Multiple sequence alignment - TraesCS5D01G031800

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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 TraesCS5D01G031800 chr5D 100.000 5885 0 0 1 5885 29162045 29167929 0.000000e+00 10868.0
1 TraesCS5D01G031800 chr5D 97.495 2515 43 10 3381 5885 29599837 29602341 0.000000e+00 4277.0
2 TraesCS5D01G031800 chr5D 89.373 574 41 7 2812 3385 29593674 29594227 0.000000e+00 704.0
3 TraesCS5D01G031800 chr5D 92.500 40 2 1 5473 5511 29167461 29167500 8.240000e-04 56.5
4 TraesCS5D01G031800 chr5D 92.500 40 2 1 5417 5456 29167517 29167555 8.240000e-04 56.5
5 TraesCS5D01G031800 chr5D 92.500 40 2 1 5473 5511 29601873 29601912 8.240000e-04 56.5
6 TraesCS5D01G031800 chr5D 92.500 40 2 1 5417 5456 29601929 29601967 8.240000e-04 56.5
7 TraesCS5D01G031800 chr5A 91.658 4555 254 58 1354 5858 19976459 19980937 0.000000e+00 6191.0
8 TraesCS5D01G031800 chr5A 88.838 439 46 3 56 492 19975034 19975471 2.410000e-148 536.0
9 TraesCS5D01G031800 chr5A 86.166 506 23 38 717 1190 19975815 19976305 2.450000e-138 503.0
10 TraesCS5D01G031800 chr5A 92.500 40 2 1 5417 5456 19980547 19980585 8.240000e-04 56.5
11 TraesCS5D01G031800 chr5B 90.883 3828 208 62 1530 5312 21538465 21534734 0.000000e+00 5005.0
12 TraesCS5D01G031800 chr5B 85.957 705 38 20 537 1203 21539388 21538707 0.000000e+00 697.0
13 TraesCS5D01G031800 chr5B 87.028 424 37 7 10 424 21539926 21539512 4.150000e-126 462.0
14 TraesCS5D01G031800 chr5B 90.780 282 20 2 5610 5885 21534479 21534198 7.200000e-99 372.0
15 TraesCS5D01G031800 chr5B 89.209 139 9 4 4342 4474 21706767 21706905 1.010000e-37 169.0
16 TraesCS5D01G031800 chrUn 100.000 416 0 0 5205 5620 477220886 477220471 0.000000e+00 769.0
17 TraesCS5D01G031800 chrUn 92.500 40 2 1 5420 5459 477220615 477220577 8.240000e-04 56.5
18 TraesCS5D01G031800 chrUn 92.500 40 2 1 5476 5514 477220671 477220632 8.240000e-04 56.5


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 TraesCS5D01G031800 chr5D 29162045 29167929 5884 False 3660.333333 10868 95.0000 1 5885 3 chr5D.!!$F2 5884
1 TraesCS5D01G031800 chr5D 29599837 29602341 2504 False 1463.333333 4277 94.1650 3381 5885 3 chr5D.!!$F3 2504
2 TraesCS5D01G031800 chr5D 29593674 29594227 553 False 704.000000 704 89.3730 2812 3385 1 chr5D.!!$F1 573
3 TraesCS5D01G031800 chr5A 19975034 19980937 5903 False 1821.625000 6191 89.7905 56 5858 4 chr5A.!!$F1 5802
4 TraesCS5D01G031800 chr5B 21534198 21539926 5728 True 1634.000000 5005 88.6620 10 5885 4 chr5B.!!$R1 5875

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
42 43 0.508213 CCGTAACGTTCGGTTTCCAC 59.492 55.0 22.78 7.13 42.62 4.02 F
1221 1458 0.039472 TGTGGGGAATGGGTCACATG 59.961 55.0 0.00 0.00 40.44 3.21 F
1422 1691 0.323451 ACCTTTTGGATTCCCCTCGC 60.323 55.0 0.00 0.00 44.07 5.03 F
1773 2076 0.531090 TGCCGTGTCAGTGTTGGTAC 60.531 55.0 0.00 0.00 0.00 3.34 F
3043 3356 0.523072 GACATGCATGGCACGTCTTT 59.477 50.0 27.99 3.81 46.24 2.52 F
3781 4110 0.389391 CCATAGTCGCCGTCTCCATT 59.611 55.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1488 0.108041 TGGAGGCGAACGATTAACCC 60.108 55.000 0.00 0.0 0.00 4.11 R
2398 2707 0.478072 ACATGCCACAGAAACAGGGA 59.522 50.000 0.00 0.0 0.00 4.20 R
2455 2768 1.209128 CGCCTAAACGCATAGACAGG 58.791 55.000 0.00 0.0 0.00 4.00 R
3287 3601 1.814429 TGGAAGAGGTGTCAAAGGGA 58.186 50.000 0.00 0.0 0.00 4.20 R
4477 4826 0.403271 AGGAGCTGTGGCATCAAGTT 59.597 50.000 0.00 0.0 41.70 2.66 R
4986 5344 2.435586 GGATGCAGCAGCGACAGT 60.436 61.111 3.51 0.0 46.23 3.55 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
42 43 0.508213 CCGTAACGTTCGGTTTCCAC 59.492 55.000 22.78 7.13 42.62 4.02
51 52 1.269012 TCGGTTTCCACGTCCCTTAT 58.731 50.000 0.00 0.00 0.00 1.73
143 148 2.500229 GGAAGTGTCGTTTCATTCCCA 58.500 47.619 0.00 0.00 34.58 4.37
179 184 7.164230 TGGTGTTTAATGGGAATTATGTGTC 57.836 36.000 0.00 0.00 0.00 3.67
