Multiple sequence alignment - TraesCS2A01G058300

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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 TraesCS2A01G058300 chr2A 100.000 4818 0 0 1 4818 24413566 24408749 0.000000e+00 8898.0
1 TraesCS2A01G058300 chr2A 81.191 2116 352 26 1745 3845 24174380 24176464 0.000000e+00 1661.0
2 TraesCS2A01G058300 chr2A 81.839 859 148 5 1745 2596 24308521 24307664 0.000000e+00 715.0
3 TraesCS2A01G058300 chr2A 76.106 226 27 17 4094 4293 766457643 766457419 5.130000e-15 93.5
4 TraesCS2A01G058300 chr2B 89.993 4157 300 39 699 4818 38416187 38420264 0.000000e+00 5265.0
5 TraesCS2A01G058300 chr2B 91.407 2665 149 42 2188 4818 39087024 39089642 0.000000e+00 3579.0
6 TraesCS2A01G058300 chr2B 91.948 2546 184 9 1669 4203 38073994 38076529 0.000000e+00 3546.0
7 TraesCS2A01G058300 chr2B 84.309 3110 426 42 744 3822 37676752 37679830 0.000000e+00 2983.0
8 TraesCS2A01G058300 chr2B 85.161 2864 380 30 974 3822 38033616 38036449 0.000000e+00 2892.0
9 TraesCS2A01G058300 chr2B 81.427 2116 346 31 1745 3845 39339823 39337740 0.000000e+00 1687.0
10 TraesCS2A01G058300 chr2B 80.306 2092 349 42 1745 3817 39184774 39186821 0.000000e+00 1522.0
11 TraesCS2A01G058300 chr2B 83.654 312 33 16 1583 1885 39184474 39184776 1.320000e-70 278.0
12 TraesCS2A01G058300 chr2B 88.304 171 18 2 211 380 38030968 38031137 2.270000e-48 204.0
13 TraesCS2A01G058300 chr2B 84.000 225 13 7 59 277 38414119 38414326 1.370000e-45 195.0
14 TraesCS2A01G058300 chr2B 82.297 209 15 12 448 641 38414324 38414525 1.390000e-35 161.0
15 TraesCS2A01G058300 chr2B 91.071 112 7 1 4710 4818 38090211 38090322 1.080000e-31 148.0
16 TraesCS2A01G058300 chr2D 90.782 3374 211 32 1468 4818 22820505 22817209 0.000000e+00 4416.0
17 TraesCS2A01G058300 chr2D 82.617 2094 324 30 1745 3821 22510456 22508386 0.000000e+00 1814.0
18 TraesCS2A01G058300 chr2D 87.688 731 68 9 699 1418 22821225 22820506 0.000000e+00 832.0
19 TraesCS2A01G058300 chr2D 81.164 584 89 16 1311 1885 22511025 22510454 2.640000e-122 449.0
20 TraesCS2A01G058300 chr2D 87.425 167 11 5 127 288 22821664 22821503 2.960000e-42 183.0
21 TraesCS2A01G058300 chr7B 84.888 536 81 0 1745 2280 744137976 744138511 4.240000e-150 542.0
22 TraesCS2A01G058300 chr6A 98.276 58 1 0 4088 4145 20245896 20245839 8.530000e-18 102.0
23 TraesCS2A01G058300 chr3D 95.000 60 3 0 4088 4147 591824198 591824257 1.430000e-15 95.3
24 TraesCS2A01G058300 chr5A 80.508 118 23 0 4621 4738 633324203 633324086 1.850000e-14 91.6
25 TraesCS2A01G058300 chr5B 78.992 119 25 0 4621 4739 636266853 636266735 1.110000e-11 82.4
26 TraesCS2A01G058300 chr4A 79.310 116 24 0 4624 4739 664181045 664180930 1.110000e-11 82.4


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 TraesCS2A01G058300 chr2A 24408749 24413566 4817 True 8898.000000 8898 100.000000 1 4818 1 chr2A.!!$R2 4817
1 TraesCS2A01G058300 chr2A 24174380 24176464 2084 False 1661.000000 1661 81.191000 1745 3845 1 chr2A.!!$F1 2100
