Multiple sequence alignment - TraesCS7D01G031800

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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 TraesCS7D01G031800 chr7D 100.000 4465 0 0 1 4465 16707735 16703271 0.000000e+00 8246.0
1 TraesCS7D01G031800 chr7D 81.593 1494 212 24 2247 3693 16692357 16690880 0.000000e+00 1177.0
2 TraesCS7D01G031800 chr7D 95.671 231 8 2 2026 2254 16705487 16705257 1.960000e-98 370.0
3 TraesCS7D01G031800 chr7D 95.671 231 8 2 2249 2479 16705710 16705482 1.960000e-98 370.0
4 TraesCS7D01G031800 chr7D 87.705 122 10 4 2039 2159 16692342 16692225 2.170000e-28 137.0
5 TraesCS7D01G031800 chr7D 93.846 65 1 2 570 631 16707123 16707059 1.320000e-15 95.3
6 TraesCS7D01G031800 chr7D 93.846 65 1 2 613 677 16707166 16707105 1.320000e-15 95.3
7 TraesCS7D01G031800 chr7D 86.364 88 11 1 2166 2252 17209557 17209644 1.320000e-15 95.3
8 TraesCS7D01G031800 chr4A 93.247 3880 190 35 623 4465 717969862 717973706 0.000000e+00 5648.0
9 TraesCS7D01G031800 chr4A 81.162 1497 218 24 2247 3693 718032784 718034266 0.000000e+00 1144.0
10 TraesCS7D01G031800 chr4A 84.929 637 60 20 1 628 717969304 717969913 2.950000e-171 612.0
11 TraesCS7D01G031800 chr4A 95.238 231 11 0 2249 2479 717971262 717971492 2.540000e-97 366.0
12 TraesCS7D01G031800 chr4A 93.966 232 12 2 2026 2255 717971487 717971718 2.560000e-92 350.0
13 TraesCS7D01G031800 chr4A 87.660 235 26 3 3816 4048 632867341 632867108 2.050000e-68 270.0
14 TraesCS7D01G031800 chr4A 71.095 685 166 21 2390 3051 717047800 717047125 6.020000e-29 139.0
15 TraesCS7D01G031800 chr4A 86.885 122 12 2 2039 2159 718032800 718032918 2.800000e-27 134.0
16 TraesCS7D01G031800 chr4A 86.364 88 11 1 2166 2252 717047800 717047713 1.320000e-15 95.3
17 TraesCS7D01G031800 chr4A 89.189 74 6 2 3707 3780 717268331 717268402 1.710000e-14 91.6
18 TraesCS7D01G031800 chr4A 89.189 74 6 2 3707 3780 717763853 717763782 1.710000e-14 91.6
19 TraesCS7D01G031800 chr4A 92.727 55 2 2 3711 3764 55384414 55384361 1.330000e-10 78.7
20 TraesCS7D01G031800 chr4A 93.023 43 3 0 114 156 5808798 5808840 3.730000e-06 63.9
21 TraesCS7D01G031800 chr7A 94.041 1611 85 6 2580 4187 15689615 15688013 0.000000e+00 2433.0
22 TraesCS7D01G031800 chr7A 92.209 1091 58 6 1464 2536 15690949 15689868 0.000000e+00 1519.0
23 TraesCS7D01G031800 chr7A 87.677 779 63 17 629 1380 15693066 15692294 0.000000e+00 876.0
24 TraesCS7D01G031800 chr7A 93.966 232 13 1 2248 2479 15690380 15690150 2.560000e-92 350.0
25 TraesCS7D01G031800 chr7A 93.074 231 14 2 2026 2254 15690155 15689925 1.990000e-88 337.0
26 TraesCS7D01G031800 chr7A 92.040 201 16 0 431 631 15693218 15693018 2.630000e-72 283.0
27 TraesCS7D01G031800 chr7A 93.023 172 11 1 4188 4358 15687967 15687796 2.670000e-62 250.0
28 TraesCS7D01G031800 chr7A 71.870 583 139 19 2390 2957 16603350 16603922 1.290000e-30 145.0
29 TraesCS7D01G031800 chr7A 87.500 88 10 1 2166 2252 16603350 16603437 2.840000e-17 100.0
30 TraesCS7D01G031800 chr2A 88.515 357 36 4 3812 4165 278463597 278463243 1.150000e-115 427.0
31 TraesCS7D01G031800 chr2A 79.649 285 52 5 348 630 515962381 515962661 2.720000e-47 200.0
32 TraesCS7D01G031800 chr2A 85.567 97 4 7 4357 4452 278463167 278463080 4.760000e-15 93.5