185 191 1.065053 TGGGAATTATGTGTCGGGGTG 60.065 52.381 0.00 0.00 0.00 4.61
200 206 3.968649 TCGGGGTGTGATAATAAAGCCTA 59.031 43.478 0.00 0.00 0.00 3.93
230 237 3.745797 GCTTGATAGAGGGGTGGATTCAC 60.746 52.174 0.00 0.00 42.91 3.18
238 245 0.834612 GGGTGGATTCACGTGGGATA 59.165 55.000 17.00 0.00 44.50 2.59
245 252 2.552599 TTCACGTGGGATAAGTGCAA 57.447 45.000 17.00 0.00 38.46 4.08
289 296 6.126409 AGGAAAGGTGAAGATGTGTGTAAAA 58.874 36.000 0.00 0.00 0.00 1.52
295 305 7.781056 AGGTGAAGATGTGTGTAAAACAATTT 58.219 30.769 0.00 0.00 37.78 1.82
296 306 7.920682 AGGTGAAGATGTGTGTAAAACAATTTC 59.079 33.333 0.00 0.00 37.78 2.17
375 387 1.145531 GTCTCCTACCTAGTCCCTCCC 59.854 61.905 0.00 0.00 0.00 4.30
378 390 1.574339 TCCTACCTAGTCCCTCCCAAG 59.426 57.143 0.00 0.00 0.00 3.61
396 408 6.068010 TCCCAAGCTTACATTCTCTCAAAAA 58.932 36.000 0.00 0.00 0.00 1.94
397 409 6.721208 TCCCAAGCTTACATTCTCTCAAAAAT 59.279 34.615 0.00 0.00 0.00 1.82
423 435 8.843262 TCTAAATTATTGTTGAGAGCATCCATG 58.157 33.333 0.00 0.00 33.66 3.66
430 442 0.883814 GAGAGCATCCATGAAGGGCG 60.884 60.000 0.00 0.00 38.24 6.13
447 459 2.288458 GGGCGCGTGCAATTTATAACTA 59.712 45.455 24.18 0.00 45.35 2.24
448 460 3.058501 GGGCGCGTGCAATTTATAACTAT 60.059 43.478 24.18 0.00 45.35 2.12
454 466 9.485591 GCGCGTGCAATTTATAACTATTTATAT 57.514 29.630 17.66 0.00 42.15 0.86
502 514 3.925913 GCCAAAATTTATCGCTCAAGCAA 59.074 39.130 2.50 0.00 42.21 3.91
508 520 7.559590 AAATTTATCGCTCAAGCAAGTCTAT 57.440 32.000 2.50 0.00 42.21 1.98
522 586 4.400567 GCAAGTCTATGAATTTTCAGCCCT 59.599 41.667 0.00 0.00 41.08 5.19
527 591 6.069731 AGTCTATGAATTTTCAGCCCTCTCTT 60.070 38.462 0.00 0.00 41.08 2.85
530 594 3.331889 TGAATTTTCAGCCCTCTCTTCCT 59.668 43.478 0.00 0.00 32.50 3.36
545 613 5.819991 TCTCTTCCTCATGCAATAAAACCT 58.180 37.500 0.00 0.00 0.00 3.50
557 625 2.404566 TAAAACCTGCCGCTCTGCCA 62.405 55.000 0.00 0.00 0.00 4.92
575 643 3.261580 GCCATTGCAATAAAACCCACTC 58.738 45.455 12.53 0.00 37.47 3.51
585 653 7.122055 TGCAATAAAACCCACTCGAATTTATCT 59.878 33.333 0.00 0.00 0.00 1.98
587 655 9.503427 CAATAAAACCCACTCGAATTTATCTTC 57.497 33.333 0.00 0.00 0.00 2.87
608 684 3.091529 GCGGCGTGCGGTTTTATA 58.908 55.556 9.37 0.00 0.00 0.98
624 700 7.042658 GCGGTTTTATAACTATGACCTCTTCAG 60.043 40.741 0.00 0.00 34.44 3.02
645 721 4.279671 CAGCCCTTCATAGTCTCGAGTTAT 59.720 45.833 13.13 9.10 0.00 1.89
646 722 4.896482 AGCCCTTCATAGTCTCGAGTTATT 59.104 41.667 13.13 0.00 0.00 1.40
647 723 6.016192 CAGCCCTTCATAGTCTCGAGTTATTA 60.016 42.308 13.13 1.43 0.00 0.98
648 724 6.550108 AGCCCTTCATAGTCTCGAGTTATTAA 59.450 38.462 13.13 8.71 0.00 1.40
649 725 7.069578 AGCCCTTCATAGTCTCGAGTTATTAAA 59.930 37.037 13.13 7.81 0.00 1.52
695 778 8.296713 TCAAACAGAGCAAACTTTATTCCATAC 58.703 33.333 0.00 0.00 0.00 2.39
696 779 6.422776 ACAGAGCAAACTTTATTCCATACG 57.577 37.500 0.00 0.00 0.00 3.06
713 879 2.125673 GCTCCATGCCACGTACGT 60.126 61.111 16.72 16.72 35.15 3.57
714 880 1.140161 GCTCCATGCCACGTACGTA 59.860 57.895 22.34 6.15 35.15 3.57
715 881 1.143969 GCTCCATGCCACGTACGTAC 61.144 60.000 22.34 15.90 35.15 3.67
905 1104 4.033776 CGGCTCAAGCAAGGGGGA 62.034 66.667 4.13 0.00 44.36 4.81
910 1134 2.036256 CAAGCAAGGGGGACAGGG 59.964 66.667 0.00 0.00 0.00 4.45
911 1135 3.984732 AAGCAAGGGGGACAGGGC 61.985 66.667 0.00 0.00 0.00 5.19
950 1174 3.530104 CGACCGCGCTACACGTTC 61.530 66.667 5.56 0.00 46.11 3.95
951 1175 2.429571 GACCGCGCTACACGTTCA 60.430 61.111 5.56 0.00 46.11 3.18
953 1177 3.475774 CCGCGCTACACGTTCACC 61.476 66.667 5.56 0.00 46.11 4.02
954 1178 3.475774 CGCGCTACACGTTCACCC 61.476 66.667 5.56 0.00 46.11 4.61
955 1179 3.116531 GCGCTACACGTTCACCCC 61.117 66.667 0.00 0.00 46.11 4.95
1171 1402 3.432782 CGCTCATCATTGCCTTTTTCTC 58.567 45.455 0.00 0.00 0.00 2.87
1172 1403 3.128242 CGCTCATCATTGCCTTTTTCTCT 59.872 43.478 0.00 0.00 0.00 3.10
