Multiple sequence alignment - TraesCS1A01G161500

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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 TraesCS1A01G161500 chr1A 100.000 2797 0 0 1 2797 290335474 290338270 0.000000e+00 5166.0
1 TraesCS1A01G161500 chr1A 100.000 166 0 0 3159 3324 290338632 290338797 1.160000e-79 307.0
2 TraesCS1A01G161500 chr1A 96.970 33 1 0 1733 1765 593752739 593752771 4.630000e-04 56.5
3 TraesCS1A01G161500 chr1B 92.155 2562 167 12 1 2559 322718286 322720816 0.000000e+00 3587.0
4 TraesCS1A01G161500 chr1B 85.000 160 22 2 3162 3320 90204418 90204260 9.540000e-36 161.0
5 TraesCS1A01G161500 chr1B 92.500 40 1 2 1737 1775 688352719 688352681 4.630000e-04 56.5
6 TraesCS1A01G161500 chr1B 92.500 40 1 2 1737 1775 688352797 688352759 4.630000e-04 56.5
7 TraesCS1A01G161500 chr1B 100.000 29 0 0 1737 1765 688383136 688383108 2.000000e-03 54.7
8 TraesCS1A01G161500 chr1D 90.583 1954 153 20 849 2797 223380872 223382799 0.000000e+00 2560.0
9 TraesCS1A01G161500 chr1D 90.738 1911 146 13 888 2797 223341225 223343105 0.000000e+00 2519.0
10 TraesCS1A01G161500 chr1D 93.103 348 23 1 1 348 223340591 223340937 2.960000e-140 508.0
11 TraesCS1A01G161500 chr1D 92.529 348 25 1 1 348 223380238 223380584 6.400000e-137 497.0
12 TraesCS1A01G161500 chr1D 86.195 297 18 5 466 761 223380580 223380854 1.940000e-77 300.0
13 TraesCS1A01G161500 chr1D 85.859 297 19 6 466 761 223340933 223341207 9.020000e-76 294.0
14 TraesCS1A01G161500 chr1D 84.615 156 23 1 3166 3320 442044174 442044019 1.600000e-33 154.0
15 TraesCS1A01G161500 chr1D 92.500 40 1 2 1737 1775 495233454 495233416 4.630000e-04 56.5
16 TraesCS1A01G161500 chr1D 100.000 29 0 0 1737 1765 495229250 495229222 2.000000e-03 54.7
17 TraesCS1A01G161500 chr1D 100.000 28 0 0 1738 1765 495223120 495223093 6.000000e-03 52.8
18 TraesCS1A01G161500 chr6B 87.441 422 43 8 2381 2797 454721426 454721842 8.340000e-131 477.0
19 TraesCS1A01G161500 chr4A 86.385 426 42 13 2382 2797 500581123 500580704 5.060000e-123 451.0
20 TraesCS1A01G161500 chr2A 86.014 429 40 13 2381 2797 19986331 19985911 3.040000e-120 442.0
21 TraesCS1A01G161500 chr2D 85.986 421 47 8 2382 2797 498809283 498809696 1.090000e-119 440.0
22 TraesCS1A01G161500 chr2D 84.810 158 23 1 3164 3320 69491474 69491631 1.230000e-34 158.0
23 TraesCS1A01G161500 chr2D 84.810 158 23 1 3164 3320 382182552 382182709 1.230000e-34 158.0
24 TraesCS1A01G161500 chr3D 85.714 427 47 10 2377 2797 513667694 513668112 3.940000e-119 438.0
25 TraesCS1A01G161500 chrUn 85.450 433 44 15 2376 2797 41914766 41914342 1.830000e-117 433.0
26 TraesCS1A01G161500 chr7D 85.185 432 50 10 2374 2797 489122868 489123293 6.590000e-117 431.0
27 TraesCS1A01G161500 chr6D 84.810 158 23 1 3164 3320 461498784 461498941 1.230000e-34 158.0
28 TraesCS1A01G161500 chr6D 83.951 162 25 1 3164 3324 379709726 379709565 1.600000e-33 154.0
29 TraesCS1A01G161500 chr5D 84.810 158 23 1 3164 3320 515800167 515800324 1.230000e-34 158.0
30 TraesCS1A01G161500 chr5D 84.177 158 24 1 3164 3320 192262439 192262282 5.740000e-33 152.0
31 TraesCS1A01G161500 chr4D 84.177 158 24 1 3164 3320 483464916 483464759 5.740000e-33 152.0


