Multiple sequence alignment - TraesCS1D01G202600

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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 TraesCS1D01G202600 chr1D 100.000 9593 0 0 1 9593 285932926 285942518 0 17716
1 TraesCS1D01G202600 chr1D 95.411 9675 351 46 1 9593 78757114 78747451 0 15320
2 TraesCS1D01G202600 chr1D 95.070 8113 305 42 1320 9356 88014024 88005931 0 12678
3 TraesCS1D01G202600 chr1D 94.551 6332 246 47 1 6263 296766285 296772586 0 9690
4 TraesCS1D01G202600 chr2D 94.205 9457 416 62 1 9356 259250047 259240622 0 14307
5 TraesCS1D01G202600 chr2D 90.395 1062 76 13 5312 6356 184180283 184179231 0 1373
6 TraesCS1D01G202600 chr3D 95.242 9037 316 35 400 9356 254425613 254416611 0 14201
7 TraesCS1D01G202600 chr3D 94.660 4307 159 33 1932 6179 353280900 353285194 0 6613
8 TraesCS1D01G202600 chr2A 93.947 7748 344 63 1932 9593 433263300 433271008 0 11594
9 TraesCS1D01G202600 chr2A 92.630 7218 426 46 2462 9593 369287157 369294354 0 10285
10 TraesCS1D01G202600 chr2A 92.640 7228 384 61 2462 9593 442318065 442325240 0 10264
11 TraesCS1D01G202600 chr2A 93.355 4590 240 24 4098 8633 377567040 377571618 0 6726
12 TraesCS1D01G202600 chr2A 92.442 3427 192 32 2462 5826 367432668 367429247 0 4831
13 TraesCS1D01G202600 chr3A 93.811 7740 370 46 1935 9593 204312980 204305269 0 11538
14 TraesCS1D01G202600 chr3A 91.943 1055 57 20 5310 6343 698773998 698775045 0 1452
15 TraesCS1D01G202600 chr7A 93.179 7213 380 62 2462 9593 421605885 421613066 0 10491
16 TraesCS1D01G202600 chr7A 89.179 4131 327 44 5312 9356 315496613 315492517 0 5042
17 TraesCS1D01G202600 chr5A 93.090 7221 386 54 2462 9593 171373203 171366007 0 10466
18 TraesCS1D01G202600 chr5A 90.067 5054 387 55 1 4970 141899825 141904847 0 6445
19 TraesCS1D01G202600 chr5A 89.859 5049 394 60 1 4970 465651852 465656861 0 6379
20 TraesCS1D01G202600 chr5D 94.921 6418 239 42 1 6347 108672370 108665969 0 9965
21 TraesCS1D01G202600 chr4D 94.175 6249 273 48 1 6179 79273737 79267510 0 9439
22 TraesCS1D01G202600 chr4D 95.312 4309 139 35 2013 6263 426270356 426266053 0 6780
23 TraesCS1D01G202600 chr4D 96.467 3510 104 10 6095 9593 426266306 426262806 0 5777
24 TraesCS1D01G202600 chr6D 95.347 4750 172 21 1 4706 428024435 428019691 0 7502
25 TraesCS1D01G202600 chr6D 94.570 3775 133 18 1914 5621 249245627 249249396 0 5770
26 TraesCS1D01G202600 chr6D 95.973 3427 117 13 6178 9593 249264292 249267708 0 5544
27 TraesCS1D01G202600 chr4B 91.710 5380 330 51 1 5306 379341248 379335911 0 7358
28 TraesCS1D01G202600 chr7B 91.470 5381 347 50 1 5306 665787412 665792755 0 7291
29 TraesCS1D01G202600 chr2B 91.445 5377 350 47 1 5306 497409130 497414467 0 7280
30 TraesCS1D01G202600 chr7D 95.724 4490 138 24 2157 6593 243735064 243730576 0 7179
