Multiple sequence alignment - TraesCS7B01G328300

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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 TraesCS7B01G328300 chr7B 100.000 8305 0 0 1 8305 582931475 582939779 0.000000e+00 15337
1 TraesCS7B01G328300 chr7B 88.345 429 44 4 635 1058 582931639 582932066 2.070000e-140 510
2 TraesCS7B01G328300 chr7B 88.345 429 44 4 165 592 582932109 582932532 2.070000e-140 510
3 TraesCS7B01G328300 chr7B 80.000 560 89 14 1327 1872 583174921 583175471 7.810000e-105 392
4 TraesCS7B01G328300 chr7D 93.758 3733 207 21 1 3720 539943537 539947256 0.000000e+00 5579
5 TraesCS7B01G328300 chr7D 93.814 3443 175 17 4886 8305 539948630 539952057 0.000000e+00 5144
6 TraesCS7B01G328300 chr7D 94.627 1154 58 4 3696 4847 539947386 539948537 0.000000e+00 1784
7 TraesCS7B01G328300 chr7D 87.559 426 49 3 167 592 539944168 539944589 2.690000e-134 490
8 TraesCS7B01G328300 chr7D 86.620 142 18 1 4585 4725 264084394 264084253 1.120000e-33 156
9 TraesCS7B01G328300 chr7A 91.927 3357 214 31 1508 4849 621307293 621310607 0.000000e+00 4645
10 TraesCS7B01G328300 chr7A 90.664 2003 130 21 6321 8305 621312179 621314142 0.000000e+00 2610
11 TraesCS7B01G328300 chr7A 92.784 1178 59 9 4893 6049 621310708 621311880 0.000000e+00 1681
12 TraesCS7B01G328300 chr7A 92.911 663 34 7 533 1191 621306052 621306705 0.000000e+00 952
13 TraesCS7B01G328300 chr7A 90.860 372 29 3 1 372 621305131 621305497 2.080000e-135 494
14 TraesCS7B01G328300 chr7A 88.489 417 34 6 177 592 621306169 621306572 7.490000e-135 492
15 TraesCS7B01G328300 chr7A 91.830 306 24 1 1203 1508 621306691 621306995 7.700000e-115 425
16 TraesCS7B01G328300 chr7A 93.617 235 14 1 6053 6287 621311950 621312183 4.770000e-92 350
17 TraesCS7B01G328300 chr7A 88.614 202 23 0 638 839 621305296 621305497 6.440000e-61 246
18 TraesCS7B01G328300 chr7A 90.625 128 10 2 4575 4700 427814852 427814979 1.430000e-37 169
19 TraesCS7B01G328300 chr7A 87.681 138 16 1 4572 4708 675529882 675529745 8.630000e-35 159
20 TraesCS7B01G328300 chr4B 89.757 2265 161 36 6050 8305 623645637 623647839 0.000000e+00 2832
21 TraesCS7B01G328300 chr4B 88.835 2266 181 37 6050 8305 623786428 623788631 0.000000e+00 2717
22 TraesCS7B01G328300 chr4B 85.171 2131 245 44 706 2782 623783719 623785832 0.000000e+00 2119
23 TraesCS7B01G328300 chr4B 85.106 1457 162 31 706 2115 623642978 623644426 0.000000e+00 1437
24 TraesCS7B01G328300 chr4B 83.514 740 86 19 1 714 623641919 623642648 0.000000e+00 658
25 TraesCS7B01G328300 chr4B 89.362 517 48 3 5544 6055 623645063 623645577 1.950000e-180 643
26 TraesCS7B01G328300 chr4B 89.628 511 46 4 5544 6049 623785854 623786362 1.950000e-180 643
27 TraesCS7B01G328300 chr4B 84.541 621 76 15 2163 2776 623644428 623645035 1.540000e-166 597
28 TraesCS7B01G328300 chr4B 85.336 491 62 5 1 490 623769470 623769951 4.480000e-137 499
29 TraesCS7B01G328300 chr4B 83.256 430 59 10 636 1058 623642080 623642503 4.700000e-102 383
30 TraesCS7B01G328300 chr4B 86.452 310 33 7 652 958 623769649 623769952 1.730000e-86 331
31 TraesCS7B01G328300 chr4B 82.895 380 36 16 236 591 623642978 623643352 1.740000e-81 315
32 TraesCS7B01G328300 chr4B 78.394 523 81 22 5488 5986 623955694 623955180 2.250000e-80 311
