Multiple sequence alignment - TraesCS5B01G178200

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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 TraesCS5B01G178200 chr5B 100.000 5463 0 0 1 5463 325966499 325961037 0.000000e+00 10089.0
1 TraesCS5B01G178200 chr5B 94.696 1150 45 7 2538 3686 705607860 705606726 0.000000e+00 1772.0
2 TraesCS5B01G178200 chr5B 78.470 562 48 30 4934 5461 325943098 325942576 3.200000e-77 300.0
3 TraesCS5B01G178200 chr5B 86.170 94 8 3 4680 4768 325944262 325944169 4.500000e-16 97.1
4 TraesCS5B01G178200 chr5D 94.463 1752 41 20 806 2531 287017788 287016067 0.000000e+00 2647.0
5 TraesCS5B01G178200 chr5D 94.195 1068 44 3 3686 4736 287016069 287015003 0.000000e+00 1613.0
6 TraesCS5B01G178200 chr5D 95.590 703 27 4 1 702 287018485 287017786 0.000000e+00 1123.0
7 TraesCS5B01G178200 chr5D 91.160 724 33 13 4742 5461 287014965 287014269 0.000000e+00 953.0
8 TraesCS5B01G178200 chr5D 93.231 458 28 3 3232 3687 154325563 154326019 0.000000e+00 671.0
9 TraesCS5B01G178200 chr5D 92.623 366 19 1 2819 3184 154313089 154313446 2.260000e-143 520.0
10 TraesCS5B01G178200 chr5D 93.286 283 19 0 2520 2802 154312822 154313104 8.460000e-113 418.0
11 TraesCS5B01G178200 chr5D 82.095 296 30 11 4930 5215 286949778 286949496 1.180000e-56 231.0
12 TraesCS5B01G178200 chr5D 85.211 142 19 2 3552 3693 494480538 494480399 1.590000e-30 145.0
13 TraesCS5B01G178200 chr5D 91.837 98 8 0 705 802 310705259 310705356 2.650000e-28 137.0
14 TraesCS5B01G178200 chr5A 94.290 1261 41 16 793 2030 379094488 379093236 0.000000e+00 1901.0
15 TraesCS5B01G178200 chr5A 91.574 1080 61 7 3686 4736 379092720 379091642 0.000000e+00 1463.0
16 TraesCS5B01G178200 chr5A 96.359 714 21 5 1 713 379095194 379094485 0.000000e+00 1170.0
17 TraesCS5B01G178200 chr5A 89.598 423 25 7 5056 5461 379091314 379090894 2.260000e-143 520.0
18 TraesCS5B01G178200 chr5A 91.901 284 13 5 4737 5010 379091602 379091319 6.640000e-104 388.0
19 TraesCS5B01G178200 chr5A 93.089 246 12 3 2246 2490 379093015 379092774 6.730000e-94 355.0
20 TraesCS5B01G178200 chr5A 81.205 415 38 16 5087 5463 379040895 379040483 1.150000e-76 298.0
21 TraesCS5B01G178200 chr5A 90.698 129 10 2 2076 2203 379093239 379093112 2.620000e-38 171.0
22 TraesCS5B01G178200 chr5A 88.028 142 13 2 4574 4711 379089202 379089061 1.220000e-36 165.0
23 TraesCS5B01G178200 chr7D 89.117 1167 91 21 833 1983 37659440 37660586 0.000000e+00 1419.0
24 TraesCS5B01G178200 chr7D 87.162 740 69 11 978 1705 37625515 37626240 0.000000e+00 817.0
25 TraesCS5B01G178200 chr7D 78.764 631 77 35 3808 4412 37661234 37661833 2.400000e-98 370.0
26 TraesCS5B01G178200 chr7D 94.444 90 5 0 709 798 498229925 498229836 7.380000e-29 139.0
27 TraesCS5B01G178200 chr7D 93.220 59 3 1 2419 2476 37661065 37661123 9.750000e-13 86.1
28 TraesCS5B01G178200 chr3D 88.898 1171 93 22 833 1986 25527112 25525962 0.000000e+00 1408.0
29 TraesCS5B01G178200 chr3D 78.727 644 80 34 3808 4412 25525317 25524692 1.440000e-100 377.0
30 TraesCS5B01G178200 chr3D 94.915 59 2 1 2419 2476 25525486 25525428 2.100000e-14 91.6
31 TraesCS5B01G178200 chr2A 88.776 1176 92 26 833 1986 720388432 720387275 0.000000e+00 1404.0
