Multiple sequence alignment - TraesCS2D01G598000

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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 TraesCS2D01G598000 chr2D 100.000 2766 0 0 1280 4045 650324247 650321482 0.000000e+00 5108
1 TraesCS2D01G598000 chr2D 100.000 1075 0 0 1 1075 650325526 650324452 0.000000e+00 1986
2 TraesCS2D01G598000 chr2B 88.688 2714 198 60 1375 4045 786228166 786225519 0.000000e+00 3210
3 TraesCS2D01G598000 chr2B 91.236 1084 68 17 1 1064 786229625 786228549 0.000000e+00 1450
4 TraesCS2D01G598000 chr2A 87.349 2071 168 52 2018 4045 774572915 774574934 0.000000e+00 2287
5 TraesCS2D01G598000 chr2A 93.669 1074 50 13 1 1062 774570905 774571972 0.000000e+00 1591
6 TraesCS2D01G598000 chr2A 92.250 400 18 6 1300 1688 774572217 774572614 4.570000e-154 555
7 TraesCS2D01G598000 chrUn 88.251 366 29 10 3274 3630 96707544 96707904 3.740000e-115 425
8 TraesCS2D01G598000 chrUn 87.000 300 34 4 3652 3946 96731576 96731875 2.330000e-87 333
9 TraesCS2D01G598000 chrUn 85.714 140 17 2 3135 3274 96702114 96702250 1.170000e-30 145
10 TraesCS2D01G598000 chr6B 88.650 326 32 5 3315 3640 47898731 47899051 3.790000e-105 392
11 TraesCS2D01G598000 chr6B 79.310 232 28 14 3013 3239 47898511 47898727 1.170000e-30 145


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 TraesCS2D01G598000 chr2D 650321482 650325526 4044 True 3547.000000 5108 100.000000 1 4045 2 chr2D.!!$R1 4044
1 TraesCS2D01G598000 chr2B 786225519 786229625 4106 True 2330.000000 3210 89.962000 1 4045 2 chr2B.!!$R1 4044
2 TraesCS2D01G598000 chr2A 774570905 774574934 4029 False 1477.666667 2287 91.089333 1 4045 3 chr2A.!!$F1 4044
3 TraesCS2D01G598000 chr6B 47898511 47899051 540 False 268.500000 392 83.980000 3013 3640 2 chr6B.!!$F1 627

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
599 602 0.760945 ATTTGGCCAAACCGGTGGAA 60.761 50.0 32.62 8.22 43.94 3.53 F
1069 1090 0.455005 CGTCGTTAAGGTCCTCCTCC 59.545 60.0 0.00 0.00 44.35 4.30 F
2307 2470 0.587768 CACAAGCGATGCTGTGTTCA 59.412 50.0 0.00 0.00 39.62 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 2628 0.240145 TGGCACGTCTCGTCTAACTG 59.760 55.0 0.0 0.0 38.32 3.16 R
2444 2632 0.885879 ACAATGGCACGTCTCGTCTA 59.114 50.0 0.0 0.0 38.32 2.59 R
3828 4034 0.395862 ATCAGACCGACGGGATCAGT 60.396 55.0 20.0 0.0 36.97 3.41 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
103 104 2.767505 CCAGTAAACTTCTTCAGGCGT 58.232 47.619 0.00 0.00 0.00 5.68
130 131 1.306148 CGAGGACGGACAGTATGCTA 58.694 55.000 0.00 0.00 36.01 3.49
140 141 4.061596 GGACAGTATGCTATGAAGAAGCC 58.938 47.826 0.00 0.00 42.53 4.35
141 142 3.722147 ACAGTATGCTATGAAGAAGCCG 58.278 45.455 0.00 0.00 42.53 5.52
234 235 6.306837 CGTGTTGTTATTTGTGACTGTTTGTT 59.693 34.615 0.00 0.00 0.00 2.83
455 456 1.815003 ACAAGCATTTCTGTGGCTAGC 59.185 47.619 6.04 6.04 36.76 3.42
472 474 2.576298 GCTTCTGCTGGGCTGATTT 58.424 52.632 0.40 0.00 36.48 2.17
568 571 7.434492 TGTTTTGACTTTTGTAACTGTTTCCA 58.566 30.769 0.00 0.00 0.00 3.53
574 577 9.295825 TGACTTTTGTAACTGTTTCCATATGAT 57.704 29.630 3.65 0.00 0.00 2.45
599 602 0.760945 ATTTGGCCAAACCGGTGGAA 60.761 50.000 32.62 8.22 43.94 3.53
