Multiple sequence alignment - TraesCS6D01G273000

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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 TraesCS6D01G273000 chr6D 100.000 4041 0 0 1 4041 381985879 381981839 0.000000e+00 7463.0
1 TraesCS6D01G273000 chr6D 93.333 60 3 1 1 59 14331742 14331683 2.000000e-13 87.9
2 TraesCS6D01G273000 chr6B 93.251 3334 166 27 51 3371 570956720 570953433 0.000000e+00 4855.0
3 TraesCS6D01G273000 chr6B 89.736 682 58 9 3367 4041 570913629 570912953 0.000000e+00 861.0
4 TraesCS6D01G273000 chr6A 92.360 3220 206 25 584 3793 523937677 523934488 0.000000e+00 4547.0
5 TraesCS6D01G273000 chr6A 95.000 40 2 0 4002 4041 523495264 523495225 3.370000e-06 63.9
6 TraesCS6D01G273000 chr3B 77.730 467 100 4 1066 1530 413865946 413865482 2.380000e-72 283.0
7 TraesCS6D01G273000 chr2D 100.000 48 0 0 1 48 561897268 561897315 5.560000e-14 89.8
8 TraesCS6D01G273000 chr2D 93.103 58 1 3 1 57 62585397 62585452 9.310000e-12 82.4
9 TraesCS6D01G273000 chr4D 97.959 49 0 1 1 49 288037657 288037704 2.590000e-12 84.2
10 TraesCS6D01G273000 chr4D 94.444 54 2 1 1 53 505524978 505525031 9.310000e-12 82.4
11 TraesCS6D01G273000 chr7D 91.803 61 1 4 1 58 144479266 144479207 9.310000e-12 82.4
12 TraesCS6D01G273000 chr7D 92.982 57 2 2 1 55 573244760 573244704 9.310000e-12 82.4
13 TraesCS6D01G273000 chr7D 86.441 59 8 0 55 113 446216596 446216538 9.370000e-07 65.8
14 TraesCS6D01G273000 chr3D 92.982 57 3 1 1 56 9858391 9858335 9.310000e-12 82.4
15 TraesCS6D01G273000 chr3D 90.385 52 5 0 62 113 390671400 390671349 7.250000e-08 69.4
16 TraesCS6D01G273000 chr3D 88.000 50 4 1 73 120 436039520 436039569 1.570000e-04 58.4
17 TraesCS6D01G273000 chr1D 97.917 48 0 1 1 48 81510363 81510409 9.310000e-12 82.4
18 TraesCS6D01G273000 chr7A 88.136 59 7 0 55 113 637823005 637823063 2.010000e-08 71.3
19 TraesCS6D01G273000 chr4A 93.617 47 3 0 64 110 535818267 535818313 2.010000e-08 71.3
20 TraesCS6D01G273000 chr1B 91.837 49 4 0 65 113 598846391 598846439 7.250000e-08 69.4
21 TraesCS6D01G273000 chr1B 95.000 40 2 0 74 113 660533694 660533655 3.370000e-06 63.9
22 TraesCS6D01G273000 chr1A 87.719 57 4 2 68 122 299234196 299234141 3.370000e-06 63.9


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 TraesCS6D01G273000 chr6D 381981839 381985879 4040 True 7463 7463 100.000 1 4041 1 chr6D.!!$R2 4040
1 TraesCS6D01G273000 chr6B 570953433 570956720 3287 True 4855 4855 93.251 51 3371 1 chr6B.!!$R2 3320
2 TraesCS6D01G273000 chr6B 570912953 570913629 676 True 861 861 89.736 3367 4041 1 chr6B.!!$R1 674
3 TraesCS6D01G273000 chr6A 523934488 523937677 3189 True 4547 4547 92.360 584 3793 1 chr6A.!!$R2 3209

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
22 23 0.238289 CAAAACTGGTGCGCCACTAG 59.762 55.0 16.89 17.26 46.13 2.57 F
31 32 0.323629 TGCGCCACTAGTAAGCCTTT 59.676 50.0 4.18 0.00 0.00 3.11 F
1539 1544 0.321122 AGCTCAAGGTCAGCGGAAAG 60.321 55.0 0.00 0.00 42.14 2.62 F
2138 2149 0.250510 TGTACCGCAGATTGTTGCCA 60.251 50.0 0.00 0.00 41.01 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1367 0.924090 GCACGTCCTTGATAAGCTCG 59.076 55.000 0.00 0.00 0.0 5.03 R
1660 1670 1.349688 TGGCAAACTATTCCAGGACGT 59.650 47.619 0.00 0.00 0.0 4.34 R
