Multiple sequence alignment - TraesCS7D01G196900

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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 TraesCS7D01G196900 chr7D 100.000 4546 0 0 1 4546 153632286 153636831 0.000000e+00 8395.0
1 TraesCS7D01G196900 chr7D 80.793 479 83 6 27 499 271053045 271053520 2.580000e-97 366.0
2 TraesCS7D01G196900 chr7D 80.376 479 87 6 52 527 586744182 586743708 1.560000e-94 357.0
3 TraesCS7D01G196900 chr7B 93.840 2857 131 21 872 3703 115401068 115403904 0.000000e+00 4259.0
4 TraesCS7D01G196900 chr7B 89.807 363 15 6 4206 4546 115404286 115404648 3.230000e-121 446.0
5 TraesCS7D01G196900 chr7B 92.818 181 10 2 3753 3930 115403920 115404100 4.510000e-65 259.0
6 TraesCS7D01G196900 chr7B 93.678 174 10 1 3975 4148 115404098 115404270 4.510000e-65 259.0
7 TraesCS7D01G196900 chr7B 88.571 70 7 1 4198 4267 115355627 115355695 2.910000e-12 84.2
8 TraesCS7D01G196900 chr7A 93.100 2290 105 26 1607 3876 155511375 155513631 0.000000e+00 3304.0
9 TraesCS7D01G196900 chr7A 93.145 671 26 7 700 1364 155510555 155511211 0.000000e+00 966.0
10 TraesCS7D01G196900 chr7A 92.068 353 14 5 1 353 155509540 155509878 6.840000e-133 484.0
11 TraesCS7D01G196900 chr7A 90.026 381 23 8 353 722 155510155 155510531 3.180000e-131 479.0
12 TraesCS7D01G196900 chr7A 88.889 207 16 4 933 1139 666158569 666158370 9.770000e-62 248.0
13 TraesCS7D01G196900 chr7A 96.552 58 2 0 4203 4260 155515021 155515078 3.740000e-16 97.1
14 TraesCS7D01G196900 chr7A 93.750 48 2 1 3907 3953 155514760 155514807 2.270000e-08 71.3
15 TraesCS7D01G196900 chr2D 100.000 329 0 0 2062 2390 574656536 574656208 3.890000e-170 608.0
16 TraesCS7D01G196900 chr2D 88.192 271 18 6 4284 4546 21829073 21828809 1.230000e-80 311.0
17 TraesCS7D01G196900 chr1B 80.945 656 100 14 1 649 667439971 667439334 3.160000e-136 496.0
18 TraesCS7D01G196900 chr1B 83.367 499 56 15 52 546 198860320 198860795 1.940000e-118 436.0
19 TraesCS7D01G196900 chr1B 88.406 207 14 5 933 1139 681868857 681868661 1.630000e-59 241.0
20 TraesCS7D01G196900 chr1B 87.440 207 16 5 933 1139 681863330 681863134 3.540000e-56 230.0
21 TraesCS7D01G196900 chr6D 82.791 430 66 7 52 478 383333358 383332934 1.190000e-100 377.0
22 TraesCS7D01G196900 chr3B 79.675 492 90 9 52 539 766801178 766801663 3.370000e-91 346.0
23 TraesCS7D01G196900 chr3B 74.883 426 79 20 57 461 379095650 379095232 7.820000e-38 169.0
24 TraesCS7D01G196900 chr3A 80.167 479 76 13 3 469 681444350 681444821 1.570000e-89 340.0
25 TraesCS7D01G196900 chr5D 91.304 207 11 4 933 1139 300557192 300556993 4.480000e-70 276.0
26 TraesCS7D01G196900 chr5B 88.119 202 14 4 938 1139 84849510 84849319 9.840000e-57 231.0


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 TraesCS7D01G196900 chr7D 153632286 153636831 4545 False 8395.000000 8395 100.000000 1 4546 1 chr7D.!!$F1 4545
1 TraesCS7D01G196900 chr7B 115401068 115404648 3580 False 1305.750000 4259 92.535750 872 4546 4 chr7B.!!$F2 3674
2 TraesCS7D01G196900 chr7A 155509540 155515078 5538 False 900.233333 3304 93.106833 1 4260 6 chr7A.!!$F1 4259
3 TraesCS7D01G196900 chr1B 667439334 667439971 637 True 496.000000 496 80.945000 1 649 1 chr1B.!!$R1 648

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
632 921 0.181114 TGGGAGATGGCTTTCGATGG 59.819 55.0 0.0 0.0 0.00 3.51 F
734 1033 0.473694 TTGGAGGTGCTTCCCTGAGA 60.474 55.0 0.0 0.0 36.35 3.27 F
1512 1865 0.178924 AAGCCAAACCAGGATGCCTT 60.179 50.0 0.0 0.0 31.97 4.35 F