31 TraesCS1D01G202600 chr7D 95.849 3421 119 10 6178 9593 387292997 387296399 0 5509
32 TraesCS1D01G202600 chr1A 93.015 4481 245 33 2462 6881 277154040 277149567 0 6479
33 TraesCS1D01G202600 chr6A 94.136 4229 191 29 1935 6120 490228624 490224410 0 6383
34 TraesCS1D01G202600 chr6A 93.097 3694 209 28 5926 9593 118303633 118307306 0 5367
35 TraesCS1D01G202600 chr5B 89.431 4816 388 56 1 4742 358462962 358458194 0 5962
36 TraesCS1D01G202600 chr5B 90.223 3682 259 38 1 3626 160760377 160764013 0 4711
37 TraesCS1D01G202600 chr1B 91.701 3181 188 35 1 3136 330402004 330405153 0 4342
38 TraesCS1D01G202600 chr3B 91.437 2686 179 29 1 2658 99634861 99637523 0 3639


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 TraesCS1D01G202600 chr1D 285932926 285942518 9592 False 17716.0 17716 100.0000 1 9593 1 chr1D.!!$F1 9592
1 TraesCS1D01G202600 chr1D 78747451 78757114 9663 True 15320.0 15320 95.4110 1 9593 1 chr1D.!!$R1 9592
2 TraesCS1D01G202600 chr1D 88005931 88014024 8093 True 12678.0 12678 95.0700 1320 9356 1 chr1D.!!$R2 8036
3 TraesCS1D01G202600 chr1D 296766285 296772586 6301 False 9690.0 9690 94.5510 1 6263 1 chr1D.!!$F2 6262
4 TraesCS1D01G202600 chr2D 259240622 259250047 9425 True 14307.0 14307 94.2050 1 9356 1 chr2D.!!$R2 9355
5 TraesCS1D01G202600 chr2D 184179231 184180283 1052 True 1373.0 1373 90.3950 5312 6356 1 chr2D.!!$R1 1044
6 TraesCS1D01G202600 chr3D 254416611 254425613 9002 True 14201.0 14201 95.2420 400 9356 1 chr3D.!!$R1 8956
7 TraesCS1D01G202600 chr3D 353280900 353285194 4294 False 6613.0 6613 94.6600 1932 6179 1 chr3D.!!$F1 4247
8 TraesCS1D01G202600 chr2A 433263300 433271008 7708 False 11594.0 11594 93.9470 1932 9593 1 chr2A.!!$F3 7661
9 TraesCS1D01G202600 chr2A 369287157 369294354 7197 False 10285.0 10285 92.6300 2462 9593 1 chr2A.!!$F1 7131
10 TraesCS1D01G202600 chr2A 442318065 442325240 7175 False 10264.0 10264 92.6400 2462 9593 1 chr2A.!!$F4 7131
11 TraesCS1D01G202600 chr2A 377567040 377571618 4578 False 6726.0 6726 93.3550 4098 8633 1 chr2A.!!$F2 4535
12 TraesCS1D01G202600 chr2A 367429247 367432668 3421 True 4831.0 4831 92.4420 2462 5826 1 chr2A.!!$R1 3364
13 TraesCS1D01G202600 chr3A 204305269 204312980 7711 True 11538.0 11538 93.8110 1935 9593 1 chr3A.!!$R1 7658
14 TraesCS1D01G202600 chr3A 698773998 698775045 1047 False 1452.0 1452 91.9430 5310 6343 1 chr3A.!!$F1 1033
15 TraesCS1D01G202600 chr7A 421605885 421613066 7181 False 10491.0 10491 93.1790 2462 9593 1 chr7A.!!$F1 7131
16 TraesCS1D01G202600 chr7A 315492517 315496613 4096 True 5042.0 5042 89.1790 5312 9356 1 chr7A.!!$R1 4044
17 TraesCS1D01G202600 chr5A 171366007 171373203 7196 True 10466.0 10466 93.0900 2462 9593 1 chr5A.!!$R1 7131
18 TraesCS1D01G202600 chr5A 141899825 141904847 5022 False 6445.0 6445 90.0670 1 4970 1 chr5A.!!$F1 4969