33 TraesCS7B01G328300 chr4B 78.218 303 54 7 5607 5905 623654666 623654960 5.120000e-42 183
34 TraesCS7B01G328300 chr4B 87.500 152 18 1 4575 4725 438375332 438375181 3.080000e-39 174
35 TraesCS7B01G328300 chr4B 86.992 123 16 0 735 857 623643224 623643102 1.120000e-28 139
36 TraesCS7B01G328300 chr4B 92.593 81 4 2 165 244 623783309 623783388 1.890000e-21 115
37 TraesCS7B01G328300 chr4B 88.889 81 7 2 165 244 623642569 623642648 1.910000e-16 99
38 TraesCS7B01G328300 chr4D 88.889 2259 191 23 6050 8305 487875125 487877326 0.000000e+00 2726
39 TraesCS7B01G328300 chr4D 85.083 2105 231 42 706 2776 487872467 487874522 0.000000e+00 2071
40 TraesCS7B01G328300 chr4D 77.369 1224 231 30 6332 7541 488172576 488173767 0.000000e+00 684
41 TraesCS7B01G328300 chr4D 90.020 511 45 3 5544 6049 487874550 487875059 0.000000e+00 656
42 TraesCS7B01G328300 chr4D 77.065 1138 218 32 6189 7306 488034129 488035243 4.260000e-172 616
43 TraesCS7B01G328300 chr4D 81.583 733 73 30 3 711 487871442 487872136 4.380000e-152 549
44 TraesCS7B01G328300 chr4D 87.465 359 38 4 236 592 487872467 487872820 2.790000e-109 407
45 TraesCS7B01G328300 chr4D 81.132 424 40 21 640 1058 487871606 487871994 3.770000e-78 303
46 TraesCS7B01G328300 chr4D 81.675 382 54 12 5473 5840 488171636 488172015 3.770000e-78 303
47 TraesCS7B01G328300 chr5A 77.843 853 157 18 6674 7522 669740996 669741820 4.480000e-137 499
48 TraesCS7B01G328300 chr5A 78.261 391 77 6 6924 7310 669987142 669987528 2.320000e-60 244
49 TraesCS7B01G328300 chr5D 86.275 153 19 2 4575 4725 220683191 220683343 1.850000e-36 165
50 TraesCS7B01G328300 chr3A 84.615 156 21 2 4575 4727 208033819 208033664 1.440000e-32 152
51 TraesCS7B01G328300 chr5B 86.667 135 16 2 4575 4708 138770129 138770262 1.870000e-31 148


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 TraesCS7B01G328300 chr7B 582931475 582939779 8304 False 15337.000000 15337 100.000000 1 8305 1 chr7B.!!$F1 8304
1 TraesCS7B01G328300 chr7B 582931639 582932532 893 False 510.000000 510 88.345000 165 1058 2 chr7B.!!$F3 893
2 TraesCS7B01G328300 chr7B 583174921 583175471 550 False 392.000000 392 80.000000 1327 1872 1 chr7B.!!$F2 545
3 TraesCS7B01G328300 chr7D 539943537 539952057 8520 False 3249.250000 5579 92.439500 1 8305 4 chr7D.!!$F1 8304
4 TraesCS7B01G328300 chr7A 621305131 621314142 9011 False 1321.666667 4645 91.299556 1 8305 9 chr7A.!!$F2 8304
5 TraesCS7B01G328300 chr4B 623783309 623788631 5322 False 1398.500000 2717 89.056750 165 8305 4 chr4B.!!$F4 8140
6 TraesCS7B01G328300 chr4B 623641919 623647839 5920 False 870.500000 2832 85.915000 1 8305 8 chr4B.!!$F2 8304
7 TraesCS7B01G328300 chr4B 623955180 623955694 514 True 311.000000 311 78.394000 5488 5986 1 chr4B.!!$R3 498
8 TraesCS7B01G328300 chr4D 487871442 487877326 5884 False 1118.666667 2726 85.695333 3 8305 6 chr4D.!!$F2 8302
9 TraesCS7B01G328300 chr4D 488034129 488035243 1114 False 616.000000 616 77.065000 6189 7306 1 chr4D.!!$F1 1117
10 TraesCS7B01G328300 chr4D 488171636 488173767 2131 False 493.500000 684 79.522000 5473 7541 2 chr4D.!!$F3 2068
11 TraesCS7B01G328300 chr5A 669740996 669741820 824 False 499.000000 499 77.843000 6674 7522 1 chr5A.!!$F1 848

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
