Multiple sequence alignment - TraesCS4D01G179800

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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 TraesCS4D01G179800 chr4D 100.000 3519 0 0 1 3519 312802842 312799324 0.000000e+00 6499.0
1 TraesCS4D01G179800 chr4A 94.425 1166 38 13 1823 2986 163818423 163819563 0.000000e+00 1768.0
2 TraesCS4D01G179800 chr4A 90.738 691 51 7 2 682 163814754 163815441 0.000000e+00 909.0
3 TraesCS4D01G179800 chr4A 87.823 813 50 25 735 1534 163816876 163817652 0.000000e+00 907.0
4 TraesCS4D01G179800 chr4A 90.800 500 43 3 3019 3518 163819830 163820326 0.000000e+00 665.0
5 TraesCS4D01G179800 chr4A 93.671 79 5 0 1711 1789 163818166 163818244 6.170000e-23 119.0
6 TraesCS4D01G179800 chr4B 92.706 1042 56 13 2019 3058 390280617 390281640 0.000000e+00 1485.0
7 TraesCS4D01G179800 chr4B 91.969 386 16 6 723 1104 390279245 390279619 8.650000e-146 527.0
8 TraesCS4D01G179800 chr4B 83.290 389 35 18 1154 1531 390279727 390280096 7.280000e-87 331.0
9 TraesCS4D01G179800 chr2B 92.593 378 28 0 2142 2519 77170293 77170670 8.590000e-151 544.0
10 TraesCS4D01G179800 chr2B 92.405 79 6 0 1000 1078 77168977 77169055 2.870000e-21 113.0
11 TraesCS4D01G179800 chr2D 92.328 378 29 0 2142 2519 49877340 49877717 4.000000e-149 538.0
12 TraesCS4D01G179800 chr2D 75.191 524 119 9 195 713 650489445 650488928 1.630000e-58 237.0
13 TraesCS4D01G179800 chr2D 92.405 79 6 0 1000 1078 49875921 49875999 2.870000e-21 113.0
14 TraesCS4D01G179800 chr2D 84.286 70 11 0 196 265 556349041 556349110 6.300000e-08 69.4
15 TraesCS4D01G179800 chr2A 92.063 378 30 0 2142 2519 51583543 51583920 1.860000e-147 532.0
16 TraesCS4D01G179800 chr2A 77.444 532 104 12 195 718 750647950 750647427 1.590000e-78 303.0
17 TraesCS4D01G179800 chr2A 77.068 532 106 12 195 718 750577275 750576752 3.440000e-75 292.0
18 TraesCS4D01G179800 chr2A 77.068 532 106 12 195 718 750613325 750612802 3.440000e-75 292.0
19 TraesCS4D01G179800 chr2A 92.405 79 6 0 1000 1078 51582360 51582438 2.870000e-21 113.0
20 TraesCS4D01G179800 chr2A 89.474 57 5 1 3124 3179 721448628 721448684 1.750000e-08 71.3
21 TraesCS4D01G179800 chr1A 90.451 377 36 0 2143 2519 499785376 499785000 6.780000e-137 497.0
22 TraesCS4D01G179800 chr1D 90.186 377 37 0 2143 2519 404138644 404138268 3.160000e-135 492.0
23 TraesCS4D01G179800 chr1B 90.186 377 37 0 2143 2519 543498119 543497743 3.160000e-135 492.0
24 TraesCS4D01G179800 chr1B 75.482 726 161 14 1 718 222317543 222316827 4.350000e-89 339.0
25 TraesCS4D01G179800 chr3B 89.390 377 37 2 2143 2519 578401424 578401797 4.110000e-129 472.0
26 TraesCS4D01G179800 chr3B 94.937 79 4 0 1000 1078 254779960 254779882 1.330000e-24 124.0
27 TraesCS4D01G179800 chr7A 81.948 421 64 11 304 718 680020449 680020863 2.600000e-91 346.0
28 TraesCS4D01G179800 chr3A 94.937 79 4 0 1000 1078 215482210 215482132 1.330000e-24 124.0
29 TraesCS4D01G179800 chr3D 93.671 79 5 0 1000 1078 175408285 175408207 6.170000e-23 119.0
30 TraesCS4D01G179800 chr3D 92.405 79 6 0 1001 1079 185790126 185790204 2.870000e-21 113.0


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 TraesCS4D01G179800 chr4D 312799324 312802842 3518 True 6499.0 6499 100.000000 1 3519 1 chr4D.!!$R1 3518
1 TraesCS4D01G179800 chr4A 163814754 163820326 5572 False 873.6 1768 91.491400 2 3518 5 chr4A.!!$F1 3516
