Multiple sequence alignment - TraesCS3B01G161200

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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 TraesCS3B01G161200 chr3B 100.000 4608 0 0 1 4608 157909853 157914460 0.000000e+00 8510
1 TraesCS3B01G161200 chr3B 92.264 530 39 2 21 549 321772508 321771980 0.000000e+00 750
2 TraesCS3B01G161200 chr3D 92.556 3224 141 41 1447 4608 107065255 107068441 0.000000e+00 4532
3 TraesCS3B01G161200 chr3D 96.290 566 13 7 884 1445 107063467 107064028 0.000000e+00 922
4 TraesCS3B01G161200 chr3D 91.682 541 44 1 18 557 559108952 559109492 0.000000e+00 749
5 TraesCS3B01G161200 chr3D 83.612 299 39 5 550 839 107063066 107063363 5.870000e-69 272
6 TraesCS3B01G161200 chr3A 89.201 2389 188 41 1663 4003 549625842 549623476 0.000000e+00 2918
7 TraesCS3B01G161200 chr3A 92.539 697 38 9 884 1570 549626539 549625847 0.000000e+00 987
8 TraesCS3B01G161200 chr4B 92.052 541 41 2 18 556 629957401 629957941 0.000000e+00 760
9 TraesCS3B01G161200 chr4B 92.105 532 42 0 18 549 647645817 647646348 0.000000e+00 750
10 TraesCS3B01G161200 chr4B 94.737 95 5 0 1578 1672 565740312 565740406 1.030000e-31 148
11 TraesCS3B01G161200 chr7B 92.308 533 40 1 21 552 74093202 74092670 0.000000e+00 756
12 TraesCS3B01G161200 chr7B 91.791 536 42 2 18 551 692876333 692876868 0.000000e+00 745
13 TraesCS3B01G161200 chr4D 92.264 530 39 2 21 549 8274948 8274420 0.000000e+00 750
14 TraesCS3B01G161200 chr4D 92.250 529 41 0 21 549 315601189 315600661 0.000000e+00 750
15 TraesCS3B01G161200 chr1B 92.264 530 40 1 21 549 269218789 269218260 0.000000e+00 750
16 TraesCS3B01G161200 chr6D 96.739 92 3 0 1574 1665 458997535 458997626 2.220000e-33 154
17 TraesCS3B01G161200 chr2B 96.739 92 2 1 1579 1670 222220578 222220668 7.990000e-33 152
18 TraesCS3B01G161200 chr6B 94.792 96 5 0 1579 1674 81652400 81652305 2.870000e-32 150
19 TraesCS3B01G161200 chr6B 87.395 119 11 4 1547 1664 62636965 62636850 2.890000e-27 134
20 TraesCS3B01G161200 chr5B 95.699 93 4 0 1572 1664 676928196 676928104 2.870000e-32 150
21 TraesCS3B01G161200 chr5B 93.878 98 5 1 1579 1676 526271476 526271380 3.720000e-31 147
22 TraesCS3B01G161200 chr7A 93.750 96 6 0 1576 1671 637982303 637982398 1.340000e-30 145
23 TraesCS3B01G161200 chr6A 93.878 98 3 3 1573 1669 563554317 563554412 1.340000e-30 145


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 TraesCS3B01G161200 chr3B 157909853 157914460 4607 False 8510.000000 8510 100.000000 1 4608 1 chr3B.!!$F1 4607
1 TraesCS3B01G161200 chr3B 321771980 321772508 528 True 750.000000 750 92.264000 21 549 1 chr3B.!!$R1 528
2 TraesCS3B01G161200 chr3D 107063066 107068441 5375 False 1908.666667 4532 90.819333 550 4608 3 chr3D.!!$F2 4058
3 TraesCS3B01G161200 chr3D 559108952 559109492 540 False 749.000000 749 91.682000 18 557 1 chr3D.!!$F1 539
4 TraesCS3B01G161200 chr3A 549623476 549626539 3063 True 1952.500000 2918 90.870000 884 4003 2 chr3A.!!$R1 3119
5 TraesCS3B01G161200 chr4B 629957401 629957941 540 False 760.000000 760 92.052000 18 556 1 chr4B.!!$F2 538
6 TraesCS3B01G161200 chr4B 647645817 647646348 531 False 750.000000 750 92.105000 18 549 1 chr4B.!!$F3 531
7 TraesCS3B01G161200 chr7B 74092670 74093202 532 True 756.000000 756 92.308000 21 552 1 chr7B.!!$R1 531
8 TraesCS3B01G161200 chr7B 692876333 692876868 535 False 745.000000 745 91.791000 18 551 1 chr7B.!!$F1 533
