.42 3.18
1659 2457 6.256912 ACAAAAAGGACAAAAGTGTTCGTA 57.743 33.333 0.00 0.00 38.42 3.43
1660 2458 5.128992 ACAAAAAGGACAAAAGTGTTCGT 57.871 34.783 0.00 0.00 38.42 3.85
1661 2459 6.364976 AGAAACAAAAAGGACAAAAGTGTTCG 59.635 34.615 0.00 0.00 38.42 3.95
1662 2460 7.652300 AGAAACAAAAAGGACAAAAGTGTTC 57.348 32.000 0.00 0.00 38.41 3.18
1663 2461 8.445275 AAAGAAACAAAAAGGACAAAAGTGTT 57.555 26.923 0.00 0.00 38.41 3.32
1664 2462 7.713073 TGAAAGAAACAAAAAGGACAAAAGTGT 59.287 29.630 0.00 0.00 42.10 3.55
1665 2463 8.082334 TGAAAGAAACAAAAAGGACAAAAGTG 57.918 30.769 0.00 0.00 0.00 3.16
1666 2464 8.669946 TTGAAAGAAACAAAAAGGACAAAAGT 57.330 26.923 0.00 0.00 0.00 2.66
1702 2500 9.528489 TTGCCCTTTAAAGTTTAGAGTTCATAT 57.472 29.630 14.03 0.00 0.00 1.78
1703 2501 8.789762 GTTGCCCTTTAAAGTTTAGAGTTCATA 58.210 33.333 14.03 0.70 0.00 2.15
1704 2502 7.286775 TGTTGCCCTTTAAAGTTTAGAGTTCAT 59.713 33.333 14.03 0.00 0.00 2.57
1705 2503 6.603997 TGTTGCCCTTTAAAGTTTAGAGTTCA 59.396 34.615 14.03 6.51 0.00 3.18
1706 2504 7.034685 TGTTGCCCTTTAAAGTTTAGAGTTC 57.965 36.000 14.03 4.48 0.00 3.01
1707 2505 7.412853 TTGTTGCCCTTTAAAGTTTAGAGTT 57.587 32.000 14.03 0.00 0.00 3.01
1708 2506 7.412853 TTTGTTGCCCTTTAAAGTTTAGAGT 57.587 32.000 14.03 0.00 0.00 3.24
1709 2507 7.762159 TGTTTTGTTGCCCTTTAAAGTTTAGAG 59.238 33.333 14.03 6.26 0.00 2.43
1710 2508 7.612677 TGTTTTGTTGCCCTTTAAAGTTTAGA 58.387 30.769 14.03 0.00 0.00 2.10
1711 2509 7.835634 TGTTTTGTTGCCCTTTAAAGTTTAG 57.164 32.000 14.03 0.00 0.00 1.85
1712 2510 8.794335 AATGTTTTGTTGCCCTTTAAAGTTTA 57.206 26.923 14.03 0.00 0.00 2.01
1713 2511 7.609918 AGAATGTTTTGTTGCCCTTTAAAGTTT 59.390 29.630 14.03 0.00 0.00 2.66
1714 2512 7.109501 AGAATGTTTTGTTGCCCTTTAAAGTT 58.890 30.769 14.03 0.00 0.00 2.66
1715 2513 6.649155 AGAATGTTTTGTTGCCCTTTAAAGT 58.351 32.000 14.03 0.00 0.00 2.66
1716 2514 8.655651 TTAGAATGTTTTGTTGCCCTTTAAAG 57.344 30.769 8.32 8.32 0.00 1.85
1717 2515 8.261522 ACTTAGAATGTTTTGTTGCCCTTTAAA 58.738 29.630 0.00 0.00 0.00 1.52
1718 2516 7.787028 ACTTAGAATGTTTTGTTGCCCTTTAA 58.213 30.769 0.00 0.00 0.00 1.52
1719 2517 7.354751 ACTTAGAATGTTTTGTTGCCCTTTA 57.645 32.000 0.00 0.00 0.00 1.85
1720 2518 6.233905 ACTTAGAATGTTTTGTTGCCCTTT 57.766 33.333 0.00 0.00 0.00 3.11