2 TraesCS4D01G179800 chr4B 390279245 390281640 2395 False 781.0 1485 89.321667 723 3058 3 chr4B.!!$F1 2335
3 TraesCS4D01G179800 chr2B 77168977 77170670 1693 False 328.5 544 92.499000 1000 2519 2 chr2B.!!$F1 1519
4 TraesCS4D01G179800 chr2D 49875921 49877717 1796 False 325.5 538 92.366500 1000 2519 2 chr2D.!!$F2 1519
5 TraesCS4D01G179800 chr2D 650488928 650489445 517 True 237.0 237 75.191000 195 713 1 chr2D.!!$R1 518
6 TraesCS4D01G179800 chr2A 51582360 51583920 1560 False 322.5 532 92.234000 1000 2519 2 chr2A.!!$F2 1519
7 TraesCS4D01G179800 chr2A 750647427 750647950 523 True 303.0 303 77.444000 195 718 1 chr2A.!!$R3 523
8 TraesCS4D01G179800 chr2A 750576752 750577275 523 True 292.0 292 77.068000 195 718 1 chr2A.!!$R1 523
9 TraesCS4D01G179800 chr2A 750612802 750613325 523 True 292.0 292 77.068000 195 718 1 chr2A.!!$R2 523
10 TraesCS4D01G179800 chr1B 222316827 222317543 716 True 339.0 339 75.482000 1 718 1 chr1B.!!$R1 717

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
997 2394 0.041833 AGGAGCCTGAGAAGGTAGCA 59.958 55.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2935 6259 0.318275 GCATTTTTCGTTGCCGGTCA 60.318 50.0 1.9 0.0 32.66 4.02 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
77 78 0.652592 CGTGAAATGATGCGAGGGAC 59.347 55.000 0.00 0.00 0.00 4.46
183 194 2.447443 GAAAGGTTCCTAAGCCAAGGG 58.553 52.381 2.26 0.00 37.24 3.95
265 276 1.092345 GCGAGGAATGGTGAGAAGGC 61.092 60.000 0.00 0.00 0.00 4.35
276 287 2.530151 AGAAGGCAGGTGGAGGCA 60.530 61.111 0.00 0.00 0.00 4.75
333 344 5.360591 CGGGAGCAAGTCAGTATCTTAAAT 58.639 41.667 0.00 0.00 0.00 1.40
367 378 2.373169 TGAAGGCTGTGGAGATTCTTGT 59.627 45.455 0.00 0.00 0.00 3.16
402 413 0.801251 ACAGCTTGCGATTGAGCTTC 59.199 50.000 0.00 0.00 46.55 3.86
467 478 5.100259 GTGCAAATGTTGAATGATCCTCAG 58.900 41.667 0.00 0.00 0.00 3.35
556 567 2.358737 CGTGGCCTGGGTTCAGTC 60.359 66.667 3.32 0.00 39.31 3.51
557 568 2.836154 GTGGCCTGGGTTCAGTCA 59.164 61.111 3.32 0.00 39.31 3.41
609 620 6.615617 TGCTAAAGTAGGAGTAGGAGATGAT 58.384 40.000 0.00 0.00 0.00 2.45
683 1749 3.713248 TCTGATGACATTCCCAGCTATGT 59.287 43.478 0.00 0.00 37.68 2.29
718 1784 5.182001 AGAAGCAGCAACGTTGATCTAAAAT 59.818 36.000 31.62 9.51 0.00 1.82
748 2141 0.250770 GTTTTGAGAAGGCGAGGGGT 60.251 55.000 0.00 0.00 0.00 4.95
781 2174 0.388391 ATTCGGTCCGCGACGTTAAA 60.388 50.000 8.23 0.22 32.65 1.52
950 2343 0.686112 CCTCTCTCCTCCACCTCCAC 60.686 65.000 0.00 0.00 0.00 4.02
953 2346 0.252467 CTCTCCTCCACCTCCACCTT 60.252 60.000 0.00 0.00 0.00 3.50
996 2393 0.750249 GAGGAGCCTGAGAAGGTAGC 59.250 60.000 0.00 0.00 0.00 3.58
997 2394 0.041833 AGGAGCCTGAGAAGGTAGCA 59.958 55.000 0.00 0.00 0.00 3.49
998 2395 1.127343 GGAGCCTGAGAAGGTAGCAT 58.873 55.000 0.00 0.00 0.00 3.79
1144 2609 3.123621 GTGATTGTTGTGATCCGTCTCAC 59.876 47.826 7.46 7.46 44.70 3.51
1179 2664 6.430451 AGAAGAAACACGAACATCAATTCAC 58.570 36.000 0.00 0.00 0.00 3.18
1225 2714 2.169832 TCTAGCATAGAATTGGGCGC 57.830 50.000 0.00 0.00 46.47 6.53
1226 2715 1.416030 TCTAGCATAGAATTGGGCGCA 59.584 47.619 10.83 0.00 46.47 6.09
1227 2716 1.802960 CTAGCATAGAATTGGGCGCAG 59.197 52.381 10.83 0.00 42.77 5.18
1228 2717 0.820891 AGCATAGAATTGGGCGCAGG 60.821 55.000 10.83 0.00 0.00 4.85
1239 2728 2.719979 GCGCAGGCAGAATGATGG 59.280 61.111 0.30 0.00 39.69 3.51
1240 2729 2.117156 GCGCAGGCAGAATGATGGT 61.117 57.895 0.30 0.00 39.69 3.55