2 TraesCS2A01G058300 chr2A 24307664 24308521 857 True 715.000000 715 81.839000 1745 2596 1 chr2A.!!$R1 851
3 TraesCS2A01G058300 chr2B 39087024 39089642 2618 False 3579.000000 3579 91.407000 2188 4818 1 chr2B.!!$F4 2630
4 TraesCS2A01G058300 chr2B 38073994 38076529 2535 False 3546.000000 3546 91.948000 1669 4203 1 chr2B.!!$F2 2534
5 TraesCS2A01G058300 chr2B 37676752 37679830 3078 False 2983.000000 2983 84.309000 744 3822 1 chr2B.!!$F1 3078
6 TraesCS2A01G058300 chr2B 38414119 38420264 6145 False 1873.666667 5265 85.430000 59 4818 3 chr2B.!!$F6 4759
7 TraesCS2A01G058300 chr2B 39337740 39339823 2083 True 1687.000000 1687 81.427000 1745 3845 1 chr2B.!!$R1 2100
8 TraesCS2A01G058300 chr2B 38030968 38036449 5481 False 1548.000000 2892 86.732500 211 3822 2 chr2B.!!$F5 3611
9 TraesCS2A01G058300 chr2B 39184474 39186821 2347 False 900.000000 1522 81.980000 1583 3817 2 chr2B.!!$F7 2234
10 TraesCS2A01G058300 chr2D 22817209 22821664 4455 True 1810.333333 4416 88.631667 127 4818 3 chr2D.!!$R2 4691
11 TraesCS2A01G058300 chr2D 22508386 22511025 2639 True 1131.500000 1814 81.890500 1311 3821 2 chr2D.!!$R1 2510
12 TraesCS2A01G058300 chr7B 744137976 744138511 535 False 542.000000 542 84.888000 1745 2280 1 chr7B.!!$F1 535

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
361 373 0.107945 GCAGAGACGGGCTCAAATCT 60.108 55.000 14.42 0.0 46.45 2.40 F
657 981 0.180171 TTCTGGTGACTGGTGGTGTG 59.820 55.000 0.00 0.0 0.00 3.82 F
1182 4508 0.320771 ACGGTGATGACTGTTGCTCC 60.321 55.000 0.00 0.0 38.67 4.70 F
1189 4515 0.397941 TGACTGTTGCTCCTGGGAAG 59.602 55.000 0.00 0.0 0.00 3.46 F
1241 4567 0.942410 TTGCGTCTCGACCTTTTCCG 60.942 55.000 0.00 0.0 0.00 4.30 F
1581 4911 1.003580 TCCCAGAATCTGTCAGCAACC 59.996 52.381 9.63 0.0 0.00 3.77 F
2194 5668 2.791383 TGCCCAATTTTCTGTTCACG 57.209 45.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 4515 1.209128 CTATTGTCGCACGTGATCCC 58.791 55.000 22.23 3.79 0.00 3.85 R
2152 5626 3.007398 TGCTTCCCCGCAAATTATTGTTT 59.993 39.130 0.00 0.00 38.85 2.83 R
2194 5668 3.925299 GGTAAACTAGTGTCGCTTCCTTC 59.075 47.826 0.00 0.00 0.00 3.46 R
2264 5738 6.039382 AGCAGTCGAAGATTAGTTTGGTTTTT 59.961 34.615 0.00 0.00 40.67 1.94 R
2779 6266 6.825944 TCCGATAGATCTAACATCTGAAGG 57.174 41.667 6.52 0.00 39.76 3.46 R
3280 6769 1.483004 TGTCCGTATGTGTATGGTGGG 59.517 52.381 0.00 0.00 38.05 4.61 R
4030 7542 0.324738 CTCCTCAGCACCCCAGTCTA 60.325 60.000 0.00 0.00 0.00 2.59 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 0.546598 ATTTCCCAGCTAACCTCCGG 59.453 55.000 0.00 0.00 0.00 5.14
20 21 2.193087 TTTCCCAGCTAACCTCCGGC 62.193 60.000 0.00 0.00 0.00 6.13
21 22 4.530857 CCCAGCTAACCTCCGGCG 62.531 72.222 0.00 0.00 0.00 6.46
25 26 4.547367 GCTAACCTCCGGCGCCAT 62.547 66.667 28.98 7.16 0.00 4.40
26 27 2.588877 CTAACCTCCGGCGCCATG 60.589 66.667 28.98 17.39 0.00 3.66
27 28 4.169696 TAACCTCCGGCGCCATGG 62.170 66.667 28.98 25.29 0.00 3.66