27 28 0.607217 TAGGACCTCTCGACAACGCA 60.607 55.000 0.00 0.00 39.58 5.24 F
57 58 0.895100 GTGCATCTGAAGTGGGCCAA 60.895 55.000 8.40 0.00 0.00 4.52 F
1655 3135 1.339610 TGGTCCAGCCAAACAAATTCG 59.660 47.619 0.00 0.00 45.94 3.34 F
1858 3339 1.994916 AAATAAGCAACGTGGCATGC 58.005 45.000 19.06 9.90 42.87 4.06 F
3479 4973 2.493278 GCCACACTAAGCAAACCATGAT 59.507 45.455 0.00 0.00 0.00 2.45 F
3956 5606 0.383949 TGCAAAGCTCGTTTGTTCCC 59.616 50.000 0.00 0.00 46.44 3.97 F
4222 5874 3.753294 ACGGGGAACATGATGACTATC 57.247 47.619 0.00 0.00 0.00 2.08 F
5442 7174 2.414058 TGTTAGCACGCCATTGTTTG 57.586 45.000 0.00 0.00 0.00 2.93 F
6636 8556 0.179009 ATGATGCAACCGGCTGCTAT 60.179 50.000 28.68 19.97 45.15 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 3366 1.265635 TGCTTTCCAACGTGAATTCCG 59.734 47.619 12.81 12.81 0.00 4.30 R
2026 3509 2.299582 TCATGACATTTGCCCAAACCTG 59.700 45.455 0.00 0.00 32.51 4.00 R
3126 4618 3.071479 ACACAAGCGTAATACAAGGTGG 58.929 45.455 0.00 0.00 0.00 4.61 R
3758 5408 1.923356 AGAAACACCCGAATGCCAAT 58.077 45.000 0.00 0.00 0.00 3.16 R
5426 7158 1.466950 GCTACAAACAATGGCGTGCTA 59.533 47.619 0.00 0.00 0.00 3.49 R
5442 7174 3.701532 AGCTCATCGTTGTCTAGCTAC 57.298 47.619 6.42 0.00 41.56 3.58 R
6145 7992 6.423604 ACTTTTGTCCACAAACTTTTTGTCTG 59.576 34.615 4.32 0.00 44.56 3.51 R
6992 8920 1.117150 GGAAGTATCCCACGCCTGTA 58.883 55.000 0.00 0.00 40.10 2.74 R
8192 10144 2.288825 TGAACTGGCAACTCCGTAGAAG 60.289 50.000 0.00 0.00 37.80 2.85 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
27 28 0.607217 TAGGACCTCTCGACAACGCA 60.607 55.000 0.00 0.00 39.58 5.24
57 58 0.895100 GTGCATCTGAAGTGGGCCAA 60.895 55.000 8.40 0.00 0.00 4.52
66 67 2.361230 GTGGGCCAACCTAGCACC 60.361 66.667 8.40 0.00 41.11 5.01
115 116 2.492088 CCATGTGTCTGTCTAACGGAGA 59.508 50.000 0.00 0.00 33.48 3.71
136 137 6.698766 GGAGATGGTTGTGAATATTTTCATGC 59.301 38.462 1.79 0.00 43.49 4.06
1085 2234 1.420430 AGAGGTGTTCGGTTCTTCCA 58.580 50.000 0.00 0.00 35.57 3.53
1235 2391 7.068593 CCATTCTTGGCCTTTTGATGAGTTATA 59.931 37.037 3.32 0.00 35.85 0.98
1238 2394 8.593945 TCTTGGCCTTTTGATGAGTTATATTT 57.406 30.769 3.32 0.00 0.00 1.40
1262 2418 3.843422 TCCAAAAGACACCATGGTTCAT 58.157 40.909 16.84 3.27 34.50 2.57
1282 2438 7.201661 GGTTCATAATAACCGTGCATAACAAGA 60.202 37.037 0.00 0.00 39.62 3.02
1360 2516 8.497910 ACACATATCTATGTTGGAAGGACTAT 57.502 34.615 0.06 0.00 43.99 2.12
1409 2571 7.338710 TCCTCTTGTAATAGTTGGATTCCAAG 58.661 38.462 18.49 3.79 44.82 3.61
1424 2586 6.129179 GGATTCCAAGAAAATCATGGGAGTA 58.871 40.000 0.00 0.00 36.02 2.59
1473 2645 8.816640 AGTAAATTTTCAAAGTGGTTAGCATG 57.183 30.769 0.00 0.00 0.00 4.06
1489 2661 6.591834 GGTTAGCATGTCTACTATTGCTATGG 59.408 42.308 4.51 0.00 44.57 2.74
1555 3027 9.930693 AGTTCTCGATTCTACAAAAGATACTTT 57.069 29.630 0.00 0.00 33.05 2.66
1576 3056 8.405418 ACTTTACATAAGTTTTTCCCCTCTTC 57.595 34.615 0.00 0.00 0.00 2.87
1629 3109 6.995511 AATGATTCATTGGCCAAAGATTTG 57.004 33.333 24.71 16.05 32.39 2.32
1655 3135 1.339610 TGGTCCAGCCAAACAAATTCG 59.660 47.619 0.00 0.00 45.94 3.34
1661 3141 3.545822 CCAGCCAAACAAATTCGCAAAAC 60.546 43.478 0.00 0.00 0.00 2.43
1827 3308 7.540474 AGGTGTAGTGACCCAATATATAGTG 57.460 40.000 3.15 3.15 36.56 2.74
1858 3339 1.994916 AAATAAGCAACGTGGCATGC 58.005 45.000 19.06 9.90 42.87 4.06