1721 2519 5.869649 ACTTAGAATGTTTTGTTGCCCTT 57.130 34.783 0.00 0.00 0.00 3.95
1722 2520 6.303839 TCTACTTAGAATGTTTTGTTGCCCT 58.696 36.000 0.00 0.00 0.00 5.19
1723 2521 6.569179 TCTACTTAGAATGTTTTGTTGCCC 57.431 37.500 0.00 0.00 0.00 5.36
1820 2618 8.255206 CGCCCTACATAAATATACAAGATGGTA 58.745 37.037 0.00 0.00 0.00 3.25
1821 2619 7.038587 TCGCCCTACATAAATATACAAGATGGT 60.039 37.037 0.00 0.00 0.00 3.55
1822 2620 7.327975 TCGCCCTACATAAATATACAAGATGG 58.672 38.462 0.00 0.00 0.00 3.51
1823 2621 8.771920 TTCGCCCTACATAAATATACAAGATG 57.228 34.615 0.00 0.00 0.00 2.90
1824 2622 9.787435 TTTTCGCCCTACATAAATATACAAGAT 57.213 29.630 0.00 0.00 0.00 2.40
1825 2623 9.616156 TTTTTCGCCCTACATAAATATACAAGA 57.384 29.630 0.00 0.00 0.00 3.02
1862 2660 3.280295 TCTTACTGCAACGTGGGAAAAA 58.720 40.909 0.00 0.00 0.00 1.94
1863 2661 2.920524 TCTTACTGCAACGTGGGAAAA 58.079 42.857 0.00 0.00 0.00 2.29
1864 2662 2.623878 TCTTACTGCAACGTGGGAAA 57.376 45.000 0.00 0.00 0.00 3.13
1865 2663 2.623878 TTCTTACTGCAACGTGGGAA 57.376 45.000 0.00 0.00 0.00 3.97
1866 2664 2.224426 ACATTCTTACTGCAACGTGGGA 60.224 45.455 0.00 0.00 0.00 4.37
1867 2665 2.151202 ACATTCTTACTGCAACGTGGG 58.849 47.619 0.00 0.00 0.00 4.61
1868 2666 3.896648 AACATTCTTACTGCAACGTGG 57.103 42.857 0.00 0.00 0.00 4.94
1869 2667 5.034152 ACAAAACATTCTTACTGCAACGTG 58.966 37.500 0.00 0.00 0.00 4.49
1870 2668 5.243426 ACAAAACATTCTTACTGCAACGT 57.757 34.783 0.00 0.00 0.00 3.99
1871 2669 5.514914 ACAACAAAACATTCTTACTGCAACG 59.485 36.000 0.00 0.00 0.00 4.10
1872 2670 6.019881 GGACAACAAAACATTCTTACTGCAAC 60.020 38.462 0.00 0.00 0.00 4.17
1873 2671 6.039616 GGACAACAAAACATTCTTACTGCAA 58.960 36.000 0.00 0.00 0.00 4.08
1874 2672 5.359576 AGGACAACAAAACATTCTTACTGCA 59.640 36.000 0.00 0.00 0.00 4.41
1875 2673 5.687285 CAGGACAACAAAACATTCTTACTGC 59.313 40.000 0.00 0.00 0.00 4.40
1876 2674 5.687285 GCAGGACAACAAAACATTCTTACTG 59.313 40.000 0.00 0.00 0.00 2.74
1877 2675 5.359576 TGCAGGACAACAAAACATTCTTACT 59.640 36.000 0.00 0.00 0.00 2.24
1878 2676 5.587289 TGCAGGACAACAAAACATTCTTAC 58.413 37.500 0.00 0.00 0.00 2.34
1879 2677 5.843673 TGCAGGACAACAAAACATTCTTA 57.156 34.783 0.00 0.00 0.00 2.10