87 88 2.046023 CACAGAGCCGCATCCCAA 60.046 61.111 0.00 0.00 0.00 4.12
96 97 3.554692 GCATCCCAACGTCGCGAG 61.555 66.667 10.24 6.53 0.00 5.03
102 103 2.050351 CAACGTCGCGAGGACTGT 60.050 61.111 32.99 13.24 43.79 3.55
114 115 2.529744 GGACTGTGGGGGAAGCTGT 61.530 63.158 0.00 0.00 0.00 4.40
118 119 4.410400 GTGGGGGAAGCTGTCGGG 62.410 72.222 0.00 0.00 0.00 5.14
246 257 4.560856 GCATCGTCTCTCGCGGCT 62.561 66.667 6.13 0.00 39.67 5.52
280 291 1.065854 CCACATCAGGAGGTCACTTCC 60.066 57.143 0.00 0.00 0.00 3.46
291 302 4.116238 GAGGTCACTTCCGATTCTGAATC 58.884 47.826 18.28 18.28 34.52 2.52
309 320 3.584406 ATCGAGTTGTTGTCTCCTCTG 57.416 47.619 0.00 0.00 0.00 3.35
344 356 1.078497 ATGCCTCCGATTTCGTGCA 60.078 52.632 10.16 10.16 39.46 4.57
350 362 0.456142 TCCGATTTCGTGCAGAGACG 60.456 55.000 0.00 0.00 40.83 4.18
361 373 0.107945 GCAGAGACGGGCTCAAATCT 60.108 55.000 14.42 0.00 46.45 2.40
362 374 1.933247 CAGAGACGGGCTCAAATCTC 58.067 55.000 14.42 1.98 46.45 2.75
365 377 2.125106 ACGGGCTCAAATCTCCGC 60.125 61.111 0.00 0.00 45.65 5.54
366 378 2.897350 CGGGCTCAAATCTCCGCC 60.897 66.667 0.00 0.00 41.75 6.13
370 382 3.264897 CTCAAATCTCCGCCGGCG 61.265 66.667 41.00 41.00 39.44 6.46
387 399 2.125793 GGCGAACTGGTACCGGAC 60.126 66.667 27.93 17.98 0.00 4.79
388 400 2.505557 GCGAACTGGTACCGGACG 60.506 66.667 27.93 27.53 0.00 4.79
398 410 2.717044 TACCGGACGGGACATGCTG 61.717 63.158 9.46 0.00 39.97 4.41
421 433 2.049063 ACGACGAGTTCTGCTGGC 60.049 61.111 0.00 0.00 0.00 4.85
442 454 3.809374 CTAGCGCCGGGGGATTCAC 62.809 68.421 21.35 1.75 0.00 3.18
470 482 2.062519 GGTCGACTGAAGCTTCTGAAC 58.937 52.381 32.44 25.00 0.00 3.18
471 483 1.716581 GTCGACTGAAGCTTCTGAACG 59.283 52.381 32.44 30.80 34.36 3.95
515 540 1.281867 TGCTTAGCTGGTATGCCACTT 59.718 47.619 18.28 0.00 40.46 3.16
516 541 1.943340 GCTTAGCTGGTATGCCACTTC 59.057 52.381 12.22 0.00 40.46 3.01
517 542 2.205074 CTTAGCTGGTATGCCACTTCG 58.795 52.381 0.00 0.00 40.46 3.79
539 564 2.044492 TCCACCTCTCTATCACCACCTT 59.956 50.000 0.00 0.00 0.00 3.50
544 569 5.833667 CACCTCTCTATCACCACCTTATGTA 59.166 44.000 0.00 0.00 0.00 2.29
547 572 6.551601 CCTCTCTATCACCACCTTATGTAACT 59.448 42.308 0.00 0.00 0.00 2.24
578 900 8.370182 AGTTGCAGGATTGAGTTATGAAATTTT 58.630 29.630 0.00 0.00 0.00 1.82
581 903 6.815142 GCAGGATTGAGTTATGAAATTTTGCT 59.185 34.615 0.00 0.00 0.00 3.91
620 942 2.086054 AGTGTCAGAGAACAATCCGC 57.914 50.000 0.00 0.00 0.00 5.54
641 965 2.444766 CCCTTTATCCATCCAGGCTTCT 59.555 50.000 0.00 0.00 37.29 2.85
642 966 3.484407 CCTTTATCCATCCAGGCTTCTG 58.516 50.000 0.00 0.00 37.29 3.02
652 976 0.604780 CAGGCTTCTGGTGACTGGTG 60.605 60.000 0.00 0.00 34.96 4.17
653 977 1.302832 GGCTTCTGGTGACTGGTGG 60.303 63.158 0.00 0.00 0.00 4.61
654 978 1.451936 GCTTCTGGTGACTGGTGGT 59.548 57.895 0.00 0.00 0.00 4.16
655 979 0.886490 GCTTCTGGTGACTGGTGGTG 60.886 60.000 0.00 0.00 0.00 4.17
656 980 0.469917 CTTCTGGTGACTGGTGGTGT 59.530 55.000 0.00 0.00 0.00 4.16
