Multiple sequence alignment - TraesCS6A01G043400

Loading Multiple Alignment...

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 TraesCS6A01G043400 chr6A 100.000 4005 0 0 1 4005 22698206 22694202 0.000000e+00 7396.0
1 TraesCS6A01G043400 chr6A 88.057 988 86 10 1793 2750 22804441 22803456 0.000000e+00 1142.0
2 TraesCS6A01G043400 chr6A 86.631 187 16 3 2927 3110 23332045 23331865 8.780000e-47 198.0
3 TraesCS6A01G043400 chr6A 81.600 250 28 6 1256 1487 22805364 22805115 1.470000e-44 191.0
4 TraesCS6A01G043400 chr6A 77.833 203 30 8 2757 2950 22803392 22803196 1.180000e-20 111.0
5 TraesCS6A01G043400 chr6A 83.495 103 12 2 3736 3834 23332373 23332272 1.530000e-14 91.6
6 TraesCS6A01G043400 chr6A 78.723 141 20 7 3452 3591 23331496 23331365 7.130000e-13 86.1
7 TraesCS6A01G043400 chr6A 87.273 55 5 2 3688 3740 23428738 23428792 1.200000e-05 62.1
8 TraesCS6A01G043400 chr6A 100.000 29 0 0 3712 3740 23259556 23259528 2.000000e-03 54.7
9 TraesCS6A01G043400 chr6B 90.402 3032 178 35 932 3871 39199946 39196936 0.000000e+00 3882.0
10 TraesCS6A01G043400 chr6B 86.842 1026 91 17 1764 2747 39339895 39338872 0.000000e+00 1107.0
11 TraesCS6A01G043400 chr6B 88.430 847 78 10 1 828 39200826 39199981 0.000000e+00 1003.0
12 TraesCS6A01G043400 chr6B 83.777 376 56 4 1062 1433 336900624 336900250 6.370000e-93 351.0
13 TraesCS6A01G043400 chr6B 81.236 453 67 9 137 576 39212695 39212248 2.290000e-92 350.0
14 TraesCS6A01G043400 chr6B 98.261 115 2 0 3891 4005 39196606 39196492 6.790000e-48 202.0
15 TraesCS6A01G043400 chr6B 89.333 150 14 1 1256 1405 39340501 39340354 1.900000e-43 187.0
16 TraesCS6A01G043400 chr6B 87.500 96 8 3 1571 1664 39340030 39339937 1.520000e-19 108.0
17 TraesCS6A01G043400 chr6B 95.833 48 2 0 1495 1542 336892489 336892442 1.190000e-10 78.7
18 TraesCS6A01G043400 chr6B 100.000 39 0 0 3862 3900 39196658 39196620 5.550000e-09 73.1
19 TraesCS6A01G043400 chr6B 84.722 72 9 2 2900 2970 39197823 39197753 2.000000e-08 71.3
20 TraesCS6A01G043400 chr6B 85.965 57 2 5 3690 3740 40592715 40592771 5.590000e-04 56.5
21 TraesCS6A01G043400 chr6D 92.335 2544 78 27 1539 3991 24231635 24229118 0.000000e+00 3509.0
22 TraesCS6A01G043400 chr6D 88.107 1051 79 15 480 1492 24232800 24231758 0.000000e+00 1206.0
23 TraesCS6A01G043400 chr6D 87.610 1025 84 19 1766 2750 24262722 24261701 0.000000e+00 1149.0
24 TraesCS6A01G043400 chr6D 83.553 304 31 5 1 286 24233100 24232798 2.370000e-67 267.0
25 TraesCS6A01G043400 chr6D 88.205 195 14 3 2907 3098 24892876 24893064 1.450000e-54 224.0
26 TraesCS6A01G043400 chr3D 88.616 571 65 0 1793 2363 459468762 459468192 0.000000e+00 695.0
27 TraesCS6A01G043400 chr3D 79.327 416 47 20 2572 2975 459467950 459467562 5.140000e-64 255.0
28 TraesCS6A01G043400 chr3D 85.792 183 18 5 2982 3161 459467653 459467476 1.900000e-43 187.0
29 TraesCS6A01G043400 chr3D 94.872 39 2 0 2497 2535 459468001 459467963 1.200000e-05 62.1