2842 2855 0.883833 CAAATGACAAGAAGGCGCCT 59.116 50.000 27.08 27.08 0.0 5.52 R
3980 4004 0.185901 TGCAGGGCTTTCCAAAGACT 59.814 50.000 4.89 0.00 43.7 3.24 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
17 18 3.605664 AGGCAAAACTGGTGCGCC 61.606 61.111 10.11 10.11 43.18 6.53
18 19 3.910490 GGCAAAACTGGTGCGCCA 61.910 61.111 19.93 19.93 43.18 5.69
19 20 2.658268 GCAAAACTGGTGCGCCAC 60.658 61.111 16.89 0.00 40.46 5.01
20 21 3.119193 CAAAACTGGTGCGCCACT 58.881 55.556 16.89 3.24 40.46 4.00
21 22 1.791103 GCAAAACTGGTGCGCCACTA 61.791 55.000 16.89 0.00 40.46 2.74
22 23 0.238289 CAAAACTGGTGCGCCACTAG 59.762 55.000 16.89 17.26 46.13 2.57
26 27 3.050703 CTGGTGCGCCACTAGTAAG 57.949 57.895 16.89 0.00 40.46 2.34
27 28 1.079405 TGGTGCGCCACTAGTAAGC 60.079 57.895 16.89 0.43 40.46 3.09
28 29 1.814169 GGTGCGCCACTAGTAAGCC 60.814 63.158 12.58 5.45 34.40 4.35
29 30 1.218316 GTGCGCCACTAGTAAGCCT 59.782 57.895 4.18 0.00 0.00 4.58
30 31 0.391263 GTGCGCCACTAGTAAGCCTT 60.391 55.000 4.18 0.00 0.00 4.35
31 32 0.323629 TGCGCCACTAGTAAGCCTTT 59.676 50.000 4.18 0.00 0.00 3.11
32 33 1.271163 TGCGCCACTAGTAAGCCTTTT 60.271 47.619 4.18 0.00 0.00 2.27
33 34 1.810755 GCGCCACTAGTAAGCCTTTTT 59.189 47.619 10.58 0.00 0.00 1.94
34 35 2.159558 GCGCCACTAGTAAGCCTTTTTC 60.160 50.000 10.58 0.00 0.00 2.29
35 36 3.335579 CGCCACTAGTAAGCCTTTTTCT 58.664 45.455 10.58 0.00 0.00 2.52
36 37 4.501071 CGCCACTAGTAAGCCTTTTTCTA 58.499 43.478 10.58 0.00 0.00 2.10
37 38 4.567159 CGCCACTAGTAAGCCTTTTTCTAG 59.433 45.833 10.58 8.45 35.59 2.43
38 39 5.489249 GCCACTAGTAAGCCTTTTTCTAGT 58.511 41.667 0.00 9.35 40.92 2.57
39 40 6.626623 CGCCACTAGTAAGCCTTTTTCTAGTA 60.627 42.308 10.58 0.00 39.10 1.82
40 41 6.757478 GCCACTAGTAAGCCTTTTTCTAGTAG 59.243 42.308 12.70 9.17 39.10 2.57
41 42 7.579146 GCCACTAGTAAGCCTTTTTCTAGTAGT 60.579 40.741 12.70 2.58 39.10 2.73
42 43 7.760340 CCACTAGTAAGCCTTTTTCTAGTAGTG 59.240 40.741 10.33 10.33 39.10 2.74
43 44 8.305317 CACTAGTAAGCCTTTTTCTAGTAGTGT 58.695 37.037 12.70 0.00 39.10 3.55
44 45 8.305317 ACTAGTAAGCCTTTTTCTAGTAGTGTG 58.695 37.037 11.93 0.00 39.26 3.82
45 46 5.932883 AGTAAGCCTTTTTCTAGTAGTGTGC 59.067 40.000 0.00 0.00 0.00 4.57
46 47 3.326747 AGCCTTTTTCTAGTAGTGTGCG 58.673 45.455 0.00 0.00 0.00 5.34
47 48 2.415512 GCCTTTTTCTAGTAGTGTGCGG 59.584 50.000 0.00 0.00 0.00 5.69
48 49 3.000727 CCTTTTTCTAGTAGTGTGCGGG 58.999 50.000 0.00 0.00 0.00 6.13
49 50 2.088950 TTTTCTAGTAGTGTGCGGGC 57.911 50.000 0.00 0.00 0.00 6.13
71 72 2.046314 CCTCCCGCATCCGTGTTT 60.046 61.111 0.00 0.00 0.00 2.83
106 107 0.741927 AGGAAATTTACGGGTCGGCG 60.742 55.000 0.00 0.00 0.00 6.46
222 223 3.118738 AGACATGAATCACCCCGTTAGAC 60.119 47.826 0.00 0.00 0.00 2.59
223 224 2.201732 CATGAATCACCCCGTTAGACG 58.798 52.381 0.00 0.00 42.11 4.18
275 276 4.041444 TCAAAACTTGGCAGGCCATTTTAT 59.959 37.500 18.93 9.12 46.64 1.40
297 298 2.810439 TTTTTGCAATTGGAGGGTCG 57.190 45.000 7.72 0.00 0.00 4.79
300 301 2.570415 TTGCAATTGGAGGGTCGTTA 57.430 45.000 7.72 0.00 0.00 3.18
315 316 1.017387 CGTTAGAGGGCCTTTCATGC 58.983 55.000 7.89 0.00 0.00 4.06
324 325 1.940613 GGCCTTTCATGCGTAAGTAGG 59.059 52.381 0.00 0.00 41.68 3.18
355 356 6.811954 TGTGAGGGGTTTTTGATAAGAAAAC 58.188 36.000 4.37 4.37 43.05 2.43
359 360 7.070571 TGAGGGGTTTTTGATAAGAAAACACAT 59.929 33.333 14.37 8.81 46.87 3.21