2950 3308 0.104672 TTCCTCAGGTTCCCCACAGA 60.105 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1839 0.037046 GGCATCCTGGTTTGGCTTTG 60.037 55.0 15.11 0.0 35.67 2.77 R
1672 2025 0.107456 AGTGAGCTCCACCAAGTGTG 59.893 55.0 12.15 0.0 46.87 3.82 R
3018 3379 0.529378 CAGCCTCCACCAAAAGCATC 59.471 55.0 0.00 0.0 0.00 3.91 R
4439 5974 0.613853 TCCTTCGAGGACCCGTTCAT 60.614 55.0 0.00 0.0 40.06 2.57 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
37 38 3.672767 TGTCGATCATGAGGATGATGG 57.327 47.619 0.09 1.99 42.84 3.51
48 49 2.045045 ATGATGGTGGTGGTGGCG 60.045 61.111 0.00 0.00 0.00 5.69
49 50 2.535485 GATGATGGTGGTGGTGGCGA 62.535 60.000 0.00 0.00 0.00 5.54
50 51 2.436646 GATGGTGGTGGTGGCGAG 60.437 66.667 0.00 0.00 0.00 5.03
122 123 5.618418 GCCGGATGGAAGTACAAAAGTAAAC 60.618 44.000 5.05 0.00 37.49 2.01
123 124 5.470777 CCGGATGGAAGTACAAAAGTAAACA 59.529 40.000 0.00 0.00 37.49 2.83
134 135 6.144078 ACAAAAGTAAACAATTCGAAGGCT 57.856 33.333 3.35 0.00 0.00 4.58
201 202 4.020573 TGAGGAAAGAGTATGCCGAAGAAA 60.021 41.667 0.00 0.00 0.00 2.52
247 248 2.364448 GAGAGGGGGAAGCCGAGT 60.364 66.667 0.00 0.00 0.00 4.18
364 642 9.072375 TCAAGTTTATGTTCATGGACACAAATA 57.928 29.630 13.55 0.00 29.73 1.40
388 666 0.250727 CCTCGACCCCAAAGCAAAGA 60.251 55.000 0.00 0.00 0.00 2.52
407 685 1.578023 GACGTATGTCGAGCTTTGTCG 59.422 52.381 0.00 0.00 42.86 4.35
487 776 0.754472 GTGCCATGGATGAAATGGGG 59.246 55.000 18.40 0.00 44.13 4.96
576 865 0.951558 GGGCGGCTACATAAACATGG 59.048 55.000 9.56 0.00 0.00 3.66
590 879 1.521764 ACATGGTGGGAGATGCCATA 58.478 50.000 0.00 0.00 40.68 2.74
593 882 2.435372 TGGTGGGAGATGCCATAAAC 57.565 50.000 0.00 0.00 38.95 2.01
602 891 3.686016 AGATGCCATAAACGGTGTCTTT 58.314 40.909 0.00 0.00 0.00 2.52
627 916 2.424956 GACAACATGGGAGATGGCTTTC 59.575 50.000 0.00 0.00 0.00 2.62
629 918 0.911769 ACATGGGAGATGGCTTTCGA 59.088 50.000 0.00 0.00 0.00 3.71
630 919 1.492176 ACATGGGAGATGGCTTTCGAT 59.508 47.619 0.00 0.00 0.00 3.59
632 921 0.181114 TGGGAGATGGCTTTCGATGG 59.819 55.000 0.00 0.00 0.00 3.51
633 922 1.169034 GGGAGATGGCTTTCGATGGC 61.169 60.000 5.71 5.71 0.00 4.40
635 924 1.382522 GAGATGGCTTTCGATGGCAA 58.617 50.000 16.54 4.72 43.05 4.52
637 926 1.747355 AGATGGCTTTCGATGGCAAAG 59.253 47.619 16.54 4.60 43.05 2.77
649 947 2.597510 GCAAAGGGTGGCTTCGGT 60.598 61.111 0.00 0.00 0.00 4.69
653 951 1.420532 AAAGGGTGGCTTCGGTGGTA 61.421 55.000 0.00 0.00 0.00 3.25
725 1024 3.583086 ACACTAGTGTTATTGGAGGTGCT 59.417 43.478 22.95 0.00 41.83 4.40
726 1025 4.041691 ACACTAGTGTTATTGGAGGTGCTT 59.958 41.667 22.95 0.00 41.83 3.91
728 1027 3.073274 AGTGTTATTGGAGGTGCTTCC 57.927 47.619 0.00 0.00 37.77 3.46
730 1029 1.992557 TGTTATTGGAGGTGCTTCCCT 59.007 47.619 0.00 0.00 36.35 4.20
731 1030 2.290896 TGTTATTGGAGGTGCTTCCCTG 60.291 50.000 0.00 0.00 36.35 4.45
732 1031 1.965414 TATTGGAGGTGCTTCCCTGA 58.035 50.000 0.00 0.00 36.35 3.86
733 1032 0.622665 ATTGGAGGTGCTTCCCTGAG 59.377 55.000 0.00 0.00 36.35 3.35
734 1033 0.473694 TTGGAGGTGCTTCCCTGAGA 60.474 55.000 0.00 0.00 36.35 3.27
735 1034 0.473694 TGGAGGTGCTTCCCTGAGAA 60.474 55.000 0.00 0.00 36.35 2.87
746 1083 2.032620 TCCCTGAGAAGATACTTCGGC 58.967 52.381 0.00 0.00 0.00 5.54
808 1145 1.013197 ACCACTACCAGGTAGGCCTA 58.987 55.000 27.50 8.91 44.97 3.93
870 1212 0.716108 CACCACGATCTGAAGCGAAC 59.284 55.000 9.72 0.00 37.81 3.95
990 1332 3.866582 GTCCAGATCCGCCCCCTG 61.867 72.222 0.00 0.00 0.00 4.45
993 1335 4.559063 CAGATCCGCCCCCTGCTG 62.559 72.222 0.00 0.00 38.05 4.41