9 TraesCS3B01G161200 chr4D 8274420 8274948 528 True 750.000000 750 92.264000 21 549 1 chr4D.!!$R1 528
10 TraesCS3B01G161200 chr4D 315600661 315601189 528 True 750.000000 750 92.250000 21 549 1 chr4D.!!$R2 528
11 TraesCS3B01G161200 chr1B 269218260 269218789 529 True 750.000000 750 92.264000 21 549 1 chr1B.!!$R1 528

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
669 672 0.179000 GTGAAGATCACCCGATGCCT 59.821 55.000 0.0 0.0 41.37 4.75 F
1595 2900 0.467659 CCTACTCCCTCCGTTCCGAT 60.468 60.000 0.0 0.0 0.00 4.18 F
1607 2912 0.643820 GTTCCGATTTACTCGCCGTG 59.356 55.000 0.0 0.0 46.25 4.94 F
1609 2914 0.742505 TCCGATTTACTCGCCGTGAT 59.257 50.000 0.0 0.0 46.25 3.06 F
1610 2915 1.135527 TCCGATTTACTCGCCGTGATT 59.864 47.619 0.0 0.0 46.25 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 3382 0.621571 TAGGGAGCAAGCCACAGGAT 60.622 55.000 0.00 0.0 0.00 3.24 R
2582 3913 1.209261 TCGCCTATGGTGAATGCTTGA 59.791 47.619 0.00 0.0 39.45 3.02 R
3340 4684 2.489938 TCAGTTGATTGGTACCTGGC 57.510 50.000 14.36 2.5 0.00 4.85 R
3521 4870 3.590720 TCATATGATTTGTCAAGCGCG 57.409 42.857 0.00 0.0 0.00 6.86 R
3772 5146 9.720667 ACGACATGAACATACATTGAAATAATG 57.279 29.630 0.00 0.0 0.00 1.90 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
101 103 2.701780 GCTCAGGAAGGCGAGACGA 61.702 63.158 0.00 0.00 0.00 4.20
104 106 2.359602 AGGAAGGCGAGACGACGA 60.360 61.111 0.00 0.00 41.28 4.20
121 123 1.667154 CGACGGCTCCCTGAAGATGA 61.667 60.000 0.00 0.00 0.00 2.92
134 136 6.215431 TCCCTGAAGATGAAATAAAGGTCTCA 59.785 38.462 0.00 0.00 0.00 3.27
240 243 1.710013 TTGCTCGGATCTCGTTGTTC 58.290 50.000 0.00 0.00 40.32 3.18
286 289 3.134081 GGTTTGGATCCTTCCGATCTACA 59.866 47.826 14.23 0.00 45.90 2.74
298 301 9.627123 TCCTTCCGATCTACATTATTTTTCATT 57.373 29.630 0.00 0.00 0.00 2.57
390 393 0.179004 ACAAGTTGTGCCCGATTCCA 60.179 50.000 7.96 0.00 0.00 3.53
435 438 2.431942 GCCTTCGGCTCGTTTCGA 60.432 61.111 0.00 0.00 46.69 3.71
449 452 2.407361 CGTTTCGATGCTTGTAGTCGTT 59.593 45.455 0.00 0.00 36.77 3.85
451 454 3.291809 TTCGATGCTTGTAGTCGTTGA 57.708 42.857 0.00 0.00 36.77 3.18
460 463 3.861276 TGTAGTCGTTGATAGGTGGTG 57.139 47.619 0.00 0.00 0.00 4.17
477 480 3.321111 GTGGTGTACGGATCTGGATGTAT 59.679 47.826 6.47 0.00 0.00 2.29
526 529 8.659925 ACTGTCATGATTGAAGATGAATAGAC 57.340 34.615 0.00 0.00 32.48 2.59
578 581 4.846779 TTTAATGGAGCAGCTTTTTCGT 57.153 36.364 0.00 0.00 0.00 3.85
579 582 5.950758 TTTAATGGAGCAGCTTTTTCGTA 57.049 34.783 0.00 0.00 0.00 3.43
580 583 5.545658 TTAATGGAGCAGCTTTTTCGTAG 57.454 39.130 0.00 0.00 0.00 3.51
581 584 1.808411 TGGAGCAGCTTTTTCGTAGG 58.192 50.000 0.00 0.00 0.00 3.18
583 586 2.224426 TGGAGCAGCTTTTTCGTAGGAA 60.224 45.455 0.00 0.00 0.00 3.36
584 587 3.010420 GGAGCAGCTTTTTCGTAGGAAT 58.990 45.455 0.00 0.00 30.88 3.01
623 626 9.695526 TCTCACCAACTTTATTGATTCAAAATG 57.304 29.630 2.68 4.93 0.00 2.32
624 627 8.830201 TCACCAACTTTATTGATTCAAAATGG 57.170 30.769 2.68 8.14 31.66 3.16
663 666 1.153628 GGGTCGTGAAGATCACCCG 60.154 63.158 5.00 0.00 44.20 5.28
665 668 0.460311 GGTCGTGAAGATCACCCGAT 59.540 55.000 5.00 0.00 44.20 4.18
666 669 1.560923 GTCGTGAAGATCACCCGATG 58.439 55.000 5.00 0.00 44.20 3.84
667 670 0.179111 TCGTGAAGATCACCCGATGC 60.179 55.000 5.00 0.00 44.20 3.91
668 671 1.154205 CGTGAAGATCACCCGATGCC 61.154 60.000 5.00 0.00 44.20 4.40
669 672 0.179000 GTGAAGATCACCCGATGCCT 59.821 55.000 0.00 0.00 41.37 4.75
702 712 7.946207 TCTAACATACAAGCAAATTTGGTGAA 58.054 30.769 22.64 11.87 39.13 3.18