627 630 4.588951 ACTGTTTTCTTCCCCTTCCATTTC 59.411 41.667 0.00 0.00 0.00 2.17
636 639 5.749422 TCCCCTTCCATTTCCATTCTAAT 57.251 39.130 0.00 0.00 0.00 1.73
641 644 9.774071 CCCCTTCCATTTCCATTCTAATAATAT 57.226 33.333 0.00 0.00 0.00 1.28
671 674 8.816640 TTAAAACTCTCCATTTCAAAGAATGC 57.183 30.769 0.00 0.00 36.04 3.56
682 685 8.741841 CCATTTCAAAGAATGCCCAAAAATAAT 58.258 29.630 0.00 0.00 36.04 1.28
686 689 9.434420 TTCAAAGAATGCCCAAAAATAATAGTG 57.566 29.630 0.00 0.00 0.00 2.74
688 691 9.868277 CAAAGAATGCCCAAAAATAATAGTGTA 57.132 29.630 0.00 0.00 0.00 2.90
689 692 9.869757 AAAGAATGCCCAAAAATAATAGTGTAC 57.130 29.630 0.00 0.00 0.00 2.90
691 694 8.466798 AGAATGCCCAAAAATAATAGTGTACAC 58.533 33.333 18.56 18.56 0.00 2.90
794 798 9.827198 AGGAATAGCCCATTCAAATATAAATGA 57.173 29.630 10.01 0.00 44.27 2.57
886 900 3.331478 AAGACTTCCTGAGATGCACAG 57.669 47.619 0.00 0.00 35.43 3.66
1064 1085 2.233271 TGACTTCGTCGTTAAGGTCCT 58.767 47.619 0.00 0.00 34.95 3.85
1065 1086 2.227388 TGACTTCGTCGTTAAGGTCCTC 59.773 50.000 0.00 0.00 34.95 3.71
1066 1087 1.543358 ACTTCGTCGTTAAGGTCCTCC 59.457 52.381 0.00 0.00 0.00 4.30
1068 1089 1.457346 TCGTCGTTAAGGTCCTCCTC 58.543 55.000 0.00 0.00 44.35 3.71
1069 1090 0.455005 CGTCGTTAAGGTCCTCCTCC 59.545 60.000 0.00 0.00 44.35 4.30
1070 1091 1.849977 GTCGTTAAGGTCCTCCTCCT 58.150 55.000 0.00 0.00 44.35 3.69
1071 1092 2.681976 CGTCGTTAAGGTCCTCCTCCTA 60.682 54.545 0.00 0.00 44.35 2.94
1072 1093 3.564264 GTCGTTAAGGTCCTCCTCCTAT 58.436 50.000 0.00 0.00 44.35 2.57
1073 1094 3.569277 GTCGTTAAGGTCCTCCTCCTATC 59.431 52.174 0.00 0.00 44.35 2.08
1074 1095 2.892215 CGTTAAGGTCCTCCTCCTATCC 59.108 54.545 0.00 0.00 44.35 2.59
1492 1585 1.358877 TTGTGAATGTCGCATCTCGG 58.641 50.000 0.00 0.00 36.69 4.63
1502 1595 1.153628 GCATCTCGGTGGTAGCGTT 60.154 57.895 0.24 0.00 40.41 4.84
1693 1840 3.701532 ATCGCAGTAGCTCTAACTGAC 57.298 47.619 17.47 8.74 45.89 3.51
1732 1879 6.325596 GGCTCTTAACCATTGTTTCTTGATC 58.674 40.000 0.00 0.00 35.87 2.92
1775 1922 8.022550 TGCTGAAACTGAACACAATATATGTTG 58.977 33.333 10.37 10.37 41.46 3.33
1867 2019 8.382030 TCGATGCATCACTTTTATATGTCATT 57.618 30.769 25.70 0.00 0.00 2.57
1931 2083 7.696992 TTGCCTTTACTATAGAAACCCAAAG 57.303 36.000 6.78 5.92 0.00 2.77
1949 2101 7.791029 ACCCAAAGTGAGTAAAATGTTTCATT 58.209 30.769 0.00 0.00 0.00 2.57
1965 2117 9.444600 AATGTTTCATTAAGACCTTATACACGT 57.555 29.630 0.00 0.00 0.00 4.49
1967 2119 8.308931 TGTTTCATTAAGACCTTATACACGTCT 58.691 33.333 0.00 0.00 38.50 4.18
1970 2122 8.697846 TCATTAAGACCTTATACACGTCTTTG 57.302 34.615 11.52 7.09 42.71 2.77
1978 2130 6.534079 ACCTTATACACGTCTTTGCTCATAAC 59.466 38.462 0.00 0.00 0.00 1.89
1979 2131 6.533723 CCTTATACACGTCTTTGCTCATAACA 59.466 38.462 0.00 0.00 0.00 2.41
1984 2143 3.244078 ACGTCTTTGCTCATAACACCTGA 60.244 43.478 0.00 0.00 0.00 3.86
1985 2144 3.369147 CGTCTTTGCTCATAACACCTGAG 59.631 47.826 0.00 0.00 42.47 3.35
1988 2147 5.645497 GTCTTTGCTCATAACACCTGAGAAT 59.355 40.000 4.57 0.00 42.22 2.40
1993 2152 5.587443 TGCTCATAACACCTGAGAATTCATG 59.413 40.000 8.44 0.00 42.22 3.07
1999 2158 4.829968 ACACCTGAGAATTCATGACAGAG 58.170 43.478 8.44 9.42 31.68 3.35
