Multiple sequence alignment - TraesCS5B01G380200

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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 TraesCS5B01G380200 chr5B 100.000 3894 0 0 1 3894 558123454 558119561 0.000000e+00 7191.0
1 TraesCS5B01G380200 chr5B 87.333 150 11 7 472 620 609842080 609841938 8.660000e-37 165.0
2 TraesCS5B01G380200 chr5B 85.333 150 14 7 472 620 40777992 40778134 8.720000e-32 148.0
3 TraesCS5B01G380200 chr5B 82.500 160 16 6 2346 2496 59926605 59926449 3.160000e-26 130.0
4 TraesCS5B01G380200 chr5D 89.565 1495 64 35 2175 3603 456342081 456340613 0.000000e+00 1812.0
5 TraesCS5B01G380200 chr5D 88.351 1528 90 47 1 1504 456344301 456342838 0.000000e+00 1755.0
6 TraesCS5B01G380200 chr5D 93.729 606 35 1 1512 2117 456342719 456342117 0.000000e+00 905.0
7 TraesCS5B01G380200 chr5D 95.114 307 13 2 3588 3894 456340596 456340292 2.100000e-132 483.0
8 TraesCS5B01G380200 chr5D 81.250 160 18 8 2346 2496 56951441 56951285 6.830000e-23 119.0
9 TraesCS5B01G380200 chr5A 88.252 1396 102 28 153 1520 574199809 574198448 0.000000e+00 1613.0
10 TraesCS5B01G380200 chr5A 86.807 902 81 27 2132 3017 574197757 574196878 0.000000e+00 972.0
11 TraesCS5B01G380200 chr5A 93.729 606 26 5 1512 2117 574198333 574197740 0.000000e+00 898.0
12 TraesCS5B01G380200 chr5A 85.762 302 27 7 3595 3894 574196081 574195794 4.890000e-79 305.0
13 TraesCS5B01G380200 chr3D 88.571 140 9 7 481 620 305658044 305657912 3.110000e-36 163.0
14 TraesCS5B01G380200 chrUn 86.667 150 12 7 472 620 86895451 86895309 4.030000e-35 159.0
15 TraesCS5B01G380200 chrUn 86.667 150 12 7 472 620 281871757 281871899 4.030000e-35 159.0
16 TraesCS5B01G380200 chr7A 86.093 151 12 8 472 620 626324356 626324499 1.870000e-33 154.0
17 TraesCS5B01G380200 chr7A 97.368 38 1 0 2032 2069 81632766 81632803 9.030000e-07 65.8
18 TraesCS5B01G380200 chr7A 84.746 59 9 0 2344 2402 100623911 100623853 4.200000e-05 60.2
19 TraesCS5B01G380200 chr2A 84.667 150 17 5 472 620 593316053 593316197 1.130000e-30 145.0
20 TraesCS5B01G380200 chr6A 100.000 37 0 0 2032 2068 254936428 254936464 6.980000e-08 69.4
21 TraesCS5B01G380200 chr6A 100.000 32 0 0 2032 2063 596750197 596750166 4.200000e-05 60.2
22 TraesCS5B01G380200 chr7D 97.368 38 1 0 2032 2069 78190279 78190316 9.030000e-07 65.8
23 TraesCS5B01G380200 chr7D 87.755 49 6 0 2345 2393 98383688 98383640 1.510000e-04 58.4
24 TraesCS5B01G380200 chr7B 97.297 37 1 0 2032 2068 25587851 25587887 3.250000e-06 63.9
25 TraesCS5B01G380200 chr7B 84.746 59 9 0 2344 2402 52923698 52923640 4.200000e-05 60.2
26 TraesCS5B01G380200 chr6D 100.000 32 0 0 2032 2063 451111124 451111093 4.200000e-05 60.2
27 TraesCS5B01G380200 chr6B 100.000 32 0 0 2032 2063 685201615 685201584 4.200000e-05 60.2


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 TraesCS5B01G380200 chr5B 558119561 558123454 3893 True 7191.00 7191 100.00000 1 3894 1 chr5B.!!$R2 3893