657 981 0.180171 TTCTGGTGACTGGTGGTGTG 59.820 55.000 0.00 0.00 0.00 3.82
658 982 0.980754 TCTGGTGACTGGTGGTGTGT 60.981 55.000 0.00 0.00 0.00 3.72
659 983 0.756294 CTGGTGACTGGTGGTGTGTA 59.244 55.000 0.00 0.00 0.00 2.90
660 984 0.756294 TGGTGACTGGTGGTGTGTAG 59.244 55.000 0.00 0.00 0.00 2.74
662 986 0.944311 GTGACTGGTGGTGTGTAGCG 60.944 60.000 0.00 0.00 0.00 4.26
663 987 2.027625 GACTGGTGGTGTGTAGCGC 61.028 63.158 0.00 0.00 0.00 5.92
689 3243 5.052172 CGTTCACATCAGCAACTTTTCTTTG 60.052 40.000 0.00 0.00 0.00 2.77
690 3244 5.581126 TCACATCAGCAACTTTTCTTTGT 57.419 34.783 0.00 0.00 0.00 2.83
691 3245 5.342433 TCACATCAGCAACTTTTCTTTGTG 58.658 37.500 0.00 0.00 34.69 3.33
692 3246 4.505191 CACATCAGCAACTTTTCTTTGTGG 59.495 41.667 0.00 0.00 0.00 4.17
697 3270 4.016444 AGCAACTTTTCTTTGTGGTCAGA 58.984 39.130 0.00 0.00 0.00 3.27
711 3284 2.288666 GGTCAGATCCAAAATAGCGCA 58.711 47.619 11.47 0.00 0.00 6.09
875 3476 4.848357 CATACCTTCTTTGACCATGGACT 58.152 43.478 21.47 0.00 0.00 3.85
882 3483 6.072452 CCTTCTTTGACCATGGACTAAAACTC 60.072 42.308 21.47 2.93 0.00 3.01
893 3494 7.176690 CCATGGACTAAAACTCTGTTTACCAAT 59.823 37.037 5.56 0.00 28.50 3.16
920 3521 8.668353 CAAGTGTATTGTATTTCACATAGCAGT 58.332 33.333 0.00 0.00 36.90 4.40
1048 4374 1.215647 CTCCTGGTCCTGTGCGTAC 59.784 63.158 0.00 0.00 0.00 3.67
1065 4391 1.555075 GTACTCCACTCCATGCTTCCA 59.445 52.381 0.00 0.00 0.00 3.53
1125 4451 5.420104 CCTCATGGAAATTAGCTCTTGGTTT 59.580 40.000 0.00 0.00 34.57 3.27
1127 4453 7.391148 TCATGGAAATTAGCTCTTGGTTTAC 57.609 36.000 0.00 0.00 0.00 2.01
1137 4463 1.941294 TCTTGGTTTACGAGCGCAAAA 59.059 42.857 11.47 1.26 0.00 2.44
1142 4468 1.136169 GTTTACGAGCGCAAAATCCGT 60.136 47.619 11.47 11.31 37.27 4.69
1182 4508 0.320771 ACGGTGATGACTGTTGCTCC 60.321 55.000 0.00 0.00 38.67 4.70
1189 4515 0.397941 TGACTGTTGCTCCTGGGAAG 59.602 55.000 0.00 0.00 0.00 3.46
1238 4564 3.306166 CGAATATTGCGTCTCGACCTTTT 59.694 43.478 0.00 0.00 33.13 2.27
1241 4567 0.942410 TTGCGTCTCGACCTTTTCCG 60.942 55.000 0.00 0.00 0.00 4.30
1242 4568 1.080974 GCGTCTCGACCTTTTCCGA 60.081 57.895 0.00 0.00 0.00 4.55
1264 4590 3.272551 ACTCTACCAGTCAATCCCTACCT 59.727 47.826 0.00 0.00 0.00 3.08
1267 4593 5.394738 TCTACCAGTCAATCCCTACCTATG 58.605 45.833 0.00 0.00 0.00 2.23
1268 4594 3.318313 ACCAGTCAATCCCTACCTATGG 58.682 50.000 0.00 0.00 0.00 2.74
1269 4595 3.051341 ACCAGTCAATCCCTACCTATGGA 60.051 47.826 0.00 0.00 34.54 3.41
1332 4658 5.129634 TGCTGGAACTTGAACTTGACAATA 58.870 37.500 0.00 0.00 0.00 1.90
1391 4717 5.119588 TCTCTGGAAATTACGCTTGTTTACG 59.880 40.000 0.00 0.00 0.00 3.18
1427 4754 1.473677 GTGGCTTCTGTTGCATGCATA 59.526 47.619 23.37 12.96 0.00 3.14
1436 4763 5.430886 TCTGTTGCATGCATACAACTCTAT 58.569 37.500 32.43 0.00 45.07 1.98
1437 4764 6.581712 TCTGTTGCATGCATACAACTCTATA 58.418 36.000 32.43 17.71 45.07 1.31
1438 4765 6.703165 TCTGTTGCATGCATACAACTCTATAG 59.297 38.462 32.43 23.94 45.07 1.31
1581 4911 1.003580 TCCCAGAATCTGTCAGCAACC 59.996 52.381 9.63 0.00 0.00 3.77