30 TraesCS6A01G043400 chr3D 91.304 46 3 1 3696 3740 598715360 598715315 1.200000e-05 62.1
31 TraesCS6A01G043400 chr3D 94.444 36 1 1 2642 2676 459468070 459468035 2.000000e-03 54.7
32 TraesCS6A01G043400 chr3B 88.636 572 63 2 1793 2363 607385473 607384903 0.000000e+00 695.0
33 TraesCS6A01G043400 chr3B 80.288 416 41 17 2572 2975 607384661 607384275 3.940000e-70 276.0
34 TraesCS6A01G043400 chr3B 79.387 359 48 17 2977 3320 607384371 607384024 3.110000e-56 230.0
35 TraesCS6A01G043400 chr3B 85.976 164 14 5 1258 1412 530702718 530702555 2.480000e-37 167.0
36 TraesCS6A01G043400 chr3B 94.872 39 2 0 2497 2535 607384712 607384674 1.200000e-05 62.1
37 TraesCS6A01G043400 chr3A 88.112 572 67 1 1793 2363 601555434 601556005 0.000000e+00 678.0
38 TraesCS6A01G043400 chr3A 79.327 416 45 17 2572 2975 601556247 601556633 1.850000e-63 254.0
39 TraesCS6A01G043400 chr3A 79.552 357 45 16 2977 3317 601556537 601556881 3.110000e-56 230.0
40 TraesCS6A01G043400 chr3A 89.796 98 10 0 2362 2459 601556031 601556128 4.200000e-25 126.0
41 TraesCS6A01G043400 chr3A 94.872 39 2 0 2497 2535 601556196 601556234 1.200000e-05 62.1
42 TraesCS6A01G043400 chr3A 94.444 36 1 1 2642 2676 601556127 601556162 2.000000e-03 54.7
43 TraesCS6A01G043400 chr5B 83.429 694 92 12 1794 2466 166167978 166167287 1.220000e-174 623.0
44 TraesCS6A01G043400 chr5B 83.285 694 93 12 1794 2466 165776643 165775952 5.690000e-173 617.0
45 TraesCS6A01G043400 chr5B 85.714 161 14 5 1258 1409 205585252 205585412 1.150000e-35 161.0
46 TraesCS6A01G043400 chr4A 90.753 292 27 0 1077 1368 696691183 696691474 1.350000e-104 390.0
47 TraesCS6A01G043400 chr4A 90.690 290 27 0 1079 1368 696667135 696667424 1.750000e-103 387.0
48 TraesCS6A01G043400 chr4A 89.726 292 30 0 1077 1368 696647196 696647487 1.360000e-99 374.0
49 TraesCS6A01G043400 chr4A 90.741 162 14 1 1539 1700 696668200 696668360 8.720000e-52 215.0
50 TraesCS6A01G043400 chr4A 90.741 162 14 1 1539 1700 696692250 696692410 8.720000e-52 215.0
51 TraesCS6A01G043400 chr4A 89.222 167 17 1 1539 1705 696648262 696648427 1.460000e-49 207.0
52 TraesCS6A01G043400 chr4A 94.444 36 1 1 1713 1747 623967084 623967119 2.000000e-03 54.7
53 TraesCS6A01G043400 chr2B 80.156 257 28 9 1256 1491 693801753 693802007 1.910000e-38 171.0
54 TraesCS6A01G043400 chr2B 88.889 54 3 2 3688 3740 681409052 681409103 3.340000e-06 63.9
55 TraesCS6A01G043400 chr2A 77.778 342 32 20 1258 1561 425814005 425813670 1.910000e-38 171.0
56 TraesCS6A01G043400 chr1B 91.667 96 6 2 1614 1708 179580982 179580888 9.030000e-27 132.0
57 TraesCS6A01G043400 chr4D 91.667 72 6 0 2942 3013 381837081 381837152 2.550000e-17 100.0
58 TraesCS6A01G043400 chr4D 92.157 51 1 2 1715 1765 281208858 281208905 7.180000e-08 69.4
59 TraesCS6A01G043400 chr7D 94.872 39 1 1 1668 1705 109922142 109922180 4.320000e-05 60.2
60 TraesCS6A01G043400 chr7D 90.476 42 3 1 1668 1708 60105568 60105527 2.000000e-03 54.7
