Multiple sequence alignment - TraesCS4D01G199300

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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 TraesCS4D01G199300 chr4D 100.000 4966 0 0 1 4966 346139387 346134422 0.000000e+00 9171.0
1 TraesCS4D01G199300 chr4D 95.449 857 35 3 2220 3074 87530350 87529496 0.000000e+00 1363.0
2 TraesCS4D01G199300 chr4D 86.096 187 22 3 4370 4555 509826603 509826420 1.090000e-46 198.0
3 TraesCS4D01G199300 chr4A 91.023 2306 117 37 1 2244 119696549 119698826 0.000000e+00 3029.0
4 TraesCS4D01G199300 chr4A 95.414 1003 41 4 2242 3240 119701359 119702360 0.000000e+00 1592.0
5 TraesCS4D01G199300 chr4A 94.279 839 40 7 3326 4157 119702363 119703200 0.000000e+00 1277.0
6 TraesCS4D01G199300 chr4A 86.298 416 39 7 4551 4966 119703563 119703960 2.120000e-118 436.0
7 TraesCS4D01G199300 chr4A 95.417 240 11 0 4156 4395 119703324 119703563 2.800000e-102 383.0
8 TraesCS4D01G199300 chr4A 93.814 97 4 2 3238 3334 428159973 428159879 1.440000e-30 145.0
9 TraesCS4D01G199300 chr4B 87.431 1631 127 40 3321 4919 427277341 427275757 0.000000e+00 1805.0
10 TraesCS4D01G199300 chr4B 93.565 979 49 7 777 1744 427280001 427279026 0.000000e+00 1447.0
11 TraesCS4D01G199300 chr4B 93.901 787 19 10 1 784 427295373 427294613 0.000000e+00 1160.0
12 TraesCS4D01G199300 chr4B 91.683 505 39 2 2739 3241 427277841 427277338 0.000000e+00 697.0
13 TraesCS4D01G199300 chr4B 88.449 303 22 9 2060 2352 427278484 427278185 2.200000e-93 353.0
14 TraesCS4D01G199300 chr4B 84.548 343 24 12 1731 2069 427278987 427278670 3.730000e-81 313.0
15 TraesCS4D01G199300 chr3D 94.645 1027 48 4 2220 3241 36679677 36678653 0.000000e+00 1585.0
16 TraesCS4D01G199300 chr3D 94.055 1026 54 4 2220 3241 546181490 546180468 0.000000e+00 1550.0
17 TraesCS4D01G199300 chr3D 90.741 162 13 2 4394 4555 104025907 104026066 1.080000e-51 215.0
18 TraesCS4D01G199300 chr3D 90.184 163 16 0 4393 4555 449740281 449740443 3.890000e-51 213.0
19 TraesCS4D01G199300 chr3D 96.667 90 3 0 3237 3326 436676985 436676896 3.100000e-32 150.0
20 TraesCS4D01G199300 chr3D 91.667 60 5 0 4728 4787 395526587 395526646 3.190000e-12 84.2
21 TraesCS4D01G199300 chr1D 94.055 1026 55 3 2220 3241 117210620 117211643 0.000000e+00 1552.0
22 TraesCS4D01G199300 chr1D 91.910 1026 57 10 2220 3241 69981541 69982544 0.000000e+00 1411.0
23 TraesCS4D01G199300 chr1D 88.372 172 17 3 4391 4561 387944779 387944948 2.340000e-48 204.0
24 TraesCS4D01G199300 chr7D 93.957 1026 55 4 2220 3241 545882916 545881894 0.000000e+00 1544.0
25 TraesCS4D01G199300 chr2D 94.111 866 45 3 2380 3241 562700380 562701243 0.000000e+00 1312.0
26 TraesCS4D01G199300 chr5D 91.225 604 44 3 2640 3241 20033077 20032481 0.000000e+00 813.0
27 TraesCS4D01G199300 chr5D 96.447 394 11 2 2220 2611 20033462 20033070 0.000000e+00 647.0
28 TraesCS4D01G199300 chr5D 92.405 158 11 1 4399 4555 475153114 475152957 1.800000e-54 224.0
29 TraesCS4D01G199300 chr5D 89.091 165 18 0 4391 4555 487413546 487413710 6.520000e-49 206.0
30 TraesCS4D01G199300 chr5D 88.757 169 16 2 4391 4556 393895833 393895665 2.340000e-48 204.0
31 TraesCS4D01G199300 chr5A 90.741 162 15 0 4394 4555 605231143 605231304 3.010000e-52 217.0
32 TraesCS4D01G199300 chr3B 90.123 162 16 0 4394 4555 154663044 154663205 1.400000e-50 211.0
33 TraesCS4D01G199300 chr6B 96.703 91 3 0 3234 3324 359864631 359864721 8.610000e-33 152.0
34 TraesCS4D01G199300 chr1A 97.701 87 2 0 3238 3324 209362154 209362068 3.100000e-32 150.0