1299 1641 4.856607 GAGCCCTTCTCCGACGCG 62.857 72.222 3.53 3.53 35.77 6.01
1340 1682 4.537433 CGCCCTCCTGCAGGTAGC 62.537 72.222 31.58 27.70 41.51 3.58
1392 1736 3.119245 TGGTTCTTCCTGCTCGTACATAC 60.119 47.826 0.00 0.00 37.07 2.39
1400 1748 3.181490 CCTGCTCGTACATACTTGCTGTA 60.181 47.826 0.00 0.00 35.37 2.74
1408 1756 8.217131 TCGTACATACTTGCTGTATCTCTTAA 57.783 34.615 0.00 0.00 39.66 1.85
1413 1761 8.531982 ACATACTTGCTGTATCTCTTAAGTTGA 58.468 33.333 1.63 3.10 39.66 3.18
1418 1766 8.846943 TTGCTGTATCTCTTAAGTTGATTTGA 57.153 30.769 15.09 0.92 0.00 2.69
1432 1780 7.472334 AGTTGATTTGATAATGCCTCAGTTT 57.528 32.000 0.00 0.00 0.00 2.66
1434 1782 5.653507 TGATTTGATAATGCCTCAGTTTGC 58.346 37.500 0.00 0.00 0.00 3.68
1440 1788 1.985473 ATGCCTCAGTTTGCTGTTGA 58.015 45.000 0.00 0.00 43.05 3.18
1447 1795 5.752955 GCCTCAGTTTGCTGTTGAATAAAAA 59.247 36.000 0.00 0.00 43.05 1.94
1449 1797 7.041848 GCCTCAGTTTGCTGTTGAATAAAAATT 60.042 33.333 0.00 0.00 43.05 1.82
1452 1800 9.474920 TCAGTTTGCTGTTGAATAAAAATTAGG 57.525 29.630 0.00 0.00 43.05 2.69
1453 1801 9.260002 CAGTTTGCTGTTGAATAAAAATTAGGT 57.740 29.630 0.00 0.00 37.92 3.08
1481 1829 9.404848 AGTGATGCTAATTGTAGTACTGTACTA 57.595 33.333 20.74 20.74 40.14 1.82
1485 1833 8.867112 TGCTAATTGTAGTACTGTACTAATGC 57.133 34.615 24.88 20.52 42.45 3.56
1491 1839 6.860080 TGTAGTACTGTACTAATGCTGTTCC 58.140 40.000 24.88 12.42 42.45 3.62
1512 1865 0.178924 AAGCCAAACCAGGATGCCTT 60.179 50.000 0.00 0.00 31.97 4.35
1545 1898 2.846206 TGAATTGGACTAGTGGGATGCT 59.154 45.455 0.00 0.00 0.00 3.79
1565 1918 8.296713 GGATGCTTAAGATGTTCACTTTGTTAA 58.703 33.333 6.67 0.00 0.00 2.01
1595 1948 6.847421 AACTACTCGTAATTCCTACCAACT 57.153 37.500 0.00 0.00 0.00 3.16
1600 1953 6.396450 ACTCGTAATTCCTACCAACTTTCTC 58.604 40.000 0.00 0.00 0.00 2.87
1625 1978 1.264288 GTTCTCAGTTTGCCTTGGTCG 59.736 52.381 0.00 0.00 0.00 4.79
1672 2025 0.469917 TTGCGAAGGATGAGGGGATC 59.530 55.000 0.00 0.00 0.00 3.36
1764 2117 3.617540 TGACGTTGCAACCAAAGTATG 57.382 42.857 23.42 9.42 42.40 2.39
2029 2382 1.795872 CGTTTGTCATTCCTGCACGTA 59.204 47.619 0.00 0.00 0.00 3.57
2040 2393 4.937201 TCCTGCACGTATAATCAGTCAT 57.063 40.909 0.00 0.00 0.00 3.06
2060 2413 6.435277 AGTCATGGAGAACACTGCATTATTTT 59.565 34.615 0.00 0.00 39.89 1.82
2159 2512 7.781324 AAATGAGAAACTAATTGTGGATGGT 57.219 32.000 0.00 0.00 0.00 3.55
2348 2701 2.224281 TGATGTTGGTGTCAGGTGAGTC 60.224 50.000 0.00 0.00 0.00 3.36
2363 2718 6.042781 TCAGGTGAGTCTTGGTTACTGTTTAT 59.957 38.462 0.00 0.00 0.00 1.40
2404 2760 8.993121 GTTCACATTGATAGATACTTATGTGGG 58.007 37.037 11.67 0.00 41.76 4.61
2461 2817 4.128925 TGGTGATGCAGATAGACTTGTC 57.871 45.455 0.00 0.00 0.00 3.18
2758 3114 2.610438 ACTTTGAGGCCAATGGACAT 57.390 45.000 8.33 0.00 29.21 3.06
2782 3138 4.274459 GGGACAGTGCTATTCAATGATGAC 59.726 45.833 0.00 0.00 42.95 3.06
2794 3150 4.881920 TCAATGATGACTTTGTCTCACGA 58.118 39.130 0.00 0.54 34.30 4.35
2797 3153 5.644977 ATGATGACTTTGTCTCACGACTA 57.355 39.130 0.00 0.00 40.86 2.59
2839 3195 1.299562 CTGAAGCTGCAGGTGAGCTG 61.300 60.000 20.97 7.39 46.32 4.24
2897 3255 6.524101 TTTTAGTTCCTGTGCTGTTTTTCT 57.476 33.333 0.00 0.00 0.00 2.52
2901 3259 3.781079 TCCTGTGCTGTTTTTCTTGTG 57.219 42.857 0.00 0.00 0.00 3.33
2915 3273 8.196771 TGTTTTTCTTGTGTTGATCTAAATGCT 58.803 29.630 0.00 0.00 0.00 3.79
2916 3274 9.034544 GTTTTTCTTGTGTTGATCTAAATGCTT 57.965 29.630 0.00 0.00 0.00 3.91
2943 3301 4.518249 CCATAACTCTTTCCTCAGGTTCC 58.482 47.826 0.00 0.00 0.00 3.62