2009 2168 4.771590 TTCATGACAGAGGCAATTCAAC 57.228 40.909 0.00 0.00 0.00 3.18
2018 2177 1.342174 AGGCAATTCAACCAGCACAAG 59.658 47.619 0.00 0.00 0.00 3.16
2019 2178 1.142474 GCAATTCAACCAGCACAAGC 58.858 50.000 0.00 0.00 42.56 4.01
2020 2179 1.538634 GCAATTCAACCAGCACAAGCA 60.539 47.619 0.00 0.00 45.49 3.91
2021 2180 2.129607 CAATTCAACCAGCACAAGCAC 58.870 47.619 0.00 0.00 45.49 4.40
2022 2181 1.401761 ATTCAACCAGCACAAGCACA 58.598 45.000 0.00 0.00 45.49 4.57
2023 2182 0.740149 TTCAACCAGCACAAGCACAG 59.260 50.000 0.00 0.00 45.49 3.66
2026 2185 1.111116 AACCAGCACAAGCACAGCAT 61.111 50.000 0.00 0.00 45.49 3.79
2036 2195 2.882761 CAAGCACAGCATATATGGCACT 59.117 45.455 14.51 0.45 0.00 4.40
2037 2196 2.501261 AGCACAGCATATATGGCACTG 58.499 47.619 14.51 14.21 0.00 3.66
2038 2197 2.105306 AGCACAGCATATATGGCACTGA 59.895 45.455 19.61 0.00 32.67 3.41
2039 2198 2.225019 GCACAGCATATATGGCACTGAC 59.775 50.000 19.61 10.91 32.67 3.51
2041 2200 2.071540 CAGCATATATGGCACTGACGG 58.928 52.381 14.51 0.00 0.00 4.79
2043 2202 2.568956 AGCATATATGGCACTGACGGAT 59.431 45.455 14.51 0.00 0.00 4.18
2049 2208 2.270352 TGGCACTGACGGATTTTCTT 57.730 45.000 0.00 0.00 0.00 2.52
2051 2210 3.745799 TGGCACTGACGGATTTTCTTTA 58.254 40.909 0.00 0.00 0.00 1.85
2057 2218 7.348201 GCACTGACGGATTTTCTTTATCATAG 58.652 38.462 0.00 0.00 0.00 2.23
2098 2259 9.953565 ATATACTTCACCTGCTTACTAAACAAA 57.046 29.630 0.00 0.00 0.00 2.83
2100 2261 5.298527 ACTTCACCTGCTTACTAAACAAACC 59.701 40.000 0.00 0.00 0.00 3.27
2105 2266 2.879646 TGCTTACTAAACAAACCGTGGG 59.120 45.455 0.00 0.00 0.00 4.61
2115 2276 1.610038 CAAACCGTGGGACTTTTACCC 59.390 52.381 0.00 0.00 46.87 3.69
2123 2284 3.893326 GGGACTTTTACCCGTAGCTTA 57.107 47.619 0.00 0.00 37.85 3.09
2175 2338 7.897864 AGGTATAGGCTTATACATGACTGAAC 58.102 38.462 22.97 6.65 42.21 3.18
2188 2351 5.106317 ACATGACTGAACGTGTTTTGAAGTT 60.106 36.000 0.00 0.00 36.76 2.66
2197 2360 6.784068 ACGTGTTTTGAAGTTGTATTTTCG 57.216 33.333 0.00 0.00 0.00 3.46
2199 2362 6.802834 ACGTGTTTTGAAGTTGTATTTTCGTT 59.197 30.769 0.00 0.00 0.00 3.85
2201 2364 7.007546 CGTGTTTTGAAGTTGTATTTTCGTTCA 59.992 33.333 0.00 0.00 0.00 3.18
2228 2391 8.827177 TTATAAGACTTAAGTGGTGTTGACTG 57.173 34.615 14.14 0.00 0.00 3.51
2229 2392 4.755266 AGACTTAAGTGGTGTTGACTGT 57.245 40.909 14.14 0.00 0.00 3.55
2230 2393 5.099042 AGACTTAAGTGGTGTTGACTGTT 57.901 39.130 14.14 0.00 0.00 3.16
2231 2394 4.876107 AGACTTAAGTGGTGTTGACTGTTG 59.124 41.667 14.14 0.00 0.00 3.33
2232 2395 4.839121 ACTTAAGTGGTGTTGACTGTTGA 58.161 39.130 7.48 0.00 0.00 3.18
2233 2396 4.876107 ACTTAAGTGGTGTTGACTGTTGAG 59.124 41.667 7.48 0.00 0.00 3.02
2242 2405 5.357257 GTGTTGACTGTTGAGAAGTCCTAA 58.643 41.667 1.40 0.00 42.85 2.69
2253 2416 5.996644 TGAGAAGTCCTAAAAGTTGAACCA 58.003 37.500 0.00 0.00 0.00 3.67
2256 2419 4.100279 AGTCCTAAAAGTTGAACCAGGG 57.900 45.455 0.00 0.00 0.00 4.45
2286 2449 2.874086 TGCCTCGCATCAAACAGATATG 59.126 45.455 0.00 0.00 34.43 1.78
2290 2453 4.025396 CCTCGCATCAAACAGATATGACAC 60.025 45.833 0.00 0.00 34.43 3.67
2295 2458 4.926860 TCAAACAGATATGACACAAGCG 57.073 40.909 0.00 0.00 0.00 4.68
2306 2469 0.588252 ACACAAGCGATGCTGTGTTC 59.412 50.000 5.34 0.00 42.97 3.18