382 385 3.952628 CTCGTTCCCAGCGGTTCCC 62.953 68.421 0.00 0.00 0.00 3.97
403 406 1.195442 TGTCCGACAGTGGGCCATAA 61.195 55.000 10.70 0.00 30.50 1.90
442 445 1.227645 GGCAGCAGATATGTCCGCA 60.228 57.895 0.23 0.00 0.00 5.69
473 476 8.372521 GGAAATGTGATTGTATTTAAAAGCACG 58.627 33.333 4.86 0.00 43.76 5.34
488 491 5.786401 AAAGCACGATCAAGTTAGATGAC 57.214 39.130 0.00 0.00 0.00 3.06
497 500 6.509199 CGATCAAGTTAGATGACTGCAATCAC 60.509 42.308 0.00 0.00 0.00 3.06
504 507 4.673441 AGATGACTGCAATCACGTACTAC 58.327 43.478 0.00 0.00 0.00 2.73
509 512 6.627243 TGACTGCAATCACGTACTACTTTAT 58.373 36.000 0.00 0.00 0.00 1.40
539 542 5.431420 TGCATCAAATTAACTGTCACGTT 57.569 34.783 0.00 0.00 0.00 3.99
555 558 7.381678 ACTGTCACGTTTAAGTTCTATGACTTC 59.618 37.037 0.00 0.00 40.24 3.01
559 562 6.645415 CACGTTTAAGTTCTATGACTTCCAGT 59.355 38.462 0.00 0.00 40.24 4.00
560 563 7.811236 CACGTTTAAGTTCTATGACTTCCAGTA 59.189 37.037 0.00 0.00 40.24 2.74
709 712 1.690352 TCCCGGTCGAACTTTCTTCTT 59.310 47.619 0.00 0.00 0.00 2.52
774 777 7.278424 CGCAAGAAATCATTTAACAAATGGGAT 59.722 33.333 10.78 0.00 44.12 3.85
781 784 6.851609 TCATTTAACAAATGGGATGAAGACG 58.148 36.000 10.78 0.00 46.40 4.18
798 801 1.944024 GACGGTGATCCAACAACACAA 59.056 47.619 0.00 0.00 36.42 3.33
939 944 1.229428 AGACGATGCCAAATATGCCG 58.771 50.000 0.00 0.00 0.00 5.69
1332 1337 1.291877 CGTGCTTCTCTTGGTTCGGG 61.292 60.000 0.00 0.00 0.00 5.14
1362 1367 2.044946 GTGGCCATCACTGACCCC 60.045 66.667 9.72 0.00 42.86 4.95
1413 1418 2.815647 GGCCACTTCGAGAAGCCG 60.816 66.667 12.32 4.64 41.99 5.52
1539 1544 0.321122 AGCTCAAGGTCAGCGGAAAG 60.321 55.000 0.00 0.00 42.14 2.62
1676 1686 4.525912 ACGTAACGTCCTGGAATAGTTT 57.474 40.909 15.41 1.68 33.69 2.66
1677 1687 4.240096 ACGTAACGTCCTGGAATAGTTTG 58.760 43.478 15.41 11.99 33.69 2.93
1680 1690 1.349688 ACGTCCTGGAATAGTTTGCCA 59.650 47.619 0.00 0.00 0.00 4.92
1681 1691 1.737793 CGTCCTGGAATAGTTTGCCAC 59.262 52.381 0.00 0.00 0.00 5.01
1686 1696 1.892474 TGGAATAGTTTGCCACCAAGC 59.108 47.619 0.00 0.00 32.96 4.01
1687 1697 1.892474 GGAATAGTTTGCCACCAAGCA 59.108 47.619 0.00 0.00 42.17 3.91
1694 1704 3.577848 AGTTTGCCACCAAGCATGATTAA 59.422 39.130 0.00 0.00 43.64 1.40
1703 1713 6.154445 CACCAAGCATGATTAATTATGGCTC 58.846 40.000 18.74 5.57 0.00 4.70
1877 1887 2.951475 TTTCCCGCACAGCTTTCGGT 62.951 55.000 14.58 0.00 41.46 4.69
1979 1989 2.406596 TTATTCCGGGTTACCTGTGC 57.593 50.000 9.62 0.00 33.28 4.57
2031 2041 5.081394 CGCTTTTGCTAATTTTTGAATGGC 58.919 37.500 0.00 0.00 44.80 4.40
2053 2063 9.649167 ATGGCTTAAATTTCTTGAAAATCTCAG 57.351 29.630 0.00 0.00 34.81 3.35
2068 2079 9.506018 TGAAAATCTCAGTCAGTATTTTCATGA 57.494 29.630 14.68 0.00 45.92 3.07
2090 2101 8.911662 CATGAATACTTTTTCCTTTTGGTTACG 58.088 33.333 0.00 0.00 41.38 3.18
2093 2104 7.748691 ATACTTTTTCCTTTTGGTTACGCTA 57.251 32.000 0.00 0.00 41.38 4.26
2100 2111 9.984190 TTTTCCTTTTGGTTACGCTATTTTTAT 57.016 25.926 0.00 0.00 41.38 1.40
2115 2126 2.969821 TTTATGTTGTGGGACCTGCT 57.030 45.000 0.00 0.00 0.00 4.24
2132 2143 2.009051 TGCTTGATGTACCGCAGATTG 58.991 47.619 0.00 0.00 0.00 2.67
2138 2149 0.250510 TGTACCGCAGATTGTTGCCA 60.251 50.000 0.00 0.00 41.01 4.92
2151 2162 3.451141 TGTTGCCAACCAAGAACAATC 57.549 42.857 4.90 0.00 33.21 2.67