1880 2678 4.734398 TGCAGGACAACAAAACATTCTT 57.266 36.364 0.00 0.00 0.00 2.52
1881 2679 4.734398 TTGCAGGACAACAAAACATTCT 57.266 36.364 0.00 0.00 31.73 2.40
1882 2680 4.869861 ACTTTGCAGGACAACAAAACATTC 59.130 37.500 0.00 0.00 38.23 2.67
1883 2681 4.831107 ACTTTGCAGGACAACAAAACATT 58.169 34.783 0.00 0.00 38.23 2.71
1884 2682 4.470334 ACTTTGCAGGACAACAAAACAT 57.530 36.364 0.00 0.00 38.23 2.71
1885 2683 3.951775 ACTTTGCAGGACAACAAAACA 57.048 38.095 0.00 0.00 38.23 2.83
1886 2684 4.688413 TCAAACTTTGCAGGACAACAAAAC 59.312 37.500 0.00 0.00 38.23 2.43
1887 2685 4.887748 TCAAACTTTGCAGGACAACAAAA 58.112 34.783 0.00 0.00 38.23 2.44
1888 2686 4.527509 TCAAACTTTGCAGGACAACAAA 57.472 36.364 0.00 0.00 38.23 2.83
1889 2687 4.021544 ACTTCAAACTTTGCAGGACAACAA 60.022 37.500 6.19 0.00 38.23 2.83
1890 2688 3.509575 ACTTCAAACTTTGCAGGACAACA 59.490 39.130 6.19 0.00 38.23 3.33
1891 2689 4.110036 ACTTCAAACTTTGCAGGACAAC 57.890 40.909 6.19 0.00 38.23 3.32
1892 2690 4.799564 AACTTCAAACTTTGCAGGACAA 57.200 36.364 6.19 0.00 36.13 3.18
1893 2691 4.799564 AAACTTCAAACTTTGCAGGACA 57.200 36.364 6.19 0.00 0.00 4.02
1894 2692 8.082242 ACATATAAACTTCAAACTTTGCAGGAC 58.918 33.333 6.19 0.00 0.00 3.85
1895 2693 8.177119 ACATATAAACTTCAAACTTTGCAGGA 57.823 30.769 6.19 0.00 0.00 3.86
1896 2694 8.702438 CAACATATAAACTTCAAACTTTGCAGG 58.298 33.333 6.19 0.00 0.00 4.85
1897 2695 9.248291 ACAACATATAAACTTCAAACTTTGCAG 57.752 29.630 0.17 0.17 0.00 4.41
1898 2696 9.593134 AACAACATATAAACTTCAAACTTTGCA 57.407 25.926 0.00 0.00 0.00 4.08
1917 2715 9.921637 TTTTGTCTCTTCAAAACTAAACAACAT 57.078 25.926 0.00 0.00 40.73 2.71
1918 2716 9.751542 TTTTTGTCTCTTCAAAACTAAACAACA 57.248 25.926 4.45 0.00 43.76 3.33
1972 2770 8.639891 CATCTGCATTGAGATATGTGCTACACA 61.640 40.741 2.45 2.45 38.44 3.72
1973 2771 5.052481 TCTGCATTGAGATATGTGCTACAC 58.948 41.667 0.00 0.00 38.37 2.90
1974 2772 5.280654 TCTGCATTGAGATATGTGCTACA 57.719 39.130 0.00 0.00 38.37 2.74
1975 2773 5.699915 ACATCTGCATTGAGATATGTGCTAC 59.300 40.000 3.97 0.00 38.37 3.58
1976 2774 5.861727 ACATCTGCATTGAGATATGTGCTA 58.138 37.500 3.97 0.00 38.37 3.49
1977 2775 4.715713 ACATCTGCATTGAGATATGTGCT 58.284 39.130 3.97 0.00 38.37 4.40
1978 2776 4.083431 GGACATCTGCATTGAGATATGTGC 60.083 45.833 3.97 0.00 38.05 4.57