32 TraesCS5B01G178200 chr2A 88.235 629 61 8 1087 1705 720354044 720353419 0.000000e+00 739.0
33 TraesCS5B01G178200 chr2A 78.315 641 83 35 3807 4412 720386368 720385749 4.020000e-96 363.0
34 TraesCS5B01G178200 chr2A 90.196 102 10 0 696 797 423207315 423207416 3.430000e-27 134.0
35 TraesCS5B01G178200 chr2A 98.611 72 1 0 2419 2490 720386640 720386569 1.600000e-25 128.0
36 TraesCS5B01G178200 chr4A 89.875 1037 80 17 981 2002 687321183 687320157 0.000000e+00 1310.0
37 TraesCS5B01G178200 chr4A 79.208 404 60 16 3801 4182 687319221 687318820 5.430000e-65 259.0
38 TraesCS5B01G178200 chr4A 95.506 89 4 0 708 796 285485363 285485451 5.700000e-30 143.0
39 TraesCS5B01G178200 chr4A 86.726 113 12 2 2218 2328 687319757 687319646 7.430000e-24 122.0
40 TraesCS5B01G178200 chr4A 94.444 72 4 0 2419 2490 687319504 687319433 1.610000e-20 111.0
41 TraesCS5B01G178200 chr3B 93.029 875 49 4 2819 3690 178481795 178482660 0.000000e+00 1267.0
42 TraesCS5B01G178200 chr3B 89.556 383 19 8 2528 2892 178481535 178481914 2.980000e-127 466.0
43 TraesCS5B01G178200 chr1B 90.722 679 29 4 2535 3212 468094687 468095332 0.000000e+00 874.0
44 TraesCS5B01G178200 chr1B 92.769 484 31 4 3207 3689 468108095 468108575 0.000000e+00 697.0
45 TraesCS5B01G178200 chr1B 84.694 196 27 3 2538 2732 612017226 612017033 5.580000e-45 193.0
46 TraesCS5B01G178200 chr1B 90.291 103 6 4 697 797 406341747 406341847 1.230000e-26 132.0
47 TraesCS5B01G178200 chr2B 93.706 572 34 2 3118 3688 41962843 41963413 0.000000e+00 856.0
48 TraesCS5B01G178200 chr2B 97.143 210 5 1 2828 3037 41962636 41962844 2.420000e-93 353.0
49 TraesCS5B01G178200 chr2B 94.000 50 3 0 2027 2076 291598899 291598948 5.870000e-10 76.8
50 TraesCS5B01G178200 chr1A 93.226 310 18 2 2869 3176 442478888 442478580 2.320000e-123 453.0
51 TraesCS5B01G178200 chr1A 96.310 271 10 0 2532 2802 442539480 442539210 3.880000e-121 446.0
52 TraesCS5B01G178200 chr1A 91.367 278 20 3 3411 3686 442478571 442478296 1.440000e-100 377.0
53 TraesCS5B01G178200 chr7B 83.004 253 36 7 2553 2802 524774950 524774702 7.120000e-54 222.0
54 TraesCS5B01G178200 chr3A 85.714 210 28 2 2526 2735 377235506 377235713 2.560000e-53 220.0
55 TraesCS5B01G178200 chr3A 84.360 211 31 2 2528 2738 156118359 156118151 7.170000e-49 206.0
56 TraesCS5B01G178200 chr2D 85.859 198 26 2 2528 2725 109550339 109550534 5.550000e-50 209.0
57 TraesCS5B01G178200 chr2D 96.629 89 3 0 710 798 117843126 117843038 1.230000e-31 148.0
58 TraesCS5B01G178200 chr2D 94.444 90 5 0 710 799 302248099 302248010 7.380000e-29 139.0
59 TraesCS5B01G178200 chr2D 97.727 44 1 0 2033 2076 220960589 220960632 5.870000e-10 76.8
60 TraesCS5B01G178200 chr7A 78.182 275 44 8 3416 3689 14500134 14499875 1.570000e-35 161.0
61 TraesCS5B01G178200 chr6D 92.632 95 6 1 703 797 1551791 1551884 9.550000e-28 135.0
62 TraesCS5B01G178200 chr6A 92.632 95 6 1 711 805 584511447 584511354 9.550000e-28 135.0
63 TraesCS5B01G178200 chr6B 86.747 83 7 4 3552 3633 133700972 133700893 7.540000e-14 89.8


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 TraesCS5B01G178200 chr5B 325961037 325966499 5462 True 10089.000000 10089 100.000000 1 5463 1 chr5B.!!$R1 5462