719 729 9.729281 ATTTGGTGAAATTATGAGCTTCAAAAT 57.271 25.926 0.00 0.00 31.21 1.82
733 743 7.117236 TGAGCTTCAAAATTAAAGATCGTACGT 59.883 33.333 16.05 2.33 40.02 3.57
756 766 9.878599 ACGTTCATAAAAGAAATTACAAGACTG 57.121 29.630 0.00 0.00 0.00 3.51
786 796 6.847421 ATTCTTTCCCTCTTGAATTTCCTG 57.153 37.500 0.00 0.00 0.00 3.86
792 802 5.891198 TCCCTCTTGAATTTCCTGAATGAA 58.109 37.500 0.00 0.00 0.00 2.57
819 829 3.806521 CCACACTCAAGACTCAAAGACTG 59.193 47.826 0.00 0.00 0.00 3.51
821 831 4.269603 CACACTCAAGACTCAAAGACTGTG 59.730 45.833 0.00 0.00 0.00 3.66
825 835 5.105146 ACTCAAGACTCAAAGACTGTGAAGT 60.105 40.000 0.00 0.00 0.00 3.01
839 849 6.926272 AGACTGTGAAGTAGTGACAGATTTTC 59.074 38.462 14.21 4.51 39.64 2.29
841 851 7.275920 ACTGTGAAGTAGTGACAGATTTTCTT 58.724 34.615 14.21 0.00 39.64 2.52
842 852 7.770897 ACTGTGAAGTAGTGACAGATTTTCTTT 59.229 33.333 14.21 0.00 39.64 2.52
844 854 9.607988 TGTGAAGTAGTGACAGATTTTCTTTTA 57.392 29.630 0.00 0.00 0.00 1.52
848 891 8.677148 AGTAGTGACAGATTTTCTTTTAGCAA 57.323 30.769 0.00 0.00 0.00 3.91
850 893 9.730420 GTAGTGACAGATTTTCTTTTAGCAAAA 57.270 29.630 0.00 0.00 0.00 2.44
1200 1277 2.817834 GCCGACATGCGCAACCTA 60.818 61.111 17.11 0.00 39.11 3.08
1448 2753 7.286775 TGAGGGTTTTGCTATACTTGTTTCTTT 59.713 33.333 0.00 0.00 0.00 2.52
1516 2821 5.660460 ACCTTGAACAATTTTGTGAAGGAC 58.340 37.500 26.28 7.35 45.55 3.85
1592 2897 1.064091 AGTACCTACTCCCTCCGTTCC 60.064 57.143 0.00 0.00 0.00 3.62
1595 2900 0.467659 CCTACTCCCTCCGTTCCGAT 60.468 60.000 0.00 0.00 0.00 4.18
1601 2906 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
1603 2908 1.197910 CTCCGTTCCGATTTACTCGC 58.802 55.000 0.00 0.00 46.25 5.03
1605 2910 1.477030 CCGTTCCGATTTACTCGCCG 61.477 60.000 0.00 0.00 46.25 6.46
1606 2911 0.799534 CGTTCCGATTTACTCGCCGT 60.800 55.000 0.00 0.00 46.25 5.68
1607 2912 0.643820 GTTCCGATTTACTCGCCGTG 59.356 55.000 0.00 0.00 46.25 4.94
1609 2914 0.742505 TCCGATTTACTCGCCGTGAT 59.257 50.000 0.00 0.00 46.25 3.06
1610 2915 1.135527 TCCGATTTACTCGCCGTGATT 59.864 47.619 0.00 0.00 46.25 2.57
1611 2916 1.931172 CCGATTTACTCGCCGTGATTT 59.069 47.619 0.00 0.00 46.25 2.17
1613 2918 3.552699 CCGATTTACTCGCCGTGATTTTA 59.447 43.478 0.00 0.00 46.25 1.52
1615 2920 4.266976 CGATTTACTCGCCGTGATTTTAGT 59.733 41.667 0.00 0.00 41.14 2.24
1617 2922 5.520022 TTTACTCGCCGTGATTTTAGTTC 57.480 39.130 0.00 0.00 0.00 3.01
1618 2923 3.034721 ACTCGCCGTGATTTTAGTTCA 57.965 42.857 0.00 0.00 0.00 3.18
1620 2925 3.810941 ACTCGCCGTGATTTTAGTTCAAA 59.189 39.130 0.00 0.00 0.00 2.69
1623 2928 5.764131 TCGCCGTGATTTTAGTTCAAATTT 58.236 33.333 0.00 0.00 0.00 1.82
1624 2929 5.627367 TCGCCGTGATTTTAGTTCAAATTTG 59.373 36.000 12.15 12.15 0.00 2.32
1646 2972 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
1694 3021 6.161855 AGAGCACTTATTAATGGACGATGA 57.838 37.500 0.00 0.00 0.00 2.92
1739 3068 2.062971 AGGATGGCCATGAACATGAC 57.937 50.000 26.56 5.49 41.20 3.06
1800 3130 9.565090 TTGAGAATATGCAGTAATGCTCTAATT 57.435 29.630 17.03 10.02 35.49 1.40
1826 3156 7.937700 AAGAGAATATTCCTTATCCAGTGGA 57.062 36.000 15.88 15.88 35.55 4.02
1953 3283 6.145534 TGCAACAGAGTAGAATAAAACAGTCG 59.854 38.462 0.00 0.00 0.00 4.18
1970 3300 4.006989 CAGTCGGTGGGATTTGAAATGTA 58.993 43.478 0.00 0.00 0.00 2.29
2017 3347 8.715998 CAGTTAAGATGTGTATGATATTCCTGC 58.284 37.037 0.00 0.00 0.00 4.85
2026 3356 5.761726 TGTATGATATTCCTGCTTGCAGAAG 59.238 40.000 22.50 8.17 0.00 2.85
2040 3370 5.049129 GCTTGCAGAAGTCTGTCATTTAGTT 60.049 40.000 9.94 0.00 45.45 2.24
