Multiple sequence alignment - TraesCS4A01G011700

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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 TraesCS4A01G011700 chr4A 100.000 3603 0 0 1 3603 6804184 6800582 0.000000e+00 6654
1 TraesCS4A01G011700 chr4A 97.917 96 2 0 2724 2819 142348617 142348522 2.230000e-37 167
2 TraesCS4A01G011700 chr4B 90.481 1996 103 38 809 2734 578069781 578071759 0.000000e+00 2553
3 TraesCS4A01G011700 chr4B 91.706 422 32 1 3183 3601 578072426 578072847 1.860000e-162 582
4 TraesCS4A01G011700 chr4B 88.155 439 42 9 4 436 109396628 109397062 6.900000e-142 514
5 TraesCS4A01G011700 chr4B 87.664 381 30 5 2775 3146 578071759 578072131 9.240000e-116 427
6 TraesCS4A01G011700 chr4B 90.604 149 10 1 632 780 578069636 578069780 1.020000e-45 195
7 TraesCS4A01G011700 chr4D 92.169 996 53 11 1752 2732 462790543 462789558 0.000000e+00 1384
8 TraesCS4A01G011700 chr4D 85.611 966 71 26 813 1718 462791504 462790547 0.000000e+00 952
9 TraesCS4A01G011700 chr4D 87.901 810 69 16 2814 3603 462789556 462788756 0.000000e+00 926
10 TraesCS4A01G011700 chr4D 88.940 434 41 6 8 436 333257172 333257603 2.460000e-146 529
11 TraesCS4A01G011700 chr5D 96.110 437 15 2 1 436 283106200 283105765 0.000000e+00 712
12 TraesCS4A01G011700 chr5D 88.938 226 10 4 433 644 283104821 283104597 7.670000e-67 265
13 TraesCS4A01G011700 chr5D 93.694 111 3 3 2712 2818 481728797 481728907 2.880000e-36 163
14 TraesCS4A01G011700 chr5D 84.058 138 21 1 502 638 9073324 9073187 8.120000e-27 132
15 TraesCS4A01G011700 chr6D 88.356 438 43 7 4 436 132004404 132003970 1.480000e-143 520
16 TraesCS4A01G011700 chr6D 94.792 96 5 0 535 630 38513373 38513278 2.240000e-32 150
17 TraesCS4A01G011700 chr7A 87.045 440 48 9 4 436 162854279 162854716 4.180000e-134 488
18 TraesCS4A01G011700 chr7A 98.947 95 1 0 2724 2818 47050822 47050728 1.720000e-38 171
19 TraesCS4A01G011700 chr7A 98.936 94 1 0 2722 2815 126551895 126551988 6.190000e-38 169
20 TraesCS4A01G011700 chr7A 79.724 217 34 6 1470 1678 20855017 20855231 8.060000e-32 148
21 TraesCS4A01G011700 chr2D 86.927 436 47 9 7 436 538274979 538274548 7.000000e-132 481
22 TraesCS4A01G011700 chr2D 95.146 103 5 0 2722 2824 384255179 384255281 2.880000e-36 163
23 TraesCS4A01G011700 chr6A 86.333 439 51 8 4 436 503593460 503593025 1.510000e-128 470
24 TraesCS4A01G011700 chr6A 76.364 605 93 25 1419 1986 185606254 185606845 2.740000e-71 279
25 TraesCS4A01G011700 chr5B 85.779 443 50 12 2 436 532699581 532699144 1.180000e-124 457
26 TraesCS4A01G011700 chr5B 94.118 102 6 0 2722 2823 287787976 287788077 4.820000e-34 156
27 TraesCS4A01G011700 chr6B 84.545 440 58 9 4 436 680699241 680699677 9.240000e-116 427
28 TraesCS4A01G011700 chr6B 78.360 573 96 15 1423 1986 97235337 97235890 2.660000e-91 346
29 TraesCS4A01G011700 chr6B 92.920 113 7 1 2724 2835 314591473 314591585 2.880000e-36 163
30 TraesCS4A01G011700 chr7D 96.078 102 4 0 535 636 94012437 94012538 2.230000e-37 167