33 TraesCS7D01G031800 chr2A 89.130 46 4 1 3735 3780 703338527 703338571 6.240000e-04 56.5
34 TraesCS7D01G031800 chr5A 86.828 372 46 3 3816 4185 546233152 546233522 3.210000e-111 412.0
35 TraesCS7D01G031800 chr5A 88.983 236 23 3 3815 4048 677745037 677745271 5.650000e-74 289.0
36 TraesCS7D01G031800 chr5A 87.500 240 26 4 3816 4052 363419259 363419497 1.580000e-69 274.0
37 TraesCS7D01G031800 chr5A 80.059 341 54 8 261 598 558241566 558241237 1.600000e-59 241.0
38 TraesCS7D01G031800 chr5A 79.235 183 26 9 451 630 22598843 22598670 2.820000e-22 117.0
39 TraesCS7D01G031800 chr5A 84.483 58 8 1 3707 3764 473231718 473231662 6.240000e-04 56.5
40 TraesCS7D01G031800 chr3B 85.523 373 42 5 3816 4183 823188021 823188386 3.260000e-101 379.0
41 TraesCS7D01G031800 chr3B 85.000 80 8 3 85 162 592692981 592693058 1.330000e-10 78.7
42 TraesCS7D01G031800 chr1A 88.841 233 23 3 3818 4048 300770371 300770140 2.630000e-72 283.0
43 TraesCS7D01G031800 chr1A 87.179 234 29 1 3816 4048 452048103 452047870 9.520000e-67 265.0
44 TraesCS7D01G031800 chr1A 97.619 42 1 0 114 155 567454814 567454773 6.200000e-09 73.1
45 TraesCS7D01G031800 chr5D 79.076 368 63 9 265 630 441793926 441793571 1.600000e-59 241.0
46 TraesCS7D01G031800 chr2B 75.227 331 62 14 303 630 451837260 451837573 6.020000e-29 139.0
47 TraesCS7D01G031800 chr3A 81.295 139 23 3 392 528 435817385 435817248 4.720000e-20 110.0
48 TraesCS7D01G031800 chr2D 75.862 203 41 7 310 511 561220907 561221102 3.680000e-16 97.1
49 TraesCS7D01G031800 chr2D 85.333 75 9 2 3707 3780 462195606 462195533 4.790000e-10 76.8
50 TraesCS7D01G031800 chr3D 83.951 81 9 3 84 162 450972430 450972508 1.720000e-09 75.0
51 TraesCS7D01G031800 chr7B 87.931 58 6 1 3707 3764 663490075 663490131 2.880000e-07 67.6


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 TraesCS7D01G031800 chr7D 16703271 16707735 4464 True 1835.32 8246 95.8068 1 4465 5 chr7D.!!$R2 4464
1 TraesCS7D01G031800 chr7D 16690880 16692357 1477 True 657.00 1177 84.6490 2039 3693 2 chr7D.!!$R1 1654
2 TraesCS7D01G031800 chr4A 717969304 717973706 4402 False 1744.00 5648 91.8450 1 4465 4 chr4A.!!$F3 4464
3 TraesCS7D01G031800 chr4A 718032784 718034266 1482 False 639.00 1144 84.0235 2039 3693 2 chr4A.!!$F4 1654
4 TraesCS7D01G031800 chr7A 15687796 15693218 5422 True 864.00 2433 92.2900 431 4358 7 chr7A.!!$R1 3927
5 TraesCS7D01G031800 chr2A 278463080 278463597 517 True 260.25 427 87.0410 3812 4452 2 chr2A.!!$R1 640

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
846 854 0.473886 ACAGGGTGCTAGACAAGGGT 60.474 55.000 0.00 0.00 0.00 4.34 F
1596 2892 0.027063 CGTCTCAACACGGCGTTTTT 59.973 50.000 11.19 3.33 34.86 1.94 F
2735 4281 1.341089 TGCCAACACCACCAACAACTA 60.341 47.619 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 3211 2.024655 ATGTCAAGGATTGCCATGGAGT 60.025 45.455 18.4 0.0 43.82 3.85 R
2918 4464 0.612174 TAGCCTCTTCCACGCTCTGT 60.612 55.000 0.0 0.0 34.03 3.41 R
3981 5559 0.545309 AGGTGCTTCTAGTGCCAGGA 60.545 55.000 0.0 0.0 0.00 3.86 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
144 148 8.109843 TGTTCACGTGTTTCAAAAATATGTTC 57.890 30.769 16.51 0.00 0.00 3.18
150 154 8.134895 ACGTGTTTCAAAAATATGTTCATGACT 58.865 29.630 0.00 0.00 0.00 3.41