2042 3372 5.858381 TGCAGAAGTCTGTCATTTAGTTCT 58.142 37.500 9.94 0.00 45.45 3.01
2174 3504 8.621532 TCACAGAAGTAAAATTTGTAGCTGAT 57.378 30.769 0.00 0.00 0.00 2.90
2204 3534 7.915397 TGTTACTTCAAAGAAAATTGTGCTCTC 59.085 33.333 0.00 0.00 0.00 3.20
2205 3535 6.455360 ACTTCAAAGAAAATTGTGCTCTCA 57.545 33.333 0.00 0.00 0.00 3.27
2292 3623 6.831868 GGAAATTATGTAGCTTAAGGTGGGAA 59.168 38.462 17.34 6.52 0.00 3.97
2485 3816 4.758674 GTCTTTTTGGTGTACTTAGGGACC 59.241 45.833 0.00 0.00 0.00 4.46
2550 3881 9.315525 GGACTCTATTGGTAAATTACTCTGTTC 57.684 37.037 2.96 0.00 0.00 3.18
2582 3913 9.203421 GCAGTTTGCCTACTTACATTTTAAATT 57.797 29.630 0.00 0.00 37.42 1.82
2610 3941 6.040842 AGCATTCACCATAGGCGAAAAATATT 59.959 34.615 0.00 0.00 27.19 1.28
2635 3966 9.967451 TTTGTATCTGGGTTTCTATGTGATTTA 57.033 29.630 0.00 0.00 0.00 1.40
2709 4041 3.303351 AACCAATGGGATCCATGAGAC 57.697 47.619 15.23 0.00 44.40 3.36
2815 4156 2.026822 TGAAAGAGTTGATGAGAGGGCC 60.027 50.000 0.00 0.00 0.00 5.80
3133 4477 6.296365 ACAGTGAATTGATCTAATGCATCG 57.704 37.500 0.00 0.00 36.70 3.84
3340 4684 9.645059 TGCTATCCTTCAGAAATATTAAGATCG 57.355 33.333 0.00 0.00 0.00 3.69
3375 4719 7.984422 ATCAACTGATGTTAGTCACATTTCA 57.016 32.000 0.00 0.00 46.96 2.69
3471 4820 5.785940 AGGTGTTTGGTCCTCTCTAAAGTAT 59.214 40.000 0.00 0.00 0.00 2.12
3769 5118 1.218047 GTGACTGACGCCCTGCATA 59.782 57.895 0.00 0.00 0.00 3.14
3772 5146 0.528684 GACTGACGCCCTGCATAGAC 60.529 60.000 0.00 0.00 0.00 2.59
3786 5160 7.040478 GCCCTGCATAGACATTATTTCAATGTA 60.040 37.037 2.78 0.00 40.62 2.29
3828 5202 5.652994 TTGTGTTTGGAGCTTGTTAACTT 57.347 34.783 7.22 0.00 0.00 2.66
3918 5295 3.745332 TGTTGCTCATCATAGTTTGCG 57.255 42.857 0.00 0.00 0.00 4.85
3919 5296 3.073678 TGTTGCTCATCATAGTTTGCGT 58.926 40.909 0.00 0.00 0.00 5.24
3920 5297 3.125146 TGTTGCTCATCATAGTTTGCGTC 59.875 43.478 0.00 0.00 0.00 5.19
3932 5309 0.237235 TTTGCGTCCGCTGATTGTTC 59.763 50.000 13.31 0.00 42.51 3.18
3948 5325 2.210116 TGTTCGAGGTTTGCTCAGTTC 58.790 47.619 0.00 0.00 0.00 3.01
3949 5326 1.531578 GTTCGAGGTTTGCTCAGTTCC 59.468 52.381 0.00 0.00 0.00 3.62
3951 5328 1.000955 TCGAGGTTTGCTCAGTTCCTC 59.999 52.381 0.00 0.00 40.62 3.71
3952 5329 1.433534 GAGGTTTGCTCAGTTCCTCG 58.566 55.000 0.00 0.00 35.94 4.63
3958 5344 4.282873 GTTTGCTCAGTTCCTCGAAAAAG 58.717 43.478 0.00 0.00 0.00 2.27
3974 5360 4.156008 CGAAAAAGGGATTGTTCAGTAGGG 59.844 45.833 0.00 0.00 0.00 3.53
3975 5361 4.741928 AAAAGGGATTGTTCAGTAGGGT 57.258 40.909 0.00 0.00 0.00 4.34
3983 5369 5.585047 GGATTGTTCAGTAGGGTTGTACATC 59.415 44.000 0.00 0.00 0.00 3.06
4007 5396 4.753107 TGTACTTTGCTACTGGCTAACAAC 59.247 41.667 0.00 0.00 42.39 3.32
4015 5404 5.048782 TGCTACTGGCTAACAACAAGAAATG 60.049 40.000 0.00 0.00 42.39 2.32
4053 5442 6.613699 TGGAGCATTATTGAGGGATACAAAT 58.386 36.000 0.00 0.00 39.74 2.32
4079 5468 4.513406 AATTTATTGCGGGAGGGAACTA 57.487 40.909 0.00 0.00 44.43 2.24
4099 5488 3.957671 AGAATATTGATGTGTGCGCAG 57.042 42.857 12.22 0.00 0.00 5.18
4118 5507 2.419324 CAGATGTTCTTTCTGCAGAGGC 59.581 50.000 17.43 7.24 34.68 4.70
4177 5566 8.881231 CGTTTTGTTTTTGAAATGAACATATGC 58.119 29.630 1.58 0.00 33.73 3.14
4191 5580 7.652300 TGAACATATGCTATTCCATTACGAC 57.348 36.000 1.58 0.00 0.00 4.34
4195 5584 3.088194 TGCTATTCCATTACGACGACC 57.912 47.619 0.00 0.00 0.00 4.79
4196 5585 2.691526 TGCTATTCCATTACGACGACCT 59.308 45.455 0.00 0.00 0.00 3.85