31 TraesCS4A01G011700 chr7D 96.970 99 3 0 2724 2822 124168125 124168223 2.230000e-37 167
32 TraesCS4A01G011700 chr2A 95.050 101 5 0 535 635 39992276 39992176 3.720000e-35 159
33 TraesCS4A01G011700 chr2A 93.578 109 4 3 2713 2819 618975015 618975122 3.720000e-35 159
34 TraesCS4A01G011700 chr1D 86.232 138 16 3 502 638 426159552 426159687 2.900000e-31 147


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 TraesCS4A01G011700 chr4A 6800582 6804184 3602 True 6654.000000 6654 100.000000 1 3603 1 chr4A.!!$R1 3602
1 TraesCS4A01G011700 chr4B 578069636 578072847 3211 False 939.250000 2553 90.113750 632 3601 4 chr4B.!!$F2 2969
2 TraesCS4A01G011700 chr4D 462788756 462791504 2748 True 1087.333333 1384 88.560333 813 3603 3 chr4D.!!$R1 2790
3 TraesCS4A01G011700 chr5D 283104597 283106200 1603 True 488.500000 712 92.524000 1 644 2 chr5D.!!$R2 643
4 TraesCS4A01G011700 chr6A 185606254 185606845 591 False 279.000000 279 76.364000 1419 1986 1 chr6A.!!$F1 567
5 TraesCS4A01G011700 chr6B 97235337 97235890 553 False 346.000000 346 78.360000 1423 1986 1 chr6B.!!$F1 563

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
692 1655 0.250640 ATCATCCTCGCCCATGCTTC 60.251 55.0 0.0 0.0 34.43 3.86 F
1262 2291 0.039527 GACCAATTTGCCGTGTCACC 60.040 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2950 2.040939 AGAGATGATGCTGGACCAGAG 58.959 52.381 26.25 0.23 32.44 3.35 R
2973 4070 1.802960 CTGTTGTGCAGTGTCATCTCC 59.197 52.381 0.00 0.00 40.27 3.71 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
184 185 7.100409 GCCATGGCAACTTAACCTAAAATTTA 58.900 34.615 32.08 0.00 41.49 1.40
260 261 3.747529 CCATGGCAAAAATGGAGTGAAAC 59.252 43.478 0.00 0.00 46.44 2.78
277 279 3.628032 TGAAACTGCCACGTCAATAAACA 59.372 39.130 0.00 0.00 0.00 2.83
346 348 6.983474 ACAAATTAAAAATGCCATGGCTAC 57.017 33.333 35.53 9.68 42.51 3.58
364 366 4.025145 GGCTACACAAGTATATTTCCGTGC 60.025 45.833 0.00 0.00 0.00 5.34
388 390 6.468000 GCTACGTAGTTAAATTTGCCATGTTC 59.532 38.462 22.98 0.00 37.78 3.18
391 393 6.205853 ACGTAGTTAAATTTGCCATGTTCTGA 59.794 34.615 0.00 0.00 37.78 3.27
407 409 7.980662 CCATGTTCTGAAAATGTATATTTGCCA 59.019 33.333 17.10 0.30 36.65 4.92
450 1399 0.538057 ATGCTTGGGAGTGTGTGGTG 60.538 55.000 0.00 0.00 0.00 4.17
453 1402 3.429372 TTGGGAGTGTGTGGTGGGC 62.429 63.158 0.00 0.00 0.00 5.36
498 1447 0.394352 GGCGTGAGGACCATGGAAAT 60.394 55.000 21.47 2.43 32.41 2.17
530 1493 2.921121 CGAACGAAAGGAATCGATGACA 59.079 45.455 0.00 0.00 45.48 3.58
542 1505 1.089112 CGATGACATGGCTGCTTTGA 58.911 50.000 0.00 0.00 0.00 2.69
558 1521 4.397103 TGCTTTGACATGCTTTAGGATCAG 59.603 41.667 0.00 0.00 0.00 2.90
577 1540 1.335182 AGTGCTGACATCCTACGATCG 59.665 52.381 14.88 14.88 0.00 3.69
616 1579 2.542595 AGAGCGTAAAAGTTGGACGTTG 59.457 45.455 10.48 0.00 38.80 4.10
630 1593 5.423704 TGGACGTTGGGAAGTTATTGATA 57.576 39.130 0.00 0.00 0.00 2.15
648 1611 9.896263 TTATTGATACCGTAAACAAAAACTTCC 57.104 29.630 5.90 0.00 0.00 3.46
654 1617 5.474532 ACCGTAAACAAAAACTTCCCTATCC 59.525 40.000 0.00 0.00 0.00 2.59
