Multiple sequence alignment - TraesCS7B01G287800

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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 TraesCS7B01G287800 chr7B 100.000 5888 0 0 1 5888 524030821 524036708 0.000000e+00 10874.0
1 TraesCS7B01G287800 chr7B 94.771 153 8 0 4752 4904 353327115 353327267 7.630000e-59 239.0
2 TraesCS7B01G287800 chr7B 86.567 201 18 4 4956 5150 353327271 353327468 4.620000e-51 213.0
3 TraesCS7B01G287800 chr7D 91.683 3018 135 37 1 2979 495691739 495694679 0.000000e+00 4076.0
4 TraesCS7B01G287800 chr7D 96.024 2465 72 14 2979 5431 495694721 495697171 0.000000e+00 3986.0
5 TraesCS7B01G287800 chr7D 95.711 443 19 0 5446 5888 495703857 495704299 0.000000e+00 713.0
6 TraesCS7B01G287800 chr7D 84.538 498 39 23 2416 2904 495693604 495694072 5.380000e-125 459.0
7 TraesCS7B01G287800 chr7D 82.258 496 48 24 1906 2370 495694115 495694601 5.530000e-105 392.0
8 TraesCS7B01G287800 chr7A 90.294 2452 136 37 1 2394 561577722 561580129 0.000000e+00 3116.0
9 TraesCS7B01G287800 chr7A 90.317 2148 119 40 3117 5243 561581034 561583113 0.000000e+00 2732.0
10 TraesCS7B01G287800 chr7A 92.500 600 32 8 5297 5888 561583126 561583720 0.000000e+00 846.0
11 TraesCS7B01G287800 chr7A 90.716 377 28 5 2475 2847 561580174 561580547 4.100000e-136 496.0
12 TraesCS7B01G287800 chr7A 82.530 498 50 16 2416 2903 561579636 561580106 2.560000e-108 403.0
13 TraesCS7B01G287800 chr7A 82.927 369 32 17 1969 2309 561580174 561580539 2.670000e-78 303.0
14 TraesCS7B01G287800 chr3A 85.822 663 48 17 3117 3773 616476023 616475401 0.000000e+00 662.0
15 TraesCS7B01G287800 chr3A 90.451 377 29 5 2475 2847 616477909 616477536 1.910000e-134 490.0
16 TraesCS7B01G287800 chr3A 82.842 373 33 18 1969 2313 616477909 616477540 7.410000e-79 305.0
17 TraesCS7B01G287800 chr3A 94.805 154 8 0 4752 4905 455229382 455229229 2.120000e-59 241.0
18 TraesCS7B01G287800 chr3A 83.085 201 17 7 4956 5150 455229226 455229037 3.650000e-37 167.0
19 TraesCS7B01G287800 chr3B 94.118 153 9 0 4752 4904 449168132 449167980 3.550000e-57 233.0
20 TraesCS7B01G287800 chr3B 87.065 201 17 4 4956 5150 449167976 449167779 9.930000e-53 219.0
21 TraesCS7B01G287800 chr3D 91.558 154 13 0 4751 4904 9423571 9423724 4.620000e-51 213.0
22 TraesCS7B01G287800 chr5A 86.070 201 18 5 4956 5150 85293534 85293338 2.150000e-49 207.0
23 TraesCS7B01G287800 chr5A 94.175 103 6 0 4802 4904 85293640 85293538 2.200000e-34 158.0
24 TraesCS7B01G287800 chr5D 81.176 255 39 5 5632 5886 413700950 413700705 4.650000e-46 196.0
25 TraesCS7B01G287800 chr4D 73.961 361 65 19 17 367 446426203 446426544 1.040000e-22 119.0
26 TraesCS7B01G287800 chr1D 88.889 63 7 0 17 79 420381153 420381091 1.760000e-10 78.7
27 TraesCS7B01G287800 chr4A 97.059 34 1 0 1459 1492 607309940 607309973 2.290000e-04 58.4


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 TraesCS7B01G287800 chr7B 524030821 524036708 5887 False 10874.000000 10874 100.000000 1 5888 1 chr7B.!!$F1 5887
1 TraesCS7B01G287800 chr7D 495691739 495697171 5432 False 2228.250000 4076 88.625750 1 5431 4 chr7D.!!$F2 5430
2 TraesCS7B01G287800 chr7A 561577722 561583720 5998 False 1316.000000 3116 88.214000 1 5888 6 chr7A.!!$F1 5887
3 TraesCS7B01G287800 chr3A 616475401 616477909 2508 True 485.666667 662 86.371667 1969 3773 3 chr3A.!!$R2 1804