2307 2470 0.587768 CACAAGCGATGCTGTGTTCA 59.412 50.000 0.00 0.00 39.62 3.18
2308 2471 1.198408 CACAAGCGATGCTGTGTTCAT 59.802 47.619 0.00 0.00 39.62 2.57
2309 2472 1.466167 ACAAGCGATGCTGTGTTCATC 59.534 47.619 0.00 0.00 39.62 2.92
2312 2475 1.206610 AGCGATGCTGTGTTCATCTCT 59.793 47.619 0.00 0.00 37.57 3.10
2319 2482 7.363431 CGATGCTGTGTTCATCTCTAACTATA 58.637 38.462 0.00 0.00 38.47 1.31
2355 2518 9.973661 TTAGTTTTCAGATTGGAGATTGGAATA 57.026 29.630 0.00 0.00 0.00 1.75
2360 2523 7.734924 TCAGATTGGAGATTGGAATAAATCG 57.265 36.000 0.00 0.00 40.75 3.34
2382 2567 5.046448 TCGTTGGGCTAAATAGTGGTAGAAA 60.046 40.000 0.00 0.00 0.00 2.52
2383 2568 5.293569 CGTTGGGCTAAATAGTGGTAGAAAG 59.706 44.000 0.00 0.00 0.00 2.62
2384 2569 6.412214 GTTGGGCTAAATAGTGGTAGAAAGA 58.588 40.000 0.00 0.00 0.00 2.52
2385 2570 6.235231 TGGGCTAAATAGTGGTAGAAAGAG 57.765 41.667 0.00 0.00 0.00 2.85
2386 2571 5.130477 TGGGCTAAATAGTGGTAGAAAGAGG 59.870 44.000 0.00 0.00 0.00 3.69
2388 2573 6.126854 GGGCTAAATAGTGGTAGAAAGAGGAA 60.127 42.308 0.00 0.00 0.00 3.36
2389 2574 7.420330 GGGCTAAATAGTGGTAGAAAGAGGAAT 60.420 40.741 0.00 0.00 0.00 3.01
2390 2575 7.658167 GGCTAAATAGTGGTAGAAAGAGGAATC 59.342 40.741 0.00 0.00 0.00 2.52
2391 2576 7.658167 GCTAAATAGTGGTAGAAAGAGGAATCC 59.342 40.741 0.00 0.00 0.00 3.01
2392 2577 5.793030 ATAGTGGTAGAAAGAGGAATCCG 57.207 43.478 0.00 0.00 0.00 4.18
2405 2590 7.414222 AAGAGGAATCCGTACAGTTTATGTA 57.586 36.000 0.00 0.00 43.66 2.29
2468 2656 0.950555 GAGACGTGCCATTGTGCAGA 60.951 55.000 0.00 0.00 43.02 4.26
2475 2663 1.273048 TGCCATTGTGCAGACCAAATC 59.727 47.619 0.00 0.00 36.04 2.17
2485 2673 2.991190 GCAGACCAAATCACTTGCATTG 59.009 45.455 0.00 0.00 33.27 2.82
2501 2692 5.940192 TGCATTGTACTTCGTCTTCAATT 57.060 34.783 0.00 0.00 0.00 2.32
2538 2730 4.813027 CATGTTTTCTGCTGCAATTAGGT 58.187 39.130 3.02 0.00 0.00 3.08
2545 2737 2.165030 CTGCTGCAATTAGGTTTGGAGG 59.835 50.000 3.02 0.00 43.09 4.30
2553 2745 4.881157 ATTAGGTTTGGAGGTATTGGCT 57.119 40.909 0.00 0.00 0.00 4.75
2663 2855 5.984725 TCCTATTTTTCGCAAGGTCTATCA 58.015 37.500 0.00 0.00 38.47 2.15
2667 2859 2.760634 TTCGCAAGGTCTATCAAGCA 57.239 45.000 0.00 0.00 38.47 3.91
2668 2860 2.760634 TCGCAAGGTCTATCAAGCAA 57.239 45.000 0.00 0.00 38.47 3.91
2669 2861 2.346803 TCGCAAGGTCTATCAAGCAAC 58.653 47.619 0.00 0.00 38.47 4.17
2670 2862 1.061131 CGCAAGGTCTATCAAGCAACG 59.939 52.381 0.00 0.00 0.00 4.10
2673 2865 3.181516 GCAAGGTCTATCAAGCAACGAAG 60.182 47.826 0.00 0.00 0.00 3.79
2675 2867 4.537135 AGGTCTATCAAGCAACGAAGAA 57.463 40.909 0.00 0.00 0.00 2.52
2676 2868 4.894784 AGGTCTATCAAGCAACGAAGAAA 58.105 39.130 0.00 0.00 0.00 2.52
2681 2873 3.963383 TCAAGCAACGAAGAAACCTTC 57.037 42.857 0.00 0.00 37.33 3.46
2773 2968 2.126071 AGGTCGACGTGAATGGCG 60.126 61.111 10.45 0.00 0.00 5.69
2826 3021 2.292292 GTCAGAGAGAGGCGGTCTATTC 59.708 54.545 0.00 0.00 34.71 1.75
3005 3200 4.764679 TTCATCTGGTGAATGTTTTCGG 57.235 40.909 0.00 0.00 41.79 4.30
3068 3265 2.187239 TCTCCAGGGAAGATCATGCT 57.813 50.000 0.00 0.00 0.00 3.79
3070 3267 0.841961 TCCAGGGAAGATCATGCTGG 59.158 55.000 6.88 6.88 0.00 4.85
3071 3268 0.178998 CCAGGGAAGATCATGCTGGG 60.179 60.000 5.61 0.00 0.00 4.45