61 TraesCS6A01G043400 chr1D 90.476 42 4 0 3699 3740 392570488 392570529 5.590000e-04 56.5
62 TraesCS6A01G043400 chr1A 86.538 52 2 3 3689 3740 492801638 492801592 7.000000e-03 52.8


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 TraesCS6A01G043400 chr6A 22694202 22698206 4004 True 7396.000000 7396 100.000000 1 4005 1 chr6A.!!$R1 4004
1 TraesCS6A01G043400 chr6A 22803196 22805364 2168 True 481.333333 1142 82.496667 1256 2950 3 chr6A.!!$R3 1694
2 TraesCS6A01G043400 chr6B 39196492 39200826 4334 True 1046.280000 3882 92.363000 1 4005 5 chr6B.!!$R4 4004
3 TraesCS6A01G043400 chr6B 39338872 39340501 1629 True 467.333333 1107 87.891667 1256 2747 3 chr6B.!!$R5 1491
4 TraesCS6A01G043400 chr6D 24229118 24233100 3982 True 1660.666667 3509 87.998333 1 3991 3 chr6D.!!$R2 3990
5 TraesCS6A01G043400 chr6D 24261701 24262722 1021 True 1149.000000 1149 87.610000 1766 2750 1 chr6D.!!$R1 984
6 TraesCS6A01G043400 chr3D 459467476 459468762 1286 True 250.760000 695 88.610200 1793 3161 5 chr3D.!!$R2 1368
7 TraesCS6A01G043400 chr3B 607384024 607385473 1449 True 315.775000 695 85.795750 1793 3320 4 chr3B.!!$R2 1527
8 TraesCS6A01G043400 chr3A 601555434 601556881 1447 False 234.133333 678 87.683833 1793 3317 6 chr3A.!!$F1 1524
9 TraesCS6A01G043400 chr5B 166167287 166167978 691 True 623.000000 623 83.429000 1794 2466 1 chr5B.!!$R2 672
10 TraesCS6A01G043400 chr5B 165775952 165776643 691 True 617.000000 617 83.285000 1794 2466 1 chr5B.!!$R1 672
11 TraesCS6A01G043400 chr4A 696691183 696692410 1227 False 302.500000 390 90.747000 1077 1700 2 chr4A.!!$F4 623
12 TraesCS6A01G043400 chr4A 696667135 696668360 1225 False 301.000000 387 90.715500 1079 1700 2 chr4A.!!$F3 621
13 TraesCS6A01G043400 chr4A 696647196 696648427 1231 False 290.500000 374 89.474000 1077 1705 2 chr4A.!!$F2 628

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
246 266 0.035725 CTGGCATGTTCTGGAGCTGA 60.036 55.000 0.00 0.0 0.0 4.26 F
530 550 0.107410 ACAGTGTTCCAACGGCTTGA 60.107 50.000 0.00 0.0 0.0 3.02 F
840 862 0.165944 CGTTGTTTGGGTCGAGCATC 59.834 55.000 17.59 0.0 0.0 3.91 F
1971 3054 1.004758 TCATGGAGGGGAGGAAGGG 59.995 63.158 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 2881 0.859232 ACTTTCACAGCTACAACGCG 59.141 50.000 3.53 3.53 34.4 6.01 R
2405 3560 0.738389 AGGTTGTTTGACTGTTGGCG 59.262 50.000 0.00 0.00 0.0 5.69 R
2867 4153 8.981659 TGTCTAGGAGAAGAATTTGATATGACA 58.018 33.333 0.00 0.00 0.0 3.58 R
3443 4774 1.270826 TCAGAGAAGAGAGGTGCGTTG 59.729 52.381 0.00 0.00 0.0 4.10 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
22 23 2.947890 GACGACGACGACGACCACT 61.948 63.158 25.15 3.08 42.66 4.00
27 28 1.154338 CGACGACGACCACTACCAC 60.154 63.158 0.00 0.00 42.66 4.16
68 73 3.965258 TGGGCATGGACCTGCGTT 61.965 61.111 9.05 0.00 43.23 4.84
71 76 2.690778 GGCATGGACCTGCGTTCAC 61.691 63.158 9.05 0.00 43.23 3.18