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
682 701 0.259938 AGAACCAATGGATCCAGGCC 59.740 55.000 21.33 11.85 0.00 5.19 F
1205 1250 0.105811 ACCACCCCCTACGAGGTATC 60.106 60.000 0.00 0.00 33.52 2.24 F
1207 1252 1.038280 CACCCCCTACGAGGTATCAC 58.962 60.000 0.00 0.00 33.52 3.06 F
1284 1361 1.074951 CCCTAATCCCCGGATTGCC 59.925 63.158 17.54 0.00 43.75 4.52 F
2750 3309 0.173935 TCACACGTTGTCCTGTCGTT 59.826 50.000 0.00 0.00 35.62 3.85 F
3297 5116 4.666512 TCTCATGATCATAGATCCACGGA 58.333 43.478 8.15 0.00 0.00 4.69 F
3298 5117 5.267587 TCTCATGATCATAGATCCACGGAT 58.732 41.667 8.15 0.00 37.59 4.18 F
4678 6529 2.176792 GAAAGAAGGCCGCAAGCG 59.823 61.111 7.60 7.60 45.17 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1815 0.836606 TGAAGATAATGGCGGGCTGA 59.163 50.000 0.00 0.0 0.00 4.26 R
2206 2759 1.017177 TATGGCGCGACAGGACAAAC 61.017 55.000 23.88 0.0 0.00 2.93 R
2465 3022 2.761208 GACTGCTACTCTAAGAGGCCAA 59.239 50.000 5.01 0.0 33.35 4.52 R
3253 5072 1.530323 ATCGTTGGCACTAACAACCC 58.470 50.000 0.00 0.0 43.95 4.11 R
3810 5656 0.035152 AGATTGCAACATCCTCGCCA 60.035 50.000 0.00 0.0 0.00 5.69 R
4205 6053 0.588252 TTGCTTCTTTCACTGCGAGC 59.412 50.000 0.00 0.0 0.00 5.03 R
4684 6535 1.258445 GGTGACTGGAGACCCGATGT 61.258 60.000 0.00 0.0 34.29 3.06 R
5499 7369 1.377202 GGAGACCAGCGCCATGAAA 60.377 57.895 2.29 0.0 36.33 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 0.959372 GACGGAGAAGGAGGACGACA 60.959 60.000 0.00 0.00 0.00 4.35
81 82 0.961358 ACGGAGAAGGAGGACGACAG 60.961 60.000 0.00 0.00 0.00 3.51
153 154 3.117372 CCGTCGGCCACCTAGTAG 58.883 66.667 2.24 0.00 0.00 2.57
193 194 7.479553 GTTGAAAACGTCGTTAAATGTCATTC 58.520 34.615 11.70 9.18 36.92 2.67
219 220 5.955488 AGTCACTAATTATAGCGATGCGAT 58.045 37.500 0.00 0.00 31.96 4.58
229 230 3.056952 AGCGATGCGATGAATTTTGTC 57.943 42.857 0.00 0.00 0.00 3.18
233 234 1.916506 TGCGATGAATTTTGTCCCCA 58.083 45.000 0.00 0.00 0.00 4.96
234 235 2.242926 TGCGATGAATTTTGTCCCCAA 58.757 42.857 0.00 0.00 0.00 4.12
236 237 4.019858 TGCGATGAATTTTGTCCCCAATA 58.980 39.130 0.00 0.00 0.00 1.90
239 240 5.463061 GCGATGAATTTTGTCCCCAATAATG 59.537 40.000 0.00 0.00 0.00 1.90
253 254 8.520351 GTCCCCAATAATGGTTTTATAGTATGC 58.480 37.037 0.00 0.00 46.01 3.14
280 281 5.245075 TGAAGCGGATTTTGGTTCCTTTTAT 59.755 36.000 2.89 0.00 41.80 1.40
281 282 6.434652 TGAAGCGGATTTTGGTTCCTTTTATA 59.565 34.615 2.89 0.00 41.80 0.98
282 283 6.451064 AGCGGATTTTGGTTCCTTTTATAG 57.549 37.500 0.00 0.00 0.00 1.31
283 284 5.949952 AGCGGATTTTGGTTCCTTTTATAGT 59.050 36.000 0.00 0.00 0.00 2.12
284 285 6.436218 AGCGGATTTTGGTTCCTTTTATAGTT 59.564 34.615 0.00 0.00 0.00 2.24
285 286 7.039293 AGCGGATTTTGGTTCCTTTTATAGTTT 60.039 33.333 0.00 0.00 0.00 2.66
286 287 7.601130 GCGGATTTTGGTTCCTTTTATAGTTTT 59.399 33.333 0.00 0.00 0.00 2.43
345 357 3.189287 CGTTTGGTTGAGCTTAATCTGCT 59.811 43.478 2.89 0.00 44.24 4.24
368 380 8.192774 TGCTCCTGCATTATTAAAGAAAATGAG 58.807 33.333 0.00 0.00 45.31 2.90
371 383 9.685276 TCCTGCATTATTAAAGAAAATGAGAGA 57.315 29.630 0.00 0.00 33.38 3.10
372 384 9.947669 CCTGCATTATTAAAGAAAATGAGAGAG 57.052 33.333 0.00 0.00 33.38 3.20
412 426 2.565841 ACAAGAAGATATGAAGGCCGC 58.434 47.619 0.00 0.00 0.00 6.53
430 444 3.734031 CCGCGATATAACGACTCTGTAG 58.266 50.000 8.23 0.00 35.09 2.74