1241 2730 0.815213 GCGCAGGCAGAATGATGGTA 60.815 55.000 0.30 0.00 39.69 3.25
1242 2731 1.224075 CGCAGGCAGAATGATGGTAG 58.776 55.000 0.00 0.00 39.69 3.18
1243 2732 1.202568 CGCAGGCAGAATGATGGTAGA 60.203 52.381 0.00 0.00 39.69 2.59
1244 2733 2.216898 GCAGGCAGAATGATGGTAGAC 58.783 52.381 0.00 0.00 39.69 2.59
1245 2734 2.420547 GCAGGCAGAATGATGGTAGACA 60.421 50.000 0.00 0.00 39.69 3.41
1246 2735 3.746751 GCAGGCAGAATGATGGTAGACAT 60.747 47.826 0.00 0.00 44.18 3.06
1279 2768 8.726988 CACTAGATAGATTACTAGAGGCTGAAC 58.273 40.741 0.00 0.00 39.25 3.18
1312 2801 0.179121 CGTACAGTAGCCGGAATGCA 60.179 55.000 5.05 0.00 0.00 3.96
1321 2810 2.301346 AGCCGGAATGCAAGATTAAGG 58.699 47.619 5.05 0.00 0.00 2.69
1351 2840 0.320683 TTGCGTCACTCACTCCATGG 60.321 55.000 4.97 4.97 0.00 3.66
1352 2841 1.184970 TGCGTCACTCACTCCATGGA 61.185 55.000 15.27 15.27 0.00 3.41
1355 2844 1.534805 CGTCACTCACTCCATGGATCG 60.535 57.143 16.63 9.62 0.00 3.69
1356 2845 1.751351 GTCACTCACTCCATGGATCGA 59.249 52.381 16.63 13.59 0.00 3.59
1406 2975 0.739561 CACCGCCCTACTGTAGTCTC 59.260 60.000 13.42 1.99 0.00 3.36
1470 3926 5.567138 AGTAACTGCTGTGGAAATTATGC 57.433 39.130 0.00 0.00 0.00 3.14
1472 3928 2.806434 ACTGCTGTGGAAATTATGCCA 58.194 42.857 0.00 0.00 0.00 4.92
1494 3950 4.220693 TCAAATCGATGTGATTGGGTCT 57.779 40.909 14.47 0.00 46.65 3.85
1507 3964 6.070021 TGTGATTGGGTCTATCAGATTTGACT 60.070 38.462 12.93 0.00 35.83 3.41
1514 3971 5.974751 GGTCTATCAGATTTGACTTCGTCTC 59.025 44.000 12.93 0.00 35.83 3.36
1524 3981 1.064357 GACTTCGTCTCGGATCCAGAC 59.936 57.143 23.73 23.73 37.51 3.51
1537 3994 2.259818 CAGACGTGGAGAAGCGCT 59.740 61.111 2.64 2.64 0.00 5.92
1538 3995 1.506718 CAGACGTGGAGAAGCGCTA 59.493 57.895 12.05 0.00 0.00 4.26
1539 3996 0.524392 CAGACGTGGAGAAGCGCTAG 60.524 60.000 12.05 0.00 0.00 3.42
1540 3997 0.677098 AGACGTGGAGAAGCGCTAGA 60.677 55.000 12.05 0.00 0.00 2.43
1541 3998 0.382515 GACGTGGAGAAGCGCTAGAT 59.617 55.000 12.05 0.00 0.00 1.98
1542 3999 0.382515 ACGTGGAGAAGCGCTAGATC 59.617 55.000 12.05 9.26 0.00 2.75
1543 4000 0.318275 CGTGGAGAAGCGCTAGATCC 60.318 60.000 22.23 22.23 0.00 3.36
1544 4001 1.036707 GTGGAGAAGCGCTAGATCCT 58.963 55.000 26.49 13.94 0.00 3.24
1545 4002 2.231529 GTGGAGAAGCGCTAGATCCTA 58.768 52.381 26.49 15.52 0.00 2.94
1546 4003 2.227865 GTGGAGAAGCGCTAGATCCTAG 59.772 54.545 26.49 0.00 0.00 3.02
1547 4004 2.158593 TGGAGAAGCGCTAGATCCTAGT 60.159 50.000 26.49 4.76 0.00 2.57
1548 4005 3.072622 TGGAGAAGCGCTAGATCCTAGTA 59.927 47.826 26.49 11.24 0.00 1.82
1549 4006 3.437741 GGAGAAGCGCTAGATCCTAGTAC 59.562 52.174 21.90 0.00 0.00 2.73
1550 4007 3.414269 AGAAGCGCTAGATCCTAGTACC 58.586 50.000 12.05 0.00 0.00 3.34
1551 4008 2.203470 AGCGCTAGATCCTAGTACCC 57.797 55.000 8.99 0.00 0.00 3.69
1552 4009 0.803740 GCGCTAGATCCTAGTACCCG 59.196 60.000 0.00 0.00 0.00 5.28
1553 4010 1.451067 CGCTAGATCCTAGTACCCGG 58.549 60.000 0.00 0.00 0.00 5.73
1554 4011 1.002888 CGCTAGATCCTAGTACCCGGA 59.997 57.143 0.73 3.46 0.00 5.14
1555 4012 2.355920 CGCTAGATCCTAGTACCCGGAT 60.356 54.545 0.73 12.08 42.55 4.18
1556 4013 3.018149 GCTAGATCCTAGTACCCGGATG 58.982 54.545 15.99 5.68 40.03 3.51
1557 4014 3.561744 GCTAGATCCTAGTACCCGGATGT 60.562 52.174 15.99 14.47 40.03 3.06
1558 4015 2.877866 AGATCCTAGTACCCGGATGTG 58.122 52.381 15.99 0.00 40.03 3.21
1559 4016 1.893801 GATCCTAGTACCCGGATGTGG 59.106 57.143 15.99 0.00 40.03 4.17