666 1629 1.087771 CCCTATCCGTTTCGTGGCAC 61.088 60.000 7.79 7.79 0.00 5.01
692 1655 0.250640 ATCATCCTCGCCCATGCTTC 60.251 55.000 0.00 0.00 34.43 3.86
701 1664 1.815421 CCCATGCTTCTTCGGACGG 60.815 63.158 0.00 0.00 0.00 4.79
733 1696 1.835483 GCCATAACCAGCGATCGCAG 61.835 60.000 38.60 31.39 44.88 5.18
780 1743 1.218316 GTACAAGGAGGGTGGCGAG 59.782 63.158 0.00 0.00 0.00 5.03
781 1744 1.229082 TACAAGGAGGGTGGCGAGT 60.229 57.895 0.00 0.00 0.00 4.18
782 1745 1.541310 TACAAGGAGGGTGGCGAGTG 61.541 60.000 0.00 0.00 0.00 3.51
783 1746 3.322466 AAGGAGGGTGGCGAGTGG 61.322 66.667 0.00 0.00 0.00 4.00
798 1761 3.680786 TGGCGACCAGTCACTCGG 61.681 66.667 0.00 0.00 0.00 4.63
799 1762 3.681835 GGCGACCAGTCACTCGGT 61.682 66.667 0.00 0.00 38.56 4.69
800 1763 2.126424 GCGACCAGTCACTCGGTC 60.126 66.667 13.61 13.61 46.88 4.79
802 1765 2.971452 GACCAGTCACTCGGTCCC 59.029 66.667 12.93 0.00 45.03 4.46
803 1766 2.989824 ACCAGTCACTCGGTCCCG 60.990 66.667 0.00 0.00 41.35 5.14
804 1767 3.760035 CCAGTCACTCGGTCCCGG 61.760 72.222 5.80 0.00 40.25 5.73
805 1768 4.436998 CAGTCACTCGGTCCCGGC 62.437 72.222 5.80 0.00 40.25 6.13
858 1821 4.796231 ACATCACCGAGCGCGTCC 62.796 66.667 8.43 0.00 35.23 4.79
879 1852 4.324991 AGTTGCCCGACCCGAACC 62.325 66.667 0.00 0.00 0.00 3.62
890 1863 1.133869 CCCGAACCGAACGATTTGC 59.866 57.895 0.00 0.00 0.00 3.68
1062 2065 2.688666 CTCTGCCCCACCCTAGCA 60.689 66.667 0.00 0.00 34.79 3.49
1063 2066 2.204074 TCTGCCCCACCCTAGCAA 60.204 61.111 0.00 0.00 35.79 3.91
1198 2216 1.209128 CGGCCGTAAGCATTCTACAG 58.791 55.000 19.50 0.00 46.50 2.74
1205 2223 5.753921 GCCGTAAGCATTCTACAGTATTTCT 59.246 40.000 0.00 0.00 42.97 2.52
1206 2224 6.258068 GCCGTAAGCATTCTACAGTATTTCTT 59.742 38.462 0.00 0.00 42.97 2.52
1207 2225 7.516943 GCCGTAAGCATTCTACAGTATTTCTTC 60.517 40.741 0.00 0.00 42.97 2.87
1213 2231 4.119442 TCTACAGTATTTCTTCGGGCAC 57.881 45.455 0.00 0.00 0.00 5.01
1214 2232 3.767673 TCTACAGTATTTCTTCGGGCACT 59.232 43.478 0.00 0.00 0.00 4.40
1262 2291 0.039527 GACCAATTTGCCGTGTCACC 60.040 55.000 0.00 0.00 0.00 4.02
1312 2342 3.624900 TCGACAACTACGTCAAGAAGTG 58.375 45.455 0.00 0.00 35.54 3.16
1322 2352 2.599082 CGTCAAGAAGTGCTAATCCGTC 59.401 50.000 0.00 0.00 0.00 4.79
1325 2355 3.119101 TCAAGAAGTGCTAATCCGTCTCC 60.119 47.826 0.00 0.00 0.00 3.71
1332 2362 2.222027 GCTAATCCGTCTCCCCATTTG 58.778 52.381 0.00 0.00 0.00 2.32
1333 2363 2.851195 CTAATCCGTCTCCCCATTTGG 58.149 52.381 0.00 0.00 0.00 3.28
1349 2383 3.802948 TTTGGTTTGCGTTAACACCAT 57.197 38.095 14.36 0.00 39.10 3.55
1354 2388 3.003897 GGTTTGCGTTAACACCATCTTGA 59.996 43.478 6.39 0.00 0.00 3.02
1369 2403 0.601046 CTTGAGGCTTCGTGCTGACA 60.601 55.000 0.00 0.00 42.39 3.58
1379 2413 2.153645 TCGTGCTGACATTCAATTGCT 58.846 42.857 0.00 0.00 0.00 3.91
1380 2414 2.095617 TCGTGCTGACATTCAATTGCTG 60.096 45.455 0.00 3.50 0.00 4.41
1381 2415 1.990563 GTGCTGACATTCAATTGCTGC 59.009 47.619 0.00 2.98 0.00 5.25
1382 2416 1.890489 TGCTGACATTCAATTGCTGCT 59.110 42.857 0.00 0.00 0.00 4.24
1410 2444 0.905357 TAGGAAGAAGCTGGAGCCAC 59.095 55.000 0.00 0.00 43.38 5.01
