Multiple sequence alignment - TraesCS1D01G026300

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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 TraesCS1D01G026300 chr1D 100.000 2915 0 0 1 2915 10721698 10724612 0.000000e+00 5384.0
1 TraesCS1D01G026300 chr1D 97.222 36 1 0 642 677 10722263 10722298 8.720000e-06 62.1
2 TraesCS1D01G026300 chr1D 97.222 36 1 0 566 601 10722339 10722374 8.720000e-06 62.1
3 TraesCS1D01G026300 chr1B 91.730 1838 73 29 768 2558 15743975 15742170 0.000000e+00 2479.0
4 TraesCS1D01G026300 chr1B 79.712 626 38 25 1 600 15744609 15744047 1.280000e-98 370.0
5 TraesCS1D01G026300 chr1B 84.519 239 30 4 2681 2915 15742138 15741903 2.260000e-56 230.0
6 TraesCS1D01G026300 chr1B 82.759 145 8 8 609 737 15744119 15743976 2.370000e-21 113.0
7 TraesCS1D01G026300 chr1B 100.000 28 0 0 925 952 144482218 144482191 5.000000e-03 52.8
8 TraesCS1D01G026300 chr1A 94.373 1564 60 17 997 2555 12371415 12372955 0.000000e+00 2375.0
9 TraesCS1D01G026300 chr1A 91.892 370 11 11 1 367 12370036 12370389 1.560000e-137 499.0
10 TraesCS1D01G026300 chr1A 92.384 302 13 4 648 949 12371032 12371323 3.470000e-114 422.0
11 TraesCS1D01G026300 chr1A 80.816 245 25 12 2672 2915 12372981 12373204 3.860000e-39 172.0
12 TraesCS1D01G026300 chr1A 94.643 56 2 1 406 460 12370454 12370509 5.180000e-13 86.1
13 TraesCS1D01G026300 chr6B 88.542 96 5 3 2555 2646 12651897 12651990 8.540000e-21 111.0
14 TraesCS1D01G026300 chr6B 87.500 96 7 2 2556 2648 12651983 12651890 3.970000e-19 106.0
15 TraesCS1D01G026300 chr6D 88.421 95 6 4 2548 2639 293153835 293153927 3.070000e-20 110.0
16 TraesCS1D01G026300 chr6D 89.655 87 6 2 2554 2639 430139582 430139666 1.100000e-19 108.0
17 TraesCS1D01G026300 chr7A 89.535 86 7 1 2556 2641 578987752 578987835 1.100000e-19 108.0
18 TraesCS1D01G026300 chr4A 89.655 87 6 2 2554 2639 460740127 460740043 1.100000e-19 108.0
19 TraesCS1D01G026300 chr3A 81.955 133 14 7 2531 2654 102841806 102841675 1.430000e-18 104.0
20 TraesCS1D01G026300 chr5B 88.506 87 6 2 2556 2640 554891230 554891314 5.140000e-18 102.0
21 TraesCS1D01G026300 chr2D 82.114 123 9 9 2540 2655 212144437 212144321 3.090000e-15 93.5


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 TraesCS1D01G026300 chr1D 10721698 10724612 2914 False 1836.066667 5384 98.1480 1 2915 3 chr1D.!!$F1 2914
1 TraesCS1D01G026300 chr1B 15741903 15744609 2706 True 798.000000 2479 84.6800 1 2915 4 chr1B.!!$R2 2914
2 TraesCS1D01G026300 chr1A 12370036 12373204 3168 False 710.820000 2375 90.8216 1 2915 5 chr1A.!!$F1 2914

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
600 1050 0.033796 CCAGTGTCCAGCCCATGAAT 60.034 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 3093 2.030007 ACGACGAGTAATTTGGAACGGA 60.03 45.455 0.0 0.0 0.0 4.69 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
106 108 0.948141 GTCAGTCAGTCAGCTGCACC 60.948 60.000 9.47 0.00 42.29 5.01
218 220 1.471287 CATCATCACCAACACCAGCAG 59.529 52.381 0.00 0.00 0.00 4.24
232 234 4.142093 ACACCAGCAGGATGATATTTTTGC 60.142 41.667 0.35 0.00 39.69 3.68
241 243 5.591877 AGGATGATATTTTTGCTGGTCACTC 59.408 40.000 0.00 0.00 0.00 3.51
278 280 3.070159 TGGTCACTTTCAGTCAGAGGAAG 59.930 47.826 0.00 0.00 0.00 3.46
279 281 3.556004 GGTCACTTTCAGTCAGAGGAAGG 60.556 52.174 0.00 0.00 0.00 3.46
280 282 3.322254 GTCACTTTCAGTCAGAGGAAGGA 59.678 47.826 1.99 0.00 0.00 3.36
281 283 3.967326 TCACTTTCAGTCAGAGGAAGGAA 59.033 43.478 1.99 0.00 0.00 3.36
291 293 1.353694 AGAGGAAGGAAATGCAGCACT 59.646 47.619 0.00 0.00 0.00 4.40