460 478 2.302952 CGCCACGGTCTGCATATCG 61.303 63.158 2.84 2.84 0.00 2.92
481 499 4.148174 TCGATATGAAACGCGCTTCATAAG 59.852 41.667 35.20 30.71 46.28 1.73
485 503 2.156891 TGAAACGCGCTTCATAAGTCAC 59.843 45.455 20.22 0.00 30.31 3.67
488 506 2.346803 ACGCGCTTCATAAGTCACATT 58.653 42.857 5.73 0.00 0.00 2.71
490 508 3.188460 ACGCGCTTCATAAGTCACATTTT 59.812 39.130 5.73 0.00 0.00 1.82
496 514 5.967674 GCTTCATAAGTCACATTTTGATCGG 59.032 40.000 0.00 0.00 36.32 4.18
518 536 3.614150 GCCATATGACGAATCCGCTAGAA 60.614 47.826 3.65 0.00 39.95 2.10
539 557 1.333177 TGCCCTAATTGCGGTGTTTT 58.667 45.000 0.00 0.00 0.00 2.43
540 558 1.689273 TGCCCTAATTGCGGTGTTTTT 59.311 42.857 0.00 0.00 0.00 1.94
541 559 2.891580 TGCCCTAATTGCGGTGTTTTTA 59.108 40.909 0.00 0.00 0.00 1.52
542 560 3.511934 TGCCCTAATTGCGGTGTTTTTAT 59.488 39.130 0.00 0.00 0.00 1.40
543 561 4.021016 TGCCCTAATTGCGGTGTTTTTATT 60.021 37.500 0.00 0.00 0.00 1.40
574 593 6.735694 GCCAAACACTCAAATGAGAGCTTTTA 60.736 38.462 16.93 0.00 44.74 1.52
599 618 4.998671 TTTGCCAAACACTCAAATGAGA 57.001 36.364 16.93 0.00 44.74 3.27
600 619 4.572985 TTGCCAAACACTCAAATGAGAG 57.427 40.909 16.93 11.42 44.74 3.20
601 620 2.294233 TGCCAAACACTCAAATGAGAGC 59.706 45.455 16.93 9.46 44.74 4.09
602 621 2.555757 GCCAAACACTCAAATGAGAGCT 59.444 45.455 16.93 0.00 44.74 4.09
603 622 3.753272 GCCAAACACTCAAATGAGAGCTA 59.247 43.478 16.93 0.00 44.74 3.32
604 623 4.142730 GCCAAACACTCAAATGAGAGCTAG 60.143 45.833 16.93 4.23 44.74 3.42
605 624 4.999950 CCAAACACTCAAATGAGAGCTAGT 59.000 41.667 16.93 4.85 44.74 2.57
606 625 5.106791 CCAAACACTCAAATGAGAGCTAGTG 60.107 44.000 16.93 7.33 44.74 2.74
607 626 5.474578 AACACTCAAATGAGAGCTAGTGA 57.525 39.130 16.93 0.00 44.74 3.41
608 627 4.815269 ACACTCAAATGAGAGCTAGTGAC 58.185 43.478 16.93 0.00 44.74 3.67
609 628 4.281941 ACACTCAAATGAGAGCTAGTGACA 59.718 41.667 16.93 0.00 44.74 3.58
610 629 5.046735 ACACTCAAATGAGAGCTAGTGACAT 60.047 40.000 16.93 1.40 44.74 3.06
658 677 5.975410 AGTCGAACACAAAAGAAGAAGAG 57.025 39.130 0.00 0.00 0.00 2.85
659 678 4.271291 AGTCGAACACAAAAGAAGAAGAGC 59.729 41.667 0.00 0.00 0.00 4.09
682 701 0.259938 AGAACCAATGGATCCAGGCC 59.740 55.000 21.33 11.85 0.00 5.19
687 706 2.087461 AATGGATCCAGGCCCCCTC 61.087 63.158 21.33 0.00 0.00 4.30
861 886 1.144057 CAATCCCTTCTCCCGTCCG 59.856 63.158 0.00 0.00 0.00 4.79
880 905 0.840617 GTCTTCCCTTCTCCATCCCC 59.159 60.000 0.00 0.00 0.00 4.81
945 986 3.798511 CTCGCCCCTCCTTTCCCC 61.799 72.222 0.00 0.00 0.00 4.81
1204 1249 0.398098 CACCACCCCCTACGAGGTAT 60.398 60.000 0.00 0.00 33.52 2.73
1205 1250 0.105811 ACCACCCCCTACGAGGTATC 60.106 60.000 0.00 0.00 33.52 2.24
1207 1252 1.038280 CACCCCCTACGAGGTATCAC 58.962 60.000 0.00 0.00 33.52 3.06
1212 1257 1.038280 CCTACGAGGTATCACCACCC 58.962 60.000 0.00 0.00 41.95 4.61
1213 1258 1.411216 CCTACGAGGTATCACCACCCT 60.411 57.143 0.00 0.00 41.95 4.34
1284 1361 1.074951 CCCTAATCCCCGGATTGCC 59.925 63.158 17.54 0.00 43.75 4.52
1285 1362 1.427072 CCCTAATCCCCGGATTGCCT 61.427 60.000 17.54 0.00 43.75 4.75
1502 1579 1.818959 GCAAGACCATGCTGGCCAAA 61.819 55.000 7.01 0.00 42.67 3.28
1656 1734 4.880120 CCTTCATGCTTCTAATCTTGCTCA 59.120 41.667 0.00 0.00 0.00 4.26
1676 1754 9.750125 TTGCTCAGTGTATATATCTGTTGTAAG 57.250 33.333 13.68 7.75 0.00 2.34
1737 1815 2.543777 TTAGTCTCGCCAACAAGCTT 57.456 45.000 0.00 0.00 0.00 3.74