201 205 7.418337 AGTGTCCACTTAGTTTTGGAAAAAT 57.582 32.000 0.00 0.00 43.67 1.82
203 207 9.143155 AGTGTCCACTTAGTTTTGGAAAAATAT 57.857 29.630 0.00 0.00 43.67 1.28
204 208 9.758651 GTGTCCACTTAGTTTTGGAAAAATATT 57.241 29.630 0.00 0.00 43.67 1.28
263 267 9.715121 TTAGAAAATGTTCGTAACACTATTCCT 57.285 29.630 3.13 0.00 45.50 3.36
264 268 8.252964 AGAAAATGTTCGTAACACTATTCCTC 57.747 34.615 3.13 0.00 45.50 3.71
266 270 8.617290 AAAATGTTCGTAACACTATTCCTCTT 57.383 30.769 3.13 0.00 45.50 2.85
267 271 8.617290 AAATGTTCGTAACACTATTCCTCTTT 57.383 30.769 3.13 0.00 45.50 2.52
269 273 8.617290 ATGTTCGTAACACTATTCCTCTTTTT 57.383 30.769 3.13 0.00 45.50 1.94
271 275 9.715121 TGTTCGTAACACTATTCCTCTTTTTAT 57.285 29.630 0.00 0.00 36.25 1.40
296 302 5.771469 AGATCAAAGTGAGATGAGATAGCG 58.229 41.667 0.00 0.00 0.00 4.26
300 306 5.823045 TCAAAGTGAGATGAGATAGCGTAGA 59.177 40.000 0.00 0.00 0.00 2.59
329 335 3.134081 GGTATGGCTAAGCACACCTCTAA 59.866 47.826 0.00 0.00 0.00 2.10
332 338 2.637872 TGGCTAAGCACACCTCTAAGTT 59.362 45.455 0.00 0.00 0.00 2.66
362 368 6.037786 TCTAATCTTAATCCATAGGGCACG 57.962 41.667 0.00 0.00 0.00 5.34
388 394 3.636231 TCACCTCAGGCAACCCCG 61.636 66.667 0.00 0.00 39.21 5.73
390 396 3.322466 ACCTCAGGCAACCCCGAG 61.322 66.667 0.00 0.00 39.21 4.63
397 403 2.241176 TCAGGCAACCCCGAGAATTATT 59.759 45.455 0.00 0.00 39.21 1.40
449 455 9.020813 TCTTTTCAATCATAATTCGTAGAGTCG 57.979 33.333 0.00 0.00 38.43 4.18
468 474 0.743345 GCCCCAATGTGAGTACCGAC 60.743 60.000 0.00 0.00 0.00 4.79
516 522 7.210718 TGCATCACATAATCTCATTGATTCC 57.789 36.000 0.00 0.00 43.69 3.01
578 584 6.313658 GGAGCAAAATCCAATTCATTACAACC 59.686 38.462 0.00 0.00 39.34 3.77
619 625 6.275494 TCACATAGTTCGACTCCATTAACA 57.725 37.500 0.00 0.00 0.00 2.41
620 626 6.693466 TCACATAGTTCGACTCCATTAACAA 58.307 36.000 0.00 0.00 0.00 2.83
621 627 6.811665 TCACATAGTTCGACTCCATTAACAAG 59.188 38.462 0.00 0.00 0.00 3.16
622 628 5.581085 ACATAGTTCGACTCCATTAACAAGC 59.419 40.000 0.00 0.00 0.00 4.01
623 629 3.335579 AGTTCGACTCCATTAACAAGCC 58.664 45.455 0.00 0.00 0.00 4.35
624 630 2.396590 TCGACTCCATTAACAAGCCC 57.603 50.000 0.00 0.00 0.00 5.19
625 631 1.626321 TCGACTCCATTAACAAGCCCA 59.374 47.619 0.00 0.00 0.00 5.36
626 632 2.238646 TCGACTCCATTAACAAGCCCAT 59.761 45.455 0.00 0.00 0.00 4.00
627 633 2.355756 CGACTCCATTAACAAGCCCATG 59.644 50.000 0.00 0.00 0.00 3.66
628 634 3.620488 GACTCCATTAACAAGCCCATGA 58.380 45.455 0.00 0.00 0.00 3.07
629 635 4.210331 GACTCCATTAACAAGCCCATGAT 58.790 43.478 0.00 0.00 0.00 2.45
630 636 5.376625 GACTCCATTAACAAGCCCATGATA 58.623 41.667 0.00 0.00 0.00 2.15
631 637 5.380043 ACTCCATTAACAAGCCCATGATAG 58.620 41.667 0.00 0.00 0.00 2.08
632 638 5.132648 ACTCCATTAACAAGCCCATGATAGA 59.867 40.000 0.00 0.00 0.00 1.98
633 639 6.012337 TCCATTAACAAGCCCATGATAGAA 57.988 37.500 0.00 0.00 0.00 2.10
634 640 6.064060 TCCATTAACAAGCCCATGATAGAAG 58.936 40.000 0.00 0.00 0.00 2.85
635 641 5.242393 CCATTAACAAGCCCATGATAGAAGG 59.758 44.000 0.00 0.00 0.00 3.46
636 642 3.303351 AACAAGCCCATGATAGAAGGG 57.697 47.619 0.00 0.00 45.68 3.95
637 643 2.492025 ACAAGCCCATGATAGAAGGGA 58.508 47.619 0.00 0.00 45.80 4.20
638 644 3.059097 ACAAGCCCATGATAGAAGGGAT 58.941 45.455 0.00 0.00 45.80 3.85
639 645 4.242811 ACAAGCCCATGATAGAAGGGATA 58.757 43.478 0.00 0.00 45.80 2.59