292 294 2.165998 GAGGAAGGAAATGCAGCACTT 58.834 47.619 0.00 0.00 0.00 3.16
293 295 1.891150 AGGAAGGAAATGCAGCACTTG 59.109 47.619 0.00 0.00 0.00 3.16
294 296 1.888512 GGAAGGAAATGCAGCACTTGA 59.111 47.619 0.00 0.00 0.00 3.02
329 333 4.223255 TGTTTTGTGGATCCAATGCATCAT 59.777 37.500 18.20 0.00 31.75 2.45
382 405 0.037975 CCCCATTTTCACACAGCAGC 60.038 55.000 0.00 0.00 0.00 5.25
384 407 1.336517 CCCATTTTCACACAGCAGCAG 60.337 52.381 0.00 0.00 0.00 4.24
423 462 3.755378 AGCTGCCAGAAGATACAAACAAG 59.245 43.478 0.00 0.00 0.00 3.16
471 561 6.406849 CCCAAAGTACATAAAATGGTCCATGG 60.407 42.308 4.97 4.97 33.60 3.66
500 590 4.102996 TGCATGAATGTATCCTAGCCAAGA 59.897 41.667 0.00 0.00 0.00 3.02
506 596 7.118723 TGAATGTATCCTAGCCAAGACAATTT 58.881 34.615 0.00 0.00 0.00 1.82
509 599 9.646522 AATGTATCCTAGCCAAGACAATTTTAT 57.353 29.630 0.00 0.00 0.00 1.40
510 600 9.646522 ATGTATCCTAGCCAAGACAATTTTATT 57.353 29.630 0.00 0.00 0.00 1.40
515 605 9.866655 TCCTAGCCAAGACAATTTTATTATCAT 57.133 29.630 0.00 0.00 0.00 2.45
573 1023 5.311265 ACTATAAGCTGTATGTGCATGCAT 58.689 37.500 25.64 11.73 33.10 3.96
582 1032 0.880441 TGTGCATGCATACACACACC 59.120 50.000 25.56 7.97 41.67 4.16
583 1033 0.880441 GTGCATGCATACACACACCA 59.120 50.000 25.64 0.00 36.77 4.17
584 1034 1.135603 GTGCATGCATACACACACCAG 60.136 52.381 25.64 0.00 36.77 4.00
585 1035 1.167851 GCATGCATACACACACCAGT 58.832 50.000 14.21 0.00 0.00 4.00
594 1044 2.281761 CACACCAGTGTCCAGCCC 60.282 66.667 0.00 0.00 42.83 5.19
595 1045 2.772191 ACACCAGTGTCCAGCCCA 60.772 61.111 0.00 0.00 40.24 5.36
596 1046 2.156098 ACACCAGTGTCCAGCCCAT 61.156 57.895 0.00 0.00 40.24 4.00
597 1047 1.676635 CACCAGTGTCCAGCCCATG 60.677 63.158 0.00 0.00 0.00 3.66
598 1048 1.847506 ACCAGTGTCCAGCCCATGA 60.848 57.895 0.00 0.00 0.00 3.07
599 1049 1.379916 CCAGTGTCCAGCCCATGAA 59.620 57.895 0.00 0.00 0.00 2.57
600 1050 0.033796 CCAGTGTCCAGCCCATGAAT 60.034 55.000 0.00 0.00 0.00 2.57
601 1051 1.617804 CCAGTGTCCAGCCCATGAATT 60.618 52.381 0.00 0.00 0.00 2.17
602 1052 2.357050 CCAGTGTCCAGCCCATGAATTA 60.357 50.000 0.00 0.00 0.00 1.40
603 1053 3.559069 CAGTGTCCAGCCCATGAATTAT 58.441 45.455 0.00 0.00 0.00 1.28
604 1054 3.956199 CAGTGTCCAGCCCATGAATTATT 59.044 43.478 0.00 0.00 0.00 1.40
605 1055 5.132502 CAGTGTCCAGCCCATGAATTATTA 58.867 41.667 0.00 0.00 0.00 0.98
606 1056 5.771666 CAGTGTCCAGCCCATGAATTATTAT 59.228 40.000 0.00 0.00 0.00 1.28
607 1057 6.266103 CAGTGTCCAGCCCATGAATTATTATT 59.734 38.462 0.00 0.00 0.00 1.40
608 1058 7.448161 CAGTGTCCAGCCCATGAATTATTATTA 59.552 37.037 0.00 0.00 0.00 0.98
609 1059 8.172741 AGTGTCCAGCCCATGAATTATTATTAT 58.827 33.333 0.00 0.00 0.00 1.28
610 1060 8.806146 GTGTCCAGCCCATGAATTATTATTATT 58.194 33.333 0.00 0.00 0.00 1.40
711 1176 1.913419 TGGAAGGGATTGGTAGTCCAC 59.087 52.381 0.00 0.00 44.22 4.02
712 1177 2.197465 GGAAGGGATTGGTAGTCCACT 58.803 52.381 0.00 0.00 44.22 4.00
737 1202 4.464951 CAGCCATGGATGCCAATTATGTAT 59.535 41.667 18.60 0.00 36.95 2.29
738 1203 4.464951 AGCCATGGATGCCAATTATGTATG 59.535 41.667 18.40 0.00 36.95 2.39
739 1204 4.221262 GCCATGGATGCCAATTATGTATGT 59.779 41.667 18.40 0.00 36.95 2.29
740 1205 5.418524 GCCATGGATGCCAATTATGTATGTA 59.581 40.000 18.40 0.00 36.95 2.29
741 1206 6.097270 GCCATGGATGCCAATTATGTATGTAT 59.903 38.462 18.40 0.00 36.95 2.29
742 1207 7.485810 CCATGGATGCCAATTATGTATGTATG 58.514 38.462 5.56 0.00 36.95 2.39
747 1212 5.996219 TGCCAATTATGTATGTATGCGTTC 58.004 37.500 0.00 0.00 0.00 3.95
889 1355 2.952978 CCGCGCTATATATCCCTCTCTT 59.047 50.000 5.56 0.00 0.00 2.85