1430 2464 4.185059 GAGACGTACGTCCCGGCC 62.185 72.222 37.43 20.98 45.59 6.13
1591 2633 0.376852 GCACGACTGTTTGAGCAACA 59.623 50.000 0.00 0.00 43.55 3.33
1619 2661 1.200948 GCTGGGTTCTTCATCTGCAAC 59.799 52.381 0.00 0.00 0.00 4.17
1623 2665 3.350219 GGTTCTTCATCTGCAACCCTA 57.650 47.619 0.00 0.00 33.42 3.53
1625 2667 2.672961 TCTTCATCTGCAACCCTACG 57.327 50.000 0.00 0.00 0.00 3.51
1636 2678 2.618053 CAACCCTACGGAATCAGTGTC 58.382 52.381 0.00 0.00 0.00 3.67
1650 2692 7.078228 GGAATCAGTGTCAAATGTACAGTTTC 58.922 38.462 5.68 3.68 0.00 2.78
1656 2698 5.901884 GTGTCAAATGTACAGTTTCGTTCAG 59.098 40.000 5.68 0.00 0.00 3.02
1678 2722 4.762251 AGAATTCTTTTGCAGGTCTACCAC 59.238 41.667 0.88 0.00 38.89 4.16
1694 2738 9.920946 AGGTCTACCACACATTATTCAATTATT 57.079 29.630 1.26 0.00 38.89 1.40
1794 2867 7.725844 AGATTCTACCTTTGTCAGATGGTTTTT 59.274 33.333 0.00 0.00 34.33 1.94
1873 2950 3.711086 TGAGAGTAGATCATTGCTTCGC 58.289 45.455 0.00 0.00 0.00 4.70
2011 3088 1.625818 CAAGCTTCAGGTGTCCTAGGT 59.374 52.381 9.08 0.00 29.64 3.08
2012 3089 1.562783 AGCTTCAGGTGTCCTAGGTC 58.437 55.000 9.08 3.43 29.64 3.85
2013 3090 1.077993 AGCTTCAGGTGTCCTAGGTCT 59.922 52.381 9.08 0.00 29.64 3.85
2015 3092 2.354203 GCTTCAGGTGTCCTAGGTCTTG 60.354 54.545 9.08 7.74 29.64 3.02
2016 3093 2.992847 TCAGGTGTCCTAGGTCTTGA 57.007 50.000 9.08 9.83 29.64 3.02
2019 3096 4.168101 TCAGGTGTCCTAGGTCTTGAAAT 58.832 43.478 9.08 0.00 29.64 2.17
2020 3097 4.597507 TCAGGTGTCCTAGGTCTTGAAATT 59.402 41.667 9.08 0.00 29.64 1.82
2026 3103 8.244113 GGTGTCCTAGGTCTTGAAATTTTATTG 58.756 37.037 9.08 0.00 0.00 1.90
2199 3276 4.850859 TGAATGCTTACGGTAAATGACG 57.149 40.909 1.79 0.00 0.00 4.35
2216 3293 4.612264 TGACGCCCTTTTTAGAAGTACT 57.388 40.909 0.00 0.00 0.00 2.73
2218 3295 4.753107 TGACGCCCTTTTTAGAAGTACTTG 59.247 41.667 14.14 0.00 0.00 3.16
2227 3304 8.188139 CCTTTTTAGAAGTACTTGCTTGTTTGA 58.812 33.333 14.14 0.00 0.00 2.69
2369 3455 0.392193 CTGTAGCCCTTGGAGCACTG 60.392 60.000 0.00 1.71 0.00 3.66
2387 3473 5.415701 AGCACTGGACAAGTATTACCAAATG 59.584 40.000 0.00 0.00 36.83 2.32
2391 3480 6.437162 ACTGGACAAGTATTACCAAATGCAAT 59.563 34.615 0.00 0.00 37.36 3.56
2638 3727 5.647589 CTGAGGTTAACGCATCTTGTACTA 58.352 41.667 0.00 0.00 0.00 1.82
2643 3732 9.090692 GAGGTTAACGCATCTTGTACTATTAAA 57.909 33.333 0.00 0.00 0.00 1.52
2683 3772 1.067295 TGCAGAGTGGGACCAAGAAT 58.933 50.000 0.00 0.00 0.00 2.40
2739 3828 9.848238 ACTTCTAGAGTATATAGTACTCCCTCT 57.152 37.037 0.00 6.77 43.61 3.69
2741 3830 9.618447 TTCTAGAGTATATAGTACTCCCTCTGT 57.382 37.037 0.00 0.00 43.61 3.41
2757 3846 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2758 3847 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2759 3848 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2760 3849 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2761 3850 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2809 3898 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2973 4070 5.124776 ACCATCACCCAAATATTGTAACGTG 59.875 40.000 0.00 0.00 0.00 4.49