1605 4062 6.595326 TCAGATGCTTAGGTTTGACTTATGTG 59.405 38.462 0.00 0.00 0.00 3.21
1623 4080 0.037697 TGCAACGGCTGAATCGTACT 60.038 50.000 0.00 0.00 40.18 2.73
1626 4083 2.479049 GCAACGGCTGAATCGTACTAGA 60.479 50.000 0.00 0.00 40.18 2.43
1627 4084 3.795826 GCAACGGCTGAATCGTACTAGAT 60.796 47.826 0.00 0.00 40.18 1.98
1628 4085 3.900388 ACGGCTGAATCGTACTAGATC 57.100 47.619 0.00 0.00 39.22 2.75
1629 4086 2.223611 ACGGCTGAATCGTACTAGATCG 59.776 50.000 0.00 0.53 39.22 3.69
1630 4087 2.479275 CGGCTGAATCGTACTAGATCGA 59.521 50.000 13.85 13.85 40.28 3.59
1651 4108 6.513180 TCGATAGCTTATAGGTTGAACTTGG 58.487 40.000 0.00 0.00 0.00 3.61
1702 4563 4.019792 TCTCCTTTGTATGCTGCTTTCA 57.980 40.909 0.00 0.00 0.00 2.69
1705 4566 6.179756 TCTCCTTTGTATGCTGCTTTCATTA 58.820 36.000 0.00 0.00 0.00 1.90
1706 4567 6.830324 TCTCCTTTGTATGCTGCTTTCATTAT 59.170 34.615 0.00 0.00 0.00 1.28
1707 4568 6.798482 TCCTTTGTATGCTGCTTTCATTATG 58.202 36.000 0.00 0.00 0.00 1.90
1708 4569 5.461078 CCTTTGTATGCTGCTTTCATTATGC 59.539 40.000 0.00 0.00 0.00 3.14
1716 4577 4.806330 CTGCTTTCATTATGCATGGATCC 58.194 43.478 10.16 4.20 36.45 3.36
1748 4609 2.919602 TCTGCTGGAAATTCTTAGGGGT 59.080 45.455 0.00 0.00 0.00 4.95
1839 4846 4.617253 GGGTTGCCCAGACTTTTAATTT 57.383 40.909 0.00 0.00 44.65 1.82
1857 4864 0.751277 TTGGCCTTCGGTGCATATGG 60.751 55.000 3.32 0.00 0.00 2.74
1874 4881 7.710907 GTGCATATGGAGTAGTACTTGAATCAA 59.289 37.037 0.00 0.00 0.00 2.57
1875 4882 8.432013 TGCATATGGAGTAGTACTTGAATCAAT 58.568 33.333 0.00 0.00 0.00 2.57
1876 4883 8.930760 GCATATGGAGTAGTACTTGAATCAATC 58.069 37.037 0.00 0.00 0.00 2.67
1877 4884 9.987272 CATATGGAGTAGTACTTGAATCAATCA 57.013 33.333 0.00 0.00 35.85 2.57
1919 4975 6.256757 GGTTTCATCTCTGAATGTACTACAGC 59.743 42.308 0.00 0.00 40.95 4.40
2006 5321 4.485163 GTTGCAGGTTTGATCCATTGTAC 58.515 43.478 0.00 0.00 0.00 2.90
2079 5394 9.645059 TTTAGTATATGCTCACTCTGAATATGC 57.355 33.333 0.00 0.00 0.00 3.14
2380 5695 2.124983 GGCTTCATCTCGGCTGCA 60.125 61.111 0.50 0.00 0.00 4.41
2410 5725 1.447838 CGTCATGACCAACCTCGGG 60.448 63.158 20.03 0.00 0.00 5.14
2428 5743 0.745468 GGGAGAAGCTAACGGACGAT 59.255 55.000 0.00 0.00 0.00 3.73
2579 5896 0.039618 GGGGAGGAGGAAATTGTGCA 59.960 55.000 0.00 0.00 0.00 4.57
2580 5897 1.342374 GGGGAGGAGGAAATTGTGCAT 60.342 52.381 0.00 0.00 0.00 3.96
2794 6112 2.363306 TGAACCCTGATTGCAGTTGT 57.637 45.000 0.00 0.00 40.63 3.32
2815 6133 2.194201 TCCGTTTGATCCAAGTTCCC 57.806 50.000 0.00 0.00 0.00 3.97
2846 6170 8.359642 ACTTCTATTTTGTACTGTACGTACCAA 58.640 33.333 22.43 15.57 46.36 3.67
2847 6171 9.362539 CTTCTATTTTGTACTGTACGTACCAAT 57.637 33.333 22.43 17.69 46.36 3.16
2848 6172 8.915871 TCTATTTTGTACTGTACGTACCAATC 57.084 34.615 22.43 11.21 46.36 2.67
2849 6173 6.973229 ATTTTGTACTGTACGTACCAATCC 57.027 37.500 22.43 7.72 46.36 3.01
2850 6174 5.726980 TTTGTACTGTACGTACCAATCCT 57.273 39.130 22.43 1.85 46.36 3.24
2851 6175 4.970662 TGTACTGTACGTACCAATCCTC 57.029 45.455 22.43 7.59 46.36 3.71
2852 6176 3.374988 TGTACTGTACGTACCAATCCTCG 59.625 47.826 22.43 4.08 46.36 4.63
2853 6177 1.747355 ACTGTACGTACCAATCCTCGG 59.253 52.381 22.43 3.22 0.00 4.63
2854 6178 0.457035 TGTACGTACCAATCCTCGGC 59.543 55.000 22.43 0.00 0.00 5.54
2855 6179 0.249197 GTACGTACCAATCCTCGGCC 60.249 60.000 15.00 0.00 0.00 6.13
2856 6180 0.683828 TACGTACCAATCCTCGGCCA 60.684 55.000 2.24 0.00 0.00 5.36