1 TraesCS5B01G380200 chr5D 456340292 456344301 4009 True 1238.75 1812 91.68975 1 3894 4 chr5D.!!$R2 3893
2 TraesCS5B01G380200 chr5A 574195794 574199809 4015 True 947.00 1613 88.63750 153 3894 4 chr5A.!!$R1 3741

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
124 137 0.263172 TAGCCTCTCCTCCCTCCAAG 59.737 60.0 0.00 0.0 0.00 3.61 F
138 151 0.326264 TCCAAGCCAAGAAGAGAGCC 59.674 55.0 0.00 0.0 0.00 4.70 F
713 741 0.394899 CATTGGCCTCCCTGTTCCTC 60.395 60.0 3.32 0.0 0.00 3.71 F
738 766 0.533951 GCATAGCCCAGCTGCTTTTT 59.466 50.0 8.66 0.0 42.75 1.94 F
2218 2419 0.458543 TCAACGAGAAGATGCGAGCC 60.459 55.0 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1755 0.178973 TGGACGAGGTCTGACTGGAA 60.179 55.0 7.85 0.00 32.47 3.53 R
1775 1963 0.525761 GCCTCTGGCGTTTGCATTTA 59.474 50.0 0.00 0.00 45.35 1.40 R
2218 2419 0.179034 GGGGTATGAGCTCTTGCAGG 60.179 60.0 16.19 0.00 42.74 4.85 R
2273 2477 0.675633 AACTGGTACGTACGTTGGCT 59.324 50.0 27.92 2.98 0.00 4.75 R
3289 3600 0.108186 TCTGGTCGCAATGGCAGTAG 60.108 55.0 0.00 0.00 41.24 2.57 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
112 113 1.623625 CTCCCCCTCACTAGCCTCT 59.376 63.158 0.00 0.00 0.00 3.69
124 137 0.263172 TAGCCTCTCCTCCCTCCAAG 59.737 60.000 0.00 0.00 0.00 3.61
125 138 2.741055 GCCTCTCCTCCCTCCAAGC 61.741 68.421 0.00 0.00 0.00 4.01
135 148 0.987294 CCCTCCAAGCCAAGAAGAGA 59.013 55.000 0.00 0.00 0.00 3.10
136 149 1.065564 CCCTCCAAGCCAAGAAGAGAG 60.066 57.143 0.00 0.00 0.00 3.20
138 151 0.326264 TCCAAGCCAAGAAGAGAGCC 59.674 55.000 0.00 0.00 0.00 4.70
139 152 1.023513 CCAAGCCAAGAAGAGAGCCG 61.024 60.000 0.00 0.00 0.00 5.52
140 153 1.376553 AAGCCAAGAAGAGAGCCGC 60.377 57.895 0.00 0.00 0.00 6.53
141 154 3.191539 GCCAAGAAGAGAGCCGCG 61.192 66.667 0.00 0.00 0.00 6.46
142 155 2.510238 CCAAGAAGAGAGCCGCGG 60.510 66.667 24.05 24.05 0.00 6.46
143 156 3.191539 CAAGAAGAGAGCCGCGGC 61.192 66.667 42.34 42.34 42.33 6.53
144 157 4.459089 AAGAAGAGAGCCGCGGCC 62.459 66.667 44.47 34.01 43.17 6.13
166 179 2.025767 CTGACTGAGCATCCTCCCGG 62.026 65.000 0.00 0.00 37.29 5.73
199 212 2.110967 CCGGTGCTGGATCTTGCAG 61.111 63.158 12.12 3.68 40.06 4.41
219 232 2.706190 AGCCAGACTGGTTAGTTCTTGT 59.294 45.455 22.58 0.00 40.46 3.16
220 233 3.136626 AGCCAGACTGGTTAGTTCTTGTT 59.863 43.478 22.58 0.00 40.46 2.83
221 234 3.498777 GCCAGACTGGTTAGTTCTTGTTC 59.501 47.826 22.58 0.00 40.46 3.18
222 235 4.743955 GCCAGACTGGTTAGTTCTTGTTCT 60.744 45.833 22.58 0.00 40.46 3.01
237 253 1.679977 TTCTTCCATGGCTGCTGGC 60.680 57.895 6.96 10.40 40.90 4.85
240 256 2.831894 CTTCCATGGCTGCTGGCTCA 62.832 60.000 17.87 7.16 41.46 4.26
267 283 2.555199 CCCTCTGCTTTCTCATTACGG 58.445 52.381 0.00 0.00 0.00 4.02
280 296 5.183228 TCTCATTACGGTTCTCCAAAATCC 58.817 41.667 0.00 0.00 0.00 3.01
304 320 2.161609 GTCCCTAATGCGTGTTTTCCAG 59.838 50.000 0.00 0.00 0.00 3.86
332 348 4.984295 TCTGAAACCTGATGTGGATTTCA 58.016 39.130 0.00 0.00 36.15 2.69
335 351 3.524095 AACCTGATGTGGATTTCACCA 57.476 42.857 0.00 0.00 45.48 4.17