640 646 4.042187 ACAAGCCCATGATAGAAGGGATAC 59.958 45.833 0.00 0.00 45.80 2.24
641 647 3.874316 AGCCCATGATAGAAGGGATACA 58.126 45.455 0.00 0.00 45.80 2.29
642 648 4.442707 AGCCCATGATAGAAGGGATACAT 58.557 43.478 0.00 0.00 45.80 2.29
643 649 4.472833 AGCCCATGATAGAAGGGATACATC 59.527 45.833 0.00 0.00 45.80 3.06
644 650 4.225942 GCCCATGATAGAAGGGATACATCA 59.774 45.833 0.00 0.00 45.80 3.07
645 651 5.738909 CCCATGATAGAAGGGATACATCAC 58.261 45.833 0.00 0.00 45.80 3.06
646 652 5.249163 CCCATGATAGAAGGGATACATCACA 59.751 44.000 0.00 0.00 45.80 3.58
647 653 6.069789 CCCATGATAGAAGGGATACATCACAT 60.070 42.308 0.00 0.00 45.80 3.21
648 654 7.126268 CCCATGATAGAAGGGATACATCACATA 59.874 40.741 0.00 0.00 45.80 2.29
649 655 8.202811 CCATGATAGAAGGGATACATCACATAG 58.797 40.741 0.00 0.00 39.74 2.23
650 656 8.756927 CATGATAGAAGGGATACATCACATAGT 58.243 37.037 0.00 0.00 39.74 2.12
651 657 8.727100 TGATAGAAGGGATACATCACATAGTT 57.273 34.615 0.00 0.00 39.74 2.24
652 658 8.807118 TGATAGAAGGGATACATCACATAGTTC 58.193 37.037 0.00 0.00 39.74 3.01
653 659 6.090483 AGAAGGGATACATCACATAGTTCG 57.910 41.667 0.00 0.00 39.74 3.95
654 660 5.833667 AGAAGGGATACATCACATAGTTCGA 59.166 40.000 0.00 0.00 39.74 3.71
655 661 5.455056 AGGGATACATCACATAGTTCGAC 57.545 43.478 0.00 0.00 39.74 4.20
656 662 5.141182 AGGGATACATCACATAGTTCGACT 58.859 41.667 0.00 0.00 39.74 4.18
657 663 5.241949 AGGGATACATCACATAGTTCGACTC 59.758 44.000 0.00 0.00 39.74 3.36
658 664 5.462405 GGATACATCACATAGTTCGACTCC 58.538 45.833 0.00 0.00 0.00 3.85
659 665 5.009710 GGATACATCACATAGTTCGACTCCA 59.990 44.000 0.00 0.00 0.00 3.86
660 666 6.294787 GGATACATCACATAGTTCGACTCCAT 60.295 42.308 0.00 0.00 0.00 3.41
661 667 5.344743 ACATCACATAGTTCGACTCCATT 57.655 39.130 0.00 0.00 0.00 3.16
662 668 6.465439 ACATCACATAGTTCGACTCCATTA 57.535 37.500 0.00 0.00 0.00 1.90
663 669 6.873997 ACATCACATAGTTCGACTCCATTAA 58.126 36.000 0.00 0.00 0.00 1.40
664 670 6.757010 ACATCACATAGTTCGACTCCATTAAC 59.243 38.462 0.00 0.00 0.00 2.01
707 713 9.070179 TCAAGATTGAAAAATGATCACAAGAGA 57.930 29.630 0.00 0.00 33.55 3.10
708 714 9.343103 CAAGATTGAAAAATGATCACAAGAGAG 57.657 33.333 0.00 0.00 0.00 3.20
709 715 8.859236 AGATTGAAAAATGATCACAAGAGAGA 57.141 30.769 0.00 0.00 0.00 3.10
750 756 1.301423 GGTACAAACGCTCAACCACA 58.699 50.000 0.00 0.00 0.00 4.17
787 795 2.366590 TGCATCACCATAGGAGTAGCAG 59.633 50.000 0.00 0.00 0.00 4.24
811 819 2.834549 TGATGGAGAGGTTGAAGAGGAC 59.165 50.000 0.00 0.00 0.00 3.85
846 854 0.473886 ACAGGGTGCTAGACAAGGGT 60.474 55.000 0.00 0.00 0.00 4.34
850 858 1.610886 GGGTGCTAGACAAGGGTTGAC 60.611 57.143 0.00 0.00 0.00 3.18
986 1004 2.351276 CCAGCCCTAGGTTGCGTT 59.649 61.111 8.29 0.00 32.46 4.84
993 1011 1.234615 CCTAGGTTGCGTTGTGGGTG 61.235 60.000 0.00 0.00 0.00 4.61
1037 1059 1.211457 CCAAGTGAGCTTCTAGCCCAT 59.789 52.381 0.00 0.00 43.77 4.00
1059 1081 3.381272 TGGTCTCTTTTGGCTTGAAAGTG 59.619 43.478 7.91 6.46 35.95 3.16
1066 1089 3.540314 TTGGCTTGAAAGTGCACAAAT 57.460 38.095 21.04 3.94 0.00 2.32
1257 1291 3.069586 CGCTTGAGATGTATCAACCCCTA 59.930 47.826 0.00 0.00 35.40 3.53
1392 1652 6.317140 CCTGAGTATCTTTAATTGCTTCTGCA 59.683 38.462 0.00 0.00 41.65 4.41
1455 2730 1.405391 CGTCACACCCATGCATGAGTA 60.405 52.381 28.31 2.97 0.00 2.59