1629 4959 6.013379 TCTCAAGAGAAATAACATGAGTGGGT 60.013 38.462 0.00 0.00 36.54 4.51
1652 4982 7.175990 GGGTCTCTTCAGAATATAGGTACTGAG 59.824 44.444 0.00 0.00 41.52 3.35
1696 5027 7.307930 CCCTTTTCAGTTTGGTGCAATTAAATC 60.308 37.037 0.00 0.00 0.00 2.17
1699 5030 8.729805 TTTCAGTTTGGTGCAATTAAATCTTT 57.270 26.923 0.00 0.00 0.00 2.52
1877 5213 8.721133 TGAAGGACATATACCTATAAGCTCAA 57.279 34.615 0.00 0.00 36.67 3.02
1940 5414 6.123651 TCTGGAAACAAGCTAAGTGGTAAAA 58.876 36.000 0.00 0.00 42.06 1.52
2074 5548 7.750229 ATTGAGAACACTAATGCTTTCTTCA 57.250 32.000 0.00 0.00 0.00 3.02
2152 5626 5.532032 TCATCTGCAGTTTCTTGATTTGTCA 59.468 36.000 14.67 0.00 0.00 3.58
2194 5668 2.791383 TGCCCAATTTTCTGTTCACG 57.209 45.000 0.00 0.00 0.00 4.35
2229 5703 6.037098 CACTAGTTTACCTGGATCTTTCGAG 58.963 44.000 0.00 0.00 0.00 4.04
2264 5738 6.672218 AGTTGGATCATTATACCCGATATGGA 59.328 38.462 0.00 0.00 42.00 3.41
2506 5984 4.206375 TCACTGATTGTTCTGCTTTGGAA 58.794 39.130 0.00 0.00 0.00 3.53
3055 6544 5.485620 TCATCAAATCTCTGTTGTCTCCAG 58.514 41.667 0.00 0.00 0.00 3.86
3256 6745 5.762179 ACAGTGATTATGAACTCCAAGGA 57.238 39.130 0.00 0.00 0.00 3.36
3280 6769 3.146847 CACCTTCACCACTAAAGGGAAC 58.853 50.000 6.15 0.00 45.27 3.62
3606 7096 0.798776 GGTCAGTTCAGCACATTCGG 59.201 55.000 0.00 0.00 0.00 4.30
3671 7161 0.038744 AAGTTCAGGTCCCATGGCAG 59.961 55.000 6.09 0.00 0.00 4.85
3857 7358 2.550978 CTAGGTGAATGGCGACGATTT 58.449 47.619 0.00 0.00 0.00 2.17
3858 7359 2.684001 AGGTGAATGGCGACGATTTA 57.316 45.000 0.00 0.00 0.00 1.40
3888 7389 7.759433 ACAACATAAATATTTGTAAGCTGTGCC 59.241 33.333 11.05 0.00 31.65 5.01
3902 7403 4.133078 AGCTGTGCCTTAATAATCTGCTC 58.867 43.478 0.00 0.00 0.00 4.26
3915 7416 6.798427 ATAATCTGCTCTCCTGTTCTGTTA 57.202 37.500 0.00 0.00 0.00 2.41
3965 7466 3.401182 AGAAGCTTTGTCTCAGCAGAAG 58.599 45.455 0.00 0.00 39.99 2.85
3966 7467 2.926778 AGCTTTGTCTCAGCAGAAGT 57.073 45.000 0.00 0.00 39.99 3.01
3967 7468 2.492012 AGCTTTGTCTCAGCAGAAGTG 58.508 47.619 0.00 0.00 39.99 3.16
3989 7501 6.701400 AGTGTATTTCCAATTTGTTCTTGTGC 59.299 34.615 0.00 0.00 0.00 4.57
3995 7507 5.291178 TCCAATTTGTTCTTGTGCATGAAG 58.709 37.500 0.00 0.00 0.00 3.02
4002 7514 2.497138 TCTTGTGCATGAAGGTGAGTG 58.503 47.619 0.00 0.00 0.00 3.51
4004 7516 2.636647 TGTGCATGAAGGTGAGTGAA 57.363 45.000 0.00 0.00 0.00 3.18
4068 7580 2.700897 GAGGTAAGAAGATGCTGCCCTA 59.299 50.000 0.00 0.00 0.00 3.53
4172 7684 3.951037 TGCATTTGTTGTTGTCTGGTAGT 59.049 39.130 0.00 0.00 0.00 2.73
4174 7686 4.036262 GCATTTGTTGTTGTCTGGTAGTGA 59.964 41.667 0.00 0.00 0.00 3.41
4210 7722 4.460263 TGAGCTGACACTTTGTTTGGTAT 58.540 39.130 0.00 0.00 0.00 2.73
4242 7754 8.351495 TCTGTTTAAACATGCTGAACAATTTC 57.649 30.769 20.83 0.00 38.41 2.17
4243 7755 7.978414 TCTGTTTAAACATGCTGAACAATTTCA 59.022 29.630 20.83 0.00 37.57 2.69
4488 8027 9.611284 GGAAATTTATTGAAAACTTGAAATGCC 57.389 29.630 0.00 0.00 0.00 4.40
4646 8198 6.984740 TTCTGAACATAATTTGAAACACGC 57.015 33.333 0.00 0.00 0.00 5.34