985 1485 2.506217 CGTGCATGACGGCGTAGT 60.506 61.111 14.74 0.58 44.85 2.73
986 1486 2.788176 CGTGCATGACGGCGTAGTG 61.788 63.158 14.74 16.09 44.85 2.74
988 1488 2.125673 GCATGACGGCGTAGTGGT 60.126 61.111 14.74 0.00 0.00 4.16
990 1490 1.296056 GCATGACGGCGTAGTGGTTT 61.296 55.000 14.74 0.00 0.00 3.27
991 1491 0.719465 CATGACGGCGTAGTGGTTTC 59.281 55.000 14.74 0.00 0.00 2.78
992 1492 0.390735 ATGACGGCGTAGTGGTTTCC 60.391 55.000 14.74 0.00 0.00 3.13
993 1493 1.005867 GACGGCGTAGTGGTTTCCA 60.006 57.895 14.74 0.00 0.00 3.53
1170 1691 3.918977 CGGGTGGTGACGGTGTCA 61.919 66.667 0.00 0.00 40.50 3.58
1797 2321 1.884926 GGCGCTCTTCATCTTCCGG 60.885 63.158 7.64 0.00 0.00 5.14
1968 2492 3.819337 CCATTGTCCATCCTCATCATCAC 59.181 47.826 0.00 0.00 0.00 3.06
2012 2538 2.476873 AGATGAGCGCAACGTAGTAG 57.523 50.000 11.47 0.00 45.00 2.57
2013 2539 0.847035 GATGAGCGCAACGTAGTAGC 59.153 55.000 11.47 0.00 45.00 3.58
2014 2540 0.172578 ATGAGCGCAACGTAGTAGCA 59.827 50.000 11.47 0.00 45.00 3.49
2036 2562 7.378181 AGCAACAATTTTCTCCGATTTTGTAT 58.622 30.769 0.00 0.00 0.00 2.29
2037 2563 7.872483 AGCAACAATTTTCTCCGATTTTGTATT 59.128 29.630 0.00 0.00 0.00 1.89
2115 2641 5.163561 CCACACAAACATAGTGGTTCACTTT 60.164 40.000 5.86 0.00 42.59 2.66
2117 2643 6.910433 CACACAAACATAGTGGTTCACTTTAC 59.090 38.462 5.86 0.00 42.59 2.01
2144 2671 6.847956 TTCTCCTGAAATTTGCATTTGTTG 57.152 33.333 0.00 0.00 32.35 3.33
2164 2691 3.603144 GCTCAAGCTCAGTGAGTGT 57.397 52.632 21.06 6.66 43.71 3.55
2165 2692 1.146637 GCTCAAGCTCAGTGAGTGTG 58.853 55.000 21.06 17.81 43.71 3.82
2166 2693 1.539929 GCTCAAGCTCAGTGAGTGTGT 60.540 52.381 21.06 1.65 43.71 3.72
2167 2694 2.133553 CTCAAGCTCAGTGAGTGTGTG 58.866 52.381 21.06 14.98 38.16 3.82
2194 2721 2.173519 CAATCTTGGCACTGTCCCATT 58.826 47.619 0.00 0.00 31.26 3.16
2212 2740 8.103935 TGTCCCATTCTACATGTGTGTAATTAA 58.896 33.333 9.11 0.00 40.16 1.40
2276 2804 1.201429 GGAGACACTGTGGGGTGGAT 61.201 60.000 13.09 0.00 41.09 3.41
2407 2935 4.157607 ACCGCAAAAGGTGACAGG 57.842 55.556 0.00 0.00 44.07 4.00
2443 2971 4.019591 CCCTAATCTGATCATGCTCATGGA 60.020 45.833 9.69 0.00 39.24 3.41
2465 2995 6.603201 TGGACCCAGATGAATTTGATTAAGTC 59.397 38.462 0.00 0.00 0.00 3.01
2489 3019 5.433855 CATTGTTTTCTTGCCAAATTCACG 58.566 37.500 0.00 0.00 0.00 4.35
2529 3059 3.942130 TCCTATGTCTATGTGATGCCG 57.058 47.619 0.00 0.00 0.00 5.69
2558 3088 4.998033 CCTCTTTCTTCCCTTGACTTGTAC 59.002 45.833 0.00 0.00 0.00 2.90
2559 3089 5.221742 CCTCTTTCTTCCCTTGACTTGTACT 60.222 44.000 0.00 0.00 0.00 2.73
2560 3090 5.855045 TCTTTCTTCCCTTGACTTGTACTC 58.145 41.667 0.00 0.00 0.00 2.59
2561 3091 4.618920 TTCTTCCCTTGACTTGTACTCC 57.381 45.455 0.00 0.00 0.00 3.85
2563 3093 2.715763 TCCCTTGACTTGTACTCCCT 57.284 50.000 0.00 0.00 0.00 4.20
2564 3094 2.537143 TCCCTTGACTTGTACTCCCTC 58.463 52.381 0.00 0.00 0.00 4.30
2565 3095 1.555533 CCCTTGACTTGTACTCCCTCC 59.444 57.143 0.00 0.00 0.00 4.30
2566 3096 1.204941 CCTTGACTTGTACTCCCTCCG 59.795 57.143 0.00 0.00 0.00 4.63
2567 3097 1.893801 CTTGACTTGTACTCCCTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
2568 3098 2.005370 TGACTTGTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
2569 3099 1.891150 TGACTTGTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
2570 3100 1.204231 GACTTGTACTCCCTCCGTTCC 59.796 57.143 0.00 0.00 0.00 3.62
2571 3101 1.263356 CTTGTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
2572 3102 1.621814 CTTGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