72 77 3.027170 GCATGGACCTGCGTTCACG 62.027 63.158 0.00 0.00 43.27 4.35
73 78 1.374125 CATGGACCTGCGTTCACGA 60.374 57.895 2.87 0.00 43.02 4.35
75 80 1.816863 ATGGACCTGCGTTCACGACT 61.817 55.000 2.87 0.00 43.02 4.18
76 81 2.022129 GGACCTGCGTTCACGACTG 61.022 63.158 2.87 0.00 43.02 3.51
77 82 1.007734 GACCTGCGTTCACGACTGA 60.008 57.895 2.87 0.00 43.02 3.41
78 83 0.388649 GACCTGCGTTCACGACTGAT 60.389 55.000 2.87 0.00 43.02 2.90
124 142 1.153249 CGGGGGATGCGCTCTTTTA 60.153 57.895 9.73 0.00 0.00 1.52
130 148 0.727398 GATGCGCTCTTTTACGGCTT 59.273 50.000 9.73 0.00 0.00 4.35
139 157 0.955905 TTTTACGGCTTGTTGGCTCC 59.044 50.000 0.00 0.00 39.32 4.70
182 200 2.772191 TCTGCACCACCACCACCT 60.772 61.111 0.00 0.00 0.00 4.00
199 217 1.600107 CTAGCGGGTGCCTTGGTTA 59.400 57.895 0.00 0.00 44.31 2.85
200 218 0.035820 CTAGCGGGTGCCTTGGTTAA 60.036 55.000 0.00 0.00 44.31 2.01
203 221 1.228306 CGGGTGCCTTGGTTAACCA 60.228 57.895 23.69 23.69 45.94 3.67
212 230 2.024464 CCTTGGTTAACCATCCATCCCA 60.024 50.000 27.57 9.53 46.97 4.37
213 231 3.565449 CCTTGGTTAACCATCCATCCCAA 60.565 47.826 27.57 8.81 46.97 4.12
233 253 1.114627 TGCATCTACGTCTCTGGCAT 58.885 50.000 0.00 0.00 0.00 4.40
238 258 2.447443 TCTACGTCTCTGGCATGTTCT 58.553 47.619 0.00 0.00 0.00 3.01
246 266 0.035725 CTGGCATGTTCTGGAGCTGA 60.036 55.000 0.00 0.00 0.00 4.26
247 267 0.401356 TGGCATGTTCTGGAGCTGAA 59.599 50.000 0.00 0.00 0.00 3.02
258 278 0.182299 GGAGCTGAATCCCCTTCCAG 59.818 60.000 0.00 0.00 32.79 3.86
268 288 1.203440 TCCCCTTCCAGCTCCTTTAGT 60.203 52.381 0.00 0.00 0.00 2.24
271 291 1.134670 CCTTCCAGCTCCTTTAGTCCG 60.135 57.143 0.00 0.00 0.00 4.79
274 294 1.187087 CCAGCTCCTTTAGTCCGTCT 58.813 55.000 0.00 0.00 0.00 4.18
322 342 1.333636 CCGGATCTGTGCCTCCTTCT 61.334 60.000 0.00 0.00 0.00 2.85
331 351 3.445008 TGTGCCTCCTTCTAGATCTTGT 58.555 45.455 0.00 0.00 0.00 3.16
335 355 4.161189 TGCCTCCTTCTAGATCTTGTCTTG 59.839 45.833 0.00 0.00 38.42 3.02
340 360 4.399618 CCTTCTAGATCTTGTCTTGTCCGA 59.600 45.833 0.00 0.00 38.42 4.55
406 426 0.543749 CACACATCCTTCCCCTCCTC 59.456 60.000 0.00 0.00 0.00 3.71
408 428 0.621571 CACATCCTTCCCCTCCTCCA 60.622 60.000 0.00 0.00 0.00 3.86
418 438 1.343884 CCCCTCCTCCAGAGTTCTCAT 60.344 57.143 2.64 0.00 41.47 2.90
446 466 1.497309 ATGCCCGGTTCCTCCTTCAA 61.497 55.000 0.00 0.00 0.00 2.69
530 550 0.107410 ACAGTGTTCCAACGGCTTGA 60.107 50.000 0.00 0.00 0.00 3.02
539 559 0.318120 CAACGGCTTGAAATTGGCCT 59.682 50.000 3.32 0.00 43.29 5.19
629 649 0.817013 CCATGGCCGTTTTATGTGCT 59.183 50.000 0.00 0.00 0.00 4.40
634 654 1.398390 GGCCGTTTTATGTGCTCTCTG 59.602 52.381 0.00 0.00 0.00 3.35
662 682 1.916777 GGGGAAACTCCAGGTCCGA 60.917 63.158 0.00 0.00 38.64 4.55
697 717 2.244695 TGACGATGGTGTCTAGGTGTT 58.755 47.619 0.00 0.00 39.64 3.32
736 758 0.790207 GTTGTCTTGATTGCTCGCGA 59.210 50.000 9.26 9.26 0.00 5.87
751 773 2.887568 CGACATCCTCGGTGCTGC 60.888 66.667 0.00 0.00 38.87 5.25
