Multiple sequence alignment - TraesCS7D01G102700

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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 TraesCS7D01G102700 chr7D 100.000 5953 0 0 1 5953 62189974 62195926 0.000000e+00 10994.0
1 TraesCS7D01G102700 chr7D 96.242 2661 87 7 2095 4751 62938450 62941101 0.000000e+00 4348.0
2 TraesCS7D01G102700 chr7D 95.413 2071 67 10 1 2050 62936256 62938319 0.000000e+00 3273.0
3 TraesCS7D01G102700 chr7D 100.000 1656 0 0 6249 7904 62196222 62197877 0.000000e+00 3059.0
4 TraesCS7D01G102700 chr7D 95.997 1249 45 2 4709 5953 62941101 62942348 0.000000e+00 2025.0
5 TraesCS7D01G102700 chr7D 87.805 1189 133 9 4629 5812 62162390 62163571 0.000000e+00 1382.0
6 TraesCS7D01G102700 chr7D 94.236 694 34 5 7216 7904 62952639 62953331 0.000000e+00 1055.0
7 TraesCS7D01G102700 chr7D 85.749 814 103 12 4629 5436 62537385 62538191 0.000000e+00 848.0
8 TraesCS7D01G102700 chr7D 97.074 376 9 1 6342 6715 62942426 62942801 4.020000e-177 632.0
9 TraesCS7D01G102700 chr7D 88.852 305 28 3 5509 5812 62538181 62538480 3.480000e-98 370.0
10 TraesCS7D01G102700 chr7D 90.132 152 14 1 5662 5812 62465983 62466134 6.260000e-46 196.0
11 TraesCS7D01G102700 chr7D 95.349 86 3 1 2709 2794 62939161 62939245 1.380000e-27 135.0
12 TraesCS7D01G102700 chr7D 96.078 51 2 0 6249 6299 62942375 62942425 5.080000e-12 84.2
13 TraesCS7D01G102700 chr7A 95.592 2450 72 12 663 3091 65514955 65517389 0.000000e+00 3893.0
14 TraesCS7D01G102700 chr7A 96.170 2089 61 9 3134 5217 65517389 65519463 0.000000e+00 3397.0
15 TraesCS7D01G102700 chr7A 96.951 1115 30 4 6249 7361 65521639 65522751 0.000000e+00 1868.0
16 TraesCS7D01G102700 chr7A 98.476 722 11 0 5225 5946 65520904 65521625 0.000000e+00 1273.0
17 TraesCS7D01G102700 chr7A 85.512 1201 149 16 4629 5812 65494710 65495902 0.000000e+00 1230.0
18 TraesCS7D01G102700 chr7A 92.527 562 31 4 7354 7904 65522913 65523474 0.000000e+00 795.0
19 TraesCS7D01G102700 chr7A 95.571 429 19 0 235 663 65513170 65513598 0.000000e+00 688.0
20 TraesCS7D01G102700 chr7A 82.119 453 62 8 6705 7139 65496425 65496876 3.480000e-98 370.0
21 TraesCS7D01G102700 chr7A 92.672 232 17 0 5 236 65510855 65511086 1.270000e-87 335.0
22 TraesCS7D01G102700 chr2B 88.374 1359 119 21 3552 4878 570896185 570897536 0.000000e+00 1598.0
23 TraesCS7D01G102700 chr2B 79.984 1239 152 57 1612 2782 570894913 570896123 0.000000e+00 826.0
24 TraesCS7D01G102700 chr2B 84.035 570 73 10 5325 5891 570897627 570898181 4.200000e-147 532.0
25 TraesCS7D01G102700 chr2B 83.264 478 51 14 602 1078 570894003 570894452 5.710000e-111 412.0
26 TraesCS7D01G102700 chr2B 100.000 46 0 0 1453 1498 620274857 620274902 1.410000e-12 86.1
27 TraesCS7D01G102700 chr2B 95.122 41 2 0 7851 7891 775338960 775339000 1.840000e-06 65.8