19 TraesCS1D01G202600 chr5A 465651852 465656861 5009 False 6379.0 6379 89.8590 1 4970 1 chr5A.!!$F2 4969
20 TraesCS1D01G202600 chr5D 108665969 108672370 6401 True 9965.0 9965 94.9210 1 6347 1 chr5D.!!$R1 6346
21 TraesCS1D01G202600 chr4D 79267510 79273737 6227 True 9439.0 9439 94.1750 1 6179 1 chr4D.!!$R1 6178
22 TraesCS1D01G202600 chr4D 426262806 426270356 7550 True 6278.5 6780 95.8895 2013 9593 2 chr4D.!!$R2 7580
23 TraesCS1D01G202600 chr6D 428019691 428024435 4744 True 7502.0 7502 95.3470 1 4706 1 chr6D.!!$R1 4705
24 TraesCS1D01G202600 chr6D 249245627 249249396 3769 False 5770.0 5770 94.5700 1914 5621 1 chr6D.!!$F1 3707
25 TraesCS1D01G202600 chr6D 249264292 249267708 3416 False 5544.0 5544 95.9730 6178 9593 1 chr6D.!!$F2 3415
26 TraesCS1D01G202600 chr4B 379335911 379341248 5337 True 7358.0 7358 91.7100 1 5306 1 chr4B.!!$R1 5305
27 TraesCS1D01G202600 chr7B 665787412 665792755 5343 False 7291.0 7291 91.4700 1 5306 1 chr7B.!!$F1 5305
28 TraesCS1D01G202600 chr2B 497409130 497414467 5337 False 7280.0 7280 91.4450 1 5306 1 chr2B.!!$F1 5305
29 TraesCS1D01G202600 chr7D 243730576 243735064 4488 True 7179.0 7179 95.7240 2157 6593 1 chr7D.!!$R1 4436
30 TraesCS1D01G202600 chr7D 387292997 387296399 3402 False 5509.0 5509 95.8490 6178 9593 1 chr7D.!!$F1 3415
31 TraesCS1D01G202600 chr1A 277149567 277154040 4473 True 6479.0 6479 93.0150 2462 6881 1 chr1A.!!$R1 4419
32 TraesCS1D01G202600 chr6A 490224410 490228624 4214 True 6383.0 6383 94.1360 1935 6120 1 chr6A.!!$R1 4185
33 TraesCS1D01G202600 chr6A 118303633 118307306 3673 False 5367.0 5367 93.0970 5926 9593 1 chr6A.!!$F1 3667
34 TraesCS1D01G202600 chr5B 358458194 358462962 4768 True 5962.0 5962 89.4310 1 4742 1 chr5B.!!$R1 4741
35 TraesCS1D01G202600 chr5B 160760377 160764013 3636 False 4711.0 4711 90.2230 1 3626 1 chr5B.!!$F1 3625
36 TraesCS1D01G202600 chr1B 330402004 330405153 3149 False 4342.0 4342 91.7010 1 3136 1 chr1B.!!$F1 3135
37 TraesCS1D01G202600 chr3B 99634861 99637523 2662 False 3639.0 3639 91.4370 1 2658 1 chr3B.!!$F1 2657

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
431 437 0.108138 ACACGCTGACCTTCTATGGC 60.108 55.000 0.00 0.0 0.00 4.40 F
1346 1358 1.005215 CTCAAGCACAAAGGGGAGGAT 59.995 52.381 0.00 0.0 0.00 3.24 F
1774 1822 1.896220 TGAAGATGACAGTGTTGGGC 58.104 50.000 0.00 0.0 0.00 5.36 F
1949 2006 3.803715 GCTTGTAGTCTCAGTTGCCTCAA 60.804 47.826 0.00 0.0 0.00 3.02 F
2807 2928 4.587891 AGTACCACAGTAGAGGAGTACAC 58.412 47.826 0.00 0.0 34.03 2.90 F
3196 3359 0.184451 ATTGCCGCTTCCATCTCCAT 59.816 50.000 0.00 0.0 0.00 3.41 F
4455 4664 2.689983 CCACCCATTCTACAAAGGCATC 59.310 50.000 0.00 0.0 0.00 3.91 F
4918 5129 0.106769 TGGAACTTTGTGGCTGCTCA 60.107 50.000 0.00 0.0 0.00 4.26 F
5626 5885 3.228017 GAGCCCCCTCGACTAGCC 61.228 72.222 0.00 0.0 0.00 3.93 F
7173 8062 0.250513 GAGCCATCGGACAAGAACCT 59.749 55.000 0.00 0.0 0.00 3.50 F