1920 3403 8.487970 CGTTGGAAAGCATACTTACATGTATAG 58.512 37.037 6.36 9.49 34.05 1.31
1955 3438 5.003160 ACTTAGTATGATGTTGCACTGCAA 58.997 37.500 12.59 12.59 46.80 4.08
2309 3796 6.270156 TGTCTGCATTTGAAGATATTTGCA 57.730 33.333 0.00 0.00 37.73 4.08
2408 3895 8.111224 ACAAAAATCGTGTTATTTTGGAAAACG 58.889 29.630 12.97 0.00 44.37 3.60
2447 3935 5.909477 ACATTAGCATGGATGGATTTGTTG 58.091 37.500 0.00 0.00 34.27 3.33
2616 4104 5.326200 ACCACCAACAATTGTTCGTTAAA 57.674 34.783 20.85 0.00 35.83 1.52
2623 4111 7.545965 ACCAACAATTGTTCGTTAAATGTTTCA 59.454 29.630 20.85 0.00 35.83 2.69
2633 4121 9.453325 GTTCGTTAAATGTTTCACCATAGAAAA 57.547 29.630 0.00 0.00 39.05 2.29
2894 4386 7.351166 TCCCGAGGAAATATTATTGGAGTTTT 58.649 34.615 0.00 0.00 0.00 2.43
2923 4415 6.569179 AATATTTTCGTAAGTGCACCAACT 57.431 33.333 14.63 0.00 39.48 3.16
3108 4600 9.054922 TGTTTGTAACAAGTACCAATACCTTAC 57.945 33.333 0.00 0.00 38.72 2.34
3153 4646 8.444715 CACCTTGTATTACGCTTGTGTTATTTA 58.555 33.333 0.00 0.00 0.00 1.40
3331 4825 6.677781 TCACACTCTTTTAACTCAACCTTG 57.322 37.500 0.00 0.00 0.00 3.61
3334 4828 7.825270 TCACACTCTTTTAACTCAACCTTGTTA 59.175 33.333 0.00 0.00 0.00 2.41
3409 4903 5.105635 ACATGTGGGTCTTTGCTATCAAATG 60.106 40.000 0.00 0.00 40.97 2.32
3479 4973 2.493278 GCCACACTAAGCAAACCATGAT 59.507 45.455 0.00 0.00 0.00 2.45
3487 4981 7.148239 ACACTAAGCAAACCATGATAACTAAGC 60.148 37.037 0.00 0.00 0.00 3.09
3575 5070 8.523523 ACACAAGTAAAACCACAAAAACTAAC 57.476 30.769 0.00 0.00 0.00 2.34
3710 5206 6.959639 TTCAGCCTCATAAAAAGTTGAAGT 57.040 33.333 0.00 0.00 0.00 3.01
3758 5408 4.347000 AGGCACACTTAGTTACTCCTTTCA 59.653 41.667 0.00 0.00 0.00 2.69
3765 5415 6.375455 CACTTAGTTACTCCTTTCATTGGCAT 59.625 38.462 0.00 0.00 0.00 4.40
3767 5417 5.904362 AGTTACTCCTTTCATTGGCATTC 57.096 39.130 0.00 0.00 0.00 2.67
3780 5430 2.035632 TGGCATTCGGGTGTTTCTTTT 58.964 42.857 0.00 0.00 0.00 2.27
3797 5447 9.959749 TGTTTCTTTTGTATCAAAACTATGGTC 57.040 29.630 3.93 0.00 32.44 4.02
3806 5456 5.925506 TCAAAACTATGGTCGGACTATCA 57.074 39.130 10.46 0.00 0.00 2.15
3825 5475 6.832384 ACTATCATTGCATGAGGTTTCTTGAT 59.168 34.615 0.00 0.00 43.53 2.57
3924 5574 8.747538 AATAGGGTTGTCCATAGAATTGTAAC 57.252 34.615 0.00 0.00 38.24 2.50
3925 5575 6.134535 AGGGTTGTCCATAGAATTGTAACA 57.865 37.500 0.00 0.00 38.24 2.41
3956 5606 0.383949 TGCAAAGCTCGTTTGTTCCC 59.616 50.000 0.00 0.00 46.44 3.97
4037 5687 4.012374 CCTTGCACAAATCTCATACTGGT 58.988 43.478 0.00 0.00 0.00 4.00
4045 5695 6.596888 CACAAATCTCATACTGGTGTTGATCT 59.403 38.462 0.00 0.00 0.00 2.75
4064 5714 6.365520 TGATCTACTGCATCTTCCACTAGTA 58.634 40.000 0.00 0.00 0.00 1.82
4099 5749 5.887214 TGCATATGGTCCTCTAAGCTTTA 57.113 39.130 3.20 0.00 0.00 1.85
4222 5874 3.753294 ACGGGGAACATGATGACTATC 57.247 47.619 0.00 0.00 0.00 2.08
4228 5880 6.102663 GGGGAACATGATGACTATCTATTCG 58.897 44.000 0.00 0.00 34.31 3.34
4286 5938 8.241497 AGCATATCATGTTAACATTGGTCATT 57.759 30.769 18.50 0.77 33.61 2.57
4537 6191 8.372459 TCCTAACTTCACAAAGCTTTACTATGA 58.628 33.333 12.25 10.46 35.81 2.15
4606 6260 9.573166 TCCATTCACTATATAAGATGTTTTGGG 57.427 33.333 0.00 0.00 0.00 4.12
4651 6305 4.568152 AACTGAAATGGGAGAACAAACG 57.432 40.909 0.00 0.00 0.00 3.60
4780 6436 6.406370 TCCATTTGATAACAGGTGTACTCTG 58.594 40.000 12.91 12.91 38.16 3.35