1174 1405 4.439837 GCTCATCATTGCCTTTTTCTCTCC 60.440 45.833 0.00 0.00 0.00 3.71
1199 1436 3.610911 GACTTCCCGTGGATGATCTTTT 58.389 45.455 11.20 0.00 32.18 2.27
1218 1455 1.710816 TTTTGTGGGGAATGGGTCAC 58.289 50.000 0.00 0.00 0.00 3.67
1219 1456 0.558220 TTTGTGGGGAATGGGTCACA 59.442 50.000 0.00 0.00 38.21 3.58
1220 1457 0.783206 TTGTGGGGAATGGGTCACAT 59.217 50.000 0.00 0.00 43.07 3.21
1221 1458 0.039472 TGTGGGGAATGGGTCACATG 59.961 55.000 0.00 0.00 40.44 3.21
1222 1459 1.000233 TGGGGAATGGGTCACATGC 60.000 57.895 0.00 0.00 40.44 4.06
1223 1460 2.120909 GGGGAATGGGTCACATGCG 61.121 63.158 0.00 0.00 40.44 4.73
1224 1461 2.120909 GGGAATGGGTCACATGCGG 61.121 63.158 0.00 0.00 40.44 5.69
1225 1462 1.077787 GGAATGGGTCACATGCGGA 60.078 57.895 0.00 0.00 40.44 5.54
1226 1463 0.679640 GGAATGGGTCACATGCGGAA 60.680 55.000 0.00 0.00 40.44 4.30
1227 1464 1.173043 GAATGGGTCACATGCGGAAA 58.827 50.000 0.00 0.00 40.44 3.13
1228 1465 1.133025 GAATGGGTCACATGCGGAAAG 59.867 52.381 0.00 0.00 40.44 2.62
1249 1486 1.871126 GCCAGCTTTGACCTGCCTTC 61.871 60.000 0.00 0.00 0.00 3.46
1250 1487 1.246737 CCAGCTTTGACCTGCCTTCC 61.247 60.000 0.00 0.00 0.00 3.46
1251 1488 1.302832 AGCTTTGACCTGCCTTCCG 60.303 57.895 0.00 0.00 0.00 4.30
1268 1505 1.149964 CCGGGTTAATCGTTCGCCTC 61.150 60.000 0.00 0.00 0.00 4.70
1313 1553 0.655733 CGCCGCGGATTGTTATCTTT 59.344 50.000 33.48 0.00 0.00 2.52
1327 1567 6.992063 TGTTATCTTTGGATCTTTCAGCTC 57.008 37.500 0.00 0.00 33.71 4.09
1332 1572 4.929808 TCTTTGGATCTTTCAGCTCGTAAC 59.070 41.667 0.00 0.00 0.00 2.50
1339 1581 4.689071 TCTTTCAGCTCGTAACAGTGAAA 58.311 39.130 0.00 0.00 36.12 2.69
1340 1582 5.113383 TCTTTCAGCTCGTAACAGTGAAAA 58.887 37.500 0.00 0.00 36.85 2.29
1389 1658 3.181491 CGTTGGTTCTGTGGTGTGATTTT 60.181 43.478 0.00 0.00 0.00 1.82
1419 1688 5.473273 AGTTTTTACCTTTTGGATTCCCCT 58.527 37.500 0.00 0.00 44.07 4.79
1420 1689 5.542635 AGTTTTTACCTTTTGGATTCCCCTC 59.457 40.000 0.00 0.00 44.07 4.30
1421 1690 3.359695 TTACCTTTTGGATTCCCCTCG 57.640 47.619 0.00 0.00 44.07 4.63
1422 1691 0.323451 ACCTTTTGGATTCCCCTCGC 60.323 55.000 0.00 0.00 44.07 5.03
1423 1692 1.376609 CCTTTTGGATTCCCCTCGCG 61.377 60.000 0.00 0.00 44.07 5.87
1424 1693 0.676782 CTTTTGGATTCCCCTCGCGT 60.677 55.000 5.77 0.00 35.38 6.01
1426 1695 1.832719 TTTGGATTCCCCTCGCGTCA 61.833 55.000 5.77 0.00 35.38 4.35
1428 1697 1.146263 GGATTCCCCTCGCGTCATT 59.854 57.895 5.77 0.00 0.00 2.57
1457 1734 0.536724 GGCCGCCAAATCCAAAATCT 59.463 50.000 3.91 0.00 0.00 2.40
1469 1746 8.408601 CCAAATCCAAAATCTGTTAGGTCTATG 58.591 37.037 0.00 0.00 0.00 2.23
1481 1758 9.797642 TCTGTTAGGTCTATGTATAATACCGAA 57.202 33.333 0.00 0.00 35.32 4.30
1486 1763 7.655490 AGGTCTATGTATAATACCGAACACAC 58.345 38.462 0.00 0.00 35.32 3.82
1493 1770 8.054152 TGTATAATACCGAACACACACTAGAA 57.946 34.615 0.00 0.00 0.00 2.10
1503 1780 7.544566 CCGAACACACACTAGAATTGTAGTAAT 59.455 37.037 14.39 4.25 31.73 1.89
1504 1781 9.563898 CGAACACACACTAGAATTGTAGTAATA 57.436 33.333 14.39 0.00 31.73 0.98
1516 1793 9.855021 AGAATTGTAGTAATAAATGTTGTTGCC 57.145 29.630 0.00 0.00 0.00 4.52
1521 1810 6.515272 AGTAATAAATGTTGTTGCCCAGAG 57.485 37.500 0.00 0.00 0.00 3.35
1522 1811 3.874392 ATAAATGTTGTTGCCCAGAGC 57.126 42.857 0.00 0.00 44.14 4.09
1596 1889 4.092237 TGAATTCAATTACTACACGCGGTG 59.908 41.667 12.47 9.20 39.75 4.94
1611 1904 1.412710 GCGGTGTGGGATCTCAATAGA 59.587 52.381 0.00 0.00 35.80 1.98
1628 1921 9.170734 TCTCAATAGAAATGTTTTGATCAGGAG 57.829 33.333 0.00 0.00 0.00 3.69
1692 1995 2.922283 ACTTTCCATGGAGGGTTGAGAT 59.078 45.455 15.53 0.00 38.24 2.75
1696 1999 3.041211 TCCATGGAGGGTTGAGATGTAG 58.959 50.000 11.44 0.00 38.24 2.74
1773 2076 0.531090 TGCCGTGTCAGTGTTGGTAC 60.531 55.000 0.00 0.00 0.00 3.34
1854 2161 5.356190 ACCTTGATGATGCATACTCTGTTTG 59.644 40.000 0.00 0.00 0.00 2.93
1880 2187 6.472016 TGTAGAAATGGTTACATGCTTCTGA 58.528 36.000 0.00 0.00 35.80 3.27