1 TraesCS5B01G178200 chr5B 705606726 705607860 1134 True 1772.000000 1772 94.696000 2538 3686 1 chr5B.!!$R2 1148
2 TraesCS5B01G178200 chr5D 287014269 287018485 4216 True 1584.000000 2647 93.852000 1 5461 4 chr5D.!!$R3 5460
3 TraesCS5B01G178200 chr5D 154312822 154313446 624 False 469.000000 520 92.954500 2520 3184 2 chr5D.!!$F3 664
4 TraesCS5B01G178200 chr5A 379089061 379095194 6133 True 766.625000 1901 91.942125 1 5461 8 chr5A.!!$R2 5460
5 TraesCS5B01G178200 chr7D 37625515 37626240 725 False 817.000000 817 87.162000 978 1705 1 chr7D.!!$F1 727
6 TraesCS5B01G178200 chr7D 37659440 37661833 2393 False 625.033333 1419 87.033667 833 4412 3 chr7D.!!$F2 3579
7 TraesCS5B01G178200 chr3D 25524692 25527112 2420 True 625.533333 1408 87.513333 833 4412 3 chr3D.!!$R1 3579
8 TraesCS5B01G178200 chr2A 720353419 720354044 625 True 739.000000 739 88.235000 1087 1705 1 chr2A.!!$R1 618
9 TraesCS5B01G178200 chr2A 720385749 720388432 2683 True 631.666667 1404 88.567333 833 4412 3 chr2A.!!$R2 3579
10 TraesCS5B01G178200 chr4A 687318820 687321183 2363 True 450.500000 1310 87.563250 981 4182 4 chr4A.!!$R1 3201
11 TraesCS5B01G178200 chr3B 178481535 178482660 1125 False 866.500000 1267 91.292500 2528 3690 2 chr3B.!!$F1 1162
12 TraesCS5B01G178200 chr1B 468094687 468095332 645 False 874.000000 874 90.722000 2535 3212 1 chr1B.!!$F2 677
13 TraesCS5B01G178200 chr2B 41962636 41963413 777 False 604.500000 856 95.424500 2828 3688 2 chr2B.!!$F2 860
14 TraesCS5B01G178200 chr1A 442478296 442478888 592 True 415.000000 453 92.296500 2869 3686 2 chr1A.!!$R2 817

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
364 366 1.879796 GCAAGTTGTAGCCAGCACTCT 60.880 52.381 4.48 0.0 0.00 3.24 F
437 439 2.102252 CCCTCTGAAGTGGCTCTATGTC 59.898 54.545 0.00 0.0 0.00 3.06 F
902 904 3.304293 GCTCGCAACTTATTTGGAATTGC 59.696 43.478 0.00 0.0 41.74 3.56 F
2080 2133 2.616842 CGGTTGTATGAGGGGTTATTGC 59.383 50.000 0.00 0.0 0.00 3.56 F
3144 3587 1.450312 CCAGGGACGATGCCAGAAC 60.450 63.158 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1502 2.799017 TCCAATGAGCTGCAAATCAGT 58.201 42.857 1.02 1.39 44.66 3.41 R
2060 2113 3.632145 CAGCAATAACCCCTCATACAACC 59.368 47.826 0.00 0.00 0.00 3.77 R
2492 2921 2.173519 CCTGGACTTGCATTTCACCAT 58.826 47.619 0.00 0.00 0.00 3.55 R
3312 3759 0.900647 CTGTTCCTCGTCCTCCCAGT 60.901 60.000 0.00 0.00 0.00 4.00 R
4701 5245 0.032815 TTTCATCGCTGTGGACGACA 59.967 50.000 0.00 0.00 43.23 4.35 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 2.034124 CCCAAGCCCCTATCAACATTG 58.966 52.381 0.00 0.00 0.00 2.82
364 366 1.879796 GCAAGTTGTAGCCAGCACTCT 60.880 52.381 4.48 0.00 0.00 3.24
429 431 4.785453 CCGGCCCTCTGAAGTGGC 62.785 72.222 0.00 4.43 44.59 5.01
437 439 2.102252 CCCTCTGAAGTGGCTCTATGTC 59.898 54.545 0.00 0.00 0.00 3.06
443 445 3.776969 TGAAGTGGCTCTATGTCAGGAAT 59.223 43.478 0.00 0.00 0.00 3.01
578 580 6.072286 CCCAGGTGATAAATCATGCTGATAAC 60.072 42.308 0.00 0.00 35.76 1.89
598 600 9.168451 TGATAACGGCTTTCTCATAATTGTTTA 57.832 29.630 0.00 0.00 0.00 2.01
677 679 5.221682 TGGGCTGTCATGTTTTTGATTTGAT 60.222 36.000 0.00 0.00 0.00 2.57
713 715 8.649841 TCACTGTGTTTATGCGTAAAATAGTAC 58.350 33.333 12.62 7.95 31.94 2.73