4855 6551 9.944376 AATGCTATAATGTTAACCTATGTCGAT 57.056 29.630 2.48 0.00 0.00 3.59
5054 6780 8.727100 AAGACCATATGTAGGATGACTTATGA 57.273 34.615 1.24 0.00 38.68 2.15
5218 6946 6.426587 ACATATAACAAGTGCCTTTGGAGAT 58.573 36.000 2.84 0.00 32.32 2.75
5251 6979 4.874970 ACATGAGAATGAACACAAAAGGC 58.125 39.130 0.00 0.00 0.00 4.35
5269 6997 9.723601 ACAAAAGGCATATTGTTGAAATGTTAT 57.276 25.926 0.00 0.00 36.39 1.89
5375 7107 9.301897 ACTAATTTCTTTTAGGCATCTTCACTT 57.698 29.630 0.00 0.00 34.19 3.16
5433 7165 5.712217 TGTGAACTATTATGTTAGCACGC 57.288 39.130 0.00 0.00 31.46 5.34
5434 7166 4.569162 TGTGAACTATTATGTTAGCACGCC 59.431 41.667 0.00 0.00 31.46 5.68
5442 7174 2.414058 TGTTAGCACGCCATTGTTTG 57.586 45.000 0.00 0.00 0.00 2.93
5480 7212 7.655328 CGATGAGCTACCTTGAATTCTAGAATT 59.345 37.037 26.98 26.98 43.14 2.17
5486 7219 9.914131 GCTACCTTGAATTCTAGAATTGTTTTT 57.086 29.630 30.65 16.11 40.77 1.94
5774 7519 7.042523 GCATTATTTTTCTTCCCATGCACATAC 60.043 37.037 0.00 0.00 36.41 2.39
6131 7978 7.486647 AGCATTTCATCCATATGTTTGTCTTC 58.513 34.615 1.24 0.00 34.50 2.87
6145 7992 3.826236 TGTCTTCTACGTGTAGCTCAC 57.174 47.619 0.00 0.00 43.03 3.51
6213 8073 9.601217 AACATCTACATGTGGAACTATTTCTAC 57.399 33.333 16.42 2.81 42.89 2.59
6269 8136 9.705290 AAATTTTGTAAATTGTGGGATCACTAC 57.295 29.630 0.00 0.00 43.94 2.73
6273 8140 6.539173 TGTAAATTGTGGGATCACTACAGTT 58.461 36.000 0.00 0.00 43.94 3.16
6312 8184 5.803461 CAGCAATCATAAACCATGACTTGTG 59.197 40.000 0.00 0.00 46.41 3.33
6388 8265 3.519510 CACATCTTCCCCTTCTTGACCTA 59.480 47.826 0.00 0.00 0.00 3.08
6390 8267 4.790790 ACATCTTCCCCTTCTTGACCTATT 59.209 41.667 0.00 0.00 0.00 1.73
6410 8289 9.200817 ACCTATTAATGTGAGGCAATGTTTATT 57.799 29.630 0.00 0.00 33.28 1.40
6444 8323 6.553100 ACCCTTTGTTGAACAGATTAATCCAA 59.447 34.615 11.92 6.34 0.00 3.53
6482 8361 0.824759 ATCCTCACTTCTACACCCGC 59.175 55.000 0.00 0.00 0.00 6.13
6500 8379 3.026630 CGCTGGACGGTATTGTGATAT 57.973 47.619 0.00 0.00 38.44 1.63
6530 8438 6.983890 GCTTTGAAAATTACTCTTTCCCACAA 59.016 34.615 0.00 0.00 32.79 3.33
6549 8457 9.042450 TCCCACAATAAAAGTGATCTTACTCTA 57.958 33.333 0.00 0.00 39.30 2.43
6610 8530 6.262944 ACAAAGACAATGTATGCAACAGAGAA 59.737 34.615 0.00 0.00 42.70 2.87
6636 8556 0.179009 ATGATGCAACCGGCTGCTAT 60.179 50.000 28.68 19.97 45.15 2.97
6813 8735 3.951563 AGCCATGCTATTCCCTTTACA 57.048 42.857 0.00 0.00 36.99 2.41
6822 8744 5.126384 TGCTATTCCCTTTACAAAAATCCGG 59.874 40.000 0.00 0.00 0.00 5.14
6852 8775 6.419791 TGGTCGATAAGGGTGTATCATTTTT 58.580 36.000 0.00 0.00 31.80 1.94
7050 8978 3.492102 ACTTAGCAGAAAAGGCAGACA 57.508 42.857 0.00 0.00 0.00 3.41
7569 9513 1.379527 CGATGGTAAAGGGAAGGTGC 58.620 55.000 0.00 0.00 0.00 5.01
7592 9536 1.076632 ACCCCAGGAACGCAAACAA 60.077 52.632 0.00 0.00 0.00 2.83
7630 9576 4.884668 TTCCGATCTAGGTTTGTCAAGT 57.115 40.909 0.00 0.00 0.00 3.16
7631 9577 5.988310 TTCCGATCTAGGTTTGTCAAGTA 57.012 39.130 0.00 0.00 0.00 2.24
7673 9619 7.814264 ACTCTTTTCTCTTGACATGAATTGT 57.186 32.000 0.00 0.00 42.79 2.71
7722 9670 5.339008 AATACTCTTACATGCCACGAAGA 57.661 39.130 0.00 0.00 0.00 2.87
7725 9673 4.579869 ACTCTTACATGCCACGAAGAAAT 58.420 39.130 0.00 0.00 0.00 2.17
7755 9703 1.198178 GTGCGAGGCGGTAAAATGAAA 59.802 47.619 0.00 0.00 0.00 2.69