35 TraesCS4D01G199300 chr6D 92.233 103 8 0 3220 3322 29232276 29232378 4.010000e-31 147.0
36 TraesCS4D01G199300 chr6D 100.000 28 0 0 4601 4628 296196857 296196884 9.000000e-03 52.8
37 TraesCS4D01G199300 chr2A 92.381 105 5 3 3225 3329 617636129 617636028 4.010000e-31 147.0
38 TraesCS4D01G199300 chr3A 93.750 96 6 0 3228 3323 22230625 22230720 1.440000e-30 145.0
39 TraesCS4D01G199300 chr2B 93.750 96 6 0 3227 3322 494265074 494265169 1.440000e-30 145.0
40 TraesCS4D01G199300 chr6A 92.079 101 6 2 3235 3334 584511359 584511458 1.860000e-29 141.0


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 TraesCS4D01G199300 chr4D 346134422 346139387 4965 True 9171.0 9171 100.0000 1 4966 1 chr4D.!!$R2 4965
1 TraesCS4D01G199300 chr4D 87529496 87530350 854 True 1363.0 1363 95.4490 2220 3074 1 chr4D.!!$R1 854
2 TraesCS4D01G199300 chr4A 119696549 119703960 7411 False 1343.4 3029 92.4862 1 4966 5 chr4A.!!$F1 4965
3 TraesCS4D01G199300 chr4B 427294613 427295373 760 True 1160.0 1160 93.9010 1 784 1 chr4B.!!$R1 783
4 TraesCS4D01G199300 chr4B 427275757 427280001 4244 True 923.0 1805 89.1352 777 4919 5 chr4B.!!$R2 4142
5 TraesCS4D01G199300 chr3D 36678653 36679677 1024 True 1585.0 1585 94.6450 2220 3241 1 chr3D.!!$R1 1021
6 TraesCS4D01G199300 chr3D 546180468 546181490 1022 True 1550.0 1550 94.0550 2220 3241 1 chr3D.!!$R3 1021
7 TraesCS4D01G199300 chr1D 117210620 117211643 1023 False 1552.0 1552 94.0550 2220 3241 1 chr1D.!!$F2 1021
8 TraesCS4D01G199300 chr1D 69981541 69982544 1003 False 1411.0 1411 91.9100 2220 3241 1 chr1D.!!$F1 1021
9 TraesCS4D01G199300 chr7D 545881894 545882916 1022 True 1544.0 1544 93.9570 2220 3241 1 chr7D.!!$R1 1021
10 TraesCS4D01G199300 chr2D 562700380 562701243 863 False 1312.0 1312 94.1110 2380 3241 1 chr2D.!!$F1 861
11 TraesCS4D01G199300 chr5D 20032481 20033462 981 True 730.0 813 93.8360 2220 3241 2 chr5D.!!$R3 1021

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
820 856 1.804396 TTTCCGGGTTCGCTGACGTA 61.804 55.0 0.00 0.00 41.18 3.57 F
1582 1627 0.037017 TGGCGGCTAAGCAGGTTAAA 59.963 50.0 11.43 0.00 39.27 1.52 F
2735 5624 0.252696 TGATGAGTGGGCCCTAGTGT 60.253 55.0 25.70 6.27 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2052 1.706866 CATTGCCTCCTGGATATGGGA 59.293 52.381 0.0 0.0 34.57 4.37 R
3310 6254 1.825474 CAACATCAGTACTCCCTCCGT 59.175 52.381 0.0 0.0 0.00 4.69 R
4138 7093 0.998226 CACAACCAAAGCATCGCACG 60.998 55.000 0.0 0.0 0.00 5.34 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
47 48 1.807142 GCAGCCTAAGAGTTCACCAAC 59.193 52.381 0.00 0.00 0.00 3.77
335 363 4.444024 CGCATGAACACCACGCCG 62.444 66.667 0.00 0.00 28.49 6.46
355 383 3.126343 CCGAACACAAACCTAATGCCTAC 59.874 47.826 0.00 0.00 0.00 3.18
361 389 3.770933 ACAAACCTAATGCCTACGACCTA 59.229 43.478 0.00 0.00 0.00 3.08
416 444 3.369400 CCAATCCGCCGGCACAAA 61.369 61.111 28.98 8.51 0.00 2.83
435 463 2.375173 ATACGGACGAAACACTTCCC 57.625 50.000 0.00 0.00 33.98 3.97
446 474 4.328169 CGAAACACTTCCCTTATAACGTCC 59.672 45.833 0.00 0.00 0.00 4.79
471 499 3.074412 ACAAGCACCGAGGTAATTCAAG 58.926 45.455 0.00 0.00 0.00 3.02
820 856 1.804396 TTTCCGGGTTCGCTGACGTA 61.804 55.000 0.00 0.00 41.18 3.57
821 857 2.476534 TTCCGGGTTCGCTGACGTAC 62.477 60.000 0.00 0.00 41.18 3.67
867 903 3.923864 AGCACAAGACGTGGCGGA 61.924 61.111 0.00 0.00 46.45 5.54
871 907 4.351938 CAAGACGTGGCGGACCGA 62.352 66.667 20.50 0.00 39.70 4.69
923 959 2.434331 CTCCGGTTCCAAGGCCAA 59.566 61.111 5.01 0.00 0.00 4.52
932 968 2.045926 CAAGGCCAACTCTCGGGG 60.046 66.667 5.01 0.00 0.00 5.73