767 789 0.593128 CTGCCTTCGGAGTTTTGGTG 59.407 55.000 0.00 0.00 0.00 4.17
840 862 0.165944 CGTTGTTTGGGTCGAGCATC 59.834 55.000 17.59 0.00 0.00 3.91
851 873 3.068873 GGGTCGAGCATCTTATGTCTCTT 59.931 47.826 17.59 0.00 33.90 2.85
860 882 4.902443 TCTTATGTCTCTTCGCTTCGAT 57.098 40.909 0.00 0.00 35.23 3.59
890 912 4.133796 GCCCCTTTGCGTCCATGC 62.134 66.667 0.00 0.00 0.00 4.06
911 933 4.039004 TGCCATGTGTTTTACAAGCTCATT 59.961 37.500 0.00 0.00 43.77 2.57
916 938 8.511321 CCATGTGTTTTACAAGCTCATTTACTA 58.489 33.333 0.00 0.00 43.77 1.82
980 1003 5.172411 CGAAAAATAAATAAACGCATCCCCG 59.828 40.000 0.00 0.00 0.00 5.73
1270 1304 3.771160 CCCCCTCCTCGACAACGG 61.771 72.222 0.00 0.00 40.21 4.44
1433 1964 1.895131 GGATTGGTGGTTGTGCTGATT 59.105 47.619 0.00 0.00 0.00 2.57
1446 1977 1.280133 TGCTGATTCTAGTGGCTGCTT 59.720 47.619 0.00 0.00 0.00 3.91
1460 1991 3.069443 TGGCTGCTTTTCTCGGAAATTTT 59.931 39.130 0.00 0.00 0.00 1.82
1533 2237 1.335810 AGTGTGCATTGCTCTGTTGTG 59.664 47.619 10.49 0.00 0.00 3.33
1608 2666 5.447818 GCATAGGTGAAGTACAGATGCAAAC 60.448 44.000 0.00 0.00 43.24 2.93
1644 2702 5.071788 TCTGTAGCTGGTTAATATCCCAAGG 59.928 44.000 0.00 0.00 0.00 3.61
1647 2705 4.312487 AGCTGGTTAATATCCCAAGGGTA 58.688 43.478 4.80 0.00 36.47 3.69
1648 2706 4.729881 AGCTGGTTAATATCCCAAGGGTAA 59.270 41.667 4.80 0.00 36.47 2.85
1669 2727 7.217906 GGTAACCTAAATGGAAGTAGAGATGG 58.782 42.308 0.00 0.00 39.71 3.51
1672 2730 7.510675 ACCTAAATGGAAGTAGAGATGGAAA 57.489 36.000 0.00 0.00 39.71 3.13
1728 2787 5.129650 GCTTCCTAAATACTCCCTCTGTCTT 59.870 44.000 0.00 0.00 0.00 3.01
1810 2884 2.190161 TCGACTCATCAAAATACCGCG 58.810 47.619 0.00 0.00 0.00 6.46
1861 2944 4.268644 GCTTGCTTGTTCTTTGAGTTTTCC 59.731 41.667 0.00 0.00 0.00 3.13
1880 2963 3.035363 TCCTGCTTACGATGACCCATTA 58.965 45.455 0.00 0.00 0.00 1.90
1918 3001 4.559862 TTCTTTCTCCTCCAGGATGTTC 57.440 45.455 0.00 0.00 44.46 3.18
1971 3054 1.004758 TCATGGAGGGGAGGAAGGG 59.995 63.158 0.00 0.00 0.00 3.95
2105 3188 2.356793 GAGATGCCCCGCGATCTG 60.357 66.667 8.23 0.00 30.84 2.90
2141 3224 4.383118 GCTTTGGTGAATGGCTAGTAGAGA 60.383 45.833 0.00 0.00 0.00 3.10
2183 3266 2.483889 GGAGACAAGTACTATGCAGGGC 60.484 54.545 0.00 0.00 0.00 5.19
2335 3418 6.409524 ACACTTGTGATGGACAAATTCAAT 57.590 33.333 7.83 0.00 44.14 2.57
2345 3428 9.411189 TGATGGACAAATTCAATCATCAGAATA 57.589 29.630 0.00 0.00 39.46 1.75
2405 3560 1.066430 TGGTGGTCAGAGCGGTAAATC 60.066 52.381 0.00 0.00 0.00 2.17
2866 4152 6.093404 TCTATATTTACTATGCGACTGCTGC 58.907 40.000 0.00 0.00 43.34 5.25
2867 4153 2.672961 TTTACTATGCGACTGCTGCT 57.327 45.000 0.00 0.00 43.34 4.24
2868 4154 1.926561 TTACTATGCGACTGCTGCTG 58.073 50.000 4.89 4.89 43.34 4.41
2996 4293 7.068839 TGGTTAATTTCTTTTCCTGTGCAAGTA 59.931 33.333 0.00 0.00 0.00 2.24
2998 4295 4.545823 TTTCTTTTCCTGTGCAAGTACG 57.454 40.909 0.00 0.00 0.00 3.67
3006 4303 0.934496 TGTGCAAGTACGTCTGCAAC 59.066 50.000 18.16 13.60 39.10 4.17