7789 9738 1.838112 TGGTAGCAAAAGGAGGCATG 58.162 50.000 0.00 0.00 0.00 4.06
8078 10029 9.778741 AACACTAACTCTCTTTGTCATTATTCA 57.221 29.630 0.00 0.00 0.00 2.57
8107 10059 9.840427 AAAAATAACTATCTTTGTCATTGACGG 57.160 29.630 11.97 5.34 34.95 4.79
8110 10062 4.174009 ACTATCTTTGTCATTGACGGACG 58.826 43.478 11.97 1.99 38.10 4.79
8192 10144 1.067516 AGCTGTTGGCACATGTTTGTC 59.932 47.619 0.00 0.00 44.79 3.18
8230 10185 6.151144 GCCAGTTCAGTTATTACTCCATTGTT 59.849 38.462 0.00 0.00 30.26 2.83
8239 10194 9.920946 AGTTATTACTCCATTGTTATCACCAAT 57.079 29.630 0.00 0.00 32.88 3.16
8262 10217 9.288576 CAATAAATGAGTCCAAATAGCTATGGA 57.711 33.333 11.37 11.37 43.32 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.417517 TCAGATGCACCATAGGCGAAT 59.582 47.619 0.00 0.00 0.00 3.34
57 58 3.246112 TTGCCACCGGTGCTAGGT 61.246 61.111 29.75 0.00 43.97 3.08
136 137 9.398170 GTATATGCCACAATTAAATGCTACTTG 57.602 33.333 0.00 0.00 0.00 3.16
151 152 8.886369 ACCAGTATTAATAAGGTATATGCCACA 58.114 33.333 12.79 0.00 0.00 4.17
1235 2391 6.933514 ACCATGGTGTCTTTTGGAATAAAT 57.066 33.333 18.99 0.00 33.36 1.40
1238 2394 5.389520 TGAACCATGGTGTCTTTTGGAATA 58.610 37.500 20.60 0.00 33.36 1.75
1262 2418 6.824196 TCCATTCTTGTTATGCACGGTTATTA 59.176 34.615 0.00 0.00 0.00 0.98
1270 2426 3.088532 TGGGTCCATTCTTGTTATGCAC 58.911 45.455 0.00 0.00 0.00 4.57
1320 2476 5.938125 AGATATGTGTTTGTGTTGGTCCTAC 59.062 40.000 0.00 0.00 0.00 3.18
1360 2516 5.887598 AGTGTACACGGTCCAGTAATGTATA 59.112 40.000 19.93 0.00 36.20 1.47
1362 2518 4.081406 AGTGTACACGGTCCAGTAATGTA 58.919 43.478 19.93 0.00 36.20 2.29
1454 2618 6.770785 AGTAGACATGCTAACCACTTTGAAAA 59.229 34.615 0.00 0.00 0.00 2.29
1473 2645 7.155328 ACATTGTAGCCATAGCAATAGTAGAC 58.845 38.462 0.00 0.00 43.56 2.59
1555 3027 6.843752 TGTGAAGAGGGGAAAAACTTATGTA 58.156 36.000 0.00 0.00 0.00 2.29
1655 3135 5.062183 GTGGAGTTTGACTTCAAAGTTTTGC 59.938 40.000 12.28 1.74 46.22 3.68
1661 3141 5.355350 ACTTCAGTGGAGTTTGACTTCAAAG 59.645 40.000 0.00 0.00 45.36 2.77
1880 3361 5.692613 TTTCCAACGTGAATTCCGTAATT 57.307 34.783 18.19 4.91 37.61 1.40
1885 3366 1.265635 TGCTTTCCAACGTGAATTCCG 59.734 47.619 12.81 12.81 0.00 4.30
1893 3374 5.001232 ACATGTAAGTATGCTTTCCAACGT 58.999 37.500 0.00 0.00 36.22 3.99
1920 3403 7.382110 ACATCATACTAAGTCATATGCCACTC 58.618 38.462 0.00 0.00 0.00 3.51
1955 3438 9.241919 TCATATTGGTGAACATGTCAAAATAGT 57.758 29.630 0.00 0.00 38.23 2.12
2013 3496 4.142249 GCCCAAACCTGATATGTTACCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2026 3509 2.299582 TCATGACATTTGCCCAAACCTG 59.700 45.455 0.00 0.00 32.51 4.00
2093 3578 4.706476 TGGGTGAAATCCTCAAATAAGCAG 59.294 41.667 0.00 0.00 35.22 4.24
2094 3579 4.671831 TGGGTGAAATCCTCAAATAAGCA 58.328 39.130 0.00 0.00 35.22 3.91
2125 3610 2.288763 GGCTTGGTGGGTGTTATTGTTG 60.289 50.000 0.00 0.00 0.00 3.33
2334 3821 2.614481 GGGGAAGCTCAAACACGTGATA 60.614 50.000 25.01 3.13 0.00 2.15
2408 3895 5.409520 TGCTAATGTTCGGATCATTATGCTC 59.590 40.000 24.15 15.33 37.22 4.26
2493 3981 6.968904 GGTGTATAAATTTCACTGCATGTCTG 59.031 38.462 0.00 0.00 33.30 3.51
2497 3985 8.761575 AAAAGGTGTATAAATTTCACTGCATG 57.238 30.769 0.00 0.00 33.30 4.06
2583 4071 6.946009 ACAATTGTTGGTGGTACTAAATAGCT 59.054 34.615 4.92 0.00 34.12 3.32