3056 4153 8.794553 TCAAATTCCAAGCATTTATTTGCAATT 58.205 25.926 0.00 0.00 45.23 2.32
3057 4154 9.413048 CAAATTCCAAGCATTTATTTGCAATTT 57.587 25.926 0.00 0.00 45.23 1.82
3058 4155 9.628746 AAATTCCAAGCATTTATTTGCAATTTC 57.371 25.926 0.00 0.00 45.23 2.17
3063 4160 7.486551 CCAAGCATTTATTTGCAATTTCCAATG 59.513 33.333 0.00 6.49 45.23 2.82
3064 4161 7.090953 AGCATTTATTTGCAATTTCCAATGG 57.909 32.000 0.00 0.00 45.23 3.16
3065 4162 6.885376 AGCATTTATTTGCAATTTCCAATGGA 59.115 30.769 0.00 0.00 45.23 3.41
3066 4163 7.066525 AGCATTTATTTGCAATTTCCAATGGAG 59.933 33.333 0.86 0.00 45.23 3.86
3067 4164 7.066043 GCATTTATTTGCAATTTCCAATGGAGA 59.934 33.333 0.86 0.00 42.31 3.71
3068 4165 8.609176 CATTTATTTGCAATTTCCAATGGAGAG 58.391 33.333 0.86 0.00 31.21 3.20
3069 4166 7.479352 TTATTTGCAATTTCCAATGGAGAGA 57.521 32.000 0.86 0.00 31.21 3.10
3117 4225 2.825532 ACATGCCATAGGGTCAACAAAC 59.174 45.455 0.00 0.00 36.17 2.93
3118 4226 2.969821 TGCCATAGGGTCAACAAACT 57.030 45.000 0.00 0.00 36.17 2.66
3129 4237 6.725364 AGGGTCAACAAACTAATCTGATCAT 58.275 36.000 0.00 0.00 0.00 2.45
3157 4368 7.551262 ACAGTTAATTTACAAGACCATATCGCA 59.449 33.333 0.00 0.00 0.00 5.10
3159 4370 7.551262 AGTTAATTTACAAGACCATATCGCACA 59.449 33.333 0.00 0.00 0.00 4.57
3180 4391 4.214119 ACAGTTTGACCAACAGATCAATCG 59.786 41.667 0.00 0.00 37.93 3.34
3186 4397 5.789521 TGACCAACAGATCAATCGAAGTAA 58.210 37.500 0.00 0.00 0.00 2.24
3187 4398 5.637810 TGACCAACAGATCAATCGAAGTAAC 59.362 40.000 0.00 0.00 0.00 2.50
3211 4583 2.428890 ACACGAAAAAGCCCATTGTCAA 59.571 40.909 0.00 0.00 0.00 3.18
3212 4584 2.794350 CACGAAAAAGCCCATTGTCAAC 59.206 45.455 0.00 0.00 0.00 3.18
3281 4653 0.695347 AGAAACCAAGAGCAGGAGGG 59.305 55.000 0.00 0.00 0.00 4.30
3305 4677 7.016268 GGGATAGAATTCCTGAGTAACCACATA 59.984 40.741 0.65 0.00 35.97 2.29
3333 4705 0.108019 GGAAGAACCACCGGTCTGTT 59.892 55.000 16.80 16.80 33.12 3.16
3337 4709 0.106149 GAACCACCGGTCTGTTGTCT 59.894 55.000 20.66 0.19 33.12 3.41
3342 4714 0.172803 ACCGGTCTGTTGTCTATCGC 59.827 55.000 0.00 0.00 0.00 4.58
3345 4717 1.146358 GGTCTGTTGTCTATCGCCGC 61.146 60.000 0.00 0.00 0.00 6.53
3366 4738 1.553704 GTCGATGTACTTGGGGAAGGT 59.446 52.381 0.00 0.00 0.00 3.50
3371 4743 1.004277 TGTACTTGGGGAAGGTGCATC 59.996 52.381 0.00 0.00 0.00 3.91
3379 4751 1.471676 GGGAAGGTGCATCGACAGTAG 60.472 57.143 0.00 0.00 0.00 2.57
3442 4814 1.666553 CTCCACAGCCGCACGTTTA 60.667 57.895 0.00 0.00 0.00 2.01
3502 4874 1.294041 TCACCCTGGCCATCATGTAA 58.706 50.000 5.51 0.00 0.00 2.41
3564 4939 2.936202 AGCAAGCTTCTTCAGTTCCAA 58.064 42.857 0.00 0.00 0.00 3.53
3592 4967 1.068741 GTCTTGTCGTTCCACAGGTCT 59.931 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 227 8.450180 CCATTTTTGCCATGGTAAATTTAACTC 58.550 33.333 25.98 0.00 37.07 3.01
237 238 2.607499 TCACTCCATTTTTGCCATGGT 58.393 42.857 14.67 0.00 41.90 3.55
260 261 4.685169 AATCTGTTTATTGACGTGGCAG 57.315 40.909 0.00 0.00 0.00 4.85
261 262 6.751514 ATTAATCTGTTTATTGACGTGGCA 57.248 33.333 0.00 0.00 0.00 4.92