1761 1839 2.936993 GCCCGCCATTATCTTCATCGAT 60.937 50.000 0.00 0.00 0.00 3.59
1954 2032 7.860373 TGAACAACGTTGTAAAGTAGTACGTAT 59.140 33.333 32.47 12.90 43.75 3.06
1976 2529 7.175293 CGTATTATCTTGGCCTCTTAGAGTAGT 59.825 40.741 3.32 0.00 0.00 2.73
2154 2707 3.365955 GCGCACGCACAATCAATG 58.634 55.556 10.65 0.00 41.49 2.82
2161 2714 3.677601 CACGCACAATCAATGATGAGTC 58.322 45.455 0.00 0.00 39.39 3.36
2178 2731 5.363979 TGAGTCGATGACATATAGCTGAC 57.636 43.478 0.00 0.00 34.60 3.51
2195 2748 1.926511 GACGCTTGTTGCATCCAGGG 61.927 60.000 10.32 10.32 43.06 4.45
2196 2749 2.575461 GCTTGTTGCATCCAGGGC 59.425 61.111 0.00 0.00 42.31 5.19
2234 2787 2.121538 TCGCGCCATAGAGCAGTCT 61.122 57.895 0.00 0.00 39.00 3.24
2264 2817 8.121305 ACAAAATGTACTCCTGATAATTTGCA 57.879 30.769 0.00 0.00 0.00 4.08
2366 2923 8.672823 TGAGGATTTACATGATTTCATCTCTG 57.327 34.615 0.00 0.00 33.61 3.35
2370 2927 8.557864 GGATTTACATGATTTCATCTCTGTCAG 58.442 37.037 0.00 0.00 33.61 3.51
2392 2949 8.822805 GTCAGATATATTACCCCATTAGAACCA 58.177 37.037 0.00 0.00 0.00 3.67
2397 2954 2.442236 ACCCCATTAGAACCATGCTG 57.558 50.000 0.00 0.00 0.00 4.41
2400 2957 1.685803 CCCATTAGAACCATGCTGGCA 60.686 52.381 0.00 0.00 42.67 4.92
2409 2966 2.041701 ACCATGCTGGCAAAAGAAACT 58.958 42.857 0.00 0.00 42.67 2.66
2643 3200 3.272334 CCAAGTCCTATGGCGCGC 61.272 66.667 25.94 25.94 0.00 6.86
2750 3309 0.173935 TCACACGTTGTCCTGTCGTT 59.826 50.000 0.00 0.00 35.62 3.85
2780 3341 4.765339 AGCAGTCCATTAACAAAAGGTACC 59.235 41.667 2.73 2.73 0.00 3.34
2890 3482 7.076842 AGTCCGTTGAAGATTTACATGATTG 57.923 36.000 0.00 0.00 0.00 2.67
3159 4977 9.829507 AACAAATTTGATGTCCAAGTTTATTGA 57.170 25.926 24.64 0.00 41.02 2.57
3253 5072 9.666626 CGTCTTACTTAGTAATCTACTGGATTG 57.333 37.037 5.21 0.00 43.68 2.67
3283 5102 4.965814 AGTGCCAACGATATTCTCATGAT 58.034 39.130 0.00 0.00 0.00 2.45
3284 5103 4.993584 AGTGCCAACGATATTCTCATGATC 59.006 41.667 0.00 0.00 0.00 2.92
3285 5104 4.751600 GTGCCAACGATATTCTCATGATCA 59.248 41.667 0.00 0.00 0.00 2.92
3286 5105 5.410746 GTGCCAACGATATTCTCATGATCAT 59.589 40.000 1.18 1.18 0.00 2.45
3287 5106 6.591448 GTGCCAACGATATTCTCATGATCATA 59.409 38.462 8.15 0.00 0.00 2.15
3288 5107 6.815142 TGCCAACGATATTCTCATGATCATAG 59.185 38.462 8.15 6.83 0.00 2.23
3289 5108 7.038048 GCCAACGATATTCTCATGATCATAGA 58.962 38.462 8.15 9.00 0.00 1.98
3290 5109 7.710044 GCCAACGATATTCTCATGATCATAGAT 59.290 37.037 8.15 0.00 0.00 1.98
3291 5110 9.247126 CCAACGATATTCTCATGATCATAGATC 57.753 37.037 8.15 4.46 0.00 2.75
3292 5111 9.247126 CAACGATATTCTCATGATCATAGATCC 57.753 37.037 8.15 2.33 0.00 3.36
3293 5112 8.530804 ACGATATTCTCATGATCATAGATCCA 57.469 34.615 8.15 0.00 0.00 3.41
3294 5113 8.412456 ACGATATTCTCATGATCATAGATCCAC 58.588 37.037 8.15 4.67 0.00 4.02
3295 5114 7.590689 CGATATTCTCATGATCATAGATCCACG 59.409 40.741 8.15 10.88 0.00 4.94
3296 5115 5.397142 TTCTCATGATCATAGATCCACGG 57.603 43.478 8.15 0.00 0.00 4.94
3297 5116 4.666512 TCTCATGATCATAGATCCACGGA 58.333 43.478 8.15 0.00 0.00 4.69
3298 5117 5.267587 TCTCATGATCATAGATCCACGGAT 58.732 41.667 8.15 0.00 37.59 4.18
3509 5352 7.143514 AGGAGTCTGTTAGTAGTTTACTTCG 57.856 40.000 0.00 0.00 40.14 3.79
3523 5366 9.189723 GTAGTTTACTTCGTGTTCTACATCTTT 57.810 33.333 0.00 0.00 32.29 2.52
3548 5391 8.023021 TGATATACTTGTCCTTGCTAGTCATT 57.977 34.615 0.00 0.00 0.00 2.57