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 TraesCS1A01G161500 chr1A 290335474 290338797 3323 False 2736.5 5166 100.000 1 3324 2 chr1A.!!$F2 3323
1 TraesCS1A01G161500 chr1B 322718286 322720816 2530 False 3587.0 3587 92.155 1 2559 1 chr1B.!!$F1 2558
2 TraesCS1A01G161500 chr1D 223380238 223382799 2561 False 1119.0 2560 89.769 1 2797 3 chr1D.!!$F2 2796
3 TraesCS1A01G161500 chr1D 223340591 223343105 2514 False 1107.0 2519 89.900 1 2797 3 chr1D.!!$F1 2796

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
939 964 1.527311 GAAGAGAAGTCGTGTTGGTGC 59.473 52.381 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 2659 0.036732 GGCGATAATCATGGAGGCCA 59.963 55.0 5.01 0.0 38.88 5.36 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
30 31 7.745155 CACAATAACGACATAGTACCTATCTCG 59.255 40.741 7.18 7.18 39.50 4.04
39 40 7.687388 ACATAGTACCTATCTCGATGAGGTTA 58.313 38.462 15.78 6.44 40.85 2.85
158 159 2.041216 TGCCACAGACCTACTCTCTACA 59.959 50.000 0.00 0.00 0.00 2.74
166 167 5.353123 CAGACCTACTCTCTACAAGTCAGAC 59.647 48.000 0.00 0.00 0.00 3.51
167 168 5.249852 AGACCTACTCTCTACAAGTCAGACT 59.750 44.000 0.00 0.00 0.00 3.24
230 231 2.270874 GATTGGTCACCCAGCCGGAT 62.271 60.000 5.05 0.00 43.15 4.18
270 271 6.438186 AAACCATCCATTTCTTGACCATTT 57.562 33.333 0.00 0.00 0.00 2.32
275 276 8.605065 ACCATCCATTTCTTGACCATTTAATTT 58.395 29.630 0.00 0.00 0.00 1.82
388 391 1.878088 AGCATCATTCCACATGATCGC 59.122 47.619 0.00 9.42 36.69 4.58
418 421 5.847111 ATGCATGTCAAGTTTCATAGCAT 57.153 34.783 0.00 14.41 35.84 3.79
518 521 3.631250 ACTTGCCAAGAAGAAAAGGTCA 58.369 40.909 12.25 0.00 0.00 4.02
519 522 3.381590 ACTTGCCAAGAAGAAAAGGTCAC 59.618 43.478 12.25 0.00 0.00 3.67
557 560 5.172934 TCTATTTTTAGGTCACGTCGCATT 58.827 37.500 0.00 0.00 0.00 3.56
561 564 3.300852 TTAGGTCACGTCGCATTAACA 57.699 42.857 0.00 0.00 0.00 2.41
608 632 9.548631 TTTTGGATATTCAATTAACCTTGGGTA 57.451 29.630 0.00 0.00 33.12 3.69
609 633 9.722317 TTTGGATATTCAATTAACCTTGGGTAT 57.278 29.630 0.00 0.00 33.12 2.73
614 638 9.875708 ATATTCAATTAACCTTGGGTATAAGCA 57.124 29.630 0.00 0.00 33.12 3.91
615 639 7.399245 TTCAATTAACCTTGGGTATAAGCAC 57.601 36.000 0.00 0.00 33.12 4.40
616 640 6.486056 TCAATTAACCTTGGGTATAAGCACA 58.514 36.000 0.00 0.00 33.12 4.57
617 641 6.948886 TCAATTAACCTTGGGTATAAGCACAA 59.051 34.615 0.00 0.00 33.12 3.33
618 642 7.122055 TCAATTAACCTTGGGTATAAGCACAAG 59.878 37.037 1.44 1.44 39.88 3.16
619 643 4.650972 AACCTTGGGTATAAGCACAAGA 57.349 40.909 9.36 0.00 42.07 3.02
620 644 4.650972 ACCTTGGGTATAAGCACAAGAA 57.349 40.909 9.36 0.00 42.07 2.52
621 645 5.193099 ACCTTGGGTATAAGCACAAGAAT 57.807 39.130 9.36 0.00 42.07 2.40
622 646 5.580022 ACCTTGGGTATAAGCACAAGAATT 58.420 37.500 9.36 0.00 42.07 2.17
623 647 6.727394 ACCTTGGGTATAAGCACAAGAATTA 58.273 36.000 9.36 0.00 42.07 1.40
624 648 7.354312 ACCTTGGGTATAAGCACAAGAATTAT 58.646 34.615 9.36 0.00 42.07 1.28
625 649 7.839200 ACCTTGGGTATAAGCACAAGAATTATT 59.161 33.333 9.36 0.00 42.07 1.40
626 650 8.137437 CCTTGGGTATAAGCACAAGAATTATTG 58.863 37.037 11.19 11.19 42.07 1.90
627 651 7.581213 TGGGTATAAGCACAAGAATTATTGG 57.419 36.000 16.65 7.23 34.36 3.16
628 652 7.122715 TGGGTATAAGCACAAGAATTATTGGT 58.877 34.615 16.65 0.61 34.36 3.67
673 697 8.800370 TTAAACAAGCAATATATCACTGACCA 57.200 30.769 0.00 0.00 0.00 4.02