28 TraesCS7D01G102700 chr2B 88.462 52 6 0 3295 3346 554291555 554291504 6.620000e-06 63.9
29 TraesCS7D01G102700 chr2A 87.452 1315 126 14 3604 4884 631538514 631539823 0.000000e+00 1478.0
30 TraesCS7D01G102700 chr2A 80.956 1234 149 49 1612 2782 631537213 631538423 0.000000e+00 898.0
31 TraesCS7D01G102700 chr2A 80.355 1013 168 21 3881 4879 631531349 631532344 0.000000e+00 739.0
32 TraesCS7D01G102700 chr2A 82.246 552 62 14 5342 5891 631539926 631540443 2.020000e-120 444.0
33 TraesCS7D01G102700 chr2A 78.328 646 101 31 5186 5812 631532379 631533004 1.610000e-101 381.0
34 TraesCS7D01G102700 chr2A 88.179 313 31 2 6265 6576 631540536 631540843 1.250000e-97 368.0
35 TraesCS7D01G102700 chr2A 91.810 232 19 0 2062 2293 631530497 631530728 2.750000e-84 324.0
36 TraesCS7D01G102700 chr2A 83.755 277 43 2 2390 2665 631530769 631531044 2.190000e-65 261.0
37 TraesCS7D01G102700 chr2A 77.872 235 43 8 4912 5139 30075381 30075613 3.850000e-28 137.0
38 TraesCS7D01G102700 chr2A 87.037 54 7 0 7851 7904 622736127 622736074 2.380000e-05 62.1
39 TraesCS7D01G102700 chr2D 89.417 1030 89 7 3875 4888 485991494 485992519 0.000000e+00 1280.0
40 TraesCS7D01G102700 chr2D 82.210 1231 131 50 1614 2782 485989921 485991125 0.000000e+00 979.0
41 TraesCS7D01G102700 chr2D 80.040 1012 168 24 3881 4879 485985193 485986183 0.000000e+00 719.0
42 TraesCS7D01G102700 chr2D 83.567 712 87 17 5179 5885 485992538 485993224 2.410000e-179 640.0
43 TraesCS7D01G102700 chr2D 84.375 480 46 14 591 1069 485989068 485989519 2.020000e-120 444.0
44 TraesCS7D01G102700 chr2D 78.889 630 105 19 5197 5812 485986229 485986844 1.240000e-107 401.0
45 TraesCS7D01G102700 chr2D 87.360 356 34 8 6251 6604 485993301 485993647 1.600000e-106 398.0
46 TraesCS7D01G102700 chr2D 82.000 450 60 13 6619 7052 485993633 485994077 5.830000e-96 363.0
47 TraesCS7D01G102700 chr2D 92.241 232 18 0 2062 2293 485984342 485984573 5.910000e-86 329.0
48 TraesCS7D01G102700 chr2D 87.215 219 27 1 6365 6583 485987095 485987312 1.700000e-61 248.0
49 TraesCS7D01G102700 chr2D 82.437 279 43 5 2378 2655 485984605 485984878 1.030000e-58 239.0
50 TraesCS7D01G102700 chr2D 78.723 235 40 10 4912 5139 27886782 27887013 1.780000e-31 148.0
51 TraesCS7D01G102700 chr2D 93.023 43 3 0 3294 3336 34682532 34682490 6.620000e-06 63.9
52 TraesCS7D01G102700 chr2D 91.304 46 3 1 3295 3339 473701184 473701139 2.380000e-05 62.1
53 TraesCS7D01G102700 chrUn 85.627 814 104 12 4629 5436 367446937 367447743 0.000000e+00 843.0
54 TraesCS7D01G102700 chrUn 88.525 305 29 3 5509 5812 367447733 367448032 1.620000e-96 364.0
55 TraesCS7D01G102700 chr4D 81.550 271 42 5 2954 3224 88146045 88146307 4.800000e-52 217.0
56 TraesCS7D01G102700 chr4B 80.903 288 39 10 2944 3231 124920031 124920302 6.210000e-51 213.0