1254 1291 0.455005 TGCTCTCAGCTCGATCTGTG 59.545 55.000 15.40 13.18 42.97 3.66
1456 1501 1.243902 TTTCGGGTGGATTTCACTGC 58.756 50.000 0.00 0.00 45.38 4.40
1462 1507 2.553028 GGGTGGATTTCACTGCTTCTGA 60.553 50.000 0.00 0.00 45.38 3.27
1463 1508 2.485814 GGTGGATTTCACTGCTTCTGAC 59.514 50.000 0.00 0.00 45.38 3.51
1464 1509 2.158449 GTGGATTTCACTGCTTCTGACG 59.842 50.000 0.00 0.00 42.86 4.35
1509 1554 7.201644 CGGTGATTATTTTGTGTAGCTGAGATT 60.202 37.037 0.00 0.00 0.00 2.40
1540 1585 0.455410 TTGTTTGCAGGTGTGTGCTC 59.545 50.000 0.00 0.00 44.32 4.26
1546 1591 4.320456 AGGTGTGTGCTCTGCCGG 62.320 66.667 0.00 0.00 0.00 6.13
1582 1627 0.037017 TGGCGGCTAAGCAGGTTAAA 59.963 50.000 11.43 0.00 39.27 1.52
1667 1721 5.163764 CCGTCAATTGCTCAAAGCTATACAA 60.164 40.000 0.00 0.00 42.97 2.41
1695 1756 2.872842 GCTTGCCATTTGCCATTGAACT 60.873 45.455 0.00 0.00 40.16 3.01
1751 1813 7.270047 GGTAACATACTAACACCTGCTGAATA 58.730 38.462 0.00 0.00 0.00 1.75
1789 1902 4.943705 AGATGTTTCAGTAATTCGGCACAT 59.056 37.500 0.00 0.00 0.00 3.21
1868 1985 9.817809 CAGTTTCATTAGTTTATGTAGCTCCTA 57.182 33.333 0.00 0.00 0.00 2.94
1876 1993 6.221659 AGTTTATGTAGCTCCTAAATACGGC 58.778 40.000 0.00 0.00 0.00 5.68
2115 2438 9.325198 GATAATATGTACTGGTGTTTGATGTGA 57.675 33.333 0.00 0.00 0.00 3.58
2158 2482 3.000727 CTGAAGTAACCACGAATCCACC 58.999 50.000 0.00 0.00 0.00 4.61
2159 2483 1.997606 GAAGTAACCACGAATCCACCG 59.002 52.381 0.00 0.00 0.00 4.94
2160 2484 1.259609 AGTAACCACGAATCCACCGA 58.740 50.000 0.00 0.00 0.00 4.69
2366 5226 5.012046 AGGAAAACTAAGGCCCTTGAAATTG 59.988 40.000 6.16 0.00 0.00 2.32
2624 5488 8.551205 AGAACAATGTTAACATGCGAGTATATG 58.449 33.333 21.46 14.18 36.56 1.78
2720 5609 1.737793 GGCCGGAGTTTAGTTGTGATG 59.262 52.381 5.05 0.00 0.00 3.07
2735 5624 0.252696 TGATGAGTGGGCCCTAGTGT 60.253 55.000 25.70 6.27 0.00 3.55
2756 5696 8.840200 AGTGTCCCTTCTAAATATAAGTCTCA 57.160 34.615 0.00 0.00 0.00 3.27
3002 5942 4.334443 CCTTCAAAATAATCAGTGTCGCG 58.666 43.478 0.00 0.00 0.00 5.87
3014 5954 0.375803 GTGTCGCGTGAAACCAGTTT 59.624 50.000 8.15 0.00 35.14 2.66
3134 6078 3.808834 AGTAGTCTTTTGGGGAAAGGG 57.191 47.619 0.00 0.00 44.00 3.95
3135 6079 2.378886 AGTAGTCTTTTGGGGAAAGGGG 59.621 50.000 0.00 0.00 44.00 4.79
3227 6171 5.484715 TCCCTCGTTAAAGGTATTTGACTG 58.515 41.667 0.00 0.00 33.83 3.51
3246 6190 8.783660 TTGACTGTATAAATCATACTCCCTCT 57.216 34.615 0.00 0.00 40.30 3.69
3247 6191 8.183104 TGACTGTATAAATCATACTCCCTCTG 57.817 38.462 0.00 0.00 40.30 3.35
3248 6192 7.785028 TGACTGTATAAATCATACTCCCTCTGT 59.215 37.037 0.00 0.00 40.30 3.41
3249 6193 9.298250 GACTGTATAAATCATACTCCCTCTGTA 57.702 37.037 0.00 0.00 40.30 2.74
3250 6194 9.656323 ACTGTATAAATCATACTCCCTCTGTAA 57.344 33.333 0.00 0.00 40.30 2.41
3264 6208 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
3265 6209 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
3266 6210 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
3267 6211 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
3268 6212 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
3285 6229 8.635877 AGAGCGTTTAGATCACTAAAGTATTG 57.364 34.615 0.00 0.00 45.42 1.90
3286 6230 8.467598 AGAGCGTTTAGATCACTAAAGTATTGA 58.532 33.333 0.00 0.00 45.42 2.57
3287 6231 9.250624 GAGCGTTTAGATCACTAAAGTATTGAT 57.749 33.333 0.00 0.00 45.42 2.57
3288 6232 9.035607 AGCGTTTAGATCACTAAAGTATTGATG 57.964 33.333 0.00 0.00 45.42 3.07
3289 6233 8.818057 GCGTTTAGATCACTAAAGTATTGATGT 58.182 33.333 0.00 0.00 45.42 3.06
3295 6239 8.818057 AGATCACTAAAGTATTGATGTAAACGC 58.182 33.333 0.00 0.00 29.52 4.84