4650 8202 4.231718 ACATAATTTGAAACACGCCGTT 57.768 36.364 0.00 0.00 40.50 4.44
4739 8301 2.172717 GAGGGTATTTGGGCTAAGCTCA 59.827 50.000 0.00 0.00 37.19 4.26
4809 8374 2.736670 ATTTACCCTCATGCACCCTC 57.263 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 4.039357 CCACAGTCCTCGCGACGT 62.039 66.667 3.71 0.00 46.92 4.34
92 93 3.316573 CTTCCCCCACAGTCCTCGC 62.317 68.421 0.00 0.00 0.00 5.03
93 94 2.982130 CTTCCCCCACAGTCCTCG 59.018 66.667 0.00 0.00 0.00 4.63
96 97 2.352805 CAGCTTCCCCCACAGTCC 59.647 66.667 0.00 0.00 0.00 3.85
291 302 2.797156 CAACAGAGGAGACAACAACTCG 59.203 50.000 0.00 0.00 35.49 4.18
294 305 3.798202 ACTCAACAGAGGAGACAACAAC 58.202 45.455 0.00 0.00 36.26 3.32
297 308 4.945246 TGTTACTCAACAGAGGAGACAAC 58.055 43.478 0.00 0.00 39.75 3.32
309 320 1.978782 GCATGCGCTTTGTTACTCAAC 59.021 47.619 9.73 0.00 35.61 3.18
344 356 0.827368 GGAGATTTGAGCCCGTCTCT 59.173 55.000 0.00 0.00 42.38 3.10
350 362 2.897350 CGGCGGAGATTTGAGCCC 60.897 66.667 0.00 0.00 46.36 5.19
370 382 2.125793 GTCCGGTACCAGTTCGCC 60.126 66.667 13.54 0.00 0.00 5.54
373 385 1.978617 TCCCGTCCGGTACCAGTTC 60.979 63.158 13.54 0.00 0.00 3.01
380 392 2.363276 AGCATGTCCCGTCCGGTA 60.363 61.111 0.00 0.00 0.00 4.02
381 393 4.082523 CAGCATGTCCCGTCCGGT 62.083 66.667 0.00 0.00 0.00 5.28
398 410 4.755614 AGAACTCGTCGTCGGCGC 62.756 66.667 15.63 0.00 38.14 6.53
400 412 3.173240 GCAGAACTCGTCGTCGGC 61.173 66.667 1.55 0.00 37.69 5.54
401 413 1.797933 CAGCAGAACTCGTCGTCGG 60.798 63.158 1.55 0.00 37.69 4.79
402 414 1.797933 CCAGCAGAACTCGTCGTCG 60.798 63.158 0.00 0.00 38.55 5.12
403 415 2.089349 GCCAGCAGAACTCGTCGTC 61.089 63.158 0.00 0.00 0.00 4.20
442 454 4.794439 TCAGTCGACCATGCGCCG 62.794 66.667 13.01 0.00 0.00 6.46
446 458 0.723981 GAAGCTTCAGTCGACCATGC 59.276 55.000 21.67 12.77 0.00 4.06
447 459 1.998315 CAGAAGCTTCAGTCGACCATG 59.002 52.381 27.57 10.34 0.00 3.66
481 493 2.755650 CTAAGCAACTTGTCAGTCCGT 58.244 47.619 0.00 0.00 30.45 4.69
490 502 2.098117 GGCATACCAGCTAAGCAACTTG 59.902 50.000 0.00 0.00 35.26 3.16
491 503 2.290896 TGGCATACCAGCTAAGCAACTT 60.291 45.455 0.00 0.00 42.67 2.66
515 540 1.283905 TGGTGATAGAGAGGTGGACGA 59.716 52.381 0.00 0.00 0.00 4.20
516 541 1.405821 GTGGTGATAGAGAGGTGGACG 59.594 57.143 0.00 0.00 0.00 4.79
517 542 1.757699 GGTGGTGATAGAGAGGTGGAC 59.242 57.143 0.00 0.00 0.00 4.02
539 564 7.880713 TCAATCCTGCAACTTGTTAGTTACATA 59.119 33.333 0.00 0.00 42.67 2.29
544 569 5.133221 ACTCAATCCTGCAACTTGTTAGTT 58.867 37.500 0.00 0.00 45.40 2.24
547 572 6.939730 TCATAACTCAATCCTGCAACTTGTTA 59.060 34.615 0.00 0.00 0.00 2.41
583 905 9.520515 TCTGACACTATGTGAATCTGCTATATA 57.479 33.333 4.61 0.00 36.96 0.86
584 906 8.414629 TCTGACACTATGTGAATCTGCTATAT 57.585 34.615 4.61 0.00 36.96 0.86
585 907 7.721399 TCTCTGACACTATGTGAATCTGCTATA 59.279 37.037 4.61 0.00 36.96 1.31
586 908 6.548993 TCTCTGACACTATGTGAATCTGCTAT 59.451 38.462 4.61 0.00 36.96 2.97