4197 5586 3.050619 GCTATTCCATTACGACGACCTG 58.949 50.000 0.00 0.00 0.00 4.00
4225 5614 3.610040 AATCACCAGCTACATCGTTCA 57.390 42.857 0.00 0.00 0.00 3.18
4245 5634 6.968904 CGTTCATTACAATCTCAGGAAAATGG 59.031 38.462 0.00 0.00 0.00 3.16
4270 5659 4.427312 GAACCAAATTTCATAGCTGCCAG 58.573 43.478 0.00 0.00 0.00 4.85
4281 5670 1.153269 GCTGCCAGTCCCTAAGCTC 60.153 63.158 0.00 0.00 0.00 4.09
4299 5688 3.065655 GCTCCATATGCAGCTAAGACAG 58.934 50.000 11.58 0.00 32.48 3.51
4310 5699 1.131883 GCTAAGACAGGTGCTGCATTG 59.868 52.381 5.27 10.46 34.37 2.82
4361 5750 9.476202 AGATTAACATTACCAAAAGCAACTTTC 57.524 29.630 0.00 0.00 31.99 2.62
4385 5774 8.991243 TCATTTTGAAATTTAATCTCCAGCAG 57.009 30.769 0.00 0.00 0.00 4.24
4389 5778 6.343716 TGAAATTTAATCTCCAGCAGCAAA 57.656 33.333 0.00 0.00 0.00 3.68
4391 5780 4.996788 ATTTAATCTCCAGCAGCAAAGG 57.003 40.909 0.00 0.00 0.00 3.11
4392 5781 1.755179 TAATCTCCAGCAGCAAAGGC 58.245 50.000 0.00 0.00 41.61 4.35
4402 5791 3.376918 GCAAAGGCTCCCAGTGGC 61.377 66.667 2.61 0.00 36.96 5.01
4412 5801 1.227380 CCCAGTGGCGCTAGATCAC 60.227 63.158 7.64 6.48 0.00 3.06
4442 5831 3.679980 GCTTGAGATCGTTTGCTTCAGTA 59.320 43.478 0.00 0.00 0.00 2.74
4452 5841 3.334583 TTGCTTCAGTACCATGGAGTC 57.665 47.619 21.47 8.08 0.00 3.36
4462 5851 5.124457 CAGTACCATGGAGTCCATTTCAAAG 59.876 44.000 22.62 9.76 42.23 2.77
4472 5861 4.219288 AGTCCATTTCAAAGATGACTTGGC 59.781 41.667 0.00 0.00 37.59 4.52
4490 5880 0.243636 GCTACACCCATGTTGGTTGC 59.756 55.000 0.00 0.00 40.48 4.17
4492 5882 2.238521 CTACACCCATGTTGGTTGCTT 58.761 47.619 0.00 0.00 40.48 3.91
4493 5883 1.494960 ACACCCATGTTGGTTGCTTT 58.505 45.000 0.00 0.00 34.46 3.51
4502 5892 5.849564 CCATGTTGGTTGCTTTATTAAGCGT 60.850 40.000 11.51 0.00 45.15 5.07
4514 5904 6.681599 GCTTTATTAAGCGTGTTTAGTAGTGC 59.318 38.462 0.00 0.00 46.53 4.40
4516 5906 1.804601 AAGCGTGTTTAGTAGTGCCC 58.195 50.000 0.00 0.00 0.00 5.36
4521 5911 2.486918 GTGTTTAGTAGTGCCCGTGTT 58.513 47.619 0.00 0.00 0.00 3.32
4523 5913 3.313249 GTGTTTAGTAGTGCCCGTGTTTT 59.687 43.478 0.00 0.00 0.00 2.43
4551 5941 4.657504 TGAAGGGCATCAGAGATATGTTCT 59.342 41.667 0.00 0.00 37.41 3.01
4555 5945 6.262980 AGGGCATCAGAGATATGTTCTAGAT 58.737 40.000 0.00 0.00 33.74 1.98
4558 5948 7.548780 GGGCATCAGAGATATGTTCTAGATTTC 59.451 40.741 0.00 0.00 33.74 2.17
4569 5959 1.134699 TCTAGATTTCCTGCACCTGCG 60.135 52.381 0.00 0.00 45.83 5.18
4599 5989 4.335082 CGTTCCGCAATCATTTCTTACA 57.665 40.909 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 103 1.682684 ATCTTCAGGGAGCCGTCGT 60.683 57.895 0.00 0.00 0.00 4.34
104 106 0.984230 TTTCATCTTCAGGGAGCCGT 59.016 50.000 0.00 0.00 0.00 5.68
121 123 3.681874 GCTAGGCGGTGAGACCTTTATTT 60.682 47.826 0.00 0.00 37.50 1.40
134 136 3.489513 GAATGGGGGCTAGGCGGT 61.490 66.667 10.58 0.00 0.00 5.68
148 151 2.047083 TAAACGCACCGCCGGAAT 60.047 55.556 11.71 0.00 0.00 3.01
163 166 1.743623 CGCCCACCAACGATGCTAA 60.744 57.895 0.00 0.00 0.00 3.09
240 243 1.967908 GACACACGAACGTAGACGAAG 59.032 52.381 9.41 9.69 43.02 3.79
286 289 2.167487 ACCGCCGCCAATGAAAAATAAT 59.833 40.909 0.00 0.00 0.00 1.28
315 318 1.076350 CCCATAGGACCAACACCCAAA 59.924 52.381 0.00 0.00 33.47 3.28
317 320 1.211567 CCCCATAGGACCAACACCCA 61.212 60.000 0.00 0.00 38.24 4.51
390 393 3.933722 CATCGCCCCTCCATCGCT 61.934 66.667 0.00 0.00 0.00 4.93
430 433 3.644823 TCAACGACTACAAGCATCGAAA 58.355 40.909 0.00 0.00 39.16 3.46
435 438 4.433615 CACCTATCAACGACTACAAGCAT 58.566 43.478 0.00 0.00 0.00 3.79