2950 3308 0.104672 TTCCTCAGGTTCCCCACAGA 60.105 55.000 0.00 0.00 0.00 3.41
2952 3310 0.771127 CCTCAGGTTCCCCACAGAAA 59.229 55.000 0.00 0.00 0.00 2.52
2958 3316 0.673985 GTTCCCCACAGAAACAAGCC 59.326 55.000 0.00 0.00 0.00 4.35
2968 3329 4.037208 CACAGAAACAAGCCTTGAGATTGT 59.963 41.667 12.25 7.41 38.76 2.71
3018 3379 2.439507 AGTGGGTGATGCTATAAGTGGG 59.560 50.000 0.00 0.00 0.00 4.61
3039 3400 1.108727 TGCTTTTGGTGGAGGCTGTG 61.109 55.000 0.00 0.00 0.00 3.66
3084 3445 6.575244 TTCCAGAATTGGTGTGACCTATAT 57.425 37.500 0.00 0.00 45.26 0.86
3180 3550 7.228150 GTCAAGCTTCTTACGACTATTTTGTC 58.772 38.462 0.00 0.00 0.00 3.18
3228 3598 5.120830 CAGGTTAAAGTGGAAGATCGAACTG 59.879 44.000 0.00 0.00 0.00 3.16
3425 3798 1.970917 CTCACGGGCGATGCTTTGTC 61.971 60.000 0.00 0.00 0.00 3.18
3514 3887 2.855180 CCTTGCAAAATCTGTAGCACG 58.145 47.619 0.00 0.00 36.62 5.34
3533 3906 0.171903 GGCATGTTGAGCGCATTCTT 59.828 50.000 11.47 0.00 0.00 2.52
3572 3945 8.340618 TGGGTTCTTCTTTTATCTTTCATCTG 57.659 34.615 0.00 0.00 0.00 2.90
3604 3977 9.654417 GAAACGTGTAATTTTCAACTTTAGCTA 57.346 29.630 0.00 0.00 32.84 3.32
3721 4094 4.710324 ACTTCAAGGTCGATGGTTTGTTA 58.290 39.130 0.00 0.00 0.00 2.41
3723 4096 4.345859 TCAAGGTCGATGGTTTGTTACT 57.654 40.909 0.00 0.00 0.00 2.24
3727 4100 1.392510 GTCGATGGTTTGTTACTCGCC 59.607 52.381 0.00 0.00 0.00 5.54
3734 4107 2.349155 GGTTTGTTACTCGCCGAAACTG 60.349 50.000 3.63 0.00 0.00 3.16
3747 4120 0.966179 GAAACTGGCGTCCCCATTTT 59.034 50.000 0.00 0.00 45.84 1.82
3759 4132 5.533482 CGTCCCCATTTTTAAAACACATGA 58.467 37.500 11.12 0.34 0.00 3.07
3793 4166 7.391148 TTGAATATTCTTAAGCAAGTGGACC 57.609 36.000 16.24 0.00 33.20 4.46
3804 4177 2.076863 CAAGTGGACCGAACTGATTCC 58.923 52.381 0.00 0.00 0.00 3.01
3806 4179 1.978580 AGTGGACCGAACTGATTCCTT 59.021 47.619 0.00 0.00 0.00 3.36
3876 4249 8.477419 TTGGAGAAAATTCAACTGAAAGGTAT 57.523 30.769 0.00 0.00 39.30 2.73
3890 4284 5.812286 TGAAAGGTATTCAAGTAGGGGAAC 58.188 41.667 0.00 0.00 0.00 3.62
3942 5414 7.062839 GCGTTAGATTATCAGGACATGATTCTC 59.937 40.741 8.06 5.82 46.97 2.87
3948 5420 4.386867 TCAGGACATGATTCTCGGTAAC 57.613 45.455 0.00 0.00 31.12 2.50
3952 5424 3.508762 GACATGATTCTCGGTAACACGT 58.491 45.455 0.00 0.00 34.94 4.49
3953 5425 3.508762 ACATGATTCTCGGTAACACGTC 58.491 45.455 0.00 0.00 34.94 4.34
3954 5426 3.057104 ACATGATTCTCGGTAACACGTCA 60.057 43.478 0.00 0.00 34.94 4.35
3955 5427 3.211803 TGATTCTCGGTAACACGTCAG 57.788 47.619 0.00 0.00 34.94 3.51
3956 5428 2.555325 TGATTCTCGGTAACACGTCAGT 59.445 45.455 0.00 0.00 34.94 3.41
3967 5439 2.584166 CACGTCAGTGTCAAGAATGC 57.416 50.000 0.00 0.00 43.15 3.56
3968 5440 1.866601 CACGTCAGTGTCAAGAATGCA 59.133 47.619 0.00 0.00 43.15 3.96
3969 5441 2.481568 CACGTCAGTGTCAAGAATGCAT 59.518 45.455 0.00 0.00 43.15 3.96
3970 5442 2.481568 ACGTCAGTGTCAAGAATGCATG 59.518 45.455 0.00 0.00 0.00 4.06
3971 5443 2.726989 CGTCAGTGTCAAGAATGCATGC 60.727 50.000 11.82 11.82 0.00 4.06
3972 5444 2.227149 GTCAGTGTCAAGAATGCATGCA 59.773 45.455 25.04 25.04 0.00 3.96
3973 5445 2.486592 TCAGTGTCAAGAATGCATGCAG 59.513 45.455 26.69 12.05 0.00 4.41
3974 5446 2.228103 CAGTGTCAAGAATGCATGCAGT 59.772 45.455 26.69 24.64 0.00 4.40
3975 5447 2.486982 AGTGTCAAGAATGCATGCAGTC 59.513 45.455 34.50 34.50 40.82 3.51
3976 5448 2.227149 GTGTCAAGAATGCATGCAGTCA 59.773 45.455 39.72 23.21 42.66 3.41
4058 5530 4.278170 CCAGGCAAGAACAATAACTTCACA 59.722 41.667 0.00 0.00 0.00 3.58
4127 5599 3.091633 AGCTACCCAATGCAAAGATGT 57.908 42.857 0.00 0.00 0.00 3.06