2171 2182 3.371168 TCTGAAGATGCGCAAAAACAAC 58.629 40.909 17.11 3.20 0.00 3.32
2276 2287 1.066303 CTAGGCCTGTTGCTAGAGTCG 59.934 57.143 17.99 0.00 40.92 4.18
2549 2560 8.486383 TGCTGAAATTGATGTATTTTGTTTTCG 58.514 29.630 0.00 0.00 0.00 3.46
2550 2561 7.475256 GCTGAAATTGATGTATTTTGTTTTCGC 59.525 33.333 0.00 0.00 0.00 4.70
2554 2565 7.945033 ATTGATGTATTTTGTTTTCGCAACT 57.055 28.000 0.00 0.00 0.00 3.16
2556 2567 6.269315 TGATGTATTTTGTTTTCGCAACTGT 58.731 32.000 0.00 0.00 0.00 3.55
2558 2569 5.403246 TGTATTTTGTTTTCGCAACTGTGT 58.597 33.333 0.00 0.00 0.00 3.72
2565 2576 4.034279 TGTTTTCGCAACTGTGTAAGGTAC 59.966 41.667 0.00 0.00 0.00 3.34
2575 2586 5.548406 ACTGTGTAAGGTACCATGACTTTC 58.452 41.667 15.94 0.00 0.00 2.62
2577 2588 5.547465 TGTGTAAGGTACCATGACTTTCAG 58.453 41.667 15.94 0.00 0.00 3.02
2656 2669 3.517901 AGGTTCTTCGGTTGTATCCATCA 59.482 43.478 0.00 0.00 0.00 3.07
2674 2687 2.695359 TCAGCTACAGTTTTTAGCCGG 58.305 47.619 0.00 0.00 42.63 6.13
2716 2729 3.993658 ATAGGAGGTGTCAGATACCCA 57.006 47.619 12.62 0.00 39.05 4.51
2731 2744 3.264574 CCCATCGGGTGTGTTCATT 57.735 52.632 0.00 0.00 38.25 2.57
2776 2789 2.914941 TCATGATCCAGACATATGGGGG 59.085 50.000 7.80 5.50 41.01 5.40
2842 2855 0.685131 CCAAGGCATCCAAGCATCCA 60.685 55.000 0.00 0.00 35.83 3.41
2980 2993 2.703416 CCATCATATACGCATGCACCT 58.297 47.619 19.57 3.20 0.00 4.00
2983 2996 3.683365 TCATATACGCATGCACCTCAT 57.317 42.857 19.57 5.21 35.31 2.90
3026 3039 2.276472 GCATGGTGCGCAAATTAAGA 57.724 45.000 14.00 0.00 31.71 2.10
3262 3277 8.408601 GTTGTCATAATGTATTGGATCTTGCTT 58.591 33.333 0.00 0.00 0.00 3.91
3364 3380 3.503363 GAGCGGAGGTGTGCATGC 61.503 66.667 11.82 11.82 39.88 4.06
3512 3528 0.321741 TCTCAGAGAACGCCGAGAGT 60.322 55.000 0.00 0.00 31.11 3.24
3523 3539 1.725164 CGCCGAGAGTGTAACCTTTTC 59.275 52.381 0.00 0.00 37.80 2.29
3524 3540 2.609737 CGCCGAGAGTGTAACCTTTTCT 60.610 50.000 0.00 0.00 37.80 2.52
3613 3631 4.540099 AGAAATGTGGTCCTATGAAAGGGA 59.460 41.667 0.00 0.00 46.55 4.20
3637 3655 4.756642 TGTGCTTCTCCACTTGAGTTTATG 59.243 41.667 0.00 0.00 42.12 1.90
3666 3684 2.426024 GTGTGAATGAGATTGCATGCCT 59.574 45.455 16.68 4.72 0.00 4.75
3681 3699 2.421739 CCTCGTCGGGGGCTATTG 59.578 66.667 2.09 0.00 0.00 1.90
3687 3705 1.349067 GTCGGGGGCTATTGATAGGT 58.651 55.000 0.59 0.00 0.00 3.08
3732 3750 1.192428 CTACCCTTCAAGGCGGTAGT 58.808 55.000 10.38 0.65 42.78 2.73
3742 3760 0.337428 AGGCGGTAGTTAGGAAGGGA 59.663 55.000 0.00 0.00 0.00 4.20
3753 3772 4.080299 AGTTAGGAAGGGAGCATTGGTAAG 60.080 45.833 0.00 0.00 0.00 2.34
3755 3774 3.460825 AGGAAGGGAGCATTGGTAAGTA 58.539 45.455 0.00 0.00 0.00 2.24
3765 3784 6.169557 AGCATTGGTAAGTATTGGTCGATA 57.830 37.500 0.00 0.00 0.00 2.92
3793 3812 5.415221 CATGAAGACTACTCAAAGGAGGTC 58.585 45.833 0.00 0.00 45.81 3.85
3794 3813 4.742012 TGAAGACTACTCAAAGGAGGTCT 58.258 43.478 0.00 0.00 45.81 3.85
3797 3816 4.484912 AGACTACTCAAAGGAGGTCTGTT 58.515 43.478 0.00 0.00 45.81 3.16
3808 3831 1.003580 GAGGTCTGTTTCCATGGCTCA 59.996 52.381 6.96 5.06 0.00 4.26
3834 3857 6.821388 TCTGAGAAACTCCTTATCCATTAGC 58.179 40.000 0.00 0.00 0.00 3.09
3858 3881 7.285858 AGCCTTAACTACCAAGTCTGATAGTAG 59.714 40.741 0.00 0.00 33.75 2.57
3859 3882 7.068470 GCCTTAACTACCAAGTCTGATAGTAGT 59.932 40.741 0.00 0.00 44.08 2.73