3644 5488 7.482654 TGACACTCAGAATCTACTTTTGTTG 57.517 36.000 0.00 0.00 0.00 3.33
4205 6053 6.576185 CAGATATTTGAAATTGGGGTTCCTG 58.424 40.000 0.00 0.00 0.00 3.86
4418 6266 8.034058 AGCAAATGTGAGTATTCAGTACTTTC 57.966 34.615 0.00 0.00 43.66 2.62
4448 6296 7.238710 ACAGTGAATTAACTTCCCTTTGGTAT 58.761 34.615 0.00 0.00 32.49 2.73
4449 6297 7.728532 ACAGTGAATTAACTTCCCTTTGGTATT 59.271 33.333 0.00 0.00 32.49 1.89
4515 6363 6.033341 TGCATTTATGTTTGGATAGCGAAAC 58.967 36.000 11.16 11.16 41.39 2.78
4568 6419 9.454585 CGTAAGTTCCTCATTATGTATTCGTTA 57.545 33.333 0.00 0.00 0.00 3.18
4678 6529 2.176792 GAAAGAAGGCCGCAAGCG 59.823 61.111 7.60 7.60 45.17 4.68
4689 6540 4.505217 GCAAGCGGTGCGACATCG 62.505 66.667 7.93 7.93 45.10 3.84
4701 6552 1.313091 CGACATCGGGTCTCCAGTCA 61.313 60.000 6.58 0.00 44.68 3.41
4706 6557 1.908793 CGGGTCTCCAGTCACCTGT 60.909 63.158 0.00 0.00 36.95 4.00
4719 6570 3.716195 CCTGTGTGGATCCGGCCA 61.716 66.667 7.39 0.00 38.35 5.36
5021 6872 4.811555 TGTTTTGAGTTCCATCGTTCTG 57.188 40.909 0.00 0.00 0.00 3.02
5034 6885 3.961477 TCGTTCTGTGTGTGGAAAATG 57.039 42.857 0.00 0.00 0.00 2.32
5102 6959 9.291664 TGTAATTTTCGTTTTGGAACTTAACTG 57.708 29.630 0.00 0.00 33.51 3.16
5182 7042 5.379732 TTCCATGGTTCAAAAATACCGTC 57.620 39.130 12.58 0.00 37.23 4.79
5206 7066 8.066595 GTCCGTTCTTTTCATATCATCTGAATG 58.933 37.037 0.00 0.00 32.94 2.67
5221 7081 3.585289 TCTGAATGTTACTTGCACCCCTA 59.415 43.478 0.00 0.00 0.00 3.53
5224 7086 3.577805 ATGTTACTTGCACCCCTATCC 57.422 47.619 0.00 0.00 0.00 2.59
5234 7096 3.205056 TGCACCCCTATCCATTGAGATTT 59.795 43.478 0.00 0.00 0.00 2.17
5309 7171 5.180117 AGCATCAATACCATAAACGATCAGC 59.820 40.000 0.00 0.00 0.00 4.26
5319 7181 1.617755 AACGATCAGCGACGCTTGTG 61.618 55.000 21.97 10.66 44.57 3.33
5323 7185 1.724623 GATCAGCGACGCTTGTGTTTA 59.275 47.619 21.97 0.01 36.40 2.01
5324 7186 1.790755 TCAGCGACGCTTGTGTTTAT 58.209 45.000 21.97 0.00 36.40 1.40
5325 7187 2.139917 TCAGCGACGCTTGTGTTTATT 58.860 42.857 21.97 0.00 36.40 1.40
5338 7202 6.486253 TTGTGTTTATTAAGAGCTGCTGAG 57.514 37.500 7.01 0.00 0.00 3.35
5342 7206 7.036220 GTGTTTATTAAGAGCTGCTGAGTCTA 58.964 38.462 7.01 0.00 0.00 2.59
5408 7272 1.798223 TGAACGATTTGAGACGCTTGG 59.202 47.619 0.00 0.00 0.00 3.61
5409 7273 1.798813 GAACGATTTGAGACGCTTGGT 59.201 47.619 0.00 0.00 0.00 3.67
5410 7274 1.148310 ACGATTTGAGACGCTTGGTG 58.852 50.000 0.00 0.00 0.00 4.17
5411 7275 1.148310 CGATTTGAGACGCTTGGTGT 58.852 50.000 0.00 0.00 0.00 4.16
5412 7276 1.126846 CGATTTGAGACGCTTGGTGTC 59.873 52.381 3.39 3.39 42.60 3.67
5422 7286 0.610232 GCTTGGTGTCTTCCAGCCAT 60.610 55.000 0.00 0.00 40.95 4.40
5506 7376 2.443887 CCTGCTTGGTGTTTTCATGG 57.556 50.000 0.00 0.00 0.00 3.66
5514 7384 0.387239 GTGTTTTCATGGCGCTGGTC 60.387 55.000 7.64 0.00 0.00 4.02
5532 7402 1.761784 GTCTCCATCATGGACAGCTCT 59.238 52.381 0.66 0.00 42.67 4.09
5535 7405 2.169978 CTCCATCATGGACAGCTCTTGA 59.830 50.000 0.66 0.00 42.67 3.02
5619 7489 3.241530 AGCGGCTTCCTGGACACA 61.242 61.111 0.00 0.00 0.00 3.72
5621 7491 2.743718 CGGCTTCCTGGACACAGT 59.256 61.111 0.00 0.00 43.36 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.237761 GACACACGAGCGACTGTAGT 59.762 55.000 0.00 0.00 0.00 2.73
60 61 0.959372 GTCGTCCTCCTTCTCCGTCA 60.959 60.000 0.00 0.00 0.00 4.35