57 TraesCS7D01G102700 chr5B 91.489 94 8 0 3091 3184 429072291 429072384 6.440000e-26 130.0
58 TraesCS7D01G102700 chr5B 94.340 53 1 2 1445 1497 509175553 509175603 6.570000e-11 80.5
59 TraesCS7D01G102700 chr7B 81.250 128 19 5 4923 5047 742664230 742664355 1.820000e-16 99.0
60 TraesCS7D01G102700 chr1D 83.019 106 18 0 4025 4130 203917219 203917114 6.530000e-16 97.1
61 TraesCS7D01G102700 chr1B 83.019 106 18 0 4025 4130 298163816 298163711 6.530000e-16 97.1
62 TraesCS7D01G102700 chr1B 89.394 66 2 3 1444 1509 17017426 17017366 2.360000e-10 78.7
63 TraesCS7D01G102700 chr6D 97.959 49 1 0 1450 1498 9346285 9346237 1.410000e-12 86.1
64 TraesCS7D01G102700 chr6D 91.379 58 3 2 1441 1498 304279402 304279457 2.360000e-10 78.7
65 TraesCS7D01G102700 chr1A 95.745 47 2 0 1449 1495 13348825 13348871 8.510000e-10 76.8
66 TraesCS7D01G102700 chr1A 95.745 47 2 0 1449 1495 13571029 13571075 8.510000e-10 76.8


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 TraesCS7D01G102700 chr7D 62189974 62197877 7903 False 7026.500000 10994 100.000000 1 7904 2 chr7D.!!$F4 7903
1 TraesCS7D01G102700 chr7D 62936256 62942801 6545 False 1749.533333 4348 96.025500 1 6715 6 chr7D.!!$F6 6714
2 TraesCS7D01G102700 chr7D 62162390 62163571 1181 False 1382.000000 1382 87.805000 4629 5812 1 chr7D.!!$F1 1183
3 TraesCS7D01G102700 chr7D 62952639 62953331 692 False 1055.000000 1055 94.236000 7216 7904 1 chr7D.!!$F3 688
4 TraesCS7D01G102700 chr7D 62537385 62538480 1095 False 609.000000 848 87.300500 4629 5812 2 chr7D.!!$F5 1183
5 TraesCS7D01G102700 chr7A 65510855 65523474 12619 False 1749.857143 3893 95.422714 5 7904 7 chr7A.!!$F2 7899
6 TraesCS7D01G102700 chr7A 65494710 65496876 2166 False 800.000000 1230 83.815500 4629 7139 2 chr7A.!!$F1 2510
7 TraesCS7D01G102700 chr2B 570894003 570898181 4178 False 842.000000 1598 83.914250 602 5891 4 chr2B.!!$F3 5289
8 TraesCS7D01G102700 chr2A 631537213 631540843 3630 False 797.000000 1478 84.708250 1612 6576 4 chr2A.!!$F3 4964
9 TraesCS7D01G102700 chr2A 631530497 631533004 2507 False 426.250000 739 83.562000 2062 5812 4 chr2A.!!$F2 3750
10 TraesCS7D01G102700 chr2D 485984342 485994077 9735 False 549.090909 1280 84.522818 591 7052 11 chr2D.!!$F2 6461
11 TraesCS7D01G102700 chrUn 367446937 367448032 1095 False 603.500000 843 87.076000 4629 5812 2 chrUn.!!$F1 1183

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
236 237 0.916358 AGTACCAGCCTGGCTCCAAT 60.916 55.000 20.49 6.98 42.67 3.16 F
632 4769 5.009210 TCACTTAAGTAACACAAATGCCACC 59.991 40.000 8.04 0.00 0.00 4.61 F
2119 7850 0.986019 ACAGTGTGGTCACCAAGGGA 60.986 55.000 0.00 0.00 44.83 4.20 F
2704 8470 1.081242 GATGCACAACGCCACCAAG 60.081 57.895 0.00 0.00 41.33 3.61 F