2573 3103 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2574 3104 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
2575 3105 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
2576 3106 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
2577 3107 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2578 3108 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2579 3109 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2580 3110 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2581 3111 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2582 3112 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2583 3113 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2584 3114 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2585 3115 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2586 3116 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2587 3117 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
2588 3118 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2589 3119 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2590 3120 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2591 3121 4.575645 TCCAAATTACTCGTCGTGGTTTTT 59.424 37.500 0.00 0.00 0.00 1.94
2592 3122 4.673311 CCAAATTACTCGTCGTGGTTTTTG 59.327 41.667 0.00 9.38 0.00 2.44
2593 3123 5.503498 CAAATTACTCGTCGTGGTTTTTGA 58.497 37.500 15.11 0.00 0.00 2.69
2594 3124 5.738118 AATTACTCGTCGTGGTTTTTGAA 57.262 34.783 0.00 0.00 0.00 2.69
2595 3125 4.519191 TTACTCGTCGTGGTTTTTGAAC 57.481 40.909 0.00 0.00 0.00 3.18
2596 3126 2.624636 ACTCGTCGTGGTTTTTGAACT 58.375 42.857 0.00 0.00 0.00 3.01
2597 3127 2.350498 ACTCGTCGTGGTTTTTGAACTG 59.650 45.455 0.00 0.00 0.00 3.16
2598 3128 2.605818 CTCGTCGTGGTTTTTGAACTGA 59.394 45.455 0.00 0.00 0.00 3.41
2599 3129 3.001414 TCGTCGTGGTTTTTGAACTGAA 58.999 40.909 0.00 0.00 0.00 3.02
2600 3130 3.623960 TCGTCGTGGTTTTTGAACTGAAT 59.376 39.130 0.00 0.00 0.00 2.57
2601 3131 4.095185 TCGTCGTGGTTTTTGAACTGAATT 59.905 37.500 0.00 0.00 0.00 2.17
2602 3132 4.436523 CGTCGTGGTTTTTGAACTGAATTC 59.563 41.667 0.00 0.00 37.88 2.17
2603 3133 5.336744 GTCGTGGTTTTTGAACTGAATTCA 58.663 37.500 8.12 8.12 45.92 2.57
2613 3143 5.568685 TGAACTGAATTCAAAAACCACGA 57.431 34.783 9.88 0.00 44.59 4.35
2614 3144 5.577835 TGAACTGAATTCAAAAACCACGAG 58.422 37.500 9.88 0.00 44.59 4.18
2615 3145 4.568152 ACTGAATTCAAAAACCACGAGG 57.432 40.909 9.88 0.00 42.21 4.63
2616 3146 4.204012 ACTGAATTCAAAAACCACGAGGA 58.796 39.130 9.88 0.00 38.69 3.71
2617 3147 4.275936 ACTGAATTCAAAAACCACGAGGAG 59.724 41.667 9.88 0.00 38.69 3.69
2618 3148 4.204012 TGAATTCAAAAACCACGAGGAGT 58.796 39.130 5.45 0.00 38.69 3.85
2619 3149 5.369833 TGAATTCAAAAACCACGAGGAGTA 58.630 37.500 5.45 0.00 38.69 2.59
2620 3150 5.823570 TGAATTCAAAAACCACGAGGAGTAA 59.176 36.000 5.45 0.00 38.69 2.24
2621 3151 6.488683 TGAATTCAAAAACCACGAGGAGTAAT 59.511 34.615 5.45 0.00 38.69 1.89
2622 3152 6.894339 ATTCAAAAACCACGAGGAGTAATT 57.106 33.333 5.68 0.00 38.69 1.40
2623 3153 6.702716 TTCAAAAACCACGAGGAGTAATTT 57.297 33.333 5.68 0.00 38.69 1.82
2624 3154 6.067263 TCAAAAACCACGAGGAGTAATTTG 57.933 37.500 5.68 9.03 38.69 2.32
2625 3155 5.009210 TCAAAAACCACGAGGAGTAATTTGG 59.991 40.000 5.68 0.00 38.69 3.28
2626 3156 4.360951 AAACCACGAGGAGTAATTTGGA 57.639 40.909 5.68 0.00 38.69 3.53
2627 3157 4.360951 AACCACGAGGAGTAATTTGGAA 57.639 40.909 5.68 0.00 38.69 3.53
2628 3158 3.671716 ACCACGAGGAGTAATTTGGAAC 58.328 45.455 5.68 0.00 38.69 3.62
2629 3159 2.671396 CCACGAGGAGTAATTTGGAACG 59.329 50.000 0.00 0.00 36.89 3.95