2597 4085 7.545965 TGAAACATTTAACGAACAATTGTTGGT 59.454 29.630 27.20 27.20 46.44 3.67
2633 4121 7.985184 TGCGTAAAGAACATAAGGAACTATCAT 59.015 33.333 0.00 0.00 38.49 2.45
2855 4347 3.576982 TCCTCGGGATGTATGTATTGGAC 59.423 47.826 0.00 0.00 0.00 4.02
2894 4386 7.024768 GGTGCACTTACGAAAATATTTAAGCA 58.975 34.615 17.98 1.33 0.00 3.91
2907 4399 3.247442 CGATAAGTTGGTGCACTTACGA 58.753 45.455 17.98 8.95 41.11 3.43
2945 4437 6.183360 GCAATAAGTCCAACCTTCTATTGTCC 60.183 42.308 0.00 0.00 0.00 4.02
3009 4501 7.606456 AGTGGCAGAGTAAAATCTAAAAATCGA 59.394 33.333 0.00 0.00 0.00 3.59
3010 4502 7.752695 AGTGGCAGAGTAAAATCTAAAAATCG 58.247 34.615 0.00 0.00 0.00 3.34
3078 4570 9.401873 GGTATTGGTACTTGTTACAAACATTTC 57.598 33.333 0.00 0.00 41.79 2.17
3126 4618 3.071479 ACACAAGCGTAATACAAGGTGG 58.929 45.455 0.00 0.00 0.00 4.61
3180 4673 6.294473 AGATTAAGGATAGCATGTGTGGAAG 58.706 40.000 0.00 0.00 0.00 3.46
3390 4884 6.719370 ACTTAACATTTGATAGCAAAGACCCA 59.281 34.615 12.26 0.00 46.27 4.51
3409 4903 7.603651 TCTATGTGTTCCAGAGAGAACTTAAC 58.396 38.462 6.04 0.00 45.25 2.01
3459 4953 5.415701 AGTTATCATGGTTTGCTTAGTGTGG 59.584 40.000 0.00 0.00 0.00 4.17
3460 4954 6.500684 AGTTATCATGGTTTGCTTAGTGTG 57.499 37.500 0.00 0.00 0.00 3.82
3487 4981 9.664332 TTTTCACCCATTTATAACATGATTTGG 57.336 29.630 0.00 0.00 0.00 3.28
3710 5206 7.956328 AGTATCATAGGATAATAGTTGCCGA 57.044 36.000 0.00 0.00 37.73 5.54
3758 5408 1.923356 AGAAACACCCGAATGCCAAT 58.077 45.000 0.00 0.00 0.00 3.16
3765 5415 6.452494 TTTGATACAAAAGAAACACCCGAA 57.548 33.333 0.00 0.00 0.00 4.30
3767 5417 6.270064 AGTTTTGATACAAAAGAAACACCCG 58.730 36.000 9.42 0.00 33.77 5.28
3780 5430 5.670792 AGTCCGACCATAGTTTTGATACA 57.329 39.130 0.00 0.00 0.00 2.29
3806 5456 3.767673 AGCATCAAGAAACCTCATGCAAT 59.232 39.130 5.10 0.00 41.98 3.56
3861 5511 9.071276 TCTTAAGAATGATGAGAGCTTTTGTTT 57.929 29.630 1.68 0.00 0.00 2.83
3897 5547 6.969043 ACAATTCTATGGACAACCCTATTCA 58.031 36.000 0.00 0.00 35.38 2.57
3924 5574 4.418392 GAGCTTTGCATGGAAATACACTG 58.582 43.478 13.13 1.62 0.00 3.66
3925 5575 3.127548 CGAGCTTTGCATGGAAATACACT 59.872 43.478 13.13 8.34 0.00 3.55
3934 5584 2.053627 GAACAAACGAGCTTTGCATGG 58.946 47.619 0.00 0.00 42.87 3.66
3956 5606 4.322424 GGGTACAAAAACAAGGGCCTATTG 60.322 45.833 6.41 16.64 0.00 1.90
4037 5687 4.223700 AGTGGAAGATGCAGTAGATCAACA 59.776 41.667 0.00 0.00 0.00 3.33
4045 5695 6.209589 GGATGATACTAGTGGAAGATGCAGTA 59.790 42.308 5.39 0.00 0.00 2.74
4064 5714 5.889853 GGACCATATGCATGTTATGGATGAT 59.110 40.000 28.87 15.48 46.05 2.45
4099 5749 7.830099 AAGAGGTTGTTGATTGAGAAGAATT 57.170 32.000 0.00 0.00 0.00 2.17
4433 6086 7.112452 AGTGTCATATGCACTATGTGAAGTA 57.888 36.000 22.94 0.00 44.41 2.24
4557 6211 8.561769 TGGAGGGAGTGGAATTGTTAATAATAA 58.438 33.333 0.00 0.00 0.00 1.40
4573 6227 7.782897 TCTTATATAGTGAATGGAGGGAGTG 57.217 40.000 0.00 0.00 0.00 3.51
4581 6235 9.354673 ACCCAAAACATCTTATATAGTGAATGG 57.645 33.333 0.00 0.00 0.00 3.16
4753 6408 7.942341 AGAGTACACCTGTTATCAAATGGAAAA 59.058 33.333 0.00 0.00 0.00 2.29
4844 6540 7.820578 AGCTAGTACTTTTATCGACATAGGT 57.179 36.000 0.00 0.00 0.00 3.08
5251 6979 9.650539 TTCCCACAATAACATTTCAACAATATG 57.349 29.630 0.00 0.00 0.00 1.78
5269 6997 6.577638 GCCTACTAATTTAGTCCTTCCCACAA 60.578 42.308 12.26 0.00 40.14 3.33