714 716 8.653338 CACTGTGTTTATGCGTAAAATAGTACT 58.347 33.333 12.62 0.00 31.94 2.73
715 717 8.866956 ACTGTGTTTATGCGTAAAATAGTACTC 58.133 33.333 12.62 2.59 31.94 2.59
716 718 8.188531 TGTGTTTATGCGTAAAATAGTACTCC 57.811 34.615 12.62 0.00 31.94 3.85
717 719 7.278424 TGTGTTTATGCGTAAAATAGTACTCCC 59.722 37.037 12.62 0.00 31.94 4.30
718 720 7.493645 GTGTTTATGCGTAAAATAGTACTCCCT 59.506 37.037 12.62 0.00 31.94 4.20
719 721 7.707893 TGTTTATGCGTAAAATAGTACTCCCTC 59.292 37.037 12.62 0.00 31.94 4.30
720 722 7.592885 TTATGCGTAAAATAGTACTCCCTCT 57.407 36.000 0.00 0.00 0.00 3.69
721 723 5.258456 TGCGTAAAATAGTACTCCCTCTG 57.742 43.478 0.00 0.00 0.00 3.35
722 724 4.708421 TGCGTAAAATAGTACTCCCTCTGT 59.292 41.667 0.00 0.00 0.00 3.41
723 725 5.887598 TGCGTAAAATAGTACTCCCTCTGTA 59.112 40.000 0.00 0.00 0.00 2.74
724 726 6.377996 TGCGTAAAATAGTACTCCCTCTGTAA 59.622 38.462 0.00 0.00 0.00 2.41
725 727 6.916932 GCGTAAAATAGTACTCCCTCTGTAAG 59.083 42.308 0.00 0.00 0.00 2.34
726 728 7.424001 CGTAAAATAGTACTCCCTCTGTAAGG 58.576 42.308 0.00 0.00 45.77 2.69
740 742 6.698359 CTCTGTAAGGAAATATAAGAGCGC 57.302 41.667 0.00 0.00 0.00 5.92
741 743 6.406692 TCTGTAAGGAAATATAAGAGCGCT 57.593 37.500 11.27 11.27 0.00 5.92
742 744 6.817184 TCTGTAAGGAAATATAAGAGCGCTT 58.183 36.000 13.26 8.09 38.15 4.68
743 745 7.948357 TCTGTAAGGAAATATAAGAGCGCTTA 58.052 34.615 13.26 12.50 40.65 3.09
744 746 8.082852 TCTGTAAGGAAATATAAGAGCGCTTAG 58.917 37.037 13.26 0.00 39.79 2.18
745 747 7.948357 TGTAAGGAAATATAAGAGCGCTTAGA 58.052 34.615 13.26 11.33 39.79 2.10
746 748 8.585881 TGTAAGGAAATATAAGAGCGCTTAGAT 58.414 33.333 13.26 13.13 39.53 1.98
747 749 9.078753 GTAAGGAAATATAAGAGCGCTTAGATC 57.921 37.037 13.26 7.23 37.50 2.75
748 750 7.233389 AGGAAATATAAGAGCGCTTAGATCA 57.767 36.000 13.26 2.70 37.50 2.92
749 751 7.846066 AGGAAATATAAGAGCGCTTAGATCAT 58.154 34.615 13.26 9.53 37.50 2.45
750 752 8.317679 AGGAAATATAAGAGCGCTTAGATCATT 58.682 33.333 13.26 9.07 37.50 2.57
751 753 9.587772 GGAAATATAAGAGCGCTTAGATCATTA 57.412 33.333 13.26 3.60 37.50 1.90
757 759 7.938563 AAGAGCGCTTAGATCATTACTTTAG 57.061 36.000 13.26 0.00 37.82 1.85
758 760 7.045126 AGAGCGCTTAGATCATTACTTTAGT 57.955 36.000 13.26 0.00 37.82 2.24
759 761 6.920758 AGAGCGCTTAGATCATTACTTTAGTG 59.079 38.462 13.26 0.00 37.82 2.74
760 762 6.806751 AGCGCTTAGATCATTACTTTAGTGA 58.193 36.000 2.64 0.00 0.00 3.41
761 763 7.437748 AGCGCTTAGATCATTACTTTAGTGAT 58.562 34.615 2.64 0.00 37.77 3.06
762 764 7.596995 AGCGCTTAGATCATTACTTTAGTGATC 59.403 37.037 2.64 9.54 46.33 2.92
790 792 8.664211 AAAGCTCTTATATTTCTTTACGGAGG 57.336 34.615 0.00 0.00 0.00 4.30
791 793 6.760291 AGCTCTTATATTTCTTTACGGAGGG 58.240 40.000 0.00 0.00 0.00 4.30
792 794 6.553852 AGCTCTTATATTTCTTTACGGAGGGA 59.446 38.462 0.00 0.00 0.00 4.20
793 795 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
794 796 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
795 797 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
902 904 3.304293 GCTCGCAACTTATTTGGAATTGC 59.696 43.478 0.00 0.00 41.74 3.56
998 1000 5.760253 ACAGAGTAACACTGTCTTCATTTGG 59.240 40.000 0.00 0.00 43.84 3.28
1009 1011 6.435277 ACTGTCTTCATTTGGAATGCTACAAT 59.565 34.615 0.00 0.00 34.32 2.71