1960 2269 7.176865 TCCCGGTGTTTTATGTTATGATGAAAA 59.823 33.333 0.00 0.00 0.00 2.29
2033 2342 0.896940 TTGGAGCCGGAGTCTACGTT 60.897 55.000 5.05 0.00 0.00 3.99
2213 2522 1.816224 GGCGAAGGGTAATTTGCTGAA 59.184 47.619 0.00 0.00 39.21 3.02
2217 2526 3.859386 CGAAGGGTAATTTGCTGAAATGC 59.141 43.478 0.00 0.00 31.83 3.56
2251 2560 3.006940 TGTTCATGAAGTGCCGTATTCC 58.993 45.455 8.80 0.00 0.00 3.01
2253 2562 3.342377 TCATGAAGTGCCGTATTCCAA 57.658 42.857 0.00 0.00 0.00 3.53
2259 2568 2.483876 AGTGCCGTATTCCAATGATCG 58.516 47.619 0.00 0.00 0.00 3.69
2271 2580 3.197549 TCCAATGATCGGATGTTCTCACA 59.802 43.478 0.00 0.00 37.31 3.58
2277 2586 4.021104 TGATCGGATGTTCTCACACTTTCT 60.021 41.667 0.00 0.00 35.03 2.52
2299 2608 7.510549 TCTTTTGACATTTTGTTCTCCTAGG 57.489 36.000 0.82 0.82 0.00 3.02
2324 2633 2.514824 GGTTGATCGGCTGGGCTC 60.515 66.667 0.00 0.00 0.00 4.70
2326 2635 1.522580 GTTGATCGGCTGGGCTCTC 60.523 63.158 0.00 0.00 0.00 3.20
2420 2729 1.000060 CCTGTTTCTGTGGCATGTTGG 60.000 52.381 0.00 0.00 0.00 3.77
2422 2731 2.101249 CTGTTTCTGTGGCATGTTGGTT 59.899 45.455 0.00 0.00 0.00 3.67
2455 2768 4.902448 ACCTTCCATCTCTCCTAACATACC 59.098 45.833 0.00 0.00 0.00 2.73
2466 2779 3.572682 TCCTAACATACCCTGTCTATGCG 59.427 47.826 0.00 0.00 36.98 4.73
2469 2782 3.906720 ACATACCCTGTCTATGCGTTT 57.093 42.857 0.00 0.00 29.94 3.60
2617 2930 2.862536 GCGTCGGGATAAAAGAGGTTAC 59.137 50.000 0.00 0.00 0.00 2.50
2788 3101 0.906066 TAGCCGGCAGTTACATTGGA 59.094 50.000 31.54 0.00 0.00 3.53
3008 3321 1.897647 GCTGAGGAGGTAAGGACAGGT 60.898 57.143 0.00 0.00 0.00 4.00
3043 3356 0.523072 GACATGCATGGCACGTCTTT 59.477 50.000 27.99 3.81 46.24 2.52
3075 3388 3.120304 GGATCGGCGGCATTATTAAGAAC 60.120 47.826 10.53 0.00 0.00 3.01
3172 3486 4.323417 TGACGATTTGCTGTTCCTTGTAT 58.677 39.130 0.00 0.00 0.00 2.29
3250 3564 1.143073 ACCCCTATTTCATCCGCCTTC 59.857 52.381 0.00 0.00 0.00 3.46
3287 3601 2.026822 CAGTGGGCAATGTAAGGACTCT 60.027 50.000 0.00 0.00 0.00 3.24
3288 3602 2.237392 AGTGGGCAATGTAAGGACTCTC 59.763 50.000 0.00 0.00 0.00 3.20
3289 3603 1.559682 TGGGCAATGTAAGGACTCTCC 59.440 52.381 0.00 0.00 36.58 3.71
3290 3604 1.134068 GGGCAATGTAAGGACTCTCCC 60.134 57.143 0.00 0.00 37.19 4.30
3298 3612 3.323979 TGTAAGGACTCTCCCTTTGACAC 59.676 47.826 0.00 0.00 43.68 3.67
3299 3613 1.353091 AGGACTCTCCCTTTGACACC 58.647 55.000 0.00 0.00 37.19 4.16
3300 3614 1.132689 AGGACTCTCCCTTTGACACCT 60.133 52.381 0.00 0.00 37.19 4.00
3315 3629 1.078426 ACCTCTTCCATTTCGCCGG 60.078 57.895 0.00 0.00 0.00 6.13
3345 3664 2.749441 GTGCTTCCTGCTGAGGCC 60.749 66.667 0.00 0.00 45.05 5.19
3394 3713 2.200373 ACCTTGTAACATCTGGTGCC 57.800 50.000 0.00 0.00 0.00 5.01
3781 4110 0.389391 CCATAGTCGCCGTCTCCATT 59.611 55.000 0.00 0.00 0.00 3.16
4125 4456 7.756722 CCATCAGACAAATTGGATGAGTTAAAC 59.243 37.037 10.79 0.00 39.52 2.01
4450 4781 4.242475 CACTTGCATCACAGCATTTTCAT 58.758 39.130 0.00 0.00 45.19 2.57
4464 4813 5.149054 CATTTTCATGCTTCTCTCCGTAC 57.851 43.478 0.00 0.00 0.00 3.67
4465 4814 4.537135 TTTTCATGCTTCTCTCCGTACT 57.463 40.909 0.00 0.00 0.00 2.73
4466 4815 5.654603 TTTTCATGCTTCTCTCCGTACTA 57.345 39.130 0.00 0.00 0.00 1.82
4467 4816 4.902443 TTCATGCTTCTCTCCGTACTAG 57.098 45.455 0.00 0.00 0.00 2.57
4468 4817 4.152284 TCATGCTTCTCTCCGTACTAGA 57.848 45.455 0.00 0.00 0.00 2.43
4469 4818 3.878103 TCATGCTTCTCTCCGTACTAGAC 59.122 47.826 0.00 0.00 0.00 2.59
4471 4820 4.750021 TGCTTCTCTCCGTACTAGACTA 57.250 45.455 0.00 0.00 0.00 2.59
4472 4821 4.440880 TGCTTCTCTCCGTACTAGACTAC 58.559 47.826 0.00 0.00 0.00 2.73
4473 4822 4.161942 TGCTTCTCTCCGTACTAGACTACT 59.838 45.833 0.00 0.00 0.00 2.57
4474 4823 4.508861 GCTTCTCTCCGTACTAGACTACTG 59.491 50.000 0.00 0.00 0.00 2.74
4475 4824 4.669206 TCTCTCCGTACTAGACTACTGG 57.331 50.000 0.00 0.00 0.00 4.00
4476 4825 4.029520 TCTCTCCGTACTAGACTACTGGT 58.970 47.826 0.00 0.00 40.73 4.00