4138 5610 6.820656 CCAATGCAAAGATGTAGAGAACTAGT 59.179 38.462 0.00 0.00 0.00 2.57
4148 5620 6.438259 TGTAGAGAACTAGTGATCCTTTCG 57.562 41.667 0.00 0.00 0.00 3.46
4150 5622 3.764434 AGAGAACTAGTGATCCTTTCGCA 59.236 43.478 0.00 0.00 37.31 5.10
4151 5623 4.404073 AGAGAACTAGTGATCCTTTCGCAT 59.596 41.667 0.00 0.00 37.31 4.73
4152 5624 4.437239 AGAACTAGTGATCCTTTCGCATG 58.563 43.478 0.00 0.00 37.31 4.06
4153 5625 4.160439 AGAACTAGTGATCCTTTCGCATGA 59.840 41.667 0.00 0.00 37.31 3.07
4154 5626 4.052159 ACTAGTGATCCTTTCGCATGAG 57.948 45.455 0.00 0.00 37.31 2.90
4162 5646 3.889815 TCCTTTCGCATGAGGATTCAAT 58.110 40.909 0.00 0.00 37.15 2.57
4163 5647 3.879295 TCCTTTCGCATGAGGATTCAATC 59.121 43.478 0.00 0.00 37.15 2.67
4172 5656 6.456853 CGCATGAGGATTCAATCGAAAGTAAA 60.457 38.462 0.00 0.00 36.78 2.01
4173 5657 6.688813 GCATGAGGATTCAATCGAAAGTAAAC 59.311 38.462 0.00 0.00 36.78 2.01
4211 5724 6.969993 ATAAACCTCCTGTTGTTGCTTTAA 57.030 33.333 0.00 0.00 37.23 1.52
4269 5782 0.817634 GCACACAGCCACACAACCTA 60.818 55.000 0.00 0.00 37.23 3.08
4270 5783 0.944386 CACACAGCCACACAACCTAC 59.056 55.000 0.00 0.00 0.00 3.18
4272 5785 1.229428 CACAGCCACACAACCTACAG 58.771 55.000 0.00 0.00 0.00 2.74
4346 5878 4.731503 GCAGCACAGCGAGCAACG 62.732 66.667 0.00 0.00 45.66 4.10
4355 5887 0.739813 AGCGAGCAACGAATACCACC 60.740 55.000 7.46 0.00 45.77 4.61
4359 5891 2.147958 GAGCAACGAATACCACCACAA 58.852 47.619 0.00 0.00 0.00 3.33
4405 5937 4.223953 AGTCCACTTCTCCACAGAAACTA 58.776 43.478 0.00 0.00 38.23 2.24
4412 5944 8.043710 CCACTTCTCCACAGAAACTATAAGATT 58.956 37.037 0.00 0.00 38.23 2.40
4531 6066 3.005554 ACTCCAGATGATGCACTTTTCG 58.994 45.455 0.00 0.00 0.00 3.46
4535 6070 3.168963 CAGATGATGCACTTTTCGCAAG 58.831 45.455 0.00 0.00 43.84 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.411361 CCTCATGATCGACAACCAAACTTTA 59.589 40.000 0.00 0.00 0.00 1.85
37 38 4.394712 CCTCCTCGCCACCACCAC 62.395 72.222 0.00 0.00 0.00 4.16
48 49 2.791868 GGCGCCTTCTCTCCTCCTC 61.792 68.421 22.15 0.00 0.00 3.71
49 50 2.762043 GGCGCCTTCTCTCCTCCT 60.762 66.667 22.15 0.00 0.00 3.69
50 51 3.855853 GGGCGCCTTCTCTCCTCC 61.856 72.222 28.56 0.41 0.00 4.30
122 123 2.099141 TGTCTCCAGCCTTCGAATTG 57.901 50.000 0.00 0.00 0.00 2.32
123 124 2.859165 TTGTCTCCAGCCTTCGAATT 57.141 45.000 0.00 0.00 0.00 2.17
134 135 7.257790 TCCTTCTTTAAGATCATTGTCTCCA 57.742 36.000 0.00 0.00 34.37 3.86
221 222 1.213926 CTTCCCCCTCTCCTCCATTTG 59.786 57.143 0.00 0.00 0.00 2.32
364 642 2.067197 CTTTGGGGTCGAGGAGGTT 58.933 57.895 0.00 0.00 0.00 3.50
388 666 1.068748 ACGACAAAGCTCGACATACGT 60.069 47.619 0.00 0.00 43.13 3.57
407 685 5.163824 TGCTTCTTCATGATCGTTTCATCAC 60.164 40.000 0.00 0.00 43.40 3.06
453 733 2.832838 TGGCACCTCTCATTCCTTCTA 58.167 47.619 0.00 0.00 0.00 2.10
487 776 0.620556 TGGCACTTCTCATTCCTCCC 59.379 55.000 0.00 0.00 0.00 4.30
576 865 1.308998 CCGTTTATGGCATCTCCCAC 58.691 55.000 1.65 0.00 37.79 4.61
602 891 2.684630 GCCATCTCCCATGTTGTCATCA 60.685 50.000 0.00 0.00 31.15 3.07
627 916 1.937546 GAAGCCACCCTTTGCCATCG 61.938 60.000 0.00 0.00 32.78 3.84
629 918 1.978617 CGAAGCCACCCTTTGCCAT 60.979 57.895 0.00 0.00 32.78 4.40
630 919 2.597217 CGAAGCCACCCTTTGCCA 60.597 61.111 0.00 0.00 32.78 4.92
632 921 2.597510 ACCGAAGCCACCCTTTGC 60.598 61.111 0.00 0.00 34.18 3.68
633 922 2.268076 CCACCGAAGCCACCCTTTG 61.268 63.158 0.00 0.00 32.78 2.77
635 924 1.838073 CTACCACCGAAGCCACCCTT 61.838 60.000 0.00 0.00 36.19 3.95