1154 1170 6.478512 TTATTTGTCTTGCTCCCTTTGTTT 57.521 33.333 0.00 0.00 0.00 2.83
1156 1172 5.923733 TTTGTCTTGCTCCCTTTGTTTTA 57.076 34.783 0.00 0.00 0.00 1.52
1409 1431 5.163571 TGTGTTCTTGTGCTGCTAATTTTGA 60.164 36.000 0.00 0.00 0.00 2.69
1414 1436 5.978919 TCTTGTGCTGCTAATTTTGAACTTG 59.021 36.000 0.00 0.00 0.00 3.16
1416 1438 4.050553 GTGCTGCTAATTTTGAACTTGCA 58.949 39.130 0.00 0.00 0.00 4.08
1419 1441 4.925054 GCTGCTAATTTTGAACTTGCATCA 59.075 37.500 0.00 0.00 0.00 3.07
1445 1483 7.171337 ACATTTTGTGTGCCATTCAAAAGATAC 59.829 33.333 12.71 0.00 41.86 2.24
1582 1621 9.793259 CATACTGGGTATTTACATATTCTTGGT 57.207 33.333 0.00 0.00 0.00 3.67
1983 2035 6.398095 CAAGTGGACACTCATCATGTAAGTA 58.602 40.000 5.30 0.00 41.58 2.24
2080 2133 2.616842 CGGTTGTATGAGGGGTTATTGC 59.383 50.000 0.00 0.00 0.00 3.56
2151 2204 8.918202 AAAACTCCATTACATACTTGAAGTCA 57.082 30.769 0.00 0.00 0.00 3.41
2492 2921 2.838202 CCTTAGCCTTGTCTCAAGGGTA 59.162 50.000 26.21 26.21 45.46 3.69
3140 3583 2.910360 CATCCAGGGACGATGCCA 59.090 61.111 0.00 0.00 31.37 4.92
3144 3587 1.450312 CCAGGGACGATGCCAGAAC 60.450 63.158 0.00 0.00 0.00 3.01
3146 3589 1.918293 AGGGACGATGCCAGAACCA 60.918 57.895 0.00 0.00 0.00 3.67
3154 3597 2.679716 GCCAGAACCAGGAGGCAT 59.320 61.111 10.72 0.00 46.26 4.40
3312 3759 2.286121 ATGGGGAGGAAGGGCGAA 60.286 61.111 0.00 0.00 0.00 4.70
3733 4182 5.192327 CAATTCAATATCAGAAGTGGGGC 57.808 43.478 9.28 0.00 37.41 5.80
3799 4271 3.459227 TCCATCAAATAGGTCATGGCTCA 59.541 43.478 0.00 0.00 36.49 4.26
4237 4754 8.483307 TTTTACCTGTTTTATCACCTATCGAC 57.517 34.615 0.00 0.00 0.00 4.20
4294 4829 1.782201 TTGCAGGACTGTGGCCTCAT 61.782 55.000 8.18 0.00 32.12 2.90
4303 4841 0.744057 TGTGGCCTCATGCATACACG 60.744 55.000 3.32 0.00 43.89 4.49
4352 4890 1.271656 GCATTGCAAACTCCTTCAGCT 59.728 47.619 1.71 0.00 0.00 4.24
4426 4967 5.591067 CCTAAGAGACACGAGTCCTATTCTT 59.409 44.000 15.69 15.69 46.15 2.52
4462 5003 3.101437 TGGCAGGAGATACGGAAACTAA 58.899 45.455 0.00 0.00 0.00 2.24
4470 5011 4.869451 AGATACGGAAACTAAGGAGGACT 58.131 43.478 0.00 0.00 0.00 3.85
4514 5055 1.202580 CCATGATCGTCCTGACCTTCC 60.203 57.143 0.00 0.00 0.00 3.46
4533 5074 1.200020 CCTCATGGGCTTGTTTTCGAC 59.800 52.381 0.00 0.00 0.00 4.20
4562 5106 0.037447 AGGGCAGAGCTGTTTTCTCC 59.963 55.000 0.00 0.00 0.00 3.71
4599 5143 2.046283 TGTAGAGCTGTCGTTTCGTG 57.954 50.000 0.00 0.00 0.00 4.35
4701 5245 4.910458 ACATTACCTAGTGGAGTGCTTT 57.090 40.909 0.00 0.00 37.04 3.51
4711 5255 0.531974 GGAGTGCTTTGTCGTCCACA 60.532 55.000 0.00 0.00 0.00 4.17
4715 5259 1.954146 GCTTTGTCGTCCACAGCGA 60.954 57.895 0.00 0.00 37.15 4.93
4720 5264 0.032815 TGTCGTCCACAGCGATGAAA 59.967 50.000 8.12 0.00 40.59 2.69
4728 5272 1.645265 CACAGCGATGAAAATGTTGCG 59.355 47.619 8.12 0.00 0.00 4.85
4729 5273 0.636733 CAGCGATGAAAATGTTGCGC 59.363 50.000 0.00 0.00 44.22 6.09
4772 5355 7.951591 TCTTGAGCAAGCAGTATGTATACATA 58.048 34.615 19.51 19.51 39.31 2.29
4782 5373 7.653713 AGCAGTATGTATACATAGTTGACTTGC 59.346 37.037 24.57 22.24 39.71 4.01
4793 5384 1.124477 GTTGACTTGCTACGCGAAGTC 59.876 52.381 23.90 23.90 41.84 3.01
4871 5462 4.608774 TGGTCGGACCGGGACTGT 62.609 66.667 21.52 0.00 42.58 3.55