3452 9239 0.323999 TGCCATGCTTGCTGAAGGAT 60.324 50.000 0.00 0.00 40.66 3.24 F
4482 10358 0.659427 CGCATATGACCACCTTGCAG 59.341 55.000 6.97 0.00 32.94 4.41 F
4833 10756 2.303890 AGGCAATATCAGATGCGGATCA 59.696 45.455 19.67 0.00 43.47 2.92 F
5603 12980 2.653366 AGAGAGGTGTCCAGGTACCTAA 59.347 50.000 15.80 2.68 46.92 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 6632 2.144482 AACGTCACGTCCTACCTTTG 57.856 50.000 1.67 0.00 39.99 2.77 R
2514 8280 2.082366 CGTGAAGCAACGCAATGGC 61.082 57.895 0.00 0.00 36.65 4.40 R
3375 9158 0.324614 TGCTCGCTGAAGGGAATTGA 59.675 50.000 0.00 0.00 36.54 2.57 R
4299 10175 3.777522 GGAGAGAATGATACCTATGGGGG 59.222 52.174 0.00 0.00 40.03 5.40 R
4833 10756 1.494721 TGAGCACTTTGACCCCTCTTT 59.505 47.619 0.00 0.00 0.00 2.52 R
6430 13849 1.004679 GTGCCCCCATTTGTTGCTG 60.005 57.895 0.00 0.00 0.00 4.41 R
6536 13955 0.822532 CTGCATTGCCTCTGGGATCC 60.823 60.000 1.92 1.92 33.58 3.36 R
7409 15025 0.824182 CTAGATCGGAGTTCGGGGCT 60.824 60.000 0.00 0.00 39.77 5.19 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
19 20 3.214123 CGAGGGCCGGACACGATA 61.214 66.667 19.05 0.00 44.60 2.92
153 154 2.728318 CTGATATCGAACACGAGCATGG 59.272 50.000 0.00 0.00 39.38 3.66
210 211 4.909880 GCCAATTCTTGTTGTAGTTCGTTC 59.090 41.667 0.00 0.00 0.00 3.95
213 214 6.018262 CCAATTCTTGTTGTAGTTCGTTCTCA 60.018 38.462 0.00 0.00 0.00 3.27
236 237 0.916358 AGTACCAGCCTGGCTCCAAT 60.916 55.000 20.49 6.98 42.67 3.16
338 2424 6.487668 TCGGTCGTACTTATCCATGATTTAGA 59.512 38.462 0.00 0.00 0.00 2.10
406 2492 8.437742 CACGTTTATGTAAACCTTGTTACCTAG 58.562 37.037 9.39 0.00 41.81 3.02
632 4769 5.009210 TCACTTAAGTAACACAAATGCCACC 59.991 40.000 8.04 0.00 0.00 4.61
1101 6632 5.130477 TCTCTGATATTAGTTGTGGGTTCCC 59.870 44.000 0.12 0.12 0.00 3.97
1254 6848 1.467342 GTAATGTCAAGTGGAACCGGC 59.533 52.381 0.00 0.00 37.80 6.13
1288 6891 1.008652 GCATGTTGCAGCGAACACA 60.009 52.632 11.20 1.64 44.26 3.72
1438 7044 4.891627 TGTTGCTTCAAGAAAACGATGA 57.108 36.364 0.00 0.00 0.00 2.92
1465 7071 3.666345 ACAGTAGTACTCCCTCCGATT 57.334 47.619 0.00 0.00 0.00 3.34
1543 7150 2.530701 AGGTACTCCCTCAGTGTCAAG 58.469 52.381 0.00 0.00 40.71 3.02
1570 7177 7.383687 TGTAAGACGGTATTTGAGTCTCAATT 58.616 34.615 15.95 14.36 43.60 2.32
1574 7181 9.449719 AAGACGGTATTTGAGTCTCAATTTAAT 57.550 29.630 15.95 9.05 43.60 1.40
1577 7184 7.827236 ACGGTATTTGAGTCTCAATTTAATCCA 59.173 33.333 15.95 0.00 36.11 3.41
1774 7392 5.593095 AGCAGCAATCAAATCATACAGATGT 59.407 36.000 0.00 0.00 36.96 3.06
1954 7599 2.028876 ACTTAAAGCCACGGCAACTTT 58.971 42.857 11.35 4.99 44.88 2.66
1955 7600 2.223711 ACTTAAAGCCACGGCAACTTTG 60.224 45.455 11.35 0.00 44.88 2.77
2053 7698 3.181455 TGATATTCTAACCATGCACCGCT 60.181 43.478 0.00 0.00 0.00 5.52