65 66 2.424246 CCTAACTGTCGTCCTCCTTCTC 59.576 54.545 0.00 0.00 0.00 2.87
68 69 2.041350 TCTCCTAACTGTCGTCCTCCTT 59.959 50.000 0.00 0.00 0.00 3.36
80 81 1.960953 GCCCTCGTCCTTCTCCTAACT 60.961 57.143 0.00 0.00 0.00 2.24
81 82 0.460722 GCCCTCGTCCTTCTCCTAAC 59.539 60.000 0.00 0.00 0.00 2.34
136 137 1.751927 ACTACTAGGTGGCCGACGG 60.752 63.158 10.29 10.29 0.00 4.79
153 154 5.447279 CGTTTTCAACCCATGCTATCTACAC 60.447 44.000 0.00 0.00 0.00 2.90
193 194 6.967199 TCGCATCGCTATAATTAGTGACTATG 59.033 38.462 0.00 0.00 45.25 2.23
211 212 2.541588 GGGGACAAAATTCATCGCATCG 60.542 50.000 0.00 0.00 0.00 3.84
236 237 7.862372 CGCTTCATTGCATACTATAAAACCATT 59.138 33.333 0.00 0.00 0.00 3.16
239 240 6.017440 TCCGCTTCATTGCATACTATAAAACC 60.017 38.462 0.00 0.00 0.00 3.27
253 254 3.056607 AGGAACCAAAATCCGCTTCATTG 60.057 43.478 0.00 0.00 42.03 2.82
345 357 9.685276 TCTCTCATTTTCTTTAATAATGCAGGA 57.315 29.630 0.00 0.00 31.08 3.86
368 380 9.868277 TGTTTATTTGATTTCTCTCTCTCTCTC 57.132 33.333 0.00 0.00 0.00 3.20
396 410 2.086054 ATCGCGGCCTTCATATCTTC 57.914 50.000 6.13 0.00 0.00 2.87
405 419 0.672342 AGTCGTTATATCGCGGCCTT 59.328 50.000 6.13 0.00 32.61 4.35
412 426 4.910456 GGCAACTACAGAGTCGTTATATCG 59.090 45.833 0.00 0.00 33.58 2.92
446 460 4.783764 TTCATATCGATATGCAGACCGT 57.216 40.909 31.84 2.35 39.90 4.83
460 478 5.051039 TGACTTATGAAGCGCGTTTCATATC 60.051 40.000 40.15 35.38 44.89 1.63
481 499 4.275689 TCATATGGCCGATCAAAATGTGAC 59.724 41.667 2.13 0.00 39.72 3.67
485 503 3.498018 TCGTCATATGGCCGATCAAAATG 59.502 43.478 12.44 0.00 0.00 2.32
488 506 2.900716 TCGTCATATGGCCGATCAAA 57.099 45.000 12.44 0.00 0.00 2.69
490 508 2.353704 GGATTCGTCATATGGCCGATCA 60.354 50.000 15.79 6.08 0.00 2.92
496 514 2.094700 TCTAGCGGATTCGTCATATGGC 60.095 50.000 2.13 0.00 38.89 4.40
518 536 1.555967 AACACCGCAATTAGGGCAAT 58.444 45.000 4.43 0.00 0.00 3.56
548 566 2.294233 GCTCTCATTTGAGTGTTTGGCA 59.706 45.455 7.42 0.00 42.60 4.92
551 569 8.807667 AATAAAAGCTCTCATTTGAGTGTTTG 57.192 30.769 10.94 0.29 42.60 2.93
580 599 2.294233 GCTCTCATTTGAGTGTTTGGCA 59.706 45.455 7.42 0.00 42.60 4.92
581 600 2.555757 AGCTCTCATTTGAGTGTTTGGC 59.444 45.455 7.42 4.61 42.60 4.52
583 602 5.698089 TCACTAGCTCTCATTTGAGTGTTTG 59.302 40.000 7.42 6.86 42.60 2.93
586 605 4.281941 TGTCACTAGCTCTCATTTGAGTGT 59.718 41.667 7.42 0.41 42.60 3.55
587 606 4.814147 TGTCACTAGCTCTCATTTGAGTG 58.186 43.478 7.42 6.40 42.60 3.51
588 607 5.421693 AGATGTCACTAGCTCTCATTTGAGT 59.578 40.000 7.42 0.00 42.60 3.41
589 608 5.904941 AGATGTCACTAGCTCTCATTTGAG 58.095 41.667 0.97 0.97 43.36 3.02
590 609 5.420104 TGAGATGTCACTAGCTCTCATTTGA 59.580 40.000 0.00 0.00 39.25 2.69
591 610 5.658468 TGAGATGTCACTAGCTCTCATTTG 58.342 41.667 0.00 0.00 39.25 2.32
592 611 5.929058 TGAGATGTCACTAGCTCTCATTT 57.071 39.130 0.00 0.00 39.25 2.32
593 612 5.929058 TTGAGATGTCACTAGCTCTCATT 57.071 39.130 4.36 0.00 42.57 2.57
594 613 5.929058 TTTGAGATGTCACTAGCTCTCAT 57.071 39.130 4.36 1.78 42.57 2.90
595 614 5.420104 TCATTTGAGATGTCACTAGCTCTCA 59.580 40.000 0.00 0.00 41.65 3.27
596 615 5.900425 TCATTTGAGATGTCACTAGCTCTC 58.100 41.667 0.00 0.00 35.72 3.20
597 616 5.655974 TCTCATTTGAGATGTCACTAGCTCT 59.344 40.000 6.17 0.00 45.48 4.09
598 617 5.900425 TCTCATTTGAGATGTCACTAGCTC 58.100 41.667 6.17 0.00 45.48 4.09