717 741 4.317671 AGAAAATAGCATGCAAGCCATC 57.682 40.909 21.98 10.55 34.23 3.51
718 742 3.702548 AGAAAATAGCATGCAAGCCATCA 59.297 39.130 21.98 0.00 34.23 3.07
786 811 4.335416 ACATCTACAATTGTGTGAAGGGG 58.665 43.478 21.42 8.43 38.82 4.79
832 857 2.697751 CTGTGAAGGTAGATGGAGAGGG 59.302 54.545 0.00 0.00 0.00 4.30
836 861 4.019231 GTGAAGGTAGATGGAGAGGGTTTT 60.019 45.833 0.00 0.00 0.00 2.43
930 955 8.934507 AAATGAATAGGTAAGAAGAGAAGTCG 57.065 34.615 0.00 0.00 0.00 4.18
939 964 1.527311 GAAGAGAAGTCGTGTTGGTGC 59.473 52.381 0.00 0.00 0.00 5.01
1039 1064 3.673484 GGCAAGCAAGCTTCGCCA 61.673 61.111 27.70 0.00 42.50 5.69
1044 1069 3.660111 GCAAGCTTCGCCACCGTT 61.660 61.111 0.00 0.00 35.54 4.44
1074 1099 1.459972 AATCCCCACCCCACCCAAAT 61.460 55.000 0.00 0.00 0.00 2.32
1081 1106 1.376249 ACCCCACCCAAATCCAAGGT 61.376 55.000 0.00 0.00 0.00 3.50
1118 1143 2.276116 TTGCCTCTCCTTCGTCGCT 61.276 57.895 0.00 0.00 0.00 4.93
1120 1145 2.995872 GCCTCTCCTTCGTCGCTGT 61.996 63.158 0.00 0.00 0.00 4.40
1225 1252 6.613679 TCCATACACTTCCCCTTTTTCTTTTT 59.386 34.615 0.00 0.00 0.00 1.94
1226 1253 6.705825 CCATACACTTCCCCTTTTTCTTTTTG 59.294 38.462 0.00 0.00 0.00 2.44
1232 1259 6.611236 ACTTCCCCTTTTTCTTTTTGATCTCA 59.389 34.615 0.00 0.00 0.00 3.27
1239 1266 5.689383 TTTCTTTTTGATCTCACTTCCCG 57.311 39.130 0.00 0.00 0.00 5.14
1386 1413 2.716244 CACGACGCGCTCCTATCT 59.284 61.111 5.73 0.00 0.00 1.98
1387 1414 1.064296 CACGACGCGCTCCTATCTT 59.936 57.895 5.73 0.00 0.00 2.40
1398 1425 0.105658 TCCTATCTTCCCACCTCCGG 60.106 60.000 0.00 0.00 0.00 5.14
1399 1426 0.398664 CCTATCTTCCCACCTCCGGT 60.399 60.000 0.00 0.00 35.62 5.28
1435 1462 2.044352 TCGTCTCCGAGGGCATCA 60.044 61.111 0.00 0.00 38.40 3.07
1454 1481 0.754217 ATCCGCAGCTTTGCATCCAT 60.754 50.000 0.00 0.00 34.41 3.41
1468 1495 3.216800 GCATCCATCTACATCTTGCCAA 58.783 45.455 0.00 0.00 0.00 4.52
1522 1549 0.034198 TGTCGGCGACCAAGAATTCA 59.966 50.000 34.28 12.10 0.00 2.57
1565 1592 2.168521 TCTAAAGGCTTACATGCGAGCT 59.831 45.455 17.35 0.00 38.89 4.09
1585 1612 4.223700 AGCTACAATGATGACAACTCCTCA 59.776 41.667 0.00 0.00 0.00 3.86
1675 1702 0.823356 ACATGCTGGGAACAAAGCGT 60.823 50.000 0.00 0.00 41.62 5.07
1678 1705 2.193536 GCTGGGAACAAAGCGTGGT 61.194 57.895 0.00 0.00 42.06 4.16
1776 1803 3.575687 CCAAGAAAGGAACCAGAAGCAAT 59.424 43.478 0.00 0.00 0.00 3.56
1779 1806 4.218312 AGAAAGGAACCAGAAGCAATGTT 58.782 39.130 0.00 0.00 0.00 2.71
1812 1839 4.392166 TGGCCCTAGTCGCCCTCA 62.392 66.667 13.93 0.00 46.48 3.86
1833 1860 0.181350 AAGGACGCATCTCCATTCCC 59.819 55.000 0.00 0.00 31.94 3.97
1957 1984 2.292267 GGTGATGGTGGTGATGATGAC 58.708 52.381 0.00 0.00 0.00 3.06
1959 1986 1.830477 TGATGGTGGTGATGATGACGA 59.170 47.619 0.00 0.00 0.00 4.20
2000 2027 1.071699 TGCTAGGAGAAAAGCGTGGTT 59.928 47.619 0.00 0.00 41.77 3.67
2007 2034 0.736053 GAAAAGCGTGGTTGTGGACA 59.264 50.000 0.00 0.00 0.00 4.02
2026 2053 3.157680 CCACGAAAGAGGGGGTGT 58.842 61.111 0.00 0.00 38.28 4.16
2030 2057 2.895424 CGAAAGAGGGGGTGTGGCT 61.895 63.158 0.00 0.00 0.00 4.75
2183 2210 2.044451 TGCCTATGCAAACCCCCG 60.044 61.111 0.00 0.00 46.66 5.73
2233 2260 2.150719 TGGGAGGCCGACAAAGGAA 61.151 57.895 0.00 0.00 0.00 3.36
2245 2272 6.316890 GGCCGACAAAGGAAACATAATAACTA 59.683 38.462 0.00 0.00 0.00 2.24