3072 3269 0.822532 CAGGGAAGATCATGCTGGGC 60.823 60.000 0.00 0.00 0.00 5.36
3074 3271 1.153086 GGAAGATCATGCTGGGCGT 60.153 57.895 0.00 0.00 0.00 5.68
3077 3274 0.322816 AAGATCATGCTGGGCGTGTT 60.323 50.000 10.83 3.74 44.84 3.32
3078 3275 0.745845 AGATCATGCTGGGCGTGTTC 60.746 55.000 10.83 11.61 44.84 3.18
3079 3276 1.002257 ATCATGCTGGGCGTGTTCA 60.002 52.632 10.83 0.00 44.84 3.18
3080 3277 1.308069 ATCATGCTGGGCGTGTTCAC 61.308 55.000 10.83 0.00 44.84 3.18
3191 3389 7.041372 GCTACTCTGTTTTCTACATGGTGAAAA 60.041 37.037 18.03 18.03 39.09 2.29
3196 3394 8.744652 TCTGTTTTCTACATGGTGAAAAGAAAA 58.255 29.630 20.71 15.71 41.10 2.29
3216 3414 8.389586 AGAAAATAACAATTTCGCCGAAATAC 57.610 30.769 23.85 8.37 40.77 1.89
3256 3454 2.492773 AACAGCAACACAGCCTGGC 61.493 57.895 11.65 11.65 34.23 4.85
3259 3457 3.286751 GCAACACAGCCTGGCGAA 61.287 61.111 13.96 0.00 0.00 4.70
3362 3560 1.064803 CTCGAGAGATGGAAGTGTCGG 59.935 57.143 6.58 0.00 40.84 4.79
3414 3612 0.237235 TCAATGTTGGAACTTCGCGC 59.763 50.000 0.00 0.00 0.00 6.86
3504 3702 2.997315 TCCTGAGCTGGGTGACGG 60.997 66.667 0.00 0.00 0.00 4.79
3701 3903 6.743575 AAATAAAGTAGATGCACGAGCTTT 57.256 33.333 6.36 11.23 42.74 3.51
3723 3925 7.587037 TTTGTTCCATGTCTGAATCTTTTCT 57.413 32.000 0.00 0.00 32.78 2.52
3738 3944 5.623956 TCTTTTCTGTTGAGGTCTGGTAA 57.376 39.130 0.00 0.00 0.00 2.85
3801 4007 2.291153 ACCCAGAACACCTCCAATGATG 60.291 50.000 0.00 0.00 0.00 3.07
3843 4049 1.139095 GACACTGATCCCGTCGGTC 59.861 63.158 11.06 2.48 44.70 4.79
3888 4094 5.235186 CAGATTGTAAGAGCCGGATAAACTG 59.765 44.000 5.05 0.00 0.00 3.16
3956 4163 4.292186 ACATACAAGTCTCAGGTGCATT 57.708 40.909 0.00 0.00 0.00 3.56
3958 4165 5.994250 ACATACAAGTCTCAGGTGCATTAT 58.006 37.500 0.00 0.00 0.00 1.28
3968 4175 7.066766 AGTCTCAGGTGCATTATTTCTTTGATC 59.933 37.037 0.00 0.00 0.00 2.92
3973 4180 7.816031 CAGGTGCATTATTTCTTTGATCTGTTT 59.184 33.333 0.00 0.00 0.00 2.83
4040 4251 1.047002 AGGAAGGAGGATGATCTGCG 58.953 55.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 0.465097 CCAGATGGCGGCTTCTTCAT 60.465 55.000 22.59 0.40 0.00 2.57
234 235 2.293677 GACAGACTCGAAGTCCTGAACA 59.706 50.000 10.24 0.00 46.18 3.18
455 456 1.475682 GGAAAATCAGCCCAGCAGAAG 59.524 52.381 0.00 0.00 0.00 2.85
465 467 4.875536 ACACAAAAACCAAGGAAAATCAGC 59.124 37.500 0.00 0.00 0.00 4.26
472 474 5.047021 TCACATGAACACAAAAACCAAGGAA 60.047 36.000 0.00 0.00 0.00 3.36
516 518 3.382546 CCTTCCAACCAAGGCATATTGAG 59.617 47.826 0.00 0.00 36.72 3.02
517 519 3.011144 TCCTTCCAACCAAGGCATATTGA 59.989 43.478 0.00 0.00 42.63 2.57
530 533 6.635030 AAGTCAAAACAGTATCCTTCCAAC 57.365 37.500 0.00 0.00 0.00 3.77
568 571 6.239008 CGGTTTGGCCAAATGTAGAATCATAT 60.239 38.462 32.52 0.00 36.97 1.78
574 577 1.889829 CCGGTTTGGCCAAATGTAGAA 59.110 47.619 32.52 6.96 36.97 2.10
599 602 5.077564 GGAAGGGGAAGAAAACAGTGTTAT 58.922 41.667 9.37 0.00 0.00 1.89
652 655 3.765511 TGGGCATTCTTTGAAATGGAGAG 59.234 43.478 0.00 0.00 37.17 3.20
653 656 3.777087 TGGGCATTCTTTGAAATGGAGA 58.223 40.909 0.00 0.00 37.17 3.71
654 657 4.540359 TTGGGCATTCTTTGAAATGGAG 57.460 40.909 0.00 0.00 37.17 3.86
655 658 4.970860 TTTGGGCATTCTTTGAAATGGA 57.029 36.364 0.00 0.00 37.17 3.41