3296 6240 8.718102 ATCACTAAAGTATTGATGTAAACGCT 57.282 30.769 0.00 0.00 28.41 5.07
3297 6241 8.181487 TCACTAAAGTATTGATGTAAACGCTC 57.819 34.615 0.00 0.00 0.00 5.03
3298 6242 8.033038 TCACTAAAGTATTGATGTAAACGCTCT 58.967 33.333 0.00 0.00 0.00 4.09
3299 6243 8.656849 CACTAAAGTATTGATGTAAACGCTCTT 58.343 33.333 0.00 0.00 0.00 2.85
3300 6244 9.865321 ACTAAAGTATTGATGTAAACGCTCTTA 57.135 29.630 0.00 0.00 0.00 2.10
3313 6257 8.810427 TGTAAACGCTCTTATATTTCTTTACGG 58.190 33.333 0.00 0.00 0.00 4.02
3314 6258 9.023967 GTAAACGCTCTTATATTTCTTTACGGA 57.976 33.333 0.00 0.00 0.00 4.69
3315 6259 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
3316 6260 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
3317 6261 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
3318 6262 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
3319 6263 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
3320 6264 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
3321 6265 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
3322 6266 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
3323 6267 8.773033 TTATATTTCTTTACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
3324 6268 4.796038 TTTCTTTACGGAGGGAGTACTG 57.204 45.455 0.00 0.00 0.00 2.74
3335 6279 4.162320 GGAGGGAGTACTGATGTTGATTCA 59.838 45.833 0.00 0.00 0.00 2.57
3483 6428 4.730949 TTTACTCCATCGGTAAGTCCTG 57.269 45.455 0.00 0.00 31.94 3.86
3520 6465 7.907389 TCCTATTGTGTAGTTTCTGTTCATCT 58.093 34.615 0.00 0.00 0.00 2.90
3695 6641 6.279513 AGCTCTGATATAATTCTCTTCGGG 57.720 41.667 0.00 0.00 0.00 5.14
3709 6655 0.693622 TTCGGGGCATTGGTTAGTCA 59.306 50.000 0.00 0.00 0.00 3.41
3713 6659 1.402787 GGGCATTGGTTAGTCATGGG 58.597 55.000 0.00 0.00 0.00 4.00
3737 6684 7.393515 GGGTCAGTTTAGGAACATTTGTCTATT 59.606 37.037 0.00 0.00 38.26 1.73
3833 6781 0.465460 AAGCAAGCCCTTCGTGACAA 60.465 50.000 0.00 0.00 0.00 3.18
3870 6819 4.522114 TCATTCGCTGGATGGTGAATTAA 58.478 39.130 0.00 0.00 42.31 1.40
3893 6842 4.799678 TGGTTGTAACTTTGTGTTGTGTG 58.200 39.130 0.00 0.00 39.55 3.82
3897 6846 5.150342 TGTAACTTTGTGTTGTGTGATCG 57.850 39.130 0.00 0.00 39.55 3.69
3899 6848 3.673746 ACTTTGTGTTGTGTGATCGTG 57.326 42.857 0.00 0.00 0.00 4.35
3989 6938 8.586570 AGATCTTTAGTATTGCTTTGATCTCG 57.413 34.615 0.00 0.00 34.46 4.04
3999 6953 9.643652 GTATTGCTTTGATCTCGAAAATAAGAG 57.356 33.333 0.00 0.00 35.91 2.85
4024 6978 6.101274 AGAACTCCTTTAGTATCCCCACTA 57.899 41.667 0.00 0.00 37.50 2.74
4138 7093 0.389391 TGAACTAGGGAGCATAGCGC 59.611 55.000 0.00 0.00 42.91 5.92
4157 7237 0.998226 CGTGCGATGCTTTGGTTGTG 60.998 55.000 0.00 0.00 0.00 3.33
4168 7248 7.148983 CGATGCTTTGGTTGTGTTTGTATAAAG 60.149 37.037 0.00 0.00 0.00 1.85
4292 7372 3.244345 CAGTACTTTCAAGCGTCAAACGA 59.756 43.478 3.28 0.00 46.05 3.85
4376 7458 0.395724 AACCTCCAAATCGCATCCCC 60.396 55.000 0.00 0.00 0.00 4.81
4395 7477 4.067896 CCCCAACATGCACTCTCATATAC 58.932 47.826 0.00 0.00 0.00 1.47
4401 7488 6.491714 ACATGCACTCTCATATACTTCCTT 57.508 37.500 0.00 0.00 0.00 3.36
4406 7493 5.688176 GCACTCTCATATACTTCCTTCGTTC 59.312 44.000 0.00 0.00 0.00 3.95
4498 7585 4.634349 CAAATTCACTCATTTTGCACCG 57.366 40.909 0.00 0.00 0.00 4.94
4499 7586 4.050553 CAAATTCACTCATTTTGCACCGT 58.949 39.130 0.00 0.00 0.00 4.83
4500 7587 5.218885 CAAATTCACTCATTTTGCACCGTA 58.781 37.500 0.00 0.00 0.00 4.02
4501 7588 5.643379 AATTCACTCATTTTGCACCGTAT 57.357 34.783 0.00 0.00 0.00 3.06
4502 7589 4.418013 TTCACTCATTTTGCACCGTATG 57.582 40.909 0.00 0.00 0.00 2.39