345 361 4.169059 TGGATTTCACCATATCCACTGG 57.831 45.455 0.00 0.00 44.04 4.00
355 371 2.973694 TATCCACTGGTCTTAACGGC 57.026 50.000 0.00 0.00 0.00 5.68
380 396 9.884465 GCATAATCCTAGTTTTTATACTGCTTG 57.116 33.333 0.00 0.00 0.00 4.01
410 426 6.239036 GCTTCCAGGTCTTTGTAAATCACTTT 60.239 38.462 0.00 0.00 0.00 2.66
417 433 8.406297 AGGTCTTTGTAAATCACTTTTCTGAAC 58.594 33.333 0.00 0.00 0.00 3.18
443 468 9.760077 CCTCTTCGCTTTTCCTATAAAATACTA 57.240 33.333 0.00 0.00 0.00 1.82
445 470 9.538508 TCTTCGCTTTTCCTATAAAATACTACC 57.461 33.333 0.00 0.00 0.00 3.18
471 496 8.627208 TCTTCTCAGCATCTTAACAGAAAAAT 57.373 30.769 0.00 0.00 30.76 1.82
472 497 9.725019 TCTTCTCAGCATCTTAACAGAAAAATA 57.275 29.630 0.00 0.00 30.76 1.40
583 611 4.265893 TGTGAAGCCTTTTCACTGTGTTA 58.734 39.130 17.74 0.00 46.53 2.41
713 741 0.394899 CATTGGCCTCCCTGTTCCTC 60.395 60.000 3.32 0.00 0.00 3.71
714 742 0.846427 ATTGGCCTCCCTGTTCCTCA 60.846 55.000 3.32 0.00 0.00 3.86
738 766 0.533951 GCATAGCCCAGCTGCTTTTT 59.466 50.000 8.66 0.00 42.75 1.94
826 863 8.680039 TTTTTAGAACTATCGGAGGTTCAAAA 57.320 30.769 20.68 19.37 42.76 2.44
884 923 1.341285 ACATGCCCTGCTTGCTTCATA 60.341 47.619 0.00 0.00 37.23 2.15
887 926 1.341285 TGCCCTGCTTGCTTCATATGT 60.341 47.619 1.90 0.00 0.00 2.29
922 961 1.679977 GCTGCAGGATCCTTGGCAA 60.680 57.895 23.04 10.65 35.59 4.52
936 975 2.818130 TGGCAAGAGGCACATTTTTC 57.182 45.000 0.00 0.00 46.46 2.29
1001 1042 1.213275 CCGCATGCACATGAAGCAA 59.787 52.632 19.57 5.84 46.27 3.91
1002 1043 0.800683 CCGCATGCACATGAAGCAAG 60.801 55.000 19.57 15.66 46.27 4.01
1019 1060 3.505293 AGCAAGGTTTCTCAGCTGATTTC 59.495 43.478 18.63 8.19 34.43 2.17
1153 1203 0.826062 CAGATTGGGGAAACATGGGC 59.174 55.000 0.00 0.00 0.00 5.36
1177 1227 2.852075 TCCAGGCCACTCGGGTTT 60.852 61.111 5.01 0.00 39.65 3.27
1205 1255 3.690628 TGAATCTTGATCGCTTGATGCAA 59.309 39.130 0.00 0.00 43.06 4.08
1210 1260 1.944709 TGATCGCTTGATGCAATGGAG 59.055 47.619 0.00 0.00 43.06 3.86
1219 1269 2.296752 TGATGCAATGGAGTTTGTGGTG 59.703 45.455 0.00 0.00 0.00 4.17
1221 1271 1.680735 TGCAATGGAGTTTGTGGTGTC 59.319 47.619 0.00 0.00 0.00 3.67
1250 1305 3.129287 GCGTTACAGGCTAGTACTGGTTA 59.871 47.826 17.20 3.36 40.23 2.85
1268 1323 5.761165 GGTTACTGACCTTTTTGTGCTTA 57.239 39.130 0.00 0.00 45.55 3.09
1273 1328 8.752254 GTTACTGACCTTTTTGTGCTTAATTTC 58.248 33.333 0.00 0.00 0.00 2.17
1284 1346 1.468054 GCTTAATTTCGTGGCTGCAGG 60.468 52.381 17.12 0.00 0.00 4.85
1434 1496 3.047877 CTGTGGTTCCCGTTCGCC 61.048 66.667 0.00 0.00 0.00 5.54
1482 1544 0.541998 TCCAGGACCTCTTCTGCGAA 60.542 55.000 0.00 0.00 0.00 4.70
1868 2056 2.431942 CGTCACCGCCACTACCAC 60.432 66.667 0.00 0.00 0.00 4.16
1869 2057 2.047560 GTCACCGCCACTACCACC 60.048 66.667 0.00 0.00 0.00 4.61
1870 2058 2.524640 TCACCGCCACTACCACCA 60.525 61.111 0.00 0.00 0.00 4.17
1918 2106 2.669569 GCAACCGGAGCAGCAAGA 60.670 61.111 9.46 0.00 0.00 3.02
1985 2173 1.536943 GCCGAGTCAGAGTCCTTGGT 61.537 60.000 0.00 0.00 35.07 3.67