656 659 6.578163 ATTTTTGGGCATTCTTTGAAATGG 57.422 33.333 0.00 0.00 37.17 3.16
671 674 8.612619 CAGCTAGTGTACACTATTATTTTTGGG 58.387 37.037 30.78 18.07 42.44 4.12
689 692 3.458189 GCCTACAATACACCAGCTAGTG 58.542 50.000 10.96 10.96 43.65 2.74
691 694 2.224305 GGGCCTACAATACACCAGCTAG 60.224 54.545 0.84 0.00 0.00 3.42
794 798 3.132925 GACAGCCACACAAATTGCAAAT 58.867 40.909 1.71 0.00 0.00 2.32
886 900 4.414337 AGCACCTGTCCTGAGATTTATC 57.586 45.455 0.00 0.00 0.00 1.75
1279 1300 6.664428 TCCACAAGAATATACGATGGATGA 57.336 37.500 0.00 0.00 29.85 2.92
1281 1302 7.244886 TCATCCACAAGAATATACGATGGAT 57.755 36.000 0.00 0.00 44.43 3.41
1282 1303 6.664428 TCATCCACAAGAATATACGATGGA 57.336 37.500 0.00 0.00 39.02 3.41
1283 1304 7.912056 AATCATCCACAAGAATATACGATGG 57.088 36.000 0.00 0.00 0.00 3.51
1284 1305 7.747799 GCAAATCATCCACAAGAATATACGATG 59.252 37.037 0.00 0.00 0.00 3.84
1287 1358 7.194607 AGCAAATCATCCACAAGAATATACG 57.805 36.000 0.00 0.00 0.00 3.06
1296 1367 1.885233 TCGCAAGCAAATCATCCACAA 59.115 42.857 0.00 0.00 37.18 3.33
1298 1369 2.253603 GTTCGCAAGCAAATCATCCAC 58.746 47.619 0.00 0.00 37.18 4.02
1347 1419 9.744468 GGAACTGTACATGAATAAAAACAAACT 57.256 29.630 0.00 0.00 0.00 2.66
1357 1429 5.109500 TGGCATGGAACTGTACATGAATA 57.891 39.130 22.06 9.52 45.55 1.75
1502 1595 8.785329 AGGATTTCAAACTAAAACTGCAAAAA 57.215 26.923 0.00 0.00 0.00 1.94
1693 1840 3.196939 AGAGCCGTACAGAGTACCTAG 57.803 52.381 2.06 0.00 0.00 3.02
1775 1922 9.027129 CCATTTGACATCAATCACATCATTTAC 57.973 33.333 0.00 0.00 35.55 2.01
1961 2113 3.067106 AGGTGTTATGAGCAAAGACGTG 58.933 45.455 0.00 0.00 0.00 4.49
1962 2114 3.067106 CAGGTGTTATGAGCAAAGACGT 58.933 45.455 0.00 0.00 0.00 4.34
1965 2117 4.890158 TCTCAGGTGTTATGAGCAAAGA 57.110 40.909 0.00 0.00 43.20 2.52
1967 2119 6.003326 TGAATTCTCAGGTGTTATGAGCAAA 58.997 36.000 7.05 0.00 43.20 3.68
1970 2122 5.819379 TCATGAATTCTCAGGTGTTATGAGC 59.181 40.000 7.05 0.00 43.20 4.26
1978 2130 4.190001 CCTCTGTCATGAATTCTCAGGTG 58.810 47.826 7.05 0.00 34.89 4.00
1979 2131 3.370315 GCCTCTGTCATGAATTCTCAGGT 60.370 47.826 7.05 0.00 34.89 4.00
1984 2143 5.258841 TGAATTGCCTCTGTCATGAATTCT 58.741 37.500 7.05 0.00 33.11 2.40
1985 2144 5.571784 TGAATTGCCTCTGTCATGAATTC 57.428 39.130 0.00 0.00 32.73 2.17
1988 2147 3.507233 GGTTGAATTGCCTCTGTCATGAA 59.493 43.478 0.00 0.00 0.00 2.57
1993 2152 1.200948 GCTGGTTGAATTGCCTCTGTC 59.799 52.381 0.00 0.00 0.00 3.51
1999 2158 1.787012 CTTGTGCTGGTTGAATTGCC 58.213 50.000 0.00 0.00 0.00 4.52
2009 2168 1.100510 ATATGCTGTGCTTGTGCTGG 58.899 50.000 0.00 0.00 40.48 4.85
2018 2177 2.225019 GTCAGTGCCATATATGCTGTGC 59.775 50.000 7.24 6.02 0.00 4.57
2019 2178 2.477754 CGTCAGTGCCATATATGCTGTG 59.522 50.000 7.24 2.37 0.00 3.66
2020 2179 2.548707 CCGTCAGTGCCATATATGCTGT 60.549 50.000 7.24 0.00 0.00 4.40
2021 2180 2.071540 CCGTCAGTGCCATATATGCTG 58.928 52.381 7.24 9.39 0.00 4.41
2022 2181 1.970640 TCCGTCAGTGCCATATATGCT 59.029 47.619 7.24 0.00 0.00 3.79
2023 2182 2.455674 TCCGTCAGTGCCATATATGC 57.544 50.000 7.24 3.97 0.00 3.14
2026 2185 5.290493 AGAAAATCCGTCAGTGCCATATA 57.710 39.130 0.00 0.00 0.00 0.86
2036 2195 7.822334 ACACACTATGATAAAGAAAATCCGTCA 59.178 33.333 0.00 0.00 0.00 4.35