599 618 5.929058 TCTCATTTGAGATGTCACTAGCT 57.071 39.130 6.17 0.00 45.48 3.32
658 677 3.368739 CCTGGATCCATTGGTTCTTTTGC 60.369 47.826 16.63 0.00 0.00 3.68
659 678 3.368739 GCCTGGATCCATTGGTTCTTTTG 60.369 47.826 16.63 0.00 0.00 2.44
861 886 0.840617 GGGGATGGAGAAGGGAAGAC 59.159 60.000 0.00 0.00 0.00 3.01
880 905 0.601558 TCGTTCGTTGAGGAAGGGAG 59.398 55.000 6.37 0.00 33.74 4.30
945 986 4.697756 TCGTTGCTTGCGGGGGAG 62.698 66.667 0.00 0.00 0.00 4.30
1204 1249 1.580059 GAATGGGTAGAGGGTGGTGA 58.420 55.000 0.00 0.00 0.00 4.02
1205 1250 0.546598 GGAATGGGTAGAGGGTGGTG 59.453 60.000 0.00 0.00 0.00 4.17
1207 1252 1.295020 TTGGAATGGGTAGAGGGTGG 58.705 55.000 0.00 0.00 0.00 4.61
1212 1257 4.141181 TGGATTGGATTGGAATGGGTAGAG 60.141 45.833 0.00 0.00 0.00 2.43
1213 1258 3.790976 TGGATTGGATTGGAATGGGTAGA 59.209 43.478 0.00 0.00 0.00 2.59
1284 1361 0.098200 CACGCAATCACATCCTGCAG 59.902 55.000 6.78 6.78 35.78 4.41
1285 1362 1.925415 GCACGCAATCACATCCTGCA 61.925 55.000 0.00 0.00 35.78 4.41
1502 1579 2.586792 GACTCCTTGGCGATGGCT 59.413 61.111 0.00 0.00 39.81 4.75
1638 1715 4.841422 ACACTGAGCAAGATTAGAAGCAT 58.159 39.130 0.00 0.00 0.00 3.79
1656 1734 9.094578 AGCATCCTTACAACAGATATATACACT 57.905 33.333 0.00 0.00 0.00 3.55
1676 1754 5.182001 ACAGAGTTACACAAAATGAGCATCC 59.818 40.000 0.00 0.00 0.00 3.51
1737 1815 0.836606 TGAAGATAATGGCGGGCTGA 59.163 50.000 0.00 0.00 0.00 4.26
1761 1839 4.349636 TGTCCCAAGAAACTATCAACCTCA 59.650 41.667 0.00 0.00 0.00 3.86
1928 2006 6.033341 ACGTACTACTTTACAACGTTGTTCA 58.967 36.000 36.26 21.75 43.63 3.18
1954 2032 9.080097 GATTACTACTCTAAGAGGCCAAGATAA 57.920 37.037 5.01 0.00 33.35 1.75
2081 2634 7.581241 CGCGTTATGATTGTCGTTTGTTAATAT 59.419 33.333 0.00 0.00 0.00 1.28
2148 2701 7.705752 GCTATATGTCATCGACTCATCATTGAT 59.294 37.037 0.00 0.00 33.15 2.57
2154 2707 6.027131 GTCAGCTATATGTCATCGACTCATC 58.973 44.000 0.00 0.00 33.15 2.92
2206 2759 1.017177 TATGGCGCGACAGGACAAAC 61.017 55.000 23.88 0.00 0.00 2.93
2366 2923 8.822805 TGGTTCTAATGGGGTAATATATCTGAC 58.177 37.037 0.00 0.00 0.00 3.51
2370 2927 8.275040 AGCATGGTTCTAATGGGGTAATATATC 58.725 37.037 0.00 0.00 0.00 1.63
2446 3003 8.276453 AGGCCAAGATACCACTACTTTATAAT 57.724 34.615 5.01 0.00 0.00 1.28
2465 3022 2.761208 GACTGCTACTCTAAGAGGCCAA 59.239 50.000 5.01 0.00 33.35 4.52
2643 3200 3.939837 ATCGCGTGGCAGACTGTGG 62.940 63.158 5.77 0.00 0.00 4.17
2750 3309 5.692115 TTGTTAATGGACTGCTCTATGGA 57.308 39.130 0.00 0.00 0.00 3.41
2780 3341 3.885297 CTGTAGGGTGCAAATTATCAGGG 59.115 47.826 0.00 0.00 0.00 4.45
3159 4977 9.233232 GAACGACACTTTTATGAAGTCAATTTT 57.767 29.630 0.00 0.00 0.00 1.82
3216 5035 8.693625 ATTACTAAGTAAGACGAAAGTAGGCAT 58.306 33.333 0.00 0.00 35.43 4.40
3253 5072 1.530323 ATCGTTGGCACTAACAACCC 58.470 50.000 0.00 0.00 43.95 4.11
3289 5108 5.946942 ATTATATGAGCAGATCCGTGGAT 57.053 39.130 0.00 0.00 37.59 3.41
3290 5109 5.745312 AATTATATGAGCAGATCCGTGGA 57.255 39.130 0.00 0.00 0.00 4.02
3291 5110 5.702670 ACAAATTATATGAGCAGATCCGTGG 59.297 40.000 0.00 0.00 0.00 4.94
3292 5111 6.791887 ACAAATTATATGAGCAGATCCGTG 57.208 37.500 0.00 0.00 0.00 4.94
3293 5112 8.314021 TCATACAAATTATATGAGCAGATCCGT 58.686 33.333 7.82 0.00 34.77 4.69
3294 5113 8.598924 GTCATACAAATTATATGAGCAGATCCG 58.401 37.037 10.99 0.00 39.22 4.18
3295 5114 9.440773 TGTCATACAAATTATATGAGCAGATCC 57.559 33.333 10.99 2.03 39.22 3.36