2630 3160 2.671396 CACGAGGAGTAATTTGGAACGG 59.329 50.000 0.00 0.00 0.00 4.44
2631 3161 2.564062 ACGAGGAGTAATTTGGAACGGA 59.436 45.455 0.00 0.00 0.00 4.69
2632 3162 3.187700 CGAGGAGTAATTTGGAACGGAG 58.812 50.000 0.00 0.00 0.00 4.63
2633 3163 3.532542 GAGGAGTAATTTGGAACGGAGG 58.467 50.000 0.00 0.00 0.00 4.30
2634 3164 3.178865 AGGAGTAATTTGGAACGGAGGA 58.821 45.455 0.00 0.00 0.00 3.71
2635 3165 3.585732 AGGAGTAATTTGGAACGGAGGAA 59.414 43.478 0.00 0.00 0.00 3.36
2636 3166 3.939592 GGAGTAATTTGGAACGGAGGAAG 59.060 47.826 0.00 0.00 0.00 3.46
2637 3167 4.565028 GGAGTAATTTGGAACGGAGGAAGT 60.565 45.833 0.00 0.00 0.00 3.01
2638 3168 5.337813 GGAGTAATTTGGAACGGAGGAAGTA 60.338 44.000 0.00 0.00 0.00 2.24
2639 3169 5.485620 AGTAATTTGGAACGGAGGAAGTAC 58.514 41.667 0.00 0.00 0.00 2.73
2640 3170 4.360951 AATTTGGAACGGAGGAAGTACA 57.639 40.909 0.00 0.00 0.00 2.90
2641 3171 2.825861 TTGGAACGGAGGAAGTACAC 57.174 50.000 0.00 0.00 0.00 2.90
2642 3172 0.599558 TGGAACGGAGGAAGTACACG 59.400 55.000 0.00 0.00 0.00 4.49
2643 3173 0.735287 GGAACGGAGGAAGTACACGC 60.735 60.000 0.00 0.00 0.00 5.34
2644 3174 0.038892 GAACGGAGGAAGTACACGCA 60.039 55.000 0.00 0.00 0.00 5.24
2645 3175 0.390124 AACGGAGGAAGTACACGCAA 59.610 50.000 0.00 0.00 0.00 4.85
2646 3176 0.390124 ACGGAGGAAGTACACGCAAA 59.610 50.000 0.00 0.00 0.00 3.68
2647 3177 1.202557 ACGGAGGAAGTACACGCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
2648 3178 1.459592 CGGAGGAAGTACACGCAAAAG 59.540 52.381 0.00 0.00 0.00 2.27
2649 3179 2.490991 GGAGGAAGTACACGCAAAAGT 58.509 47.619 0.00 0.00 0.00 2.66
2654 3184 5.225642 AGGAAGTACACGCAAAAGTAGTAC 58.774 41.667 0.00 0.00 36.26 2.73
2663 3193 7.769220 ACACGCAAAAGTAGTACTAGTGATAT 58.231 34.615 18.01 0.00 0.00 1.63
2800 3334 2.945447 TGCTGGCTGATTTGTATTGC 57.055 45.000 0.00 0.00 0.00 3.56
2886 3421 3.629398 GCCTAACTGATGGTCAAATCTGG 59.371 47.826 0.00 0.00 31.69 3.86
2888 3423 2.134789 ACTGATGGTCAAATCTGGGC 57.865 50.000 0.00 0.00 31.69 5.36
2900 3435 0.706433 ATCTGGGCCTGGAAATGTGT 59.294 50.000 10.79 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 108 4.503910 TGTAACACAGATCCGAATTCTGG 58.496 43.478 3.52 6.92 43.95 3.86
218 220 5.591877 AGAGTGACCAGCAAAAATATCATCC 59.408 40.000 0.00 0.00 0.00 3.51
232 234 0.972134 TTGCCTCTGAGAGTGACCAG 59.028 55.000 8.88 0.00 0.00 4.00
241 243 2.227388 GTGACCAACATTTGCCTCTGAG 59.773 50.000 0.00 0.00 0.00 3.35
278 280 3.015327 AGATCTCAAGTGCTGCATTTCC 58.985 45.455 5.27 0.00 0.00 3.13
279 281 4.155462 TCAAGATCTCAAGTGCTGCATTTC 59.845 41.667 5.27 0.00 0.00 2.17
280 282 4.077108 TCAAGATCTCAAGTGCTGCATTT 58.923 39.130 5.27 4.79 0.00 2.32
281 283 3.682696 TCAAGATCTCAAGTGCTGCATT 58.317 40.909 5.27 0.00 0.00 3.56
291 293 6.772233 TCCACAAAACAATCTCAAGATCTCAA 59.228 34.615 0.00 0.00 32.75 3.02
292 294 6.298361 TCCACAAAACAATCTCAAGATCTCA 58.702 36.000 0.00 0.00 32.75 3.27
293 295 6.808008 TCCACAAAACAATCTCAAGATCTC 57.192 37.500 0.00 0.00 32.75 2.75
294 296 6.376581 GGATCCACAAAACAATCTCAAGATCT 59.623 38.462 6.95 0.00 32.75 2.75
329 333 2.003937 GGGGGTTTGTTTCTTAGCCA 57.996 50.000 0.00 0.00 0.00 4.75
382 405 0.187361 TGGTTTGGGGGTTTCTCCTG 59.813 55.000 0.00 0.00 36.25 3.86
384 407 1.185618 GCTGGTTTGGGGGTTTCTCC 61.186 60.000 0.00 0.00 0.00 3.71
423 462 5.121454 GGACAAATCTGATGTGTTGTCTCTC 59.879 44.000 22.90 10.72 45.85 3.20
471 561 5.448768 GCTAGGATACATTCATGCATGCATC 60.449 44.000 30.07 16.83 41.41 3.91
551 1000 5.874895 ATGCATGCACATACAGCTTATAG 57.125 39.130 25.37 0.00 0.00 1.31
580 1030 1.426251 TTCATGGGCTGGACACTGGT 61.426 55.000 0.00 0.00 0.00 4.00