4477 4826 5.204292 TCTCTCCGTACTAGACTACTGGTA 58.796 45.833 0.00 0.00 38.69 3.25
4478 4827 5.658634 TCTCTCCGTACTAGACTACTGGTAA 59.341 44.000 0.00 0.00 40.67 2.85
4479 4828 5.665459 TCTCCGTACTAGACTACTGGTAAC 58.335 45.833 0.00 0.00 40.67 2.50
4480 4829 5.423610 TCTCCGTACTAGACTACTGGTAACT 59.576 44.000 0.00 0.00 40.67 2.24
4481 4830 6.054860 TCCGTACTAGACTACTGGTAACTT 57.945 41.667 0.00 0.00 40.67 2.66
4482 4831 5.877012 TCCGTACTAGACTACTGGTAACTTG 59.123 44.000 0.00 0.00 40.67 3.16
4483 4832 5.877012 CCGTACTAGACTACTGGTAACTTGA 59.123 44.000 0.00 0.00 40.67 3.02
4484 4833 6.541641 CCGTACTAGACTACTGGTAACTTGAT 59.458 42.308 0.00 0.00 40.67 2.57
4485 4834 7.408123 CGTACTAGACTACTGGTAACTTGATG 58.592 42.308 0.00 0.00 40.67 3.07
4486 4835 6.210287 ACTAGACTACTGGTAACTTGATGC 57.790 41.667 0.00 0.00 36.11 3.91
4606 4962 7.622081 TCATAAATCTAGGGTGAGTACCTCAAA 59.378 37.037 0.00 0.00 46.66 2.69
4607 4963 5.941555 AATCTAGGGTGAGTACCTCAAAG 57.058 43.478 0.00 0.00 46.66 2.77
4608 4964 3.097614 TCTAGGGTGAGTACCTCAAAGC 58.902 50.000 0.00 0.00 46.66 3.51
4609 4965 2.031495 AGGGTGAGTACCTCAAAGCT 57.969 50.000 0.00 0.00 46.66 3.74
4610 4966 1.903183 AGGGTGAGTACCTCAAAGCTC 59.097 52.381 0.00 0.00 46.66 4.09
4611 4967 1.623811 GGGTGAGTACCTCAAAGCTCA 59.376 52.381 0.00 0.00 46.66 4.26
4612 4968 2.038557 GGGTGAGTACCTCAAAGCTCAA 59.961 50.000 0.00 0.00 46.66 3.02
4625 4981 7.094463 ACCTCAAAGCTCAAACAATTATCTCAG 60.094 37.037 0.00 0.00 0.00 3.35
5746 6170 0.527565 GCCAGTTGATTCAACCGCAT 59.472 50.000 22.70 4.77 44.49 4.73
5784 6208 0.321298 TCTTCCTTTGCGCCCTACAC 60.321 55.000 4.18 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.645415 CGGTAAACAATATTAGAATCGCTCCT 59.355 38.462 0.00 0.00 0.00 3.69
1 2 6.423001 ACGGTAAACAATATTAGAATCGCTCC 59.577 38.462 0.00 0.00 0.00 4.70
2 3 7.404139 ACGGTAAACAATATTAGAATCGCTC 57.596 36.000 0.00 0.00 0.00 5.03
3 4 8.758715 GTTACGGTAAACAATATTAGAATCGCT 58.241 33.333 1.47 0.00 0.00 4.93
4 5 7.733011 CGTTACGGTAAACAATATTAGAATCGC 59.267 37.037 1.47 0.00 0.00 4.58
5 6 8.745837 ACGTTACGGTAAACAATATTAGAATCG 58.254 33.333 10.20 0.00 0.00 3.34
8 9 8.582930 CGAACGTTACGGTAAACAATATTAGAA 58.417 33.333 10.20 0.00 0.00 2.10
38 39 6.488769 ACAATACATTATAAGGGACGTGGA 57.511 37.500 0.00 0.00 0.00 4.02
42 43 8.897872 AGGTTAACAATACATTATAAGGGACG 57.102 34.615 8.10 0.00 0.00 4.79
143 148 5.280934 CCATTAAACACCAAATGGGGGATTT 60.281 40.000 6.65 1.34 46.16 2.17
159 164 5.221165 CCCCGACACATAATTCCCATTAAAC 60.221 44.000 0.00 0.00 0.00 2.01
179 184 3.208747 AGGCTTTATTATCACACCCCG 57.791 47.619 0.00 0.00 0.00 5.73
185 191 8.171164 AGCAAAGGAATAGGCTTTATTATCAC 57.829 34.615 0.00 0.00 31.34 3.06
200 206 3.529319 ACCCCTCTATCAAGCAAAGGAAT 59.471 43.478 0.00 0.00 0.00 3.01
230 237 2.355756 CCATCTTTGCACTTATCCCACG 59.644 50.000 0.00 0.00 0.00 4.94
238 245 6.655078 AACTTATGTTCCATCTTTGCACTT 57.345 33.333 0.00 0.00 0.00 3.16
245 252 9.401058 CTTTCCTCATAACTTATGTTCCATCTT 57.599 33.333 8.37 0.00 37.59 2.40
266 273 6.183360 TGTTTTACACACATCTTCACCTTTCC 60.183 38.462 0.00 0.00 0.00 3.13
270 277 6.959639 ATTGTTTTACACACATCTTCACCT 57.040 33.333 0.00 0.00 33.98 4.00
271 278 7.169140 GGAAATTGTTTTACACACATCTTCACC 59.831 37.037 0.00 0.00 33.98 4.02
289 296 2.365582 CGGAAATCGGGAGGAAATTGT 58.634 47.619 0.00 0.00 34.75 2.71
346 358 6.101005 GGGACTAGGTAGGAGACTTAAGAGTA 59.899 46.154 10.09 0.00 43.67 2.59
396 408 8.985315 TGGATGCTCTCAACAATAATTTAGAT 57.015 30.769 0.00 0.00 0.00 1.98
397 409 8.843262 CATGGATGCTCTCAACAATAATTTAGA 58.157 33.333 0.00 0.00 0.00 2.10
420 432 2.546645 AATTGCACGCGCCCTTCATG 62.547 55.000 5.73 0.00 37.32 3.07
423 435 0.100503 ATAAATTGCACGCGCCCTTC 59.899 50.000 5.73 0.00 37.32 3.46
454 466 6.366877 GTGTTTTATTGCACCGAGTAGAGTAA 59.633 38.462 0.00 0.00 0.00 2.24
457 469 4.201589 CGTGTTTTATTGCACCGAGTAGAG 60.202 45.833 0.00 0.00 32.40 2.43