3860 3883 9.624373 CCTTAACTACCAAGTCTGATAGTAGTA 57.376 37.037 10.40 0.00 42.01 1.82
3866 3889 9.610705 CTACCAAGTCTGATAGTAGTAGTTGTA 57.389 37.037 0.00 0.00 0.00 2.41
3868 3891 9.476928 ACCAAGTCTGATAGTAGTAGTTGTATT 57.523 33.333 0.00 0.00 0.00 1.89
3919 3942 7.027874 TGTTTCTCTGTATGTATCCCCTTTT 57.972 36.000 0.00 0.00 0.00 2.27
3923 3946 5.018539 TCTGTATGTATCCCCTTTTGTCG 57.981 43.478 0.00 0.00 0.00 4.35
3925 3948 2.052782 ATGTATCCCCTTTTGTCGCC 57.947 50.000 0.00 0.00 0.00 5.54
3938 3961 1.343821 GTCGCCGACAATGCTAACG 59.656 57.895 13.23 0.00 32.09 3.18
3939 3962 2.021380 CGCCGACAATGCTAACGC 59.979 61.111 0.00 0.00 0.00 4.84
3955 3979 4.743644 GCTAACGCGGAAACTACAATAGAT 59.256 41.667 12.47 0.00 0.00 1.98
3957 3981 4.119442 ACGCGGAAACTACAATAGATGT 57.881 40.909 12.47 0.00 46.36 3.06
3968 3992 3.347216 ACAATAGATGTTGGAGCACACC 58.653 45.455 0.00 0.00 40.06 4.16
3972 3996 1.589716 GATGTTGGAGCACACCAGGC 61.590 60.000 0.00 0.00 41.19 4.85
3978 4002 1.003355 GAGCACACCAGGCAGCTAA 60.003 57.895 1.09 0.00 37.48 3.09
3980 4004 0.178992 AGCACACCAGGCAGCTAAAA 60.179 50.000 0.00 0.00 35.19 1.52
3986 4010 2.887152 CACCAGGCAGCTAAAAGTCTTT 59.113 45.455 0.00 0.00 0.00 2.52
3990 4014 3.569701 CAGGCAGCTAAAAGTCTTTGGAA 59.430 43.478 0.00 0.00 0.00 3.53
3999 4023 0.185901 AGTCTTTGGAAAGCCCTGCA 59.814 50.000 0.00 0.00 35.99 4.41
4004 4028 0.538057 TTGGAAAGCCCTGCAGTCAG 60.538 55.000 13.81 1.89 40.02 3.51
4005 4029 2.338785 GGAAAGCCCTGCAGTCAGC 61.339 63.158 13.81 12.50 45.96 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.605664 GGCGCACCAGTTTTGCCT 61.606 61.111 10.83 0.00 42.44 4.75
1 2 3.910490 TGGCGCACCAGTTTTGCC 61.910 61.111 10.83 0.00 42.67 4.52
9 10 1.079405 GCTTACTAGTGGCGCACCA 60.079 57.895 10.83 0.00 46.51 4.17
10 11 1.814169 GGCTTACTAGTGGCGCACC 60.814 63.158 10.83 0.00 34.49 5.01
11 12 0.391263 AAGGCTTACTAGTGGCGCAC 60.391 55.000 10.83 5.73 34.10 5.34
12 13 0.323629 AAAGGCTTACTAGTGGCGCA 59.676 50.000 10.83 0.00 0.00 6.09
13 14 1.450025 AAAAGGCTTACTAGTGGCGC 58.550 50.000 5.39 0.00 0.00 6.53
14 15 3.335579 AGAAAAAGGCTTACTAGTGGCG 58.664 45.455 5.39 0.00 0.00 5.69
15 16 5.489249 ACTAGAAAAAGGCTTACTAGTGGC 58.511 41.667 25.91 9.73 41.05 5.01
16 17 7.760340 CACTACTAGAAAAAGGCTTACTAGTGG 59.240 40.741 29.91 29.14 43.29 4.00
17 18 8.305317 ACACTACTAGAAAAAGGCTTACTAGTG 58.695 37.037 29.91 24.03 42.07 2.74
18 19 8.305317 CACACTACTAGAAAAAGGCTTACTAGT 58.695 37.037 27.66 27.66 43.62 2.57
19 20 7.275999 GCACACTACTAGAAAAAGGCTTACTAG 59.724 40.741 22.51 22.51 37.25 2.57
20 21 7.095270 GCACACTACTAGAAAAAGGCTTACTA 58.905 38.462 0.00 4.54 0.00 1.82
21 22 5.932883 GCACACTACTAGAAAAAGGCTTACT 59.067 40.000 0.00 3.52 0.00 2.24
22 23 5.163982 CGCACACTACTAGAAAAAGGCTTAC 60.164 44.000 0.00 0.00 0.00 2.34
23 24 4.927425 CGCACACTACTAGAAAAAGGCTTA 59.073 41.667 0.00 0.00 0.00 3.09
24 25 3.746492 CGCACACTACTAGAAAAAGGCTT 59.254 43.478 0.00 0.00 0.00 4.35
25 26 3.326747 CGCACACTACTAGAAAAAGGCT 58.673 45.455 0.00 0.00 0.00 4.58
26 27 2.415512 CCGCACACTACTAGAAAAAGGC 59.584 50.000 0.00 0.00 0.00 4.35
27 28 3.000727 CCCGCACACTACTAGAAAAAGG 58.999 50.000 0.00 0.00 0.00 3.11
28 29 2.415512 GCCCGCACACTACTAGAAAAAG 59.584 50.000 0.00 0.00 0.00 2.27
29 30 2.419667 GCCCGCACACTACTAGAAAAA 58.580 47.619 0.00 0.00 0.00 1.94