2897 6221 3.508793 AGATGCTGCTGTTGTATTGCTTT 59.491 39.130 0.00 0.00 0.00 3.51
2976 6300 1.001020 TTGAATGGCCTGGTCGCAT 60.001 52.632 3.32 0.00 0.00 4.73
2977 6301 1.314534 TTGAATGGCCTGGTCGCATG 61.315 55.000 3.32 0.00 0.00 4.06
2978 6302 1.750399 GAATGGCCTGGTCGCATGT 60.750 57.895 3.32 0.00 0.00 3.21
2979 6303 1.996786 GAATGGCCTGGTCGCATGTG 61.997 60.000 3.32 0.00 0.00 3.21
2980 6304 2.482796 AATGGCCTGGTCGCATGTGA 62.483 55.000 4.45 4.45 0.00 3.58
2981 6305 2.359850 GGCCTGGTCGCATGTGAA 60.360 61.111 11.25 0.00 0.00 3.18
3010 6334 1.871676 GGACCTCCGTTGAACTGAAAC 59.128 52.381 0.00 0.00 0.00 2.78
3099 6662 1.207329 AGTCCAAGGCGTGTTATCTCC 59.793 52.381 0.00 0.00 0.00 3.71
3180 6743 2.112190 TGCACCAGATACATTCCCGTA 58.888 47.619 0.00 0.00 0.00 4.02
3204 6767 4.541973 ACAAGTGTGAGTGCATCAGATA 57.458 40.909 0.00 0.00 39.07 1.98
3209 6772 5.114780 AGTGTGAGTGCATCAGATACATTC 58.885 41.667 0.00 0.07 39.07 2.67
3213 6776 4.652881 TGAGTGCATCAGATACATTCCTCT 59.347 41.667 4.16 0.00 32.77 3.69
3215 6778 6.015603 TGAGTGCATCAGATACATTCCTCTAG 60.016 42.308 4.16 0.00 32.77 2.43
3228 6791 5.723887 ACATTCCTCTAGGTGACTTGATCTT 59.276 40.000 0.00 0.00 41.36 2.40
3229 6792 6.897966 ACATTCCTCTAGGTGACTTGATCTTA 59.102 38.462 0.00 0.00 41.36 2.10
3240 6803 1.261619 CTTGATCTTATCGGGCGTTGC 59.738 52.381 0.00 0.00 0.00 4.17
3252 6815 2.730672 GCGTTGCCGTCTGCTACTG 61.731 63.158 0.13 0.00 42.57 2.74
3329 6892 1.867233 GTGTCGCTGTTGTGAAGACAT 59.133 47.619 0.00 0.00 42.68 3.06
3330 6893 3.057019 GTGTCGCTGTTGTGAAGACATA 58.943 45.455 0.00 0.00 42.68 2.29
3366 6929 1.913317 ATACTAACCGGCGAACGTTC 58.087 50.000 18.47 18.47 42.24 3.95
3367 6930 0.109319 TACTAACCGGCGAACGTTCC 60.109 55.000 22.07 14.33 42.24 3.62
3369 6932 3.912820 TAACCGGCGAACGTTCCCG 62.913 63.158 33.19 33.19 42.24 5.14
3375 6938 4.446413 CGAACGTTCCCGGGGAGG 62.446 72.222 23.50 21.82 38.78 4.30
3450 7013 6.767524 ACAATTTGTGTCAGTTTCTACCAA 57.232 33.333 0.15 0.00 34.38 3.67
3451 7014 7.164230 ACAATTTGTGTCAGTTTCTACCAAA 57.836 32.000 0.15 0.00 34.38 3.28
3453 7016 8.257306 ACAATTTGTGTCAGTTTCTACCAAAAT 58.743 29.630 0.15 0.00 34.38 1.82
3454 7017 9.743057 CAATTTGTGTCAGTTTCTACCAAAATA 57.257 29.630 0.00 0.00 0.00 1.40
3486 7049 3.426695 CCTTCCAGAAAATGTCATGCGTC 60.427 47.826 0.00 0.00 0.00 5.19
3488 7051 3.002791 TCCAGAAAATGTCATGCGTCTC 58.997 45.455 0.00 0.00 0.00 3.36
3489 7052 3.005554 CCAGAAAATGTCATGCGTCTCT 58.994 45.455 0.00 0.00 0.00 3.10
3490 7053 3.181513 CCAGAAAATGTCATGCGTCTCTG 60.182 47.826 0.00 2.08 0.00 3.35
3491 7054 3.681417 CAGAAAATGTCATGCGTCTCTGA 59.319 43.478 11.68 0.00 32.58 3.27
3494 7057 5.239306 AGAAAATGTCATGCGTCTCTGAAAA 59.761 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 0.461870 CCGTCCCTCGCATCATTTCA 60.462 55.000 0.00 0.00 38.35 2.69
77 78 1.148498 GGGGGCAATCTTCCTACCG 59.852 63.158 0.00 0.00 0.00 4.02
104 111 7.010923 GTGAGTAGACTGATTCCATGATTTCAC 59.989 40.741 0.00 0.00 0.00 3.18
183 194 3.010420 GAGGCTCCCATTTCTGTACAAC 58.990 50.000 2.15 0.00 0.00 3.32
265 276 0.687354 AAGTACTGTGCCTCCACCTG 59.313 55.000 0.00 0.00 41.35 4.00
276 287 2.093658 CACCGCAATCCCTAAGTACTGT 60.094 50.000 0.00 0.00 0.00 3.55
333 344 1.985159 AGCCTTCAGGTCAACCATGTA 59.015 47.619 1.33 0.00 38.89 2.29
402 413 4.186926 TCAAGATGGATTCTCTGAAAGCG 58.813 43.478 0.00 0.00 31.78 4.68