449 452 2.956333 CAGATCCGTACACCACCTATCA 59.044 50.000 0.00 0.00 0.00 2.15
451 454 2.091499 TCCAGATCCGTACACCACCTAT 60.091 50.000 0.00 0.00 0.00 2.57
490 493 7.326968 TCAATCATGACAGTACAACAAACAA 57.673 32.000 0.00 0.00 0.00 2.83
559 562 3.938963 CCTACGAAAAAGCTGCTCCATTA 59.061 43.478 1.00 0.00 0.00 1.90
591 594 9.383519 GAATCAATAAAGTTGGTGAGATGTCTA 57.616 33.333 0.00 0.00 0.00 2.59
593 596 8.044060 TGAATCAATAAAGTTGGTGAGATGTC 57.956 34.615 0.00 0.00 0.00 3.06
595 598 9.695526 TTTTGAATCAATAAAGTTGGTGAGATG 57.304 29.630 0.00 0.00 0.00 2.90
598 601 8.928733 CCATTTTGAATCAATAAAGTTGGTGAG 58.071 33.333 0.00 0.00 0.00 3.51
600 603 8.497554 CACCATTTTGAATCAATAAAGTTGGTG 58.502 33.333 16.54 16.54 40.87 4.17
601 604 8.210265 ACACCATTTTGAATCAATAAAGTTGGT 58.790 29.630 0.00 0.36 35.92 3.67
604 607 9.829507 TGAACACCATTTTGAATCAATAAAGTT 57.170 25.926 0.00 0.00 0.00 2.66
622 625 5.885352 CCAATCCTTGTACATATGAACACCA 59.115 40.000 10.38 0.00 0.00 4.17
623 626 5.299279 CCCAATCCTTGTACATATGAACACC 59.701 44.000 10.38 0.00 0.00 4.16
624 627 5.885912 ACCCAATCCTTGTACATATGAACAC 59.114 40.000 10.38 4.94 0.00 3.32
633 636 1.972075 TCACGACCCAATCCTTGTACA 59.028 47.619 0.00 0.00 0.00 2.90
650 653 0.179000 AGGCATCGGGTGATCTTCAC 59.821 55.000 0.00 0.00 46.23 3.18
653 656 0.759346 GGTAGGCATCGGGTGATCTT 59.241 55.000 0.00 0.00 30.49 2.40
665 668 7.453439 TGCTTGTATGTTAGATATAGGTAGGCA 59.547 37.037 0.00 0.00 0.00 4.75
666 669 7.837863 TGCTTGTATGTTAGATATAGGTAGGC 58.162 38.462 0.00 0.00 0.00 3.93
762 772 7.698912 TCAGGAAATTCAAGAGGGAAAGAATA 58.301 34.615 0.00 0.00 31.01 1.75
766 776 6.435277 TCATTCAGGAAATTCAAGAGGGAAAG 59.565 38.462 0.00 0.00 0.00 2.62
771 781 6.040878 GCATTCATTCAGGAAATTCAAGAGG 58.959 40.000 0.00 0.00 0.00 3.69
772 782 6.864342 AGCATTCATTCAGGAAATTCAAGAG 58.136 36.000 0.00 0.00 0.00 2.85
777 787 5.105635 TGTGGAGCATTCATTCAGGAAATTC 60.106 40.000 0.00 0.00 0.00 2.17
786 796 4.005650 TCTTGAGTGTGGAGCATTCATTC 58.994 43.478 0.00 0.00 42.23 2.67
792 802 1.973515 TGAGTCTTGAGTGTGGAGCAT 59.026 47.619 0.00 0.00 0.00 3.79
821 831 8.774586 TGCTAAAAGAAAATCTGTCACTACTTC 58.225 33.333 0.00 0.00 0.00 3.01
880 923 8.960591 CCTTTACACCACATCATCTAAAAATCT 58.039 33.333 0.00 0.00 0.00 2.40
881 924 8.190784 CCCTTTACACCACATCATCTAAAAATC 58.809 37.037 0.00 0.00 0.00 2.17
882 925 7.893302 TCCCTTTACACCACATCATCTAAAAAT 59.107 33.333 0.00 0.00 0.00 1.82
974 1050 5.355350 CCTAGATTTTCAGATGCGGTTTCTT 59.645 40.000 0.00 0.00 0.00 2.52
977 1053 3.378427 GCCTAGATTTTCAGATGCGGTTT 59.622 43.478 0.00 0.00 0.00 3.27
1072 1149 4.224274 ACGGTTGTCGGTGCGGAA 62.224 61.111 0.00 0.00 44.45 4.30
1391 1468 9.419297 GATGCATATCATGTGAAGCAAAAATAT 57.581 29.630 0.00 0.00 35.05 1.28
1422 1500 6.303839 AGAAACAAGTATAGCAAAACCCTCA 58.696 36.000 0.00 0.00 0.00 3.86
1460 2765 8.754230 TGCGAATTTGACAATTTGATTATTCA 57.246 26.923 2.79 0.00 36.24 2.57
1516 2821 6.661669 TCAAGCATAATTGATAAGATGTGCG 58.338 36.000 0.00 0.00 34.31 5.34
1595 2900 4.989797 TGAACTAAAATCACGGCGAGTAAA 59.010 37.500 16.62 0.00 0.00 2.01
1601 2906 5.627367 TCAAATTTGAACTAAAATCACGGCG 59.373 36.000 18.45 4.80 33.55 6.46
1615 2920 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
1617 2922 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
1618 2923 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
1620 2925 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
1623 2928 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1624 2929 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