1471 2766 7.806690 TGCATGAGTATTGTAACAAGAGAAAC 58.193 34.615 0.00 0.00 0.00 2.78
1478 2773 9.216117 AGTATTGTAACAAGAGAAACCACATAC 57.784 33.333 0.00 0.00 0.00 2.39
1487 2782 5.008331 AGAGAAACCACATACTACGAGACA 58.992 41.667 0.00 0.00 0.00 3.41
1512 2807 4.270084 GCCCTTGACTAAAAGTTTTTGTGC 59.730 41.667 18.14 11.73 0.00 4.57
1589 2885 1.080705 GGACCTCGTCTCAACACGG 60.081 63.158 0.00 0.00 40.35 4.94
1596 2892 0.027063 CGTCTCAACACGGCGTTTTT 59.973 50.000 11.19 3.33 34.86 1.94
1739 3035 8.786826 ACCATTTCAACGTTAAGATCTTGATA 57.213 30.769 18.47 2.09 0.00 2.15
1826 3122 1.916181 AGTATGGTTGGGCTTAGCAGT 59.084 47.619 6.53 0.00 0.00 4.40
1900 3211 5.534278 TCAGTTTCACAACATTGGAGCATAA 59.466 36.000 0.00 0.00 35.05 1.90
2091 3403 7.194112 TCATGTACAAGATTACAGAATGGGA 57.806 36.000 0.00 0.00 43.62 4.37
2219 3531 3.838317 AGATTAGACTTGTAGTGCCACCA 59.162 43.478 0.00 0.00 0.00 4.17
2220 3532 3.678056 TTAGACTTGTAGTGCCACCAG 57.322 47.619 0.00 0.00 0.00 4.00
2242 3555 6.090493 CCAGCACAATAATACGAGATGATCAG 59.910 42.308 0.09 0.00 0.00 2.90
2275 3588 4.163441 TGGAGTGTGTGAATGGAAAAGA 57.837 40.909 0.00 0.00 0.00 2.52
2332 3645 7.603404 CAGAATGGGTTTTGCAAAAAGATATGA 59.397 33.333 25.40 6.80 0.00 2.15
2395 3731 4.041321 AGTCATATGCAGGTGATATGTGCT 59.959 41.667 7.03 3.70 38.09 4.40
2559 3895 8.210946 ACAACTATAAGTATGCATGTACCATGT 58.789 33.333 10.16 1.06 0.00 3.21
2570 3906 4.425772 CATGTACCATGTAGATCCCCCTA 58.574 47.826 0.00 0.00 0.00 3.53
2735 4281 1.341089 TGCCAACACCACCAACAACTA 60.341 47.619 0.00 0.00 0.00 2.24
2918 4464 4.813235 GCCCGGTGCAAGGCCATA 62.813 66.667 5.01 0.00 43.76 2.74
2990 4536 2.564721 GCCCCAACAGGAAGCACAC 61.565 63.158 0.00 0.00 38.24 3.82
3010 4556 4.125703 CACCTTAAGAGCATGAGGATGTC 58.874 47.826 3.36 0.00 33.47 3.06
3766 5338 9.734620 CTTTGAATTAACAAAGTCATCAACTGA 57.265 29.630 10.16 0.00 46.41 3.41
3772 5344 6.798315 AACAAAGTCATCAACTGATCTGAG 57.202 37.500 6.60 0.00 38.58 3.35
4111 5691 0.108520 GTCGCTCCGGAATACCAACA 60.109 55.000 5.23 0.00 35.59 3.33
4112 5692 0.609151 TCGCTCCGGAATACCAACAA 59.391 50.000 5.23 0.00 35.59 2.83
4172 5752 2.581208 TTCGGTGGACTGCGTTGTGT 62.581 55.000 0.00 0.00 0.00 3.72
4216 5841 1.157585 GGTTCCGGCTTGAGAAACTC 58.842 55.000 0.00 0.00 0.00 3.01
4334 5959 6.672266 TTAGAATGCTAGATCGATTCCCTT 57.328 37.500 0.00 0.00 0.00 3.95
4344 5970 3.536956 TCGATTCCCTTAAATCAGCGT 57.463 42.857 0.00 0.00 35.75 5.07
4395 6045 4.563580 CCCTAGAAACAAGCTAGCTCACAA 60.564 45.833 19.65 0.00 35.19 3.33
4396 6046 4.997395 CCTAGAAACAAGCTAGCTCACAAA 59.003 41.667 19.65 0.00 35.19 2.83
4397 6047 4.820284 AGAAACAAGCTAGCTCACAAAC 57.180 40.909 19.65 8.51 0.00 2.93
4398 6048 4.199310 AGAAACAAGCTAGCTCACAAACA 58.801 39.130 19.65 0.00 0.00 2.83
4399 6049 3.971032 AACAAGCTAGCTCACAAACAC 57.029 42.857 19.65 0.00 0.00 3.32
4400 6050 3.199880 ACAAGCTAGCTCACAAACACT 57.800 42.857 19.65 0.00 0.00 3.55
4401 6051 3.545703 ACAAGCTAGCTCACAAACACTT 58.454 40.909 19.65 0.00 0.00 3.16
4442 6092 6.200665 CGATTGATTTTCCTCTAGAAGCAGAG 59.799 42.308 0.00 0.00 41.54 3.35
4449 6099 1.337703 CTCTAGAAGCAGAGCGAGCAT 59.662 52.381 0.00 0.00 35.95 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 121 8.641499 ACATATTTTTGAAACACGTGAACATT 57.359 26.923 25.01 11.22 0.00 2.71