8323 9356 0.108992 CATGCAGCGCAAGTGGAAAT 60.109 50.000 11.47 0.0 43.62 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1818 0.181587 TTTCAGTTTCCTCGTGCCCA 59.818 50.000 0.00 0.00 0.00 5.36 R
2152 2213 1.135972 GGTCGACAGTAGCGTTTCGTA 60.136 52.381 18.91 0.00 33.20 3.43 R
2807 2928 1.683011 GGGTTGGTGATGATGGAGGTG 60.683 57.143 0.00 0.00 0.00 4.00 R
2918 3040 1.737793 CTAAATCCCACTTGCACGTCC 59.262 52.381 0.00 0.00 0.00 4.79 R
4276 4460 0.321919 ACGTCTCATGGTGCAGCAAT 60.322 50.000 24.18 8.80 0.00 3.56 R
4502 4711 2.674380 GGTTGTCTGGCAGCTGGG 60.674 66.667 17.12 0.00 0.00 4.45 R
5877 6136 1.003118 TCCGTGGTGCAGAGCTAAATT 59.997 47.619 0.00 0.00 0.00 1.82 R
6633 7500 0.472925 TCAGTGCCCTGGGAGTTGTA 60.473 55.000 19.27 0.00 39.31 2.41 R
7419 8314 0.671781 CACCAAGCAGAGTTCCTCGG 60.672 60.000 0.00 0.00 35.36 4.63 R
8444 9483 0.321919 GATGAGGTTGTCTGGCAGCA 60.322 55.000 10.34 8.61 0.00 4.41 R
9147 10240 3.713288 TGTTCAAGTGTACCAGAACTCG 58.287 45.455 14.26 0.00 40.62 4.18 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
92 93 1.000394 TGGAACGAGCGTGAGAAATGA 60.000 47.619 0.00 0.00 0.00 2.57
99 100 5.109210 ACGAGCGTGAGAAATGAATATCAA 58.891 37.500 0.00 0.00 0.00 2.57
182 183 7.441836 TGAACTATGTGCTCAAGAAGAACTTA 58.558 34.615 0.00 0.00 37.03 2.24
194 195 8.466617 TCAAGAAGAACTTAGTAAGTGAGAGT 57.533 34.615 16.22 0.00 41.91 3.24
231 232 1.429930 TGTCAGCCAGGTAAACTCCA 58.570 50.000 0.00 0.00 0.00 3.86
280 281 4.657814 ACCAAGAGACAATGGGTAACAT 57.342 40.909 0.00 0.00 43.07 2.71
431 437 0.108138 ACACGCTGACCTTCTATGGC 60.108 55.000 0.00 0.00 0.00 4.40
662 668 1.915078 GCAGGCTATGGGACCACACT 61.915 60.000 0.00 0.00 0.00 3.55
663 669 1.496060 CAGGCTATGGGACCACACTA 58.504 55.000 0.00 0.00 0.00 2.74
821 833 2.025037 TCCAGACAATTAAGGCTGCCAT 60.025 45.455 22.65 12.21 0.00 4.40
844 856 5.847304 TCATTCCAGAGAAATACATCCTCG 58.153 41.667 0.00 0.00 35.09 4.63
848 860 3.580458 CCAGAGAAATACATCCTCGGGAT 59.420 47.826 0.00 0.05 44.21 3.85
900 912 5.541845 ACATTCGACAGAAATGACTTGAGA 58.458 37.500 1.16 0.00 40.15 3.27
1080 1092 1.204704 GCTAAAAATGGAGGTGTGGCC 59.795 52.381 0.00 0.00 37.58 5.36
1249 1261 3.189618 TGCGAGATCATGAGCTTGATT 57.810 42.857 28.52 0.46 36.48 2.57
1331 1343 7.557719 AGTGATTAAACCACCCATATTCTCAAG 59.442 37.037 7.49 0.00 35.23 3.02
1346 1358 1.005215 CTCAAGCACAAAGGGGAGGAT 59.995 52.381 0.00 0.00 0.00 3.24
1347 1359 2.239654 CTCAAGCACAAAGGGGAGGATA 59.760 50.000 0.00 0.00 0.00 2.59
1469 1499 3.380486 CAGATTCTGCAATGTCGTGAC 57.620 47.619 0.00 0.00 0.00 3.67
1717 1765 7.912056 TCAAATGAAGACGATGAAGAAGAAT 57.088 32.000 0.00 0.00 0.00 2.40
1730 1778 7.433719 CGATGAAGAAGAATAGTTTGACGAGAT 59.566 37.037 0.00 0.00 0.00 2.75
1750 1798 2.060326 TGACGACCAATCAGACGAAC 57.940 50.000 0.00 0.00 0.00 3.95
1752 1800 2.029380 TGACGACCAATCAGACGAACAT 60.029 45.455 0.00 0.00 0.00 2.71