1633 2938 2.267188 TTCCGATTTACTCGTCGTGG 57.733 50.000 0.00 0.00 46.18 4.94
1634 2939 2.534349 CCATTCCGATTTACTCGTCGTG 59.466 50.000 0.00 0.00 46.18 4.35
1635 2940 2.424601 TCCATTCCGATTTACTCGTCGT 59.575 45.455 0.00 0.00 46.18 4.34
1636 2941 3.043586 CTCCATTCCGATTTACTCGTCG 58.956 50.000 0.00 0.00 46.18 5.12
1646 2972 1.343069 GCTACTCCCTCCATTCCGAT 58.657 55.000 0.00 0.00 0.00 4.18
1649 2975 1.840635 ACTTGCTACTCCCTCCATTCC 59.159 52.381 0.00 0.00 0.00 3.01
1653 2979 3.366396 CTCTTACTTGCTACTCCCTCCA 58.634 50.000 0.00 0.00 0.00 3.86
1694 3021 6.751514 TGCAATACTCACATTTAATTCGGT 57.248 33.333 0.00 0.00 0.00 4.69
1739 3068 0.754217 CCTCATTGGGCCATGGTGAG 60.754 60.000 25.40 25.40 36.83 3.51
1800 3130 9.447279 TCCACTGGATAAGGAATATTCTCTTTA 57.553 33.333 18.38 13.51 0.00 1.85
1953 3283 3.447229 CCACCTACATTTCAAATCCCACC 59.553 47.826 0.00 0.00 0.00 4.61
1970 3300 5.163131 ACTGACACATTTTAACCTACCACCT 60.163 40.000 0.00 0.00 0.00 4.00
2040 3370 3.776969 AGCCACAGGATGATTAGTTGAGA 59.223 43.478 0.00 0.00 39.69 3.27
2042 3372 4.264253 CAAGCCACAGGATGATTAGTTGA 58.736 43.478 0.00 0.00 39.69 3.18
2052 3382 0.621571 TAGGGAGCAAGCCACAGGAT 60.622 55.000 0.00 0.00 0.00 3.24
2181 3511 7.566760 TGAGAGCACAATTTTCTTTGAAGTA 57.433 32.000 0.00 0.00 0.00 2.24
2200 3530 4.001652 ACACATTCAGCAGAACATGAGAG 58.998 43.478 0.00 0.00 36.39 3.20
2204 3534 4.492791 TTGACACATTCAGCAGAACATG 57.507 40.909 0.00 0.00 36.39 3.21
2205 3535 5.242171 TCATTTGACACATTCAGCAGAACAT 59.758 36.000 0.00 0.00 36.39 2.71
2582 3913 1.209261 TCGCCTATGGTGAATGCTTGA 59.791 47.619 0.00 0.00 39.45 3.02
2610 3941 9.613428 CTAAATCACATAGAAACCCAGATACAA 57.387 33.333 0.00 0.00 0.00 2.41
2652 3984 9.761504 AAGAACATTCAGATCAGATACATAGTG 57.238 33.333 0.00 0.00 0.00 2.74
2709 4041 4.568152 AAACATTCGTCTCAACAAAGGG 57.432 40.909 0.00 0.00 0.00 3.95
2815 4156 3.001330 GCGAGATCAAACAAGATAACCCG 59.999 47.826 0.00 0.00 0.00 5.28
2897 4238 5.354513 GCCGATATTAGAATAAAGAAGCCCC 59.645 44.000 0.00 0.00 0.00 5.80
3157 4501 7.225931 TGCACCGAGATACCAATTAAATAAGAC 59.774 37.037 0.00 0.00 0.00 3.01
3340 4684 2.489938 TCAGTTGATTGGTACCTGGC 57.510 50.000 14.36 2.50 0.00 4.85
3375 4719 4.909001 AGAAAGCAGCTCTTCAGAGAAAT 58.091 39.130 8.09 0.00 44.74 2.17
3497 4846 7.254795 GCGATTAACTACAGAAGCAATTGGTAT 60.255 37.037 11.15 0.00 0.00 2.73
3521 4870 3.590720 TCATATGATTTGTCAAGCGCG 57.409 42.857 0.00 0.00 0.00 6.86
3772 5146 9.720667 ACGACATGAACATACATTGAAATAATG 57.279 29.630 0.00 0.00 0.00 1.90
3786 5160 4.335315 ACAAACAACTCACGACATGAACAT 59.665 37.500 0.00 0.00 36.69 2.71
3828 5202 2.507484 CTCCAATGTTTCTGCTGGTCA 58.493 47.619 0.00 0.00 0.00 4.02
3918 5295 0.389948 ACCTCGAACAATCAGCGGAC 60.390 55.000 0.00 0.00 0.00 4.79
3919 5296 0.320374 AACCTCGAACAATCAGCGGA 59.680 50.000 0.00 0.00 0.00 5.54
3920 5297 1.135972 CAAACCTCGAACAATCAGCGG 60.136 52.381 0.00 0.00 0.00 5.52
3932 5309 1.433534 GAGGAACTGAGCAAACCTCG 58.566 55.000 0.00 0.00 43.82 4.63
3948 5325 3.821033 ACTGAACAATCCCTTTTTCGAGG 59.179 43.478 0.00 0.00 36.52 4.63
3949 5326 5.122396 CCTACTGAACAATCCCTTTTTCGAG 59.878 44.000 0.00 0.00 0.00 4.04
3951 5328 4.156008 CCCTACTGAACAATCCCTTTTTCG 59.844 45.833 0.00 0.00 0.00 3.46
3952 5329 5.077564 ACCCTACTGAACAATCCCTTTTTC 58.922 41.667 0.00 0.00 0.00 2.29
3958 5344 3.434940 ACAACCCTACTGAACAATCCC 57.565 47.619 0.00 0.00 0.00 3.85
3974 5360 9.203244 GCCAGTAGCAAAGTACAGATGTACAAC 62.203 44.444 21.70 0.00 46.15 3.32