30 31 1.670674 CGCCCGCACACTACTAGAAAA 60.671 52.381 0.00 0.00 0.00 2.29
31 32 0.108992 CGCCCGCACACTACTAGAAA 60.109 55.000 0.00 0.00 0.00 2.52
32 33 1.509463 CGCCCGCACACTACTAGAA 59.491 57.895 0.00 0.00 0.00 2.10
33 34 3.060020 GCGCCCGCACACTACTAGA 62.060 63.158 7.91 0.00 41.49 2.43
34 35 2.582498 GCGCCCGCACACTACTAG 60.582 66.667 7.91 0.00 41.49 2.57
35 36 4.137872 GGCGCCCGCACACTACTA 62.138 66.667 18.11 0.00 44.11 1.82
56 57 3.053291 GCAAACACGGATGCGGGA 61.053 61.111 18.37 0.00 32.17 5.14
118 119 8.321353 TGATAGTTTTGTCATCTATGTGAGGTT 58.679 33.333 0.00 0.00 0.00 3.50
206 207 2.094338 AACTCGTCTAACGGGGTGATTC 60.094 50.000 4.21 0.00 42.58 2.52
222 223 6.773099 CAGCAAGCATTGATAGCCAACTCG 62.773 50.000 0.00 0.00 46.84 4.18
223 224 3.488721 CAGCAAGCATTGATAGCCAACTC 60.489 47.826 0.00 0.00 46.84 3.01
275 276 4.282195 ACGACCCTCCAATTGCAAAAATTA 59.718 37.500 1.71 0.00 0.00 1.40
297 298 1.017387 CGCATGAAAGGCCCTCTAAC 58.983 55.000 0.00 0.00 43.34 2.34
300 301 0.618458 TTACGCATGAAAGGCCCTCT 59.382 50.000 0.00 0.00 43.34 3.69
331 332 6.381420 TGTTTTCTTATCAAAAACCCCTCACA 59.619 34.615 8.50 0.00 42.98 3.58
340 341 9.959749 GAGGTGTATGTGTTTTCTTATCAAAAA 57.040 29.630 0.00 0.00 0.00 1.94
344 345 6.460781 ACGAGGTGTATGTGTTTTCTTATCA 58.539 36.000 0.00 0.00 0.00 2.15
350 351 3.187842 GGGAACGAGGTGTATGTGTTTTC 59.812 47.826 0.00 0.00 0.00 2.29
355 356 2.007049 GCTGGGAACGAGGTGTATGTG 61.007 57.143 0.00 0.00 0.00 3.21
359 360 2.642254 CCGCTGGGAACGAGGTGTA 61.642 63.158 0.00 0.00 34.06 2.90
408 411 4.771127 CCTGTGTGGCACGTTAGT 57.229 55.556 13.77 0.00 37.14 2.24
422 425 2.910205 CGGACATATCTGCTGCCTG 58.090 57.895 0.00 0.00 0.00 4.85
447 450 8.372521 CGTGCTTTTAAATACAATCACATTTCC 58.627 33.333 0.00 0.00 0.00 3.13
458 461 9.210329 TCTAACTTGATCGTGCTTTTAAATACA 57.790 29.630 0.00 0.00 0.00 2.29
473 476 6.509199 CGTGATTGCAGTCATCTAACTTGATC 60.509 42.308 15.51 0.00 0.00 2.92
580 583 9.847224 TTCTTATCCAGGTTAAATTACTGATCC 57.153 33.333 0.00 0.00 34.21 3.36
694 697 4.084276 GCTTGGAGAAGAAGAAAGTTCGAC 60.084 45.833 0.00 0.00 0.00 4.20
709 712 1.375140 CTTGCAGCGAGCTTGGAGA 60.375 57.895 2.37 0.00 45.94 3.71
774 777 2.158885 TGTTGTTGGATCACCGTCTTCA 60.159 45.455 0.00 0.00 39.42 3.02
781 784 3.317711 TGTCATTGTGTTGTTGGATCACC 59.682 43.478 0.00 0.00 0.00 4.02
798 801 2.164827 TCGTGTTATGTAGCGGTGTCAT 59.835 45.455 0.00 4.89 0.00 3.06
939 944 1.242076 AAGAGTGTGCATTGACTGGC 58.758 50.000 0.00 0.00 0.00 4.85
1032 1037 1.147153 GAGGTAGCTCCATGGCACC 59.853 63.158 10.97 11.35 39.02 5.01
1362 1367 0.924090 GCACGTCCTTGATAAGCTCG 59.076 55.000 0.00 0.00 0.00 5.03
1413 1418 2.435059 GTGAGAGCCGGGAACTGC 60.435 66.667 2.18 0.00 41.43 4.40
1467 1472 2.553904 CCTGTGCTTGACCCATTTCTCT 60.554 50.000 0.00 0.00 0.00 3.10
1561 1566 6.831353 TCATACCACAGAAACTGAAAGGAAAA 59.169 34.615 5.76 0.00 39.30 2.29
1653 1663 5.643379 AACTATTCCAGGACGTTACGTAA 57.357 39.130 11.32 3.29 41.37 3.18
1659 1669 2.224670 TGGCAAACTATTCCAGGACGTT 60.225 45.455 0.00 0.00 0.00 3.99
1660 1670 1.349688 TGGCAAACTATTCCAGGACGT 59.650 47.619 0.00 0.00 0.00 4.34
1662 1672 2.092323 GGTGGCAAACTATTCCAGGAC 58.908 52.381 0.00 0.00 0.00 3.85
1663 1673 1.707989 TGGTGGCAAACTATTCCAGGA 59.292 47.619 0.00 0.00 0.00 3.86