2037 2196 8.116753 CACACACTATGATAAAGAAAATCCGTC 58.883 37.037 0.00 0.00 0.00 4.79
2038 2197 7.414098 GCACACACTATGATAAAGAAAATCCGT 60.414 37.037 0.00 0.00 0.00 4.69
2039 2198 6.907212 GCACACACTATGATAAAGAAAATCCG 59.093 38.462 0.00 0.00 0.00 4.18
2043 2202 9.225436 TGTATGCACACACTATGATAAAGAAAA 57.775 29.630 0.00 0.00 0.00 2.29
2051 2210 9.645059 GTATATTCTGTATGCACACACTATGAT 57.355 33.333 0.00 0.00 0.00 2.45
2057 2218 7.254455 GGTGAAGTATATTCTGTATGCACACAC 60.254 40.741 0.00 0.00 0.00 3.82
2075 2236 6.484308 GGTTTGTTTAGTAAGCAGGTGAAGTA 59.516 38.462 0.00 0.00 0.00 2.24
2098 2259 1.372307 CGGGTAAAAGTCCCACGGT 59.628 57.895 1.91 0.00 44.81 4.83
2100 2261 2.000429 CTACGGGTAAAAGTCCCACG 58.000 55.000 1.91 0.00 44.81 4.94
2105 2266 4.462508 AGGTAAGCTACGGGTAAAAGTC 57.537 45.455 0.00 0.00 0.00 3.01
2123 2284 1.209019 CCATGCTCTGAACAGCTAGGT 59.791 52.381 0.00 0.00 40.39 3.08
2132 2293 1.065636 CCTGAGAAGCCATGCTCTGAA 60.066 52.381 0.00 0.00 38.25 3.02
2175 2338 6.784068 ACGAAAATACAACTTCAAAACACG 57.216 33.333 0.00 0.00 0.00 4.49
2213 2376 4.746535 TCTCAACAGTCAACACCACTTA 57.253 40.909 0.00 0.00 0.00 2.24
2223 2386 6.235231 ACTTTTAGGACTTCTCAACAGTCA 57.765 37.500 2.68 0.00 42.28 3.41
2224 2387 6.761714 TCAACTTTTAGGACTTCTCAACAGTC 59.238 38.462 0.00 0.00 40.12 3.51
2226 2389 7.410485 GTTCAACTTTTAGGACTTCTCAACAG 58.590 38.462 0.00 0.00 0.00 3.16
2227 2390 6.317893 GGTTCAACTTTTAGGACTTCTCAACA 59.682 38.462 0.00 0.00 0.00 3.33
2228 2391 6.317893 TGGTTCAACTTTTAGGACTTCTCAAC 59.682 38.462 0.00 0.00 0.00 3.18
2229 2392 6.419791 TGGTTCAACTTTTAGGACTTCTCAA 58.580 36.000 0.00 0.00 0.00 3.02
2230 2393 5.996644 TGGTTCAACTTTTAGGACTTCTCA 58.003 37.500 0.00 0.00 0.00 3.27
2231 2394 5.470437 CCTGGTTCAACTTTTAGGACTTCTC 59.530 44.000 0.00 0.00 0.00 2.87
2232 2395 5.377478 CCTGGTTCAACTTTTAGGACTTCT 58.623 41.667 0.00 0.00 0.00 2.85
2233 2396 4.519350 CCCTGGTTCAACTTTTAGGACTTC 59.481 45.833 0.00 0.00 0.00 3.01
2242 2405 1.756538 CTGTTGCCCTGGTTCAACTTT 59.243 47.619 21.61 0.00 42.11 2.66
2268 2431 4.567959 TGTGTCATATCTGTTTGATGCGAG 59.432 41.667 0.00 0.00 36.65 5.03
2271 2434 5.032863 GCTTGTGTCATATCTGTTTGATGC 58.967 41.667 0.00 0.00 36.65 3.91
2286 2449 0.588252 AACACAGCATCGCTTGTGTC 59.412 50.000 18.01 0.00 43.87 3.67
2290 2453 1.736126 AGATGAACACAGCATCGCTTG 59.264 47.619 0.00 0.00 45.18 4.01
2295 2458 8.138074 TGTATAGTTAGAGATGAACACAGCATC 58.862 37.037 0.00 0.00 41.85 3.91
2319 2482 7.556275 TCCAATCTGAAAACTAACTCAACTTGT 59.444 33.333 0.00 0.00 0.00 3.16
2355 2518 4.595986 ACCACTATTTAGCCCAACGATTT 58.404 39.130 0.00 0.00 0.00 2.17
2358 2521 4.025360 TCTACCACTATTTAGCCCAACGA 58.975 43.478 0.00 0.00 0.00 3.85
2360 2523 6.412214 TCTTTCTACCACTATTTAGCCCAAC 58.588 40.000 0.00 0.00 0.00 3.77
2382 2567 5.934402 ACATAAACTGTACGGATTCCTCT 57.066 39.130 9.17 0.00 35.91 3.69
2383 2568 7.695869 CTTACATAAACTGTACGGATTCCTC 57.304 40.000 9.17 0.00 40.06 3.71
2384 2569 8.995111 AGCCTTACATAAACTGTACGGATTCCT 61.995 40.741 9.17 0.00 43.59 3.36
2385 2570 6.907151 AGCCTTACATAAACTGTACGGATTCC 60.907 42.308 9.17 0.00 43.59 3.01
2386 2571 6.018994 CAGCCTTACATAAACTGTACGGATTC 60.019 42.308 9.17 0.00 43.59 2.52