581 1031 0.033796 ATTCATGGGCTGGACACTGG 60.034 55.000 0.00 0.00 0.00 4.00
582 1032 1.843368 AATTCATGGGCTGGACACTG 58.157 50.000 0.00 0.00 0.00 3.66
583 1033 3.959495 ATAATTCATGGGCTGGACACT 57.041 42.857 0.00 0.00 0.00 3.55
584 1034 6.655078 AATAATAATTCATGGGCTGGACAC 57.345 37.500 0.00 0.00 0.00 3.67
585 1035 8.954834 AATAATAATAATTCATGGGCTGGACA 57.045 30.769 0.00 0.00 0.00 4.02
638 1088 3.860641 TGGTGTGTGTATGCATACAGAG 58.139 45.455 34.29 0.00 45.16 3.35
640 1090 3.371898 CACTGGTGTGTGTATGCATACAG 59.628 47.826 34.29 23.72 45.16 2.74
737 1202 1.135489 GGAGACAGACGAACGCATACA 60.135 52.381 0.00 0.00 0.00 2.29
738 1203 1.135489 TGGAGACAGACGAACGCATAC 60.135 52.381 0.00 0.00 35.01 2.39
739 1204 1.170442 TGGAGACAGACGAACGCATA 58.830 50.000 0.00 0.00 35.01 3.14
740 1205 1.964448 TGGAGACAGACGAACGCAT 59.036 52.632 0.00 0.00 35.01 4.73
741 1206 3.439008 TGGAGACAGACGAACGCA 58.561 55.556 0.00 0.00 35.01 5.24
979 1479 0.170339 GCCAATGGAAACCACTACGC 59.830 55.000 2.05 0.00 35.80 4.42
980 1480 0.808755 GGCCAATGGAAACCACTACG 59.191 55.000 2.05 0.00 35.80 3.51
982 1482 2.455557 CATGGCCAATGGAAACCACTA 58.544 47.619 10.96 0.00 35.80 2.74
983 1483 1.269012 CATGGCCAATGGAAACCACT 58.731 50.000 10.96 0.00 35.80 4.00
985 1485 0.835115 TGCATGGCCAATGGAAACCA 60.835 50.000 10.96 0.61 36.71 3.67
986 1486 0.542805 ATGCATGGCCAATGGAAACC 59.457 50.000 10.96 0.00 40.37 3.27
988 1488 1.408340 CGTATGCATGGCCAATGGAAA 59.592 47.619 10.96 0.00 40.37 3.13
990 1490 1.454572 GCGTATGCATGGCCAATGGA 61.455 55.000 10.96 10.83 41.34 3.41
991 1491 1.007038 GCGTATGCATGGCCAATGG 60.007 57.895 10.96 3.32 42.15 3.16
992 1492 4.639824 GCGTATGCATGGCCAATG 57.360 55.556 10.96 10.29 42.15 2.82
1797 2321 2.821366 CTGGACAGCACGATGGGC 60.821 66.667 0.00 0.00 0.00 5.36
1921 2445 7.020010 GCTATGATGGATCGAATGAAATTGTC 58.980 38.462 0.00 0.00 36.07 3.18
1926 2450 4.971939 TGGCTATGATGGATCGAATGAAA 58.028 39.130 0.00 0.00 0.00 2.69
1930 2454 4.914983 ACAATGGCTATGATGGATCGAAT 58.085 39.130 0.00 0.00 0.00 3.34
1968 2492 9.500864 CTTGGTTTCACATTTTTGTTTTTATGG 57.499 29.630 0.00 0.00 0.00 2.74
2012 2538 5.905480 ACAAAATCGGAGAAAATTGTTGC 57.095 34.783 0.00 0.00 43.58 4.17
2014 2540 9.981114 AGAAATACAAAATCGGAGAAAATTGTT 57.019 25.926 0.00 0.00 43.58 2.83
2115 2641 7.707624 AATGCAAATTTCAGGAGAATGAGTA 57.292 32.000 0.00 0.00 32.89 2.59
2117 2643 6.872020 ACAAATGCAAATTTCAGGAGAATGAG 59.128 34.615 0.00 0.00 32.89 2.90
2165 2692 2.880890 AGTGCCAAGATTGTGAACTCAC 59.119 45.455 2.78 2.78 46.59 3.51
2166 2693 2.880268 CAGTGCCAAGATTGTGAACTCA 59.120 45.455 0.00 0.00 0.00 3.41
2167 2694 2.880890 ACAGTGCCAAGATTGTGAACTC 59.119 45.455 0.00 0.00 0.00 3.01
2212 2740 8.696374 AGCTACTAATTACAGTGTCACACATAT 58.304 33.333 11.40 0.00 36.74 1.78
2276 2804 2.046988 CTCTCACCGCATGTGCCA 60.047 61.111 0.00 0.00 45.03 4.92
2285 2813 2.055042 CCCACTCTCCCTCTCACCG 61.055 68.421 0.00 0.00 0.00 4.94
2443 2971 6.493166 TGGACTTAATCAAATTCATCTGGGT 58.507 36.000 0.00 0.00 0.00 4.51
2465 2995 5.558653 CGTGAATTTGGCAAGAAAACAATGG 60.559 40.000 0.00 0.00 0.00 3.16
2489 3019 4.472833 AGGATACCCCAGATCAATGATAGC 59.527 45.833 0.00 0.00 37.41 2.97
2529 3059 3.325135 TCAAGGGAAGAAAGAGGTGAGAC 59.675 47.826 0.00 0.00 0.00 3.36
2558 3088 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2559 3089 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2560 3090 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2561 3091 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2563 3093 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