4873 5464 1.755783 GGTCGGACCGGGACTGTAT 60.756 63.158 15.25 0.00 34.82 2.29
4879 5470 1.202651 GGACCGGGACTGTATTGGATG 60.203 57.143 6.32 0.00 0.00 3.51
4880 5471 0.837272 ACCGGGACTGTATTGGATGG 59.163 55.000 6.32 0.00 0.00 3.51
4901 5492 2.167075 GCCCATTGCAAAGCTGTAATCT 59.833 45.455 1.71 0.00 35.89 2.40
4947 5538 4.371681 TCTTAAGAAGTAGGGCCTGGAAT 58.628 43.478 18.53 0.00 0.00 3.01
5008 5599 2.025155 TGCGTGCCTTGGTTCTTTTTA 58.975 42.857 0.00 0.00 0.00 1.52
5014 5605 4.082190 GTGCCTTGGTTCTTTTTATCCCTC 60.082 45.833 0.00 0.00 0.00 4.30
5054 5645 2.333688 GGATTTCTCCCTACTGTGCC 57.666 55.000 0.00 0.00 35.28 5.01
5123 5715 1.000274 GCATTTGGGAGTTTCGTGCTT 60.000 47.619 0.00 0.00 0.00 3.91
5150 5742 1.206610 ACGAGAGAATGTGATGCTGCT 59.793 47.619 0.00 0.00 0.00 4.24
5173 5765 8.835439 TGCTTTCGTATTATCTTGCATTAATCA 58.165 29.630 0.00 0.00 0.00 2.57
5206 5799 5.278561 GGCATCCATATATAGCGACTAGACC 60.279 48.000 0.00 0.00 0.00 3.85
5207 5800 5.299531 GCATCCATATATAGCGACTAGACCA 59.700 44.000 0.00 0.00 0.00 4.02
5333 5932 3.071580 GAAGCCATCTTCTCCGGTG 57.928 57.895 0.00 0.00 44.08 4.94
5388 5999 1.610967 TATCCACCACCACCAGCGA 60.611 57.895 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 160 5.947663 TGAAACCTCTGAGATTTGGGTAAA 58.052 37.500 0.72 0.00 0.00 2.01
272 274 3.826157 CCAGGAAAGTAGCATGTTCCAAA 59.174 43.478 12.97 0.00 42.81 3.28
429 431 6.176183 ACCAAGTCAAATTCCTGACATAGAG 58.824 40.000 11.80 0.70 46.81 2.43
437 439 5.706916 CATGAAGACCAAGTCAAATTCCTG 58.293 41.667 0.00 0.00 34.60 3.86
443 445 3.569701 GGAAGCATGAAGACCAAGTCAAA 59.430 43.478 0.00 0.00 34.60 2.69
484 486 7.773864 TTGTTCTCGTAGTAAACATCACAAA 57.226 32.000 0.00 0.00 34.37 2.83
521 523 4.698304 GCAGGCTATAACTACAAACCACAA 59.302 41.667 0.00 0.00 0.00 3.33
598 600 5.124776 TCGCCCGATCAAATTTGAAGTAATT 59.875 36.000 23.91 7.18 41.13 1.40
616 618 1.097547 AGCATGAAAATCCTCGCCCG 61.098 55.000 0.00 0.00 0.00 6.13
677 679 7.551262 ACGCATAAACACAGTGATTAAGGAATA 59.449 33.333 7.81 0.00 0.00 1.75
713 715 7.382898 GCTCTTATATTTCCTTACAGAGGGAG 58.617 42.308 0.00 0.00 46.31 4.30
714 716 6.015350 CGCTCTTATATTTCCTTACAGAGGGA 60.015 42.308 4.76 0.00 46.31 4.20
715 717 6.159988 CGCTCTTATATTTCCTTACAGAGGG 58.840 44.000 0.00 0.00 46.31 4.30
717 719 6.451393 AGCGCTCTTATATTTCCTTACAGAG 58.549 40.000 2.64 0.00 0.00 3.35
718 720 6.406692 AGCGCTCTTATATTTCCTTACAGA 57.593 37.500 2.64 0.00 0.00 3.41
719 721 8.082852 TCTAAGCGCTCTTATATTTCCTTACAG 58.917 37.037 12.06 0.00 34.54 2.74
720 722 7.948357 TCTAAGCGCTCTTATATTTCCTTACA 58.052 34.615 12.06 0.00 34.54 2.41
721 723 8.989653 ATCTAAGCGCTCTTATATTTCCTTAC 57.010 34.615 12.06 0.00 34.54 2.34
722 724 8.803235 TGATCTAAGCGCTCTTATATTTCCTTA 58.197 33.333 12.06 0.00 34.54 2.69
723 725 7.671302 TGATCTAAGCGCTCTTATATTTCCTT 58.329 34.615 12.06 0.00 34.54 3.36
724 726 7.233389 TGATCTAAGCGCTCTTATATTTCCT 57.767 36.000 12.06 0.00 34.54 3.36
725 727 8.485976 AATGATCTAAGCGCTCTTATATTTCC 57.514 34.615 12.06 0.00 34.54 3.13
731 733 9.632807 CTAAAGTAATGATCTAAGCGCTCTTAT 57.367 33.333 12.06 3.87 34.54 1.73
732 734 8.630917 ACTAAAGTAATGATCTAAGCGCTCTTA 58.369 33.333 12.06 0.00 33.85 2.10
733 735 7.436673 CACTAAAGTAATGATCTAAGCGCTCTT 59.563 37.037 12.06 2.09 36.35 2.85