2119 7850 0.986019 ACAGTGTGGTCACCAAGGGA 60.986 55.000 0.00 0.00 44.83 4.20
2329 8060 7.758980 CACAGCCTGCTATATATTCACTTCTAG 59.241 40.741 0.00 0.00 0.00 2.43
2330 8061 7.453126 ACAGCCTGCTATATATTCACTTCTAGT 59.547 37.037 0.00 0.00 0.00 2.57
2331 8062 8.310382 CAGCCTGCTATATATTCACTTCTAGTT 58.690 37.037 0.00 0.00 0.00 2.24
2332 8063 8.310382 AGCCTGCTATATATTCACTTCTAGTTG 58.690 37.037 0.00 0.00 0.00 3.16
2333 8064 8.091449 GCCTGCTATATATTCACTTCTAGTTGT 58.909 37.037 0.00 0.00 0.00 3.32
2514 8280 2.289565 GGGAAACAAAGGGAGCTATCG 58.710 52.381 0.00 0.00 0.00 2.92
2515 8281 1.671328 GGAAACAAAGGGAGCTATCGC 59.329 52.381 0.00 0.00 38.64 4.58
2519 8285 1.212935 ACAAAGGGAGCTATCGCCATT 59.787 47.619 0.00 0.00 37.77 3.16
2692 8458 4.189231 AGAGGGTTAATACAACGATGCAC 58.811 43.478 0.00 0.00 0.00 4.57
2704 8470 1.081242 GATGCACAACGCCACCAAG 60.081 57.895 0.00 0.00 41.33 3.61
2771 8548 3.004734 AGTGGCATTAAGTTCACAAGTGC 59.995 43.478 0.00 0.00 33.01 4.40
2782 8559 5.431765 AGTTCACAAGTGCCTAGATTATGG 58.568 41.667 0.00 0.00 0.00 2.74
2911 8690 2.702592 TCGGGTTGAGTTCACAAGTT 57.297 45.000 0.00 0.00 0.00 2.66
2949 8728 7.060600 ACATTGTACACAATACAGATTCACG 57.939 36.000 7.25 0.00 44.10 4.35
3053 8835 1.134946 GCGGCAGCACTAAAAATCCAT 59.865 47.619 3.18 0.00 44.35 3.41
3147 8929 6.372381 AGCAAATCCAATGGCTAAAACAATTC 59.628 34.615 0.00 0.00 34.25 2.17
3172 8954 2.289382 TGACGTGGAAGCACACATGTAT 60.289 45.455 0.00 0.00 41.38 2.29
3375 9158 5.699001 TCGAATTACCGTATTGCAAGCATAT 59.301 36.000 4.94 0.00 0.00 1.78
3402 9189 1.741706 CCTTCAGCGAGCATGACAAAT 59.258 47.619 0.00 0.00 0.00 2.32
3403 9190 2.223203 CCTTCAGCGAGCATGACAAATC 60.223 50.000 0.00 0.00 0.00 2.17
3405 9192 1.065926 TCAGCGAGCATGACAAATCCT 60.066 47.619 0.00 0.00 0.00 3.24
3406 9193 1.063616 CAGCGAGCATGACAAATCCTG 59.936 52.381 0.00 0.00 0.00 3.86
3452 9239 0.323999 TGCCATGCTTGCTGAAGGAT 60.324 50.000 0.00 0.00 40.66 3.24
3483 9270 2.210961 TCGTGTCACGTAATTTGCCAA 58.789 42.857 23.82 0.00 43.14 4.52
3591 9378 5.165911 CATCTGTACATGCATCAAAGTCC 57.834 43.478 0.00 0.00 0.00 3.85
3627 9417 8.682936 AGTTACAATATCCATTCTGATTCCAC 57.317 34.615 0.00 0.00 0.00 4.02
3866 9662 9.458727 AGCATCTTGATTTGGTATATATGAAGG 57.541 33.333 0.00 0.00 0.00 3.46
4020 9831 3.270877 GTGTTGTCCTATACCTGGCTTG 58.729 50.000 0.00 0.00 0.00 4.01
4166 9990 3.855689 ACCTTGCAATCATGTTAGTGC 57.144 42.857 0.00 0.28 40.73 4.40
4401 10277 2.687425 CAACACCATGGACAAGTCAACA 59.313 45.455 21.47 0.00 0.00 3.33
4408 10284 1.754803 TGGACAAGTCAACAGACGAGT 59.245 47.619 2.29 0.00 37.36 4.18
4482 10358 0.659427 CGCATATGACCACCTTGCAG 59.341 55.000 6.97 0.00 32.94 4.41
4593 10469 3.650461 TGGCATGGCTATCAATGGTACTA 59.350 43.478 21.08 0.00 0.00 1.82
4666 10542 3.728076 AGATCATGATGCAAACATGGC 57.272 42.857 25.84 20.34 45.92 4.40