2564 3094 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
2565 3095 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2566 3096 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
2567 3097 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2568 3098 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2569 3099 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2570 3100 5.503498 TCAAAAACCACGACGAGTAATTTG 58.497 37.500 0.00 12.84 0.00 2.32
2571 3101 5.738118 TCAAAAACCACGACGAGTAATTT 57.262 34.783 0.00 1.88 0.00 1.82
2572 3102 5.295045 AGTTCAAAAACCACGACGAGTAATT 59.705 36.000 0.00 0.00 35.92 1.40
2573 3103 4.812626 AGTTCAAAAACCACGACGAGTAAT 59.187 37.500 0.00 0.00 35.92 1.89
2574 3104 4.033129 CAGTTCAAAAACCACGACGAGTAA 59.967 41.667 0.00 0.00 35.92 2.24
2575 3105 3.552699 CAGTTCAAAAACCACGACGAGTA 59.447 43.478 0.00 0.00 35.92 2.59
2576 3106 2.350498 CAGTTCAAAAACCACGACGAGT 59.650 45.455 0.00 0.00 35.92 4.18
2577 3107 2.605818 TCAGTTCAAAAACCACGACGAG 59.394 45.455 0.00 0.00 35.92 4.18
2578 3108 2.619147 TCAGTTCAAAAACCACGACGA 58.381 42.857 0.00 0.00 35.92 4.20
2579 3109 3.392769 TTCAGTTCAAAAACCACGACG 57.607 42.857 0.00 0.00 35.92 5.12
2580 3110 5.336744 TGAATTCAGTTCAAAAACCACGAC 58.663 37.500 3.38 0.00 43.64 4.34
2581 3111 5.568685 TGAATTCAGTTCAAAAACCACGA 57.431 34.783 3.38 0.00 43.64 4.35
2590 3120 8.972364 TCCTCGTGGTTTTTGAATTCAGTTCAA 61.972 37.037 8.41 0.00 43.00 2.69
2591 3121 5.449862 CCTCGTGGTTTTTGAATTCAGTTCA 60.450 40.000 8.41 2.17 44.87 3.18
2592 3122 4.976116 CCTCGTGGTTTTTGAATTCAGTTC 59.024 41.667 8.41 1.48 37.35 3.01
2593 3123 4.642885 TCCTCGTGGTTTTTGAATTCAGTT 59.357 37.500 8.41 0.00 34.23 3.16
2594 3124 4.204012 TCCTCGTGGTTTTTGAATTCAGT 58.796 39.130 8.41 0.00 34.23 3.41
2595 3125 4.275936 ACTCCTCGTGGTTTTTGAATTCAG 59.724 41.667 8.41 0.00 34.23 3.02
2596 3126 4.204012 ACTCCTCGTGGTTTTTGAATTCA 58.796 39.130 3.38 3.38 34.23 2.57
2597 3127 4.830826 ACTCCTCGTGGTTTTTGAATTC 57.169 40.909 2.99 0.00 34.23 2.17
2598 3128 6.894339 ATTACTCCTCGTGGTTTTTGAATT 57.106 33.333 2.99 0.00 34.23 2.17
2599 3129 6.894339 AATTACTCCTCGTGGTTTTTGAAT 57.106 33.333 2.99 0.00 34.23 2.57
2600 3130 6.460399 CCAAATTACTCCTCGTGGTTTTTGAA 60.460 38.462 2.99 0.00 34.23 2.69
2601 3131 5.009210 CCAAATTACTCCTCGTGGTTTTTGA 59.991 40.000 2.99 0.00 34.23 2.69
2602 3132 5.009210 TCCAAATTACTCCTCGTGGTTTTTG 59.991 40.000 2.99 7.59 34.23 2.44
2603 3133 5.134661 TCCAAATTACTCCTCGTGGTTTTT 58.865 37.500 2.99 0.00 34.23 1.94
2604 3134 4.721132 TCCAAATTACTCCTCGTGGTTTT 58.279 39.130 2.99 0.00 34.23 2.43
2605 3135 4.360951 TCCAAATTACTCCTCGTGGTTT 57.639 40.909 2.99 0.00 34.23 3.27
2606 3136 4.070009 GTTCCAAATTACTCCTCGTGGTT 58.930 43.478 2.99 0.00 34.23 3.67
2607 3137 3.671716 GTTCCAAATTACTCCTCGTGGT 58.328 45.455 2.99 0.00 34.23 4.16
2608 3138 2.671396 CGTTCCAAATTACTCCTCGTGG 59.329 50.000 0.00 0.00 0.00 4.94
2609 3139 2.671396 CCGTTCCAAATTACTCCTCGTG 59.329 50.000 0.00 0.00 0.00 4.35
2610 3140 2.564062 TCCGTTCCAAATTACTCCTCGT 59.436 45.455 0.00 0.00 0.00 4.18
2611 3141 3.187700 CTCCGTTCCAAATTACTCCTCG 58.812 50.000 0.00 0.00 0.00 4.63
2612 3142 3.197116 TCCTCCGTTCCAAATTACTCCTC 59.803 47.826 0.00 0.00 0.00 3.71
2613 3143 3.178865 TCCTCCGTTCCAAATTACTCCT 58.821 45.455 0.00 0.00 0.00 3.69
2614 3144 3.622166 TCCTCCGTTCCAAATTACTCC 57.378 47.619 0.00 0.00 0.00 3.85
2615 3145 4.576879 ACTTCCTCCGTTCCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2616 3146 4.635699 ACTTCCTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2617 3147 5.121298 GTGTACTTCCTCCGTTCCAAATTAC 59.879 44.000 0.00 0.00 0.00 1.89