3027 4324 6.761242 GCAACCTGTTTAAAATTTCTTCTGGT 59.239 34.615 0.00 0.58 0.00 4.00
3029 4326 9.981114 CAACCTGTTTAAAATTTCTTCTGGTAT 57.019 29.630 0.00 0.00 0.00 2.73
3182 4502 6.710597 ACTACAGAGTGTTCTTGTGAGTTA 57.289 37.500 0.00 0.00 33.41 2.24
3496 4830 4.444591 CCTTCTCAGCTCTTCCATGCTTAT 60.445 45.833 0.00 0.00 37.44 1.73
3563 4900 4.518211 GCAGCTATCTATGCAGTTCCAAAT 59.482 41.667 0.00 0.00 42.11 2.32
3583 4920 6.128742 CCAAATTGCATTGAGTTGCTCTTAAC 60.129 38.462 1.52 0.00 43.18 2.01
3586 4923 5.512753 TGCATTGAGTTGCTCTTAACAAA 57.487 34.783 0.00 0.00 43.18 2.83
3604 4941 5.151632 ACAAAATGATACGATACAACGGC 57.848 39.130 0.00 0.00 37.61 5.68
3607 4944 2.847959 TGATACGATACAACGGCGAA 57.152 45.000 16.62 0.00 37.61 4.70
3829 5171 2.889045 TGTACTATGAGATACCCACGGC 59.111 50.000 0.00 0.00 0.00 5.68
4001 5678 0.038251 CGCAGGCAAGTGTAGAGACA 60.038 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.211190 GGTGGTAGTGGTCGTCGTC 59.789 63.158 0.00 0.00 0.00 4.20
13 14 2.653087 GGGGGTGGTAGTGGTCGTC 61.653 68.421 0.00 0.00 0.00 4.20
16 17 2.298661 CCTGGGGGTGGTAGTGGTC 61.299 68.421 0.00 0.00 0.00 4.02
68 73 2.178273 CGCACCGATCAGTCGTGA 59.822 61.111 0.00 0.00 46.25 4.35
72 77 2.125512 AAGCCGCACCGATCAGTC 60.126 61.111 0.00 0.00 0.00 3.51
73 78 2.125512 GAAGCCGCACCGATCAGT 60.126 61.111 0.00 0.00 0.00 3.41
75 80 4.812476 CCGAAGCCGCACCGATCA 62.812 66.667 6.07 0.00 0.00 2.92
76 81 4.508128 TCCGAAGCCGCACCGATC 62.508 66.667 6.07 0.00 0.00 3.69
77 82 4.814294 GTCCGAAGCCGCACCGAT 62.814 66.667 6.07 0.00 0.00 4.18
110 128 1.090052 AGCCGTAAAAGAGCGCATCC 61.090 55.000 11.47 0.00 0.00 3.51
120 138 0.955905 GGAGCCAACAAGCCGTAAAA 59.044 50.000 0.00 0.00 0.00 1.52
124 142 1.152756 AAAGGAGCCAACAAGCCGT 60.153 52.632 0.00 0.00 0.00 5.68
130 148 1.600636 CGAGCCAAAGGAGCCAACA 60.601 57.895 0.00 0.00 0.00 3.33
139 157 1.301677 GAGGAGCCAACGAGCCAAAG 61.302 60.000 0.00 0.00 0.00 2.77
182 200 0.321830 GTTAACCAAGGCACCCGCTA 60.322 55.000 0.00 0.00 38.60 4.26
199 217 2.090943 AGATGCATTGGGATGGATGGTT 60.091 45.455 0.00 0.00 43.39 3.67
200 218 1.502039 AGATGCATTGGGATGGATGGT 59.498 47.619 0.00 0.00 43.39 3.55
203 221 2.373169 ACGTAGATGCATTGGGATGGAT 59.627 45.455 0.00 0.00 45.65 3.41
212 230 1.482182 TGCCAGAGACGTAGATGCATT 59.518 47.619 0.00 0.00 0.00 3.56
213 231 1.114627 TGCCAGAGACGTAGATGCAT 58.885 50.000 0.00 0.00 0.00 3.96
233 253 0.620556 GGGGATTCAGCTCCAGAACA 59.379 55.000 0.00 0.00 37.01 3.18
238 258 0.549902 TGGAAGGGGATTCAGCTCCA 60.550 55.000 0.00 0.00 39.91 3.86
246 266 1.387119 AAAGGAGCTGGAAGGGGATT 58.613 50.000 0.00 0.00 0.00 3.01
247 267 2.131023 CTAAAGGAGCTGGAAGGGGAT 58.869 52.381 0.00 0.00 0.00 3.85
258 278 0.246635 TGCAGACGGACTAAAGGAGC 59.753 55.000 0.00 0.00 0.00 4.70
308 328 3.678965 AGATCTAGAAGGAGGCACAGA 57.321 47.619 0.00 0.00 0.00 3.41
322 342 2.427453 GCCTCGGACAAGACAAGATCTA 59.573 50.000 0.00 0.00 36.27 1.98