1989 2177 0.683973 AGTCAGAGTCCTTGGTGCTG 59.316 55.000 0.00 0.00 0.00 4.41
2080 2268 1.004320 AGGGTGCGTTGCGTCATTA 60.004 52.632 0.00 0.00 0.00 1.90
2105 2293 3.002791 TCTTCTTGTGCGATCAATGGTC 58.997 45.455 0.00 0.00 0.00 4.02
2117 2305 5.230726 GCGATCAATGGTCAATTGTTCATTC 59.769 40.000 18.76 11.64 45.14 2.67
2118 2306 5.745294 CGATCAATGGTCAATTGTTCATTCC 59.255 40.000 18.76 12.96 45.14 3.01
2119 2307 5.058149 TCAATGGTCAATTGTTCATTCCG 57.942 39.130 18.76 12.65 45.14 4.30
2120 2308 4.764308 TCAATGGTCAATTGTTCATTCCGA 59.236 37.500 18.76 14.02 45.14 4.55
2121 2309 5.418524 TCAATGGTCAATTGTTCATTCCGAT 59.581 36.000 18.76 3.89 45.14 4.18
2122 2310 4.963276 TGGTCAATTGTTCATTCCGATC 57.037 40.909 5.13 0.00 0.00 3.69
2123 2311 4.331108 TGGTCAATTGTTCATTCCGATCA 58.669 39.130 5.13 0.00 0.00 2.92
2124 2312 4.764308 TGGTCAATTGTTCATTCCGATCAA 59.236 37.500 5.13 0.00 37.64 2.57
2125 2313 5.242615 TGGTCAATTGTTCATTCCGATCAAA 59.757 36.000 5.13 0.00 36.99 2.69
2126 2314 6.155827 GGTCAATTGTTCATTCCGATCAAAA 58.844 36.000 5.13 0.00 36.99 2.44
2127 2315 6.644592 GGTCAATTGTTCATTCCGATCAAAAA 59.355 34.615 5.13 0.00 36.99 1.94
2218 2419 0.458543 TCAACGAGAAGATGCGAGCC 60.459 55.000 0.00 0.00 0.00 4.70
2252 2453 1.152777 CCCCACTGCAACAAGGTGA 60.153 57.895 4.70 0.00 33.32 4.02
2254 2455 1.455383 CCCACTGCAACAAGGTGACC 61.455 60.000 4.70 0.00 33.32 4.02
2256 2457 1.102154 CACTGCAACAAGGTGACCAA 58.898 50.000 3.63 0.00 33.32 3.67
2261 2465 3.791245 TGCAACAAGGTGACCAAATTTC 58.209 40.909 3.63 0.00 0.00 2.17
2265 2469 5.220643 GCAACAAGGTGACCAAATTTCTTTG 60.221 40.000 3.63 0.00 41.22 2.77
2273 2477 4.518590 TGACCAAATTTCTTTGCTCGATCA 59.481 37.500 0.00 0.00 40.39 2.92
2282 2486 4.806571 GCTCGATCAGCCAACGTA 57.193 55.556 6.02 0.00 43.17 3.57
2283 2487 2.288969 GCTCGATCAGCCAACGTAC 58.711 57.895 6.02 0.00 43.17 3.67
2284 2488 1.472276 GCTCGATCAGCCAACGTACG 61.472 60.000 15.01 15.01 43.17 3.67
2286 2490 1.063027 CTCGATCAGCCAACGTACGTA 59.937 52.381 23.12 4.86 0.00 3.57
2287 2491 1.186030 CGATCAGCCAACGTACGTAC 58.814 55.000 23.12 15.90 0.00 3.67
2288 2492 1.553308 GATCAGCCAACGTACGTACC 58.447 55.000 23.12 12.63 0.00 3.34
2294 2503 2.295909 AGCCAACGTACGTACCAGTTTA 59.704 45.455 23.12 0.00 0.00 2.01
2303 2512 6.636850 ACGTACGTACCAGTTTAGTTTTACTG 59.363 38.462 21.41 2.36 41.08 2.74
2320 2529 9.167311 AGTTTTACTGATTAATCTGCTCGATTT 57.833 29.630 19.07 4.09 42.26 2.17
2593 2821 3.952628 CTTCCTCGGCGTCAACCCC 62.953 68.421 6.85 0.00 0.00 4.95
2698 2942 3.053896 CCCGCCGTCTTTTCCACC 61.054 66.667 0.00 0.00 0.00 4.61
2822 3071 1.082169 CACGTGTCCAATGGCAACG 60.082 57.895 19.94 19.94 42.51 4.10
2933 3196 0.676151 CTTCTCCAGGCAAGGTGCTC 60.676 60.000 0.00 0.00 44.28 4.26
2936 3199 2.743928 CCAGGCAAGGTGCTCGAC 60.744 66.667 0.00 0.00 44.28 4.20
2937 3200 2.031012 CAGGCAAGGTGCTCGACA 59.969 61.111 0.00 0.00 44.28 4.35
2938 3201 2.031516 CAGGCAAGGTGCTCGACAG 61.032 63.158 0.00 0.00 44.28 3.51