4798 10721 3.086493 AGGGAGAGGGAATCCATCAAT 57.914 47.619 16.75 0.00 38.70 2.57
4832 10755 2.676839 CAGGCAATATCAGATGCGGATC 59.323 50.000 9.16 9.16 43.47 3.36
4833 10756 2.303890 AGGCAATATCAGATGCGGATCA 59.696 45.455 19.67 0.00 43.47 2.92
4888 10820 5.273674 TCAATCAGGCATGTTGACAAAAA 57.726 34.783 10.79 0.00 0.00 1.94
4923 10855 4.030216 ACCACCACCTTTTTCACTTTGAT 58.970 39.130 0.00 0.00 0.00 2.57
5175 11113 5.123502 TGAAGTTAAAACCACGTGCTAAACA 59.876 36.000 10.91 4.10 0.00 2.83
5217 11155 4.307432 CACGTGACACCTAACTTCTGATT 58.693 43.478 10.90 0.00 0.00 2.57
5603 12980 2.653366 AGAGAGGTGTCCAGGTACCTAA 59.347 50.000 15.80 2.68 46.92 2.69
6277 13683 6.380095 ACGGAAAACAGTAGCAAACATTAA 57.620 33.333 0.00 0.00 0.00 1.40
6293 13699 8.616076 GCAAACATTAAGCTATAGTGTCATCTT 58.384 33.333 0.84 0.00 0.00 2.40
6340 13747 6.169557 TGTAAACCCATGTAGCTACCATAG 57.830 41.667 21.01 10.00 0.00 2.23
6536 13955 2.286872 CTTGAGTAGCCCTGCAATGAG 58.713 52.381 0.00 0.00 0.00 2.90
6866 14293 3.411446 TGATGGACATCGAGCAAGTTTT 58.589 40.909 7.70 0.00 40.63 2.43
6943 14370 6.697395 TGAATCCTCCCATATATGTTACACG 58.303 40.000 11.73 0.00 0.00 4.49
7067 14514 9.722056 GGTATCAATAGCAAAAACTTATGAGTG 57.278 33.333 0.00 0.00 35.91 3.51
7141 14588 6.769822 ACCCATTATCAGTGACATTCAGATTC 59.230 38.462 0.00 0.00 0.00 2.52
7147 14594 5.541845 TCAGTGACATTCAGATTCGAACTT 58.458 37.500 0.00 0.00 0.00 2.66
7167 14614 6.484364 ACTTTAAATGGCCATGGAATAAGG 57.516 37.500 21.63 17.47 0.00 2.69
7378 14994 6.748198 GTCGAGATTAGACACTACTGGAAAAG 59.252 42.308 0.00 0.00 38.42 2.27
7440 15056 3.005554 TCCGATCTAGAACGTTCGACTT 58.994 45.455 21.87 7.78 33.59 3.01
7513 15129 5.179368 TCACCGAACTCAAATCAATCTCAAC 59.821 40.000 0.00 0.00 0.00 3.18
7530 15146 5.208121 TCTCAACTTTTCTCCCCATTTGTT 58.792 37.500 0.00 0.00 0.00 2.83
7679 15303 0.250467 AGCTCCTGTTGTGCATCGTT 60.250 50.000 0.00 0.00 35.92 3.85
7712 15336 2.741055 GGCTCCTCTCCTGCTTCCC 61.741 68.421 0.00 0.00 0.00 3.97
7847 15474 6.822667 AATTGCTCACATACACAAGAATCA 57.177 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.403225 CTGCGTGTGTATCGTGTCCG 61.403 60.000 0.00 0.00 0.00 4.79
19 20 1.067776 GCTTCTACCTACTGCGTGTGT 60.068 52.381 0.00 0.00 0.00 3.72
153 154 2.184579 GGCCACTACTGGACTCGC 59.815 66.667 0.00 0.00 43.43 5.03
210 211 1.745141 GCCAGGCTGGTACTCAATGAG 60.745 57.143 32.80 8.98 40.46 2.90
213 214 0.543749 GAGCCAGGCTGGTACTCAAT 59.456 55.000 32.80 11.66 39.88 2.57
236 237 2.987821 TCGATGTATTGAAAACGCGACA 59.012 40.909 15.93 3.83 0.00 4.35
406 2492 6.355747 AGAGGATGTTTGGATTGAGAGATTC 58.644 40.000 0.00 0.00 0.00 2.52
443 2529 8.558700 AGGAAAACAAATTATGTGATTTTGTGC 58.441 29.630 1.47 0.00 42.99 4.57
632 4769 6.454583 GCATAAAACATGTTGTTGCTATGCTG 60.455 38.462 24.64 9.96 46.34 4.41
1101 6632 2.144482 AACGTCACGTCCTACCTTTG 57.856 50.000 1.67 0.00 39.99 2.77