118 122 8.641499 AACATATTTTTGAAACACGTGAACAT 57.359 26.923 25.01 6.68 0.00 2.71
125 129 8.506140 AGTCATGAACATATTTTTGAAACACG 57.494 30.769 0.00 0.00 0.00 4.49
177 181 6.844097 TTTTTCCAAAACTAAGTGGACACT 57.156 33.333 0.00 0.00 43.67 3.55
178 182 9.758651 AATATTTTTCCAAAACTAAGTGGACAC 57.241 29.630 0.00 0.00 43.67 3.67
271 275 7.013750 ACGCTATCTCATCTCACTTTGATCTAA 59.986 37.037 0.00 0.00 0.00 2.10
272 276 6.488344 ACGCTATCTCATCTCACTTTGATCTA 59.512 38.462 0.00 0.00 0.00 1.98
274 278 5.527951 ACGCTATCTCATCTCACTTTGATC 58.472 41.667 0.00 0.00 0.00 2.92
276 280 4.991153 ACGCTATCTCATCTCACTTTGA 57.009 40.909 0.00 0.00 0.00 2.69
278 282 5.277586 CGTCTACGCTATCTCATCTCACTTT 60.278 44.000 0.00 0.00 0.00 2.66
296 302 4.734917 CTTAGCCATACCTATGCGTCTAC 58.265 47.826 0.00 0.00 32.40 2.59
300 306 1.691976 TGCTTAGCCATACCTATGCGT 59.308 47.619 0.29 0.00 39.81 5.24
303 309 3.403038 GGTGTGCTTAGCCATACCTATG 58.597 50.000 0.29 0.00 41.95 2.23
345 351 1.523758 GGCGTGCCCTATGGATTAAG 58.476 55.000 0.00 0.00 0.00 1.85
362 368 1.598701 GCCTGAGGTGACAATTGGGC 61.599 60.000 10.83 6.37 0.00 5.36
366 372 1.620822 GGTTGCCTGAGGTGACAATT 58.379 50.000 0.00 0.00 0.00 2.32
368 374 1.150536 GGGTTGCCTGAGGTGACAA 59.849 57.895 0.00 0.00 0.00 3.18
449 455 0.743345 GTCGGTACTCACATTGGGGC 60.743 60.000 0.00 0.00 0.00 5.80
619 625 4.242811 TGTATCCCTTCTATCATGGGCTT 58.757 43.478 0.00 0.00 39.09 4.35
620 626 3.874316 TGTATCCCTTCTATCATGGGCT 58.126 45.455 0.00 0.00 39.09 5.19
621 627 4.225942 TGATGTATCCCTTCTATCATGGGC 59.774 45.833 0.00 0.00 39.09 5.36
622 628 5.249163 TGTGATGTATCCCTTCTATCATGGG 59.751 44.000 0.00 0.00 40.42 4.00
623 629 6.364568 TGTGATGTATCCCTTCTATCATGG 57.635 41.667 0.00 0.00 31.28 3.66
624 630 8.756927 ACTATGTGATGTATCCCTTCTATCATG 58.243 37.037 0.00 0.00 31.28 3.07
625 631 8.907829 ACTATGTGATGTATCCCTTCTATCAT 57.092 34.615 0.00 0.00 31.28 2.45
626 632 8.727100 AACTATGTGATGTATCCCTTCTATCA 57.273 34.615 0.00 0.00 0.00 2.15
627 633 7.971168 CGAACTATGTGATGTATCCCTTCTATC 59.029 40.741 0.00 0.00 0.00 2.08
628 634 7.670140 TCGAACTATGTGATGTATCCCTTCTAT 59.330 37.037 0.00 0.00 0.00 1.98
629 635 7.002276 TCGAACTATGTGATGTATCCCTTCTA 58.998 38.462 0.00 0.00 0.00 2.10
630 636 5.833667 TCGAACTATGTGATGTATCCCTTCT 59.166 40.000 0.00 0.00 0.00 2.85
631 637 5.921408 GTCGAACTATGTGATGTATCCCTTC 59.079 44.000 0.00 0.00 0.00 3.46
632 638 5.598830 AGTCGAACTATGTGATGTATCCCTT 59.401 40.000 0.00 0.00 0.00 3.95
633 639 5.141182 AGTCGAACTATGTGATGTATCCCT 58.859 41.667 0.00 0.00 0.00 4.20
634 640 5.455056 AGTCGAACTATGTGATGTATCCC 57.545 43.478 0.00 0.00 0.00 3.85
635 641 5.009710 TGGAGTCGAACTATGTGATGTATCC 59.990 44.000 0.00 0.00 0.00 2.59
636 642 6.073327 TGGAGTCGAACTATGTGATGTATC 57.927 41.667 0.00 0.00 0.00 2.24
637 643 6.656632 ATGGAGTCGAACTATGTGATGTAT 57.343 37.500 0.00 0.00 0.00 2.29
638 644 6.465439 AATGGAGTCGAACTATGTGATGTA 57.535 37.500 0.00 0.00 0.00 2.29
639 645 5.344743 AATGGAGTCGAACTATGTGATGT 57.655 39.130 0.00 0.00 0.00 3.06
640 646 6.756542 TGTTAATGGAGTCGAACTATGTGATG 59.243 38.462 0.00 0.00 0.00 3.07
641 647 6.873997 TGTTAATGGAGTCGAACTATGTGAT 58.126 36.000 0.00 0.00 0.00 3.06
642 648 6.275494 TGTTAATGGAGTCGAACTATGTGA 57.725 37.500 0.00 0.00 0.00 3.58
643 649 6.455646 GCTTGTTAATGGAGTCGAACTATGTG 60.456 42.308 0.00 0.00 0.00 3.21