734 736 6.920758 CACTAAAGTAATGATCTAAGCGCTCT 59.079 38.462 12.06 3.55 0.00 4.09
735 737 6.918569 TCACTAAAGTAATGATCTAAGCGCTC 59.081 38.462 12.06 0.00 0.00 5.03
736 738 6.806751 TCACTAAAGTAATGATCTAAGCGCT 58.193 36.000 2.64 2.64 0.00 5.92
737 739 7.644986 ATCACTAAAGTAATGATCTAAGCGC 57.355 36.000 0.00 0.00 0.00 5.92
764 766 9.110502 CCTCCGTAAAGAAATATAAGAGCTTTT 57.889 33.333 0.00 0.00 31.85 2.27
765 767 7.715686 CCCTCCGTAAAGAAATATAAGAGCTTT 59.284 37.037 0.00 0.00 33.76 3.51
766 768 7.070821 TCCCTCCGTAAAGAAATATAAGAGCTT 59.929 37.037 0.00 0.00 0.00 3.74
767 769 6.553852 TCCCTCCGTAAAGAAATATAAGAGCT 59.446 38.462 0.00 0.00 0.00 4.09
768 770 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
769 771 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
770 772 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
774 776 9.151177 TGTAATACTCCCTCCGTAAAGAAATAT 57.849 33.333 0.00 0.00 0.00 1.28
775 777 8.537728 TGTAATACTCCCTCCGTAAAGAAATA 57.462 34.615 0.00 0.00 0.00 1.40
776 778 7.125356 ACTGTAATACTCCCTCCGTAAAGAAAT 59.875 37.037 0.00 0.00 0.00 2.17
777 779 6.438425 ACTGTAATACTCCCTCCGTAAAGAAA 59.562 38.462 0.00 0.00 0.00 2.52
778 780 5.954150 ACTGTAATACTCCCTCCGTAAAGAA 59.046 40.000 0.00 0.00 0.00 2.52
779 781 5.513233 ACTGTAATACTCCCTCCGTAAAGA 58.487 41.667 0.00 0.00 0.00 2.52
780 782 5.848833 ACTGTAATACTCCCTCCGTAAAG 57.151 43.478 0.00 0.00 0.00 1.85
781 783 7.685155 GCAATACTGTAATACTCCCTCCGTAAA 60.685 40.741 0.00 0.00 0.00 2.01
782 784 6.239120 GCAATACTGTAATACTCCCTCCGTAA 60.239 42.308 0.00 0.00 0.00 3.18
783 785 5.242393 GCAATACTGTAATACTCCCTCCGTA 59.758 44.000 0.00 0.00 0.00 4.02
784 786 4.038883 GCAATACTGTAATACTCCCTCCGT 59.961 45.833 0.00 0.00 0.00 4.69
785 787 4.281182 AGCAATACTGTAATACTCCCTCCG 59.719 45.833 0.00 0.00 0.00 4.63
786 788 5.810080 AGCAATACTGTAATACTCCCTCC 57.190 43.478 0.00 0.00 0.00 4.30
787 789 7.527568 ACTAGCAATACTGTAATACTCCCTC 57.472 40.000 0.00 0.00 0.00 4.30
788 790 7.916077 AACTAGCAATACTGTAATACTCCCT 57.084 36.000 0.00 0.00 0.00 4.20
789 791 8.959705 AAAACTAGCAATACTGTAATACTCCC 57.040 34.615 0.00 0.00 0.00 4.30
919 921 8.624367 TCCCTTTATTTCGTCAGTTTAATCAA 57.376 30.769 0.00 0.00 0.00 2.57
966 968 5.127194 AGACAGTGTTACTCTGTTTGACTGA 59.873 40.000 19.03 0.00 44.68 3.41
998 1000 7.669098 CACAAATACTTGCAATTGTAGCATTC 58.331 34.615 14.10 0.00 42.33 2.67
1009 1011 3.221771 ACAGGAGCACAAATACTTGCAA 58.778 40.909 0.00 0.00 41.48 4.08
1125 1135 4.706962 AGGGAGCAAGACAAATAATTGGTC 59.293 41.667 7.60 7.60 45.87 4.02
1154 1170 8.812972 GGATATCCGCCATTATGTCCTATATAA 58.187 37.037 5.86 0.00 32.32 0.98
1156 1172 6.787458 TGGATATCCGCCATTATGTCCTATAT 59.213 38.462 17.04 0.00 39.43 0.86
1224 1246 4.867086 TCCAGTCATACATGTGGAGTCTA 58.133 43.478 9.11 0.00 34.03 2.59
1445 1483 9.533253 AAATCAGTTGAGTTACAAAATTGGAAG 57.467 29.630 0.00 0.00 40.36 3.46
1464 1502 2.799017 TCCAATGAGCTGCAAATCAGT 58.201 42.857 1.02 1.39 44.66 3.41
2060 2113 3.632145 CAGCAATAACCCCTCATACAACC 59.368 47.826 0.00 0.00 0.00 3.77
2492 2921 2.173519 CCTGGACTTGCATTTCACCAT 58.826 47.619 0.00 0.00 0.00 3.55
2809 3250 9.874205 TCAGATTCATATGTATATTCGATGCAA 57.126 29.630 1.90 0.00 0.00 4.08