1667 1677 1.892474 TGCTTGGTGGCAAACTATTCC 59.108 47.619 0.00 0.00 39.43 3.01
1676 1686 5.221481 CCATAATTAATCATGCTTGGTGGCA 60.221 40.000 0.00 0.00 46.63 4.92
1677 1687 5.232463 CCATAATTAATCATGCTTGGTGGC 58.768 41.667 0.00 0.00 0.00 5.01
1680 1690 5.834742 TGAGCCATAATTAATCATGCTTGGT 59.165 36.000 0.00 0.00 0.00 3.67
1681 1691 6.335471 TGAGCCATAATTAATCATGCTTGG 57.665 37.500 0.00 0.00 0.00 3.61
1694 1704 9.632638 AGTCATAAACTAACAATGAGCCATAAT 57.367 29.630 0.00 0.00 36.07 1.28
1877 1887 3.068307 GCCTTCCTTCGAGATAACTGCTA 59.932 47.826 0.00 0.00 0.00 3.49
1979 1989 6.598753 AAACCCGAGAATCACATAATAACG 57.401 37.500 0.00 0.00 33.17 3.18
2063 2074 9.974980 GTAACCAAAAGGAAAAAGTATTCATGA 57.025 29.630 0.00 0.00 0.00 3.07
2064 2075 8.911662 CGTAACCAAAAGGAAAAAGTATTCATG 58.088 33.333 0.00 0.00 0.00 3.07
2065 2076 7.597369 GCGTAACCAAAAGGAAAAAGTATTCAT 59.403 33.333 0.00 0.00 0.00 2.57
2066 2077 6.919115 GCGTAACCAAAAGGAAAAAGTATTCA 59.081 34.615 0.00 0.00 0.00 2.57
2067 2078 7.143340 AGCGTAACCAAAAGGAAAAAGTATTC 58.857 34.615 0.00 0.00 0.00 1.75
2068 2079 7.046292 AGCGTAACCAAAAGGAAAAAGTATT 57.954 32.000 0.00 0.00 0.00 1.89
2070 2081 7.748691 ATAGCGTAACCAAAAGGAAAAAGTA 57.251 32.000 0.00 0.00 0.00 2.24
2071 2082 4.994907 AGCGTAACCAAAAGGAAAAAGT 57.005 36.364 0.00 0.00 0.00 2.66
2072 2083 7.940178 AAATAGCGTAACCAAAAGGAAAAAG 57.060 32.000 0.00 0.00 0.00 2.27
2090 2101 5.650543 CAGGTCCCACAACATAAAAATAGC 58.349 41.667 0.00 0.00 0.00 2.97
2093 2104 4.159557 AGCAGGTCCCACAACATAAAAAT 58.840 39.130 0.00 0.00 0.00 1.82
2100 2111 0.478072 ATCAAGCAGGTCCCACAACA 59.522 50.000 0.00 0.00 0.00 3.33
2115 2126 2.161410 GCAACAATCTGCGGTACATCAA 59.839 45.455 0.00 0.00 31.50 2.57
2132 2143 3.068024 TCAGATTGTTCTTGGTTGGCAAC 59.932 43.478 21.92 21.92 0.00 4.17
2138 2149 4.083110 CGCATCTTCAGATTGTTCTTGGTT 60.083 41.667 0.00 0.00 31.21 3.67
2151 2162 3.114809 TGTTGTTTTTGCGCATCTTCAG 58.885 40.909 12.75 0.00 0.00 3.02
2171 2182 7.599998 CCTTGTAAAATTGATTCAACCTCCTTG 59.400 37.037 0.15 0.00 0.00 3.61
2276 2287 3.066342 TCTCGTCCACGTCCTTCATATTC 59.934 47.826 0.00 0.00 40.80 1.75
2396 2407 6.238842 GCATGCTTAGTACAATCATTGTCCAT 60.239 38.462 11.37 0.00 44.12 3.41
2549 2560 3.435671 GTCATGGTACCTTACACAGTTGC 59.564 47.826 14.36 0.00 0.00 4.17
2550 2561 4.894784 AGTCATGGTACCTTACACAGTTG 58.105 43.478 14.36 0.00 0.00 3.16
2554 2565 5.512404 CCTGAAAGTCATGGTACCTTACACA 60.512 44.000 14.36 9.01 0.00 3.72
2556 2567 4.019681 CCCTGAAAGTCATGGTACCTTACA 60.020 45.833 14.36 0.00 29.02 2.41
2558 2569 4.172807 ACCCTGAAAGTCATGGTACCTTA 58.827 43.478 14.36 0.00 42.40 2.69
2565 2576 8.840321 CAACTATTTATACCCTGAAAGTCATGG 58.160 37.037 0.00 0.00 38.03 3.66
2656 2669 3.412237 TTCCGGCTAAAAACTGTAGCT 57.588 42.857 0.00 0.00 42.98 3.32
2698 2711 2.683768 GATGGGTATCTGACACCTCCT 58.316 52.381 4.92 0.00 36.25 3.69
2716 2729 1.351017 ACCTCAATGAACACACCCGAT 59.649 47.619 0.00 0.00 0.00 4.18
2731 2744 3.519107 TGATGAATAGAACTGGCACCTCA 59.481 43.478 0.00 0.00 0.00 3.86
2776 2789 5.239306 TGGTTTGAACTCATTGACATCACTC 59.761 40.000 0.00 0.00 0.00 3.51
2842 2855 0.883833 CAAATGACAAGAAGGCGCCT 59.116 50.000 27.08 27.08 0.00 5.52
2980 2993 3.258971 TGCAATGTCATCACGGTATGA 57.741 42.857 0.00 0.00 43.13 2.15
2983 2996 2.080693 GGTTGCAATGTCATCACGGTA 58.919 47.619 0.59 0.00 0.00 4.02