637 926 1.259840 TACTACCACCGAAGCCACCC 61.260 60.000 0.00 0.00 0.00 4.61
647 945 1.955080 CCCATCTCTCGTACTACCACC 59.045 57.143 0.00 0.00 0.00 4.61
648 946 2.652590 ACCCATCTCTCGTACTACCAC 58.347 52.381 0.00 0.00 0.00 4.16
649 947 3.285484 GAACCCATCTCTCGTACTACCA 58.715 50.000 0.00 0.00 0.00 3.25
653 951 1.340795 ACCGAACCCATCTCTCGTACT 60.341 52.381 0.00 0.00 0.00 2.73
677 975 4.643387 AAGCCACCCCGCTGTGTC 62.643 66.667 2.49 0.00 39.64 3.67
707 1006 3.054655 GGGAAGCACCTCCAATAACACTA 60.055 47.826 2.38 0.00 37.20 2.74
716 1015 0.473694 TTCTCAGGGAAGCACCTCCA 60.474 55.000 2.38 0.00 39.34 3.86
725 1024 2.431057 GCCGAAGTATCTTCTCAGGGAA 59.569 50.000 7.70 0.00 0.00 3.97
726 1025 2.032620 GCCGAAGTATCTTCTCAGGGA 58.967 52.381 7.70 0.00 0.00 4.20
728 1027 1.269309 CCGCCGAAGTATCTTCTCAGG 60.269 57.143 7.70 3.63 0.00 3.86
730 1029 0.102481 GCCGCCGAAGTATCTTCTCA 59.898 55.000 7.70 0.00 0.00 3.27
731 1030 0.102481 TGCCGCCGAAGTATCTTCTC 59.898 55.000 7.70 0.22 0.00 2.87
732 1031 0.103208 CTGCCGCCGAAGTATCTTCT 59.897 55.000 7.70 0.00 0.00 2.85
733 1032 1.491505 GCTGCCGCCGAAGTATCTTC 61.492 60.000 0.00 0.03 0.00 2.87
734 1033 1.521681 GCTGCCGCCGAAGTATCTT 60.522 57.895 0.00 0.00 0.00 2.40
735 1034 2.107141 GCTGCCGCCGAAGTATCT 59.893 61.111 0.00 0.00 0.00 1.98
736 1035 2.202878 TGCTGCCGCCGAAGTATC 60.203 61.111 0.00 0.00 34.43 2.24
746 1083 2.981560 GAACATGGGTGTGCTGCCG 61.982 63.158 0.00 0.00 38.92 5.69
756 1093 2.749076 TGCTTCTCAATTCGAACATGGG 59.251 45.455 0.00 2.81 0.00 4.00
855 1197 1.478510 AGATGGTTCGCTTCAGATCGT 59.521 47.619 0.00 0.00 0.00 3.73
1370 1713 1.334160 TGTACGAGCAGGAAGAACCA 58.666 50.000 0.00 0.00 42.04 3.67
1392 1736 8.939929 TCAAATCAACTTAAGAGATACAGCAAG 58.060 33.333 10.09 0.00 0.00 4.01
1400 1748 9.638176 AGGCATTATCAAATCAACTTAAGAGAT 57.362 29.630 10.09 9.20 0.00 2.75
1408 1756 7.318141 CAAACTGAGGCATTATCAAATCAACT 58.682 34.615 0.00 0.00 0.00 3.16
1413 1761 5.927281 AGCAAACTGAGGCATTATCAAAT 57.073 34.783 0.00 0.00 0.00 2.32
1432 1780 9.906660 CACTAACCTAATTTTTATTCAACAGCA 57.093 29.630 0.00 0.00 0.00 4.41
1449 1797 9.417561 AGTACTACAATTAGCATCACTAACCTA 57.582 33.333 0.00 0.00 43.60 3.08
1452 1800 8.928270 ACAGTACTACAATTAGCATCACTAAC 57.072 34.615 0.00 0.00 43.60 2.34
1481 1829 2.485302 GGTTTGGCTTTGGAACAGCATT 60.485 45.455 0.00 0.00 42.39 3.56
1485 1833 1.069049 CCTGGTTTGGCTTTGGAACAG 59.931 52.381 0.00 0.00 42.39 3.16
1491 1839 0.037046 GGCATCCTGGTTTGGCTTTG 60.037 55.000 15.11 0.00 35.67 2.77
1512 1865 8.739039 CACTAGTCCAATTCAATGATAAAACCA 58.261 33.333 0.00 0.00 0.00 3.67
1574 1927 7.545489 AGAAAGTTGGTAGGAATTACGAGTAG 58.455 38.462 0.00 0.00 32.79 2.57
1583 1936 4.243270 CGAACGAGAAAGTTGGTAGGAAT 58.757 43.478 0.00 0.00 34.00 3.01
1595 1948 3.000925 GCAAACTGAGAACGAACGAGAAA 59.999 43.478 0.14 0.00 0.00 2.52
1600 1953 1.217882 AGGCAAACTGAGAACGAACG 58.782 50.000 0.00 0.00 0.00 3.95
1625 1978 2.733227 GCACCAGCTGCATATGAACAAC 60.733 50.000 8.66 0.00 46.29 3.32
1672 2025 0.107456 AGTGAGCTCCACCAAGTGTG 59.893 55.000 12.15 0.00 46.87 3.82
1686 2039 1.301244 AGCACTTGTGCCGAGTGAG 60.301 57.895 20.39 2.55 45.84 3.51
1764 2117 2.301346 CAGAGGGTGTTAATGCCATCC 58.699 52.381 8.62 0.00 36.33 3.51
1765 2118 3.004752 ACAGAGGGTGTTAATGCCATC 57.995 47.619 5.21 5.21 34.94 3.51
1808 2161 7.550597 TCAGATCAACTCAGCCAATAGATAT 57.449 36.000 0.00 0.00 0.00 1.63
1814 2167 5.999044 AGTAATCAGATCAACTCAGCCAAT 58.001 37.500 0.00 0.00 0.00 3.16
2029 2382 5.121811 GCAGTGTTCTCCATGACTGATTAT 58.878 41.667 12.72 0.00 38.49 1.28