467 478 0.529378 CCACAGCAGCCAAATTCCTC 59.471 55.000 0.00 0.00 0.00 3.71
553 564 3.058914 GCAACAACGTTAGCAGAATGACT 60.059 43.478 0.00 0.00 39.69 3.41
554 565 3.226347 GCAACAACGTTAGCAGAATGAC 58.774 45.455 0.00 0.00 39.69 3.06
556 567 2.233355 CGCAACAACGTTAGCAGAATG 58.767 47.619 16.44 0.00 40.87 2.67
557 568 1.399727 GCGCAACAACGTTAGCAGAAT 60.400 47.619 16.44 0.00 34.88 2.40
609 620 2.108601 CCCCAACCACACCCTAGTTAAA 59.891 50.000 0.00 0.00 0.00 1.52
614 625 0.840722 AGACCCCAACCACACCCTAG 60.841 60.000 0.00 0.00 0.00 3.02
683 1749 5.009210 ACGTTGCTGCTTCTTATTTAACCAA 59.991 36.000 0.00 0.00 0.00 3.67
718 1784 5.964958 CCTTCTCAAAACAAGGCATCTAA 57.035 39.130 0.00 0.00 32.98 2.10
748 2141 0.322997 CCGAATTACCCCCAACTGCA 60.323 55.000 0.00 0.00 0.00 4.41
979 2372 1.069978 GATGCTACCTTCTCAGGCTCC 59.930 57.143 0.00 0.00 45.56 4.70
996 2393 0.392863 TGAGTTGGTCCGCCATGATG 60.393 55.000 0.00 0.00 45.56 3.07
997 2394 0.392998 GTGAGTTGGTCCGCCATGAT 60.393 55.000 0.00 0.00 45.56 2.45
998 2395 1.003839 GTGAGTTGGTCCGCCATGA 60.004 57.895 0.00 0.00 45.56 3.07
1144 2609 5.955488 TCGTGTTTCTTCTTCTATCCAGAG 58.045 41.667 0.00 0.00 30.73 3.35
1179 2664 4.133820 AGACAGAGAGTAGACATCGATGG 58.866 47.826 28.09 11.30 0.00 3.51
1223 2712 1.202568 TCTACCATCATTCTGCCTGCG 60.203 52.381 0.00 0.00 0.00 5.18
1224 2713 2.216898 GTCTACCATCATTCTGCCTGC 58.783 52.381 0.00 0.00 0.00 4.85
1225 2714 3.548745 TGTCTACCATCATTCTGCCTG 57.451 47.619 0.00 0.00 0.00 4.85
1236 2725 9.679661 CTATCTAGTGTATCAGATGTCTACCAT 57.320 37.037 0.00 0.00 33.58 3.55
1238 2727 9.899661 ATCTATCTAGTGTATCAGATGTCTACC 57.100 37.037 0.00 0.00 33.58 3.18
1248 2737 9.893634 GCCTCTAGTAATCTATCTAGTGTATCA 57.106 37.037 0.00 0.00 36.17 2.15
1250 2739 9.899661 CAGCCTCTAGTAATCTATCTAGTGTAT 57.100 37.037 0.00 0.00 36.17 2.29
1251 2740 9.102453 TCAGCCTCTAGTAATCTATCTAGTGTA 57.898 37.037 0.00 0.00 36.17 2.90
1252 2741 7.980032 TCAGCCTCTAGTAATCTATCTAGTGT 58.020 38.462 0.00 0.00 36.17 3.55
1253 2742 8.726988 GTTCAGCCTCTAGTAATCTATCTAGTG 58.273 40.741 0.00 0.00 36.17 2.74
1254 2743 8.441572 TGTTCAGCCTCTAGTAATCTATCTAGT 58.558 37.037 0.00 0.00 36.17 2.57
1255 2744 8.856153 TGTTCAGCCTCTAGTAATCTATCTAG 57.144 38.462 0.00 0.00 36.10 2.43
1256 2745 9.815306 AATGTTCAGCCTCTAGTAATCTATCTA 57.185 33.333 0.00 0.00 0.00 1.98
1257 2746 8.719645 AATGTTCAGCCTCTAGTAATCTATCT 57.280 34.615 0.00 0.00 0.00 1.98
1265 2754 4.441079 GGCGTAAATGTTCAGCCTCTAGTA 60.441 45.833 0.00 0.00 44.06 1.82
1296 2785 0.613260 TCTTGCATTCCGGCTACTGT 59.387 50.000 0.00 0.00 34.04 3.55
1312 2801 6.246420 GCAATATGTGCGATCCTTAATCTT 57.754 37.500 0.00 0.00 45.10 2.40
1381 2870 4.489771 AGTAGGGCGGTGGCATGC 62.490 66.667 9.90 9.90 42.47 4.06
1382 2871 1.966901 TACAGTAGGGCGGTGGCATG 61.967 60.000 0.00 0.00 42.47 4.06
1383 2872 1.686325 CTACAGTAGGGCGGTGGCAT 61.686 60.000 0.00 0.00 42.47 4.40
1396 2885 2.493414 ACGGCAGTAGAGACTACAGT 57.507 50.000 10.78 3.67 33.32 3.55
1406 2975 1.755161 CGTGCACTATACGGCAGTAG 58.245 55.000 16.19 0.00 41.35 2.57
1472 3928 4.785301 AGACCCAATCACATCGATTTGAT 58.215 39.130 19.02 19.02 41.83 2.57
1514 3971 0.101399 CTTCTCCACGTCTGGATCCG 59.899 60.000 7.39 2.06 46.18 4.18
1524 3981 0.318275 GGATCTAGCGCTTCTCCACG 60.318 60.000 18.68 0.00 0.00 4.94
1530 3987 2.488937 GGGTACTAGGATCTAGCGCTTC 59.511 54.545 18.68 7.24 0.00 3.86
1531 3988 2.516906 GGGTACTAGGATCTAGCGCTT 58.483 52.381 18.68 0.00 0.00 4.68