1979 2777 5.061179 TGGACATCTGCATTGAGATATGTG 58.939 41.667 3.97 0.00 31.14 3.21
1980 2778 5.071384 TCTGGACATCTGCATTGAGATATGT 59.929 40.000 3.97 0.00 31.14 2.29
1981 2779 5.548406 TCTGGACATCTGCATTGAGATATG 58.452 41.667 3.97 0.00 31.14 1.78
1982 2780 5.820404 TCTGGACATCTGCATTGAGATAT 57.180 39.130 3.97 0.00 31.14 1.63
1983 2781 5.608449 CTTCTGGACATCTGCATTGAGATA 58.392 41.667 3.97 0.00 31.14 1.98
1984 2782 4.452825 CTTCTGGACATCTGCATTGAGAT 58.547 43.478 3.97 0.00 32.59 2.75
1985 2783 3.870274 CTTCTGGACATCTGCATTGAGA 58.130 45.455 3.97 0.00 0.00 3.27
1986 2784 2.355132 GCTTCTGGACATCTGCATTGAG 59.645 50.000 3.97 0.00 0.00 3.02
1987 2785 2.362736 GCTTCTGGACATCTGCATTGA 58.637 47.619 3.97 0.00 0.00 2.57
1988 2786 1.404391 GGCTTCTGGACATCTGCATTG 59.596 52.381 0.00 0.00 0.00 2.82
1989 2787 1.684248 GGGCTTCTGGACATCTGCATT 60.684 52.381 0.00 0.00 0.00 3.56
1990 2788 0.106819 GGGCTTCTGGACATCTGCAT 60.107 55.000 0.00 0.00 0.00 3.96
1991 2789 1.300963 GGGCTTCTGGACATCTGCA 59.699 57.895 0.00 0.00 0.00 4.41
1992 2790 1.817099 CGGGCTTCTGGACATCTGC 60.817 63.158 0.00 0.00 0.00 4.26
1993 2791 0.179089 CTCGGGCTTCTGGACATCTG 60.179 60.000 0.00 0.00 0.00 2.90
1994 2792 1.965754 GCTCGGGCTTCTGGACATCT 61.966 60.000 0.00 0.00 35.22 2.90
1995 2793 1.522580 GCTCGGGCTTCTGGACATC 60.523 63.158 0.00 0.00 35.22 3.06
1996 2794 2.586792 GCTCGGGCTTCTGGACAT 59.413 61.111 0.00 0.00 35.22 3.06
2006 2804 5.500645 AAGTTGATTTATAAAGCTCGGGC 57.499 39.130 14.13 0.00 39.06 6.13
2007 2805 7.321745 AGAAAGTTGATTTATAAAGCTCGGG 57.678 36.000 14.13 0.00 0.00 5.14
2008 2806 7.910683 GGAAGAAAGTTGATTTATAAAGCTCGG 59.089 37.037 14.13 0.00 0.00 4.63
2009 2807 8.450964 TGGAAGAAAGTTGATTTATAAAGCTCG 58.549 33.333 14.13 0.00 0.00 5.03
2010 2808 9.780413 CTGGAAGAAAGTTGATTTATAAAGCTC 57.220 33.333 14.13 7.78 34.07 4.09
2011 2809 8.743714 CCTGGAAGAAAGTTGATTTATAAAGCT 58.256 33.333 14.13 2.60 34.07 3.74
2012 2810 8.523658 ACCTGGAAGAAAGTTGATTTATAAAGC 58.476 33.333 6.51 6.51 34.07 3.51
2015 2813 9.807921 AGAACCTGGAAGAAAGTTGATTTATAA 57.192 29.630 0.00 0.00 34.07 0.98
2016 2814 9.231297 CAGAACCTGGAAGAAAGTTGATTTATA 57.769 33.333 0.00 0.00 34.07 0.98