4503 7590 3.407698 TCACTCATTTTGCACCGTATGT 58.592 40.909 0.00 0.00 0.00 2.29
4504 7591 4.570930 TCACTCATTTTGCACCGTATGTA 58.429 39.130 0.00 0.00 0.00 2.29
4505 7592 4.629634 TCACTCATTTTGCACCGTATGTAG 59.370 41.667 0.00 0.00 0.00 2.74
4507 7594 4.630069 ACTCATTTTGCACCGTATGTAGTC 59.370 41.667 0.00 0.00 0.00 2.59
4508 7595 3.936453 TCATTTTGCACCGTATGTAGTCC 59.064 43.478 0.00 0.00 0.00 3.85
4509 7596 3.404224 TTTTGCACCGTATGTAGTCCA 57.596 42.857 0.00 0.00 0.00 4.02
4510 7597 3.620427 TTTGCACCGTATGTAGTCCAT 57.380 42.857 0.00 0.00 37.58 3.41
4511 7598 4.739587 TTTGCACCGTATGTAGTCCATA 57.260 40.909 0.00 0.00 34.86 2.74
4513 7600 4.948341 TGCACCGTATGTAGTCCATATT 57.052 40.909 0.00 0.00 38.29 1.28
4514 7601 6.408107 TTGCACCGTATGTAGTCCATATTA 57.592 37.500 0.00 0.00 38.29 0.98
4521 7608 8.958506 ACCGTATGTAGTCCATATTAGAATCTC 58.041 37.037 0.00 0.00 38.29 2.75
4549 7636 8.622948 AAAAGACTTGTATTTAGGAACAGAGG 57.377 34.615 0.00 0.00 0.00 3.69
4550 7637 7.554959 AAGACTTGTATTTAGGAACAGAGGA 57.445 36.000 0.00 0.00 0.00 3.71
4586 7673 6.812160 ACTTAAGATCACGTAACTAAGCAAGG 59.188 38.462 10.09 0.00 0.00 3.61
4686 7781 3.275143 AGACATGTGTTTGTTCCAACGA 58.725 40.909 1.15 0.00 0.00 3.85
4687 7782 3.692101 AGACATGTGTTTGTTCCAACGAA 59.308 39.130 1.15 0.00 0.00 3.85
4722 7817 1.135024 CATTGGCAAAATAGCGCTGGT 60.135 47.619 22.90 5.61 34.64 4.00
4738 7833 4.023707 GCGCTGGTCTTGAAATATGCTATT 60.024 41.667 0.00 0.00 0.00 1.73
4741 7836 5.766222 CTGGTCTTGAAATATGCTATTGGC 58.234 41.667 0.00 0.00 42.22 4.52
4753 7848 9.565090 AAATATGCTATTGGCGTGATATATCAT 57.435 29.630 18.18 4.28 45.43 2.45
4832 7927 6.757897 TTCAAGATATCAATGCGAAAACCT 57.242 33.333 5.32 0.00 0.00 3.50
4881 7978 5.215160 GGATGCCTAGCAAAACATATTTCG 58.785 41.667 0.00 0.00 43.62 3.46
4886 7983 7.990917 TGCCTAGCAAAACATATTTCGATTTA 58.009 30.769 0.00 0.00 34.76 1.40
4917 8014 7.609760 AGATCGCACAAAAATAAGATGTACA 57.390 32.000 0.00 0.00 0.00 2.90
4959 8056 0.537143 TTGACAGATGGGGCACACAC 60.537 55.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.577919 ACTGCAGGGAGGTAGTAATAGG 58.422 50.000 19.93 0.00 31.65 2.57
150 151 5.351740 GCTCAAGTGGAAATAACTCCAGTAC 59.648 44.000 0.48 0.00 46.54 2.73
285 313 8.060679 GTCAATTTGACTACAGATCATCGATTG 58.939 37.037 19.90 0.00 43.73 2.67
335 363 3.998341 TCGTAGGCATTAGGTTTGTGTTC 59.002 43.478 0.00 0.00 0.00 3.18
355 383 6.043327 TGCGTTATTTCATCAAATAGGTCG 57.957 37.500 0.00 1.47 36.13 4.79
384 412 1.097547 ATTGGCGACATGTGCTAGGC 61.098 55.000 1.15 4.94 42.32 3.93
416 444 1.897802 AGGGAAGTGTTTCGTCCGTAT 59.102 47.619 0.00 0.00 43.88 3.06
422 450 4.886579 ACGTTATAAGGGAAGTGTTTCGT 58.113 39.130 9.79 0.00 33.98 3.85
471 499 1.444895 CGGAACCTGCTGCATTTGC 60.445 57.895 1.31 4.20 42.50 3.68
923 959 2.203640 TGTCACTGCCCCGAGAGT 60.204 61.111 0.00 0.00 0.00 3.24
932 968 3.279116 TTGTGCGGCTGTCACTGC 61.279 61.111 17.24 0.00 42.55 4.40
1114 1150 3.319198 GTTGGTGAGGGAGCCGGA 61.319 66.667 5.05 0.00 0.00 5.14
1254 1291 1.841663 ATGTCGTGCGTGTGGCTTTC 61.842 55.000 0.00 0.00 44.05 2.62
1385 1430 1.413382 CTTCCATAGATCAGCGACGC 58.587 55.000 13.03 13.03 0.00 5.19
1398 1443 0.622665 CAGCCTTCCTGTCCTTCCAT 59.377 55.000 0.00 0.00 36.79 3.41
1456 1501 4.430007 TCGACAAATTATCCCGTCAGAAG 58.570 43.478 0.00 0.00 0.00 2.85
1462 1507 2.981859 AGCTCGACAAATTATCCCGT 57.018 45.000 0.00 0.00 0.00 5.28
1463 1508 2.724690 CGTAGCTCGACAAATTATCCCG 59.275 50.000 0.00 0.00 42.86 5.14
1464 1509 3.057734 CCGTAGCTCGACAAATTATCCC 58.942 50.000 7.07 0.00 42.86 3.85
1509 1554 0.108424 GCAAACAACCAGCACCAACA 60.108 50.000 0.00 0.00 0.00 3.33