2040 2393 6.003326 TCAGAAAATAATGCAGTGTTCTCCA 58.997 36.000 0.00 0.00 0.00 3.86
2159 2512 2.301296 CAACCCACCAATACCATTTGCA 59.699 45.455 0.00 0.00 0.00 4.08
2348 2701 6.468956 CGCAGCAAATATAAACAGTAACCAAG 59.531 38.462 0.00 0.00 0.00 3.61
2363 2718 5.559427 ATGTGAACATAACGCAGCAAATA 57.441 34.783 0.00 0.00 34.26 1.40
2404 2760 7.358066 CACACCTGAATGTTATATCAGAATGC 58.642 38.462 4.43 0.00 44.64 3.56
2461 2817 6.202762 TGCTAGGCGATGTAACATGAAAATAG 59.797 38.462 0.00 0.00 0.00 1.73
2758 3114 3.998913 TCATTGAATAGCACTGTCCCA 57.001 42.857 0.00 0.00 0.00 4.37
2794 3150 3.445805 GCCTAGCAGTCAAAGACTCTAGT 59.554 47.826 19.90 0.00 41.37 2.57
2797 3153 2.534990 AGCCTAGCAGTCAAAGACTCT 58.465 47.619 0.00 1.45 41.37 3.24
2839 3195 1.528161 GCTTTTGCACAAGCCATGAAC 59.472 47.619 24.02 0.00 43.03 3.18
2880 3238 3.509575 ACACAAGAAAAACAGCACAGGAA 59.490 39.130 0.00 0.00 0.00 3.36
2883 3241 4.484236 TCAACACAAGAAAAACAGCACAG 58.516 39.130 0.00 0.00 0.00 3.66
2897 3255 6.454795 GGGAAAAGCATTTAGATCAACACAA 58.545 36.000 0.00 0.00 37.28 3.33
2901 3259 5.659440 TGGGGAAAAGCATTTAGATCAAC 57.341 39.130 0.00 0.00 37.28 3.18
2915 3273 5.516591 CCTGAGGAAAGAGTTATGGGGAAAA 60.517 44.000 0.00 0.00 0.00 2.29
2916 3274 4.018415 CCTGAGGAAAGAGTTATGGGGAAA 60.018 45.833 0.00 0.00 0.00 3.13
2943 3301 1.610522 CTCAAGGCTTGTTTCTGTGGG 59.389 52.381 25.39 0.00 0.00 4.61
2950 3308 4.584325 TGCTAACAATCTCAAGGCTTGTTT 59.416 37.500 25.39 15.07 41.77 2.83
2952 3310 3.754965 TGCTAACAATCTCAAGGCTTGT 58.245 40.909 25.39 8.20 34.71 3.16
3018 3379 0.529378 CAGCCTCCACCAAAAGCATC 59.471 55.000 0.00 0.00 0.00 3.91
3039 3400 6.203723 GGAATGACCATCTCTTATGCTGTAAC 59.796 42.308 0.00 0.00 38.79 2.50
3142 3511 6.378710 AGAAGCTTGACCAAGAAGTTAAAC 57.621 37.500 2.10 0.00 40.79 2.01
3180 3550 8.267620 TGAACAACAGTCACATTATTATGGAG 57.732 34.615 0.00 0.00 36.01 3.86
3216 3586 6.887376 TGTAACAATAGCAGTTCGATCTTC 57.113 37.500 0.00 0.00 0.00 2.87
3228 3598 3.621268 TCTGCATCGGTTGTAACAATAGC 59.379 43.478 0.00 0.00 0.00 2.97
3383 3755 8.830580 TGAGAGTAATTAACTGCAATAGAATGC 58.169 33.333 0.00 0.00 46.58 3.56
3388 3761 6.201044 CCCGTGAGAGTAATTAACTGCAATAG 59.799 42.308 0.00 0.00 39.07 1.73
3425 3798 1.153289 CTCAGTTCCAGATGGCCGG 60.153 63.158 0.00 0.00 34.44 6.13
3514 3887 0.171903 AAGAATGCGCTCAACATGCC 59.828 50.000 9.73 0.00 0.00 4.40
3533 3906 2.091555 AGAACCCAACTAGCAAAACCCA 60.092 45.455 0.00 0.00 0.00 4.51
3572 3945 8.389586 AGTTGAAAATTACACGTTTCAGAAAC 57.610 30.769 15.16 15.16 42.86 2.78
3604 3977 7.272037 ACATTCTTCAAAACGTAGGTGAATT 57.728 32.000 8.42 0.00 31.21 2.17
3609 3982 6.518493 TGTCTACATTCTTCAAAACGTAGGT 58.482 36.000 0.00 0.00 0.00 3.08
3727 4100 1.241315 AAATGGGGACGCCAGTTTCG 61.241 55.000 17.49 0.00 0.00 3.46
3734 4107 3.061322 GTGTTTTAAAAATGGGGACGCC 58.939 45.455 1.31 0.53 0.00 5.68
3747 4120 9.993454 TTCAATTCCATGATTCATGTGTTTTAA 57.007 25.926 21.95 9.30 39.94 1.52
3774 4147 4.811969 TCGGTCCACTTGCTTAAGAATA 57.188 40.909 6.67 0.00 0.00 1.75
3793 4166 7.364522 TCACAAGATAAAAGGAATCAGTTCG 57.635 36.000 0.00 0.00 35.10 3.95
3804 4177 9.681692 TGAAACACATCAATCACAAGATAAAAG 57.318 29.630 0.00 0.00 33.08 2.27
3806 4179 9.065798 TCTGAAACACATCAATCACAAGATAAA 57.934 29.630 0.00 0.00 33.08 1.40
3876 4249 2.375174 ACTGCATGTTCCCCTACTTGAA 59.625 45.455 0.00 0.00 0.00 2.69
3890 4284 9.697250 CATTTTTCAGCATTATAAAACTGCATG 57.303 29.630 11.15 7.22 38.37 4.06
3948 5420 1.866601 TGCATTCTTGACACTGACGTG 59.133 47.619 0.00 0.00 46.63 4.49