644 650 5.581085 GCTTGTTAATGGAGTCGAACTATGT 59.419 40.000 0.00 0.00 0.00 2.29
645 651 5.006746 GGCTTGTTAATGGAGTCGAACTATG 59.993 44.000 0.00 0.00 0.00 2.23
646 652 5.116882 GGCTTGTTAATGGAGTCGAACTAT 58.883 41.667 0.00 0.00 0.00 2.12
647 653 4.501071 GGCTTGTTAATGGAGTCGAACTA 58.499 43.478 0.00 0.00 0.00 2.24
648 654 3.335579 GGCTTGTTAATGGAGTCGAACT 58.664 45.455 0.00 0.00 0.00 3.01
649 655 2.418976 GGGCTTGTTAATGGAGTCGAAC 59.581 50.000 0.00 0.00 0.00 3.95
650 656 2.039216 TGGGCTTGTTAATGGAGTCGAA 59.961 45.455 0.00 0.00 0.00 3.71
651 657 1.626321 TGGGCTTGTTAATGGAGTCGA 59.374 47.619 0.00 0.00 0.00 4.20
652 658 2.107950 TGGGCTTGTTAATGGAGTCG 57.892 50.000 0.00 0.00 0.00 4.18
653 659 3.620488 TCATGGGCTTGTTAATGGAGTC 58.380 45.455 0.00 0.00 0.00 3.36
654 660 3.737559 TCATGGGCTTGTTAATGGAGT 57.262 42.857 0.00 0.00 0.00 3.85
655 661 5.593909 TGTTATCATGGGCTTGTTAATGGAG 59.406 40.000 0.00 0.00 0.00 3.86
656 662 5.514169 TGTTATCATGGGCTTGTTAATGGA 58.486 37.500 0.00 0.00 0.00 3.41
657 663 5.850557 TGTTATCATGGGCTTGTTAATGG 57.149 39.130 0.00 0.00 0.00 3.16
658 664 7.490840 TGATTGTTATCATGGGCTTGTTAATG 58.509 34.615 0.00 0.00 35.87 1.90
659 665 7.658525 TGATTGTTATCATGGGCTTGTTAAT 57.341 32.000 0.00 0.00 35.87 1.40
660 666 7.395772 TCTTGATTGTTATCATGGGCTTGTTAA 59.604 33.333 0.00 0.00 40.37 2.01
661 667 6.889177 TCTTGATTGTTATCATGGGCTTGTTA 59.111 34.615 0.00 0.00 40.37 2.41
662 668 5.716228 TCTTGATTGTTATCATGGGCTTGTT 59.284 36.000 0.00 0.00 40.37 2.83
663 669 5.263599 TCTTGATTGTTATCATGGGCTTGT 58.736 37.500 0.00 0.00 40.37 3.16
664 670 5.840243 TCTTGATTGTTATCATGGGCTTG 57.160 39.130 0.00 0.00 40.37 4.01
707 713 9.247861 ACCAAAAGCAATATGTTTTATCTCTCT 57.752 29.630 0.00 0.00 30.58 3.10
728 734 2.097791 GTGGTTGAGCGTTTGTACCAAA 59.902 45.455 0.00 0.00 40.31 3.28
750 756 4.082026 GTGATGCAATTTTAGCCCACTCTT 60.082 41.667 0.00 0.00 34.16 2.85
787 795 3.181456 CCTCTTCAACCTCTCCATCATCC 60.181 52.174 0.00 0.00 0.00 3.51
811 819 0.460284 CTGTCGGAGGGTCGAATTGG 60.460 60.000 0.00 0.00 41.05 3.16
836 844 3.119602 CGATCTTCGTCAACCCTTGTCTA 60.120 47.826 0.00 0.00 34.72 2.59
913 930 3.458163 CGCCCCCTCGCTCTACAA 61.458 66.667 0.00 0.00 0.00 2.41
937 955 1.614824 CCTTGACCTCCTCCCTGCT 60.615 63.158 0.00 0.00 0.00 4.24
986 1004 2.751036 CCATCGCATGCACCCACA 60.751 61.111 19.57 0.00 0.00 4.17
993 1011 3.896133 CACCAGGCCATCGCATGC 61.896 66.667 7.91 7.91 45.40 4.06
1037 1059 3.381272 CACTTTCAAGCCAAAAGAGACCA 59.619 43.478 9.34 0.00 37.22 4.02
1176 1205 5.999205 TTGTTCCATAACTTTGGCATCAT 57.001 34.783 0.00 0.00 36.66 2.45
1187 1216 7.095816 GCTGTTTTTGTACCATTGTTCCATAAC 60.096 37.037 0.00 0.00 36.07 1.89
1193 1222 7.865385 TCTTATGCTGTTTTTGTACCATTGTTC 59.135 33.333 0.00 0.00 0.00 3.18
1257 1291 6.239487 GGCTATTGGAAAAGTTTTAACCCTGT 60.239 38.462 0.00 0.00 0.00 4.00
1353 1387 8.948401 AAGATACTCAGGCTTATCTTGATAGA 57.052 34.615 15.70 0.00 41.47 1.98
1392 1652 4.074970 GCATAATTCCTCGATTCACCCAT 58.925 43.478 0.00 0.00 0.00 4.00
1400 1660 9.520204 CTTTTTAAACATGCATAATTCCTCGAT 57.480 29.630 0.00 0.00 0.00 3.59
1455 2730 9.216117 GTAGTATGTGGTTTCTCTTGTTACAAT 57.784 33.333 0.00 0.00 0.00 2.71
1471 2766 2.545952 GGGCATGTCTCGTAGTATGTGG 60.546 54.545 0.00 0.00 0.00 4.17