459 471 3.723835 GCGTGTTTTATTGCACCGAGTAG 60.724 47.826 0.00 0.00 32.40 2.57
502 514 5.428131 AGAGAGGGCTGAAAATTCATAGACT 59.572 40.000 0.00 0.00 36.46 3.24
508 520 3.331889 AGGAAGAGAGGGCTGAAAATTCA 59.668 43.478 0.00 0.00 35.57 2.57
522 586 5.649395 CAGGTTTTATTGCATGAGGAAGAGA 59.351 40.000 0.00 0.00 0.00 3.10
527 591 2.760092 GGCAGGTTTTATTGCATGAGGA 59.240 45.455 0.00 0.00 42.02 3.71
530 594 1.135141 GCGGCAGGTTTTATTGCATGA 60.135 47.619 0.00 0.00 42.02 3.07
557 625 5.659440 ATTCGAGTGGGTTTTATTGCAAT 57.341 34.783 17.56 17.56 0.00 3.56
608 684 2.839228 AGGGCTGAAGAGGTCATAGTT 58.161 47.619 0.00 0.00 35.07 2.24
624 700 4.857509 ATAACTCGAGACTATGAAGGGC 57.142 45.455 21.68 0.00 0.00 5.19
645 721 5.950758 ACGCCAACATGAGTGTAATTTAA 57.049 34.783 0.00 0.00 37.67 1.52
646 722 6.819146 TGATACGCCAACATGAGTGTAATTTA 59.181 34.615 0.00 0.00 37.67 1.40
647 723 5.645929 TGATACGCCAACATGAGTGTAATTT 59.354 36.000 0.00 0.00 37.67 1.82
648 724 5.182487 TGATACGCCAACATGAGTGTAATT 58.818 37.500 0.00 0.00 37.67 1.40
649 725 4.765273 TGATACGCCAACATGAGTGTAAT 58.235 39.130 0.00 0.00 37.67 1.89
658 741 2.420022 GCTCTGTTTGATACGCCAACAT 59.580 45.455 0.00 0.00 0.00 2.71
696 779 1.140161 TACGTACGTGGCATGGAGC 59.860 57.895 30.25 0.00 44.65 4.70
774 949 1.737735 TGCCGCTGTCTGAATCGTG 60.738 57.895 0.00 0.00 0.00 4.35
1140 1370 2.354656 GATGAGCGCGCACCGATA 60.355 61.111 35.10 11.67 40.02 2.92
1171 1402 1.192146 TCCACGGGAAGTCCAAGGAG 61.192 60.000 0.00 0.00 34.40 3.69
1172 1403 0.546747 ATCCACGGGAAGTCCAAGGA 60.547 55.000 0.00 3.65 40.82 3.36
1174 1405 0.613260 TCATCCACGGGAAGTCCAAG 59.387 55.000 0.00 0.00 34.34 3.61
1199 1436 1.062886 TGTGACCCATTCCCCACAAAA 60.063 47.619 0.00 0.00 36.69 2.44
1203 1440 1.322538 GCATGTGACCCATTCCCCAC 61.323 60.000 0.00 0.00 0.00 4.61
1206 1443 2.120909 CCGCATGTGACCCATTCCC 61.121 63.158 8.11 0.00 0.00 3.97
1207 1444 0.679640 TTCCGCATGTGACCCATTCC 60.680 55.000 8.11 0.00 0.00 3.01
1208 1445 1.133025 CTTTCCGCATGTGACCCATTC 59.867 52.381 8.11 0.00 0.00 2.67
1209 1446 1.176527 CTTTCCGCATGTGACCCATT 58.823 50.000 8.11 0.00 0.00 3.16
1210 1447 1.315257 GCTTTCCGCATGTGACCCAT 61.315 55.000 8.11 0.00 38.92 4.00
1213 1450 2.480555 CGCTTTCCGCATGTGACC 59.519 61.111 8.11 0.00 39.08 4.02
1228 1465 4.410743 GCAGGTCAAAGCTGGCGC 62.411 66.667 0.00 0.00 43.49 6.53
1231 1468 1.246737 GGAAGGCAGGTCAAAGCTGG 61.247 60.000 8.11 0.00 43.49 4.85
1232 1469 1.580845 CGGAAGGCAGGTCAAAGCTG 61.581 60.000 1.88 1.88 45.86 4.24
1233 1470 1.302832 CGGAAGGCAGGTCAAAGCT 60.303 57.895 0.00 0.00 0.00 3.74
1234 1471 3.267974 CGGAAGGCAGGTCAAAGC 58.732 61.111 0.00 0.00 0.00 3.51
1249 1486 1.149964 GAGGCGAACGATTAACCCGG 61.150 60.000 0.00 0.00 0.00 5.73
1250 1487 1.149964 GGAGGCGAACGATTAACCCG 61.150 60.000 0.00 0.00 0.00 5.28
1251 1488 0.108041 TGGAGGCGAACGATTAACCC 60.108 55.000 0.00 0.00 0.00 4.11
1298 1538 5.757850 AAGATCCAAAGATAACAATCCGC 57.242 39.130 0.00 0.00 30.90 5.54
1303 1543 7.383102 GAGCTGAAAGATCCAAAGATAACAA 57.617 36.000 0.00 0.00 45.38 2.83
1339 1581 4.816925 GCCTATCGGAGCAGAGTAATTTTT 59.183 41.667 0.00 0.00 0.00 1.94
1340 1582 4.381411 GCCTATCGGAGCAGAGTAATTTT 58.619 43.478 0.00 0.00 0.00 1.82
1351 1593 4.767633 CGATACGCCTATCGGAGC 57.232 61.111 14.92 0.00 45.50 4.70
1356 1598 3.050619 CAGAACCAACGATACGCCTATC 58.949 50.000 0.00 0.00 0.00 2.08
1357 1599 2.429610 ACAGAACCAACGATACGCCTAT 59.570 45.455 0.00 0.00 0.00 2.57
1358 1600 1.820519 ACAGAACCAACGATACGCCTA 59.179 47.619 0.00 0.00 0.00 3.93
1359 1601 0.606604 ACAGAACCAACGATACGCCT 59.393 50.000 0.00 0.00 0.00 5.52
1364 1633 2.365941 TCACACCACAGAACCAACGATA 59.634 45.455 0.00 0.00 0.00 2.92
1367 1636 1.593196 ATCACACCACAGAACCAACG 58.407 50.000 0.00 0.00 0.00 4.10
1389 1658 5.197451 TCCAAAAGGTAAAAACTCTGCAGA 58.803 37.500 17.19 17.19 0.00 4.26
1422 1691 3.487202 CCGTGTGGGCGAATGACG 61.487 66.667 0.00 0.00 45.66 4.35