2368 2395 7.201794 GGTTATAAAGGCCCAAGTGAATAAGAC 60.202 40.741 0.00 0.00 0.00 3.01
2473 2500 1.905894 GGAGAGTCTTCTTGCCCTCTT 59.094 52.381 0.00 0.00 34.54 2.85
2575 2602 5.216622 TCTAACATGGTATCAGCCTAACCT 58.783 41.667 0.00 0.00 34.23 3.50
2590 2617 1.129058 AACCTATCCAACCCTAGCCG 58.871 55.000 0.00 0.00 0.00 5.52
2593 2620 1.383386 TATCCAACCCTAGCCGCCA 60.383 57.895 0.00 0.00 0.00 5.69
2596 2623 4.796495 CAACCCTAGCCGCCACCC 62.796 72.222 0.00 0.00 0.00 4.61
2618 2645 3.041351 CTTACGCACTGCACGCCA 61.041 61.111 1.11 0.00 0.00 5.69
2644 2671 0.846693 GGGTAGTTGGCCTCCATGAT 59.153 55.000 3.32 0.00 31.53 2.45
2645 2672 1.215423 GGGTAGTTGGCCTCCATGATT 59.785 52.381 3.32 0.00 31.53 2.57
2646 2673 2.441750 GGGTAGTTGGCCTCCATGATTA 59.558 50.000 3.32 0.00 31.53 1.75
2647 2674 3.074538 GGGTAGTTGGCCTCCATGATTAT 59.925 47.826 3.32 0.00 31.53 1.28
2652 2679 1.021390 GGCCTCCATGATTATCGCCG 61.021 60.000 0.00 0.00 0.00 6.46
2684 2711 1.718757 CCCGTACCTAGGGTTCGTCG 61.719 65.000 14.81 7.94 43.23 5.12
2685 2712 1.063166 CGTACCTAGGGTTCGTCGC 59.937 63.158 14.81 0.00 40.63 5.19
2724 2752 3.517500 CTGCCCTAGAGAGTCTTTTTCCT 59.482 47.826 0.00 0.00 0.00 3.36
2733 2761 3.910627 AGAGTCTTTTTCCTGAGCCCTTA 59.089 43.478 0.00 0.00 0.00 2.69
2737 2765 3.009143 TCTTTTTCCTGAGCCCTTACTCC 59.991 47.826 0.00 0.00 35.72 3.85
2738 2766 2.344093 TTTCCTGAGCCCTTACTCCT 57.656 50.000 0.00 0.00 35.72 3.69
2740 2768 0.325671 TCCTGAGCCCTTACTCCTGG 60.326 60.000 0.00 0.00 35.72 4.45
2763 2791 0.516001 TTTCTCTCTCACGTCGGTCG 59.484 55.000 0.00 0.00 46.00 4.79
3181 3209 2.818132 GGCCTCTCCTCCGACATG 59.182 66.667 0.00 0.00 0.00 3.21
3182 3210 2.801631 GGCCTCTCCTCCGACATGG 61.802 68.421 0.00 0.00 40.09 3.66
3183 3211 2.818132 CCTCTCCTCCGACATGGC 59.182 66.667 0.00 0.00 37.80 4.40
3184 3212 2.415010 CTCTCCTCCGACATGGCG 59.585 66.667 15.88 15.88 37.80 5.69
3211 3239 2.669569 GCCGAAGCAGCCTGTCAA 60.670 61.111 0.00 0.00 39.53 3.18
3212 3240 2.684843 GCCGAAGCAGCCTGTCAAG 61.685 63.158 0.00 0.00 39.53 3.02
3221 3249 2.674380 CCTGTCAAGGCCAGCCAC 60.674 66.667 12.03 0.78 36.56 5.01
3222 3250 2.674380 CTGTCAAGGCCAGCCACC 60.674 66.667 12.03 0.00 38.92 4.61
3223 3251 4.641645 TGTCAAGGCCAGCCACCG 62.642 66.667 12.03 0.00 38.92 4.94
3224 3252 4.643387 GTCAAGGCCAGCCACCGT 62.643 66.667 12.03 0.00 38.92 4.83
3225 3253 4.329545 TCAAGGCCAGCCACCGTC 62.330 66.667 12.03 0.00 38.92 4.79
3232 3260 4.988598 CAGCCACCGTCCGTGCTT 62.989 66.667 0.00 0.00 41.53 3.91
3233 3261 3.307906 AGCCACCGTCCGTGCTTA 61.308 61.111 0.00 0.00 41.53 3.09
3234 3262 2.357760 GCCACCGTCCGTGCTTAA 60.358 61.111 0.00 0.00 41.53 1.85
3235 3263 2.388232 GCCACCGTCCGTGCTTAAG 61.388 63.158 0.00 0.00 41.53 1.85
3236 3264 2.388232 CCACCGTCCGTGCTTAAGC 61.388 63.158 20.84 20.84 41.53 3.09
3237 3265 2.047560 ACCGTCCGTGCTTAAGCC 60.048 61.111 24.30 14.34 41.18 4.35
3238 3266 3.186047 CCGTCCGTGCTTAAGCCG 61.186 66.667 24.30 23.69 41.18 5.52
3239 3267 3.849953 CGTCCGTGCTTAAGCCGC 61.850 66.667 24.30 15.65 41.18 6.53
3240 3268 3.497031 GTCCGTGCTTAAGCCGCC 61.497 66.667 24.30 14.93 41.18 6.13
3241 3269 4.770874 TCCGTGCTTAAGCCGCCC 62.771 66.667 24.30 8.91 41.18 6.13
3244 3272 3.497031 GTGCTTAAGCCGCCCGTC 61.497 66.667 24.30 3.21 41.18 4.79