1546 1591 0.251634 CCAGAAGGTCAGCCCTCTTC 59.748 60.000 0.00 0.00 45.47 2.87
1555 1600 1.596934 CTTAGCCGCCAGAAGGTCA 59.403 57.895 0.00 0.00 37.19 4.02
1582 1627 5.070180 AGTGAGGAATCAATGAGACATCGAT 59.930 40.000 0.00 0.00 0.00 3.59
1636 1690 2.161855 TGAGCAATTGACGGCATTTCT 58.838 42.857 10.34 0.00 0.00 2.52
1667 1721 2.088950 GCAAATGGCAAGCAACAGAT 57.911 45.000 0.00 0.00 43.97 2.90
1695 1756 7.471399 GCCTCTGAAAAAGGGAGTTTCATTTTA 60.471 37.037 0.45 0.00 42.49 1.52
1751 1813 2.005095 ATCTGGGCAGCCAACAGAT 58.995 52.632 21.63 21.63 44.27 2.90
1789 1902 6.886178 AACTAACTTAGGAAGGCCTTATGA 57.114 37.500 20.54 6.23 43.90 2.15
1868 1985 7.334171 AGTTTACAAAAGGTATACGCCGTATTT 59.666 33.333 15.77 1.28 38.49 1.40
1872 1989 4.389687 CAGTTTACAAAAGGTATACGCCGT 59.610 41.667 0.00 0.00 38.49 5.68
1876 1993 7.662604 AAGGACAGTTTACAAAAGGTATACG 57.337 36.000 0.00 0.00 38.49 3.06
1934 2052 1.706866 CATTGCCTCCTGGATATGGGA 59.293 52.381 0.00 0.00 34.57 4.37
2045 2166 3.135225 TGTATTTCACAACCACCGAGTG 58.865 45.455 0.00 0.00 32.95 3.51
2158 2482 5.984627 TCAAACCATGATAATAACGCATCG 58.015 37.500 0.00 0.00 31.50 3.84
2366 5226 6.520104 GCAACTTTTCTTCGCAAGTTATACTC 59.480 38.462 0.00 0.00 40.52 2.59
2681 5568 3.435890 GGCCCCATGCTACCACTTTAATA 60.436 47.826 0.00 0.00 40.92 0.98
2720 5609 2.368011 GGGACACTAGGGCCCACTC 61.368 68.421 27.56 10.05 41.64 3.51
2877 5817 5.062528 TCACAACACTGAATCATTGCTACA 58.937 37.500 0.24 0.00 0.00 2.74
3035 5975 1.946081 TCTGTGCAAAGCGTTTCATGA 59.054 42.857 0.00 0.00 0.00 3.07
3074 6014 7.822658 TGCATAGTTACTGGGAATTTGTAAAC 58.177 34.615 0.00 0.00 0.00 2.01
3182 6126 8.488668 AGGGATCCAAATAATTTTCATTTCCAG 58.511 33.333 15.23 0.00 0.00 3.86
3185 6129 8.197439 ACGAGGGATCCAAATAATTTTCATTTC 58.803 33.333 15.23 0.00 0.00 2.17
3202 6146 6.258068 CAGTCAAATACCTTTAACGAGGGATC 59.742 42.308 0.00 0.00 39.55 3.36
3241 6185 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
3242 6186 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
3259 6203 9.088512 CAATACTTTAGTGATCTAAACGCTCTT 57.911 33.333 0.00 0.00 40.05 2.85
3260 6204 8.467598 TCAATACTTTAGTGATCTAAACGCTCT 58.532 33.333 0.00 0.00 40.05 4.09
3261 6205 8.630278 TCAATACTTTAGTGATCTAAACGCTC 57.370 34.615 0.00 0.00 40.05 5.03
3262 6206 9.035607 CATCAATACTTTAGTGATCTAAACGCT 57.964 33.333 0.00 0.00 41.06 5.07
3263 6207 8.818057 ACATCAATACTTTAGTGATCTAAACGC 58.182 33.333 0.00 0.00 41.06 4.84
3269 6213 8.818057 GCGTTTACATCAATACTTTAGTGATCT 58.182 33.333 0.00 0.00 41.06 2.75
3270 6214 8.818057 AGCGTTTACATCAATACTTTAGTGATC 58.182 33.333 0.00 0.00 41.06 2.92
3271 6215 8.718102 AGCGTTTACATCAATACTTTAGTGAT 57.282 30.769 0.00 0.00 43.48 3.06
3272 6216 8.033038 AGAGCGTTTACATCAATACTTTAGTGA 58.967 33.333 0.00 0.00 37.18 3.41
3273 6217 8.186178 AGAGCGTTTACATCAATACTTTAGTG 57.814 34.615 0.00 0.00 0.00 2.74
3274 6218 8.773404 AAGAGCGTTTACATCAATACTTTAGT 57.227 30.769 0.00 0.00 0.00 2.24
3287 6231 8.810427 CCGTAAAGAAATATAAGAGCGTTTACA 58.190 33.333 0.00 0.00 31.53 2.41
3288 6232 9.023967 TCCGTAAAGAAATATAAGAGCGTTTAC 57.976 33.333 0.00 0.00 0.00 2.01
3289 6233 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
3290 6234 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
3291 6235 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
3292 6236 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
3293 6237 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