262 263 8.460831 AAAATTAATCTGTTTATTGACGTGGC 57.539 30.769 0.00 0.00 0.00 5.01
346 348 5.311016 CGTAGCACGGAAATATACTTGTG 57.689 43.478 1.40 0.00 38.08 3.33
364 366 7.692291 CAGAACATGGCAAATTTAACTACGTAG 59.308 37.037 20.97 20.97 0.00 3.51
450 1399 0.541863 TCCATTTTCTCTCCTCGCCC 59.458 55.000 0.00 0.00 0.00 6.13
453 1402 4.061596 GCCTTATCCATTTTCTCTCCTCG 58.938 47.826 0.00 0.00 0.00 4.63
498 1447 2.614983 CCTTTCGTTCGGAAAAGGAACA 59.385 45.455 12.38 0.74 43.73 3.18
530 1493 1.263356 AAGCATGTCAAAGCAGCCAT 58.737 45.000 0.00 0.00 0.00 4.40
542 1505 3.054875 TCAGCACTGATCCTAAAGCATGT 60.055 43.478 0.00 0.00 34.14 3.21
558 1521 1.333931 TCGATCGTAGGATGTCAGCAC 59.666 52.381 15.94 0.00 31.51 4.40
577 1540 3.116531 CGCCCCGAACGACCTTTC 61.117 66.667 0.00 0.00 0.00 2.62
616 1579 7.614124 TTGTTTACGGTATCAATAACTTCCC 57.386 36.000 0.00 0.00 0.00 3.97
630 1593 5.474532 GGATAGGGAAGTTTTTGTTTACGGT 59.525 40.000 0.00 0.00 0.00 4.83
647 1610 1.087771 GTGCCACGAAACGGATAGGG 61.088 60.000 0.00 0.00 0.00 3.53
648 1611 0.108329 AGTGCCACGAAACGGATAGG 60.108 55.000 0.00 0.00 0.00 2.57
654 1617 0.938713 TAAACCAGTGCCACGAAACG 59.061 50.000 0.00 0.00 0.00 3.60
666 1629 1.140852 TGGGCGAGGATGATAAACCAG 59.859 52.381 0.00 0.00 0.00 4.00
708 1671 0.541392 TCGCTGGTTATGGCATGAGT 59.459 50.000 10.98 0.00 0.00 3.41
719 1682 3.121030 GCACTGCGATCGCTGGTT 61.121 61.111 38.48 23.32 43.03 3.67
756 1719 0.883833 CACCCTCCTTGTACGTACGT 59.116 55.000 25.98 25.98 0.00 3.57
757 1720 0.171903 CCACCCTCCTTGTACGTACG 59.828 60.000 20.18 15.01 0.00 3.67
758 1721 0.108472 GCCACCCTCCTTGTACGTAC 60.108 60.000 18.90 18.90 0.00 3.67
759 1722 1.597797 CGCCACCCTCCTTGTACGTA 61.598 60.000 0.00 0.00 0.00 3.57
780 1743 2.430921 CGAGTGACTGGTCGCCAC 60.431 66.667 10.19 5.23 40.77 5.01
781 1744 3.680786 CCGAGTGACTGGTCGCCA 61.681 66.667 10.19 0.00 40.77 5.69
782 1745 3.628280 GACCGAGTGACTGGTCGCC 62.628 68.421 15.08 2.67 44.68 5.54
783 1746 2.126424 GACCGAGTGACTGGTCGC 60.126 66.667 15.08 6.21 44.68 5.19
786 1749 2.989824 CGGGACCGAGTGACTGGT 60.990 66.667 4.40 6.45 42.83 4.00
787 1750 3.760035 CCGGGACCGAGTGACTGG 61.760 72.222 13.13 0.00 42.83 4.00
788 1751 4.436998 GCCGGGACCGAGTGACTG 62.437 72.222 13.13 0.00 42.83 3.51
806 1769 2.076622 CTATCCGTCGCCACCAGGAG 62.077 65.000 0.00 0.00 36.08 3.69
807 1770 2.043752 TATCCGTCGCCACCAGGA 60.044 61.111 0.00 0.00 36.89 3.86
817 1780 0.593263 CGTTACGTGGGCTATCCGTC 60.593 60.000 0.00 0.00 38.76 4.79
862 1825 4.324991 GGTTCGGGTCGGGCAACT 62.325 66.667 0.00 0.00 0.00 3.16
996 1999 2.764314 CGAGGCGGAGGGCATTTTG 61.764 63.158 0.00 0.00 46.16 2.44
1046 2049 2.204074 TTGCTAGGGTGGGGCAGA 60.204 61.111 0.00 0.00 37.28 4.26
1192 2207 3.767673 AGTGCCCGAAGAAATACTGTAGA 59.232 43.478 0.00 0.00 0.00 2.59
1198 2216 1.062148 GCGAAGTGCCCGAAGAAATAC 59.938 52.381 0.00 0.00 37.76 1.89
1225 2243 3.588906 ACTCACGTCGCACACCGA 61.589 61.111 0.00 0.00 45.15 4.69
1226 2244 3.394874 CACTCACGTCGCACACCG 61.395 66.667 0.00 0.00 38.61 4.94
1227 2245 2.027024 TCACTCACGTCGCACACC 59.973 61.111 0.00 0.00 0.00 4.16