1770 1818 6.650807 ACGAACATAATGAAGATGACAGTGTT 59.349 34.615 0.00 0.00 0.00 3.32
1774 1822 1.896220 TGAAGATGACAGTGTTGGGC 58.104 50.000 0.00 0.00 0.00 5.36
1949 2006 3.803715 GCTTGTAGTCTCAGTTGCCTCAA 60.804 47.826 0.00 0.00 0.00 3.02
2386 2474 6.964741 TTTGTACTGACGAAAAACACTACA 57.035 33.333 0.00 0.00 0.00 2.74
2777 2898 8.783093 TGGTAAGTTCAATTACACTTCAATCAG 58.217 33.333 5.00 0.00 37.38 2.90
2807 2928 4.587891 AGTACCACAGTAGAGGAGTACAC 58.412 47.826 0.00 0.00 34.03 2.90
3196 3359 0.184451 ATTGCCGCTTCCATCTCCAT 59.816 50.000 0.00 0.00 0.00 3.41
3855 4028 5.992217 AGTGTAGTTTCTGAACTTGATCCAC 59.008 40.000 0.00 0.00 43.48 4.02
3866 4039 6.688578 TGAACTTGATCCACTAGTGTAGTTC 58.311 40.000 25.57 25.57 40.18 3.01
3978 4153 7.923414 ATAAACTAAGGACTTGGTAAAGCAG 57.077 36.000 1.40 0.00 36.84 4.24
4276 4460 3.353836 GCCAAGCGCCTGAACGAA 61.354 61.111 7.79 0.00 34.06 3.85
4455 4664 2.689983 CCACCCATTCTACAAAGGCATC 59.310 50.000 0.00 0.00 0.00 3.91
4466 4675 4.574599 ACAAAGGCATCAAGAAGAACAC 57.425 40.909 0.00 0.00 0.00 3.32
4473 4682 3.316308 GCATCAAGAAGAACACCAACACT 59.684 43.478 0.00 0.00 0.00 3.55
4803 5012 9.562408 TGTCATGGTTGAACAAGTTTACTTATA 57.438 29.630 0.00 0.00 31.91 0.98
4825 5034 7.686438 ATATCATCAAGTACAGTGTTTTGCA 57.314 32.000 0.00 0.00 0.00 4.08
4918 5129 0.106769 TGGAACTTTGTGGCTGCTCA 60.107 50.000 0.00 0.00 0.00 4.26
5626 5885 3.228017 GAGCCCCCTCGACTAGCC 61.228 72.222 0.00 0.00 0.00 3.93
5971 6234 7.213678 ACAAGAGAACTTAATAGCCTATCTGC 58.786 38.462 0.00 0.00 34.70 4.26
6043 6391 9.515020 TCAACTACTAAAATGCAAAAAGTTCAG 57.485 29.630 0.00 0.00 0.00 3.02
6123 6473 9.900264 GTTCAACTACTAAAATGCAAAAAGTTG 57.100 29.630 14.24 14.24 42.33 3.16
6124 6474 9.862371 TTCAACTACTAAAATGCAAAAAGTTGA 57.138 25.926 16.99 16.99 45.76 3.18
6125 6475 9.862371 TCAACTACTAAAATGCAAAAAGTTGAA 57.138 25.926 17.89 8.31 44.97 2.69
6128 6478 9.646427 ACTACTAAAATGCAAAAAGTTGAAACA 57.354 25.926 0.00 0.00 36.83 2.83
6363 7216 3.252944 TGTACACACCTCAACGAACGATA 59.747 43.478 0.14 0.00 0.00 2.92
6538 7403 5.826601 TTACATTTCAGTTCACACAGCAA 57.173 34.783 0.00 0.00 0.00 3.91
6800 7670 1.271379 ACGTGCAAGTGGGATTTAGCT 60.271 47.619 3.91 0.00 0.00 3.32
6837 7709 3.198409 TGACAAGACAAGTCAGTGCAT 57.802 42.857 2.72 0.00 40.80 3.96
6912 7787 2.281070 ACTGAGCGGTTGCCACAG 60.281 61.111 9.39 9.39 45.35 3.66
6949 7831 4.980805 CCCACGACCACCACACCG 62.981 72.222 0.00 0.00 0.00 4.94
6975 7858 2.505557 GACGAACCGCCTACCACG 60.506 66.667 0.00 0.00 0.00 4.94
6985 7868 2.582436 CTACCACGCATCCCCGTT 59.418 61.111 0.00 0.00 39.83 4.44
7172 8061 1.084370 CGAGCCATCGGACAAGAACC 61.084 60.000 0.00 0.00 45.39 3.62
7173 8062 0.250513 GAGCCATCGGACAAGAACCT 59.749 55.000 0.00 0.00 0.00 3.50
7182 8071 1.149148 GACAAGAACCTCAACCTCGC 58.851 55.000 0.00 0.00 0.00 5.03