3263 3291 2.126071 CCTTGCGTCGTCCGTCAT 60.126 61.111 0.00 0.00 39.32 3.06
3264 3292 1.736645 CCTTGCGTCGTCCGTCATT 60.737 57.895 0.00 0.00 39.32 2.57
3265 3293 1.416049 CTTGCGTCGTCCGTCATTG 59.584 57.895 0.00 0.00 39.32 2.82
3266 3294 2.548587 CTTGCGTCGTCCGTCATTGC 62.549 60.000 0.00 0.00 39.32 3.56
3267 3295 2.809601 GCGTCGTCCGTCATTGCT 60.810 61.111 0.00 0.00 39.32 3.91
3268 3296 2.380410 GCGTCGTCCGTCATTGCTT 61.380 57.895 0.00 0.00 39.32 3.91
3269 3297 1.897398 GCGTCGTCCGTCATTGCTTT 61.897 55.000 0.00 0.00 39.32 3.51
3270 3298 0.179250 CGTCGTCCGTCATTGCTTTG 60.179 55.000 0.00 0.00 0.00 2.77
3271 3299 0.452784 GTCGTCCGTCATTGCTTTGC 60.453 55.000 0.00 0.00 0.00 3.68
3272 3300 0.602638 TCGTCCGTCATTGCTTTGCT 60.603 50.000 0.00 0.00 0.00 3.91
3273 3301 0.179215 CGTCCGTCATTGCTTTGCTC 60.179 55.000 0.00 0.00 0.00 4.26
3274 3302 0.169009 GTCCGTCATTGCTTTGCTCC 59.831 55.000 0.00 0.00 0.00 4.70
3275 3303 1.135315 CCGTCATTGCTTTGCTCCG 59.865 57.895 0.00 0.00 0.00 4.63
3276 3304 1.298157 CCGTCATTGCTTTGCTCCGA 61.298 55.000 0.00 0.00 0.00 4.55
3277 3305 0.179215 CGTCATTGCTTTGCTCCGAC 60.179 55.000 0.00 0.00 0.00 4.79
3278 3306 1.160137 GTCATTGCTTTGCTCCGACT 58.840 50.000 0.00 0.00 0.00 4.18
3279 3307 1.135859 GTCATTGCTTTGCTCCGACTG 60.136 52.381 0.00 0.00 0.00 3.51
3280 3308 0.169672 CATTGCTTTGCTCCGACTGG 59.830 55.000 0.00 0.00 0.00 4.00
3281 3309 0.962356 ATTGCTTTGCTCCGACTGGG 60.962 55.000 0.00 0.00 35.24 4.45
3282 3310 2.050836 TTGCTTTGCTCCGACTGGGA 62.051 55.000 0.00 0.00 44.68 4.37
3283 3311 2.035442 GCTTTGCTCCGACTGGGAC 61.035 63.158 0.00 0.00 40.94 4.46
3284 3312 1.674057 CTTTGCTCCGACTGGGACT 59.326 57.895 0.00 0.00 40.94 3.85
3285 3313 0.390472 CTTTGCTCCGACTGGGACTC 60.390 60.000 0.00 0.00 40.94 3.36
3286 3314 1.827399 TTTGCTCCGACTGGGACTCC 61.827 60.000 0.00 0.00 40.94 3.85
3287 3315 2.363147 GCTCCGACTGGGACTCCT 60.363 66.667 0.00 0.00 40.94 3.69
3288 3316 1.076923 GCTCCGACTGGGACTCCTA 60.077 63.158 0.00 0.00 40.94 2.94
3289 3317 1.385756 GCTCCGACTGGGACTCCTAC 61.386 65.000 0.00 0.00 40.94 3.18
3290 3318 0.034380 CTCCGACTGGGACTCCTACA 60.034 60.000 0.00 0.00 40.94 2.74
3291 3319 0.629596 TCCGACTGGGACTCCTACAT 59.370 55.000 0.00 0.00 40.94 2.29
3292 3320 1.033574 CCGACTGGGACTCCTACATC 58.966 60.000 0.00 0.00 38.47 3.06
3293 3321 0.663688 CGACTGGGACTCCTACATCG 59.336 60.000 0.00 0.00 0.00 3.84
3294 3322 0.386113 GACTGGGACTCCTACATCGC 59.614 60.000 0.00 0.00 0.00 4.58
3295 3323 1.043673 ACTGGGACTCCTACATCGCC 61.044 60.000 0.00 0.00 0.00 5.54
3296 3324 1.749334 CTGGGACTCCTACATCGCCC 61.749 65.000 0.00 0.00 36.11 6.13
3297 3325 2.508751 GGGACTCCTACATCGCCCC 61.509 68.421 0.00 0.00 0.00 5.80
3298 3326 2.728817 GACTCCTACATCGCCCCG 59.271 66.667 0.00 0.00 0.00 5.73
3299 3327 1.826921 GACTCCTACATCGCCCCGA 60.827 63.158 0.00 0.00 41.13 5.14
3300 3328 2.073037 GACTCCTACATCGCCCCGAC 62.073 65.000 0.00 0.00 39.18 4.79
3301 3329 2.836360 TCCTACATCGCCCCGACC 60.836 66.667 0.00 0.00 39.18 4.79
3302 3330 3.925090 CCTACATCGCCCCGACCC 61.925 72.222 0.00 0.00 39.18 4.46
3303 3331 4.280494 CTACATCGCCCCGACCCG 62.280 72.222 0.00 0.00 39.18 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 9.289303 CCGTTTATCATTTTTCGATGATTTTCT 57.711 29.630 4.67 0.00 42.57 2.52