1236 2265 0.110238 CGGCAAATTGGTCACTCACG 60.110 55.000 0.00 0.00 0.00 4.35
1312 2342 2.222027 CAAATGGGGAGACGGATTAGC 58.778 52.381 0.00 0.00 0.00 3.09
1322 2352 0.678950 AACGCAAACCAAATGGGGAG 59.321 50.000 4.17 0.00 42.91 4.30
1325 2355 2.797719 GTGTTAACGCAAACCAAATGGG 59.202 45.455 14.22 0.00 44.81 4.00
1332 2362 3.003897 TCAAGATGGTGTTAACGCAAACC 59.996 43.478 20.13 12.82 0.00 3.27
1333 2363 4.217754 TCAAGATGGTGTTAACGCAAAC 57.782 40.909 20.13 8.51 0.00 2.93
1369 2403 0.895530 AGCAGCAGCAGCAATTGAAT 59.104 45.000 12.92 0.00 45.49 2.57
1379 2413 1.078637 CTTCCTAGCAGCAGCAGCA 60.079 57.895 12.92 0.00 45.49 4.41
1380 2414 0.392193 TTCTTCCTAGCAGCAGCAGC 60.392 55.000 3.17 0.46 45.49 5.25
1381 2415 1.654317 CTTCTTCCTAGCAGCAGCAG 58.346 55.000 3.17 0.00 45.49 4.24
1382 2416 0.392193 GCTTCTTCCTAGCAGCAGCA 60.392 55.000 3.17 0.00 45.49 4.41
1430 2464 2.031012 TCTTGGGTCAGCAGCACG 59.969 61.111 0.00 0.00 0.00 5.34
1591 2633 3.439857 TGAAGAACCCAGCTGCTAATT 57.560 42.857 8.66 0.00 0.00 1.40
1621 2663 5.867174 TGTACATTTGACACTGATTCCGTAG 59.133 40.000 0.00 0.00 0.00 3.51
1623 2665 4.637276 TGTACATTTGACACTGATTCCGT 58.363 39.130 0.00 0.00 0.00 4.69
1625 2667 6.560253 AACTGTACATTTGACACTGATTCC 57.440 37.500 0.00 0.00 0.00 3.01
1636 2678 8.070171 AGAATTCTGAACGAAACTGTACATTTG 58.930 33.333 7.30 0.00 34.79 2.32
1650 2692 4.023707 AGACCTGCAAAAGAATTCTGAACG 60.024 41.667 9.17 0.00 0.00 3.95
1656 2698 4.518970 TGTGGTAGACCTGCAAAAGAATTC 59.481 41.667 0.00 0.00 36.82 2.17
1694 2738 5.127519 CCATTTCCATTGGAAGAAGCACATA 59.872 40.000 17.29 1.03 43.06 2.29
1794 2867 8.704668 TCTCTGTAATGAAGCATATGAAGGTTA 58.295 33.333 6.97 0.00 0.00 2.85
1801 2874 8.618702 AGGATTTCTCTGTAATGAAGCATATG 57.381 34.615 0.00 0.00 0.00 1.78
1873 2950 2.040939 AGAGATGATGCTGGACCAGAG 58.959 52.381 26.25 0.23 32.44 3.35
1970 3047 5.068215 TGAGAAGTAGAAGGGCTAGCTAT 57.932 43.478 15.72 0.00 0.00 2.97
2012 3089 9.034544 GCTATGGCCTAACAATAAAATTTCAAG 57.965 33.333 3.32 0.00 0.00 3.02
2013 3090 8.535335 TGCTATGGCCTAACAATAAAATTTCAA 58.465 29.630 3.32 0.00 37.74 2.69
2015 3092 9.546428 AATGCTATGGCCTAACAATAAAATTTC 57.454 29.630 3.32 0.00 37.74 2.17
2026 3103 8.145122 GGATACTCTATAATGCTATGGCCTAAC 58.855 40.741 3.32 0.00 37.74 2.34
2079 3156 8.855110 ACACAGTTTCAGTATCCATAGATAGAG 58.145 37.037 0.00 0.00 35.61 2.43
2084 3161 5.417894 ACGACACAGTTTCAGTATCCATAGA 59.582 40.000 0.00 0.00 0.00 1.98
2090 3167 7.404139 AAGTTTACGACACAGTTTCAGTATC 57.596 36.000 0.00 0.00 0.00 2.24
2199 3276 5.009710 ACAAGCAAGTACTTCTAAAAAGGGC 59.990 40.000 4.77 2.90 0.00 5.19
2216 3293 6.066054 TCAATACATTCGTCAAACAAGCAA 57.934 33.333 0.00 0.00 0.00 3.91
2218 3295 4.554973 GCTCAATACATTCGTCAAACAAGC 59.445 41.667 0.00 0.00 0.00 4.01
2227 3304 4.875536 TGCATAACAGCTCAATACATTCGT 59.124 37.500 0.00 0.00 34.99 3.85
2369 3455 8.850156 AGATATTGCATTTGGTAATACTTGTCC 58.150 33.333 0.00 0.00 36.97 4.02
2387 3473 8.355169 TGCTTTCAAGATGGATAAAGATATTGC 58.645 33.333 0.00 0.00 31.96 3.56