397 417 0.336737 GAGAACTCTGGAGGAGGGGA 59.663 60.000 2.58 0.00 45.83 4.81
406 426 0.460987 GCCGGACATGAGAACTCTGG 60.461 60.000 5.05 1.21 34.02 3.86
408 428 0.965866 TCGCCGGACATGAGAACTCT 60.966 55.000 5.05 0.00 0.00 3.24
436 456 1.006571 GCACGACGTTGAAGGAGGA 60.007 57.895 10.51 0.00 0.00 3.71
484 504 3.537874 GGTCGTCGGGCATAGGCT 61.538 66.667 0.00 0.00 40.87 4.58
530 550 1.275666 GGTTTAGCCCAGGCCAATTT 58.724 50.000 5.01 0.00 43.17 1.82
587 607 1.630244 CGCCTTCAAGAAGCGGACAG 61.630 60.000 14.47 0.08 37.11 3.51
588 608 1.667830 CGCCTTCAAGAAGCGGACA 60.668 57.895 14.47 0.00 37.11 4.02
593 613 2.177778 GCAGCGCCTTCAAGAAGC 59.822 61.111 2.29 0.00 37.11 3.86
634 654 1.657751 GAGTTTCCCCCAATGCTCGC 61.658 60.000 0.00 0.00 0.00 5.03
674 694 2.032620 ACCTAGACACCATCGTCATCC 58.967 52.381 0.00 0.00 38.43 3.51
726 748 1.589993 CGAGGATGTCGCGAGCAAT 60.590 57.895 10.24 3.34 43.03 3.56
736 758 2.527951 GAAGGCAGCACCGAGGATGT 62.528 60.000 0.00 0.00 46.52 3.06
767 789 4.702131 AGCAATCCAATCAACAACTAGACC 59.298 41.667 0.00 0.00 0.00 3.85
840 862 4.602006 TGATCGAAGCGAAGAGACATAAG 58.398 43.478 0.00 0.00 39.99 1.73
851 873 2.860136 GTGAACATGATGATCGAAGCGA 59.140 45.455 0.00 0.00 41.13 4.93
860 882 0.327924 AAGGGGCGTGAACATGATGA 59.672 50.000 0.00 0.00 0.00 2.92
890 912 7.370383 AGTAAATGAGCTTGTAAAACACATGG 58.630 34.615 0.00 0.00 36.90 3.66
934 956 5.467063 TCGCCAATACGCAATCATTACATTA 59.533 36.000 0.00 0.00 0.00 1.90
937 959 3.198872 TCGCCAATACGCAATCATTACA 58.801 40.909 0.00 0.00 0.00 2.41
938 960 3.870723 TCGCCAATACGCAATCATTAC 57.129 42.857 0.00 0.00 0.00 1.89
939 961 4.884458 TTTCGCCAATACGCAATCATTA 57.116 36.364 0.00 0.00 0.00 1.90
1115 1149 1.453379 CTACGGAGGAAGCGAGGGA 60.453 63.158 0.00 0.00 0.00 4.20
1270 1304 3.844090 GAGGAGGCAGAGTCGGGC 61.844 72.222 8.84 8.84 0.00 6.13
1331 1365 2.185608 GGAAGAGGAGCTCACCGC 59.814 66.667 17.19 0.92 39.57 5.68
1433 1964 1.066858 CCGAGAAAAGCAGCCACTAGA 60.067 52.381 0.00 0.00 0.00 2.43
1460 1991 6.817641 ACACATGCTTCAACTGAAAAATTGAA 59.182 30.769 0.00 0.00 41.38 2.69
1472 2003 2.350772 GCCTGTGTACACATGCTTCAAC 60.351 50.000 35.01 15.48 45.43 3.18
1644 2702 7.070821 TCCATCTCTACTTCCATTTAGGTTACC 59.929 40.741 0.00 0.00 39.02 2.85
1647 2705 7.510675 TTCCATCTCTACTTCCATTTAGGTT 57.489 36.000 0.00 0.00 39.02 3.50
1648 2706 7.510675 TTTCCATCTCTACTTCCATTTAGGT 57.489 36.000 0.00 0.00 39.02 3.08
1657 2715 9.906660 CAGTACTGATATTTCCATCTCTACTTC 57.093 37.037 18.45 0.00 0.00 3.01
1748 2807 2.769663 ACACTTGTACTCCCTTGTGTCA 59.230 45.455 0.00 0.00 34.10 3.58
1749 2808 3.470645 ACACTTGTACTCCCTTGTGTC 57.529 47.619 0.00 0.00 34.10 3.67
1750 2809 3.541632 CAACACTTGTACTCCCTTGTGT 58.458 45.455 0.00 0.00 39.85 3.72
1751 2810 2.878406 CCAACACTTGTACTCCCTTGTG 59.122 50.000 0.00 0.00 0.00 3.33
1752 2811 2.508300 ACCAACACTTGTACTCCCTTGT 59.492 45.455 0.00 0.00 0.00 3.16
1753 2812 3.208747 ACCAACACTTGTACTCCCTTG 57.791 47.619 0.00 0.00 0.00 3.61