2618 3148 5.240121 GTGTACTTCCTCCGTTCCAAATTA 58.760 41.667 0.00 0.00 0.00 1.40
2619 3149 4.070009 GTGTACTTCCTCCGTTCCAAATT 58.930 43.478 0.00 0.00 0.00 1.82
2620 3150 3.671716 GTGTACTTCCTCCGTTCCAAAT 58.328 45.455 0.00 0.00 0.00 2.32
2621 3151 2.546373 CGTGTACTTCCTCCGTTCCAAA 60.546 50.000 0.00 0.00 0.00 3.28
2622 3152 1.000060 CGTGTACTTCCTCCGTTCCAA 60.000 52.381 0.00 0.00 0.00 3.53
2623 3153 0.599558 CGTGTACTTCCTCCGTTCCA 59.400 55.000 0.00 0.00 0.00 3.53
2624 3154 0.735287 GCGTGTACTTCCTCCGTTCC 60.735 60.000 0.00 0.00 0.00 3.62
2625 3155 0.038892 TGCGTGTACTTCCTCCGTTC 60.039 55.000 0.00 0.00 0.00 3.95
2626 3156 0.390124 TTGCGTGTACTTCCTCCGTT 59.610 50.000 0.00 0.00 0.00 4.44
2627 3157 0.390124 TTTGCGTGTACTTCCTCCGT 59.610 50.000 0.00 0.00 0.00 4.69
2628 3158 1.459592 CTTTTGCGTGTACTTCCTCCG 59.540 52.381 0.00 0.00 0.00 4.63
2629 3159 2.490991 ACTTTTGCGTGTACTTCCTCC 58.509 47.619 0.00 0.00 0.00 4.30
2630 3160 4.304939 ACTACTTTTGCGTGTACTTCCTC 58.695 43.478 0.00 0.00 0.00 3.71
2631 3161 4.332428 ACTACTTTTGCGTGTACTTCCT 57.668 40.909 0.00 0.00 0.00 3.36
2632 3162 5.225642 AGTACTACTTTTGCGTGTACTTCC 58.774 41.667 0.00 0.00 40.27 3.46
2633 3163 7.060403 CACTAGTACTACTTTTGCGTGTACTTC 59.940 40.741 8.97 0.00 42.28 3.01
2634 3164 6.860023 CACTAGTACTACTTTTGCGTGTACTT 59.140 38.462 8.97 0.00 42.28 2.24
2635 3165 6.205464 TCACTAGTACTACTTTTGCGTGTACT 59.795 38.462 13.01 0.00 43.85 2.73
2636 3166 6.373779 TCACTAGTACTACTTTTGCGTGTAC 58.626 40.000 13.01 0.00 35.18 2.90
2637 3167 6.558771 TCACTAGTACTACTTTTGCGTGTA 57.441 37.500 13.01 2.31 0.00 2.90
2638 3168 5.443185 TCACTAGTACTACTTTTGCGTGT 57.557 39.130 13.01 0.00 0.00 4.49
2639 3169 8.630278 AATATCACTAGTACTACTTTTGCGTG 57.370 34.615 0.00 4.34 0.00 5.34
2679 3209 9.814899 CCCAAATTACTCATATTTGCACAAATA 57.185 29.630 15.98 15.98 44.47 1.40
2680 3210 8.538701 TCCCAAATTACTCATATTTGCACAAAT 58.461 29.630 12.82 12.82 40.15 2.32
2776 3307 6.072342 TGCAATACAAATCAGCCAGCATATAG 60.072 38.462 0.00 0.00 0.00 1.31
2783 3314 3.853831 TGTGCAATACAAATCAGCCAG 57.146 42.857 0.00 0.00 36.06 4.85
2825 3360 9.103048 CAAGTTGATTACGTGACATAAAAAGTC 57.897 33.333 0.00 0.00 38.34 3.01
2832 3367 7.485418 AAACACAAGTTGATTACGTGACATA 57.515 32.000 10.54 0.00 38.34 2.29
2833 3368 6.371809 AAACACAAGTTGATTACGTGACAT 57.628 33.333 10.54 0.00 38.34 3.06
2834 3369 5.804692 AAACACAAGTTGATTACGTGACA 57.195 34.783 10.54 0.00 38.34 3.58
2835 3370 8.678510 CAATAAAACACAAGTTGATTACGTGAC 58.321 33.333 10.54 0.00 38.34 3.67
2836 3371 7.858382 CCAATAAAACACAAGTTGATTACGTGA 59.142 33.333 10.54 0.00 38.34 4.35
2837 3372 7.646130 ACCAATAAAACACAAGTTGATTACGTG 59.354 33.333 10.54 0.00 41.34 4.49
2838 3373 7.646130 CACCAATAAAACACAAGTTGATTACGT 59.354 33.333 10.54 0.00 38.17 3.57
2839 3374 7.358023 GCACCAATAAAACACAAGTTGATTACG 60.358 37.037 10.54 0.00 38.17 3.18
2840 3375 7.095816 GGCACCAATAAAACACAAGTTGATTAC 60.096 37.037 10.54 0.00 38.17 1.89
2841 3376 6.926272 GGCACCAATAAAACACAAGTTGATTA 59.074 34.615 10.54 4.09 38.17 1.75
2843 3378 5.070313 AGGCACCAATAAAACACAAGTTGAT 59.930 36.000 10.54 0.00 38.17 2.57
2845 3380 4.692228 AGGCACCAATAAAACACAAGTTG 58.308 39.130 0.00 0.00 38.17 3.16
2846 3381 6.097696 AGTTAGGCACCAATAAAACACAAGTT 59.902 34.615 0.00 0.00 40.40 2.66
2886 3421 2.649129 GCCCACACATTTCCAGGCC 61.649 63.158 0.00 0.00 34.23 5.19
2888 3423 2.993471 GCGCCCACACATTTCCAGG 61.993 63.158 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.