2947 3210 4.683432 GCTCGACAGCTGGAAACT 57.317 55.556 19.93 0.00 43.09 2.66
2948 3211 3.814577 GCTCGACAGCTGGAAACTA 57.185 52.632 19.93 0.00 43.09 2.24
2949 3212 1.351153 GCTCGACAGCTGGAAACTAC 58.649 55.000 19.93 0.00 43.09 2.73
2950 3213 1.067495 GCTCGACAGCTGGAAACTACT 60.067 52.381 19.93 0.00 43.09 2.57
2951 3214 2.610727 GCTCGACAGCTGGAAACTACTT 60.611 50.000 19.93 0.00 43.09 2.24
2952 3215 3.654414 CTCGACAGCTGGAAACTACTTT 58.346 45.455 19.93 0.00 0.00 2.66
2953 3216 4.058817 CTCGACAGCTGGAAACTACTTTT 58.941 43.478 19.93 0.00 0.00 2.27
2954 3217 4.448210 TCGACAGCTGGAAACTACTTTTT 58.552 39.130 19.93 0.00 0.00 1.94
3107 3380 4.168014 CACATGGGATCAAAAATCACGTG 58.832 43.478 9.94 9.94 42.53 4.49
3193 3476 8.937634 TTTCCTACTATACGAAATGAAAGGTC 57.062 34.615 0.00 0.00 0.00 3.85
3229 3540 3.823330 ACCGCATCTCCCGTCGAC 61.823 66.667 5.18 5.18 0.00 4.20
3276 3587 1.745653 CCAATTTTCTTCCTCTCCGCC 59.254 52.381 0.00 0.00 0.00 6.13
3331 3642 0.250038 GCCGCTAGATCATGGAAGCA 60.250 55.000 0.00 0.00 34.60 3.91
3342 3653 7.925043 AGATCATGGAAGCATTAATCTCATC 57.075 36.000 0.00 0.00 0.00 2.92
3349 3660 3.906998 AGCATTAATCTCATCGTCCTCG 58.093 45.455 0.00 0.00 38.55 4.63
3356 3667 1.095600 CTCATCGTCCTCGTCTTCCA 58.904 55.000 0.00 0.00 38.33 3.53
3375 3694 1.737735 CTTCACGCCGCTCATCACA 60.738 57.895 0.00 0.00 0.00 3.58
3376 3695 1.291184 CTTCACGCCGCTCATCACAA 61.291 55.000 0.00 0.00 0.00 3.33
3392 3711 4.257536 TCACAACATATCGACGCAATTG 57.742 40.909 0.00 0.00 0.00 2.32
3446 3771 6.398095 CCTGCCCCTAAATTTTAACTCAAAG 58.602 40.000 0.00 0.00 0.00 2.77
3500 3825 9.587772 GTAGAAAGTATGAAAGTGCTCATCTAA 57.412 33.333 0.00 0.00 37.27 2.10
3511 3862 3.942115 GTGCTCATCTAACCCTTTTCCTC 59.058 47.826 0.00 0.00 0.00 3.71
3543 3894 8.116651 AGCCTTTCTTCTTCTTTCCTTAATTC 57.883 34.615 0.00 0.00 0.00 2.17
3548 3899 5.555941 TCTTCTTCTTTCCTTAATTCCCCCT 59.444 40.000 0.00 0.00 0.00 4.79
3550 3901 5.827756 TCTTCTTTCCTTAATTCCCCCTTC 58.172 41.667 0.00 0.00 0.00 3.46
3552 3903 4.191963 TCTTTCCTTAATTCCCCCTTCCT 58.808 43.478 0.00 0.00 0.00 3.36
3555 3906 4.331159 TCCTTAATTCCCCCTTCCTTTG 57.669 45.455 0.00 0.00 0.00 2.77
3556 3907 3.665618 TCCTTAATTCCCCCTTCCTTTGT 59.334 43.478 0.00 0.00 0.00 2.83
3617 4269 5.240891 CACGGATATGGCAATGTCTATTCT 58.759 41.667 0.00 0.00 0.00 2.40
3667 4319 1.294659 CTCGCCTCAAAGAGCACCAC 61.295 60.000 0.00 0.00 0.00 4.16
3769 4421 1.363807 GCCAACCACAACTTCTGCC 59.636 57.895 0.00 0.00 0.00 4.85
3790 4443 6.408035 TGCCGGTAGATAATGTAAAAACTCA 58.592 36.000 1.90 0.00 0.00 3.41
3796 4449 9.444600 GGTAGATAATGTAAAAACTCACCAAGA 57.555 33.333 0.00 0.00 0.00 3.02
3824 4477 2.452937 GGGTCTCCTATGTGCCCCC 61.453 68.421 0.00 0.00 33.40 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 0.475632 TTCTTGGCTTGGAGGGAGGA 60.476 55.000 0.00 0.00 0.00 3.71
124 137 3.191539 CGCGGCTCTCTTCTTGGC 61.192 66.667 0.00 0.00 0.00 4.52
125 138 2.510238 CCGCGGCTCTCTTCTTGG 60.510 66.667 14.67 0.00 0.00 3.61