1532 3989 1.611148 CGGGTACTAGGATCTAGCGCT 60.611 57.143 17.26 17.26 0.00 5.92
1533 3990 0.803740 CGGGTACTAGGATCTAGCGC 59.196 60.000 0.00 0.00 0.00 5.92
1534 3991 1.002888 TCCGGGTACTAGGATCTAGCG 59.997 57.143 0.00 0.00 31.25 4.26
1535 3992 2.875094 TCCGGGTACTAGGATCTAGC 57.125 55.000 0.00 0.00 31.25 3.42
1536 3993 4.011023 CACATCCGGGTACTAGGATCTAG 58.989 52.174 16.23 10.31 41.92 2.43
1537 3994 3.245158 CCACATCCGGGTACTAGGATCTA 60.245 52.174 16.23 0.00 41.92 1.98
1538 3995 2.491086 CCACATCCGGGTACTAGGATCT 60.491 54.545 16.23 6.06 41.92 2.75
1539 3996 1.893801 CCACATCCGGGTACTAGGATC 59.106 57.143 16.23 0.00 41.92 3.36
1540 3997 1.482553 CCCACATCCGGGTACTAGGAT 60.483 57.143 14.20 14.20 43.81 3.24
1541 3998 0.105862 CCCACATCCGGGTACTAGGA 60.106 60.000 0.00 11.24 41.83 2.94
1542 3999 2.437625 CCCACATCCGGGTACTAGG 58.562 63.158 0.00 0.00 41.83 3.02
1550 4007 1.686325 CCCTGACTACCCACATCCGG 61.686 65.000 0.00 0.00 0.00 5.14
1551 4008 1.823295 CCCTGACTACCCACATCCG 59.177 63.158 0.00 0.00 0.00 4.18
1552 4009 1.527370 GCCCTGACTACCCACATCC 59.473 63.158 0.00 0.00 0.00 3.51
1553 4010 1.527370 GGCCCTGACTACCCACATC 59.473 63.158 0.00 0.00 0.00 3.06
1554 4011 2.367202 CGGCCCTGACTACCCACAT 61.367 63.158 0.00 0.00 0.00 3.21
1555 4012 3.000819 CGGCCCTGACTACCCACA 61.001 66.667 0.00 0.00 0.00 4.17
1556 4013 3.001406 ACGGCCCTGACTACCCAC 61.001 66.667 0.00 0.00 0.00 4.61
1557 4014 2.682494 GACGGCCCTGACTACCCA 60.682 66.667 0.00 0.00 0.00 4.51
1558 4015 3.468140 GGACGGCCCTGACTACCC 61.468 72.222 0.00 0.00 0.00 3.69
1559 4016 1.623542 ATTGGACGGCCCTGACTACC 61.624 60.000 3.83 0.00 35.38 3.18
1605 4062 1.852895 CTAGTACGATTCAGCCGTTGC 59.147 52.381 0.00 0.00 40.95 4.17
1623 4080 8.865420 AGTTCAACCTATAAGCTATCGATCTA 57.135 34.615 0.00 0.00 0.00 1.98
1626 4083 7.155328 CCAAGTTCAACCTATAAGCTATCGAT 58.845 38.462 2.16 2.16 0.00 3.59
1627 4084 6.513180 CCAAGTTCAACCTATAAGCTATCGA 58.487 40.000 0.00 0.00 0.00 3.59
1628 4085 5.177696 GCCAAGTTCAACCTATAAGCTATCG 59.822 44.000 0.00 0.00 0.00 2.92
1629 4086 5.470437 GGCCAAGTTCAACCTATAAGCTATC 59.530 44.000 0.00 0.00 0.00 2.08
1630 4087 5.104109 TGGCCAAGTTCAACCTATAAGCTAT 60.104 40.000 0.61 0.00 0.00 2.97
1685 4546 6.037726 TGCATAATGAAAGCAGCATACAAAG 58.962 36.000 0.00 0.00 33.75 2.77
1702 4563 5.191124 TCTGCAGATAGGATCCATGCATAAT 59.809 40.000 24.92 0.00 45.08 1.28
1705 4566 2.910977 TCTGCAGATAGGATCCATGCAT 59.089 45.455 24.92 10.14 45.08 3.96
1706 4567 2.332117 TCTGCAGATAGGATCCATGCA 58.668 47.619 23.86 23.86 44.10 3.96
1707 4568 3.198200 AGATCTGCAGATAGGATCCATGC 59.802 47.826 28.78 17.74 37.24 4.06
1708 4569 4.760878 CAGATCTGCAGATAGGATCCATG 58.239 47.826 28.78 13.00 37.24 3.66
1748 4609 2.978156 AGCTGGATCTGGGTTTCAAA 57.022 45.000 0.00 0.00 0.00 2.69
1874 4881 3.568007 ACCACGCTGTTACAACAATTGAT 59.432 39.130 13.59 0.00 38.66 2.57
1875 4882 2.946329 ACCACGCTGTTACAACAATTGA 59.054 40.909 13.59 0.00 38.66 2.57
1876 4883 3.347958 ACCACGCTGTTACAACAATTG 57.652 42.857 3.24 3.24 38.66 2.32
1877 4884 4.142359 TGAAACCACGCTGTTACAACAATT 60.142 37.500 0.00 0.00 38.66 2.32
1919 4975 8.550376 CCCAAAACAAAAGTTACTCATCAATTG 58.450 33.333 0.00 0.00 0.00 2.32
2006 5321 0.457166 CGCATGAAGCAACCACCATG 60.457 55.000 0.00 0.00 46.13 3.66
2079 5394 4.929211 TGACTGAGTCGGTAATCACATTTG 59.071 41.667 4.10 0.00 34.95 2.32