5373 7105 8.822855 GTTTGGTTTTGTAGTAAAATTCCCAAG 58.177 33.333 0.00 0.00 30.22 3.61
5375 7107 7.848128 TGTTTGGTTTTGTAGTAAAATTCCCA 58.152 30.769 0.00 0.00 0.00 4.37
5426 7158 1.466950 GCTACAAACAATGGCGTGCTA 59.533 47.619 0.00 0.00 0.00 3.49
5433 7165 4.688879 TCGTTGTCTAGCTACAAACAATGG 59.311 41.667 20.41 13.52 40.85 3.16
5434 7166 5.839262 TCGTTGTCTAGCTACAAACAATG 57.161 39.130 17.35 17.35 40.85 2.82
5442 7174 3.701532 AGCTCATCGTTGTCTAGCTAC 57.298 47.619 6.42 0.00 41.56 3.58
6057 7902 8.736244 GGTTAACATCTAAACATACATGTGGTT 58.264 33.333 9.11 10.14 41.61 3.67
6071 7916 7.775053 AATTTGGCAGAAGGTTAACATCTAA 57.225 32.000 8.10 2.68 0.00 2.10
6145 7992 6.423604 ACTTTTGTCCACAAACTTTTTGTCTG 59.576 34.615 4.32 0.00 44.56 3.51
6187 8040 9.601217 GTAGAAATAGTTCCACATGTAGATGTT 57.399 33.333 2.09 0.00 41.12 2.71
6269 8136 4.214758 TGCTGACATTTGTCTCATGAACTG 59.785 41.667 11.67 0.00 44.99 3.16
6273 8140 5.005094 TGATTGCTGACATTTGTCTCATGA 58.995 37.500 11.67 0.00 44.99 3.07
6293 8160 7.177216 ACACAATCACAAGTCATGGTTTATGAT 59.823 33.333 0.00 0.00 46.85 2.45
6312 8184 6.426328 TGAATTGGTTTGCCATTTACACAATC 59.574 34.615 0.00 0.00 45.56 2.67
6390 8267 9.311916 GCATAAAATAAACATTGCCTCACATTA 57.688 29.630 0.00 0.00 0.00 1.90
6410 8289 4.579340 TGTTCAACAAAGGGTACGCATAAA 59.421 37.500 12.95 0.00 0.00 1.40
6460 8339 2.159226 CGGGTGTAGAAGTGAGGATGTC 60.159 54.545 0.00 0.00 0.00 3.06
6482 8361 6.650807 AGCATAAATATCACAATACCGTCCAG 59.349 38.462 0.00 0.00 0.00 3.86
6500 8379 9.705290 GGGAAAGAGTAATTTTCAAAGCATAAA 57.295 29.630 0.00 0.00 36.50 1.40
6564 8484 6.142818 TGTGTGTGGGTTAGAAAATTTCTG 57.857 37.500 17.70 0.00 40.94 3.02
6610 8530 4.559300 GCAGCCGGTTGCATCATAATTATT 60.559 41.667 34.95 0.00 44.83 1.40
6636 8556 2.917713 AACCAGGGCAATCCATGTTA 57.082 45.000 0.00 0.00 42.34 2.41
6808 8730 4.767928 ACCATGTAGCCGGATTTTTGTAAA 59.232 37.500 5.05 0.00 0.00 2.01
6813 8735 2.014128 CGACCATGTAGCCGGATTTTT 58.986 47.619 5.05 0.00 0.00 1.94
6822 8744 2.102588 ACACCCTTATCGACCATGTAGC 59.897 50.000 0.00 0.00 0.00 3.58
6992 8920 1.117150 GGAAGTATCCCACGCCTGTA 58.883 55.000 0.00 0.00 40.10 2.74
7422 9366 2.745821 TGCATGTTTGTTGCAAGCAAAA 59.254 36.364 20.95 11.48 46.48 2.44
7569 9513 3.443045 GCGTTCCTGGGGTGCATG 61.443 66.667 0.00 0.00 0.00 4.06
7592 9536 8.915057 AGATCGGAAATGATAAGAACAATGAT 57.085 30.769 0.00 0.00 0.00 2.45
7612 9556 8.873215 ACAATATACTTGACAAACCTAGATCG 57.127 34.615 0.00 0.00 0.00 3.69
7755 9703 6.403866 TTGCTACCATCATTGTCAAGTTTT 57.596 33.333 0.00 0.00 0.00 2.43
7763 9711 4.019174 CCTCCTTTTGCTACCATCATTGT 58.981 43.478 0.00 0.00 0.00 2.71
7789 9738 7.413438 CCAGAGATAGCAAACTTGTTGTATGAC 60.413 40.741 0.00 0.00 0.00 3.06
7946 9896 5.826737 ACTGGAATTAGGATCAAGCTGAATG 59.173 40.000 0.00 0.00 0.00 2.67
8086 10038 5.803461 CGTCCGTCAATGACAAAGATAGTTA 59.197 40.000 14.24 0.00 32.91 2.24
8107 10059 2.837883 AATGCATGGATGGCGCGTC 61.838 57.895 2.29 2.29 0.00 5.19
8192 10144 2.288825 TGAACTGGCAACTCCGTAGAAG 60.289 50.000 0.00 0.00 37.80 2.85
8230 10185 9.066892 GCTATTTGGACTCATTTATTGGTGATA 57.933 33.333 0.00 0.00 0.00 2.15
8262 10217 5.683681 TGACAATGGCAGTGATACATATGT 58.316 37.500 23.05 13.93 0.00 2.29


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

AutoCloner maintained by Alex Coulton.