3096 3109 6.321181 ACAGAGTTCATCTTACAAAAGCCAAA 59.679 34.615 0.00 0.00 35.47 3.28
3148 3161 9.632638 AATGCATAGATTATCTTACACAAACCT 57.367 29.630 0.00 0.00 0.00 3.50
3249 3264 3.659183 AGCCTACAAGCAAGATCCAAT 57.341 42.857 0.00 0.00 34.23 3.16
3262 3277 5.447683 CGTATACGTGTAACTCAAGCCTACA 60.448 44.000 17.16 0.00 31.75 2.74
3330 3346 6.114187 TCCGCTCATATTATTCTTGACCAT 57.886 37.500 0.00 0.00 0.00 3.55
3512 3528 5.382664 AGGGAGTTTCAGAAAAGGTTACA 57.617 39.130 0.00 0.00 0.00 2.41
3523 3539 3.718815 GCCGATAGTTAGGGAGTTTCAG 58.281 50.000 0.00 0.00 0.00 3.02
3524 3540 2.100252 CGCCGATAGTTAGGGAGTTTCA 59.900 50.000 0.00 0.00 0.00 2.69
3637 3655 1.896220 TCTCATTCACACCCACTTGC 58.104 50.000 0.00 0.00 0.00 4.01
3646 3664 2.686405 GAGGCATGCAATCTCATTCACA 59.314 45.455 21.36 0.00 0.00 3.58
3666 3684 1.254026 CTATCAATAGCCCCCGACGA 58.746 55.000 0.00 0.00 0.00 4.20
3681 3699 5.367945 TTGTCAAGGACCCATAACCTATC 57.632 43.478 0.00 0.00 35.25 2.08
3687 3705 6.833416 CCTTATCATTTGTCAAGGACCCATAA 59.167 38.462 6.96 0.00 40.02 1.90
3732 3750 3.850173 ACTTACCAATGCTCCCTTCCTAA 59.150 43.478 0.00 0.00 0.00 2.69
3742 3760 4.481368 TCGACCAATACTTACCAATGCT 57.519 40.909 0.00 0.00 0.00 3.79
3753 3772 7.657761 AGTCTTCATGGATTTATCGACCAATAC 59.342 37.037 0.00 0.00 37.24 1.89
3755 3774 6.595682 AGTCTTCATGGATTTATCGACCAAT 58.404 36.000 0.00 0.00 37.24 3.16
3765 3784 7.020827 TCCTTTGAGTAGTCTTCATGGATTT 57.979 36.000 0.00 0.00 0.00 2.17
3793 3812 3.349927 TCAGAATGAGCCATGGAAACAG 58.650 45.455 18.40 0.41 43.32 3.16
3794 3813 3.438216 TCAGAATGAGCCATGGAAACA 57.562 42.857 18.40 12.06 42.56 2.83
3808 3831 7.936301 GCTAATGGATAAGGAGTTTCTCAGAAT 59.064 37.037 0.00 0.00 31.08 2.40
3834 3857 8.522542 ACTACTATCAGACTTGGTAGTTAAGG 57.477 38.462 5.86 0.00 46.65 2.69
3876 3899 7.628234 AGAAACAACACCTCATATGATCTCTT 58.372 34.615 5.72 0.00 0.00 2.85
3877 3900 7.125507 AGAGAAACAACACCTCATATGATCTCT 59.874 37.037 17.84 17.84 36.15 3.10
3919 3942 1.348538 CGTTAGCATTGTCGGCGACA 61.349 55.000 36.29 36.29 41.09 4.35
3923 3946 2.021380 CGCGTTAGCATTGTCGGC 59.979 61.111 0.00 0.00 45.49 5.54
3925 3948 0.440758 TTTCCGCGTTAGCATTGTCG 59.559 50.000 4.92 0.00 45.49 4.35
3938 3961 4.873827 TCCAACATCTATTGTAGTTTCCGC 59.126 41.667 0.00 0.00 37.68 5.54
3939 3962 5.006746 GCTCCAACATCTATTGTAGTTTCCG 59.993 44.000 0.00 0.00 37.68 4.30
3955 3979 2.203337 GCCTGGTGTGCTCCAACA 60.203 61.111 0.00 0.00 38.85 3.33
3957 3981 2.113774 CTGCCTGGTGTGCTCCAA 59.886 61.111 0.00 0.00 37.01 3.53
3968 3992 3.149196 TCCAAAGACTTTTAGCTGCCTG 58.851 45.455 0.00 0.00 0.00 4.85
3972 3996 4.550422 GGCTTTCCAAAGACTTTTAGCTG 58.450 43.478 15.24 0.72 40.95 4.24
3978 4002 1.688735 GCAGGGCTTTCCAAAGACTTT 59.311 47.619 4.89 0.00 43.70 2.66
3980 4004 0.185901 TGCAGGGCTTTCCAAAGACT 59.814 50.000 4.89 0.00 43.70 3.24
3986 4010 1.073722 CTGACTGCAGGGCTTTCCA 59.926 57.895 19.93 3.30 38.51 3.53
3999 4023 2.160219 CACACACAATAATGCGCTGACT 59.840 45.455 9.73 0.00 0.00 3.41
4004 4028 3.120338 ACACTACACACACAATAATGCGC 60.120 43.478 0.00 0.00 0.00 6.09
4005 4029 4.151512 TGACACTACACACACAATAATGCG 59.848 41.667 0.00 0.00 0.00 4.73
4006 4030 5.605564 TGACACTACACACACAATAATGC 57.394 39.130 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.