71 72 8.247562 TCCCGTTTATCATTTTTCGATGATTTT 58.752 29.630 4.67 0.00 42.57 1.82
82 83 7.548780 CACCATCATTTTCCCGTTTATCATTTT 59.451 33.333 0.00 0.00 0.00 1.82
93 94 2.965572 AATGCACCATCATTTTCCCG 57.034 45.000 0.00 0.00 33.18 5.14
158 159 6.936968 AGGGTTAATCAACTAGTCTGACTT 57.063 37.500 16.53 0.00 34.88 3.01
223 224 1.511613 CCATATATGGGGATCCGGCT 58.488 55.000 22.31 0.00 44.31 5.52
230 231 7.959153 GGATGGTTTCCTTCCATATATGGGGA 61.959 46.154 27.86 23.74 44.38 4.81
297 298 7.267857 TGTTGATCTCCTTATGACATGTGTAG 58.732 38.462 1.15 0.00 0.00 2.74
366 369 3.499537 GCGATCATGTGGAATGATGCTTA 59.500 43.478 5.58 0.00 38.73 3.09
497 500 3.381590 GTGACCTTTTCTTCTTGGCAAGT 59.618 43.478 25.39 4.91 0.00 3.16
499 502 3.381272 CAGTGACCTTTTCTTCTTGGCAA 59.619 43.478 0.00 0.00 0.00 4.52
501 504 2.287849 GCAGTGACCTTTTCTTCTTGGC 60.288 50.000 0.00 0.00 0.00 4.52
557 560 7.661127 AAGTGATAGTGTAAACGCAATGTTA 57.339 32.000 0.00 0.00 40.84 2.41
649 673 8.800370 TTGGTCAGTGATATATTGCTTGTTTA 57.200 30.769 0.00 0.00 0.00 2.01
673 697 2.071778 ACAAGTGTTGGCATGTCCTT 57.928 45.000 0.00 0.00 35.26 3.36
717 741 8.837788 TTGTAGATATGAAAGCTCCATGTATG 57.162 34.615 10.74 0.00 0.00 2.39
780 805 7.830099 ATGAAAGATATGAATGAACCCCTTC 57.170 36.000 0.00 0.00 0.00 3.46
781 806 9.887862 ATAATGAAAGATATGAATGAACCCCTT 57.112 29.630 0.00 0.00 0.00 3.95
810 835 3.370104 CCTCTCCATCTACCTTCACAGT 58.630 50.000 0.00 0.00 0.00 3.55
812 837 2.044492 ACCCTCTCCATCTACCTTCACA 59.956 50.000 0.00 0.00 0.00 3.58
836 861 9.847224 AAAACAAAACCTCTCTCTATGTCTAAA 57.153 29.630 0.00 0.00 0.00 1.85
910 935 6.837471 ACACGACTTCTCTTCTTACCTATT 57.163 37.500 0.00 0.00 0.00 1.73
930 955 0.730265 TTTCACTCACGCACCAACAC 59.270 50.000 0.00 0.00 0.00 3.32
939 964 0.888736 TGGGCCATGTTTCACTCACG 60.889 55.000 0.00 0.00 0.00 4.35
1016 1041 0.167689 GAAGCTTGCTTGCCTTCGAG 59.832 55.000 12.92 0.00 0.00 4.04
1039 1064 2.224450 GGGATTATTGGATCCGAACGGT 60.224 50.000 5.57 0.94 45.40 4.83
1044 1069 1.702957 GGTGGGGATTATTGGATCCGA 59.297 52.381 3.49 3.49 45.40 4.55
1074 1099 3.632645 CCATACCTCCTTCCTACCTTGGA 60.633 52.174 0.00 0.00 0.00 3.53
1081 1106 1.336347 ACCCCCATACCTCCTTCCTA 58.664 55.000 0.00 0.00 0.00 2.94
1138 1163 3.849951 CGGGTGCGGGCTATCAGT 61.850 66.667 0.00 0.00 0.00 3.41
1225 1252 1.137675 CATGAGCGGGAAGTGAGATCA 59.862 52.381 0.00 0.00 34.71 2.92
1226 1253 1.539929 CCATGAGCGGGAAGTGAGATC 60.540 57.143 0.00 0.00 0.00 2.75
1232 1259 1.274703 ACCATCCATGAGCGGGAAGT 61.275 55.000 0.00 0.00 38.09 3.01
1239 1266 6.002704 AGATTAGATTCAACCATCCATGAGC 58.997 40.000 0.00 0.00 0.00 4.26
1311 1338 1.067416 GGCGATGGCATCACGACTA 59.933 57.895 25.88 0.00 42.47 2.59
1454 1481 0.251916 CGGGGTTGGCAAGATGTAGA 59.748 55.000 0.00 0.00 0.00 2.59
1492 1519 4.530857 GCCGACACGATGAGGGGG 62.531 72.222 0.00 0.00 0.00 5.40
1493 1520 4.873129 CGCCGACACGATGAGGGG 62.873 72.222 0.00 0.00 34.06 4.79
1548 1575 1.207089 TGTAGCTCGCATGTAAGCCTT 59.793 47.619 15.20 3.95 39.39 4.35
1565 1592 5.934043 CACTTGAGGAGTTGTCATCATTGTA 59.066 40.000 0.00 0.00 42.85 2.41
1585 1612 3.129462 AGTCATCGTCATCGTCATCACTT 59.871 43.478 0.00 0.00 38.33 3.16
1669 1696 2.660552 CGTCCACGACCACGCTTT 60.661 61.111 0.00 0.00 43.96 3.51
1675 1702 1.471287 CTTGATACTCGTCCACGACCA 59.529 52.381 0.00 0.00 44.22 4.02