147 160 1.440893 CGGGAGGATGCTCAGTCAG 59.559 63.158 16.72 0.00 0.00 3.51
148 161 3.621225 CGGGAGGATGCTCAGTCA 58.379 61.111 16.72 0.00 0.00 3.41
199 212 3.127425 ACAAGAACTAACCAGTCTGGC 57.873 47.619 19.40 1.16 42.67 4.85
219 232 1.679977 GCCAGCAGCCATGGAAGAA 60.680 57.895 18.40 0.00 40.51 2.52
220 233 2.044650 GCCAGCAGCCATGGAAGA 60.045 61.111 18.40 0.00 40.51 2.87
221 234 2.044252 AGCCAGCAGCCATGGAAG 60.044 61.111 18.40 7.81 45.47 3.46
222 235 2.044650 GAGCCAGCAGCCATGGAA 60.045 61.111 18.40 0.00 45.47 3.53
267 283 0.446616 GGACGCGGATTTTGGAGAAC 59.553 55.000 12.47 0.00 0.00 3.01
304 320 3.999663 CCACATCAGGTTTCAGAAGAGAC 59.000 47.826 0.00 0.00 0.00 3.36
335 351 2.769663 TGCCGTTAAGACCAGTGGATAT 59.230 45.455 18.40 3.27 0.00 1.63
345 361 7.549615 AAAACTAGGATTATGCCGTTAAGAC 57.450 36.000 0.00 0.00 0.00 3.01
380 396 6.628919 TTTACAAAGACCTGGAAGCTTTAC 57.371 37.500 0.00 0.00 31.21 2.01
391 407 8.406297 GTTCAGAAAAGTGATTTACAAAGACCT 58.594 33.333 0.00 0.00 0.00 3.85
392 408 7.648112 GGTTCAGAAAAGTGATTTACAAAGACC 59.352 37.037 0.00 0.00 0.00 3.85
410 426 3.139077 GGAAAAGCGAAGAGGTTCAGAA 58.861 45.455 0.00 0.00 40.06 3.02
417 433 8.664211 AGTATTTTATAGGAAAAGCGAAGAGG 57.336 34.615 0.00 0.00 0.00 3.69
443 468 4.774726 TCTGTTAAGATGCTGAGAAGAGGT 59.225 41.667 0.00 0.00 0.00 3.85
444 469 5.336150 TCTGTTAAGATGCTGAGAAGAGG 57.664 43.478 0.00 0.00 0.00 3.69
445 470 7.664082 TTTTCTGTTAAGATGCTGAGAAGAG 57.336 36.000 0.00 0.00 30.72 2.85
495 520 5.766150 AGTCTACAGAGCACTAGCAATAG 57.234 43.478 0.00 0.00 45.49 1.73
496 521 5.652452 TCAAGTCTACAGAGCACTAGCAATA 59.348 40.000 0.00 0.00 45.49 1.90
497 522 4.464244 TCAAGTCTACAGAGCACTAGCAAT 59.536 41.667 0.00 0.00 45.49 3.56
713 741 1.077930 AGCTGGGCTATGCAGTGTG 60.078 57.895 0.00 0.00 36.99 3.82
714 742 1.077930 CAGCTGGGCTATGCAGTGT 60.078 57.895 5.57 0.00 36.40 3.55
801 836 8.562052 GTTTTGAACCTCCGATAGTTCTAAAAA 58.438 33.333 15.81 10.88 43.83 1.94
802 837 7.716123 TGTTTTGAACCTCCGATAGTTCTAAAA 59.284 33.333 15.81 13.75 43.83 1.52
803 838 7.218614 TGTTTTGAACCTCCGATAGTTCTAAA 58.781 34.615 12.68 12.68 41.79 1.85
804 839 6.761312 TGTTTTGAACCTCCGATAGTTCTAA 58.239 36.000 10.96 7.95 42.32 2.10
805 840 6.349243 TGTTTTGAACCTCCGATAGTTCTA 57.651 37.500 10.96 3.47 42.32 2.10
807 842 6.496338 AATGTTTTGAACCTCCGATAGTTC 57.504 37.500 5.03 5.03 42.20 3.01
848 887 0.036105 ATGTGCGATGCCAGACAGAA 60.036 50.000 0.00 0.00 0.00 3.02
849 888 0.741927 CATGTGCGATGCCAGACAGA 60.742 55.000 0.00 0.00 0.00 3.41
1001 1042 3.409026 ACGAAATCAGCTGAGAAACCT 57.591 42.857 22.96 0.23 0.00 3.50
1002 1043 3.251004 ACAACGAAATCAGCTGAGAAACC 59.749 43.478 22.96 8.23 0.00 3.27
1019 1060 4.161333 GAGATGGCAAGAATCAAACAACG 58.839 43.478 0.00 0.00 0.00 4.10
1069 1114 1.670087 CGATTCACTTCACCGCAGAGT 60.670 52.381 0.00 0.00 0.00 3.24
1153 1203 1.142748 GAGTGGCCTGGAGATGTCG 59.857 63.158 3.32 0.00 0.00 4.35
1177 1227 3.257469 AGCGATCAAGATTCAAGAGCA 57.743 42.857 0.00 0.00 0.00 4.26