2810 3251 9.305925 GTCAGATTCATATGTATATTCGATGCA 57.694 33.333 1.90 0.00 0.00 3.96
2811 3252 9.526713 AGTCAGATTCATATGTATATTCGATGC 57.473 33.333 1.90 0.00 0.00 3.91
3140 3583 1.566298 GGGTCATGCCTCCTGGTTCT 61.566 60.000 6.20 0.00 37.43 3.01
3144 3587 2.593978 CTGGGTCATGCCTCCTGG 59.406 66.667 6.20 0.00 37.43 4.45
3146 3589 3.415087 GCCTGGGTCATGCCTCCT 61.415 66.667 0.00 0.00 37.43 3.69
3312 3759 0.900647 CTGTTCCTCGTCCTCCCAGT 60.901 60.000 0.00 0.00 0.00 4.00
3520 3967 2.355756 CCATCCGCAATACAGAGGTTTG 59.644 50.000 0.00 0.00 0.00 2.93
3522 3969 1.134098 CCCATCCGCAATACAGAGGTT 60.134 52.381 0.00 0.00 0.00 3.50
3733 4182 2.807967 TGAAAGATTGAGACTTGCCGTG 59.192 45.455 0.00 0.00 0.00 4.94
3826 4314 5.133221 CCCTGGAATAGATTAACACAAGGG 58.867 45.833 0.00 0.00 0.00 3.95
4116 4633 2.243736 AGGGAACAGGGAACAACAGAAA 59.756 45.455 0.00 0.00 0.00 2.52
4118 4635 1.518367 AGGGAACAGGGAACAACAGA 58.482 50.000 0.00 0.00 0.00 3.41
4209 4726 7.012044 CGATAGGTGATAAAACAGGTAAAAGGG 59.988 40.741 0.00 0.00 0.00 3.95
4237 4754 6.215121 TGTTATCACTGCAAAACATGGAAAG 58.785 36.000 0.00 0.00 0.00 2.62
4303 4841 4.600576 GCCTCGGCTAGCTGGAGC 62.601 72.222 23.27 20.74 42.05 4.70
4352 4890 4.308458 CTCCGTGGGTGGTCGCAA 62.308 66.667 0.00 0.00 38.21 4.85
4426 4967 1.126948 TGCCAGACTCCATGGTGTCA 61.127 55.000 36.07 20.95 40.03 3.58
4462 5003 0.626382 TCGTCTGATCCAGTCCTCCT 59.374 55.000 0.00 0.00 32.61 3.69
4470 5011 2.801077 TCAGGTAGTCGTCTGATCCA 57.199 50.000 0.00 0.00 35.37 3.41
4514 5055 1.135972 CGTCGAAAACAAGCCCATGAG 60.136 52.381 0.00 0.00 0.00 2.90
4547 5088 1.534595 GTGCAGGAGAAAACAGCTCTG 59.465 52.381 0.00 0.00 32.98 3.35
4562 5106 3.988379 ACAATACACCAAACTGTGCAG 57.012 42.857 0.00 0.00 39.93 4.41
4599 5143 4.455877 CACTGAAAACCCATACAGAGGTTC 59.544 45.833 0.00 0.00 45.68 3.62
4701 5245 0.032815 TTTCATCGCTGTGGACGACA 59.967 50.000 0.00 0.00 43.23 4.35
4711 5255 0.523072 AGCGCAACATTTTCATCGCT 59.477 45.000 11.47 0.84 46.56 4.93
4715 5259 4.980590 TCGAAATAGCGCAACATTTTCAT 58.019 34.783 11.47 0.00 0.00 2.57
4720 5264 4.572389 AGAAGATCGAAATAGCGCAACATT 59.428 37.500 11.47 2.77 0.00 2.71
4728 5272 5.521735 TCAAGAGCAAGAAGATCGAAATAGC 59.478 40.000 0.00 0.00 37.82 2.97
4729 5273 7.164226 CTCAAGAGCAAGAAGATCGAAATAG 57.836 40.000 0.00 0.00 37.82 1.73
4782 5373 2.408704 CCAAACTTCAGACTTCGCGTAG 59.591 50.000 11.50 11.50 0.00 3.51
4793 5384 2.539547 CGTGCAGACAACCAAACTTCAG 60.540 50.000 0.00 0.00 0.00 3.02
4879 5470 0.607620 TTACAGCTTTGCAATGGGCC 59.392 50.000 13.62 0.00 43.89 5.80
4880 5471 2.167075 AGATTACAGCTTTGCAATGGGC 59.833 45.455 13.62 11.84 45.13 5.36
4947 5538 4.011698 CCATCCATGTGAACTGAATGTGA 58.988 43.478 0.00 0.00 0.00 3.58
5014 5605 3.191371 CCCTTCTGTTTCCCTCAAAATCG 59.809 47.826 0.00 0.00 0.00 3.34
5123 5715 4.488879 CATCACATTCTCTCGTCACTCAA 58.511 43.478 0.00 0.00 0.00 3.02
5173 5765 7.557358 TCGCTATATATGGATGCCAAAATCAAT 59.443 33.333 0.00 0.00 36.95 2.57
5206 5799 8.719648 GGAATGTTATGATAATTGCTCTCTCTG 58.280 37.037 0.00 0.00 0.00 3.35
5207 5800 8.435187 TGGAATGTTATGATAATTGCTCTCTCT 58.565 33.333 0.00 0.00 0.00 3.10
5366 5971 0.179000 CTGGTGGTGGTGGATAGCTC 59.821 60.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.