2391 2576 3.930229 TGCAGCCTTACATAAACTGTACG 59.070 43.478 0.00 0.00 40.06 3.67
2392 2577 5.411669 ACTTGCAGCCTTACATAAACTGTAC 59.588 40.000 0.00 0.00 40.06 2.90
2405 2590 3.008375 TCATACTGAAGACTTGCAGCCTT 59.992 43.478 12.02 0.00 35.57 4.35
2440 2628 0.240145 TGGCACGTCTCGTCTAACTG 59.760 55.000 0.00 0.00 38.32 3.16
2444 2632 0.885879 ACAATGGCACGTCTCGTCTA 59.114 50.000 0.00 0.00 38.32 2.59
2449 2637 0.950555 TCTGCACAATGGCACGTCTC 60.951 55.000 0.00 0.00 39.25 3.36
2453 2641 1.794151 TTGGTCTGCACAATGGCACG 61.794 55.000 0.00 0.00 39.25 5.34
2468 2656 5.562696 CGAAGTACAATGCAAGTGATTTGGT 60.563 40.000 7.69 0.00 34.17 3.67
2501 2692 8.497554 GCAGAAAACATGCAAAGATAAATGAAA 58.502 29.630 0.00 0.00 43.31 2.69
2538 2730 2.558800 GGGGAAAGCCAATACCTCCAAA 60.559 50.000 0.00 0.00 35.15 3.28
2545 2737 1.555967 TTGCAGGGGAAAGCCAATAC 58.444 50.000 0.00 0.00 35.15 1.89
2670 2862 6.486993 ACACACAGAAATAGGAAGGTTTCTTC 59.513 38.462 0.00 0.00 46.47 2.87
2673 2865 5.531287 ACACACACAGAAATAGGAAGGTTTC 59.469 40.000 0.00 0.00 35.18 2.78
2675 2867 4.821805 CACACACACAGAAATAGGAAGGTT 59.178 41.667 0.00 0.00 0.00 3.50
2676 2868 4.389374 CACACACACAGAAATAGGAAGGT 58.611 43.478 0.00 0.00 0.00 3.50
2681 2873 3.372206 GCTAGCACACACACAGAAATAGG 59.628 47.826 10.63 0.00 0.00 2.57
2773 2968 3.818787 CAGCGGGGCAGCATTGTC 61.819 66.667 6.94 0.00 40.15 3.18
2826 3021 2.509052 TCCATTTGATACGCTCTCCG 57.491 50.000 0.00 0.00 44.21 4.63
2859 3054 1.351017 TGCCCCTCTTTGTCAACTAGG 59.649 52.381 0.00 5.67 0.00 3.02
3068 3265 1.449782 ACATGAGTGAACACGCCCA 59.550 52.632 0.00 3.89 36.20 5.36
3079 3276 5.411831 ACAGATGACACATACACATGAGT 57.588 39.130 0.00 0.00 38.49 3.41
3080 3277 6.104665 AGAACAGATGACACATACACATGAG 58.895 40.000 0.00 0.00 35.96 2.90
3154 3352 5.483685 AAACAGAGTAGCATACAACAGGA 57.516 39.130 0.00 0.00 46.26 3.86
3191 3389 8.024285 TGTATTTCGGCGAAATTGTTATTTTCT 58.976 29.630 41.55 22.81 41.64 2.52
3196 3394 7.085116 TGTTTGTATTTCGGCGAAATTGTTAT 58.915 30.769 41.55 25.79 41.64 1.89
3236 3434 1.299620 CAGGCTGTGTTGCTGTTGC 60.300 57.895 6.28 0.00 40.20 4.17
3237 3435 1.361271 CCAGGCTGTGTTGCTGTTG 59.639 57.895 14.43 0.00 0.00 3.33
3239 3437 2.908940 GCCAGGCTGTGTTGCTGT 60.909 61.111 14.43 0.00 0.00 4.40
3242 3440 1.305219 TATTCGCCAGGCTGTGTTGC 61.305 55.000 14.43 8.56 0.00 4.17
3243 3441 1.164411 TTATTCGCCAGGCTGTGTTG 58.836 50.000 14.43 0.00 0.00 3.33
3362 3560 7.835822 TCTTCTAGAGGATAGCTCATATTTGC 58.164 38.462 0.00 0.00 0.00 3.68
3414 3612 3.862642 GCCTAGCTCTGGGATATTTGACG 60.863 52.174 3.27 0.00 32.26 4.35
3701 3903 6.064060 ACAGAAAAGATTCAGACATGGAACA 58.936 36.000 0.00 0.00 39.87 3.18
3723 3925 3.820467 CAGCAATTTACCAGACCTCAACA 59.180 43.478 0.00 0.00 0.00 3.33
3828 4034 0.395862 ATCAGACCGACGGGATCAGT 60.396 55.000 20.00 0.00 36.97 3.41
3843 4049 0.962356 ACGAGGGCCAGCAAAATCAG 60.962 55.000 6.18 0.00 0.00 2.90
3930 4137 4.562757 GCACCTGAGACTTGTATGTAACCA 60.563 45.833 0.00 0.00 0.00 3.67
3956 4163 7.707624 ATGCAGGAAACAGATCAAAGAAATA 57.292 32.000 0.00 0.00 0.00 1.40
3958 4165 7.707624 ATATGCAGGAAACAGATCAAAGAAA 57.292 32.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.