7220 8109 0.811915 AGAGAAGCGCGAGTACACAT 59.188 50.000 12.10 0.00 0.00 3.21
7234 8123 1.434188 ACACATGAACCCTCACAGGA 58.566 50.000 0.00 0.00 37.67 3.86
7293 8182 1.071471 CCAGCGAACCAGACAAGGT 59.929 57.895 0.00 0.00 45.91 3.50
7403 8298 1.451504 CCTCCATAGATGGCGGCAA 59.548 57.895 18.31 0.00 44.98 4.52
7458 8353 0.673333 TACCACATCGCAACAGCCAG 60.673 55.000 0.00 0.00 0.00 4.85
7706 8645 9.695526 CCAAATTAATTTCTGAACTTGATGTGA 57.304 29.630 10.53 0.00 0.00 3.58
8022 9045 8.964420 ACATGGTGTAGTTGAATTTAATTTCG 57.036 30.769 0.00 0.00 0.00 3.46
8323 9356 0.108992 CATGCAGCGCAAGTGGAAAT 60.109 50.000 11.47 0.00 43.62 2.17
8397 9430 1.153168 CCACCCATTCTACAGCGGG 60.153 63.158 0.00 0.00 44.88 6.13
8648 9696 5.358160 GCACTTCTGCCTGTCCTTAATATTT 59.642 40.000 0.00 0.00 37.45 1.40
8853 9936 7.703328 TGAAACTAGTCATGGAGAAACAAAAC 58.297 34.615 0.00 0.00 0.00 2.43
8937 10025 5.064707 GCAAATAGTAGAATTGGACGCTCAA 59.935 40.000 0.00 0.00 0.00 3.02
8938 10026 6.478588 CAAATAGTAGAATTGGACGCTCAAC 58.521 40.000 0.00 0.00 0.00 3.18
9174 10269 1.671845 TGGTACACTTGAACAAACGGC 59.328 47.619 0.00 0.00 0.00 5.68
9335 10431 7.048629 TCATACAAAACATTGCCTTGAGAAA 57.951 32.000 5.57 0.00 0.00 2.52
9383 10484 4.385977 CCCCCGGAGACCTATTTAATTGTT 60.386 45.833 0.73 0.00 0.00 2.83
9403 10504 6.885952 TGTTGCTAATTTAAACCAGTGCTA 57.114 33.333 0.00 0.00 0.00 3.49
9462 10563 7.173907 TCAAGAAGTTCAAACAAAAATTTGGCA 59.826 29.630 5.50 0.00 42.34 4.92
9514 10615 9.504708 CTTGAATAAAATCTGGCTAGAGATGAT 57.495 33.333 5.82 0.00 36.14 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 6.438763 CGCAGAAAATTTCTTTGAAGTAGGT 58.561 36.000 5.36 0.00 38.11 3.08
182 183 6.462628 GGTGTAGGTTTTGACTCTCACTTACT 60.463 42.308 0.00 0.00 0.00 2.24
231 232 0.550914 TGCCTCCTGGTTTTGACACT 59.449 50.000 0.00 0.00 35.27 3.55
280 281 4.072839 CGACAGGTGATAGAGCTATACCA 58.927 47.826 1.81 0.00 33.88 3.25
357 362 5.298276 ACCAAATTGTTAGTTTTCTCGCAGA 59.702 36.000 0.00 0.00 0.00 4.26
431 437 1.619654 TTGCCATCTGGGTGTCAAAG 58.380 50.000 0.00 0.00 39.65 2.77
821 833 5.221521 CCGAGGATGTATTTCTCTGGAATGA 60.222 44.000 0.00 0.00 0.00 2.57
844 856 2.158871 TCAGGCGTTTGGTGTATATCCC 60.159 50.000 0.00 0.00 0.00 3.85
848 860 3.404224 TGTTCAGGCGTTTGGTGTATA 57.596 42.857 0.00 0.00 0.00 1.47
900 912 1.602377 GCCTTGTTTGACGCTACTGTT 59.398 47.619 0.00 0.00 0.00 3.16
1249 1261 1.372499 GTCGTTCGCCTACAGCACA 60.372 57.895 0.00 0.00 44.04 4.57
1331 1343 1.340991 TGCTTATCCTCCCCTTTGTGC 60.341 52.381 0.00 0.00 0.00 4.57
1346 1358 0.955428 CCCTGCTTGCGTCTTGCTTA 60.955 55.000 0.00 0.00 46.63 3.09
1347 1359 2.263741 CCCTGCTTGCGTCTTGCTT 61.264 57.895 0.00 0.00 46.63 3.91
1469 1499 3.181497 GCATGTGCAGTAGTTATGGTTGG 60.181 47.826 0.00 0.00 41.59 3.77
1717 1765 3.253921 TGGTCGTCAATCTCGTCAAACTA 59.746 43.478 0.00 0.00 0.00 2.24
1730 1778 2.223852 TGTTCGTCTGATTGGTCGTCAA 60.224 45.455 0.00 0.00 40.01 3.18