1432 1709 4.114997 GATTTGGCGGCCGTGTGG 62.115 66.667 28.70 0.00 38.77 4.17
1438 1715 0.536724 AGATTTTGGATTTGGCGGCC 59.463 50.000 13.32 13.32 0.00 6.13
1457 1734 9.353431 TGTTCGGTATTATACATAGACCTAACA 57.647 33.333 4.67 13.12 41.11 2.41
1469 1746 9.525409 AATTCTAGTGTGTGTTCGGTATTATAC 57.475 33.333 0.00 0.00 0.00 1.47
1472 1749 7.380536 ACAATTCTAGTGTGTGTTCGGTATTA 58.619 34.615 0.00 0.00 0.00 0.98
1493 1770 8.128322 TGGGCAACAACATTTATTACTACAAT 57.872 30.769 0.00 0.00 39.74 2.71
1503 1780 1.539388 CGCTCTGGGCAACAACATTTA 59.461 47.619 0.00 0.00 41.91 1.40
1504 1781 0.314935 CGCTCTGGGCAACAACATTT 59.685 50.000 0.00 0.00 41.91 2.32
1505 1782 1.959085 CGCTCTGGGCAACAACATT 59.041 52.632 0.00 0.00 41.91 2.71
1506 1783 2.629656 GCGCTCTGGGCAACAACAT 61.630 57.895 0.00 0.00 41.23 2.71
1514 1791 4.774503 AGCTTCTGCGCTCTGGGC 62.775 66.667 9.73 6.89 45.42 5.36
1515 1792 2.046507 AAGCTTCTGCGCTCTGGG 60.047 61.111 9.73 0.00 45.42 4.45
1516 1793 2.105466 GGAAGCTTCTGCGCTCTGG 61.105 63.158 25.05 0.00 45.42 3.86
1521 1810 1.230635 TTCAGTGGAAGCTTCTGCGC 61.231 55.000 25.05 15.87 45.42 6.09
1522 1811 0.795085 CTTCAGTGGAAGCTTCTGCG 59.205 55.000 25.05 11.92 43.67 5.18
1579 1868 1.392168 CCACACCGCGTGTAGTAATTG 59.608 52.381 4.92 0.00 45.65 2.32
1596 1889 8.055279 TCAAAACATTTCTATTGAGATCCCAC 57.945 34.615 0.00 0.00 0.00 4.61
1611 1904 6.251471 AGTCCATCTCCTGATCAAAACATTT 58.749 36.000 0.00 0.00 0.00 2.32
1628 1921 5.177326 GGAATCTGCATCTCATAGTCCATC 58.823 45.833 0.00 0.00 36.44 3.51
1683 1986 7.285858 ACTTCAGATAGTACTACATCTCAACCC 59.714 40.741 4.31 0.00 28.88 4.11
1726 2029 5.163343 ACCAAACAAGCACAAGAGTAGTAGA 60.163 40.000 0.00 0.00 0.00 2.59
1812 2119 4.170468 AGGTATGTAGCAAGATTTGGGG 57.830 45.455 0.00 0.00 0.00 4.96
1854 2161 7.280876 TCAGAAGCATGTAACCATTTCTACATC 59.719 37.037 0.00 0.00 36.77 3.06
1904 2211 5.390356 GCAAGACAGAAAATAGACTCTGCAC 60.390 44.000 0.00 0.00 42.39 4.57
1960 2269 7.776969 ACAAAATAGATGTTCCATGAGCACTAT 59.223 33.333 0.00 0.00 0.00 2.12
2217 2526 2.815503 TCATGAACAATGTGCACTCCAG 59.184 45.455 19.41 7.93 37.56 3.86
2251 2560 4.186926 AGTGTGAGAACATCCGATCATTG 58.813 43.478 0.00 0.00 0.00 2.82
2253 2562 4.478206 AAGTGTGAGAACATCCGATCAT 57.522 40.909 0.00 0.00 0.00 2.45
2259 2568 6.183360 TGTCAAAAGAAAGTGTGAGAACATCC 60.183 38.462 0.00 0.00 0.00 3.51
2271 2580 7.840931 AGGAGAACAAAATGTCAAAAGAAAGT 58.159 30.769 0.00 0.00 0.00 2.66
2277 2586 6.133356 ACCCTAGGAGAACAAAATGTCAAAA 58.867 36.000 11.48 0.00 0.00 2.44
2299 2608 1.139520 GCCGATCAACCATGCAACC 59.860 57.895 0.00 0.00 0.00 3.77
2324 2633 5.635280 CGCCAATTGTATACTCCAGTATGAG 59.365 44.000 9.17 0.00 41.03 2.90
2326 2635 4.690748 CCGCCAATTGTATACTCCAGTATG 59.309 45.833 9.17 0.00 41.03 2.39
2398 2707 0.478072 ACATGCCACAGAAACAGGGA 59.522 50.000 0.00 0.00 0.00 4.20
2401 2710 1.682854 ACCAACATGCCACAGAAACAG 59.317 47.619 0.00 0.00 0.00 3.16
2410 2719 4.517453 GTGAAACTACTAACCAACATGCCA 59.483 41.667 0.00 0.00 0.00 4.92
2411 2720 4.082949 GGTGAAACTACTAACCAACATGCC 60.083 45.833 0.00 0.00 36.74 4.40
2420 2729 6.937392 AGAGATGGAAGGTGAAACTACTAAC 58.063 40.000 0.00 0.00 36.74 2.34
2422 2731 5.657302 GGAGAGATGGAAGGTGAAACTACTA 59.343 44.000 0.00 0.00 36.74 1.82
2455 2768 1.209128 CGCCTAAACGCATAGACAGG 58.791 55.000 0.00 0.00 0.00 4.00
2483 2796 1.559682 GGCAGACTATTTGGTCCTCCA 59.440 52.381 0.00 0.00 42.66 3.86
2617 2930 3.378112 TGTTTCTGAAGTGTTGAAGCCTG 59.622 43.478 0.00 0.00 0.00 4.85
2655 2968 8.458573 AATATCATAGGCTATACTTCTCGAGG 57.541 38.462 13.56 0.00 0.00 4.63
2701 3014 4.024048 CCTTGCACGAATGTACTCTGTTTT 60.024 41.667 0.00 0.00 0.00 2.43
2702 3015 3.498397 CCTTGCACGAATGTACTCTGTTT 59.502 43.478 0.00 0.00 0.00 2.83
2866 3179 5.540400 AGTGGTTAAGCACACTACTTACA 57.460 39.130 32.69 0.00 45.45 2.41
3008 3321 4.041321 TGCATGTCAATTTGGGAAATGGAA 59.959 37.500 0.00 0.00 32.79 3.53