3975 5361 7.289310 GCCAGTAGCAAAGTACAGATGTACAA 61.289 42.308 21.70 1.55 46.15 2.41
4007 5396 3.293311 CTGGTGGAGCAACATTTCTTG 57.707 47.619 0.00 0.00 27.67 3.02
4053 5442 2.763448 CCCTCCCGCAATAAATTTTCCA 59.237 45.455 0.00 0.00 0.00 3.53
4079 5468 3.534554 TCTGCGCACACATCAATATTCT 58.465 40.909 5.66 0.00 0.00 2.40
4099 5488 1.742268 GGCCTCTGCAGAAAGAACATC 59.258 52.381 18.85 0.00 40.13 3.06
4118 5507 0.250467 CCATACCCGAAGAGCCATGG 60.250 60.000 7.63 7.63 0.00 3.66
4151 5540 8.881231 GCATATGTTCATTTCAAAAACAAAACG 58.119 29.630 4.29 0.00 36.57 3.60
4152 5541 9.934190 AGCATATGTTCATTTCAAAAACAAAAC 57.066 25.926 4.29 0.00 36.57 2.43
4167 5556 6.364976 CGTCGTAATGGAATAGCATATGTTCA 59.635 38.462 4.29 0.00 30.96 3.18
4177 5566 3.050619 GCAGGTCGTCGTAATGGAATAG 58.949 50.000 0.00 0.00 0.00 1.73
4183 5572 2.665777 CCAGCAGGTCGTCGTAATG 58.334 57.895 0.00 0.00 0.00 1.90
4210 5599 5.755375 AGATTGTAATGAACGATGTAGCTGG 59.245 40.000 0.00 0.00 31.87 4.85
4219 5608 7.148255 CCATTTTCCTGAGATTGTAATGAACGA 60.148 37.037 0.00 0.00 0.00 3.85
4225 5614 4.339247 CGGCCATTTTCCTGAGATTGTAAT 59.661 41.667 2.24 0.00 0.00 1.89
4245 5634 3.438360 CAGCTATGAAATTTGGTTCGGC 58.562 45.455 0.00 0.00 0.00 5.54
4260 5649 0.761802 GCTTAGGGACTGGCAGCTAT 59.238 55.000 15.89 0.57 41.52 2.97
4261 5650 0.325671 AGCTTAGGGACTGGCAGCTA 60.326 55.000 15.89 5.29 43.01 3.32
4263 5652 1.153269 GAGCTTAGGGACTGGCAGC 60.153 63.158 15.89 7.42 41.52 5.25
4270 5659 3.051081 CTGCATATGGAGCTTAGGGAC 57.949 52.381 11.59 0.00 0.00 4.46
4281 5670 3.136763 CACCTGTCTTAGCTGCATATGG 58.863 50.000 4.56 0.00 0.00 2.74
4299 5688 1.200020 GTCCTGTAACAATGCAGCACC 59.800 52.381 0.00 0.00 37.89 5.01
4303 5692 2.489329 CCAAGGTCCTGTAACAATGCAG 59.511 50.000 0.00 0.00 38.83 4.41
4310 5699 4.546829 TGTATGTCCAAGGTCCTGTAAC 57.453 45.455 0.00 0.00 0.00 2.50
4361 5750 7.332430 TGCTGCTGGAGATTAAATTTCAAAATG 59.668 33.333 0.00 0.00 0.00 2.32
4385 5774 3.376918 GCCACTGGGAGCCTTTGC 61.377 66.667 0.00 0.00 35.59 3.68
4392 5781 1.365633 GATCTAGCGCCACTGGGAG 59.634 63.158 2.29 0.00 35.59 4.30
4394 5783 1.227380 GTGATCTAGCGCCACTGGG 60.227 63.158 2.29 0.00 37.18 4.45
4402 5791 1.135915 AGCCAGAACTGTGATCTAGCG 59.864 52.381 0.00 0.00 36.77 4.26
4412 5801 2.376808 ACGATCTCAAGCCAGAACTG 57.623 50.000 0.00 0.00 0.00 3.16
4442 5831 4.387026 TCTTTGAAATGGACTCCATGGT 57.613 40.909 12.58 2.88 44.40 3.55
4452 5841 4.796038 AGCCAAGTCATCTTTGAAATGG 57.204 40.909 4.68 4.68 40.42 3.16
4462 5851 2.292267 CATGGGTGTAGCCAAGTCATC 58.708 52.381 6.91 0.00 39.65 2.92
4490 5880 7.178074 GGCACTACTAAACACGCTTAATAAAG 58.822 38.462 0.00 0.00 35.68 1.85
4492 5882 5.581874 GGGCACTACTAAACACGCTTAATAA 59.418 40.000 0.00 0.00 0.00 1.40
4493 5883 5.111293 GGGCACTACTAAACACGCTTAATA 58.889 41.667 0.00 0.00 0.00 0.98
4502 5892 2.914695 AACACGGGCACTACTAAACA 57.085 45.000 0.00 0.00 0.00 2.83
4514 5904 1.472480 CCCTTCATGCTAAAACACGGG 59.528 52.381 0.00 0.00 0.00 5.28
4516 5906 1.539388 TGCCCTTCATGCTAAAACACG 59.461 47.619 0.00 0.00 0.00 4.49
4521 5911 3.200605 TCTCTGATGCCCTTCATGCTAAA 59.799 43.478 0.00 0.00 35.05 1.85
4523 5913 2.401568 TCTCTGATGCCCTTCATGCTA 58.598 47.619 0.00 0.00 35.05 3.49
4551 5941 3.458872 CGCAGGTGCAGGAAATCTA 57.541 52.632 2.33 0.00 42.21 1.98
4579 5969 5.296813 ACTGTAAGAAATGATTGCGGAAC 57.703 39.130 0.00 0.00 37.43 3.62


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

AutoCloner maintained by Alex Coulton.