1438 7044 5.184671 CGGAGGGAGTACTACTGTTTACTTT 59.815 44.000 4.77 0.00 0.00 2.66
1465 7071 7.556733 ACTAAAACCACGACACTTATTTTGA 57.443 32.000 0.00 0.00 0.00 2.69
1543 7150 6.561614 TGAGACTCAAATACCGTCTTACATC 58.438 40.000 1.64 0.00 38.07 3.06
1954 7599 4.391830 GCAATTAGATCTGTGACCGTTTCA 59.608 41.667 5.18 0.00 0.00 2.69
1955 7600 4.201822 GGCAATTAGATCTGTGACCGTTTC 60.202 45.833 5.18 0.00 0.00 2.78
2053 7698 4.344102 GCCAAGACCAGGTACTACATATGA 59.656 45.833 10.38 0.00 36.02 2.15
2119 7850 3.136641 ACTAGGTTCATGTCTCCCCAT 57.863 47.619 0.00 0.00 0.00 4.00
2329 8060 7.667043 TCAGGTAATTTGAGTGTGATACAAC 57.333 36.000 0.00 0.00 0.00 3.32
2330 8061 8.684386 TTTCAGGTAATTTGAGTGTGATACAA 57.316 30.769 0.00 0.00 0.00 2.41
2331 8062 8.862325 ATTTCAGGTAATTTGAGTGTGATACA 57.138 30.769 0.00 0.00 0.00 2.29
2332 8063 9.167311 AGATTTCAGGTAATTTGAGTGTGATAC 57.833 33.333 0.00 0.00 0.00 2.24
2334 8065 9.739276 TTAGATTTCAGGTAATTTGAGTGTGAT 57.261 29.630 0.00 0.00 0.00 3.06
2514 8280 2.082366 CGTGAAGCAACGCAATGGC 61.082 57.895 0.00 0.00 36.65 4.40
2515 8281 4.135570 CGTGAAGCAACGCAATGG 57.864 55.556 0.00 0.00 36.65 3.16
2665 8431 5.272283 TCGTTGTATTAACCCTCTCATCC 57.728 43.478 0.00 0.00 0.00 3.51
2692 8458 2.292016 TGTGAATAACTTGGTGGCGTTG 59.708 45.455 0.00 0.00 0.00 4.10
2704 8470 4.851558 GTGCGATCCTTGTTTGTGAATAAC 59.148 41.667 0.00 0.00 0.00 1.89
2771 8548 3.181454 ACCCGAAGCAACCATAATCTAGG 60.181 47.826 0.00 0.00 0.00 3.02
2782 8559 3.907894 TGATTTGTTACCCGAAGCAAC 57.092 42.857 0.00 0.00 29.95 4.17
2926 8705 7.060600 ACGTGAATCTGTATTGTGTACAATG 57.939 36.000 17.94 4.35 45.34 2.82
3012 8793 6.267817 CCGCATTTCATTCATGACATAGTTT 58.732 36.000 0.00 0.00 36.36 2.66
3086 8868 2.936498 ACATCCGTCCGATTTGAACATC 59.064 45.455 0.00 0.00 0.00 3.06
3147 8929 1.374125 TGTGCTTCCACGTCATCCG 60.374 57.895 0.00 0.00 45.04 4.18
3226 9008 6.988622 ATTGGTCAAATTGGTTGCAATATG 57.011 33.333 0.59 0.00 37.13 1.78
3375 9158 0.324614 TGCTCGCTGAAGGGAATTGA 59.675 50.000 0.00 0.00 36.54 2.57
3452 9239 0.391130 GTGACACGAGCCTGGCAATA 60.391 55.000 22.65 0.00 28.17 1.90
3591 9378 4.334481 GGATATTGTAACTCCAACCAACGG 59.666 45.833 0.00 0.00 0.00 4.44
4020 9831 8.015658 GTCCCATATTATTTATGAAGTCGTTGC 58.984 37.037 0.00 0.00 0.00 4.17
4166 9990 7.560368 AGAACATAATGGACCTAAAGTCTCAG 58.440 38.462 0.00 0.00 45.54 3.35
4299 10175 3.777522 GGAGAGAATGATACCTATGGGGG 59.222 52.174 0.00 0.00 40.03 5.40
4401 10277 4.762765 AGTGTTCTCTCATACAACTCGTCT 59.237 41.667 0.00 0.00 0.00 4.18
4408 10284 6.358974 TCCAATCAGTGTTCTCTCATACAA 57.641 37.500 0.00 0.00 0.00 2.41
4482 10358 5.290386 CCAACCCTTAGATGATAAGTCGAC 58.710 45.833 7.70 7.70 0.00 4.20
4593 10469 4.404640 CAGATGATCCATAAACCCATGCT 58.595 43.478 0.00 0.00 0.00 3.79