3294 6238 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3295 6239 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3296 6240 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3297 6241 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
3298 6242 8.636213 CAGTACTCCCTCCGTAAAGAAATATAA 58.364 37.037 0.00 0.00 0.00 0.98
3299 6243 8.000709 TCAGTACTCCCTCCGTAAAGAAATATA 58.999 37.037 0.00 0.00 0.00 0.86
3300 6244 6.837568 TCAGTACTCCCTCCGTAAAGAAATAT 59.162 38.462 0.00 0.00 0.00 1.28
3301 6245 6.189859 TCAGTACTCCCTCCGTAAAGAAATA 58.810 40.000 0.00 0.00 0.00 1.40
3302 6246 5.021458 TCAGTACTCCCTCCGTAAAGAAAT 58.979 41.667 0.00 0.00 0.00 2.17
3303 6247 4.410099 TCAGTACTCCCTCCGTAAAGAAA 58.590 43.478 0.00 0.00 0.00 2.52
3304 6248 4.038271 TCAGTACTCCCTCCGTAAAGAA 57.962 45.455 0.00 0.00 0.00 2.52
3305 6249 3.726557 TCAGTACTCCCTCCGTAAAGA 57.273 47.619 0.00 0.00 0.00 2.52
3306 6250 3.700038 ACATCAGTACTCCCTCCGTAAAG 59.300 47.826 0.00 0.00 0.00 1.85
3307 6251 3.705051 ACATCAGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 0.00 2.01
3308 6252 3.377253 ACATCAGTACTCCCTCCGTAA 57.623 47.619 0.00 0.00 0.00 3.18
3309 6253 3.021695 CAACATCAGTACTCCCTCCGTA 58.978 50.000 0.00 0.00 0.00 4.02
3310 6254 1.825474 CAACATCAGTACTCCCTCCGT 59.175 52.381 0.00 0.00 0.00 4.69
3311 6255 2.100197 TCAACATCAGTACTCCCTCCG 58.900 52.381 0.00 0.00 0.00 4.63
3312 6256 4.162320 TGAATCAACATCAGTACTCCCTCC 59.838 45.833 0.00 0.00 0.00 4.30
3313 6257 5.127845 TCTGAATCAACATCAGTACTCCCTC 59.872 44.000 0.00 0.00 43.77 4.30
3314 6258 5.026121 TCTGAATCAACATCAGTACTCCCT 58.974 41.667 0.00 0.00 43.77 4.20
3315 6259 5.344743 TCTGAATCAACATCAGTACTCCC 57.655 43.478 0.00 0.00 43.77 4.30
3316 6260 6.259608 CCAATCTGAATCAACATCAGTACTCC 59.740 42.308 0.00 0.00 43.77 3.85
3317 6261 7.010923 GTCCAATCTGAATCAACATCAGTACTC 59.989 40.741 0.00 0.00 43.77 2.59
3318 6262 6.820656 GTCCAATCTGAATCAACATCAGTACT 59.179 38.462 3.72 0.00 43.77 2.73
3319 6263 6.595326 TGTCCAATCTGAATCAACATCAGTAC 59.405 38.462 3.72 0.00 43.77 2.73
3320 6264 6.710278 TGTCCAATCTGAATCAACATCAGTA 58.290 36.000 3.72 0.00 43.77 2.74
3321 6265 5.563592 TGTCCAATCTGAATCAACATCAGT 58.436 37.500 3.72 0.00 43.77 3.41
3322 6266 6.505044 TTGTCCAATCTGAATCAACATCAG 57.495 37.500 0.00 0.00 44.53 2.90
3323 6267 7.470935 AATTGTCCAATCTGAATCAACATCA 57.529 32.000 0.00 0.00 0.00 3.07
3324 6268 7.816031 ACAAATTGTCCAATCTGAATCAACATC 59.184 33.333 0.56 0.00 0.00 3.06
3335 6279 5.797051 CAATTCCCACAAATTGTCCAATCT 58.203 37.500 0.00 0.00 40.28 2.40
3384 6329 2.472861 CGGCATATACTTCTGCGAAGTG 59.527 50.000 24.56 14.14 39.30 3.16
3483 6428 7.048512 ACTACACAATAGGAAAGTTATCCAGC 58.951 38.462 6.80 0.00 42.27 4.85
3666 6612 7.609097 AGAGAATTATATCAGAGCTCCAACA 57.391 36.000 10.93 0.00 0.00 3.33
3695 6641 2.024414 GACCCATGACTAACCAATGCC 58.976 52.381 0.00 0.00 0.00 4.40
3709 6655 5.393866 ACAAATGTTCCTAAACTGACCCAT 58.606 37.500 0.00 0.00 36.30 4.00
3713 6659 9.220767 AGAATAGACAAATGTTCCTAAACTGAC 57.779 33.333 0.00 0.00 36.30 3.51
3833 6781 7.067372 TCCAGCGAATGATCAAATAGAAAATGT 59.933 33.333 0.00 0.00 0.00 2.71
3870 6819 5.184096 TCACACAACACAAAGTTACAACCAT 59.816 36.000 0.00 0.00 38.74 3.55
3893 6842 2.143122 TCTTTGTCCTGTTGCACGATC 58.857 47.619 0.00 0.00 0.00 3.69
3897 6846 1.678101 AGCTTCTTTGTCCTGTTGCAC 59.322 47.619 0.00 0.00 0.00 4.57
3899 6848 1.000938 CCAGCTTCTTTGTCCTGTTGC 60.001 52.381 0.00 0.00 0.00 4.17
3999 6953 5.898397 AGTGGGGATACTAAAGGAGTTCTAC 59.102 44.000 0.00 0.00 39.81 2.59
4024 6978 6.561614 ACGACTATACACGAGAACATTTGAT 58.438 36.000 0.00 0.00 0.00 2.57
4138 7093 0.998226 CACAACCAAAGCATCGCACG 60.998 55.000 0.00 0.00 0.00 5.34