1478 2773 1.478510 AGTCAAGGGCATGTCTCGTAG 59.521 52.381 0.00 0.00 0.00 3.51
1487 2782 6.048509 CACAAAAACTTTTAGTCAAGGGCAT 58.951 36.000 0.00 0.00 0.00 4.40
1512 2807 5.738693 ACATAAAATTCGATGAACACATGCG 59.261 36.000 6.55 0.00 0.00 4.73
1596 2892 4.810345 ACCTTCATGTTGGGGTAAAAGAA 58.190 39.130 10.50 0.00 0.00 2.52
1739 3035 2.939353 GGGTTGGGTGGGCCTAGT 60.939 66.667 4.53 0.00 34.45 2.57
1768 3064 7.518848 GCCCTTCTTTTAGTCAAAAGCAAATTG 60.519 37.037 5.23 0.00 46.84 2.32
1826 3122 8.561536 TTGTAATCCTCCAAGGTTGATATCTA 57.438 34.615 3.98 0.00 36.53 1.98
1900 3211 2.024655 ATGTCAAGGATTGCCATGGAGT 60.025 45.455 18.40 0.00 43.82 3.85
2001 3312 5.755849 ACTCGATTAATTGTTCCCTGGAAT 58.244 37.500 1.26 0.00 36.45 3.01
2091 3403 4.081752 TGGGTCGCATATCTTTTTGCAAAT 60.082 37.500 13.65 0.00 38.80 2.32
2219 3531 6.753180 ACTGATCATCTCGTATTATTGTGCT 58.247 36.000 0.00 0.00 0.00 4.40
2220 3532 7.413475 AACTGATCATCTCGTATTATTGTGC 57.587 36.000 0.00 0.00 0.00 4.57
2242 3555 5.587289 TCACACACTCCATGCTTTTTAAAC 58.413 37.500 0.00 0.00 0.00 2.01
2332 3645 3.788227 TGTCAAGCATAGTTTGGGTCT 57.212 42.857 0.00 0.00 0.00 3.85
2395 3731 8.578448 TGGATGATCATCAAATGTACTTTTCA 57.422 30.769 31.49 15.65 39.54 2.69
2514 3850 2.038952 TGTCATGGTCTAGTTTGCTGCT 59.961 45.455 0.00 0.00 0.00 4.24
2559 3895 4.295905 AAGGTTGATGTAGGGGGATCTA 57.704 45.455 0.00 0.00 0.00 1.98
2570 3906 4.787551 TGTGGTTGTCTAAAGGTTGATGT 58.212 39.130 0.00 0.00 0.00 3.06
2918 4464 0.612174 TAGCCTCTTCCACGCTCTGT 60.612 55.000 0.00 0.00 34.03 3.41
2990 4536 3.388308 CGACATCCTCATGCTCTTAAGG 58.612 50.000 1.85 0.00 32.57 2.69
3010 4556 4.379243 ACGGCAGGGTCTGAAGCG 62.379 66.667 0.00 0.00 32.44 4.68
3269 4818 6.209589 GCCTGATAGACTCTACCACATTATGA 59.790 42.308 0.00 0.00 0.00 2.15
3564 5136 6.737254 TGTAGCTTTATTTAGACAAGTGCC 57.263 37.500 0.00 0.00 0.00 5.01
3766 5338 5.598416 TGATGGTCGTTGTAATCTCAGAT 57.402 39.130 0.00 0.00 0.00 2.90
3772 5344 4.634004 TGTTGGATGATGGTCGTTGTAATC 59.366 41.667 0.00 0.00 0.00 1.75
3981 5559 0.545309 AGGTGCTTCTAGTGCCAGGA 60.545 55.000 0.00 0.00 0.00 3.86
4111 5691 1.852633 GGCAAGGAAGGCCTACATTT 58.147 50.000 5.16 0.00 46.28 2.32
4112 5692 3.596362 GGCAAGGAAGGCCTACATT 57.404 52.632 5.16 0.00 46.28 2.71
4154 5734 1.736365 TACACAACGCAGTCCACCGA 61.736 55.000 0.00 0.00 45.00 4.69
4172 5752 2.346766 TTAGTATGCGGACGACCCTA 57.653 50.000 0.00 0.00 0.00 3.53
4231 5856 0.608582 GCTGCTCCCATGATCCCATC 60.609 60.000 0.00 0.00 0.00 3.51
4288 5913 3.626924 ACTCCACCACACGGGCTC 61.627 66.667 0.00 0.00 42.05 4.70
4334 5959 3.490800 TGCAGTACGTACGCTGATTTA 57.509 42.857 29.00 14.63 34.87 1.40
4344 5970 2.921121 CAATCGAGCTTTGCAGTACGTA 59.079 45.455 0.00 0.00 0.00 3.57
4395 6045 4.436852 CGAGCTGTTTGTGTGTTAAGTGTT 60.437 41.667 0.00 0.00 0.00 3.32
4396 6046 3.063452 CGAGCTGTTTGTGTGTTAAGTGT 59.937 43.478 0.00 0.00 0.00 3.55
4397 6047 3.308595 TCGAGCTGTTTGTGTGTTAAGTG 59.691 43.478 0.00 0.00 0.00 3.16
4398 6048 3.527533 TCGAGCTGTTTGTGTGTTAAGT 58.472 40.909 0.00 0.00 0.00 2.24
4399 6049 4.732285 ATCGAGCTGTTTGTGTGTTAAG 57.268 40.909 0.00 0.00 0.00 1.85
4400 6050 4.572795 TCAATCGAGCTGTTTGTGTGTTAA 59.427 37.500 0.00 0.00 0.00 2.01
4401 6051 4.123506 TCAATCGAGCTGTTTGTGTGTTA 58.876 39.130 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.