2476 3565 4.067972 TCCTTTATCCATAACGGCTGAC 57.932 45.455 0.00 0.00 33.17 3.51
2648 3737 7.230108 CCCACTCTGCAATTTAATCATACTGAT 59.770 37.037 0.00 0.00 39.09 2.90
2683 3772 5.178623 CACAGGTAATTGTTCTGCTACGAAA 59.821 40.000 0.00 0.00 32.19 3.46
2733 3822 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2734 3823 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2735 3824 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2798 3887 6.864151 AAAGTAATACTCCCTCCGTAAACT 57.136 37.500 0.00 0.00 0.00 2.66
2799 3888 7.099120 TGAAAAGTAATACTCCCTCCGTAAAC 58.901 38.462 0.00 0.00 0.00 2.01
2891 3981 4.636206 AGGATTATGCTCAAACTTCCGTTC 59.364 41.667 0.00 0.00 31.66 3.95
2973 4070 1.802960 CTGTTGTGCAGTGTCATCTCC 59.197 52.381 0.00 0.00 40.27 3.71
3015 4112 6.680810 TGGAATTTGAGAATGCAAGTTACAG 58.319 36.000 0.00 0.00 34.59 2.74
3056 4153 5.250543 TCCACTTATGTTCTCTCCATTGGAA 59.749 40.000 6.88 0.00 28.57 3.53
3057 4154 4.782691 TCCACTTATGTTCTCTCCATTGGA 59.217 41.667 5.05 5.05 28.84 3.53
3058 4155 5.102953 TCCACTTATGTTCTCTCCATTGG 57.897 43.478 0.00 0.00 0.00 3.16
3063 4160 5.596361 TCTGAGATCCACTTATGTTCTCTCC 59.404 44.000 9.23 0.00 35.60 3.71
3064 4161 6.707440 TCTGAGATCCACTTATGTTCTCTC 57.293 41.667 9.23 7.37 35.60 3.20
3065 4162 6.894654 TCTTCTGAGATCCACTTATGTTCTCT 59.105 38.462 9.23 0.00 35.60 3.10
3066 4163 7.106439 TCTTCTGAGATCCACTTATGTTCTC 57.894 40.000 0.00 3.21 35.35 2.87
3067 4164 7.364585 CCTTCTTCTGAGATCCACTTATGTTCT 60.365 40.741 0.00 0.00 0.00 3.01
3068 4165 6.760770 CCTTCTTCTGAGATCCACTTATGTTC 59.239 42.308 0.00 0.00 0.00 3.18
3069 4166 6.214412 ACCTTCTTCTGAGATCCACTTATGTT 59.786 38.462 0.00 0.00 0.00 2.71
3146 4254 2.351726 GGTCAAACTGTGCGATATGGTC 59.648 50.000 0.00 0.00 0.00 4.02
3151 4259 2.805671 CTGTTGGTCAAACTGTGCGATA 59.194 45.455 0.00 0.00 39.70 2.92
3157 4368 4.214119 CGATTGATCTGTTGGTCAAACTGT 59.786 41.667 0.00 0.00 39.70 3.55
3159 4370 4.641396 TCGATTGATCTGTTGGTCAAACT 58.359 39.130 0.00 0.00 39.70 2.66
3180 4391 4.501559 GGGCTTTTTCGTGTTTGTTACTTC 59.498 41.667 0.00 0.00 0.00 3.01
3186 4397 3.194062 CAATGGGCTTTTTCGTGTTTGT 58.806 40.909 0.00 0.00 0.00 2.83
3187 4398 3.194062 ACAATGGGCTTTTTCGTGTTTG 58.806 40.909 0.00 0.00 0.00 2.93
3212 4584 5.034554 AGAATGTTTATGTGTTGACGCAG 57.965 39.130 3.62 0.00 39.97 5.18
3281 4653 9.482627 CTTATGTGGTTACTCAGGAATTCTATC 57.517 37.037 5.23 0.00 0.00 2.08
3305 4677 3.477530 CGGTGGTTCTTCCTTCTTTCTT 58.522 45.455 0.00 0.00 37.07 2.52
3342 4714 1.876714 CCCAAGTACATCGACGCGG 60.877 63.158 12.47 0.00 0.00 6.46
3345 4717 1.470979 CCTTCCCCAAGTACATCGACG 60.471 57.143 0.00 0.00 0.00 5.12
3366 4738 1.616374 TCACAACCTACTGTCGATGCA 59.384 47.619 0.00 0.00 0.00 3.96
3371 4743 1.995484 CTGCATCACAACCTACTGTCG 59.005 52.381 0.00 0.00 0.00 4.35
3379 4751 4.465512 CGCCGCTGCATCACAACC 62.466 66.667 0.00 0.00 37.32 3.77
3502 4874 1.066858 ACGCAGGATGATGACTTCGTT 60.067 47.619 0.00 0.00 39.69 3.85
3564 4939 1.880027 GGAACGACAAGACCAAGCAAT 59.120 47.619 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.