587 909 5.888161 TCTCTGACACTATGTGAATCTGCTA 59.112 40.000 4.61 0.00 36.96 3.49
597 919 4.748892 CGGATTGTTCTCTGACACTATGT 58.251 43.478 0.00 0.00 0.00 2.29
600 922 2.094182 GGCGGATTGTTCTCTGACACTA 60.094 50.000 0.00 0.00 29.23 2.74
620 942 2.444766 AGAAGCCTGGATGGATAAAGGG 59.555 50.000 0.00 0.00 38.35 3.95
641 965 0.756294 CTACACACCACCAGTCACCA 59.244 55.000 0.00 0.00 0.00 4.17
642 966 0.602905 GCTACACACCACCAGTCACC 60.603 60.000 0.00 0.00 0.00 4.02
644 968 1.365999 CGCTACACACCACCAGTCA 59.634 57.895 0.00 0.00 0.00 3.41
646 970 2.030562 GCGCTACACACCACCAGT 59.969 61.111 0.00 0.00 0.00 4.00
655 979 0.093026 GATGTGAACGTGCGCTACAC 59.907 55.000 9.73 11.83 46.45 2.90
656 980 0.319125 TGATGTGAACGTGCGCTACA 60.319 50.000 9.73 5.72 0.00 2.74
657 981 0.366871 CTGATGTGAACGTGCGCTAC 59.633 55.000 9.73 4.27 0.00 3.58
658 982 1.351430 GCTGATGTGAACGTGCGCTA 61.351 55.000 9.73 0.00 0.00 4.26
659 983 2.671177 GCTGATGTGAACGTGCGCT 61.671 57.895 9.73 0.00 0.00 5.92
660 984 2.202222 GCTGATGTGAACGTGCGC 60.202 61.111 0.00 0.00 0.00 6.09
662 986 0.588252 AGTTGCTGATGTGAACGTGC 59.412 50.000 0.00 0.00 0.00 5.34
663 987 3.338818 AAAGTTGCTGATGTGAACGTG 57.661 42.857 0.00 0.00 0.00 4.49
689 3243 2.032178 GCGCTATTTTGGATCTGACCAC 59.968 50.000 0.00 0.00 39.85 4.16
690 3244 2.288666 GCGCTATTTTGGATCTGACCA 58.711 47.619 0.00 0.00 38.24 4.02
691 3245 2.288666 TGCGCTATTTTGGATCTGACC 58.711 47.619 9.73 0.00 0.00 4.02
692 3246 4.558538 AATGCGCTATTTTGGATCTGAC 57.441 40.909 9.73 0.00 0.00 3.51
697 3270 3.709987 GCAGAAATGCGCTATTTTGGAT 58.290 40.909 9.73 0.00 39.06 3.41
831 3432 2.928801 TGGACAGCAACTTGAGCTAA 57.071 45.000 0.00 0.00 41.14 3.09
875 3476 8.514330 ACACTTGATTGGTAAACAGAGTTTTA 57.486 30.769 0.03 0.00 0.00 1.52
893 3494 8.785329 TGCTATGTGAAATACAATACACTTGA 57.215 30.769 0.00 0.00 43.77 3.02
912 3513 6.283694 TCTGCTCCTTTATACAACTGCTATG 58.716 40.000 0.00 0.00 0.00 2.23
1048 4374 1.004044 ACTTGGAAGCATGGAGTGGAG 59.996 52.381 0.00 0.00 0.00 3.86
1065 4391 2.645838 TGAAGCAGCCTGAAGAACTT 57.354 45.000 0.00 0.00 0.00 2.66
1125 4451 1.355796 CCACGGATTTTGCGCTCGTA 61.356 55.000 9.73 0.00 33.30 3.43
1127 4453 2.098298 CCACGGATTTTGCGCTCG 59.902 61.111 9.73 5.67 33.30 5.03
1182 4508 1.450312 GCACGTGATCCCTTCCCAG 60.450 63.158 22.23 0.00 0.00 4.45
1189 4515 1.209128 CTATTGTCGCACGTGATCCC 58.791 55.000 22.23 3.79 0.00 3.85
1214 4540 2.293677 AGGTCGAGACGCAATATTCGAT 59.706 45.455 12.27 3.29 43.03 3.59
1215 4541 1.674441 AGGTCGAGACGCAATATTCGA 59.326 47.619 12.27 3.18 39.48 3.71
1242 4568 3.272551 AGGTAGGGATTGACTGGTAGAGT 59.727 47.826 0.00 0.00 37.76 3.24
1267 4593 3.071874 TGACATGGAACCATCACTTCC 57.928 47.619 3.10 0.00 38.18 3.46
1268 4594 4.201851 CGATTGACATGGAACCATCACTTC 60.202 45.833 3.10 1.36 33.90 3.01
1269 4595 3.691118 CGATTGACATGGAACCATCACTT 59.309 43.478 3.10 0.00 33.90 3.16
1391 4717 2.676342 AGCCACATACCGTCGAAATTTC 59.324 45.455 8.20 8.20 0.00 2.17
1512 4842 4.499183 AGGTTGAGATACTTGAGCTTTCG 58.501 43.478 0.00 0.00 0.00 3.46