4666 10542 6.051717 CCTGGAAGTTGTATCTTGGTATCAG 58.948 44.000 0.00 0.00 0.00 2.90
4798 10721 6.600388 TGATATTGCCTGCTCAATTAACCTA 58.400 36.000 5.11 0.00 37.75 3.08
4832 10755 1.882623 GAGCACTTTGACCCCTCTTTG 59.117 52.381 0.00 0.00 0.00 2.77
4833 10756 1.494721 TGAGCACTTTGACCCCTCTTT 59.505 47.619 0.00 0.00 0.00 2.52
4888 10820 7.432148 AAAGGTGGTGGTTAAGAAAGAATTT 57.568 32.000 0.00 0.00 43.98 1.82
4889 10821 7.432148 AAAAGGTGGTGGTTAAGAAAGAATT 57.568 32.000 0.00 0.00 0.00 2.17
4890 10822 7.125053 TGAAAAAGGTGGTGGTTAAGAAAGAAT 59.875 33.333 0.00 0.00 0.00 2.40
5175 11113 5.171476 CGTGGAAGAATGTATGAAGAGTGT 58.829 41.667 0.00 0.00 0.00 3.55
5217 11155 5.599732 CATTTCTGAATGTTTTGTGACCCA 58.400 37.500 0.00 0.00 38.25 4.51
5603 12980 4.947388 TCAACAAAGTAGCAAGGTGAAAGT 59.053 37.500 0.00 0.00 0.00 2.66
5779 13177 7.092712 TGAGGTATCTCATCACTGGAGAATTTT 60.093 37.037 0.14 0.00 44.39 1.82
6277 13683 3.963374 TGCTGGAAGATGACACTATAGCT 59.037 43.478 0.00 0.00 34.07 3.32
6293 13699 4.574892 TCTAATCGTTGTCATTTGCTGGA 58.425 39.130 0.00 0.00 0.00 3.86
6340 13747 7.971183 ATCAGAGTGTTTCTTTTCTTCCTAC 57.029 36.000 0.00 0.00 32.41 3.18
6430 13849 1.004679 GTGCCCCCATTTGTTGCTG 60.005 57.895 0.00 0.00 0.00 4.41
6536 13955 0.822532 CTGCATTGCCTCTGGGATCC 60.823 60.000 1.92 1.92 33.58 3.36
6731 14156 7.690301 GCCAATTCTATTCATGAAGGGAGTAGA 60.690 40.741 14.54 12.12 33.45 2.59
6742 14167 6.704289 TCTTGGAAGCCAATTCTATTCATG 57.296 37.500 0.00 0.00 43.07 3.07
6943 14370 4.691860 AACACTGCAGCTCAACATTATC 57.308 40.909 15.27 0.00 0.00 1.75
7067 14514 4.227512 TGGCGATTCATACATTTCATGC 57.772 40.909 0.00 0.00 0.00 4.06
7141 14588 4.448537 TTCCATGGCCATTTAAAGTTCG 57.551 40.909 17.92 0.57 0.00 3.95
7147 14594 4.293494 TGCCTTATTCCATGGCCATTTAA 58.707 39.130 17.92 13.78 45.00 1.52
7167 14614 5.048504 TGTGTTGGATCTCTCTTTGAATTGC 60.049 40.000 0.00 0.00 0.00 3.56
7378 14994 3.445857 GAATCTGGTAGGCGTAGTTGAC 58.554 50.000 0.00 0.00 0.00 3.18
7409 15025 0.824182 CTAGATCGGAGTTCGGGGCT 60.824 60.000 0.00 0.00 39.77 5.19
7462 15078 2.607635 GCAGCGATTTCCAATCGAACTA 59.392 45.455 20.27 0.00 43.59 2.24
7471 15087 1.077787 AATCGGGCAGCGATTTCCA 60.078 52.632 5.69 0.00 32.91 3.53
7513 15129 6.523840 TGAAATCAACAAATGGGGAGAAAAG 58.476 36.000 0.00 0.00 0.00 2.27
7563 15180 6.438259 GCGTCTAGCCTGTAATAGATGATA 57.562 41.667 5.79 0.00 37.26 2.15
7744 15368 1.006813 TATTGCACACCCCATCCCTT 58.993 50.000 0.00 0.00 0.00 3.95
7825 15452 6.432162 ACTTGATTCTTGTGTATGTGAGCAAT 59.568 34.615 0.00 0.00 0.00 3.56
7827 15454 5.308014 ACTTGATTCTTGTGTATGTGAGCA 58.692 37.500 0.00 0.00 0.00 4.26
7847 15474 3.873801 GCATGTGTTCATAGGGGTGACTT 60.874 47.826 0.00 0.00 32.47 3.01


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

AutoCloner maintained by Alex Coulton.