3952 5424 2.486592 CTGCATGCATTCTTGACACTGA 59.513 45.455 22.97 0.00 0.00 3.41
3953 5425 2.228103 ACTGCATGCATTCTTGACACTG 59.772 45.455 22.97 7.24 0.00 3.66
3954 5426 2.486982 GACTGCATGCATTCTTGACACT 59.513 45.455 25.92 0.00 0.00 3.55
3955 5427 2.227149 TGACTGCATGCATTCTTGACAC 59.773 45.455 30.70 10.69 0.00 3.67
3956 5428 2.506444 TGACTGCATGCATTCTTGACA 58.494 42.857 30.70 18.69 0.00 3.58
3957 5429 3.564235 TTGACTGCATGCATTCTTGAC 57.436 42.857 30.70 16.64 0.00 3.18
3958 5430 4.587584 TTTTGACTGCATGCATTCTTGA 57.412 36.364 30.70 17.97 0.00 3.02
3959 5431 5.168569 AGATTTTGACTGCATGCATTCTTG 58.831 37.500 30.70 18.44 0.00 3.02
3960 5432 5.047590 TGAGATTTTGACTGCATGCATTCTT 60.048 36.000 30.70 17.17 0.00 2.52
3961 5433 4.461431 TGAGATTTTGACTGCATGCATTCT 59.539 37.500 30.70 19.04 0.00 2.40
3962 5434 4.740268 TGAGATTTTGACTGCATGCATTC 58.260 39.130 26.32 26.32 0.00 2.67
3963 5435 4.794278 TGAGATTTTGACTGCATGCATT 57.206 36.364 22.97 16.79 0.00 3.56
3964 5436 4.794278 TTGAGATTTTGACTGCATGCAT 57.206 36.364 22.97 11.62 0.00 3.96
3965 5437 4.038282 ACTTTGAGATTTTGACTGCATGCA 59.962 37.500 21.29 21.29 0.00 3.96
3966 5438 4.553323 ACTTTGAGATTTTGACTGCATGC 58.447 39.130 11.82 11.82 0.00 4.06
3967 5439 6.088824 GGTACTTTGAGATTTTGACTGCATG 58.911 40.000 0.00 0.00 0.00 4.06
3968 5440 5.769662 TGGTACTTTGAGATTTTGACTGCAT 59.230 36.000 0.00 0.00 0.00 3.96
3969 5441 5.129634 TGGTACTTTGAGATTTTGACTGCA 58.870 37.500 0.00 0.00 0.00 4.41
3970 5442 5.689383 TGGTACTTTGAGATTTTGACTGC 57.311 39.130 0.00 0.00 0.00 4.40
3971 5443 9.533253 AAAAATGGTACTTTGAGATTTTGACTG 57.467 29.630 0.00 0.00 0.00 3.51
3998 5470 1.556591 CGTTTCTACGCAGCACAGCA 61.557 55.000 0.00 0.00 41.41 4.41
4009 5481 6.753279 TGTGTTACATAGCCATACGTTTCTAC 59.247 38.462 0.00 0.00 0.00 2.59
4018 5490 3.433031 GCCTGGTGTGTTACATAGCCATA 60.433 47.826 8.68 0.00 0.00 2.74
4020 5492 1.339631 GCCTGGTGTGTTACATAGCCA 60.340 52.381 8.68 7.00 0.00 4.75
4021 5493 1.339631 TGCCTGGTGTGTTACATAGCC 60.340 52.381 8.68 2.89 0.00 3.93
4058 5530 0.681733 ACGACACACTGATGAGGCTT 59.318 50.000 0.00 0.00 0.00 4.35
4127 5599 4.948004 TGCGAAAGGATCACTAGTTCTCTA 59.052 41.667 0.00 0.00 0.00 2.43
4148 5620 4.889832 ACTTTCGATTGAATCCTCATGC 57.110 40.909 0.00 0.00 33.20 4.06
4150 5622 8.567285 AAGTTTACTTTCGATTGAATCCTCAT 57.433 30.769 0.00 0.00 33.20 2.90
4151 5623 7.979444 AAGTTTACTTTCGATTGAATCCTCA 57.021 32.000 0.00 0.00 33.20 3.86
4189 5673 5.889289 AGTTAAAGCAACAACAGGAGGTTTA 59.111 36.000 0.00 0.00 39.81 2.01
4196 5680 4.096382 ACTGTCAGTTAAAGCAACAACAGG 59.904 41.667 18.59 8.03 46.76 4.00
4211 5724 0.823769 TGCCGAGTGAGACTGTCAGT 60.824 55.000 4.81 4.81 41.97 3.41
4269 5782 3.762823 GGTAAGCAGACTACACTACCTGT 59.237 47.826 0.00 0.00 36.82 4.00
4270 5783 3.762288 TGGTAAGCAGACTACACTACCTG 59.238 47.826 5.88 0.00 0.00 4.00
4272 5785 3.130693 CCTGGTAAGCAGACTACACTACC 59.869 52.174 0.00 0.00 0.00 3.18
4274 5787 2.758979 GCCTGGTAAGCAGACTACACTA 59.241 50.000 0.00 0.00 0.00 2.74
4346 5878 6.751888 GCAAACTATGAATTGTGGTGGTATTC 59.248 38.462 0.00 0.00 0.00 1.75
4381 5913 1.248486 TCTGTGGAGAAGTGGACTCG 58.752 55.000 0.00 0.00 35.49 4.18
4405 5937 3.829601 CGAGGGAGGACAGCTAATCTTAT 59.170 47.826 0.00 0.00 0.00 1.73
4412 5944 2.442272 GGCGAGGGAGGACAGCTA 60.442 66.667 0.00 0.00 0.00 3.32
4439 5974 0.613853 TCCTTCGAGGACCCGTTCAT 60.614 55.000 0.00 0.00 40.06 2.57


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

AutoCloner maintained by Alex Coulton.