1756 1783 4.218312 ACATTGCTTCTGGTTCCTTTCTT 58.782 39.130 0.00 0.00 0.00 2.52
1776 1803 2.076100 CACGCTTGATGCTCCTTAACA 58.924 47.619 0.00 0.00 40.11 2.41
1779 1806 0.744414 GCCACGCTTGATGCTCCTTA 60.744 55.000 0.00 0.00 40.11 2.69
1812 1839 1.407437 GGAATGGAGATGCGTCCTTGT 60.407 52.381 1.23 0.00 37.52 3.16
1957 1984 4.377839 AGGAGTGTAGTCAACATCATCG 57.622 45.455 0.00 0.00 41.10 3.84
1959 1986 5.365025 AGCATAGGAGTGTAGTCAACATCAT 59.635 40.000 0.00 0.00 41.10 2.45
2007 2034 2.122099 ACCCCCTCTTTCGTGGGT 60.122 61.111 0.00 0.00 46.50 4.51
2024 2051 1.074775 CCTTACAAGGCCAGCCACA 59.925 57.895 12.03 0.00 39.76 4.17
2131 2158 6.243900 TCCATTCTGAAAAGAAGCTTCTGAT 58.756 36.000 29.09 20.21 37.65 2.90
2183 2210 4.789012 TTGGCATCAAGAAATCACCTTC 57.211 40.909 0.00 0.00 0.00 3.46
2245 2272 3.322254 CGCCCTCTCTGGATACTTGTTAT 59.678 47.826 0.00 0.00 38.35 1.89
2250 2277 1.115467 CACGCCCTCTCTGGATACTT 58.885 55.000 0.00 0.00 38.35 2.24
2277 2304 6.966534 ACTTGTGATTGTTCATCCTTTCTT 57.033 33.333 0.00 0.00 33.56 2.52
2329 2356 9.582648 GGGCCTTTATAACCTATAATTTCTGAA 57.417 33.333 0.84 0.00 31.27 3.02
2575 2602 1.383386 TGGCGGCTAGGGTTGGATA 60.383 57.895 11.43 0.00 0.00 2.59
2601 2628 3.041351 TGGCGTGCAGTGCGTAAG 61.041 61.111 11.20 2.63 43.44 2.34
2623 2650 2.375345 ATGGAGGCCAACTACCCCG 61.375 63.158 5.01 0.00 36.95 5.73
2629 2656 2.811873 GCGATAATCATGGAGGCCAACT 60.812 50.000 5.01 0.00 36.95 3.16
2632 2659 0.036732 GGCGATAATCATGGAGGCCA 59.963 55.000 5.01 0.00 38.88 5.36
2636 2663 0.391661 CCCCGGCGATAATCATGGAG 60.392 60.000 9.30 0.00 0.00 3.86
2684 2711 2.028484 TCAGTCAACACGACCGGC 59.972 61.111 0.00 0.00 46.69 6.13
2685 2712 0.939577 CAGTCAGTCAACACGACCGG 60.940 60.000 0.00 0.00 46.69 5.28
2691 2719 1.618837 TCTAGGGCAGTCAGTCAACAC 59.381 52.381 0.00 0.00 0.00 3.32
2699 2727 2.909504 AAGACTCTCTAGGGCAGTCA 57.090 50.000 18.54 0.00 39.29 3.41
2701 2729 3.262151 GGAAAAAGACTCTCTAGGGCAGT 59.738 47.826 0.00 0.00 0.00 4.40
2724 2752 1.742308 AAACCAGGAGTAAGGGCTCA 58.258 50.000 0.00 0.00 37.24 4.26
2756 2784 1.542544 CACCGATTAAGACGACCGAC 58.457 55.000 6.44 0.00 0.00 4.79
2757 2785 0.179156 GCACCGATTAAGACGACCGA 60.179 55.000 6.44 0.00 0.00 4.69
2763 2791 5.390991 CCAAAGAAGAAGCACCGATTAAGAC 60.391 44.000 0.00 0.00 0.00 3.01
2768 2796 2.863809 ACCAAAGAAGAAGCACCGATT 58.136 42.857 0.00 0.00 0.00 3.34
3164 3192 2.801631 CCATGTCGGAGGAGAGGCC 61.802 68.421 0.00 0.00 36.56 5.19
3165 3193 2.818132 CCATGTCGGAGGAGAGGC 59.182 66.667 0.00 0.00 36.56 4.70
3166 3194 2.818132 GCCATGTCGGAGGAGAGG 59.182 66.667 0.00 0.00 36.56 3.69
3167 3195 2.415010 CGCCATGTCGGAGGAGAG 59.585 66.667 0.00 0.00 36.56 3.20
3194 3222 2.669569 TTGACAGGCTGCTTCGGC 60.670 61.111 15.89 0.00 42.19 5.54
3195 3223 2.037136 CCTTGACAGGCTGCTTCGG 61.037 63.158 15.89 6.76 31.53 4.30
3196 3224 3.571119 CCTTGACAGGCTGCTTCG 58.429 61.111 15.89 0.74 31.53 3.79
3204 3232 2.674380 GTGGCTGGCCTTGACAGG 60.674 66.667 13.05 0.00 39.45 4.00
3205 3233 2.674380 GGTGGCTGGCCTTGACAG 60.674 66.667 13.05 0.00 42.51 3.51
3206 3234 4.641645 CGGTGGCTGGCCTTGACA 62.642 66.667 13.05 1.74 36.94 3.58
3207 3235 4.643387 ACGGTGGCTGGCCTTGAC 62.643 66.667 13.05 0.00 36.94 3.18
3208 3236 4.329545 GACGGTGGCTGGCCTTGA 62.330 66.667 13.05 0.00 36.94 3.02