4157 7237 9.881649 AGTAGGTTTACTAGGCTTTATACAAAC 57.118 33.333 0.00 0.00 38.35 2.93
4168 7248 4.750598 GCTAATGCAGTAGGTTTACTAGGC 59.249 45.833 21.67 1.40 38.05 3.93
4253 7333 2.522185 ACTGATGCAGGTGAAAGCAAT 58.478 42.857 0.00 0.00 44.88 3.56
4292 7372 3.005155 GTGTTTTGCTGGAGATGCTCTTT 59.995 43.478 0.00 0.00 0.00 2.52
4376 7458 6.286758 AGGAAGTATATGAGAGTGCATGTTG 58.713 40.000 0.00 0.00 0.00 3.33
4395 7477 9.819267 AAGACTTATATTTAGGAACGAAGGAAG 57.181 33.333 0.00 0.00 0.00 3.46
4432 7519 9.895138 CATTCATCCATATGTAGTCCATATTCA 57.105 33.333 1.24 0.00 42.87 2.57
4433 7520 9.896645 ACATTCATCCATATGTAGTCCATATTC 57.103 33.333 1.24 0.00 42.87 1.75
4477 7564 4.050553 ACGGTGCAAAATGAGTGAATTTG 58.949 39.130 0.00 0.00 37.17 2.32
4478 7565 4.320608 ACGGTGCAAAATGAGTGAATTT 57.679 36.364 0.00 0.00 0.00 1.82
4480 7567 4.458989 ACATACGGTGCAAAATGAGTGAAT 59.541 37.500 0.00 0.00 0.00 2.57
4481 7568 3.818210 ACATACGGTGCAAAATGAGTGAA 59.182 39.130 0.00 0.00 0.00 3.18
4483 7570 3.829886 ACATACGGTGCAAAATGAGTG 57.170 42.857 0.00 0.00 0.00 3.51
4484 7571 4.575885 ACTACATACGGTGCAAAATGAGT 58.424 39.130 0.00 0.00 0.00 3.41
4485 7572 4.034048 GGACTACATACGGTGCAAAATGAG 59.966 45.833 0.00 0.00 0.00 2.90
4487 7574 3.687212 TGGACTACATACGGTGCAAAATG 59.313 43.478 0.00 0.00 31.30 2.32
4488 7575 3.945346 TGGACTACATACGGTGCAAAAT 58.055 40.909 0.00 0.00 31.30 1.82
4489 7576 3.404224 TGGACTACATACGGTGCAAAA 57.596 42.857 0.00 0.00 31.30 2.44
4491 7578 4.948341 ATATGGACTACATACGGTGCAA 57.052 40.909 0.00 0.00 44.41 4.08
4492 7579 4.948341 AATATGGACTACATACGGTGCA 57.052 40.909 0.00 0.00 44.41 4.57
4493 7580 6.263516 TCTAATATGGACTACATACGGTGC 57.736 41.667 0.00 0.00 44.41 5.01
4494 7581 8.740906 AGATTCTAATATGGACTACATACGGTG 58.259 37.037 0.00 0.00 44.41 4.94
4495 7582 8.880991 AGATTCTAATATGGACTACATACGGT 57.119 34.615 0.00 0.00 44.41 4.83
4496 7583 9.179909 AGAGATTCTAATATGGACTACATACGG 57.820 37.037 0.00 0.00 44.41 4.02
4528 7615 7.387643 ACTTCCTCTGTTCCTAAATACAAGTC 58.612 38.462 0.00 0.00 0.00 3.01
4562 7649 6.812160 ACCTTGCTTAGTTACGTGATCTTAAG 59.188 38.462 0.00 0.00 0.00 1.85
4652 7739 9.534565 ACAAACACATGTCTATATACATCTGAC 57.465 33.333 11.69 0.00 38.01 3.51
4703 7798 1.134946 GACCAGCGCTATTTTGCCAAT 59.865 47.619 10.99 0.00 0.00 3.16
4718 7813 5.561532 CGCCAATAGCATATTTCAAGACCAG 60.562 44.000 0.00 0.00 44.04 4.00
4722 7817 5.122519 TCACGCCAATAGCATATTTCAAGA 58.877 37.500 0.00 0.00 44.04 3.02
4738 7833 6.485648 ACGCTATAGTATGATATATCACGCCA 59.514 38.462 17.60 4.70 40.03 5.69
4741 7836 7.577107 AGCACGCTATAGTATGATATATCACG 58.423 38.462 17.60 15.12 40.03 4.35
4753 7848 9.923143 ATGTTTCATTAATAGCACGCTATAGTA 57.077 29.630 11.80 0.00 38.20 1.82
4754 7849 8.833231 ATGTTTCATTAATAGCACGCTATAGT 57.167 30.769 11.80 0.68 38.20 2.12
4801 7896 8.893219 TCGCATTGATATCTTGAAACTAGATT 57.107 30.769 3.98 0.00 34.35 2.40
4832 7927 9.619316 CAAATTATGAACTATTTTCACCGTTGA 57.381 29.630 0.00 0.00 0.00 3.18
4847 7944 5.772825 TGCTAGGCATCCAAATTATGAAC 57.227 39.130 0.00 0.00 31.71 3.18
4893 7990 7.334421 ACTGTACATCTTATTTTTGTGCGATCT 59.666 33.333 0.00 0.00 0.00 2.75
4909 8006 9.950496 ATAGAGTTTCATTTTCACTGTACATCT 57.050 29.630 0.00 0.00 0.00 2.90
4926 8023 9.442047 CCCCATCTGTCAATATTATAGAGTTTC 57.558 37.037 0.00 0.00 0.00 2.78
4937 8034 2.241941 TGTGTGCCCCATCTGTCAATAT 59.758 45.455 0.00 0.00 0.00 1.28
4940 8037 0.537143 GTGTGTGCCCCATCTGTCAA 60.537 55.000 0.00 0.00 0.00 3.18
4947 8044 1.688811 AATACCGTGTGTGCCCCAT 59.311 52.632 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.