1205 1255 5.188434 CAGATATGACACCACAAACTCCAT 58.812 41.667 0.00 0.00 0.00 3.41
1210 1260 2.742053 ACGCAGATATGACACCACAAAC 59.258 45.455 0.00 0.00 0.00 2.93
1250 1305 5.977129 CGAAATTAAGCACAAAAAGGTCAGT 59.023 36.000 0.00 0.00 0.00 3.41
1268 1323 0.539438 TTCCCTGCAGCCACGAAATT 60.539 50.000 8.66 0.00 0.00 1.82
1273 1328 2.743928 GTCTTCCCTGCAGCCACG 60.744 66.667 8.66 0.00 0.00 4.94
1284 1346 1.757118 TCCATGAGGTCATCGTCTTCC 59.243 52.381 0.00 0.00 33.61 3.46
1434 1496 3.500642 TCGAGCGAGTCAGCGAGG 61.501 66.667 0.00 0.00 43.00 4.63
1440 1502 1.170290 TGTCCTTGTCGAGCGAGTCA 61.170 55.000 0.00 0.00 0.00 3.41
1567 1755 0.178973 TGGACGAGGTCTGACTGGAA 60.179 55.000 7.85 0.00 32.47 3.53
1571 1759 1.979693 GCCTGGACGAGGTCTGACT 60.980 63.158 7.85 0.00 44.97 3.41
1575 1763 2.752238 CGAGCCTGGACGAGGTCT 60.752 66.667 5.32 3.02 44.97 3.85
1775 1963 0.525761 GCCTCTGGCGTTTGCATTTA 59.474 50.000 0.00 0.00 45.35 1.40
1854 2042 2.358247 GTGGTGGTAGTGGCGGTG 60.358 66.667 0.00 0.00 0.00 4.94
1863 2051 3.243053 CCGGTGGTGGTGGTGGTA 61.243 66.667 0.00 0.00 0.00 3.25
1932 2120 2.745100 TCCGAGTCCTCCGTGTCG 60.745 66.667 0.00 0.00 0.00 4.35
1974 2162 1.835927 GCTCCAGCACCAAGGACTCT 61.836 60.000 0.00 0.00 41.59 3.24
2004 2192 2.811317 GCCGTCGTGAGCTTCTGG 60.811 66.667 0.00 0.00 0.00 3.86
2072 2260 4.260656 CGCACAAGAAGAAATTAATGACGC 59.739 41.667 0.00 0.00 0.00 5.19
2080 2268 5.047802 ACCATTGATCGCACAAGAAGAAATT 60.048 36.000 0.00 0.00 33.22 1.82
2140 2328 4.154015 CGCCAGAGATGTTGTAATGAACAA 59.846 41.667 0.00 0.00 45.90 2.83
2141 2329 3.684305 CGCCAGAGATGTTGTAATGAACA 59.316 43.478 0.00 0.00 40.08 3.18
2142 2330 3.485877 GCGCCAGAGATGTTGTAATGAAC 60.486 47.826 0.00 0.00 0.00 3.18
2143 2331 2.677836 GCGCCAGAGATGTTGTAATGAA 59.322 45.455 0.00 0.00 0.00 2.57
2144 2332 2.093500 AGCGCCAGAGATGTTGTAATGA 60.093 45.455 2.29 0.00 0.00 2.57
2145 2333 2.031314 CAGCGCCAGAGATGTTGTAATG 59.969 50.000 2.29 0.00 0.00 1.90
2146 2334 2.093500 TCAGCGCCAGAGATGTTGTAAT 60.093 45.455 2.29 0.00 0.00 1.89
2147 2335 1.275010 TCAGCGCCAGAGATGTTGTAA 59.725 47.619 2.29 0.00 0.00 2.41
2148 2336 0.894835 TCAGCGCCAGAGATGTTGTA 59.105 50.000 2.29 0.00 0.00 2.41
2218 2419 0.179034 GGGGTATGAGCTCTTGCAGG 60.179 60.000 16.19 0.00 42.74 4.85
2252 2453 5.051891 CTGATCGAGCAAAGAAATTTGGT 57.948 39.130 4.32 5.20 44.27 3.67
2273 2477 0.675633 AACTGGTACGTACGTTGGCT 59.324 50.000 27.92 2.98 0.00 4.75
2276 2480 5.888412 AAACTAAACTGGTACGTACGTTG 57.112 39.130 27.92 16.03 0.00 4.10
2280 2484 8.748380 ATCAGTAAAACTAAACTGGTACGTAC 57.252 34.615 17.56 17.56 42.72 3.67
2282 2486 9.762933 TTAATCAGTAAAACTAAACTGGTACGT 57.237 29.630 0.00 0.00 42.72 3.57
2287 2491 9.774742 GCAGATTAATCAGTAAAACTAAACTGG 57.225 33.333 17.56 0.00 42.72 4.00
2294 2503 8.723942 AATCGAGCAGATTAATCAGTAAAACT 57.276 30.769 17.56 1.92 46.99 2.66
2320 2529 1.459455 CGCCCATCACAAAACCCACA 61.459 55.000 0.00 0.00 0.00 4.17
2663 2907 1.029681 GGGGCGTTGGAAATGGATAC 58.970 55.000 0.00 0.00 32.13 2.24