3220 3248 2.047560 GGCTTAAGCACGGACGGT 60.048 61.111 27.83 0.00 44.36 4.83
3221 3249 3.186047 CGGCTTAAGCACGGACGG 61.186 66.667 27.83 4.97 44.36 4.79
3222 3250 3.849953 GCGGCTTAAGCACGGACG 61.850 66.667 27.83 21.29 44.36 4.79
3223 3251 3.497031 GGCGGCTTAAGCACGGAC 61.497 66.667 27.83 15.19 44.36 4.79
3224 3252 4.770874 GGGCGGCTTAAGCACGGA 62.771 66.667 27.83 0.00 44.36 4.69
3227 3255 3.497031 GACGGGCGGCTTAAGCAC 61.497 66.667 27.83 18.74 44.36 4.40
3252 3280 0.452784 GCAAAGCAATGACGGACGAC 60.453 55.000 0.00 0.00 0.00 4.34
3253 3281 0.602638 AGCAAAGCAATGACGGACGA 60.603 50.000 0.00 0.00 0.00 4.20
3254 3282 0.179215 GAGCAAAGCAATGACGGACG 60.179 55.000 0.00 0.00 0.00 4.79
3255 3283 0.169009 GGAGCAAAGCAATGACGGAC 59.831 55.000 0.00 0.00 0.00 4.79
3256 3284 1.298157 CGGAGCAAAGCAATGACGGA 61.298 55.000 0.00 0.00 0.00 4.69
3257 3285 1.135315 CGGAGCAAAGCAATGACGG 59.865 57.895 0.00 0.00 0.00 4.79
3258 3286 0.179215 GTCGGAGCAAAGCAATGACG 60.179 55.000 0.00 0.00 0.00 4.35
3259 3287 1.135859 CAGTCGGAGCAAAGCAATGAC 60.136 52.381 0.00 0.00 0.00 3.06
3260 3288 1.159285 CAGTCGGAGCAAAGCAATGA 58.841 50.000 0.00 0.00 0.00 2.57
3261 3289 0.169672 CCAGTCGGAGCAAAGCAATG 59.830 55.000 0.00 0.00 0.00 2.82
3262 3290 0.962356 CCCAGTCGGAGCAAAGCAAT 60.962 55.000 0.00 0.00 0.00 3.56
3263 3291 1.600636 CCCAGTCGGAGCAAAGCAA 60.601 57.895 0.00 0.00 0.00 3.91
3264 3292 2.032528 CCCAGTCGGAGCAAAGCA 59.967 61.111 0.00 0.00 0.00 3.91
3265 3293 2.035442 GTCCCAGTCGGAGCAAAGC 61.035 63.158 0.00 0.00 43.19 3.51
3266 3294 0.390472 GAGTCCCAGTCGGAGCAAAG 60.390 60.000 0.00 0.00 43.19 2.77
3267 3295 1.671742 GAGTCCCAGTCGGAGCAAA 59.328 57.895 0.00 0.00 43.19 3.68
3268 3296 2.283529 GGAGTCCCAGTCGGAGCAA 61.284 63.158 0.00 0.00 43.19 3.91
3269 3297 1.859841 TAGGAGTCCCAGTCGGAGCA 61.860 60.000 5.25 0.00 43.19 4.26
3270 3298 1.076923 TAGGAGTCCCAGTCGGAGC 60.077 63.158 5.25 0.00 43.19 4.70
3271 3299 0.034380 TGTAGGAGTCCCAGTCGGAG 60.034 60.000 5.25 0.00 43.19 4.63
3272 3300 0.629596 ATGTAGGAGTCCCAGTCGGA 59.370 55.000 5.25 0.00 38.83 4.55
3273 3301 1.033574 GATGTAGGAGTCCCAGTCGG 58.966 60.000 5.25 0.00 33.88 4.79
3274 3302 0.663688 CGATGTAGGAGTCCCAGTCG 59.336 60.000 5.25 7.46 33.88 4.18
3275 3303 0.386113 GCGATGTAGGAGTCCCAGTC 59.614 60.000 5.25 0.00 33.88 3.51
3276 3304 1.043673 GGCGATGTAGGAGTCCCAGT 61.044 60.000 5.25 0.00 33.88 4.00
3277 3305 1.742768 GGCGATGTAGGAGTCCCAG 59.257 63.158 5.25 0.00 33.88 4.45
3278 3306 1.760875 GGGCGATGTAGGAGTCCCA 60.761 63.158 5.25 0.00 34.01 4.37
3279 3307 2.508751 GGGGCGATGTAGGAGTCCC 61.509 68.421 5.25 0.00 43.15 4.46
3280 3308 2.857744 CGGGGCGATGTAGGAGTCC 61.858 68.421 0.00 0.00 0.00 3.85
3281 3309 1.826921 TCGGGGCGATGTAGGAGTC 60.827 63.158 0.00 0.00 0.00 3.36
3282 3310 2.125961 GTCGGGGCGATGTAGGAGT 61.126 63.158 0.00 0.00 38.42 3.85
3283 3311 2.728817 GTCGGGGCGATGTAGGAG 59.271 66.667 0.00 0.00 38.42 3.69
3284 3312 2.836360 GGTCGGGGCGATGTAGGA 60.836 66.667 0.00 0.00 38.42 2.94
3285 3313 3.925090 GGGTCGGGGCGATGTAGG 61.925 72.222 0.00 0.00 38.42 3.18
3286 3314 4.280494 CGGGTCGGGGCGATGTAG 62.280 72.222 0.00 0.00 38.42 2.74


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

AutoCloner maintained by Alex Coulton.