3043 3356 2.717044 CGCCGATCCAGTGGGTGTA 61.717 63.158 9.92 0.00 32.13 2.90
3075 3388 6.467677 TGGAATGGAAGTTTAGACAGAAGAG 58.532 40.000 0.00 0.00 0.00 2.85
3172 3486 6.348132 CGACAATAACAACTGAAACCAGCATA 60.348 38.462 0.00 0.00 35.09 3.14
3274 3588 4.597507 TGTCAAAGGGAGAGTCCTTACATT 59.402 41.667 0.00 0.00 45.67 2.71
3287 3601 1.814429 TGGAAGAGGTGTCAAAGGGA 58.186 50.000 0.00 0.00 0.00 4.20
3288 3602 2.887151 ATGGAAGAGGTGTCAAAGGG 57.113 50.000 0.00 0.00 0.00 3.95
3289 3603 3.189287 CGAAATGGAAGAGGTGTCAAAGG 59.811 47.826 0.00 0.00 0.00 3.11
3290 3604 3.365364 GCGAAATGGAAGAGGTGTCAAAG 60.365 47.826 0.00 0.00 0.00 2.77
3298 3612 1.819632 CCCGGCGAAATGGAAGAGG 60.820 63.158 9.30 0.00 0.00 3.69
3299 3613 2.472909 GCCCGGCGAAATGGAAGAG 61.473 63.158 9.30 0.00 0.00 2.85
3300 3614 2.437716 GCCCGGCGAAATGGAAGA 60.438 61.111 9.30 0.00 0.00 2.87
3353 3672 3.214328 ACCTAAAACAAGACAGTGCAGG 58.786 45.455 0.00 0.00 0.00 4.85
3358 3677 5.997843 ACAAGGTACCTAAAACAAGACAGT 58.002 37.500 16.67 0.00 0.00 3.55
3366 3685 6.938596 ACCAGATGTTACAAGGTACCTAAAAC 59.061 38.462 16.67 18.65 0.00 2.43
3708 4037 5.300792 TGCAACCAAACTTAACTCCTTTAGG 59.699 40.000 0.00 0.00 0.00 2.69
4450 4781 3.630892 AGTCTAGTACGGAGAGAAGCA 57.369 47.619 1.18 0.00 0.00 3.91
4464 4813 5.127194 TGGCATCAAGTTACCAGTAGTCTAG 59.873 44.000 0.00 0.00 0.00 2.43
4465 4814 5.020795 TGGCATCAAGTTACCAGTAGTCTA 58.979 41.667 0.00 0.00 0.00 2.59
4466 4815 3.838317 TGGCATCAAGTTACCAGTAGTCT 59.162 43.478 0.00 0.00 0.00 3.24
4467 4816 3.933332 GTGGCATCAAGTTACCAGTAGTC 59.067 47.826 0.00 0.00 31.46 2.59
4468 4817 3.326588 TGTGGCATCAAGTTACCAGTAGT 59.673 43.478 0.00 0.00 31.46 2.73
4469 4818 3.935203 CTGTGGCATCAAGTTACCAGTAG 59.065 47.826 0.00 0.00 31.46 2.57
4471 4820 2.783135 CTGTGGCATCAAGTTACCAGT 58.217 47.619 0.00 0.00 31.46 4.00
4472 4821 1.470098 GCTGTGGCATCAAGTTACCAG 59.530 52.381 0.00 0.00 38.54 4.00
4473 4822 1.073763 AGCTGTGGCATCAAGTTACCA 59.926 47.619 0.00 0.00 41.70 3.25
4474 4823 1.740025 GAGCTGTGGCATCAAGTTACC 59.260 52.381 0.00 0.00 41.70 2.85
4475 4824 1.740025 GGAGCTGTGGCATCAAGTTAC 59.260 52.381 0.00 0.00 41.70 2.50
4476 4825 1.630369 AGGAGCTGTGGCATCAAGTTA 59.370 47.619 0.00 0.00 41.70 2.24
4477 4826 0.403271 AGGAGCTGTGGCATCAAGTT 59.597 50.000 0.00 0.00 41.70 2.66
4478 4827 0.403271 AAGGAGCTGTGGCATCAAGT 59.597 50.000 0.00 0.00 41.70 3.16
4479 4828 1.471684 GAAAGGAGCTGTGGCATCAAG 59.528 52.381 0.00 0.00 41.70 3.02
4480 4829 1.074405 AGAAAGGAGCTGTGGCATCAA 59.926 47.619 0.00 0.00 41.70 2.57
4481 4830 0.694771 AGAAAGGAGCTGTGGCATCA 59.305 50.000 0.00 0.00 41.70 3.07
4482 4831 1.093159 CAGAAAGGAGCTGTGGCATC 58.907 55.000 0.00 0.00 41.70 3.91
4483 4832 0.964358 GCAGAAAGGAGCTGTGGCAT 60.964 55.000 0.00 0.00 41.70 4.40
4484 4833 1.601759 GCAGAAAGGAGCTGTGGCA 60.602 57.895 0.00 0.00 41.70 4.92
4485 4834 2.338785 GGCAGAAAGGAGCTGTGGC 61.339 63.158 0.00 0.00 35.81 5.01
4486 4835 2.037136 CGGCAGAAAGGAGCTGTGG 61.037 63.158 0.00 0.00 35.81 4.17
4606 4962 4.331168 GCGACTGAGATAATTGTTTGAGCT 59.669 41.667 0.00 0.00 0.00 4.09
4607 4963 4.331168 AGCGACTGAGATAATTGTTTGAGC 59.669 41.667 0.00 0.00 0.00 4.26
4608 4964 5.578336 TCAGCGACTGAGATAATTGTTTGAG 59.422 40.000 5.59 0.00 35.39 3.02
4609 4965 5.478407 TCAGCGACTGAGATAATTGTTTGA 58.522 37.500 5.59 0.00 35.39 2.69
4610 4966 5.784750 TCAGCGACTGAGATAATTGTTTG 57.215 39.130 5.59 0.00 35.39 2.93
4611 4967 7.766278 ACTTATCAGCGACTGAGATAATTGTTT 59.234 33.333 13.55 0.00 44.08 2.83
4612 4968 7.268586 ACTTATCAGCGACTGAGATAATTGTT 58.731 34.615 13.55 0.00 44.08 2.83
4625 4981 4.492085 GGCGAAAGTAAACTTATCAGCGAC 60.492 45.833 0.00 0.00 34.61 5.19
4986 5344 2.435586 GGATGCAGCAGCGACAGT 60.436 61.111 3.51 0.00 46.23 3.55
5746 6170 7.125792 GGAAGATCCTACTTGTTGATCCTTA 57.874 40.000 0.00 0.00 36.41 2.69
5784 6208 0.882927 TTCCTTTCACGCCCTTGTCG 60.883 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.