1754 2813 3.551846 CAACCAACACTTGTACTCCCTT 58.448 45.455 0.00 0.00 0.00 3.95
1807 2881 0.859232 ACTTTCACAGCTACAACGCG 59.141 50.000 3.53 3.53 34.40 6.01
1810 2884 4.142469 ACCAAACACTTTCACAGCTACAAC 60.142 41.667 0.00 0.00 0.00 3.32
1861 2944 4.212004 CACATAATGGGTCATCGTAAGCAG 59.788 45.833 0.00 0.00 37.18 4.24
1880 2963 8.743714 GGAGAAAGAAAATAGTTTCATCCACAT 58.256 33.333 17.15 0.86 44.82 3.21
1918 3001 5.215252 TCGATTCCTTGGATTTAGCTAGG 57.785 43.478 0.00 0.00 0.00 3.02
1971 3054 1.463831 CAGTGTCTGACTCTTGCATGC 59.536 52.381 11.82 11.82 32.44 4.06
2105 3188 2.096496 CACCAAAGCGATGATCAACTCC 59.904 50.000 0.00 0.00 0.00 3.85
2141 3224 3.954258 CCAAACCACTTTCTCACTTTCCT 59.046 43.478 0.00 0.00 0.00 3.36
2335 3418 5.883685 AGTCAGGAGCAATATTCTGATGA 57.116 39.130 7.59 2.90 38.34 2.92
2345 3428 6.070538 ACATTAGTTCTGTAGTCAGGAGCAAT 60.071 38.462 0.00 0.00 41.59 3.56
2405 3560 0.738389 AGGTTGTTTGACTGTTGGCG 59.262 50.000 0.00 0.00 0.00 5.69
2866 4152 9.474920 GTCTAGGAGAAGAATTTGATATGACAG 57.525 37.037 0.00 0.00 0.00 3.51
2867 4153 8.981659 TGTCTAGGAGAAGAATTTGATATGACA 58.018 33.333 0.00 0.00 0.00 3.58
2868 4154 9.823647 TTGTCTAGGAGAAGAATTTGATATGAC 57.176 33.333 0.00 0.00 0.00 3.06
2996 4293 4.911514 ATTTTAAACAGGTTGCAGACGT 57.088 36.364 0.00 0.00 0.00 4.34
2998 4295 7.706607 AGAAGAAATTTTAAACAGGTTGCAGAC 59.293 33.333 0.00 0.00 0.00 3.51
3027 4324 6.109156 TCCACAAGAAGTTGCAAGACTATA 57.891 37.500 0.00 0.00 37.14 1.31
3029 4326 4.415881 TCCACAAGAAGTTGCAAGACTA 57.584 40.909 0.00 0.00 37.14 2.59
3182 4502 6.995364 TGTGATGGACAAATTCAAACATCAT 58.005 32.000 14.72 0.00 44.21 2.45
3335 4666 3.973206 ATGGTGTTGATACCGTCTCAA 57.027 42.857 0.00 0.00 43.87 3.02
3443 4774 1.270826 TCAGAGAAGAGAGGTGCGTTG 59.729 52.381 0.00 0.00 0.00 4.10
3444 4775 1.621992 TCAGAGAAGAGAGGTGCGTT 58.378 50.000 0.00 0.00 0.00 4.84
3445 4776 1.621992 TTCAGAGAAGAGAGGTGCGT 58.378 50.000 0.00 0.00 0.00 5.24
3496 4830 4.081142 TGTTCTGTTTTCCTGTCTGTCAGA 60.081 41.667 0.00 0.00 46.27 3.27
3567 4904 9.846248 GTATCATTTTGTTAAGAGCAACTCAAT 57.154 29.630 0.00 0.00 32.06 2.57
3583 4920 4.026393 TCGCCGTTGTATCGTATCATTTTG 60.026 41.667 0.00 0.00 0.00 2.44
3586 4923 3.358707 TCGCCGTTGTATCGTATCATT 57.641 42.857 0.00 0.00 0.00 2.57
3641 4978 4.507710 TGTCAGCCAAGCTCATTAAGTAG 58.492 43.478 0.00 0.00 36.40 2.57
3642 4979 4.551702 TGTCAGCCAAGCTCATTAAGTA 57.448 40.909 0.00 0.00 36.40 2.24
3646 4983 3.011818 CACATGTCAGCCAAGCTCATTA 58.988 45.455 0.00 0.00 36.40 1.90
3647 4984 1.816835 CACATGTCAGCCAAGCTCATT 59.183 47.619 0.00 0.00 36.40 2.57
3648 4985 1.271762 ACACATGTCAGCCAAGCTCAT 60.272 47.619 0.00 0.00 36.40 2.90
3729 5071 2.108168 CCACTAGGAATCTCCGGTTCA 58.892 52.381 0.00 0.00 42.75 3.18
3829 5171 9.212641 TGAAATTAGAAGACTGTTCAGAATCTG 57.787 33.333 3.38 3.38 0.00 2.90


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

AutoCloner maintained by Alex Coulton.