1750 1798 5.449588 GCCCAACACTGTCATCTTCATTATG 60.450 44.000 0.00 0.00 0.00 1.90
1752 1800 4.009675 GCCCAACACTGTCATCTTCATTA 58.990 43.478 0.00 0.00 0.00 1.90
1770 1818 0.181587 TTTCAGTTTCCTCGTGCCCA 59.818 50.000 0.00 0.00 0.00 5.36
1774 1822 2.218759 CGTCAGTTTCAGTTTCCTCGTG 59.781 50.000 0.00 0.00 0.00 4.35
1949 2006 5.593909 TCTGAAATGTTTCCTCATTGTGTGT 59.406 36.000 3.26 0.00 37.96 3.72
2152 2213 1.135972 GGTCGACAGTAGCGTTTCGTA 60.136 52.381 18.91 0.00 33.20 3.43
2386 2474 5.449107 TTTTGCTGAGTTACTAGTCGACT 57.551 39.130 23.66 23.66 0.00 4.18
2777 2898 2.561419 TCTACTGTGGTACTTGGACTGC 59.439 50.000 0.00 0.00 0.00 4.40
2807 2928 1.683011 GGGTTGGTGATGATGGAGGTG 60.683 57.143 0.00 0.00 0.00 4.00
2918 3040 1.737793 CTAAATCCCACTTGCACGTCC 59.262 52.381 0.00 0.00 0.00 4.79
2983 3112 5.374071 AGAAGTAACCGTCCAAGTCAATTT 58.626 37.500 0.00 0.00 0.00 1.82
3030 3160 1.845809 CTTGTGGCAACCGCTCAGTC 61.846 60.000 0.00 0.00 38.60 3.51
3093 3251 2.119484 ATTTGTGGGAGGCGGTTCGA 62.119 55.000 0.00 0.00 0.00 3.71
3196 3359 3.006323 AGAAGTTTGTGGTTTGTGTGCAA 59.994 39.130 0.00 0.00 0.00 4.08
3759 3932 6.506500 AATCTAGTGCATCAGGTTCAAAAG 57.493 37.500 0.00 0.00 0.00 2.27
3855 4028 7.017498 ACATCGAGTACATGAACTACACTAG 57.983 40.000 0.00 0.00 0.00 2.57
3978 4153 8.500753 TGTTGAATAGGATAACACATAACCAC 57.499 34.615 0.00 0.00 30.06 4.16
4021 4197 6.696583 TCAATGTTGTATGTTCTGCTTTGTTG 59.303 34.615 0.00 0.00 0.00 3.33
4023 4199 6.039717 AGTCAATGTTGTATGTTCTGCTTTGT 59.960 34.615 0.00 0.00 0.00 2.83
4276 4460 0.321919 ACGTCTCATGGTGCAGCAAT 60.322 50.000 24.18 8.80 0.00 3.56
4455 4664 3.313526 CCTGAGTGTTGGTGTTCTTCTTG 59.686 47.826 0.00 0.00 0.00 3.02
4466 4675 4.336889 TTGTAGTCTTCCTGAGTGTTGG 57.663 45.455 0.00 0.00 0.00 3.77
4473 4682 3.071023 CCCACAGTTTGTAGTCTTCCTGA 59.929 47.826 0.00 0.00 0.00 3.86
4502 4711 2.674380 GGTTGTCTGGCAGCTGGG 60.674 66.667 17.12 0.00 0.00 4.45
4803 5012 6.579666 ATGCAAAACACTGTACTTGATGAT 57.420 33.333 0.00 0.00 0.00 2.45
5060 5272 8.731605 TGAGAACACTACATGAAGTACTAAGAG 58.268 37.037 0.00 0.00 0.00 2.85
5249 5464 1.586422 TCGTAGTAGCGCTTACGGAT 58.414 50.000 30.66 10.34 40.57 4.18
5420 5639 4.335647 CTGCGCCTGACCTTGGGT 62.336 66.667 4.18 0.00 39.44 4.51
5877 6136 1.003118 TCCGTGGTGCAGAGCTAAATT 59.997 47.619 0.00 0.00 0.00 1.82
5947 6210 7.441017 AGCAGATAGGCTATTAAGTTCTCTTG 58.559 38.462 8.71 0.00 43.70 3.02
6092 6441 8.850454 TTTGCATTTTAGTAGTTGAACTTGTC 57.150 30.769 1.97 0.00 0.00 3.18
6171 6521 8.507249 GCATTTTAGTAGTTGAACTTGTCAGAT 58.493 33.333 1.97 0.00 37.61 2.90
6172 6522 7.497579 TGCATTTTAGTAGTTGAACTTGTCAGA 59.502 33.333 1.97 0.00 37.61 3.27
6173 6523 7.639039 TGCATTTTAGTAGTTGAACTTGTCAG 58.361 34.615 1.97 0.00 37.61 3.51
6174 6524 7.561021 TGCATTTTAGTAGTTGAACTTGTCA 57.439 32.000 1.97 0.00 0.00 3.58