1514 4844 5.012561 ACTGAGGTTGAGATACTTGAGCTTT 59.987 40.000 0.00 0.00 0.00 3.51
1581 4911 4.826274 TTATGACCTCCAGAGAAACCAG 57.174 45.455 0.00 0.00 0.00 4.00
1629 4959 7.658167 CGTCTCAGTACCTATATTCTGAAGAGA 59.342 40.741 0.00 0.00 36.67 3.10
1664 4994 5.306678 TGCACCAAACTGAAAAGGGATATTT 59.693 36.000 0.00 0.00 0.00 1.40
1667 4997 3.838565 TGCACCAAACTGAAAAGGGATA 58.161 40.909 0.00 0.00 0.00 2.59
1940 5414 9.638176 ACAATATCTTAGCCAGAAGAAATCAAT 57.362 29.630 0.00 0.00 38.89 2.57
1961 5435 8.753497 TCTATCTCTTTGAGCTCAGTACAATA 57.247 34.615 17.43 12.02 0.00 1.90
1963 5437 7.559533 AGATCTATCTCTTTGAGCTCAGTACAA 59.440 37.037 17.43 7.45 29.30 2.41
2074 5548 9.277783 GTAATCATGCTCTTATCAAGGTTACAT 57.722 33.333 0.00 0.00 0.00 2.29
2152 5626 3.007398 TGCTTCCCCGCAAATTATTGTTT 59.993 39.130 0.00 0.00 38.85 2.83
2194 5668 3.925299 GGTAAACTAGTGTCGCTTCCTTC 59.075 47.826 0.00 0.00 0.00 3.46
2264 5738 6.039382 AGCAGTCGAAGATTAGTTTGGTTTTT 59.961 34.615 0.00 0.00 40.67 1.94
2779 6266 6.825944 TCCGATAGATCTAACATCTGAAGG 57.174 41.667 6.52 0.00 39.76 3.46
3256 6745 3.655777 TCCCTTTAGTGGTGAAGGTGAAT 59.344 43.478 0.00 0.00 40.65 2.57
3280 6769 1.483004 TGTCCGTATGTGTATGGTGGG 59.517 52.381 0.00 0.00 38.05 4.61
3281 6770 2.093921 TGTGTCCGTATGTGTATGGTGG 60.094 50.000 0.00 0.00 38.05 4.61
3282 6771 3.239587 TGTGTCCGTATGTGTATGGTG 57.760 47.619 0.00 0.00 38.05 4.17
3456 6945 2.955660 AGGTCTAAGCTCTCAATCTCGG 59.044 50.000 0.00 0.00 0.00 4.63
3606 7096 5.310451 TGTTCCCTTTGTAACTGTCCATAC 58.690 41.667 0.00 0.00 0.00 2.39
3881 7382 4.133078 AGAGCAGATTATTAAGGCACAGC 58.867 43.478 0.00 0.00 0.00 4.40
3888 7389 7.271511 ACAGAACAGGAGAGCAGATTATTAAG 58.728 38.462 0.00 0.00 0.00 1.85
3902 7403 9.988815 ATAGCATAGTTTATAACAGAACAGGAG 57.011 33.333 0.00 0.00 0.00 3.69
3965 7466 6.478344 TGCACAAGAACAAATTGGAAATACAC 59.522 34.615 0.00 0.00 31.76 2.90
3966 7467 6.577103 TGCACAAGAACAAATTGGAAATACA 58.423 32.000 0.00 0.00 31.76 2.29
3967 7468 7.384660 TCATGCACAAGAACAAATTGGAAATAC 59.615 33.333 0.00 0.00 31.76 1.89
3989 7501 3.131709 ACAGGTTCACTCACCTTCATG 57.868 47.619 0.00 0.00 45.76 3.07
3995 7507 4.918810 ATTTTCAACAGGTTCACTCACC 57.081 40.909 0.00 0.00 37.04 4.02
4002 7514 9.528018 TTTCAAGTTCATATTTTCAACAGGTTC 57.472 29.630 0.00 0.00 0.00 3.62
4030 7542 0.324738 CTCCTCAGCACCCCAGTCTA 60.325 60.000 0.00 0.00 0.00 2.59
4068 7580 3.117512 CCTTAAGCACCATTCTACCCCAT 60.118 47.826 0.00 0.00 0.00 4.00
4172 7684 3.749609 CAGCTCAACATGTCTCAACATCA 59.250 43.478 0.00 0.00 44.41 3.07
4210 7722 6.472016 TCAGCATGTTTAAACAGATACAGGA 58.528 36.000 24.22 12.89 43.04 3.86
4619 8171 9.782028 CGTGTTTCAAATTATGTTCAGAAATTG 57.218 29.630 2.72 2.72 0.00 2.32
4634 8186 0.101399 TGCAACGGCGTGTTTCAAAT 59.899 45.000 15.70 0.00 45.35 2.32
4739 8301 3.953775 CCTGCACGGGACCACCTT 61.954 66.667 0.00 0.00 36.97 3.50


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

AutoCloner maintained by Alex Coulton.