3297 5116 9.224267 GGTGTCATACAAATTATATGAGCAGAT 57.776 33.333 10.99 0.00 39.22 2.90
3298 5117 8.432013 AGGTGTCATACAAATTATATGAGCAGA 58.568 33.333 10.99 0.00 39.22 4.26
3299 5118 8.501580 CAGGTGTCATACAAATTATATGAGCAG 58.498 37.037 10.99 3.82 39.22 4.24
3300 5119 7.445096 CCAGGTGTCATACAAATTATATGAGCA 59.555 37.037 10.99 9.78 39.22 4.26
3301 5120 7.661437 TCCAGGTGTCATACAAATTATATGAGC 59.339 37.037 10.99 8.20 39.22 4.26
3302 5121 9.730705 ATCCAGGTGTCATACAAATTATATGAG 57.269 33.333 10.99 2.56 39.22 2.90
3461 5304 5.798132 TGTCTGCTCATTTAGTTCTCACAT 58.202 37.500 0.00 0.00 0.00 3.21
3523 5366 7.603180 ATGACTAGCAAGGACAAGTATATCA 57.397 36.000 0.00 0.00 0.00 2.15
3548 5391 3.892284 TGTTAAAAGCACCTCACCTCAA 58.108 40.909 0.00 0.00 0.00 3.02
3644 5488 6.672147 AGCAACACAGAAAGAAATACATGTC 58.328 36.000 0.00 0.00 0.00 3.06
3810 5656 0.035152 AGATTGCAACATCCTCGCCA 60.035 50.000 0.00 0.00 0.00 5.69
3858 5704 8.943002 GTTTACATGTATAGCCACAACTACTTT 58.057 33.333 6.36 0.00 30.84 2.66
3955 5802 4.261578 ACTGGGCATCAGAACAAATTTG 57.738 40.909 16.67 16.67 46.18 2.32
4205 6053 0.588252 TTGCTTCTTTCACTGCGAGC 59.412 50.000 0.00 0.00 0.00 5.03
4541 6392 6.420008 ACGAATACATAATGAGGAACTTACGC 59.580 38.462 0.00 0.00 41.55 4.42
4568 6419 5.652452 AGTTACAAGCAAAAAGGTCAGAACT 59.348 36.000 0.00 0.00 0.00 3.01
4684 6535 1.258445 GGTGACTGGAGACCCGATGT 61.258 60.000 0.00 0.00 34.29 3.06
4686 6537 1.388531 AGGTGACTGGAGACCCGAT 59.611 57.895 0.00 0.00 41.13 4.18
4701 6552 3.717294 GGCCGGATCCACACAGGT 61.717 66.667 13.41 0.00 39.02 4.00
4728 6579 2.480416 GCTCTGTACCTGGTCATCTTCG 60.480 54.545 0.63 0.00 0.00 3.79
5021 6872 4.874970 AGAATTCTGCATTTTCCACACAC 58.125 39.130 7.30 0.00 0.00 3.82
5102 6959 7.052873 TGTATAGAGTCTGTCTACCCTACAAC 58.947 42.308 1.86 0.00 40.76 3.32
5182 7042 7.923888 ACATTCAGATGATATGAAAAGAACGG 58.076 34.615 6.58 0.00 39.92 4.44
5206 7066 3.577805 ATGGATAGGGGTGCAAGTAAC 57.422 47.619 0.00 0.00 0.00 2.50
5249 7111 2.951475 AAAACACGGCGCTTCTCCCA 62.951 55.000 6.90 0.00 0.00 4.37
5309 7171 4.091509 AGCTCTTAATAAACACAAGCGTCG 59.908 41.667 0.00 0.00 33.62 5.12
5319 7181 7.923344 TGATAGACTCAGCAGCTCTTAATAAAC 59.077 37.037 0.00 0.00 0.00 2.01
5323 7185 6.088016 CTGATAGACTCAGCAGCTCTTAAT 57.912 41.667 0.00 0.00 44.73 1.40
5324 7186 5.512753 CTGATAGACTCAGCAGCTCTTAA 57.487 43.478 0.00 0.00 44.73 1.85
5356 7220 0.957395 CATGAAGACGCCAAGCAGGT 60.957 55.000 0.00 0.00 40.61 4.00
5366 7230 1.577328 AAACCAGCGCCATGAAGACG 61.577 55.000 2.29 0.00 0.00 4.18
5411 7275 7.522073 GCGATTAATTAATTCATGGCTGGAAGA 60.522 37.037 17.27 0.00 34.07 2.87
5412 7276 6.583806 GCGATTAATTAATTCATGGCTGGAAG 59.416 38.462 17.27 0.00 0.00 3.46
5450 7314 2.242564 CGTGATACGATACGATGCCAG 58.757 52.381 0.00 0.00 46.05 4.85
5499 7369 1.377202 GGAGACCAGCGCCATGAAA 60.377 57.895 2.29 0.00 36.33 2.69
5506 7376 1.890979 CCATGATGGAGACCAGCGC 60.891 63.158 5.27 0.00 43.67 5.92
5532 7402 3.072915 TCAAGGGCATTTCTCTGTCTCAA 59.927 43.478 0.00 0.00 0.00 3.02
5535 7405 2.617532 GCTCAAGGGCATTTCTCTGTCT 60.618 50.000 0.00 0.00 0.00 3.41
5619 7489 2.418910 CGAGGAGATCCACGCCACT 61.419 63.158 5.78 0.00 42.60 4.00
5851 7721 4.681978 GGACAGCTTCGCCCACGT 62.682 66.667 0.00 0.00 41.18 4.49


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

AutoCloner maintained by Alex Coulton.