2017 2815 7.725844 ACAGAACCTGGAAGAAAGTTGATTTAT 59.274 33.333 0.00 0.00 35.51 1.40
2018 2816 7.013274 CACAGAACCTGGAAGAAAGTTGATTTA 59.987 37.037 0.00 0.00 35.51 1.40
2019 2817 5.893824 ACAGAACCTGGAAGAAAGTTGATTT 59.106 36.000 0.00 0.00 35.51 2.17
2020 2818 5.300286 CACAGAACCTGGAAGAAAGTTGATT 59.700 40.000 0.00 0.00 35.51 2.57
2021 2819 4.823989 CACAGAACCTGGAAGAAAGTTGAT 59.176 41.667 0.00 0.00 35.51 2.57
2022 2820 4.199310 CACAGAACCTGGAAGAAAGTTGA 58.801 43.478 0.00 0.00 35.51 3.18
2023 2821 3.243201 GCACAGAACCTGGAAGAAAGTTG 60.243 47.826 0.00 0.00 35.51 3.16
2024 2822 2.952310 GCACAGAACCTGGAAGAAAGTT 59.048 45.455 0.00 0.00 35.51 2.66
2025 2823 2.576615 GCACAGAACCTGGAAGAAAGT 58.423 47.619 0.00 0.00 35.51 2.66
2026 2824 1.532868 CGCACAGAACCTGGAAGAAAG 59.467 52.381 0.00 0.00 35.51 2.62
2027 2825 1.140052 TCGCACAGAACCTGGAAGAAA 59.860 47.619 0.00 0.00 35.51 2.52
2028 2826 0.756294 TCGCACAGAACCTGGAAGAA 59.244 50.000 0.00 0.00 35.51 2.52
2029 2827 0.318441 CTCGCACAGAACCTGGAAGA 59.682 55.000 0.00 0.00 35.51 2.87
2030 2828 1.294659 GCTCGCACAGAACCTGGAAG 61.295 60.000 0.00 0.00 35.51 3.46
2031 2829 1.301716 GCTCGCACAGAACCTGGAA 60.302 57.895 0.00 0.00 35.51 3.53
2032 2830 2.343758 GCTCGCACAGAACCTGGA 59.656 61.111 0.00 0.00 35.51 3.86
2033 2831 2.031012 TGCTCGCACAGAACCTGG 59.969 61.111 0.00 0.00 35.51 4.45
2457 3270 3.618750 GGTCCCGTCCGTGTCCAA 61.619 66.667 0.00 0.00 0.00 3.53
2502 3319 3.185299 TTTGGGCGTCGGTCATGGT 62.185 57.895 0.00 0.00 0.00 3.55
2609 3426 0.321671 CCAACATCCAGTCCGTGAGT 59.678 55.000 0.00 0.00 0.00 3.41
2656 3473 1.227118 TTGAACTCGTGCTGCGTCA 60.227 52.632 0.00 0.00 42.13 4.35
3052 3915 6.630203 TTTTGGTGCTCTACTCCCTTATTA 57.370 37.500 0.00 0.00 0.00 0.98
3086 3949 6.757478 TCTTCCCGTTCCAACAAAAATTAAAC 59.243 34.615 0.00 0.00 0.00 2.01
3125 3994 7.321908 ACTAAAAAGGGACTAATCTCGAGAAC 58.678 38.462 20.91 8.55 38.49 3.01
3142 4016 6.616947 TGTTGCCCGAAATCATACTAAAAAG 58.383 36.000 0.00 0.00 0.00 2.27
3520 6259 4.163078 AGCTACAGTTGATAGTTCAGCCAT 59.837 41.667 0.00 0.00 33.88 4.40
3977 6743 1.944024 CGGTCAAGTAAGTTTGGTGCA 59.056 47.619 0.00 0.00 0.00 4.57
3980 6746 2.946990 CAACCGGTCAAGTAAGTTTGGT 59.053 45.455 8.04 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.