2698 2942 3.028850 TCCATCTTACGTGTTAGGGAGG 58.971 50.000 0.00 0.00 0.00 4.30
2933 3196 4.813296 AAAAAGTAGTTTCCAGCTGTCG 57.187 40.909 13.81 0.00 0.00 4.35
3077 3346 4.415881 TTTGATCCCATGTGCGTACTAT 57.584 40.909 4.97 0.00 0.00 2.12
3079 3348 2.779755 TTTGATCCCATGTGCGTACT 57.220 45.000 4.97 0.00 0.00 2.73
3080 3349 3.840890 TTTTTGATCCCATGTGCGTAC 57.159 42.857 0.00 0.00 0.00 3.67
3081 3350 4.013050 TGATTTTTGATCCCATGTGCGTA 58.987 39.130 0.00 0.00 0.00 4.42
3082 3351 2.824936 TGATTTTTGATCCCATGTGCGT 59.175 40.909 0.00 0.00 0.00 5.24
3083 3352 3.181397 GTGATTTTTGATCCCATGTGCG 58.819 45.455 0.00 0.00 0.00 5.34
3084 3353 3.181397 CGTGATTTTTGATCCCATGTGC 58.819 45.455 0.00 0.00 0.00 4.57
3085 3354 4.168014 CACGTGATTTTTGATCCCATGTG 58.832 43.478 10.90 0.00 38.07 3.21
3107 3380 9.624697 TGCTGAAATTATTTGATGTTAGTGAAC 57.375 29.630 0.00 0.00 36.00 3.18
3213 3524 4.570663 GGTCGACGGGAGATGCGG 62.571 72.222 9.92 0.00 0.00 5.69
3241 3552 4.817318 AAATTGGTGAGAGAGGAGAGAC 57.183 45.455 0.00 0.00 0.00 3.36
3289 3600 0.108186 TCTGGTCGCAATGGCAGTAG 60.108 55.000 0.00 0.00 41.24 2.57
3317 3628 7.763071 CGATGAGATTAATGCTTCCATGATCTA 59.237 37.037 0.00 0.00 36.29 1.98
3331 3642 5.278561 GGAAGACGAGGACGATGAGATTAAT 60.279 44.000 0.00 0.00 42.66 1.40
3342 3653 0.596577 TGAAGTGGAAGACGAGGACG 59.403 55.000 0.00 0.00 45.75 4.79
3349 3660 2.668280 GCGGCGTGAAGTGGAAGAC 61.668 63.158 9.37 0.00 0.00 3.01
3356 3667 1.738099 GTGATGAGCGGCGTGAAGT 60.738 57.895 9.37 0.00 0.00 3.01
3375 3694 5.499139 AATTCCAATTGCGTCGATATGTT 57.501 34.783 0.00 0.00 0.00 2.71
3376 3695 5.065859 TGAAATTCCAATTGCGTCGATATGT 59.934 36.000 0.00 0.00 0.00 2.29
3392 3711 6.049790 AGATACTCTTAAGGCGTGAAATTCC 58.950 40.000 1.85 0.00 0.00 3.01
3420 3745 3.104512 AGTTAAAATTTAGGGGCAGGGC 58.895 45.455 0.00 0.00 0.00 5.19
3464 3789 9.793259 ACTTTCATACTTTCTACAATTGAGGAA 57.207 29.630 13.59 12.31 0.00 3.36
3472 3797 8.097038 AGATGAGCACTTTCATACTTTCTACAA 58.903 33.333 0.00 0.00 37.90 2.41
3477 3802 7.201652 GGGTTAGATGAGCACTTTCATACTTTC 60.202 40.741 0.00 0.00 37.90 2.62
3500 3825 4.324521 TCCACGGAGGAAAAGGGT 57.675 55.556 0.00 0.00 45.65 4.34
3529 3880 4.610703 AGGAAGGGGGAATTAAGGAAAGAA 59.389 41.667 0.00 0.00 0.00 2.52
3530 3881 4.191963 AGGAAGGGGGAATTAAGGAAAGA 58.808 43.478 0.00 0.00 0.00 2.52
3534 3885 3.665618 ACAAAGGAAGGGGGAATTAAGGA 59.334 43.478 0.00 0.00 0.00 3.36
3550 3901 3.096852 GGGAATTAACCCCTCACAAAGG 58.903 50.000 7.37 0.00 43.81 3.11
3617 4269 2.763215 GTGGTGGATGCCTCCCAA 59.237 61.111 5.49 0.00 41.29 4.12
3769 4421 7.837202 TGGTGAGTTTTTACATTATCTACCG 57.163 36.000 0.00 0.00 0.00 4.02
3790 4443 3.641436 GAGACCCCATTGTTTTTCTTGGT 59.359 43.478 0.00 0.00 0.00 3.67
3796 4449 4.772100 CACATAGGAGACCCCATTGTTTTT 59.228 41.667 0.00 0.00 37.41 1.94
3824 4477 0.943673 TTCCATGTTGTGCAGTCACG 59.056 50.000 0.00 0.00 46.01 4.35


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

AutoCloner maintained by Alex Coulton.