2410 5725 1.404391 TCATCGTCCGTTAGCTTCTCC 59.596 52.381 0.00 0.00 0.00 3.71
2428 5743 1.309950 GGATCATCTCGTCGACCTCA 58.690 55.000 10.58 0.00 0.00 3.86
2579 5896 7.334421 CCGCATTCCTTACTACTAATATGCAAT 59.666 37.037 0.00 0.00 0.00 3.56
2580 5897 6.649141 CCGCATTCCTTACTACTAATATGCAA 59.351 38.462 0.00 0.00 0.00 4.08
2673 5991 1.063183 GGGGAGGAGGATTCCATGAG 58.937 60.000 5.29 0.00 46.64 2.90
2794 6112 3.521937 AGGGAACTTGGATCAAACGGATA 59.478 43.478 0.00 0.00 37.44 2.59
2815 6133 9.837525 ACGTACAGTACAAAATAGAAGTAGAAG 57.162 33.333 11.37 0.00 0.00 2.85
2854 6178 2.037136 CAACTGAAGGAGCCGCTGG 61.037 63.158 0.00 0.00 0.00 4.85
2855 6179 2.037136 CCAACTGAAGGAGCCGCTG 61.037 63.158 0.00 0.00 0.00 5.18
2856 6180 2.348998 CCAACTGAAGGAGCCGCT 59.651 61.111 0.00 0.00 0.00 5.52
2897 6221 5.227569 ACATATTACTTCCATCCATCGCA 57.772 39.130 0.00 0.00 0.00 5.10
2935 6259 0.318275 GCATTTTTCGTTGCCGGTCA 60.318 50.000 1.90 0.00 32.66 4.02
2976 6300 2.290260 GGAGGTCCACATCACATTCACA 60.290 50.000 0.00 0.00 35.64 3.58
2977 6301 2.359900 GGAGGTCCACATCACATTCAC 58.640 52.381 0.00 0.00 35.64 3.18
2978 6302 1.066215 CGGAGGTCCACATCACATTCA 60.066 52.381 0.00 0.00 35.14 2.57
2979 6303 1.066143 ACGGAGGTCCACATCACATTC 60.066 52.381 0.00 0.00 35.14 2.67
2980 6304 0.984230 ACGGAGGTCCACATCACATT 59.016 50.000 0.00 0.00 35.14 2.71
2981 6305 0.984230 AACGGAGGTCCACATCACAT 59.016 50.000 0.00 0.00 35.14 3.21
3010 6334 4.326766 CACCAAACGGCGCACTGG 62.327 66.667 10.83 17.78 34.95 4.00
3068 6631 2.019156 GCCTTGGACTAACATCAGGCC 61.019 57.143 0.00 0.00 44.94 5.19
3099 6662 1.604278 TCCGATCACATAGAGCTGTCG 59.396 52.381 0.00 0.00 0.00 4.35
3147 6710 2.040544 GGTGCATCCACACTTCCGG 61.041 63.158 0.00 0.00 43.88 5.14
3150 6713 2.119801 ATCTGGTGCATCCACACTTC 57.880 50.000 0.00 0.00 43.88 3.01
3156 6719 2.158623 GGGAATGTATCTGGTGCATCCA 60.159 50.000 0.00 0.76 45.01 3.41
3200 6763 6.436027 TCAAGTCACCTAGAGGAATGTATCT 58.564 40.000 1.60 0.00 38.94 1.98
3204 6767 5.276440 AGATCAAGTCACCTAGAGGAATGT 58.724 41.667 1.60 0.00 38.94 2.71
3209 6772 5.048364 CCGATAAGATCAAGTCACCTAGAGG 60.048 48.000 0.00 0.00 42.17 3.69
3213 6776 3.321111 GCCCGATAAGATCAAGTCACCTA 59.679 47.826 0.00 0.00 0.00 3.08
3215 6778 2.484889 GCCCGATAAGATCAAGTCACC 58.515 52.381 0.00 0.00 0.00 4.02
3252 6815 1.001815 ACAAGCACAACACGGTTATGC 60.002 47.619 10.77 10.77 36.52 3.14
3287 6850 0.169672 CTGGATGCAAAACTCGCCAG 59.830 55.000 0.00 0.00 37.21 4.85
3310 6873 2.238942 ATGTCTTCACAACAGCGACA 57.761 45.000 0.00 0.00 38.75 4.35
3312 6875 3.660501 ACTATGTCTTCACAACAGCGA 57.339 42.857 0.00 0.00 35.64 4.93
3313 6876 5.576774 TCATAACTATGTCTTCACAACAGCG 59.423 40.000 0.00 0.00 35.64 5.18
3369 6932 2.439245 GTTTGTCACCCCCTCCCC 59.561 66.667 0.00 0.00 0.00 4.81
3375 6938 3.513680 AAAAAGTTCGTTTGTCACCCC 57.486 42.857 0.00 0.00 0.00 4.95
3455 7018 8.021898 TGACATTTTCTGGAAGGAAGATTTTT 57.978 30.769 0.00 0.00 29.38 1.94
3465 7028 3.438087 AGACGCATGACATTTTCTGGAAG 59.562 43.478 0.00 0.00 0.00 3.46
3467 7030 3.002791 GAGACGCATGACATTTTCTGGA 58.997 45.455 0.00 0.00 0.00 3.86
3469 7032 3.681417 TCAGAGACGCATGACATTTTCTG 59.319 43.478 0.00 1.64 33.81 3.02
3494 7057 2.378445 ACGTTTTTGCTGGCAGTTTT 57.622 40.000 17.16 0.00 0.00 2.43
3500 7063 2.635305 CGCGAACGTTTTTGCTGGC 61.635 57.895 0.00 0.00 39.71 4.85


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

AutoCloner maintained by Alex Coulton.