6175 6525 8.850454 TTTGCATTTTAGTAGTTGAACTTGTC 57.150 30.769 1.97 0.00 0.00 3.18
6176 6526 9.646427 TTTTTGCATTTTAGTAGTTGAACTTGT 57.354 25.926 1.97 0.00 0.00 3.16
6363 7216 6.481976 TGCGATTGAGATTATTTTACGACCAT 59.518 34.615 0.00 0.00 0.00 3.55
6412 7275 7.848223 TGTCATATGTATGTTTGAACTGAGG 57.152 36.000 1.90 0.00 35.26 3.86
6538 7403 9.461312 TCTCATTTTAGTGCACTTATGGTTTAT 57.539 29.630 27.06 5.02 0.00 1.40
6633 7500 0.472925 TCAGTGCCCTGGGAGTTGTA 60.473 55.000 19.27 0.00 39.31 2.41
6800 7670 4.882842 TGTCAAGCTGTACTTATGACCA 57.117 40.909 9.37 0.00 36.04 4.02
6837 7709 6.442952 CGTCCAATTCAAATGGTTTTACTGA 58.557 36.000 0.00 0.00 39.09 3.41
6970 7853 3.632080 TCAACGGGGATGCGTGGT 61.632 61.111 0.00 0.00 0.00 4.16
6985 7868 0.878416 GGGTATTTTGCAGTGCGTCA 59.122 50.000 11.20 0.00 0.00 4.35
7172 8061 2.049433 AACGTCGGCGAGGTTGAG 60.049 61.111 37.32 16.42 38.85 3.02
7173 8062 2.049802 GAACGTCGGCGAGGTTGA 60.050 61.111 41.15 6.13 40.09 3.18
7220 8109 1.694150 CTCAACTCCTGTGAGGGTTCA 59.306 52.381 0.00 0.00 43.29 3.18
7234 8123 0.886490 CTTTGCCGTGGAGCTCAACT 60.886 55.000 19.09 0.00 0.00 3.16
7293 8182 1.657751 CCTGCTCATCACCTCGTCGA 61.658 60.000 0.00 0.00 0.00 4.20
7403 8298 3.058160 GGCGCACAACTGCAGGAT 61.058 61.111 19.93 3.18 44.50 3.24
7419 8314 0.671781 CACCAAGCAGAGTTCCTCGG 60.672 60.000 0.00 0.00 35.36 4.63
7517 8425 7.761038 AGTTGGGAAACTAGTTTATTGAAGG 57.239 36.000 20.58 0.00 32.11 3.46
7706 8645 7.549842 GTGCATCAAGATCAGAATCTATGCTAT 59.450 37.037 17.51 0.00 45.79 2.97
7959 8981 4.397417 GCTATCTTCAGTGCTTCACCAAAT 59.603 41.667 0.00 0.00 34.49 2.32
7960 8982 3.753272 GCTATCTTCAGTGCTTCACCAAA 59.247 43.478 0.00 0.00 34.49 3.28
7961 8983 3.244526 TGCTATCTTCAGTGCTTCACCAA 60.245 43.478 0.00 0.00 34.49 3.67
7962 8984 2.302733 TGCTATCTTCAGTGCTTCACCA 59.697 45.455 0.00 0.00 34.49 4.17
7963 8985 2.977914 TGCTATCTTCAGTGCTTCACC 58.022 47.619 0.00 0.00 34.49 4.02
8022 9045 4.995487 CCAGAAACTAGTACACAAAGTCCC 59.005 45.833 0.00 0.00 0.00 4.46
8323 9356 6.046593 CGTAGTATTTGCTGGTCTTTGGATA 58.953 40.000 0.00 0.00 0.00 2.59
8397 9430 4.163078 TCTCCCTTGTCCATCTTCTTCATC 59.837 45.833 0.00 0.00 0.00 2.92
8444 9483 0.321919 GATGAGGTTGTCTGGCAGCA 60.322 55.000 10.34 8.61 0.00 4.41
8648 9696 8.770438 AAAGCAAACTACAAATCTGAAACAAA 57.230 26.923 0.00 0.00 0.00 2.83
8937 10025 4.267349 ACCGTAAATGTCTAAGCTGTGT 57.733 40.909 0.00 0.00 0.00 3.72
8938 10026 5.408356 ACTACCGTAAATGTCTAAGCTGTG 58.592 41.667 0.00 0.00 0.00 3.66
9008 10099 3.442977 GTCCTCGGCTGAAACTTAGTCTA 59.557 47.826 0.00 0.00 0.00 2.59
9147 10240 3.713288 TGTTCAAGTGTACCAGAACTCG 58.287 45.455 14.26 0.00 40.62 4.18
9335 10431 5.254115 GACCTATTTTCTAGGCTGTGGTTT 58.746 41.667 0.00 0.00 38.25 3.27
9514 10615 7.675962 AATTATTTACGACCAAGTTGCTACA 57.324 32.000 0.13 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.